Comparing spatial diversification and meta-population models in the Indo-Australian Archipelago.

PubMed

Chalmandrier, Loïc; Albouy, Camille; Descombes, Patrice; Sandel, Brody; Faurby, Soren; Svenning, Jens-Christian; Zimmermann, Niklaus E; Pellissier, Loïc

2018-03-01

Reconstructing the processes that have shaped the emergence of biodiversity gradients is critical to understand the dynamics of diversification of life on Earth. Islands have traditionally been used as model systems to unravel the processes shaping biological diversity. MacArthur and Wilson's island biogeographic model predicts diversity to be based on dynamic interactions between colonization and extinction rates, while treating islands themselves as geologically static entities. The current spatial configuration of islands should influence meta-population dynamics, but long-term geological changes within archipelagos are also expected to have shaped island biodiversity, in part by driving diversification. Here, we compare two mechanistic models providing inferences on species richness at a biogeographic scale: a mechanistic spatial-temporal model of species diversification and a spatial meta-population model. While the meta-population model operates over a static landscape, the diversification model is driven by changes in the size and spatial configuration of islands through time. We compare the inferences of both models to floristic diversity patterns among land patches of the Indo-Australian Archipelago. Simulation results from the diversification model better matched observed diversity than a meta-population model constrained only by the contemporary landscape. The diversification model suggests that the dynamic re-positioning of islands promoting land disconnection and reconnection induced an accumulation of particularly high species diversity on Borneo, which is central within the island network. By contrast, the meta-population model predicts a higher diversity on the mainlands, which is less compatible with empirical data. Our analyses highlight that, by comparing models with contrasting assumptions, we can pinpoint the processes that are most compatible with extant biodiversity patterns.

Unique parallel radiations of high-mountainous species of the genus Sedum (Crassulaceae) on the continental island of Taiwan.

PubMed

Ito, Takuro; Yu, Chih-Chieh; Nakamura, Koh; Chung, Kuo-Fang; Yang, Qin-Er; Fu, Cheng-Xin; Qi, Zhe-Chen; Kokubugata, Goro

2017-08-01

We explored the temporal and spatial diversification of the plant genus Sedum L. (Crassulaceae) in Taiwan based on molecular analysis of nrITS and cpDNA sequences from East Asian Sedum members. Our phylogenetic and ancestral area reconstruction analysis showed that Taiwanese Sedum comprised two lineages that independently migrated from Japan and Eastern China. Furthermore, the genetic distances among species in these two clades were smaller than those of other East Asian Sedum clades, and the Taiwanese members of each clade occupy extremely varied habitats with similar niches in high-mountain regions. These data indicate that species diversification occurred in parallel in the two Taiwanese Sedum lineages, and that these parallel radiations could have occurred within the small continental island of Taiwan. Moreover, the estimated time of divergence for Taiwanese Sedum indicates that the two radiations might have been correlated to the formation of mountains in Taiwan during the early Pleistocene. We suggest that these parallel radiations may be attributable to the geographical dynamics of Taiwan and specific biological features of Sedum that allow them to adapt to new ecological niches. Copyright © 2017 Elsevier Inc. All rights reserved.

Experimental evolution in biofilm populations

PubMed Central

Steenackers, Hans P.; Parijs, Ilse; Foster, Kevin R.; Vanderleyden, Jozef

2016-01-01

Biofilms are a major form of microbial life in which cells form dense surface associated communities that can persist for many generations. The long-life of biofilm communities means that they can be strongly shaped by evolutionary processes. Here, we review the experimental study of evolution in biofilm communities. We first provide an overview of the different experimental models used to study biofilm evolution and their associated advantages and disadvantages. We then illustrate the vast amount of diversification observed during biofilm evolution, and we discuss (i) potential ecological and evolutionary processes behind the observed diversification, (ii) recent insights into the genetics of adaptive diversification, (iii) the striking degree of parallelism between evolution experiments and real-life biofilms and (iv) potential consequences of diversification. In the second part, we discuss the insights provided by evolution experiments in how biofilm growth and structure can promote cooperative phenotypes. Overall, our analysis points to an important role of biofilm diversification and cooperation in bacterial survival and productivity. Deeper understanding of both processes is of key importance to design improved antimicrobial strategies and diagnostic techniques. PMID:26895713

Experimental evolution in biofilm populations.

PubMed

Steenackers, Hans P; Parijs, Ilse; Dubey, Akanksha; Foster, Kevin R; Vanderleyden, Jozef

2016-05-01

Biofilms are a major form of microbial life in which cells form dense surface associated communities that can persist for many generations. The long-life of biofilm communities means that they can be strongly shaped by evolutionary processes. Here, we review the experimental study of evolution in biofilm communities. We first provide an overview of the different experimental models used to study biofilm evolution and their associated advantages and disadvantages. We then illustrate the vast amount of diversification observed during biofilm evolution, and we discuss (i) potential ecological and evolutionary processes behind the observed diversification, (ii) recent insights into the genetics of adaptive diversification, (iii) the striking degree of parallelism between evolution experiments and real-life biofilms and (iv) potential consequences of diversification. In the second part, we discuss the insights provided by evolution experiments in how biofilm growth and structure can promote cooperative phenotypes. Overall, our analysis points to an important role of biofilm diversification and cooperation in bacterial survival and productivity. Deeper understanding of both processes is of key importance to design improved antimicrobial strategies and diagnostic techniques. © FEMS 2016.

Pleistocene aridification cycles shaped the contemporary genetic architecture of Southern African baboons.

PubMed

Sithaldeen, Riashna; Ackermann, Rebecca Rogers; Bishop, Jacqueline M

2015-01-01

Plio-Pleistocene environmental change influenced the evolutionary history of many animal lineages in Africa, highlighting key roles for both climate and tectonics in the evolution of Africa's faunal diversity. Here, we explore diversification in the southern African chacma baboon Papio ursinus sensu lato and reveal a dominant role for increasingly arid landscapes during past glacial cycles in shaping contemporary genetic structure. Recent work on baboons (Papio spp.) supports complex lineage structuring with a dominant pulse of diversification occurring 1-2Ma, and yet the link to palaeoenvironmental change remains largely untested. Phylogeographic reconstruction based on mitochondrial DNA sequence data supports a scenario where chacma baboon populations were likely restricted to refugia during periods of regional cooling and drying through the Late Pleistocene. The two lineages of chacma baboon, ursinus and griseipes, are strongly geographically structured, and demographic reconstruction together with spatial analysis of genetic variation point to possible climate-driven isolating events where baboons may have retreated to more optimum conditions during cooler, drier periods. Our analysis highlights a period of continuous population growth beginning in the Middle to Late Pleistocene in both the ursinus and the PG2 griseipes lineages. All three clades identified in the study then enter a state of declining population size (Nef) through to the Holocene; this is particularly marked in the last 20,000 years, most likely coincident with the Last Glacial Maximum. The pattern recovered here conforms to expectations based on the dynamic regional climate trends in southern Africa through the Pleistocene and provides further support for complex patterns of diversification in the region's biodiversity.

Morphological Diversity and the Roles of Contingency, Chance and Determinism in African Cichlid Radiations

PubMed Central

Young, Kyle A.; Snoeks, Jos; Seehausen, Ole

2009-01-01

Background Deterministic evolution, phylogenetic contingency and evolutionary chance each can influence patterns of morphological diversification during adaptive radiation. In comparative studies of replicate radiations, convergence in a common morphospace implicates determinism, whereas non-convergence suggests the importance of contingency or chance. Methodology/Principal Findings The endemic cichlid fish assemblages of the three African great lakes have evolved similar sets of ecomorphs but show evidence of non-convergence when compared in a common morphospace, suggesting the importance of contingency and/or chance. We then analyzed the morphological diversity of each assemblage independently and compared their axes of diversification in the unconstrained global morphospace. We find that despite differences in phylogenetic composition, invasion history, and ecological setting, the three assemblages are diversifying along parallel axes through morphospace and have nearly identical variance-covariance structures among morphological elements. Conclusions/Significance By demonstrating that replicate adaptive radiations are diverging along parallel axes, we have shown that non-convergence in the common morphospace is associated with convergence in the global morphospace. Applying these complimentary analyses to future comparative studies will improve our understanding of the relationship between morphological convergence and non-convergence, and the roles of contingency, chance and determinism in driving morphological diversification. PMID:19270732

Evolutionary Roots and Diversification of the Genus Aeromonas.

PubMed

Sanglas, Ariadna; Albarral, Vicenta; Farfán, Maribel; Lorén, J G; Fusté, M C

2017-01-01

Despite the importance of diversification rates in the study of prokaryote evolution, they have not been quantitatively assessed for the majority of microorganism taxa. The investigation of evolutionary patterns in prokaryotes constitutes a challenge due to a very scarce fossil record, limited morphological differentiation and frequently complex taxonomic relationships, which make even species recognition difficult. Although the speciation models and speciation rates in eukaryotes have traditionally been established by analyzing the fossil record data, this is frequently incomplete, and not always available. More recently, several methods based on molecular sequence data have been developed to estimate speciation and extinction rates from phylogenies reconstructed from contemporary taxa. In this work, we determined the divergence time and temporal diversification of the genus Aeromonas by applying these methods widely used with eukaryotic taxa. Our analysis involved 150 Aeromonas strains using the concatenated sequences of two housekeeping genes (approximately 2,000 bp). Dating and diversification model analyses were performed using two different approaches: obtaining the consensus sequence from the concatenated sequences corresponding to all the strains belonging to the same species, or generating the species tree from multiple alignments of each gene. We used BEAST to perform a Bayesian analysis to estimate both the phylogeny and the divergence times. A global molecular clock cannot be assumed for any gene. From the chronograms obtained, we carried out a diversification analysis using several approaches. The results suggest that the genus Aeromonas began to diverge approximately 250 millions of years (Ma) ago. All methods used to determine Aeromonas diversification gave similar results, suggesting that the speciation process in this bacterial genus followed a rate-constant (Yule) diversification model, although there is a small probability that a slight deceleration occurred in recent times. We also determined the constant of diversification (λ) values, which in all cases were very similar, about 0.01 species/Ma, a value clearly lower than those described for different eukaryotes.

Evolutionary Roots and Diversification of the Genus Aeromonas

PubMed Central

Sanglas, Ariadna; Albarral, Vicenta; Farfán, Maribel; Lorén, J. G.; Fusté, M. C.

2017-01-01

Despite the importance of diversification rates in the study of prokaryote evolution, they have not been quantitatively assessed for the majority of microorganism taxa. The investigation of evolutionary patterns in prokaryotes constitutes a challenge due to a very scarce fossil record, limited morphological differentiation and frequently complex taxonomic relationships, which make even species recognition difficult. Although the speciation models and speciation rates in eukaryotes have traditionally been established by analyzing the fossil record data, this is frequently incomplete, and not always available. More recently, several methods based on molecular sequence data have been developed to estimate speciation and extinction rates from phylogenies reconstructed from contemporary taxa. In this work, we determined the divergence time and temporal diversification of the genus Aeromonas by applying these methods widely used with eukaryotic taxa. Our analysis involved 150 Aeromonas strains using the concatenated sequences of two housekeeping genes (approximately 2,000 bp). Dating and diversification model analyses were performed using two different approaches: obtaining the consensus sequence from the concatenated sequences corresponding to all the strains belonging to the same species, or generating the species tree from multiple alignments of each gene. We used BEAST to perform a Bayesian analysis to estimate both the phylogeny and the divergence times. A global molecular clock cannot be assumed for any gene. From the chronograms obtained, we carried out a diversification analysis using several approaches. The results suggest that the genus Aeromonas began to diverge approximately 250 millions of years (Ma) ago. All methods used to determine Aeromonas diversification gave similar results, suggesting that the speciation process in this bacterial genus followed a rate-constant (Yule) diversification model, although there is a small probability that a slight deceleration occurred in recent times. We also determined the constant of diversification (λ) values, which in all cases were very similar, about 0.01 species/Ma, a value clearly lower than those described for different eukaryotes. PMID:28228750

Rates of ecological divergence and body size evolution are correlated with species diversification in scaly tree ferns

PubMed Central

Ramírez-Barahona, Santiago; Barrera-Redondo, Josué; Eguiarte, Luis E.

2016-01-01

Variation in species richness across regions and between different groups of organisms is a major feature of evolution. Several factors have been proposed to explain these differences, including heterogeneity in the rates of species diversification and the age of clades. It has been frequently assumed that rapid rates of diversification are coupled to high rates of ecological and morphological evolution, leading to a prediction that remains poorly explored for most species: the positive association between ecological niche divergence, morphological evolution and species diversification. We combined a time-calibrated phylogeny with distribution, ecological and body size data for scaly tree ferns (Cyatheaceae) to test whether rates of species diversification are predicted by the rates at which clades have evolved distinct ecological niches and body sizes. We found that rates of species diversification are positively correlated with rates of ecological and morphological evolution, with rapidly diversifying clades also showing rapidly evolving ecological niches and body sizes. Our results show that rapid diversification of scaly tree ferns is associated with the evolution of species with comparable morphologies that diversified into similar, yet distinct, environments. This suggests parallel evolutionary pathways opening in different tropical regions whenever ecological and geographical opportunities arise. Accordingly, rates of ecological niche and body size evolution are relevant to explain the current patterns of species richness in this ‘ancient’ fern lineage across the tropics. PMID:27412279

Rates of ecological divergence and body size evolution are correlated with species diversification in scaly tree ferns.

PubMed

Ramírez-Barahona, Santiago; Barrera-Redondo, Josué; Eguiarte, Luis E

2016-07-13

Variation in species richness across regions and between different groups of organisms is a major feature of evolution. Several factors have been proposed to explain these differences, including heterogeneity in the rates of species diversification and the age of clades. It has been frequently assumed that rapid rates of diversification are coupled to high rates of ecological and morphological evolution, leading to a prediction that remains poorly explored for most species: the positive association between ecological niche divergence, morphological evolution and species diversification. We combined a time-calibrated phylogeny with distribution, ecological and body size data for scaly tree ferns (Cyatheaceae) to test whether rates of species diversification are predicted by the rates at which clades have evolved distinct ecological niches and body sizes. We found that rates of species diversification are positively correlated with rates of ecological and morphological evolution, with rapidly diversifying clades also showing rapidly evolving ecological niches and body sizes. Our results show that rapid diversification of scaly tree ferns is associated with the evolution of species with comparable morphologies that diversified into similar, yet distinct, environments. This suggests parallel evolutionary pathways opening in different tropical regions whenever ecological and geographical opportunities arise. Accordingly, rates of ecological niche and body size evolution are relevant to explain the current patterns of species richness in this 'ancient' fern lineage across the tropics. © 2016 The Author(s).

Evolutionary origin and early biogeography of otophysan fishes (Ostariophysi: Teleostei).

PubMed

Chen, Wei-Jen; Lavoué, Sébastien; Mayden, Richard L

2013-08-01

The biogeography of the mega-diverse, freshwater, and globally distributed Otophysi has received considerable attention. This attraction largely stems from assumptions as to their ancient origin, the clade being almost exclusively freshwater, and their suitability as to explanations of trans-oceanic distributions. Despite multiple hypotheses explaining present-day distributions, problems remain, precluding more parsimonious explanations. Underlying previous hypotheses are alternative phylogenies for Otophysi, uncertainties as to temporal diversification and assumptions integral to various explanations. We reexamine the origin and early diversification of this clade based on a comprehensive time-calibrated, molecular-based phylogenetic analysis and event-based approaches for ancestral range inference of lineages. Our results do not corroborate current phylogenetic classifications of otophysans. We demonstrate Siluriformes are never sister to Gymnotiformes and Characiformes are most likely nonmonophyletic. Divergence time estimates specify a split between Cypriniformes and Characiphysi with the fragmentation of Pangea. The early diversification of characiphysans either predated, or was contemporary with, the separation of Africa and South America, and involved a combination of within- and between-continental divergence events for these lineages. The intercontinental diversification of siluroids and characoids postdated major intercontinental tectonic fragmentations (<90 Mya). Post-tectonic drift dispersal events are hypothesized to account for their current distribution patterns. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Genetic diversification of chemokine CXCL16 and its receptor CXCR6 in primates.

PubMed

Xu, Feifei; He, Dan; Liu, Jiabin; Ni, Qingyong; Lyu, Yongqing; Xiong, Shiqiu; Li, Yan

2018-08-01

Chemokine CXCL16 and its receptor CXCR6 are associated with a series of physiological and pathological processes in cooperative and stand-alone fashions. To shed insight into their versatile nature, we studied genetic variations of CXCL16 and CXCR6 in primates. Evolutionary analyses revealed that these genes underwent a similar evolutionary fate. Both genes experienced adaptive diversification with the phylogenetic division of cercopithecoids (Old World monkeys) and hominoids (humans, great apes, and gibbons) from their common ancestor. In contrast, they were conserved in the periods preceding and following the dividing process. In terms of the adaptive diversification between cercopithecoids and hominoids, the adaptive genetic changes have occurred in the mucin-like and chemokine domains of CXCL16 and the N-terminus and transmembrane helixes of CXCR6. In combination with currently available structural and functional information for CXCL16 and CXCR6, the parallels between the evolutionary footprints and the co-occurrence of adaptive diversification at some evolutionary stage suggest that interplay could exist between the diversification-related amino acid sites, or between the domains on which the identified sites are located, in physiological processes such as chemotaxis and/or cell adhesion. Copyright © 2018 Elsevier Ltd. All rights reserved.

Kenya's Harambee Institutes of Technology.

ERIC Educational Resources Information Center

Kintzer, Frederick C.

1989-01-01

Reviews the history and current status of the Harambee Institutes of Technology in Kenya. Offers a critique of the parallel vocationalized system. Discusses the vocational-technical/general education controversy, diversification among types of schools, financing, and the 8-4-4 Plan. (DMM)

Parallel diversifications of Cremastosperma and Mosannona (Annonaceae), tropical rainforest trees tracking Neogene upheaval of South America

PubMed Central

Maas, Paul J. M.; Melchers-Sharrott, Heleen

2018-01-01

Much of the immense present day biological diversity of Neotropical rainforests originated from the Miocene onwards, a period of geological and ecological upheaval in South America. We assess the impact of the Andean orogeny, drainage of Lake Pebas and closure of the Panama isthmus on two clades of tropical trees (Cremastosperma, ca 31 spp.; and Mosannona, ca 14 spp.; both Annonaceae). Phylogenetic inference revealed similar patterns of geographically restricted clades and molecular dating showed diversifications in the different areas occurred in parallel, with timing consistent with Andean vicariance and Central American geodispersal. Ecological niche modelling approaches show phylogenetically conserved niche differentiation, particularly within Cremastosperma. Niche similarity and recent common ancestry of Amazon and Guianan Mosannona species contrast with dissimilar niches and more distant ancestry of Amazon, Venezuelan and Guianan species of Cremastosperma, suggesting that this element of the similar patterns of disjunct distributions in the two genera is instead a biogeographic parallelism, with differing origins. The results provide further independent evidence for the importance of the Andean orogeny, the drainage of Lake Pebas, and the formation of links between South and Central America in the evolutionary history of Neotropical lowland rainforest trees. PMID:29410860

Parallel diversifications of Cremastosperma and Mosannona (Annonaceae), tropical rainforest trees tracking Neogene upheaval of South America.

PubMed

Pirie, Michael D; Maas, Paul J M; Wilschut, Rutger A; Melchers-Sharrott, Heleen; Chatrou, Lars W

2018-01-01

Much of the immense present day biological diversity of Neotropical rainforests originated from the Miocene onwards, a period of geological and ecological upheaval in South America. We assess the impact of the Andean orogeny, drainage of Lake Pebas and closure of the Panama isthmus on two clades of tropical trees ( Cremastosperma , ca 31 spp.; and Mosannona , ca 14 spp.; both Annonaceae). Phylogenetic inference revealed similar patterns of geographically restricted clades and molecular dating showed diversifications in the different areas occurred in parallel, with timing consistent with Andean vicariance and Central American geodispersal. Ecological niche modelling approaches show phylogenetically conserved niche differentiation, particularly within Cremastosperma . Niche similarity and recent common ancestry of Amazon and Guianan Mosannona species contrast with dissimilar niches and more distant ancestry of Amazon, Venezuelan and Guianan species of Cremastosperma , suggesting that this element of the similar patterns of disjunct distributions in the two genera is instead a biogeographic parallelism, with differing origins. The results provide further independent evidence for the importance of the Andean orogeny, the drainage of Lake Pebas, and the formation of links between South and Central America in the evolutionary history of Neotropical lowland rainforest trees.

Host-driven diversification of gall-inducing Acacia thrips and the aridification of Australia

PubMed Central

McLeish, Michael J; Chapman, Thomas W; Schwarz, Michael P

2007-01-01

Background Insects that feed on plants contribute greatly to the generation of biodiversity. Hypotheses explaining rate increases in phytophagous insect diversification and mechanisms driving speciation in such specialists remain vexing despite considerable attention. The proliferation of plant-feeding insects and their hosts are expected to broadly parallel one another where climate change over geological timescales imposes consequences for the diversification of flora and fauna via habitat modification. This work uses a phylogenetic approach to investigate the premise that the aridification of Australia, and subsequent expansion and modification of arid-adapted host flora, has implications for the diversification of insects that specialise on them. Results Likelihood ratio tests indicated the possibility of hard molecular polytomies within two co-radiating gall-inducing species complexes specialising on the same set of host species. Significant tree asymmetry is indicated at a branch adjacent to an inferred transition to a Plurinerves ancestral host species. Lineage by time diversification plots indicate gall-thrips that specialise on Plurinerves hosts differentially experienced an explosive period of speciation contemporaneous with climatic cycling during the Quaternary period. Chronological analyses indicated that the approximate age of origin of gall-inducing thrips on Acacia might be as recent as 10 million years ago during the Miocene, as truly arid landscapes first developed in Australia. Conclusion Host-plant diversification and spatial heterogeneity of hosts have increased the potential for specialisation, resource partitioning, and unoccupied ecological niche availability for gall-thrips on Australian Acacia. PMID:17257412

Evolution caused by extreme events.

PubMed

Grant, Peter R; Grant, B Rosemary; Huey, Raymond B; Johnson, Marc T J; Knoll, Andrew H; Schmitt, Johanna

2017-06-19

Extreme events can be a major driver of evolutionary change over geological and contemporary timescales. Outstanding examples are evolutionary diversification following mass extinctions caused by extreme volcanism or asteroid impact. The evolution of organisms in contemporary time is typically viewed as a gradual and incremental process that results from genetic change, environmental perturbation or both. However, contemporary environments occasionally experience strong perturbations such as heat waves, floods, hurricanes, droughts and pest outbreaks. These extreme events set up strong selection pressures on organisms, and are small-scale analogues of the dramatic changes documented in the fossil record. Because extreme events are rare, almost by definition, they are difficult to study. So far most attention has been given to their ecological rather than to their evolutionary consequences. We review several case studies of contemporary evolution in response to two types of extreme environmental perturbations, episodic (pulse) or prolonged (press). Evolution is most likely to occur when extreme events alter community composition. We encourage investigators to be prepared for evolutionary change in response to rare events during long-term field studies.This article is part of the themed issue 'Behavioural, ecological and evolutionary responses to extreme climatic events'. © 2017 The Author(s).

Phylogenetic relationships in Epidendroideae (Orchidaceae), one of the great flowering plant radiations: progressive specialization and diversification.

PubMed

Freudenstein, John V; Chase, Mark W

2015-03-01

The largest subfamily of orchids, Epidendroideae, represents one of the most significant diversifications among flowering plants in terms of pollination strategy, vegetative adaptation and number of species. Although many groups in the subfamily have been resolved, significant relationships in the tree remain unclear, limiting conclusions about diversification and creating uncertainty in the classification. This study brings together DNA sequences from nuclear, plastid and mitochrondrial genomes in order to clarify relationships, to test associations of key characters with diversification and to improve the classification. Sequences from seven loci were concatenated in a supermatrix analysis for 312 genera representing most of epidendroid diversity. Maximum-likelihood and parsimony analyses were performed on this matrix and on subsets of the data to generate trees and to investigate the effect of missing values. Statistical character-associated diversification analyses were performed. Likelihood and parsimony analyses yielded highly resolved trees that are in strong agreement and show significant support for many key clades. Many previously proposed relationships among tribes and subtribes are supported, and some new relationships are revealed. Analyses of subsets of the data suggest that the relatively high number of missing data for the full analysis is not problematic. Diversification analyses show that epiphytism is most strongly associated with diversification among epidendroids, followed by expansion into the New World and anther characters that are involved with pollinator specificity, namely early anther inflexion, cellular pollinium stalks and the superposed pollinium arrangement. All tested characters show significant association with speciation in Epidendroideae, suggesting that no single character accounts for the success of this group. Rather, it appears that a succession of key features appeared that have contributed to diversification, sometimes in parallel. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Multiple shifts to different pollinators fuelled rapid diversification in sexually deceptive Ophrys orchids.

PubMed

Breitkopf, Hendrik; Onstein, Renske E; Cafasso, Donata; Schlüter, Philipp M; Cozzolino, Salvatore

2015-07-01

Episodes of rapid speciation provide unique insights into evolutionary processes underlying species radiations and patterns of biodiversity. Here we investigated the radiation of sexually deceptive bee orchids (Ophrys). Based on a time-calibrated phylogeny and by means of ancestral character reconstruction and divergence time estimation, we estimated the tempo and mode of this radiation within a state-dependent evolutionary framework. It appears that, in the Pleistocene, the evolution of Ophrys was marked by episodes of rapid diversification coinciding with shifts to different pollinator types: from wasps to Eucera bees to Andrena and other bees. An abrupt increase in net diversification rate was detected in three clades. Among these, two phylogenetically distant lineages switched from Eucera to Andrena and other bees in a parallel fashion and at about the same time in their evolutionary history. Lack of early radiation associated with the evolution of the key innovation of sexual deception suggests that Ophrys diversification was mainly driven by subsequent ecological opportunities provided by the exploitation of novel pollinator groups, encompassing many bee species slightly differing in their sex pheromone communication systems, and by spatiotemporal fluctuations in the pollinator mosaic. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary

PubMed Central

Liu, Liang; Zhang, Jin; Rheindt, Frank E.; Lei, Fumin; Qu, Yanhua; Wang, Yu; Zhang, Yu; Sullivan, Corwin; Nie, Wenhui; Wang, Jinhuan; Yang, Fengtang; Chen, Jinping; Edwards, Scott V.; Meng, Jin; Wu, Shaoyuan

2017-01-01

The timing of the diversification of placental mammals relative to the Cretaceous–Paleogene (KPg) boundary mass extinction remains highly controversial. In particular, there have been seemingly irreconcilable differences in the dating of the early placental radiation not only between fossil-based and molecular datasets but also among molecular datasets. To help resolve this discrepancy, we performed genome-scale analyses using 4,388 loci from 90 taxa, including representatives of all extant placental orders and transcriptome data from flying lemurs (Dermoptera) and pangolins (Pholidota). Depending on the gene partitioning scheme, molecular clock model, and genic deviation from molecular clock assumptions, extensive sensitivity analyses recovered widely varying diversification scenarios for placental mammals from a given gene set, ranging from a deep Cretaceous origin and diversification to a scenario spanning the KPg boundary, suggesting that the use of suboptimal molecular clock markers and methodologies is a major cause of controversies regarding placental diversification timing. We demonstrate that reconciliation between molecular and paleontological estimates of placental divergence times can be achieved using the appropriate clock model and gene partitioning scheme while accounting for the degree to which individual genes violate molecular clock assumptions. A birth-death-shift analysis suggests that placental mammals underwent a continuous radiation across the KPg boundary without apparent interruption by the mass extinction, paralleling a genus-level radiation of multituberculates and ecomorphological diversification of both multituberculates and therians. These findings suggest that the KPg catastrophe evidently played a limited role in placental diversification, which, instead, was likely a delayed response to the slightly earlier radiation of angiosperms. PMID:28808022

Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary.

PubMed

Liu, Liang; Zhang, Jin; Rheindt, Frank E; Lei, Fumin; Qu, Yanhua; Wang, Yu; Zhang, Yu; Sullivan, Corwin; Nie, Wenhui; Wang, Jinhuan; Yang, Fengtang; Chen, Jinping; Edwards, Scott V; Meng, Jin; Wu, Shaoyuan

2017-08-29

The timing of the diversification of placental mammals relative to the Cretaceous-Paleogene (KPg) boundary mass extinction remains highly controversial. In particular, there have been seemingly irreconcilable differences in the dating of the early placental radiation not only between fossil-based and molecular datasets but also among molecular datasets. To help resolve this discrepancy, we performed genome-scale analyses using 4,388 loci from 90 taxa, including representatives of all extant placental orders and transcriptome data from flying lemurs (Dermoptera) and pangolins (Pholidota). Depending on the gene partitioning scheme, molecular clock model, and genic deviation from molecular clock assumptions, extensive sensitivity analyses recovered widely varying diversification scenarios for placental mammals from a given gene set, ranging from a deep Cretaceous origin and diversification to a scenario spanning the KPg boundary, suggesting that the use of suboptimal molecular clock markers and methodologies is a major cause of controversies regarding placental diversification timing. We demonstrate that reconciliation between molecular and paleontological estimates of placental divergence times can be achieved using the appropriate clock model and gene partitioning scheme while accounting for the degree to which individual genes violate molecular clock assumptions. A birth-death-shift analysis suggests that placental mammals underwent a continuous radiation across the KPg boundary without apparent interruption by the mass extinction, paralleling a genus-level radiation of multituberculates and ecomorphological diversification of both multituberculates and therians. These findings suggest that the KPg catastrophe evidently played a limited role in placental diversification, which, instead, was likely a delayed response to the slightly earlier radiation of angiosperms.

Climate Change: A "Green" Approach to Teaching Contemporary Germany

ERIC Educational Resources Information Center

Melin, Charlotte

2013-01-01

This article describes a newly designed upper division German language course, "Contemporary Germany: Food, Energy Politics," and two sampling methods of assessment for measuring parallel gains in German skills and sustainable development (SD) thinking. Second Language Acquisition (SLA) informed course design, key assignments, and…

Preferential host switching and codivergence shaped radiation of bark beetle symbionts, nematodes of Micoletzkya (Nematoda: Diplogastridae).

PubMed

Susoy, V; Herrmann, M

2014-05-01

Host-symbiont systems are of particular interest to evolutionary biology because they allow testable inferences of diversification processes while also providing both a historical basis and an ecological context for studies of adaptation. Our investigations of bark beetle symbionts, predatory nematodes of the genus Micoletzkya, have revealed remarkable diversity of the group along with a high level of host specificity. Cophylogenetic analyses suggest that evolution of the nematodes was largely influenced by the evolutionary history of beetles. The diversification of the symbionts, however, could not be attributed to parallel divergence alone; our results indicate that adaptive radiation of the nematodes was shaped by preferential host shifts among closely related beetles along with codivergence. Whereas ecological and geographic isolation have played a major role in the diversification of Micoletzkya at shallow phylogenetic depths, adaptations towards related hosts have played a role in shaping cophylogenetic structure at a larger evolutionary scale. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Computability, Gödel's incompleteness theorem, and an inherent limit on the predictability of evolution

PubMed Central

Day, Troy

2012-01-01

The process of evolutionary diversification unfolds in a vast genotypic space of potential outcomes. During the past century, there have been remarkable advances in the development of theory for this diversification, and the theory's success rests, in part, on the scope of its applicability. A great deal of this theory focuses on a relatively small subset of the space of potential genotypes, chosen largely based on historical or contemporary patterns, and then predicts the evolutionary dynamics within this pre-defined set. To what extent can such an approach be pushed to a broader perspective that accounts for the potential open-endedness of evolutionary diversification? There have been a number of significant theoretical developments along these lines but the question of how far such theory can be pushed has not been addressed. Here a theorem is proven demonstrating that, because of the digital nature of inheritance, there are inherent limits on the kinds of questions that can be answered using such an approach. In particular, even in extremely simple evolutionary systems, a complete theory accounting for the potential open-endedness of evolution is unattainable unless evolution is progressive. The theorem is closely related to Gödel's incompleteness theorem, and to the halting problem from computability theory. PMID:21849390

Parallel evolution of a type IV secretion system in radiating lineages of the host-restricted bacterial pathogen Bartonella.

PubMed

Engel, Philipp; Salzburger, Walter; Liesch, Marius; Chang, Chao-Chin; Maruyama, Soichi; Lanz, Christa; Calteau, Alexandra; Lajus, Aurélie; Médigue, Claudine; Schuster, Stephan C; Dehio, Christoph

2011-02-10

Adaptive radiation is the rapid origination of multiple species from a single ancestor as the result of concurrent adaptation to disparate environments. This fundamental evolutionary process is considered to be responsible for the genesis of a great portion of the diversity of life. Bacteria have evolved enormous biological diversity by exploiting an exceptional range of environments, yet diversification of bacteria via adaptive radiation has been documented in a few cases only and the underlying molecular mechanisms are largely unknown. Here we show a compelling example of adaptive radiation in pathogenic bacteria and reveal their genetic basis. Our evolutionary genomic analyses of the α-proteobacterial genus Bartonella uncover two parallel adaptive radiations within these host-restricted mammalian pathogens. We identify a horizontally-acquired protein secretion system, which has evolved to target specific bacterial effector proteins into host cells as the evolutionary key innovation triggering these parallel adaptive radiations. We show that the functional versatility and adaptive potential of the VirB type IV secretion system (T4SS), and thereby translocated Bartonella effector proteins (Beps), evolved in parallel in the two lineages prior to their radiations. Independent chromosomal fixation of the virB operon and consecutive rounds of lineage-specific bep gene duplications followed by their functional diversification characterize these parallel evolutionary trajectories. Whereas most Beps maintained their ancestral domain constitution, strikingly, a novel type of effector protein emerged convergently in both lineages. This resulted in similar arrays of host cell-targeted effector proteins in the two lineages of Bartonella as the basis of their independent radiation. The parallel molecular evolution of the VirB/Bep system displays a striking example of a key innovation involved in independent adaptive processes and the emergence of bacterial pathogens. Furthermore, our study highlights the remarkable evolvability of T4SSs and their effector proteins, explaining their broad application in bacterial interactions with the environment.

Parallel Evolution of a Type IV Secretion System in Radiating Lineages of the Host-Restricted Bacterial Pathogen Bartonella

PubMed Central

Engel, Philipp; Salzburger, Walter; Liesch, Marius; Chang, Chao-Chin; Maruyama, Soichi; Lanz, Christa; Calteau, Alexandra; Lajus, Aurélie; Médigue, Claudine; Schuster, Stephan C.; Dehio, Christoph

2011-01-01

Adaptive radiation is the rapid origination of multiple species from a single ancestor as the result of concurrent adaptation to disparate environments. This fundamental evolutionary process is considered to be responsible for the genesis of a great portion of the diversity of life. Bacteria have evolved enormous biological diversity by exploiting an exceptional range of environments, yet diversification of bacteria via adaptive radiation has been documented in a few cases only and the underlying molecular mechanisms are largely unknown. Here we show a compelling example of adaptive radiation in pathogenic bacteria and reveal their genetic basis. Our evolutionary genomic analyses of the α-proteobacterial genus Bartonella uncover two parallel adaptive radiations within these host-restricted mammalian pathogens. We identify a horizontally-acquired protein secretion system, which has evolved to target specific bacterial effector proteins into host cells as the evolutionary key innovation triggering these parallel adaptive radiations. We show that the functional versatility and adaptive potential of the VirB type IV secretion system (T4SS), and thereby translocated Bartonella effector proteins (Beps), evolved in parallel in the two lineages prior to their radiations. Independent chromosomal fixation of the virB operon and consecutive rounds of lineage-specific bep gene duplications followed by their functional diversification characterize these parallel evolutionary trajectories. Whereas most Beps maintained their ancestral domain constitution, strikingly, a novel type of effector protein emerged convergently in both lineages. This resulted in similar arrays of host cell-targeted effector proteins in the two lineages of Bartonella as the basis of their independent radiation. The parallel molecular evolution of the VirB/Bep system displays a striking example of a key innovation involved in independent adaptive processes and the emergence of bacterial pathogens. Furthermore, our study highlights the remarkable evolvability of T4SSs and their effector proteins, explaining their broad application in bacterial interactions with the environment. PMID:21347280

Origin, adaptive radiation and diversification of the Hawaiian lobeliads (Asterales: Campanulaceae)

PubMed Central

Givnish, Thomas J.; Millam, Kendra C.; Mast, Austin R.; Paterson, Thomas B.; Theim, Terra J.; Hipp, Andrew L.; Henss, Jillian M.; Smith, James F.; Wood, Kenneth R.; Sytsma, Kenneth J.

2008-01-01

The endemic Hawaiian lobeliads are exceptionally species rich and exhibit striking diversity in habitat, growth form, pollination biology and seed dispersal, but their origins and pattern of diversification remain shrouded in mystery. Up to five independent colonizations have been proposed based on morphological differences among extant taxa. We present a molecular phylogeny showing that the Hawaiian lobeliads are the product of one immigration event; that they are the largest plant clade on any single oceanic island or archipelago; that their ancestor arrived roughly 13 Myr ago; and that this ancestor was most likely woody, wind-dispersed, bird-pollinated, and adapted to open habitats at mid-elevations. Invasion of closed tropical forests is associated with evolution of fleshy fruits. Limited dispersal of such fruits in wet-forest understoreys appears to have accelerated speciation and led to a series of parallel adaptive radiations in Cyanea, with most species restricted to single islands. Consistency of Cyanea diversity across all tall islands except Hawai `i suggests that diversification of Cyanea saturates in less than 1.5 Myr. Lobeliad diversity appears to reflect a hierarchical adaptive radiation in habitat, then elevation and flower-tube length, and provides important insights into the pattern and tempo of diversification in a species-rich clade of tropical plants. PMID:18854299

Side effects of problem-solving strategies in large-scale nutrition science: towards a diversification of health.

PubMed

Penders, Bart; Vos, Rein; Horstman, Klasien

2009-11-01

Solving complex problems in large-scale research programmes requires cooperation and division of labour. Simultaneously, large-scale problem solving also gives rise to unintended side effects. Based upon 5 years of researching two large-scale nutrigenomic research programmes, we argue that problems are fragmented in order to be solved. These sub-problems are given priority for practical reasons and in the process of solving them, various changes are introduced in each sub-problem. Combined with additional diversity as a result of interdisciplinarity, this makes reassembling the original and overall goal of the research programme less likely. In the case of nutrigenomics and health, this produces a diversification of health. As a result, the public health goal of contemporary nutrition science is not reached in the large-scale research programmes we studied. Large-scale research programmes are very successful in producing scientific publications and new knowledge; however, in reaching their political goals they often are less successful.

Long-term effects of inducible mutagenic DNA repair on relative fitness and phenotypic diversification in Pseudomonas cichorii 302959.

PubMed

Weigand, Michael R; Sundin, George W

2009-01-01

Mutagenic DNA repair (MDR) employs low-fidelity DNA polymerases capable of replicating past DNA lesions resulting from exposure to high-energy ultraviolet radiation (UVR). MDR confers UVR tolerance and activation initiates a transient mutator phenotype that may provide opportunities for adaptation. To investigate the potential role of MDR in adaptation, we have propagated parallel lineages of the highly mutable epiphytic plant pathogen Pseudomonas cichorii 302959 with daily UVR activation (UVR lineages) for approximately 500 generations. Here we examine those lineages through the measurement of relative fitness and observation of distinct colony morphotypes that emerged. Isolates and population samples from UVR lineages displayed gains in fitness relative to the ancestor despite increased rates of inducible mutation to rifampicin resistance. Regular activation of MDR resulted in the maintenance of genetic diversity within UVR lineages, including the reproducible diversification and coexistence of "round" and "fuzzy" colony morphotypes. These results suggest that inducible mutability may present a reasonable strategy for adaptive evolution in stressful environments by contributing to gains in relative fitness and diversification.

Evolutionary bursts in Euphorbia (Euphorbiaceae) are linked with photosynthetic pathway.

PubMed

Horn, James W; Xi, Zhenxiang; Riina, Ricarda; Peirson, Jess A; Yang, Ya; Dorsey, Brian L; Berry, Paul E; Davis, Charles C; Wurdack, Kenneth J

2014-12-01

The mid-Cenozoic decline of atmospheric CO2 levels that promoted global climate change was critical to shaping contemporary arid ecosystems. Within angiosperms, two CO2 -concentrating mechanisms (CCMs)-crassulacean acid metabolism (CAM) and C4 -evolved from the C3 photosynthetic pathway, enabling more efficient whole-plant function in such environments. Many angiosperm clades with CCMs are thought to have diversified rapidly due to Miocene aridification, but links between this climate change, CCM evolution, and increased net diversification rates (r) remain to be further understood. Euphorbia (∼2000 species) includes a diversity of CAM-using stem succulents, plus a single species-rich C4 subclade. We used ancestral state reconstructions with a dated molecular phylogeny to reveal that CCMs independently evolved 17-22 times in Euphorbia, principally from the Miocene onwards. Analyses assessing among-lineage variation in r identified eight Euphorbia subclades with significantly increased r, six of which have a close temporal relationship with a lineage-corresponding CCM origin. Our trait-dependent diversification analysis indicated that r of Euphorbia CCM lineages is approximately threefold greater than C3 lineages. Overall, these results suggest that CCM evolution in Euphorbia was likely an adaptive strategy that enabled the occupation of increased arid niche space accompanying Miocene expansion of arid ecosystems. These opportunities evidently facilitated recent, replicated bursts of diversification in Euphorbia. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

The anatomy of a 'suture zone' in Amazonian butterflies: a coalescent-based test for vicariant geographic divergence and speciation.

PubMed

Dasmahapatra, Kanchon K; Lamas, Gerardo; Simpson, Fraser; Mallet, James

2010-10-01

Attempts by biogeographers to understand biotic diversification in the Amazon have often employed contemporary species distribution patterns to support particular theories, such as Pleistocene rainforest refugia, rather than to test among alternative hypotheses. Suture zones, narrow regions where multiple contact zones and hybrid zones between taxa cluster, have been seen as evidence for past expansion of whole biotas that have undergone allopatric divergence in vicariant refuges. We used coalescent analysis of mutilocus sequence data to examine population split times in 22 pairs of geminate taxa in ithomiine and heliconiine butterflies. We test a hypothesis of simultaneous divergence across a suture zone in NE Peru. Our results reveal a scattered time course of diversification in this suture zone, rather than a tight cluster of split times. Additionally, we find rapid diversification within some lineages such as Melinaea contrasting with older divergence within lineages such as the Oleriina (Hyposcada and Oleria). These results strongly reject simple vicariance as a cause of the suture zone. At the same time, observed lineage effects are incompatible with a series of geographically coincident vicariant events which should affect all lineages similarly. Our results suggest that Pleistocene climatic forcing cannot readily explain this Peruvian suture zone. Lineage-specific biological traits, such as characteristic distances of gene flow or varying rates of parapatric divergence, may be of greater importance. © 2010 Blackwell Publishing Ltd.

Structure versus time in the evolutionary diversification of avian carotenoid metabolic networks.

PubMed

Morrison, Erin S; Badyaev, Alexander V

2018-05-01

Historical associations of genes and proteins are thought to delineate pathways available to subsequent evolution; however, the effects of past functional involvements on contemporary evolution are rarely quantified. Here, we examined the extent to which the structure of a carotenoid enzymatic network persists in avian evolution. Specifically, we tested whether the evolution of carotenoid networks was most concordant with phylogenetically structured expansion from core reactions of common ancestors or with subsampling of biochemical pathway modules from an ancestral network. We compared structural and historical associations in 467 carotenoid networks of extant and ancestral species and uncovered the overwhelming effect of pre-existing metabolic network structure on carotenoid diversification over the last 50 million years of avian evolution. Over evolutionary time, birds repeatedly subsampled and recombined conserved biochemical modules, which likely maintained the overall structure of the carotenoid metabolic network during avian evolution. These findings explain the recurrent convergence of evolutionary distant species in carotenoid metabolism and weak phylogenetic signal in avian carotenoid evolution. Remarkable retention of an ancient metabolic structure throughout extensive and prolonged ecological diversification in avian carotenoid metabolism illustrates a fundamental requirement of organismal evolution - historical continuity of a deterministic network that links past and present functional associations of its components. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

Communication overhead on the Intel Paragon, IBM SP2 and Meiko CS-2

NASA Technical Reports Server (NTRS)

Bokhari, Shahid H.

1995-01-01

Interprocessor communication overhead is a crucial measure of the power of parallel computing systems-its impact can severely limit the performance of parallel programs. This report presents measurements of communication overhead on three contemporary commercial multicomputer systems: the Intel Paragon, the IBM SP2 and the Meiko CS-2. In each case the time to communicate between processors is presented as a function of message length. The time for global synchronization and memory access is discussed. The performance of these machines in emulating hypercubes and executing random pairwise exchanges is also investigated. It is shown that the interprocessor communication time depends heavily on the specific communication pattern required. These observations contradict the commonly held belief that communication overhead on contemporary machines is independent of the placement of tasks on processors. The information presented in this report permits the evaluation of the efficiency of parallel algorithm implementations against standard baselines.

Old diseases and contemporary crisis. Inherited blood disorders in the Sultanate of Oman.

PubMed

Beaudevin, Claire

2013-01-01

This contribution draws on ethnographic research conducted in Oman on inherited blood disorders (IBD). By interpreting results from population genomics studies that trace mutation processes over centuries of human activities, lay-representations of IBD often consider them historical evidence. The perceived spread of IBD in Oman may thus provide unusual historical depth in a country where past conflicts have been erased from historiography and representations of time are politically prescribed. Through the notions of crisis and diversification, this contribution shows how IBD's chronicity challenges the healthcare system and became a national issue, politically labelled as urgent. The paper casts light on several aspects of contemporary Omani society: it first addresses the dynamics of disease taxonomies - although biomedically described in the early twentieth century, IBD were not individualized within local nosologies until the 1970s. Secondly, it shows how biomedical knowledge about IBD led to diversification within the healthcare system, through the introduction of clinical genetics, genomics, and community genetics. Thirdly, it attempts to broach modalities of the biopower exerted by the Omani regime over its citizens: IBD are targeted by various public health measures that jeopardize patients' autonomy by aiming to control their bodies through their matrimonial behaviour. In addition, two aspects of the intersections between Omani social hierarchy and IBD are noteworthy: the creation of a patients' association that constitutes a potential disturbance of the social order; and the way IBD mutations traced by genomics are considered direct historical documents that challenge representations of the recently crafted 'Omanity' in a context of regional concern regarding national identities' durability.

Postfire response and genetic diversity in Erica coccinea: connecting population dynamics and diversification in a biodiversity hotspot.

PubMed

Segarra-Moragues, José Gabriel; Ojeda, Fernando

2010-12-01

Understanding the processes of biological diversification is a central topic in evolutionary biology. The South African Cape fynbos, one of the major plant biodiversity hotspots out of the tropics, has prompted several hypotheses about the causes of generation and maintenance of biodiversity. Fire has been traditionally invoked as a key element to explain high levels of biodiversity in highly speciose fynbos taxa, such as the genus Erica. In this study, we have implemented a microevolutionary approach to elucidate how plant-response to fire may contribute to explain high levels of diversification in Erica. By using microsatellite markers, we investigated the genetic background of seeder (fire-sensitive) and resprouter (fire-resistant) populations of the fynbos species Erica coccinea. We found higher within-population genetic diversity and higher among-population differentiation in seeder populations and interpreted these higher levels of genetic diversification as a consequence of the comparatively shorter generation times and faster population turnover in the seeder form of this species. Considering that genetic divergence among populations may be seen as the initial step to speciation, the parallelism between these results and the pattern of biodiversity at the genus level offers stimulating insights into understanding causes of speciation of the genus Erica in the Cape fynbos. © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.

The reanalysis of biogeography of the Asian tree frog, Rhacophorus (Anura: Rhacophoridae): geographic shifts and climatic change influenced the dispersal process and diversification

PubMed Central

Wang, Hui; Wu, Jun; Kang, Xing; Qian, Lifu; Chen, Jinyun; Rao, Dingqi; Jiang, Jianping

2017-01-01

Rapid uplifts of the Tibetan Plateau and climate change in Asia are thought to have profoundly modulated the diversification of most of the species distributed throughout Asia. The ranoid tree frog genus Rhacophorus, the largest genus in the Rhacophoridae, is widely distributed in Asia and especially speciose in the areas south and east of the Tibetan Plateau. Here, we infer phylogenetic relationships among species and estimate divergence times, asking whether the spatiotemporal characteristics of diversification within Rhacophorus were related to rapid uplifts of the Tibetan Plateau and concomitant climate change. Phylogenetic analysis recovered distinct lineage structures in Rhacophorus, which indicated a clear distribution pattern from Southeast Asia toward East Asia and India. Molecular dating suggests that the first split within the genus date back to the Middle Oligocene (approx. 30 Ma). The Rhacophorus lineage through time (LTT) showed that there were periods of increased speciation rate: 14–12 Ma and 10–4 Ma. In addition, ancestral area reconstructions supported Southeast Asia as the ancestral area of Rhacophorus. According to the results of molecular dating, ancestral area reconstructions and LTT we think the geographic shifts, the staged rapid rises of the Tibetan Plateau with parallel climatic changes and reinforcement of the Asian monsoons (15 Ma, 8 Ma and 4–3 Ma), possibly prompted a burst of diversification in Rhacophorus. PMID:29177111

Historical factors shaped species diversity and composition of Salix in eastern Asia.

PubMed

Wang, Qinggang; Su, Xiangyan; Shrestha, Nawal; Liu, Yunpeng; Wang, Siyang; Xu, Xiaoting; Wang, Zhiheng

2017-02-08

Ambient energy, niche conservatism, historical climate stability and habitat heterogeneity hypothesis have been proposed to explain the broad-scale species diversity patterns and species compositions, while their relative importance have been controversial. Here, we assessed the relative contributions of contemporary climate, historical climate changes and habitat heterogeneity in shaping Salix species diversity and species composition in whole eastern Asia as well as mountains and lowlands using linear regressions and distance-based redundancy analyses, respectively. Salix diversity was negatively related with mean annual temperature. Habitat heterogeneity was more important than contemporary climate in shaping Salix diversity patterns, and their relative contributions were different in mountains and lowlands. In contrast, the species composition was strongly influenced by contemporary climate and historical climate change than habitat heterogeneity, and their relative contributions were nearly the same both in mountains and lowlands. Our findings supported niche conservatism and habitat heterogeneity hypotheses, but did not support ambient energy and historical climate stability hypotheses. The diversity pattern and species composition of Salix could not be well-explained by any single hypothesis tested, suggesting that other factors such as disturbance history and diversification rate may be also important in shaping the diversity pattern and composition of Salix species.

Historical factors shaped species diversity and composition of Salix in eastern Asia

PubMed Central

Wang, Qinggang; Su, Xiangyan; Shrestha, Nawal; Liu, Yunpeng; Wang, Siyang; Xu, Xiaoting; Wang, Zhiheng

2017-01-01

Ambient energy, niche conservatism, historical climate stability and habitat heterogeneity hypothesis have been proposed to explain the broad-scale species diversity patterns and species compositions, while their relative importance have been controversial. Here, we assessed the relative contributions of contemporary climate, historical climate changes and habitat heterogeneity in shaping Salix species diversity and species composition in whole eastern Asia as well as mountains and lowlands using linear regressions and distance-based redundancy analyses, respectively. Salix diversity was negatively related with mean annual temperature. Habitat heterogeneity was more important than contemporary climate in shaping Salix diversity patterns, and their relative contributions were different in mountains and lowlands. In contrast, the species composition was strongly influenced by contemporary climate and historical climate change than habitat heterogeneity, and their relative contributions were nearly the same both in mountains and lowlands. Our findings supported niche conservatism and habitat heterogeneity hypotheses, but did not support ambient energy and historical climate stability hypotheses. The diversity pattern and species composition of Salix could not be well-explained by any single hypothesis tested, suggesting that other factors such as disturbance history and diversification rate may be also important in shaping the diversity pattern and composition of Salix species. PMID:28176816

The genetic architecture of novel trophic specialists: larger effect sizes are associated with exceptional oral jaw diversification in a pupfish adaptive radiation.

PubMed

Martin, Christopher H; Erickson, Priscilla A; Miller, Craig T

2017-01-01

The genetic architecture of adaptation is fundamental to understanding the mechanisms and constraints governing diversification. However, most case studies focus on loss of complex traits or parallel speciation in similar environments. It is still unclear how the genetic architecture of these local adaptive processes compares to the architecture of evolutionary transitions contributing to morphological and ecological novelty. Here, we identify quantitative trait loci (QTL) between two trophic specialists in an excellent case study for examining the origins of ecological novelty: a sympatric radiation of pupfishes endemic to San Salvador Island, Bahamas, containing a large-jawed scale-eater and a short-jawed molluscivore with a skeletal nasal protrusion. These specialized niches and trophic traits are unique among over 2000 related species. Measurements of the fitness landscape on San Salvador demonstrate multiple fitness peaks and a larger fitness valley isolating the scale-eater from the putative ancestral intermediate phenotype of the generalist, suggesting that more large-effect QTL should contribute to its unique phenotype. We evaluated this prediction using an F2 intercross between these specialists. We present the first linkage map for pupfishes and detect significant QTL for sex and eight skeletal traits. Large-effect QTL contributed more to enlarged scale-eater jaws than the molluscivore nasal protrusion, consistent with predictions from the adaptive landscape. The microevolutionary genetic architecture of large-effect QTL for oral jaws parallels the exceptional diversification rates of oral jaws within the San Salvador radiation observed over macroevolutionary timescales and may have facilitated exceptional trophic novelty in this system. © 2016 John Wiley & Sons Ltd.

Design, Sustainable Synthesis, and Programmed Reactions of Templated N-Heteroaryl-Fused Vinyl Sultams.

PubMed

Laha, Joydev K; Sharma, Shubhra; Kirar, Seema; Banerjee, Uttam C

2017-09-15

A de novo design and synthesis of N-heteroaryl-fused vinyl sultams as templates for programming chemical reactions on vinyl sultam periphery or (hetero)aryl ring is described. The key features include rational designing and sustainable synthesis of the template, customized reactions of vinyl sultams at C═C bond or involving N-S bond cleavage, and reactions on the periphery of the heteroaryl ring for late-stage diversification. The simple, easy access to the template coupled with opportunities for the synthesis of diversely functionalized heterocyles from a single template constitutes a rare study in contemporary organic synthesis.

Reduce, reuse, and recycle: developmental evolution of trait diversification.

PubMed

Preston, Jill C; Hileman, Lena C; Cubas, Pilar

2011-03-01

A major focus of evolutionary developmental (evo-devo) studies is to determine the genetic basis of variation in organismal form and function, both of which are fundamental to biological diversification. Pioneering work on metazoan and flowering plant systems has revealed conserved sets of genes that underlie the bauplan of organisms derived from a common ancestor. However, the extent to which variation in the developmental genetic toolkit mirrors variation at the phenotypic level is an active area of research. Here we explore evidence from the angiosperm evo-devo literature supporting the frugal use of genes and genetic pathways in the evolution of developmental patterning. In particular, these examples highlight the importance of genetic pleiotropy in different developmental modules, thus reducing the number of genes required in growth and development, and the reuse of particular genes in the parallel evolution of ecologically important traits.

Converging evolution leads to near maximal junction diversity through parallel mechanisms in B and T cell receptors

NASA Astrophysics Data System (ADS)

Benichou, Jennifer I. C.; van Heijst, Jeroen W. J.; Glanville, Jacob; Louzoun, Yoram

2017-08-01

T and B cell receptor (TCR and BCR) complementarity determining region 3 (CDR3) genetic diversity is produced through multiple diversification and selection stages. Potential holes in the CDR3 repertoire were argued to be linked to immunodeficiencies and diseases. In contrast with BCRs, TCRs have practically no Dβ germline genetic diversity, and the question emerges as to whether they can produce a diverse CDR3 repertoire. In order to address the genetic diversity of the adaptive immune system, appropriate quantitative measures for diversity and large-scale sequencing are required. Such a diversity method should incorporate the complex diversification mechanisms of the adaptive immune response and the BCR and TCR loci structure. We combined large-scale sequencing and diversity measures to show that TCRs have a near maximal CDR3 genetic diversity. Specifically, TCR have a larger junctional and V germline diversity, which starts more 5‧ in Vβ than BCRs. Selection decreases the TCR repertoire diversity, but does not affect BCR repertoire. As a result, TCR is as diverse as BCR repertoire, with a biased CDR3 length toward short TCRs and long BCRs. These differences suggest parallel converging evolutionary tracks to reach the required diversity to avoid holes in the CDR3 repertoire.

The Role of microRNAs in the Repeated Parallel Diversification of Lineages of Midas Cichlid Fish from Nicaragua

PubMed Central

Franchini, Paolo; Xiong, Peiwen; Fruciano, Carmelo; Meyer, Axel

2016-01-01

Cichlid fishes are an ideal model system for studying biological diversification because they provide textbook examples of rapid speciation. To date, there has been little focus on the role of gene regulation during cichlid speciation. However, in recent years, gene regulation has been recognized as a powerful force linking diversification in gene function to speciation. Here, we investigated the potential role of miRNA regulation in the diversification of six cichlid species of the Midas cichlid lineage (Amphilophus spp.) inhabiting the Nicaraguan crater lakes. Using several genomic resources, we inferred 236 Midas miRNA genes that were used to predict the miRNA target sites on 8,232 Midas 3′-UTRs. Using population genomic calculations of SNP diversity, we found the miRNA genes to be more conserved than protein coding genes. In contrast to what has been observed in other cichlid fish, but similar to what has been typically found in other groups, we observed genomic signatures of purifying selection on the miRNA targets by comparing these sites with the less conserved nontarget portion of the 3′-UTRs. However, in one species pair that has putatively speciated sympatrically in crater Lake Apoyo, we recovered a different pattern of relaxed purifying selection and high genetic divergence at miRNA targets. Our results suggest that sequence evolution at miRNA binding sites could be a critical genomic mechanism contributing to the rapid phenotypic evolution of Midas cichlids. PMID:27189980

A Phylogeographic Assessment of the Malagasy Giant Chameleons (Furcifer verrucosus and Furcifer oustaleti)

PubMed Central

Raxworthy, Christopher J.

2016-01-01

The Malagasy giant chameleons (Furcifer oustaleti and Furcifer verrucosus) are sister species that are both broadly distributed in Madagascar, and also endemic to the island. These species are also morphologically similar and, because of this, have been frequently misidentified in the field. Previous studies have suggested that cryptic species are nested within this chameleon group, and two subspecies have been described in F. verrucosus. In this study, we utilized a phylogeographic approach to assess genetic diversification within these chameleons. This was accomplished by (1) identifying clades within each species supported by both mitochondrial and nuclear DNA, (2) assessing divergence times between clades, and (3) testing for niche divergence or conservatism. We found that both F. oustaleti and F. verrucosus could be readily identified based on genetic data, and within each species, there are two well-supported clades. However, divergence times are not contemporary and spatial patterns are not congruent. Diversification within F. verrucosus occurred during the Plio-Pleistocene, and there is evidence for niche divergence between a southwestern and southeastern clade, in a region of Madagascar that shows no obvious landscape barriers to dispersal. Diversification in F. oustaleti occurred earlier in the Pliocene or Miocene, and niche conservatism is supported with two genetically distinct clades separated at the Sofia River in northwestern Madagascar. Divergence within F. verrucosus is most consistent with patterns expected from ecologically mediated speciation, whereas divergence in F. oustaleti most strongly matches the patterns expected from the riverine barrier hypothesis. PMID:27257819

Ethical Issues Revisited.

ERIC Educational Resources Information Center

Wolfensberger, Wolf; And Others

1981-01-01

The author reviews the program of extermination of handicapped and mentally retarded persons in Nazi Germany during World War II and suggests possible parallels with contemporary developments such as euthanasia. (Author)

The Role of microRNAs in the Repeated Parallel Diversification of Lineages of Midas Cichlid Fish from Nicaragua.

PubMed

Franchini, Paolo; Xiong, Peiwen; Fruciano, Carmelo; Meyer, Axel

2016-06-03

Cichlid fishes are an ideal model system for studying biological diversification because they provide textbook examples of rapid speciation. To date, there has been little focus on the role of gene regulation during cichlid speciation. However, in recent years, gene regulation has been recognized as a powerful force linking diversification in gene function to speciation. Here, we investigated the potential role of miRNA regulation in the diversification of six cichlid species of the Midas cichlid lineage (Amphilophus spp.) inhabiting the Nicaraguan crater lakes. Using several genomic resources, we inferred 236 Midas miRNA genes that were used to predict the miRNA target sites on 8,232 Midas 3'-UTRs. Using population genomic calculations of SNP diversity, we found the miRNA genes to be more conserved than protein coding genes. In contrast to what has been observed in other cichlid fish, but similar to what has been typically found in other groups, we observed genomic signatures of purifying selection on the miRNA targets by comparing these sites with the less conserved nontarget portion of the 3'-UTRs. However, in one species pair that has putatively speciated sympatrically in crater Lake Apoyo, we recovered a different pattern of relaxed purifying selection and high genetic divergence at miRNA targets. Our results suggest that sequence evolution at miRNA binding sites could be a critical genomic mechanism contributing to the rapid phenotypic evolution of Midas cichlids. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Getting there and around: Host range oscillations during colonization of the Canary Islands by the parasitic nematode Spauligodon.

PubMed

Jorge, Fátima; Perera, Ana; Poulin, Robert; Roca, Vicente; Carretero, Miguel A

2018-01-01

Episodes of expansion and isolation in geographic range over space and time, during which parasites have the opportunity to expand their host range, are linked to the development of host-parasite mosaic assemblages and parasite diversification. In this study, we investigated whether island colonization events lead to host range oscillations in a taxon of host-specific parasitic nematodes of the genus Spauligodon in the Canary Islands. We further investigated whether range oscillations also resulted in shifts in host breadth (i.e., specialization), as expected for parasites on islands. Parasite phylogeny and divergence time estimates were inferred from molecular data with Bayesian methods. Host divergence times were set as calibration priors after a priori evaluation with a global-fit method of which individual host-parasite associations likely represent cospeciation links. Parasite colonization history was reconstructed, followed by an estimation of oscillation events and specificity level. The results indicate the presence of four Spauligodon clades in the Canary Islands, which originated from at least three different colonization events. We found evidence of host range oscillations to truly novel hosts, which in one case led to higher diversification. Contemporary host-parasite associations show strong host specificity, suggesting that changes in host breadth were limited to the shift period. Lineages with more frequent and wider taxonomic host range oscillations prior to the initial colonization event showed wider range oscillations during colonization and diversification within the archipelago. Our results suggest that a lineage's evolutionary past may be the best indicator of a parasite's potential for future range expansions. © 2017 John Wiley & Sons Ltd.

Local variation and parallel evolution: morphological and genetic diversity across a species complex of neotropical crater lake cichlid fishes

PubMed Central

Elmer, Kathryn R.; Kusche, Henrik; Lehtonen, Topi K.; Meyer, Axel

2010-01-01

The polychromatic and trophically polymorphic Midas cichlid fish species complex (Amphilophus cf. citrinellus) is an excellent model system for studying the mechanisms of speciation and patterns of phenotypic diversification in allopatry and in sympatry. Here, we first review research to date on the species complex and the geological history of its habitat. We analyse body shape variation from all currently described species in the complex, sampled from six crater lakes (maximally 1.2–23.9 kyr old) and both great lakes in Nicaragua. We find that Midas cichlid populations in each lake have their own characteristic body shape. In lakes with multiple sympatric species of Midas cichlid, each species has a distinct body shape. Across the species complex, most body shape change relates to body depth, head, snout and mouth shape and caudal peduncle length. There is independent parallel evolution of an elongate limnetic species in at least two crater lakes. Mitochondrial genetic diversity is higher in crater lakes with multiple species. Midas cichlid species richness increases with the size and age of the crater lakes, though no such relationship exists for the other syntopic fishes. We suggest that crater lake Midas cichlids follow the predicted pattern of an adaptive radiation, with early divergence of each crater lake colonization, followed by intralacustrine diversification and speciation by ecological adaptation and sexual selection. PMID:20439280

Drivers of Cape Verde archipelagic endemism in keyhole limpets.

PubMed

Cunha, Regina L; Assis, Jorge M; Madeira, Celine; Seabra, Rui; Lima, Fernando P; Lopes, Evandro P; Williams, Suzanne T; Castilho, Rita

2017-02-02

Oceanic archipelagos are the ideal setting for investigating processes that shape species assemblages. Focusing on keyhole limpets, genera Fissurella and Diodora from Cape Verde Islands, we used an integrative approach combining molecular phylogenetics with ocean transport simulations to infer species distribution patterns and analyse connectivity. Dispersal simulations, using pelagic larval duration and ocean currents as proxies, showed a reduced level of connectivity despite short distances between some of the islands. It is suggested that dispersal and persistence driven by patterns of oceanic circulation favouring self-recruitment played a primary role in explaining contemporary species distributions. Mitochondrial and nuclear data revealed the existence of eight Cape Verde endemic lineages, seven within Fissurella, distributed across the archipelago, and one within Diodora restricted to Boavista. The estimated origins for endemic Fissurella and Diodora were 10.2 and 6.7 MY, respectively. Between 9.5 and 4.5 MY, an intense period of volcanism in Boavista might have affected Diodora, preventing its diversification. Having originated earlier, Fissurella might have had more opportunities to disperse to other islands and speciate before those events. Bayesian analyses showed increased diversification rates in Fissurella possibly promoted by low sea levels during Plio-Pleistocene, which further explain differences in species richness between both genera.

Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion.

PubMed

Hadfield, James; Harris, Simon R; Seth-Smith, Helena M B; Parmar, Surendra; Andersson, Patiyan; Giffard, Philip M; Schachter, Julius; Moncada, Jeanne; Ellison, Louise; Vaulet, María Lucía Gallo; Fermepin, Marcelo Rodríguez; Radebe, Frans; Mendoza, Suyapa; Ouburg, Sander; Morré, Servaas A; Sachse, Konrad; Puolakkainen, Mirja; Korhonen, Suvi J; Sonnex, Chris; Wiggins, Rebecca; Jalal, Hamid; Brunelli, Tamara; Casprini, Patrizia; Pitt, Rachel; Ison, Cathy; Savicheva, Alevtina; Shipitsyna, Elena; Hadad, Ronza; Kari, Laszlo; Burton, Matthew J; Mabey, David; Solomon, Anthony W; Lewis, David; Marsh, Peter; Unemo, Magnus; Clarke, Ian N; Parkhill, Julian; Thomson, Nicholas R

2017-07-01

Chlamydia trachomatis is the world's most prevalent bacterial sexually transmitted infection and leading infectious cause of blindness, yet it is one of the least understood human pathogens, in part due to the difficulties of in vitro culturing and the lack of available tools for genetic manipulation. Genome sequencing has reinvigorated this field, shedding light on the contemporary history of this pathogen. Here, we analyze 563 full genomes, 455 of which are novel, to show that the history of the species comprises two phases, and conclude that the currently circulating lineages are the result of evolution in different genomic ecotypes. Temporal analysis indicates these lineages have recently expanded in the space of thousands of years, rather than the millions of years as previously thought, a finding that dramatically changes our understanding of this pathogen's history. Finally, at a time when almost every pathogen is becoming increasingly resistant to antimicrobials, we show that there is no evidence of circulating genomic resistance in C. trachomatis . © 2017 Hadfield et al.; Published by Cold Spring Harbor Laboratory Press.

Top hits in contemporary JAZ: New information on jasmonate signaling

PubMed Central

Chung, Hoo Sun; Niu, Yajie; Browse, John; Howe, Gregg A.

2012-01-01

The phytohormone jasmonate (JA) regulates a wide range of growth, developmental, and defense-related processes during the plant life cycle. Identification of the JAZ family of proteins that repress JA responses has facilitated rapid progress in understanding how this lipid-derived hormone controls gene expression. Recent analysis of JAZ proteins has provided new insight into the nature of the JA receptor, the chemical specificity of signal perception, and cross-talk between JA and other hormone response pathways. Functional diversification of JAZ proteins by alternative splicing, together with the ability of JAZ proteins to homo- and heterodimerize, provide mechanisms to enhance combinatorial diversity and versatility in gene regulation by JA. PMID:19800644

Simulation/Emulation Techniques: Compressing Schedules With Parallel (HW/SW) Development

NASA Technical Reports Server (NTRS)

Mangieri, Mark L.; Hoang, June

2014-01-01

NASA has always been in the business of balancing new technologies and techniques to achieve human space travel objectives. NASA's Kedalion engineering analysis lab has been validating and using many contemporary avionics HW/SW development and integration techniques, which represent new paradigms to NASA's heritage culture. Kedalion has validated many of the Orion HW/SW engineering techniques borrowed from the adjacent commercial aircraft avionics solution space, inserting new techniques and skills into the Multi - Purpose Crew Vehicle (MPCV) Orion program. Using contemporary agile techniques, Commercial-off-the-shelf (COTS) products, early rapid prototyping, in-house expertise and tools, and extensive use of simulators and emulators, NASA has achieved cost effective paradigms that are currently serving the Orion program effectively. Elements of long lead custom hardware on the Orion program have necessitated early use of simulators and emulators in advance of deliverable hardware to achieve parallel design and development on a compressed schedule.

Muroid rodent phylogenetics: 900-species tree reveals increasing diversification rates

PubMed Central

Schenk, John J.

2017-01-01

We combined new sequence data for more than 300 muroid rodent species with our previously published sequences for up to five nuclear and one mitochondrial genes to generate the most widely and densely sampled hypothesis of evolutionary relationships across Muroidea. An exhaustive screening procedure for publically available sequences was implemented to avoid the propagation of taxonomic errors that are common to supermatrix studies. The combined data set of carefully screened sequences derived from all available sequences on GenBank with our new data resulted in a robust maximum likelihood phylogeny for 900 of the approximately 1,620 muroids. Several regions that were equivocally resolved in previous studies are now more decisively resolved, and we estimated a chronogram using 28 fossil calibrations for the most integrated age and topological estimates to date. The results were used to update muroid classification and highlight questions needing additional data. We also compared the results of multigene supermatrix studies like this one with the principal published supertrees and concluded that the latter are unreliable for any comparative study in muroids. In addition, we explored diversification patterns as an explanation for why muroid rodents represent one of the most species-rich groups of mammals by detecting evidence for increasing net diversification rates through time across the muroid tree. We suggest the observation of increasing rates may be due to a combination of parallel increases in rate across clades and high average extinction rates. Five increased diversification-rate-shifts were inferred, suggesting that multiple, but perhaps not independent, events have led to the remarkable species diversity in the superfamily. Our results provide a phylogenetic framework for comparative studies that is not highly dependent upon the signal from any one gene. PMID:28813483

Parallel selective pressures drive convergent diversification of phenotypes in pythons and boas.

PubMed

Esquerré, Damien; Scott Keogh, J

2016-07-01

Pythons and boas are globally distributed and distantly related radiations with remarkable phenotypic and ecological diversity. We tested whether pythons, boas and their relatives have evolved convergent phenotypes when they display similar ecology. We collected geometric morphometric data on head shape for 1073 specimens representing over 80% of species. We show that these two groups display strong and widespread convergence when they occupy equivalent ecological niches and that the history of phenotypic evolution strongly matches the history of ecological diversification, suggesting that both processes are strongly coupled. These results are consistent with replicated adaptive radiation in both groups. We argue that strong selective pressures related to habitat-use have driven this convergence. Pythons and boas provide a new model system for the study of macro-evolutionary patterns of morphological and ecological evolution and they do so at a deeper level of divergence and global scale than any well-established adaptive radiation model systems. © 2016 John Wiley & Sons Ltd/CNRS.

The ubiquity of alpine plant radiations: from the Andes to the Hengduan Mountains.

PubMed

Hughes, Colin E; Atchison, Guy W

2015-07-01

Alpine plant radiations are compared across the world's major mountain ranges and shown to be overwhelmingly young and fast, largely confined to the Pliocene and Pleistocene, and some of them apparently in the early explosive phase of radiation. Accelerated diversification triggered by island-like ecological opportunities following the final phases of mountain uplift, and in many cases enabled by the key adaptation of perennial habit, provides a general model for alpine plant radiations. Accelerated growth form evolution facilitated by perenniality provides compelling evidence of ecological release and suggests striking parallels between island-like alpine, and especially tropicalpine radiations, and island radiations more generally. These parallels suggest that the world's mountains offer an excellent comparative system for explaining evolutionary radiation. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Comparative mtDNA phylogeography of neotropical freshwater fishes: testing shared history to infer the evolutionary landscape of lower Central America.

PubMed

Bermingham, E; Martin, A P

1998-04-01

Historical biogeography seeks to explain contemporary distributions of taxa in the context of intrinsic biological and extrinsic geological and climatic factors. To decipher the relative importance of biological characteristics vs. environmental conditions, it is necessary to ask whether groups of taxa with similar distributions share the same history of diversification. Because all of the taxa will have shared the same climatic and geological history, evidence of shared history across multiple species provides an estimate of the role of extrinsic factors in shaping contemporary biogeographic patterns. Similarly, differences in the records of evolutionary history across species will probably be signatures of biological differences. In this study, we focus on inferring the evolutionary history for geographical populations and closely related species representing three genera of primary freshwater fishes that are widely distributed in lower Central America (LCA) and northwestern Colombia. Analysis of mitochondrial gene trees provides the opportunity for robust tests of shared history across taxa. Moreover, because mtDNA permits inference of the temporal scale of diversification we can test hypotheses regarding the chronological development of the Isthmian corridor linking North and South America. We have focused attention on two issues. First, we show that many of the distinct populations of LCA fishes diverged in a relatively brief period of time thus limiting the phylogenetic signal available for tests of shared history. Second, our results provide reduced evidence of shared history when all drainages are included in the analysis because of inferred dispersion events that obscure the evolutionary history among drainage basins. When we restrict the analysis to areas that harbour endemic mitochondrial lineages, there is evidence of shared history across taxa. We hypothesize that there were two to three distinct waves of invasion into LCA from putative source populations in northwestern Colombia. The first probably happened in the late Miocene, prior to the final emergence of the Isthmus in the mid-Pliocene; the second was probably coincident with the rise of the Isthmus in the mid-Pliocene, and the third event occurred more recently, perhaps in the Pleistocene. In each case the geographical scale of the dispersion of lineages was progressively more limited, a pattern we attribute to the continuing development of the landscape due to orogeny and the consequent increase in the insularization of drainage basins. Thus, the fisheye view of LCA suggests a complex biogeographic history of overlaid cycles of colonization, diversification, sorting and extinction of lineages.

The Impact of Rise of the Andes and Amazon Landscape Evolution on Diversification of Lowland terra-firme Forest Birds

NASA Technical Reports Server (NTRS)

Aleixo, Alexandre; Wilkinson, M. Justin

2011-01-01

Since the 19th Century, the unmatched biological diversity of Amazonia has stimulated a diverse set of hypotheses accounting for patterns of species diversity and distribution in mega-diverse tropical environments. Unfortunately, the evidence supporting particular hypotheses to date is at best described as ambiguous, and no generalizations have emerged yet, mostly due to the lack of comprehensive comparative phylogeographic studies with thorough trans-Amazonian sampling of lineages. Here we report on spatial and temporal patterns of diversification estimated from mitochondrial gene trees for 31 lineages of birds associated with upland terra-firme forest, the dominant habitat in modern lowland Amazonia. The results confirm the pervasive role of Amazonian rivers as primary barriers separating sister lineages of birds, and a protracted spatio-temporal pattern of diversification, with a gradual reduction of earlier (1st and 2nd) and older (> 2 mya) splits associated with each lineage in an eastward direction. (The easternmost tributaries of the Amazon, the Xingu and Tocantins Rivers, are not associated with any splits older than > 2 mya). For the suboscine passerines, maximum-likelihood estimates of rates of diversification point to an overall constant rate over the past 5 my (up to a significant downturn at 300,000 y ago). This "younging-eastward" pattern may have an abiotic explanation related to landscape evolution. Triggered by a new pulse of Andean uplift, it has been proposed that modern Amazon basin landscapes may have evolved successively eastward, away from the mountain chain, starting approximately 10 mya. This process was likely based on the deposition of vast fluvial sediment masses, known as megafans, that may have extended progressively and in series eastward from Andean sources. This process plausibly explains the progressive extinction of original Pebas wetland of western-central Amazonia by the present fluvial landsurfaces of a more terra-firme type. The youngest landsurfaces thus lie furthest from the mountains. In this scenario major drainages were also reoriented in wholesale fashion away from a northerly orientation generally towards the east and an Atlantic Ocean outlet. The advance of megafans is best seen by the location of axial rivers such as the Orinoco and Mamore which lie against the cratonic margins furthest from the Andes, at the distal ends of major megafan ramparts. More importantly, other major river courses in western-central Amazonia will have been established at progressively younger dates with distance eastward. If this landscape-sequence scenario is accurate, it parallels the progressive younging of the passerine lineages. The bird DNA data appears to confirm strongly the pervasive role of Amazonian rivers--as primary barriers separating sister lineages of birds, and thus probably as facilitaters of bird speciation. We show for the first time that a general spatio-temporal pattern of diversification for terra-firme lineages in the Amazon is associated with rivers ("younging-eastward"), and furthermore parallels a specific scenario of regional drainage evolution.

Evolutionary pathway to increased virulence and epidemic group A Streptococcus disease derived from 3,615 genome sequences.

PubMed

Nasser, Waleed; Beres, Stephen B; Olsen, Randall J; Dean, Melissa A; Rice, Kelsey A; Long, S Wesley; Kristinsson, Karl G; Gottfredsson, Magnus; Vuopio, Jaana; Raisanen, Kati; Caugant, Dominique A; Steinbakk, Martin; Low, Donald E; McGeer, Allison; Darenberg, Jessica; Henriques-Normark, Birgitta; Van Beneden, Chris A; Hoffmann, Steen; Musser, James M

2014-04-29

We sequenced the genomes of 3,615 strains of serotype Emm protein 1 (M1) group A Streptococcus to unravel the nature and timing of molecular events contributing to the emergence, dissemination, and genetic diversification of an unusually virulent clone that now causes epidemic human infections worldwide. We discovered that the contemporary epidemic clone emerged in stepwise fashion from a precursor cell that first contained the phage encoding an extracellular DNase virulence factor (streptococcal DNase D2, SdaD2) and subsequently acquired the phage encoding the SpeA1 variant of the streptococcal pyrogenic exotoxin A superantigen. The SpeA2 toxin variant evolved from SpeA1 by a single-nucleotide change in the M1 progenitor strain before acquisition by horizontal gene transfer of a large chromosomal region encoding secreted toxins NAD(+)-glycohydrolase and streptolysin O. Acquisition of this 36-kb region in the early 1980s into just one cell containing the phage-encoded sdaD2 and speA2 genes was the final major molecular event preceding the emergence and rapid intercontinental spread of the contemporary epidemic clone. Thus, we resolve a decades-old controversy about the type and sequence of genomic alterations that produced this explosive epidemic. Analysis of comprehensive, population-based contemporary invasive strains from seven countries identified strong patterns of temporal population structure. Compared with a preepidemic reference strain, the contemporary clone is significantly more virulent in nonhuman primate models of pharyngitis and necrotizing fasciitis. A key finding is that the molecular evolutionary events transpiring in just one bacterial cell ultimately have produced millions of human infections worldwide.

Evolutionary pathway to increased virulence and epidemic group A Streptococcus disease derived from 3,615 genome sequences

PubMed Central

Nasser, Waleed; Beres, Stephen B.; Olsen, Randall J.; Dean, Melissa A.; Rice, Kelsey A.; Long, S. Wesley; Kristinsson, Karl G.; Gottfredsson, Magnus; Vuopio, Jaana; Raisanen, Kati; Caugant, Dominique A.; Steinbakk, Martin; Low, Donald E.; McGeer, Allison; Darenberg, Jessica; Henriques-Normark, Birgitta; Van Beneden, Chris A.; Hoffmann, Steen; Musser, James M.

2014-01-01

We sequenced the genomes of 3,615 strains of serotype Emm protein 1 (M1) group A Streptococcus to unravel the nature and timing of molecular events contributing to the emergence, dissemination, and genetic diversification of an unusually virulent clone that now causes epidemic human infections worldwide. We discovered that the contemporary epidemic clone emerged in stepwise fashion from a precursor cell that first contained the phage encoding an extracellular DNase virulence factor (streptococcal DNase D2, SdaD2) and subsequently acquired the phage encoding the SpeA1 variant of the streptococcal pyrogenic exotoxin A superantigen. The SpeA2 toxin variant evolved from SpeA1 by a single-nucleotide change in the M1 progenitor strain before acquisition by horizontal gene transfer of a large chromosomal region encoding secreted toxins NAD+-glycohydrolase and streptolysin O. Acquisition of this 36-kb region in the early 1980s into just one cell containing the phage-encoded sdaD2 and speA2 genes was the final major molecular event preceding the emergence and rapid intercontinental spread of the contemporary epidemic clone. Thus, we resolve a decades-old controversy about the type and sequence of genomic alterations that produced this explosive epidemic. Analysis of comprehensive, population-based contemporary invasive strains from seven countries identified strong patterns of temporal population structure. Compared with a preepidemic reference strain, the contemporary clone is significantly more virulent in nonhuman primate models of pharyngitis and necrotizing fasciitis. A key finding is that the molecular evolutionary events transpiring in just one bacterial cell ultimately have produced millions of human infections worldwide. PMID:24733896

Diversification in continental island archipelagos: new evidence on the roles of fragmentation, colonization and gene flow on the genetic divergence of Aegean Nigella (Ranunculaceae).

PubMed

Jaros, Ursula; Tribsch, Andreas; Comes, Hans Peter

2018-02-12

Disentangling the relative roles of past fragmentation (vicariance), colonization (dispersal) and post-divergence gene flow in the genetic divergence of continental island organisms remains a formidable challenge. Amplified fragment length polymorphisms (AFLPs) were used to (1) gain further insights into the biogeographical processes underlying the Pleistocene diversification of the Aegean Nigella arvensis complex; (2) evaluate the role of potential key factors driving patterns of population genetic variability (mating system, geographical isolation and historical contingencies); and (3) test the robustness of conclusions previously drawn from chloroplast (cp) DNA. Genetic diversity was analysed for 235 AFLP markers from 48 populations (497 individuals) representing 11 taxa of the complex using population genetic methods and Bayesian assignment tests. Most designated taxa are identifiable as genetically distinct units. Both fragmentation and dispersal-driven diversification processes occurred at different geological time scales, from Early to Late Pleistocene, specifically (1) sea barrier-induced vicariant speciation in the Cyclades, the Western Cretan Strait and Ikaria; and (2) bi-regional colonizations of the 'Southern Aegean Island Arc' from the Western vs. Eastern Aegean mainland, followed by allopatric divergences in Crete vs. Rhodos and Karpathos/Kasos. Outcrossing island taxa experienced drift-related demographic processes that are magnified in the two insular selfing species. Population genetic differentiation on the mainland seems largely driven by dispersal limitation, while in the Central Aegean it may still be influenced by historical events (island fragmentation and sporadic long-distance colonization). The biogeographical history of Aegean Nigella is more complex than expected for a strictly allopatric vicariant model of divergence. Nonetheless, the major phylogeographical boundaries of this radiation are largely congruent with the geography and history of islands, with little evidence for ongoing gene exchange between divergent taxa. The present results emphasize the need to investigate further biological and landscape features and contemporary vs. historical processes in driving population divergence and taxon diversification in Aegean plant radiations. © The Author(s) 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Comparative Analysis of Proteomes and Functionomes Provides Insights into Origins of Cellular Diversification

PubMed Central

Caetano-Anollés, Gustavo

2013-01-01

Reconstructing the evolutionary history of modern species is a difficult problem complicated by the conceptual and technical limitations of phylogenetic tree building methods. Here, we propose a comparative proteomic and functionomic inferential framework for genome evolution that allows resolving the tripartite division of cells and sketching their history. Evolutionary inferences were derived from the spread of conserved molecular features, such as molecular structures and functions, in the proteomes and functionomes of contemporary organisms. Patterns of use and reuse of these traits yielded significant insights into the origins of cellular diversification. Results uncovered an unprecedented strong evolutionary association between Bacteria and Eukarya while revealing marked evolutionary reductive tendencies in the archaeal genomic repertoires. The effects of nonvertical evolutionary processes (e.g., HGT, convergent evolution) were found to be limited while reductive evolution and molecular innovation appeared to be prevalent during the evolution of cells. Our study revealed a strong vertical trace in the history of proteins and associated molecular functions, which was reliably recovered using the comparative genomics approach. The trace supported the existence of a stem line of descent and the very early appearance of Archaea as a diversified superkingdom, but failed to uncover a hidden canonical pattern in which Bacteria was the first superkingdom to deploy superkingdom-specific structures and functions. PMID:24492748

Drivers of Cape Verde archipelagic endemism in keyhole limpets

PubMed Central

Cunha, Regina L.; Assis, Jorge M.; Madeira, Celine; Seabra, Rui; Lima, Fernando P.; Lopes, Evandro P.; Williams, Suzanne T.; Castilho, Rita

2017-01-01

Oceanic archipelagos are the ideal setting for investigating processes that shape species assemblages. Focusing on keyhole limpets, genera Fissurella and Diodora from Cape Verde Islands, we used an integrative approach combining molecular phylogenetics with ocean transport simulations to infer species distribution patterns and analyse connectivity. Dispersal simulations, using pelagic larval duration and ocean currents as proxies, showed a reduced level of connectivity despite short distances between some of the islands. It is suggested that dispersal and persistence driven by patterns of oceanic circulation favouring self-recruitment played a primary role in explaining contemporary species distributions. Mitochondrial and nuclear data revealed the existence of eight Cape Verde endemic lineages, seven within Fissurella, distributed across the archipelago, and one within Diodora restricted to Boavista. The estimated origins for endemic Fissurella and Diodora were 10.2 and 6.7 MY, respectively. Between 9.5 and 4.5 MY, an intense period of volcanism in Boavista might have affected Diodora, preventing its diversification. Having originated earlier, Fissurella might have had more opportunities to disperse to other islands and speciate before those events. Bayesian analyses showed increased diversification rates in Fissurella possibly promoted by low sea levels during Plio-Pleistocene, which further explain differences in species richness between both genera. PMID:28150720

Solution-phase parallel synthesis of hexahydro-1H-isoindolone libraries via tactical combination of Cu-catalyzed three-component coupling and Diels-Alder reactions.

PubMed

Zhang, Lei; Lushington, Gerald H; Neuenswander, Benjamin; Hershberger, John C; Malinakova, Helena C

2008-01-01

Parallel solution-phase synthesis of combinatorial libraries of hexahydro-1 H-isoindolones exploiting a novel "tactical combination" of Cu-catalyzed three-component coupling and Diels-Alder reactions was accomplished. Three distinct libraries consisting of 24 members (library I), 60 members (library II), and 32 members (library III) were constructed. Variation of three substituents on the isoindolone scaffold in library I was exclusively achieved by the choice of the building blocks. In the syntheses of libraries II and III, sublibraries of isoindolone scaffolds were prepared initially in a one-pot/two-step process and were further diversified via Pd-catalyzed Suzuki cross-coupling reaction with boronic acids at two different diversification points. The Lipinski profiles and calculated ADME properties of the compounds are also reported.

Light fluorous-tagged traceless one-pot synthesis of benzimidazoles facilitated by microwave irradiation.

PubMed

Tseng, Chih-Chung; Tasi, Cheng-Hsun; Sun, Chung-Ming

2012-06-01

A novel protocol for rapid assemble of benzimidazole framework has been demonstrated. This method incorporated with light fluorous-tag provides a convenient method for diversification of benzimidazoles and for easy purification via fluorous solid-phase extraction (F-SPE) in a parallel manner. The key transformation of this study involves in situ reduction of aromatic nitro compound, amide formation, cyclization and aromatization promoted by microwave irradiation in a one-pot fashion. The strategy is envisaged to be applied for the establishment of drug-like small molecule libraries for high throughput screening.

Capital finance and ownership conversions in health care.

PubMed

Robinson, J C

2000-01-01

This paper analyzes the for-profit transformation of health care, with emphasis on Internet start-ups, physician practice management firms, insurance plans, and hospitals at various stages in the industry life cycle. Venture capital, conglomerate diversification, publicly traded equity, convertible bonds, retained earnings, and taxable corporate debt come with forms of financial accountability that are distinct from those inherent in the capital sources available to nonprofit organizations. The pattern of for-profit conversions varies across health sectors, parallel with the relative advantages and disadvantages of for-profit and nonprofit capital sources in those sectors.

"The Human Condition" as social ontology: Hannah Arendt on society, action and knowledge.

PubMed

Walsh, Philip

2011-01-01

Hannah Arendt is widely regarded as a political theorist who sought to rescue politics from "society," and political theory from the social sciences. This conventional view has had the effect of distracting attention from many of Arendt's most important insights concerning the constitution of "society" and the significance of the social sciences. In this article, I argue that Hannah Arendt's distinctions between labor, work, and action, as these are discussed in "The Human Condition" and elsewhere, are best understood as a set of claims about the fundamental structures of human societies. Understanding Arendt in this way introduces interesting parallels between Arendt's work and both classical and contemporary sociology. From this I draw a number of conclusions concerning Arendt's conception of "society," and extend these insights into two contemporary debates within contemporary theoretical sociology: the need for a differentiated ontology of the social world, and the changing role that novel forms of knowledge play in contemporary society as major sources of social change and order.

University-Community Engagement: Case Study of University Social Responsibility

ERIC Educational Resources Information Center

Chile, Love M.; Black, Xavier M.

2015-01-01

Corporatisation of universities has drawn parallels between contemporary universities and business corporations, and extended analysis of corporate social responsibility to universities. This article reports on a case study of university-community engagement with schools and school communities through youth engagement programmes to enhance…

Parallels in the Arts

ERIC Educational Resources Information Center

Laffey, Grace

1972-01-01

A mini-course of nine weeks was organized as a laboratory course to survey relationships in literature, music, and art. Three periods in the arts (Romanticism, Impressionism, and Contemporary) were matched with three major activities; the basic areas of study and activity were poetry, short story, and novel. (Author)

The philosophical core of King's conceptual system.

PubMed

Whelton, B J

1999-04-01

Aristotelian understanding of being human is presented as the philosophical core of King's conceptual system. A summary of King's thought is organized according to contemporary influences. The article then turns to what Aristotle teaches about the composition of the world and what it means to be a human being. Wallace's life-powers model of the soul brings these insights into contemporary thought. Aristotelian philosophy completes King's account of the personal system by providing insight into what it is to be human. Parallels in the reasoning of transaction and Aristotelian deliberation are further evidence of classical influences within King's work.

Coevolution Pattern and Functional Conservation or Divergence of miR167s and their targets across Diverse Plant Species

PubMed Central

Barik, Suvakanta; Kumar, Ashutosh; Sarkar Das, Shabari; Yadav, Sandeep; Gautam, Vibhav; Singh, Archita; Singh, Sharmila; Sarkar, Ananda K.

2015-01-01

microRNAs (miRNAs), a class of endogenously produced small non-coding RNAs of 20–21 nt length, processed from precursor miRNAs, regulate many developmental processes by negatively regulating the target genes in both animals and plants. The coevolutionary pattern of a miRNA family and their targets underscores its functional conservation or diversification. The miR167 regulates various aspects of plant development in Arabidopsis by targeting ARF6 and ARF8. The evolutionary conservation or divergence of miR167s and their target genes are poorly understood till now. Here we show the evolutionary relationship among 153 MIR167 genes obtained from 33 diverse plant species. We found that out of the 153 of miR167 sequences retrieved from the “miRBase”, 27 have been annotated to be processed from the 3′ end, and have diverged distinctively from the other miR167s produced from 5′ end. Our analysis reveals that gma-miR167h/i and mdm-miR167a are processed from 3′ end and have evolved separately, diverged most resulting in novel targets other than their known ones, and thus led to functional diversification, especially in apple and soybean. We also show that mostly conserved miR167 sequences and their target AUXIN RESPONSE FACTORS (ARFs) have gone through parallel evolution leading to functional diversification among diverse plant species. PMID:26459056

Coevolution Pattern and Functional Conservation or Divergence of miR167s and their targets across Diverse Plant Species.

PubMed

Barik, Suvakanta; Kumar, Ashutosh; Sarkar Das, Shabari; Yadav, Sandeep; Gautam, Vibhav; Singh, Archita; Singh, Sharmila; Sarkar, Ananda K

2015-10-13

microRNAs (miRNAs), a class of endogenously produced small non-coding RNAs of 20-21 nt length, processed from precursor miRNAs, regulate many developmental processes by negatively regulating the target genes in both animals and plants. The coevolutionary pattern of a miRNA family and their targets underscores its functional conservation or diversification. The miR167 regulates various aspects of plant development in Arabidopsis by targeting ARF6 and ARF8. The evolutionary conservation or divergence of miR167s and their target genes are poorly understood till now. Here we show the evolutionary relationship among 153 MIR167 genes obtained from 33 diverse plant species. We found that out of the 153 of miR167 sequences retrieved from the "miRBase", 27 have been annotated to be processed from the 3' end, and have diverged distinctively from the other miR167s produced from 5' end. Our analysis reveals that gma-miR167h/i and mdm-miR167a are processed from 3' end and have evolved separately, diverged most resulting in novel targets other than their known ones, and thus led to functional diversification, especially in apple and soybean. We also show that mostly conserved miR167 sequences and their target AUXIN RESPONSE FACTORS (ARFs) have gone through parallel evolution leading to functional diversification among diverse plant species.

Early Paleocene landbird supports rapid phylogenetic and morphological diversification of crown birds after the K-Pg mass extinction.

PubMed

Ksepka, Daniel T; Stidham, Thomas A; Williamson, Thomas E

2017-07-25

Evidence is accumulating for a rapid diversification of birds following the K-Pg extinction. Recent molecular divergence dating studies suggest that birds radiated explosively during the first few million years of the Paleocene; however, fossils from this interval remain poorly represented, hindering our understanding of morphological and ecological specialization in early neoavian birds. Here we report a small fossil bird from the Nacimiento Formation of New Mexico, constrained to 62.221-62.517 Ma. This partial skeleton represents the oldest arboreal crown group bird known. Phylogenetic analyses recovered Tsidiiyazhi abini gen. et sp. nov. as a member of the Sandcoleidae, an extinct basal clade of stem mousebirds (Coliiformes). The discovery of Tsidiiyazhi pushes the minimum divergence ages of as many as nine additional major neoavian lineages into the earliest Paleocene, compressing the duration of the proposed explosive post-K-Pg radiation of modern birds into a very narrow temporal window parallel to that suggested for placental mammals. Simultaneously, Tsidiiyazhi provides evidence for the rapid morphological (and likely ecological) diversification of crown birds. Features of the foot indicate semizygodactyly (the ability to facultatively reverse the fourth pedal digit), and the arcuate arrangement of the pedal trochleae bears a striking resemblance to the conformation in owls (Strigiformes). Inclusion of fossil taxa and branch length estimates impacts ancestral state reconstructions, revealing support for the independent evolution of semizygodactyly in Coliiformes, Leptosomiformes, and Strigiformes, none of which is closely related to extant clades exhibiting full zygodactyly.

Early Paleocene landbird supports rapid phylogenetic and morphological diversification of crown birds after the K-Pg mass extinction

NASA Astrophysics Data System (ADS)

Ksepka, Daniel T.; Stidham, Thomas A.; Williamson, Thomas E.

2017-07-01

Evidence is accumulating for a rapid diversification of birds following the K-Pg extinction. Recent molecular divergence dating studies suggest that birds radiated explosively during the first few million years of the Paleocene; however, fossils from this interval remain poorly represented, hindering our understanding of morphological and ecological specialization in early neoavian birds. Here we report a small fossil bird from the Nacimiento Formation of New Mexico, constrained to 62.221-62.517 Ma. This partial skeleton represents the oldest arboreal crown group bird known. Phylogenetic analyses recovered Tsidiiyazhi abini gen. et sp. nov. as a member of the Sandcoleidae, an extinct basal clade of stem mousebirds (Coliiformes). The discovery of Tsidiiyazhi pushes the minimum divergence ages of as many as nine additional major neoavian lineages into the earliest Paleocene, compressing the duration of the proposed explosive post-K-Pg radiation of modern birds into a very narrow temporal window parallel to that suggested for placental mammals. Simultaneously, Tsidiiyazhi provides evidence for the rapid morphological (and likely ecological) diversification of crown birds. Features of the foot indicate semizygodactyly (the ability to facultatively reverse the fourth pedal digit), and the arcuate arrangement of the pedal trochleae bears a striking resemblance to the conformation in owls (Strigiformes). Inclusion of fossil taxa and branch length estimates impacts ancestral state reconstructions, revealing support for the independent evolution of semizygodactyly in Coliiformes, Leptosomiformes, and Strigiformes, none of which is closely related to extant clades exhibiting full zygodactyly.

Early Paleocene landbird supports rapid phylogenetic and morphological diversification of crown birds after the K–Pg mass extinction

PubMed Central

Ksepka, Daniel T.; Stidham, Thomas A.; Williamson, Thomas E.

2017-01-01

Evidence is accumulating for a rapid diversification of birds following the K–Pg extinction. Recent molecular divergence dating studies suggest that birds radiated explosively during the first few million years of the Paleocene; however, fossils from this interval remain poorly represented, hindering our understanding of morphological and ecological specialization in early neoavian birds. Here we report a small fossil bird from the Nacimiento Formation of New Mexico, constrained to 62.221–62.517 Ma. This partial skeleton represents the oldest arboreal crown group bird known. Phylogenetic analyses recovered Tsidiiyazhi abini gen. et sp. nov. as a member of the Sandcoleidae, an extinct basal clade of stem mousebirds (Coliiformes). The discovery of Tsidiiyazhi pushes the minimum divergence ages of as many as nine additional major neoavian lineages into the earliest Paleocene, compressing the duration of the proposed explosive post–K–Pg radiation of modern birds into a very narrow temporal window parallel to that suggested for placental mammals. Simultaneously, Tsidiiyazhi provides evidence for the rapid morphological (and likely ecological) diversification of crown birds. Features of the foot indicate semizygodactyly (the ability to facultatively reverse the fourth pedal digit), and the arcuate arrangement of the pedal trochleae bears a striking resemblance to the conformation in owls (Strigiformes). Inclusion of fossil taxa and branch length estimates impacts ancestral state reconstructions, revealing support for the independent evolution of semizygodactyly in Coliiformes, Leptosomiformes, and Strigiformes, none of which is closely related to extant clades exhibiting full zygodactyly. PMID:28696285

Convergence across a continent: adaptive diversification in a recent radiation of Australian lizards

PubMed Central

Horner, Paul; Moritz, Craig

2016-01-01

Recent radiations are important to evolutionary biologists, because they provide an opportunity to study the mechanisms that link micro- and macroevolution. The role of ecological speciation during adaptive radiation has been intensively studied, but radiations can arise from a diversity of evolutionary processes; in particular, on large continental landmasses where allopatric speciation might frequently precede ecological differentiation. It is therefore important to establish a phylogenetic and ecological framework for recent continental-scale radiations that are species-rich and ecologically diverse. Here, we use a genomic (approx. 1 200 loci, exon capture) approach to fit branch lengths on a summary-coalescent species tree and generate a time-calibrated phylogeny for a recent and ecologically diverse radiation of Australian scincid lizards; the genus Cryptoblepharus. We then combine the phylogeny with a comprehensive phenotypic dataset for over 800 individuals across the 26 species, and use comparative methods to test whether habitat specialization can explain current patterns of phenotypic variation in ecologically relevant traits. We find significant differences in morphology between species that occur in distinct environments and convergence in ecomorphology with repeated habitat shifts across the continent. These results suggest that isolated analogous habitats have provided parallel ecological opportunity and have repeatedly promoted adaptive diversification. By contrast, speciation processes within the same habitat have resulted in distinct lineages with relatively limited morphological variation. Overall, our study illustrates how alternative diversification processes might have jointly stimulated species proliferation across the continent and generated a remarkably diverse group of Australian lizards. PMID:27306048

Hypnotic Overdoses and Fairy Tales: Snow White and the Uses of Disenchantment.

ERIC Educational Resources Information Center

Pommereau, Xavier; And Others

1987-01-01

Considers explanations for women's use of less violent methods to commit suicide. Reinterprets "Snow White" and makes parallel with contemporary clinical cases to show that illusion of a nondefinitive death is often assimilated, in western culture, with step toward rebirth. (Author/NB)

Matrix metalloproteinases: structures, evolution, and diversification.

PubMed

Massova, I; Kotra, L P; Fridman, R; Mobashery, S

1998-09-01

A comprehensive sequence alignment of 64 members of the family of matrix metalloproteinases (MMPs) for the entire sequences, and subsequently the catalytic and the hemopexin-like domains, have been performed. The 64 MMPs were selected from plants, invertebrates, and vertebrates. The analyses disclosed that as many as 23 distinct subfamilies of these proteins are known to exist. Information from the sequence alignments was correlated with structures, both crystallographic as well as computational, of the catalytic domains for the 23 representative members of the MMP family. A survey of the metal binding sites and two loops containing variable sequences of amino acids, which are important for substrate interactions, are discussed. The collective data support the proposal that the assembly of the domains into multidomain enzymes was likely to be an early evolutionary event. This was followed by diversification, perhaps in parallel among the MMPs, in a subsequent evolutionary time scale. Analysis indicates that a retrograde structure simplification may have accounted for the evolution of MMPs with simple domain constituents, such as matrilysin, from the larger and more elaborate enzymes.

Protein expression parallels thermal tolerance and ecologic changes in the diversification of a diving beetle species complex.

PubMed

Hidalgo-Galiana, A; Monge, M; Biron, D G; Canals, F; Ribera, I; Cieslak, A

2016-01-01

Physiological changes associated with evolutionary and ecological processes such as diversification, range expansion or speciation are still incompletely understood, especially for non-model species. Here we study differences in protein expression in response to temperature in a western Mediterranean diving beetle species complex, using two-dimensional differential gel electrophoresis with one Moroccan and one Iberian population each of Agabus ramblae and Agabus brunneus. We identified proteins with significant expression differences after thermal treatments comparing them with a reference EST library generated from one of the species of the complex (A. ramblae). The colonisation during the Middle Pleistocene of the Iberian peninsula by A. ramblae, where maximum temperatures and seasonality are lower than in the ancestral north African range, was associated with changes in the response to 27 °C in proteins related to energy metabolism. The subsequent speciation of A. brunneus from within populations of Iberian A. ramblae was associated with changes in the expression of several stress-related proteins (mostly chaperons) when exposed to 4 °C. These changes are in agreement with the known tolerance to lower temperatures of A. brunneus, which occupies a larger geographical area with a wider range of climatic conditions. In both cases, protein expression changes paralleled the evolution of thermal tolerance and the climatic conditions experienced by the species. However, although the colonisation of the Iberian peninsula did not result in morphological change, the speciation process of A. brunneus within Iberia involved genetic isolation and substantial differences in male genitalia and body size and shape.

Protein expression parallels thermal tolerance and ecologic changes in the diversification of a diving beetle species complex

PubMed Central

Hidalgo-Galiana, A; Monge, M; Biron, D G; Canals, F; Ribera, I; Cieslak, A

2016-01-01

Physiological changes associated with evolutionary and ecological processes such as diversification, range expansion or speciation are still incompletely understood, especially for non-model species. Here we study differences in protein expression in response to temperature in a western Mediterranean diving beetle species complex, using two-dimensional differential gel electrophoresis with one Moroccan and one Iberian population each of Agabus ramblae and Agabus brunneus. We identified proteins with significant expression differences after thermal treatments comparing them with a reference EST library generated from one of the species of the complex (A. ramblae). The colonisation during the Middle Pleistocene of the Iberian peninsula by A. ramblae, where maximum temperatures and seasonality are lower than in the ancestral north African range, was associated with changes in the response to 27 °C in proteins related to energy metabolism. The subsequent speciation of A. brunneus from within populations of Iberian A. ramblae was associated with changes in the expression of several stress-related proteins (mostly chaperons) when exposed to 4 °C. These changes are in agreement with the known tolerance to lower temperatures of A. brunneus, which occupies a larger geographical area with a wider range of climatic conditions. In both cases, protein expression changes paralleled the evolution of thermal tolerance and the climatic conditions experienced by the species. However, although the colonisation of the Iberian peninsula did not result in morphological change, the speciation process of A. brunneus within Iberia involved genetic isolation and substantial differences in male genitalia and body size and shape. PMID:26328758

Techniques and Tools for Performance Tuning of Parallel and Distributed Scientific Applications

NASA Technical Reports Server (NTRS)

Sarukkai, Sekhar R.; VanderWijngaart, Rob F.; Castagnera, Karen (Technical Monitor)

1994-01-01

Performance degradation in scientific computing on parallel and distributed computer systems can be caused by numerous factors. In this half-day tutorial we explain what are the important methodological issues involved in obtaining codes that have good performance potential. Then we discuss what are the possible obstacles in realizing that potential on contemporary hardware platforms, and give an overview of the software tools currently available for identifying the performance bottlenecks. Finally, some realistic examples are used to illustrate the actual use and utility of such tools.

Caring science and the science of unitary human beings: a trans-theoretical discourse for nursing knowledge development.

PubMed

Watson, Jean; Smith, Marlaine C

2002-03-01

Two dominant discourses in contemporary nursing theory and knowledge development have evolved over the past few decades, in part by unitary science views and caring theories. Rogers' science of unitary human beings (SUHB) represents the unitary directions in nursing. Caring theories and related caring science (CS) scholarship represent the other. These two contemporary initiatives have generated two parallel, often controversial, seemingly separate and unrelated, trees of knowledge for nursing science. This paper explores the evolution of CS and its intersection with SUHB that have emerged in contemporary nursing literature. We present a case for integration, convergence, and creative synthesis of CS with SUHB. A trans-theoretical, trans-disciplinary context emerges, allowing nursing to sustain its caring ethic and ontology, within a unitary science. The authors critique and review the seminal, critical issues that have separated contemporary knowledge developments in CS and SUHB. Foundational issues of CS, and Watson's theory of transpersonal caring science (TCS), as a specific exemplar, are analysed, alongside parallel themes in SUHB. By examining hidden ethical-ontological and paradigmatic commonalities, trans-theoretical themes and connections are explored and revealed between TCS and SUHB. Through a creative synthesis of TCS and SUHB we explicate a distinct unitary view of human with a relational caring ontology and ethic that informs nursing as well as other sciences. The result: is a trans-theoretical, trans-disciplinary view for nursing knowledge development. Nursing's history has been to examine theoretical differences rather than commonalities. This trans-theoretical position moves nursing toward theoretical integration and creative synthesis, vs. separation, away from the 'Balkanization' of different theories. This initiative still maintains the integrity of different theories, while facilitating and inviting a new discourse for nursing science. The result: Unitary Caring Science that evokes both science and spirit.

Rainfall Patterns and U.S. Migration from Rural Mexico

PubMed Central

Hunter, Lori M.; Murray, Sheena; Riosmena, Fernando

2014-01-01

In many rural regions of developing countries, natural resource dependency means changes in climate patterns hold tremendous potential to impact livelihoods. When environmentally-based livelihood options are constrained, migration can become an important adaptive strategy. Using data from the Mexican Migration Project, we model U.S. emigration from rural communities as related to community, household and climate factors. The results suggest that households subjected to recent drought conditions are far more likely to send a U.S. migrant, but only in communities with strong migration histories. In regions lacking such social networks, rainfall deficits actually reduce migration propensities, perhaps reflecting constraints in the ability to engage in migration as a coping strategy. Policy implications emphasize diversification of rural Mexican livelihoods in the face of contemporary climate change. PMID:25473143

The Foundations of Telegraphy and Telephony in Latin America.

ERIC Educational Resources Information Center

Baur, Cynthia

1994-01-01

Synthesizes empirical evidence on the participation of state and capital in the establishment of domestic telegraphic and telephonic communication in Latin America. Suggests that, in many ways, the contemporary period of telecommunication system organization in the region parallels the early years of telegraphy and telephony. Discusses these…

Cultural Narratives: Developing a Three-Dimensional Learning Community through Braided Understanding

ERIC Educational Resources Information Center

Heck, Marsha L.

2004-01-01

Paula Underwood's "Learning Stories" braid together body, mind, and spirit to enable understanding that does not easily unravel. They tell of relationships among individual and community learning that parallel other ancient and contemporary ideas about learning in caring communities. Underwood's tradition considers learning sacred; everyone's…

Control Yourself, or at Least Your Core Self

ERIC Educational Resources Information Center

Austin, Lisa M.

2010-01-01

Contemporary privacy debates regarding new technologies often define privacy in terms of control over personal information such that the privacy "problem" is a lack of control and the privacy "solution" is increased control. This article questions the control-paradigm by pointing to its parallels with earlier debates in the…

Learning from Programmed Instruction: Examining Implications for Modern Instructional Technology

ERIC Educational Resources Information Center

McDonald, Jason K.; Yanchar, Stephen C.; Osguthorpe, Russell T.

2005-01-01

This article reports a theoretical examination of several parallels between contemporary instructional technology (as manifest in one of its most current manifestations, online learning) and one of its direct predecessors, programmed instruction. We place particular focus on the underlying assumptions of the two movements. Our analysis suggests…

Phylogenetic diversity anomaly in angiosperms between eastern Asia and eastern North America.

PubMed

Qian, Hong; Jin, Yi; Ricklefs, Robert E

2017-10-24

Although eastern Asia (EAS) and eastern North America (ENA) have similar climates, plant species richness in EAS greatly exceeds that in ENA. The degree to which this diversity difference reflects the ages of the floras or their rates of evolutionary diversification has not been quantified. Measures of species diversity that do not incorporate the ages of lineages disregard the evolutionary distinctiveness of species. In contrast, phylogenetic diversity integrates both the number of species and their history of evolutionary diversification. Here we compared species diversity and phylogenetic diversity in a large number of flowering plant (angiosperm) floras distributed across EAS and ENA, two regions with similar contemporary environments and broadly shared floristic history. After accounting for climate and sample area, we found both species diversity and phylogenetic diversity to be significantly higher in EAS than in ENA. When we controlled the number of species statistically, we found that phylogenetic diversity remained substantially higher in EAS than in ENA, although it tended to converge at high latitude. This pattern held independently for herbs, shrubs, and trees. The anomaly in species and phylogenetic diversity likely resulted from differences in regional processes, related in part to high climatic and topographic heterogeneity, and a strong monsoon climate, in EAS. The broad connection between tropical and temperate floras in southern Asia also might have played a role in creating the phylogenetic diversity anomaly.

Diversification: Far term (2000 - )

NASA Technical Reports Server (NTRS)

1975-01-01

Diversification, intended to underly the far term of the energy conservation program, was defined to imply conservation through substitution for scarce energy resources by maximizing the total number of viable energy system types in every sector. The following requirements or aspects of diversification that must be studied were given: fuel mix and end use patterns for various alternative diversification plans, current status of diversification, advantages and disadvantages of diversification, constraints and criteria, diversification actions and their controls, and means for implementing the chosen diversification strategy. The following advantages resulting from diversification were described: competition, crisis-related situations, local energy production, decentralized plant locations, long range energy policy, and environmental overloads. The major criteria by which a diversification program should be judged, the major constraints affecting the approaches, and the road to diversification, were elaborated.

Genetic structure in the European endemic seabird, Phalacrocorax aristotelis, shaped by a complex interaction of historical and contemporary, physical and nonphysical drivers.

PubMed

Thanou, Evanthia; Sponza, Stefano; Nelson, Emily J; Perry, Annika; Wanless, Sarah; Daunt, Francis; Cavers, Stephen

2017-05-01

Geographically separated populations tend to be less connected by gene flow, as a result of physical or nonphysical barriers preventing dispersal, and this can lead to genetic structure. In this context, highly mobile organisms such as seabirds are interesting because the small effect of physical barriers means nonphysical ones may be relatively more important. Here, we use microsatellite and mitochondrial data to explore the genetic structure and phylogeography of Atlantic and Mediterranean populations of a European endemic seabird, the European shag, Phalacrocorax aristotelis, and identify the primary drivers of their diversification. Analyses of mitochondrial markers revealed three phylogenetic lineages grouping the North Atlantic, Spanish/Corsican and eastern Mediterranean populations, apparently arising from fragmentation during the Pleistocene followed by range expansion. These traces of historical fragmentation were also evident in the genetic structure estimated by microsatellite markers, despite significant contemporary gene flow among adjacent populations. Stronger genetic structure, probably promoted by landscape, philopatry and local adaptation, was found among distant populations and those separated by physical and ecological barriers. This study highlights the enduring effect of Pleistocene climatic changes on shag populations, especially within the Mediterranean Basin, and suggests a role for cryptic northern refugia, as well as known southern refugia, on the genetic structure of European seabirds. Finally, it outlines how contemporary ecological barriers and behavioural traits may maintain population divergence, despite long-distance dispersal triggered by extreme environmental conditions (e.g. population crashes). © 2017 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

The Nazi Physicians as Leaders in Eugenics and "Euthanasia": Lessons for Today.

PubMed

Grodin, Michael A; Miller, Erin L; Kelly, Johnathan I

2018-01-01

This article, in commemoration of the 70th anniversary of the Doctors' Trial at Nuremberg, reflects on the Nazi eugenics and "euthanasia" programs and their relevance for today. The Nazi doctors used eugenic ideals to justify sterilizations, child and adult "euthanasia," and, ultimately, genocide. Contemporary euthanasia has experienced a progression from voluntary to nonvoluntary and from passive to active killing. Modern eugenics has included both positive and negative selective activities. The 70th anniversary of the Doctors' Trial at Nuremberg provides an important opportunity to reflect on the implications of the Nazi eugenics and "euthanasia" programs for contemporary health law, bioethics, and human rights. In this article, we will examine the role that health practitioners played in the promotion and implementation of State-sponsored eugenics and "euthanasia" in Nazi Germany, followed by an exploration of contemporary parallels and debates in modern bioethics. 1 .

Convergence across a continent: adaptive diversification in a recent radiation of Australian lizards.

PubMed

Blom, Mozes P K; Horner, Paul; Moritz, Craig

2016-06-15

Recent radiations are important to evolutionary biologists, because they provide an opportunity to study the mechanisms that link micro- and macroevolution. The role of ecological speciation during adaptive radiation has been intensively studied, but radiations can arise from a diversity of evolutionary processes; in particular, on large continental landmasses where allopatric speciation might frequently precede ecological differentiation. It is therefore important to establish a phylogenetic and ecological framework for recent continental-scale radiations that are species-rich and ecologically diverse. Here, we use a genomic (approx. 1 200 loci, exon capture) approach to fit branch lengths on a summary-coalescent species tree and generate a time-calibrated phylogeny for a recent and ecologically diverse radiation of Australian scincid lizards; the genus Cryptoblepharus We then combine the phylogeny with a comprehensive phenotypic dataset for over 800 individuals across the 26 species, and use comparative methods to test whether habitat specialization can explain current patterns of phenotypic variation in ecologically relevant traits. We find significant differences in morphology between species that occur in distinct environments and convergence in ecomorphology with repeated habitat shifts across the continent. These results suggest that isolated analogous habitats have provided parallel ecological opportunity and have repeatedly promoted adaptive diversification. By contrast, speciation processes within the same habitat have resulted in distinct lineages with relatively limited morphological variation. Overall, our study illustrates how alternative diversification processes might have jointly stimulated species proliferation across the continent and generated a remarkably diverse group of Australian lizards. © 2016 The Author(s).

Repeated evolution of tricellular (and bicellular) pollen.

PubMed

Williams, Joseph H; Taylor, Mackenzie L; O'Meara, Brian C

2014-04-01

Male gametophytes of seed plants are sexually immature at the time they are dispersed as pollen, but approximately 30% of flowering plants have tricellular pollen containing fully formed sperm at anthesis. The classic study of Brewbaker (1967: American Journal of Botany 54: 1069-1083) provided a powerful confirmation of the long-standing hypothesis that tricellular pollen had many parallel and irreversible origins within angiosperms. We readdressed the main questions of that study with modern comparative phylogenetic methods. We used our own and more recent reports to greatly expand the Brewbaker data set. We modeled trait evolution for 2511 species on a time-calibrated angiosperm phylogeny using (1) Binary State Speciation and Extinction (BiSSE), which accounts for the effect of species diversification rates on character transition rates and, (2) the hidden rates model (HRM), which incorporates variation in transition rates across a phylogeny. Seventy percent of species had bicellular pollen. BiSSE found a 1.9-fold higher bicellular to tricellular transition rate than in the reverse direction, and bicellular lineages had a 1.8-fold higher diversification rate than tricellular lineages. HRM found heterogeneity in evolutionary rates, with bidirectional transition rates in three of four rate classes. The tricellular condition is not irreversible. Pollen cell numbers are maintained at intermediate frequencies because lower net diversification rates of tricellular lineages are counterbalanced by slower state shifts to the bicellular condition. That tricellular lineages diversify slowly and give rise to bicellular lineages slowly reflects a linkage between the evolution of sporophyte lifestyles and the developmental lability of male gametophytes.

"Dissoi Logoi," Civic Friendship, and the Politics of Education

ERIC Educational Resources Information Center

Olbrys, Stephen Gencarella

2006-01-01

This essay examines the recent debate over the politics of American education, particularly the accusation of liberal bias by members of the Right such as David Horowitz and Students for Academic Freedom. It draws parallels between the contemporary movement for an "Academic Bill of Rights" and the historical context of the "Powell…

The Variability Hypothesis: The History of a Biological Model of Sex Differences in Intelligence.

ERIC Educational Resources Information Center

Shields, Stephanie A.

1982-01-01

Describes the origin and development of the variability hypothesis as applied to the study of social and psychological sex differences. Explores changes in the hypothesis over time, social and scientific factors that fostered its acceptance, and possible parallels between the variability hypothesis and contemporary theories of sex differences.…

Darwin's Difficulties and Students' Struggles with Trait Loss: Cognitive-Historical Parallelisms in Evolutionary Explanation

ERIC Educational Resources Information Center

Ha, Minsu; Nehm, Ross H.

2014-01-01

Although historical changes in scientific ideas sometimes display striking similarities with students' conceptual progressions, some scholars have cautioned that such similarities lack meaningful commonalities. In the history of evolution, while Darwin and his contemporaries often used natural selection to explain evolutionary trait gain or…

Living the Orwellian Nightmare: New Media and Digital Dystopia

ERIC Educational Resources Information Center

Diglin, Greg

2014-01-01

This article offers an academic critique of new media culture, as viewed comparatively with George Orwell's "1984." The author makes the argument that a number of plot elements of "1984" are reflected within contemporary Western societies. The assertion is made that these parallels have developed as a consequence of new…

Working with the Young Child: Clinical Implications of Contemporary Developmental Science

ERIC Educational Resources Information Center

Gold, Claudia M.

2017-01-01

The recognition that adverse childhood experiences have long-term negative effects parallels the explosion of evidence demonstrating how early experience gets into the body and brain. This knowledge, in turn, has significant implications for treatment of emotional and behavioral problems in early childhood. In this article, I offer a guide to…

Multicultural Education in a Post-Race Political Age: Our Movement at Risk?

ERIC Educational Resources Information Center

Marshall, Patricia L.

2009-01-01

The 2008 elections ushered in a new era in U.S. politics with implications for race relations and social justice activity. Drawing parallels between the contemporary African American community and splintering undercurrents in the National Association for Multicultural Education (NAME), the author urges cross-generational coalescence around an…

Refining the oak-fire hypothesis for management of oak-dominated forests of the eastern United States

Treesearch

Mary A. Arthur; Heather D. Alexander; Daniel C. Dey; Callie J. Schweitzer; David L. Loftis

2012-01-01

Prescribed fires are increasingly implemented throughout eastern deciduous forests to accomplish various management objectives, including maintenance of oak-dominated (Quercus spp.) forests. Despite a regional research-based understanding of prehistoric and historic fire regimes, a parallel understanding of contemporary fire use to preserve oak...

Clinical appraisal of arterial stiffness: the Argonauts in front of the Golden Fleece

PubMed Central

Vlachopoulos, C; Aznaouridis, K; Stefanadis, C

2006-01-01

Interest in evaluating arterial elastic properties has grown in parallel with the widespread availability of non‐invasive methods for assessing arterial stiffness. A clinically useful diagnostic index must be pathophysiologically relevant, must be readily measurable, and must indicate the severity of the disease and predict the corresponding risk. Interventional modification of this index must parallel disease regression and benefit prognosis. The current evidence for the clinical value of estimating arterial stiffness (mainly of large, elastic‐type arteries, such as the aorta and the carotids) in the contemporary era of cardiovascular medicine is reviewed. PMID:16339817

Ars Moriendi: Coping with death in the Late Middle Ages.

PubMed

Espi Forcén, Fernando; Espi Forcén, Carlos

2016-10-01

The Ars moriendi was a book written in the early 15th century with the goal of assisting friars in their work of helping the dying. The aim of our study was to review the current literature on the Ars Moriendi concerning the field of medicine, to analyze the psychological mechanisms for coping with death anxiety within Ars Moriendi, and to explore parallels between the strategies used in the medieval book and in contemporary literature about death and dying. A review of literature using Pubmed, EMBASE, JSTOR, Project MUSE, and the New York Public Library was undertaken first. The primary source was then interpreted from a medical/psychological point of view. Seven articles were selected by literature review. These works comment on the importance of the Ars Moriendi in its historical context and explore the possibility of retrieving the principles of the text in contemporary society. The original text of Ars Moriendi, the primary source, presents death as a relief from the sufferings of earthly life and a gateway to eternal glory. According to the author, a good death implied the triumph over five demonic temptations in agonizing people: a lack of faith, despair, impatience, pride and greed. Analyzed from a modern psychiatric perspective, the Ars Moriendi offers descriptions of behavioral manifestations compatible with delirium, mood and anxiety disorders that characterize people with terminal illnesses. Moreover, we also explored parallels between the strategies used to cope with death anxiety in the Late Middle Ages and in contemporary society.

Ancient human genomes suggest three ancestral populations for present-day Europeans

PubMed Central

Lazaridis, Iosif; Patterson, Nick; Mittnik, Alissa; Renaud, Gabriel; Mallick, Swapan; Kirsanow, Karola; Sudmant, Peter H.; Schraiber, Joshua G.; Castellano, Sergi; Lipson, Mark; Berger, Bonnie; Economou, Christos; Bollongino, Ruth; Fu, Qiaomei; Bos, Kirsten I.; Nordenfelt, Susanne; Li, Heng; de Filippo, Cesare; Prüfer, Kay; Sawyer, Susanna; Posth, Cosimo; Haak, Wolfgang; Hallgren, Fredrik; Fornander, Elin; Rohland, Nadin; Delsate, Dominique; Francken, Michael; Guinet, Jean-Michel; Wahl, Joachim; Ayodo, George; Babiker, Hamza A.; Bailliet, Graciela; Balanovska, Elena; Balanovsky, Oleg; Barrantes, Ramiro; Bedoya, Gabriel; Ben-Ami, Haim; Bene, Judit; Berrada, Fouad; Bravi, Claudio M.; Brisighelli, Francesca; Busby, George B. J.; Cali, Francesco; Churnosov, Mikhail; Cole, David E. C.; Corach, Daniel; Damba, Larissa; van Driem, George; Dryomov, Stanislav; Dugoujon, Jean-Michel; Fedorova, Sardana A.; Romero, Irene Gallego; Gubina, Marina; Hammer, Michael; Henn, Brenna M.; Hervig, Tor; Hodoglugil, Ugur; Jha, Aashish R.; Karachanak-Yankova, Sena; Khusainova, Rita; Khusnutdinova, Elza; Kittles, Rick; Kivisild, Toomas; Klitz, William; Kučinskas, Vaidutis; Kushniarevich, Alena; Laredj, Leila; Litvinov, Sergey; Loukidis, Theologos; Mahley, Robert W.; Melegh, Béla; Metspalu, Ene; Molina, Julio; Mountain, Joanna; Näkkäläjärvi, Klemetti; Nesheva, Desislava; Nyambo, Thomas; Osipova, Ludmila; Parik, Jüri; Platonov, Fedor; Posukh, Olga; Romano, Valentino; Rothhammer, Francisco; Rudan, Igor; Ruizbakiev, Ruslan; Sahakyan, Hovhannes; Sajantila, Antti; Salas, Antonio; Starikovskaya, Elena B.; Tarekegn, Ayele; Toncheva, Draga; Turdikulova, Shahlo; Uktveryte, Ingrida; Utevska, Olga; Vasquez, René; Villena, Mercedes; Voevoda, Mikhail; Winkler, Cheryl; Yepiskoposyan, Levon; Zalloua, Pierre; Zemunik, Tatijana; Cooper, Alan; Capelli, Cristian; Thomas, Mark G.; Ruiz-Linares, Andres; Tishkoff, Sarah A.; Singh, Lalji; Thangaraj, Kumarasamy; Villems, Richard; Comas, David; Sukernik, Rem; Metspalu, Mait; Meyer, Matthias; Eichler, Evan E.; Burger, Joachim; Slatkin, Montgomery; Pääbo, Svante; Kelso, Janet; Reich, David; Krause, Johannes

2014-01-01

We sequenced the genomes of a ~7,000 year old farmer from Germany and eight ~8,000 year old hunter-gatherers from Luxembourg and Sweden. We analyzed these and other ancient genomes1–4 with 2,345 contemporary humans to show that most present Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE) related to Upper Paleolithic Siberians3, who contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations’ deep relationships and show that EEF had ~44% ancestry from a “Basal Eurasian” population that split prior to the diversification of other non-African lineages. PMID:25230663

Ancient human genomes suggest three ancestral populations for present-day Europeans.

PubMed

Lazaridis, Iosif; Patterson, Nick; Mittnik, Alissa; Renaud, Gabriel; Mallick, Swapan; Kirsanow, Karola; Sudmant, Peter H; Schraiber, Joshua G; Castellano, Sergi; Lipson, Mark; Berger, Bonnie; Economou, Christos; Bollongino, Ruth; Fu, Qiaomei; Bos, Kirsten I; Nordenfelt, Susanne; Li, Heng; de Filippo, Cesare; Prüfer, Kay; Sawyer, Susanna; Posth, Cosimo; Haak, Wolfgang; Hallgren, Fredrik; Fornander, Elin; Rohland, Nadin; Delsate, Dominique; Francken, Michael; Guinet, Jean-Michel; Wahl, Joachim; Ayodo, George; Babiker, Hamza A; Bailliet, Graciela; Balanovska, Elena; Balanovsky, Oleg; Barrantes, Ramiro; Bedoya, Gabriel; Ben-Ami, Haim; Bene, Judit; Berrada, Fouad; Bravi, Claudio M; Brisighelli, Francesca; Busby, George B J; Cali, Francesco; Churnosov, Mikhail; Cole, David E C; Corach, Daniel; Damba, Larissa; van Driem, George; Dryomov, Stanislav; Dugoujon, Jean-Michel; Fedorova, Sardana A; Gallego Romero, Irene; Gubina, Marina; Hammer, Michael; Henn, Brenna M; Hervig, Tor; Hodoglugil, Ugur; Jha, Aashish R; Karachanak-Yankova, Sena; Khusainova, Rita; Khusnutdinova, Elza; Kittles, Rick; Kivisild, Toomas; Klitz, William; Kučinskas, Vaidutis; Kushniarevich, Alena; Laredj, Leila; Litvinov, Sergey; Loukidis, Theologos; Mahley, Robert W; Melegh, Béla; Metspalu, Ene; Molina, Julio; Mountain, Joanna; Näkkäläjärvi, Klemetti; Nesheva, Desislava; Nyambo, Thomas; Osipova, Ludmila; Parik, Jüri; Platonov, Fedor; Posukh, Olga; Romano, Valentino; Rothhammer, Francisco; Rudan, Igor; Ruizbakiev, Ruslan; Sahakyan, Hovhannes; Sajantila, Antti; Salas, Antonio; Starikovskaya, Elena B; Tarekegn, Ayele; Toncheva, Draga; Turdikulova, Shahlo; Uktveryte, Ingrida; Utevska, Olga; Vasquez, René; Villena, Mercedes; Voevoda, Mikhail; Winkler, Cheryl A; Yepiskoposyan, Levon; Zalloua, Pierre; Zemunik, Tatijana; Cooper, Alan; Capelli, Cristian; Thomas, Mark G; Ruiz-Linares, Andres; Tishkoff, Sarah A; Singh, Lalji; Thangaraj, Kumarasamy; Villems, Richard; Comas, David; Sukernik, Rem; Metspalu, Mait; Meyer, Matthias; Eichler, Evan E; Burger, Joachim; Slatkin, Montgomery; Pääbo, Svante; Kelso, Janet; Reich, David; Krause, Johannes

2014-09-18

We sequenced the genomes of a ∼7,000-year-old farmer from Germany and eight ∼8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations' deep relationships and show that early European farmers had ∼44% ancestry from a 'basal Eurasian' population that split before the diversification of other non-African lineages.

Novel microsatellites for Calibrachoa heterophylla (Solanaceae) endemic to the South Atlantic Coastal Plain of South America1

PubMed Central

Silva-Arias, Gustavo Adolfo; Mäder, Geraldo; Bonatto, Sandro L.; Freitas, Loreta B.

2015-01-01

Premise of the study: Calibrachoa heterophylla (Solanaceae) is a petunia species restricted to the South Atlantic Coastal Plain of South America and presents a recent history of colonization from continental to coastal environments and diversification following the formation of the Coastal Plain during the Quaternary period. Methods and Results: This study reports a suite of 16 microsatellite loci for C. heterophylla. The applicability of these markers was assessed by genotyping 57 individuals from two natural populations. Of the 16 described loci, 12 were found to be polymorphic. Successful cross-amplification tests were obtained using 12 Calibrachoa species. Conclusions: The development of microsatellite markers will be useful to recover the contemporary history of the colonization of the Coastal Plain and to provide information for the conservation of this endemic species. PMID:26191462

The Role of Context in Producing Item Interactions and False Memories

ERIC Educational Resources Information Center

Tehan, Gerald; Humphreys, Michael S.; Tolan, Georgina Anne; Pitcher, Cameron

2004-01-01

Cued recall with an extralist cue poses a challenge for contemporary memory theory in that there is a need to explain how episodic and semantic information are combined. A parallel activation and intersection approach proposes one such means by assuming that an experimental cue will elicit its preexisting semantic network and a context cue will…

Lysenkoism and the population control movement.

PubMed

Simon, J L

1997-09-01

The case of Lysenkoism in the Soviet Union helps us understand how people's wrong beliefs can be influenced by what the information they receive from outside, especially when there is a large volume of media coverage and there is no contrary information to be heard. The population control movement in contemporary United States has many parallels to the Lysenko episode.

An Anthropologist's Reflections on Defining Quality in Education Research

ERIC Educational Resources Information Center

Tobin, Joseph

2007-01-01

In the USA there is a contemporary discourse of crisis about the state of education and a parallel discourse that lays a large portion of the blame onto the poor quality of educational research. The solution offered is "scientific research." This article presents critiques of the core assumptions of the scientific research as secure argument.…

"You Don't Look Like Your Profile Picture": The Ethical Implications of Researching Online Identities in Higher Education

ERIC Educational Resources Information Center

Blanco Ramírez, Gerardo; Palu-ay, Lyssa

2015-01-01

Social media sites and other contemporary technologies open the possibility for the construction of online identities that are loosely connected to physical bodies; this construction allows individuals to edit their identities constantly, in a continuous process of self-recreation. In parallel, universities utilise printed and electronic media to…

Emulating the logic of monoterpenoid alkaloid biogenesis to access a skeletally diverse chemical library.

PubMed

Liu, Song; Scotti, John S; Kozmin, Sergey A

2013-09-06

We have developed a synthetic strategy that mimics the diversity-generating power of monoterpenoid indole alkaloid biosynthesis. Our general approach goes beyond diversification of a single natural product-like substructure and enables production of a highly diverse collection of small molecules. The reaction sequence begins with rapid and highly modular assembly of the tetracyclic indoloquinolizidine core, which can be chemoselectively processed into several additional skeletally diverse structural frameworks. The general utility of this approach was demonstrated by parallel synthesis of two representative chemical libraries containing 847 compounds with favorable physicochemical properties to enable its subsequent broad pharmacological evaluation.

Testing the Relationships between Diversification, Species Richness, and Trait Evolution.

PubMed

Kozak, Kenneth H; Wiens, John J

2016-11-01

Understanding which traits drive species diversification is essential for macroevolutionary studies and to understand patterns of species richness among clades. An important tool for testing if traits influence diversification is to estimate rates of net diversification for each clade, and then test for a relationship between traits and diversification rates among clades. However, this general approach has become very controversial. Numerous papers have now stated that it is inappropriate to analyze net diversification rates in groups in which clade richness is not positively correlated with clade age. Similarly, some have stated that variation in net diversification rates does not explain variation in species richness patterns among clades across the Tree of Life. Some authors have also suggested that strong correlations between richness and diversification rates are a statistical artifact and effectively inevitable. If this latter point is true, then correlations between richness and diversification rates would be uninformative (or even misleading) for identifying how much variation in species richness among clades is explained by variation in net diversification rates. Here, we use simulations (based on empirical data for plethodontid salamanders) to address three main questions. First, how is variation in net diversification rates among clades related to the relationship between clade age and species richness? Second, how accurate are these net diversification rate estimators, and does the age-richness relationship have any relevance to their accuracy? Third, is a relationship between species richness and diversification rates an inevitable, statistical artifact? Our simulations show that strong, positive age-richness relationships arise when diversification rates are invariant among clades, whereas realistic variation in diversification rates among clades frequently disrupts this relationship. Thus, a significant age-richness relationship should not be a requirement for utilizing net diversification rates in macroevolutionary studies. Moreover, we find no difference in the accuracy of net diversification rate estimators between conditions in which there are strong, positive relationships between clade age and richness and conditions in which these strong relationships are absent. We find that net diversification rate estimators are reasonably accurate under many conditions (true and estimated rates are strongly corrrelated, and typically differ by ∼10-20%), but become more accurate when clades are older and less accurate when using incorrect assumptions about extinction. We also find that significant relationships between richness and diversification rates fail to arise under many conditions, especially when there are faster rates in younger clades. Therefore, a significant relationship between richness and diversification rates is not inevitable. Given this latter result, we suggest that relationships between richness and diversification should be tested for when attempting to explain the causes of richness patterns, to avoid potential misinterpretations (e.g., high diversification rates associated with low-richness clades). Similarly, our results also provide some support for previous studies suggesting that variation in diversification rates might explain much of the variation in species richness among major clades, based on strong relationships between clade richness and diversification rates. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

The Phylogeny and Biogeographic History of Ashes (Fraxinus, Oleaceae) Highlight the Roles of Migration and Vicariance in the Diversification of Temperate Trees

PubMed Central

Hinsinger, Damien Daniel; Basak, Jolly; Gaudeul, Myriam; Cruaud, Corinne; Bertolino, Paola; Frascaria-Lacoste, Nathalie; Bousquet, Jean

2013-01-01

The cosmopolitan genus Fraxinus, which comprises about 40 species of temperate trees and shrubs occupying various habitats in the Northern Hemisphere, represents a useful model to study speciation in long-lived angiosperms. We used nuclear external transcribed spacers (nETS), phantastica gene sequences, and two chloroplast loci (trnH-psbA and rpl32-trnL) in combination with previously published and newly obtained nITS sequences to produce a time-calibrated multi-locus phylogeny of the genus. We then inferred the biogeographic history and evolution of floral morphology. An early dispersal event could be inferred from North America to Asia during the Oligocene, leading to the diversification of the section Melioides sensus lato. Another intercontinental dispersal originating from the Eurasian section of Fraxinus could be dated from the Miocene and resulted in the speciation of F. nigra in North America. In addition, vicariance was inferred to account for the distribution of the other Old World species (sections Sciadanthus, Fraxinus and Ornus). Geographic speciation likely involving dispersal and vicariance could also be inferred from the phylogenetic grouping of geographically close taxa. Molecular dating suggested that the initial divergence of the taxonomical sections occurred during the middle and late Eocene and Oligocene periods, whereas diversification within sections occurred mostly during the late Oligocene and Miocene, which is consistent with the climate warming and accompanying large distributional changes observed during these periods. These various results underline the importance of dispersal and vicariance in promoting geographic speciation and diversification in Fraxinus. Similarities in life history, reproductive and demographic attributes as well as geographical distribution patterns suggest that many other temperate trees should exhibit similar speciation patterns. On the other hand, the observed parallel evolution and reversions in floral morphology would imply a major influence of environmental pressure. The phylogeny obtained and its biogeographical implications should facilitate future studies on the evolution of complex adaptive characters, such as habitat preference, and their possible roles in promoting divergent evolution in trees. PMID:24278282

The phylogeny and biogeographic history of ashes (fraxinus, oleaceae) highlight the roles of migration and vicariance in the diversification of temperate trees.

PubMed

Hinsinger, Damien Daniel; Basak, Jolly; Gaudeul, Myriam; Cruaud, Corinne; Bertolino, Paola; Frascaria-Lacoste, Nathalie; Bousquet, Jean

2013-01-01

The cosmopolitan genus Fraxinus, which comprises about 40 species of temperate trees and shrubs occupying various habitats in the Northern Hemisphere, represents a useful model to study speciation in long-lived angiosperms. We used nuclear external transcribed spacers (nETS), phantastica gene sequences, and two chloroplast loci (trnH-psbA and rpl32-trnL) in combination with previously published and newly obtained nITS sequences to produce a time-calibrated multi-locus phylogeny of the genus. We then inferred the biogeographic history and evolution of floral morphology. An early dispersal event could be inferred from North America to Asia during the Oligocene, leading to the diversification of the section Melioides sensus lato. Another intercontinental dispersal originating from the Eurasian section of Fraxinus could be dated from the Miocene and resulted in the speciation of F. nigra in North America. In addition, vicariance was inferred to account for the distribution of the other Old World species (sections Sciadanthus, Fraxinus and Ornus). Geographic speciation likely involving dispersal and vicariance could also be inferred from the phylogenetic grouping of geographically close taxa. Molecular dating suggested that the initial divergence of the taxonomical sections occurred during the middle and late Eocene and Oligocene periods, whereas diversification within sections occurred mostly during the late Oligocene and Miocene, which is consistent with the climate warming and accompanying large distributional changes observed during these periods. These various results underline the importance of dispersal and vicariance in promoting geographic speciation and diversification in Fraxinus. Similarities in life history, reproductive and demographic attributes as well as geographical distribution patterns suggest that many other temperate trees should exhibit similar speciation patterns. On the other hand, the observed parallel evolution and reversions in floral morphology would imply a major influence of environmental pressure. The phylogeny obtained and its biogeographical implications should facilitate future studies on the evolution of complex adaptive characters, such as habitat preference, and their possible roles in promoting divergent evolution in trees.

HIV-1 Env C2-V4 Diversification in a Slow-Progressor Infant Reveals a Flat but Rugged Fitness Landscape

PubMed Central

Smith, S. Abigail; Wood, Charles; West, John T.

2013-01-01

Human immunodeficiency virus type-1 (HIV-1) fitness has been associated with virus entry, a process mediated by the envelope glycoprotein (Env). We previously described Env genetic diversification in a Zambian, subtype C infected, slow-progressor child (1157i) in parallel with an evolving neutralizing antibody response. Because of the role the Variable-3 loop (V3) plays in transmission, cell tropism, neutralization sensitivity, and fitness, longitudinally isolated 1157i C2-V4 alleles were cloned into HIV-1NL4-3-eGFP and -DsRed2 infectious molecular clones. The fluorescent reporters allowed for dual-infection competitions between all patient-derived C2-V4 chimeras to quantify the effect of V3 diversification and selection on fitness. ‘Winners’ and ‘losers’ were readily discriminated among the C2-V4 alleles. Exceptional sensitivity for detection of subtle fitness differences was revealed through analysis of two alleles differing in a single synonymous amino acid. However, when the outcomes of N = 33 competitions were averaged for each chimera, the aggregate analysis showed that despite increasing diversification and divergence with time, natural selection of C2-V4 sequences in this individual did not appear to be producing a ‘survival of the fittest’ evolutionary pattern. Rather, we detected a relatively flat fitness landscape consistent with mutational robustness. Fitness outcomes were then correlated with individual components of the entry process. Env incorporation into particles correlated best with fitness, suggesting a role for Env avidity, as opposed to receptor/coreceptor affinity, in defining fitness. Nevertheless, biochemical analyses did not identify any step in HIV-1 entry as a dominant determinant of fitness. Our results lead us to conclude that multiple aspects of entry contribute to maintaining adequate HIV-1 fitness, and there is no surrogate analysis for determining fitness. The capacity for subtle polymorphisms in Env to nevertheless significantly impact viral fitness suggests fitness is best defined by head-to-head competition. PMID:23638182

Functional diversification of duplicated CYC2 clade genes in regulation of inflorescence development in Gerbera hybrida (Asteraceae).

PubMed

Juntheikki-Palovaara, Inka; Tähtiharju, Sari; Lan, Tianying; Broholm, Suvi K; Rijpkema, Anneke S; Ruonala, Raili; Kale, Liga; Albert, Victor A; Teeri, Teemu H; Elomaa, Paula

2014-09-01

The complex inflorescences (capitula) of Asteraceae consist of different types of flowers. In Gerbera hybrida (gerbera), the peripheral ray flowers are bilaterally symmetrical and lack functional stamens while the central disc flowers are more radially symmetrical and hermaphroditic. Proteins of the CYC2 subclade of the CYC/TB1-like TCP domain transcription factors have been recruited several times independently for parallel evolution of bilaterally symmetrical flowers in various angiosperm plant lineages, and have also been shown to regulate flower-type identity in Asteraceae. The CYC2 subclade genes in gerbera show largely overlapping gene expression patterns. At the level of single flowers, their expression domain in petals shows a spatial shift from the dorsal pattern known so far in species with bilaterally symmetrical flowers, suggesting that this change in expression may have evolved after the origin of Asteraceae. Functional analysis indicates that GhCYC2, GhCYC3 and GhCYC4 mediate positional information at the proximal-distal axis of the inflorescence, leading to differentiation of ray flowers, but that they also regulate ray flower petal growth by affecting cell proliferation until the final size and shape of the petals is reached. Moreover, our data show functional diversification for the GhCYC5 gene. Ectopic activation of GhCYC5 increases flower density in the inflorescence, suggesting that GhCYC5 may promote the flower initiation rate during expansion of the capitulum. Our data thus indicate that modification of the ancestral network of TCP factors has, through gene duplications, led to the establishment of new expression domains and to functional diversification. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

Making the most of your host: the Metrosideros-feeding psyllids (Hemiptera, Psylloidea) of the Hawaiian Islands

PubMed Central

Percy, Diana M.

2017-01-01

Abstract The Hawaiian psyllids (Psylloidea, Triozidae) feeding on Metrosideros (Myrtaceae) constitute a remarkable radiation of more than 35 species. This monophyletic group has diversified on a single, highly polymorphic host plant species, Metrosideros polymorpha. Eleven Metrosideros-feeding species included in the Insects of Hawaii by Zimmerman are redescribed, and an additional 25 new species are described. Contrary to previous classifications that placed the Metrosideros-feeders in two genera, Trioza Foerster, 1848 and Kuwayama Crawford, 1911, all 36 named species are placed in Pariaconus Enderlein, 1926; and the relationship of this genus to other Pacific taxa within the family Triozidae, and other Austro-Pacific taxa feeding on host plants in Myrtaceae is clarified. The processes of diversification in Pariaconus include shifts in galling habit, geographic isolation within and between islands, and preferences for different morphotypes of the host plant. Four species groups are recognized: the bicoloratus and minutus groups are free-living or form pit galls, and together with the kamua group (composing all of the Kauai species) form a basal assemblage; the more derived closed gall species in the ohialoha group are found on all major islands except Kauai. The diversification of Pariaconus has likely occurred over several million years. Within island diversification is exemplified in the kamua group, and within species variation in the ohialoha group, but species discovery rates suggest this radiation remains undersampled. Mitochondrial DNA barcodes are provided for 28 of the 36 species. Genetic divergence, intraspecific genetic structure, and parallel evolution of different galling biologies and morphological traits are discussed within a phylogenetic framework. Outgroup analysis for the genus Pariaconus and ancestral character state reconstruction suggest pit-galling may be the ancestral state, and the closest outgroups are Palaearctic-Australasian taxa rather than other Pacific Metrosideros-feeders. PMID:28325970

Herbivory increases diversification across insect clades

PubMed Central

Wiens, John J.; Lapoint, Richard T.; Whiteman, Noah K.

2015-01-01

Insects contain more than half of all living species, but the causes of their remarkable diversity remain poorly understood. Many authors have suggested that herbivory has accelerated diversification in many insect clades. However, others have questioned the role of herbivory in insect diversification. Here, we test the relationships between herbivory and insect diversification across multiple scales. We find a strong, positive relationship between herbivory and diversification among insect orders. However, herbivory explains less variation in diversification within some orders (Diptera, Hemiptera) or shows no significant relationship with diversification in others (Coleoptera, Hymenoptera, Orthoptera). Thus, we support the overall importance of herbivory for insect diversification, but also show that its impacts can vary across scales and clades. In summary, our results illuminate the causes of species richness patterns in a group containing most living species, and show the importance of ecological impacts on diversification in explaining the diversity of life. PMID:26399434

Herbivory increases diversification across insect clades.

PubMed

Wiens, John J; Lapoint, Richard T; Whiteman, Noah K

2015-09-24

Insects contain more than half of all living species, but the causes of their remarkable diversity remain poorly understood. Many authors have suggested that herbivory has accelerated diversification in many insect clades. However, others have questioned the role of herbivory in insect diversification. Here, we test the relationships between herbivory and insect diversification across multiple scales. We find a strong, positive relationship between herbivory and diversification among insect orders. However, herbivory explains less variation in diversification within some orders (Diptera, Hemiptera) or shows no significant relationship with diversification in others (Coleoptera, Hymenoptera, Orthoptera). Thus, we support the overall importance of herbivory for insect diversification, but also show that its impacts can vary across scales and clades. In summary, our results illuminate the causes of species richness patterns in a group containing most living species, and show the importance of ecological impacts on diversification in explaining the diversity of life.

Tightly congruent bursts of lineage and phenotypic diversification identified in a continental ant radiation.

PubMed

Price, Shauna L; Etienne, Rampal S; Powell, Scott

2016-04-01

Adaptive diversification is thought to be shaped by ecological opportunity. A prediction of this ecological process of diversification is that it should result in congruent bursts of lineage and phenotypic diversification, but few studies have found this expected association. Here, we study the relationship between rates of lineage diversification and body size evolution in the turtle ants, a diverse Neotropical clade. Using a near complete, time-calibrated phylogeny we investigated lineage diversification dynamics and body size disparity through model fitting analyses and estimation of per-lineage rates of cladogenesis and phenotypic evolution. We identify an exceptionally high degree of congruence between the high rates of lineage and body size diversification in a young clade undergoing renewed diversification in the ecologically distinct Chacoan biogeographical region of South America. It is likely that the region presented turtle ants with novel ecological opportunity, which facilitated a nested burst of diversification and phenotypic evolution within the group. Our results provide a compelling quantitative example of tight congruence between rates of lineage and phenotypic diversification, meeting the key predicted pattern of adaptive diversification shaped by ecological opportunity. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications.

PubMed

Tank, David C; Eastman, Jonathan M; Pennell, Matthew W; Soltis, Pamela S; Soltis, Douglas E; Hinchliff, Cody E; Brown, Joseph W; Sessa, Emily B; Harmon, Luke J

2015-07-01

Our growing understanding of the plant tree of life provides a novel opportunity to uncover the major drivers of angiosperm diversity. Using a time-calibrated phylogeny, we characterized hot and cold spots of lineage diversification across the angiosperm tree of life by modeling evolutionary diversification using stepwise AIC (MEDUSA). We also tested the whole-genome duplication (WGD) radiation lag-time model, which postulates that increases in diversification tend to lag behind established WGD events. Diversification rates have been incredibly heterogeneous throughout the evolutionary history of angiosperms and reveal a pattern of 'nested radiations' - increases in net diversification nested within other radiations. This pattern in turn generates a negative relationship between clade age and diversity across both families and orders. We suggest that stochastically changing diversification rates across the phylogeny explain these patterns. Finally, we demonstrate significant statistical support for the WGD radiation lag-time model. Across angiosperms, nested shifts in diversification led to an overall increasing rate of net diversification and declining relative extinction rates through time. These diversification shifts are only rarely perfectly associated with WGD events, but commonly follow them after a lag period. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua.

PubMed

Manousaki, Tereza; Hull, Pincelli M; Kusche, Henrik; Machado-Schiaffino, Gonzalo; Franchini, Paolo; Harrod, Chris; Elmer, Kathryn R; Meyer, Axel

2013-02-01

The study of parallel evolution facilitates the discovery of common rules of diversification. Here, we examine the repeated evolution of thick lips in Midas cichlid fishes (the Amphilophus citrinellus species complex)-from two Great Lakes and two crater lakes in Nicaragua-to assess whether similar changes in ecology, phenotypic trophic traits and gene expression accompany parallel trait evolution. Using next-generation sequencing technology, we characterize transcriptome-wide differential gene expression in the lips of wild-caught sympatric thick- and thin-lipped cichlids from all four instances of repeated thick-lip evolution. Six genes (apolipoprotein D, myelin-associated glycoprotein precursor, four-and-a-half LIM domain protein 2, calpain-9, GTPase IMAP family member 8-like and one hypothetical protein) are significantly underexpressed in the thick-lipped morph across all four lakes. However, other aspects of lips' gene expression in sympatric morphs differ in a lake-specific pattern, including the magnitude of differentially expressed genes (97-510). Generally, fewer genes are differentially expressed among morphs in the younger crater lakes than in those from the older Great Lakes. Body shape, lower pharyngeal jaw size and shape, and stable isotopes (δ(13)C and δ(15)N) differ between all sympatric morphs, with the greatest differentiation in the Great Lake Nicaragua. Some ecological traits evolve in parallel (those related to foraging ecology; e.g. lip size, body and head shape) but others, somewhat surprisingly, do not (those related to diet and food processing; e.g. jaw size and shape, stable isotopes). Taken together, this case of parallelism among thick- and thin-lipped cichlids shows a mosaic pattern of parallel and nonparallel evolution. © 2012 Blackwell Publishing Ltd.

The Core Competencies and MFT Education: Practical Aspects of Transitioning to a Learning-Centered, Outcome-Based Pedagogy

ERIC Educational Resources Information Center

Gehart, Diane

2011-01-01

The MFT core competencies and latest COAMFTE accreditation standards usher in a new paradigm for MFT education. This transition necessitates not only measuring student mastery of competencies but also, more importantly, adopting a contemporary pedagogical model. This article provides an overview of the changes, a review of parallel trends in other…

Solution-Phase Synthesis of Dipeptides: A Capstone Project That Employs Key Techniques in an Organic Laboratory Course

ERIC Educational Resources Information Center

Marchetti, Louis; DeBoef, Brenton

2015-01-01

A contemporary approach to the synthesis and purification of several UV-active dipeptides has been developed for the second-year organic laboratory. This experiment exposes students to the important technique of solution-phase peptide synthesis and allows an instructor to highlight the parallel between what they are accomplishing in the laboratory…

"Anti-American Studies" in the Deep South: Dissenting Rhetorics, the Practice of Democracy, and Academic Freedom in Wartime Universities

ERIC Educational Resources Information Center

Powers, M. Karen; Chaput, Catherine

2007-01-01

Using Frederic Jameson, we outline concentric circles of the political unconscious structuring debates about academic freedom at the national and state levels. By drawing parallels between the World War I university and the contemporary university, we suggest that such circles function historically, always bearing traces of an earlier time. To…

Parallel Distributed Processing at 25: further explorations in the microstructure of cognition.

PubMed

Rogers, Timothy T; McClelland, James L

2014-08-01

This paper introduces a special issue of Cognitive Science initiated on the 25th anniversary of the publication of Parallel Distributed Processing (PDP), a two-volume work that introduced the use of neural network models as vehicles for understanding cognition. The collection surveys the core commitments of the PDP framework, the key issues the framework has addressed, and the debates the framework has spawned, and presents viewpoints on the current status of these issues. The articles focus on both historical roots and contemporary developments in learning, optimality theory, perception, memory, language, conceptual knowledge, cognitive control, and consciousness. Here we consider the approach more generally, reviewing the original motivations, the resulting framework, and the central tenets of the underlying theory. We then evaluate the impact of PDP both on the field at large and within specific subdomains of cognitive science and consider the current role of PDP models within the broader landscape of contemporary theoretical frameworks in cognitive science. Looking to the future, we consider the implications for cognitive science of the recent success of machine learning systems called "deep networks"-systems that build on key ideas presented in the PDP volumes. Copyright © 2014 Cognitive Science Society, Inc.

Natural Constraints to Species Diversification.

PubMed

Lewitus, Eric; Morlon, Hélène

2016-08-01

Identifying modes of species diversification is fundamental to our understanding of how biodiversity changes over evolutionary time. Diversification modes are captured in species phylogenies, but characterizing the landscape of diversification has been limited by the analytical tools available for directly comparing phylogenetic trees of groups of organisms. Here, we use a novel, non-parametric approach and 214 family-level phylogenies of vertebrates representing over 500 million years of evolution to identify major diversification modes, to characterize phylogenetic space, and to evaluate the bounds and central tendencies of species diversification. We identify five principal patterns of diversification to which all vertebrate families hold. These patterns, mapped onto multidimensional space, constitute a phylogenetic space with distinct properties. Firstly, phylogenetic space occupies only a portion of all possible tree space, showing family-level phylogenies to be constrained to a limited range of diversification patterns. Secondly, the geometry of phylogenetic space is delimited by quantifiable trade-offs in tree size and the heterogeneity and stem-to-tip distribution of branching events. These trade-offs are indicative of the instability of certain diversification patterns and effectively bound speciation rates (for successful clades) within upper and lower limits. Finally, both the constrained range and geometry of phylogenetic space are established by the differential effects of macroevolutionary processes on patterns of diversification. Given these properties, we show that the average path through phylogenetic space over evolutionary time traverses several diversification stages, each of which is defined by a different principal pattern of diversification and directed by a different macroevolutionary process. The identification of universal patterns and natural constraints to diversification provides a foundation for understanding the deep-time evolution of biodiversity.

Earliest filter-feeding pterosaur from the Jurassic of China and ecological evolution of Pterodactyloidea

NASA Astrophysics Data System (ADS)

Zhou, Chang-Fu; Gao, Ke-Qin; Yi, Hongyu; Xue, Jinzhuang; Li, Quanguo; Fox, Richard C.

2017-02-01

Pterosaurs were a unique clade of flying reptiles that were contemporaries of dinosaurs in Mesozoic ecosystems. The Pterodactyloidea as the most species-diverse group of pterosaurs dominated the sky during Cretaceous time, but earlier phases of their evolution remain poorly known. Here, we describe a 160 Ma filter-feeding pterosaur from western Liaoning, China, representing the geologically oldest record of the Ctenochasmatidae, a group of exclusive filter feeders characterized by an elongated snout and numerous fine teeth. The new pterosaur took the lead of a major ecological transition in pterosaur evolution from fish-catching to filter-feeding adaptation, prior to the Tithonian (145-152 Ma) diversification of the Ctenochasmatidae. Our research shows that the rise of ctenochasmatid pterosaurs was followed by the burst of eco-morphological divergence of other pterodactyloid clades, which involved a wide range of feeding adaptations that considerably altered the terrestrial ecosystems of the Cretaceous world.

Unifying ecology and macroevolution with individual-based theory

PubMed Central

Rosindell, James; Harmon, Luke J; Etienne, Rampal S

2015-01-01

A contemporary goal in both ecology and evolutionary biology is to develop theory that transcends the boundary between the two disciplines, to understand phenomena that cannot be explained by either field in isolation. This is challenging because macroevolution typically uses lineage-based models, whereas ecology often focuses on individual organisms. Here, we develop a new parsimonious individual-based theory by adding mild selection to the neutral theory of biodiversity. We show that this model generates realistic phylogenies showing a slowdown in diversification and also improves on the ecological predictions of neutral theory by explaining the occurrence of very common species. Moreover, we find the distribution of individual fitness changes over time, with average fitness increasing at a pace that depends positively on community size. Consequently, large communities tend to produce fitter species than smaller communities. These findings have broad implications beyond biodiversity theory, potentially impacting, for example, invasion biology and paleontology. PMID:25818618

Earliest filter-feeding pterosaur from the Jurassic of China and ecological evolution of Pterodactyloidea.

PubMed

Zhou, Chang-Fu; Gao, Ke-Qin; Yi, Hongyu; Xue, Jinzhuang; Li, Quanguo; Fox, Richard C

2017-02-01

Pterosaurs were a unique clade of flying reptiles that were contemporaries of dinosaurs in Mesozoic ecosystems. The Pterodactyloidea as the most species-diverse group of pterosaurs dominated the sky during Cretaceous time, but earlier phases of their evolution remain poorly known. Here, we describe a 160 Ma filter-feeding pterosaur from western Liaoning, China, representing the geologically oldest record of the Ctenochasmatidae, a group of exclusive filter feeders characterized by an elongated snout and numerous fine teeth. The new pterosaur took the lead of a major ecological transition in pterosaur evolution from fish-catching to filter-feeding adaptation, prior to the Tithonian (145-152 Ma) diversification of the Ctenochasmatidae. Our research shows that the rise of ctenochasmatid pterosaurs was followed by the burst of eco-morphological divergence of other pterodactyloid clades, which involved a wide range of feeding adaptations that considerably altered the terrestrial ecosystems of the Cretaceous world.

On the evolution of primitive genetic codes.

PubMed

Weberndorfer, Günter; Hofacker, Ivo L; Stadler, Peter F

2003-10-01

The primordial genetic code probably has been a drastically simplified ancestor of the canonical code that is used by contemporary cells. In order to understand how the present-day code came about we first need to explain how the language of the building plan can change without destroying the encoded information. In this work we introduce a minimal organism model that is based on biophysically reasonable descriptions of RNA and protein, namely secondary structure folding and knowledge based potentials. The evolution of a population of such organism under competition for a common resource is simulated explicitly at the level of individual replication events. Starting with very simple codes, and hence greatly reduced amino acid alphabets, we observe a diversification of the codes in most simulation runs. The driving force behind this effect is the possibility to produce fitter proteins when the repertoire of amino acids is enlarged.

Technological Diversification of Japanese Industry.

ERIC Educational Resources Information Center

Kodama, Fumio

1986-01-01

Describes an approach for measuring industrial technological diversification behavior. Identifies sectoral patterns of Japanese industry as related to diversification behaviors. Delineates the mechanisms and effectiveness of Japanese corporate and government policies relevant to diversification. (ML)

Rapid and recent diversification patterns in Anseriformes birds: Inferred from molecular phylogeny and diversification analyses.

PubMed

Sun, Zhonglou; Pan, Tao; Hu, Chaochao; Sun, Lu; Ding, Hengwu; Wang, Hui; Zhang, Chenling; Jin, Hong; Chang, Qing; Kan, Xianzhao; Zhang, Baowei

2017-01-01

The Anseriformes is a well-known and widely distributed bird order, with more than 150 species in the world. This paper aims to revise the classification, determine the phylogenetic relationships and diversification patterns in Anseriformes by exploring the Cyt b, ND2, COI genes and the complete mitochondrial genomes (mito-genomes). Molecular phylogeny and genetic distance analyses suggest that the Dendrocygna species should be considered as an independent family, Dendrocygnidae, rather than a member of Anatidae. Molecular timescale analyses suggests that the ancestral diversification occurred during the Early Eocene Climatic Optimum (58 ~ 50 Ma). Furthermore, diversification analyses showed that, after a long period of constant diversification, the median initial speciation rate was accelerated three times, and finally increased to approximately 0.3 sp/My. In the present study, both molecular phylogeny and diversification analyses results support that Anseriformes birds underwent rapid and recent diversification in their evolutionary history, especially in modern ducks, which show extreme diversification during the Plio-Pleistocene (~ 5.3 Ma). Therefore, our study support that the Plio-Pleistocene climate fluctuations are likely to have played a significant role in promoting the recent diversification for Anseriformes.

Perspectives on the history of evo-devo and the contemporary research landscape in the genomics era.

PubMed

Tickle, Cheryll; Urrutia, Araxi O

2017-02-05

A fundamental question in biology is how the extraordinary range of living organisms arose. In this theme issue, we celebrate how evolutionary studies on the origins of morphological diversity have changed over the past 350 years since the first publication of the Philosophical Transactions of The Royal Society Current understanding of this topic is enriched by many disciplines, including anatomy, palaeontology, developmental biology, genetics and genomics. Development is central because it is the means by which genetic information of an organism is translated into morphology. The discovery of the genetic basis of development has revealed how changes in form can be inherited, leading to the emergence of the field known as evolutionary developmental biology (evo-devo). Recent approaches include imaging, quantitative morphometrics and, in particular, genomics, which brings a new dimension. Articles in this issue illustrate the contemporary evo-devo field by considering general principles emerging from genomics and how this and other approaches are applied to specific questions about the evolution of major transitions and innovations in morphology, diversification and modification of structures, intraspecific morphological variation and developmental plasticity. Current approaches enable a much broader range of organisms to be studied, thus building a better appreciation of the origins of morphological diversity.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'. © 2016 The Author(s).

Natural Constraints to Species Diversification

PubMed Central

Lewitus, Eric; Morlon, Hélène

2016-01-01

Identifying modes of species diversification is fundamental to our understanding of how biodiversity changes over evolutionary time. Diversification modes are captured in species phylogenies, but characterizing the landscape of diversification has been limited by the analytical tools available for directly comparing phylogenetic trees of groups of organisms. Here, we use a novel, non-parametric approach and 214 family-level phylogenies of vertebrates representing over 500 million years of evolution to identify major diversification modes, to characterize phylogenetic space, and to evaluate the bounds and central tendencies of species diversification. We identify five principal patterns of diversification to which all vertebrate families hold. These patterns, mapped onto multidimensional space, constitute a phylogenetic space with distinct properties. Firstly, phylogenetic space occupies only a portion of all possible tree space, showing family-level phylogenies to be constrained to a limited range of diversification patterns. Secondly, the geometry of phylogenetic space is delimited by quantifiable trade-offs in tree size and the heterogeneity and stem-to-tip distribution of branching events. These trade-offs are indicative of the instability of certain diversification patterns and effectively bound speciation rates (for successful clades) within upper and lower limits. Finally, both the constrained range and geometry of phylogenetic space are established by the differential effects of macroevolutionary processes on patterns of diversification. Given these properties, we show that the average path through phylogenetic space over evolutionary time traverses several diversification stages, each of which is defined by a different principal pattern of diversification and directed by a different macroevolutionary process. The identification of universal patterns and natural constraints to diversification provides a foundation for understanding the deep-time evolution of biodiversity. PMID:27505866

Diversification of energy sources

NASA Technical Reports Server (NTRS)

1975-01-01

The concept of energy source diversification was introduced as a substitution conservation action. The current status and philosophy behind a diversification program is presented in the context of a national energy policy. Advantages, disadvantages (constraints), and methods of implementation for diversification are discussed. The energy source systems for diversification are listed and an example impact assessment is outlined which deals with the water requirements of the specific energy systems.

Divergence and diversification in North American Psoraleeae (Fabaceae) due to climate change

PubMed Central

Egan, Ashley N; Crandall, Keith A

2008-01-01

Background Past studies in the legume family (Fabaceae) have uncovered several evolutionary trends including differential mutation and diversification rates across varying taxonomic levels. The legume tribe Psoraleeae is shown herein to exemplify these trends at the generic and species levels. This group includes a sizable diversification within North America dated at approximately 6.3 million years ago with skewed species distribution to the most recently derived genus, Pediomelum, suggesting a diversification rate shift. We estimate divergence dates of North American (NAm) Psoraleeae using Bayesian MCMC sampling in BEAST based on eight DNA regions (ITS, waxy, matK, trnD-trnT, trnL-trnF, trnK, trnS-trnG, and rpoB-trnC). We also test the hypothesis of a diversification rate shift within NAm Psoraleeae using topological and temporal methods. We investigate the impact of climate change on diversification in this group by (1) testing the hypothesis that a shift from mesic to xeric habitats acted as a key innovation and (2) investigating diversification rate shifts along geologic time, discussing the impact of Quaternary climate oscillations on diversification. Results NAm Psoraleeae represents a recent, rapid radiation with several genera originating during the Pleistocene, 1 to 2 million years ago. A shift in diversification rate is supported by both methods with a 2.67-fold increase suggested around 2 million years ago followed by a 8.73-fold decrease 440,000 years ago. The hypothesis that a climate regime shift from mesic to xeric habitats drove increased diversification in affected taxa was not supported. Timing of the diversification rate increase supports the hypothesis that glaciation-induced climate changes during the Quaternary influenced diversification of the group. Nonrandom spatial diversification also exists, with greater species richness in the American Southwest. Conclusion This study outlines NAm Psoraleeae as a model example of a recent, rapid radiation. Diversification rate shifts in NAm Psoraleeae are not due to current climate regimes as represented by habitat, but instead to past global climate change resulting from Quaternary glaciations. NAm Psoraleeae diversification is a good example of how earthly dynamics including global climate change and topography work together to shape biodiversity. PMID:19091055

Impact of whole-genome duplication events on diversification rates in angiosperms.

PubMed

Landis, Jacob B; Soltis, Douglas E; Li, Zheng; Marx, Hannah E; Barker, Michael S; Tank, David C; Soltis, Pamela S

2018-03-01

Polyploidy or whole-genome duplication (WGD) pervades the evolutionary history of angiosperms. Despite extensive progress in our understanding of WGD, the role of these events in promoting diversification is still not well understood. We seek to clarify the possible association between WGD and diversification rates in flowering plants. Using a previously published phylogeny spanning all land plants (31,749 tips) and WGD events inferred from analyses of the 1000 Plants (1KP) transcriptome data, we analyzed the association of WGDs and diversification rates following numerous WGD events across the angiosperms. We used a stepwise AIC approach (MEDUSA), a Bayesian mixture model approach (BAMM), and state-dependent diversification analyses (MuSSE) to investigate patterns of diversification. Sister-clade comparisons were used to investigate species richness after WGDs. Based on the density of 1KP taxon sampling, 106 WGDs were unambiguously placed on the angiosperm phylogeny. We identified 334-530 shifts in diversification rates. We found that 61 WGD events were tightly linked to changes in diversification rates, and state-dependent diversification analyses indicated higher speciation rates for subsequent rounds of WGD. Additionally, 70 of 99 WGD events showed an increase in species richness compared to the sister clade. Forty-six of the 106 WGDs analyzed appear to be closely associated with upshifts in the rate of diversification in angiosperms. Shifts in diversification do not appear more likely than random within a four-node lag phase following a WGD; however, younger WGD events are more likely to be followed by an upshift in diversification than older WGD events. © 2018 Botanical Society of America.

Paleoclimate determines diversification patterns in the fossorial snake family Uropeltidae Cuvier, 1829.

PubMed

Cyriac, Vivek Philip; Kodandaramaiah, Ullasa

2017-11-01

Understanding how and why diversification rates vary across evolutionary time is central to understanding how biodiversity is generated and maintained. Recent mathematical models that allow estimation of diversification rates across time from reconstructed phylogenies have enabled us to make inferences on how biodiversity copes with environmental change. Here, we explore patterns of temporal diversification in Uropeltidae, a diverse fossorial snake family. We generate a time-calibrated phylogenetic hypothesis for Uropeltidae and show a significant correlation between diversification rate and paleotemperature during the Cenozoic. We show that the temporal diversification pattern of this group is punctuated by one rate shift event with a decrease in diversification and turnover rate between ca. 11Ma to present, but there is no strong support for mass extinction events. The analysis indicates higher turnover during periods of drastic climatic fluctuations and reduced diversification rates associated with contraction and fragmentation of forest habitats during the late Miocene. Our study highlights the influence of environmental fluctuations on diversification rates in fossorial taxa such as uropeltids, and raises conservation concerns related to present rate of climate change. Copyright © 2017 Elsevier Inc. All rights reserved.

Patient Centered Outcomes Assessment of Retreatment and Endodontic Microsurgery Using CBCT Volumetric Analysis

DTIC Science & Technology

2018-11-09

Retreatment and EMS were completed using a dental operating microscope (Zeiss OPMJ PROergo) and contemporary materials and techniques. Retreatrnent...paralleling technique and external cone positioning device (XCP) using size 2 digital sensors (Kodak RVG 6100). A dental x-ray machine (Planmeca...EMS and retreatment were calculated. Examiners used MiPACS dental enterprise viewer (LEAD Technologies Inc, Charlotte, NC) to interpret randomized

A master-slave parallel hybrid multi-objective evolutionary algorithm for groundwater remediation design under general hydrogeological conditions

NASA Astrophysics Data System (ADS)

Wu, J.; Yang, Y.; Luo, Q.; Wu, J.

2012-12-01

This study presents a new hybrid multi-objective evolutionary algorithm, the niched Pareto tabu search combined with a genetic algorithm (NPTSGA), whereby the global search ability of niched Pareto tabu search (NPTS) is improved by the diversification of candidate solutions arose from the evolving nondominated sorting genetic algorithm II (NSGA-II) population. Also, the NPTSGA coupled with the commonly used groundwater flow and transport codes, MODFLOW and MT3DMS, is developed for multi-objective optimal design of groundwater remediation systems. The proposed methodology is then applied to a large-scale field groundwater remediation system for cleanup of large trichloroethylene (TCE) plume at the Massachusetts Military Reservation (MMR) in Cape Cod, Massachusetts. Furthermore, a master-slave (MS) parallelization scheme based on the Message Passing Interface (MPI) is incorporated into the NPTSGA to implement objective function evaluations in distributed processor environment, which can greatly improve the efficiency of the NPTSGA in finding Pareto-optimal solutions to the real-world application. This study shows that the MS parallel NPTSGA in comparison with the original NPTS and NSGA-II can balance the tradeoff between diversity and optimality of solutions during the search process and is an efficient and effective tool for optimizing the multi-objective design of groundwater remediation systems under complicated hydrogeologic conditions.

Anuran radiations and the evolution of tadpole morphospace

PubMed Central

Roelants, Kim; Haas, Alexander; Bossuyt, Franky

2011-01-01

Anurans (frogs and toads) are unique among land vertebrates in possessing a free-living larval stage that, parallel to adult frogs, diversified into an impressive range of ecomorphs. The tempo and mode at which tadpole morphology evolved through anuran history as well as its relationship to lineage diversification remain elusive. We used a molecular phylogenetic framework to examine patterns of morphological evolution in tadpoles in light of observed episodes of accelerated lineage diversification. Our reconstructions show that the expansion of tadpole morphospace during the basal anuran radiation in the Triassic/Early Jurassic was unparalleled by the basal neobatrachian radiation in the Late Jurassic/Early Cretaceous or any subsequent radiation in the Late Cretaceous/Early Tertiary. Comparative analyses of radiation episodes indicate that the slowdown of morphospace expansion was caused not only by a drop in evolutionary rate after the basal anuran radiation but also by an overall increase in homoplasy in the characters that did evolve during later radiations. The overlapping sets of evolving characters among more recent radiations may have enhanced tadpole diversity by creating unique combinations of homoplastic traits, but the lack of innovative character changes prevented the exploration of fundamental regions in morphospace. These complex patterns transcend the four traditionally recognized tadpole morphotypes and apply to most tissue types and body parts. PMID:21555583

IgV gene intraclonal diversification and clonal evolution in B-cell chronic lymphocytic leukaemia.

PubMed

Bagnara, Davide; Callea, Vincenzo; Stelitano, Caterina; Morabito, Fortunato; Fabris, Sonia; Neri, Antonino; Zanardi, Sabrina; Ghiotto, Fabio; Ciccone, Ermanno; Grossi, Carlo Enrico; Fais, Franco

2006-04-01

Intraclonal diversification of immunoglobulin (Ig) variable (V) genes was evaluated in leukaemic cells from a B-cell chronic lymphocytic leukaemia (B-CLL) case over a 2-year period at four time points. Intraclonal heterogeneity was analysed by sequencing 305 molecular clones derived from polymerase chain reaction amplification of B-CLL cell IgV heavy (H) and light (C) chain gene rearrangements. Sequences were compared with evaluating intraclonal variation and the nature of somatic mutations. Although IgV intraclonal variation was detected at all time points, its level decreased with time and a parallel emergence of two more represented V(H)DJ(H) clones was observed. They differed by nine nucleotide substitutions one of which only caused a conservative replacement aminoacid change. In addition, one V(L)J(L) rearrangement became more represented over time. Analyses of somatic mutations suggest antigen selection and impairment of negative selection of neoplastic cells. In addition, a genealogical tree representing a model of clonal evolution of the neoplastic cells was created. It is of note that, during the period of study, the patient showed clinical progression of disease. We conclude that antigen stimulation and somatic hypermutation may participate in disease progression through the selection and expansion of neoplastic subclone(s).

The Hyalella (Crustacea: Amphipoda) species cloud of the ancient Lake Titicaca originated from multiple colonizations.

PubMed

Adamowicz, Sarah J; Marinone, María Cristina; Menu-Marque, Silvina; Martin, Jeffrey W; Allen, Daniel C; Pyle, Michelle N; De Los Ríos, Patricio; Sobel, Crystal N; Ibañez, Carla; Pinto, Julio; Witt, Jonathan D S

2018-08-01

Ancient lakes are renowned for their exceptional diversity of endemic species. As model systems for the study of sympatric speciation, it is necessary to understand whether a given hypothesized species flock is of monophyletic or polyphyletic origin. Here, we present the first molecular characterization of the Hyalella (Crustacea: Amphipoda) species complex of Lake Titicaca, using COI and 28S DNA sequences, including samples from the connected Small and Large Lakes that comprise Lake Titicaca as well as from a broader survey of southern South American sites. At least five evolutionarily distant lineages are present within Lake Titicaca, which were estimated to have diverged from one another 12-20 MYA. These major lineages are dispersed throughout the broader South American Hyalella phylogeny, with each lineage representing at least one independent colonization of the lake. Moreover, complex genetic relationships are revealed between Lake Titicaca individuals and those from surrounding water bodies, which may be explained by repeated dispersal into and out of the lake, combined with parallel intralacustrine diversification within two separate clades. Although further work in deeper waters will be required to determine the number of species present and modes of diversification, our results strongly indicate that this amphipod species cloud is polyphyletic with a complex geographic history. Copyright © 2018 Elsevier Inc. All rights reserved.

Whole genome-based phylogeny of reptile-associated Helicobacter indicates independent niche adaptation followed by diversification in a poikilothermic host.

PubMed

Gilbert, Maarten J; Duim, Birgitta; Timmerman, Arjen J; Zomer, Aldert L; Wagenaar, Jaap A

2017-08-21

Reptiles have been shown to host a significant Helicobacter diversity. In order to survive, reptile-associated Helicobacter lineages need to be adapted to the thermally dynamic environment encountered in a poikilothermic host. The whole genomes of reptile-associated Helicobacter lineages can provide insights in Helicobacter host adaptation and coevolution. These aspects were explored by comparing the genomes of reptile-, bird-, and mammal-associated Helicobacter lineages. Based on average nucleotide identity, all reptile-associated Helicobacter lineages in this study could be considered distinct species. A whole genome-based phylogeny showed two distinct clades, one associated with chelonians and one associated with lizards. The phylogeny indicates initial adaptation to an anatomical niche, which is followed by an ancient host jump and subsequent diversification. Furthermore, the ability to grow at low temperatures, which might reflect thermal adaptation to a reptilian host, originated at least twice in Helicobacter evolution. A putative tricarballylate catabolism locus was specifically present in Campylobacter and Helicobacter isolates from reptiles. The phylogeny of reptile-associated Helicobacter parallels host association, indicating a high level of host specificity. The high diversity and deep branching within these clades supports long-term coevolution with, and extensive radiation within the respective reptilian host type.

Diversification and Competition in Higher Education.

ERIC Educational Resources Information Center

Ruegg, Walter

1987-01-01

Understanding the issues involved in the diversifications of missions and functions in higher education requires (1) distinguishing between vertical and horizontal diversification, either between or within institutions and (2) identifying the agents and mechanisms causing diversification within different higher education systems, including both…

Playing in parallel: the effects of multiplayer modes in active video game on motivation and physical exertion.

PubMed

Peng, Wei; Crouse, Julia

2013-06-01

Although multiplayer modes are common among contemporary video games, the bulk of game research focuses on the single-player mode. To fill the gap in the literature, the current study investigated the effects of different multiplayer modes on enjoyment, future play motivation, and the actual physical activity intensity in an active video game. One hundred sixty-two participants participated in a one-factor between-subject laboratory experiment with three conditions: (a) single player: play against self pretest score; (b) cooperation with another player in the same physical space; (c) parallel competition with another player in separated physical spaces. We found that parallel competition in separate physical spaces was the optimal mode, since it resulted in both high enjoyment and future play motivation and high physical intensity. Implications for future research on multiplayer mode and play space as well as active video game-based physical activity interventions are discussed.

Testing for coevolutionary diversification: linking pattern with process.

PubMed

Althoff, David M; Segraves, Kari A; Johnson, Marc T J

2014-02-01

Coevolutionary diversification is cited as a major mechanism driving the evolution of diversity, particularly in plants and insects. However, tests of coevolutionary diversification have focused on elucidating macroevolutionary patterns rather than the processes giving rise to such patterns. Hence, there is weak evidence that coevolution promotes diversification. This is in part due to a lack of understanding about the mechanisms by which coevolution can cause speciation and the difficulty of integrating results across micro- and macroevolutionary scales. In this review, we highlight potential mechanisms of coevolutionary diversification, outline approaches to examine this process across temporal scales, and propose a set of minimal requirements for demonstrating coevolutionary diversification. Our aim is to stimulate research that tests more rigorously for coevolutionary diversification. Copyright © 2013 Elsevier Ltd. All rights reserved.

Courting disaster: How diversification rate affects fitness under risk

PubMed Central

Ratcliff, William C; Hawthorne, Peter; Libby, Eric

2015-01-01

Life is full of risk. To deal with this uncertainty, many organisms have evolved bet-hedging strategies that spread risk through phenotypic diversification. These rates of diversification can vary by orders of magnitude in different species. Here we examine how key characteristics of risk and organismal ecology affect the fitness consequences of variation in diversification rate. We find that rapid diversification is strongly favored when the risk faced has a wide spatial extent, with a single disaster affecting a large fraction of the population. This advantage is especially great in small populations subject to frequent disaster. In contrast, when risk is correlated through time, slow diversification is favored because it allows adaptive tracking of disasters that tend to occur in series. Naturally evolved diversification mechanisms in diverse organisms facing a broad array of environmental risks largely support these results. The theory presented in this article provides a testable ecological hypothesis to explain the prevalence of slow stochastic switching among microbes and rapid, within-clutch diversification strategies among plants and animals. PMID:25410817

Depth as a driver of evolution in the deep sea: Insights from grenadiers (Gadiformes: Macrouridae) of the genus Coryphaenoides.

PubMed

Gaither, Michelle R; Violi, Biagio; Gray, Howard W I; Neat, Francis; Drazen, Jeffrey C; Grubbs, R Dean; Roa-Varón, Adela; Sutton, Tracey; Hoelzel, A Rus

2016-11-01

Here we consider the role of depth as a driver of evolution in a genus of deep-sea fishes. We provide a phylogeny for the genus Coryphaenoides (Gadiformes: Macrouridae) that represents the breadth of habitat use and distributions for these species. In our consensus phylogeny species found at abyssal depths (>4000m) form a well-supported lineage, which interestingly also includes two non-abyssal species, C. striaturus and C. murrayi, diverging from the basal node of that lineage. Biogeographic analyses suggest the genus may have originated in the Southern and Pacific Oceans where contemporary species diversity is highest. The abyssal lineage seems to have arisen secondarily and likely originated in the Southern/Pacific Oceans but diversification of this lineage occurred in the Northern Atlantic Ocean. All abyssal species are found in the North Atlantic with the exception of C. yaquinae in the North Pacific and C. filicauda in the Southern Ocean. Abyssal species tend to have broad depth ranges and wide distributions, indicating that the stability of the deep oceans and the ability to live across wide depths may promote population connectivity and facilitate large ranges. We also confirm that morphologically defined subgenera do not agree with our phylogeny and that the Giant grenadier (formerly Albatrossia pectoralis) belongs to Coryphaenoides, indicating that a taxonomic revision of the genus is needed. We discuss the implications of our findings for understanding the radiation and diversification of this genus, and the likely role of adaptation to the abyss. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Global patterns of insect diversification: towards a reconciliation of fossil and molecular evidence?

PubMed

Condamine, Fabien L; Clapham, Matthew E; Kergoat, Gael J

2016-01-18

Macroevolutionary studies of insects at diverse taxonomic scales often reveal dynamic evolutionary patterns, with multiple inferred diversification rate shifts. Responses to major past environmental changes, such as the Cretaceous Terrestrial Revolution, or the development of major key innovations, such as wings or complete metamorphosis are usually invoked as potential evolutionary triggers. However this view is partially contradicted by studies on the family-level fossil record showing that insect diversification was relatively constant through time. In an attempt to reconcile both views, we investigate large-scale insect diversification dynamics at family level using two distinct types of diversification analyses on a molecular timetree representing ca. 82% of the extant families, and reassess the insect fossil diversity using up-to-date records. Analyses focusing on the fossil record recovered an early burst of diversification, declining to low and steady rates through time, interrupted by extinction events. Phylogenetic analyses showed that major shifts of diversification rates only occurred in the four richest holometabolous orders. Both suggest that neither the development of flight or complete metamorphosis nor the Cretaceous Terrestrial Revolution environmental changes induced immediate changes in diversification regimes; instead clade-specific innovations likely promoted the diversification of major insect orders.

Global patterns of insect diversification: towards a reconciliation of fossil and molecular evidence?

PubMed Central

Condamine, Fabien L.; Clapham, Matthew E.; Kergoat, Gael J.

2016-01-01

Macroevolutionary studies of insects at diverse taxonomic scales often reveal dynamic evolutionary patterns, with multiple inferred diversification rate shifts. Responses to major past environmental changes, such as the Cretaceous Terrestrial Revolution, or the development of major key innovations, such as wings or complete metamorphosis are usually invoked as potential evolutionary triggers. However this view is partially contradicted by studies on the family-level fossil record showing that insect diversification was relatively constant through time. In an attempt to reconcile both views, we investigate large-scale insect diversification dynamics at family level using two distinct types of diversification analyses on a molecular timetree representing ca. 82% of the extant families, and reassess the insect fossil diversity using up-to-date records. Analyses focusing on the fossil record recovered an early burst of diversification, declining to low and steady rates through time, interrupted by extinction events. Phylogenetic analyses showed that major shifts of diversification rates only occurred in the four richest holometabolous orders. Both suggest that neither the development of flight or complete metamorphosis nor the Cretaceous Terrestrial Revolution environmental changes induced immediate changes in diversification regimes; instead clade-specific innovations likely promoted the diversification of major insect orders. PMID:26778170

Host shifts enhance diversification of ectomycorrhizal fungi: diversification rate analysis of the ectomycorrhizal fungal genera Strobilomyces and Afroboletus with an 80-gene phylogeny.

PubMed

Sato, Hirotoshi; Tanabe, Akifumi S; Toju, Hirokazu

2017-04-01

Mutualisms with new host lineages can provide symbionts with novel ecological opportunities to expand their geographical distribution, thereby leading to evolutionary diversification. Because ectomycorrhizal (ECM) fungi provide ideal opportunities to test the relationship between host shifts and diversification, we tested whether mutualism with new host lineages could increase the diversification rates of ECM fungi. Using a Bayesian tree inferred from 23 027-base nucleotide sequences of 80 single-copy genes, we tested whether the diversification rate had changed through host-shift events in the monophyletic clade containing the ECM fungal genera Strobilomyces and Afroboletus. The results indicated that these fungi were initially associated with Caesalpinioideae/Monotoideae in Africa, acquired associations with Dipterocarpoideae in tropical Asia, and then switched to Fagaceae/Pinaceae and Nothofagaceae/Eucalyptus. Fungal lineages associated with Fagaceae/Pinaceae were inferred to have approximately four-fold and two-fold greater diversification rates than those associated with Caesalpinioideae/Monotoideae and Dipterocarpoideae or Nothofagaceae/Eucalyptus, respectively. Moreover, the diversification rate shift was inferred to follow the host shift to Fagaceae/Pinaceae. Our study suggests that host-shift events, particularly those occurring with respect to Fagaceae/Pinaceae, can provide ecological opportunities for the rapid diversification of Strobilomyces-Afroboletus. Although further studies are needed for generalization, we propose a possible diversification scenario of ECM fungi. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

The Tera Multithreaded Architecture and Unstructured Meshes

NASA Technical Reports Server (NTRS)

Bokhari, Shahid H.; Mavriplis, Dimitri J.

1998-01-01

The Tera Multithreaded Architecture (MTA) is a new parallel supercomputer currently being installed at San Diego Supercomputing Center (SDSC). This machine has an architecture quite different from contemporary parallel machines. The computational processor is a custom design and the machine uses hardware to support very fine grained multithreading. The main memory is shared, hardware randomized and flat. These features make the machine highly suited to the execution of unstructured mesh problems, which are difficult to parallelize on other architectures. We report the results of a study carried out during July-August 1998 to evaluate the execution of EUL3D, a code that solves the Euler equations on an unstructured mesh, on the 2 processor Tera MTA at SDSC. Our investigation shows that parallelization of an unstructured code is extremely easy on the Tera. We were able to get an existing parallel code (designed for a shared memory machine), running on the Tera by changing only the compiler directives. Furthermore, a serial version of this code was compiled to run in parallel on the Tera by judicious use of directives to invoke the "full/empty" tag bits of the machine to obtain synchronization. This version achieves 212 and 406 Mflop/s on one and two processors respectively, and requires no attention to partitioning or placement of data issues that would be of paramount importance in other parallel architectures.

The risks of innovation in health care.

PubMed

Enzmann, Dieter R

2015-04-01

Innovation in health care creates risks that are unevenly distributed. An evolutionary analogy using species to represent business models helps categorize innovation experiments and their risks. This classification reveals two qualitative categories: early and late diversification experiments. Early diversification has prolific innovations with high risk because they encounter a "decimation" stage, during which most experiments disappear. Participants face high risk. The few decimation survivors can be sustaining or disruptive according to Christensen's criteria. Survivors enter late diversification, during which they again expand, but within a design range limited to variations of the previous surviving designs. Late diversifications carry lower risk. The exception is when disruptive survivors "diversify," which amplifies their disruption. Health care and radiology will experience both early and late diversifications, often simultaneously. Although oversimplifying Christensen's concepts, early diversifications are likely to deliver disruptive innovation, whereas late diversifications tend to produce sustaining innovations. Current health care consolidation is a manifestation of late diversification. Early diversifications will appear outside traditional care models and physical health care sites, as well as with new science such as molecular diagnostics. They warrant attention because decimation survivors will present both disruptive and sustaining opportunities to radiology. Radiology must participate in late diversification by incorporating sustaining innovations to its value chain. Given the likelihood of disruptive survivors, radiology should seriously consider disrupting itself rather than waiting for others to do so. Disruption entails significant modifications of its value chain, hence, its business model, for which lessons may become available from the pharmaceutical industry's current simultaneous experience with early and late diversifications. Copyright © 2015. Published by Elsevier Inc.

Interpreting the gamma statistic in phylogenetic diversification rate studies: a rate decrease does not necessarily indicate an early burst.

PubMed

Fordyce, James A

2010-07-23

Phylogenetic hypotheses are increasingly being used to elucidate historical patterns of diversification rate-variation. Hypothesis testing is often conducted by comparing the observed vector of branching times to a null, pure-birth expectation. A popular method for inferring a decrease in speciation rate, which might suggest an early burst of diversification followed by a decrease in diversification rate is the gamma statistic. Using simulations under varying conditions, I examine the sensitivity of gamma to the distribution of the most recent branching times. Using an exploratory data analysis tool for lineages through time plots, tree deviation, I identified trees with a significant gamma statistic that do not appear to have the characteristic early accumulation of lineages consistent with an early, rapid rate of cladogenesis. I further investigated the sensitivity of the gamma statistic to recent diversification by examining the consequences of failing to simulate the full time interval following the most recent cladogenic event. The power of gamma to detect rate decrease at varying times was assessed for simulated trees with an initial high rate of diversification followed by a relatively low rate. The gamma statistic is extraordinarily sensitive to recent diversification rates, and does not necessarily detect early bursts of diversification. This was true for trees of various sizes and completeness of taxon sampling. The gamma statistic had greater power to detect recent diversification rate decreases compared to early bursts of diversification. Caution should be exercised when interpreting the gamma statistic as an indication of early, rapid diversification.

Fighting Islamic Terrorists With Democracy: A Critique

DTIC Science & Technology

2007-05-21

other hand, translations of the Bible from its Aramaic, Hebrew , and Koine Greek yield no such unlimited, violent imperatives requiring contemporary...pronouncements of a mere man who claimed to speak with the authority of Christ, and yet repeatedly contradicted the clear teachings of the Bible . Thus, the...faithful. And here is where the parallel between “fundamentalist” worshippers seeking to understand the Qur’an and the Bible —both written in tongues

The Great Beyond: Higher Dimensions, Parallel Universes and the Extraordinary Search for a Theory of Everything

NASA Astrophysics Data System (ADS)

Halpern, Paul

2005-08-01

Praise for The Great Beyond "A marvelous book-very clear, very readable. A brilliant introduction to the math and physics of higher dimensions, from Flatland to superstrings. Its greatest strength is a wealth of fascinating historical narrative and anecdote. I enjoyed it enormously." -Ian Stewart, author of Flatterland "A remarkable journey from Plato's cave to the farthest reaches of human thought and scientific knowledge. This mind-boggling book allows readers to dream strange visions of hyperspace, chase light waves, explore Klein's quantum odyssey and Kaluza's cocoon, leap through parallel universes, and grasp the very essence of conscience and cosmos. Buy this book and feed your head." -Clifford Pickover, author of A Passion for Mathematics "Halpern looks with a bemused eye at the wildest ideas currently afoot in physics. He takes us into the personal world of those who relish and explore seemingly outlandish notions, and does it with a light, engaging style." -Gregory Benford, author of Foundation's Fear "An informative, stimulating, and thoughtful presentation at the very frontiers of contemporary physics. It is quite on a par with Brian Greene's The Elegant Universe or his more recent The Fabric of the Cosmos, and as such, deserves to receive wide non-specialist coverage among an intelligent, curious, thinking public." -Professor E. Sheldon, Contemporary Physics

Parallel changes in genital morphology delineate cryptic diversification of planktonic nudibranchs

PubMed Central

Churchill, Celia K. C.; Alejandrino, Alvin; Valdés, Ángel; Ó Foighil, Diarmaid

2013-01-01

The relative roles of geographical and non-geographical barriers in the genesis of genetic isolation are highly debated in evolutionary biology, yet knowing how speciation occurs is essential to our understanding of biodiversity. In the open ocean, differentiating between the two is particularly difficult, because of the high levels of gene flow found in pelagic communities. Here, we use molecular phylogenetics to test the hypothesis that geography is the primary isolating mechanism in a clade of pelagic nudibranchs, Glaucinae. Our results contradict allopatric expectations: the cosmopolitan Glaucus atlanticus is panmictic, whereas the Indo-Pacific Glaucus marginatus contains two pairs of cryptic species with overlapping distributions. Within the G. marginatus species complex, a parallel reproductive change has occurred in each cryptic species pair: the loss of a bursa copulatrix. Available G. marginatus data are most consistent with non-geographical speciation events, but we cannot rule out the possibility of allopatric speciation, followed by iterative range extension and secondary overlap. Irrespective of ancestral range distributions, our results implicate a central role for reproductive character differentiation in glaucinin speciation—a novel result in a planktonic system. PMID:23825213

Cortical organization in insectivora: the parallel evolution of the sensory periphery and the brain.

PubMed

Catania, K C

2000-06-01

Insectivores are traditionally described as a primitive group that has not changed much in the course of mammalian evolution. In contrast, recent studies reveal a great diversity of sensorimotor specializations among insectivores adapted to a number of different ecological niches, indicating that there has been significant diversification and change in the course of their evolution. Here the organization of sensory cortex is compared in the African hedgehog (Atelerix albiventris), the masked shrew (Sorex cinereus), the eastern mole (Scalopus aquaticus), and the star-nosed mole (Condylura cristata). Each of these four closely related species lives in a unique ecological niche, exhibits a different repertoire of behaviors, and has a different configuration of peripheral sensory receptors. Corresponding specializations of cortical sensory areas reveal a number of ways in which the cortex has evolved in parallel with changes to the sensory periphery. These specializations include expansion of cortical representations (cortical magnification), the addition or loss of cortical areas in the processing network, and the subdivision of areas into modules (barrels and stripes). Copyright 2000 S. Karger AG, Basel

Diversity spurs diversification in ecological communities

PubMed Central

Calcagno, Vincent; Jarne, Philippe; Loreau, Michel; Mouquet, Nicolas; David, Patrice

2017-01-01

Diversity is a fundamental, yet threatened, property of ecological systems. The idea that diversity can itself favour diversification, in an autocatalytic process, is very appealing but remains controversial. Here, we study a generalized model of ecological communities and investigate how the level of initial diversity influences the possibility of evolutionary diversification. We show that even simple models of intra- and inter-specific ecological interactions can predict a positive effect of diversity on diversification: adaptive radiations may require a threshold number of species before kicking-off. We call this phenomenon DDAR (diversity-dependent adaptive radiations) and identify mathematically two distinct pathways connecting diversity to diversification, involving character displacement and the positive diversity-productivity relationship. Our results may explain observed delays in adaptive radiations at the macroscale and diversification patterns reported in experimental microbial communities, and shed new light on the dynamics of ecological diversity, the diversity-dependence of diversification rates, and the consequences of biodiversity loss. PMID:28598423

Diversity spurs diversification in ecological communities

NASA Astrophysics Data System (ADS)

Calcagno, Vincent; Jarne, Philippe; Loreau, Michel; Mouquet, Nicolas; David, Patrice

2017-06-01

Diversity is a fundamental, yet threatened, property of ecological systems. The idea that diversity can itself favour diversification, in an autocatalytic process, is very appealing but remains controversial. Here, we study a generalized model of ecological communities and investigate how the level of initial diversity influences the possibility of evolutionary diversification. We show that even simple models of intra- and inter-specific ecological interactions can predict a positive effect of diversity on diversification: adaptive radiations may require a threshold number of species before kicking-off. We call this phenomenon DDAR (diversity-dependent adaptive radiations) and identify mathematically two distinct pathways connecting diversity to diversification, involving character displacement and the positive diversity-productivity relationship. Our results may explain observed delays in adaptive radiations at the macroscale and diversification patterns reported in experimental microbial communities, and shed new light on the dynamics of ecological diversity, the diversity-dependence of diversification rates, and the consequences of biodiversity loss.

Diversity spurs diversification in ecological communities.

PubMed

Calcagno, Vincent; Jarne, Philippe; Loreau, Michel; Mouquet, Nicolas; David, Patrice

2017-06-09

Diversity is a fundamental, yet threatened, property of ecological systems. The idea that diversity can itself favour diversification, in an autocatalytic process, is very appealing but remains controversial. Here, we study a generalized model of ecological communities and investigate how the level of initial diversity influences the possibility of evolutionary diversification. We show that even simple models of intra- and inter-specific ecological interactions can predict a positive effect of diversity on diversification: adaptive radiations may require a threshold number of species before kicking-off. We call this phenomenon DDAR (diversity-dependent adaptive radiations) and identify mathematically two distinct pathways connecting diversity to diversification, involving character displacement and the positive diversity-productivity relationship. Our results may explain observed delays in adaptive radiations at the macroscale and diversification patterns reported in experimental microbial communities, and shed new light on the dynamics of ecological diversity, the diversity-dependence of diversification rates, and the consequences of biodiversity loss.

Curriculum Diversification Re-examined--A Case Study of Sierra Leone.

ERIC Educational Resources Information Center

Wright, Cream A. H.

This paper deals with a case study of secondary curriculum diversification as a vocationalization strategy in Sierra Leone. It explores diversification issues from four crucial standpoints that are distinct but highly interrelated. First, diversification is dealt with as a policy that was adopted and actively pursued by Sierra Leone for over a…

Niche evolution and diversification in a Neotropical radiation of birds (Aves: Furnariidae).

PubMed

Seeholzer, Glenn F; Claramunt, Santiago; Brumfield, Robb T

2017-03-01

Rapid diversification may be caused by ecological adaptive radiation via niche divergence. In this model, speciation is coupled with niche divergence and lineage diversification is predicted to be correlated with rates of niche evolution. Studies of the role of niche evolution in diversification have generally focused on ecomorphological diversification but climatic-niche evolution may also be important. We tested these alternatives using a phylogeny of 298 species of ovenbirds (Aves: Furnariidae). We found that within Furnariidae, variation in species richness and diversification rates of subclades were best predicted by rate of climatic-niche evolution than ecomorphological evolution. Although both are clearly important, univariate regression and multivariate model averaging more consistently supported the climatic-niche as the best predictor of lineage diversification. Our study adds to the growing body of evidence, suggesting that climatic-niche divergence may be an important driver of rapid diversification in addition to ecomorphological evolution. However, this pattern may depend on the phylogenetic scale at which rate heterogeneity is examined. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Exploring Diversification as A Management Strategy in Substance Use Disorder Treatment Organizations.

PubMed

Fields, Dail; Riesenmy, Kelly; Roman, Paul M

2015-10-01

Implementation of the Affordable Care Act (ACA) creates both environmental uncertainties and opportunities for substance use disorder (SUD) treatment providers. One managerial response to uncertainties and emergent opportunities is strategic diversification of various dimensions of organizational activity. This paper explored organizational outcomes related to diversification of funding sources, services offered, and referral sources in a national sample of 590 SUD treatment organizations. Funding diversification was related to higher average levels of census, organization size, and recent expansion of operations. Service diversification was related to higher average levels of use of medication-assisted treatment (MAT), organization size, and expansion. Referral source diversification was related only to greater average use of MAT. Overall, strategic diversification in the three areas explored was related to positive organizational outcomes. Considering alternative strategies of diversification may help position SUD treatment centers to deliver more innovative treatments such as MAT as well as enhance capacity to satisfy current unmet treatment needs of individuals with behavioral health coverage provided under the ACA. Copyright © 2015 Elsevier Inc. All rights reserved.

Patterns of diversification in islands: A comparative study across three gecko genera in the Socotra Archipelago.

PubMed

Garcia-Porta, Joan; Morales, Hernán E; Gómez-Díaz, Elena; Sindaco, Roberto; Carranza, Salvador

2016-05-01

In this study we used the complete fauna of geckos of the Socotra Archipelago to test whether the three gecko genera co-occurring in the islands (Pristurus, Hemidactylus and Haemodracon) produced similar outcomes of morphological and climatic diversification. To test this, we produced a time-calibrated tree of 346 geckos including all 16 endemic species of the archipelago and 26 potential close-relatives in the continent. Our dating estimates revealed that most of the diversity of geckos in the archipelago was the consequence of in situ diversification. However not all genera shared similar patterns of diversification. While in Hemidactylus and Haemodracon this involved great differences in body size and low levels of climatic diversification (mostly involving sympatric distributions), an opposite pattern appeared in Pristurus in which most of the diversification involved shifts in climatic envelopes (mostly involving allopatric and parapatric distributions) but almost no size differentiation. Consistently with this, Pristurus was the only genus in which rates of size diversification in islands were substantially lower than in the continent. This illustrates how different groups can greatly differ in their patterns of intra-island diversification and highlights the importance of taxon-dependent factors at determining different patterns of diversification in the same insular context. Copyright © 2016 Elsevier Inc. All rights reserved.

Diversification rates are more strongly related to microhabitat than climate in squamate reptiles (lizards and snakes).

PubMed

Bars-Closel, Melissa; Kohlsdorf, Tiana; Moen, Daniel S; Wiens, John J

2017-09-01

Patterns of species richness among clades can be directly explained by the ages of clades or their rates of diversification. The factors that most strongly influence diversification rates remain highly uncertain, since most studies typically consider only a single predictor variable. Here, we explore the relative impacts of macroclimate (i.e., occurring in tropical vs. temperate regions) and microhabitat use (i.e., terrestrial, fossorial, arboreal, aquatic) on diversification rates of squamate reptile clades (lizards and snakes). We obtained data on microhabitat, macroclimatic distribution, and phylogeny for >4000 species. We estimated diversification rates of squamate clades (mostly families) from a time-calibrated tree, and used phylogenetic methods to test relationships between diversification rates and microhabitat and macroclimate. Across 72 squamate clades, the best-fitting model included microhabitat but not climatic distribution. Microhabitat explained ∼37% of the variation in diversification rates among clades, with a generally positive impact of arboreal microhabitat use on diversification, and negative impacts of fossorial and aquatic microhabitat use. Overall, our results show that the impacts of microhabitat on diversification rates can be more important than those of climate, despite much greater emphasis on climate in previous studies. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

The impact of rise of the Andes and Amazon landscape evolution on diversification of lowland terra-firme forest birds

NASA Astrophysics Data System (ADS)

Aleixo, A.; Wilkinson, M. J.

2011-12-01

Since the 19th Century, the unmatched biological diversity of Amazonia has stimulated a diverse set of hypotheses accounting for patterns of species diversity and distribution in mega-diverse tropical environments. Unfortunately, the evidence supporting particular hypotheses to date is at best described as ambiguous, and no generalizations have emerged yet, mostly due to the lack of comprehensive comparative phylogeographic studies with thorough trans-Amazonian sampling of lineages. Here we report on spatial and temporal patterns of diversification estimated from mitochondrial gene trees for 31 lineages of birds associated with upland terra-firme forest, the dominant habitat in modern lowland Amazonia. The results confirm the pervasive role of Amazonian rivers as primary barriers separating sister lineages of birds, and a protracted spatio-temporal pattern of diversification, with a gradual reduction of earlier (1st and 2nd) and older (> 2 mya) splits associated with each lineage in an eastward direction (the easternmost tributaries of the Amazon, the Xingu and Tocantins Rivers, are not associated with any splits older than > 2 mya). This "younging-eastward" pattern may have an abiotic explanation related to landscape evolution. Triggered by a new pulse of Andean uplift, it has been proposed that modern Amazon basin landscapes may have evolved successively eastward, away from the mountain chain, starting ~10 mya. This process was likely based on the deposition of vast fluvial sediment masses, known as megafans, which apparently extended in series progressively eastward from Andean sources. The effects on drainage patterns are apparent from the location of axial rivers such as the Negro / Orinoco and Madeira which lie at the distal ends of major megafan ramparts at cratonic margins furthest from the Andes. Megafan extension plausibly explains the progressive extinction of the original Pebas wetland of west-central Amazonia by the present fluvial landsurfaces where upland terra-firme forest develop. The youngest landsurfaces thus appear to lie furthest from the mountains. In this scenario major drainages were also reoriented in wholesale fashion from a northward (Caribbean) outlet to a generally eastward, Atlantic Ocean outlet. More importantly, other major river courses in western-central Amazonia will have been established at progressively younger dates with distance eastward. The bird DNA data appears to confirm the role of Amazonian rivers as primary diversification barriers, and thus probably as promoters of bird speciation. We show for the first time that a general spatio-temporal pattern of diversification for terra-firme lineages in the Amazon is associated with rivers of apparently different ages ("younging-eastward"), and furthermore parallels a specific scenario of regional drainage evolution.

Were Oceanic Plateaus Instrumental for Calcareous Nannoplankton Evolution?

NASA Astrophysics Data System (ADS)

Erba, E.; Casellato, C.; Bottini, C.

2011-12-01

The history of calcareous nannoplankton shows a general increase in species richness through the Mesozoic. Fertility and chemistry of the oceans, climate and pCO2 seem instrumental for nannoplankton abundance, diversification and adaptation, but high-resolution chronology of paleobiological and geological events is crucial for the understanding of evolutionary processes relative to ecosystem perturbations. Natural variations in atmospheric CO2 are essentially triggered by igneous activity and the role of ocean crust production in the evolution of seawater composition, nutrient cycling, climate change and, consequently, in calcareous nannoplankton biodiversity, might be more relevant than generally thought. Indeed, two major steps in nannofloral Mesozoic evolution correlate with construction of gigantic oceanic plateaus, namely the Shatsky Rise (SR) (Tithonian/Berriasian boundary interval) and the Ontong Java Plateau (OJP) (Barremian/Aptian boundary interval). During the latest Jurassic calcareous nannoplankton experienced a rapid diversification and rise in abundance of several taxa including heavily calcified nannoliths with consequent major increase in biogenic calcite production. The Tithonian origination of coccoliths and nannoliths suggests ideal paleoecological conditions for calcareous nannoplankton, presumably thriving in stable, relatively oligotrophic and cool oceans under low pCO2. Recent data indicate that this speciation and calcification episode was interrupted during magnetochron CM19r, prior to massive diversification of nannoconids. In the late Barremian-early Aptian interval, the nannoconid decline and crisis are paralleled by a major nannoplankton (mainly coccolith) speciation episode. Such calcification failure and coccolith diversification might reflect disruption of the thermocline, increased fertility and warming under excess CO2 levels. These evolutionary steps show rapid speciation, but differ because nannoliths became dominant in the late Tithonian whereas suffered a major crisis in the early Aptian, although without extinctions. Can SR and OJP be used to understand evolutionary patterns of oceanic calcifiers? Was the massive emplacement of submarine and/or subaerial basalts and CO2 outgassing instrumental for directing biological innovation? Increased volcanic CO2 could induce ocean acidification and hamper nannoplankton calcification, presumably favoring production and diversification of small coccoliths and perhaps inducing extinctions. The appearance and rapid development of heavily calcified nannoliths in the late Tithonian is odd if took place during the construction of the huge SR. However, early subaerial volcanism of the vast paleoequatorial Shatsky archipelago might have turned the climate into cooler conditions and altered oceanic structure and circulation, possibly establishing a thermocline in the lower photic zone. Perhaps the marked decrease in nannolith calcification during CM 19r was triggered by the rapid eruption of SR submarine edifice, similarly to the nannoconid crisis linked to OJP volcanism. The combination of climate change, alteration of ocean chemistry, structure, circulation and fertility during formation of oceanic plateaus might explain diverse tempo and mode of nannoplankton innovation.

How Well Can We Detect Lineage-Specific Diversification-Rate Shifts? A Simulation Study of Sequential AIC Methods.

PubMed

May, Michael R; Moore, Brian R

2016-11-01

Evolutionary biologists have long been fascinated by the extreme differences in species numbers across branches of the Tree of Life. This has motivated the development of statistical methods for detecting shifts in the rate of lineage diversification across the branches of phylogenic trees. One of the most frequently used methods, MEDUSA, explores a set of diversification-rate models, where each model assigns branches of the phylogeny to a set of diversification-rate categories. Each model is first fit to the data, and the Akaike information criterion (AIC) is then used to identify the optimal diversification model. Surprisingly, the statistical behavior of this popular method is uncharacterized, which is a concern in light of: (1) the poor performance of the AIC as a means of choosing among models in other phylogenetic contexts; (2) the ad hoc algorithm used to visit diversification models, and; (3) errors that we reveal in the likelihood function used to fit diversification models to the phylogenetic data. Here, we perform an extensive simulation study demonstrating that MEDUSA (1) has a high false-discovery rate (on average, spurious diversification-rate shifts are identified [Formula: see text] of the time), and (2) provides biased estimates of diversification-rate parameters. Understanding the statistical behavior of MEDUSA is critical both to empirical researchers-in order to clarify whether these methods can make reliable inferences from empirical datasets-and to theoretical biologists-in order to clarify the specific problems that need to be solved in order to develop more reliable approaches for detecting shifts in the rate of lineage diversification. [Akaike information criterion; extinction; lineage-specific diversification rates; phylogenetic model selection; speciation.]. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

How Well Can We Detect Lineage-Specific Diversification-Rate Shifts? A Simulation Study of Sequential AIC Methods

PubMed Central

May, Michael R.; Moore, Brian R.

2016-01-01

Evolutionary biologists have long been fascinated by the extreme differences in species numbers across branches of the Tree of Life. This has motivated the development of statistical methods for detecting shifts in the rate of lineage diversification across the branches of phylogenic trees. One of the most frequently used methods, MEDUSA, explores a set of diversification-rate models, where each model assigns branches of the phylogeny to a set of diversification-rate categories. Each model is first fit to the data, and the Akaike information criterion (AIC) is then used to identify the optimal diversification model. Surprisingly, the statistical behavior of this popular method is uncharacterized, which is a concern in light of: (1) the poor performance of the AIC as a means of choosing among models in other phylogenetic contexts; (2) the ad hoc algorithm used to visit diversification models, and; (3) errors that we reveal in the likelihood function used to fit diversification models to the phylogenetic data. Here, we perform an extensive simulation study demonstrating that MEDUSA (1) has a high false-discovery rate (on average, spurious diversification-rate shifts are identified ≈30% of the time), and (2) provides biased estimates of diversification-rate parameters. Understanding the statistical behavior of MEDUSA is critical both to empirical researchers—in order to clarify whether these methods can make reliable inferences from empirical datasets—and to theoretical biologists—in order to clarify the specific problems that need to be solved in order to develop more reliable approaches for detecting shifts in the rate of lineage diversification. [Akaike information criterion; extinction; lineage-specific diversification rates; phylogenetic model selection; speciation.] PMID:27037081

Ancient diversification of eukaryotic MCM DNA replication proteins

PubMed Central

Liu, Yuan; Richards, Thomas A; Aves, Stephen J

2009-01-01

Background Yeast and animal cells require six mini-chromosome maintenance proteins (Mcm2-7) for pre-replication complex formation, DNA replication initiation and DNA synthesis. These six individual MCM proteins form distinct heterogeneous subunits within a hexamer which is believed to form the replicative helicase and which associates with the essential but non-homologous Mcm10 protein during DNA replication. In contrast Archaea generally only possess one MCM homologue which forms a homohexameric MCM helicase. In some eukaryotes Mcm8 and Mcm9 paralogues also appear to be involved in DNA replication although their exact roles are unclear. Results We used comparative genomics and phylogenetics to reconstruct the diversification of the eukaryotic Mcm2-9 gene family, demonstrating that Mcm2-9 were formed by seven gene duplication events before the last common ancestor of the eukaryotes. Mcm2-7 protein paralogues were present in all eukaryote genomes studied suggesting that no gene loss or functional replacements have been tolerated during the evolutionary diversification of eukaryotes. Mcm8 and 9 are widely distributed in eukaryotes and group together on the MCM phylogenetic tree to the exclusion of all other MCM paralogues suggesting co-ancestry. Mcm8 and Mcm9 are absent in some taxa, including Trichomonas and Giardia, and appear to have been secondarily lost in some fungi and some animals. The presence and absence of Mcm8 and 9 is concordant in all taxa sampled with the exception of Drosophila species. Mcm10 is present in most eukaryotes sampled but shows no concordant pattern of presence or absence with Mcm8 or 9. Conclusion A multifaceted and heterogeneous Mcm2-7 hexamer evolved during the early evolution of the eukaryote cell in parallel with numerous other acquisitions in cell complexity and prior to the diversification of extant eukaryotes. The conservation of all six paralogues throughout the eukaryotes suggests that each Mcm2-7 hexamer component has an exclusive functional role, either by a combination of unique lock and key interactions between MCM hexamer subunits and/or by a range of novel side interactions. Mcm8 and 9 evolved early in eukaryote cell evolution and their pattern of presence or absence suggests that they may have linked functions. Mcm8 is highly divergent in all Drosophila species and may not provide a good model for Mcm8 in other eukaryotes. PMID:19292915

Estimating diversification rates for higher taxa: BAMM can give problematic estimates of rates and rate shifts.

PubMed

Meyer, Andreas L S; Wiens, John J

2018-01-01

Estimates of diversification rates are invaluable for many macroevolutionary studies. Recently, an approach called BAMM (Bayesian Analysis of Macro-evolutionary Mixtures) has become widely used for estimating diversification rates and rate shifts. At the same time, several articles have concluded that estimates of net diversification rates from the method-of-moments (MS) estimators are inaccurate. Yet, no studies have compared the ability of these two methods to accurately estimate clade diversification rates. Here, we use simulations to compare their performance. We found that BAMM yielded relatively weak relationships between true and estimated diversification rates. This occurred because BAMM underestimated the number of rates shifts across each tree, and assigned high rates to small clades with low rates. Errors in both speciation and extinction rates contributed to these errors, showing that using BAMM to estimate only speciation rates is also problematic. In contrast, the MS estimators (particularly using stem group ages), yielded stronger relationships between true and estimated diversification rates, by roughly twofold. Furthermore, the MS approach remained relatively accurate when diversification rates were heterogeneous within clades, despite the widespread assumption that it requires constant rates within clades. Overall, we caution that BAMM may be problematic for estimating diversification rates and rate shifts. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Quantitative traits and diversification.

PubMed

FitzJohn, Richard G

2010-12-01

Quantitative traits have long been hypothesized to affect speciation and extinction rates. For example, smaller body size or increased specialization may be associated with increased rates of diversification. Here, I present a phylogenetic likelihood-based method (quantitative state speciation and extinction [QuaSSE]) that can be used to test such hypotheses using extant character distributions. This approach assumes that diversification follows a birth-death process where speciation and extinction rates may vary with one or more traits that evolve under a diffusion model. Speciation and extinction rates may be arbitrary functions of the character state, allowing much flexibility in testing models of trait-dependent diversification. I test the approach using simulated phylogenies and show that a known relationship between speciation and a quantitative character could be recovered in up to 80% of the cases on large trees (500 species). Consistent with other approaches, detecting shifts in diversification due to differences in extinction rates was harder than when due to differences in speciation rates. Finally, I demonstrate the application of QuaSSE to investigate the correlation between body size and diversification in primates, concluding that clade-specific differences in diversification may be more important than size-dependent diversification in shaping the patterns of diversity within this group.

Diversification rates have declined in the Malagasy herpetofauna.

PubMed

Scantlebury, Daniel P

2013-09-07

The evolutionary origins of Madagascar's biodiversity remain mysterious despite the fact that relative to land area, there is no other place with consistently high levels of species richness and endemism across a range of taxonomic levels. Most efforts to explain diversification on the island have focused on geographical models of speciation, but recent studies have begun to address the island's accumulation of species through time, although with conflicting results. Prevailing hypotheses for diversification on the island involve either constant diversification rates or scenarios where rates decline through time. Using relative-time-calibrated phylogenies for seven endemic vertebrate clades and a model-fitting framework, I find evidence that diversification rates have declined through time on Madagascar. I show that diversification rates have clearly declined throughout the history of each clade, and models invoking diversity-dependent reductions to diversification rates best explain the diversification histories for each clade. These results are consistent with the ecological theory of adaptive radiation, and, coupled with ancillary observations about ecomorphological and life-history evolution, strongly suggest that adaptive radiation was an important formative process for one of the most species-rich regions on the Earth. These results cast the Malagasy biota in a new light and provide macroevolutionary justification for conservation initiatives.

Biological factors contributing to bark and ambrosia beetle species diversification.

PubMed

Gohli, Jostein; Kirkendall, Lawrence R; Smith, Sarah M; Cognato, Anthony I; Hulcr, Jiri; Jordal, Bjarte H

2017-05-01

The study of species diversification can identify the processes that shape patterns of species richness across the tree of life. Here, we perform comparative analyses of species diversification using a large dataset of bark beetles. Three examined covariates-permanent inbreeding (sibling mating), fungus farming, and major host type-represent a range of factors that may be important for speciation. We studied the association of these covariates with species diversification while controlling for evolutionary lag on adaptation. All three covariates were significantly associated with diversification, but fungus farming showed conflicting patterns between different analyses. Genera that exhibited interspecific variation in host type had higher rates of species diversification, which may suggest that host switching is a driver of species diversification or that certain host types or forest compositions facilitate colonization and thus allopatric speciation. Because permanent inbreeding is thought to facilitate dispersal, the positive association between permanent inbreeding and diversification rates suggests that dispersal ability may contribute to species richness. Bark beetles are ecologically unique; however, our results indicate that their impressive species diversity is largely driven by mechanisms shown to be important for many organism groups. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Courting disaster: How diversification rate affects fitness under risk.

PubMed

Ratcliff, William C; Hawthorne, Peter; Libby, Eric

2015-01-01

Life is full of risk. To deal with this uncertainty, many organisms have evolved bet-hedging strategies that spread risk through phenotypic diversification. These rates of diversification can vary by orders of magnitude in different species. Here we examine how key characteristics of risk and organismal ecology affect the fitness consequences of variation in diversification rate. We find that rapid diversification is strongly favored when the risk faced has a wide spatial extent, with a single disaster affecting a large fraction of the population. This advantage is especially great in small populations subject to frequent disaster. In contrast, when risk is correlated through time, slow diversification is favored because it allows adaptive tracking of disasters that tend to occur in series. Naturally evolved diversification mechanisms in diverse organisms facing a broad array of environmental risks largely support these results. The theory presented in this article provides a testable ecological hypothesis to explain the prevalence of slow stochastic switching among microbes and rapid, within-clutch diversification strategies among plants and animals. © 2014 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

EXPLOSIVE RADIATION OF A BACTERIAL SPECIES GROUP

PubMed Central

Morlon, Hélène; Kemps, Brian D.; Plotkin, Joshua B.; Brisson, Dustin

2013-01-01

The current diversity of life on earth is the product of macroevolutionary processes that have shaped the dynamics of diversification. Although the tempo of diversification has been studied extensively in macroorganisms, much less is known about the rates of diversification in the exceedingly diverse and species-rich microbiota. Decreases in diversification rates over time, a signature of explosive radiations, are commonly observed in plant and animal lineages. However, the few existing analyses of microbial lineages suggest that the tempo of diversification in prokaryotes may be fundamentally different. Here, we use multilocus and genomic sequence data to test hypotheses about the rate of diversification in a well-studied pathogenic bacterial lineage, Borrelia burgdorferi sensu lato (sl). Our analyses support the hypothesis that an explosive radiation of lineages occurred near the origin of the clade, followed by a sharp decay in diversification rates. These results suggest that explosive radiations may be a general feature of evolutionary history across the tree of life. PMID:22834754

Putting all your eggs in one basket: life-history strategies, bet hedging, and diversification.

PubMed

White, Andrew Edward; Li, Yexin Jessica; Griskevicius, Vladas; Neuberg, Steven L; Kenrick, Douglas T

2013-05-01

Diversification of resources is a strategy found everywhere from the level of microorganisms to that of giant Wall Street investment firms. We examine the functional nature of diversification using life-history theory-a framework for understanding how organisms navigate resource-allocation trade-offs. This framework suggests that diversification may be adaptive or maladaptive depending on one's life-history strategy and that these differences should be observed under conditions of threat. In three studies, we found that cues of mortality threat interact with one index of life-history strategy, childhood socioeconomic status (SES), to affect diversification. Among those from low-SES backgrounds, mortality threat increased preferences for diversification. However, among those from high-SES backgrounds, mortality threat had the opposite effect, inclining people to put all their eggs in one basket. The same interaction pattern emerged with a potential biomarker of life-history strategy, oxidative stress. These findings highlight when, and for whom, different diversification strategies can be advantageous.

Critically evaluating the theory and performance of Bayesian analysis of macroevolutionary mixtures

PubMed Central

Moore, Brian R.; Höhna, Sebastian; May, Michael R.; Rannala, Bruce; Huelsenbeck, John P.

2016-01-01

Bayesian analysis of macroevolutionary mixtures (BAMM) has recently taken the study of lineage diversification by storm. BAMM estimates the diversification-rate parameters (speciation and extinction) for every branch of a study phylogeny and infers the number and location of diversification-rate shifts across branches of a tree. Our evaluation of BAMM reveals two major theoretical errors: (i) the likelihood function (which estimates the model parameters from the data) is incorrect, and (ii) the compound Poisson process prior model (which describes the prior distribution of diversification-rate shifts across branches) is incoherent. Using simulation, we demonstrate that these theoretical issues cause statistical pathologies; posterior estimates of the number of diversification-rate shifts are strongly influenced by the assumed prior, and estimates of diversification-rate parameters are unreliable. Moreover, the inability to correctly compute the likelihood or to correctly specify the prior for rate-variable trees precludes the use of Bayesian approaches for testing hypotheses regarding the number and location of diversification-rate shifts using BAMM. PMID:27512038

Epistasis can accelerate adaptive diversification in haploid asexual populations.

PubMed

Griswold, Cortland K

2015-03-07

A fundamental goal of the biological sciences is to determine processes that facilitate the evolution of diversity. These processes can be separated into ecological, physiological, developmental and genetic. An ecological process that facilitates diversification is frequency-dependent selection caused by competition. Models of frequency-dependent adaptive diversification have generally assumed a genetic basis of phenotype that is non-epistatic. Here, we present a model that indicates diversification is accelerated by an epistatic basis of phenotype in combination with a competition model that invokes frequency-dependent selection. Our model makes use of a genealogical model of epistasis and insights into the effects of balancing selection on the genealogical structure of a population to understand how epistasis can facilitate diversification. The finding that epistasis facilitates diversification may be informative with respect to empirical results that indicate an epistatic basis of phenotype in experimental bacterial populations that experienced adaptive diversification. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Regional Diversity and Diversification in Mammals.

PubMed

Machac, Antonin; Graham, Catherine H

2017-01-01

The effects of regional diversity on diversification remain controversial. The classic hypothesis that diversification decelerates as regional diversity increases has been recently revived. Yet, there is little geographic evidence for slower diversification across regions of high diversity, and diversity is often thought to promote diversification through its effects on ecological divergence and speciation. Here, we use the newest phylogeny for mammals (4,990 species) and two different methods to test the effects of regional diversity on diversification. We find that regions of high diversity are dominated by expanding clades that are far from their estimated carrying capacities. Regions of low diversity host clades that are small and mostly saturated. These results were supported across mammals and their six largest orders. They were corroborated by the two methods when controlling for clade relatedness, clade nestedness, and clade size. Together, these results reject the hypothesis that high geographic concentration of mammals effectively suppresses their further diversification. Instead, highly diverse regions (especially the tropics) seem to act as the engine of mammalian richness.

Madness and sanity at the time of Indian independence

PubMed Central

Jain, Sanjeev; Murthy, Pratima; Sarin, Alok

2016-01-01

The backdrop of the Indian Independence offers glimpses of many ‘metaphors of madness’. In this article, we explore this through a few instances, starting from 1857, around the time of the First War of Independence, to 1947, when India became an independent nation. Such metaphors have their parallels both in historical as well as in contemporary times, where instances of one man's imagination becoming another's concept of irrationality and insanity continue. PMID:28066017

Madness and sanity at the time of Indian independence.

PubMed

Jain, Sanjeev; Murthy, Pratima; Sarin, Alok

2016-01-01

The backdrop of the Indian Independence offers glimpses of many 'metaphors of madness'. In this article, we explore this through a few instances, starting from 1857, around the time of the First War of Independence, to 1947, when India became an independent nation. Such metaphors have their parallels both in historical as well as in contemporary times, where instances of one man's imagination becoming another's concept of irrationality and insanity continue.

Linking micro- and macroevolutionary perspectives to evaluate the role of Quaternary sea-level oscillations in island diversification.

PubMed

Papadopoulou, Anna; Knowles, L Lacey

2017-12-01

With shifts in island area, isolation, and cycles of island fusion-fission, the role of Quaternary sea-level oscillations as drivers of diversification is complex and not well understood. Here, we conduct parallel comparisons of population and species divergence between two island areas of equivalent size that have been affected differently by sea-level oscillations, with the aim to understand the micro- and macroevolutionary dynamics associated with sea-level change. Using genome-wide datasets for a clade of seven Amphiacusta ground cricket species endemic to the Puerto Rico Bank (PRB), we found consistently deeper interspecific divergences and higher population differentiation across the unfragmented Western PRB, in comparison to the currently fragmented Eastern PRB that has experienced extreme changes in island area and connectivity during the Quaternary. We evaluate alternative hypotheses related to the microevolutionary processes (population splitting, extinction, and merging) that regulate the frequency of completed speciation across the PRB. Our results suggest that under certain combinations of archipelago characteristics and taxon traits, the repeated changes in island area and connectivity may create an opposite effect to the hypothesized "species pump" action of oscillating sea levels. Our study highlights how a microevolutionary perspective can complement current macroecological work on the Quaternary dynamics of island biodiversity. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Cultural and climatic changes shape the evolutionary history of the Uralic languages.

PubMed

Honkola, T; Vesakoski, O; Korhonen, K; Lehtinen, J; Syrjänen, K; Wahlberg, N

2013-06-01

Quantitative phylogenetic methods have been used to study the evolutionary relationships and divergence times of biological species, and recently, these have also been applied to linguistic data to elucidate the evolutionary history of language families. In biology, the factors driving macroevolutionary processes are assumed to be either mainly biotic (the Red Queen model) or mainly abiotic (the Court Jester model) or a combination of both. The applicability of these models is assumed to depend on the temporal and spatial scale observed as biotic factors act on species divergence faster and in smaller spatial scale than the abiotic factors. Here, we used the Uralic language family to investigate whether both 'biotic' interactions (i.e. cultural interactions) and abiotic changes (i.e. climatic fluctuations) are also connected to language diversification. We estimated the times of divergence using Bayesian phylogenetics with a relaxed-clock method and related our results to climatic, historical and archaeological information. Our timing results paralleled the previous linguistic studies but suggested a later divergence of Finno-Ugric, Finnic and Saami languages. Some of the divergences co-occurred with climatic fluctuation and some with cultural interaction and migrations of populations. Thus, we suggest that both 'biotic' and abiotic factors contribute either directly or indirectly to the diversification of languages and that both models can be applied when studying language evolution. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

Complex dynamics underlie the evolution of imperfect wing pattern convergence in butterflies.

PubMed

Finkbeiner, Susan D; Briscoe, Adriana D; Mullen, Sean P

2017-04-01

Adaptive radiation is characterized by rapid diversification that is strongly associated with ecological specialization. However, understanding the evolutionary mechanisms fueling adaptive diversification requires a detailed knowledge of how natural selection acts at multiple life-history stages. Butterflies within the genus Adelpha represent one of the largest and most diverse butterfly lineages in the Neotropics. Although Adelpha species feed on an extraordinary diversity of larval hosts, convergent evolution is widespread in this group, suggesting that selection for mimicry may contribute to adaptive divergence among species. To investigate this hypothesis, we conducted predation studies in Costa Rica using artificial butterfly facsimiles. Specifically, we predicted that nontoxic, palatable Adelpha species that do not feed on host plants in the family Rubiaceae would benefit from sharing a locally convergent wing pattern with the presumably toxic Rubiaceae-feeding species via reduced predation. Contrary to expectations, we found that the presumed mimic was attacked significantly more than its locally convergent model at a frequency paralleling attack rates on both novel and palatable prey. Although these data reveal the first evidence for protection from avian predators by the supposed toxic, Rubiaceae-feeding Adelpha species, we conclude that imprecise mimetic patterns have high costs for Batesian mimics in the tropics. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Does evolutionary innovation in pharyngeal jaws lead to rapid lineage diversification in labrid fishes?

PubMed Central

2009-01-01

Background Major modifications to the pharyngeal jaw apparatus are widely regarded as a recurring evolutionary key innovation that has enabled adaptive radiation in many species-rich clades of percomorph fishes. However one of the central predictions of this hypothesis, that the acquisition of a modified pharyngeal jaw apparatus will be positively correlated with explosive lineage diversification, has never been tested. We applied comparative methods to a new time-calibrated phylogeny of labrid fishes to test whether diversification rates shifted at two scales where major pharyngeal jaw innovations have evolved: across all of Labridae and within the subclade of parrotfishes. Results Diversification patterns within early labrids did not reflect rapid initial radiation. Much of modern labrid diversity stems from two recent rapid diversification events; one within julidine fishes and the other with the origin of the most species-rich clade of reef-associated parrotfishes. A secondary pharyngeal jaw innovation was correlated with rapid diversification within the parrotfishes. However diversification rate shifts within parrotfishes are more strongly correlated with the evolution of extreme dichromatism than with pharyngeal jaw modifications. Conclusion The temporal lag between pharyngeal jaw modifications and changes in diversification rates casts doubt on the key innovation hypothesis as a simple explanation for much of the richness seen in labrids and scarines. Although the possession of a secondarily modified PJA was correlated with increased diversification rates, this pattern is better explained by the evolution of extreme dichromatism (and other social and behavioral characters relating to sexual selection) within Scarus and Chlorurus. The PJA-innovation hypothesis also fails to explain the most dominant aspect of labrid lineage diversification, the radiation of the julidines. We suggest that pharyngeal jaws might have played a more important role in enabling morphological evolution of the feeding apparatus in labrids and scarines rather than in accelerating lineage diversification. PMID:19849854

Are rates of species diversification and body size evolution coupled in the ferns?

PubMed

Testo, Weston L; Sundue, Michael A

2018-03-01

Understanding the relationship between phenotypic evolution and lineage diversification is a central goal of evolutionary biology. To extend our understanding of the role morphological evolution plays in the diversification of plants, we examined the relationship between leaf size evolution and lineage diversification across ferns. We tested for an association between body size evolution and lineage diversification using a comparative phylogenetic approach that combined a time-calibrated phylogeny and leaf size data set for 2654 fern species. Rates of leaf size change and lineage diversification were estimated using BAMM, and rate correlations were performed for rates obtained for all families and individual species. Rates and patterns of rate-rate correlation were also analyzed separately for terrestrial and epiphytic taxa. We find no significant correlation between rates of leaf area change and lineage diversification, nor was there a difference in this pattern when growth habit is considered. Our results are consistent with the findings of an earlier study that reported decoupled rates of body size evolution and diversification in the Polypodiaceae, but conflict with a recent study that reported a positive correlation between body size evolution and lineage diversification rates in the tree fern family Cyatheaceae. Our findings indicate that lineage diversification in ferns is largely decoupled from shifts in body size, in contrast to several other groups of organisms. Speciation in ferns appears to be primarily driven by hybridization and isolation along elevational gradients, rather than adaptive radiations featuring prominent morphological restructuring. The exceptional diversity of leaf morphologies in ferns appears to reflect a combination of ecophysiological constraints and adaptations that are not key innovations. © 2018 Botanical Society of America.

Managing to harvest? Perspectives on the potential of aquaculture

PubMed Central

Muir, James

2005-01-01

Aquaculture has been one of the most rapid and technically innovative of food production sectors globally, with significant investment, scientific and technical development and production growth in many parts of the world over the past two decades. While this has had a significant effect on the global supply of aquatic food products and had an important impact in rural and urban food supply and employment in many developing economies, growth and increasing internationalization has not been without concern for natural resource use, environmental impact and social disruption. The expectations for production and diversification are now significant and while the scientific and technical means are already available to meet much of the intended targets, practical constraints of investment, profitability, resource access and system efficiency are likely to become far more important constraints for the future. This review offers a contemporary perspective on the ways in which the sector might develop, its interactions with constraints and the strategies that may be required to ensure that future development is both positive and sustainable. PMID:15713597

Unifying ecology and macroevolution with individual-based theory.

PubMed

Rosindell, James; Harmon, Luke J; Etienne, Rampal S

2015-05-01

A contemporary goal in both ecology and evolutionary biology is to develop theory that transcends the boundary between the two disciplines, to understand phenomena that cannot be explained by either field in isolation. This is challenging because macroevolution typically uses lineage-based models, whereas ecology often focuses on individual organisms. Here, we develop a new parsimonious individual-based theory by adding mild selection to the neutral theory of biodiversity. We show that this model generates realistic phylogenies showing a slowdown in diversification and also improves on the ecological predictions of neutral theory by explaining the occurrence of very common species. Moreover, we find the distribution of individual fitness changes over time, with average fitness increasing at a pace that depends positively on community size. Consequently, large communities tend to produce fitter species than smaller communities. These findings have broad implications beyond biodiversity theory, potentially impacting, for example, invasion biology and paleontology. © 2015 The Authors. Ecology Letters published by John Wiley & Sons Ltd and CNRS.

Evolution of Epiphytism and Fruit Traits Act Unevenly on the Diversification of the Species-Rich Genus Peperomia (Piperaceae).

PubMed

Frenzke, Lena; Goetghebeur, Paul; Neinhuis, Christoph; Samain, Marie-Stéphanie; Wanke, Stefan

2016-01-01

The species-rich genus Peperomia (Black Pepper relatives) is the only genus among early diverging angiosperms where epiphytism evolved. The majority of fruits of Peperomia release sticky secretions or exhibit hook-shaped appendages indicative of epizoochorous dispersal, which is in contrast to other flowering plants, where epiphytes are generally characterized by fruit morphological adaptations for anemochory or endozoochory. We investigate fruit characters using Cryo-SEM. Comparative phylogenetic analyses are applied for the first time to include life form and fruit character information to study diversification in Peperomia. Likelihood ratio tests uncover correlated character evolution. We demonstrate that diversification within Peperomia is not homogenous across its phylogeny, and that net diversification rates increase by twofold within the most species-rich subgenus. In contrast to former land plant studies that provide general evidence for increased diversification in epiphytic lineages, we demonstrate that the evolution of epiphytism within Peperomia predates the diversification shift. An epiphytic-dependent diversification is only observed for the background phylogeny. An elevated frequency of life form transitions between epiphytes and terrestrials and thus evolutionary flexibility of life forms is uncovered to coincide with the diversification shift. The evolution of fruits showing dispersal related structures is key to diversification in the foreground region of the phylogeny and postdates the evolution of epiphytism. We conclude that the success of Peperomia, measured in species numbers, is likely the result of enhanced vertical and horizontal dispersal ability and life form flexibility but not the evolution of epiphytism itself.

Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes

PubMed Central

Near, Thomas J.; Dornburg, Alex; Eytan, Ron I.; Keck, Benjamin P.; Smith, W. Leo; Kuhn, Kristen L.; Moore, Jon A.; Price, Samantha A.; Burbrink, Frank T.; Friedman, Matt; Wainwright, Peter C.

2013-01-01

Spiny-rayed fishes, or acanthomorphs, comprise nearly one-third of all living vertebrates. Despite their dominant role in aquatic ecosystems, the evolutionary history and tempo of acanthomorph diversification is poorly understood. We investigate the pattern of lineage diversification in acanthomorphs by using a well-resolved time-calibrated phylogeny inferred from a nuclear gene supermatrix that includes 520 acanthomorph species and 37 fossil age constraints. This phylogeny provides resolution for what has been classically referred to as the “bush at the top” of the teleost tree, and indicates acanthomorphs originated in the Early Cretaceous. Paleontological evidence suggests acanthomorphs exhibit a pulse of morphological diversification following the end Cretaceous mass extinction; however, the role of this event on the accumulation of living acanthomorph diversity remains unclear. Lineage diversification rates through time exhibit no shifts associated with the end Cretaceous mass extinction, but there is a global decrease in lineage diversification rates 50 Ma that occurs during a period when morphological disparity among fossil acanthomorphs increases sharply. Analysis of clade-specific shifts in diversification rates reveal that the hyperdiversity of living acanthomorphs is highlighted by several rapidly radiating lineages including tunas, gobies, blennies, snailfishes, and Afro-American cichlids. These lineages with high diversification rates are not associated with a single habitat type, such as coral reefs, indicating there is no single explanation for the success of acanthomorphs, as exceptional bouts of diversification have occurred across a wide array of marine and freshwater habitats. PMID:23858462

Diversification rates have declined in the Malagasy herpetofauna

PubMed Central

Scantlebury, Daniel P.

2013-01-01

The evolutionary origins of Madagascar's biodiversity remain mysterious despite the fact that relative to land area, there is no other place with consistently high levels of species richness and endemism across a range of taxonomic levels. Most efforts to explain diversification on the island have focused on geographical models of speciation, but recent studies have begun to address the island's accumulation of species through time, although with conflicting results. Prevailing hypotheses for diversification on the island involve either constant diversification rates or scenarios where rates decline through time. Using relative-time-calibrated phylogenies for seven endemic vertebrate clades and a model-fitting framework, I find evidence that diversification rates have declined through time on Madagascar. I show that diversification rates have clearly declined throughout the history of each clade, and models invoking diversity-dependent reductions to diversification rates best explain the diversification histories for each clade. These results are consistent with the ecological theory of adaptive radiation, and, coupled with ancillary observations about ecomorphological and life-history evolution, strongly suggest that adaptive radiation was an important formative process for one of the most species-rich regions on the Earth. These results cast the Malagasy biota in a new light and provide macroevolutionary justification for conservation initiatives. PMID:23843388

Diversification rates and species richness across the Tree of Life.

PubMed

Scholl, Joshua P; Wiens, John J

2016-09-14

Species richness varies dramatically among clades across the Tree of Life, by over a million-fold in some cases (e.g. placozoans versus arthropods). Two major explanations for differences in richness among clades are the clade-age hypothesis (i.e. species-rich clades are older) and the diversification-rate hypothesis (i.e. species-rich clades diversify more rapidly, where diversification rate is the net balance of speciation and extinction over time). Here, we examine patterns of variation in diversification rates across the Tree of Life. We address how rates vary across higher taxa, whether rates within higher taxa are related to the subclades within them, and how diversification rates of clades are related to their species richness. We find substantial variation in diversification rates, with rates in plants nearly twice as high as in animals, and rates in some eukaryotes approximately 10-fold faster than prokaryotes. Rates for each kingdom-level clade are then significantly related to the subclades within them. Although caution is needed when interpreting relationships between diversification rates and richness, a positive relationship between the two is not inevitable. We find that variation in diversification rates seems to explain most variation in richness among clades across the Tree of Life, in contrast to the conclusions of previous studies. © 2016 The Author(s).

Diversification rates and species richness across the Tree of Life

PubMed Central

Scholl, Joshua P.

2016-01-01

Species richness varies dramatically among clades across the Tree of Life, by over a million-fold in some cases (e.g. placozoans versus arthropods). Two major explanations for differences in richness among clades are the clade-age hypothesis (i.e. species-rich clades are older) and the diversification-rate hypothesis (i.e. species-rich clades diversify more rapidly, where diversification rate is the net balance of speciation and extinction over time). Here, we examine patterns of variation in diversification rates across the Tree of Life. We address how rates vary across higher taxa, whether rates within higher taxa are related to the subclades within them, and how diversification rates of clades are related to their species richness. We find substantial variation in diversification rates, with rates in plants nearly twice as high as in animals, and rates in some eukaryotes approximately 10-fold faster than prokaryotes. Rates for each kingdom-level clade are then significantly related to the subclades within them. Although caution is needed when interpreting relationships between diversification rates and richness, a positive relationship between the two is not inevitable. We find that variation in diversification rates seems to explain most variation in richness among clades across the Tree of Life, in contrast to the conclusions of previous studies. PMID:27605507

Evaluating the role of Pleistocene refugia, rivers and environmental variation in the diversification of central African duikers (genera Cephalophus and Philantomba).

PubMed

Ntie, Stephan; Davis, Anne R; Hils, Katrin; Mickala, Patrick; Thomassen, Henri A; Morgan, Katy; Vanthomme, Hadrien; Gonder, Mary K; Anthony, Nicola M

2017-09-06

This study aims to assess the role that Pleistocene refugia, rivers and local habitat conditions may have played in the evolutionary diversification of three central African duiker species (Cephalophus dorsalis, C. callipygus and Philantomba monticola). Genetic data from geo-referenced feces were collected from a wide range of sites across Central Africa. Historical patterns of population genetic structure were assessed using a ~ 650 bp fragment of the mitochondrial control region and contemporary patterns of genetic differentiation were evaluated using 12 polymorphic microsatellite loci. Mitochondrial analyses revealed that populations of C. callipygus and P. monticola in the Gulf of Guinea refugium are distinct from other populations in west central Africa. All three species exhibit signatures of past population expansion across much of the study area consistent with a history of postglacial expansion. There was no strong evidence for a riverine barrier effect in any of the three species, suggesting that duikers can readily cross major rivers. Generalized dissimilarity models (GDM) showed that environmental variation explains most of the nuclear genetic differentiation in both C. callipygus and P. monticola. The forest-savanna transition across central Cameroon and the Plateaux Batéké region in southeastern Gabon show the highest environmentally-associated turnover in genetic variability. A pattern of genetic differentiation was also evident between the coast and forest interior that may reflect differences in precipitation and/or vegetation. Findings from this study highlight the historical impact of Pleistocene fragmentation and current influence of environmental variation on genetic structure in duikers. Conservation efforts should therefore target areas that harbor as much environmentally-associated genetic variation as possible in order to maximize species' capacity to adapt to environmental change.

Dynamics of clade diversification on the morphological hypercube

PubMed Central

Gavrilets, S.

1999-01-01

Understanding the relationship between taxonomic and morphological changes is important in identifying the reasons for accelerated morphological diversification early in the history of animal phyla. Here, a simple general model describing the joint dynamics of taxonomic diversity and morphological disparity is presented and applied to the data on the diversification of blastozoans. I show that the observed patterns of deceleration in clade diversification can be explicable in terms of the geometric structure of the morphospace and the effects of extinction and speciation on morphological disparity without invoking major declines in the size of morphological transitions or taxonomic turnover rates. The model allows testing of hypotheses about patterns of diversification and estimation of rates of morphological evolution. In the case of blastozoans, I find no evidence that major changes in evolutionary rates and mechanisms are responsible for the deceleration of morphological diversification seen during the period of this clade's expansion. At the same time, there is evidence for a moderate decline in overall rates of morphological diversification concordant with a major change (from positive to negative values) in the clade's growth rate.

Distinct Processes Drive Diversification in Different Clades of Gesneriaceae.

PubMed

Roalson, Eric H; Roberts, Wade R

2016-07-01

Using a time-calibrated phylogenetic hypothesis including 768 Gesneriaceae species (out of [Formula: see text]3300 species) and more than 29,000 aligned bases from 26 gene regions, we test Gesneriaceae for diversification rate shifts and the possible proximal drivers of these shifts: geographic distributions, growth forms, and pollination syndromes. Bayesian Analysis of Macroevolutionary Mixtures analyses found five significant rate shifts in Beslerieae, core Nematanthus, core Columneinae, core Streptocarpus, and Pacific Cyrtandra These rate shifts correspond with shifts in diversification rates, as inferred by Binary State Speciation and Extinction Model and Geographic State Speciation and Extinction model, associated with hummingbird pollination, epiphytism, unifoliate growth, and geographic area. Our results suggest that diversification processes are extremely variable across Gesneriaceae clades with different combinations of characters influencing diversification rates in different clades. Diversification patterns between New and Old World lineages show dramatic differences, suggesting that the processes of diversification in Gesneriaceae are very different in these two geographic regions. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A comparative study of diversification events: the early Paleozoic versus the Mesozoic

NASA Technical Reports Server (NTRS)

Erwin, D. H.; Valentine, J. W.; Sepkoski, J. J. Jr; Sepkoski JJ, J. r. (Principal Investigator)

1987-01-01

We compare two major long-term diversifications of marine animal families that began during periods of low diversity but produced strikingly different numbers of phyla, classes, and orders. The first is the early-Paleozoic diversification (late Vendian-Ordovician; 182 MY duration) and the other the Mesozoic phase of the post-Paleozoic diversification (183 MY duration). The earlier diversification was associated with a great burst of morphological invention producing many phyla, classes, and orders and displaying high per taxon rates of family origination. The later diversification lacked novel morphologies recognized as phyla and classes, produced fewer orders, and displayed lower per taxon rates of family appearances. The chief difference between the diversifications appears to be that the earlier one proceeded from relatively narrow portions of adaptive space, whereas the latter proceeded from species widely scattered among adaptive zones and representing a variety of body plans. This difference is believed to explain the major differences in the products of these great radiations. Our data support those models that hold that evolutionary opportunity is a major factor in the outcome of evolutionary processes.

Has the connection between polyploidy and diversification actually been tested?

PubMed

Kellogg, Elizabeth A

2016-04-01

Many major clades of angiosperms have several whole genome duplications (polyploidization events) in their distant past, suggesting that polyploidy drives or at least permits diversification. However, data on recently diverged groups are more equivocal, finding little evidence of elevated diversification following polyploidy. The discrepancy may be attributable at least in part to methodology. Many studies use indirect methods, such as chromosome numbers, genome size, and Ks plots, to test polyploidy, although these approaches can be misleading, and often lack sufficient resolution. A direct test of diversification following polyploidy requires a sequence-based approach that traces the history of nuclear genomes rather than species. These methods identify the point of coalescence of ancestral genomes, but may be misleading about the time and thus the extent of diversification. Limitations of existing methods mean that the connection between polyploidy and diversification has not been rigorously tested and remains unknown. Copyright © 2016 Elsevier Ltd. All rights reserved.

Diversification and Challenges of Software Engineering Standards

NASA Technical Reports Server (NTRS)

Poon, Peter T.

1994-01-01

The author poses certain questions in this paper: 'In the future, should there be just one software engineering standards set? If so, how can we work towards that goal? What are the challenges of internationalizing standards?' Based on the author's personal view, the statement of his position is as follows: 'There should NOT be just one set of software engineering standards in the future. At the same time, there should NOT be the proliferation of standards, and the number of sets of standards should be kept to a minimum.It is important to understand the diversification of the areas which are spanned by the software engineering standards.' The author goes on to describe the diversification of processes, the diversification in the national and international character of standards organizations, the diversification of the professional organizations producing standards, the diversification of the types of businesses and industries, and the challenges of internationalizing standards.

The Interactive Effect of Diversification and Farming Scale on Productivity of Family Farm:Taking Rice Cultivation as An Example

NASA Astrophysics Data System (ADS)

Wei, Zhou

2017-05-01

Based on the diversification and cultivation scale, the rice cropping data of rural fixed observation points in 2011 were selected and the effect of diversification degree on rice productivity was analyzed by the Tobit model. The empirical results of the model show that diversification of sample farm will lead to loss of rice production efficiency. With the increase of rice planting scale, the loss of rice production efficiency will need to be further increased by diversification. Thus, we should stick to the family farm of specialized production operation. The transfer of land, the price and quantity of leasing, respecting the law of the market; the raising of funds can be considered non-subsidized capital market financing to help, while maintaining a certain degree of diversification, to avoid idle assets, low resource efficiency loss.

Mixed methods in gerontological research: Do the qualitative and quantitative data “touch”?

PubMed Central

Happ, Mary Beth

2010-01-01

This paper distinguishes between parallel and integrated mixed methods research approaches. Barriers to integrated mixed methods approaches in gerontological research are discussed and critiqued. The author presents examples of mixed methods gerontological research to illustrate approaches to data integration at the levels of data analysis, interpretation, and research reporting. As a summary of the methodological literature, four basic levels of mixed methods data combination are proposed. Opportunities for mixing qualitative and quantitative data are explored using contemporary examples from published studies. Data transformation and visual display, judiciously applied, are proposed as pathways to fuller mixed methods data integration and analysis. Finally, practical strategies for mixing qualitative and quantitative data types are explicated as gerontological research moves beyond parallel mixed methods approaches to achieve data integration. PMID:20077973

Phylogenetic estimates of diversification rate are affected by molecular rate variation.

PubMed

Duchêne, D A; Hua, X; Bromham, L

2017-10-01

Molecular phylogenies are increasingly being used to investigate the patterns and mechanisms of macroevolution. In particular, node heights in a phylogeny can be used to detect changes in rates of diversification over time. Such analyses rest on the assumption that node heights in a phylogeny represent the timing of diversification events, which in turn rests on the assumption that evolutionary time can be accurately predicted from DNA sequence divergence. But there are many influences on the rate of molecular evolution, which might also influence node heights in molecular phylogenies, and thus affect estimates of diversification rate. In particular, a growing number of studies have revealed an association between the net diversification rate estimated from phylogenies and the rate of molecular evolution. Such an association might, by influencing the relative position of node heights, systematically bias estimates of diversification time. We simulated the evolution of DNA sequences under several scenarios where rates of diversification and molecular evolution vary through time, including models where diversification and molecular evolutionary rates are linked. We show that commonly used methods, including metric-based, likelihood and Bayesian approaches, can have a low power to identify changes in diversification rate when molecular substitution rates vary. Furthermore, the association between the rates of speciation and molecular evolution rate can cause the signature of a slowdown or speedup in speciation rates to be lost or misidentified. These results suggest that the multiple sources of variation in molecular evolutionary rates need to be considered when inferring macroevolutionary processes from phylogenies. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Evolutionary history, immigration history, and the extent of diversification in community assembly.

PubMed

Knope, Matthew L; Forde, Samantha E; Fukami, Tadashi

2011-01-01

During community assembly, species may accumulate not only by immigration, but also by in situ diversification. Diversification has intrigued biologists because its extent varies even among closely related lineages under similar ecological conditions. Recent research has suggested that some of this puzzling variation may be caused by stochastic differences in the history of immigration (relative timing and order of immigration by founding populations), indicating that immigration and diversification may affect community assembly interactively. However, the conditions under which immigration history affects diversification remain unclear. Here we propose the hypothesis that whether or not immigration history influences the extent of diversification depends on the founding populations' prior evolutionary history, using evidence from a bacterial experiment. To create genotypes with different evolutionary histories, replicate populations of Pseudomonas fluorescens were allowed to adapt to a novel environment for a short or long period of time (approximately 10 or 100 bacterial generations) with or without exploiters (viral parasites). Each evolved genotype was then introduced to a new habitat either before or after a standard competitor genotype. Most genotypes diversified to a greater extent when introduced before, rather than after, the competitor. However, introduction order did not affect the extent of diversification when the evolved genotype had previously adapted to the environment for a long period of time without exploiters. Diversification of these populations was low regardless of introduction order. These results suggest that the importance of immigration history in diversification can be predicted by the immigrants' evolutionary past. The hypothesis proposed here may be generally applicable in both micro- and macro-organisms.

Evolution of Epiphytism and Fruit Traits Act Unevenly on the Diversification of the Species-Rich Genus Peperomia (Piperaceae)

PubMed Central

Frenzke, Lena; Goetghebeur, Paul; Neinhuis, Christoph; Samain, Marie-Stéphanie; Wanke, Stefan

2016-01-01

The species-rich genus Peperomia (Black Pepper relatives) is the only genus among early diverging angiosperms where epiphytism evolved. The majority of fruits of Peperomia release sticky secretions or exhibit hook-shaped appendages indicative of epizoochorous dispersal, which is in contrast to other flowering plants, where epiphytes are generally characterized by fruit morphological adaptations for anemochory or endozoochory. We investigate fruit characters using Cryo-SEM. Comparative phylogenetic analyses are applied for the first time to include life form and fruit character information to study diversification in Peperomia. Likelihood ratio tests uncover correlated character evolution. We demonstrate that diversification within Peperomia is not homogenous across its phylogeny, and that net diversification rates increase by twofold within the most species-rich subgenus. In contrast to former land plant studies that provide general evidence for increased diversification in epiphytic lineages, we demonstrate that the evolution of epiphytism within Peperomia predates the diversification shift. An epiphytic-dependent diversification is only observed for the background phylogeny. An elevated frequency of life form transitions between epiphytes and terrestrials and thus evolutionary flexibility of life forms is uncovered to coincide with the diversification shift. The evolution of fruits showing dispersal related structures is key to diversification in the foreground region of the phylogeny and postdates the evolution of epiphytism. We conclude that the success of Peperomia, measured in species numbers, is likely the result of enhanced vertical and horizontal dispersal ability and life form flexibility but not the evolution of epiphytism itself. PMID:27555851

A learnable parallel processing architecture towards unity of memory and computing

NASA Astrophysics Data System (ADS)

Li, H.; Gao, B.; Chen, Z.; Zhao, Y.; Huang, P.; Ye, H.; Liu, L.; Liu, X.; Kang, J.

2015-08-01

Developing energy-efficient parallel information processing systems beyond von Neumann architecture is a long-standing goal of modern information technologies. The widely used von Neumann computer architecture separates memory and computing units, which leads to energy-hungry data movement when computers work. In order to meet the need of efficient information processing for the data-driven applications such as big data and Internet of Things, an energy-efficient processing architecture beyond von Neumann is critical for the information society. Here we show a non-von Neumann architecture built of resistive switching (RS) devices named “iMemComp”, where memory and logic are unified with single-type devices. Leveraging nonvolatile nature and structural parallelism of crossbar RS arrays, we have equipped “iMemComp” with capabilities of computing in parallel and learning user-defined logic functions for large-scale information processing tasks. Such architecture eliminates the energy-hungry data movement in von Neumann computers. Compared with contemporary silicon technology, adder circuits based on “iMemComp” can improve the speed by 76.8% and the power dissipation by 60.3%, together with a 700 times aggressive reduction in the circuit area.

A learnable parallel processing architecture towards unity of memory and computing.

PubMed

Li, H; Gao, B; Chen, Z; Zhao, Y; Huang, P; Ye, H; Liu, L; Liu, X; Kang, J

2015-08-14

Developing energy-efficient parallel information processing systems beyond von Neumann architecture is a long-standing goal of modern information technologies. The widely used von Neumann computer architecture separates memory and computing units, which leads to energy-hungry data movement when computers work. In order to meet the need of efficient information processing for the data-driven applications such as big data and Internet of Things, an energy-efficient processing architecture beyond von Neumann is critical for the information society. Here we show a non-von Neumann architecture built of resistive switching (RS) devices named "iMemComp", where memory and logic are unified with single-type devices. Leveraging nonvolatile nature and structural parallelism of crossbar RS arrays, we have equipped "iMemComp" with capabilities of computing in parallel and learning user-defined logic functions for large-scale information processing tasks. Such architecture eliminates the energy-hungry data movement in von Neumann computers. Compared with contemporary silicon technology, adder circuits based on "iMemComp" can improve the speed by 76.8% and the power dissipation by 60.3%, together with a 700 times aggressive reduction in the circuit area.

What defines an adaptive radiation? Macroevolutionary diversification dynamics of an exceptionally species-rich continental lizard radiation.

PubMed

Pincheira-Donoso, Daniel; Harvey, Lilly P; Ruta, Marcello

2015-08-07

Adaptive radiation theory posits that ecological opportunity promotes rapid proliferation of phylogenetic and ecological diversity. Given that adaptive radiation proceeds via occupation of available niche space in newly accessed ecological zones, theory predicts that: (i) evolutionary diversification follows an 'early-burst' process, i.e., it accelerates early in the history of a clade (when available niche space facilitates speciation), and subsequently slows down as niche space becomes saturated by new species; and (ii) phylogenetic branching is accompanied by diversification of ecologically relevant phenotypic traits among newly evolving species. Here, we employ macroevolutionary phylogenetic model-selection analyses to address these two predictions about evolutionary diversification using one of the most exceptionally species-rich and ecologically diverse lineages of living vertebrates, the South American lizard genus Liolaemus. Our phylogenetic analyses lend support to a density-dependent lineage diversification model. However, the lineage through-time diversification curve does not provide strong support for an early burst. In contrast, the evolution of phenotypic (body size) relative disparity is high, significantly different from a Brownian model during approximately the last 5 million years of Liolaemus evolution. Model-fitting analyses also reject the 'early-burst' model of phenotypic evolution, and instead favour stabilizing selection (Ornstein-Uhlenbeck, with three peaks identified) as the best model for body size diversification. Finally, diversification rates tend to increase with smaller body size. Liolaemus have diversified under a density-dependent process with slightly pronounced apparent episodic pulses of lineage accumulation, which are compatible with the expected episodic ecological opportunity created by gradual uplifts of the Andes over the last ~25My. We argue that ecological opportunity can be strong and a crucial driver of adaptive radiations in continents, but may emerge less frequently (compared to islands) when major events (e.g., climatic, geographic) significantly modify environments. In contrast, body size diversification conforms to an Ornstein-Uhlenbeck model with multiple trait optima. Despite this asymmetric diversification between both lineages and phenotype, links are expected to exist between the two processes, as shown by our trait-dependent analyses of diversification. We finally suggest that the definition of adaptive radiation should not be conditioned by the existence of early-bursts of diversification, and should instead be generalized to lineages in which species and ecological diversity have evolved from a single ancestor.

Universal Principles of Depicting Oneself across the Centuries: From Renaissance Self-Portraits to Selfie-Photographs.

PubMed

Carbon, Claus-Christian

2017-01-01

Selfie-photography is generally thought of as a cultural mass phenomenon of the early 21st century, inseparably related to the development and triumph of the smartphone with integrated camera. Western culture, however, has been highly familiar with self-depictions since the Renaissance days. Putting the contemporary selfie into this historic context covering more than five centuries of cultural development from Dürer's (1500) famous "Self-Portrait at 28" (also known as "Selbstbildnis im Pelzrock") to today's Instagram galleries allows for identifying central parallels concerning the technical and social antecedents as well as common underlying psychological factors and shared properties of different kinds of self-depiction. The article provides an overview of the types of contemporary photographic selfies and compares them with painted self-portraits. Finally, this historic perspective leads us to the insight that self-portraits as well as selfies are both referring to nothing less than the "conditio humana."

The Porosity of Autonomy: Social and Biological Constitution of the Patient in Biomedicine.

PubMed

Beever, Jonathan; Morar, Nicolae

2016-01-01

The nature and role of the patient in biomedicine comprise issues central to bioethical inquiry. Given its developmental history grounded firmly in a backlash against 20th-century cases of egregious human subjects abuse, contemporary medical bioethics has come to rely on a fundamental assumption: the unit of care (and the unit of value) is the autonomous self-directing patient. In this article we examine first the structure of the feminist social critique of autonomy. Then we show that a parallel argument can be made against relational autonomy as well, demonstrating how this second concept of autonomy fails to take sufficiently into account an array of biological determinants, particularly those from microbial biology. Finally, in light of this biological critique, we question whether or to what extent any relevant and meaningful view of autonomy can be recovered in the contemporary landscape of bioethics.

Toward ethnocultural diversification of higher education.

PubMed

Hall, Gordon C Nagayama; Martinez, Charles R; Tuan, Mia; McMahon, Timothy R; Chain, Jennifer

2011-07-01

Attitudes toward ethnocultural diversification in higher education mirror attitudes toward paying taxes. Dissenters are opposed to paying taxes or to ethnocultural diversification. Passive Supporters value the benefits of taxes or ethnocultural diversification, but pay taxes or engage in diversity efforts only when required to do so. Active Supporters pay taxes or support diversity efforts even if they are not required to do so. Mandatory approaches to decrease the resistance of Dissenters to ethnocultural diversification may be necessary, whereas compelling voluntary approaches may be useful to mobilize Passive Supporters. Solutions need to be tailored to the needs of European Americans and persons of color. This article offers a conceptual framework for future research and interventions.

Toward Ethnocultural Diversification of Higher Education

PubMed Central

Nagayama Hall, Gordon C.; Martinez, Charles R.; Tuan, Mia; McMahon, Timothy R.; Chain, Jennifer

2011-01-01

Attitudes toward ethnocultural diversification in higher education mirror attitudes toward paying taxes. Dissenters are opposed to paying taxes or to ethnocultural diversification. Passive Supporters value the benefits of taxes or ethnocultural diversification, but pay taxes or engage in diversity efforts only when required to do so. Active Supporters pay taxes or support diversity efforts even if they are not required to do so. Mandatory approaches to decrease the resistance of Dissenters to ethnocultural diversification may be necessary, whereas compelling voluntary approaches may be useful to mobilize Passive Supporters. Solutions need to be tailored to the needs of European Americans and persons of color. This article offers a conceptual framework for future research and interventions. PMID:21787056

Using phylogenomics to understand the link between biogeographic origins and regional diversification in ratsnakes.

PubMed

Chen, Xin; Lemmon, Alan R; Lemmon, Emily Moriarty; Pyron, R Alexander; Burbrink, Frank T

2017-06-01

Globally distributed groups may show regionally distinct rates of diversification, where speciation is elevated given timing and sources of ecological opportunity. However, for most organisms, nearly complete sampling at genomic-data scales to reduce topological error in all regions is unattainable, thus hampering conclusions related to biogeographic origins and rates of diversification. We explore processes leading to the diversity of global ratsnakes and test several important hypotheses related to areas of origin and enhanced diversification upon colonizing new continents. We estimate species trees inferred from phylogenomic scale data (304 loci) while exploring several strategies that consider topological error from each individual gene tree. With a dated species tree, we examine taxonomy and test previous hypotheses that suggest the ratsnakes originated in the Old World (OW) and dispersed to New World (NW). Furthermore, we determine if dispersal to the NW represented a source of ecological opportunity, which should show elevated rates of species diversification. We show that ratsnakes originated in the OW during the mid-Oligocene and subsequently dispersed to the NW by the mid-Miocene; diversification was also elevated in a subclade of NW taxa. Finally, the optimal biogeographic region-dependent speciation model shows that the uptick in ratsnake diversification was associated with colonization of the NW. We consider several alternative explanations that account for regionally distinct diversification rates. Copyright © 2017 Elsevier Inc. All rights reserved.

Defense mutualisms enhance plant diversification

PubMed Central

Weber, Marjorie G.; Agrawal, Anurag A.

2014-01-01

The ability of plants to form mutualistic relationships with animal defenders has long been suspected to influence their evolutionary success, both by decreasing extinction risk and by increasing opportunity for speciation through an expanded realized niche. Nonetheless, the hypothesis that defense mutualisms consistently enhance plant diversification across lineages has not been well tested due to a lack of phenotypic and phylogenetic information. Using a global analysis, we show that the >100 vascular plant families in which species have evolved extrafloral nectaries (EFNs), sugar-secreting organs that recruit arthropod mutualists, have twofold higher diversification rates than families that lack species with EFNs. Zooming in on six distantly related plant clades, trait-dependent diversification models confirmed the tendency for lineages with EFNs to display increased rates of diversification. These results were consistent across methodological approaches. Inference using reversible-jump Markov chain Monte Carlo (MCMC) to model the placement and number of rate shifts revealed that high net diversification rates in EFN clades were driven by an increased number of positive rate shifts following EFN evolution compared with sister clades, suggesting that EFNs may be indirect facilitators of diversification. Our replicated analysis indicates that defense mutualisms put lineages on a path toward increased diversification rates within and between clades, and is concordant with the hypothesis that mutualistic interactions with animals can have an impact on deep macroevolutionary patterns and enhance plant diversity. PMID:25349406

Hummingbird pollination and the diversification of angiosperms: an old and successful association in Gesneriaceae

PubMed Central

Rolland, Jonathan; Clark, John L.; Salamin, Nicolas

2017-01-01

The effects of specific functional groups of pollinators in the diversification of angiosperms are still to be elucidated. We investigated whether the pollination shifts or the specific association with hummingbirds affected the diversification of a highly diverse angiosperm lineage in the Neotropics. We reconstructed a phylogeny of 583 species from the Gesneriaceae family and detected diversification shifts through time, inferred the timing and amount of transitions among pollinator functional groups, and tested the association between hummingbird pollination and speciation and extinction rates. We identified a high frequency of pollinator transitions, including reversals to insect pollination. Diversification rates of the group increased through time since 25 Ma, coinciding with the evolution of hummingbird-adapted flowers and the arrival of hummingbirds in South America. We showed that plants pollinated by hummingbirds have a twofold higher speciation rate compared with plants pollinated by insects, and that transitions among functional groups of pollinators had little impact on the diversification process. We demonstrated that floral specialization on hummingbirds for pollination has triggered rapid diversification in the Gesneriaceae family since the Early Miocene, and that it represents one of the oldest identified plant–hummingbird associations. Biotic drivers of plant diversification in the Neotropics could be more related to this specific type of pollinator (hummingbirds) than to shifts among different functional groups of pollinators. PMID:28381621

Ecological opportunities, habitat, and past climatic fluctuations influenced the diversification of modern turtles.

PubMed

Rodrigues, João Fabrício Mota; Diniz-Filho, José Alexandre Felizola

2016-08-01

Habitat may be viewed as an important life history component potentially related to diversification patterns. However, differences in diversification rates between aquatic and terrestrial realms are still poorly explored. Testudines is a group distributed worldwide that lives in aquatic and terrestrial environments, but until now no-one has evaluated the diversification history of the group as a whole. We aim here to investigate the diversification history of turtles and to test if habitat influenced speciation rate in these animals. We reconstructed the phylogeny of the modern species of chelonians and estimated node divergence dates using molecular markers and a Bayesian approach. Then, we used Bayesian Analyses of Macroevolutionary Mixtures to evaluate the diversification history of turtles and evaluate the effect of habitat on this pattern. Our reconstructed phylogeny covered 300 species (87% of the total diversity of the group). We found that the emydid subfamily Deirochelyinae, which forms the turtle hotspot in south-eastern United States, had an increase in its speciation rate, and that Galapagos tortoises had similar increases. Current speciation rates are lower in terrestrial turtles, contradicting studies supporting the idea terrestrial animals diversify more than aquatic species. Our results suggest that habitat, ecological opportunities, island invasions, and climatic factors are important drivers of diversification in modern turtles and reinforce the importance of habitat as a diversification driver. Copyright © 2016 Elsevier Inc. All rights reserved.

Diversity Dynamics in Nymphalidae Butterflies: Effect of Phylogenetic Uncertainty on Diversification Rate Shift Estimates

PubMed Central

Peña, Carlos; Espeland, Marianne

2015-01-01

The species rich butterfly family Nymphalidae has been used to study evolutionary interactions between plants and insects. Theories of insect-hostplant dynamics predict accelerated diversification due to key innovations. In evolutionary biology, analysis of maximum credibility trees in the software MEDUSA (modelling evolutionary diversity using stepwise AIC) is a popular method for estimation of shifts in diversification rates. We investigated whether phylogenetic uncertainty can produce different results by extending the method across a random sample of trees from the posterior distribution of a Bayesian run. Using the MultiMEDUSA approach, we found that phylogenetic uncertainty greatly affects diversification rate estimates. Different trees produced diversification rates ranging from high values to almost zero for the same clade, and both significant rate increase and decrease in some clades. Only four out of 18 significant shifts found on the maximum clade credibility tree were consistent across most of the sampled trees. Among these, we found accelerated diversification for Ithomiini butterflies. We used the binary speciation and extinction model (BiSSE) and found that a hostplant shift to Solanaceae is correlated with increased net diversification rates in Ithomiini, congruent with the diffuse cospeciation hypothesis. Our results show that taking phylogenetic uncertainty into account when estimating net diversification rate shifts is of great importance, as very different results can be obtained when using the maximum clade credibility tree and other trees from the posterior distribution. PMID:25830910

Diversity dynamics in Nymphalidae butterflies: effect of phylogenetic uncertainty on diversification rate shift estimates.

PubMed

Peña, Carlos; Espeland, Marianne

2015-01-01

The species rich butterfly family Nymphalidae has been used to study evolutionary interactions between plants and insects. Theories of insect-hostplant dynamics predict accelerated diversification due to key innovations. In evolutionary biology, analysis of maximum credibility trees in the software MEDUSA (modelling evolutionary diversity using stepwise AIC) is a popular method for estimation of shifts in diversification rates. We investigated whether phylogenetic uncertainty can produce different results by extending the method across a random sample of trees from the posterior distribution of a Bayesian run. Using the MultiMEDUSA approach, we found that phylogenetic uncertainty greatly affects diversification rate estimates. Different trees produced diversification rates ranging from high values to almost zero for the same clade, and both significant rate increase and decrease in some clades. Only four out of 18 significant shifts found on the maximum clade credibility tree were consistent across most of the sampled trees. Among these, we found accelerated diversification for Ithomiini butterflies. We used the binary speciation and extinction model (BiSSE) and found that a hostplant shift to Solanaceae is correlated with increased net diversification rates in Ithomiini, congruent with the diffuse cospeciation hypothesis. Our results show that taking phylogenetic uncertainty into account when estimating net diversification rate shifts is of great importance, as very different results can be obtained when using the maximum clade credibility tree and other trees from the posterior distribution.

Defense mutualisms enhance plant diversification.

PubMed

Weber, Marjorie G; Agrawal, Anurag A

2014-11-18

The ability of plants to form mutualistic relationships with animal defenders has long been suspected to influence their evolutionary success, both by decreasing extinction risk and by increasing opportunity for speciation through an expanded realized niche. Nonetheless, the hypothesis that defense mutualisms consistently enhance plant diversification across lineages has not been well tested due to a lack of phenotypic and phylogenetic information. Using a global analysis, we show that the >100 vascular plant families in which species have evolved extrafloral nectaries (EFNs), sugar-secreting organs that recruit arthropod mutualists, have twofold higher diversification rates than families that lack species with EFNs. Zooming in on six distantly related plant clades, trait-dependent diversification models confirmed the tendency for lineages with EFNs to display increased rates of diversification. These results were consistent across methodological approaches. Inference using reversible-jump Markov chain Monte Carlo (MCMC) to model the placement and number of rate shifts revealed that high net diversification rates in EFN clades were driven by an increased number of positive rate shifts following EFN evolution compared with sister clades, suggesting that EFNs may be indirect facilitators of diversification. Our replicated analysis indicates that defense mutualisms put lineages on a path toward increased diversification rates within and between clades, and is concordant with the hypothesis that mutualistic interactions with animals can have an impact on deep macroevolutionary patterns and enhance plant diversity.

Hummingbird pollination and the diversification of angiosperms: an old and successful association in Gesneriaceae.

PubMed

Serrano-Serrano, Martha Liliana; Rolland, Jonathan; Clark, John L; Salamin, Nicolas; Perret, Mathieu

2017-04-12

The effects of specific functional groups of pollinators in the diversification of angiosperms are still to be elucidated. We investigated whether the pollination shifts or the specific association with hummingbirds affected the diversification of a highly diverse angiosperm lineage in the Neotropics. We reconstructed a phylogeny of 583 species from the Gesneriaceae family and detected diversification shifts through time, inferred the timing and amount of transitions among pollinator functional groups, and tested the association between hummingbird pollination and speciation and extinction rates. We identified a high frequency of pollinator transitions, including reversals to insect pollination. Diversification rates of the group increased through time since 25 Ma, coinciding with the evolution of hummingbird-adapted flowers and the arrival of hummingbirds in South America. We showed that plants pollinated by hummingbirds have a twofold higher speciation rate compared with plants pollinated by insects, and that transitions among functional groups of pollinators had little impact on the diversification process. We demonstrated that floral specialization on hummingbirds for pollination has triggered rapid diversification in the Gesneriaceae family since the Early Miocene, and that it represents one of the oldest identified plant-hummingbird associations. Biotic drivers of plant diversification in the Neotropics could be more related to this specific type of pollinator (hummingbirds) than to shifts among different functional groups of pollinators. © 2017 The Author(s).

Contrasting patterns of Andean diversification among three diverse clades of Neotropical clearwing butterflies.

PubMed

Chazot, Nicolas; De-Silva, Donna Lisa; Willmott, Keith R; Freitas, André V L; Lamas, Gerardo; Mallet, James; Giraldo, Carlos E; Uribe, Sandra; Elias, Marianne

2018-04-01

The Neotropical region is the most biodiverse on Earth, in a large part due to the highly diverse tropical Andean biota. The Andes are a potentially important driver of diversification within the mountains and for neighboring regions. We compared the role of the Andes in diversification among three subtribes of Ithomiini butterflies endemic to the Neotropics, Dircennina, Oleriina, and Godyridina. The diversification patterns of Godyridina have been studied previously. Here, we generate the first time-calibrated phylogeny for the largest ithomiine subtribe, Dircennina, and we reanalyze a published phylogeny of Oleriina to test different biogeographic scenarios involving the Andes within an identical framework. We found common diversification patterns across the three subtribes, as well as major differences. In Dircennina and Oleriina, our results reveal a congruent pattern of diversification related to the Andes with an Andean origin, which contrasts with the Amazonian origin and multiple Andean colonizations of Godyridina. In each of the three subtribes, a clade diversified in the Northern Andes at a faster rate. Diversification within Amazonia occurred in Oleriina and Godyridina, while virtually no speciation occurred in Dircennina in this region. Dircennina was therefore characterized by higher diversification rates within the Andes compared to non-Andean regions, while in Oleriina and Godyridina, we found no difference between these regions. Our results and discussion highlight the importance of comparative approaches in biogeographic studies.

A parametric method for assessing diversification-rate variation in phylogenetic trees.

PubMed

Shah, Premal; Fitzpatrick, Benjamin M; Fordyce, James A

2013-02-01

Phylogenetic hypotheses are frequently used to examine variation in rates of diversification across the history of a group. Patterns of diversification-rate variation can be used to infer underlying ecological and evolutionary processes responsible for patterns of cladogenesis. Most existing methods examine rate variation through time. Methods for examining differences in diversification among groups are more limited. Here, we present a new method, parametric rate comparison (PRC), that explicitly compares diversification rates among lineages in a tree using a variety of standard statistical distributions. PRC can identify subclades of the tree where diversification rates are at variance with the remainder of the tree. A randomization test can be used to evaluate how often such variance would appear by chance alone. The method also allows for comparison of diversification rate among a priori defined groups. Further, the application of the PRC method is not restricted to monophyletic groups. We examined the performance of PRC using simulated data, which showed that PRC has acceptable false-positive rates and statistical power to detect rate variation. We apply the PRC method to the well-studied radiation of North American Plethodon salamanders, and support the inference that the large-bodied Plethodon glutinosus clade has a higher historical rate of diversification compared to other Plethodon salamanders. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Comparative analysis reveals that polyploidy does not decelerate diversification in fish.

PubMed

Zhan, S H; Glick, L; Tsigenopoulos, C S; Otto, S P; Mayrose, I

2014-02-01

While the proliferation of the species-rich teleost fish has been ascribed to an ancient genome duplication event at the base of this group, the broader impact of polyploidy on fish evolution and diversification remains poorly understood. Here, we investigate the association between polyploidy and diversification in several fish lineages: the sturgeons (Acipenseridae: Acipenseriformes), the botiid loaches (Botiidae: Cypriniformes), Cyprininae fishes (Cyprinidae: Cypriniformes) and the salmonids (Salmonidae: Salmoniformes). Using likelihood-based evolutionary methodologies, we co-estimate speciation and extinction rates associated with polyploid vs. diploid fish lineages. Family-level analysis of Acipenseridae and Botiidae revealed no significant difference in diversification rates between polyploid and diploid relatives, while analysis of the subfamily Cyprininae revealed higher polyploid diversification. Additionally, order-level analysis of the polyploid Salmoniformes and its diploid sister clade, the Esociformes, did not support a significantly different net diversification rate between the two groups. Taken together, our results suggest that polyploidy is generally not associated with decreased diversification in fish - a pattern that stands in contrast to that previously observed in plants. While there are notable differences in the time frame examined in the two studies, our results suggest that polyploidy is associated with different diversification patterns in these two major branches of the eukaryote tree of life. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

78 FR 40828 - Proposed Collection; Comment Request for Notice 2006-107

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-08

... Notice 2006-107, Diversification Requirements for Qualified Defined Contribution Plans Holding Publicly...: Title: Diversification Requirements for Qualified Defined Contribution Plans Holding Publicly Traded... diversification rights with respect to publicly traded employer securities held by a defined contribution plan...

75 FR 21149 - Proposed Collection; Comment Request for Notice 2006-107

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-22

... Notice 2006-107, Diversification Requirements for Qualified Defined Contribution Plans Holding Publicly... INFORMATION: Title: Diversification Requirements for Qualified Defined Contribution Plans Holding Publicly... provides diversification rights with respect to publicly traded employer securities held by a defined...

Macroevolutionary diversification with limited niche disparity in a species-rich lineage of cold-climate lizards.

PubMed

Reaney, Ashley M; Saldarriaga-Córdoba, Mónica; Pincheira-Donoso, Daniel

2018-02-06

Life diversifies via adaptive radiation when natural selection drives the evolution of ecologically distinct species mediated by their access to novel niche space, or via non-adaptive radiation when new species diversify while retaining ancestral niches. However, while cases of adaptive radiation are widely documented, examples of non-adaptively radiating lineages remain rarely observed. A prolific cold-climate lizard radiation from South America (Phymaturus), sister to a hyper-diverse adaptive radiation (Liolaemus), has extensively diversified phylogenetically and geographically, but with exceptionally minimal ecological and life-history diversification. This lineage, therefore, may offer unique opportunities to investigate the non-adaptive basis of diversification, and in combination with Liolaemus, to cover the whole spectrum of modes of diversification predicted by theory, from adaptive to non-adaptive. Using phylogenetic macroevolutionary modelling performed on a newly created 58-species molecular tree, we establish the tempo and mode of diversification in the Phymaturus radiation. Lineage accumulation in Phymaturus opposes a density-dependent (or 'niche-filling') process of diversification. Concurrently, we found that body size diversification is better described by an Ornstein-Uhlenbeck evolutionary model, suggesting stabilizing selection as the mechanism underlying niche conservatism (i.e., maintaining two fundamental size peaks), and which has predominantly evolved around two major adaptive peaks on a 'Simpsonian' adaptive landscape. Lineage diversification of the Phymaturus genus does not conform to an adaptive radiation, as it is characterised by a constant rate of species accumulation during the clade's history. Their strict habitat requirements (rocky outcrops), predominantly invariant herbivory, and especially the constant viviparous reproduction across species have likely limited their opportunities for adaptive diversifications throughout novel environments. This mode of diversification contrasts dramatically with its sister lineage Liolaemus, which geographically overlaps with Phymaturus, but exploits all possible microhabitats in these and other bioclimatic areas. Our study contributes importantly to consolidate these lizards (liolaemids) as promising model systems to investigate the entire spectrum of modes of species formations, from the adaptive to the non-adaptive extremes of the continuum.

Evidence for determinism in species diversification and contingency in phenotypic evolution during adaptive radiation.

PubMed

Burbrink, Frank T; Chen, Xin; Myers, Edward A; Brandley, Matthew C; Pyron, R Alexander

2012-12-07

Adaptive radiation (AR) theory predicts that groups sharing the same source of ecological opportunity (EO) will experience deterministic species diversification and morphological evolution. Thus, deterministic ecological and morphological evolution should be correlated with deterministic patterns in the tempo and mode of speciation for groups in similar habitats and time periods. We test this hypothesis using well-sampled phylogenies of four squamate groups that colonized the New World (NW) in the Late Oligocene. We use both standard and coalescent models to assess species diversification, as well as likelihood models to examine morphological evolution. All squamate groups show similar early pulses of speciation, as well as diversity-dependent ecological limits on clade size at a continental scale. In contrast, processes of morphological evolution are not easily predictable and do not show similar pulses of early and rapid change. Patterns of morphological and species diversification thus appear uncoupled across these groups. This indicates that the processes that drive diversification and disparification are not mechanistically linked, even among similar groups of taxa experiencing the same sources of EO. It also suggests that processes of phenotypic diversification cannot be predicted solely from the existence of an AR or knowledge of the process of diversification.

Temperate radiations and dying embers of a tropical past: the diversification of Viburnum.

PubMed

Spriggs, Elizabeth L; Clement, Wendy L; Sweeney, Patrick W; Madriñán, Santiago; Edwards, Erika J; Donoghue, Michael J

2015-07-01

We used a near-complete phylogeny for the angiosperm clade Viburnum to assess lineage diversification rates, and to examine possible morphological and ecological factors driving radiations. Maximum-likelihood and Bayesian approaches identified shifts in diversification rate and possible links to character evolution. We inferred the ancestral environment for Viburnum and changes in diversification dynamics associated with subsequent biome shifts. Viburnum probably diversified in tropical forests of Southeast Asia in the Eocene, with three subsequent radiations in temperate clades during the Miocene. Four traits (purple fruits, extrafloral nectaries, bud scales and toothed leaves) were statistically associated with higher rates of diversification. However, we argue that these traits are unlikely to be driving diversification directly. Instead, two radiations were associated with the occupation of mountainous regions and a third with repeated shifts between colder and warmer temperate forests. Early-branching depauperate lineages imply that the rare lowland tropical species are 'dying embers' of once more diverse lineages; net diversification rates in Viburnum likely decreased in these tropical environments after the Oligocene. We suggest that 'taxon pulse' dynamics might characterize other temperate plant lineages. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Hybridisation and diversification in the adaptive radiation of clownfishes.

PubMed

Litsios, Glenn; Salamin, Nicolas

2014-11-30

The importance of hybridisation during species diversification has long been debated among evolutionary biologists. It is increasingly recognised that hybridisation events occurred during the evolutionary history of numerous species, especially during the early stages of adaptive radiation. We study the effect of hybridisation on diversification in the clownfishes, a clade of coral reef fish that diversified through an adaptive radiation process. While two species of clownfish are likely to have been described from hybrid specimens, the occurrence and effect of hybridisation on the clade diversification is yet unknown. We generate sequences of three mitochondrial genes to complete an existing dataset of nuclear sequences and document cytonuclear discordance at a node, which shows a drastic increase of diversification rate. Then, using a tree-based jack-knife method, we identify clownfish species likely stemming from hybridisation events. Finally, we use molecular cloning and identify the putative parental species of four clownfish specimens that display the morphological characteristics of hybrids. Our results show that consistently with the syngameon hypothesis, hybridisation events are linked with a burst of diversification in the clownfishes. Moreover, several recently diverged clownfish lineages likely originated through hybridisation, which indicates that diversification, catalysed by hybridisation events, may still be happening.

Structuring evolution: biochemical networks and metabolic diversification in birds.

PubMed

Morrison, Erin S; Badyaev, Alexander V

2016-08-25

Recurrence and predictability of evolution are thought to reflect the correspondence between genomic and phenotypic dimensions of organisms, and the connectivity in deterministic networks within these dimensions. Direct examination of the correspondence between opportunities for diversification imbedded in such networks and realized diversity is illuminating, but is empirically challenging because both the deterministic networks and phenotypic diversity are modified in the course of evolution. Here we overcome this problem by directly comparing the structure of a "global" carotenoid network - comprising of all known enzymatic reactions among naturally occurring carotenoids - with the patterns of evolutionary diversification in carotenoid-producing metabolic networks utilized by birds. We found that phenotypic diversification in carotenoid networks across 250 species was closely associated with enzymatic connectivity of the underlying biochemical network - compounds with greater connectivity occurred the most frequently across species and were the hotspots of metabolic pathway diversification. In contrast, we found no evidence for diversification along the metabolic pathways, corroborating findings that the utilization of the global carotenoid network was not strongly influenced by history in avian evolution. The finding that the diversification in species-specific carotenoid networks is qualitatively predictable from the connectivity of the underlying enzymatic network points to significant structural determinism in phenotypic evolution.

Evidence for determinism in species diversification and contingency in phenotypic evolution during adaptive radiation

PubMed Central

Burbrink, Frank T.; Chen, Xin; Myers, Edward A.; Brandley, Matthew C.; Pyron, R. Alexander

2012-01-01

Adaptive radiation (AR) theory predicts that groups sharing the same source of ecological opportunity (EO) will experience deterministic species diversification and morphological evolution. Thus, deterministic ecological and morphological evolution should be correlated with deterministic patterns in the tempo and mode of speciation for groups in similar habitats and time periods. We test this hypothesis using well-sampled phylogenies of four squamate groups that colonized the New World (NW) in the Late Oligocene. We use both standard and coalescent models to assess species diversification, as well as likelihood models to examine morphological evolution. All squamate groups show similar early pulses of speciation, as well as diversity-dependent ecological limits on clade size at a continental scale. In contrast, processes of morphological evolution are not easily predictable and do not show similar pulses of early and rapid change. Patterns of morphological and species diversification thus appear uncoupled across these groups. This indicates that the processes that drive diversification and disparification are not mechanistically linked, even among similar groups of taxa experiencing the same sources of EO. It also suggests that processes of phenotypic diversification cannot be predicted solely from the existence of an AR or knowledge of the process of diversification. PMID:23034709

Hospital diversification strategy.

PubMed

Eastaugh, Steven R

2014-01-01

To determine the impact of health system restructuring on the levels of hospital diversification and operating ratio this article analyzed 94 teaching hospitals and 94 community hospitals during the period 2008-2013. The 47 teaching hospitals are matched with 47 other teaching hospitals experiencing the same financial market position in 2008, but with different levels of preference for risk and diversification in their strategic plan. Covariates in the analysis included levels of hospital competition and the degree of local government planning (for example, highly regulated in New York, in contrast to Texas). Moreover, 47 nonteaching community hospitals are matched with 47 other community hospitals in 2008, having varying manager preferences for service-line diversification and risk. Diversification and operating ratio are modeled in a two-stage least squares (TSLS) framework as jointly dependent. Institutional diversification is found to yield better financial position, and the better operating profits provide the firm the wherewithal to diversify. Some services are in a growth phase, like bariatric weight-loss surgery and sleep disorder clinics. Hospital managers' preferences for risk/return potential were considered. An institution life cycle hypothesis is advanced to explain hospital behavior: boom and bust, diversification, and divestiture, occasionally leading to closure or merger.

Convergent, Parallel and Correlated Evolution of Trophic Morphologies in the Subfamily Schizothoracinae from the Qinghai-Tibetan Plateau

PubMed Central

Qi, Delin; Chao, Yan; Guo, Songchang; Zhao, Lanying; Li, Taiping; Wei, Fulei; Zhao, Xinquan

2012-01-01

Schizothoracine fishes distributed in the water system of the Qinghai-Tibetan plateau (QTP) and adjacent areas are characterized by being highly adaptive to the cold and hypoxic environment of the plateau, as well as by a high degree of diversity in trophic morphology due to resource polymorphisms. Although convergent and parallel evolution are prevalent in the organisms of the QTP, it remains unknown whether similar evolutionary patterns have occurred in the schizothoracine fishes. Here, we constructed for the first time a tentative molecular phylogeny of the schizothoracine fishes based on the complete sequences of the cytochrome b gene. We employed this molecular phylogenetic framework to examine the evolution of trophic morphologies. We used Pagel's maximum likelihood method to estimate the evolutionary associations of trophic morphologies and food resource use. Our results showed that the molecular and published morphological phylogenies of Schizothoracinae are partially incongruent with respect to some intergeneric relationships. The phylogenetic results revealed that four character states of five trophic morphologies and of food resource use evolved at least twice during the diversification of the subfamily. State transitions are the result of evolutionary patterns including either convergence or parallelism or both. Furthermore, our analyses indicate that some characters of trophic morphologies in the Schizothoracinae have undergone correlated evolution, which are somewhat correlated with different food resource uses. Collectively, our results reveal new examples of convergent and parallel evolution in the organisms of the QTP. The adaptation to different trophic niches through the modification of trophic morphologies and feeding behaviour as found in the schizothoracine fishes may account for the formation and maintenance of the high degree of diversity and radiations in fish communities endemic to QTP. PMID:22470515

Parallel Mitogenome Sequencing Alleviates Random Rooting Effect in Phylogeography.

PubMed

Hirase, Shotaro; Takeshima, Hirohiko; Nishida, Mutsumi; Iwasaki, Wataru

2016-04-28

Reliably rooted phylogenetic trees play irreplaceable roles in clarifying diversification in the patterns of species and populations. However, such trees are often unavailable in phylogeographic studies, particularly when the focus is on rapidly expanded populations that exhibit star-like trees. A fundamental bottleneck is known as the random rooting effect, where a distant outgroup tends to root an unrooted tree "randomly." We investigated whether parallel mitochondrial genome (mitogenome) sequencing alleviates this effect in phylogeography using a case study on the Sea of Japan lineage of the intertidal goby Chaenogobius annularis Eighty-three C. annularis individuals were collected and their mitogenomes were determined by high-throughput and low-cost parallel sequencing. Phylogenetic analysis of these mitogenome sequences was conducted to root the Sea of Japan lineage, which has a star-like phylogeny and had not been reliably rooted. The topologies of the bootstrap trees were investigated to determine whether the use of mitogenomes alleviated the random rooting effect. The mitogenome data successfully rooted the Sea of Japan lineage by alleviating the effect, which hindered phylogenetic analysis that used specific gene sequences. The reliable rooting of the lineage led to the discovery of a novel, northern lineage that expanded during an interglacial period with high bootstrap support. Furthermore, the finding of this lineage suggested the existence of additional glacial refugia and provided a new recent calibration point that revised the divergence time estimation between the Sea of Japan and Pacific Ocean lineages. This study illustrates the effectiveness of parallel mitogenome sequencing for solving the random rooting problem in phylogeographic studies. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Post-Eocene climate change across continental Australia and the diversification of Australasian spiny trapdoor spiders (Idiopidae: Arbanitinae).

PubMed

Rix, Michael G; Cooper, Steven J B; Meusemann, Karen; Klopfstein, Seraina; Harrison, Sophie E; Harvey, Mark S; Austin, Andrew D

2017-04-01

The formation and spread of the Australian arid zone during the Neogene was a profoundly transformative event in the biogeographic history of Australia, resulting in extinction or range contraction in lineages adapted to mesic habitats, as well as diversification and range expansion in arid-adapted taxa (most of which evolved from mesic ancestors). However, the geographic origins of the arid zone biota are still relatively poorly understood, especially among highly diverse invertebrate lineages, many of which are themselves poorly documented at the species level. Spiny trapdoor spiders (Idiopidae: Arbanitinae) are one such lineage, having mesic 'on-the-continent' Gondwanan origins, while also having experienced major arid zone radiations in select clades. In this study, we present new orthologous nuclear markers for the phylogenetic inference of mygalomorph spiders, and use them to infer the phylogeny of Australasian Idiopidae with a 12-gene parallel tagged amplicon next-generation sequencing approach. We use these data to test the mode and timing of diversification of arid-adapted idiopid lineages across mainland Australia, and employ a continent-wide sampling of the fauna's phylogenetic and geographic diversity to facilitate ancestral area inference. We further explore the evolution of phenotypic and behavioural characters associated with both arid and mesic environments, and test an 'out of south-western Australia' hypothesis for the origin of arid zone clades. Three lineages of Idiopidae are shown to have diversified in the arid zone during the Miocene, one (genus Euoplos) exclusively in Western Australia. Arid zone Blakistonia likely had their origins in South Australia, whereas in the most widespread genus Aganippe, a more complex scenario is evident, with likely range expansion from southern Western Australia to southern South Australia, from where the bulk of the arid zone fauna then originated. In Aganippe, remarkable adaptations to phragmotic burrow-plugging in transitional arid zone taxa have evolved twice independently in Western Australia, while in Misgolas and Cataxia, burrow door-building behaviours have likely been independently lost at least three times in the eastern Australian mesic zone. We also show that the presence of idiopids in New Zealand (Cantuaria) is likely to be the result of recent dispersal from Australia, rather than ancient continental vicariance. By providing the first comprehensive, continental synopsis of arid zone biogeography in an Australian arachnid lineage, we show that the diversification of arbanitine Idiopidae was intimately associated with climate shifts during the Neogene, resulting in multiple Mio-Pliocene radiations. Copyright © 2017 Elsevier Inc. All rights reserved.

Ants sow the seeds of global diversification in flowering plants.

PubMed

Lengyel, Szabolcs; Gove, Aaron D; Latimer, Andrew M; Majer, Jonathan D; Dunn, Robert R

2009-01-01

The extraordinary diversification of angiosperm plants in the Cretaceous and Tertiary periods has produced an estimated 250,000-300,000 living angiosperm species and has fundamentally altered terrestrial ecosystems. Interactions with animals as pollinators or seed dispersers have long been suspected as drivers of angiosperm diversification, yet empirical examples remain sparse or inconclusive. Seed dispersal by ants (myrmecochory) may drive diversification as it can reduce extinction by providing selective advantages to plants and can increase speciation by enhancing geographical isolation by extremely limited dispersal distances. Using the most comprehensive sister-group comparison to date, we tested the hypothesis that myrmecochory leads to higher diversification rates in angiosperm plants. As predicted, diversification rates were substantially higher in ant-dispersed plants than in their non-myrmecochorous relatives. Data from 101 angiosperm lineages in 241 genera from all continents except Antarctica revealed that ant-dispersed lineages contained on average more than twice as many species as did their non-myrmecochorous sister groups. Contrasts in species diversity between sister groups demonstrated that diversification rates did not depend on seed dispersal mode in the sister group and were higher in myrmecochorous lineages in most biogeographic regions. Myrmecochory, which has evolved independently at least 100 times in angiosperms and is estimated to be present in at least 77 families and 11 000 species, is a key evolutionary innovation and a globally important driver of plant diversity. Myrmecochory provides the best example to date for a consistent effect of any mutualism on large-scale diversification.

Into and out of the tropics: global diversification patterns in a hyperdiverse clade of ectomycorrhizal fungi.

PubMed

Looney, Brian P; Ryberg, Martin; Hampe, Felix; Sánchez-García, Marisol; Matheny, P Brandon

2016-01-01

Ectomycorrhizal (ECM) fungi, symbiotic mutualists of many dominant tree and shrub species, exhibit a biogeographic pattern counter to the established latitudinal diversity gradient of most macroflora and fauna. However, an evolutionary basis for this pattern has not been explicitly tested in a diverse lineage. In this study, we reconstructed a mega-phylogeny of a cosmopolitan and hyperdiverse genus of ECM fungi, Russula, sampling from annotated collections and utilizing publically available sequences deposited in GenBank. Metadata from molecular operational taxonomic unit cluster sets were examined to infer the distribution and plant association of the genus. This allowed us to test for differences in patterns of diversification between tropical and extratropical taxa, as well as how their associations with different plant lineages may be a driver of diversification. Results show that Russula is most species-rich at temperate latitudes and ancestral state reconstruction shows that the genus initially diversified in temperate areas. Migration into and out of the tropics characterizes the early evolution of the genus, and these transitions have been frequent since this time. We propose the 'generalized diversification rate' hypothesis to explain the reversed latitudinal diversity gradient pattern in Russula as we detect a higher net diversification rate in extratropical lineages. Patterns of diversification with plant associates support host switching and host expansion as driving diversification, with a higher diversification rate in lineages associated with Pinaceae and frequent transitions to association with angiosperms. © 2015 John Wiley & Sons Ltd.

Understanding the genetic effects of recent habitat fragmentation in the context of evolutionary history: Phylogeography and landscape genetics of a southern California endemic Jerusalem cricket (Orthoptera: Stenopelmatidae: Stenopelmatus)

USGS Publications Warehouse

Vandergast, A.G.; Bohonak, A.J.; Weissman, D.B.; Fisher, R.N.

2007-01-01

Habitat loss and fragmentation due to urbanization are the most pervasive threats to biodiversity in southern California. Loss of habitat and fragmentation can lower migration rates and genetic connectivity among remaining populations of native species, reducing genetic variability and increasing extinction risk. However, it may be difficult to separate the effects of recent anthropogenic fragmentation from the genetic signature of prehistoric fragmentation due to previous natural geological and climatic changes. To address these challenges, we examined the phylogenetic and population genetic structure of a flightless insect endemic to cismontane southern California, Stenopelmatus 'mahogani' (Orthoptera: Stenopelmatidae). Analyses of mitochondrial DNA sequence data suggest that diversification across southern California began during the Pleistocene, with most haplotypes currently restricted to a single population. Patterns of genetic divergence correlate with contemporary urbanization, even after correcting for (geographical information system) GIS-based reconstructions of fragmentation during the Pleistocene. Theoretical simulations confirm that contemporary patterns of genetic structure could be produced by recent urban fragmentation using biologically reasonable assumptions about model parameters. Diversity within populations was positively correlated with current fragment size, but not prehistoric fragment size, suggesting that the effects of increased drift following anthropogenic fragmentation are already being seen. Loss of genetic connectivity and diversity can hinder a population's ability to adapt to ecological perturbations commonly associated with urbanization, such as habitat degradation, climatic changes and introduced species. Consequently, our results underscore the importance of preserving and restoring landscape connectivity for long-term persistence of low vagility native species. Journal compilation ?? 2006 Blackwell Publishing Ltd.

26 CFR 1.351-1 - Transfer to corporation controlled by transferor.

Code of Federal Regulations, 2010 CFR

2010-04-01

... diversification of the transferors' interests, and (ii) The transferee is (a) a regulated investment company, (b... stock outstanding. (5) A transfer ordinarily results in the diversification of the transferors... be disregarded in determining whether diversification has occurred. If there is only one transferor...

7 CFR 4290.740 - Portfolio diversification (“overline” limitation).

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 15 2010-01-01 2010-01-01 false Portfolio diversification (âoverlineâ limitation). 4290.740 Section 4290.740 Agriculture Regulations of the Department of Agriculture (Continued) RURAL... Enterprise for Rbic Financing § 4290.740 Portfolio diversification (“overline” limitation). (a) Without the...

Funding Reforms and Revenue Diversification--Patterns, Challenges and Rhetoric

ERIC Educational Resources Information Center

Teixeira, Pedro; Koryakina, Tatyana

2013-01-01

In recent years, much has been written about the challenging financial context faced by many European higher education institutions, and the pressures towards funding diversification. However, the evidence available indicates that funding diversification has seldom lived up to the rhetorical expectations of marketization and privatization that…

Rough Electrode Creates Excess Capacitance in Thin-Film Capacitors

PubMed Central

2017-01-01

The parallel-plate capacitor equation is widely used in contemporary material research for nanoscale applications and nanoelectronics. To apply this equation, flat and smooth electrodes are assumed for a capacitor. This essential assumption is often violated for thin-film capacitors because the formation of nanoscale roughness at the electrode interface is very probable for thin films grown via common deposition methods. In this work, we experimentally and theoretically show that the electrical capacitance of thin-film capacitors with realistic interface roughness is significantly larger than the value predicted by the parallel-plate capacitor equation. The degree of the deviation depends on the strength of the roughness, which is described by three roughness parameters for a self-affine fractal surface. By applying an extended parallel-plate capacitor equation that includes the roughness parameters of the electrode, we are able to calculate the excess capacitance of the electrode with weak roughness. Moreover, we introduce the roughness parameter limits for which the simple parallel-plate capacitor equation is sufficiently accurate for capacitors with one rough electrode. Our results imply that the interface roughness beyond the proposed limits cannot be dismissed unless the independence of the capacitance from the interface roughness is experimentally demonstrated. The practical protocols suggested in our work for the reliable use of the parallel-plate capacitor equation can be applied as general guidelines in various fields of interest. PMID:28745040

Rough Electrode Creates Excess Capacitance in Thin-Film Capacitors.

PubMed

Torabi, Solmaz; Cherry, Megan; Duijnstee, Elisabeth A; Le Corre, Vincent M; Qiu, Li; Hummelen, Jan C; Palasantzas, George; Koster, L Jan Anton

2017-08-16

The parallel-plate capacitor equation is widely used in contemporary material research for nanoscale applications and nanoelectronics. To apply this equation, flat and smooth electrodes are assumed for a capacitor. This essential assumption is often violated for thin-film capacitors because the formation of nanoscale roughness at the electrode interface is very probable for thin films grown via common deposition methods. In this work, we experimentally and theoretically show that the electrical capacitance of thin-film capacitors with realistic interface roughness is significantly larger than the value predicted by the parallel-plate capacitor equation. The degree of the deviation depends on the strength of the roughness, which is described by three roughness parameters for a self-affine fractal surface. By applying an extended parallel-plate capacitor equation that includes the roughness parameters of the electrode, we are able to calculate the excess capacitance of the electrode with weak roughness. Moreover, we introduce the roughness parameter limits for which the simple parallel-plate capacitor equation is sufficiently accurate for capacitors with one rough electrode. Our results imply that the interface roughness beyond the proposed limits cannot be dismissed unless the independence of the capacitance from the interface roughness is experimentally demonstrated. The practical protocols suggested in our work for the reliable use of the parallel-plate capacitor equation can be applied as general guidelines in various fields of interest.

Parallel evolution of Streptococcus pneumoniae and Streptococcus mitis to pathogenic and mutualistic lifestyles.

PubMed

Kilian, Mogens; Riley, David R; Jensen, Anders; Brüggemann, Holger; Tettelin, Hervé

2014-07-22

The bacterium Streptococcus pneumoniae is one of the leading causes of fatal infections affecting humans. Intriguingly, phylogenetic analysis shows that the species constitutes one evolutionary lineage in a cluster of the otherwise commensal Streptococcus mitis strains, with which humans live in harmony. In a comparative analysis of 35 genomes, including phylogenetic analyses of all predicted genes, we have shown that the pathogenic pneumococcus has evolved into a master of genomic flexibility while lineages that evolved into the nonpathogenic S. mitis secured harmonious coexistence with their host by stabilizing an approximately 15%-reduced genome devoid of many virulence genes. Our data further provide evidence that interspecies gene transfer between S. pneumoniae and S. mitis occurs in a unidirectional manner, i.e., from S. mitis to S. pneumoniae. Import of genes from S. mitis and other mitis, anginosus, and salivarius group streptococci ensured allelic replacements and antigenic diversification and has been driving the evolution of the remarkable structural diversity of capsular polysaccharides of S. pneumoniae. Our study explains how the unique structural diversity of the pneumococcal capsule emerged and conceivably will continue to increase and reveals a striking example of the fragile border between the commensal and pathogenic lifestyles. While genomic plasticity enabling quick adaptation to environmental stress is a necessity for the pathogenic streptococci, the commensal lifestyle benefits from stability. Importance: One of the leading causes of fatal infections affecting humans, Streptococcus pneumoniae, and the commensal Streptococcus mitis are closely related obligate symbionts associated with hominids. Faced with a shortage of accessible hosts, the two opposing lifestyles evolved in parallel. We have shown that the nonpathogenic S. mitis secured harmonious coexistence with its host by stabilizing a reduced genome devoid of many virulence genes. Meanwhile, the pathogenic pneumococcus evolved into a master of genomic flexibility and imports genes from S. mitis and other related streptococci. This process ensured antigenic diversification and has been driving the evolution of the remarkable structural diversity of capsular polysaccharides of S. pneumoniae, which conceivably will continue to increase and present a challenge to disease prevention. Copyright © 2014 Kilian et al.

Changing Tertiary Education in Modern European Society.

ERIC Educational Resources Information Center

Council for Cultural Cooperation, Strasbourg (France).

Reports on recent developments and problems in the diversification of tertiary education in seven Western European countries are presented by members of the Working Party on the Diversification of Tertiary Education. Policy analysis and evaluation and recommendations for future policy are also provided. As a policy, diversification refers to the…

13 CFR 107.740 - Portfolio diversification (“overline” limitation).

Code of Federal Regulations, 2010 CFR

2010-01-01

... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false Portfolio diversification (âoverlineâ limitation). 107.740 Section 107.740 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION... Eligibility of A Small Business for Sbic Financing § 107.740 Portfolio diversification (“overline” limitation...

Primate diversification inferred from phylogenies and fossils.

PubMed

Herrera, James P

2017-12-01

Biodiversity arises from the balance between speciation and extinction. Fossils record the origins and disappearance of organisms, and the branching patterns of molecular phylogenies allow estimation of speciation and extinction rates, but the patterns of diversification are frequently incongruent between these two data sources. I tested two hypotheses about the diversification of primates based on ∼600 fossil species and 90% complete phylogenies of living species: (1) diversification rates increased through time; (2) a significant extinction event occurred in the Oligocene. Consistent with the first hypothesis, analyses of phylogenies supported increasing speciation rates and negligible extinction rates. In contrast, fossils showed that while speciation rates increased, speciation and extinction rates tended to be nearly equal, resulting in zero net diversification. Partially supporting the second hypothesis, the fossil data recorded a clear pattern of diversity decline in the Oligocene, although diversification rates were near zero. The phylogeny supported increased extinction ∼34 Ma, but also elevated extinction ∼10 Ma, coinciding with diversity declines in some fossil clades. The results demonstrated that estimates of speciation and extinction ignoring fossils are insufficient to infer diversification and information on extinct lineages should be incorporated into phylogenetic analyses. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Non-reef environments impact the diversification of extant jacks, remoras and allies (Carangoidei, Percomorpha)

PubMed Central

Marramà, Giuseppe; Carnevale, Giorgio; Santini, Francesco

2016-01-01

Various factors may impact the processes of diversification of a clade. In the marine realm, it has been shown that coral reef environments have promoted diversification in various fish groups. With the exception of requiem sharks, all the groups showing a higher level of diversity in reefs than in non-reef habitats have diets based predominantly on plankton, algae or benthic invertebrates. Here we explore the pattern of diversification of carangoid fishes, a clade that includes numerous piscivorous species (e.g. trevallies, jacks and dolphinfishes), using time-calibrated phylogenies as well as ecological and morphological data from both extant and fossil species. The study of carangoid morphospace suggests that reef environments played a role in their early radiation during the Eocene. However, contrary to the hypothesis of a reef-association-promoting effect, we show that habitat shifts to non-reef environments have increased the rates of morphological diversification (i.e. size and body shape) in extant carangoids. Piscivory did not have a major impact on the tempo of diversification of this group. Through the ecological radiation of carangoid fishes, we demonstrate that non-reef environments may sustain and promote processes of diversification of different marine fish groups, at least those including a large proportion of piscivorous species. PMID:27807262

Pleistocene glacial cycles drive isolation, gene flow and speciation in the high-elevation Andes.

PubMed

Nevado, Bruno; Contreras-Ortiz, Natalia; Hughes, Colin; Filatov, Dmitry A

2018-06-04

Mountain ranges are amongst the most species-rich habitats, with many large and rapid evolutionary radiations. The tempo and mode of diversification in these systems are key unanswered questions in evolutionary biology. Here we study the Andean Lupinus radiation to understand the processes driving very rapid diversification in montane systems. We use genomic and transcriptomic data of multiple species and populations, and apply phylogenomic and demographic analyses to test whether diversification proceeded without interspecific gene flow - as expected if Andean orogeny and geographic isolation were the main drivers of diversification - or if diversification was accompanied by gene flow, in which case other processes were probably involved. We uncover several episodes of gene flow between species, including very recent events likely to have been prompted by changes in habitat connectivity during Pleistocene glacial cycles. Furthermore, we find that gene flow between species was heterogeneously distributed across the genome. We argue that exceptionally fast diversification of Andean Lupinus was partly a result of Late Pleistocene glacial cycles, with associated cycles of expansion and contraction driving geographic isolation or secondary contact of species. Furthermore, heterogeneous gene flow across the genome suggests a role for selection and ecological speciation in rapid diversification in this system. © 2018 The Authors New Phytologist © 2018 New Phytologist Trust.

What Explains Patterns of Diversification and Richness among Animal Phyla?

PubMed Central

Jezkova, Tereza; Wiens, John J.

2016-01-01

Animal phyla vary dramatically in species richness (from 1 species to >1.2 million), but the causes of this variation remain largely unknown. Animals have also evolved striking variation in morphology and ecology, including sessile marine taxa lacking heads, eyes, limbs, and complex organs (e.g. sponges), parasitic worms (e.g. nematodes, platyhelminths), and taxa with eyes, skeletons, limbs, and complex organs that dominate terrestrial ecosystems (arthropods, chordates). Relating this remarkable variation in traits to the diversification and richness of animal phyla is a fundamental yet unresolved problem in biology. Here, we test the impacts of 18 traits (including morphology, ecology, reproduction, and development) on diversification and richness of extant animal phyla. Using phylogenetic multiple regression, the best-fitting model includes five traits that explain ~74% of the variation in diversification rates (dioecy, parasitism, eyes/photoreceptors, a skeleton, non-marine habitat). However, a model including just three (skeleton, parasitism, habitat) explains nearly as much variation (~67%). Diversification rates then largely explain richness patterns. Our results also identify many striking traits that have surprisingly little impact on diversification (e.g. head, limbs, and complex circulatory and digestive systems). Overall, our results reveal the key factors that shape large-scale patterns of diversification and richness across >80% of all extant, described species. PMID:28221832

Elevated Extinction Rates as a Trigger for Diversification Rate Shifts: Early Amniotes as a Case Study

PubMed Central

Brocklehurst, Neil; Ruta, Marcello; Müller, Johannes; Fröbisch, Jörg

2015-01-01

Tree shape analyses are frequently used to infer the location of shifts in diversification rate within the Tree of Life. Many studies have supported a causal relationship between shifts and temporally coincident events such as the evolution of “key innovations”. However, the evidence for such relationships is circumstantial. We investigated patterns of diversification during the early evolution of Amniota from the Carboniferous to the Triassic, subjecting a new supertree to analyses of tree balance in order to infer the timing and location of diversification shifts. We investigated how uneven origination and extinction rates drive diversification shifts, and use two case studies (herbivory and an aquatic lifestyle) to examine whether shifts tend to be contemporaneous with evolutionary novelties. Shifts within amniotes tend to occur during periods of elevated extinction, with mass extinctions coinciding with numerous and larger shifts. Diversification shifts occurring in clades that possess evolutionary innovations do not coincide temporally with the appearance of those innovations, but are instead deferred to periods of high extinction rate. We suggest such innovations did not cause increases in the rate of cladogenesis, but allowed clades to survive extinction events. We highlight the importance of examining general patterns of diversification before interpreting specific shifts. PMID:26592209

Buccal venom gland associates with increased of diversification rate in the fang blenny fish Meiacanthus (Blenniidae; Teleostei).

PubMed

Liu, Shang-Yin Vanson; Frédérich, Bruno; Lavoué, Sébastien; Chang, Jonathan; Erdmann, Mark V; Mahardika, Gusti Ngurah; Barber, Paul H

2018-08-01

At the macroevolutionary level, many mechanisms have been proposed to explain explosive species diversification. Among them morphological and/or physiological novelty is considered to have a great impact on the tempo and the mode of diversification. Meiacanthus is a genus of Blenniidae possessing a unique buccal venom gland at the base of an elongated canine tooth. This unusual trait has been hypothesized to aid escape from predation and thus potentially play an important role in their pattern of diversification. Here, we produce the first time-calibrated phylogeny of Blenniidae and we test the impact of two morphological novelties on their diversification, i.e. the presence of swim bladder and buccal venom gland, using various comparative methods. We found an increase in the tempo of lineage diversification at the root of the Meiacanthus clade, associated with the evolution of the buccal venom gland, but not the swim bladder. Neither morphological novelty was associated with the pattern of size disparification in blennies. Our results support the hypothesis that the buccal venom gland has contributed to the explosive diversification of Meiacanthus, but further analyses are needed to fully understand the factors sustaining this burst of speciation. Copyright © 2018 Elsevier Inc. All rights reserved.

Diversification dynamics of rhynchostomatian ciliates: the impact of seven intrinsic traits on speciation and extinction in a microbial group.

PubMed

Vďačný, Peter; Rajter, Ľubomír; Shazib, Shahed Uddin Ahmed; Jang, Seok Won; Shin, Mann Kyoon

2017-08-30

Ciliates are a suitable microbial model to investigate trait-dependent diversification because of their comparatively complex morphology and high diversity. We examined the impact of seven intrinsic traits on speciation, extinction, and net-diversification of rhynchostomatians, a group of comparatively large, predatory ciliates with proboscis carrying a dorsal brush (sensoric structure) and toxicysts (organelles used to kill the prey). Bayesian estimates under the binary-state speciation and extinction model indicate that two types of extrusomes and two-rowed dorsal brush raise diversification through decreasing extinction. On the other hand, the higher number of contractile vacuoles and their dorsal location likely increase diversification via elevating speciation rate. Particular nuclear characteristics, however, do not significantly differ in their diversification rates and hence lineages with various macronuclear patterns and number of micronuclei have similar probabilities to generate new species. Likelihood-based quantitative state diversification analyses suggest that rhynchostomatians conform to Cope's rule in that their diversity linearly grows with increasing body length and relative length of the proboscis. Comparison with other litostomatean ciliates indicates that rhynchostomatians are not among the cladogenically most successful lineages and their survival over several hundred million years could be associated with their comparatively large and complex bodies that reduce the risk of extinction.

Non-reef environments impact the diversification of extant jacks, remoras and allies (Carangoidei, Percomorpha).

PubMed

Frédérich, Bruno; Marramà, Giuseppe; Carnevale, Giorgio; Santini, Francesco

2016-11-16

Various factors may impact the processes of diversification of a clade. In the marine realm, it has been shown that coral reef environments have promoted diversification in various fish groups. With the exception of requiem sharks, all the groups showing a higher level of diversity in reefs than in non-reef habitats have diets based predominantly on plankton, algae or benthic invertebrates. Here we explore the pattern of diversification of carangoid fishes, a clade that includes numerous piscivorous species (e.g. trevallies, jacks and dolphinfishes), using time-calibrated phylogenies as well as ecological and morphological data from both extant and fossil species. The study of carangoid morphospace suggests that reef environments played a role in their early radiation during the Eocene. However, contrary to the hypothesis of a reef-association-promoting effect, we show that habitat shifts to non-reef environments have increased the rates of morphological diversification (i.e. size and body shape) in extant carangoids. Piscivory did not have a major impact on the tempo of diversification of this group. Through the ecological radiation of carangoid fishes, we demonstrate that non-reef environments may sustain and promote processes of diversification of different marine fish groups, at least those including a large proportion of piscivorous species. © 2016 The Author(s).

Adaptive radiation versus 'radiation' and 'explosive diversification': why conceptual distinctions are fundamental to understanding evolution.

PubMed

Givnish, Thomas J

2015-07-01

Adaptive radiation is the rise of a diversity of ecological roles and role-specific adaptations within a lineage. Recently, some researchers have begun to use 'adaptive radiation' or 'radiation' as synonymous with 'explosive species diversification'. This essay aims to clarify distinctions between these concepts, and the related ideas of geographic speciation, sexual selection, key innovations, key landscapes and ecological keys. Several examples are given to demonstrate that adaptive radiation and explosive diversification are not the same phenomenon, and that focusing on explosive diversification and the analysis of phylogenetic topology ignores much of the rich biology associated with adaptive radiation, and risks generating confusion about the nature of the evolutionary forces driving species diversification. Some 'radiations' involve bursts of geographic speciation or sexual selection, rather than adaptive diversification; some adaptive radiations have little or no effect on speciation, or even a negative effect. Many classic examples of 'adaptive radiation' appear to involve effects driven partly by geographic speciation, species' dispersal abilities, and the nature of extrinsic dispersal barriers; partly by sexual selection; and partly by adaptive radiation in the classical sense, including the origin of traits and invasion of adaptive zones that result in decreased diversification rates but add to overall diversity. © 2015 The Author. New Phytologist © 2015 New Phytologist Trust.

Dioecy does not consistently accelerate or slow lineage diversification across multiple genera of angiosperms.

PubMed

Sabath, Niv; Goldberg, Emma E; Glick, Lior; Einhorn, Moshe; Ashman, Tia-Lynn; Ming, Ray; Otto, Sarah P; Vamosi, Jana C; Mayrose, Itay

2016-02-01

Dioecy, the sexual system in which male and female organs are found in separate individuals, allows greater specialization for sex-specific functions and can be advantageous under various ecological and environmental conditions. However, dioecy is rare among flowering plants. Previous studies identified contradictory trends regarding the relative diversification rates of dioecious lineages vs their nondioecious counterparts, depending on the methods and data used. We gathered detailed species-level data for dozens of genera that contain both dioecious and nondioecious species. We then applied a probabilistic approach that accounts for differential speciation, extinction, and transition rates between states to examine whether there is an association between dioecy and lineage diversification. We found a bimodal distribution, whereby dioecious lineages exhibited higher diversification in certain genera but lower diversification in others. Additional analyses did not uncover an ecological or life history trait that could explain a context-dependent effect of dioecy on diversification. Furthermore, in-depth simulations of neutral characters demonstrated that such bimodality is also found when simulating neutral characters across the observed trees. Our analyses suggest that - at least for these genera with the currently available data - dioecy neither consistently places a strong brake on diversification nor is a strong driver. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets.

PubMed

Zeng, Liping; Zhang, Ning; Zhang, Qiang; Endress, Peter K; Huang, Jie; Ma, Hong

2017-05-01

Explosive diversification is widespread in eukaryotes, making it difficult to resolve phylogenetic relationships. Eudicots contain c. 75% of extant flowering plants, are important for human livelihood and terrestrial ecosystems, and have probably experienced explosive diversifications. The eudicot phylogenetic relationships, especially among those of the Pentapetalae, remain unresolved. Here, we present a highly supported eudicot phylogeny and diversification rate shifts using 31 newly generated transcriptomes and 88 other datasets covering 70% of eudicot orders. A highly supported eudicot phylogeny divided Pentapetalae into two groups: one with rosids, Saxifragales, Vitales and Santalales; the other containing asterids, Caryophyllales and Dilleniaceae, with uncertainty for Berberidopsidales. Molecular clock analysis estimated that crown eudicots originated c. 146 Ma, considerably earlier than earliest tricolpate pollen fossils and most other molecular clock estimates, and Pentapetalae sequentially diverged into eight major lineages within c. 15 Myr. Two identified increases of diversification rate are located in the stems leading to Pentapetalae and asterids, and lagged behind the gamma hexaploidization. The nuclear genes from newly generated transcriptomes revealed a well-resolved eudicot phylogeny, sequential separation of major core eudicot lineages and temporal mode of diversifications, providing new insights into the evolutionary trend of morphologies and contributions to the diversification of eudicots. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

What Explains Patterns of Diversification and Richness among Animal Phyla?

PubMed

Jezkova, Tereza; Wiens, John J

2017-03-01

Animal phyla vary dramatically in species richness (from one species to >1.2 million), but the causes of this variation remain largely unknown. Animals have also evolved striking variation in morphology and ecology, including sessile marine taxa lacking heads, eyes, limbs, and complex organs (e.g., sponges), parasitic worms (e.g., nematodes, platyhelminths), and taxa with eyes, skeletons, limbs, and complex organs that dominate terrestrial ecosystems (arthropods, chordates). Relating this remarkable variation in traits to the diversification and richness of animal phyla is a fundamental yet unresolved problem in biology. Here, we test the impacts of 18 traits (including morphology, ecology, reproduction, and development) on diversification and richness of extant animal phyla. Using phylogenetic multiple regression, the best-fitting model includes five traits that explain ∼74% of the variation in diversification rates (dioecy, parasitism, eyes/photoreceptors, a skeleton, nonmarine habitat). However, a model including just three (skeleton, parasitism, habitat) explains nearly as much variation (∼67%). Diversification rates then largely explain richness patterns. Our results also identify many striking traits that have surprisingly little impact on diversification (e.g., head, limbs, and complex circulatory and digestive systems). Overall, our results reveal the key factors that shape large-scale patterns of diversification and richness across >80% of all extant, described species.

Impact of Insertion Sequences and Recombination on the Population Structure of Staphylococcus haemolyticus.

PubMed

Bouchami, Ons; de Lencastre, Herminia; Miragaia, Maria

2016-01-01

Staphylococcus haemolyticus is one of the most common pathogens associated with medical-device related infections, but its molecular epidemiology is poorly explored. In the current study, we aimed to better understand the genetic mechanisms contributing to S. haemolyticus diversity in the hospital environment and their impact on the population structure and clinical relevant phenotypic traits. The analysis of a representative S. haemolyticus collection by multilocus sequence typing (MLST) has identified a single highly prevalent and diverse genetic lineage of nosocomial S. haemolyticus clonal complex (CC) 29 accounting for 91% of the collection of isolates disseminated worldwide. The examination of the sequence changes at MLST loci during clonal diversification showed that recombination had a higher impact than mutation in shaping the S. haemolyticus population. Also, we ascertained that another mechanism contributing significantly to clonal diversification and adaptation was mediated by insertion sequence (IS) elements. We found that all nosocomial S. haemolyticus, belonging to different STs, were rich in IS1272 copies, as determined by Southern hybridization of macrorestriction patterns. In particular, we observed that the chromosome of a S. haemolyticus strain within CC29 was highly unstable during serial growth in vitro which paralleled with IS1272 transposition events and changes in clinically relevant phenotypic traits namely, mannitol fermentation, susceptibility to beta-lactams, biofilm formation and hemolysis. Our results suggest that recombination and IS transposition might be a strategy of adaptation, evolution and pathogenicity of the major S. haemolyticus prevalent lineage in the hospital environment.

Impact of Insertion Sequences and Recombination on the Population Structure of Staphylococcus haemolyticus

PubMed Central

Bouchami, Ons; de Lencastre, Herminia; Miragaia, Maria

2016-01-01

Staphylococcus haemolyticus is one of the most common pathogens associated with medical-device related infections, but its molecular epidemiology is poorly explored. In the current study, we aimed to better understand the genetic mechanisms contributing to S. haemolyticus diversity in the hospital environment and their impact on the population structure and clinical relevant phenotypic traits. The analysis of a representative S. haemolyticus collection by multilocus sequence typing (MLST) has identified a single highly prevalent and diverse genetic lineage of nosocomial S. haemolyticus clonal complex (CC) 29 accounting for 91% of the collection of isolates disseminated worldwide. The examination of the sequence changes at MLST loci during clonal diversification showed that recombination had a higher impact than mutation in shaping the S. haemolyticus population. Also, we ascertained that another mechanism contributing significantly to clonal diversification and adaptation was mediated by insertion sequence (IS) elements. We found that all nosocomial S. haemolyticus, belonging to different STs, were rich in IS1272 copies, as determined by Southern hybridization of macrorestriction patterns. In particular, we observed that the chromosome of a S. haemolyticus strain within CC29 was highly unstable during serial growth in vitro which paralleled with IS1272 transposition events and changes in clinically relevant phenotypic traits namely, mannitol fermentation, susceptibility to beta-lactams, biofilm formation and hemolysis. Our results suggest that recombination and IS transposition might be a strategy of adaptation, evolution and pathogenicity of the major S. haemolyticus prevalent lineage in the hospital environment. PMID:27249649

Development and evolution of the mammalian limb: adaptive diversification of nails, hooves, and claws.

PubMed

Hamrick, M W

2001-01-01

Paleontological evidence indicates that the evolutionary diversification of mammals early in the Cenozoic era was characterized by an adaptive radiation of distal limb structures. Likewise, neontological data show that morphological variation in distal limb integumentary appendages (e.g., nails, hooves, and claws) can be observed not only among distantly related mammalian taxa but also among closely related species within the same clade. Comparative analysis of nail, claw, and hoof morphogenesis reveals relatively subtle differences in mesenchymal and epithelial patterning underlying these adult differences in distal limb appendage morphology. Furthermore, studies of regulatory gene expression during vertebrate claw development demonstrate that many of the signaling molecules involved in patterning ectodermal derivatives such as teeth, hair, and feathers are also involved in organizing mammalian distal limb appendages. For example, Bmp4 signaling plays an important role during the recruitment of mesenchymal cells into the condensations forming the terminal phalanges, whereas Msx2 affects the length of nails and claws by suppressing proliferation of germinal epidermal cells. Evolutionary changes in the form of distal integumentary appendages may therefore result from changes in gene expression during formation of mesenchymal condensations (Bmp4, posterior Hox genes), induction of the claw fold and germinal matrix (shh), and/or proliferation of epidermal cells in the claw matrix (Msx1, Msx2). The prevalence of convergences and parallelisms in nail and claw structure among mammals underscores the existence of multiple morphogenetic pathways for evolutionary change in distal limb appendages.

The Evolutionary Dynamics of the Odorant Receptor Gene Family in Corbiculate Bees

PubMed Central

Ramírez, Santiago R.

2017-01-01

Abstract Insects rely on chemical information to locate food, choose mates, and detect potential predators. It has been hypothesized that adaptive changes in the olfactory system facilitated the diversification of numerous insect lineages. For instance, evolutionary changes of Odorant Receptor (OR) genes often occur in parallel with modifications in life history strategies. Corbiculate bees display a diverse array of behaviors that are controlled through olfaction, including varying degrees of social organization, and manifold associations with floral resources. Here we investigated the molecular mechanisms driving the evolution of the OR gene family in corbiculate bees in comparison to other chemosensory gene families. Our results indicate that the genomic organization of the OR gene family has remained highly conserved for ∼80 Myr, despite exhibiting major changes in repertoire size among bee lineages. Moreover, the evolution of OR genes appears to be driven mostly by lineage-specific gene duplications in few genomic regions that harbor large numbers of OR genes. A selection analysis revealed that OR genes evolve under positive selection, with the strongest signals detected in recently duplicated copies. Our results indicate that chromosomal translocations had a minimal impact on OR evolution, and instead local molecular mechanisms appear to be main drivers of OR repertoire size. Our results provide empirical support to the longstanding hypothesis that positive selection shaped the diversification of the OR gene family. Together, our results shed new light on the molecular mechanisms underlying the evolution of olfaction in insects. PMID:28854688

Can you sequence ecology? Metagenomics of adaptive diversification.

PubMed

Marx, Christopher J

2013-01-01

Few areas of science have benefited more from the expansion in sequencing capability than the study of microbial communities. Can sequence data, besides providing hypotheses of the functions the members possess, detect the evolutionary and ecological processes that are occurring? For example, can we determine if a species is adapting to one niche, or if it is diversifying into multiple specialists that inhabit distinct niches? Fortunately, adaptation of populations in the laboratory can serve as a model to test our ability to make such inferences about evolution and ecology from sequencing. Even adaptation to a single niche can give rise to complex temporal dynamics due to the transient presence of multiple competing lineages. If there are multiple niches, this complexity is augmented by segmentation of the population into multiple specialists that can each continue to evolve within their own niche. For a known example of parallel diversification that occurred in the laboratory, sequencing data gave surprisingly few obvious, unambiguous signs of the ecological complexity present. Whereas experimental systems are open to direct experimentation to test hypotheses of selection or ecological interaction, the difficulty in "seeing ecology" from sequencing for even such a simple system suggests translation to communities like the human microbiome will be quite challenging. This will require both improved empirical methods to enhance the depth and time resolution for the relevant polymorphisms and novel statistical approaches to rigorously examine time-series data for signs of various evolutionary and ecological phenomena within and between species.

A glimpse on the pattern of rodent diversification: a phylogenetic approach

PubMed Central

2012-01-01

Background Development of phylogenetic methods that do not rely on fossils for the study of evolutionary processes through time have revolutionized the field of evolutionary biology and resulted in an unprecedented expansion of our knowledge about the tree of life. These methods have helped to shed light on the macroevolution of many taxonomic groups such as the placentals (Mammalia). However, despite the increase of studies addressing the diversification patterns of organisms, no synthesis has addressed the case of the most diversified mammalian clade: the Rodentia. Results Here we present a rodent maximum likelihood phylogeny inferred from a molecular supermatrix. It is based on 11 mitochondrial and nuclear genes that covers 1,265 species, i.e., respectively 56% and 81% of the known specific and generic rodent diversity. The inferred topology recovered all Rodentia clades proposed by recent molecular works. A relaxed molecular clock dating approach provided a time framework for speciation events. We found that the Myomorpha clade shows a greater degree of variation in diversification rates than Sciuroidea, Caviomorpha, Castorimorpha and Anomaluromorpha. We identified a number of shifts in diversification rates within the major clades: two in Castorimorpha, three in Ctenohystrica, 6 within the squirrel-related clade and 24 in the Myomorpha clade. The majority of these shifts occurred within the most recent familial rodent radiations: the Cricetidae and Muridae clades. Using the topological imbalances and the time line we discuss the potential role of different diversification factors that might have shaped the rodents radiation. Conclusions The present glimpse on the diversification pattern of rodents can be used for further comparative meta-analyses. Muroid lineages have a greater degree of variation in their diversification rates than any other rodent group. Different topological signatures suggest distinct diversification processes among rodent lineages. In particular, Muroidea and Sciuroidea display widespread distribution and have undergone evolutionary and adaptive radiation on most of the continents. Our results show that rodents experienced shifts in diversification rate regularly through the Tertiary, but at different periods for each clade. A comparison between the rodent fossil record and our results suggest that extinction led to the loss of diversification signal for most of the Paleogene nodes. PMID:22697210

Darwinism for the Genomic Age: Connecting Mutation to Diversification

PubMed Central

Hua, Xia; Bromham, Lindell

2017-01-01

A growing body of evidence suggests that rates of diversification of biological lineages are correlated with differences in genome-wide mutation rate. Given that most research into differential patterns of diversification rate have focused on species traits or ecological parameters, a connection to the biochemical processes of genome change is an unexpected observation. While the empirical evidence for a significant association between mutation rate and diversification rate is mounting, there has been less effort in explaining the factors that mediate this connection between genetic change and species richness. Here we draw together empirical studies and theoretical concepts that may help to build links in the explanatory chain that connects mutation to diversification. First we consider the way that mutation rates vary between species. We then explore how differences in mutation rates have flow-through effects to the rate at which populations acquire substitutions, which in turn influences the speed at which populations become reproductively isolated from each other due to the acquisition of genomic incompatibilities. Since diversification rate is commonly measured from phylogenetic analyses, we propose a conceptual approach for relating events of reproductive isolation to bifurcations on molecular phylogenies. As we examine each of these relationships, we consider theoretical models that might shine a light on the observed association between rate of molecular evolution and diversification rate, and critically evaluate the empirical evidence for these links, focusing on phylogenetic comparative studies. Finally, we ask whether we are getting closer to a real understanding of the way that the processes of molecular evolution connect to the observable patterns of diversification. PMID:28224003

Phylogenetic patterns of geographical and ecological diversification in the subgenus Drosophila.

PubMed

Morales-Hojas, Ramiro; Vieira, Jorge

2012-01-01

Colonisation of new geographic regions and/or of new ecological resources can result in rapid species diversification into the new ecological niches available. Members of the subgenus Drosophila are distributed across the globe and show a large diversity of ecological niches. Furthermore, taxonomic classification of Drosophila includes the rank radiation, which refers to closely related species groups. Nevertheless, it has never been tested if these taxonomic radiations correspond to evolutionary radiations. Here we present a study of the patterns of diversification of Drosophila to test for increased diversification rates in relation to the geographic and ecological diversification processes. For this, we have estimated and dated a phylogeny of 218 species belonging to the major species groups of the subgenus. The obtained phylogenies are largely consistent with previous studies and indicate that the major groups appeared during the Oligocene/Miocene transition or early Miocene, characterized by a trend of climate warming with brief periods of glaciation. Ancestral reconstruction of geographic ranges and ecological resource use suggest at least two dispersals to the Neotropics from the ancestral Asiatic tropical disribution, and several transitions to specialized ecological resource use (mycophagous and cactophilic). Colonisation of new geographic regions and/or of new ecological resources can result in rapid species diversification into the new ecological niches available. However, diversification analyses show no significant support for adaptive radiations as a result of geographic dispersal or ecological resource shift. Also, cactophily has not resulted in an increase in the diversification rate of the repleta and related groups. It is thus concluded that the taxonomic radiations do not correspond to adaptive radiations.

Ants Sow the Seeds of Global Diversification in Flowering Plants

PubMed Central

Lengyel, Szabolcs; Gove, Aaron D.; Latimer, Andrew M.; Majer, Jonathan D.; Dunn, Robert R.

2009-01-01

Background The extraordinary diversification of angiosperm plants in the Cretaceous and Tertiary periods has produced an estimated 250,000–300,000 living angiosperm species and has fundamentally altered terrestrial ecosystems. Interactions with animals as pollinators or seed dispersers have long been suspected as drivers of angiosperm diversification, yet empirical examples remain sparse or inconclusive. Seed dispersal by ants (myrmecochory) may drive diversification as it can reduce extinction by providing selective advantages to plants and can increase speciation by enhancing geographical isolation by extremely limited dispersal distances. Methodology/Principal Findings Using the most comprehensive sister-group comparison to date, we tested the hypothesis that myrmecochory leads to higher diversification rates in angiosperm plants. As predicted, diversification rates were substantially higher in ant-dispersed plants than in their non-myrmecochorous relatives. Data from 101 angiosperm lineages in 241 genera from all continents except Antarctica revealed that ant-dispersed lineages contained on average more than twice as many species as did their non-myrmecochorous sister groups. Contrasts in species diversity between sister groups demonstrated that diversification rates did not depend on seed dispersal mode in the sister group and were higher in myrmecochorous lineages in most biogeographic regions. Conclusions/Significance Myrmecochory, which has evolved independently at least 100 times in angiosperms and is estimated to be present in at least 77 families and 11 000 species, is a key evolutionary innovation and a globally important driver of plant diversity. Myrmecochory provides the best example to date for a consistent effect of any mutualism on large-scale diversification. PMID:19436714

Darwinism for the Genomic Age: Connecting Mutation to Diversification.

PubMed

Hua, Xia; Bromham, Lindell

2017-01-01

A growing body of evidence suggests that rates of diversification of biological lineages are correlated with differences in genome-wide mutation rate. Given that most research into differential patterns of diversification rate have focused on species traits or ecological parameters, a connection to the biochemical processes of genome change is an unexpected observation. While the empirical evidence for a significant association between mutation rate and diversification rate is mounting, there has been less effort in explaining the factors that mediate this connection between genetic change and species richness. Here we draw together empirical studies and theoretical concepts that may help to build links in the explanatory chain that connects mutation to diversification. First we consider the way that mutation rates vary between species. We then explore how differences in mutation rates have flow-through effects to the rate at which populations acquire substitutions, which in turn influences the speed at which populations become reproductively isolated from each other due to the acquisition of genomic incompatibilities. Since diversification rate is commonly measured from phylogenetic analyses, we propose a conceptual approach for relating events of reproductive isolation to bifurcations on molecular phylogenies. As we examine each of these relationships, we consider theoretical models that might shine a light on the observed association between rate of molecular evolution and diversification rate, and critically evaluate the empirical evidence for these links, focusing on phylogenetic comparative studies. Finally, we ask whether we are getting closer to a real understanding of the way that the processes of molecular evolution connect to the observable patterns of diversification.

Is the diversification of Mediterranean Basin plant lineages coupled to karyotypic changes?

PubMed

Escudero, M; Balao, F; Martín-Bravo, S; Valente, L; Valcárcel, V

2018-01-01

The Mediterranean Basin region, home to 25,000 plant species, is included in the worldwide list of hotspots of biodiversity. Despite the indisputably important role of chromosome transitions in plant evolution and diversification, no reference study to date has dealt with the possible relationship between chromosome evolution and lineage diversification in the Mediterranean Basin. Here we study patterns of diversification, patterns of chromosome number transition (either polyploidy or dysploidy) and the relationship between the two for 14 Mediterranean Basin angiosperm lineages using previously published phylogenies. We found a mixed pattern, with half of the lineages displaying a change in chromosome transition rates after the onset of the Mediterranean climate (six increases, one decrease) and the other half (six) experiencing constant rates of chromosome transitions through time. We have also found a heterogeneous pattern regarding diversification rates, with lineages exhibiting moderate (five phylogenies) or low (six) initial diversification rates that either increased (six) or declined (five) through time. Our results reveal no clear link between diversification rates and chromosome number transition rates. By promoting the formation of new habitats and driving the extinction of many species, the Mediterranean onset and the posterior Quaternary climatic oscillations could have been key for the establishment of new chromosomal variants in some plant phylogenies but not in others. While the biodiversity of the Mediterranean Basin may be partly influenced by the chromosomal diversity of its lineages, this study concludes that lineage diversification in the region is largely decoupled from karyotypic evolution. © 2017 German Botanical Society and The Royal Botanical Society of the Netherlands.

Going to extremes: contrasting rates of diversification in a recent radiation of new world passerine birds.

PubMed

Barker, F Keith; Burns, Kevin J; Klicka, John; Lanyon, Scott M; Lovette, Irby J

2013-03-01

Recent analyses suggest that a few major shifts in diversification rate may be enough to explain most of the disparity in diversity among vertebrate lineages. At least one significant increase in diversification rate appears to have occurred within the birds; however, several nested lineages within birds have been identified as hyperdiverse by different studies. A clade containing the finches and relatives (within the avian order Passeriformes), including a large radiation endemic to the New World that comprises ~8% of all bird species, may be the true driver of this rate increase. Understanding the patterns and processes of diversification of this diverse lineage may go a long way toward explaining the apparently rapid diversification rates of both passerines and of birds as a whole. We present the first multilocus phylogenetic analyses of this endemic New World radiation of finch relatives that include sampling of all recognized genera, a relaxed molecular clock analysis of its divergence history, and an analysis of its broad-scale diversification patterns. These analyses recovered 5 major lineages traditionally recognized as avian families, but identified an additional 10 relatively ancient lineages worthy of recognition at the family level. Time-calibrated diversification analyses suggested that at least 3 of the 15 family-level lineages were significantly species poor given the entire group's background diversification rate, whereas at least one-the tanagers of family Thraupidae-appeared significantly more diverse. Lack of an age-diversity relationship within this clade suggests that, due to rapid initial speciation, it may have experienced density-dependent ecological limits on its overall diversity.

Kokkos: Enabling manycore performance portability through polymorphic memory access patterns

DOE PAGES

Carter Edwards, H.; Trott, Christian R.; Sunderland, Daniel

2014-07-22

The manycore revolution can be characterized by increasing thread counts, decreasing memory per thread, and diversity of continually evolving manycore architectures. High performance computing (HPC) applications and libraries must exploit increasingly finer levels of parallelism within their codes to sustain scalability on these devices. We found that a major obstacle to performance portability is the diverse and conflicting set of constraints on memory access patterns across devices. Contemporary portable programming models address manycore parallelism (e.g., OpenMP, OpenACC, OpenCL) but fail to address memory access patterns. The Kokkos C++ library enables applications and domain libraries to achieve performance portability on diversemore » manycore architectures by unifying abstractions for both fine-grain data parallelism and memory access patterns. In this paper we describe Kokkos’ abstractions, summarize its application programmer interface (API), present performance results for unit-test kernels and mini-applications, and outline an incremental strategy for migrating legacy C++ codes to Kokkos. Furthermore, the Kokkos library is under active research and development to incorporate capabilities from new generations of manycore architectures, and to address a growing list of applications and domain libraries.« less

Multiphase complete exchange on Paragon, SP2 and CS-2

NASA Technical Reports Server (NTRS)

Bokhari, Shahid H.

1995-01-01

The overhead of interprocessor communication is a major factor in limiting the performance of parallel computer systems. The complete exchange is the severest communication pattern in that it requires each processor to send a distinct message to every other processor. This pattern is at the heart of many important parallel applications. On hypercubes, multiphase complete exchange has been developed and shown to provide optimal performance over varying message sizes. Most commercial multicomputer systems do not have a hypercube interconnect. However, they use special purpose hardware and dedicated communication processors to achieve very high performance communication and can be made to emulate the hypercube quite well. Multiphase complete exchange has been implemented on three contemporary parallel architectures: the Intel Paragon, IBM SP2 and Meiko CS-2. The essential features of these machines are described and their basic interprocessor communication overheads are discussed. The performance of multiphase complete exchange is evaluated on each machine. It is shown that the theoretical ideas developed for hypercubes are also applicable in practice to these machines and that multiphase complete exchange can lead to major savings in execution time over traditional solutions.

Diversification Management at Tertiary Education Level: A Review

ERIC Educational Resources Information Center

Takwate, Kwaji Tizhe

2016-01-01

This paper examines the concept of management of diversification at tertiary education level in view of the growth of national secondary education system which vested high scramble for tertiary education was made in relation to question of access and expansion. This paper examines management of diversification at tertiary education level as a…

The Diversification of Secondary Education: School Curricula in Comparative Perspective. IBE Working Papers on Curriculum Issues Number 6

ERIC Educational Resources Information Center

Benavot, Aaron

2006-01-01

Secondary education continues to expand rapidly worldwide. Equally important is its diversification. The present paper contends that the diversification of secondary education, while acknowledged, is not well studied. Despite the widespread expansion of secondary education in different world regions, the information available to researchers--and…

29 CFR 2560.502c-7 - Civil penalties under section 502(c)(7).

Code of Federal Regulations, 2010 CFR

2010-07-01

...) of the Act), who fails or refuses to provide notice of diversification rights to applicable... a notice of diversification rights shall mean a failure or refusal, in whole or in part, to provide notice of diversification rights to an applicable individual at the time and in the manner prescribed by...

Vertical integration and diversification of acute care hospitals: conceptual definitions.

PubMed

Clement, J P

1988-01-01

The terms vertical integration and diversification, although used quite frequently, are ill-defined for use in the health care field. In this article, the concepts are defined--specifically for nonuniversity acute care hospitals. The resulting definitions are more useful than previous ones for predicting the effects of vertical integration and diversification.

The role of ecological opportunity in shaping disparate diversification trajectories in a bicontinental primate radiation.

PubMed

Tran, Lucy A P

2014-04-22

Exceptional species and phenotypic diversity commonly are attributed to ecological opportunity (EO). The conventional EO model predicts that rates of lineage diversification and phenotypic evolution are elevated early in a radiation only to decline later in response to niche availability. Foregut fermentation is hypothesized to be a key innovation that allowed colobine monkeys (subfamily Colobinae), the only primates with this trait, to successfully colonize folivore adaptive zones unavailable to other herbivorous species. Therefore, diversification rates also are expected to be strongly linked with the evolution of traits related to folivory in these monkeys. Using dated molecular phylogenies and a dataset of feeding morphology, I test predictions of the EO model to evaluate the role of EO conferred by foregut fermentation in shaping the African and Asian colobine radiations. Findings from diversification methods coupled with colobine biogeographic history provide compelling evidence that decreasing availability of new adaptive zones during colonization of Asia together with constraints presented by dietary specialization underlie temporal changes in diversification in the Asian but not African clade. Additionally, departures from the EO model likely reflect iterative diversification events in Asia.

Diversification of land plants: insights from a family-level phylogenetic analysis.

PubMed

Fiz-Palacios, Omar; Schneider, Harald; Heinrichs, Jochen; Savolainen, Vincent

2011-11-21

Some of the evolutionary history of land plants has been documented based on the fossil record and a few broad-scale phylogenetic analyses, especially focusing on angiosperms and ferns. Here, we reconstructed phylogenetic relationships among all 706 families of land plants using molecular data. We dated the phylogeny using multiple fossils and a molecular clock technique. Applying various tests of diversification that take into account topology, branch length, numbers of extant species as well as extinction, we evaluated diversification rates through time. We also compared these diversification profiles against the distribution of the climate modes of the Phanerozoic. We found evidence for the radiations of ferns and mosses in the shadow of angiosperms coinciding with the rather warm Cretaceous global climate. In contrast, gymnosperms and liverworts show a signature of declining diversification rates during geological time periods of cool global climate. This broad-scale phylogenetic analysis helps to reveal the successive waves of diversification that made up the diversity of land plants we see today. Both warm temperatures and wet climate may have been necessary for the rise of the diversity under a successive lineage replacement scenario.

Crop diversification and livelihoods of smallholder farmers in Zimbabwe: adaptive management for environmental change.

PubMed

Makate, Clifton; Wang, Rongchang; Makate, Marshall; Mango, Nelson

2016-01-01

This paper demonstrates how crop diversification impacts on two outcomes of climate smart agriculture; increased productivity (legume and cereal crop productivity) and enhanced resilience (household income, food security, and nutrition) in rural Zimbabwe. Using data from over 500 smallholder farmers, we jointly estimate crop diversification and each of the outcome variables within a conditional (recursive) mixed process framework that corrects for selectivity bias arising due to the voluntary nature of crop diversification. We find that crop diversification depends on the land size, farming experience, asset wealth, location, access to agricultural extension services, information on output prices, low transportation costs and general information access. Our results also indicate that an increase in the rate of adoption improves crop productivity, income, food security and nutrition at household level. Overall, our results are indicative of the importance of crop diversification as a viable climate smart agriculture practice that significantly enhances crop productivity and consequently resilience in rural smallholder farming systems. We, therefore, recommend wider adoption of diversified cropping systems notably those currently less diversified for greater adaptation to the ever-changing climate.

Diversification of visual media retrieval results using saliency detection

NASA Astrophysics Data System (ADS)

Muratov, Oleg; Boato, Giulia; De Natale, Franesco G. B.

2013-03-01

Diversification of retrieval results allows for better and faster search. Recently there has been proposed different methods for diversification of image retrieval results mainly utilizing text information and techniques imported from natural language processing domain. However, images contain visual information that is impossible to describe in text and the use of visual features is inevitable. Visual saliency is information about the main object of an image implicitly included by humans while creating visual content. For this reason it is naturally to exploit this information for the task of diversification of the content. In this work we study whether visual saliency can be used for the task of diversification and propose a method for re-ranking image retrieval results using saliency. The evaluation has shown that the use of saliency information results in higher diversity of retrieval results.

Syphilis 1855 and HIV-AIDS 2007: Historical reflections on the tendency to blame human anatomy for the action of micro-organisms.

PubMed

Darby, Robert

2015-01-01

In this paper, I discuss the parallels between responses to syphilis in nineteenth century Britain and HIV/AIDS in contemporary Africa. In each case, an incurable disease connected with sexual behaviour aroused fear, stigmatisation and moralistic responses, as well as a desperate scramble to find an effective means of control. In both cases, circumcision of adult males, and then of children or infants, was proposed as the key tactic. In the ensuing debates over the effectiveness and propriety of this approach, three questions occupied health authorities in both Victorian Britain and the contemporary world: (1) Were circumcised men at significantly lower risk of these diseases? (2) If there was evidence pointing to an affirmative answer, was it altered anatomy or different behaviour that explained the difference? (3) Given that circumcision was a surgical procedure with attendant risks of infection, was it possible that circumcision spread syphilis or HIV? I show that in both situations the answers to these questions were inconclusive, argue that circumcision played little or no role in the eventual control of syphilis and suggest that attention to nineteenth century debates may assist contemporary policy-makers to avoid the treatment dead-ends and ethical transgressions that marked the war on syphilis.

Detecting Hidden Diversification Shifts in Models of Trait-Dependent Speciation and Extinction.

PubMed

Beaulieu, Jeremy M; O'Meara, Brian C

2016-07-01

The distribution of diversity can vary considerably from clade to clade. Attempts to understand these patterns often employ state-dependent speciation and extinction models to determine whether the evolution of a particular novel trait has increased speciation rates and/or decreased extinction rates. It is still unclear, however, whether these models are uncovering important drivers of diversification, or whether they are simply pointing to more complex patterns involving many unmeasured and co-distributed factors. Here we describe an extension to the popular state-dependent speciation and extinction models that specifically accounts for the presence of unmeasured factors that could impact diversification rates estimated for the states of any observed trait, addressing at least one major criticism of BiSSE (Binary State Speciation and Extinction) methods. Specifically, our model, which we refer to as HiSSE (Hidden State Speciation and Extinction), assumes that related to each observed state in the model are "hidden" states that exhibit potentially distinct diversification dynamics and transition rates than the observed states in isolation. We also demonstrate how our model can be used as character-independent diversification models that allow for a complex diversification process that is independent of the evolution of a character. Under rigorous simulation tests and when applied to empirical data, we find that HiSSE performs reasonably well, and can at least detect net diversification rate differences between observed and hidden states and detect when diversification rate differences do not correlate with the observed states. We discuss the remaining issues with state-dependent speciation and extinction models in general, and the important ways in which HiSSE provides a more nuanced understanding of trait-dependent diversification. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Parallelized Kalman-Filter-Based Reconstruction of Particle Tracks on Many-Core Architectures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cerati, Giuseppe; Elmer, Peter; Krutelyov, Slava

Faced with physical and energy density limitations on clock speed, contemporary microprocessor designers have increasingly turned to on-chip parallelism for performance gains. Examples include the Intel Xeon Phi, GPGPUs, and similar technologies. Algorithms should accordingly be designed with ample amounts of fine-grained parallelism if they are to realize the full performance of the hardware. This requirement can be challenging for algorithms that are naturally expressed as a sequence of small-matrix operations, such as the Kalman filter methods widely in use in high-energy physics experiments. In the High-Luminosity Large Hadron Collider (HL-LHC), for example, one of the dominant computational problems ismore » expected to be finding and fitting charged-particle tracks during event reconstruction; today, the most common track-finding methods are those based on the Kalman filter. Experience at the LHC, both in the trigger and offline, has shown that these methods are robust and provide high physics performance. Previously we reported the significant parallel speedups that resulted from our efforts to adapt Kalman-filter-based tracking to many-core architectures such as Intel Xeon Phi. Here we report on how effectively those techniques can be applied to more realistic detector configurations and event complexity.« less

Sub-inhibitory concentrations of some antibiotics can drive diversification of Pseudomonas aeruginosa populations in artificial sputum medium

PubMed Central

2013-01-01

Background Pseudomonas aeruginosa populations within the cystic fibrosis lung exhibit extensive phenotypic and genetic diversification. The resultant population diversity is thought to be crucial to the persistence of infection and may underpin the progression of disease. However, because cystic fibrosis lungs represent ecologically complex and hostile environments, the selective forces driving this diversification in vivo remain unclear. We took an experimental evolution approach to test the hypothesis that sub-inhibitory antibiotics can drive diversification of P. aeruginosa populations. Replicate populations of P. aeruginosa LESB58 were cultured for seven days in artificial sputum medium with and without sub-inhibitory concentrations of various clinically relevant antibiotics. We then characterised diversification with respect to 13 phenotypic and genotypic characteristics. Results We observed that higher population diversity evolved in the presence of azithromycin, ceftazidime or colistin relative to antibiotic-free controls. Divergence occurred due to alterations in antimicrobial susceptibility profiles following exposure to azithromycin, ceftazidime and colistin. Alterations in colony morphology and pyocyanin production were observed following exposure to ceftazidime and colistin only. Diversification was not observed in the presence of meropenem. Conclusions Our study indicates that certain antibiotics can promote population diversification when present in sub-inhibitory concentrations. Hence, the choice of antibiotic may have previously unforeseen implications for the development of P. aeruginosa infections in the lungs of cystic fibrosis patients. PMID:23879797

A Robust Semi-Parametric Test for Detecting Trait-Dependent Diversification.

PubMed

Rabosky, Daniel L; Huang, Huateng

2016-03-01

Rates of species diversification vary widely across the tree of life and there is considerable interest in identifying organismal traits that correlate with rates of speciation and extinction. However, it has been challenging to develop methodological frameworks for testing hypotheses about trait-dependent diversification that are robust to phylogenetic pseudoreplication and to directionally biased rates of character change. We describe a semi-parametric test for trait-dependent diversification that explicitly requires replicated associations between character states and diversification rates to detect effects. To use the method, diversification rates are reconstructed across a phylogenetic tree with no consideration of character states. A test statistic is then computed to measure the association between species-level traits and the corresponding diversification rate estimates at the tips of the tree. The empirical value of the test statistic is compared to a null distribution that is generated by structured permutations of evolutionary rates across the phylogeny. The test is applicable to binary discrete characters as well as continuous-valued traits and can accommodate extremely sparse sampling of character states at the tips of the tree. We apply the test to several empirical data sets and demonstrate that the method has acceptable Type I error rates. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Geological and climatic changes in quaternary shaped the evolutionary history of Calibrachoa heterophylla, an endemic South-Atlantic species of petunia

PubMed Central

2013-01-01

Background The glacial and interglacial cycles that characterized the Quaternary greatly affected the distribution and genetic diversity of plants. In the Neotropics, few phylogeographic studies have focused on coastal species outside of the Atlantic Rainforest. Climatic and sea level changes during the Quaternary played an important role in the evolutionary history of many organisms found in coastal regions. To contribute to a better understanding of plant evolution in this environment in Southern South America, we focused on Calibrachoa heterophylla (Solanaceae), an endemic and vulnerable wild petunia species from the South Atlantic Coastal Plain (SACP). Results We assessed DNA sequences from two cpDNA intergenic spacers and analyzed them using a phylogeographic approach. The present phylogeographic study reveals the influence of complex geologic and climatic events on patterns of genetic diversification. The results indicate that C. heterophylla originated inland and subsequently colonized the SACP; the data show that the inland haplogroup is more ancient than the coastal one and that the inland was not affected by sea level changes in the Quaternary. The major diversification of C. heterophylla that occurred after 0.4 Myr was linked to sea level oscillations in the Quaternary, and any diversification that occurred before this time was obscured by marine transgressions that occurred before the coastal sand barrier’s formation. Results of the Bayesian skyline plot showed a recent population expansion detected in C. heterophylla seems to be related to an increase in temperature and humidity that occurred at the beginning of the Holocene. Conclusions The geographic clades have been formed when the coastal plain was deeply dissected by paleochannels and these correlate very well with the distributional limits of the clades. The four major sea transgressions formed a series of four sand barriers parallel to the coast that progressively increased the availability of coastal areas after the regressions and that may have promoted the geographic structuring of genetic diversity observed today. The recent population expansion for the entire species may be linked with the event of marine regression after the most recent sea transgression at ~5 kya. PMID:23987105

Phylogenetics of tribe Orchideae (Orchidaceae: Orchidoideae) based on combined DNA matrices: inferences regarding timing of diversification and evolution of pollination syndromes

PubMed Central

Inda, Luis A.; Pimentel, Manuel; Chase, Mark W.

2012-01-01

Background and aims Tribe Orchideae (Orchidaceae: Orchidoideae) comprises around 62 mostly terrestrial genera, which are well represented in the Northern Temperate Zone and less frequently in tropical areas of both the Old and New Worlds. Phylogenetic relationships within this tribe have been studied previously using only nuclear ribosomal DNA (nuclear ribosomal internal transcribed spacer, nrITS). However, different parts of the phylogenetic tree in these analyses were weakly supported, and integrating information from different plant genomes is clearly necessary in orchids, where reticulate evolution events are putatively common. The aims of this study were to: (1) obtain a well-supported and dated phylogenetic hypothesis for tribe Orchideae, (ii) assess appropriateness of recent nomenclatural changes in this tribe in the last decade, (3) detect possible examples of reticulate evolution and (4) analyse in a temporal context evolutionary trends for subtribe Orchidinae with special emphasis on pollination systems. Methods The analyses included 118 samples, belonging to 103 species and 25 genera, for three DNA regions (nrITS, mitochondrial cox1 intron and plastid rpl16 intron). Bayesian and maximum-parsimony methods were used to construct a well-supported and dated tree. Evolutionary trends in the subtribe were analysed using Bayesian and maximum-likelihood methods of character evolution. Key Results The dated phylogenetic tree strongly supported the recently recircumscribed generic concepts of Bateman and collaborators. Moreover, it was found that Orchidinae have diversified in the Mediterranean basin during the last 15 million years, and one potential example of reticulate evolution in the subtribe was identified. In Orchidinae, pollination systems have shifted on numerous occasions during the last 23 million years. Conclusions The results indicate that ancestral Orchidinae were hymenopteran-pollinated, food-deceptive plants and that these traits have been dominant throughout the evolutionary history of the subtribe in the Mediterranean. Evidence was also obtained that the onset of sexual deception might be linked to an increase in labellum size, and the possibility is discussed that diversification in Orchidinae developed in parallel with diversification of bees and wasps from the Miocene onwards. PMID:22539542

75 FR 3871 - Promoting Diversification of Ownership in Broadcast Services; Suspension of Filing Date

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-25

... FEDERAL COMMUNICATIONS COMMISSION 47 CFR Part 73 [MB Docket Nos. 07-294, 06-121, 02-277, 04-228; MM Docket Nos. 01-235, 01-317, 00-244; DA 09-2618] Promoting Diversification of Ownership in...); Promoting Diversification in the Broadcasting Services, Order, DA 09-2165 (rel. Oct. 2, 2009). See also...

Agricultural Adjustment and the Diversification of Farm Households and Corporate Farms in Central Europe

ERIC Educational Resources Information Center

Chaplin, Hannah; Davidova, Sophia; Gorton, Matthew

2004-01-01

Survey evidence from three Central European Countries (Czech Republic, Hungary and Poland) is analysed to identify the degree of non-agricultural farm diversification and the factors facilitating or impeding it in individual and corporate farms. The effect of diversification on rural job creation and household incomes is investigated. The results…

Place of Manufacture Diversification in Cyclical Development of the Enterprise

ERIC Educational Resources Information Center

Erofeev, Alexander G.; Smolin, Georgy K.

2016-01-01

The relevance of the researched problem is caused by the fact that diversification is one of the best options for reforming enterprises. The aim of the research: to consider changes in production of outputs in development cycles of the enterprise. This will help to reveal the nature of manufacture diversification. The leading method to the…

Phylogenetic and paleobotanical evidence for late Miocene diversification of the Tertiary subtropical lineage of ivies (Hedera L., Araliaceae).

PubMed

Valcárcel, V; Guzmán, B; Medina, N G; Vargas, P; Wen, J

2017-06-22

Hedera (ivies) is one of the few temperate genera of the primarily tropical Asian Palmate group of the Araliaceae, which extends its range out of Asia to Europe and the Mediterranean basin. Phylogenetic and phylogeographic results suggested Asia as the center of origin and the western Mediterranean region as one of the secondary centers of diversification. The bird-dispersed fleshy fruits of ivies suggest frequent dispersal over long distances (e.g. Macaronesian archipelagos), although reducing the impact of geographic barriers to gene flow in mainland species. Genetic isolation associated with geographic barriers and independent polyploidization events have been postulated as the main driving forces of diversification. In this study we aim to evaluate past and present diversification patterns in Hedera within a geographic and temporal framework to clarify the biogeographic history of the genus. Phylogenetic (biogeographic, time divergence and diversification) and phylogeographic (coalescence) analyses using four DNA regions (nrITS, trnH-psbA, trnT-trnL, rpl32) revealed a complex spatial pattern of lineage divergence. Scarce geographic limitation to gene flow and limited diversification are observed during the early-mid Miocene, followed by a diversification rate increase related to geographic divergence from the Tortonian/Messinian. Genetic and palaeobotanical evidence points the origin of the Hedera clade in Asia, followed by a gradual E-W Asian extinction and the progressive E-W Mediterranean colonization. The temporal framework for the E Asia - W Mediterranean westward colonization herein reported is congruent with the fossil record. Subsequent range expansion in Europe and back colonization to Asia is also inferred. Uneven diversification among geographic areas occurred from the Tortonian/Messinian onwards with limited diversification in the newly colonized European and Asian regions. Eastern and western Mediterranean regions acted as refugia for Miocene and post-Miocene lineages, with a similar role as consecutive centers of centrifugal dispersal (including islands) and speciation. The Miocene Asian extinction and European survival of Hedera question the general pattern of Tertiary regional extinction of temperate angiosperms in Europe while they survived in Asia. The Tortonian/Messinian diversification increase of ivies in the Mediterranean challenges the idea that this aridity period was responsible for the extinction of the Mediterranean subtropical Tertiary flora. Differential responses of Hedera to geographic barriers throughout its evolutionary history, linked to spatial isolation related to historical geologic and climatic constraints may have shaped diversification of ivies in concert with recurrent polyploidy.

Temporal and spatial diversification of Pteroglossus araçaris (AVES: Ramphastidae) in the neotropics: constant rate of diversification does not support an increase in radiation during the Pleistocene.

PubMed

Patel, Swati; Weckstein, Jason D; Patané, José S L; Bates, John M; Aleixo, Alexandre

2011-01-01

We use the small-bodied toucan genus Pteroglossus to test hypotheses about diversification in the lowland Neotropics. We sequenced three mitochondrial genes and one nuclear intron from all Pteroglossus species and used these data to reconstruct phylogenetic trees based on maximum parsimony, maximum likelihood, and Bayesian analyses. These phylogenetic trees were used to make inferences regarding both the pattern and timing of diversification for the group. We used the uplift of the Talamanca highlands of Costa Rica and western Panama as a geologic calibration for estimating divergence times on the Pteroglossus tree and compared these results with a standard molecular clock calibration. Then, we used likelihood methods to model the rate of diversification. Based on our analyses, the onset of the Pteroglossus radiation predates the Pleistocene, which has been predicted to have played a pivotal role in diversification in the Amazon rainforest biota. We found a constant rate of diversification in Pteroglossus evolutionary history, and thus no support that events during the Pleistocene caused an increase in diversification. We compare our data to other avian phylogenies to better understand major biogeographic events in the Neotropics. These comparisons support recurring forest connections between the Amazonian and Atlantic forests, and the splitting of cis/trans Andean species after the final uplift of the Andes. At the subspecies level, there is evidence for reciprocal monophyly and groups are often separated by major rivers, demonstrating the important role of rivers in causing or maintaining divergence. Because some of the results presented here conflict with current taxonomy of Pteroglossus, new taxonomic arrangements are suggested. Copyright © 2010 Elsevier Inc. All rights reserved.

Widespread correlations between climatic niche evolution and species diversification in birds.

PubMed

Cooney, Christopher R; Seddon, Nathalie; Tobias, Joseph A

2016-07-01

The adaptability of species' climatic niches can influence the dynamics of colonization and gene flow across climatic gradients, potentially increasing the likelihood of speciation or reducing extinction in the face of environmental change. However, previous comparative studies have tested these ideas using geographically, taxonomically and ecologically restricted samples, yielding mixed results, and thus the processes linking climatic niche evolution with diversification remain poorly understood. Focusing on birds, the largest and most widespread class of terrestrial vertebrates, we test whether variation in species diversification among clades is correlated with rates of climatic niche evolution and the extent to which these patterns are modified by underlying gradients in biogeography and species' ecology. We quantified climatic niches, latitudinal distribution and ecological traits for 7657 (˜75%) bird species based on geographical range polygons and then used Bayesian phylogenetic analyses to test whether niche evolution was related to species richness and rates of diversification across genus- and family-level clades. We found that the rate of climatic niche evolution has a positive linear relationship with both species richness and diversification rate at two different taxonomic levels (genus and family). Furthermore, this positive association between labile climatic niches and diversification was detected regardless of variation in clade latitude or key ecological traits. Our findings suggest either that rapid adaptation to unoccupied areas of climatic niche space promotes avian diversification, or that diversification promotes adaptation. Either way, we propose that climatic niche evolution is a fundamental process regulating the link between climate and biodiversity at global scales, irrespective of the geographical and ecological context of speciation and extinction. © 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.

Diversification patterns in cosmopolitan earthworms: similar mode but different tempo.

PubMed

Fernández, Rosa; Novo, Marta; Marchán, Daniel F; Díaz Cosín, Darío J

2016-01-01

Comparative phylogeography of widespread species that span the same geographic areas can elucidate the influence of historical events on current patterns of biodiversity, identify patterns of co-vicariance, and therefore aid the understanding of general evolutionary processes. Soil-dwelling animals present characteristics that make them suitable for testing the effect of the palaeogeographical events on their distribution and diversification, such as their low vagility and population structure. In this study, we shed light on the spatial lineage diversification and cladogenesis of two widely-distributed cosmopolitan and invasive earthworms (Aporrectodea rosea and A. trapezoides) in their putative ancestral area of origin, the Western Palearctic, and a few populations in North America. Molecular analyses were conducted on mitochondrial and nuclear markers from 220 (A. rosea) and 198 (A. trapezoides) individuals collected in 56 and 57 localities, respectively. We compared the lineage diversification pattern, genetic variability and cladogenesis in both species. Our findings showed that both species underwent a similar diversification from the Western Mediterranean plates to (i) Northern Europe and (ii) the Iberian Peninsula, establishing their two main lineages. Their diversification was in concordance with the main palaeogeographical events in the Iberian Peninsula and Western Mediterranean, followed by a later colonization of North America from individuals derived exclusively from the Eurosiberian lineage. Their diversification occurred at different times, with the diversification of A. rosea being potentially more ancient. Cladogenesis in both species seems to have been modelled only by the Mediterranean plate shifts, ignoring historical climatic oscillations such as the Messinian salinity crisis. Their high genetic variability, strong population structure, lack of gene flow and stepping-stone-like cladogenesis suggest the existence of different cryptic lineages. Our results may indicate a recurrent event in invasive earthworms within their ancestral distribution areas in the Western Palearctic. Copyright © 2015 Elsevier Inc. All rights reserved.

Asynchronous diversification in a specialized plant-pollinator mutualism.

PubMed

Ramírez, Santiago R; Eltz, Thomas; Fujiwara, Mikiko K; Gerlach, Günter; Goldman-Huertas, Benjamin; Tsutsui, Neil D; Pierce, Naomi E

2011-09-23

Most flowering plants establish mutualistic associations with insect pollinators to facilitate sexual reproduction. However, the evolutionary processes that gave rise to these associations remain poorly understood. We reconstructed the times of divergence, diversification patterns, and interaction networks of a diverse group of specialized orchids and their bee pollinators. In contrast to a scenario of coevolution by race formation, we show that fragrance-producing orchids originated at least three times independently after their fragrance-collecting bee mutualists. Whereas orchid diversification has apparently tracked the diversification of orchids' bee pollinators, bees appear to have depended on the diverse chemical environment of neotropical forests. We corroborated this apparent asymmetrical dependency by simulating co-extinction cascades in real interaction networks that lacked reciprocal specialization. These results suggest that the diversification of insect-pollinated angiosperms may have been facilitated by the exploitation of preexisting sensory biases of insect pollinators.

Viviparity stimulates diversification in an order of fish.

PubMed

Helmstetter, Andrew J; Papadopulos, Alexander S T; Igea, Javier; Van Dooren, Tom J M; Leroi, Armand M; Savolainen, Vincent

2016-04-12

Species richness is distributed unevenly across the tree of life and this may be influenced by the evolution of novel phenotypes that promote diversification. Viviparity has originated ∼150 times in vertebrates and is considered to be an adaptation to highly variable environments. Likewise, possessing an annual life cycle is common in plants and insects, where it enables the colonization of seasonal environments, but rare in vertebrates. The extent to which these reproductive life-history traits have enhanced diversification and their relative importance in the process remains unknown. We show that convergent evolution of viviparity causes bursts of diversification in fish. We built a phylogenetic tree for Cyprinodontiformes, an order in which both annualism and viviparity have arisen, and reveal that while both traits have evolved multiple times, only viviparity played a major role in shaping the patterns of diversity. These results demonstrate that changes in reproductive life-history strategy can stimulate diversification.

Competition both drives and impedes diversification in a model adaptive radiation

PubMed Central

Bailey, Susan F.; Dettman, Jeremy R.; Rainey, Paul B.; Kassen, Rees

2013-01-01

Competitors are known to be important in governing the outcome of evolutionary diversification during an adaptive radiation, but the precise mechanisms by which they exert their effects remain elusive. Using the model adaptive radiation of Pseudomonas fluorescens, we show experimentally that the effect of competition on diversification of a focal lineage depends on both the strength of competition and the ability of the competitors to diversify. We provide evidence that the extent of diversification in the absence of interspecific competitors depends on the strength of resource competition. We also show that the presence of competitors can actually increase diversity by increasing interspecific resource competition. Competitors that themselves are able to diversify prevent diversification of the focal lineage by removing otherwise available ecological opportunities. These results suggest that the progress of an adaptive radiation depends ultimately on the strength of resource competition, an effect that can be exaggerated or impeded by the presence of competitors. PMID:23843392

Host shifts and evolutionary radiations of butterflies

PubMed Central

Fordyce, James A.

2010-01-01

Ehrlich and Raven proposed a model of coevolution where major host plant shifts of butterflies facilitate a burst of diversification driven by their arrival to a new adaptive zone. One prediction of this model is that reconstructions of historical diversification of butterflies should indicate an increase in diversification rate following major host shifts. Using reconstructed histories of 15 butterfly groups, I tested this prediction and found general agreement with Ehrlich and Raven's model. Butterfly lineages with an inferred major historical host shift showed evidence of diversification rate variation, with a significant acceleration following the host shift. Lineages without an inferred major host shift generally agreed with a constant-rate model of diversification. These results are consistent with the view that host plant associations have played a profound role in the evolutionary history of butterflies, and show that major shifts to chemically distinct plant groups leave a historical footprint that remains detectable today. PMID:20610430

Viviparity stimulates diversification in an order of fish

PubMed Central

Helmstetter, Andrew J.; Papadopulos, Alexander S. T.; Igea, Javier; Van Dooren, Tom J. M.; Leroi, Armand M.; Savolainen, Vincent

2016-01-01

Species richness is distributed unevenly across the tree of life and this may be influenced by the evolution of novel phenotypes that promote diversification. Viviparity has originated ∼150 times in vertebrates and is considered to be an adaptation to highly variable environments. Likewise, possessing an annual life cycle is common in plants and insects, where it enables the colonization of seasonal environments, but rare in vertebrates. The extent to which these reproductive life-history traits have enhanced diversification and their relative importance in the process remains unknown. We show that convergent evolution of viviparity causes bursts of diversification in fish. We built a phylogenetic tree for Cyprinodontiformes, an order in which both annualism and viviparity have arisen, and reveal that while both traits have evolved multiple times, only viviparity played a major role in shaping the patterns of diversity. These results demonstrate that changes in reproductive life-history strategy can stimulate diversification. PMID:27070759

Estimation of main diversification time-points of hantaviruses using phylogenetic analyses of complete genomes.

PubMed

Castel, Guillaume; Tordo, Noël; Plyusnin, Alexander

2017-04-02

Because of the great variability of their reservoir hosts, hantaviruses are excellent models to evaluate the dynamics of virus-host co-evolution. Intriguing questions remain about the timescale of the diversification events that influenced this evolution. In this paper we attempted to estimate the first ever timing of hantavirus diversification based on thirty five available complete genomes representing five major groups of hantaviruses and the assumption of co-speciation of hantaviruses with their respective mammal hosts. Phylogenetic analyses were used to estimate the main diversification points during hantavirus evolution in mammals while host diversification was mostly estimated from independent calibrators taken from fossil records. Our results support an earlier developed hypothesis of co-speciation of known hantaviruses with their respective mammal hosts and hence a common ancestor for all hantaviruses carried by placental mammals. Copyright © 2017 Elsevier B.V. All rights reserved.

Comparative diversification dynamics among palaeocontinents during the Ordovician Radiation

NASA Technical Reports Server (NTRS)

Miller, A. I.

1997-01-01

The Ordovician Radiation was among the most extensive intervals of diversification in the history of life. However, a delineation of the proximal cause(s) of the Radiation remains elusive. Any such determination should involve an analysis of geographic overprints on diversification: did the Radiation occur randomly around the world or, alternatively, was it focused in particular geographic or depositional regimes? Here, I present a comparative evaluation of Ordovician diversification among several palaeocontinents to determine whether biotas associated with certain palaeocontinents exhibited different diversification patterns than others; in part, this involves a numerical "correction" to raw diversity trajectories. Clear disparities among palaeocontinents are indicated by the data, which appear to reflect differences in the extent of siliciclastic input partly in association with tectonic activity. Further testing will be required to fully substantiate the implication that siliciclastic influx was a predominant factor in the Ordovician Radiation, affecting a variety of higher taxa among all three Phanerozoic evolutionary faunas.

Multiple Geographical Origins of Environmental Sex Determination enhanced the diversification of Darwin's Favourite Orchids.

PubMed

Pérez-Escobar, Oscar Alejandro; Chomicki, Guillaume; Condamine, Fabien L; de Vos, Jurriaan M; Martins, Aline C; Smidt, Eric C; Klitgård, Bente; Gerlach, Günter; Heinrichs, Jochen

2017-10-10

Environmental sex determination (ESD) - a change in sexual function during an individual life span driven by environmental cues - is an exceedingly rare sexual system among angiosperms. Because ESD can directly affect reproduction success, it could influence diversification rate as compared with lineages that have alternative reproductive systems. Here we test this hypothesis using a solid phylogenetic framework of Neotropical Catasetinae, the angiosperm lineage richest in taxa with ESD. We assess whether gains of ESD are associated with higher diversification rates compared to lineages with alternative systems while considering additional traits known to positively affect diversification rates in orchids. We found that ESD has evolved asynchronously three times during the last ~5 Myr. Lineages with ESD have consistently higher diversification rates than related lineages with other sexual systems. Habitat fragmentation due to mega-wetlands extinction, and climate instability are suggested as the driving forces for ESD evolution.

A phosphatidylinositol transfer protein integrates phosphoinositide signaling with lipid droplet metabolism to regulate a developmental program of nutrient stress-induced membrane biogenesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ren, J.; Pei-Chen Lin, C.; Pathak, M. C.

2016-07-06

Lipid droplet (LD) utilization is an important cellular activity that regulates energy balance and release of lipid second messengers. Because fatty acids exhibit both beneficial and toxic properties, their release from LDs must be controlled. Here we demonstrate that yeast Sfh3, an unusual Sec14-like phosphatidylinositol transfer protein, is an LD-associated protein that inhibits lipid mobilization from these particles. We further document a complex biochemical diversification of LDs during sporulation in which Sfh3 and select other LD proteins redistribute into discrete LD subpopulations. The data show that Sfh3 modulates the efficiency with which a neutral lipid hydrolase-rich LD subclass is consumedmore » during biogenesis of specialized membrane envelopes that package replicated haploid meiotic genomes. These results present novel insights into the interface between phosphoinositide signaling and developmental regulation of LD metabolism and unveil meiosis-specific aspects of Sfh3 (and phosphoinositide) biology that are invisible to contemporary haploid-centric cell biological, proteomic, and functional genomics approaches.« less

Molecular systematics of European Hyalodaphnia: the role of contemporary hybridization in ancient species.

PubMed Central

Schwenk, K; Posada, D; Hebert, P D

2000-01-01

We examined phylogenetic relationships among Daphnia using mitochondrial DNA (mtDNA) sequences from the small subunit ribosomal RNA (12S), cytochrome c oxidase subunit I and nuclear DNA sequences from the first and second internal transcribed spacer representing 1612 base positions. Phylogenetic analyses using several species of the three main Daphnia subgenera, Ctenodaphnia, Hyalodaphnia and Daphnia, revealed that the Hyalodaphnia are a monophyletic sister group of the Daphnia. Most Hyalodaphnia species occur on one continent, whereas only three are found in North America and Europe. Endemicity of species is associated with variation in thermal tolerance and habitat differentiation. Although many species of the Hyalodaphnia are known to hybridize in nature, mtDNA divergence is relatively high ca. 9%) compared to other hybridizing arthropods (ca. 3%). Reproductive isolation in Daphnia seems to evolve significantly slower than genetic isolation. We related these findings to what is known about the ecology and genetics of Daphnia in order to better understand the evolutionary diversification of lineages. The relationship of these data to phylogenetic patterns is discussed in the context of speciation processes in Daphnia. PMID:11052533

A phosphatidylinositol transfer protein integrates phosphoinositide signaling with lipid droplet metabolism to regulate a developmental program of nutrient stress-induced membrane biogenesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ren, Jihui; Lin, Coney Pei-Chen; Pathak, Manish C.

2014-07-11

Lipid droplet (LD) utilization is an important cellular activity that regulates energy balance and release of lipid second messengers. Because fatty acids exhibit both beneficial and toxic properties, their release from LDs must be controlled. Here we demonstrate that yeast Sfh3, an unusual Sec14-like phosphatidylinositol transfer protein, is an LD-associated protein that inhibits lipid mobilization from these particles. We further document a complex biochemical diversification of LDs during sporulation in which Sfh3 and select other LD proteins redistribute into discrete LD subpopulations. The data show that Sfh3 modulates the efficiency with which a neutral lipid hydrolase-rich LD subclass is consumedmore » during biogenesis of specialized membrane envelopes that package replicated haploid meiotic genomes. These results present novel insights into the interface between phosphoinositide signaling and developmental regulation of LD metabolism and unveil meiosis-specific aspects of Sfh3 (and phosphoinositide) biology that are invisible to contemporary haploid-centric cell biological, proteomic, and functional genomics approaches.« less

Diversification patterns of pebble-mimic dragons are consistent with historical disruption of important habitat corridors in arid Australia.

PubMed

Shoo, L P; Rose, R; Doughty, P; Austin, J J; Melville, J

2008-08-01

The pebble-mimic dragon lineage of Tympanocryptis is widely distributed in the stony, or 'gibber', deserts of Australia but is noticeably absent from intersecting areas of sand deserts. Past fluctuations in the extent and configuration of sandy desert habitat barriers are likely to have been an import factor promoting genetic differentiation in this group. We sequenced a approximately 1400bp region of mitochondrial DNA and a approximately 1400bp nuclear gene (RAG-1) to investigate phylogeographic structuring of species of pebble-mimic dragons. Our topology indicates an early split in this lineage between eastern and western parts of the arid zone that probably dates to the mid-Miocene. This split corresponds directly with large expanses of contemporary sandy habitat in the form of Great Sandy and Great Victoria Deserts. Our data indicate that this biogeographic barrier established very early on in the development of the arid zone and has persisted to present. Additional genetic structuring in the absence of recognized barriers suggests that an expanded view of potential habitat barriers in the arid zone is required.

A living fossil tale of Pangaean biogeography.

PubMed

Murienne, Jerome; Daniels, Savel R; Buckley, Thomas R; Mayer, Georg; Giribet, Gonzalo

2014-01-22

The current distributions of widespread groups of terrestrial animals and plants are supposedly the result of a mixture of either vicariance owing to continental split or more recent trans-oceanic dispersal. For organisms exhibiting a vicariant biogeographic pattern-achieving their current distribution by riding on the plates of former supercontinents-this view is largely inspired by the belief that Pangaea lacked geographical or ecological barriers, or that extinctions and dispersal would have erased any biogeographic signal since the early Mesozoic. We here present a time-calibrated molecular phylogeny of Onychophora (velvet worms), an ancient and exclusively terrestrial panarthropod group distributed throughout former Pangaean landmasses. Our data not only demonstrate that trans-oceanic dispersal does not need be invoked to explain contemporary distributions, but also reveal that the early diversification of the group pre-dates the break-up of Pangaea, maintaining regionalization even in landmasses that have remained contiguous throughout the history of the group. These results corroborate a growing body of evidence from palaeontology, palaeogeography and palaeoclimatic modelling depicting ancient biogeographic regionalization over the continuous landmass of Pangaea.

A living fossil tale of Pangaean biogeography

PubMed Central

Murienne, Jerome; Daniels, Savel R.; Buckley, Thomas R.; Mayer, Georg; Giribet, Gonzalo

2014-01-01

The current distributions of widespread groups of terrestrial animals and plants are supposedly the result of a mixture of either vicariance owing to continental split or more recent trans-oceanic dispersal. For organisms exhibiting a vicariant biogeographic pattern—achieving their current distribution by riding on the plates of former supercontinents—this view is largely inspired by the belief that Pangaea lacked geographical or ecological barriers, or that extinctions and dispersal would have erased any biogeographic signal since the early Mesozoic. We here present a time-calibrated molecular phylogeny of Onychophora (velvet worms), an ancient and exclusively terrestrial panarthropod group distributed throughout former Pangaean landmasses. Our data not only demonstrate that trans-oceanic dispersal does not need be invoked to explain contemporary distributions, but also reveal that the early diversification of the group pre-dates the break-up of Pangaea, maintaining regionalization even in landmasses that have remained contiguous throughout the history of the group. These results corroborate a growing body of evidence from palaeontology, palaeogeography and palaeoclimatic modelling depicting ancient biogeographic regionalization over the continuous landmass of Pangaea. PMID:24285200

The dynamics and limits of corporate growth in health care.

PubMed

Robinson, J C

1996-01-01

This paper analyzes the economic dynamics of five forms of organizational growth in health care: horizontal integration within a single geographic market; horizontal integration across different geographic markets; diversification among multiple products and types of service; diversification among multiple distribution channels; and vertical integration with suppliers. These principles are illustrated through brief case studies of three firms that have grown by way of internal expansion, mergers, acquisitions, and diversification: WellPoint Health Networks, UniHealth America, and Mullikin Medical Enterprises. The paper analyzes the potential limits of organizational growth in health care and explores the implications of integration and diversification for antitrust policy.

Rapid diversification and dispersal during periods of global warming by plethodontid salamanders

PubMed Central

Vieites, David R.; Min, Mi-Sook; Wake, David B.

2007-01-01

A phylogeny and timescale derived from analyses of multilocus nuclear DNA sequences for Holarctic genera of plethodontid salamanders reveal them to be an old radiation whose common ancestor diverged from sister taxa in the late Jurassic and underwent rapid diversification during the late Cretaceous. A North American origin of plethodontids was followed by a continental-wide diversification, not necessarily centered only in the Appalachian region. The colonization of Eurasia by plethodontids most likely occurred once, by dispersal during the late Cretaceous. Subsequent diversification in Asia led to the origin of Hydromantes and Karsenia, with the former then dispersing both to Europe and back to North America. Salamanders underwent rapid episodes of diversification and dispersal that coincided with major global warming events during the late Cretaceous and again during the Paleocene–Eocene thermal optimum. The major clades of plethodontids were established during these episodes, contemporaneously with similar phenomena in angiosperms, arthropods, birds, and mammals. Periods of global warming may have promoted diversification and both inter- and transcontinental dispersal in northern hemisphere salamanders by making available terrain that shortened dispersal routes and offered new opportunities for adaptive and vicariant evolution. PMID:18077422

Diversification of land plants: insights from a family-level phylogenetic analysis

PubMed Central

2011-01-01

Background Some of the evolutionary history of land plants has been documented based on the fossil record and a few broad-scale phylogenetic analyses, especially focusing on angiosperms and ferns. Here, we reconstructed phylogenetic relationships among all 706 families of land plants using molecular data. We dated the phylogeny using multiple fossils and a molecular clock technique. Applying various tests of diversification that take into account topology, branch length, numbers of extant species as well as extinction, we evaluated diversification rates through time. We also compared these diversification profiles against the distribution of the climate modes of the Phanerozoic. Results We found evidence for the radiations of ferns and mosses in the shadow of angiosperms coinciding with the rather warm Cretaceous global climate. In contrast, gymnosperms and liverworts show a signature of declining diversification rates during geological time periods of cool global climate. Conclusions This broad-scale phylogenetic analysis helps to reveal the successive waves of diversification that made up the diversity of land plants we see today. Both warm temperatures and wet climate may have been necessary for the rise of the diversity under a successive lineage replacement scenario. PMID:22103931

Tree of Life Reveals Clock-Like Speciation and Diversification

PubMed Central

Hedges, S. Blair; Marin, Julie; Suleski, Michael; Paymer, Madeline; Kumar, Sudhir

2015-01-01

Genomic data are rapidly resolving the tree of living species calibrated to time, the timetree of life, which will provide a framework for research in diverse fields of science. Previous analyses of taxonomically restricted timetrees have found a decline in the rate of diversification in many groups of organisms, often attributed to ecological interactions among species. Here, we have synthesized a global timetree of life from 2,274 studies representing 50,632 species and examined the pattern and rate of diversification as well as the timing of speciation. We found that species diversity has been mostly expanding overall and in many smaller groups of species, and that the rate of diversification in eukaryotes has been mostly constant. We also identified, and avoided, potential biases that may have influenced previous analyses of diversification including low levels of taxon sampling, small clade size, and the inclusion of stem branches in clade analyses. We found consistency in time-to-speciation among plants and animals, ∼2 My, as measured by intervals of crown and stem species times. Together, this clock-like change at different levels suggests that speciation and diversification are processes dominated by random events and that adaptive change is largely a separate process. PMID:25739733

Competition, virulence, host body mass and the diversification of macro-parasites

PubMed Central

Rascalou, Guilhem; Gourbière, Sébastien

2014-01-01

Adaptive speciation has been much debated in recent years, with a strong emphasis on how competition can lead to the diversification of ecological and sexual traits. Surprisingly, little attention has been paid to this evolutionary process to explain intrahost diversification of parasites. We expanded the theory of competitive speciation to look at the effect of key features of the parasite lifestyle, namely fragmentation, aggregation and virulence, on the conditions and rate of sympatric speciation under the standard ‘pleiotropic scenario’. The conditions for competitive speciation were found similar to those for non-parasite species, but not the rate of diversification. Adaptive evolution proceeds faster in highly fragmented parasite populations and for weakly aggregated and virulent parasites. Combining these theoretical results with standard empirical allometric relationships, we showed that parasite diversification can be faster in host species of intermediate body mass. The increase in parasite load with body mass, indeed, fuels evolution by increasing mutants production, but because of the deleterious effect of virulence, it simultaneously weakens selection for resource specialization. Those two antagonistic effects lead to optimal parasite burden and host body mass for diversification. Data on the diversity of fishes' gills parasites were found consistent with the existence of such optimum. PMID:24522783

The role of ecological opportunity in shaping disparate diversification trajectories in a bicontinental primate radiation

PubMed Central

Tran, Lucy A. P.

2014-01-01

Exceptional species and phenotypic diversity commonly are attributed to ecological opportunity (EO). The conventional EO model predicts that rates of lineage diversification and phenotypic evolution are elevated early in a radiation only to decline later in response to niche availability. Foregut fermentation is hypothesized to be a key innovation that allowed colobine monkeys (subfamily Colobinae), the only primates with this trait, to successfully colonize folivore adaptive zones unavailable to other herbivorous species. Therefore, diversification rates also are expected to be strongly linked with the evolution of traits related to folivory in these monkeys. Using dated molecular phylogenies and a dataset of feeding morphology, I test predictions of the EO model to evaluate the role of EO conferred by foregut fermentation in shaping the African and Asian colobine radiations. Findings from diversification methods coupled with colobine biogeographic history provide compelling evidence that decreasing availability of new adaptive zones during colonization of Asia together with constraints presented by dietary specialization underlie temporal changes in diversification in the Asian but not African clade. Additionally, departures from the EO model likely reflect iterative diversification events in Asia. PMID:24598417

Heterostyly accelerates diversification via reduced extinction in primroses.

PubMed

de Vos, Jurriaan M; Hughes, Colin E; Schneeweiss, Gerald M; Moore, Brian R; Conti, Elena

2014-06-07

The exceptional species diversity of flowering plants, exceeding that of their sister group more than 250-fold, is especially evident in floral innovations, interactions with pollinators and sexual systems. Multiple theories, emphasizing flower-pollinator interactions, genetic effects of mating systems or high evolvability, predict that floral evolution profoundly affects angiosperm diversification. However, consequences for speciation and extinction dynamics remain poorly understood. Here, we investigate trajectories of species diversification focusing on heterostyly, a remarkable floral syndrome where outcrossing is enforced via cross-compatible floral morphs differing in placement of their respective sexual organs. Heterostyly evolved at least 20 times independently in angiosperms. Using Darwin's model for heterostyly, the primrose family, we show that heterostyly accelerates species diversification via decreasing extinction rates rather than increasing speciation rates, probably owing to avoidance of the negative genetic effects of selfing. However, impact of heterostyly appears to differ over short and long evolutionary time-scales: the accelerating effect of heterostyly on lineage diversification is manifest only over long evolutionary time-scales, whereas recent losses of heterostyly may prompt ephemeral bursts of speciation. Our results suggest that temporal or clade-specific conditions may ultimately determine the net effects of specific traits on patterns of species diversification.

Diversification in the Mexican horned lizard Phrynosoma orbiculare across a dynamic landscape.

PubMed

Bryson, Robert W; García-Vázquez, Uri Omar; Riddle, Brett R

2012-01-01

The widespread montane Mexican horned lizard Phrynosoma orbiculare (Squamata: Phrynosomatidae) represents an ideal species to investigate the relative impacts of Neogene vicariance and Quaternary climate change on lineage diversification across the Mexican highlands. We used mitochondrial DNA to examine the maternal history of P. orbiculare and estimate the timing and tempo of lineage diversification. Based on our results, we inferred 11 geographically structured, well supported mitochondrial lineages within this species, suggesting P. orbiculare represents a species complex. Six divergences between lineages likely occurred during the Late Miocene and Pliocene, and four splits probably happened during the Pleistocene. Diversification rate appeared relatively constant through time. Spatial and temporal divergences between lineages of P. orbiculare and co-distributed taxa suggest that a distinct period of uplifting of the Transvolcanic Belt around 7.5-3 million years ago broadly impacted diversification in taxa associated with this mountain range. To the north, several river drainages acting as filter barriers differentially subdivided co-distributed highland taxa through time. Diversification patterns observed in P. orbiculare provide additional insight into the mechanisms that impacted differentiation of highland taxa across the complex Mexican highlands. Copyright © 2011 Elsevier Inc. All rights reserved.

Heterostyly accelerates diversification via reduced extinction in primroses

PubMed Central

de Vos, Jurriaan M.; Hughes, Colin E.; Schneeweiss, Gerald M.; Moore, Brian R.; Conti, Elena

2014-01-01

The exceptional species diversity of flowering plants, exceeding that of their sister group more than 250-fold, is especially evident in floral innovations, interactions with pollinators and sexual systems. Multiple theories, emphasizing flower–pollinator interactions, genetic effects of mating systems or high evolvability, predict that floral evolution profoundly affects angiosperm diversification. However, consequences for speciation and extinction dynamics remain poorly understood. Here, we investigate trajectories of species diversification focusing on heterostyly, a remarkable floral syndrome where outcrossing is enforced via cross-compatible floral morphs differing in placement of their respective sexual organs. Heterostyly evolved at least 20 times independently in angiosperms. Using Darwin's model for heterostyly, the primrose family, we show that heterostyly accelerates species diversification via decreasing extinction rates rather than increasing speciation rates, probably owing to avoidance of the negative genetic effects of selfing. However, impact of heterostyly appears to differ over short and long evolutionary time-scales: the accelerating effect of heterostyly on lineage diversification is manifest only over long evolutionary time-scales, whereas recent losses of heterostyly may prompt ephemeral bursts of speciation. Our results suggest that temporal or clade-specific conditions may ultimately determine the net effects of specific traits on patterns of species diversification. PMID:24759859

Individual-based models for adaptive diversification in high-dimensional phenotype spaces.

PubMed

Ispolatov, Iaroslav; Madhok, Vaibhav; Doebeli, Michael

2016-02-07

Most theories of evolutionary diversification are based on equilibrium assumptions: they are either based on optimality arguments involving static fitness landscapes, or they assume that populations first evolve to an equilibrium state before diversification occurs, as exemplified by the concept of evolutionary branching points in adaptive dynamics theory. Recent results indicate that adaptive dynamics may often not converge to equilibrium points and instead generate complicated trajectories if evolution takes place in high-dimensional phenotype spaces. Even though some analytical results on diversification in complex phenotype spaces are available, to study this problem in general we need to reconstruct individual-based models from the adaptive dynamics generating the non-equilibrium dynamics. Here we first provide a method to construct individual-based models such that they faithfully reproduce the given adaptive dynamics attractor without diversification. We then show that a propensity to diversify can be introduced by adding Gaussian competition terms that generate frequency dependence while still preserving the same adaptive dynamics. For sufficiently strong competition, the disruptive selection generated by frequency-dependence overcomes the directional evolution along the selection gradient and leads to diversification in phenotypic directions that are orthogonal to the selection gradient. Copyright © 2015 Elsevier Ltd. All rights reserved.

Independent evolution of the sexes promotes amphibian diversification

PubMed Central

De Lisle, Stephen P.; Rowe, Locke

2015-01-01

Classic ecological theory predicts that the evolution of sexual dimorphism constrains diversification by limiting morphospace available for speciation. Alternatively, sexual selection may lead to the evolution of reproductive isolation and increased diversification. We test contrasting predictions of these hypotheses by examining the relationship between sexual dimorphism and diversification in amphibians. Our analysis shows that the evolution of sexual size dimorphism (SSD) is associated with increased diversification and speciation, contrary to the ecological theory. Further, this result is unlikely to be explained by traditional sexual selection models because variation in amphibian SSD is unlikely to be driven entirely by sexual selection. We suggest that relaxing a central assumption of classic ecological models—that the sexes share a common adaptive landscape—leads to the alternative hypothesis that independent evolution of the sexes may promote diversification. Once the constraints of sexual conflict are relaxed, the sexes can explore morphospace that would otherwise be inaccessible. Consistent with this novel hypothesis, the evolution of SSD in amphibians is associated with reduced current extinction threat status, and an historical reduction in extinction rate. Our work reconciles conflicting predictions from ecological and evolutionary theory and illustrates that the ability of the sexes to evolve independently is associated with a spectacular vertebrate radiation. PMID:25694616

Impact of catch shares on diversification of fishers' income and risk.

PubMed

Holland, Daniel S; Speir, Cameron; Agar, Juan; Crosson, Scott; DePiper, Geret; Kasperski, Stephen; Kitts, Andrew W; Perruso, Larry

2017-08-29

Many fishers diversify their income by participating in multiple fisheries, which has been shown to significantly reduce year-to-year variation in income. The ability of fishers to diversify has become increasingly constrained in the last few decades, and catch share programs could further reduce diversification as a result of consolidation. This could increase income variation and thus financial risk. However, catch shares can also offer fishers opportunities to enter or increase participation in catch share fisheries by purchasing or leasing quota. Thus, the net effect on diversification is uncertain. We tested whether diversification and variation in fishing revenues changed after implementation of catch shares for 6,782 vessels in 13 US fisheries that account for 20% of US landings revenue. For each of these fisheries, we tested whether diversification levels, trends, and variation in fishing revenues changed after implementation of catch shares, both for fishers that remained in the catch share fishery and for those that exited but remained active in other fisheries. We found that diversification for both groups was nearly always reduced. However, in most cases, we found no significant change in interannual variation of revenues, and, where changes were significant, variation decreased nearly as often as it increased.

Modeling bivalve diversification: the effect of interaction on a macroevolutionary system

NASA Technical Reports Server (NTRS)

Miller, A. I.; Sepkoski, J. J. Jr; Sepkoski JJ, J. r. (Principal Investigator)

1988-01-01

The global diversification of the class Bivalvia has historically received two conflicting interpretations. One is that a major upturn in diversification was associated with, and a consequence of, the Lake Permian mass extinction. The other is that mass extinctions have had little influence and that bivalves have experienced slow but nearly steady exponential diversification through most of their history, unaffected by interactions with other clades. We find that the most likely explanation lies between these two interpretations. Through most of the Phanerozoic, the diversity of bivalves did indeed exhibit slow growth, which was not substantially altered by mass extinctions. However, the presence of "hyperexponential bursts" in diversification during the initial Ordovician radiation and following the Late Permian and Late Cretaceous mass extinctions suggests a more complex history in which a higher characteristic diversification rate was dampened through most of the Phanerozoic. The observed pattern can be accounted for with a two-phase coupled (i.e., interactive) logistic model, where one phase is treated as the "bivalves" and the other phase is treated as a hypothetical group of clades with which the "bivalves" might have interacted. Results of this analysis suggest that interactions with other taxa have substantially affected bivalve global diversity through the Phanerozoic.

Influence of sexual selection and feeding functional morphology on diversification rate of parrotfishes (Scaridae).

PubMed

Kazancioglu, Erem; Near, Thomas J; Hanel, Reinhold; Wainwright, Peter C

2009-10-07

Scaridae (parrotfishes) is a prominent clade of 96 species that shape coral reef communities worldwide through their actions as grazing herbivores. Phylogenetically nested within Labridae, the profound ecological impact and high species richness of parrotfishes suggest that their diversification and ecological success may be linked. Here, we ask whether parrotfish evolution is characterized by a significant burst of lineage diversification and whether parrotfish diversity is shaped more strongly by sexual selection or modifications of the feeding mechanism. We first examined scarid diversification within the greater context of labrid diversity. We used a supermatrix approach for 252 species to propose the most extensive phylogenetic hypothesis of Labridae to date, and time-calibrated the phylogeny with fossil and biogeographical data. Using divergence date estimates, we find that several parrotfish clades exhibit the highest diversification rates among all labrid lineages. Furthermore, we pinpoint a rate shift at the shared ancestor of Scarus and Chlorurus, a scarid subclade characterized by territorial behaviour and strong sexual dichromatism, suggesting that sexual selection was a major factor in parrotfish diversification. Modifications of the pharyngeal and oral jaws that happened earlier in parrotfish evolution may have contributed to this diversity by establishing parrotfishes as uniquely capable reef herbivores.

The influence of an innovative locomotor strategy on the phenotypic diversification of triggerfish (family: Balistidae).

PubMed

Dornburg, Alex; Sidlauskas, Brian; Santini, Francesco; Sorenson, Laurie; Near, Thomas J; Alfaro, Michael E

2011-07-01

Innovations in locomotor morphology have been invoked as important drivers of vertebrate diversification, although the influence of novel locomotion strategies on marine fish diversification remains largely unexplored. Using triggerfish as a case study, we determine whether the evolution of the distinctive synchronization of enlarged dorsal and anal fins that triggerfish use to swim may have catalyzed the ecological diversification of the group. By adopting a comparative phylogenetic approach to quantify median fin and body shape integration and to assess the tempo of functional and morphological evolution in locomotor traits, we find that: (1) functional and morphological components of the locomotive system exhibit a strong signal of correlated evolution; (2) triggerfish partitioned locomotor morphological and functional spaces early in their history; and (3) there is no strong evidence that a pulse of lineage diversification accompanied the major episode of phenotypic diversification. Together these findings suggest that the acquisition of a distinctive mode of locomotion drove an early radiation of shape and function in triggerfish, but not an early radiation of species. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Impact of catch shares on diversification of fishers’ income and risk

PubMed Central

Speir, Cameron; Agar, Juan; Crosson, Scott; DePiper, Geret; Kasperski, Stephen; Kitts, Andrew W.; Perruso, Larry

2017-01-01

Many fishers diversify their income by participating in multiple fisheries, which has been shown to significantly reduce year-to-year variation in income. The ability of fishers to diversify has become increasingly constrained in the last few decades, and catch share programs could further reduce diversification as a result of consolidation. This could increase income variation and thus financial risk. However, catch shares can also offer fishers opportunities to enter or increase participation in catch share fisheries by purchasing or leasing quota. Thus, the net effect on diversification is uncertain. We tested whether diversification and variation in fishing revenues changed after implementation of catch shares for 6,782 vessels in 13 US fisheries that account for 20% of US landings revenue. For each of these fisheries, we tested whether diversification levels, trends, and variation in fishing revenues changed after implementation of catch shares, both for fishers that remained in the catch share fishery and for those that exited but remained active in other fisheries. We found that diversification for both groups was nearly always reduced. However, in most cases, we found no significant change in interannual variation of revenues, and, where changes were significant, variation decreased nearly as often as it increased. PMID:28808006

Universal Principles of Depicting Oneself across the Centuries: From Renaissance Self-Portraits to Selfie-Photographs

PubMed Central

Carbon, Claus-Christian

2017-01-01

Selfie-photography is generally thought of as a cultural mass phenomenon of the early 21st century, inseparably related to the development and triumph of the smartphone with integrated camera. Western culture, however, has been highly familiar with self-depictions since the Renaissance days. Putting the contemporary selfie into this historic context covering more than five centuries of cultural development from Dürer's (1500) famous “Self-Portrait at 28” (also known as “Selbstbildnis im Pelzrock”) to today's Instagram galleries allows for identifying central parallels concerning the technical and social antecedents as well as common underlying psychological factors and shared properties of different kinds of self-depiction. The article provides an overview of the types of contemporary photographic selfies and compares them with painted self-portraits. Finally, this historic perspective leads us to the insight that self-portraits as well as selfies are both referring to nothing less than the “conditio humana.” PMID:28270789

Radiosensitivity of cancer-initiating cells and normal stem cells (or what the Heisenberg uncertainly principle has to do with biology).

PubMed

Woodward, Wendy Ann; Bristow, Robert Glen

2009-04-01

Mounting evidence suggests that parallels between normal stem cell biology and cancer biology may provide new targets for cancer therapy. Prospective identification and isolation of cancer-initiating cells from solid tumors has promoted the descriptive and functional identification of these cells allowing for characterization of their response to contemporary cancer therapies, including chemotherapy and radiation. In clinical radiation therapy, the failure to clinically eradicate all tumor cells (eg, a lack of response, partial response, or nonpermanent complete response by imaging) is considered a treatment failure. As such, biologists have explored the characteristics of the small population of clonogenic cancer cells that can survive and are capable of repopulating the tumor after subcurative therapy. Herein, we discuss the convergence of these clonogenic studies with contemporary radiosensitivity studies that use cell surface markers to identify cancer-initiating cells. Implications for and uncertainties regarding incorporation of these concepts into the practice of modern radiation oncology are discussed.

Parallelizing a peanut butter sandwich

NASA Astrophysics Data System (ADS)

Quenette, S. M.

2005-12-01

This poster aims to demonstrate, in a novel way, why contemporary computational code development is seemingly hard to a geodynamics modeler (i.e. a non-computer-scientist). For example, to utilise comtemporary computer hardware, parallelisation is required. But why do we chose the explicit approach (MPI) over an implicit (OpenMP) one? How does this relate to the typical geodynamics codes. And do we face this same style of problems in every day life? We aim to demonstrate that the little bit of complexity, fore-thought and effort is worth its while.

Range expansion and habitat shift triggered elevated diversification of the rice genus (Oryza, Poaceae) during the Pleistocene.

PubMed

Lin, Li; Tang, Liang; Bai, Yun-Jun; Tang, Zhi-Yao; Wang, Wei; Chen, Zhi-Duan

2015-09-03

The rice genus (Oryza) contains many wild genetic resources that are vital to the well-being of humans. However, little is known about the process by which the genus diversified or the factors that drove its speciation. Here, we integrated the phylogenetic, molecular dating and biogeographic methods to investigate the spatial-temporal patterns of Oryza diversification, and used a series of model tests to examine whether intercontinental migrations and/or key innovations were associated with significant changes in diversification rates in the genus. Oryza became differentiated in tropical Asia in the Miocene. There were two migrations from the ancestral area into Africa and Australia during the Miocene. We inferred at least 10 migration events out of tropical Asia since the Pleistocene, mainly involving the species adapting open habitat. A rapid increase in diversification rates of the whole Oryza occurred during the Pleistocene. Intercontinental migrations from tropical Asia to other tropical regions were positively correlated with shift in habitat, but not with changes in life history. A habitat preference shift from shade tolerant to open habitat predated the burst in diversification rates. Rice species may have been pre-adapted to invade open habitat. Significant increase in diversification rates occurred during the Pleistocene and is associated with range expansion and habitat shift, but not with life history. The rice genus provides an excellent case supporting the idea that range expansion and invasion of novel habitats can drive the diversification of a group.

Extinction probabilities and stationary distributions of mobile genetic elements in prokaryotes: The birth-death-diversification model.

PubMed

Drakos, Nicole E; Wahl, Lindi M

2015-12-01

Theoretical approaches are essential to our understanding of the complex dynamics of mobile genetic elements (MGEs) within genomes. Recently, the birth-death-diversification model was developed to describe the dynamics of mobile promoters (MPs), a particular class of MGEs in prokaryotes. A unique feature of this model is that genetic diversification of elements was included. To explore the implications of diversification on the longterm fate of MGE lineages, in this contribution we analyze the extinction probabilities, extinction times and equilibrium solutions of the birth-death-diversification model. We find that diversification increases both the survival and growth rate of MGE families, but the strength of this effect depends on the rate of horizontal gene transfer (HGT). We also find that the distribution of MGE families per genome is not necessarily monotonically decreasing, as observed for MPs, but may have a peak in the distribution that is related to the HGT rate. For MPs specifically, we find that new families have a high extinction probability, and predict that the number of MPs is increasing, albeit at a very slow rate. Additionally, we develop an extension of the birth-death-diversification model which allows MGEs in different regions of the genome, for example coding and non-coding, to be described by different rates. This extension may offer a potential explanation as to why the majority of MPs are located in non-promoter regions of the genome. Copyright © 2015 Elsevier Inc. All rights reserved.

Character combinations, convergence and diversification in ectoparasitic arthropods.

PubMed

Poulin, Robert

2009-08-01

Different lineages of organisms diversify over time at different rates, in part as a consequence of the characteristics of the species in these lineages. Certain suites of traits possessed by species within a clade may determine rates of diversification, with some particular combinations of characters acting synergistically to either limit or promote diversification; the most successful combinations may also emerge repeatedly in different clades via convergent evolution. Here, the association between species characters and diversification is investigated amongst 21 independent lineages of arthropods ectoparasitic on vertebrate hosts. Using nine characters (each with two to four states) that capture general life history strategy, transmission mode and host-parasite interaction, each lineage was described by the set of character states it possesses. The results show, firstly, that most possible pair-wise combinations of character states have been adopted at least once, sometimes several times independently by different lineages; thus, ectoparasitic arthropods have explored most of the life history character space available to them. Secondly, lineages possessing commonly observed combinations of character states are not necessarily the ones that have experienced the highest rates of diversification (measured as a clade's species-per-genus ratio). Thirdly, some specific traits are associated with higher rates of diversification. Using more than one host per generation, laying eggs away from the host and intermediate levels of fecundity are features that appear to have promoted diversification. These findings indicate that particular species characters may be evolutionary drivers of diversity, whose effects could also apply in other taxa.

Trait-based diversification shifts reflect differential extinction among fossil taxa.

PubMed

Wagner, Peter J; Estabrook, George F

2014-11-18

Evolution provides many cases of apparent shifts in diversification associated with particular anatomical traits. Three general models connect these patterns to anatomical evolution: (i) elevated net extinction of taxa bearing particular traits, (ii) elevated net speciation of taxa bearing particular traits, and (iii) elevated evolvability expanding the range of anatomies available to some species. Trait-based diversification shifts predict elevated hierarchical stratigraphic compatibility (i.e., primitive→derived→highly derived sequences) among pairs of anatomical characters. The three specific models further predict (i) early loss of diversity for taxa retaining primitive conditions (elevated net extinction), (ii) increased diversification among later members of a clade (elevated net speciation), and (iii) increased disparity among later members in a clade (elevated evolvability). Analyses of 319 anatomical and stratigraphic datasets for fossil species and genera show that hierarchical stratigraphic compatibility exceeds the expectations of trait-independent diversification in the vast majority of cases, which was expected if trait-dependent diversification shifts are common. Excess hierarchical stratigraphic compatibility correlates with early loss of diversity for groups retaining primitive conditions rather than delayed bursts of diversity or disparity across entire clades. Cambrian clades (predominantly trilobites) alone fit null expectations well. However, it is not clear whether evolution was unusual among Cambrian taxa or only early trilobites. At least among post-Cambrian taxa, these results implicate models, such as competition and extinction selectivity/resistance, as major drivers of trait-based diversification shifts at the species and genus levels while contradicting the predictions of elevated net speciation and elevated evolvability models.

Are diversification rates and chromosome evolution in the temperate grasses (Pooideae) associated with major environmental changes in the Oligocene-Miocene?

PubMed

Pimentel, Manuel; Escudero, Marcial; Sahuquillo, Elvira; Minaya, Miguel Ángel; Catalán, Pilar

2017-01-01

The Pooideae are a highly diverse C3 grass subfamily that includes some of the most economically important crops, nested within the highly speciose core-pooid clade. Here, we build and explore the phylogeny of the Pooideae within a temporal framework, assessing its patterns of diversification and its chromosomal evolutionary changes in the light of past environmental transformations. We sequenced five plastid DNA loci, two coding ( ndhF , matk ) and three non-coding ( trnH-psbA , trnT-L and trnL-F ), in 163 Poaceae taxa, including representatives for all subfamilies of the grasses and all but four ingroup Pooideae tribes. Parsimony and Bayesian phylogenetic analyses were conducted and divergence times were inferred in BEAST using a relaxed molecular clock. Diversification rates were assessed using the MEDUSA approach, and chromosome evolution was analyzed using the chromEvol software. Diversification of the Pooideae started in the Late-Eocene and was especially intense during the Oligocene-Miocene. The background diversification rate increased significantly at the time of the origin of the Poodae + Triticodae clade. This shift in diversification occurred in a context of falling temperatures that potentially increased ecological opportunities for grasses adapted to open areas around the world. The base haploid chromosome number n  = 7 has remained stable throughout the phylogenetic history of the core pooids and we found no link between chromosome transitions and major diversification events in the Pooideae.

Uplift-driven diversification in the Hengduan Mountains, a temperate biodiversity hotspot.

PubMed

Xing, Yaowu; Ree, Richard H

2017-04-25

A common hypothesis for the rich biodiversity found in mountains is uplift-driven diversification-that orogeny creates conditions favoring rapid in situ speciation of resident lineages. We tested this hypothesis in the context of the Qinghai-Tibetan Plateau (QTP) and adjoining mountain ranges, using the phylogenetic and geographic histories of multiple groups of plants to infer the tempo (rate) and mode (colonization versus in situ diversification) of biotic assembly through time and across regions. We focused on the Hengduan Mountains region, which in comparison with the QTP and Himalayas was uplifted more recently (since the late Miocene) and is smaller in area and richer in species. Time-calibrated phylogenetic analyses show that about 8 million y ago the rate of in situ diversification increased in the Hengduan Mountains, significantly exceeding that in the geologically older QTP and Himalayas. By contrast, in the QTP and Himalayas during the same period the rate of in situ diversification remained relatively flat, with colonization dominating lineage accumulation. The Hengduan Mountains flora was thus assembled disproportionately by recent in situ diversification, temporally congruent with independent estimates of orogeny. This study shows quantitative evidence for uplift-driven diversification in this region, and more generally, tests the hypothesis by comparing the rate and mode of biotic assembly jointly across time and space. It thus complements the more prevalent method of examining endemic radiations individually and could be used as a template to augment such studies in other biodiversity hotspots.

Are diversification rates and chromosome evolution in the temperate grasses (Pooideae) associated with major environmental changes in the Oligocene-Miocene?

PubMed Central

Escudero, Marcial; Sahuquillo, Elvira; Minaya, Miguel Ángel; Catalán, Pilar

2017-01-01

The Pooideae are a highly diverse C3 grass subfamily that includes some of the most economically important crops, nested within the highly speciose core-pooid clade. Here, we build and explore the phylogeny of the Pooideae within a temporal framework, assessing its patterns of diversification and its chromosomal evolutionary changes in the light of past environmental transformations. We sequenced five plastid DNA loci, two coding (ndhF, matk) and three non-coding (trnH-psbA, trnT-L and trnL-F), in 163 Poaceae taxa, including representatives for all subfamilies of the grasses and all but four ingroup Pooideae tribes. Parsimony and Bayesian phylogenetic analyses were conducted and divergence times were inferred in BEAST using a relaxed molecular clock. Diversification rates were assessed using the MEDUSA approach, and chromosome evolution was analyzed using the chromEvol software. Diversification of the Pooideae started in the Late-Eocene and was especially intense during the Oligocene-Miocene. The background diversification rate increased significantly at the time of the origin of the Poodae + Triticodae clade. This shift in diversification occurred in a context of falling temperatures that potentially increased ecological opportunities for grasses adapted to open areas around the world. The base haploid chromosome number n = 7 has remained stable throughout the phylogenetic history of the core pooids and we found no link between chromosome transitions and major diversification events in the Pooideae. PMID:28951814

Do freshwater fishes diversify faster than marine fishes? A test using state-dependent diversification analyses and molecular phylogenetics of new world silversides (atherinopsidae).

PubMed

Bloom, Devin D; Weir, Jason T; Piller, Kyle R; Lovejoy, Nathan R

2013-07-01

Freshwater habitats make up only ∼0.01% of available aquatic habitat and yet harbor 40% of all fish species, whereas marine habitats comprise >99% of available aquatic habitat and have only 60% of fish species. One possible explanation for this pattern is that diversification rates are higher in freshwater habitats than in marine habitats. We investigated diversification in marine and freshwater lineages in the New World silverside fish clade Menidiinae (Teleostei, Atherinopsidae). Using a time-calibrated phylogeny and a state-dependent speciation-extinction framework, we determined the frequency and timing of habitat transitions in Menidiinae and tested for differences in diversification parameters between marine and freshwater lineages. We found that Menidiinae is an ancestrally marine lineage that independently colonized freshwater habitats four times followed by three reversals to the marine environment. Our state-dependent diversification analyses showed that freshwater lineages have higher speciation and extinction rates than marine lineages. Net diversification rates were higher (but not significant) in freshwater than marine environments. The marine lineage-through time (LTT) plot shows constant accumulation, suggesting that ecological limits to clade growth have not slowed diversification in marine lineages. Freshwater lineages exhibited an upturn near the recent in their LTT plot, which is consistent with our estimates of high background extinction rates. All sequence data are currently being archived on Genbank and phylogenetic trees archived on Treebase. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Ecological transition predictably associated with gene degeneration.

PubMed

Wessinger, Carolyn A; Rausher, Mark D

2015-02-01

Gene degeneration or loss can significantly contribute to phenotypic diversification, but may generate genetic constraints on future evolutionary trajectories, potentially restricting phenotypic reversal. Such constraints may manifest as directional evolutionary trends when parallel phenotypic shifts consistently involve gene degeneration or loss. Here, we demonstrate that widespread parallel evolution in Penstemon from blue to red flowers predictably involves the functional inactivation and degeneration of the enzyme flavonoid 3',5'-hydroxylase (F3'5'H), an anthocyanin pathway enzyme required for the production of blue floral pigments. Other types of genetic mutations do not consistently accompany this phenotypic shift. This pattern may be driven by the relatively large mutational target size of degenerative mutations to this locus and the apparent lack of associated pleiotropic effects. The consistent degeneration of F3'5'H may provide a mechanistic explanation for the observed asymmetry in the direction of flower color evolution in Penstemon: Blue to red transitions are common, but reverse transitions have not been observed. Although phenotypic shifts in this system are likely driven by natural selection, internal constraints may generate predictable genetic outcomes and may restrict future evolutionary trajectories. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Diversification or Homogenization: How Governments and Markets Have Combined to (Re)Shape Chinese Higher Education in Its Recent Massification Process

ERIC Educational Resources Information Center

Zha, Qiang

2009-01-01

The expansion and diversification of higher education are twin phenomena that have been associated with the development of higher education in many countries around the world. This study attempts to use enrolment expansion as a lens to examine the effects of governmental intervention and market forces on diversification of the Chinese system,…

Is sexual selection driving diversification of the bioluminescent ponyfishes (Teleostei: Leiognathidae)?

PubMed

Chakrabarty, Prosanta; Davis, Matthew P; Smith, W Leo; Baldwin, Zachary H; Sparks, John S

2011-07-01

Sexual selection may facilitate genetic isolation among populations and result in increased rates of diversification. As a mechanism driving diversification, sexual selection has been invoked and upheld in numerous empirical studies across disparate taxa, including birds, plants and spiders. In this study, we investigate the potential impact of sexual selection on the tempo and mode of ponyfish evolution. Ponyfishes (Leiognathidae) are bioluminescent marine fishes that exhibit sexually dimorphic features of their unique light-organ system (LOS). Although sexual selection is widely considered to be the driving force behind ponyfish speciation, this hypothesis has never been formally tested. Given that some leiognathid species have a sexually dimorphic LOS, whereas others do not, this family provides an excellent system within which to study the potential role of sexual selection in diversification and morphological differentiation. In this study, we estimate the phylogenetic relationships and divergence times for Leiognathidae, investigate the tempo and mode of ponyfish diversification, and explore morphological shape disparity among leiognathid clades. We recover strong support for a monophyletic Leiognathidae and estimate that all major ponyfish lineages evolved during the Paleogene. Our studies of ponyfish diversification demonstrate that there is no conclusive evidence that sexually dimorphic clades are significantly more species rich than nonsexually dimorphic lineages and that evidence is lacking to support any significant diversification rate increases within ponyfishes. Further, we detected a lineage-through-time signal indicating that ponyfishes have continuously diversified through time, which is in contrast to many recent diversification studies that identify lineage-through-time patterns that support mechanisms of density-dependent speciation. Additionally, there is no evidence of sexual selection hindering morphological diversity, as sexually dimorphic taxa are shown to be more disparate in overall shape morphology than nonsexually dimorphic taxa. Our results suggest that if sexual selection is occurring in ponyfish evolution, it is likely acting only as a genetic isolating mechanism that has allowed ponyfishes to continuously diversify over time, with no overall impact on increases in diversification rate or morphological disparity. © 2011 Blackwell Publishing Ltd.

Emergence of Complexity in Protein Functions and Metabolic Networks

NASA Technical Reports Server (NTRS)

Pohorille, Andzej

2009-01-01

In modern organisms proteins perform a majority of cellular functions, such as chemical catalysis, energy transduction and transport of material across cell walls. Although great strides have been made towards understanding protein evolution, a meaningful extrapolation from contemporary proteins to their earliest ancestors is virtually impossible. In an alternative approach, the origin of water-soluble proteins was probed through the synthesis of very large libraries of random amino acid sequences and subsequently subjecting them to in vitro evolution. In combination with computer modeling and simulations, these experiments allow us to address a number of fundamental questions about the origins of proteins. Can functionality emerge from random sequences of proteins? How did the initial repertoire of functional proteins diversify to facilitate new functions? Did this diversification proceed primarily through drawing novel functionalities from random sequences or through evolution of already existing proto-enzymes? Did protein evolution start from a pool of proteins defined by a frozen accident and other collections of proteins could start a different evolutionary pathway? Although we do not have definitive answers to these questions, important clues have been uncovered. Considerable progress has been also achieved in understanding the origins of membrane proteins. We will address this issue in the example of ion channels - proteins that mediate transport of ions across cell walls. Remarkably, despite overall complexity of these proteins in contemporary cells, their structural motifs are quite simple, with -helices being most common. By combining results of experimental and computer simulation studies on synthetic models and simple, natural channels, I will show that, even though architectures of membrane proteins are not nearly as diverse as those of water-soluble proteins, they are sufficiently flexible to adapt readily to the functional demands arising during evolution.

Implementation of Controlled Traffic in the Canadian Prairies: Soil and Plant Dynamics under Simulated and Field Conditions

NASA Astrophysics Data System (ADS)

Guenette, Kris; Hernandez-Ramirez, Guillermo

2017-04-01

Achieving resiliency in agroecosystems may be accomplished through the incorporation of contemporary management systems and the diversification of crop rotations with pulse crops, such as controlled traffic farming (CTF) and faba beans (Vicia faba L.). As these practices become more common in the Canadian Prairies, it is imperative to have a well-rounded understanding of how faba beans interact with the soil-plant-atmosphere continuum in conditions found in contemporary management systems. Simulated field conditions emulated soil compaction found in both the trafficked and un-trafficked areas of a CTF system, in which the presence of high water availability was shown to offset the negative results of large applications of compactive effort. Furthermore, low water availability exacerbated differences in plant responses between compaction treatments. The simulated treatment of 1.2 gcm-3 coupled with high water content yielded the most optimal results for most measured parameters, with a contrasting detrimental treatment of 1.4 gcm-3 at low water availability. The simulated field conditions were further bridged through an analysis of two commercial sites in Alberta, Canada that compared both trafficked and un-trafficked soil properties. Soil properties such as available nitrogen (AN), pH, soil total nitrogen (STN), soil organic carbon (SOC), bulk density, macroporosity, soil quality S-Index, plant available water capacity (PAWC) and unsaturated hydraulic conductivity (Km) were analysed and compared among trafficked and un-trafficked areas. The measured soil physical and hydraulic properties of bulk density, macroporosity, S-Index, PAWC and Km were shown to be heavily influenced by the CTF traffic regime, while soil nutrient properties of AN, pH, STN SOC were determined to be dependent on both management and landscape features.

Evolutionary diversification of galactinol synthases in Rosaceae: adaptive roles of galactinol and raffinose during apple bud dormancy.

PubMed

Falavigna, Vítor da Silveira; Porto, Diogo Denardi; Miotto, Yohanna Evelyn; Santos, Henrique Pessoa Dos; Oliveira, Paulo Ricardo Dias de; Margis-Pinheiro, Márcia; Pasquali, Giancarlo; Revers, Luís Fernando

2018-01-24

Galactinol synthase (GolS) is a key enzyme in the biosynthetic pathway of raffinose family oligosaccharides (RFOs), which play roles in carbon storage, signal transduction, and osmoprotection. The present work assessed the evolutionary history of GolS genes across the Rosaceae using several bioinformatic tools. Apple (Malus × domestica) GolS genes were transcriptionally characterized during bud dormancy, in parallel with galactinol and raffinose measurements. Additionally, MdGolS2, a candidate to regulate seasonal galactinol and RFO content during apple bud dormancy, was functionally characterized in Arabidopsis. Evolutionary analyses revealed that whole genome duplications have driven GolS gene evolution and diversification in Rosaceae speciation. The strong purifying selection identified in duplicated GolS genes suggests that differential gene expression might define gene function better than protein structure. Interestingly, MdGolS2 was differentially expressed during bud dormancy, concomitantly with the highest galactinol and raffinose levels. One of the intrinsic adaptive features of bud dormancy is limited availability of free water; therefore, we generated transgenic Arabidopsis plants expressing MdGolS2. They showed higher galactinol and raffinose contents and increased tolerance to water deficit. Our results suggest that MdGolS2 is the major GolS responsible for RFO accumulation during apple dormancy, and these carbohydrates help to protect dormant buds against limited water supply. © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

The Evolutionary Dynamics of the Odorant Receptor Gene Family in Corbiculate Bees.

PubMed

Brand, Philipp; Ramírez, Santiago R

2017-08-01

Insects rely on chemical information to locate food, choose mates, and detect potential predators. It has been hypothesized that adaptive changes in the olfactory system facilitated the diversification of numerous insect lineages. For instance, evolutionary changes of Odorant Receptor (OR) genes often occur in parallel with modifications in life history strategies. Corbiculate bees display a diverse array of behaviors that are controlled through olfaction, including varying degrees of social organization, and manifold associations with floral resources. Here we investigated the molecular mechanisms driving the evolution of the OR gene family in corbiculate bees in comparison to other chemosensory gene families. Our results indicate that the genomic organization of the OR gene family has remained highly conserved for ∼80 Myr, despite exhibiting major changes in repertoire size among bee lineages. Moreover, the evolution of OR genes appears to be driven mostly by lineage-specific gene duplications in few genomic regions that harbor large numbers of OR genes. A selection analysis revealed that OR genes evolve under positive selection, with the strongest signals detected in recently duplicated copies. Our results indicate that chromosomal translocations had a minimal impact on OR evolution, and instead local molecular mechanisms appear to be main drivers of OR repertoire size. Our results provide empirical support to the longstanding hypothesis that positive selection shaped the diversification of the OR gene family. Together, our results shed new light on the molecular mechanisms underlying the evolution of olfaction in insects. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Trans-biome diversity in Australian grass-specialist lizards (Diplodactylidae: Strophurus).

PubMed

Laver, Rebecca J; Nielsen, Stuart V; Rosauer, Dan F; Oliver, Paul M

2017-10-01

Comparisons of biodiversity patterns within lineages that occur across major climate gradients and biomes, can provide insights into the relative roles that lineage history, landscape and climatic variation, and environmental change have played in shaping regional biotas. In Australia, while there has been extensive research into the origins and patterns of diversity in the Australian Arid Zone (AAZ), how diversity is distributed across this biome and the Australian Monsoonal Tropics (AMT) to the north, has been less studied. We compared the timing and patterns of diversification across this broad aridity gradient in a clade of lizards (Strophurus: phasmid geckos) that only occur in association with a unique Australian radiation of sclerophyllous grasses (Triodia: spinifex). Our results indicate that overall genetic diversity is much higher, older and more finely geographically structured within the AMT, including distantly related clades endemic to the sandstone escarpments of the Kimberley and Arnhem Plateau. Niche modelling analyses also suggest that the distribution of taxa in the AMT is more strongly correlated with variation in topographic relief than in the AAZ. The two broad patterns that we recovered - (i) lineage endemism increases as latitude decreases, and (ii) endemism is tightly correlated to rocky regions - parallel and corroborate other recent studies of habitat generalists and specialised saxicoline lineages occurring across these same regions. Early Miocene diversification estimates also suggest that, soon after Triodia grasses colonised Australia and began to diversify in the Miocene, phasmid geckos with Gondwanan ancestry shifted into these grasses, and have subsequently remained closely associated with this unique vegetation type. Copyright © 2017 Elsevier Inc. All rights reserved.

Comprehensive evolutionary analysis of the Anthroherpon radiation (Coleoptera, Leiodidae, Leptodirini).

PubMed

Njunjić, Iva; Perrard, Adrien; Hendriks, Kasper; Schilthuizen, Menno; Perreau, Michel; Merckx, Vincent; Baylac, Michel; Deharveng, Louis

2018-01-01

The genus Anthroherpon Reitter, 1889 exhibits the most pronounced troglomorphic characters among Coleoptera, and represents one of the most spectacular radiations of subterranean beetles. However, radiation, diversification, and biogeography of this genus have never been studied in a phylogenetic context. This study provides a comprehensive evolutionary analysis of the Anthroherpon radiation, using a dated molecular phylogeny as a framework for understanding Anthroherpon diversification, reconstructing the ancestral range, and exploring troglomorphic diversity. Based on 16 species and 22 subspecies, i.e. the majority of Anthroherpon diversity, we reconstructed the phylogeny using Bayesian analysis of six loci, both mitochondrial and nuclear, comprising a total of 4143 nucleotides. In parallel, a morphometric analysis was carried out with 79 landmarks on the body that were subjected to geometric morphometrics. We optimized morphometric features to phylogeny, in order to recognize the way troglomorphy was expressed in different clades of the tree, and did character evolution analyses. Finally, we reconstructed the ancestral range of the genus using BioGeoBEARS. Besides further elucidating the suprageneric classification of the East-Mediterranean Leptodirini, our main findings also show that Anthroherpon dates back to the Early Miocene (ca. 22 MYA) and that the genus diversified entirely underground. Biogeographic reconstruction of the ancestral range shows the origin of the genus in the area comprising three high mountains in western Montenegro, which is in the accordance with the available data on the paleogeography of the Balkan Peninsula. Character evolution analysis indicates that troglomorphic morphometric traits in Anthroherpon mostly evolve neutrally but may diverge adaptively under syntopic competition.

Phylogeographic dispersion and diversification of rabies virus lineages associated with dogs and crab-eating foxes (Cerdocyon thous) in Brazil.

PubMed

Carnieli, Pedro; Ruthner Batista, Helena B C; de Novaes Oliveira, Rafael; Castilho, Juliana Galera; Vieira, Luiz Fernando Pereira

2013-11-01

Genetic lineages of dog-associated RABV still circulate in some areas of the North and Northeast of Brazil. In parallel, another RABV lineage circulates among wild canids in the Northeast, particularly the crab-eating fox (Cerdocyon thous). Although previous studies and phylogenetic analyses have been carried out, the way in which these lineages are dispersed temporally and spatially remained to be elucidated. In this study, RABV N gene sequences isolated from canids in North and Northeast Brazil were analyzed by the Bayesian Markov Chain Monte Carlo Method, and the results were then used in a phylogeographic study. It was inferred from the findings that the most recent common ancestor became established at the end of the nineteenth century on the border of the Brazilian states of Paraíba and Pernambuco and diversified into the lineages associated with dogs and C. thous. Around 1910, the original C. thous lineage diversified into two main sublineages in the same area, one of which migrated to the south and the other to the north. The dog-associated lineage diversified around 1945 and moved toward the north and south. From the phylogeographic analysis it was possible to infer not only the movement of the virus lineages but also the probable location where dispersion and diversification occurred. The methodology used here enabled the phylogeographic history of RABV in the region to be reconstructed, and the dispersion pattern of the virus can be used to predict its movements, making it easier to stop the advance of a rabies epidemic.

The Variable Regions of Lactobacillus rhamnosus Genomes Reveal the Dynamic Evolution of Metabolic and Host-Adaptation Repertoires

PubMed Central

Ceapa, Corina; Davids, Mark; Ritari, Jarmo; Lambert, Jolanda; Wels, Michiel; Douillard, François P.; Smokvina, Tamara; de Vos, Willem M.; Knol, Jan; Kleerebezem, Michiel

2016-01-01

Lactobacillus rhamnosus is a diverse Gram-positive species with strains isolated from different ecological niches. Here, we report the genome sequence analysis of 40 diverse strains of L. rhamnosus and their genomic comparison, with a focus on the variable genome. Genomic comparison of 40 L. rhamnosus strains discriminated the conserved genes (core genome) and regions of plasticity involving frequent rearrangements and horizontal transfer (variome). The L. rhamnosus core genome encompasses 2,164 genes, out of 4,711 genes in total (the pan-genome). The accessory genome is dominated by genes encoding carbohydrate transport and metabolism, extracellular polysaccharides (EPS) biosynthesis, bacteriocin production, pili production, the cas system, and the associated clustered regularly interspaced short palindromic repeat (CRISPR) loci, and more than 100 transporter functions and mobile genetic elements like phages, plasmid genes, and transposons. A clade distribution based on amino acid differences between core (shared) proteins matched with the clade distribution obtained from the presence–absence of variable genes. The phylogenetic and variome tree overlap indicated that frequent events of gene acquisition and loss dominated the evolutionary segregation of the strains within this species, which is paralleled by evolutionary diversification of core gene functions. The CRISPR-Cas system could have contributed to this evolutionary segregation. Lactobacillus rhamnosus strains contain the genetic and metabolic machinery with strain-specific gene functions required to adapt to a large range of environments. A remarkable congruency of the evolutionary relatedness of the strains’ core and variome functions, possibly favoring interspecies genetic exchanges, underlines the importance of gene-acquisition and loss within the L. rhamnosus strain diversification. PMID:27358423

Tempo and rates of diversification in the South American cichlid genus Apistogramma (Teleostei: Perciformes: Cichlidae).

PubMed

Tougard, Christelle; García Dávila, Carmen R; Römer, Uwe; Duponchelle, Fabrice; Cerqueira, Frédérique; Paradis, Emmanuel; Guinand, Bruno; Angulo Chávez, Carlos; Salas, Vanessa; Quérouil, Sophie; Sirvas, Susana; Renno, Jean-François

2017-01-01

Evaluating biodiversity and understanding the processes involved in diversification are noticeable conservation issues in fishes subject to large, sometimes illegal, ornamental trade purposes. Here, the diversity and evolutionary history of the Neotropical dwarf cichlid genus Apistogramma from several South American countries are investigated. Mitochondrial and nuclear markers are used to infer phylogenetic relationships between 31 genetically identified species. The monophyly of Apistogramma is suggested, and Apistogramma species are distributed into four clades, corresponding to three morphological lineages. Divergence times estimated with the Yule process and an uncorrelated lognormal clock dated the Apistogramma origin to the beginning of the Eocene (≈ 50 Myr) suggesting that diversification might be related to marine incursions. Our molecular dating also suggests that the Quaternary glacial cycles coincide with the phases leading to Apistogramma speciation. These past events did not influence diversification rates in the speciose genus Apistogramma, since diversification appeared low and constant through time. Further characterization of processes involved in recent Apistogramma diversity will be necessary.

Tempo and rates of diversification in the South American cichlid genus Apistogramma (Teleostei: Perciformes: Cichlidae)

PubMed Central

García Dávila, Carmen R.; Römer, Uwe; Duponchelle, Fabrice; Cerqueira, Frédérique; Paradis, Emmanuel; Guinand, Bruno; Angulo Chávez, Carlos; Salas, Vanessa; Quérouil, Sophie; Sirvas, Susana; Renno, Jean-François

2017-01-01

Evaluating biodiversity and understanding the processes involved in diversification are noticeable conservation issues in fishes subject to large, sometimes illegal, ornamental trade purposes. Here, the diversity and evolutionary history of the Neotropical dwarf cichlid genus Apistogramma from several South American countries are investigated. Mitochondrial and nuclear markers are used to infer phylogenetic relationships between 31 genetically identified species. The monophyly of Apistogramma is suggested, and Apistogramma species are distributed into four clades, corresponding to three morphological lineages. Divergence times estimated with the Yule process and an uncorrelated lognormal clock dated the Apistogramma origin to the beginning of the Eocene (≈ 50 Myr) suggesting that diversification might be related to marine incursions. Our molecular dating also suggests that the Quaternary glacial cycles coincide with the phases leading to Apistogramma speciation. These past events did not influence diversification rates in the speciose genus Apistogramma, since diversification appeared low and constant through time. Further characterization of processes involved in recent Apistogramma diversity will be necessary. PMID:28873089

Limited by the roof of the world: mountain radiations of Apollo swallowtails controlled by diversity-dependence processes.

PubMed

Condamine, Fabien L

2018-03-01

Mountainous areas contain a substantial part of the world species richness, but the evolutionary origins and diversification of this biodiversity remain elusive. Diversification may result from differences in clade age (longer time to diversify), net diversification rates (faster speciation rate) or carrying capacities (number of niches). The likelihood of these macroevolutionary scenarios was assessed for six clades of Apollo swallowtails ( Parnassius ) that diversified mainly in the Himalayan-Tibetan region. The analyses suggest that neither the clade age nor the speciation rate could explain the mountain butterfly diversification. Instead diversity-dependence models were strongly supported for each group. Models further estimated clades' carrying capacities, which approximate to the current number of species, indicating that diversity equilibrium has been reached (or close to being reached). The results suggest that diversification of mountain butterflies was controlled by ecological limits, which governed the number of niches, and provide macroevolutionary justification for regarding mountains as islands. © 2018 The Author(s).

Independent evolution of the sexes promotes amphibian diversification.

PubMed

De Lisle, Stephen P; Rowe, Locke

2015-03-22

Classic ecological theory predicts that the evolution of sexual dimorphism constrains diversification by limiting morphospace available for speciation. Alternatively, sexual selection may lead to the evolution of reproductive isolation and increased diversification. We test contrasting predictions of these hypotheses by examining the relationship between sexual dimorphism and diversification in amphibians. Our analysis shows that the evolution of sexual size dimorphism (SSD) is associated with increased diversification and speciation, contrary to the ecological theory. Further, this result is unlikely to be explained by traditional sexual selection models because variation in amphibian SSD is unlikely to be driven entirely by sexual selection. We suggest that relaxing a central assumption of classic ecological models-that the sexes share a common adaptive landscape-leads to the alternative hypothesis that independent evolution of the sexes may promote diversification. Once the constraints of sexual conflict are relaxed, the sexes can explore morphospace that would otherwise be inaccessible. Consistent with this novel hypothesis, the evolution of SSD in amphibians is associated with reduced current extinction threat status, and an historical reduction in extinction rate. Our work reconciles conflicting predictions from ecological and evolutionary theory and illustrates that the ability of the sexes to evolve independently is associated with a spectacular vertebrate radiation. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Diet and Diversification in the Evolution of Coral Reef Fishes

PubMed Central

Lobato, Fabio L.; Barneche, Diego R.; Siqueira, Alexandre C.; Liedke, Ana M. R.; Lindner, Alberto; Pie, Marcio R.; Bellwood, David R.; Floeter, Sergio R.

2014-01-01

The disparity in species richness among evolutionary lineages is one of the oldest and most intriguing issues in evolutionary biology. Although geographical factors have been traditionally thought to promote speciation, recent studies have underscored the importance of ecological interactions as one of the main drivers of diversification. Here, we test if differences in species richness of closely related lineages match predictions based on the concept of density-dependent diversification. As radiation progresses, ecological niche-space would become increasingly saturated, resulting in fewer opportunities for speciation. To assess this hypothesis, we tested whether reef fish niche shifts toward usage of low-quality food resources (i.e. relatively low energy/protein per unit mass), such as algae, detritus, sponges and corals are accompanied by rapid net diversification. Using available molecular information, we reconstructed phylogenies of four major reef fish clades (Acanthuroidei, Chaetodontidae, Labridae and Pomacentridae) to estimate the timing of radiations of their subclades. We found that the evolution of species-rich clades was associated with a switch to low quality food in three of the four clades analyzed, which is consistent with a density-dependent model of diversification. We suggest that ecological opportunity may play an important role in understanding the diversification of reef-fish lineages. PMID:25029229

Ecological opportunity and predator–prey interactions: linking eco-evolutionary processes and diversification in adaptive radiations

PubMed Central

2018-01-01

Much of life's diversity has arisen through ecological opportunity and adaptive radiations, but the mechanistic underpinning of such diversification is not fully understood. Competition and predation can affect adaptive radiations, but contrasting theoretical and empirical results show that they can both promote and interrupt diversification. A mechanistic understanding of the link between microevolutionary processes and macroevolutionary patterns is thus needed, especially in trophic communities. Here, we use a trait-based eco-evolutionary model to investigate the mechanisms linking competition, predation and adaptive radiations. By combining available micro-evolutionary theory and simulations of adaptive radiations we show that intraspecific competition is crucial for diversification as it induces disruptive selection, in particular in early phases of radiation. The diversification rate is however decreased in later phases owing to interspecific competition as niche availability, and population sizes are decreased. We provide new insight into how predation tends to have a negative effect on prey diversification through decreased population sizes, decreased disruptive selection and through the exclusion of prey from parts of niche space. The seemingly disparate effects of competition and predation on adaptive radiations, listed in the literature, may thus be acting and interacting in the same adaptive radiation at different relative strength as the radiation progresses. PMID:29514970

Early stages of functional diversification in the Rab GTPase gene family revealed by genomic and localization studies in Paramecium species

PubMed Central

Bright, Lydia J.; Gout, Jean-Francois; Lynch, Michael

2017-01-01

New gene functions arise within existing gene families as a result of gene duplication and subsequent diversification. To gain insight into the steps that led to the functional diversification of paralogues, we tracked duplicate retention patterns, expression-level divergence, and subcellular markers of functional diversification in the Rab GTPase gene family in three Paramecium aurelia species. After whole-genome duplication, Rab GTPase duplicates are more highly retained than other genes in the genome but appear to be diverging more rapidly in expression levels, consistent with early steps in functional diversification. However, by localizing specific Rab proteins in Paramecium cells, we found that paralogues from the two most recent whole-genome duplications had virtually identical localization patterns, and that less closely related paralogues showed evidence of both conservation and diversification. The functionally conserved paralogues appear to target to compartments associated with both endocytic and phagocytic recycling functions, confirming evolutionary and functional links between the two pathways in a divergent eukaryotic lineage. Because the functionally diversifying paralogues are still closely related to and derived from a clade of functionally conserved Rab11 genes, we were able to pinpoint three specific amino acid residues that may be driving the change in the localization and thus the function in these proteins. PMID:28251922

Investigating Processes of Neotropical Rain Forest Tree Diversification By Examining the Evolution and Historical Biogeography of the Protieae (BURSERACEAE)

NASA Astrophysics Data System (ADS)

Fine, P.; Zapata, F.; Daly, D.

2014-12-01

Andean uplift and the collision of North and South America are thought to have major implications for the diversification of the Neotropical biota. However, few studies have investigated how these geological events may have influenced diversification. We present a multilocus phylogeny of 102 Protieae taxa (73% of published species), sampled pantropically, to test hypotheses about the relative importance of dispersal, vicariance, habitat specialization, and biotic factors in the diversification of this ecologically dominant tribe of Neotropical trees. Bayesian fossil-calibrated analyses date the Protieae stem at 55 Mya. Biogeographic analyses reconstruct an initial late Oligocene/early Miocene radiation in Amazonia for Neotropical Protieae, with several subsequent late Miocene dispersal events to Central America, the Caribbean, Brazil's Atlantic Forest, and the Chocó. Regional phylogenetic structure results indicate frequent dispersal among regions throughout the Miocene and many instances of more recent regional in situ speciation. Habitat specialization to white sand or flooded soils was common, especially in Amazonia. There was one significant increase in diversification rate coincident with colonization of the Neotropics, followed by a gradual decrease consistent with models of diversity-dependent cladogenesis. Dispersal, biotic interactions, and habitat specialization are thus hypothesized to be the most important processes underlying the diversification of the Protieae.

Beyond aridification: multiple explanations for the elevated diversification of cacti in the New World Succulent Biome.

PubMed

Hernández-Hernández, Tania; Brown, Joseph W; Schlumpberger, Boris O; Eguiarte, Luis E; Magallón, Susana

2014-06-01

Succulent plants are widely distributed, reaching their highest diversity in arid and semi-arid regions. Their origin and diversification is thought to be associated with a global expansion of aridity. We test this hypothesis by investigating the tempo and pattern of Cactaceae diversification. Our results contribute to the understanding of the evolution of New World Succulent Biomes. We use the most taxonomically complete dataset currently available for Cactaceae. We estimate divergence times and utilize Bayesian and maximum likelihood methods that account for nonrandom taxonomic sampling, possible extinction scenarios and phylogenetic uncertainty to analyze diversification rates, and evolution of growth form and pollination syndrome. Cactaceae originated shortly after the Eocene-Oligocene global drop in CO2 , and radiation of its richest genera coincided with the expansion of aridity in North America during the late Miocene. A significant correlation between growth form and pollination syndrome was found, as well as a clear state dependence between diversification rate, and pollination and growth-form evolution. This study suggests a complex picture underlying the diversification of Cactaceae. It not only responded to the availability of new niches resulting from aridification, but also to the correlated evolution of novel growth forms and reproductive strategies. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

Investigating the timing of origin and evolutionary processes shaping regional species diversity: Insights from simulated data and neotropical butterfly diversification rates.

PubMed

Matos-Maraví, Pável

2016-07-01

Different diversification scenarios have been proposed to explain the origin of extant biodiversity. However, most existing meta-analyses of time-calibrated phylogenies rely on approaches that do not quantitatively test alternative diversification processes. Here, I highlight the shortcomings of using species divergence ranks, which is a method widely used in meta-analyses. Divergence ranks consist of categorizing cladogenetic events to certain periods of time, typically to either Pleistocene or to pre-Pleistocene ages. This approach has been claimed to shed light on the origin of most extant species and the timing and dynamics of diversification in any biogeographical region. However, interpretations drawn from such method often confound two fundamental questions in macroevolutionary studies, tempo (timing of evolutionary rate shifts) and mode ("how" and "why" of speciation). By using simulated phylogenies under four diversification scenarios, constant-rate, diversity-dependence, high extinction, and high speciation rates in the Pleistocene, I showed that interpretations based on species divergence ranks might have been seriously misleading. Future meta-analyses of dated phylogenies need to be aware of the impacts of incomplete taxonomic sampling, tree topology, and divergence time uncertainties, as well as they might be benefited by including quantitative tests of alternative diversification models that acknowledge extinction and diversity dependence. © 2016 The Author(s).

Host conservatism, geography, and elevation in the evolution of a Neotropical moth radiation.

PubMed

Jahner, Joshua P; Forister, Matthew L; Parchman, Thomas L; Smilanich, Angela M; Miller, James S; Wilson, Joseph S; Walla, Thomas R; Tepe, Eric J; Richards, Lora A; Quijano-Abril, Mario Alberto; Glassmire, Andrea E; Dyer, Lee A

2017-12-01

The origins of evolutionary radiations are often traced to the colonization of novel adaptive zones, including unoccupied habitats or unutilized resources. For herbivorous insects, the predominant mechanism of diversification is typically assumed to be a shift onto a novel lineage of host plants. However, other drivers of diversification are important in shaping evolutionary history, especially for groups residing in regions with complex geological histories. We evaluated the contributions of shifts in host plant clade, bioregion, and elevation to diversification in Eois (Lepidoptera: Geometridae), a hyper-diverse genus of moths found throughout the Neotropics. Relationships among 107 taxa were reconstructed using one mitochondrial and two nuclear genes. In addition, we used a genotyping-by-sequencing approach to generate 4641 SNPs for 137 taxa. Both datasets yielded similar phylogenetic histories, with relationships structured by host plant clade, bioregion, and elevation. While diversification of basal lineages often coincided with host clade shifts, more recent speciation events were more typically associated with shifts across bioregions or elevational gradients. Overall, patterns of diversification in Eois are consistent with the perspective that shifts across multiple adaptive zones synergistically drive diversification in hyper-diverse lineages. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Microhabitat and Climatic Niche Change Explain Patterns of Diversification among Frog Families.

PubMed

Moen, Daniel S; Wiens, John J

2017-07-01

A major goal of ecology and evolutionary biology is to explain patterns of species richness among clades. Differences in rates of net diversification (speciation minus extinction over time) may often explain these patterns, but the factors that drive variation in diversification rates remain uncertain. Three important candidates are climatic niche position (e.g., whether clades are primarily temperate or tropical), rates of climatic niche change among species within clades, and microhabitat (e.g., aquatic, terrestrial, arboreal). The first two factors have been tested separately in several studies, but the relative importance of all three is largely unknown. Here we explore the correlates of diversification among families of frogs, which collectively represent ∼88% of amphibian species. We assemble and analyze data on phylogeny, climate, and microhabitat for thousands of species. We find that the best-fitting phylogenetic multiple regression model includes all three types of variables: microhabitat, rates of climatic niche change, and climatic niche position. This model explains 67% of the variation in diversification rates among frog families, with arboreal microhabitat explaining ∼31%, niche rates ∼25%, and climatic niche position ∼11%. Surprisingly, we show that microhabitat can have a much stronger influence on diversification than climatic niche position or rates of climatic niche change.

Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics.

PubMed

Zhang, Shu-Dong; Jin, Jian-Jun; Chen, Si-Yun; Chase, Mark W; Soltis, Douglas E; Li, Hong-Tao; Yang, Jun-Bo; Li, De-Zhu; Yi, Ting-Shuang

2017-05-01

Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their historical diversification has not been clarified. With 87 genera representing all subfamilies and tribes of Rosaceae and six of the other eight families of Rosales (outgroups), we analysed 130 newly sequenced plastomes together with 12 from GenBank in an attempt to reconstruct deep relationships and reveal temporal diversification of this family. Our results highlight the importance of improving sequence alignment and the use of appropriate substitution models in plastid phylogenomics. Three subfamilies and 16 tribes (as previously delimited) were strongly supported as monophyletic, and their relationships were fully resolved and strongly supported at most nodes. Rosaceae were estimated to have originated during the Late Cretaceous with evidence for rapid diversification events during several geological periods. The major lineages rapidly diversified in warm and wet habits during the Late Cretaceous, and the rapid diversification of genera from the early Oligocene onwards occurred in colder and drier environments. Plastid phylogenomics offers new and important insights into deep phylogenetic relationships and the diversification history of Rosaceae. The robust phylogenetic backbone and time estimates we provide establish a framework for future comparative studies on rosaceous evolution. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Increased diversification rates follow shifts to bisexuality in liverworts.

PubMed

Laenen, Benjamin; Machac, Antonin; Gradstein, S Robbert; Shaw, Blanka; Patiño, Jairo; Désamoré, Aurélie; Goffinet, Bernard; Cox, Cymon J; Shaw, A Jonathan; Vanderpoorten, Alain

2016-05-01

Shifts in sexual systems are one of the key drivers of species diversification. In contrast to angiosperms, unisexuality prevails in bryophytes. Here, we test the hypotheses that bisexuality evolved from an ancestral unisexual condition and is a key innovation in liverworts. We investigate whether shifts in sexual systems influence diversification using hidden state speciation and extinction analysis (HiSSE). This new method compares the effects of the variable of interest to the best-fitting latent variable, yielding robust and conservative tests. We find that the transitions in sexual systems are significantly biased toward unisexuality, even though bisexuality is coupled with increased diversification. Sexual systems are strongly conserved deep within the liverwort tree but become much more labile toward the present. Bisexuality appears to be a key innovation in liverworts. Its effects on diversification are presumably mediated by the interplay of high fertilization rates, massive spore production and long-distance dispersal, which may separately or together have facilitated liverwort speciation, suppressed their extinction, or both. Importantly, shifts in liverwort sexual systems have the opposite effect when compared to angiosperms, leading to contrasting diversification patterns between the two groups. The high prevalence of unisexuality among liverworts suggests, however, a strong selection for sexual dimorphism. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Sex-specific patterns of morphological diversification: evolution of reaction norms and static allometries in neriid flies.

PubMed

Cassidy, Elizabeth J; Bath, Eleanor; Chenoweth, Stephen F; Bonduriansky, Russell

2014-02-01

The consequences of sex-specific selection for patterns of diversification remain poorly known. Because male secondary sexual traits are typically costly to express, and both costs and benefits are likely to depend on ambient environment and individual condition, such traits may be expected to diversify via changes in reaction norms as well as the scaling of trait size with body size (static allometry). We investigated morphological diversification within two species of Australian neriid flies (Telostylinus angusticollis, Telostylinus lineolatus) by rearing larvae from several populations on larval diets varying sixfold in nutrient concentration. Mean body size varied among populations of T. angusticollis, but body size reaction norms did not vary within either species. However, we detected diversification of reaction norms for body shape in males and females within both species. Moreover, unlike females, males also diversified in static allometry slope and reaction norms for static allometry slope of sexual and nonsexual traits. Our findings reveal qualitative sex differences in patterns of morphological diversification, whereby shape-size relationships diversify extensively in males, but remain conserved in females despite extensive evolution of trait means. Our results highlight the importance of incorporating plasticity and allometry in studies of adaptation and diversification. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Rapid diversification of falcons (Aves: Falconidae) due to expansion of open habitats in the Late Miocene.

PubMed

Fuchs, Jérôme; Johnson, Jeff A; Mindell, David P

2015-01-01

Understanding how and why lineages diversify is central to understanding the origins of biological diversity. The avian family Falconidae (caracaras, forest-falcons, falcons) has an uneven distribution of species among multiple well-supported clades, and provides a useful system for testing hypotheses about diversification rate and correlation with environmental changes. We analyzed eight independent loci for 1-7 individuals from each of the 64 currently recognized Falconidae species, together with two fossil falconid temporal calibrations, to assess phylogeny, absolute divergence times and potential shifts in diversification rate. Our analyses supported similar diversification ages in the Early to Middle Miocene for the three traditional subfamilies, Herpetotherinae, Polyborinae and Falconinae. We estimated that divergences within the subfamily Falconinae began about 16mya and divergences within the most species-rich genus, Falco, including about 60% of all Falconidae species, began about 7.5mya. We found evidence for a significant increase in diversification rate at the basal phylogenetic node for the genus Falco, and the timing for this rate shift correlates generally with expansion of C4 grasslands beginning around the Miocene/Pliocene transition. Concomitantly, Falco lineages that are distributed primarily in grassland or savannah habitats, as opposed to woodlands, and exhibit migratory, as opposed to sedentary, behavior experienced a higher diversification rate. Published by Elsevier Inc.

Presence in Mediterranean hotspots and floral symmetry affect speciation and extinction rates in Proteaceae.

PubMed

Reyes, Elisabeth; Morlon, Hélène; Sauquet, Hervé

2015-07-01

The Proteaceae is a large angiosperm family displaying the common pattern of uneven distribution of species among genera. Previous studies have shown that this disparity is a result of variation in diversification rates across lineages, but the reasons for this variation are still unclear. Here, we tested the impact of floral symmetry and occurrence in Mediterranean climate regions on speciation and extinction rates in the Proteaceae. A rate shift analysis was conducted on dated genus-level phylogenetic trees of the Proteaceae. Character-dependent analyses were used to test for differences in diversification rates between actinomorphic and zygomorphic lineages and between lineages located within or outside Mediterranean climate regions. The rate shift analysis identified 5-10 major diversification rate shifts in the Proteaceae tree. The character-dependent analyses showed that speciation rates, extinction rates and net diversification rates of the Proteaceae were significantly higher for lineages occurring in Mediterranean hotspots. Higher speciation and extinction rates were also detected for zygomorphic species, but net diversification rates appeared to be similar in actinomorphic and zygomorphic Proteaceae. Presence in Mediterranean hotspots favors Proteaceae diversification. In contrast with observations at the scale of angiosperms, floral symmetry is not a trait that strongly influences their evolutionary success. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

Evolutionary diversifications of plants on the Qinghai-Tibetan Plateau

PubMed Central

Wen, Jun; Zhang, Jian-Qiang; Nie, Ze-Long; Zhong, Yang; Sun, Hang

2014-01-01

The Qinghai-Tibetan Plateau (QTP) is the highest and one of the most extensive plateaus in the world. Phylogenetic, phylogeographic, and ecological studies support plant diversifications on the QTP through multiple mechanisms such as allopatric speciation via geographic isolation, climatic oscillations and divergences, pollinator-mediated isolation, diploid hybridization and introgression, and allopolyploidy. These mechanisms have driven spectacular radiations and/or species diversifications in various groups of plants such as Pedicularis L., Saussurea DC., Rhododendron L., Primula L., Meconopsis Vig., Rhodiola L., and many lineages of gymnosperms. Nevertheless, much work is needed toward understanding the evolutionary mechanisms of plant diversifications on the QTP. Well-sampled biogeographic analyses of the QTP plants in the broad framework of the Northern Hemisphere as well as the Southern Hemisphere are still relatively few and should be encouraged in the next decade. This paper reviews recent evidence from phylogenetic and biogeographic studies in plants, in the context of rapid radiations, mechanisms of species diversifications on the QTP, and the biogeographic significance of the QTP in the broader context of both the Northern and Southern Hemisphere biogeography. Integrative multidimensional analyses of phylogeny, morphological innovations, geography, ecology, development, species interactions and diversifications, and geology are needed and should shed insights into the patterns of evolutionary assembly and radiations in this fascinating region. PMID:24575120

The uncertain role of diversity dependence in species diversification and the need to incorporate time-varying carrying capacities

PubMed Central

Marshall, Charles R.; Quental, Tiago B.

2016-01-01

There is no agreement among palaeobiologists or biologists as to whether, or to what extent, there are limits on diversification and species numbers. Here, we posit that part of the disagreement stems from: (i) the lack of explicit criteria for defining the relevant species pools, which may be defined phylogenetically, ecologically or geographically; (ii) assumptions that must be made when extrapolating from population-level logistic growth to macro-evolutionary diversification; and (iii) too much emphasis being placed on fixed carrying capacities, rather than taking into account the opportunities for increased species richness on evolutionary timescales, for example, owing to increased biologically available energy, increased habitat complexity and the ability of many clades to better extract resources from the environment, or to broaden their resource base. Thus, we argue that a more effective way of assessing the evidence for and against the ideas of bound versus unbound diversification is through appropriate definition of the relevant species pools, and through explicit modelling of diversity-dependent diversification with time-varying carrying capacities. Here, we show that time-varying carrying capacities, either increases or decreases, can be accommodated through changing intrinsic diversification rates (diversity-independent effects), or changing the effects of crowding (diversity-dependent effects). PMID:26977059

Relative roles of Neogene vicariance and Quaternary climate change on the historical diversification of bunchgrass lizards (Sceloporus scalaris group) in Mexico.

PubMed

Bryson, Robert W; García-Vázquez, Uri Omar; Riddle, Brett R

2012-01-01

Neogene vicariance during the Miocene and Pliocene and Quaternary climate change have synergistically driven diversification in Mexican highland taxa. We investigated the impacts of these processes on genetic diversification in the widely distributed bunchgrass lizards in the Sceloporus scalaris group. We searched for correlations between timing in diversification and timing of (1) a period of marked volcanism across the Trans-Mexican Volcanic Belt in central Mexico 3-7.5million years ago (Ma) and (2) a transition to larger glacial-interglacial cycles during the mid-Pleistocene. From our phylogenetic analyses of mitochondrial DNA we identified two major clades that contained 13 strongly supported lineages. One clade contained lineages from the two northern sierras of Mexico, and the other clade included lineages associated with the Trans-Mexican Volcanic Belt and Central Mexican Plateau. Results provided support for Neogene divergences within the S. scalaris group in response to uplift of the Trans-Mexican Volcanic Belt, a pattern observed in several co-distributed taxa, and suggested that Quaternary climate change likely had little effect on diversification between lineages. Uplift of the Trans-Mexican Volcanic Belt during specific time periods appears to have strongly impacted diversification in Mexican highland taxa. Copyright © 2011 Elsevier Inc. All rights reserved.

Genetic and phenotypic variation along an ecological gradient in lake trout Salvelinus namaycush

USGS Publications Warehouse

Baillie, Shauna M.; Muir, Andrew M.; Hansen, Michael J.; Krueger, Charles C.; Bentzen, Paul

2016-01-01

BackgroundAdaptive radiation involving a colonizing phenotype that rapidly evolves into at least one other ecological variant, or ecotype, has been observed in a variety of freshwater fishes in post-glacial environments. However, few studies consider how phenotypic traits vary with regard to neutral genetic partitioning along ecological gradients. Here, we present the first detailed investigation of lake trout Salvelinus namaycushthat considers variation as a cline rather than discriminatory among ecotypes. Genetic and phenotypic traits organized along common ecological gradients of water depth and geographic distance provide important insights into diversification processes in a lake with high levels of human disturbance from over-fishing.ResultsFour putative lake trout ecotypes could not be distinguished using population genetic methods, despite morphological differences. Neutral genetic partitioning in lake trout was stronger along a gradient of water depth, than by locality or ecotype. Contemporary genetic migration patterns were consistent with isolation-by-depth. Historical gene flow patterns indicated colonization from shallow to deep water. Comparison of phenotypic (Pst) and neutral genetic variation (Fst) revealed that morphological traits related to swimming performance (e.g., buoyancy, pelvic fin length) departed more strongly from neutral expectations along a depth gradient than craniofacial feeding traits. Elevated phenotypic variance with increasing water depth in pelvic fin length indicated possible ongoing character release and diversification. Finally, differences in early growth rate and asymptotic fish length across depth strata may be associated with limiting factors attributable to cold deep-water environments.ConclusionWe provide evidence of reductions in gene flow and divergent natural selection associated with water depth in Lake Superior. Such information is relevant for documenting intraspecific biodiversity in the largest freshwater lake in the world for a species that recently lost considerable genetic diversity and is now in recovery. Unknown is whether observed patterns are a result of an early stage of incipient speciation, gene flow-selection equilibrium, or reverse speciation causing formerly divergent ecotypes to collapse into a single gene pool.

IgA Function in Relation to the Intestinal Microbiota.

PubMed

Macpherson, Andrew J; Yilmaz, Bahtiyar; Limenitakis, Julien P; Ganal-Vonarburg, Stephanie C

2018-04-26

IgA is the dominant immunoglobulin isotype produced in mammals, largely secreted across the intestinal mucosal surface. Although induction of IgA has been a hallmark feature of microbiota colonization following colonization in germ-free animals, until recently appreciation of the function of IgA in host-microbial mutualism has depended mainly on indirect evidence of alterations in microbiota composition or penetration of microbes in the absence of somatic mutations in IgA (or compensatory IgM). Highly parallel sequencing techniques that enable high-resolution analysis of either microbial consortia or IgA sequence diversity are now giving us new perspectives on selective targeting of microbial taxa and the trajectory of IgA diversification according to induction mechanisms, between different individuals and over time. The prospects are to link the range of diversified IgA clonotypes to specific antigenic functions in modulating the microbiota composition, position and metabolism to ensure host mutualism.

Anxiety from a Phylogenetic Perspective: Is there a Qualitative Difference between Human and Animal Anxiety?

PubMed Central

Belzung, Catherine; Philippot, Pierre

2007-01-01

A phylogenetic approach to anxiety is proposed. The different facets of human anxiety and their presence at different levels of the phylum are examined. All organisms, including unicellular such as protozoan, can display a specific reaction to danger. The mechanisms enabling the appraisal of harmful stimuli are fully present in insects. In higher invertebrates, fear is associated with a specific physiological response. In mammals, anxiety is accompanied by specific cognitive responses. The expression of emotions diversifies in higher vertebrates, only primates displaying facial expressions. Finally, autonoetic consciousness, a feature essential for human anxiety, appears only in great apes. This evolutive feature parallels the progress in the complexity of the logistic systems supporting it (e.g., the vegetative and central nervous systems). The ability to assess one's coping potential, the diversification of the anxiety responses, and autonoetic consciousness seem relevant markers in a phylogenetic perspective. PMID:17641735

Solarnorth '81 by Tymura Solardesigns: diverse residential, commercial and industrial projects at and above the 48th parallel in Ontario, Canada

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tymura, E.J.

1981-01-01

Solar Energy Heating Applications are On the Rise in and above the Northwestern City of Thunder Bay, on the northern shore of Lake Superior. Unique in their diversifications, the architectural commissions range from pure passive residential design thru hybrid systems; residential Greenhouse-Solarium active swimming pool and commercial hotel pool to inexpensive hybrid system for Canada's First Commercial Solar Lumber Drying Kiln; as well as combined earth sheltered with solar system design for a dormitory complex and shopping center. By May 1981, 7 buildings designed by Tymura Solardesigns in the Thunder Bay area will have been subjected to the Extreme Canadianmore » climate (10,500/sup 0/F degree days, yearly temperature maximums from -41/sup 0/F to 90/sup 0/F, and solar fractions vary from 50% to 75%, with economic payback periods ranging between 7 and 10 years.« less

Expected time-invariant effects of biological traits on mammal species duration.

PubMed

Smits, Peter D

2015-10-20

Determining which biological traits influence differences in extinction risk is vital for understanding the differential diversification of life and for making predictions about species' vulnerability to anthropogenic impacts. Here I present a hierarchical Bayesian survival model of North American Cenozoic mammal species durations in relation to species-level ecological factors, time of origination, and phylogenetic relationships. I find support for the survival of the unspecialized as a time-invariant generalization of trait-based extinction risk. Furthermore, I find that phylogenetic and temporal effects are both substantial factors associated with differences in species durations. Finally, I find that the estimated effects of these factors are partially incongruous with how these factors are correlated with extinction risk of the extant species. These findings parallel previous observations that background extinction is a poor predictor of mass extinction events and suggest that attention should be focused on mass extinctions to gain insight into modern species loss.

Trait-based diversification shifts reflect differential extinction among fossil taxa

PubMed Central

Wagner, Peter J.; Estabrook, George F.

2014-01-01

Evolution provides many cases of apparent shifts in diversification associated with particular anatomical traits. Three general models connect these patterns to anatomical evolution: (i) elevated net extinction of taxa bearing particular traits, (ii) elevated net speciation of taxa bearing particular traits, and (iii) elevated evolvability expanding the range of anatomies available to some species. Trait-based diversification shifts predict elevated hierarchical stratigraphic compatibility (i.e., primitive→derived→highly derived sequences) among pairs of anatomical characters. The three specific models further predict (i) early loss of diversity for taxa retaining primitive conditions (elevated net extinction), (ii) increased diversification among later members of a clade (elevated net speciation), and (iii) increased disparity among later members in a clade (elevated evolvability). Analyses of 319 anatomical and stratigraphic datasets for fossil species and genera show that hierarchical stratigraphic compatibility exceeds the expectations of trait-independent diversification in the vast majority of cases, which was expected if trait-dependent diversification shifts are common. Excess hierarchical stratigraphic compatibility correlates with early loss of diversity for groups retaining primitive conditions rather than delayed bursts of diversity or disparity across entire clades. Cambrian clades (predominantly trilobites) alone fit null expectations well. However, it is not clear whether evolution was unusual among Cambrian taxa or only early trilobites. At least among post-Cambrian taxa, these results implicate models, such as competition and extinction selectivity/resistance, as major drivers of trait-based diversification shifts at the species and genus levels while contradicting the predictions of elevated net speciation and elevated evolvability models. PMID:25331898

Both temperature fluctuations and East Asian monsoons have driven plant diversification in the karst ecosystems from southern China.

PubMed

Kong, Hanghui; Condamine, Fabien L; Harris, A J; Chen, Junlin; Pan, Bo; Möller, Michael; Hoang, Van Sam; Kang, Ming

2017-11-01

Karst ecosystems in southern China are species-rich and have high levels of endemism, yet little is known regarding the evolutionary processes responsible for the origin and diversification of karst biodiversity. The genus Primulina (Gesneriaceae) comprises ca. 170 species endemic to southern China with high levels of ecological (edaphic) specialization, providing an exceptional model to study the plant diversification in karsts. We used molecular data from nine chloroplast and 11 nuclear regions and macroevolutionary analyses to assess the origin and cause of species diversification due to palaeoenvironmental changes and edaphic specialization in Primulina. We found that speciation was positively associated with changes in past temperatures and East Asian monsoons through the evolutionary history of Primulina. Climatic change around the mid-Miocene triggered an early burst followed by a slowdown of diversification rate towards the present with the climate cooling. We detected different speciation rates among edaphic types, and transitions among soil types were infrequently and did not impact the overall speciation rate. Our findings suggest that both global temperature changes and East Asian monsoons have played crucial roles in floristic diversification within the karst ecosystems in southern China, such that speciation was higher when climate was warmer and wetter. This is the first study to directly demonstrate that past monsoon activity is positively correlated with speciation rate in East Asia. This case study could motivate further investigations to assess the impacts of past environmental changes on the origin and diversification of biodiversity in global karst ecosystems, most of which are under threat. © 2017 John Wiley & Sons Ltd.

SRSF1-3 contributes to diversification of the immunoglobulin variable region gene by promoting accumulation of AID in the nucleus.

PubMed

Kawaguchi, Yuka; Nariki, Hiroaki; Kawamoto, Naoko; Kanehiro, Yuichi; Miyazaki, Satoshi; Suzuki, Mari; Magari, Masaki; Tokumitsu, Hiroshi; Kanayama, Naoki

2017-04-01

Activation-induced cytidine deaminase (AID) is essential for diversification of the Ig variable region (IgV). AID is excluded from the nucleus, where it normally functions. However, the molecular mechanisms responsible for regulating AID localization remain to be elucidated. The SR-protein splicing factor SRSF1 is a nucleocytoplasmic shuttling protein, a splicing isoform of which called SRSF1-3, has previously been shown to contribute to IgV diversification in chicken DT40 cells. In this study, we examined whether SRSF1-3 functions in IgV diversification by promoting nuclear localization of AID. AID expressed alone was localized predominantly in the cytoplasm. In contrast, co-expression of AID with SRSF1-3 led to the nuclear accumulation of both AID and SRSF1-3 and the formation of a protein complex that contained them both, although SRSF1-3 was dispensable for nuclear import of AID. Expression of either SRSF1-3 or a C-terminally-truncated AID mutant increased IgV diversification in DT40 cells. However, overexpression of exogenous SRSF1-3 was unable to further enhance IgV diversification in DT40 cells expressing the truncated AID mutant, although SRSF1-3 was able to form a protein complex with the AID mutant. These results suggest that SRSF1-3 promotes nuclear localization of AID probably by forming a nuclear protein complex, which might stabilize nuclear AID and induce IgV diversification in an AID C-terminus-dependent manner. Copyright © 2017 Elsevier Inc. All rights reserved.

Early diversification trend and Asian origin for extent bat lineages.

PubMed

Yu, W; Wu, Y; Yang, G

2014-10-01

Bats are a unique mammalian group, which belong to one of the largest and most diverse mammalian radiations, but their early diversification is still poorly understood, and conflicting hypotheses have emerged regarding their biogeographic history. Understanding their diversification is crucial for untangling the enigmatic evolutionary history of bats. In this study, we elucidated the rate of diversification and the biogeographic history of extant bat lineages using genus-level chronograms. The results suggest that a rapid adaptive radiation persisted from the emergence of crown bats until the Early Eocene Climatic Optimum, whereas there was a major deceleration in diversification around 35-49 Ma. There was a positive association between changes in the palaeotemperature and the net diversification rate until 35 Ma, which suggests that the palaeotemperature may have played an important role in the regulation of ecological opportunities. By contrast, there were unexpectedly higher diversification rates around 25-35 Ma during a period characterized by intense and long-lasting global cooling, which implies that intrinsic innovations or adaptations may have released some lineages from the intense selective pressures associated with these severe conditions. Our reconstruction of the ancestral distribution suggests an Asian origin for bats, thereby indicating that the current panglobal but disjunct distribution pattern of extant bats may be related to events involving seriate cross-continental dispersal and local extinction, as well as the influence of geological events and the expansion and contraction of megathermal rainforests during the Tertiary. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

The influence of habitat on the evolution of plants: a case study across Saxifragales

PubMed Central

de Casas, Rafael Rubio; Mort, Mark E.; Soltis, Douglas E.

2016-01-01

Background and Aims Organismal evolution tends to be closely associated with ecological conditions. However, the extent to which this association constrains adaptation or diversification into new habitats remains unclear. We studied habitat evolution in the hyper-diverse angiosperm clade Saxifragales. Methods We used species-level phylogenies for approx. 950 species to analyse the evolution of habitat shifts as well as their influence on plant diversification. We combined habitat characterization based on floristic assignments and state-of-the art phylogenetic comparative methods to estimate within- and across-habitat diversification patterns. Key Results Our analyses showed that Saxifragales diversified into multiple habitats from a forest-inhabiting ancestor and that this diversification is governed by relatively rare habitat shifts. Lineages are likely to stay within inferred ancestral ecological conditions. Adaptation to some habitat types (e.g. aquatic, desert) may be canalizing events that lineages do not escape. Although associations between increased diversification rates and shifts in habitat preferences are occasionally observed, extreme macroevolutionary rates are closely associated with specific habitats. Lineages occurring in shrubland, and especially tundra and rock cliffs, exhibit comparatively high diversification, whereas forest, grassland, desert and aquatic habitats are associated with low diversification. Conclusions The likelihood of occupation of new habitats appears to be asymmetric. Shifts to aquatic and desert habitats may be canalizing events. Other habitats, such as tundra, might act as evolutionary sources, while forests provide the only habitat seemingly colonized easily by lineages originating elsewhere. However, habitat shifts are very rare, and any major environmental alteration is expected to have dramatic evolutionary consequences. PMID:27551029

The shape and temporal dynamics of phylogenetic trees arising from geographic speciation.

PubMed

Pigot, Alex L; Phillimore, Albert B; Owens, Ian P F; Orme, C David L

2010-12-01

Phylogenetic trees often depart from the expectations of stochastic models, exhibiting imbalance in diversification among lineages and slowdowns in the rate of lineage accumulation through time. Such departures have led to a widespread perception that ecological differences among species or adaptation and subsequent niche filling are required to explain patterns of diversification. However, a key element missing from models of diversification is the geographical context of speciation and extinction. In this study, we develop a spatially explicit model of geographic range evolution and cladogenesis, where speciation arises via vicariance or peripatry, and explore the effects of these processes on patterns of diversification. We compare the results with those observed in 41 reconstructed avian trees. Our model shows that nonconstant rates of speciation and extinction are emergent properties of the apportioning of geographic ranges that accompanies speciation. The dynamics of diversification exhibit wide variation, depending on the mode of speciation, tendency for range expansion, and rate of range evolution. By varying these parameters, the model is able to capture many, but not all, of the features exhibited by birth-death trees and extant bird clades. Under scenarios with relatively stable geographic ranges, strong slowdowns in diversification rates are produced, with faster rates of range dynamics leading to constant or accelerating rates of apparent diversification. A peripatric model of speciation with stable ranges also generates highly unbalanced trees typical of bird phylogenies but fails to produce realistic range size distributions among the extant species. Results most similar to those of a birth-death process are reached under a peripatric speciation scenario with highly volatile range dynamics. Taken together, our results demonstrate that considering the geographical context of speciation and extinction provides a more conservative null model of diversification and offers a very different perspective on the phylogenetic patterns expected in the absence of ecology.

Multiple continental radiations and correlates of diversification in Lupinus (Leguminosae): testing for key innovation with incomplete taxon sampling.

PubMed

Drummond, Christopher S; Eastwood, Ruth J; Miotto, Silvia T S; Hughes, Colin E

2012-05-01

Replicate radiations provide powerful comparative systems to address questions about the interplay between opportunity and innovation in driving episodes of diversification and the factors limiting their subsequent progression. However, such systems have been rarely documented at intercontinental scales. Here, we evaluate the hypothesis of multiple radiations in the genus Lupinus (Leguminosae), which exhibits some of the highest known rates of net diversification in plants. Given that incomplete taxon sampling, background extinction, and lineage-specific variation in diversification rates can confound macroevolutionary inferences regarding the timing and mechanisms of cladogenesis, we used Bayesian relaxed clock phylogenetic analyses as well as MEDUSA and BiSSE birth-death likelihood models of diversification, to evaluate the evolutionary patterns of lineage accumulation in Lupinus. We identified 3 significant shifts to increased rates of net diversification (r) relative to background levels in the genus (r = 0.18-0.48 lineages/myr). The primary shift occurred approximately 4.6 Ma (r = 0.48-1.76) in the montane regions of western North America, followed by a secondary shift approximately 2.7 Ma (r = 0.89-3.33) associated with range expansion and diversification of allopatrically distributed sister clades in the Mexican highlands and Andes. We also recovered evidence for a third independent shift approximately 6.5 Ma at the base of a lower elevation eastern South American grassland and campo rupestre clade (r = 0.36-1.33). Bayesian ancestral state reconstructions and BiSSE likelihood analyses of correlated diversification indicated that increased rates of speciation are strongly associated with the derived evolution of perennial life history and invasion of montane ecosystems. Although we currently lack hard evidence for "replicate adaptive radiations" in the sense of convergent morphological and ecological trajectories among species in different clades, these results are consistent with the hypothesis that iteroparity functioned as an adaptive key innovation, providing a mechanism for range expansion and rapid divergence in upper elevation regions across much of the New World.

Biogeographic and diversification patterns of Neotropical Troidini butterflies (Papilionidae) support a museum model of diversity dynamics for Amazonia.

PubMed

Condamine, Fabien L; Silva-Brandão, Karina L; Kergoat, Gael J; Sperling, Felix A H

2012-06-12

The temporal and geographical diversification of Neotropical insects remains poorly understood because of the complex changes in geological and climatic conditions that occurred during the Cenozoic. To better understand extant patterns in Neotropical biodiversity, we investigated the evolutionary history of three Neotropical swallowtail Troidini genera (Papilionidae). First, DNA-based species delimitation analyses were conducted to assess species boundaries within Neotropical Troidini using an enlarged fragment of the standard barcode gene. Molecularly delineated species were then used to infer a time-calibrated species-level phylogeny based on a three-gene dataset and Bayesian dating analyses. The corresponding chronogram was used to explore their temporal and geographical diversification through distinct likelihood-based methods. The phylogeny for Neotropical Troidini was well resolved and strongly supported. Molecular dating and biogeographic analyses indicate that the extant lineages of Neotropical Troidini have a late Eocene (33-42 Ma) origin in North America. Two independent lineages (Battus and Euryades+Parides) reached South America via the GAARlandia temporary connection, and later became extinct in North America. They only began substantive diversification during the early Miocene in Amazonia. Macroevolutionary analysis supports the "museum model" of diversification, rather than Pleistocene refugia, as the best explanation for the diversification of these lineages. This study demonstrates that: (i) current Neotropical biodiversity may have originated ex situ; (ii) the GAARlandia bridge was important in facilitating invasions of South America; (iii) colonization of Amazonia initiated the crown diversification of these swallowtails; and (iv) Amazonia is not only a species-rich region but also acted as a sanctuary for the dynamics of this diversity. In particular, Amazonia probably allowed the persistence of old lineages and contributed to the steady accumulation of diversity over time with constant net diversification rates, a result that contrasts with previous studies on other South American butterflies.

Biogeographic and diversification patterns of Neotropical Troidini butterflies (Papilionidae) support a museum model of diversity dynamics for Amazonia

PubMed Central

2012-01-01

Background The temporal and geographical diversification of Neotropical insects remains poorly understood because of the complex changes in geological and climatic conditions that occurred during the Cenozoic. To better understand extant patterns in Neotropical biodiversity, we investigated the evolutionary history of three Neotropical swallowtail Troidini genera (Papilionidae). First, DNA-based species delimitation analyses were conducted to assess species boundaries within Neotropical Troidini using an enlarged fragment of the standard barcode gene. Molecularly delineated species were then used to infer a time-calibrated species-level phylogeny based on a three-gene dataset and Bayesian dating analyses. The corresponding chronogram was used to explore their temporal and geographical diversification through distinct likelihood-based methods. Results The phylogeny for Neotropical Troidini was well resolved and strongly supported. Molecular dating and biogeographic analyses indicate that the extant lineages of Neotropical Troidini have a late Eocene (33–42 Ma) origin in North America. Two independent lineages (Battus and Euryades + Parides) reached South America via the GAARlandia temporary connection, and later became extinct in North America. They only began substantive diversification during the early Miocene in Amazonia. Macroevolutionary analysis supports the “museum model” of diversification, rather than Pleistocene refugia, as the best explanation for the diversification of these lineages. Conclusions This study demonstrates that: (i) current Neotropical biodiversity may have originated ex situ; (ii) the GAARlandia bridge was important in facilitating invasions of South America; (iii) colonization of Amazonia initiated the crown diversification of these swallowtails; and (iv) Amazonia is not only a species-rich region but also acted as a sanctuary for the dynamics of this diversity. In particular, Amazonia probably allowed the persistence of old lineages and contributed to the steady accumulation of diversity over time with constant net diversification rates, a result that contrasts with previous studies on other South American butterflies. PMID:22690927

Microscale vicariance and diversification of Western Balkan caddisflies linked to karstification.

PubMed

Previšić, Ana; Schnitzler, Jan; Kučinić, Mladen; Graf, Wolfram; Ibrahimi, Halil; Kerovec, Mladen; Pauls, Steffen U

2014-03-01

The karst areas in the Dinaric region of the Western Balkan Peninsula are a hotspot of freshwater biodiversity. Many investigators have examined diversification of the subterranean freshwater fauna in these karst systems. However, diversification of surface-water fauna remains largely unexplored. We assessed local and regional diversification of surface-water species in karst systems and asked whether patterns of population differentiation could be explained by dispersal-diversification processes or allopatric diversification following karst-related microscale vicariance. We analyzed mitochondrial cytochrome c oxidase subunit I (mtCOI) sequence data of 4 caddisfly species (genus Drusus ) in a phylogeographic framework to assess local and regional population genetic structure and Pliocene/Pleistocene history. We used BEAST software to assess the timing of intraspecific diversification of the target species. We compared climate envelopes of the study species and projected climatically suitable areas during the last glacial maximum (LGM) to assess differences in the species climatic niches and infer potential LGM refugia. The haplotype distribution of the 4 species (324 individuals from 32 populations) was characterized by strong genetic differentiation with few haplotypes shared among populations (16%) and deep divergence among populations of the 3 endemic species, even at local scales. Divergence among local populations of endemics often exceeded divergence among regional and continental clades of the widespread D. discolor . Major divergences among regional populations dated to 2.0 to 0.5 Mya. Species distribution model projections and genetic structure suggest that the endemic species persisted in situ and diversified locally throughout multiple Pleistocene climate cycles. The pattern for D. discolor was different and consistent with multiple invasions into the region. Patterns of population genetic structure and diversification were similar for the 3 regional endemic Drusus species and consistent with microscale vicariance after the onset of intensified karstification in the Dinaric region. Karstification may induce microscale vicariance of running surface-water habitats and probably promotes allopatric fragmentation of stream insects at small spatial scales.

Burning phylogenies: fire, molecular evolutionary rates, and diversification.

PubMed

Verdú, Miguel; Pausas, Juli G; Segarra-Moragues, José Gabriel; Ojeda, Fernando

2007-09-01

Mediterranean-type ecosystems are among the most remarkable plant biodiversity "hot spots" on the earth, and fire has traditionally been invoked as one of the evolutionary forces explaining this exceptional diversity. In these ecosystems, adult plants of some species are able to survive after fire (resprouters), whereas in other species fire kills the adults and populations are only maintained by an effective post-fire recruitment (seeders). Seeders tend to have shorter generation times than resprouters, particularly under short fire return intervals, thus potentially increasing their molecular evolutionary rates and, ultimately, their diversification. We explored whether seeder lineages actually have higher rates of molecular evolution and diversification than resprouters. Molecular evolutionary rates in different DNA regions were compared in 45 phylogenetically paired congeneric taxa from fire-prone Mediterranean-type ecosystems with contrasting seeder and resprouter life histories. Differential diversification was analyzed with both topological and chronological approaches in five genera (Banksia, Daviesia, Lachnaea, Leucadendron, and Thamnochortus) from two fire-prone regions (Australia and South Africa). We found that seeders had neither higher molecular rates nor higher diversification than resprouters. Such lack of differences in molecular rates between seeders and resprouters-which did not agree with theoretical predictions-may occur if (1) the timing of the switch from seeding to resprouting (or vice versa) occurs near the branch tip, so that most of the branch length evolves under the opposite life-history form; (2) resprouters suffer more somatic mutations and therefore counterbalancing the replication-induced mutations of seeders; and (3) the rate of mutations is not related to shorter generation times because plants do not undergo determinate germ-line replication. The absence of differential diversification is to be expected if seeders and resprouters do not differ from each other in their molecular evolutionary rate, which is the fuel for speciation. Although other factors such as the formation of isolated populations may trigger diversification, we can conclude that fire acting as a throttle for diversification is by no means the rule in fire-prone ecosystems.

Evolution of exceptional species richness among lineages of fleshy-fruited Myrtaceae

PubMed Central

Biffin, Ed; Lucas, Eve J.; Craven, Lyn A.; Ribeiro da Costa, Itayguara; Harrington, Mark G.; Crisp, Michael D.

2010-01-01

Background and Aims The angiosperm family Myrtaceae comprises 17 tribes with more than half of the estimated 5500 species being referred to the fleshy-fruited and predominantly rainforest associated Syzygieae and Myrteae. Previous studies suggest that fleshy fruits have evolved separately in these lineages, whereas generally shifts in fruit morphology have been variously implicated in diversification rate shifts among angiosperms. A phylogenetic hypothesis and estimate divergence times for Myrtaceae is developed as a basis to explore the evidence for, and drivers of, elevated diversification rates among the fleshy-fruited tribes of Myrtaceae. Methods Bayesian phylogenetic analyses of plastid and nuclear DNA sequences were used to estimate intertribal relationships and lineage divergence times in Myrtaceae. Focusing on the fleshy-fruited tribes, a variety of statistical approaches were used to assess diversification rates and diversification rate shifts across the family. Key Results Analyses of the sequence data provide a strongly supported phylogenetic hypothesis for Myrtaceae. Relative to previous studies, substantially younger ages for many of the clades are reported, and it is argued that the use of flexible calibrations to incorporate fossil data provides more realistic divergence estimates than the use of errorless point calibrations. It is found that Syzygieae and Myrteae have experienced elevated diversification rates relative to other lineages of Myrtaceae. Positive shifts in diversification rate have occurred separately in each lineage, associated with a shift from dry to fleshy fruit. Conclusions Fleshy fruits have evolved independently in Syzygieae and Myrteae, and this is accompanied by exceptional diversification rate shifts in both instances, suggesting that the evolution of fleshy fruits is a key innovation for rainforest Myrtaceae. Noting the scale dependency of this hypothesis, more complex explanations may be required to explain diversification rate shifts occurring within the fleshy-fruited tribes, and the suggested phylogenetic hypothesis provides an appropriate framework for this undertaking. PMID:20462850

Darwin's Difficulties and Students' Struggles with Trait Loss: Cognitive-Historical Parallelisms in Evolutionary Explanation

NASA Astrophysics Data System (ADS)

Ha, Minsu; Nehm, Ross H.

2014-05-01

Although historical changes in scientific ideas sometimes display striking similarities with students' conceptual progressions, some scholars have cautioned that such similarities lack meaningful commonalities. In the history of evolution, while Darwin and his contemporaries often used natural selection to explain evolutionary trait gain or increase, they struggled to use it to convincingly account for cases of trait loss or decrease. This study examines Darwin's evolutionary writings about trait gain and loss in the Origin of Species (On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. D. Appleton, New York, 1859) and compares them to written evolutionary explanations for trait gain and loss in a large (n > 500), cross-cultural and cross-sectional sample (novices and experts from the USA and Korea). Findings indicate that significantly more students and experts applied natural selection to cases of trait gain, but like Darwin and his contemporaries, they more often applied `use and disuse' and `inheritance of acquired characteristics' to episodes of trait loss. Although the parallelism between Darwin's difficulties and students' struggles with trait loss are striking, significant differences also characterize explanatory model structure. Overall, however, students and scientists struggles to explain trait loss—which is a very common phenomenon in the history of life—appear to transcend time, place, and level of biological expertise. The significance of these findings for evolution education are discussed; in particular, the situated nature of biological reasoning, and the important role that the history of science can play in understanding cognitive constraints on science learning.

The effect of electrodes on 11 acene molecular spin valve: Semi-empirical study

NASA Astrophysics Data System (ADS)

Aadhityan, A.; Preferencial Kala, C.; John Thiruvadigal, D.

2017-10-01

A new revolution in electronics is molecular spintronics, with the contemporary evolution of the two novel disciplines of spintronics and molecular electronics. The key point is the creation of molecular spin valve which consists of a diamagnetic molecule in between two magnetic leads. In this paper, non-equilibrium Green's function (NEGF) combined with Extended Huckel Theory (EHT); a semi-empirical approach is used to analyse the electron transport characteristics of 11 acene molecular spin valve. We examine the spin-dependence transport on 11 acene molecular junction with various semi-infinite electrodes as Iron, Cobalt and Nickel. To analyse the spin-dependence transport properties the left and right electrodes are joined to the central region in parallel and anti-parallel configurations. We computed spin polarised device density of states, projected device density of states of carbon and the electrode element, and transmission of these devices. The results demonstrate that the effect of electrodes modifying the spin-dependence behaviours of these systems in a controlled way. In Parallel and anti-parallel configuration the separation of spin up and spin down is lager in the case of iron electrode than nickel and cobalt electrodes. It shows that iron is the best electrode for 11 acene spin valve device. Our theoretical results are reasonably impressive and trigger our motivation for comprehending the transport properties of these molecular-sized contacts.

Massively Multithreaded Maxflow for Image Segmentation on the Cray XMT-2

PubMed Central

Bokhari, Shahid H.; Çatalyürek, Ümit V.; Gurcan, Metin N.

2014-01-01

SUMMARY Image segmentation is a very important step in the computerized analysis of digital images. The maxflow mincut approach has been successfully used to obtain minimum energy segmentations of images in many fields. Classical algorithms for maxflow in networks do not directly lend themselves to efficient parallel implementations on contemporary parallel processors. We present the results of an implementation of Goldberg-Tarjan preflow-push algorithm on the Cray XMT-2 massively multithreaded supercomputer. This machine has hardware support for 128 threads in each physical processor, a uniformly accessible shared memory of up to 4 TB and hardware synchronization for each 64 bit word. It is thus well-suited to the parallelization of graph theoretic algorithms, such as preflow-push. We describe the implementation of the preflow-push code on the XMT-2 and present the results of timing experiments on a series of synthetically generated as well as real images. Our results indicate very good performance on large images and pave the way for practical applications of this machine architecture for image analysis in a production setting. The largest images we have run are 320002 pixels in size, which are well beyond the largest previously reported in the literature. PMID:25598745

Lead Diversification through a Prins-Driven Macrocyclization Strategy: Application to C13-Diversified Bryostatin Analogues.

PubMed

Wender, Paul A; Billingsley, Kelvin L

2013-01-01

The design, synthesis, and biological evaluation of a novel class of C13-diversified bryostatin analogues are described. An innovative and general strategy based on a Prins macrocyclization-nucleophilic trapping cascade was used to achieve late-stage diversification. In vitro analysis of selected library members revealed that modification at the C13 position of the bryostatin scaffold can be used as a diversification handle to regulate biological activity.

Can Google Trends search queries contribute to risk diversification?

PubMed

Kristoufek, Ladislav

2013-01-01

Portfolio diversification and active risk management are essential parts of financial analysis which became even more crucial (and questioned) during and after the years of the Global Financial Crisis. We propose a novel approach to portfolio diversification using the information of searched items on Google Trends. The diversification is based on an idea that popularity of a stock measured by search queries is correlated with the stock riskiness. We penalize the popular stocks by assigning them lower portfolio weights and we bring forward the less popular, or peripheral, stocks to decrease the total riskiness of the portfolio. Our results indicate that such strategy dominates both the benchmark index and the uniformly weighted portfolio both in-sample and out-of-sample.

Can Google Trends search queries contribute to risk diversification?

PubMed Central

Kristoufek, Ladislav

2013-01-01

Portfolio diversification and active risk management are essential parts of financial analysis which became even more crucial (and questioned) during and after the years of the Global Financial Crisis. We propose a novel approach to portfolio diversification using the information of searched items on Google Trends. The diversification is based on an idea that popularity of a stock measured by search queries is correlated with the stock riskiness. We penalize the popular stocks by assigning them lower portfolio weights and we bring forward the less popular, or peripheral, stocks to decrease the total riskiness of the portfolio. Our results indicate that such strategy dominates both the benchmark index and the uniformly weighted portfolio both in-sample and out-of-sample. PMID:24048448

Endogenous technological and demographic change under increasing water scarcity

NASA Astrophysics Data System (ADS)

Pande, S.; Ertsen, M.; Sivapalan, M.

2013-12-01

Many ancient civilizations such as the Indus Valley civilization dispersed under extreme dry conditions. Even contemporary societies such as the one in Murrumbidgee river basin, Australia, have started to witness a decline in overall population under increasing water scarcity. Skeptics of hydroclimatic determinism have often cautioned against the use of hydroclimatic change as the sole predictor of the fate of contemporary societies in water scarce regions by suggesting that technological change may ameliorate the effects of increasing water scarcity. We here develop a simple overlapping generations model of endogenous technological and demographic change. It models technological change not as an exogenous random sequence of events but as an endogenous process (as is widely accepted in contemporary literature) that depends on factors such as the investments that are (endogenously) made in a society, the endogenous diversification of a society into skilled and unskilled workers, individuals' patience in terms of its present consumption versus future consumption, the production technology and the (endogenous) interaction of these factors. The population growth rate is modeled to decline once consumption per capita crosses a ';survival' threshold. The model demonstrates that technological change may ameliorate the effects of increasing water scarcity but only to a certain extent in many cases. It is possible that technological change may allow a society to escape the effect of increasing water society, leading to an exponential rise in technology and population. However, such cases require that the rate of success of investment in technological advancement is high. In other more realistic cases of technological success, we find that endogenous technology change has an effect delaying the peak of population before it starts to decline. While the model is a rather simple model of societal growth, it is capable of replicating (not to scale) patterns of technological change (proxies of which in ancient technology include irrigation canals, metal tools, and the use of horses for labor while in contemporary societies its proxies may be the advent of drip irrigation, increasing reservoir storage capacity etc) and population change. It is capable of replicating the pattern of declining consumption per capita in presence of growth in aggregate production. It is also capable of modeling the exponential population rise even under increasing water scarcity. The results of the model suggest, as one of the many other possible explanations, that ancient societies that declined in the face of extreme water scarcity may have done so due to slower rate of success of investment in technological advancement. The model suggests that the population decline occurs after a prolonged decline in consumption per capita, which in turn is due to the joint effect of initially increasing population and increasing water scarcity. This is despite technological advancement and increase in aggregate production. Thus declining consumption per capita despite technological advancement and increase in aggregate production may serve as a useful predictor of upcoming decline in contemporary societies in water scarce basins.

The explosive radiation of Cheirolophus (Asteraceae, Cardueae) in Macaronesia

PubMed Central

2014-01-01

Background Considered a biodiversity hotspot, the Canary Islands have been the key subjects of numerous evolutionary studies concerning a large variety of organisms. The genus Cheirolophus (Asteraceae) represents one of the largest plant radiations in the Canarian archipelago. In contrast, only a few species occur in the Mediterranean region, the putative ancestral area of the genus. Here, our main aim was to reconstruct the phylogenetic and biogeographic history of Cheirolophus with special focus on explaining the origin of the large Canarian radiation. Results We found significant incongruence in phylogenetic relationships between nuclear and plastid markers. Each dataset provided resolution at different levels in Cheirolophus: the nuclear markers resolved the backbone of the phylogeny while the plastid data provided better resolution within the Canarian clade. The origin of Cheirolophus was dated in the Mid-Late Miocene, followed by rapid diversification into the three main Mediterranean lineages and the Macaronesian clade. A decrease in diversification rates was inferred at the end of the Miocene, with a new increase in the Late Pliocene concurrent with the onset of the Mediterranean climate. Diversification within the Macaronesian clade started in the Early-Mid Pleistocene, with unusually high speciation rates giving rise to the extant insular diversity. Conclusions Climate-driven diversification likely explains the early evolutionary history of Cheirolophus in the Mediterranean region. It appears that the exceptionally high diversification rate in the Canarian clade was mainly driven by allopatric speciation (including intra- and interisland diversification). Several intrinsic (e.g. breeding system, polyploid origin, seed dispersal syndrome) and extrinsic (e.g. fragmented landscape, isolated habitats, climatic and geological changes) factors probably contributed to the progressive differentiation of populations resulting in numerous microendemisms. Finally, hybridization events and emerging ecological adaptation may have also reinforced the diversification process. PMID:24888240

The explosive radiation of Cheirolophus (Asteraceae, Cardueae) in Macaronesia.

PubMed

Vitales, Daniel; Garnatje, Teresa; Pellicer, Jaume; Vallès, Joan; Santos-Guerra, Arnoldo; Sanmartín, Isabel

2014-06-02

Considered a biodiversity hotspot, the Canary Islands have been the key subjects of numerous evolutionary studies concerning a large variety of organisms. The genus Cheirolophus (Asteraceae) represents one of the largest plant radiations in the Canarian archipelago. In contrast, only a few species occur in the Mediterranean region, the putative ancestral area of the genus. Here, our main aim was to reconstruct the phylogenetic and biogeographic history of Cheirolophus with special focus on explaining the origin of the large Canarian radiation. We found significant incongruence in phylogenetic relationships between nuclear and plastid markers. Each dataset provided resolution at different levels in Cheirolophus: the nuclear markers resolved the backbone of the phylogeny while the plastid data provided better resolution within the Canarian clade. The origin of Cheirolophus was dated in the Mid-Late Miocene, followed by rapid diversification into the three main Mediterranean lineages and the Macaronesian clade. A decrease in diversification rates was inferred at the end of the Miocene, with a new increase in the Late Pliocene concurrent with the onset of the Mediterranean climate. Diversification within the Macaronesian clade started in the Early-Mid Pleistocene, with unusually high speciation rates giving rise to the extant insular diversity. Climate-driven diversification likely explains the early evolutionary history of Cheirolophus in the Mediterranean region. It appears that the exceptionally high diversification rate in the Canarian clade was mainly driven by allopatric speciation (including intra- and interisland diversification). Several intrinsic (e.g. breeding system, polyploid origin, seed dispersal syndrome) and extrinsic (e.g. fragmented landscape, isolated habitats, climatic and geological changes) factors probably contributed to the progressive differentiation of populations resulting in numerous microendemisms. Finally, hybridization events and emerging ecological adaptation may have also reinforced the diversification process.

Phylogenetics and diversification of tanagers (Passeriformes: Thraupidae), the largest radiation of Neotropical songbirds.

PubMed

Burns, Kevin J; Shultz, Allison J; Title, Pascal O; Mason, Nicholas A; Barker, F Keith; Klicka, John; Lanyon, Scott M; Lovette, Irby J

2014-06-01

Thraupidae is the second largest family of birds and represents about 4% of all avian species and 12% of the Neotropical avifauna. Species in this family display a wide range of plumage colors and patterns, foraging behaviors, vocalizations, ecotypes, and habitat preferences. The lack of a complete phylogeny for tanagers has hindered the study of this evolutionary diversity. Here, we present a comprehensive, species-level phylogeny for tanagers using six molecular markers. Our analyses identified 13 major clades of tanagers that we designate as subfamilies. In addition, two species are recognized as distinct branches on the tanager tree. Our topologies disagree in many places with previous estimates of relationships within tanagers, and many long-recognized genera are not monophyletic in our analyses. Our trees identify several cases of convergent evolution in plumage ornaments and bill morphology, and two cases of social mimicry. The phylogeny produced by this study provides a robust framework for studying macroevolutionary patterns and character evolution. We use our new phylogeny to study diversification processes, and find that tanagers show a background model of exponentially declining diversification rates. Thus, the evolution of tanagers began with an initial burst of diversification followed by a rate slowdown. In addition to this background model, two later, clade-specific rate shifts are supported, one increase for Darwin's finches and another increase for some species of Sporophila. The rate of diversification within these two groups is exceptional, even when compared to the overall rapid rate of diversification found within tanagers. This study provides the first robust assessment of diversification rates for the Darwin's finches in the context of the larger group within which they evolved. Copyright © 2014 Elsevier Inc. All rights reserved.

Rate heterogeneity across Squamata, misleading ancestral state reconstruction and the importance of proper null model specification.

PubMed

Harrington, S; Reeder, T W

2017-02-01

The binary-state speciation and extinction (BiSSE) model has been used in many instances to identify state-dependent diversification and reconstruct ancestral states. However, recent studies have shown that the standard procedure of comparing the fit of the BiSSE model to constant-rate birth-death models often inappropriately favours the BiSSE model when diversification rates vary in a state-independent fashion. The newly developed HiSSE model enables researchers to identify state-dependent diversification rates while accounting for state-independent diversification at the same time. The HiSSE model also allows researchers to test state-dependent models against appropriate state-independent null models that have the same number of parameters as the state-dependent models being tested. We reanalyse two data sets that originally used BiSSE to reconstruct ancestral states within squamate reptiles and reached surprising conclusions regarding the evolution of toepads within Gekkota and viviparity across Squamata. We used this new method to demonstrate that there are many shifts in diversification rates across squamates. We then fit various HiSSE submodels and null models to the state and phylogenetic data and reconstructed states under these models. We found that there is no single, consistent signal for state-dependent diversification associated with toepads in gekkotans or viviparity across all squamates. Our reconstructions show limited support for the recently proposed hypotheses that toepads evolved multiple times independently in Gekkota and that transitions from viviparity to oviparity are common in Squamata. Our results highlight the importance of considering an adequate pool of models and null models when estimating diversification rate parameters and reconstructing ancestral states. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Recent radiation and dispersal of an ancient lineage: The case of Fouquieria (Fouquiericeae, Ericales) in North American deserts.

PubMed

De-Nova, José Arturo; Sánchez-Reyes, Luna L; Eguiarte, Luis E; Magallón, Susana

2018-09-01

Arid biomes are particularly prominent in the Neotropics providing some of its most emblematic landscapes and a substantial part of its species diversity. To understand some of the evolutionary processes underlying the speciation of lineages in the Mexican Deserts, the diversification of Fouquieria is investigated, which includes eleven species, all endemic to the warm deserts and dry subtropical regions of North America. Using a phylogeny from plastid DNA sequences with samples of individuals from populations of all the species recognized in Fouquieria, we estimate divergence times, test for temporal diversification heterogeneity, test for geographical structure, and conduct ancestral area reconstruction. Fouquieria is an ancient lineage that diverged from Polemoniaceae ca. 75.54 Ma. A Mio-Pliocene diversification of Fouquieria with vicariance, associated with Neogene orogenesis underlying the early development of regional deserts is strongly supported. Test for temporal diversification heterogeneity indicates that during its evolutionary history, Fouquieria had a drastic diversification rate shift at ca.12.72 Ma, agreeing with hypotheses that some of the lineages in North American deserts diversified as early as the late Miocene to Pliocene, and not during the Pleistocene. Long-term diversification dynamics analyses suggest that extinction also played a significant role in Fouquieria's evolution, with a very high rate at the onset of the process. From the late Miocene onwards, Fouquieria underwent substantial diversification change, involving high speciation decreasing to the present and negligible extinction, which is congruent with its scant fossil record during this period. Geographic phylogenetic structure and the pattern of most sister species inhabiting different desert nucleus support that isolation by distance could be the main driver of speciation. Copyright © 2018 Elsevier Inc. All rights reserved.

The evolution of defense mechanisms correlate with the explosive diversification of autodigesting Coprinellus mushrooms (Agaricales, Fungi).

PubMed

Nagy, László G; Házi, Judit; Szappanos, Balázs; Kocsubé, Sándor; Bálint, Balázs; Rákhely, Gábor; Vágvölgyi, Csaba; Papp, Tamás

2012-07-01

Bursts of diversification are known to have contributed significantly to the extant morphological and species diversity, but evidence for many of the theoretical predictions about adaptive radiations have remained contentious. Despite their tremendous diversity, patterns of evolutionary diversification and the contribution of explosive episodes in fungi are largely unknown. Here, using the genus Coprinellus (Psathyrellaceae, Agaricales) as a model, we report the first explosive fungal radiation and infer that the onset of the radiation correlates with a change from a multilayered to a much simpler defense structure on the fruiting bodies. We hypothesize that this change constitutes a key innovation, probably relaxing constraints on diversification imposed by nutritional investment into the development of protective tissues of fruiting bodies. Fossil calibration suggests that Coprinellus mushrooms radiated during the Miocene coinciding with global radiation of large grazing mammals following expansion of dry open grasslands. In addition to diversification rate-based methods, we test the hard polytomy hypothesis, by analyzing the resolvability of internal nodes of the backbone of the putative radiation using Reversible-Jump MCMC. We discuss potential applications and pitfalls of this approach as well as how biologically meaningful polytomies can be distinguished from alignment shortcomings. Our data provide insights into the nature of adaptive radiations in general by revealing a deceleration of morphological diversification through time. The dynamics of morphological diversification was approximated by obtaining the temporal distribution of state changes in discrete traits along the trees and comparing it with the tempo of lineage accumulation. We found that the number of state changes correlate with the number of lineages, even in parts of the tree with short internal branches, and peaks around the onset of the explosive radiation followed by a slowdown, most likely because of the decrease in available niches.

The influence of habitat on the evolution of plants: a case study across Saxifragales.

PubMed

de Casas, Rafael Rubio; Mort, Mark E; Soltis, Douglas E

2016-12-01

Organismal evolution tends to be closely associated with ecological conditions. However, the extent to which this association constrains adaptation or diversification into new habitats remains unclear. We studied habitat evolution in the hyper-diverse angiosperm clade Saxifragales. We used species-level phylogenies for approx. 950 species to analyse the evolution of habitat shifts as well as their influence on plant diversification. We combined habitat characterization based on floristic assignments and state-of-the art phylogenetic comparative methods to estimate within- and across-habitat diversification patterns. Our analyses showed that Saxifragales diversified into multiple habitats from a forest-inhabiting ancestor and that this diversification is governed by relatively rare habitat shifts. Lineages are likely to stay within inferred ancestral ecological conditions. Adaptation to some habitat types (e.g. aquatic, desert) may be canalizing events that lineages do not escape. Although associations between increased diversification rates and shifts in habitat preferences are occasionally observed, extreme macroevolutionary rates are closely associated with specific habitats. Lineages occurring in shrubland, and especially tundra and rock cliffs, exhibit comparatively high diversification, whereas forest, grassland, desert and aquatic habitats are associated with low diversification. The likelihood of occupation of new habitats appears to be asymmetric. Shifts to aquatic and desert habitats may be canalizing events. Other habitats, such as tundra, might act as evolutionary sources, while forests provide the only habitat seemingly colonized easily by lineages originating elsewhere. However, habitat shifts are very rare, and any major environmental alteration is expected to have dramatic evolutionary consequences. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company.

Farmer's response to changing climate in North East India

NASA Astrophysics Data System (ADS)

De, Utpal Kumar

2015-02-01

Diversification of land use in the cultivation of various crops provides an alternative way to moderate the climate risk. By choosing alternative crops that are resilient to various weather parameters, farmers can reduce the crop damage and achieve optimum output from their limited land resources. Apart from other adaptation measures, crop diversity can reflect farmers' response towards changing climate uncertainty. This paper tries to examine the changing climatic condition through spatio-temporal variation of two important weather variables (precipitation and temperature) in the largest North-East Indian state, Assam, since 1950. It is examined by the variation in crop diversification index. We have used (1) Herfindahl Index for measuring degree of diversification and (2) locational quotient for measuring the changes in the regional crop concentration. The results show that, in almost all the districts, crop specialization has been taking place slowly and that happened mostly in the last phase of our study. The hilly and backward districts recorded more diversification but towards lower value crops. It goes against the normal feature of crop diversification where farmers diversify in favour of high value crops. Employing ordinary least squares method and/or Fixed Effect model, irrigation is found to have significant impact on crop diversification; while the flood plain zones and hill zones are found to have better progress in this regard, which has been due to the survival necessity of poor farmers living the zone. Thus crop diversity does not reflect very significant response from the farmers' side towards changing weather factors (except rainfall) though they have significant impact on the productivity of various crops, and thus profitability. The study thus suggests the necessity for rapid and suitable diversification as alternative climate change mitigation in the long run.

A review of interventions based on dietary diversification or modification strategies with the potential to enhance intakes of total and absorbable zinc.

PubMed

Gibson, Rosalind S; Anderson, Victoria P

2009-03-01

Dietary diversification or modification has the potential to prevent deficiencies of zinc and other coexisting limiting micronutrients simultaneously, without risk of antagonistic interactions. In this review, we have addressed the following. The first section focuses on strategies with the potential to enhance intake and/or bioavailability of zinc, and includes interventions (with and without nutrition education) based on agriculture, production or promotion of animal-source foods through animal husbandry or aquaculture, and commercial and household processing strategies to enhance zinc absorption. Outcome indicators include intakes of foods or nutrients (although rarely zinc) and, in some cases, zinc status, or zinc-related functional responses. The next two sections address whether dietary diversification or modification can achieve increases in absorbable zinc that are sufficient to enhance zinc status or zinc-related functional responses in breastfed infants and toddlers and in older children and women of reproductive age. Evidence for the impact of dietary diversification or modification on behavior change and on nutritional status in the short and long term, and the possible role of modifying factors (e.g., baseline nutritional status, socioeconomic status, infection, sex, age, and life-stage group) is the emphasis of the next section. The following section highlights the evidence for three potential adverse effects of dietary diversification or modification: aflatoxin contamination from germinated cereals, loss of water-soluble nutrients, and displacement of breastmilk. Finally, an example of a dietary diversification or modification program (Homestead Food Production) developed and implemented by Helen Keller International is given, together with the critical steps needed to scale up dietary diversification or modification for programs and future research needs.

Diversification strategy and performance: implications for health services research.

PubMed

Rivers, P A; Glover, S H; Munchus, G

1999-01-01

Health care represents a promising area of research due to its uniqueness. In recent years, considerable progress has been made in diversification strategy and performance research but not the study of health services strategy research. This article reviews diversification strategy and performance in health services domains. Adopting Datta, Rajagopalan, and Rasheed's (1991) framework, the authors evaluate the theoretical and empirical contributions of this research. The limitations and theoretical implications of these efforts are also explored.

Analysis of adaptive evolution in Lyssavirus genomes reveals pervasive diversifying selection during species diversification.

PubMed

Voloch, Carolina M; Capellão, Renata T; Mello, Beatriz; Schrago, Carlos G

2014-11-19

Lyssavirus is a diverse genus of viruses that infect a variety of mammalian hosts, typically causing encephalitis. The evolution of this lineage, particularly the rabies virus, has been a focus of research because of the extensive occurrence of cross-species transmission, and the distinctive geographical patterns present throughout the diversification of these viruses. Although numerous studies have examined pattern-related questions concerning Lyssavirus evolution, analyses of the evolutionary processes acting on Lyssavirus diversification are scarce. To clarify the relevance of positive natural selection in Lyssavirus diversification, we conducted a comprehensive scan for episodic diversifying selection across all lineages and codon sites of the five coding regions in lyssavirus genomes. Although the genomes of these viruses are generally conserved, the glycoprotein (G), RNA-dependent RNA polymerase (L) and polymerase (P) genes were frequently targets of adaptive evolution during the diversification of the genus. Adaptive evolution is particularly manifest in the glycoprotein gene, which was inferred to have experienced the highest density of positively selected codon sites along branches. Substitutions in the L gene were found to be associated with the early diversification of phylogroups. A comparison between the number of positively selected sites inferred along the branches of RABV population branches and Lyssavirus intespecies branches suggested that the occurrence of positive selection was similar on the five coding regions of the genome in both groups.

Analysis of Adaptive Evolution in Lyssavirus Genomes Reveals Pervasive Diversifying Selection during Species Diversification

PubMed Central

Voloch, Carolina M.; Capellão, Renata T.; Mello, Beatriz; Schrago, Carlos G.

2014-01-01

Lyssavirus is a diverse genus of viruses that infect a variety of mammalian hosts, typically causing encephalitis. The evolution of this lineage, particularly the rabies virus, has been a focus of research because of the extensive occurrence of cross-species transmission, and the distinctive geographical patterns present throughout the diversification of these viruses. Although numerous studies have examined pattern-related questions concerning Lyssavirus evolution, analyses of the evolutionary processes acting on Lyssavirus diversification are scarce. To clarify the relevance of positive natural selection in Lyssavirus diversification, we conducted a comprehensive scan for episodic diversifying selection across all lineages and codon sites of the five coding regions in lyssavirus genomes. Although the genomes of these viruses are generally conserved, the glycoprotein (G), RNA-dependent RNA polymerase (L) and polymerase (P) genes were frequently targets of adaptive evolution during the diversification of the genus. Adaptive evolution is particularly manifest in the glycoprotein gene, which was inferred to have experienced the highest density of positively selected codon sites along branches. Substitutions in the L gene were found to be associated with the early diversification of phylogroups. A comparison between the number of positively selected sites inferred along the branches of RABV population branches and Lyssavirus intespecies branches suggested that the occurrence of positive selection was similar on the five coding regions of the genome in both groups. PMID:25415197

Plural provision of primary medical care in England, 2002-2012.

PubMed

Sheaff, Rod

2013-10-01

Health care reforms often include provider diversification, including privatization, to increase competition and thereby health care quality and efficiency. Donabedian's organizational theory implies that the consequences will vary according to the providers' ownership. The aim was to examine how far that theory applies to changes in English NHS primary medical care (general practice) since 1998, and the consequences for patterns of service provision. Framework analysis whose categories and structure reflected Donabedian's theory and its implications, populated with data from a systematic review, administrative sources and press rapportage. Two patterns of provider diversification occurred: 'native' diversification among existing providers and plural provision as providers with different types of ownership were introduced. Native diversification occurred through: extensive recruitment of salaried GPs; extending the range of services provided by general practices; introducing limited liability partnerships; establishing GPs with special clinical interests; and introducing a wider range of services for GPs to refer to. All of these had little apparent effect on competition between general practices. Plural provision involved: increased primary care provision by corporations; introducing GP-owned firms; establishing social enterprises (initially mostly out-of-hours cooperatives); and Primary Care Trusts taking over general practices. Plural provision was on a smaller scale than native diversification and appeared to go into reverse in 2011. Although the available data confirm the implications of Donabedian's theory, there are exceptions. Native diversification and plural provision policies differ in their implications for service development.

Higher speciation and lower extinction rates influence mammal diversity gradients in Asia.

PubMed

Tamma, Krishnapriya; Ramakrishnan, Uma

2015-02-04

Little is known about the patterns and correlates of mammal diversity gradients in Asia. In this study, we examine patterns of species distributions and phylogenetic diversity in Asia and investigate if the observed diversity patterns are associated with differences in diversification rates between the tropical and non-tropical regions. We used species distribution maps and phylogenetic trees to generate species and phylogenetic diversity measures for 1° × 1° cells across mainland Asia. We constructed lineage-through-time plots and estimated diversification shift-times to examine the temporal patterns of diversifications across orders. Finally, we tested if the observed gradients in Asia could be associated with geographical differences in diversification rates across the tropical and non-tropical biomes. We estimated speciation, extinction and dispersal rates across these two regions for mammals, both globally and for Asian mammals. Our results demonstrate strong latitudinal and longitudinal gradients of species and phylogenetic diversity with Southeast Asia and the Himalayas showing highest diversity. Importantly, our results demonstrate that differences in diversification (speciation, extinction and dispersal) rates between the tropical and the non-tropical biomes influence the observed diversity gradients globally and in Asia. For the first time, we demonstrate that Asian tropics act as both cradles and museums of mammalian diversity. Temporal and spatial variation in diversification rates across different lineages of mammals is an important correlate of species diversity gradients observed in Asia.

Diversity-dependent evolutionary rates in early Palaeozoic zooplankton.

PubMed

Foote, Michael; Cooper, Roger A; Crampton, James S; Sadler, Peter M

2018-02-28

The extent to which biological diversity affects rates of diversification is central to understanding macroevolutionary dynamics, yet no consensus has emerged on the importance of diversity-dependence of evolutionary rates. Here, we analyse the species-level fossil record of early Palaeozoic graptoloids, documented with high temporal resolution, to test directly whether rates of diversification were influenced by levels of standing diversity within this major clade of marine zooplankton. To circumvent the statistical regression-to-the-mean artefact, whereby higher- and lower-than-average values of diversity tend to be followed by negative and positive diversification rates, we construct a non-parametric, empirically scaled, diversity-independent null model by randomizing the observed diversification rates with respect to time. Comparing observed correlations between diversity and diversification rate to those expected from this diversity-independent model, we find evidence for negative diversity-dependence, accounting for up to 12% of the variance in diversification rate, with maximal correlation at a temporal lag of approximately 1 Myr. Diversity-dependence persists throughout the Ordovician and Silurian, despite a major increase in the strength and frequency of extinction and speciation pulses in the Silurian. By contrast to some previous work, we find that diversity-dependence affects rates of speciation and extinction nearly equally on average, although subtle differences emerge when we compare the Ordovician and Silurian. © 2018 The Author(s).

Investigating processes of neotropical rain forest tree diversification by examining the evolution and historical biogeography of the Protieae (Burseraceae).

PubMed

Fine, Paul V A; Zapata, Felipe; Daly, Douglas C

2014-07-01

Andean uplift and the collision of North and South America are thought to have major implications for the diversification of the Neotropical biota. However, few studies have investigated how these geological events may have influenced diversification. We present a multilocus phylogeny of 102 Protieae taxa (73% of published species), sampled pantropically, to test hypotheses about the relative importance of dispersal, vicariance, habitat specialization, and biotic factors in the diversification of this ecologically dominant tribe of Neotropical trees. Bayesian fossil-calibrated analyses date the Protieae stem at 55 Mya. Biogeographic analyses reconstruct an initial late Oligocene/early Miocene radiation in Amazonia for Neotropical Protieae, with several subsequent late Miocene dispersal events to Central America, the Caribbean, Brazil's Atlantic Forest, and the Chocó. Regional phylogenetic structure results indicate frequent dispersal among regions throughout the Miocene and many instances of more recent regional in situ speciation. Habitat specialization to white sand or flooded soils was common, especially in Amazonia. There was one significant increase in diversification rate coincident with colonization of the Neotropics, followed by a gradual decrease consistent with models of diversity-dependent cladogenesis. Dispersal, biotic interactions, and habitat specialization are thus hypothesized to be the most important processes underlying the diversification of the Protieae. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Aridification driven diversification of fan-throated lizards from the Indian subcontinent.

PubMed

Deepak, V; Karanth, Praveen

2018-03-01

The establishment of monsoon climate and the consequent aridification has been one of the most important climate change episodes in the Indian subcontinent. However, little is known about how these events might have shaped the diversification patterns among the widely distributed taxa. Fan-throated lizards (FTL) (Genus: Sitana, Sarada) are widespread, diurnal and restricted to the semi-arid zones of the Indian subcontinent. We sampled FTL in 107 localities across its range. We used molecular species delimitation method and delineated 15 species including six putative species. Thirteen of them were distinguishable based on morphology but two sister species were indistinguishable and have minor overlaps in distribution. Five fossils were used to calibrate and date the phylogeny. Diversification of fan-throated lizards lineage started ~18 mya and higher lineage diversification was observed after 11 my. The initial diversification corresponds to the time when monsoon climate was established and the latter was a period of intensification of monsoon and initiation of aridification. Thirteen out of the fifteen FTL species delimited are from Peninsular India; this is probably due to the landscape heterogeneity in this region. The species poor sister genus Otocryptis is paraphyletic and probably represents relict lineages which are now confined to forested areas. Thus, the seasonality led changes in habitat, from forests to open habitats appear to have driven diversification of fan-throated lizards. Copyright © 2017 Elsevier Inc. All rights reserved.

Phylogenomics, Diversification Dynamics, and Comparative Transcriptomics across the Spider Tree of Life.

PubMed

Fernández, Rosa; Kallal, Robert J; Dimitrov, Dimitar; Ballesteros, Jesús A; Arnedo, Miquel A; Giribet, Gonzalo; Hormiga, Gustavo

2018-05-07

Dating back to almost 400 mya, spiders are among the most diverse terrestrial predators [1]. However, despite considerable effort [1-9], their phylogenetic relationships and diversification dynamics remain poorly understood. Here, we use a synergistic approach to study spider evolution through phylogenomics, comparative transcriptomics, and lineage diversification analyses. Our analyses, based on ca. 2,500 genes from 159 spider species, reject a single origin of the orb web (the "ancient orb-web hypothesis") and suggest that orb webs evolved multiple times since the late Triassic-Jurassic. We find no significant association between the loss of foraging webs and increases in diversification rates, suggesting that other factors (e.g., habitat heterogeneity or biotic interactions) potentially played a key role in spider diversification. Finally, we report notable genomic differences in the main spider lineages: while araneoids (ecribellate orb-weavers and their allies) reveal an enrichment in genes related to behavior and sensory reception, the retrolateral tibial apophysis (RTA) clade-the most diverse araneomorph spider lineage-shows enrichment in genes related to immune responses and polyphenic determination. This study, one of the largest invertebrate phylogenomic analyses to date, highlights the usefulness of transcriptomic data not only to build a robust backbone for the Spider Tree of Life, but also to address the genetic basis of diversification in the spider evolutionary chronicle. Copyright © 2018 Elsevier Ltd. All rights reserved.

Does the colonization of new biogeographic regions influence the diversification and accumulation of clade richness among the Corvides (Aves: Passeriformes)?

PubMed

Kennedy, Jonathan D; Borregaard, Michael K; Jønsson, Knud A; Holt, Ben; Fjeldså, Jon; Rahbek, Carsten

2017-01-01

Regional variation in clade richness can be vast, reflecting differences in the dynamics of historical dispersal and diversification among lineages. Although it has been proposed that dispersal into new biogeographic regions may facilitate diversification, to date there has been limited assessment of the importance of this process in the generation, and maintenance, of broad-scale biodiversity gradients. To address this issue, we analytically derive biogeographic regions for a global radiation of passerine birds (the Corvides, c. 790 species) that are highly variable in the geographic and taxonomic distribution of species. Subsequently, we determine rates of historical dispersal between regions, the dynamics of diversification following regional colonization, and spatial variation in the distribution of species that differ in their rates of lineage diversification. The results of these analyses reveal spatiotemporal differences in the build-up of lineages across regions. The number of regions occupied and the rate of transition between regions both predict family richness well, indicating that the accumulation of high clade richness is associated with repeated expansion into new geographic areas. However, only the largest family (the Corvidae) had significantly heightened rates of both speciation and regional transition, implying that repeated regional colonization is not a general mechanism promoting lineage diversification among the Corvides. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Modeling lineage and phenotypic diversification in the New World monkey (Platyrrhini, Primates) radiation.

PubMed

Aristide, Leandro; Rosenberger, Alfred L; Tejedor, Marcelo F; Perez, S Ivan

2015-01-01

Adaptive radiations that have taken place in the distant past can now be more thoroughly studied with the availability of large molecular phylogenies and comparative data drawn from extant and fossil species. Platyrrhines are a good example of a major mammalian evolutionary radiation confined to a single continent, involving a relatively large temporal scale and documented by a relatively small but informative fossil record. Here, we present comparative evidence using data on extant and fossil species to explore alternative evolutionary models in an effort to better understand the process of platyrrhine lineage and phenotypic diversification. Specifically, we compare the likelihood of null models of lineage and phenotypic diversification versus various models of adaptive evolution. Moreover, we statistically explore the main ecological dimension behind the platyrrhine diversification. Contrary to the previous proposals, our study did not find evidence of a rapid lineage accumulation in the phylogenetic tree of extant platyrrhine species. However, the fossil-based diversity curve seems to show a slowdown in diversification rates toward present times. This also suggests an early high rate of extinction among lineages within crown Platyrrhini. Finally, our analyses support the hypothesis that the platyrrhine phenotypic diversification appears to be characterized by an early and profound differentiation in body size related to a multidimensional niche model, followed by little subsequent change (i.e., stasis). Copyright © 2013 Elsevier Inc. All rights reserved.

Next-generation sequencing shows West Nile virus quasispecies diversification after a single passage in a carrion crow (Corvus corone) in vivo infection model.

PubMed

Dridi, M; Rosseel, T; Orton, R; Johnson, P; Lecollinet, S; Muylkens, B; Lambrecht, B; Van Borm, S

2015-10-01

West Nile virus (WNV) occurs as a population of genetic variants (quasispecies) infecting a single animal. Previous low-resolution viral genetic diversity estimates in sampled wild birds and mosquitoes, and in multiple-passage adaptation studies in vivo or in cell culture, suggest that WNV genetic diversification is mostly limited to the mosquito vector. This study investigated genetic diversification of WNV in avian hosts during a single passage using next-generation sequencing. Wild-captured carrion crows were subcutaneously infected using a clonal Middle-East WNV. Blood samples were collected 2 and 4 days post-infection. A reverse-transcription (RT)-PCR approach was used to amplify the WNV genome directly from serum samples prior to next-generation sequencing resulting in an average depth of at least 700 ×  in each sample. Appropriate controls were sequenced to discriminate biologically relevant low-frequency variants from experimentally introduced errors. The WNV populations in the wild crows showed significant diversification away from the inoculum virus quasispecies structure. By contrast, WNV populations in intracerebrally infected day-old chickens did not diversify from that of the inoculum. Where previous studies concluded that WNV genetic diversification is only experimentally demonstrated in its permissive insect vector species, we have experimentally shown significant diversification of WNV populations in a wild bird reservoir species.

The pollination niche and its role in the diversification and maintenance of the southern African flora

PubMed Central

Johnson, Steven D.

2010-01-01

The flora of southern Africa has exceptional species richness and endemism, making it an ideal system for studying the patterns and processes of evolutionary diversification. Using a wealth of recent case studies, I examine the evidence for pollinator-driven diversification in this flora. Pollination systems, which represent available niches for ecological diversification, are characterized in southern Africa by a high level of ecological and evolutionary specialization on the part of plants, and, in some cases, by pollinators as well. These systems are asymmetric, with entire plant guilds commonly specialized for a particular pollinator species or functional type, resulting in obvious convergent floral evolution among guild members. Identified modes of plant lineage diversification involving adaptation to pollinators in these guilds include (i) shifts between pollination systems, (ii) divergent use of the same pollinator, (iii) coevolution, (iv) trait tracking, and (v) floral mimicry of different model species. Microevolutionary studies confirm that pollinator shifts can be precipitated when a plant species encounters a novel pollinator fauna on its range margin, and macroevolutionary studies confirm frequent pollinator shifts associated with lineage diversification. As Darwin first noted, evolutionary specialization for particular pollinators, when resulting in ecological dependency, may increase the risk of plant extinction. I thus also consider the evidence that disturbance provokes pollination failure in some southern African plants with specialized pollination systems. PMID:20047876

The pollination niche and its role in the diversification and maintenance of the southern African flora.

PubMed

Johnson, Steven D

2010-02-12

The flora of southern Africa has exceptional species richness and endemism, making it an ideal system for studying the patterns and processes of evolutionary diversification. Using a wealth of recent case studies, I examine the evidence for pollinator-driven diversification in this flora. Pollination systems, which represent available niches for ecological diversification, are characterized in southern Africa by a high level of ecological and evolutionary specialization on the part of plants, and, in some cases, by pollinators as well. These systems are asymmetric, with entire plant guilds commonly specialized for a particular pollinator species or functional type, resulting in obvious convergent floral evolution among guild members. Identified modes of plant lineage diversification involving adaptation to pollinators in these guilds include (i) shifts between pollination systems, (ii) divergent use of the same pollinator, (iii) coevolution, (iv) trait tracking, and (v) floral mimicry of different model species. Microevolutionary studies confirm that pollinator shifts can be precipitated when a plant species encounters a novel pollinator fauna on its range margin, and macroevolutionary studies confirm frequent pollinator shifts associated with lineage diversification. As Darwin first noted, evolutionary specialization for particular pollinators, when resulting in ecological dependency, may increase the risk of plant extinction. I thus also consider the evidence that disturbance provokes pollination failure in some southern African plants with specialized pollination systems.

A method for investigating relative timing information on phylogenetic trees.

PubMed

Ford, Daniel; Matsen, Frederick A; Stadler, Tanja

2009-04-01

In this paper, we present a new way to describe the timing of branching events in phylogenetic trees. Our description is in terms of the relative timing of diversification events between sister clades; as such it is complementary to existing methods using lineages-through-time plots which consider diversification in aggregate. The method can be applied to look for evidence of diversification happening in lineage-specific "bursts", or the opposite, where diversification between 2 clades happens in an unusually regular fashion. In order to be able to distinguish interesting events from stochasticity, we discuss 2 classes of neutral models on trees with relative timing information and develop a statistical framework for testing these models. These model classes include both the coalescent with ancestral population size variation and global rate speciation-extinction models. We end the paper with 2 example applications: first, we show that the evolution of the hepatitis C virus deviates from the coalescent with arbitrary population size. Second, we analyze a large tree of ants, demonstrating that a period of elevated diversification rates does not appear to have occurred in a bursting manner.

Coral reefs as drivers of cladogenesis: expanding coral reefs, cryptic extinction events, and the development of biodiversity hotspots.

PubMed

Cowman, P F; Bellwood, D R

2011-12-01

Diversification rates within four conspicuous coral reef fish families (Labridae, Chaetodontidae, Pomacentridae and Apogonidae) were estimated using Bayesian inference. Lineage through time plots revealed a possible late Eocene/early Oligocene cryptic extinction event coinciding with the collapse of the ancestral Tethyan/Arabian hotspot. Rates of diversification analysis revealed elevated cladogenesis in all families in the Oligocene/Miocene. Throughout the Miocene, lineages with a high percentage of coral reef-associated taxa display significantly higher net diversification rates than expected. The development of a complex mosaic of reef habitats in the Indo-Australian Archipelago (IAA) during the Oligocene/Miocene appears to have been a significant driver of cladogenesis. Patterns of diversification suggest that coral reefs acted as a refuge from high extinction, as reef taxa are able to sustain diversification at high extinction rates. The IAA appears to support both cladogenesis and survival in associated lineages, laying the foundation for the recent IAA marine biodiversity hotspot. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

Rapid action in the Palaeogene, the relationship between phenotypic and taxonomic diversification in Coenozoic mammals

PubMed Central

Raia, P.; Carotenuto, F.; Passaro, F.; Piras, P.; Fulgione, D.; Werdelin, L.; Saarinen, J.; Fortelius, M.

2013-01-01

A classic question in evolutionary biology concerns the tempo and mode of lineage evolution. Considered variously in relation to resource utilization, intrinsic constraints or hierarchic level, the question of how evolutionary change occurs in general has continued to draw the attention of the field for over a century and a half. Here we use the largest species-level phylogeny of Coenozoic fossil mammals (1031 species) ever assembled and their body size estimates, to show that body size and taxonomic diversification rates declined from the origin of placentals towards the present, and very probably correlate to each other. These findings suggest that morphological and taxic diversifications of mammals occurred hierarchically, with major shifts in body size coinciding with the birth of large clades, followed by taxonomic diversification within these newly formed clades. As the clades expanded, rates of taxonomic diversification proceeded independently of phenotypic evolution. Such a dynamic is consistent with the idea, central to the Modern Synthesis, that mammals radiated adaptively, with the filling of adaptive zones following the radiation. PMID:23173207

Metabolic flexibility in health and disease

PubMed Central

Goodpaster, Bret H.; Sparks, Lauren M.

2017-01-01

Summary Metabolic flexibility is the ability to respond or adapt to conditional changes in metabolic demand. This broad concept has been propagated to explain insulin resistance and mechanisms governing fuel selection between glucose and fatty acids, highlighting the metabolic inflexibility of obesity and type 2 diabetes. In parallel, contemporary exercise physiology research has helped to identify potential mechanisms underlying altered fuel metabolism in obesity and diabetes. Advances in ‘omics’ technologies have further stimulated additional basic and clinical-translational research to further interrogate mechanisms for improved metabolic flexibility in skeletal muscle and adipose tissue with the goal to prevent and treat metabolic disease. PMID:28467922

Hey Wait! I Just Thought of Something Else! Advaita and Clinical Hypnosis.

PubMed

Amundson, Jon K; Ross, Marc W; Campbell, Debra

2018-07-01

While much has been made of the value of Buddhist mindfulness in clinical treatment, little attention has been given over to its parallels, if not antecedents in Hindu philosophy. Buddhist traditions in the vipassana, ch'an and zen tradition, and the practices associated, find their roots in Advaita philosophy and practice. This article looks at the useful/effective nature of Advaita and its specific application in clinical hypnosis. The linkage between traditional wisdom sources, psychological investigations of the self and contemporary hypnosis is articulated in the article which follows, and a case example, regarding clinical application, is provided.

Choice.

PubMed

Greenberg, Jay

2008-09-01

Understanding how and why analysands make the choices they do is central to both the clinical and the theoretical projects of psychoanalysis. And yet we know very little about the process of choice or about the relationship between choices and motives. A striking parallel is to be found between the ways choice is narrated in ancient Greek texts and the experience of analysts as they observe patients making choices in everyday clinical work. Pursuing this convergence of classical and contemporary sensibilities will illuminate crucial elements of the various meanings of choice, and of the way that these meanings change over the course of psychoanalytic treatment.

Voluntarism and Diversification of Undergraduate Geoscience Programs.

ERIC Educational Resources Information Center

Greenberg, Jeffrey King

1990-01-01

Strategies that can be used to revitalize geoscience education are discussed. Stressed are the ideas of providing voluntary assistance to science and science teacher education and program diversification. (CW)

Large-scale diversification without genetic isolation in nematode symbionts of figs

PubMed Central

Susoy, Vladislav; Herrmann, Matthias; Kanzaki, Natsumi; Kruger, Meike; Nguyen, Chau N.; Rödelsperger, Christian; Röseler, Waltraud; Weiler, Christian; Giblin-Davis, Robin M.; Ragsdale, Erik J.; Sommer, Ralf J.

2016-01-01

Diversification is commonly understood to be the divergence of phenotypes accompanying that of lineages. In contrast, alternative phenotypes arising from a single genotype are almost exclusively limited to dimorphism in nature. We report a remarkable case of macroevolutionary-scale diversification without genetic divergence. Upon colonizing the island-like microecosystem of individual figs, symbiotic nematodes of the genus Pristionchus accumulated a polyphenism with up to five discrete adult morphotypes per species. By integrating laboratory and field experiments with extensive genotyping of individuals, including the analysis of 49 genomes from a single species, we show that rapid filling of potential ecological niches is possible without diversifying selection on genotypes. This uncoupling of morphological diversification and speciation in fig-associated nematodes has resulted from a remarkable expansion of discontinuous developmental plasticity. PMID:26824073

Rapid radiation of Impatiens (Balsaminaceae) during Pliocene and Pleistocene: result of a global climate change.

PubMed

Janssens, Steven B; Knox, Eric B; Huysmans, Suzy; Smets, Erik F; Merckx, Vincent S F T

2009-09-01

Impatiens comprises more than 1000 species and is one of the largest genera of flowering plants. The genus has a subcosmopolitan distribution, yet most of its evolutionary history is unknown. Diversification analyses, divergence time estimates and historical biogeography, illustrated that the extant species of Impatiens originated in Southwest China and started to diversify in the Early Miocene. Until the Early Pliocene, the net diversification rate within the genus was fairly slow. Since that time, however, approximately 80% of all Impatiens lineages have originated. This period of rapid diversification coincides with the global cooling of the Earth's climate and subsequent glacial oscillations. Without this accelerated diversification rate, Impatiens would only have contained 1/5th of its current number of species, thereby indicating the rapid radiation of the genus.

Diversification of Angraecum (Orchidaceae, Vandeae) in Madagascar: Revised Phylogeny Reveals Species Accumulation through Time Rather than Rapid Radiation

PubMed Central

2016-01-01

Angraecum is the largest genus of subtribe Angraecinae (Orchidaceae) with about 221 species. Madagascar is the center of the diversity for the genus with ca. 142 species, of which 90% are endemic. The great morphological diversity associated with species diversification in the genus on the island of Madagascar offers valuable insights for macroevolutionary studies. Phylogenies of the Angraecinae have been published but a lack of taxon and character sampling and their limited taxonomic resolution limit their uses for macroevolutionary studies. We present a new phylogeny of Angraecum based on chloroplast sequence data (matk, rps16, trnL), nuclear ribosomal (ITS2) and 39 morphological characters from 194 Angraecinae species of which 69 were newly sampled. Using this phylogeny, we evaluated the monophyly of the sections of Angraecum as defined by Garay and investigated the patterns of species diversification within the genus. We used maximum parsimony and bayesian analyses to generate phylogenetic trees and dated divergence times of the phylogeny. We analyzed diversification patterns within Angraecinae and Angraecum with an emphasis on four floral characters (flower color, flower size, labellum position, spur length) using macroevolutionary models to evaluate which characters or character states are associated with speciation rates, and inferred ancestral states of these characters. The phylogenetic analysis showed the polyphyly of Angraecum sensu lato and of all Angraecum sections except sect. Hadrangis, and that morphology can be consistent with the phylogeny. It appeared that the characters (flower color, flower size, spur length) formerly used by many authors to delineate Angraecum groups were insufficient to do so. However, the newly described character, position of the labellum (uppermost and lowermost), was the main character delimiting clades within a monophyletic Angraecum sensu stricto. This character also appeared to be associated with speciation rates in Angraecum. The macroevolutionary model-based phylogeny failed to detect shifts in diversification that could be associated directly with morphological diversification. Diversification in Angraecum resulted from gradual species accumulation through time rather than from rapid radiation, a diversification pattern often encountered in tropical rain forests. PMID:27669569

Multiple Continental Radiations and Correlates of Diversification in Lupinus (Leguminosae): Testing for Key Innovation with Incomplete Taxon Sampling

PubMed Central

Drummond, Christopher S.; Eastwood, Ruth J.; Miotto, Silvia T. S.; Hughes, Colin E.

2012-01-01

Replicate radiations provide powerful comparative systems to address questions about the interplay between opportunity and innovation in driving episodes of diversification and the factors limiting their subsequent progression. However, such systems have been rarely documented at intercontinental scales. Here, we evaluate the hypothesis of multiple radiations in the genus Lupinus (Leguminosae), which exhibits some of the highest known rates of net diversification in plants. Given that incomplete taxon sampling, background extinction, and lineage-specific variation in diversification rates can confound macroevolutionary inferences regarding the timing and mechanisms of cladogenesis, we used Bayesian relaxed clock phylogenetic analyses as well as MEDUSA and BiSSE birth–death likelihood models of diversification, to evaluate the evolutionary patterns of lineage accumulation in Lupinus. We identified 3 significant shifts to increased rates of net diversification (r) relative to background levels in the genus (r = 0.18–0.48 lineages/myr). The primary shift occurred approximately 4.6 Ma (r = 0.48–1.76) in the montane regions of western North America, followed by a secondary shift approximately 2.7 Ma (r = 0.89–3.33) associated with range expansion and diversification of allopatrically distributed sister clades in the Mexican highlands and Andes. We also recovered evidence for a third independent shift approximately 6.5 Ma at the base of a lower elevation eastern South American grassland and campo rupestre clade (r = 0.36–1.33). Bayesian ancestral state reconstructions and BiSSE likelihood analyses of correlated diversification indicated that increased rates of speciation are strongly associated with the derived evolution of perennial life history and invasion of montane ecosystems. Although we currently lack hard evidence for “replicate adaptive radiations” in the sense of convergent morphological and ecological trajectories among species in different clades, these results are consistent with the hypothesis that iteroparity functioned as an adaptive key innovation, providing a mechanism for range expansion and rapid divergence in upper elevation regions across much of the New World. PMID:22228799

Diversification of Angraecum (Orchidaceae, Vandeae) in Madagascar: Revised Phylogeny Reveals Species Accumulation through Time Rather than Rapid Radiation.

PubMed

Andriananjamanantsoa, Herinandrianina N; Engberg, Shannon; Louis, Edward E; Brouillet, Luc

Angraecum is the largest genus of subtribe Angraecinae (Orchidaceae) with about 221 species. Madagascar is the center of the diversity for the genus with ca. 142 species, of which 90% are endemic. The great morphological diversity associated with species diversification in the genus on the island of Madagascar offers valuable insights for macroevolutionary studies. Phylogenies of the Angraecinae have been published but a lack of taxon and character sampling and their limited taxonomic resolution limit their uses for macroevolutionary studies. We present a new phylogeny of Angraecum based on chloroplast sequence data (matk, rps16, trnL), nuclear ribosomal (ITS2) and 39 morphological characters from 194 Angraecinae species of which 69 were newly sampled. Using this phylogeny, we evaluated the monophyly of the sections of Angraecum as defined by Garay and investigated the patterns of species diversification within the genus. We used maximum parsimony and bayesian analyses to generate phylogenetic trees and dated divergence times of the phylogeny. We analyzed diversification patterns within Angraecinae and Angraecum with an emphasis on four floral characters (flower color, flower size, labellum position, spur length) using macroevolutionary models to evaluate which characters or character states are associated with speciation rates, and inferred ancestral states of these characters. The phylogenetic analysis showed the polyphyly of Angraecum sensu lato and of all Angraecum sections except sect. Hadrangis, and that morphology can be consistent with the phylogeny. It appeared that the characters (flower color, flower size, spur length) formerly used by many authors to delineate Angraecum groups were insufficient to do so. However, the newly described character, position of the labellum (uppermost and lowermost), was the main character delimiting clades within a monophyletic Angraecum sensu stricto. This character also appeared to be associated with speciation rates in Angraecum. The macroevolutionary model-based phylogeny failed to detect shifts in diversification that could be associated directly with morphological diversification. Diversification in Angraecum resulted from gradual species accumulation through time rather than from rapid radiation, a diversification pattern often encountered in tropical rain forests.

The philosophical "mind-body problem" and its relevance for the relationship between psychiatry and the neurosciences.

PubMed

Van Oudenhove, Lukas; Cuypers, Stefaan E

2010-01-01

Parallel to psychiatry, "philosophy of mind" investigates the relationship between mind (mental domain) and body/brain (physical domain). Unlike older forms of philosophy of mind, contemporary analytical philosophy is not exclusively based on introspection and conceptual analysis, but also draws upon the empirical methods and findings of the sciences. This article outlines the conceptual framework of the "mind-body problem" as formulated in contemporary analytical philosophy and argues that this philosophical debate has potentially far-reaching implications for psychiatry as a clinical-scientific discipline, especially for its own autonomy and its relationship to neurology/neuroscience. This point is illustrated by a conceptual analysis of the five principles formulated in Kandel's 1998 article "A New Intellectual Framework for Psychiatry." Kandel's position in the philosophical mind-body debate is ambiguous, ranging from reductive physicalism (psychophysical identity theory) to non-reductive physicalism (in which the mental "supervenes" on the physical) to epiphenomenalist dualism or even emergent dualism. We illustrate how these diverging interpretations result in radically different views on the identity of psychiatry and its relationship with the rapidly expanding domain of neurology/neuroscience.

Adaptive evolution and functional constraint at TLR4 during the secondary aquatic adaptation and diversification of cetaceans.

PubMed

Shen, Tong; Xu, Shixia; Wang, Xiaohong; Yu, Wenhua; Zhou, Kaiya; Yang, Guang

2012-03-24

Cetaceans (whales, dolphins and porpoises) are a group of adapted marine mammals with an enigmatic history of transition from terrestrial to full aquatic habitat and rapid radiation in waters around the world. Throughout this evolution, the pathogen stress-response proteins must have faced challenges from the dramatic change of environmental pathogens in the completely different ecological niches cetaceans occupied. For this reason, cetaceans could be one of the most ideal candidate taxa for studying evolutionary process and associated driving mechanism of vertebrate innate immune systems such as Toll-like receptors (TLRs), which are located at the direct interface between the host and the microbial environment, act at the first line in recognizing specific conserved components of microorganisms, and translate them rapidly into a defense reaction. We used TLR4 as an example to test whether this traditionally regarded pattern recognition receptor molecule was driven by positive selection across cetacean evolutionary history. Overall, the lineage-specific selection test showed that the dN/dS (ω) values along most (30 out of 33) examined cetartiodactylan lineages were less than 1, suggesting a common effect of functional constraint. However, some specific codons made radical changes, fell adjacent to the residues interacting with lipopolysaccharides (LPS), and showed parallel evolution between independent lineages, suggesting that TLR4 was under positive selection. Especially, strong signatures of adaptive evolution on TLR4 were identified in two periods, one corresponding to the early evolutionary transition of the terrestrial ancestors of cetaceans from land to semi-aquatic (represented by the branch leading to whale + hippo) and from semi-aquatic to full aquatic (represented by the ancestral branch leading to cetaceans) habitat, and the other to the rapid diversification and radiation of oceanic dolphins. This is the first study thus far to characterize the TLR gene in cetaceans. Our data present evidences that cetacean TLR4 has undergone adaptive evolution against the background of purifying selection in response to the secondary aquatic adaptation and rapid diversification in the sea. It is suggested that microbial pathogens in different environments are important factors that promote adaptive changes at cetacean TLR4 and new functions of some amino acid sites specialized for recognizing pathogens in dramatically contrasted environments to enhance the fitness for the adaptation and survival of cetaceans.

Phylogeography and diversification history of the day-gecko genus Phelsuma in the Seychelles islands.

PubMed

Rocha, Sara; Posada, David; Harris, D James

2013-01-05

Lying in a shallow continental shelf cyclically affected by oscillating sea levels since the Miocene, the Seychelles islands are particularly interesting for evolutionary studies. Recent molecular studies are generating an emerging picture of the origin of its biota, yet very little is known regarding their phylogeographic structure or on the factors promoting diversification within the archipelago. Here we aimed to obtain a detailed depiction of the genetic structure and evolution of one of the most widespread vertebrate groups in the archipelago: the day-geckos of the genus Phelsuma. In parallel, we aimed to infer divergence times between species and subspecies, testing a long-standing hypothesis that argues for different time since sympatry between species as the cause of their different morphological differentiation across the archipelago. Molecular data corroborated the existence of two main lineages, corresponding to the two currently recognized species. Divergences between species likely date back to the Mio-Pliocene, while more recent, Pleistocenic, divergences are suggested within each species. Populations from outer islands share mtDNA haplotypes with inner island populations, suggesting very recent dispersals (or introductions). We found no evidence of current gene flow between species, but results pointed to the possibility of gene flow between (now allopatric) subspecies. Time estimates suggest a synchronous divergence within each species (between island groups). The geographic patterns of genetic variation agree with previous taxonomic subdivisions within each species and the origin of outer islands populations is clearly tracked. The similar intraspecific divergence time estimates obtained suggest that the differential body-size differentiation between species within each group of islands may be driven by factors other than character displacement proportional to time since sympatry, as previously suggested. These factors could include different habitats/resources available within each island group, niche differentiation and/or character displacement. We also bring again into consideration the hypothesis of body size being influenced by the distribution of native vegetation and social systems within this group, although it remains to be tested. Our results highlight not only the necessity of clarifying the role of ecology and interspecific interactions in this group's morphological diversification and community assemblage, but also the importance of co-evolutionary mechanisms and their importance for appropriate conservation of island biodiversity. Further, we provide a detailed description of the phylogeographic structure of these taxa across these islands, which still remain poorly characterized in this respect.

Adaptive evolution and functional constraint at TLR4 during the secondary aquatic adaptation and diversification of cetaceans

PubMed Central

2012-01-01

Background Cetaceans (whales, dolphins and porpoises) are a group of adapted marine mammals with an enigmatic history of transition from terrestrial to full aquatic habitat and rapid radiation in waters around the world. Throughout this evolution, the pathogen stress-response proteins must have faced challenges from the dramatic change of environmental pathogens in the completely different ecological niches cetaceans occupied. For this reason, cetaceans could be one of the most ideal candidate taxa for studying evolutionary process and associated driving mechanism of vertebrate innate immune systems such as Toll-like receptors (TLRs), which are located at the direct interface between the host and the microbial environment, act at the first line in recognizing specific conserved components of microorganisms, and translate them rapidly into a defense reaction. Results We used TLR4 as an example to test whether this traditionally regarded pattern recognition receptor molecule was driven by positive selection across cetacean evolutionary history. Overall, the lineage-specific selection test showed that the dN/dS (ω) values along most (30 out of 33) examined cetartiodactylan lineages were less than 1, suggesting a common effect of functional constraint. However, some specific codons made radical changes, fell adjacent to the residues interacting with lipopolysaccharides (LPS), and showed parallel evolution between independent lineages, suggesting that TLR4 was under positive selection. Especially, strong signatures of adaptive evolution on TLR4 were identified in two periods, one corresponding to the early evolutionary transition of the terrestrial ancestors of cetaceans from land to semi-aquatic (represented by the branch leading to whale + hippo) and from semi-aquatic to full aquatic (represented by the ancestral branch leading to cetaceans) habitat, and the other to the rapid diversification and radiation of oceanic dolphins. Conclusions This is the first study thus far to characterize the TLR gene in cetaceans. Our data present evidences that cetacean TLR4 has undergone adaptive evolution against the background of purifying selection in response to the secondary aquatic adaptation and rapid diversification in the sea. It is suggested that microbial pathogens in different environments are important factors that promote adaptive changes at cetacean TLR4 and new functions of some amino acid sites specialized for recognizing pathogens in dramatically contrasted environments to enhance the fitness for the adaptation and survival of cetaceans. PMID:22443485

On portfolio risk diversification

NASA Astrophysics Data System (ADS)

Takada, Hellinton H.; Stern, Julio M.

2017-06-01

The first portfolio risk diversification strategy was put into practice by the All Weather fund in 1996. The idea of risk diversification is related to the risk contribution of each available asset class or investment factor to the total portfolio risk. The maximum diversification or the risk parity allocation is achieved when the set of risk contributions is given by a uniform distribution. Meucci (2009) introduced the maximization of the Rényi entropy as part of a leverage constrained optimization problem to achieve such diversified risk contributions when dealing with uncorrelated investment factors. A generalization of the risk parity is the risk budgeting when there is a prior for the distribution of the risk contributions. Our contribution is the generalization of the existent optimization frameworks to be able to solve the risk budgeting problem. In addition, our framework does not possess any leverage constraint.

Big bang in the evolution of extant malaria parasites.

PubMed

Hayakawa, Toshiyuki; Culleton, Richard; Otani, Hiroto; Horii, Toshihiro; Tanabe, Kazuyuki

2008-10-01

Malaria parasites (genus Plasmodium) infect all classes of terrestrial vertebrates and display host specificity in their infections. It is therefore assumed that malaria parasites coevolved intimately with their hosts. Here, we propose a novel scenario of malaria parasite-host coevolution. A phylogenetic tree constructed using the malaria parasite mitochondrial genome reveals that the extant primate, rodent, bird, and reptile parasite lineages rapidly diverged from a common ancestor during an evolutionary short time period. This rapid diversification occurred long after the establishment of the primate, rodent, bird, and reptile host lineages, which implies that host-switch events contributed to the rapid diversification of extant malaria parasite lineages. Interestingly, the rapid diversification coincides with the radiation of the mammalian genera, suggesting that adaptive radiation to new mammalian hosts triggered the rapid diversification of extant malaria parasite lineages.

Brain shape convergence in the adaptive radiation of New World monkeys

PubMed Central

Aristide, Leandro; dos Reis, Sergio Furtado; Machado, Alessandra C.; Lima, Inaya; Lopes, Ricardo T.; Perez, S. Ivan

2016-01-01

Primates constitute one of the most diverse mammalian clades, and a notable feature of their diversification is the evolution of brain morphology. However, the evolutionary processes and ecological factors behind these changes are largely unknown. In this work, we investigate brain shape diversification of New World monkeys during their adaptive radiation in relation to different ecological dimensions. Our results reveal that brain diversification in this clade can be explained by invoking a model of adaptive peak shifts to unique and shared optima, defined by a multidimensional ecological niche hypothesis. Particularly, we show that the evolution of convergent brain phenotypes may be related to ecological factors associated with group size (e.g., social complexity). Together, our results highlight the complexity of brain evolution and the ecological significance of brain shape changes during the evolutionary diversification of a primate clade. PMID:26858427

A multilocus evaluation of ermine (Mustela erminea) across the Holarctic, testing hypotheses of Pleistocene diversification in response to climate change

USGS Publications Warehouse

Dawson, Natalie G.; Hope, Andrew G.; Talbot, Sandra L.; Cook, Joseph A.

2013-01-01

Aim: We examined data for ermine (Mustela erminea) to test two sets of diversification hypotheses concerning the number and location of late Pleistocene refugia, the timing and mode of diversification, and the evolutionary influence of insularization. Location: Temperate and sub-Arctic Northern Hemisphere. Methods: We used up to two mitochondrial and four nuclear loci from 237 specimens for statistical phylogeographical and demographic analyses. Coalescent species-tree estimation used a Bayesian approach for clade divergence based on external mutation rate calibrations. Approximate Bayesian methods were used to assess population size, timing of divergence and gene flow. Results: Limited structure coupled with evidence of population growth across broad regions, including previously ice-covered areas, indicated expansion from multiple centres of differentiation, but high endemism along the North Pacific coast (NPC). A bifurcating model of diversification with recent growth spanning three glacial cycles best explained the empirical data. Main conclusions: A newly identified clade in North America indicated a fourth refugial area for ermine. The shallow coalescence of all extant ermine reflects a recent history of diversification overlying a deeper fossil record. Post-glacial colonization has led to potential contact zones for multiple lineages in north-western North America. A model of diversification of ermine accompanied by recent gene flow was marginally less well supported than a model of divergence of major clades in response to the most recent glacial cycles.

Income diversification and risk for fishermen.

PubMed

Kasperski, Stephen; Holland, Daniel S

2013-02-05

Catches and prices from many fisheries exhibit high interannual variability, leading to variability in the income derived by fishery participants. The economic risk posed by this may be mitigated in some cases if individuals participate in several different fisheries, particularly if revenues from those fisheries are uncorrelated or vary asynchronously. We construct indices of gross income diversification from fisheries at the level of individual vessels and find that the income of the current fleet of vessels on the US West Coast and in Alaska is less diverse than at any point in the past 30 y. We also find a dome-shaped relationship between the variability of individuals' income and income diversification, which implies that a small amount of diversification does not reduce income risk but that higher levels of diversification can substantially reduce the variability of income from fishing. Moving from a single fishery strategy to a 50-25-25 split in revenues reduces the expected coefficient of variation of gross revenues between 24% and 65% for the vessels included in this study. The increasing access restrictions in many marine fisheries through license reductions and moratoriums have the potential to limit fishermen's ability to diversify their income risk across multiple fisheries. Catch share programs often result in consolidation initially and may reduce diversification. However, catch share programs also make it feasible for fishermen to build a portfolio of harvest privileges and potentially reduce their income risk. Therefore, catch share programs create both threats and opportunities for fishermen wishing to maintain diversified fishing strategies.

Explosive ice age diversification of kiwi.

PubMed

Weir, Jason T; Haddrath, Oliver; Robertson, Hugh A; Colbourne, Rogan M; Baker, Allan J

2016-09-20

Molecular dating largely overturned the paradigm that global cooling during recent Pleistocene glacial cycles resulted in a burst of species diversification although some evidence exists that speciation was commonly promoted in habitats near the expanding and retracting ice sheets. Here, we used a genome-wide dataset of more than half a million base pairs of DNA to test for a glacially induced burst of diversification in kiwi, an avian family distributed within several hundred kilometers of the expanding and retracting glaciers of the Southern Alps of New Zealand. By sampling across the geographic range of the five kiwi species, we discovered many cryptic lineages, bringing the total number of kiwi taxa that currently exist to 11 and the number that existed just before human arrival to 16 or 17. We found that 80% of kiwi diversification events date to the major glacial advances of the Middle and Late Pleistocene. During this period, New Zealand was repeatedly fragmented by glaciers into a series of refugia, with the tiny geographic ranges of many kiwi lineages currently distributed in areas adjacent to these refugia. Estimates of effective population size through time show a dramatic bottleneck during the last glacial cycle in all but one kiwi lineage, as expected if kiwi were isolated in glacially induced refugia. Our results support a fivefold increase in diversification rates during key glacial periods, comparable with levels observed in classic adaptive radiations, and confirm that at least some lineages distributed near glaciated regions underwent rapid ice age diversification.

Paraphyly changes understanding of timing and tempo of diversification in subtribe Hakeinae (Proteaceae), a giant Australian plant radiation.

PubMed

Mast, Austin R; Olde, Peter M; Makinson, Robert O; Jones, Eric; Kubes, Amanda; Miller, Eliot T; Weston, Peter H

2015-10-01

Subtribe Hakeinae (526 spp.) represents a large Australian plant radiation central to our understanding of that flora's evolution and ecology. It contains Grevillea-the third largest plant genus in Australia and a group inferred to have among the highest diversification rates in the angiosperms. However, we lack a robust phylogenetic framework for understanding subtribe Hakeinae and recognize that Grevillea lacks an unambiguous synapomorphy supporting its monophyly. We used four plastid and one nuclear DNA region from a taxonomically even sampling of a third of the species to infer a time-calibrated phylogeny of Hakeinae and absolute diversification rates of major clades. We developed the R package addTaxa to add unsampled taxa to the tree for diversification rate inference. Grevillea is paraphyletic with respect to Hakea and Finschia. Under most parameter combinations, Hakea contains the major clade with the highest diversification rate in Hakeinae, rather than Grevillea. The crown age of the Grevillea+Hakea+Finschia crown group is about double that of prior estimates. We demonstrate that the paraphyly of Grevillea considerably enlarges the number of Australian descendants from its most recent common ancestor but has also misled investigators who considered a single operational taxonomic unit as adequate to represent the genus for inferences of diversification rate and timing. Our time-calibrated phylogeny can form the basis of future evolutionary, comparative ecology, and biogeography studies involving this large Australian plant radiation, as well as nomenclatural changes. © 2015 Botanical Society of America.

Diversification of clearwing butterflies with the rise of the Andes.

PubMed

De-Silva, Donna Lisa; Elias, Marianne; Willmott, Keith; Mallet, James; Day, Julia J

2016-01-01

Despite the greatest butterfly diversity on Earth occurring in the Neotropical Andes and Amazonia, there is still keen debate about the origins of this exceptional biota. A densely sampled calibrated phylogeny for a widespread butterfly subtribe, Oleriina (Nymphalidae: Ithomiini) was used to estimate the origin, colonization history and diversification of this species-rich group. Neotropics. Ancestral elevation and biogeographical ranges were reconstructed using data generated from detailed range maps and applying the dispersal-extinction-cladogenesis model using stratified palaeogeographical time slice matrices. The pattern of diversification through time was examined by comparing constant and variable rate models. We also tested the hypothesis that a change in elevation is associated with speciation. The Oleriina likely originated in the Andes in the Early to Middle Miocene and rapidly diversified to include four genera all of which also originated in the Andes. These clades, together with four species groups, experienced varying spatial and temporal patterns of diversification. An overall early burst and decreasing diversification rate is identified, and this pattern is reflected for most subclades. Changes in the palaeogeological landscape, particularly the prolonged uplift of the Andes, had a profound impact on the diversification of the subtribe. The Oleriina mostly remained within the Andes and vicariant speciation resulted in some instances. Dynamic dispersal occurred with the disappearance of geological barriers such as the Acre System and the subtribe exploited newly available habitats. Our results confirm the role of the Andean uplift in the evolution of Neotropical biodiversity.

Diversification of C(4) grasses (Poaceae) does not coincide with their ecological dominance.

PubMed

Bouchenak-Khelladi, Yanis; Slingsby, Jasper A; Verboom, G Anthony; Bond, William J

2014-02-01

The radiation of a lineage and its rise to ecological dominance are distinct phenomena and driven by different processes. For example, paleoecological data has been used to show that the Cretaceous angiosperm radiation did not coincide with their rise to dominance. Using a phylogenetic approach, we here explored the evolution of C4 grasses and evaluated whether the diversification of this group and its rise to ecological dominance in the late Miocene were decoupled. We assembled a matrix including 675 grass species of the PACMAD clade and 2784 characters (ITS and ndhF) to run a molecular dating analysis using three fossils as reference calibrations. We coded species as C3 vs. C4 and reconstructed ancestral states under maximum likelihood. We used the program BiSSE to test whether rates of diversification are correlated with photosynthetic pathway and whether the radiation of C4 lineages preceded or coincided with their rise to ecological dominance from ∼10 Ma. C4 grass lineages first originated around 35 Ma at the time of the Eocene-Oligocene transition. Accelerated diversification of C4 lineages did not coincide with their rise to ecological dominance. C4-dominated grasslands have expanded only since the Late Miocene and Pliocene. The initial diversification of their biotic elements can be tracked back as far as the Eocene-Oligocene transition. We suggest that shifts in taxonomic diversification and ecological dominance were stimulated by different factors, as in the case of the early angiosperms in the Cretaceous.

Evaluating mechanisms of diversification in a Guineo-Congolian tropical forest frog using demographic model selection.

PubMed

Portik, Daniel M; Leaché, Adam D; Rivera, Danielle; Barej, Michael F; Burger, Marius; Hirschfeld, Mareike; Rödel, Mark-Oliver; Blackburn, David C; Fujita, Matthew K

2017-10-01

The accumulation of biodiversity in tropical forests can occur through multiple allopatric and parapatric models of diversification, including forest refugia, riverine barriers and ecological gradients. Considerable debate surrounds the major diversification process, particularly in the West African Lower Guinea forests, which contain a complex geographic arrangement of topographic features and historical refugia. We used genomic data to investigate alternative mechanisms of diversification in the Gaboon forest frog, Scotobleps gabonicus, by first identifying population structure and then performing demographic model selection and spatially explicit analyses. We found that a majority of population divergences are best explained by allopatric models consistent with the forest refugia hypothesis and involve divergence in isolation with subsequent expansion and gene flow. These population divergences occurred simultaneously and conform to predictions based on climatically stable regions inferred through ecological niche modelling. Although forest refugia played a prominent role in the intraspecific diversification of S. gabonicus, we also find evidence for potential interactions between landscape features and historical refugia, including major rivers and elevational barriers such as the Cameroonian Volcanic Line. We outline the advantages of using genomewide variation in a model-testing framework to distinguish between alternative allopatric hypotheses, and the pitfalls of limited geographic and molecular sampling. Although phylogeographic patterns are often species-specific and related to life-history traits, additional comparative studies incorporating genomic data are necessary for separating shared historical processes from idiosyncratic responses to environmental, climatic and geological influences on diversification. © 2017 John Wiley & Sons Ltd.

Income diversification and risk for fishermen

PubMed Central

Kasperski, Stephen; Holland, Daniel S.

2013-01-01

Catches and prices from many fisheries exhibit high interannual variability, leading to variability in the income derived by fishery participants. The economic risk posed by this may be mitigated in some cases if individuals participate in several different fisheries, particularly if revenues from those fisheries are uncorrelated or vary asynchronously. We construct indices of gross income diversification from fisheries at the level of individual vessels and find that the income of the current fleet of vessels on the US West Coast and in Alaska is less diverse than at any point in the past 30 y. We also find a dome-shaped relationship between the variability of individuals' income and income diversification, which implies that a small amount of diversification does not reduce income risk but that higher levels of diversification can substantially reduce the variability of income from fishing. Moving from a single fishery strategy to a 50-25-25 split in revenues reduces the expected coefficient of variation of gross revenues between 24% and 65% for the vessels included in this study. The increasing access restrictions in many marine fisheries through license reductions and moratoriums have the potential to limit fishermen's ability to diversify their income risk across multiple fisheries. Catch share programs often result in consolidation initially and may reduce diversification. However, catch share programs also make it feasible for fishermen to build a portfolio of harvest privileges and potentially reduce their income risk. Therefore, catch share programs create both threats and opportunities for fishermen wishing to maintain diversified fishing strategies. PMID:23341621

Mass extinction in tetraodontiform fishes linked to the Palaeocene-Eocene thermal maximum.

PubMed

Arcila, Dahiana; Tyler, James C

2017-11-15

Integrative evolutionary analyses based upon fossil and extant species provide a powerful approach for understanding past diversification events and for assessing the tempo of evolution across the Tree of Life. Herein, we demonstrate the importance of integrating fossil and extant species for inferring patterns of lineage diversification that would otherwise be masked in analyses that examine only one source of evidence. We infer the phylogeny and macroevolutionary history of the Tetraodontiformes (triggerfishes, pufferfishes and allies), a group with one of the most extensive fossil records among fishes. Our analyses combine molecular and morphological data, based on an expanded matrix that adds newly coded fossil species and character states. Beyond confidently resolving the relationships and divergence times of tetraodontiforms, our diversification analyses detect a major mass-extinction event during the Palaeocene-Eocene Thermal Maximum (PETM), followed by a marked increase in speciation rates. This pattern is consistently obtained when fossil and extant species are integrated, whereas examination of the fossil occurrences alone failed to detect major diversification changes during the PETM. When taking into account non-homogeneous models, our analyses also detect a rapid lineage diversification increase in one of the groups (tetraodontoids) during the middle Miocene, which is considered a key period in the evolution of reef fishes associated with trophic changes and ecological opportunity. In summary, our analyses show distinct diversification dynamics estimated from phylogenies and the fossil record, suggesting that different episodes shaped the evolution of tetraodontiforms during the Cenozoic. © 2017 The Author(s).

Uplift-driven diversification in the Hengduan Mountains, a temperate biodiversity hotspot

PubMed Central

Xing, Yaowu; Ree, Richard H.

2017-01-01

A common hypothesis for the rich biodiversity found in mountains is uplift-driven diversification—that orogeny creates conditions favoring rapid in situ speciation of resident lineages. We tested this hypothesis in the context of the Qinghai–Tibetan Plateau (QTP) and adjoining mountain ranges, using the phylogenetic and geographic histories of multiple groups of plants to infer the tempo (rate) and mode (colonization versus in situ diversification) of biotic assembly through time and across regions. We focused on the Hengduan Mountains region, which in comparison with the QTP and Himalayas was uplifted more recently (since the late Miocene) and is smaller in area and richer in species. Time-calibrated phylogenetic analyses show that about 8 million y ago the rate of in situ diversification increased in the Hengduan Mountains, significantly exceeding that in the geologically older QTP and Himalayas. By contrast, in the QTP and Himalayas during the same period the rate of in situ diversification remained relatively flat, with colonization dominating lineage accumulation. The Hengduan Mountains flora was thus assembled disproportionately by recent in situ diversification, temporally congruent with independent estimates of orogeny. This study shows quantitative evidence for uplift-driven diversification in this region, and more generally, tests the hypothesis by comparing the rate and mode of biotic assembly jointly across time and space. It thus complements the more prevalent method of examining endemic radiations individually and could be used as a template to augment such studies in other biodiversity hotspots. PMID:28373546

[Internationalization, science and health: global regenerative medicine and the parallel markets].

PubMed

Acero, Liliana

2015-02-01

Regenerative medicine involves a paradigm change due to organism regeneration at cellular and tissue level - a controversial contemporary issue and difficult to regulate. This article presents a summary of the main scientific, economic, social and regulatory global trends, analyzed according to relevant theoretical dilemmas in medical anthropology and in the sociology of science and health. This is especially true of the construction of a 'collective frame of reference' on the new biological and ontological entities, the shaping of biological citizenship, and governance through uncertainty. Empirical evidence is also presented on a key aspect in regulation and governance, namely the emergence of a new transnational demand in health research through the establishment of parallel markets for ova and experimental cellular therapies. Qualitative data collected for a broader research paper is analyzed, as well as journal reviews and information gathered during interviews with international leaders. The paper concludes with a discussion on the importance on international governance of clinical trials and on further exploration, towards a multilevel harmonization of a diversity of normative practices.

Conservation of native Pacific trout diversity in western North America

USGS Publications Warehouse

Penaluna, Brooke E.; Abadía-Cardoso, Alicia; Dunham, Jason B.; García de León, Francisco J; Gresswell, Robert E.; Luna, Arturo Ruiz; Taylor, Eric B.; Shepard, Bradley B.; Al-Chokhachy, Robert K.; Muhlfeld, Clint C.; Bestgen, Kevin R.; Rogers, Kevin H.; Escalante, Marco A; Keeley, Ernest R; Temple, Gabriel; Williams, Jack E.; Matthews, Kathleen; Pierce, Ron; Mayden, Richard L.; Kovach, Ryan; Garza, John Carlos; Fausch, Kurt D.

2016-01-01

Pacific trout Oncorhynchus spp. in western North America are strongly valued in ecological, socioeconomic, and cultural views, and have been the subject of substantial research and conservation efforts. Despite this, the understanding of their evolutionary histories, overall diversity, and challenges to their conservation is incomplete. We review the state of knowledge on these important issues, focusing on Pacific trout in the genus Oncorhynchus. Although most research on salmonid fishes emphasizes Pacific salmon, we focus on Pacific trout because they share a common evolutionary history, and many taxa in western North America have not been formally described, particularly in the southern extent of their ranges. Research in recent decades has led to the revision of many hypotheses concerning the origin and diversification of Pacific trout throughout their range. Although there has been significant success at addressing past threats to Pacific trout, contemporary and future threats represented by nonnative species, land and water use activities, and climate change pose challenges and uncertainties. Ultimately, conservation of Pacific trout depends on how well these issues are understood and addressed, and on solutions that allow these species to coexist with a growing scope of human influences.

Mobile DNA and evolution in the 21st century

PubMed Central

2010-01-01

Scientific history has had a profound effect on the theories of evolution. At the beginning of the 21st century, molecular cell biology has revealed a dense structure of information-processing networks that use the genome as an interactive read-write (RW) memory system rather than an organism blueprint. Genome sequencing has documented the importance of mobile DNA activities and major genome restructuring events at key junctures in evolution: exon shuffling, changes in cis-regulatory sites, horizontal transfer, cell fusions and whole genome doublings (WGDs). The natural genetic engineering functions that mediate genome restructuring are activated by multiple stimuli, in particular by events similar to those found in the DNA record: microbial infection and interspecific hybridization leading to the formation of allotetraploids. These molecular genetic discoveries, plus a consideration of how mobile DNA rearrangements increase the efficiency of generating functional genomic novelties, make it possible to formulate a 21st century view of interactive evolutionary processes. This view integrates contemporary knowledge of the molecular basis of genetic change, major genome events in evolution, and stimuli that activate DNA restructuring with classical cytogenetic understanding about the role of hybridization in species diversification. PMID:20226073

Clade age and species richness are decoupled across the eukaryotic tree of life.

PubMed

Rabosky, Daniel L; Slater, Graham J; Alfaro, Michael E

2012-08-01

Explaining the dramatic variation in species richness across the tree of life remains a key challenge in evolutionary biology. At the largest phylogenetic scales, the extreme heterogeneity in species richness observed among different groups of organisms is almost certainly a function of many complex and interdependent factors. However, the most fundamental expectation in macroevolutionary studies is simply that species richness in extant clades should be correlated with clade age: all things being equal, older clades will have had more time for diversity to accumulate than younger clades. Here, we test the relationship between stem clade age and species richness across 1,397 major clades of multicellular eukaryotes that collectively account for more than 1.2 million described species. We find no evidence that clade age predicts species richness at this scale. We demonstrate that this decoupling of age and richness is unlikely to result from variation in net diversification rates among clades. At the largest phylogenetic scales, contemporary patterns of species richness are inconsistent with unbounded diversity increase through time. These results imply that a fundamentally different interpretative paradigm may be needed in the study of phylogenetic diversity patterns in many groups of organisms.

Evolutionary relationships among sympatric life history forms of Dolly Varden inhabiting the landlocked Kronotsky Lake, Kamchatka, and a neighboring anadromous population

USGS Publications Warehouse

Ostberg, C.O.; Pavlov, S.D.; Hauser, L.

2009-01-01

We investigated the evolutionary relationships among five sympatric morphs of Dolly Varden Salvelinus malma (white, Schmidti, longhead, river, and dwarf) inhabiting landlocked Kronotsky Lake on the Kamchatka Peninsula, Russia, and an anadromous population below the barrier waterfall on the outflowing Kronotsky River. Morphological analyses indicated phenotypic differentiation corresponding to preferred habitat, the longhead (a limnetic piscivorous morph) having a fusiform body, long jaw, and short fins and the Schmidti (a benthic morph) having a robust body, small jaw, and long fins. Analysis of molecular variance among the Kronotsky Lake morphs indicated that contemporary gene flow is restricted both among morphs within locations and among locations within morphs. Gene flow from Kronotsky Lake into the anadromous population also appears to be restricted. Our findings indicate that there are two divergent evolutionary lineages, one consisting of the white, Schmidti, river, and dwarf morphs and the other of the longhead morph and the anadromous population, which suggests that Kronotsky Lake was subject to separate waves of immigration. The Kronotsky Lake Dolly Varden morphs may represent an example of ecological speciation in progress, and we present a working hypothesis for the diversification of morphs within Kronotsky Lake.

A New 13 Million Year Old Gavialoid Crocodylian from Proto-Amazonian Mega-Wetlands Reveals Parallel Evolutionary Trends in Skull Shape Linked to Longirostry

PubMed Central

Salas-Gismondi, Rodolfo; Flynn, John J.; Baby, Patrice; Tejada-Lara, Julia V.; Claude, Julien; Antoine, Pierre-Olivier

2016-01-01

Gavialoid crocodylians are the archetypal longirostrine archosaurs and, as such, understanding their patterns of evolution is fundamental to recognizing cranial rearrangements and reconstructing adaptive pathways associated with elongation of the rostrum (longirostry). The living Indian gharial Gavialis gangeticus is the sole survivor of the group, thus providing unique evidence on the distinctive biology of its fossil kin. Yet phylogenetic relationships and evolutionary ecology spanning ~70 million-years of longirostrine crocodylian diversification remain unclear. Analysis of cranial anatomy of a new proto-Amazonian gavialoid, Gryposuchus pachakamue sp. nov., from the Miocene lakes and swamps of the Pebas Mega-Wetland System reveals that acquisition of both widely separated and protruding eyes (telescoped orbits) and riverine ecology within South American and Indian gavialoids is the result of parallel evolution. Phylogenetic and morphometric analyses show that, in association with longirostry, circumorbital bone configuration can evolve rapidly for coping with trends in environmental conditions and may reflect shifts in feeding strategy. Our results support a long-term radiation of the South American forms, with taxa occupying either extreme of the gavialoid morphospace showing preferences for coastal marine versus fluvial environments. The early biogeographic history of South American gavialoids was strongly linked to the northward drainage system connecting proto-Amazonian wetlands to the Caribbean region. PMID:27097031

A New 13 Million Year Old Gavialoid Crocodylian from Proto-Amazonian Mega-Wetlands Reveals Parallel Evolutionary Trends in Skull Shape Linked to Longirostry.

PubMed

Salas-Gismondi, Rodolfo; Flynn, John J; Baby, Patrice; Tejada-Lara, Julia V; Claude, Julien; Antoine, Pierre-Olivier

2016-01-01

Gavialoid crocodylians are the archetypal longirostrine archosaurs and, as such, understanding their patterns of evolution is fundamental to recognizing cranial rearrangements and reconstructing adaptive pathways associated with elongation of the rostrum (longirostry). The living Indian gharial Gavialis gangeticus is the sole survivor of the group, thus providing unique evidence on the distinctive biology of its fossil kin. Yet phylogenetic relationships and evolutionary ecology spanning ~70 million-years of longirostrine crocodylian diversification remain unclear. Analysis of cranial anatomy of a new proto-Amazonian gavialoid, Gryposuchus pachakamue sp. nov., from the Miocene lakes and swamps of the Pebas Mega-Wetland System reveals that acquisition of both widely separated and protruding eyes (telescoped orbits) and riverine ecology within South American and Indian gavialoids is the result of parallel evolution. Phylogenetic and morphometric analyses show that, in association with longirostry, circumorbital bone configuration can evolve rapidly for coping with trends in environmental conditions and may reflect shifts in feeding strategy. Our results support a long-term radiation of the South American forms, with taxa occupying either extreme of the gavialoid morphospace showing preferences for coastal marine versus fluvial environments. The early biogeographic history of South American gavialoids was strongly linked to the northward drainage system connecting proto-Amazonian wetlands to the Caribbean region.

Shape - but Not Size - Codivergence between Male and Female Copulatory Structures in Onthophagus Beetles

PubMed Central

Macagno, Anna L. M.; Pizzo, Astrid; Parzer, Harald F.; Palestrini, Claudia; Rolando, Antonio; Moczek, Armin P.

2011-01-01

Genitalia are among the fastest evolving morphological traits in arthropods. Among the many hypotheses aimed at explaining this observation, some explicitly or implicitly predict concomitant male and female changes of genital traits that interact during copulation (i.e., lock and key, sexual conflict, cryptic female choice and pleiotropy). Testing these hypotheses requires insights into whether male and female copulatory structures that physically interact during mating also affect each other's evolution and patterns of diversification. Here we compare and contrast size and shape evolution of male and female structures that are known to interact tightly during copulation using two model systems: (a) the sister species O. taurus (1 native, 3 recently established populations) and O. illyricus, and (b) the species-complex O. fracticornis-similis-opacicollis. Partial Least Squares analyses indicated very little to no correlation between size and shape of copulatory structures, both in males and females. Accordingly, comparing shape and size diversification patterns of genitalia within each sex showed that the two components diversify readily - though largely independently of each other - within and between species. Similarly, comparing patterns of divergence across sexes showed that relative sizes of male and female copulatory organs diversify largely independent of each other. However, performing this analysis for genital shape revealed a signature of parallel divergence. Our results therefore suggest that male and female copulatory structures that are linked mechanically during copulation may diverge in concert with respect to their shapes. Furthermore, our results suggest that genital divergence in general, and co-divergence of male and female genital shape in particular, can evolve over an extraordinarily short time frame. Results are discussed in the framework of the hypotheses that assume or predict concomitant evolutionary changes in male and female copulatory organs. PMID:22194942

Tol2 transposon-mediated transgenesis in the Midas cichlid (Amphilophus citrinellus) - towards understanding gene function and regulatory evolution in an ecological model system for rapid phenotypic diversification.

PubMed

Kratochwil, Claudius F; Sefton, Maggie M; Liang, Yipeng; Meyer, Axel

2017-11-23

The Midas cichlid species complex (Amphilophus spp.) is widely known among evolutionary biologists as a model system for sympatric speciation and adaptive phenotypic divergence within extremely short periods of time (a few hundred generations). The repeated parallel evolution of adaptive phenotypes in this radiation, combined with their near genetic identity, makes them an excellent model for studying phenotypic diversification. While many ecological and evolutionary studies have been performed on Midas cichlids, the molecular basis of specific phenotypes, particularly adaptations, and their underlying coding and cis-regulatory changes have not yet been studied thoroughly. For the first time in any New World cichlid, we use Tol2 transposon-mediated transgenesis in the Midas cichlid (Amphilophus citrinellus). By adapting existing microinjection protocols, we established an effective protocol for transgenesis in Midas cichlids. Embryos were injected with a Tol2 plasmid construct that drives enhanced green fluorescent protein (eGFP) expression under the control of the ubiquitin promoter. The transgene was successfully integrated into the germline, driving strong ubiquitous expression of eGFP in the first transgenic Midas cichlid line. Additionally, we show transient expression of two further transgenic constructs, ubiquitin::tdTomato and mitfa::eGFP. Transgenesis in Midas cichlids will facilitate further investigation of the genetic basis of species-specific traits, many of which are adaptations. Transgenesis is a versatile tool not only for studying regulatory elements such as promoters and enhancers, but also for testing gene function through overexpression of allelic gene variants. As such, it is an important first step in establishing the Midas cichlid as a powerful model for studying adaptive coding and non-coding changes in an ecological and evolutionary context.

Processes Driving the Adaptive Radiation of a Tropical Tree ( Diospyros , Ebenaceae) in New Caledonia, a Biodiversity Hotspot

PubMed Central

Paun, Ovidiu; Turner, Barbara; Trucchi, Emiliano; Munzinger, Jérôme; Chase, Mark W.; Samuel, Rosabelle

2016-01-01

Abstract Due to its special geological history, the New Caledonian Archipelago is a mosaic of soil types, and in combination with climatic conditions this results in a heterogeneous environment across relatively small distances. A group of over 20 endemic species of Diospyros (Ebenaceae) has rapidly and recently radiated on the archipelago after a single long-distance dispersal event. Most of the Diospyros species in the radiating group are morphologically and ecologically well differentiated, but they exhibit low levels of DNA variability. To investigate the processes that shaped the diversification of this group we employed restriction site associated DNA sequencing (RADseq). Over 8400 filtered SNPs generally confirm species delimitations and produce a well-supported phylogenetic tree. Our analyses document local introgression, but only a limited potential for gene flow over longer distances. The phylogenetic relationships point to an early regional clustering among populations and species, indicating that allopatric speciation with respect to macrohabitat (i.e., climatic conditions) may have had a role in the initial differentiation within the group. A later, more rapid radiation involved divergence with respect to microhabitat (i.e., soil preference). Several sister species in the group show a parallel divergence in edaphic preference. Searches for genomic regions that are systematically differentiated in this replicated phenotypic divergence pointed to loci potentially involved in ion binding and cellular transport. These loci appear meaningful in the context of adaptations to soil types that differ in heavy-metal and mineral content. Identical nucleotide changes affected only two of these loci, indicating that introgression may have played a limited role in their evolution. Our results suggest that both allopatric diversification and (parapatric) ecological divergence shaped successive rounds of speciation in the Diospyros radiation on New Caledonia. PMID:26430059

The assembly of montane biotas: linking Andean tectonics and climatic oscillations to independent regimes of diversification in Pionus parrots

PubMed Central

Ribas, Camila C; Moyle, Robert G; Miyaki, Cristina Y; Cracraft, Joel

2007-01-01

The mechanisms underlying the taxonomic assembly of montane biotas are still poorly understood. Most hypotheses have assumed that the diversification of montane biotas is loosely coupled to Earth history and have emphasized instead the importance of multiple long-distance dispersal events and biotic interactions, particularly competition, for structuring the taxonomic composition and distribution of montane biotic elements. Here we use phylogenetic and biogeographic analyses of species in the parrot genus Pionus to demonstrate that standing diversity within montane lineages is directly attributable to events of Earth history. Phylogenetic relationships confirm three independent biogeographic disjunctions between montane lineages, on one hand, and lowland dry-forest/wet-forest lineages on the other. Temporal estimates of lineage diversification are consistent with the interpretation that the three lineages were transported passively to high elevations by mountain building, and that subsequent diversification within the Andes was driven primarily by Pleistocene climatic oscillations and their large-scale effects on habitat change. These results support a mechanistic link between diversification and Earth history and have general implications for explaining high altitudinal disjuncts and the origin of montane biotas. PMID:17686731

Deep under the sea: unraveling the evolutionary history of the deep-sea squat lobster Paramunida (Decapoda, Munididae).

PubMed

Cabezas, Patricia; Sanmartín, Isabel; Paulay, Gustav; Macpherson, Enrique; Machordom, Annie

2012-06-01

The diversification of Indo-Pacific marine fauna has long captivated the attention of evolutionary biologists. Previous studies have mainly focused on coral reef or shallow water-associated taxa. Here, we present the first attempt to reconstruct the evolutionary history--phylogeny, diversification, and biogeography--of a deep-water lineage. We sequenced the molecular markers 16S, COI, ND1, 18S, and 28S for nearly 80% of the nominal species of the squat lobster genus Paramunida. Analyses of the molecular phylogeny revealed an accelerated diversification in the late Oligocene-Miocene followed by a slowdown in the rate of lineage accumulation over time. A parametric biogeographical reconstruction showed the importance of the southwest Pacific area, specifically the island arc of Fiji, Tonga, Vanuatu, Wallis, and Futuna, for diversification of squat lobsters, probably associated with the global warming, high tectonic activity, and changes in oceanic currents that took place in this region during the Oligocene-Miocene period. These results add strong evidence to the hypothesis that the Neogene was a period of major diversification for marine organisms in both shallow and deep waters. © 2012 The Author(s). Evolution © 2012 The Society for the Study of Evolution.

A Bayesian framework to estimate diversification rates and their variation through time and space

PubMed Central

2011-01-01

Background Patterns of species diversity are the result of speciation and extinction processes, and molecular phylogenetic data can provide valuable information to derive their variability through time and across clades. Bayesian Markov chain Monte Carlo methods offer a promising framework to incorporate phylogenetic uncertainty when estimating rates of diversification. Results We introduce a new approach to estimate diversification rates in a Bayesian framework over a distribution of trees under various constant and variable rate birth-death and pure-birth models, and test it on simulated phylogenies. Furthermore, speciation and extinction rates and their posterior credibility intervals can be estimated while accounting for non-random taxon sampling. The framework is particularly suitable for hypothesis testing using Bayes factors, as we demonstrate analyzing dated phylogenies of Chondrostoma (Cyprinidae) and Lupinus (Fabaceae). In addition, we develop a model that extends the rate estimation to a meta-analysis framework in which different data sets are combined in a single analysis to detect general temporal and spatial trends in diversification. Conclusions Our approach provides a flexible framework for the estimation of diversification parameters and hypothesis testing while simultaneously accounting for uncertainties in the divergence times and incomplete taxon sampling. PMID:22013891

Unparalleled rates of species diversification in Europe

PubMed Central

Valente, Luis M.; Savolainen, Vincent; Vargas, Pablo

2010-01-01

The most rapid species radiations have been reported from ‘evolutionary laboratories’, such as the Andes and the Cape of South Africa, leading to the prevailing view that diversification elsewhere has not been as dramatic. However, few studies have explicitly assessed rates of diversification in northern regions such as Europe. Here, we show that carnations (Dianthus, Caryophyllaceae), a well-known group of plants from temperate Eurasia, have diversified at the most rapid rate ever reported in plants or terrestrial vertebrates. Using phylogenetic methods, we found that the majority of species of carnations belong to a lineage that is remarkably species-rich in Europe, and arose at the rate of 2.2–7.6 species per million years. Unlike most previous studies that have inferred rates of diversification in young diverse groups, we use a conservative approach throughout that explicitly incorporates the uncertainties associated with phylogenetic inference, molecular dating and incomplete taxon sampling. We detected a shift in diversification rates of carnations coinciding with a period of increase in climatic aridity in the Pleistocene, suggesting a link between climate and biodiversity. This explosive radiation suggests that Europe, the continent with the world's best-studied flora, has been underestimated as a cradle of recent and rapid speciation. PMID:20106850

North Andean origin and diversification of the largest ithomiine butterfly genus

PubMed Central

Lisa De-Silva, Donna; Mota, Luísa L.; Chazot, Nicolas; Mallarino, Ricardo; Silva-Brandão, Karina L.; Piñerez, Luz Miryam Gómez; Freitas, André V.L.; Lamas, Gerardo; Joron, Mathieu; Mallet, James; Giraldo, Carlos E.; Uribe, Sandra; Särkinen, Tiina; Knapp, Sandra; Jiggins, Chris D.; Willmott, Keith R.; Elias, Marianne

2017-01-01

The Neotropics harbour the most diverse flora and fauna on Earth. The Andes are a major centre of diversification and source of diversity for adjacent areas in plants and vertebrates, but studies on insects remain scarce, even though they constitute the largest fraction of terrestrial biodiversity. Here, we combine molecular and morphological characters to generate a dated phylogeny of the butterfly genus Pteronymia (Nymphalidae: Danainae), which we use to infer spatial, elevational and temporal diversification patterns. We first propose six taxonomic changes that raise the generic species total to 53, making Pteronymia the most diverse genus of the tribe Ithomiini. Our biogeographic reconstruction shows that Pteronymia originated in the Northern Andes, where it diversified extensively. Some lineages colonized lowlands and adjacent montane areas, but diversification in those areas remained scarce. The recent colonization of lowland areas was reflected by an increase in the rate of evolution of species’ elevational ranges towards present. By contrast, speciation rate decelerated with time, with no extinction. The geological history of the Andes and adjacent regions have likely contributed to Pteronymia diversification by providing compartmentalized habitats and an array of biotic and abiotic conditions, and by limiting dispersal between some areas while promoting interchange across others. PMID:28387233

Convergence, recurrence and diversification of complex sperm traits in diving beetles (Dytiscidae)

PubMed Central

Higginson, Dawn M.; Miller, Kelly B.; Segraves, Kari A.; Pitnick, Scott

2013-01-01

Sperm display remarkable morphological diversity among even closely related species, a pattern that is widely attributed to postcopulatory sexual selection. Surprisingly few studies have used phylogenetic analyses to discern the details of evolutionary diversification in ornaments and armaments subject to sexual selection, and the origins of novel sperm traits and their subsequent modification are particularly poorly understood. Here we investigate sperm evolution in diving beetles (Dytiscidae), revealing dramatic diversification in flagellum length, head shape, presence of sperm heteromorphism, and the presence/type of sperm conjugation, an unusual trait where two or more sperm unite for motility or transport. Sperm conjugation was found to be the ancestral condition in diving beetles, with subsequent diversification into three forms, each exhibiting varying degrees of evolutionary loss, convergence and recurrence. Sperm head shape, but not length or heteromorphism, was found to evolve in a significantly correlated manner with conjugation, consistent with the different mechanisms of head alignment and binding required for the different forms of conjugation. Our study reveals that sperm morphological evolution is channeled along particular evolutionary pathways (i.e., conjugate form), yet subject to considerable diversification within those pathways through modification in sperm length, head shape and heteromorphism. PMID:22519797

Evolutionary origins and diversification of proteobacterial mutualists.

PubMed

Sachs, Joel L; Skophammer, Ryan G; Bansal, Nidhanjali; Stajich, Jason E

2014-01-22

Mutualistic bacteria infect most eukaryotic species in nearly every biome. Nonetheless, two dilemmas remain unresolved about bacterial-eukaryote mutualisms: how do mutualist phenotypes originate in bacterial lineages and to what degree do mutualists traits drive or hinder bacterial diversification? Here, we reconstructed the phylogeny of the hyperdiverse phylum Proteobacteria to investigate the origins and evolutionary diversification of mutualistic bacterial phenotypes. Our ancestral state reconstructions (ASRs) inferred a range of 34-39 independent origins of mutualist phenotypes in Proteobacteria, revealing the surprising frequency with which host-beneficial traits have evolved in this phylum. We found proteobacterial mutualists to be more often derived from parasitic than from free-living ancestors, consistent with the untested paradigm that bacterial mutualists most often evolve from pathogens. Strikingly, we inferred that mutualists exhibit a negative net diversification rate (speciation minus extinction), which suggests that mutualism evolves primarily via transitions from other states rather than diversification within mutualist taxa. Moreover, our ASRs infer that proteobacterial mutualist lineages exhibit a paucity of reversals to parasitism or to free-living status. This evolutionary conservatism of mutualism is contrary to long-standing theory, which predicts that selection should often favour mutants in microbial mutualist populations that exploit or abandon more slowly evolving eukaryotic hosts.

Adaptive Diversification Between Yellow Fever Virus West African and South American Lineages: A Genome-Wide Study.

PubMed

Li, Yan; Yang, Zexiao

2017-03-01

AbstractYellow fever virus (YFV) has emerged as the causative agent of a vector-borne disease with devastating mortality in the tropics of Africa and the Americas. YFV phylogenies indicate that the isolates collected from West Africa, East and Central Africa, and South America cluster into different lineages and the virus spread into the Americas from Africa. To determine the nature of genetic variation accompanying the intercontinental epidemic, we performed a genome-wide evolutionary study on the West African and South American lineages of YFV. Our results reveal that adaptive genetic diversification has occurred on viral nonstructural protein 5 (NS5), which is crucially required for viral genome replication, in the early epidemic phase of these currently circulating lineages. Furthermore, major amino acid changes relevant to the adaptive diversification generally cluster in different structural regions of NS5 in a lineage-specific manner. These results suggest that YFV has experienced adaptive diversification in the epidemic spread between the continents and shed insights into the genetic determinants of such diversification, which might be beneficial for understanding the emergence and re-emergence of yellow fever as an important global public health issue.

Signatures of microevolutionary processes in phylogenetic patterns.

PubMed

Costa, Carolina L N; Lemos-Costa, Paula; Marquitti, Flavia M D; Fernandes, Lucas D; Ramos, Marlon F; Schneider, David M; Martins, Ayana B; Aguiar, Marcus A M

2018-06-23

Phylogenetic trees are representations of evolutionary relationships among species and contain signatures of the processes responsible for the speciation events they display. Inferring processes from tree properties, however, is challenging. To address this problem we analysed a spatially-explicit model of speciation where genome size and mating range can be controlled. We simulated parapatric and sympatric (narrow and wide mating range, respectively) radiations and constructed their phylogenetic trees, computing structural properties such as tree balance and speed of diversification. We showed that parapatric and sympatric speciation are well separated by these structural tree properties. Balanced trees with constant rates of diversification only originate in sympatry and genome size affected both the balance and the speed of diversification of the simulated trees. Comparison with empirical data showed that most of the evolutionary radiations considered to have developed in parapatry or sympatry are in good agreement with model predictions. Even though additional forces other than spatial restriction of gene flow, genome size, and genetic incompatibilities, do play a role in the evolution of species formation, the microevolutionary processes modeled here capture signatures of the diversification pattern of evolutionary radiations, regarding the symmetry and speed of diversification of lineages.

North Andean origin and diversification of the largest ithomiine butterfly genus

NASA Astrophysics Data System (ADS)

Lisa de-Silva, Donna; Mota, Luísa L.; Chazot, Nicolas; Mallarino, Ricardo; Silva-Brandão, Karina L.; Piñerez, Luz Miryam Gómez; Freitas, André V. L.; Lamas, Gerardo; Joron, Mathieu; Mallet, James; Giraldo, Carlos E.; Uribe, Sandra; Särkinen, Tiina; Knapp, Sandra; Jiggins, Chris D.; Willmott, Keith R.; Elias, Marianne

2017-04-01

The Neotropics harbour the most diverse flora and fauna on Earth. The Andes are a major centre of diversification and source of diversity for adjacent areas in plants and vertebrates, but studies on insects remain scarce, even though they constitute the largest fraction of terrestrial biodiversity. Here, we combine molecular and morphological characters to generate a dated phylogeny of the butterfly genus Pteronymia (Nymphalidae: Danainae), which we use to infer spatial, elevational and temporal diversification patterns. We first propose six taxonomic changes that raise the generic species total to 53, making Pteronymia the most diverse genus of the tribe Ithomiini. Our biogeographic reconstruction shows that Pteronymia originated in the Northern Andes, where it diversified extensively. Some lineages colonized lowlands and adjacent montane areas, but diversification in those areas remained scarce. The recent colonization of lowland areas was reflected by an increase in the rate of evolution of species’ elevational ranges towards present. By contrast, speciation rate decelerated with time, with no extinction. The geological history of the Andes and adjacent regions have likely contributed to Pteronymia diversification by providing compartmentalized habitats and an array of biotic and abiotic conditions, and by limiting dispersal between some areas while promoting interchange across others.

Enemy at the gates: Rapid defensive trait diversification in an adaptive radiation of lizards.

PubMed

Broeckhoven, Chris; Diedericks, Genevieve; Hui, Cang; Makhubo, Buyisile G; Mouton, P le Fras N

2016-11-01

Adaptive radiation (AR), the product of rapid diversification of an ancestral species into novel adaptive zones, has become pivotal in our understanding of biodiversity. Although it has widely been accepted that predators may drive the process of AR by creating ecological opportunity (e.g., enemy-free space), the role of predators as selective agents in defensive trait diversification remains controversial. Using phylogenetic comparative methods, we provide evidence for an "early burst" in the diversification of antipredator phenotypes in Cordylinae, a relatively small AR of morphologically diverse southern African lizards. The evolution of body armor appears to have been initially rapid, but slowed down over time, consistent with the ecological niche-filling model. We suggest that the observed "early burst" pattern could be attributed to shifts in vulnerability to different types of predators (i.e., aerial versus terrestrial) associated with thermal habitat partitioning. These results provide empirical evidence supporting the hypothesis that predators or the interaction therewith might be key components of ecological opportunity, although the way in which predators influence morphological diversification requires further study. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Parallels between astronauts and terrestrial patients - Taking physiotherapy rehabilitation "To infinity and beyond".

PubMed

Hides, Julie; Lambrecht, Gunda; Ramdharry, Gita; Cusack, Rebecca; Bloomberg, Jacob; Stokes, Maria

2017-01-01

Exposure to the microgravity environment induces physiological changes in the cardiovascular, musculoskeletal and sensorimotor systems in healthy astronauts. As space agencies prepare for extended duration missions, it is difficult to predict the extent of the effects that prolonged exposure to microgravity will have on astronauts. Prolonged bed rest is a model used by space agencies to simulate the effects of spaceflight on the human body, and bed rest studies have provided some insights into the effects of immobilisation and inactivity. Whilst microgravity exposure is confined to a relatively small population, on return to Earth, the physiological changes seen in astronauts parallel many changes routinely seen by physiotherapists on Earth in people with low back pain (LBP), muscle wasting diseases, exposure to prolonged bed rest, elite athletes and critically ill patients in intensive care. The medical operations team at the European Space Agency are currently involved in preparing astronauts for spaceflight, advising on exercises whilst astronauts are on the International Space Station, and reconditioning astronauts following their return. There are a number of parallels between this role and contemporary roles performed by physiotherapists working with elite athletes and muscle wasting conditions. This clinical commentary will draw parallels between changes which occur to the neuromuscular system in the absence of gravity and conditions which occur on Earth. Implications for physiotherapy management of astronauts and terrestrial patients will be discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Pharmacophore mapping in the laulimalide series: total synthesis of a vinylogue for a late-stage metathesis diversification strategy.

PubMed

Wender, Paul A; Hilinski, Michael K; Skaanderup, Philip R; Soldermann, Nicolas G; Mooberry, Susan L

2006-08-31

An efficient synthesis of the macrocyclic core of laulimalide with a pendant vinyl group at C20 is described, allowing for late-stage introduction of various side chains through a selective and efficient cross metathesis diversification step. Representative analogues reported herein are the first to contain modifications to only the side chain dihydropyran of laulimalide and des-epoxy laulimalide. This step-economical strategy enables the rapid synthesis of new analogues using alkenes as an inexpensive, abundantly available diversification feedstock.

Model-based analyses reveal insular population diversification and cryptic frog species in the Ischnocnema parva complex in the Atlantic forest of Brazil.

PubMed

Gehara, Marcelo; Barth, Adriane; Oliveira, Eliana Faria de; Costa, Marco Antonio; Haddad, Célio Fernando Baptista; Vences, Miguel

2017-07-01

The Atlantic Forest (AF) of Brazil has long been recognized as a biodiversity conservation hotspot. Despite decades of studies the species inventory of this biome continues to increase with the discovery of cryptic diversity and the description of new species. Different diversification mechanisms have been proposed to explain the diversity in the region, including models of forest dynamics, barriers to gene flow and dispersal. Also, sea level change is thought to have influenced coastal diversification and isolated populations on continental islands. However, the timing and mode of diversification of insular populations in the AF region were rarely investigated. Here, we analyze the phylogeography and species diversity of the small-sized direct-developing frog Ischnocnema parva. These frogs are independent from water bodies but dependent on forest cover and high humidity, and provide good models to understand forest dynamics and insular diversification. Our analysis was based on DNA sequences for one mitochondrial and four nuclear genes of 71 samples from 18 localities including two islands, São Sebastião, municipality of Ilhabela, and Mar Virado, municipality of Ubatuba, both in the state of São Paulo. We use molecular taxonomic methods to show that I. parva is composed of six independently evolving lineages, with the nominal I. parva likely endemic to the type locality. The time-calibrated species tree shows that these lineages have diverged in the Pliocene and Pleistocene, suggesting the persistence of micro-refuges of forest in the AF. For the two insular populations we used approximate Bayesian computation to test different diversification hypotheses. Our findings support isolation with migration for São Sebastião population, with ∼1Mya divergence time, and isolation without migration for Mar Virado population, with ∼13Kya divergence time, suggesting a combination of different processes for diversification on AF islands. Copyright © 2017. Published by Elsevier Inc.

In and out of Madagascar: Dispersal to Peripheral Islands, Insular Speciation and Diversification of Indian Ocean Daisy Trees (Psiadia, Asteraceae)

PubMed Central

Strijk, Joeri S.; Noyes, Richard D.; Strasberg, Dominique; Cruaud, Corinne; Gavory, Fredéric; Chase, Mark W.; Abbott, Richard J.; Thébaud, Christophe

2012-01-01

Madagascar is surrounded by archipelagos varying widely in origin, age and structure. Although small and geologically young, these archipelagos have accumulated disproportionate numbers of unique lineages in comparison to Madagascar, highlighting the role of waif-dispersal and rapid in situ diversification processes in generating endemic biodiversity. We reconstruct the evolutionary and biogeographical history of the genus Psiadia (Asteraceae), a plant genus with near equal numbers of species in Madagascar and surrounding islands. Analyzing patterns and processes of diversification, we explain species accumulation on peripheral islands and aim to offer new insights on the origin and potential causes for diversification in the Madagascar and Indian Ocean Islands biodiversity hotspot. Our results provide support for an African origin of the group, with strong support for non-monophyly. Colonization of the Mascarenes took place by two evolutionary distinct lineages from Madagascar, via two independent dispersal events, each unique for their spatial and temporal properties. Significant shifts in diversification rate followed regional expansion, resulting in co-occurring and phenotypically convergent species on high-elevation volcanic slopes. Like other endemic island lineages, Psiadia have been highly successful in dispersing to and radiating on isolated oceanic islands, typified by high habitat diversity and dynamic ecosystems fuelled by continued geological activity. Results stress the important biogeographical role for Rodrigues in serving as an outlying stepping stone from which regional colonization took place. We discuss how isolated volcanic islands contribute to regional diversity by generating substantial numbers of endemic species on short temporal scales. Factors pertaining to the mode and tempo of archipelago formation and its geographical isolation strongly govern evolutionary pathways available for species diversification, and the potential for successful diversification of dispersed lineages, therefore, appears highly dependent on the timing of arrival, as habitat and resource properties change dramatically over the course of oceanic island evolution. PMID:22900068

Environmental and genetic sources of diversification in the timing of seed germination: implications for the evolution of bet hedging.

PubMed

Simons, Andrew M; Johnston, Mark O

2006-11-01

Environmental variation that is not predictably related to cues is expected to drive the evolution of bet-hedging strategies. The high variance observed in the timing of seed germination has led to it being the most cited diversification strategy in the theoretical bet-hedging literature. Despite this theoretical focus, virtually nothing is known about the mechanisms responsible for the generation of individual-level diversification. Here we report analyses of sources of variation in timing of germination within seasons, germination fraction over two generations and three sequential seasons, and the genetic correlation structure of these traits using almost 10,000 seeds from more than 100 genotypes of the monocarpic perennial Lobelia inflata. Microenvironmental analysis of time to germination suggests that extreme sensitivity to environmental gradients, or microplasticity, even within a homogeneous growth chamber, may act as an effective individual-level diversification mechanism and explains more than 30% of variance in time to germination. The heritability of within-season timing of germination was low (h(2) = 0.07) but significant under homogeneous conditions. Consistent with individual-level diversification, this low h(2) was attributable not to low additive genetic variance, but to an unusually high coefficient of residual variation in time to germination. Despite high power to detect additive genetic variance in within-season diversification, it was low and indistinguishable from zero. Restricted maximum likelihood detected significant genetic variation for germination fraction (h(2) = 0.18) under homogeneous conditions. Unexpectedly, this heritability was positive when measured within a generation by sibling analysis and negative when measured across generations by offspring-on-parent regression. The consistency of dormancy fraction over multiple delays, a major premise of Cohen's classic model, was supported by a strong genetic correlation (r = 0.468) observed for a cohort's germination fraction over two seasons. We discuss implications of the results for the evolution of bet hedging and highlight the need for further empirical study of the causal components of diversification.

Rotational diversification and intensification

USDA-ARS?s Scientific Manuscript database

Diversification and intensification of inland Pacific Northwest (PNW) dryland cereal cropping systems can present win-win scenarios that deliver short and long-term benefits for producers and the environment, stabilizing profit and increasing adaptability to and mitigation of climate change. Improvi...

Habitat use affects morphological diversification in dragon lizards

PubMed Central

COLLAR, D C; SCHULTE, J A; O’MEARA, B C; LOSOS, J B

2010-01-01

Habitat use may lead to variation in diversity among evolutionary lineages because habitats differ in the variety of ways they allow for species to make a living. Here, we show that structural habitats contribute to differential diversification of limb and body form in dragon lizards (Agamidae). Based on phylogenetic analysis and ancestral state reconstructions for 90 species, we find that multiple lineages have independently adopted each of four habitat use types: rock-dwelling, terrestriality, semi-arboreality and arboreality. Given these reconstructions, we fit models of evolution to species’ morphological trait values and find that rock-dwelling and arboreality limit diversification relative to terrestriality and semi-arboreality. Models preferred by Akaike information criterion infer slower rates of size and shape evolution in lineages inferred to occupy rocks and trees, and model-averaged rate estimates are slowest for these habitat types. These results suggest that ground-dwelling facilitates ecomorphological differentiation and that use of trees or rocks impedes diversification. PMID:20345808

A role for Runx transcription factor signaling in dorsal root ganglion sensory neuron diversification.

PubMed

Kramer, Ina; Sigrist, Markus; de Nooij, Joriene C; Taniuchi, Ichiro; Jessell, Thomas M; Arber, Silvia

2006-02-02

Subpopulations of sensory neurons in the dorsal root ganglion (DRG) can be characterized on the basis of sensory modalities that convey distinct peripheral stimuli, but the molecular mechanisms that underlie sensory neuronal diversification remain unclear. Here, we have used genetic manipulations in the mouse embryo to examine how Runx transcription factor signaling controls the acquisition of distinct DRG neuronal subtype identities. Runx3 acts to diversify an Ngn1-independent neuronal cohort by promoting the differentiation of proprioceptive sensory neurons through erosion of TrkB expression in prospective TrkC+ sensory neurons. In contrast, Runx1 controls neuronal diversification within Ngn1-dependent TrkA+ neurons by repression of neuropeptide CGRP expression and controlling the fine pattern of laminar termination in the dorsal spinal cord. Together, our findings suggest that Runx transcription factor signaling plays a key role in sensory neuron diversification.

Large-scale parallel genome assembler over cloud computing environment.

PubMed

Das, Arghya Kusum; Koppa, Praveen Kumar; Goswami, Sayan; Platania, Richard; Park, Seung-Jong

2017-06-01

The size of high throughput DNA sequencing data has already reached the terabyte scale. To manage this huge volume of data, many downstream sequencing applications started using locality-based computing over different cloud infrastructures to take advantage of elastic (pay as you go) resources at a lower cost. However, the locality-based programming model (e.g. MapReduce) is relatively new. Consequently, developing scalable data-intensive bioinformatics applications using this model and understanding the hardware environment that these applications require for good performance, both require further research. In this paper, we present a de Bruijn graph oriented Parallel Giraph-based Genome Assembler (GiGA), as well as the hardware platform required for its optimal performance. GiGA uses the power of Hadoop (MapReduce) and Giraph (large-scale graph analysis) to achieve high scalability over hundreds of compute nodes by collocating the computation and data. GiGA achieves significantly higher scalability with competitive assembly quality compared to contemporary parallel assemblers (e.g. ABySS and Contrail) over traditional HPC cluster. Moreover, we show that the performance of GiGA is significantly improved by using an SSD-based private cloud infrastructure over traditional HPC cluster. We observe that the performance of GiGA on 256 cores of this SSD-based cloud infrastructure closely matches that of 512 cores of traditional HPC cluster.

A revised and dated phylogeny of cobweb spiders (Araneae, Araneoidea, Theridiidae): A predatory Cretaceous lineage diversifying in the era of the ants (Hymenoptera, Formicidae).

PubMed

Liu, Jie; May-Collado, Laura J; Pekár, Stano; Agnarsson, Ingi

2016-01-01

Cobweb spiders (Theridiidae) are highly diverse from the perspective of species richness, morphological diversity, variety of web architecture, and behavioral repertoires. The family includes over 50% of social spiders, a behavioral rarity among the order, and members of the family are furthermore the subject of research on venom, silk biomechanics, kleptoparasitism and web building, among other traits. Theridiidae is one of the most abundant groups of spiders, and thus key insect predators in many different ecosystems and is among relatively few spider families that show high degree of myrmecophagy. Modern comparative studies on all these fronts are best buttressed on a phylogenetic foundation. Our goal here is to offer a revised, dated, phylogenetic hypothesis for the family by summarizing previously published data from multiple molecular and morphological studies through data-mining, and adding novel data from several genera. We also test the hypothesis that the origin and diversification of cobweb spiders coincides with that of ants on which many species specialize as prey. The new phylogeny is largely congruent with prior studies and current taxonomy and should provide a useful tool for theridiid classification and for comparative analyses. Nevertheless, we also highlight the limitations of currently available data-the state of the art in Theridiidae phylogenetics-offering weak support for most of the deeper nodes in the phylogeny. Thus the need is clear for modern phylogenomic approaches to obtain a more solid understanding, especially of relationships among subfamilies. We recover the monophyly of currently recognized theridiid subfamilies with the exception of some enigmatic 'pholcommatines' (Styposis, Phoroncidia) and putative 'hadrotarsines' (Audifia, Tekellina) whose placement is uncertain in our analyses. Theridiidae dates back some 100 mya to the Cretaceous, a period of diversification in flowering plants and many groups of insects, including ants. The origin of cobweb spiders, and hence the cobweb-a speciallized trap for pedestrian prey-coincides with a major diversification shift in ants. The family becomes abundant in fossil record 50-40 mya as ants also diversify and reach dominance and contemporary patterns of abundances of theridiids and ants show the same trends, with increasing relative abundance towards the equator and at lower altitudes. We find that among orbiculariae, lineages that specialize on ant prey are non-randomly clustered within Theridiidae. Given these findings we hypothesize that the origin of the gumfoot web was a stepping stone that facilitated the capture of ants and resulted in specialized myrmecophagy in a number of 'basal' theridiids. We also document a subsequent loss in myrmecophagy, and associated increase in speciation rates, as 'recent' theridiid groups evolve diverse web forms and many return to the capture of aerial prey. Copyright © 2015 Elsevier Inc. All rights reserved.

Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota.

PubMed

Gubry-Rangin, Cécile; Kratsch, Christina; Williams, Tom A; McHardy, Alice C; Embley, T Martin; Prosser, James I; Macqueen, Daniel J

2015-07-28

The Thaumarchaeota is an abundant and ubiquitous phylum of archaea that plays a major role in the global nitrogen cycle. Previous analyses of the ammonia monooxygenase gene amoA suggest that pH is an important driver of niche specialization in these organisms. Although the ecological distribution and ecophysiology of extant Thaumarchaeota have been studied extensively, the evolutionary rise of these prokaryotes to ecological dominance in many habitats remains poorly understood. To characterize processes leading to their diversification, we investigated coevolutionary relationships between amoA, a conserved marker gene for Thaumarchaeota, and soil characteristics, by using deep sequencing and comprehensive environmental data in Bayesian comparative phylogenetics. These analyses reveal a large and rapid increase in diversification rates during early thaumarchaeotal evolution; this finding was verified by independent analyses of 16S rRNA. Our findings suggest that the entire Thaumarchaeota diversification regime was strikingly coupled to pH adaptation but less clearly correlated with several other tested environmental factors. Interestingly, the early radiation event coincided with a period of pH adaptation that enabled the terrestrial Thaumarchaeota ancestor to initially move from neutral to more acidic and alkaline conditions. In contrast to classic evolutionary models, whereby niches become rapidly filled after adaptive radiation, global diversification rates have remained stably high in Thaumarchaeota during the past 400-700 million years, suggesting an ongoing high rate of niche formation or switching for these microbes. Our study highlights the enduring importance of environmental adaptation during thaumarchaeotal evolution and, to our knowledge, is the first to link evolutionary diversification to environmental adaptation in a prokaryotic phylum.

The relative importance of body size and paleoclimatic change as explanatory variables influencing lineage diversification rate: an evolutionary analysis of bullhead catfishes (Siluriformes: Ictaluridae).

PubMed

Hardman, Michael; Hardman, Lotta M

2008-02-01

We applied Bayesian phylogenetics, divergence time estimation, diversification pattern analysis, and parsimony-based methods of ancestral state reconstruction to a combination of nucleotide sequences, maximum body sizes, fossils, and paleoclimate data to explore the influence of an extrinsic (climate change) and an intrinsic (maximum body size) factor on diversification rates in a North American clade of catfishes (Ictaluridae). We found diversification rate to have been significantly variable over time, with significant (or nearly significant) rate increases in the early history of Noturus. Though the latter coincided closely with a period of dramatic climate change at the Eocene-Oligocene boundary, we did not detect evidence for a general association between climate change and diversification rate during the entire history of Ictaluridae. Within Ictaluridae, small body size was found to be a near significant predictor of species richness. Morphological stasis of several species appears to be a consequence of a homoplastic increase in body size. We estimated the maximum standard length of the ictalurid ancestor to be approximately 50 cm, comparable to Eocene ictalurids (Astephus) and similar to modern sizes of Ameiurus and their Asian sister-taxon Cranoglanis. During the late Paleocene and early Eocene, the ictalurid ancestor diversified into the lineages represented by the modern epigean genera. The majority of modern species originated in the Oligocene and Miocene, most likely according to a peripheral isolates model of speciation. We discuss the difficulties of detecting macroevolutionary patterns within a lineage history and encourage the scrutiny of the terminal Eocene climatic event as a direct promoter of diversification.

Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota

PubMed Central

Gubry-Rangin, Cécile; Kratsch, Christina; Williams, Tom A.; McHardy, Alice C.; Embley, T. Martin; Prosser, James I.; Macqueen, Daniel J.

2015-01-01

The Thaumarchaeota is an abundant and ubiquitous phylum of archaea that plays a major role in the global nitrogen cycle. Previous analyses of the ammonia monooxygenase gene amoA suggest that pH is an important driver of niche specialization in these organisms. Although the ecological distribution and ecophysiology of extant Thaumarchaeota have been studied extensively, the evolutionary rise of these prokaryotes to ecological dominance in many habitats remains poorly understood. To characterize processes leading to their diversification, we investigated coevolutionary relationships between amoA, a conserved marker gene for Thaumarchaeota, and soil characteristics, by using deep sequencing and comprehensive environmental data in Bayesian comparative phylogenetics. These analyses reveal a large and rapid increase in diversification rates during early thaumarchaeotal evolution; this finding was verified by independent analyses of 16S rRNA. Our findings suggest that the entire Thaumarchaeota diversification regime was strikingly coupled to pH adaptation but less clearly correlated with several other tested environmental factors. Interestingly, the early radiation event coincided with a period of pH adaptation that enabled the terrestrial Thaumarchaeota ancestor to initially move from neutral to more acidic and alkaline conditions. In contrast to classic evolutionary models, whereby niches become rapidly filled after adaptive radiation, global diversification rates have remained stably high in Thaumarchaeota during the past 400–700 million years, suggesting an ongoing high rate of niche formation or switching for these microbes. Our study highlights the enduring importance of environmental adaptation during thaumarchaeotal evolution and, to our knowledge, is the first to link evolutionary diversification to environmental adaptation in a prokaryotic phylum. PMID:26170282

Putative floral brood-site mimicry, loss of autonomous selfing, and reduced vegetative growth are significantly correlated with increased diversification in Asarum (Aristolochiaceae).

PubMed

Sinn, Brandon T; Kelly, Lawrence M; Freudenstein, John V

2015-08-01

The drivers of angiosperm diversity have long been sought and the flower-arthropod association has often been invoked as the most powerful driver of the angiosperm radiation. We now know that features that influence arthropod interactions cannot only affect the diversification of lineages, but also expedite or constrain their rate of extinction, which can equally influence the observed asymmetric richness of extant angiosperm lineages. The genus Asarum (Aristolochiaceae; ∼100 species) is widely distributed in north temperate forests, with substantial vegetative and floral divergence between its three major clades, Euasarum, Geotaenium, and Heterotropa. We used Binary-State Speciation and Extinction Model (BiSSE) Net Diversification tests of character state distributions on a Maximum Likelihood phylogram and a Coalescent Bayesian species tree, inferred from seven chloroplast markers and nuclear rDNA, to test for signal of asymmetric diversification, character state transition, and extinction rates of floral and vegetative characters. We found that reduction in vegetative growth, loss of autonomous self-pollination, and the presence of putative fungal-mimicking floral structures are significantly correlated with increased diversification in Asarum. No significant difference in model likelihood was identified between symmetric and asymmetric rates of character state transitions or extinction. We conclude that the flowers of the Heterotropa clade may have converged on some aspects of basidiomycete sporocarp morphology and that brood-site mimicry, coupled with a reduction in vegetative growth and the loss of autonomous self-pollination, may have driven diversification within Asarum. Copyright © 2015 Elsevier Inc. All rights reserved.

How the Aridification of Australia Structured the Biogeography and Influenced the Diversification of a Large Lineage of Australian Cicadas.

PubMed

Owen, Christopher L; Marshall, David C; Hill, Kathy B R; Simon, Chris

2017-07-01

Over the last 30 million years, Australia's landscape has undergone dramatic cooling and drying due to the establishment of the Antarctic Circumpolar Current and change in global CO$_{2}$ levels. Studies have shown that many Australian organisms went extinct during these major cooling events, while others experienced adaptive radiations and increases in diversification rates as a result of exploiting new niches in the arid zone. Despite the many studies on diversification and biogeography in Australia, few have been continent-wide and none have focused on a group of organisms adapted to feeding on plants. We studied 162 species of cicadas in the Australian Pauropsalta complex, a large generic lineage within the tribe Cicadettini. We asked whether there were changes in the diversification rate of Pauropsalta over time and if so: 1) which clades were associated with the rate change? 2) did timing of rate shifts correspond to known periods of dramatic historical climate change, 3) did increases in diversification rate along select lineages correspond to adaptive radiations with movement into the arid zone? To address these questions, we estimated a molecular phylogeny of the Pauropsalta complex using ${\\sim}$5300 bp of nucleotide sequence data distributed among five loci (one mtDNA locus and four nDNA loci). We found that this large group of cicadas did not diversify at a constant rate as they spread through Australia; instead the signature of decreasing diversification rate changed roughly around the time of the expansion of the east Antarctic ice sheets ${\\sim}$16 Ma and the glaciation of the northern hemisphere ${\\sim}$3 Ma. Unlike other Australian taxa, the Pauropsalta complex did not explosively radiate in response to an early invasion of the arid zone. Instead multiple groups invaded the arid zone and experienced rates of diversification similar to mesic-distributed taxa. We found evidence for relictual groups, located in pre-Mesozoic habitat, that have not diversified and continue to reside on mesic hosts in isolated "habitat islands". Future work should focus on groups of similar ages with similar distribution patterns to determine whether this tempo and pattern of diversification and biogeography is consistent with evidence from other phytophagous insects. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Diversification of non-visual photopigment parapinopsin in spectral sensitivity for diverse pineal functions.

PubMed

Koyanagi, Mitsumasa; Wada, Seiji; Kawano-Yamashita, Emi; Hara, Yuichiro; Kuraku, Shigehiro; Kosaka, Shigeaki; Kawakami, Koichi; Tamotsu, Satoshi; Tsukamoto, Hisao; Shichida, Yoshinori; Terakita, Akihisa

2015-09-15

Recent genome projects of various animals have uncovered an unexpectedly large number of opsin genes, which encode protein moieties of photoreceptor molecules, in most animals. In visual systems, the biological meanings of this diversification are clear; multiple types of visual opsins with different spectral sensitivities are responsible for color vision. However, the significance of the diversification of non-visual opsins remains uncertain, in spite of the importance of understanding the molecular mechanism and evolution of varied non-visual photoreceptions. Here, we investigated the diversification of the pineal photopigment parapinopsin, which serves as the UV-sensitive photopigment for the pineal wavelength discrimination in the lamprey, linking it with other pineal photoreception. Spectroscopic analyses of the recombinant pigments of the two teleost parapinopsins PP1 and PP2 revealed that PP1 is a UV-sensitive pigment, similar to lamprey parapinopsin, but PP2 is a blue-sensitive pigment, with an absorption maximum at 460-480 nm, showing the diversification of non-visual pigment with respect to spectral sensitivity. We also found that PP1 and PP2 exhibit mutually exclusive expressions in the pineal organs of three teleost species. By using transgenic zebrafish in which these parapinopsin-expressing cells are labeled, we found that PP1-expressing cells basically possess neuronal processes, which is consistent with their involvement in wavelength discrimination. Interestingly, however, PP2-expressing cells rarely possess neuronal processes, raising the possibility that PP2 could be involved in non-neural responses rather than neural responses. Furthermore, we found that PP2-expressing cells contain serotonin and aanat2, the key enzyme involved in melatonin synthesis from serotonin, whereas PP1-expressing cells do not contain either, suggesting that blue-sensitive PP2 is instead involved in light-regulation of melatonin secretion. In this paper, we have clearly shown the different molecular properties of duplicated non-visual opsins by demonstrating the diversification of parapinopsin with respect to spectral sensitivity. Moreover, we have shown a plausible link between the diversification and its physiological impact by discovering a strong candidate for the underlying pigment in light-regulated melatonin secretion in zebrafish; the diversification could generate a new contribution of parapinopsin to pineal photoreception. Current findings could also provide an opportunity to understand the "color" preference of non-visual photoreception.