Molecular mechanisms underlying origin and diversification of the angiosperm flower.

PubMed

Theissen, Guenter; Melzer, Rainer

2007-09-01

Understanding the mode and mechanisms of the evolution of the angiosperm flower is a long-standing and central problem of evolutionary biology and botany. It has essentially remained unsolved, however. In contrast, considerable progress has recently been made in our understanding of the genetic basis of flower development in some extant model species. The knowledge that accumulated this way has been pulled together in two major hypotheses, termed the 'ABC model' and the 'floral quartet model'. These models explain how the identity of the different types of floral organs is specified during flower development by homeotic selector genes encoding transcription factors. We intend to explain how the 'ABC model' and the 'floral quartet model' are now guiding investigations that help to understand the origin and diversification of the angiosperm flower. Investigation of orthologues of class B and class C floral homeotic genes in gymnosperms suggest that bisexuality was one of the first innovations during the origin of the flower. The transition from dimer to tetramer formation of floral homeotic proteins after establishment of class E proteins may have increased cooperativity of DNA binding of the transcription factors controlling reproductive growth. That way, we hypothesize, better 'developmental switches' originated that facilitated the early evolution of the flower. Expression studies of ABC genes in basally diverging angiosperm lineages, monocots and basal eudicots suggest that the 'classical' ABC system known from core eudicots originated from a more fuzzy system with fading borders of gene expression and gradual transitions in organ identity, by sharpening of ABC gene expression domains and organ borders. Shifting boundaries of ABC gene expression may have contributed to the diversification of the angiosperm flower many times independently, as may have changes in interactions between ABC genes and their target genes.

Molecular Mechanisms Underlying Origin and Diversification of the Angiosperm Flower

PubMed Central

Theissen, Guenter; Melzer, Rainer

2007-01-01

Background Understanding the mode and mechanisms of the evolution of the angiosperm flower is a long-standing and central problem of evolutionary biology and botany. It has essentially remained unsolved, however. In contrast, considerable progress has recently been made in our understanding of the genetic basis of flower development in some extant model species. The knowledge that accumulated this way has been pulled together in two major hypotheses, termed the ‘ABC model’ and the ‘floral quartet model’. These models explain how the identity of the different types of floral organs is specified during flower development by homeotic selector genes encoding transcription factors. Scope We intend to explain how the ‘ABC model’ and the ‘floral quartet model’ are now guiding investigations that help to understand the origin and diversification of the angiosperm flower. Conclusions Investigation of orthologues of class B and class C floral homeotic genes in gymnosperms suggest that bisexuality was one of the first innovations during the origin of the flower. The transition from dimer to tetramer formation of floral homeotic proteins after establishment of class E proteins may have increased cooperativity of DNA binding of the transcription factors controlling reproductive growth. That way, we hypothesize, better ‘developmental switches’ originated that facilitated the early evolution of the flower. Expression studies of ABC genes in basally diverging angiosperm lineages, monocots and basal eudicots suggest that the ‘classical’ ABC system known from core eudicots originated from a more fuzzy system with fading borders of gene expression and gradual transitions in organ identity, by sharpening of ABC gene expression domains and organ borders. Shifting boundaries of ABC gene expression may have contributed to the diversification of the angiosperm flower many times independently, as may have changes in interactions between ABC genes and their target

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

Studying the evolutionary significance of thermal adaptation in ectotherms: The diversification of amphibians' energetics.

PubMed

Nespolo, Roberto F; Figueroa, Julio; Solano-Iguaran, Jaiber J

2017-08-01

A fundamental problem in evolutionary biology is the understanding of the factors that promote or constrain adaptive evolution, and assessing the role of natural selection in this process. Here, comparative phylogenetics, that is, using phylogenetic information and traits to infer evolutionary processes has been a major paradigm . In this study, we discuss Ornstein-Uhlenbeck models (OU) in the context of thermal adaptation in ectotherms. We specifically applied this approach to study amphibians's evolution and energy metabolism. It has been hypothesized that amphibians exploit adaptive zones characterized by low energy expenditure, which generate specific predictions in terms of the patterns of diversification in standard metabolic rate (SMR). We complied whole-animal metabolic rates for 122 species of amphibians, and adjusted several models of diversification. According to the adaptive zone hypothesis, we expected: (1) to find "accelerated evolution" in SMR (i.e., diversification above Brownian Motion expectations, BM), (2) that a model assuming evolutionary optima (i.e., an OU model) fits better than a white-noise model and (3) that a model assuming multiple optima (according to the three amphibians's orders) fits better than a model assuming a single optimum. As predicted, we found that the diversification of SMR occurred most of the time, above BM expectations. Also, we found that a model assuming an optimum explained the data in a better way than a white-noise model. However, we did not find evidence that an OU model with multiple optima fits the data better, suggesting a single optimum in SMR for Anura, Caudata and Gymnophiona. These results show how comparative phylogenetics could be applied for testing adaptive hypotheses regarding history and physiological performance in ectotherms. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evolutionary rates of mitochondrial genomes correspond to diversification rates and to contemporary species richness in birds and reptiles

PubMed Central

Eo, Soo Hyung; DeWoody, J. Andrew

2010-01-01

Rates of biological diversification should ultimately correspond to rates of genome evolution. Recent studies have compared diversification rates with phylogenetic branch lengths, but incomplete phylogenies hamper such analyses for many taxa. Herein, we use pairwise comparisons of confamilial sauropsid (bird and reptile) mitochondrial DNA (mtDNA) genome sequences to estimate substitution rates. These molecular evolutionary rates are considered in light of the age and species richness of each taxonomic family, using a random-walk speciation–extinction process to estimate rates of diversification. We find the molecular clock ticks at disparate rates in different families and at different genes. For example, evolutionary rates are relatively fast in snakes and lizards, intermediate in crocodilians and slow in turtles and birds. There was also rate variation across genes, where non-synonymous substitution rates were fastest at ATP8 and slowest at CO3. Family-by-gene interactions were significant, indicating that local clocks vary substantially among sauropsids. Most importantly, we find evidence that mitochondrial genome evolutionary rates are positively correlated with speciation rates and with contemporary species richness. Nuclear sequences are poorly represented among reptiles, but the correlation between rates of molecular evolution and species diversification also extends to 18 avian nuclear genes we tested. Thus, the nuclear data buttress our mtDNA findings. PMID:20610427

Origins, evolution and diversification of cleptoparasitic lineages in long-tongued bees

USDA-ARS?s Scientific Manuscript database

The evolution of parasitic behavior may catalyze the exploitation of new ecological niches yet also binds the fate of a parasite to that of its host. It is thus not clear whether evolutionary transitions from free-living organism to parasite lead to increased or decreased rates of diversification. W...

Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower

PubMed Central

Chanderbali, André S.; Yoo, Mi-Jeong; Zahn, Laura M.; Brockington, Samuel F.; Wall, P. Kerr; Gitzendanner, Matthew A.; Albert, Victor A.; Leebens-Mack, James; Altman, Naomi S.; Ma, Hong; dePamphilis, Claude W.; Soltis, Douglas E.; Soltis, Pamela S.

2010-01-01

The origin and rapid diversification of the angiosperms (Darwin's “Abominable Mystery”) has engaged generations of researchers. Here, we examine the floral genetic programs of phylogenetically pivotal angiosperms (water lily, avocado, California poppy, and Arabidopsis) and a nonflowering seed plant (a cycad) to obtain insight into the origin and subsequent evolution of the flower. Transcriptional cascades with broadly overlapping spatial domains, resembling the hypothesized ancestral gymnosperm program, are deployed across morphologically intergrading organs in water lily and avocado flowers. In contrast, spatially discrete transcriptional programs in distinct floral organs characterize the more recently derived angiosperm lineages represented by California poppy and Arabidopsis. Deep evolutionary conservation in the genetic programs of putatively homologous floral organs traces to those operating in gymnosperm reproductive cones. Female gymnosperm cones and angiosperm carpels share conserved genetic features, which may be associated with the ovule developmental program common to both organs. However, male gymnosperm cones share genetic features with both perianth (sterile attractive and protective) organs and stamens, supporting the evolutionary origin of the floral perianth from the male genetic program of seed plants. PMID:21149731

Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower.

PubMed

Chanderbali, André S; Yoo, Mi-Jeong; Zahn, Laura M; Brockington, Samuel F; Wall, P Kerr; Gitzendanner, Matthew A; Albert, Victor A; Leebens-Mack, James; Altman, Naomi S; Ma, Hong; dePamphilis, Claude W; Soltis, Douglas E; Soltis, Pamela S

2010-12-28

The origin and rapid diversification of the angiosperms (Darwin's "Abominable Mystery") has engaged generations of researchers. Here, we examine the floral genetic programs of phylogenetically pivotal angiosperms (water lily, avocado, California poppy, and Arabidopsis) and a nonflowering seed plant (a cycad) to obtain insight into the origin and subsequent evolution of the flower. Transcriptional cascades with broadly overlapping spatial domains, resembling the hypothesized ancestral gymnosperm program, are deployed across morphologically intergrading organs in water lily and avocado flowers. In contrast, spatially discrete transcriptional programs in distinct floral organs characterize the more recently derived angiosperm lineages represented by California poppy and Arabidopsis. Deep evolutionary conservation in the genetic programs of putatively homologous floral organs traces to those operating in gymnosperm reproductive cones. Female gymnosperm cones and angiosperm carpels share conserved genetic features, which may be associated with the ovule developmental program common to both organs. However, male gymnosperm cones share genetic features with both perianth (sterile attractive and protective) organs and stamens, supporting the evolutionary origin of the floral perianth from the male genetic program of seed plants.

Impact of gene gains, losses and duplication modes on the origin and diversification of vertebrates.

PubMed

Cañestro, Cristian; Albalat, Ricard; Irimia, Manuel; Garcia-Fernàndez, Jordi

2013-02-01

The study of the evolutionary origin of vertebrates has been linked to the study of genome duplications since Susumo Ohno suggested that the successful diversification of vertebrate innovations was facilitated by two rounds of whole-genome duplication (2R-WGD) in the stem vertebrate. Since then, studies on the functional evolution of many genes duplicated in the vertebrate lineage have provided the grounds to support experimentally this link. This article reviews cases of gene duplications derived either from the 2R-WGD or from local gene duplication events in vertebrates, analyzing their impact on the evolution of developmental innovations. We analyze how gene regulatory networks can be rewired by the activity of transposable elements after genome duplications, discuss how different mechanisms of duplication might affect the fate of duplicated genes, and how the loss of gene duplicates might influence the fate of surviving paralogs. We also discuss the evolutionary relationships between gene duplication and alternative splicing, in particular in the vertebrate lineage. Finally, we discuss the role that the 2R-WGD might have played in the evolution of vertebrate developmental gene networks, paying special attention to those related to vertebrate key features such as neural crest cells, placodes, and the complex tripartite brain. In this context, we argue that current evidences points that the 2R-WGD may not be linked to the origin of vertebrate innovations, but to their subsequent diversification in a broad variety of complex structures and functions that facilitated the successful transition from peaceful filter-feeding non-vertebrate ancestors to voracious vertebrate predators. Copyright © 2013 Elsevier Ltd. All rights reserved.

Evolutionary innovation and diversification of carotenoid-based pigmentation in finches.

PubMed

Ligon, Russell A; Simpson, Richard K; Mason, Nicholas A; Hill, Geoffrey E; McGraw, Kevin J

2016-12-01

The ornaments used by animals to mediate social interactions are diverse, and by reconstructing their evolutionary pathways we can gain new insights into the mechanisms underlying ornamental innovation and variability. Here, we examine variation in plumage carotenoids among the true finches (Aves: Fringillidae) using biochemical and comparative phylogenetic analyses to reconstruct the evolutionary history of carotenoid states and evaluate competing models of carotenoid evolution. Our comparative analyses reveal that the most likely ancestor of finches used dietary carotenoids as yellow plumage colorants, and that the ability to metabolically modify dietary carotenoids into more complex pigments arose secondarily once finches began to use modified carotenoids to create red plumage. Following the evolutionary "innovation" that enabled modified red carotenoid pigments to be deposited as plumage colorants, many finch species subsequently modified carotenoid biochemical pathways to create yellow plumage. However, no reversions to dietary carotenoids were observed. The finding that ornaments and their underlying mechanisms may be operating under different selection regimes-where ornamental trait colors undergo frequent reversions (e.g., between red and yellow plumage) while carotenoid metabolization mechanisms are more conserved-supports a growing empirical framework suggesting different evolutionary patterns for ornaments and the mechanistic innovations that facilitate their diversification. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Large-scale patterns of diversification in the widespread legume genus Senna and the evolutionary role of extrafloral nectaries.

PubMed

Marazzi, Brigitte; Sanderson, Michael J

2010-12-01

Unraveling the diversification history of old, species-rich and widespread clades is difficult because of extinction, undersampling, and taxonomic uncertainty. In the context of these challenges, we investigated the timing and mode of lineage diversification in Senna (Leguminosae) to gain insights into the evolutionary role of extrafloral nectaries (EFNs). EFNs secrete nectar, attracting ants and forming ecologically important ant-plant mutualisms. In Senna, EFNs characterize one large clade (EFN clade), including 80% of its 350 species. Taxonomic accounts make Senna the largest caesalpinioid genus, but quantitative comparisons to other taxa require inferences about rates. Molecular dating analyses suggest that Senna originated in the early Eocene, and its major lineages appeared during early/mid Eocene to early Oligocene. EFNs evolved in the late Eocene, after the main radiation of ants. The EFN clade diversified faster, becoming significantly more species-rich than non-EFN clades. The shift in diversification rates associated with EFN evolution supports the hypothesis that EFNs represent a (relatively old) key innovation in Senna. EFNs may have promoted the colonization of new habitats appearing with the early uplift of the Andes. This would explain the distinctive geographic concentration of the EFN clade in South America. © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.

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.

Origin and diversification of the California flora: re-examining classic hypotheses with molecular phylogenies.

PubMed

Lancaster, Lesley T; Kay, Kathleen M

2013-04-01

The California Floristic Province exhibits one of the richest floras on the planet, with more than 5500 native plant species, approximately 40% of which are endemic. Despite its impressive diversity and the attention it has garnered from ecologists and evolutionary biologists, historical causes of species richness and endemism in California remain poorly understood. Using a phylogenetic analysis of 16 angiosperm clades, each containing California natives in addition to species found only outside California, we show that CA's current biodiversity primarily results from low extinction rates, as opposed to elevated speciation or immigration rates. Speciation rates in California were lowest among Arcto-Tertiary lineages (i.e., those colonizing California from the north, during the Tertiary), but extinction rates were universally low across California native plants of all historical, geographic origins. In contrast to long-accepted ideas, we find that California diversification rates were generally unaffected by the onset of the Mediterranean climate. However, the Mediterranean climate coincided with immigration of many desert species, validating one previous hypothesis regarding origins of CA's plant diversity. This study implicates topographic complexity and climatic buffering as key, long-standing features of CA's landscape favoring plant species persistence and diversification, and highlights California as an important refuge under changing climates. © 2013 The Author(s). Evolution© 2013 The Society for the Study of Evolution.

AFLP markers provide insights into the evolutionary relationships and diversification of New Caledonian Araucaria species (Araucariaceae).

PubMed

Gaudeul, Myriam; Rouhan, Germinal; Gardner, Martin F; Hollingsworth, Peter M

2012-01-01

Despite its small size, New Caledonia is characterized by a very diverse flora and striking environmental gradients, which make it an ideal setting to study species diversification. Thirteen of the 19 Araucaria species are endemic to the territory and form a monophyletic group, but patterns and processes that lead to such a high species richness are largely unexplored. We used 142 polymorphic AFLP markers and performed analyses based on Bayesian clustering algorithms, genetic distances, and cladistics on 71 samples representing all New Caledonian Araucaria species. We examined correlations between the inferred evolutionary relationships and shared morphological, ecological, or geographic parameters among species, to investigate evolutionary processes that may have driven speciation. We showed that genetic divergence among the present New Caledonian Araucaria species is low, suggesting recent diversification rather than pre-existence on Gondwana. We identified three genetic groups that included small-leaved, large-leaved, and coastal species, but detected no association with soil preference, ecological habitat, or rainfall. The observed patterns suggested that speciation events resulted from both differential adaptation and vicariance. Last, we hypothesize that speciation is ongoing and/or there are cryptic species in some genetically (sometimes also morphologically) divergent populations. Further data are required to provide better resolution and understanding of the diversification of New Caledonian Araucaria species. Nevertheless, our study allowed insights into their evolutionary relationships and provides a framework for future investigations on the evolution of this emblematic group of plants in one of the world's biodiversity hotspots.

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.

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.

Top predators induce the evolutionary diversification of intermediate predator species.

PubMed

Zu, Jian; Yuan, Bo; Du, Jianqiang

2015-12-21

We analyze the evolutionary branching phenomenon of intermediate predator species in a tritrophic food chain model by using adaptive dynamics theory. Specifically, we consider the adaptive diversification of an intermediate predator species that feeds on a prey species and is fed upon by a top predator species. We assume that the intermediate predator׳s ability to forage on the prey can adaptively improve, but this comes at the cost of decreased defense ability against the top predator. First, we identify the general properties of trade-off relationships that lead to a continuously stable strategy or to evolutionary branching in the intermediate predator species. We find that if there is an accelerating cost near the singular strategy, then that strategy is continuously stable. In contrast, if there is a mildly decelerating cost near the singular strategy, then that strategy may be an evolutionary branching point. Second, we find that after branching has occurred, depending on the specific shape and strength of the trade-off relationship, the intermediate predator species may reach an evolutionarily stable dimorphism or one of the two resultant predator lineages goes extinct. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Evolutionary cell biology: two origins, one objective.

PubMed

Lynch, Michael; Field, Mark C; Goodson, Holly V; Malik, Harmit S; Pereira-Leal, José B; Roos, David S; Turkewitz, Aaron P; Sazer, Shelley

2014-12-02

All aspects of biological diversification ultimately trace to evolutionary modifications at the cellular level. This central role of cells frames the basic questions as to how cells work and how cells come to be the way they are. Although these two lines of inquiry lie respectively within the traditional provenance of cell biology and evolutionary biology, a comprehensive synthesis of evolutionary and cell-biological thinking is lacking. We define evolutionary cell biology as the fusion of these two eponymous fields with the theoretical and quantitative branches of biochemistry, biophysics, and population genetics. The key goals are to develop a mechanistic understanding of general evolutionary processes, while specifically infusing cell biology with an evolutionary perspective. The full development of this interdisciplinary field has the potential to solve numerous problems in diverse areas of biology, including the degree to which selection, effectively neutral processes, historical contingencies, and/or constraints at the chemical and biophysical levels dictate patterns of variation for intracellular features. These problems can now be examined at both the within- and among-species levels, with single-cell methodologies even allowing quantification of variation within genotypes. Some results from this emerging field have already had a substantial impact on cell biology, and future findings will significantly influence applications in agriculture, medicine, environmental science, and synthetic biology.

Evolutionary origin of the latitudinal diversity gradient in liverworts.

PubMed

Laenen, Benjamin; Patiño, Jairo; Hagborg, Anders; Désamoré, Aurélie; Wang, Jian; Jonathan Shaw, A; Goffinet, Bernard; Vanderpoorten, Alain

2018-06-08

A latitudinal diversity gradient towards the tropics appears as one most recurrent patterns in ecology, but the mechanisms underlying this pattern remain an area of controversy. In angiosperms, the tropical conservatism hypothesis proposes that most groups originated in the tropics and are adapted to a tropical climatic regime, and that relatively few species have evolved physiological adaptations to cold, dry or unpredictable climates. This mechanism is, however, unlikely to apply across land plants, and in particular, to liverworts, a group of about 7500 species, whose ability to withstand cold much better than their tracheophyte counterparts is at odds with the tropical conservatism hypothesis. Molecular dating, diversification rate analyses and ancestral area reconstructions were employed to explore the evolutionary mechanisms that account for the latitudinal diversity gradient in liverworts. As opposed to angiosperms, tropical liverwort genera are not older than their extra-tropical counterparts (median stem age of tropical and extra-tropical liverwort genera of 24.35±39.65 Ma and 39.57±49.07 Ma, respectively), weakening the 'time for speciation hypothesis'. Models of ancestral area reconstructions with equal migration rates between tropical and extra-tropical regions outperformed models with asymmetrical migration rates in either direction. The symmetry and intensity of migrations between tropical and extra-tropical regions suggested by the lack of resolution in ancestral area reconstructions towards the deepest nodes are at odds with the tropical niche conservatism hypothesis. In turn, tropical genera exhibited significantly higher net diversification rates than extra-tropical ones, suggesting that the observed latitudinal diversity gradient results from either higher extinction rates in extra-tropical lineages or higher speciation rates in the tropics. We discuss a series of experiments to help deciphering the underlying evolutionary mechanisms. Copyright

Origin and Diversification Dynamics of Self-Incompatibility Haplotypes

PubMed Central

Gervais, Camille E.; Castric, Vincent; Ressayre, Adrienne; Billiard, Sylvain

2011-01-01

Self-incompatibility (SI) is a genetic system found in some hermaphrodite plants. Recognition of pollen by pistils expressing cognate specificities at two linked genes leads to rejection of self pollen and pollen from close relatives, i.e., to avoidance of self-fertilization and inbred matings, and thus increased outcrossing. These genes generally have many alleles, yet the conditions allowing the evolution of new alleles remain mysterious. Evolutionary changes are clearly necessary in both genes, since any mutation affecting only one of them would result in a nonfunctional self-compatible haplotype. Here, we study diversification at the S-locus (i.e., a stable increase in the total number of SI haplotypes in the population, through the incorporation of new SI haplotypes), both deterministically (by investigating analytically the fate of mutations in an infinite population) and by simulations of finite populations. We show that the conditions allowing diversification are far less stringent in finite populations with recurrent mutations of the pollen and pistil genes, suggesting that diversification is possible in a panmictic population. We find that new SI haplotypes emerge fastest in populations with few SI haplotypes, and we discuss some implications for empirical data on S-alleles. However, allele numbers in our simulations never reach values as high as observed in plants whose SI systems have been studied, and we suggest extensions of our models that may reconcile the theory and data. PMID:21515570

Cretaceous origin and repeated tertiary diversification of the redefined butterflies

PubMed Central

Heikkilä, Maria; Kaila, Lauri; Mutanen, Marko; Peña, Carlos; Wahlberg, Niklas

2012-01-01

Although the taxonomy of the ca 18 000 species of butterflies and skippers is well known, the family-level relationships are still debated. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the superfamilies Papilionoidea, Hesperioidea and Hedyloidea to date based on morphological and molecular data. We reconstructed their phylogenetic relationships using parsimony and Bayesian approaches. We estimated times and rates of diversification along lineages in order to reconstruct their evolutionary history. Our results suggest that the butterflies, as traditionally understood, are paraphyletic, with Papilionidae being the sister-group to Hesperioidea, Hedyloidea and all other butterflies. Hence, the families in the current three superfamilies should be placed in a single superfamily Papilionoidea. In addition, we find that Hedylidae is sister to Hesperiidae, and this novel relationship is supported by two morphological characters. The families diverged in the Early Cretaceous but diversified after the Cretaceous–Palaeogene event. The diversification of butterflies is characterized by a slow speciation rate in the lineage leading to Baronia brevicornis, a period of stasis by the skippers after divergence and a burst of diversification in the lineages leading to Nymphalidae, Riodinidae and Lycaenidae. PMID:21920981

Cretaceous origin and repeated tertiary diversification of the redefined butterflies.

PubMed

Heikkilä, Maria; Kaila, Lauri; Mutanen, Marko; Peña, Carlos; Wahlberg, Niklas

2012-03-22

Although the taxonomy of the ca 18 000 species of butterflies and skippers is well known, the family-level relationships are still debated. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the superfamilies Papilionoidea, Hesperioidea and Hedyloidea to date based on morphological and molecular data. We reconstructed their phylogenetic relationships using parsimony and Bayesian approaches. We estimated times and rates of diversification along lineages in order to reconstruct their evolutionary history. Our results suggest that the butterflies, as traditionally understood, are paraphyletic, with Papilionidae being the sister-group to Hesperioidea, Hedyloidea and all other butterflies. Hence, the families in the current three superfamilies should be placed in a single superfamily Papilionoidea. In addition, we find that Hedylidae is sister to Hesperiidae, and this novel relationship is supported by two morphological characters. The families diverged in the Early Cretaceous but diversified after the Cretaceous-Palaeogene event. The diversification of butterflies is characterized by a slow speciation rate in the lineage leading to Baronia brevicornis, a period of stasis by the skippers after divergence and a burst of diversification in the lineages leading to Nymphalidae, Riodinidae and Lycaenidae.

Evolutionary cell biology: Two origins, one objective

PubMed Central

Lynch, Michael; Field, Mark C.; Goodson, Holly V.; Malik, Harmit S.; Pereira-Leal, José B.; Roos, David S.; Turkewitz, Aaron P.; Sazer, Shelley

2014-01-01

All aspects of biological diversification ultimately trace to evolutionary modifications at the cellular level. This central role of cells frames the basic questions as to how cells work and how cells come to be the way they are. Although these two lines of inquiry lie respectively within the traditional provenance of cell biology and evolutionary biology, a comprehensive synthesis of evolutionary and cell-biological thinking is lacking. We define evolutionary cell biology as the fusion of these two eponymous fields with the theoretical and quantitative branches of biochemistry, biophysics, and population genetics. The key goals are to develop a mechanistic understanding of general evolutionary processes, while specifically infusing cell biology with an evolutionary perspective. The full development of this interdisciplinary field has the potential to solve numerous problems in diverse areas of biology, including the degree to which selection, effectively neutral processes, historical contingencies, and/or constraints at the chemical and biophysical levels dictate patterns of variation for intracellular features. These problems can now be examined at both the within- and among-species levels, with single-cell methodologies even allowing quantification of variation within genotypes. Some results from this emerging field have already had a substantial impact on cell biology, and future findings will significantly influence applications in agriculture, medicine, environmental science, and synthetic biology. PMID:25404324

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

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.

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.

Hill-Climbing search and diversification within an evolutionary approach to protein structure prediction.

PubMed

Chira, Camelia; Horvath, Dragos; Dumitrescu, D

2011-07-30

Proteins are complex structures made of amino acids having a fundamental role in the correct functioning of living cells. The structure of a protein is the result of the protein folding process. However, the general principles that govern the folding of natural proteins into a native structure are unknown. The problem of predicting a protein structure with minimum-energy starting from the unfolded amino acid sequence is a highly complex and important task in molecular and computational biology. Protein structure prediction has important applications in fields such as drug design and disease prediction. The protein structure prediction problem is NP-hard even in simplified lattice protein models. An evolutionary model based on hill-climbing genetic operators is proposed for protein structure prediction in the hydrophobic - polar (HP) model. Problem-specific search operators are implemented and applied using a steepest-ascent hill-climbing approach. Furthermore, the proposed model enforces an explicit diversification stage during the evolution in order to avoid local optimum. The main features of the resulting evolutionary algorithm - hill-climbing mechanism and diversification strategy - are evaluated in a set of numerical experiments for the protein structure prediction problem to assess their impact to the efficiency of the search process. Furthermore, the emerging consolidated model is compared to relevant algorithms from the literature for a set of difficult bidimensional instances from lattice protein models. The results obtained by the proposed algorithm are promising and competitive with those of related methods.

Early vertebrate origin and diversification of small transmembrane regulators of cellular ion transport.

PubMed

Pirkmajer, Sergej; Kirchner, Henriette; Lundell, Leonidas S; Zelenin, Pavel V; Zierath, Juleen R; Makarova, Kira S; Wolf, Yuri I; Chibalin, Alexander V

2017-07-15

Small transmembrane proteins such as FXYDs, which interact with Na + ,K + -ATPase, and the micropeptides that interact with sarco/endoplasmic reticulum Ca 2+ -ATPase play fundamental roles in regulation of ion transport in vertebrates. Uncertain evolutionary origins and phylogenetic relationships among these regulators of ion transport have led to inconsistencies in their classification across vertebrate species, thus hampering comparative studies of their functions. We discovered the first FXYD homologue in sea lamprey, a basal jawless vertebrate, which suggests small transmembrane regulators of ion transport emerged early in the vertebrate lineage. We also identified 13 gene subfamilies of FXYDs and propose a revised, phylogeny-based FXYD classification that is consistent across vertebrate species. These findings provide an improved framework for investigating physiological and pathophysiological functions of small transmembrane regulators of ion transport. Small transmembrane proteins are important for regulation of cellular ion transport. The most prominent among these are members of the FXYD family (FXYD1-12), which regulate Na + ,K + -ATPase, and phospholamban, sarcolipin, myoregulin and DWORF, which regulate the sarco/endoplasmic reticulum Ca 2+ -ATPase (SERCA). FXYDs and regulators of SERCA are present in fishes, as well as terrestrial vertebrates; however, their evolutionary origins and phylogenetic relationships are obscure, thus hampering comparative physiological studies. Here we discovered that sea lamprey (Petromyzon marinus), a representative of extant jawless vertebrates (Cyclostomata), expresses an FXYD homologue, which strongly suggests that FXYDs predate the emergence of fishes and other jawed vertebrates (Gnathostomata). Using a combination of sequence-based phylogenetic analysis and conservation of local chromosome context, we determined that FXYDs markedly diversified in the lineages leading to cartilaginous fishes (Chondrichthyes) and bony

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 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.

Evolutionary origin and phylogeny of the modern holocephalans (Chondrichthyes: Chimaeriformes): a mitogenomic perspective.

PubMed

Inoue, Jun G; Miya, Masaki; Lam, Kevin; Tay, Boon-Hui; Danks, Janine A; Bell, Justin; Walker, Terrence I; Venkatesh, Byrappa

2010-11-01

With our increasing ability for generating whole-genome sequences, comparative analysis of whole genomes has become a powerful tool for understanding the structure, function, and evolutionary history of human and other vertebrate genomes. By virtue of their position basal to bony vertebrates, cartilaginous fishes (class Chondrichthyes) are a valuable outgroup in comparative studies of vertebrates. Recently, a holocephalan cartilaginous fish, the elephant shark, Callorhinchus milii (Subclass Holocephali: Order Chimaeriformes), has been proposed as a model genome, and low-coverage sequence of its genome has been generated. Despite such an increasing interest, the evolutionary history of the modern holocephalans-a previously successful and diverse group but represented by only 39 extant species-and their relationship with elasmobranchs and other jawed vertebrates has been poorly documented largely owing to a lack of well-preserved fossil materials after the end-Permian about 250 Ma. In this study, we assembled the whole mitogenome sequences for eight representatives from all the three families of the modern holocephalans and investigated their phylogenetic relationships and evolutionary history. Unambiguously aligned sequences from these holocephalans together with 17 other vertebrates (9,409 nt positions excluding entire third codon positions) were subjected to partitioned maximum likelihood analysis. The resulting tree strongly supported a single origin of the modern holocephalans and their sister-group relationship with elasmobranchs. The mitogenomic tree recovered the most basal callorhinchids within the chimaeriforms, which is sister to a clade comprising the remaining two families (rhinochimaerids and chimaerids). The timetree derived from a relaxed molecular clock Bayesian method suggests that the holocephalans originated in the Silurian about 420 Ma, having survived from the end-Permian (250 Ma) mass extinction and undergoing familial diversifications during

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

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

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

Phylogenetic investigation of the complex evolutionary history of dispersal mode and diversification rates across living and fossil Fagales.

PubMed

Larson-Johnson, Kathryn

2016-01-01

As a primary determinant of spatial structure in angiosperm populations, fruit dispersal may impact large-scale ecological and evolutionary processes. Essential to understanding these mechanisms is an accurate reconstruction of dispersal mode over the entire history of an angiosperm lineage. A total-evidence phylogeny is presented for most fossil fruit and all extant genera in Fagales over its c. 95 million yr history. This phylogeny - the largest of its kind to include plant fossils - was used to reconstruct an evolutionary history directly informed by fossil morphologies and to assess relationships among dispersal mode, biogeographic range size, and diversification rate. Reconstructions indicate four transitions to wind dispersal and seven to biotic dispersal, with the phylogenetic integration of fossils crucial to understanding these patterns. Complexity further increased when more specialized behaviors were considered, with fluttering, gliding, autorotating, and scatter-hoarding evolving multiple times across the order. Preliminary biogeographic analyses suggest larger range sizes in biotically dispersed lineages, especially when pollination mode was held constant. Biotically dispersed lineages had significantly higher diversification rates than abiotically dispersed lineages, although transitions in dispersal mode alone cannot explain all detected diversification rate shifts across Fagales. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

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.

Evolutionary transition in symbiotic syndromes enabled diversification of phytophagous insects on an imbalanced diet

PubMed Central

Sudakaran, Sailendharan; Retz, Franziska; Kikuchi, Yoshitomo; Kost, Christian; Kaltenpoth, Martin

2015-01-01

Evolutionary adaptations for the exploitation of nutritionally challenging or toxic host plants represent a major force driving the diversification of phytophagous insects. Although symbiotic bacteria are known to have essential nutritional roles for insects, examples of radiations into novel ecological niches following the acquisition of specific symbionts remain scarce. Here we characterized the microbiota across bugs of the family Pyrrhocoridae and investigated whether the acquisition of vitamin-supplementing symbionts enabled the hosts to diversify into the nutritionally imbalanced and chemically well-defended seeds of Malvales plants as a food source. Our results indicate that vitamin-provisioning Actinobacteria (Coriobacterium and Gordonibacter), as well as Firmicutes (Clostridium) and Proteobacteria (Klebsiella) are widespread across Pyrrhocoridae, but absent from the sister family Largidae and other outgroup taxa. Despite the consistent association with a specific microbiota, the Pyrrhocoridae phylogeny is neither congruent with a dendrogram based on the hosts' microbial community profiles nor phylogenies of individual symbiont strains, indicating frequent horizontal exchange of symbiotic partners. Phylogenetic dating analyses based on the fossil record reveal an origin of the Pyrrhocoridae core microbiota in the late Cretaceous (81.2–86.5 million years ago), following the transition from crypt-associated beta-proteobacterial symbionts to an anaerobic community localized in the M3 region of the midgut. The change in symbiotic syndromes (that is, symbiont identity and localization) and the acquisition of the pyrrhocorid core microbiota followed the evolution of their preferred host plants (Malvales), suggesting that the symbionts facilitated their hosts' adaptation to this imbalanced nutritional resource and enabled the subsequent diversification in a competition-poor ecological niche. PMID:26023876

Origins, evolution, and diversification of cleptoparasitic lineages in long-tongued bees.

PubMed

Litman, Jessica R; Praz, Christophe J; Danforth, Bryan N; Griswold, Terry L; Cardinal, Sophie

2013-10-01

The evolution of parasitic behavior may catalyze the exploitation of new ecological niches yet also binds the fate of a parasite to that of its host. It is thus not clear whether evolutionary transitions from free-living organism to parasite lead to increased or decreased rates of diversification. We explore the evolution of brood parasitism in long-tongued bees and find decreased rates of diversification in eight of 10 brood parasitic clades. We propose a pathway for the evolution of brood parasitic strategy and find that a strategy in which a closed host nest cell is parasitized and the host offspring is killed by the adult parasite represents an obligate first step in the appearance of a brood parasitic lineage; this ultimately evolves into a strategy in which an open host cell is parasitized and the host offspring is killed by a specialized larval instar. The transition to parasitizing open nest cells expanded the range of potential hosts for brood parasitic bees and played a fundamental role in the patterns of diversification seen in brood parasitic clades. We address the prevalence of brood parasitic lineages in certain families of bees and examine the evolution of brood parasitism in other groups of organisms. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Late Cretaceous origin of the rice tribe provides evidence for early diversification in Poaceae.

PubMed

Prasad, V; Strömberg, C A E; Leaché, A D; Samant, B; Patnaik, R; Tang, L; Mohabey, D M; Ge, S; Sahni, A

2011-09-20

Rice and its relatives are a focal point in agricultural and evolutionary science, but a paucity of fossils has obscured their deep-time history. Previously described cuticles with silica bodies (phytoliths) from the Late Cretaceous period (67-65 Ma) of India indicate that, by the latest Cretaceous, the grass family (Poaceae) consisted of members of the modern subclades PACMAD (Panicoideae-Aristidoideae-Chloridoideae-Micrairoideae-Arundinoideae-Danthonioideae) and BEP (Bambusoideae-Ehrhartoideae-Pooideae), including a taxon with proposed affinities to Ehrhartoideae. Here we describe additional fossils and show that, based on phylogenetic analyses that combine molecular genetic data and epidermal and phytolith features across Poaceae, these can be assigned to the rice tribe, Oryzeae, of grass subfamily Ehrhartoideae. The new Oryzeae fossils suggest substantial diversification within Ehrhartoideae by the Late Cretaceous, pushing back the time of origin of Poaceae as a whole. These results, therefore, necessitate a re-evaluation of current models for grass evolution and palaeobiogeography.

Evolutionary origins of the endosperm in flowering plants

PubMed Central

Baroux, Célia; Spillane, Charles; Grossniklaus, Ueli

2002-01-01

The evolutionary origin of double fertilization and the resultant endosperm tissue in flowering plants remains a puzzle, despite over a century of research. The recent resurgence of approaches to evolutionary developmental biology combining comparative biology with phylogenetics provides new understanding of endosperm origins. PMID:12225592

Evolutionary consequences of polyploidy in prokaryotes and the origin of mitosis and meiosis.

PubMed

Markov, Alexander V; Kaznacheev, Ilya S

2016-06-08

The origin of eukaryote-specific traits such as mitosis and sexual reproduction remains disputable. There is growing evidence that both mitosis and eukaryotic sex (i.e., the alternation of syngamy and meiosis) may have already existed in the basal eukaryotes. The mating system of the halophilic archaeon Haloferax volcanii probably represents an intermediate stage between typical prokaryotic and eukaryotic sex. H. volcanii is highly polyploid, as well as many other Archaea. Here, we use computer simulation to explore genetic and evolutionary outcomes of polyploidy in amitotic prokaryotes and its possible role in the origin of mitosis, meiosis and eukaryotic sex. Modeling suggests that polyploidy can confer strong short-term evolutionary advantage to amitotic prokaryotes. However, it also promotes the accumulation of recessive deleterious mutations and the risk of extinction in the long term, especially in highly mutagenic environment. There are several possible strategies that amitotic polyploids can use in order to reduce the genetic costs of polyploidy while retaining its benefits. Interestingly, most of these strategies resemble different components or aspects of eukaryotic sex. They include asexual ploidy cycles, equalization of genome copies by gene conversion, high-frequency lateral gene transfer between relatives, chromosome exchange coupled with homologous recombination, and the evolution of more accurate chromosome distribution during cell division (mitosis). Acquisition of mitosis by an amitotic polyploid results in chromosome diversification and specialization. Ultimately, it transforms a polyploid cell into a functionally monoploid one with multiple unique, highly redundant chromosomes. Specialization of chromosomes makes the previously evolved modes of promiscuous chromosome shuffling deleterious. This can result in selective pressure to develop accurate mechanisms of homolog pairing, and, ultimately, meiosis. Emergence of mitosis and the first

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 Diversification of Alanine Transaminases in Yeast: Catabolic Specialization and Biosynthetic Redundancy.

PubMed

Escalera-Fanjul, Ximena; Campero-Basaldua, Carlos; Colón, Maritrini; González, James; Márquez, Dariel; González, Alicia

2017-01-01

Gene duplication is one of the major evolutionary mechanisms providing raw material for the generation of genes with new or modified functions. The yeast Saccharomyces cerevisiae originated after an allopolyploidization event, which involved mating between two different ancestral yeast species. ScALT1 and ScALT2 codify proteins with 65% identity, which were proposed to be paralogous alanine transaminases. Further analysis of their physiological role showed that while ScALT1 encodes an alanine transaminase which constitutes the main pathway for alanine biosynthesis and the sole pathway for alanine catabolism, Sc Alt2 does not display alanine transaminase activity and is not involved in alanine metabolism. Moreover, phylogenetic studies have suggested that ScALT1 and ScALT2 come from each one of the two parental strains which gave rise to the ancestral hybrid. The present work has been aimed to the understanding of the properties of the ancestral type Lacchancea kluyveri LkALT1 and Kluyveromyces lactis KlALT1 , alanine transaminases in order to better understand the ScALT1 and ScALT2 evolutionary history. These ancestral -type species were chosen since they harbor ALT1 genes, which are related to ScALT2. Presented results show that, although LkALT1 and KlALT1 constitute ScALT1 orthologous genes, encoding alanine transaminases, both yeasts display Lk Alt1 and Kl Alt1 independent alanine transaminase activity and additional unidentified alanine biosynthetic and catabolic pathway(s). Furthermore, phenotypic analysis of null mutants uncovered the fact that Kl Alt1 and Lk Alt1 have an additional role, not related to alanine metabolism but is necessary to achieve wild type growth rate. Our study shows that the ancestral alanine transaminase function has been retained by the ScALT1 encoded enzyme, which has specialized its catabolic character, while losing the alanine independent role observed in the ancestral type enzymes. The fact that Sc Alt2 conserves 64% identity with

Evolutionary Diversification of Alanine Transaminases in Yeast: Catabolic Specialization and Biosynthetic Redundancy

PubMed Central

Escalera-Fanjul, Ximena; Campero-Basaldua, Carlos; Colón, Maritrini; González, James; Márquez, Dariel; González, Alicia

2017-01-01

Gene duplication is one of the major evolutionary mechanisms providing raw material for the generation of genes with new or modified functions. The yeast Saccharomyces cerevisiae originated after an allopolyploidization event, which involved mating between two different ancestral yeast species. ScALT1 and ScALT2 codify proteins with 65% identity, which were proposed to be paralogous alanine transaminases. Further analysis of their physiological role showed that while ScALT1 encodes an alanine transaminase which constitutes the main pathway for alanine biosynthesis and the sole pathway for alanine catabolism, ScAlt2 does not display alanine transaminase activity and is not involved in alanine metabolism. Moreover, phylogenetic studies have suggested that ScALT1 and ScALT2 come from each one of the two parental strains which gave rise to the ancestral hybrid. The present work has been aimed to the understanding of the properties of the ancestral type Lacchancea kluyveri LkALT1 and Kluyveromyces lactis KlALT1, alanine transaminases in order to better understand the ScALT1 and ScALT2 evolutionary history. These ancestral -type species were chosen since they harbor ALT1 genes, which are related to ScALT2. Presented results show that, although LkALT1 and KlALT1 constitute ScALT1 orthologous genes, encoding alanine transaminases, both yeasts display LkAlt1 and KlAlt1 independent alanine transaminase activity and additional unidentified alanine biosynthetic and catabolic pathway(s). Furthermore, phenotypic analysis of null mutants uncovered the fact that KlAlt1 and LkAlt1 have an additional role, not related to alanine metabolism but is necessary to achieve wild type growth rate. Our study shows that the ancestral alanine transaminase function has been retained by the ScALT1 encoded enzyme, which has specialized its catabolic character, while losing the alanine independent role observed in the ancestral type enzymes. The fact that ScAlt2 conserves 64% identity with LkAlt1

Transformation and diversification in early mammal evolution.

PubMed

Luo, Zhe-Xi

2007-12-13

Evolution of the earliest mammals shows successive episodes of diversification. Lineage-splitting in Mesozoic mammals is coupled with many independent evolutionary experiments and ecological specializations. Classic scenarios of mammalian morphological evolution tend to posit an orderly acquisition of key evolutionary innovations leading to adaptive diversification, but newly discovered fossils show that evolution of such key characters as the middle ear and the tribosphenic teeth is far more labile among Mesozoic mammals. Successive diversifications of Mesozoic mammal groups multiplied the opportunities for many dead-end lineages to iteratively evolve developmental homoplasies and convergent ecological specializations, parallel to those in modern mammal groups.

Bats, Primates, and the Evolutionary Origins and Diversification of Mammalian Gammaherpesviruses

PubMed Central

Rojas-Anaya, Edith; Kolokotronis, Sergios-Orestis; Taboada, Blanca; Loza-Rubio, Elizabeth; Méndez-Ojeda, Maria L.; Osterrieder, Nikolaus

2016-01-01

ABSTRACT Gammaherpesviruses (γHVs) are generally considered host specific and to have codiverged with their hosts over millions of years. This tenet is challenged here by broad-scale phylogenetic analysis of two viral genes using the largest sample of mammalian γHVs to date, integrating for the first time bat γHV sequences available from public repositories and newly generated viral sequences from two vampire bat species (Desmodus rotundus and Diphylla ecaudata). Bat and primate viruses frequently represented deep branches within the supported phylogenies and clustered among viruses from distantly related mammalian taxa. Following evolutionary scenario testing, we determined the number of host-switching and cospeciation events. Cross-species transmissions have occurred much more frequently than previously estimated, and most of the transmissions were attributable to bats and primates. We conclude that the evolution of the Gammaherpesvirinae subfamily has been driven by both cross-species transmissions and subsequent cospeciation within specific viral lineages and that the bat and primate orders may have potentially acted as superspreaders to other mammalian taxa throughout evolutionary history. PMID:27834200

Evolutionary diversification of Mesobuthus α-scorpion toxins affecting sodium channels.

PubMed

Zhu, Shunyi; Peigneur, Steve; Gao, Bin; Lu, Xiuxiu; Cao, Chunyang; Tytgat, Jan

2012-01-01

α-Scorpion toxins constitute a family of peptide modulators that induce a prolongation of the action potential of excitable cells by inhibiting voltage-gated sodium channel inactivation. Although they all adopt a conserved structural scaffold, the potency and phylogentic preference of these toxins largely vary, which render them an intriguing model for studying evolutionary diversification among family members. Here, we report molecular characterization of a new multigene family of α-toxins comprising 13 members (named MeuNaTxα-1 to MeuNaTxα-13) from the scorpion Mesobuthus eupeus. Of them, five native toxins (MeuNaTxα-1 to -5) were purified to homogeneity from the venom and the solution structure of MeuNaTxα-5 was solved by nuclear magnetic resonance. A systematic functional evaluation of MeuNaTxα-1, -2, -4, and -5 was conducted by two-electrode voltage-clamp recordings on seven cloned mammalian voltage-gated sodium channels (Na(v)1.2 to Na(v)1.8) and the insect counterpart DmNa(v)1 expressed in Xenopus oocytes. Results show that all these four peptides slow inactivation of DmNa(v)1 and are inactive on Na(v)1.8 at micromolar concentrations. However, they exhibit differential specificity for the other six channel isoforms (Na(v)1.2 to Na(v)1.7), in which MeuNaTxα-4 shows no activity on these isoforms and thus represents the first Mesobuthus-derived insect-selective α-toxin identified so far with a half maximal effective concentration of 130 ± 2 nm on DmNa(v)1 and a half maximal lethal dose of about 200 pmol g(-1) on the insect Musca domestica; MeuNaTxα-2 only affects Na(v)1.4; MeuNaTxα-1 and MeuNaTxα-5 have a wider range of channel spectrum, the former active on Na(v)1.2, Na(v)1.3, Na(v)1.6, and Na(v)1.7, whereas the latter acting on Na(v)1.3-Na(v)1.7. Remarkably, MeuNaTxα-4 and MeuNaTxα-5 are two nearly identical peptides differing by only one point mutation at site 50 (A50V) but exhibit rather different channel subtype selectivity, highlighting a

Evolutionary diversification of TTX-resistant sodium channels in a predator-prey interaction.

PubMed

Geffeney, Shana L; Fujimoto, Esther; Brodie, Edmund D; Brodie, Edmund D; Ruben, Peter C

2005-04-07

Understanding the molecular genetic basis of adaptations provides incomparable insight into the genetic mechanisms by which evolutionary diversification takes place. Whether the evolution of common traits in different lineages proceeds by similar or unique mutations, and the degree to which phenotypic evolution is controlled by changes in gene regulation as opposed to gene function, are fundamental questions in evolutionary biology that require such an understanding of genetic mechanisms. Here we identify novel changes in the molecular structure of a sodium channel expressed in snake skeletal muscle, tsNa(V)1.4, that are responsible for differences in tetrodotoxin (TTX) resistance among garter snake populations coevolving with toxic newts. By the functional expression of tsNa(V)1.4, we show how differences in the amino-acid sequence of the channel affect TTX binding and impart different levels of resistance in four snake populations. These results indicate that the evolution of a physiological trait has occurred through a series of unique functional changes in a gene that is otherwise highly conserved among vertebrates.

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

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

The human dark side: evolutionary psychology and original sin.

PubMed

Lee, Joseph; Theol, M

2014-04-01

Human nature has a dark side, something important to religions. Evolutionary psychology has been used to illuminate the human shadow side, although as a discipline it has attracted criticism. This article seeks to examine the evolutionary psychology's understanding of human nature and to propose an unexpected dialog with an enduring account of human evil known as original sin. Two cases are briefly considered: murder and rape. To further the exchange, numerous theoretical and methodological criticisms and replies of evolutionary psychology are explored jointly with original sin. Evolutionary psychology can partner with original sin since they share some theoretical likenesses and together they offer insights into the nature of what it means to be human.

Evolutionary origins of leadership and followership.

PubMed

Van Vugt, Mark

2006-01-01

Drawing upon evolutionary logic, leadership is reconceptualized in terms of the outcome of strategic interactions among individuals who are following different, yet complementary, decision rules to solve recurrent coordination problems. This article uses the vast psychological literature on leadership as a database to test several evolutionary hypotheses about the origins of leadership and followership in humans. As expected, leadership correlates with initiative taking, trait measures of intelligence, specific task competencies, and several indicators of generosity. The review finds no link between leadership and dominance. The evolutionary analysis accounts for reliable age, health, and sex differences in leadership emergence. In general, evolutionary theory provides a useful, integrative framework for studying leader-follower relationships and generates various novel research hypotheses.

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

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.

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.

Evolution of microgastropods (Ellobioidea, Carychiidae): integrating taxonomic, phylogenetic and evolutionary hypotheses

PubMed Central

2013-01-01

Background Current biodiversity patterns are considered largely the result of past climatic and tectonic changes. In an integrative approach, we combine taxonomic and phylogenetic hypotheses to analyze temporal and geographic diversification of epigean (Carychium) and subterranean (Zospeum) evolutionary lineages in Carychiidae (Eupulmonata, Ellobioidea). We explicitly test three hypotheses: 1) morphospecies encompass unrecognized evolutionary lineages, 2) limited dispersal results in a close genetic relationship of geographical proximally distributed taxa and 3) major climatic and tectonic events had an impact on lineage diversification within Carychiidae. Results Initial morphospecies assignments were investigated by different molecular delimitation approaches (threshold, ABGD, GMYC and SP). Despite a conservative delimitation strategy, carychiid morphospecies comprise a great number of unrecognized evolutionary lineages. We attribute this phenomenon to historic underestimation of morphological stasis and phenotypic variability amongst lineages. The first molecular phylogenetic hypothesis for the Carychiidae (based on COI, 16S and H3) reveals Carychium and Zospeum to be reciprocally monophyletic. Geographical proximally distributed lineages are often closely related. The temporal diversification of Carychiidae is best described by a constant rate model of diversification. The evolution of Carychiidae is characterized by relatively few (long distance) colonization events. We find support for an Asian origin of Carychium. Zospeum may have arrived in Europe before extant members of Carychium. Distantly related Carychium clades inhabit a wide spectrum of the available bioclimatic niche and demonstrate considerable niche overlap. Conclusions Carychiid taxonomy is in dire need of revision. An inferred wide distribution and variable phenotype suggest underestimated diversity in Zospeum. Several Carychium morphospecies are results of past taxonomic lumping. By collecting

Do holocentric chromosomes represent an evolutionary advantage? A study of paired analyses of diversification rates of lineages with holocentric chromosomes and their monocentric closest relatives.

PubMed

Márquez-Corro, José Ignacio; Escudero, Marcial; Luceño, Modesto

2017-10-17

Despite most of the cytogenetic research is focused on monocentric chromosomes, chromosomes with kinetochoric activity localized in a single centromere, several studies have been centered on holocentric chromosomes which have diffuse kinetochoric activity along the chromosomes. The eukaryotic organisms that present this type of chromosomes have been relatively understudied despite they constitute rather diversified species lineages. On the one hand, holocentric chromosomes may present intrinsic benefits (chromosome mutations such as fissions and fusions are potentially neutral in holocentrics). On the other hand, they present restrictions to the spatial separation of the functions of recombination and segregation during meiotic divisions (functions that may interfere), separation that is found in monocentric chromosomes. In this study, we compare the diversification rates of all known holocentric lineages in animals and plants with their most related monocentric lineages in order to elucidate whether holocentric chromosomes constitute an evolutionary advantage in terms of diversification and species richness. The results showed that null hypothesis of equal mean diversification rates cannot be rejected, leading us to surmise that shifts in diversification rates between holocentric and monocentric lineages might be due to other factors, such as the idiosyncrasy of each lineage or the interplay of evolutionary selections with the benefits of having either monocentric or holocentric chromosomes.

Evolutionary history of the recruitment of conserved developmental genes in association to the formation and diversification of a novel trait.

PubMed

Shirai, Leila T; Saenko, Suzanne V; Keller, Roberto A; Jerónimo, Maria A; Brakefield, Paul M; Descimon, Henri; Wahlberg, Niklas; Beldade, Patrícia

2012-02-15

The origin and modification of novel traits are important aspects of biological diversification. Studies combining concepts and approaches of developmental genetics and evolutionary biology have uncovered many examples of the recruitment, or co-option, of genes conserved across lineages for the formation of novel, lineage-restricted traits. However, little is known about the evolutionary history of the recruitment of those genes, and of the relationship between them -for example, whether the co-option involves whole or parts of existing networks, or whether it occurs by redeployment of individual genes with de novo rewiring. We use a model novel trait, color pattern elements on butterfly wings called eyespots, to explore these questions. Eyespots have greatly diversified under natural and sexual selection, and their formation involves genetic circuitries shared across insects. We investigated the evolutionary history of the recruitment and co-recruitment of four conserved transcription regulators to the larval wing disc region where circular pattern elements develop. The co-localization of Antennapedia, Notch, Distal-less, and Spalt with presumptive (eye)spot organizers was examined in 13 butterfly species, providing the largest comparative dataset available for the system. We found variation between families, between subfamilies, and between tribes. Phylogenetic reconstructions by parsimony and maximum likelihood methods revealed an unambiguous evolutionary history only for Antennapedia, with a resolved single origin of eyespot-associated expression, and many homoplastic events for Notch, Distal-less, and Spalt. The flexibility in the (co-)recruitment of the targeted genes includes cases where different gene combinations are associated with morphologically similar eyespots, as well as cases where identical protein combinations are associated with very different phenotypes. The evolutionary history of gene (co-)recruitment is consistent with both divergence from a

Synchronic historical patterns of species diversification in seasonal aplocheiloid killifishes of the semi-arid Brazilian Caatinga

PubMed Central

Amorim, Pedro F.; Mattos, José Leonardo O.

2018-01-01

The Caatinga is the largest nucleus of seasonally dry tropical forests in South America, but little is known about the evolutionary history and biogeography of endemic organisms. Evolutionary diversification and distribution of terrestrial vertebrates endemic to the Caatinga have been explained by palaeogeographical Neogene episodes, mostly related to changes in the course of the São Francisco River, the largest river in the region. Our objective is to estimate the timing of divergence of two endemic groups of short-lived seasonal killifishes inhabiting all ecoregions of the Caatinga, testing the occurrence of synchronic events of spatial diversification in light of available data on regional palaeogeography. We performed independent time-calibrated phylogenetic molecular analyses for two clades of sympatric and geographically widespread seasonal killifishes endemic to the Caatinga, the Hypsolebias antenori group and the Cynolebias alpha-clade. Our results consistently indicate that species diversification took place synchronically in both groups, as well as it is contemporary to diversification of other organisms adapted to life in the semi-arid Caatinga, including lizards and small mammals. Both groups originated during the Miocene, but species diversification started between the Late Miocene and Early Pliocene, when global cooling probably favoured the expansion of semi-arid areas. Synchronic diversification patterns found are chronologically related to Tertiary palaeogeographical reorganizations associated to continental drift and to Quaternary climatic changes, corroborating the recent proposal that South American biodiversity has been continuously shaped between the Late Paleogene and Pleistocene. PMID:29451915

Synchronic historical patterns of species diversification in seasonal aplocheiloid killifishes of the semi-arid Brazilian Caatinga.

PubMed

Costa, Wilson J E M; Amorim, Pedro F; Mattos, José Leonardo O

2018-01-01

The Caatinga is the largest nucleus of seasonally dry tropical forests in South America, but little is known about the evolutionary history and biogeography of endemic organisms. Evolutionary diversification and distribution of terrestrial vertebrates endemic to the Caatinga have been explained by palaeogeographical Neogene episodes, mostly related to changes in the course of the São Francisco River, the largest river in the region. Our objective is to estimate the timing of divergence of two endemic groups of short-lived seasonal killifishes inhabiting all ecoregions of the Caatinga, testing the occurrence of synchronic events of spatial diversification in light of available data on regional palaeogeography. We performed independent time-calibrated phylogenetic molecular analyses for two clades of sympatric and geographically widespread seasonal killifishes endemic to the Caatinga, the Hypsolebias antenori group and the Cynolebias alpha-clade. Our results consistently indicate that species diversification took place synchronically in both groups, as well as it is contemporary to diversification of other organisms adapted to life in the semi-arid Caatinga, including lizards and small mammals. Both groups originated during the Miocene, but species diversification started between the Late Miocene and Early Pliocene, when global cooling probably favoured the expansion of semi-arid areas. Synchronic diversification patterns found are chronologically related to Tertiary palaeogeographical reorganizations associated to continental drift and to Quaternary climatic changes, corroborating the recent proposal that South American biodiversity has been continuously shaped between the Late Paleogene and Pleistocene.

Novelties of the flowering plant pollen tube underlie diversification of a key life history stage.

PubMed

Williams, Joseph H

2008-08-12

The origin and rapid diversification of flowering plants has puzzled evolutionary biologists, dating back to Charles Darwin. Since that time a number of key life history and morphological traits have been proposed as developmental correlates of the extraordinary diversity and ecological success of angiosperms. Here, I identify several innovations that were fundamental to the evolutionary lability of angiosperm reproduction, and hence to their diversification. In gymnosperms pollen reception must be near the egg largely because sperm swim or are transported by pollen tubes that grow at very slow rates (< approximately 20 microm/h). In contrast, pollen tube growth rates of taxa in ancient angiosperm lineages (Amborella, Nuphar, and Austrobaileya) range from approximately 80 to 600 microm/h. Comparative analyses point to accelerated pollen tube growth rate as a critical innovation that preceded the origin of the true closed carpel, long styles, multiseeded ovaries, and, in monocots and eudicots, much faster pollen tube growth rates. Ancient angiosperm pollen tubes all have callosic walls and callose plugs (in contrast, no gymnosperms have these features). The early association of the callose-walled growth pattern with accelerated pollen tube growth rate underlies a striking repeated pattern of faster and longer-distance pollen tube growth often within solid pathways in phylogenetically derived angiosperms. Pollen tube innovations are a key component of the spectacular diversification of carpel (flower and fruit) form and reproductive cycles in flowering plants.

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.

Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics

PubMed Central

Simionato, Elena; Ledent, Valérie; Richards, Gemma; Thomas-Chollier, Morgane; Kerner, Pierre; Coornaert, David; Degnan, Bernard M; Vervoort, Michel

2007-01-01

Background Molecular and genetic analyses conducted in model organisms such as Drosophila and vertebrates, have provided a wealth of information about how networks of transcription factors control the proper development of these species. Much less is known, however, about the evolutionary origin of these elaborated networks and their large-scale evolution. Here we report the first evolutionary analysis of a whole superfamily of transcription factors, the basic helix-loop-helix (bHLH) proteins, at the scale of the whole metazoan kingdom. Results We identified in silico the putative full complement of bHLH genes in the sequenced genomes of 12 different species representative of the main metazoan lineages, including three non-bilaterian metazoans, the cnidarians Nematostella vectensis and Hydra magnipapillata and the demosponge Amphimedon queenslandica. We have performed extensive phylogenetic analyses of the 695 identified bHLHs, which has allowed us to allocate most of these bHLHs to defined evolutionary conserved groups of orthology. Conclusion Three main features in the history of the bHLH gene superfamily can be inferred from these analyses: (i) an initial diversification of the bHLHs has occurred in the pre-Cambrian, prior to metazoan cladogenesis; (ii) a second expansion of the bHLH superfamily occurred early in metazoan evolution before bilaterians and cnidarians diverged; and (iii) the bHLH complement during the evolution of the bilaterians has been remarkably stable. We suggest that these features may be extended to other developmental gene families and reflect a general trend in the evolution of the developmental gene repertoires of metazoans. PMID:17335570

An Evolutionary Framework for Understanding the Origin of Eukaryotes

PubMed Central

Blackstone, Neil W.

2016-01-01

Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real—the endosymbiosis that led to the mitochondrion is often described as “non-Darwinian” because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious—all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes. PMID:27128953

An Evolutionary Framework for Understanding the Origin of Eukaryotes.

PubMed

Blackstone, Neil W

2016-04-27

Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real-the endosymbiosis that led to the mitochondrion is often described as "non-Darwinian" because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious-all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes.

Evolutionary dynamics and biogeography of Musaceae reveal a correlation between the diversification of the banana family and the geological and climatic history of Southeast Asia.

PubMed

Janssens, Steven B; Vandelook, Filip; De Langhe, Edmond; Verstraete, Brecht; Smets, Erik; Vandenhouwe, Ines; Swennen, Rony

2016-06-01

Tropical Southeast Asia, which harbors most of the Musaceae biodiversity, is one of the most species-rich regions in the world. Its high degree of endemism is shaped by the region's tectonic and climatic history, with large differences between northern Indo-Burma and the Malayan Archipelago. Here, we aim to find a link between the diversification and biogeography of Musaceae and geological history of the Southeast Asian subcontinent. The Musaceae family (including five Ensete, 45 Musa and one Musella species) was dated using a large phylogenetic framework encompassing 163 species from all Zingiberales families. Evolutionary patterns within Musaceae were inferred using ancestral area reconstruction and diversification rate analyses. All three Musaceae genera - Ensete, Musa and Musella - originated in northern Indo-Burma during the early Eocene. Musa species dispersed from 'northwest to southeast' into Southeast Asia with only few back-dispersals towards northern Indo-Burma. Musaceae colonization events of the Malayan Archipelago subcontinent are clearly linked to the geological and climatic history of the region. Musa species were only able to colonize the region east of Wallace's line after the availability of emergent land from the late Miocene onwards. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

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.

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

Diversification in the Andes: age and origins of South American Heliotropium lineages (Heliotropiaceae, Boraginales).

PubMed

Luebert, Federico; Hilger, Hartmut H; Weigend, Maximilian

2011-10-01

The uplift of the Andes was a major factor for plant diversification in South America and had significant effects on the climatic patterns at the continental scale. It was crucial for the formation of the arid environments in south-eastern and western South America. However, both the timing of the major stages of the Andean uplift and the onset of aridity in western South America remain controversial. In this paper we examine the hypothesis that the Andean South American groups of Heliotropium originated and diversified in response to Andean orogeny during the late Miocene and a the subsequent development of aridity. To this end, we estimate divergence times and likely biogeographical origins of the major clades in the phylogeny of Heliotropium, using both Bayesian and likelihood methods. Divergence times of all Andean clades in Heliotropium are estimated to be of late Miocene or Pliocene ages. At least three independent Andean diversification events can be recognized within Heliotropium. Timing of the diversification in the Andean lineages Heliotropium sects.Heliothamnus, Cochranea, Heliotrophytum, Hypsogenia, Plagiomeris, Platygyne clearly correspond to a rapid, late Miocene uplift of the Andes and a Pliocene development of arid environments in South America. Copyright © 2011 Elsevier Inc. All rights reserved.

Evolutionary diversification of protein-protein interactions by interface add-ons.

PubMed

Plach, Maximilian G; Semmelmann, Florian; Busch, Florian; Busch, Markus; Heizinger, Leonhard; Wysocki, Vicki H; Merkl, Rainer; Sterner, Reinhard

2017-10-03

Cells contain a multitude of protein complexes whose subunits interact with high specificity. However, the number of different protein folds and interface geometries found in nature is limited. This raises the question of how protein-protein interaction specificity is achieved on the structural level and how the formation of nonphysiological complexes is avoided. Here, we describe structural elements called interface add-ons that fulfill this function and elucidate their role for the diversification of protein-protein interactions during evolution. We identified interface add-ons in 10% of a representative set of bacterial, heteromeric protein complexes. The importance of interface add-ons for protein-protein interaction specificity is demonstrated by an exemplary experimental characterization of over 30 cognate and hybrid glutamine amidotransferase complexes in combination with comprehensive genetic profiling and protein design. Moreover, growth experiments showed that the lack of interface add-ons can lead to physiologically harmful cross-talk between essential biosynthetic pathways. In sum, our complementary in silico, in vitro, and in vivo analysis argues that interface add-ons are a practical and widespread evolutionary strategy to prevent the formation of nonphysiological complexes by specializing protein-protein interactions.

Evolutionary diversification of protein–protein interactions by interface add-ons

PubMed Central

Plach, Maximilian G.; Semmelmann, Florian; Busch, Florian; Busch, Markus; Heizinger, Leonhard; Wysocki, Vicki H.; Sterner, Reinhard

2017-01-01

Cells contain a multitude of protein complexes whose subunits interact with high specificity. However, the number of different protein folds and interface geometries found in nature is limited. This raises the question of how protein–protein interaction specificity is achieved on the structural level and how the formation of nonphysiological complexes is avoided. Here, we describe structural elements called interface add-ons that fulfill this function and elucidate their role for the diversification of protein–protein interactions during evolution. We identified interface add-ons in 10% of a representative set of bacterial, heteromeric protein complexes. The importance of interface add-ons for protein–protein interaction specificity is demonstrated by an exemplary experimental characterization of over 30 cognate and hybrid glutamine amidotransferase complexes in combination with comprehensive genetic profiling and protein design. Moreover, growth experiments showed that the lack of interface add-ons can lead to physiologically harmful cross-talk between essential biosynthetic pathways. In sum, our complementary in silico, in vitro, and in vivo analysis argues that interface add-ons are a practical and widespread evolutionary strategy to prevent the formation of nonphysiological complexes by specializing protein–protein interactions. PMID:28923934

Macroevolutionary dynamics in the early diversification of Asteraceae.

PubMed

Panero, Jose L; Crozier, Bonnie S

2016-06-01

Spatial and temporal differences in ecological opportunity can result in disparity of net species diversification rates and consequently uneven distribution of taxon richness across the tree of life. The largest eudicotyledonous plant family Asteraceae has a global distribution and at least 460 times more species than its South American endemic sister family Calyceraceae. In this study, diversification rate dynamics across Asteraceae are examined in light of the several hypothesized causes for the family's evolutionary success that could be responsible for rate change. The innovations of racemose capitulum and pappus, and a whole genome duplication event occurred near the origin of the family, yet we found the basal lineages of Asteraceae that evolved in South America share background diversification rates with Calyceraceae and their Australasian sister Goodeniaceae. Instead we found diversification rates increased gradually from the origin of Asteraceae approximately 69.5Ma in the late Cretaceous through the Early Eocene Climatic Optimum at least. In contrast to earlier studies, significant rate shifts were not strongly correlated with intercontinental dispersals or polyploidization. The difference is due primarily to sampling more backbone nodes, as well as calibrations placed internally in Asteraceae that resulted in earlier divergence times than those found in most previous relaxed clock studies. Two clades identified as having transformed rate processes are the Vernonioid Clade and a clade within the Heliantheae alliance characterized by phytomelanic fruit (PF Clade) that represents an American radiation. In Africa, subfamilies Carduoideae, Pertyoideae, Gymnarrhenoideae, Cichorioideae, Corymbioideae, and Asteroideae diverged in a relatively short span of only 6.5millionyears during the Middle Eocene. Copyright © 2016 Elsevier Inc. All rights reserved.

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

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.

The complex evolutionary dynamics of ancient and recent polyploidy in Leucaena (Leguminosae; Mimosoideae).

PubMed

Govindarajulu, Rajanikanth; Hughes, Colin E; Alexander, Patrick J; Bailey, C Donovan

2011-12-01

The evolutionary history of Leucaena has been impacted by polyploidy, hybridization, and divergent allopatric species diversification, suggesting that this is an ideal group to investigate the evolutionary tempo of polyploidy and the complexities of reticulation and divergence in plant diversification. Parsimony- and ML-based phylogenetic approaches were applied to 105 accessions sequenced for six sequence characterized amplified region-based nuclear encoded loci, nrDNA ITS, and four cpDNA regions. Hypotheses for the origin of tetraploid species were inferred using results derived from a novel species tree and established gene tree methods and from data on genome sizes and geographic distributions. The combination of comprehensively sampled multilocus DNA sequence data sets and a novel methodology provide strong resolution and support for the origins of all five tetraploid species. A minimum of four allopolyploidization events are required to explain the origins of these species. The origin(s) of one tetraploid pair (L. involucrata/L. pallida) can be equally explained by two unique allopolyploidizations or a single event followed by divergent speciation. Alongside other recent findings, a comprehensive picture of the complex evolutionary dynamics of polyploidy in Leucaena is emerging that includes paleotetraploidization, diploidization of the last common ancestor to Leucaena, allopatric divergence among diploids, and recent allopolyploid origins for tetraploid species likely associated with human translocation of seed. These results provide insights into the role of divergence and reticulation in a well-characterized angiosperm lineage and into traits of diploid parents and derived tetraploids (particularly self-compatibility and year-round flowering) favoring the formation and establishment of novel tetraploids combinations.

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

Plastome phylogeny and early diversification of Brassicaceae.

PubMed

Guo, Xinyi; Liu, Jianquan; Hao, Guoqian; Zhang, Lei; Mao, Kangshan; Wang, Xiaojuan; Zhang, Dan; Ma, Tao; Hu, Quanjun; Al-Shehbaz, Ihsan A; Koch, Marcus A

2017-02-16

The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies. Bayesian and maximum likelihood phylogenetic analyses using a partitioned supermatrix of 77 protein coding genes resulted in nearly identical tree topologies exemplified by highly supported relationships between clades. All four lineages were well identified and interrelationships between them were resolved. The previously defined Clade C was found to be paraphyletic (the genus Megadenia formed a separate lineage), while the remaining clades were monophyletic. Clade E (lineage III) was sister to clades B + C rather than to all core Brassicaceae (clades A + B + C or lineages I + II), as suggested by a previous transcriptome study. Molecular dating based on plastome phylogeny supported the origin of major lineages or clades between late Oligocene and early Miocene, and the following radiative diversification across the family took place within a short timescale. In addition, gene losses in the plastomes occurred multiple times during the evolutionary diversification of the family. Plastome phylogeny illustrates the early diversification of cruciferous species. This phylogeny will facilitate our further understanding of evolution and adaptation of numerous species in the model family Brassicaceae.

Novelties of the flowering plant pollen tube underlie diversification of a key life history stage

PubMed Central

Williams, Joseph H.

2008-01-01

The origin and rapid diversification of flowering plants has puzzled evolutionary biologists, dating back to Charles Darwin. Since that time a number of key life history and morphological traits have been proposed as developmental correlates of the extraordinary diversity and ecological success of angiosperms. Here, I identify several innovations that were fundamental to the evolutionary lability of angiosperm reproduction, and hence to their diversification. In gymnosperms pollen reception must be near the egg largely because sperm swim or are transported by pollen tubes that grow at very slow rates (< ≈20 μm/h). In contrast, pollen tube growth rates of taxa in ancient angiosperm lineages (Amborella, Nuphar, and Austrobaileya) range from ≈80 to 600 μm/h. Comparative analyses point to accelerated pollen tube growth rate as a critical innovation that preceded the origin of the true closed carpel, long styles, multiseeded ovaries, and, in monocots and eudicots, much faster pollen tube growth rates. Ancient angiosperm pollen tubes all have callosic walls and callose plugs (in contrast, no gymnosperms have these features). The early association of the callose-walled growth pattern with accelerated pollen tube growth rate underlies a striking repeated pattern of faster and longer-distance pollen tube growth often within solid pathways in phylogenetically derived angiosperms. Pollen tube innovations are a key component of the spectacular diversification of carpel (flower and fruit) form and reproductive cycles in flowering plants. PMID:18678915

Rapid diversification of Tragopogon and ecological associates in Eurasia.

PubMed

Bell, C D; Mavrodiev, E V; Soltis, P S; Calaminus, A K; Albach, D C; Cellinese, N; Garcia-Jacas, N; Soltis, D E

2012-12-01

Tragopogon comprises approximately 150 described species distributed throughout Eurasia from Ireland and the UK to India and China with a few species in North Africa. Most of the species diversity is found in Eastern Europe to Western Asia. Previous phylogenetic analyses identified several major clades, generally corresponding to recognized taxonomic sections, although relationships both among these clades and among species within clades remain largely unresolved. These patterns are consistent with rapid diversification following the origin of Tragopogon, and this study addresses the timing and rate of diversification in Tragopogon. Using BEAST to simultaneously estimate a phylogeny and divergence times, we estimate the age of a major split and subsequent rapid divergence within Tragopogon to be ~2.6 Ma (and 1.7-5.4 Ma using various clock estimates). Based on the age estimates obtained with BEAST (HPD 1.7-5.4 Ma) for the origin of crown group Tragopogon and 200 estimated species (to accommodate a large number of cryptic species), the diversification rate of Tragopogon is approximately 0.84-2.71 species/Myr for the crown group, assuming low levels of extinction. This estimate is comparable in rate to a rapid Eurasian radiation in Dianthus (0.66-3.89 species/Myr), which occurs in the same or similar habitats. Using available data, we show that subclades of various plant taxa that occur in the same semi-arid habitats of Eurasia also represent rapid radiations occurring during roughly the same window of time (1.7-5.4 Ma), suggesting similar causal events. However, not all species-rich plant genera from the same habitats diverged at the same time, or at the same tempo. Radiations of several other clades in this same habitat (e.g. Campanula, Knautia, Scabiosa) occurred at earlier dates (45-4.28 Ma). Existing phylogenetic data and diversification estimates therefore indicate that, although some elements of these semi-arid communities radiated during the Plio

The evolutionary origins of Syngnathidae: pipefishes and seahorses.

PubMed

Wilson, A B; Orr, J W

2011-06-01

Despite their importance as evolutionary and ecological model systems, the phylogenetic relationships among gasterosteiforms remain poorly understood, complicating efforts to understand the evolutionary origins of the exceptional morphological and behavioural diversity of this group. The present review summarizes current knowledge on the origin and evolution of syngnathids, a gasterosteiform family with a highly developed form of male parental care, combining inferences based on morphological and molecular data with paleontological evidence documenting the evolutionary history of the group. Molecular methods have provided new tools for the study of syngnathid relationships and have played an important role in recent conservation efforts. Despite recent insights into syngnathid evolution, however, a survey of the literature reveals a strong taxonomic bias towards studies on the species-rich genera Hippocampus and Syngnathus, with a lack of data for many morphologically unique members of the family. The study of the evolutionary pressures responsible for generating the high diversity of syngnathids would benefit from a wider perspective, providing a comparative framework in which to investigate the evolution of the genetic, morphological and behavioural traits of the group as a whole. © 2011 The Authors. Journal of Fish Biology © 2011 The Fisheries Society of the British Isles.

Sex-specific evolution during the diversification of live-bearing fishes.

PubMed

Culumber, Zachary W; Tobler, Michael

2017-08-01

Natural selection is often assumed to drive parallel functional diversification of the sexes. But males and females exhibit fundamental differences in their biology, and it remains largely unknown how sex differences affect macroevolutionary patterns. On microevolutionary scales, we understand how natural and sexual selection interact to give rise to sex-specific evolution during phenotypic diversification and speciation. Here we show that ignoring sex-specific patterns of functional trait evolution misrepresents the macroevolutionary adaptive landscape and evolutionary rates for 112 species of live-bearing fishes (Poeciliidae). Males and females of the same species evolve in different adaptive landscapes. Major axes of female morphology were correlated with environmental variables but not reproductive investment, while male morphological variation was primarily associated with sexual selection. Despite the importance of both natural and sexual selection in shaping sex-specific phenotypic diversification, species diversification was overwhelmingly associated with ecological divergence. Hence, the inter-predictability of mechanisms of phenotypic and species diversification may be limited in many systems. These results underscore the importance of explicitly addressing sex-specific diversification in empirical and theoretical frameworks of evolutionary radiations to elucidate the roles of different sources of selection and constraint.

Disentangling adaptive evolutionary radiations and the role of diet in promoting diversification on islands

NASA Astrophysics Data System (ADS)

Demiguel, Daniel

2016-07-01

Although the initial formulation of modern concepts of adaptive radiation arose from consideration of the fossil data, rigorous attempts to identify this phenomenon in the fossil record are largely uncommon. Here I focus on direct evidence of the diet (through tooth-wear patterns) and ecologically-relevant traits of one of the most renowned fossil vertebrates-the Miocene ruminant Hoplitomeryx from the island of Gargano-to deepen our understanding of the most likely causal forces under which adaptive radiations emerge on islands. Results show how accelerated accumulation of species and early-bursts of ecological diversification occur after invading an island, and provide insights on the interplay between diet and demographic (population-density), ecological (competition/food requirements) and abiotic (climate-instability) factors, identified as drivers of adaptive diversification. A pronounced event of overpopulation and a phase of aridity determined most of the rate and magnitude of radiation, and pushed species to expand diets from soft-leafy foods to tougher-harder items. Unexpectedly, results show that herbivorous mammals are restricted to browsing habits on small-islands, even if bursts of ecological diversification and dietary divergence occur. This study deepens our understanding of the mechanisms promoting adaptive radiations, and forces us to reevaluate the role of diet in the origins and evolution of islands mammals.

Disentangling adaptive evolutionary radiations and the role of diet in promoting diversification on islands

PubMed Central

DeMiguel, Daniel

2016-01-01

Although the initial formulation of modern concepts of adaptive radiation arose from consideration of the fossil data, rigorous attempts to identify this phenomenon in the fossil record are largely uncommon. Here I focus on direct evidence of the diet (through tooth-wear patterns) and ecologically-relevant traits of one of the most renowned fossil vertebrates-the Miocene ruminant Hoplitomeryx from the island of Gargano-to deepen our understanding of the most likely causal forces under which adaptive radiations emerge on islands. Results show how accelerated accumulation of species and early-bursts of ecological diversification occur after invading an island, and provide insights on the interplay between diet and demographic (population-density), ecological (competition/food requirements) and abiotic (climate-instability) factors, identified as drivers of adaptive diversification. A pronounced event of overpopulation and a phase of aridity determined most of the rate and magnitude of radiation, and pushed species to expand diets from soft-leafy foods to tougher-harder items. Unexpectedly, results show that herbivorous mammals are restricted to browsing habits on small-islands, even if bursts of ecological diversification and dietary divergence occur. This study deepens our understanding of the mechanisms promoting adaptive radiations, and forces us to reevaluate the role of diet in the origins and evolution of islands mammals. PMID:27405690

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.

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

Boom and bust: ancient and recent diversification in bichirs (Polypteridae: Actinopterygii), a relictual lineage of ray-finned fishes.

PubMed

Near, Thomas J; Dornburg, Alex; Tokita, Masayoshi; Suzuki, Dai; Brandley, Matthew C; Friedman, Matt

2014-04-01

Understanding the history that underlies patterns of species richness across the Tree of Life requires an investigation of the mechanisms that not only generate young species-rich clades, but also those that maintain species-poor lineages over long stretches of evolutionary time. However, diversification dynamics that underlie ancient species-poor lineages are often hidden due to a lack of fossil evidence. Using information from the fossil record and time calibrated molecular phylogenies, we investigate the history of lineage diversification in Polypteridae, which is the sister lineage of all other ray-finned fishes (Actinopterygii). Despite originating at least 390 million years (Myr) ago, molecular timetrees support a Neogene origin for the living polypterid species. Our analyses demonstrate polypterids are exceptionally species depauperate with a stem lineage duration that exceeds 380 million years (Ma) and is significantly longer than the stem lineage durations observed in other ray-finned fish lineages. Analyses of the fossil record show an early Late Cretaceous (100.5-83.6 Ma) peak in polypterid genus richness, followed by 60 Ma of low richness. The Neogene species radiation and evidence for high-diversity intervals in the geological past suggest a "boom and bust" pattern of diversification that contrasts with common perceptions of relative evolutionary stasis in so-called "living fossils." © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Eocene diversification of crown group rails (Aves: Gruiformes: Rallidae).

PubMed

García-R, Juan C; Gibb, Gillian C; Trewick, Steve A

2014-01-01

Central to our understanding of the timing of bird evolution is debate about an apparent conflict between fossil and molecular data. A deep age for higher level taxa within Neoaves is evident from molecular analyses but much remains to be learned about the age of diversification in modern bird families and their evolutionary ecology. In order to better understand the timing and pattern of diversification within the family Rallidae we used a relaxed molecular clock, fossil calibrations, and complete mitochondrial genomes from a range of rallid species analysed in a Bayesian framework. The estimated time of origin of Rallidae is Eocene, about 40.5 Mya, with evidence of intrafamiliar diversification from the Late Eocene to the Miocene. This timing is older than previously suggested for crown group Rallidae, but fossil calibrations, extent of taxon sampling and substantial sequence data give it credence. We note that fossils of Eocene age tentatively assigned to Rallidae are consistent with our findings. Compared to available studies of other bird lineages, the rail clade is old and supports an inference of deep ancestry of ground-dwelling habits among Neoaves.

Evolutionary history of aphid-plant associations and their role in aphid diversification.

PubMed

Peccoud, Jean; Simon, Jean-Christophe; von Dohlen, Carol; Coeur d'acier, Armelle; Plantegenest, Manuel; Vanlerberghe-Masutti, Flavie; Jousselin, Emmanuelle

2010-01-01

Aphids are intimately linked with their host plants that constitute their only food resource and habitat, and thus impose considerable selective pressure on their evolution. It is therefore commonly assumed that host plants have greatly influenced the diversification of aphids. Here, we review what is known about the role of host plant association on aphid speciation by examining both macroevolutionary and population-level studies. Phylogenetic studies conducted at different taxonomic levels show that, as in many phytophagous insect groups, the radiation of angiosperms has probably favoured the major Tertiary diversification of aphids. These studies also highlight many aphid lineages constrained to sets of related host plants, suggesting strong evolutionary commitment in aphids' host plant choice, but they fail to document cospeciation events between aphid and host lineages. Instead, phylogenies of several aphid genera reveal that divergence events are often accompanied by host shifts, and suggest, without constituting a formal demonstration, that aphid speciation could be a consequence of adaptation to new hosts. Experimental and field studies below the species level support reproductive isolation between host races as partly due to divergent selection by their host plants. Selected traits are mainly feeding performances and life cycle adaptations to plant phenology. Combined with behavioural preference for favourable host species, these divergent adaptations can induce pre- and post-zygotic barriers between host-specialized aphid populations. However, the hypothesis of host-driven speciation is seldom tested formally and must be weighed against overlooked explanations involving geographic isolation and non-ecological reproductive barriers in the process of speciation. Copyright 2010 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification.

PubMed

Robertson, Fiona M; Gundappa, Manu Kumar; Grammes, Fabian; Hvidsten, Torgeir R; Redmond, Anthony K; Lien, Sigbjørn; Martin, Samuel A M; Holland, Peter W H; Sandve, Simen R; Macqueen, Daniel J

2017-06-14

The functional divergence of duplicate genes (ohnologues) retained from whole genome duplication (WGD) is thought to promote evolutionary diversification. However, species radiation and phenotypic diversification are often temporally separated from WGD. Salmonid fish, whose ancestor underwent WGD by autotetraploidization ~95 million years ago, fit such a 'time-lag' model of post-WGD radiation, which occurred alongside a major delay in the rediploidization process. Here we propose a model, 'lineage-specific ohnologue resolution' (LORe), to address the consequences of delayed rediploidization. Under LORe, speciation precedes rediploidization, allowing independent ohnologue divergence in sister lineages sharing an ancestral WGD event. Using cross-species sequence capture, phylogenomics and genome-wide analyses of ohnologue expression divergence, we demonstrate the major impact of LORe on salmonid evolution. One-quarter of each salmonid genome, harbouring at least 4550 ohnologues, has evolved under LORe, with rediploidization and functional divergence occurring on multiple independent occasions >50 million years post-WGD. We demonstrate the existence and regulatory divergence of many LORe ohnologues with functions in lineage-specific physiological adaptations that potentially facilitated salmonid species radiation. We show that LORe ohnologues are enriched for different functions than 'older' ohnologues that began diverging in the salmonid ancestor. LORe has unappreciated significance as a nested component of post-WGD divergence that impacts the functional properties of genes, whilst providing ohnologues available solely for lineage-specific adaptation. Under LORe, which is predicted following many WGD events, the functional outcomes of WGD need not appear 'explosively', but can arise gradually over tens of millions of years, promoting lineage-specific diversification regimes under prevailing ecological pressures.

An evolutionary scenario for the origin of flowers.

PubMed

Frohlich, Michael W

2003-07-01

The Mostly Male theory is the first to use evidence from gene phylogenies, genetics, modern plant morphology and fossils to explain the evolutionary origin of flowers. It proposes that flower organization derives more from the male structures of ancestral gymnosperms than from female structures. The theory arose from a hypothesis-based study. Such studies are the most likely to generate testable evolutionary scenarios, which should be the ultimate goal of evo-devo.

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

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.

Origin, evolution, and biogeography of Juglans: a phylogenetic perspective

USDA-ARS?s Scientific Manuscript database

Phylogenetic analyses of extant Juglans (Juglandaceae) using five cpDNA intergenic spacer (IGS) sequences (trnT-trnF, psbA-trnH, atpB-rbcL, trnV-16S rRNA, and trnS-trnfM) were performed to elucidate the origin, diversification, historical biogeography, and evolutionary relationships within the genus...

The Complex Demographic History and Evolutionary Origin of the Western Honey Bee, Apis Mellifera

PubMed Central

Tsutsui, Neil D.; Ramírez, Santiago R.

2017-01-01

The western honey bee, Apis mellifera, provides critical pollination services to agricultural crops worldwide. However, despite substantial interest and prior investigation, the early evolution and subsequent diversification of this important pollinator remain uncertain. The primary hypotheses place the origin of A. mellifera in either Asia or Africa, with subsequent radiations proceeding from one of these regions. Here, we use two publicly available whole-genome data sets plus newly sequenced genomes and apply multiple population genetic analysis methods to investigate the patterns of ancestry and admixture in native honey bee populations from Europe, Africa, and the Middle East. The combination of these data sets is critical to the analyses, as each contributes samples from geographic locations lacking in the other, thereby producing the most complete set of honey bee populations available to date. We find evidence supporting an origin of A. mellifera in the Middle East or North Eastern Africa, with the A and Y lineages representing the earliest branching lineages. This finding has similarities with multiple contradictory hypotheses and represents a disentangling of genetic relationships, geographic proximity, and secondary contact to produce a more accurate picture of the origins of A. mellifera. We also investigate how previous studies came to their various conclusions based on incomplete sampling of populations, and illustrate the importance of complete sampling in understanding evolutionary processes. These results provide fundamental knowledge about genetic diversity within Old World honey bee populations and offer insight into the complex history of an important pollinator. PMID:28164223

Approaches to Macroevolution: 1. General Concepts and Origin of Variation.

PubMed

Jablonski, David

2017-01-01

Approaches to macroevolution require integration of its two fundamental components, i.e. the origin and the sorting of variation, in a hierarchical framework. Macroevolution occurs in multiple currencies that are only loosely correlated, notably taxonomic diversity, morphological disparity, and functional variety. The origin of variation within this conceptual framework is increasingly understood in developmental terms, with the semi-hierarchical structure of gene regulatory networks (GRNs, used here in a broad sense incorporating not just the genetic circuitry per se but the factors controlling the timing and location of gene expression and repression), the non-linear relation between magnitude of genetic change and the phenotypic results, the evolutionary potential of co-opting existing GRNs, and developmental responsiveness to nongenetic signals (i.e. epigenetics and plasticity), all requiring modification of standard microevolutionary models, and rendering difficult any simple definition of evolutionary novelty. The developmental factors underlying macroevolution create anisotropic probabilities-i.e., an uneven density distribution-of evolutionary change around any given phenotypic starting point, and the potential for coordinated changes among traits that can accommodate change via epigenetic mechanisms. From this standpoint, "punctuated equilibrium" and "phyletic gradualism" simply represent two cells in a matrix of evolutionary models of phenotypic change, and the origin of trends and evolutionary novelty are not simply functions of ecological opportunity. Over long timescales, contingency becomes especially important, and can be viewed in terms of macroevolutionary lags (the temporal separation between the origin of a trait or clade and subsequent diversification); such lags can arise by several mechanisms: as geological or phylogenetic artifacts, or when diversifications require synergistic interactions among traits, or between traits and external events

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.

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

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.

Is specialization an evolutionary dead end? Testing for differences in speciation, extinction and trait transition rates across diverse phylogenies of specialists and generalists.

PubMed

Day, E H; Hua, X; Bromham, L

2016-06-01

Specialization has often been claimed to be an evolutionary dead end, with specialist lineages having a reduced capacity to persist or diversify. In a phylogenetic comparative framework, an evolutionary dead end may be detectable from the phylogenetic distribution of specialists, if specialists rarely give rise to large, diverse clades. Previous phylogenetic studies of the influence of specialization on macroevolutionary processes have demonstrated a range of patterns, including examples where specialists have both higher and lower diversification rates than generalists, as well as examples where the rates of evolutionary transitions from generalists to specialists are higher, lower or equal to transitions from specialists to generalists. Here, we wish to ask whether these varied answers are due to the differences in macroevolutionary processes in different clades, or partly due to differences in methodology. We analysed ten phylogenies containing multiple independent origins of specialization and quantified the phylogenetic distribution of specialists by applying a common set of metrics to all datasets. We compared the tip branch lengths of specialists to generalists, the size of specialist clades arising from each evolutionary origin of a specialized trait and whether specialists tend to be clustered or scattered on phylogenies. For each of these measures, we compared the observed values to expectations under null models of trait evolution and expected outcomes under alternative macroevolutionary scenarios. We found that specialization is sometimes an evolutionary dead end: in two of the ten case studies (pollinator-specific plants and host-specific flies), specialization is associated with a reduced rate of diversification or trait persistence. However, in the majority of studies, we could not distinguish the observed phylogenetic distribution of specialists from null models in which specialization has no effect on diversification or trait persistence. © 2016

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.

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.

A molecular genetic time scale demonstrates Cretaceous origins and multiple diversification rate shifts within the order Galliformes (Aves).

PubMed

Stein, R Will; Brown, Joseph W; Mooers, Arne Ø

2015-11-01

The phylogeny of Galliformes (landfowl) has been studied extensively; however, the associated chronologies have been criticized recently due to misplaced or misidentified fossil calibrations. As a consequence, it is unclear whether any crown-group lineages arose in the Cretaceous and survived the Cretaceous-Paleogene (K-Pg; 65.5 Ma) mass extinction. Using Bayesian phylogenetic inference on an alignment spanning 14,539 bp of mitochondrial and nuclear DNA sequence data, four fossil calibrations, and a combination of uncorrelated lognormally distributed relaxed-clock and strict-clock models, we inferred a time-calibrated molecular phylogeny for 225 of the 291 extant Galliform taxa. These analyses suggest that crown Galliformes diversified in the Cretaceous and that three-stem lineages survived the K-Pg mass extinction. Ideally, characterizing the tempo and mode of diversification involves a taxonomically complete phylogenetic hypothesis. We used simple constraint structures to incorporate 66 data-deficient taxa and inferred the first taxon-complete phylogenetic hypothesis for the Galliformes. Diversification analyses conducted on 10,000 timetrees sampled from the posterior distribution of candidate trees show that the evolutionary history of the Galliformes is best explained by a rate-shift model including 1-3 clade-specific increases in diversification rate. We further show that the tempo and mode of diversification in the Galliformes conforms to a three-pulse model, with three-stem lineages arising in the Cretaceous and inter and intrafamilial diversification occurring after the K-Pg mass extinction, in the Paleocene-Eocene (65.5-33.9 Ma) or in association with the Eocene-Oligocene transition (33.9 Ma). Copyright © 2015 Elsevier Inc. All rights reserved.

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

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

The fossil record of evolution: Data on diversification and extinction

NASA Technical Reports Server (NTRS)

Sepkoski, J. John, Jr.

1990-01-01

The two principle efforts include: (1) a compilation of a synoptic, mesoscale data base on times of origination and extinction of animal genera in the oceans over the last 600 million years of geologic time; and (2) an analysis of statistical patterns in these data that relate to the diversification of complex life and to the occurrence of mass extinctions, especially those that might be associated with extraterrestrial phenomena. The data base is unique in its taxonomic scope and detail and in its temporal resolution. It is a valuable resource for investigating evolutionary expansions and extinctions of complex life.

Diversification rates, host plant shifts and an updated molecular phylogeny of Andean Eois moths (Lepidoptera: Geometridae)

PubMed Central

Brehm, Gunnar; Gottsberger, Brigitte; Bodner, Florian; Seifert, Carlo Lutz; Fiedler, Konrad

2017-01-01

Eois is one of the best-investigated genera of tropical moths. Its close association with Piper plants has inspired numerous studies on life histories, phylogeny and evolutionary biology. This study provides an updated view on phylogeny, host plant use and temporal patterns of speciation in Eois. Using sequence data (2776 bp) from one mitochondrial (COI) and one nuclear gene (Ef1-alpha) for 221 Eois species, we confirm and reinforce previous findings regarding temporal patterns of diversification. Deep diversification within Andean Eois took place in the Miocene followed by a sustained high rate of diversification until the Pleistocene when a pronounced slowdown of speciation is evident. In South America, Eois diversification is very likely to be primarily driven by the Andean uplift which occurred concurrently with the entire evolutionary history of Eois. A massively expanded dataset enabled an in-depth look into the phylogenetic signal contained in host plant usage. This revealed several independent shifts from Piper to other host plant genera and families. Seven shifts to Peperomia, the sister genus of Piper were detected, indicating that the shift to Peperomia was an easy one compared to the singular shifts to the Chloranthaceae, Siparunaceae and the Piperacean genus Manekia. The potential for close co-evolution of Eois with Piper host plants is therefore bound to be limited to smaller subsets within Neotropical Eois instead of a frequently proposed genus-wide co-evolutionary scenario. In regards to Eois systematics we confirm the monophyly of Neotropical Eois in relation to their Old World counterparts. A tentative biogeographical hypothesis is presented suggesting that Eois originated in tropical Asia and subsequently colonized the Neotropics and Africa. Within Neotropical Eois we were able to identify the existence of six clades not recognized in previous studies and confirm and reinforce the monophyly of all 9 previously delimited infrageneric clades. PMID

Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling

PubMed Central

Pardo-Diaz, Carolina; Hanly, Joseph J.; Martin, Simon H.; Mallet, James; Dasmahapatra, Kanchon K.; Salazar, Camilo; Joron, Mathieu; Nadeau, Nicola; McMillan, W. Owen; Jiggins, Chris D.

2016-01-01

An important goal in evolutionary biology is to understand the genetic changes underlying novel morphological structures. We investigated the origins of a complex wing pattern found among Amazonian Heliconius butterflies. Genome sequence data from 142 individuals across 17 species identified narrow regions associated with two distinct red colour pattern elements, dennis and ray. We hypothesise that these modules in non-coding sequence represent distinct cis-regulatory loci that control expression of the transcription factor optix, which in turn controls red pattern variation across Heliconius. Phylogenetic analysis of the two elements demonstrated that they have distinct evolutionary histories and that novel adaptive morphological variation was created by shuffling these cis-regulatory modules through recombination between divergent lineages. In addition, recombination of modules into different combinations within species further contributes to diversity. Analysis of the timing of diversification in these two regions supports the hypothesis of introgression moving regulatory modules between species, rather than shared ancestral variation. The dennis phenotype introgressed into Heliconius melpomene at about the same time that ray originated in this group, while ray introgressed back into H. elevatus much more recently. We show that shuffling of existing enhancer elements both within and between species provides a mechanism for rapid diversification and generation of novel morphological combinations during adaptive radiation. PMID:26771987

Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling.

PubMed

Wallbank, Richard W R; Baxter, Simon W; Pardo-Diaz, Carolina; Hanly, Joseph J; Martin, Simon H; Mallet, James; Dasmahapatra, Kanchon K; Salazar, Camilo; Joron, Mathieu; Nadeau, Nicola; McMillan, W Owen; Jiggins, Chris D

2016-01-01

An important goal in evolutionary biology is to understand the genetic changes underlying novel morphological structures. We investigated the origins of a complex wing pattern found among Amazonian Heliconius butterflies. Genome sequence data from 142 individuals across 17 species identified narrow regions associated with two distinct red colour pattern elements, dennis and ray. We hypothesise that these modules in non-coding sequence represent distinct cis-regulatory loci that control expression of the transcription factor optix, which in turn controls red pattern variation across Heliconius. Phylogenetic analysis of the two elements demonstrated that they have distinct evolutionary histories and that novel adaptive morphological variation was created by shuffling these cis-regulatory modules through recombination between divergent lineages. In addition, recombination of modules into different combinations within species further contributes to diversity. Analysis of the timing of diversification in these two regions supports the hypothesis of introgression moving regulatory modules between species, rather than shared ancestral variation. The dennis phenotype introgressed into Heliconius melpomene at about the same time that ray originated in this group, while ray introgressed back into H. elevatus much more recently. We show that shuffling of existing enhancer elements both within and between species provides a mechanism for rapid diversification and generation of novel morphological combinations during adaptive radiation.

Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation

PubMed Central

2011-01-01

Background Freshwater harbors approximately 12,000 fish species accounting for 43% of the diversity of all modern fish. A single ancestral lineage evolved into about two-thirds of this enormous biodiversity (≈ 7900 spp.) and is currently distributed throughout the world's continents except Antarctica. Despite such remarkable species diversity and ubiquity, the evolutionary history of this major freshwater fish clade, Otophysi, remains largely unexplored. To gain insight into the history of otophysan diversification, we constructed a timetree based on whole mitogenome sequences across 110 species representing 55 of the 64 families. Results Partitioned maximum likelihood analysis based on unambiguously aligned sequences (9923 bp) confidently recovered the monophyly of Otophysi and the two constituent subgroups (Cypriniformes and Characiphysi). The latter clade comprised three orders (Gymnotiformes, Characiformes, Siluriformes), and Gymnotiformes was sister to the latter two groups. One of the two suborders in Characiformes (Characoidei) was more closely related to Siluriformes than to its own suborder (Citharinoidei), rendering the characiforms paraphyletic. Although this novel relationship did not receive strong statistical support, it was supported by analyzing independent nuclear markers. A relaxed molecular clock Bayesian analysis of the divergence times and reconstruction of ancestral habitats on the timetree suggest a Pangaean origin and Mesozoic radiation of otophysans. Conclusions The present timetree demonstrates that survival of the ancestral lineages through the two consecutive mass extinctions on Pangaea, and subsequent radiations during the Jurassic through early Cretaceous shaped the modern familial diversity of otophysans. This evolutionary scenario is consistent with recent arguments based on biogeographic inferences and molecular divergence time estimates. No fossil otophysan, however, has been recorded before the Albian, the early Cretaceous 100

Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation.

PubMed

Nakatani, Masanori; Miya, Masaki; Mabuchi, Kohji; Saitoh, Kenji; Nishida, Mutsumi

2011-06-22

Freshwater harbors approximately 12,000 fish species accounting for 43% of the diversity of all modern fish. A single ancestral lineage evolved into about two-thirds of this enormous biodiversity (≈ 7900 spp.) and is currently distributed throughout the world's continents except Antarctica. Despite such remarkable species diversity and ubiquity, the evolutionary history of this major freshwater fish clade, Otophysi, remains largely unexplored. To gain insight into the history of otophysan diversification, we constructed a timetree based on whole mitogenome sequences across 110 species representing 55 of the 64 families. Partitioned maximum likelihood analysis based on unambiguously aligned sequences (9923 bp) confidently recovered the monophyly of Otophysi and the two constituent subgroups (Cypriniformes and Characiphysi). The latter clade comprised three orders (Gymnotiformes, Characiformes, Siluriformes), and Gymnotiformes was sister to the latter two groups. One of the two suborders in Characiformes (Characoidei) was more closely related to Siluriformes than to its own suborder (Citharinoidei), rendering the characiforms paraphyletic. Although this novel relationship did not receive strong statistical support, it was supported by analyzing independent nuclear markers. A relaxed molecular clock Bayesian analysis of the divergence times and reconstruction of ancestral habitats on the timetree suggest a Pangaean origin and Mesozoic radiation of otophysans. The present timetree demonstrates that survival of the ancestral lineages through the two consecutive mass extinctions on Pangaea, and subsequent radiations during the Jurassic through early Cretaceous shaped the modern familial diversity of otophysans. This evolutionary scenario is consistent with recent arguments based on biogeographic inferences and molecular divergence time estimates. No fossil otophysan, however, has been recorded before the Albian, the early Cretaceous 100-112 Ma, creating an over 100

The vertebrate Hox gene regulatory network for hindbrain segmentation: Evolution and diversification: Coupling of a Hox gene regulatory network to hindbrain segmentation is an ancient trait originating at the base of vertebrates.

PubMed

Parker, Hugo J; Bronner, Marianne E; Krumlauf, Robb

2016-06-01

Hindbrain development is orchestrated by a vertebrate gene regulatory network that generates segmental patterning along the anterior-posterior axis via Hox genes. Here, we review analyses of vertebrate and invertebrate chordate models that inform upon the evolutionary origin and diversification of this network. Evidence from the sea lamprey reveals that the hindbrain regulatory network generates rhombomeric compartments with segmental Hox expression and an underlying Hox code. We infer that this basal feature was present in ancestral vertebrates and, as an evolutionarily constrained developmental state, is fundamentally important for patterning of the vertebrate hindbrain across diverse lineages. Despite the common ground plan, vertebrates exhibit neuroanatomical diversity in lineage-specific patterns, with different vertebrates revealing variations of Hox expression in the hindbrain that could underlie this diversification. Invertebrate chordates lack hindbrain segmentation but exhibit some conserved aspects of this network, with retinoic acid signaling playing a role in establishing nested domains of Hox expression. © 2016 WILEY Periodicals, Inc.

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

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

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.

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

Near-Stasis in the Long-Term Diversification of Mesozoic Tetrapods

PubMed Central

Benson, Roger B. J.; Butler, Richard J.; Alroy, John; Mannion, Philip D.; Carrano, Matthew T.; Lloyd, Graeme T.

2016-01-01

How did evolution generate the extraordinary diversity of vertebrates on land? Zero species are known prior to ~380 million years ago, and more than 30,000 are present today. An expansionist model suggests this was achieved by large and unbounded increases, leading to substantially greater diversity in the present than at any time in the geological past. This model contrasts starkly with empirical support for constrained diversification in marine animals, suggesting different macroevolutionary processes on land and in the sea. We quantify patterns of vertebrate standing diversity on land during the Mesozoic–early Paleogene interval, applying sample-standardization to a global fossil dataset containing 27,260 occurrences of 4,898 non-marine tetrapod species. Our results show a highly stable pattern of Mesozoic tetrapod diversity at regional and local levels, underpinned by a weakly positive, but near-zero, long-term net diversification rate over 190 million years. Species diversity of non-flying terrestrial tetrapods less than doubled over this interval, despite the origins of exceptionally diverse extant groups within mammals, squamates, amphibians, and dinosaurs. Therefore, although speciose groups of modern tetrapods have Mesozoic origins, rates of Mesozoic diversification inferred from the fossil record are slow compared to those inferred from molecular phylogenies. If high speciation rates did occur in the Mesozoic, then they seem to have been balanced by extinctions among older clades. An apparent 4-fold expansion of species richness after the Cretaceous/Paleogene (K/Pg) boundary deserves further examination in light of potential taxonomic biases, but is consistent with the hypothesis that global environmental disturbances such as mass extinction events can rapidly adjust limits to diversity by restructuring ecosystems, and suggests that the gradualistic evolutionary diversification of tetrapods was punctuated by brief but dramatic episodes of radiation

Neutral stability, drift, and the diversification of languages.

PubMed

Pawlowitsch, Christina; Mertikopoulos, Panayotis; Ritt, Nikolaus

2011-10-21

The diversification of languages is one of the most interesting facts about language that seek explanation from an evolutionary point of view. Conceptually the question is related to explaining mechanisms of speciation. An argument that prominently figures in evolutionary accounts of language diversification is that it serves the formation of group markers which help to enhance in-group cooperation. In this paper we use the theory of evolutionary games to show that language diversification on the level of the meaning of lexical items can come about in a perfectly cooperative world solely as a result of the effects of frequency-dependent selection. Importantly, our argument does not rely on some stipulated function of language diversification in some co-evolutionary process, but comes about as an endogenous feature of the model. The model that we propose is an evolutionary language game in the style of Nowak et al. (1999) [The evolutionary language game. J. Theor. Biol. 200, 147-162], which has been used to explain the rise of a signaling system or protolanguage from a prelinguistic environment. Our analysis focuses on the existence of neutrally stable polymorphisms in this model, where, on the level of the population, a signal can be used for more than one concept or a concept can be inferred by more than one signal. Specifically, such states cannot be invaded by a mutation for bidirectionality, that is, a mutation that tries to resolve the existing ambiguity by linking each concept to exactly one signal in a bijective way. However, such states are not resistant against drift between the selectively neutral variants that are present in such a state. Neutral drift can be a pathway for a mutation for bidirectionality that was blocked before but that finally will take over the population. Different directions of neutral drift open the door for a mutation for bidirectionality to appear on different resident types. This mechanism-which can be seen as a form of shifting

Evolutionary process of deep-sea bathymodiolus mussels.

PubMed

Miyazaki, Jun-Ichi; de Oliveira Martins, Leonardo; Fujita, Yuko; Matsumoto, Hiroto; Fujiwara, Yoshihiro

2010-04-27

Since the discovery of deep-sea chemosynthesis-based communities, much work has been done to clarify their organismal and environmental aspects. However, major topics remain to be resolved, including when and how organisms invade and adapt to deep-sea environments; whether strategies for invasion and adaptation are shared by different taxa or unique to each taxon; how organisms extend their distribution and diversity; and how they become isolated to speciate in continuous waters. Deep-sea mussels are one of the dominant organisms in chemosynthesis-based communities, thus investigations of their origin and evolution contribute to resolving questions about life in those communities. We investigated worldwide phylogenetic relationships of deep-sea Bathymodiolus mussels and their mytilid relatives by analyzing nucleotide sequences of the mitochondrial cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 4 (ND4) genes. Phylogenetic analysis of the concatenated sequence data showed that mussels of the subfamily Bathymodiolinae from vents and seeps were divided into four groups, and that mussels of the subfamily Modiolinae from sunken wood and whale carcasses assumed the outgroup position and shallow-water modioline mussels were positioned more distantly to the bathymodioline mussels. We provisionally hypothesized the evolutionary history of Bathymodilolus mussels by estimating evolutionary time under a relaxed molecular clock model. Diversification of bathymodioline mussels was initiated in the early Miocene, and subsequently diversification of the groups occurred in the early to middle Miocene. The phylogenetic relationships support the "Evolutionary stepping stone hypothesis," in which mytilid ancestors exploited sunken wood and whale carcasses in their progressive adaptation to deep-sea environments. This hypothesis is also supported by the evolutionary transition of symbiosis in that nutritional adaptation to the deep sea proceeded from extracellular

Myrteae phylogeny, calibration, biogeography and diversification patterns: Increased understanding in the most species rich tribe of Myrtaceae.

PubMed

Vasconcelos, Thais N C; Proença, Carol E B; Ahmad, Berhaman; Aguilar, Daniel S; Aguilar, Reinaldo; Amorim, Bruno S; Campbell, Keron; Costa, Itayguara R; De-Carvalho, Plauto S; Faria, Jair E Q; Giaretta, Augusto; Kooij, Pepijn W; Lima, Duane F; Mazine, Fiorella F; Peguero, Brigido; Prenner, Gerhard; Santos, Matheus F; Soewarto, Julia; Wingler, Astrid; Lucas, Eve J

2017-04-01

Myrteae (c. 2500 species; 51 genera) is the largest tribe of Myrtaceae and an ecologically important groups of angiosperms in the Neotropics. Systematic relationships in Myrteae are complex, hindering conservation initiatives and jeopardizing evolutionary modelling. A well-supported and robust phylogenetic hypothesis was here targeted towards a comprehensive understanding of the relationships within the tribe. The resultant topology was used as a base for key evolutionary analyses such as age estimation, historical biogeography and diversification rate patterns. One nuclear (ITS) and seven chloroplast (psbA-trnH, matK, ndhF, trnl-trnF, trnQ-rps16, rpl16 and rpl32-trnL) DNA regions for 115 taxa representing 46 out of the 51 genera in the tribe were accessed and analysed using maximum likelihood and Bayesian inference tools for phylogenetic reconstruction. Dates of diversification events were estimated and contrasted using two distinct fossil sets (macro and pollen) in BEAST. The subsequent dated phylogenies were compared and analysed for biogeographical patterns using BioGeoBEARS and diversification rates using BAMM. Myrteae phylogeny presents strong statistical support for three major clades within the tribe: Australasian group, Myrtus group and Main Neotropical Lineage. Dating results from calibration using macrofossil are an average of 20 million years older and show an early Paleocene origin of Myrteae, against a mid-Eocene one from the pollen fossil calibration. Biogeographic analysis shows the origin of Myrteae in Zealandia in both calibration approaches, followed by a widespread distribution throughout the still-linked Gondwana continents and diversification of Neotropical endemic lineages by later vicariance. Best configuration shift indicates three points of acceleration in diversification rates, all of them occurring in the Main Neotropical Lineage. Based on the reconstructed topology, several new taxonomic placements were recovered, including: the

The influence of body size and net diversification rate on molecular evolution during the radiation of animal phyla

PubMed Central

Fontanillas, Eric; Welch, John J; Thomas, Jessica A; Bromham, Lindell

2007-01-01

Background Molecular clock dates, which place the origin of animal phyla deep in the Precambrian, have been used to reject the hypothesis of a rapid evolutionary radiation of animal phyla supported by the fossil record. One possible explanation of the discrepancy is the potential for fast substitution rates early in the metazoan radiation. However, concerted rate variation, occurring simultaneously in multiple lineages, cannot be detected by "clock tests", and so another way to explore such variation is to look for correlated changes between rates and other biological factors. Here we investigate two possible causes of fast early rates: change in average body size or diversification rate of deep metazoan lineages. Results For nine genes for phylogenetically independent comparisons between 50 metazoan phyla, orders, and classes, we find a significant correlation between average body size and rate of molecular evolution of mitochondrial genes. The data also indicate that diversification rate may have a positive effect on rates of mitochondrial molecular evolution. Conclusion If average body sizes were significantly smaller in the early history of the Metazoa, and if rates of diversification were much higher, then it is possible that mitochondrial genes have undergone a slow-down in evolutionary rate, which could affect date estimates made from these genes. PMID:17592650

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.

Origin and Evolutionary Alteration of the Mitochondrial Import System in Eukaryotic Lineages

PubMed Central

Fukasawa, Yoshinori; Oda, Toshiyuki; Tomii, Kentaro

2017-01-01

Abstract Protein transport systems are fundamentally important for maintaining mitochondrial function. Nevertheless, mitochondrial protein translocases such as the kinetoplastid ATOM complex have recently been shown to vary in eukaryotic lineages. Various evolutionary hypotheses have been formulated to explain this diversity. To resolve any contradiction, estimating the primitive state and clarifying changes from that state are necessary. Here, we present more likely primitive models of mitochondrial translocases, specifically the translocase of the outer membrane (TOM) and translocase of the inner membrane (TIM) complexes, using scrutinized phylogenetic profiles. We then analyzed the translocases’ evolution in eukaryotic lineages. Based on those results, we propose a novel evolutionary scenario for diversification of the mitochondrial transport system. Our results indicate that presequence transport machinery was mostly established in the last eukaryotic common ancestor, and that primitive translocases already had a pathway for transporting presequence-containing proteins. Moreover, secondary changes including convergent and migrational gains of a presequence receptor in TOM and TIM complexes, respectively, likely resulted from constrained evolution. The nature of a targeting signal can constrain alteration to the protein transport complex. PMID:28369657

[The Evolutionary Origin of Placodes and Neural Crest Cells

NASA Technical Reports Server (NTRS)

Bronner-Fraser, Marianne

2003-01-01

The long-term goal of this NASA-supported research is to understand the evolutionary origin of placodes and neural crest cells, with particular reference to evolution of the inner ear, and their evolutionary and developmental relationships. The cephalochordcate amphioxus, the closest living invertebrate relative of the vertebrates is used as a stand-in for the ancestral vertebrate. The research, which has supported one graduate student, Jr-Kai Yu, has resulted in ten publications by the Holland laboratory in peer-reviewed journals.

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.

The evolutionary origins of Lévy walk foraging

PubMed Central

Wosniack, Marina E.

2017-01-01

We study through a reaction-diffusion algorithm the influence of landscape diversity on the efficiency of search dynamics. Remarkably, the identical optimal search strategy arises in a wide variety of environments, provided the target density is sparse and the searcher’s information is restricted to its close vicinity. Our results strongly impact the current debate on the emergentist vs. evolutionary origins of animal foraging. The inherent character of the optimal solution (i.e., independent on the landscape for the broad scenarios assumed here) suggests an interpretation favoring the evolutionary view, as originally implied by the Lévy flight foraging hypothesis. The latter states that, under conditions of scarcity of information and sparse resources, some organisms must have evolved to exploit optimal strategies characterized by heavy-tailed truncated power-law distributions of move lengths. These results strongly suggest that Lévy strategies—and hence the selection pressure for the relevant adaptations—are robust with respect to large changes in habitat. In contrast, the usual emergentist explanation seems not able to explain how very similar Lévy walks can emerge from all the distinct non-Lévy foraging strategies that are needed for the observed large variety of specific environments. We also report that deviations from Lévy can take place in plentiful ecosystems, where locomotion truncation is very frequent due to high encounter rates. So, in this case normal diffusion strategies—performing as effectively as the optimal one—can naturally emerge from Lévy. Our results constitute the strongest theoretical evidence to date supporting the evolutionary origins of experimentally observed Lévy walks. PMID:28972973

Contrasting biogeographic and diversification patterns in two Mediterranean-type ecosystems.

PubMed

Buerki, Sven; Jose, Sarah; Yadav, Shrirang R; Goldblatt, Peter; Manning, John C; Forest, Félix

2012-01-01

The five Mediterranean regions of the world comprise almost 50,000 plant species (ca 20% of the known vascular plants) despite accounting for less than 5% of the world's land surface. The ecology and evolutionary history of two of these regions, the Cape Floristic Region and the Mediterranean Basin, have been extensively investigated, but there have been few studies aimed at understanding the historical relationships between them. Here, we examine the biogeographic and diversification processes that shaped the evolution of plant diversity in the Cape and the Mediterranean Basin using a large plastid data set for the geophyte family Hyacinthaceae (comprising ca. 25% of the total diversity of the group), a group found mainly throughout Africa and Eurasia. Hyacinthaceae is a predominant group in the Cape and the Mediterranean Basin both in terms of number of species and their morphological and ecological variability. Using state-of-the-art methods in biogeography and diversification, we found that the Old World members of the family originated in sub-Saharan Africa at the Paleocene-Eocene boundary and that the two Mediterranean regions both have high diversification rates, but contrasting biogeographic histories. While the Cape diversity has been greatly influenced by its relationship with sub-Saharan Africa throughout the history of the family, the Mediterranean Basin had no connection with the latter after the onset of the Mediterranean climate in the region and the aridification of the Sahara. The Mediterranean Basin subsequently contributed significantly to the diversity of neighbouring areas, especially Northern Europe and the Middle East, whereas the Cape can be seen as a biogeographical cul-de-sac, with only a few dispersals toward sub-Saharan Africa. The understanding of the evolutionary history of these two important repositories of biodiversity would benefit from the application of the framework developed here to other groups of plants present in the two

Evolutionary Origins of Cancer Driver Genes and Implications for Cancer Prognosis

PubMed Central

Chu, Xin-Yi; Zhou, Xiong-Hui; Cui, Ze-Jia; Zhang, Hong-Yu

2017-01-01

The cancer atavistic theory suggests that carcinogenesis is a reverse evolution process. It is thus of great interest to explore the evolutionary origins of cancer driver genes and the relevant mechanisms underlying the carcinogenesis. Moreover, the evolutionary features of cancer driver genes could be helpful in selecting cancer biomarkers from high-throughput data. In this study, through analyzing the cancer endogenous molecular networks, we revealed that the subnetwork originating from eukaryota could control the unlimited proliferation of cancer cells, and the subnetwork originating from eumetazoa could recapitulate the other hallmarks of cancer. In addition, investigations based on multiple datasets revealed that cancer driver genes were enriched in genes originating from eukaryota, opisthokonta, and eumetazoa. These results have important implications for enhancing the robustness of cancer prognosis models through selecting the gene signatures by the gene age information. PMID:28708071

Evolutionary Origins of Cancer Driver Genes and Implications for Cancer Prognosis.

PubMed

Chu, Xin-Yi; Jiang, Ling-Han; Zhou, Xiong-Hui; Cui, Ze-Jia; Zhang, Hong-Yu

2017-07-14

The cancer atavistic theory suggests that carcinogenesis is a reverse evolution process. It is thus of great interest to explore the evolutionary origins of cancer driver genes and the relevant mechanisms underlying the carcinogenesis. Moreover, the evolutionary features of cancer driver genes could be helpful in selecting cancer biomarkers from high-throughput data. In this study, through analyzing the cancer endogenous molecular networks, we revealed that the subnetwork originating from eukaryota could control the unlimited proliferation of cancer cells, and the subnetwork originating from eumetazoa could recapitulate the other hallmarks of cancer. In addition, investigations based on multiple datasets revealed that cancer driver genes were enriched in genes originating from eukaryota, opisthokonta, and eumetazoa. These results have important implications for enhancing the robustness of cancer prognosis models through selecting the gene signatures by the gene age information.

The Complex Demographic History and Evolutionary Origin of the Western Honey Bee, Apis Mellifera.

PubMed

Cridland, Julie M; Tsutsui, Neil D; Ramírez, Santiago R

2017-02-01

The western honey bee, Apis mellifera, provides critical pollination services to agricultural crops worldwide. However, despite substantial interest and prior investigation, the early evolution and subsequent diversification of this important pollinator remain uncertain. The primary hypotheses place the origin of A. mellifera in either Asia or Africa, with subsequent radiations proceeding from one of these regions. Here, we use two publicly available whole-genome data sets plus newly sequenced genomes and apply multiple population genetic analysis methods to investigate the patterns of ancestry and admixture in native honey bee populations from Europe, Africa, and the Middle East. The combination of these data sets is critical to the analyses, as each contributes samples from geographic locations lacking in the other, thereby producing the most complete set of honey bee populations available to date. We find evidence supporting an origin of A. mellifera in the Middle East or North Eastern Africa, with the A and Y lineages representing the earliest branching lineages. This finding has similarities with multiple contradictory hypotheses and represents a disentangling of genetic relationships, geographic proximity, and secondary contact to produce a more accurate picture of the origins of A. mellifera. We also investigate how previous studies came to their various conclusions based on incomplete sampling of populations, and illustrate the importance of complete sampling in understanding evolutionary processes. These results provide fundamental knowledge about genetic diversity within Old World honey bee populations and offer insight into the complex history of an important pollinator. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Evolutionary origin of the Asteraceae capitulum: Insights from Calyceraceae.

PubMed

Pozner, Raúl; Zanotti, Christian; Johnson, Leigh A

2012-01-01

Phylogenies based on molecular data are revealing that generalizations about complex morphological structures often obscure variation and developmental patterns important for understanding the evolution of forms, as is the case for inflorescence morphology within the well-supported MGCA clade (Menyanthaceae + Goodeniaceae + Calyceraceae + Asteraceae). While the basal families share a basic thyrsic/thyrsoid structure of their inflorescences, Asteraceae possesses a capitulum that is widely interpreted as a racemose, condensed inflorescence. Elucidating the poorly known inflorescence structure of Calyceraceae, sister to Asteraceae, should help clarify how the Asteraceae capitulum evolved from thyrsic/thyrsoid inflorescences. The early development and structure of the inflorescence of eight species (five genera) of Calyceraceae were studied by SEM, and patterns of evolutionary change were interpreted via phylogenetic character mapping. The basic inflorescence structure of Calyceraceae is a cephalioid (a very condensed botryoid/thyrsoid). Optimization of inflorescence characters on a DNA sequence-derived tree suggests that the Asteraceae capitulum derives from a simple cephalioid through two morphological changes: loss of the terminal flower and suppression of the cymose branching pattern in the peripheral branches. Widely understood as a condensed raceme, the Asteraceae capitulum is the evolutionary result of a very reduced, condensed thyrsoid. Starting from that point, evolution worked separately only on the racemose developmental control/pattern within Asteraceae and mainly on the cymose developmental control/pattern within Calyceraceae, producing head-like inflorescences in both groups but with very different diversification potential. We also discuss possible remnants of the ancestral cephalioid structure in some Asteraceae.

The life and adventures of an eight-legged castaway: Colonization and diversification of Philisca ghost spiders on Robinson Crusoe Island (Araneae, Anyphaenidae).

PubMed

Soto, Eduardo M; Labarque, Facundo M; Ceccarelli, F Sara; Arnedo, Miquel A; Pizarro-Araya, Jaime; Ramírez, Martín J

2017-02-01

Oceanic archipelagoes, by their young origin and isolation, provide privileged settings to study the origin and diversification of species. Here, we study the anyphaenid spider genus Philisca, endemic to the Valdivian temperate rainforest, which includes species living both on the mainland as well as on the Robison Crusoe Island in the Juan Fernández archipelago. Anyphaenids, as many spiders, are potentially good colonizers due their ability for ballooning, an airborne dispersal mediated by strands of silk that are caught in the wind. We use a molecular approach to estimate both the phylogenetic relationships and the timeframe of species diversification of Philisca, with the aim to infer its evolutionary history. We further estimate the rates of speciation on both the insular and continental Philisca species and score the microhabitat used by each species and their sizes as a proxy to evaluate ecological niche diversification within the island. Most analyses support the monophyly of Philisca, with the exclusion of Philisca tripunctata. Our results reveal colonization from a single lineage that postdated the origin of the island, followed by rapid (∼2Ma) diversification. The ancestral microhabitat was most likely leaf-dwelling but we identify two independent microhabitat shifts. Our data provides evidence that Philisca has undergone an adaptive radiation on the Robison Crusoe Island. Copyright © 2016 Elsevier Inc. All rights reserved.

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

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

Origin and global diversification patterns of tropical rain forests: inferences from a complete genus-level phylogeny of palms

PubMed Central

2011-01-01

Background Understanding how biodiversity is shaped through time is a fundamental question in biology. Even though tropical rain forests (TRF) represent the most diverse terrestrial biomes on the planet, the timing, location and mechanisms of their diversification remain poorly understood. Molecular phylogenies are valuable tools for exploring these issues, but to date most studies have focused only on recent time scales, which minimises their explanatory potential. In order to provide a long-term view of TRF diversification, we constructed the first complete genus-level dated phylogeny of a largely TRF-restricted plant family with a known history dating back to the Cretaceous. Palms (Arecaceae/Palmae) are one of the most characteristic and ecologically important components of TRF worldwide, and represent a model group for the investigation of TRF evolution. Results We provide evidence that diversification of extant lineages of palms started during the mid-Cretaceous period about 100 million years ago. Ancestral biome and area reconstructions for the whole family strongly support the hypothesis that palms diversified in a TRF-like environment at northern latitudes. Finally, our results suggest that palms conform to a constant diversification model (the 'museum' model or Yule process), at least until the Neogene, with no evidence for any change in diversification rates even through the Cretaceous/Paleogene mass extinction event. Conclusions Because palms are restricted to TRF and assuming biome conservatism over time, our results suggest the presence of a TRF-like biome in the mid-Cretaceous period of Laurasia, consistent with controversial fossil evidence of the earliest TRF. Throughout its history, the TRF biome is thought to have been highly dynamic and to have fluctuated greatly in extent, but it has persisted even during climatically unfavourable periods. This may have allowed old lineages to survive and contribute to the steady accumulation of diversity over

The evolutionary sequence: origin and emergences.

PubMed

Fox, S W

1986-03-01

The evolutionary sequence is being reexamined experimentally from a "Big Bang"origin to the protocell and from the emergence of protocell and variety of species to Darwin's mental power (mind) and society (The Descent of Man). A most fundamentally revisionary consequence of experiments is an emphasis on endogenous ordering. This principle, seen vividly in ordered copolymerization of amino acids, has had new impact on the theory of Darwinian evolution and has been found to apply to the entire sequence. Herein, I will discuss some problems of dealing with teaching controversial subjects.

The evolutionary sequence: origin and emergences

NASA Technical Reports Server (NTRS)

Fox, S. W.

1986-01-01

The evolutionary sequence is being reexamined experimentally from a "Big Bang"origin to the protocell and from the emergence of protocell and variety of species to Darwin's mental power (mind) and society (The Descent of Man). A most fundamentally revisionary consequence of experiments is an emphasis on endogenous ordering. This principle, seen vividly in ordered copolymerization of amino acids, has had new impact on the theory of Darwinian evolution and has been found to apply to the entire sequence. Herein, I will discuss some problems of dealing with teaching controversial subjects.

Community assembly and diversification in Indo-Pacific coral reef fishes

PubMed Central

Hubert, Nicolas; Paradis, Emmanuel; Bruggemann, Henrich; Planes, Serge

2011-01-01

Theories of species coexistence have played a central role in ecology and evolutionary studies of the origin and maintenance of biodiversity in highly diverse communities. The concept of niche and associated theories predict that competition for available ecological space leads to a ceiling in species richness that influences further diversification patterns. By contrast, the neutral theory supports that speciation is stochastic and diversity independent. We examined the phylogenetic community structure and diversification rates in three families and 14 sites within coral reef fish communities from the Indian and Pacific oceans. Using the phylogenetic relationships among 157 species estimated with 2300 bp of mitochondrial DNA, we tested predictions in terms of species coexistence from the neutral and niche theories. At the regional scale, our findings suggest that phylogenetic community structure shifts during community assembly to a pattern of dispersion as a consequence of allopatric speciation in recent times but overall, variations in diversification rates did not relate with sea level changes. At the local scale, the phylogenetic community structure is consistent with a neutral model of community assembly since no departure from a random sorting of species was observed. The present results support a neutral model of community assembly as a consequence of the stochastic and unpredictable nature of coral reefs favoring generalist and sedentary species competing for living space rather than trophic resources. As a consequence, the observed decrease in diversification rates may be seen as the result of a limited supply of living space as expected in a finite island model. PMID:22393499

Emergence of a novel prey life history promotes contemporary sympatric diversification in a top predator.

PubMed

Brodersen, Jakob; Howeth, Jennifer G; Post, David M

2015-09-14

Intraspecific phenotypic variation can strongly impact community and ecosystem dynamics. Effects of intraspecific variation in keystone species have been shown to propagate down through the food web by altering the adaptive landscape for other species and creating a cascade of ecological and evolutionary change. However, similar bottom-up eco-evolutionary effects are poorly described. Here we show that life history diversification in a keystone prey species, the alewife (Alosa pseudoharengus), propagates up through the food web to promote phenotypic diversification in its native top predator, the chain pickerel (Esox niger), on contemporary timescales. The landlocking of alewife by human dam construction has repeatedly created a stable open water prey resource, novel to coastal lakes, that has promoted the parallel emergence of a habitat polymorphism in chain pickerel. Understanding how strong interactions propagate through food webs to influence diversification across multiple trophic levels is critical to understand eco-evolutionary interactions in complex natural ecosystems.

The evolutionary history of Melianthus (Melianthaceae).

PubMed

Linder, H Peter; Dlamini, Titus; Henning, Jack; Verboom, G Anthony

2006-07-01

The evolutionary origins of the morphological and taxonomic diversity of angiosperms is poorly known. We used the genus Melianthus to explore the diversification of the southern African flora. Melianthus comprises eight species, and a phylogeny based on one nuclear and two plastid genes, as well as a morphological data set, confirmed that the genus is monophyletic. The two earliest diverging lineages are found in relatively mesic habitats, whereas the two terminal clades (an eastern and a western clade), each with three species, favor more arid habitats. The eastern clade is largely restricted to the summer-rainfall parts of southern Africa, and the western clade is found in winter-rainfall region. Molecular dating indicates a mid-Tertiary origin of the genus, with diversification of the eastern and western clades coincident with the Late Miocene-Pliocene uplift of the Escarpment mountains and the establishment of summer aridity along the west coast. The remarkably complex flowers are indicative of sunbird pollination, but many smaller birds can also visit. Speciation may be the consequence of allopatric divergence into edaphic-climatic niches. Divergence in flower and inflorescence morphology might be in response to the divergent pressures for nectar conservation in arid regions coupled with the need for signaling to avian pollinators in generally shrubby vegetation.

Avian skin development and the evolutionary origin of feathers.

PubMed

Sawyer, Roger H; Knapp, Loren W

2003-08-15

The discovery of several dinosaurs with filamentous integumentary appendages of different morphologies has stimulated models for the evolutionary origin of feathers. In order to understand these models, knowledge of the development of the avian integument must be put into an evolutionary context. Thus, we present a review of avian scale and feather development, which summarizes the morphogenetic events involved, as well as the expression of the beta (beta) keratin multigene family that characterizes the epidermal appendages of reptiles and birds. First we review information on the evolution of the ectodermal epidermis and its beta (beta) keratins. Then we examine the morphogenesis of scutate scales and feathers including studies in which the extraembryonic ectoderm of the chorion is used to examine dermal induction. We also present studies on the scaleless (sc) mutant, and, because of the recent discovery of "four-winged" dinosaurs, we review earlier studies of a chicken strain, Silkie, that expresses ptilopody (pti), "feathered feet." We conclude that the ability of the ectodermal epidermis to generate discrete cell populations capable of forming functional structural elements consisting of specific members of the beta keratin multigene family was a plesiomorphic feature of the archosaurian ancestor of crocodilians and birds. Evidence suggests that the discrete epidermal lineages that make up the embryonic feather filament of extant birds are homologous with similar embryonic lineages of the developing scutate scales of birds and the scales of alligators. We believe that the early expression of conserved signaling modules in the embryonic skin of the avian ancestor led to the early morphogenesis of the embryonic feather filament, with its periderm, sheath, and barb ridge lineages forming the first protofeather. Invagination of the epidermis of the protofeather led to formation of the follicle providing for feather renewal and diversification. The observations that

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.

Missing links: the genetic architecture of flowers [correction of flower] and floral diversification.

PubMed

Soltis, Douglas E; Soltis, Pamela S; Albert, Victor A; Oppenheimer, David G; dePamphilis, Claude W; Ma, Hong; Frohlich, Michael W; Theissen, Günter

2002-01-01

To understand the genetic architecture of floral development, including the origin and subsequent diversification of the flower, data are needed not only for a few model organisms but also for gymnosperms, basal angiosperm lineages and early-diverging eudicots. We must link what is known about derived model plants such as Arabidopsis, snapdragon and maize with other angiosperms. To this end, we suggest a massive evolutionary genomics effort focused on the identification and expression patterns of floral genes and elucidation of their expression patterns in 'missing-link' taxa differing in the arrangement, number and organization of floral parts.

Diversification and the evolution of dispersal ability in the tribe Brassiceae (Brassicaceae).

PubMed

Willis, C G; Hall, J C; Rubio de Casas, R; Wang, T Y; Donohue, K

2014-12-01

Dispersal and establishment ability can influence evolutionary processes such as geographic isolation, adaptive divergence and extinction probability. Through these population-level dynamics, dispersal ability may also influence macro-evolutionary processes such as species distributions and diversification. This study examined patterns of evolution of dispersal-related fruit traits, and how the evolution of these traits is correlated with shifts in geographic range size, habitat and diversification rates in the tribe Brassiceae (Brassicaceae). The phylogenetic analysis included 72 taxa sampled from across the Brassiceae and included both nuclear and chloroplast markers. Dispersal-related fruit characters were scored and climate information for each taxon was retrieved from a database. Correlations between fruit traits, seed characters, habitat, range and climate were determined, together with trait-dependent diversification rates. It was found that the evolution of traits associated with limited dispersal evolved only in association with compensatory traits that increase dispersal ability. The evolution of increased dispersal ability occurred in multiple ways through the correlated evolution of different combinations of fruit traits. The evolution of traits that increase dispersal ability was in turn associated with larger seed size, increased geographic range size and higher diversification rates. This study provides evidence that the evolution of increased dispersal ability and larger seed size, which may increase establishment ability, can also influence macro-evolutionary processes, possibly by increasing the propensity for long-distance dispersal. In particular, it may increase speciation and consequent diversification rates by increasing the likelihood of geographic and thereby reproductive isolation. © The Author 2014. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Unveiling the diversification dynamics of Australasian predaceous diving beetles in the Cenozoic.

PubMed

Toussaint, Emmanuel F A; Condamine, Fabien L; Hawlitschek, Oliver; Watts, Chris H; Porch, Nick; Hendrich, Lars; Balke, Michael

2015-01-01

During the Cenozoic, Australia experienced major climatic shifts that have had dramatic ecological consequences for the modern biota. Mesic tropical ecosystems were progressively restricted to the coasts and replaced by arid-adapted floral and faunal communities. Whilst the role of aridification has been investigated in a wide range of terrestrial lineages, the response of freshwater clades remains poorly investigated. To gain insights into the diversification processes underlying a freshwater radiation, we studied the evolutionary history of the Australasian predaceous diving beetles of the tribe Hydroporini (147 described species). We used an integrative approach including the latest methods in phylogenetics, divergence time estimation, ancestral character state reconstruction, and likelihood-based methods of diversification rate estimation. Phylogenies and dating analyses were reconstructed with molecular data from seven genes (mitochondrial and nuclear) for 117 species (plus 12 outgroups). Robust and well-resolved phylogenies indicate a late Oligocene origin of Australasian Hydroporini. Biogeographic analyses suggest an origin in the East Coast region of Australia, and a dynamic biogeographic scenario implying dispersal events. The group successfully colonized the tropical coastal regions carved by a rampant desertification, and also colonized groundwater ecosystems in Central Australia. Diversification rate analyses suggest that the ongoing aridification of Australia initiated in the Miocene contributed to a major wave of extinctions since the late Pliocene probably attributable to an increasing aridity, range contractions and seasonally disruptions resulting from Quaternary climatic changes. When comparing subterranean and epigean genera, our results show that contrasting mechanisms drove their diversification and therefore current diversity pattern. The Australasian Hydroporini radiation reflects a combination of processes that promoted both diversification

Origin and Evolutionary Alteration of the Mitochondrial Import System in Eukaryotic Lineages.

PubMed

Fukasawa, Yoshinori; Oda, Toshiyuki; Tomii, Kentaro; Imai, Kenichiro

2017-07-01

Protein transport systems are fundamentally important for maintaining mitochondrial function. Nevertheless, mitochondrial protein translocases such as the kinetoplastid ATOM complex have recently been shown to vary in eukaryotic lineages. Various evolutionary hypotheses have been formulated to explain this diversity. To resolve any contradiction, estimating the primitive state and clarifying changes from that state are necessary. Here, we present more likely primitive models of mitochondrial translocases, specifically the translocase of the outer membrane (TOM) and translocase of the inner membrane (TIM) complexes, using scrutinized phylogenetic profiles. We then analyzed the translocases' evolution in eukaryotic lineages. Based on those results, we propose a novel evolutionary scenario for diversification of the mitochondrial transport system. Our results indicate that presequence transport machinery was mostly established in the last eukaryotic common ancestor, and that primitive translocases already had a pathway for transporting presequence-containing proteins. Moreover, secondary changes including convergent and migrational gains of a presequence receptor in TOM and TIM complexes, respectively, likely resulted from constrained evolution. The nature of a targeting signal can constrain alteration to the protein transport complex. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The Impact of Organismal Innovation on Functional and Ecological Diversification.

PubMed

Wainwright, Peter C; Price, Samantha A

2016-09-01

Innovations in organismal functional morphology are thought to be a major force in shaping evolutionary patterns, with the potential to drive adaptive radiation and influence the evolutionary prospects for lineages. But the evolutionary consequences of innovation are diverse and usually do not result in adaptive radiation. What factors shape the macroevolutionary impact of innovations? We assert that little is known in general about the macroevolutionary outcomes associated with functional innovations and we discuss a framework for studying biological innovations in an evolutionary context. Innovations are novel functional mechanisms that enhance organismal performance. The ubiquity of trade-offs in functional systems means that enhanced performance on one axis often occurs at the expense of performance on another axis, such that many innovations result in an exchange of performance capabilities, rather than an expansion. Innovations may open up new resources for exploitation but their consequences for functional and ecological diversification depend heavily on the adaptive landscape around these novel resources. As an example of a broader program that we imagine, we survey five feeding innovations in labrid fishes, an exceptionally successful and ecologically diverse group of reef fishes, and explore their impact on the rate of evolution of jaw functional morphology. All of the innovations provide performance enhancements and result in changes in patterns of resource use, but most are not associated with subsequent functional diversification or substantial ecological diversification. Because selection acts on a specific performance enhancement and not on the evolutionary potential of an innovation, the enhancement of diversity may be highly serendipitous. The macroevolutionary potential of innovations depends critically on the interaction between the performance enhancement and the ecological opportunity that is exposed. © The Author 2016. Published by Oxford

Impact of parental Bos taurus and Bos indicus origins on copy number variation in traditional Chinese cattle breeds

USDA-ARS?s Scientific Manuscript database

Copy number variation (CNV) is an important component of genomic structural variation and plays a role not only in evolutionary diversification but also domestication. Chinese cattle were derived from Bos taurus and Bos indicus, and several breeds presumably are of hybrid origin, but the evolution o...

The Evolutionary Origin of Female Orgasm.

PubMed

Pavličev, Mihaela; Wagner, Günter

2016-09-01

The evolutionary explanation of female orgasm has been difficult to come by. The orgasm in women does not obviously contribute to the reproductive success, and surprisingly unreliably accompanies heterosexual intercourse. Two types of explanations have been proposed: one insisting on extant adaptive roles in reproduction, another explaining female orgasm as a byproduct of selection on male orgasm, which is crucial for sperm transfer. We emphasize that these explanations tend to focus on evidence from human biology and thus address the modification of a trait rather than its evolutionary origin. To trace the trait through evolution requires identifying its homologue in other species, which may have limited similarity with the human trait. Human female orgasm is associated with an endocrine surge similar to the copulatory surges in species with induced ovulation. We suggest that the homolog of human orgasm is the reflex that, ancestrally, induced ovulation. This reflex became superfluous with the evolution of spontaneous ovulation, potentially freeing female orgasm for other roles. This is supported by phylogenetic evidence showing that induced ovulation is ancestral, while spontaneous ovulation is derived within eutherians. In addition, the comparative anatomy of female reproductive tract shows that evolution of spontaneous ovulation is correlated with increasing distance of clitoris from the copulatory canal. In summary, we suggest that the female orgasm-like trait may have been adaptive, however for a different role, namely for inducing ovulation. With the evolution of spontaneous ovulation, orgasm was freed to gain secondary roles, which may explain its maintenance, but not its origin. © 2016 Wiley Periodicals, Inc.

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.

Evolutionary history of the Afro-Madagascan Ixora species (Rubiaceae): species diversification and distribution of key morphological traits inferred from dated molecular phylogenetic trees

PubMed Central

Tosh, J.; Dessein, S.; Buerki, S.; Groeninckx, I.; Mouly, A.; Bremer, B.; Smets, E. F.; De Block, P.

2013-01-01

Background and Aims Previous work on the pantropical genus Ixora has revealed an Afro-Madagascan clade, but as yet no study has focused in detail on the evolutionary history and morphological trends in this group. Here the evolutionary history of Afro-Madagascan Ixora spp. (a clade of approx. 80 taxa) is investigated and the phylogenetic trees compared with several key morphological traits in taxa occurring in Madagascar. Methods Phylogenetic relationships of Afro-Madagascan Ixora are assessed using sequence data from four plastid regions (petD, rps16, rpoB-trnC and trnL-trnF) and nuclear ribosomal external transcribed spacer (ETS) and internal transcribed spacer (ITS) regions. The phylogenetic distribution of key morphological characters is assessed. Bayesian inference (implemented in BEAST) is used to estimate the temporal origin of Ixora based on fossil evidence. Key Results Two separate lineages of Madagascan taxa are recovered, one of which is nested in a group of East African taxa. Divergence in Ixora is estimated to have commenced during the mid Miocene, with extensive cladogenesis occurring in the Afro-Madagascan clade during the Pliocene onwards. Conclusions Both lineages of Madagascan Ixora exhibit morphological innovations that are rare throughout the rest of the genus, including a trend towards pauciflorous inflorescences and a trend towards extreme corolla tube length, suggesting that the same ecological and selective pressures are acting upon taxa from both Madagascan lineages. Novel ecological opportunities resulting from climate-induced habitat fragmentation and corolla tube length diversification are likely to have facilitated species radiation on Madagascar. PMID:24142919

Drosophila sex combs as a model of evolutionary innovations.

PubMed

Kopp, Artyom

2011-01-01

The diversity of animal and plant forms is shaped by nested evolutionary innovations. Understanding the genetic and molecular changes responsible for these innovations is therefore one of the key goals of evolutionary biology. From the genetic point of view, the origin of novel traits implies the origin of new regulatory pathways to control their development. To understand how these new pathways are assembled in the course of evolution, we need model systems that combine relatively recent innovations with a powerful set of genetic and molecular tools. One such model is provided by the Drosophila sex comb-a male-specific morphological structure that evolved in a relatively small lineage related to the model species D. melanogaster. Our extensive knowledge of sex comb development in D. melanogaster provides the basis for investigating the genetic changes responsible for sex comb origin and diversification. At the same time, sex combs can change on microevolutionary timescales and differ spectacularly among closely related species, providing opportunities for direct genetic analysis and for integrating developmental and population-genetic approaches. Sex comb evolution is associated with the origin of novel interactions between Hox and sex determination genes. Activity of the sex determination pathway was brought under the control of the Hox code to become segment-specific, while Hox gene expression became sexually dimorphic. At the same time, both Hox and sex determination genes were integrated into the intrasegmental spatial patterning network, and acquired new joint downstream targets. Phylogenetic analysis shows that similar sex comb morphologies evolved independently in different lineages. Convergent evolution at the phenotypic level reflects convergent changes in the expression of Hox and sex determination genes, involving both independent gains and losses of regulatory interactions. However, the downstream cell-differentiation programs have diverged between

Drosophila Sex Combs as a Model of Evolutionary Innovations

PubMed Central

Kopp, Artyom

2011-01-01

The diversity of animal and plant forms is shaped by nested evolutionary innovations. Understanding the genetic and molecular changes responsible for these innovations is therefore one of the key goals of evolutionary biology. From the genetic point of view, the origin of novel traits implies the origin of new regulatory pathways to control their development. To understand how these new pathways are assembled in the course of evolution, we need model systems that combine relatively recent innovations with a powerful set of genetic and molecular tools. One such model is provided by the Drosophila sex comb – a male-specific morphological structure that evolved in a relatively small lineage related to the model species D. melanogaster. Our extensive knowledge of sex comb development in D. melanogaster provides the basis for investigating the genetic changes responsible for sex comb origin and diversification. At the same time, sex combs can change on microevolutionary timescales and differ spectacularly among closely related species, providing opportunities for direct genetic analysis and for integrating developmental and population-genetic approaches. Sex comb evolution is associated with the origin of novel interactions between HOX and sex determination genes. Activity of the sex determination pathway was brought under the control of the HOX code to become segment-specific, while HOX gene expression became sexually dimorphic. At the same time, both HOX and sex determination genes were integrated into the intrasegmental spatial patterning network, and acquired new joint downstream targets. Phylogenetic analysis shows that similar sex comb morphologies evolved independently in different lineages. Convergent evolution at the phenotypic level reflects convergent changes in the expression of HOX and sex determination genes, involving both independent gains and losses of regulatory interactions. However, the downstream cell differentiation programs have diverged between

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.

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

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.

Conservatism and diversification of plant functional traits: Evolutionary rates versus phylogenetic signal

PubMed Central

Ackerly, David

2009-01-01

The concepts of niche conservatism and adaptive radiation have played central roles in the study of evolution and ecological diversification. With respect to phenotypic evolution, the two processes may be seen as opposite ends of a spectrum; however, there is no straightforward method for the comparative analysis of trait evolution that will identify these contrasting scenarios. Analysis of the rate of phenotypic evolution plays an important role in this context and merits increased attention. In this article, independent contrasts are used to estimate rates of evolution for continuous traits under a Brownian motion model of evolution. A unit for the rate of phenotypic diversification is introduced: the felsen, in honor of J. Felsenstein, is defined as an increase of one unit per million years in the variance among sister taxa of ln-transformed trait values. The use of a standardized unit of measurement facilitates comparisons among clades and traits. Rates of diversification of three functional traits (plant height, leaf size, and seed size) were estimated for four to six woody plant clades (Acer, Aesculus, Ceanothus, Arbutoideae, Hawaiian lobeliads, and the silversword alliance) for which calibrated phylogenies were available. For height and leaf size, rates were two to ≈300 times greater in the Hawaiian silversword alliance than in the other clades considered. These results highlight the value of direct estimates of rates of trait evolution for comparative analysis of adaptive radiation, niche conservatism, and trait diversification. PMID:19843698

Conservatism and diversification of plant functional traits: Evolutionary rates versus phylogenetic signal.

PubMed

Ackerly, David

2009-11-17

The concepts of niche conservatism and adaptive radiation have played central roles in the study of evolution and ecological diversification. With respect to phenotypic evolution, the two processes may be seen as opposite ends of a spectrum; however, there is no straightforward method for the comparative analysis of trait evolution that will identify these contrasting scenarios. Analysis of the rate of phenotypic evolution plays an important role in this context and merits increased attention. In this article, independent contrasts are used to estimate rates of evolution for continuous traits under a Brownian motion model of evolution. A unit for the rate of phenotypic diversification is introduced: the felsen, in honor of J. Felsenstein, is defined as an increase of one unit per million years in the variance among sister taxa of ln-transformed trait values. The use of a standardized unit of measurement facilitates comparisons among clades and traits. Rates of diversification of three functional traits (plant height, leaf size, and seed size) were estimated for four to six woody plant clades (Acer, Aesculus, Ceanothus, Arbutoideae, Hawaiian lobeliads, and the silversword alliance) for which calibrated phylogenies were available. For height and leaf size, rates were two to approximately 300 times greater in the Hawaiian silversword alliance than in the other clades considered. These results highlight the value of direct estimates of rates of trait evolution for comparative analysis of adaptive radiation, niche conservatism, and trait diversification.

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.

Evolutionary melting pots: a biodiversity hotspot shaped by ring diversifications around the Black Sea in the Eastern tree frog (Hyla orientalis).

PubMed

Dufresnes, Christophe; Litvinchuk, Spartak N; Leuenberger, Julien; Ghali, Karim; Zinenko, Oleksandr; Stöck, Matthias; Perrin, Nicolas

2016-09-01

Hotspots of intraspecific genetic diversity, which are of primary importance for the conservation of species, have been associated with glacial refugia, that is areas where species survived the Quaternary climatic oscillations. However, the proximate mechanisms generating these hotspots remain an open issue. Hotspots may reflect the long-term persistence of large refugial populations; alternatively, they may result from allopatric differentiation between small and isolated populations, that later admixed. Here, we test these two scenarios in a widely distributed species of tree frog, Hyla orientalis, which inhabits Asia Minor and southeastern Europe. We apply a fine-scale phylogeographic survey, combining fast-evolving mitochondrial and nuclear markers, with a dense sampling throughout the range, as well as ecological niche modelling, to understand what shaped the genetic variation of this species. We documented an important diversity centre around the Black Sea, composed of multiple allopatric and/or parapatric diversifications, likely driven by a combination of Pleistocene climatic fluctuations and complex regional topography. Remarkably, this diversification forms a ring around the Black Sea, from the Caucasus through Anatolia and eastern Europe, with terminal forms coming into contact and partially admixing in Crimea. Our results support the view that glacial refugia generate rather than host genetic diversity and can also function as evolutionary melting pots of biodiversity. Moreover, we report a new case of ring diversification, triggered by a large, yet cohesive dispersal barrier, a very rare situation in nature. Finally, we emphasize the Black Sea region as an important centre of intraspecific diversity in the Palearctic with implications for conservation. © 2016 John Wiley & Sons Ltd.

Large-Scale Evolutionary Analysis of Genes and Supergene Clusters from Terpenoid Modular Pathways Provides Insights into Metabolic Diversification in Flowering Plants

PubMed Central

Hofberger, Johannes A.; Ramirez, Aldana M.; van den Bergh, Erik; Zhu, Xinguang; Bouwmeester, Harro J.; Schuurink, Robert C.; Schranz, M. Eric

2015-01-01

An important component of plant evolution is the plethora of pathways producing more than 200,000 biochemically diverse specialized metabolites with pharmacological, nutritional and ecological significance. To unravel dynamics underlying metabolic diversification, it is critical to determine lineage-specific gene family expansion in a phylogenomics framework. However, robust functional annotation is often only available for core enzymes catalyzing committed reaction steps within few model systems. In a genome informatics approach, we extracted information from early-draft gene-space assemblies and non-redundant transcriptomes to identify protein families involved in isoprenoid biosynthesis. Isoprenoids comprise terpenoids with various roles in plant-environment interaction, such as pollinator attraction or pathogen defense. Combining lines of evidence provided by synteny, sequence homology and Hidden-Markov-Modelling, we screened 17 genomes including 12 major crops and found evidence for 1,904 proteins associated with terpenoid biosynthesis. Our terpenoid genes set contains evidence for 840 core terpene-synthases and 338 triterpene-specific synthases. We further identified 190 prenyltransferases, 39 isopentenyl-diphosphate isomerases as well as 278 and 219 proteins involved in mevalonate and methylerithrol pathways, respectively. Assessing the impact of gene and genome duplication to lineage-specific terpenoid pathway expansion, we illustrated key events underlying terpenoid metabolic diversification within 250 million years of flowering plant radiation. By quantifying Angiosperm-wide versatility and phylogenetic relationships of pleiotropic gene families in terpenoid modular pathways, our analysis offers significant insight into evolutionary dynamics underlying diversification of plant secondary metabolism. Furthermore, our data provide a blueprint for future efforts to identify and more rapidly clone terpenoid biosynthetic genes from any plant species. PMID

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.

Intercontinental and intracontinental biogeography of the eastern Asian - Eastern North American disjunct Panax (the ginseng genus, Araliaceae), emphasizing its diversification processes in eastern Asia.

PubMed

Zuo, Yun-Juan; Wen, Jun; Zhou, Shi-Liang

2017-12-01

The intercontinental biogeography between eastern Asia and eastern North America has attracted much attention from evolutionary biologists. Further insights into understanding the evolution of the intercontinental disjunctions have been hampered by the lack of studies on the intracontinental biogeography in eastern Asia, a region with complex geology, geography, climates and habitats. Herein we studied the biogeographic history of the eastern Asian-eastern North American disjunct genus Panax with special emphasis on the investigation of its uneven diversification in Asia. This study reconstructs the diversification history of Panax and also emphasizes a large clade of Panax taxa, which has a wide distribution in eastern Asia, but was unresolved in previous studies. We examined the noncoding plastid DNA fragments of trnH-psbA, rps16, and psbM-trnD, the mitochondrial b/c intron of NAD1, and the nuclear ribosomal internal transcribed spacer (ITS) region of 356 samples from 47 populations. The results revealed the subtropical Northern Hemisphere origin (Asia or Asia and North America) of Panax in the Paleocene. Intercontinental disjunctions between eastern Asia and eastern North America formed twice in Panax, once estimated in early Eocene for the split of P. trifolius and another in mid-Miocene for the divergence of P. quinquefolius. Intercontinental diversifications in Panax showed temporal correlation with the increase of global temperature. The evolutionary radiation of the P. bipinnatifidus species complex occurred around the boundary of Oligocene and Miocene. Strong genetic structure among populations of the species complex was detected and the populations may be isolated by distance. The backbone network and the Bayesian clustering analysis revealed a major evolutionary radiation centered in the Hengduan Mountains of western China. Our results suggested that the evolutionary radiation of Panax was promoted by geographic barriers, including mountain ranges

Ecological opportunity and the adaptive diversification of lineages

PubMed Central

Wellborn, Gary A; Langerhans, R Brian

2015-01-01

The tenet that ecological opportunity drives adaptive diversification has been central to theories of speciation since Darwin, yet no widely accepted definition or mechanistic framework for the concept currently exists. We propose a definition for ecological opportunity that provides an explicit mechanism for its action. In our formulation, ecological opportunity refers to environmental conditions that both permit the persistence of a lineage within a community, as well as generate divergent natural selection within that lineage. Thus, ecological opportunity arises from two fundamental elements: (1) niche availability, the ability of a population with a phenotype previously absent from a community to persist within that community and (2) niche discordance, the diversifying selection generated by the adaptive mismatch between a population's niche-related traits and the newly encountered ecological conditions. Evolutionary response to ecological opportunity is primarily governed by (1) spatiotemporal structure of ecological opportunity, which influences dynamics of selection and development of reproductive isolation and (2) diversification potential, the biological properties of a lineage that determine its capacity to diversify. Diversification under ecological opportunity proceeds as an increase in niche breadth, development of intraspecific ecotypes, speciation, and additional cycles of diversification that may themselves be triggered by speciation. Extensive ecological opportunity may exist in depauperate communities, but it is unclear whether ecological opportunity abates in species-rich communities. Because ecological opportunity should generally increase during times of rapid and multifarious environmental change, human activities may currently be generating elevated ecological opportunity – but so far little work has directly addressed this topic. Our framework highlights the need for greater synthesis of community ecology and evolutionary biology, unifying

Ecological opportunity and the adaptive diversification of lineages.

PubMed

Wellborn, Gary A; Langerhans, R Brian

2015-01-01

The tenet that ecological opportunity drives adaptive diversification has been central to theories of speciation since Darwin, yet no widely accepted definition or mechanistic framework for the concept currently exists. We propose a definition for ecological opportunity that provides an explicit mechanism for its action. In our formulation, ecological opportunity refers to environmental conditions that both permit the persistence of a lineage within a community, as well as generate divergent natural selection within that lineage. Thus, ecological opportunity arises from two fundamental elements: (1) niche availability, the ability of a population with a phenotype previously absent from a community to persist within that community and (2) niche discordance, the diversifying selection generated by the adaptive mismatch between a population's niche-related traits and the newly encountered ecological conditions. Evolutionary response to ecological opportunity is primarily governed by (1) spatiotemporal structure of ecological opportunity, which influences dynamics of selection and development of reproductive isolation and (2) diversification potential, the biological properties of a lineage that determine its capacity to diversify. Diversification under ecological opportunity proceeds as an increase in niche breadth, development of intraspecific ecotypes, speciation, and additional cycles of diversification that may themselves be triggered by speciation. Extensive ecological opportunity may exist in depauperate communities, but it is unclear whether ecological opportunity abates in species-rich communities. Because ecological opportunity should generally increase during times of rapid and multifarious environmental change, human activities may currently be generating elevated ecological opportunity - but so far little work has directly addressed this topic. Our framework highlights the need for greater synthesis of community ecology and evolutionary biology, unifying

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.

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.

Evolutionary persistence in Gunnera and the contribution of southern plant groups to the tropical Andes biodiversity hotspot.

PubMed

Bacon, Christine D; Velásquez-Puentes, Francisco J; Hinojosa, Luis Felipe; Schwartz, Thomas; Oxelman, Bengt; Pfeil, Bernard; Arroyo, Mary T K; Wanntorp, Livia; Antonelli, Alexandre

2018-01-01

Several studies have demonstrated the contribution of northern immigrants to the flora of the tropical Andes-the world's richest and most diverse biodiversity hotspot. However, much less is known about the biogeographic history and diversification of Andean groups with southern origins, although it has been suggested that northern and southern groups have contributed roughly equally to the high Andean (i.e., páramo) flora. Here we infer the evolutionary history of the southern hemisphere plant genus Gunnera , a lineage with a rich fossil history and an important ecological role as an early colonising species characteristic of wet, montane environments. Our results show striking contrasts in species diversification, where some species may have persisted for some 90 million years, and whereas others date to less than 2 Ma since origination. The outstanding longevity of the group is likely linked to a high degree of niche conservatism across its highly disjunct range, whereby Gunnera tracks damp and boggy soils in cool habitats. Colonisation of the northern Andes is related to Quaternary climate change, with subsequent rapid diversification appearing to be driven by their ability to take advantage of environmental opportunities. This study demonstrates the composite origin of a mega-diverse biota.

Evolutionary origin of the turtle skull.

PubMed

Bever, G S; Lyson, Tyler R; Field, Daniel J; Bhullar, Bhart-Anjan S

2015-09-10

Transitional fossils informing the origin of turtles are among the most sought-after discoveries in palaeontology. Despite strong genomic evidence indicating that turtles evolved from within the diapsid radiation (which includes all other living reptiles), evidence of the inferred transformation between an ancestral turtle with an open, diapsid skull to the closed, anapsid condition of modern turtles remains elusive. Here we use high-resolution computed tomography and a novel character/taxon matrix to study the skull of Eunotosaurus africanus, a 260-million-year-old fossil reptile from the Karoo Basin of South Africa, whose distinctive postcranial skeleton shares many unique features with the shelled body plan of turtles. Scepticism regarding the status of Eunotosaurus as the earliest stem turtle arises from the possibility that these shell-related features are the products of evolutionary convergence. Our phylogenetic analyses indicate strong cranial support for Eunotosaurus as a critical transitional form in turtle evolution, thus fortifying a 40-million-year extension to the turtle stem and moving the ecological context of its origin back onto land. Furthermore, we find unexpected evidence that Eunotosaurus is a diapsid reptile in the process of becoming secondarily anapsid. This is important because categorizing the skull based on the number of openings in the complex of dermal bone covering the adductor chamber has long held sway in amniote systematics, and still represents a common organizational scheme for teaching the evolutionary history of the group. These discoveries allow us to articulate a detailed and testable hypothesis of fenestral closure along the turtle stem. Our results suggest that Eunotosaurus represents a crucially important link in a chain that will eventually lead to consilience in reptile systematics, paving the way for synthetic studies of amniote evolution and development.

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.

Patterns of genetic variability and habitat occupancy in Crepis triasii (Asteraceae) at different spatial scales: insights on evolutionary processes leading to diversification in continental islands

PubMed Central

Mayol, Maria; Palau, Carles; Rosselló, Josep A.; González-Martínez, Santiago C.; Molins, Arántzazu; Riba, Miquel

2012-01-01

Background and Aims Archipelagos are unique systems for studying evolutionary processes promoting diversification and speciation. The islands of the Mediterranean basin are major areas of plant richness, including a high proportion of narrow endemics. Many endemic plants are currently found in rocky habitats, showing varying patterns of habitat occupancy at different spatial scales throughout their range. The aim of the present study was to understand the impact of varying patterns of population distribution on genetic diversity and structure to shed light on demographic and evolutionary processes leading to population diversification in Crepis triasii, an endemic plant from the eastern Balearic Islands. Methods Using allozyme and chloroplast markers, we related patterns of genetic structure and diversity to those of habitat occupancy at a regional (between islands and among populations within islands) and landscape (population size and connectivity) scale. Key Results Genetic diversity was highly structured both at the regional and at the landscape level, and was positively correlated with population connectivity in the landscape. Populations located in small isolated mountains and coastal areas, with restricted patterns of regional occupancy, were genetically less diverse and much more differentiated. In addition, more isolated populations had stronger fine-scale genetic structure than well-connected ones. Changes in habitat availability and quality arising from marine transgressions during the Quaternary, as well as progressive fragmentation associated with the aridification of the climate since the last glaciation, are the most plausible factors leading to the observed patterns of genetic diversity and structure. Conclusions Our results emphasize the importance of gene flow in preventing genetic erosion and maintaining the evolutionary potential of populations. They also agree with recent studies highlighting the importance of restricted gene flow and genetic

Patterns of genetic variability and habitat occupancy in Crepis triasii (Asteraceae) at different spatial scales: insights on evolutionary processes leading to diversification in continental islands.

PubMed

Mayol, Maria; Palau, Carles; Rosselló, Josep A; González-Martínez, Santiago C; Molins, Arántzazu; Riba, Miquel

2012-02-01

Archipelagos are unique systems for studying evolutionary processes promoting diversification and speciation. The islands of the Mediterranean basin are major areas of plant richness, including a high proportion of narrow endemics. Many endemic plants are currently found in rocky habitats, showing varying patterns of habitat occupancy at different spatial scales throughout their range. The aim of the present study was to understand the impact of varying patterns of population distribution on genetic diversity and structure to shed light on demographic and evolutionary processes leading to population diversification in Crepis triasii, an endemic plant from the eastern Balearic Islands. Using allozyme and chloroplast markers, we related patterns of genetic structure and diversity to those of habitat occupancy at a regional (between islands and among populations within islands) and landscape (population size and connectivity) scale. Genetic diversity was highly structured both at the regional and at the landscape level, and was positively correlated with population connectivity in the landscape. Populations located in small isolated mountains and coastal areas, with restricted patterns of regional occupancy, were genetically less diverse and much more differentiated. In addition, more isolated populations had stronger fine-scale genetic structure than well-connected ones. Changes in habitat availability and quality arising from marine transgressions during the Quaternary, as well as progressive fragmentation associated with the aridification of the climate since the last glaciation, are the most plausible factors leading to the observed patterns of genetic diversity and structure. Our results emphasize the importance of gene flow in preventing genetic erosion and maintaining the evolutionary potential of populations. They also agree with recent studies highlighting the importance of restricted gene flow and genetic drift as drivers of plant evolution in Mediterranean

An investigation of the evolutionary origin of reciprocal communication using simulated autonomous agents.

PubMed

Tuci, Elio

2009-09-01

How does communication originates in a population of originally non-communicating individuals? Providing an answer to this question from a neo-Darwinian epistemological perspective is not a trivial task. The reason is that, for non-communicating agents, the capabilities of emitting signals and responding to them are both adaptively neutral traits if they are not simultaneously present. Research studies based on rather general and theoretically oriented evolutionary simulation models have, so far, demonstrated that at least two different processes can account for the origin of communication. On the one hand, communicative behaviour may first evolve in a non-communicative context and only subsequently acquire its adaptive function.On the other hand, communication may originate thanks to cognitive constraints; that is, communication may originate thanks to the existence of neural substrates that are common to the signalling and categorising capabilities. This article provides a proof-of-concept demonstration of the origin of communication in a novel-simulated scenario in which groups of two homogeneous (i.e. genetically identical) agents exploit reciprocal communication to develop common perceptual categories nd to perform a collective task. In particular, in circumstances in which communication is evolutionarily advantageous, simulated agents evolve from scratch social behaviour through acoustic interactions.We look into the phylogeny of successful communication protocol, and we describe the evolutionary phenomena that, in early evolutionary stages, paved the way for the subsequent development of reciprocal communication, categorisation capabilities and successful cooperative strategies.

Eco-geographical diversification of bitter taste receptor genes (TAS2Rs) among subspecies of chimpanzees (Pan troglodytes).

PubMed

Hayakawa, Takashi; Sugawara, Tohru; Go, Yasuhiro; Udono, Toshifumi; Hirai, Hirohisa; Imai, Hiroo

2012-01-01

Chimpanzees (Pan troglodytes) have region-specific difference in dietary repertoires from East to West across tropical Africa. Such differences may result from different genetic backgrounds in addition to cultural variations. We analyzed the sequences of all bitter taste receptor genes (cTAS2Rs) in a total of 59 chimpanzees, including 4 putative subspecies. We identified genetic variations including single-nucleotide variations (SNVs), insertions and deletions (indels), gene-conversion variations, and copy-number variations (CNVs) in cTAS2Rs. Approximately two-thirds of all cTAS2R haplotypes in the amino acid sequence were unique to each subspecies. We analyzed the evolutionary backgrounds of natural selection behind such diversification. Our previous study concluded that diversification of cTAS2Rs in western chimpanzees (P. t. verus) may have resulted from balancing selection. In contrast, the present study found that purifying selection dominates as the evolutionary form of diversification of the so-called human cluster of cTAS2Rs in eastern chimpanzees (P. t. schweinfurthii) and that the other cTAS2Rs were under no obvious selection as a whole. Such marked diversification of cTAS2Rs with different evolutionary backgrounds among subspecies of chimpanzees probably reflects their subspecies-specific dietary repertoires.

Eco-Geographical Diversification of Bitter Taste Receptor Genes (TAS2Rs) among Subspecies of Chimpanzees (Pan troglodytes)

PubMed Central

Hayakawa, Takashi; Sugawara, Tohru; Go, Yasuhiro; Udono, Toshifumi; Hirai, Hirohisa; Imai, Hiroo

2012-01-01

Chimpanzees (Pan troglodytes) have region-specific difference in dietary repertoires from East to West across tropical Africa. Such differences may result from different genetic backgrounds in addition to cultural variations. We analyzed the sequences of all bitter taste receptor genes (cTAS2Rs) in a total of 59 chimpanzees, including 4 putative subspecies. We identified genetic variations including single-nucleotide variations (SNVs), insertions and deletions (indels), gene-conversion variations, and copy-number variations (CNVs) in cTAS2Rs. Approximately two-thirds of all cTAS2R haplotypes in the amino acid sequence were unique to each subspecies. We analyzed the evolutionary backgrounds of natural selection behind such diversification. Our previous study concluded that diversification of cTAS2Rs in western chimpanzees (P. t. verus) may have resulted from balancing selection. In contrast, the present study found that purifying selection dominates as the evolutionary form of diversification of the so-called human cluster of cTAS2Rs in eastern chimpanzees (P. t. schweinfurthii) and that the other cTAS2Rs were under no obvious selection as a whole. Such marked diversification of cTAS2Rs with different evolutionary backgrounds among subspecies of chimpanzees probably reflects their subspecies-specific dietary repertoires. PMID:22916235

Environmental Adaptation from the Origin of Life to the Last Universal Common Ancestor

NASA Astrophysics Data System (ADS)

Cantine, Marjorie D.; Fournier, Gregory P.

2018-03-01

Extensive fundamental molecular and biological evolution took place between the prebiotic origins of life and the state of the Last Universal Common Ancestor (LUCA). Considering the evolutionary innovations between these two endpoints from the perspective of environmental adaptation, we explore the hypothesis that LUCA was temporally, spatially, and environmentally distinct from life's earliest origins in an RNA world. Using this lens, we interpret several molecular biological features as indicating an environmental transition between a cold, radiation-shielded origin of life and a mesophilic, surface-dwelling LUCA. Cellularity provides motility and permits Darwinian evolution by connecting genetic material and its products, and thus establishing heredity and lineage. Considering the importance of compartmentalization and motility, we propose that the early emergence of cellularity is required for environmental dispersal and diversification during these transitions. Early diversification and the emergence of ecology before LUCA could be an important pre-adaptation for life's persistence on a changing planet.

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

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

Freshwater Biodiversity and Insect Diversification

PubMed Central

Dijkstra, Klaas-Douwe B.; Monaghan, Michael T.; Pauls, Steffen U.

2016-01-01

Inland waters cover less than one percent of Earth’s surface, but harbor more than six percent of all insect species: nearly 100,000 species from 12 orders spend one or more life stages in freshwater. Little is known about how this remarkable diversity arose, although allopatric speciation and ecological adaptation are thought to be primary mechanisms. Freshwater habitats are exceptionally susceptible to environmental change, and exhibit marked ecological gradients. The amphibiotic lifestyles of aquatic insects result in complex contributions of extinction and allopatric and non-allopatric speciation in species diversification. In contrast to the lack of evolutionary studies, the ecology and habitat preferences of aquatic insects have been intensively studied, in part because of their widespread use as bio-indicators. The combination of phylogenetics with the extensive ecological data provides a promising avenue for future research, making aquatic insects highly suitable models for the study of ecological diversification. PMID:24160433

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.

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

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.

Ecological diversification associated with the benthic-to-pelagic transition by North American minnows.

PubMed

Burress, E D; Holcomb, J M; Tan, M; Armbruster, J W

2017-03-01

Ecological opportunity is often regarded as a key factor that explains why diversity is unevenly distributed across life. Colonization of novel environments or adaptive zones may promote diversification. North American minnows exhibit an ancestral benthic-to-pelagic habitat shift that coincided with a burst in diversification. Here, we evaluate the phenotypic and ecological implications of this habitat shift by assessing craniofacial and dietary traits among 34 species and testing for morphology-diet covariation, convergence and adaptive optima. There were several instances of morphology-diet covariation such as correlations between mouth angle and the consumption of terrestrial insects and between relative gut length and the consumption of algae. After accounting for size and phylogenetic nonindependence, benthic species had longer heads, longer snouts, eyes positioned higher on their head, smaller mouth angles and longer digestive tracts than pelagic minnows. Benthic minnows also consumed more algae but less terrestrial insects, by volume, than pelagic minnows. Lastly, there were three distinct evolutionary regimes and more convergence in morphology and dietary characteristics than expected under a Brownian motion model of evolution. These findings indicate that colonization of the pelagic zone by minnows involved myriad phenotypic and dietary changes associated with exploitation of terrestrial subsidies. Thus, minnows exhibit phenotype-dietary covariation, an expansion of ecological roles and a burst in diversification rates in response to the ecological opportunity afforded by the colonization of a novel habitat. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

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

Evolution and diversification of the Toxicofera reptile venom system.

PubMed

Fry, Bryan G; Vidal, Nicolas; van der Weerd, Louise; Kochva, Elazar; Renjifo, Camila

2009-03-06

The diversification of the reptile venom system has been an area of major research but of great controversy. In this review we examine the historical and modern-day efforts of all aspects of the venom system including dentition, glands and secreted toxins and highlight areas of future research opportunities. We use multidisciplinary techniques, including magnetic resonance imaging of venom glands through to molecular phylogenetic reconstruction of toxin evolutionary history, to illustrate the diversity within this integrated weapons system and map the timing of toxin recruitment events over the toxicoferan organismal evolutionary tree.

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

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

Physalis and physaloids: A recent and complex evolutionary history.

PubMed

Zamora-Tavares, María Del Pilar; Martínez, Mahinda; Magallón, Susana; Guzmán-Dávalos, Laura; Vargas-Ponce, Ofelia

2016-07-01

The complex evolutionary history of the subtribe Physalinae is reflected in the poor resolution of the relationships of Physalis and the physaloid genera. We hypothesize that this low resolution is caused by recent evolutionary history in a complex geographic setting. The aims of this study were twofold: (1) To determine the phylogenetic relationships of the current genera recognized in Physalinae in order to identify monophyletic groups and resolve the physaloid grade; and (2) to determine the probable causes of the recent divergence in Physalinae. We conducted phylogenetic analyses with maximum likelihood (ML) and Bayesian inference with 50 Physalinae species and 19 others as outgroups, using morphological and molecular data from five plastid and two nuclear regions. A relaxed molecular clock was obtained from the ML topology and ancestral area reconstruction was conducted using the DEC model. The genera Chamaesaracha, Leucophysalis, and Physalis subgenus Rydbergis were recovered as monophyletic. Three clades, Alkekengi-Calliphysalis, Schraderanthus-Tzeltalia, and Witheringia-Brachistus, also received good support. However, even with morphological data and that of the DNA of seven regions, the tree was not completely resolved and many clades remained unsupported. Physalinae diverged at the end of the Miocene (∼9.22Mya) with one trend indicating that the greatest diversification within the subtribe occurred during the last 5My. The Neotropical region presented the highest probability (45%) of being the ancestral area of Physalinae followed by the Mexican Transition Zone (35%). During the Pliocene and Pleistocene, the geographical areas where species were found experienced significant geological and climatic changes, giving rise to rapid and relatively recent diversification events in Physalinae. Thus, recent origin, high diversification, and morphological complexity have contributed, at least with the currently available methods, to the inability to completely

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.

Disruptive selection as a driver of evolutionary branching and caste evolution in social insects.

PubMed

Planqué, R; Powell, S; Franks, N R; van den Berg, J B

2016-11-01

Theory suggests that evolutionary branching via disruptive selection may be a relatively common and powerful force driving phenotypic divergence. Here, we extend this theory to social insects, which have novel social axes of phenotypic diversification. Our model, built around turtle ant (Cephalotes) biology, is used to explore whether disruptive selection can drive the evolutionary branching of divergent colony phenotypes that include a novel soldier caste. Soldier evolution is a recurrent theme in social insect diversification that is exemplified in the turtle ants. We show that phenotypic mutants can gain competitive advantages that induce disruptive selection and subsequent branching. A soldier caste does not generally appear before branching, but can evolve from subsequent competition. The soldier caste then evolves in association with specialized resource preferences that maximize defensive performance. Overall, our model indicates that resource specialization may occur in the absence of morphological specialization, but that when morphological specialization evolves, it is always in association with resource specialization. This evolutionary coupling of ecological and morphological specialization is consistent with recent empirical evidence, but contrary to predictions of classical caste theory. Our model provides a new theoretical understanding of the ecology of caste evolution that explicitly considers the process of adaptive phenotypic divergence and diversification. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Extinction vs. Rapid Radiation: The Juxtaposed Evolutionary Histories of Coelotine Spiders Support the Eocene-Oligocene Orogenesis of the Tibetan Plateau.

PubMed

Zhao, Zhe; Li, Shuqiang

2017-11-01

Evolutionary biology has long been concerned with how changing environments affect and drive the spatiotemporal development of organisms. Coelotine spiders (Agelenidae: Coelotinae) are common species in the temperate and subtropical areas of the Northern Hemisphere. Their long evolutionary history and the extremely imbalanced distribution of species richness suggest that Eurasian environments, especially since the Cenozoic, are the drivers of their diversification. We use phylogenetics, molecular dating, ancestral area reconstructions, diversity, and ecological niche analyses to investigate the spatiotemporal evolution of 286 coelotine species from throughout the region. Based on eight genes (6.5 kb) and 2323 de novo DNA sequences, analyses suggest an Eocene South China origin for them. Most extant, widespread species belong to the southern (SCG) or northern (NCG) clades. The origin of coelotine spiders appears to associate with either the Paleocene-Eocene Thermal Maximum or the hot period in early Eocene. Tibetan uplifting events influenced the current diversity patterns of coelotines. The origin of SCG lies outside of the Tibetan Plateau. Uplifting in the southeastern area of the plateau blocked dispersal since the Late Eocene. Continuous orogenesis appears to have created localized vicariant events, which drove rapid radiation in SCG. North-central Tibet is the likely location of origin for NCG and many lineages likely experienced extinction owing to uplifting since early Oligocene. Their evolutionary histories correspond with recent geological evidence that high-elevation orographical features existed in the Tibetan region as early as 40-35 Ma. Our discoveries may be the first empirical evidence that links the evolution of organisms to the Eocene-Oligocene uplifting of the Tibetan Plateau. [Tibet; biogeography; ecology; molecular clock; diversification.]. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic

The extended evolutionary synthesis: its structure, assumptions and predictions

PubMed Central

Laland, Kevin N.; Uller, Tobias; Feldman, Marcus W.; Sterelny, Kim; Müller, Gerd B.; Moczek, Armin; Jablonka, Eva; Odling-Smee, John

2015-01-01

Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the ‘extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism–environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology. PMID:26246559

Evolution Stings: The Origin and Diversification of Scorpion Toxin Peptide Scaffolds

PubMed Central

Sunagar, Kartik; Undheim, Eivind A. B.; Chan, Angelo H. C.; Koludarov, Ivan; Muñoz-Gómez, Sergio A.; Antunes, Agostinho; Fry, Bryan G.

2013-01-01

The episodic nature of natural selection and the accumulation of extreme sequence divergence in venom-encoding genes over long periods of evolutionary time can obscure the signature of positive Darwinian selection. Recognition of the true biocomplexity is further hampered by the limited taxon selection, with easy to obtain or medically important species typically being the subject of intense venom research, relative to the actual taxonomical diversity in nature. This holds true for scorpions, which are one of the most ancient terrestrial venomous animal lineages. The family Buthidae that includes all the medically significant species has been intensely investigated around the globe, while almost completely ignoring the remaining non-buthid families. Australian scorpion lineages, for instance, have been completely neglected, with only a single scorpion species (Urodacus yaschenkoi) having its venom transcriptome sequenced. Hence, the lack of venom composition and toxin sequence information from an entire continent’s worth of scorpions has impeded our understanding of the molecular evolution of scorpion venom. The molecular origin, phylogenetic relationships and evolutionary histories of most scorpion toxin scaffolds remain enigmatic. In this study, we have sequenced venom gland transcriptomes of a wide taxonomical diversity of scorpions from Australia, including buthid and non-buthid representatives. Using state-of-art molecular evolutionary analyses, we show that a majority of CSα/β toxin scaffolds have experienced episodic influence of positive selection, while most non-CSα/β linear toxins evolve under the extreme influence of negative selection. For the first time, we have unraveled the molecular origin of the major scorpion toxin scaffolds, such as scorpion venom single von Willebrand factor C-domain peptides (SV-SVC), inhibitor cystine knot (ICK), disulphide-directed beta-hairpin (DDH), bradykinin potentiating peptides (BPP), linear non-disulphide bridged

Evolution stings: the origin and diversification of scorpion toxin peptide scaffolds.

PubMed

Sunagar, Kartik; Undheim, Eivind A B; Chan, Angelo H C; Koludarov, Ivan; Muñoz-Gómez, Sergio A; Antunes, Agostinho; Fry, Bryan G

2013-12-13

The episodic nature of natural selection and the accumulation of extreme sequence divergence in venom-encoding genes over long periods of evolutionary time can obscure the signature of positive Darwinian selection. Recognition of the true biocomplexity is further hampered by the limited taxon selection, with easy to obtain or medically important species typically being the subject of intense venom research, relative to the actual taxonomical diversity in nature. This holds true for scorpions, which are one of the most ancient terrestrial venomous animal lineages. The family Buthidae that includes all the medically significant species has been intensely investigated around the globe, while almost completely ignoring the remaining non-buthid families. Australian scorpion lineages, for instance, have been completely neglected, with only a single scorpion species (Urodacus yaschenkoi) having its venom transcriptome sequenced. Hence, the lack of venom composition and toxin sequence information from an entire continent's worth of scorpions has impeded our understanding of the molecular evolution of scorpion venom. The molecular origin, phylogenetic relationships and evolutionary histories of most scorpion toxin scaffolds remain enigmatic. In this study, we have sequenced venom gland transcriptomes of a wide taxonomical diversity of scorpions from Australia, including buthid and non-buthid representatives. Using state-of-art molecular evolutionary analyses, we show that a majority of CSα/β toxin scaffolds have experienced episodic influence of positive selection, while most non-CSα/β linear toxins evolve under the extreme influence of negative selection. For the first time, we have unraveled the molecular origin of the major scorpion toxin scaffolds, such as scorpion venom single von Willebrand factor C-domain peptides (SV-SVC), inhibitor cystine knot (ICK), disulphide-directed beta-hairpin (DDH), bradykinin potentiating peptides (BPP), linear non-disulphide bridged

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

Phylogeny of Dictyoptera: Dating the Origin of Cockroaches, Praying Mantises and Termites with Molecular Data and Controlled Fossil Evidence

PubMed Central

Legendre, Frédéric; Nel, André; Svenson, Gavin J.; Robillard, Tony; Pellens, Roseli; Grandcolas, Philippe

2015-01-01

Understanding the origin and diversification of organisms requires a good phylogenetic estimate of their age and diversification rates. This estimate can be difficult to obtain when samples are limited and fossil records are disputed, as in Dictyoptera. To choose among competing hypotheses of origin for dictyopteran suborders, we root a phylogenetic analysis (~800 taxa, 10 kbp) within a large selection of outgroups and calibrate datings with fossils attributed to lineages with clear synapomorphies. We find the following topology: (mantises, (other cockroaches, (Cryptocercidae, termites)). Our datings suggest that crown-Dictyoptera—and stem-mantises—would date back to the Late Carboniferous (~ 300 Mya), a result compatible with the oldest putative fossil of stem-dictyoptera. Crown-mantises, however, would be much more recent (~ 200 Mya; Triassic/Jurassic boundary). This pattern (i.e., old origin and more recent diversification) suggests a scenario of replacement in carnivory among polyneopterous insects. The most recent common ancestor of (cockroaches + termites) would date back to the Permian (~275 Mya), which contradicts the hypothesis of a Devonian origin of cockroaches. Stem-termites would date back to the Triassic/Jurassic boundary, which refutes a Triassic origin. We suggest directions in extant and extinct species sampling to sharpen this chronological framework and dictyopteran evolutionary studies. PMID:26200914

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.

Tracing the evolutionary origin of vertebrate skeletal tissues: insights from cephalochordate amphioxus.

PubMed

Yong, Luok Wen; Yu, Jr-Kai

2016-08-01

Vertebrate mineralized skeletal tissues are widely considered as an evolutionary novelty. Despite the importance of these tissues to the adaptation and radiation of vertebrate animals, the evolutionary origin of vertebrate skeletal tissues remains largely unclear. Cephalochordates (Amphioxus) occupy a key phylogenetic position and can serve as a valuable model for studying the evolution of vertebrate skeletal tissues. Here we summarize recent advances in amphioxus developmental biology and comparative genomics that can help to elucidate the evolutionary origins of the vertebrate skeletal tissues and their underlying developmental gene regulatory networks (GRN). By making comparisons to the developmental studies in vertebrate models and recent discoveries in paleontology and genomics, it becomes evident that the collagen matrix-based connective tissues secreted by the somite-derived cells in amphioxus likely represent the rudimentary skeletal tissues in chordates. We propose that upon the foundation of this collagenous precursor, novel tissue mineralization genes that arose from gene duplications were incorporated into an ancestral mesodermal GRN that makes connective and supporting tissues, leading to the emergence of highly-mineralized skeletal tissues in early vertebrates. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

The ancient evolutionary origins of Scleractinia revealed by azooxanthellate corals

PubMed Central

2011-01-01

Background Scleractinian corals are currently a focus of major interest because of their ecological importance and the uncertain fate of coral reefs in the face of increasing anthropogenic pressure. Despite this, remarkably little is known about the evolutionary origins of corals. The Scleractinia suddenly appear in the fossil record about 240 Ma, but the range of morphological variation seen in these Middle Triassic fossils is comparable to that of modern scleractinians, implying much earlier origins that have so far remained elusive. A significant weakness in reconstruction(s) of early coral evolution is that deep-sea corals have been poorly represented in molecular phylogenetic analyses. Results By adding new data from a large and representative range of deep-water species to existing molecular datasets and applying a relaxed molecular clock, we show that two exclusively deep-sea families, the Gardineriidae and Micrabaciidae, diverged prior to the Complexa/Robusta coral split around 425 Ma, thereby pushing the evolutionary origin of scleractinian corals deep into the Paleozoic. Conclusions The early divergence and distinctive morphologies of the extant gardineriid and micrabaciid corals suggest a link with Ordovician "scleractiniamorph" fossils that were previously assumed to represent extinct anthozoan skeletonized lineages. Therefore, scleractinian corals most likely evolved from Paleozoic soft-bodied ancestors. Modern shallow-water Scleractinia, which are dependent on symbionts, appear to have had several independent origins from solitary, non-symbiotic precursors. The Scleractinia have survived periods of massive climate change in the past, suggesting that as a lineage they may be less vulnerable to future changes than often assumed. PMID:22034946

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.

Genomic insights into the origin and diversification of late maritime hunter-gatherers from the Chilean Patagonia.

PubMed

de la Fuente, Constanza; Ávila-Arcos, María C; Galimany, Jacqueline; Carpenter, Meredith L; Homburger, Julian R; Blanco, Alejandro; Contreras, Paloma; Cruz Dávalos, Diana; Reyes, Omar; San Roman, Manuel; Moreno-Estrada, Andrés; Campos, Paula F; Eng, Celeste; Huntsman, Scott; Burchard, Esteban G; Malaspinas, Anna-Sapfo; Bustamante, Carlos D; Willerslev, Eske; Llop, Elena; Verdugo, Ricardo A; Moraga, Mauricio

2018-04-24

Patagonia was the last region of the Americas reached by humans who entered the continent from Siberia ∼15,000-20,000 y ago. Despite recent genomic approaches to reconstruct the continental evolutionary history, regional characterization of ancient and modern genomes remains understudied. Exploring the genomic diversity within Patagonia is not just a valuable strategy to gain a better understanding of the history and diversification of human populations in the southernmost tip of the Americas, but it would also improve the representation of Native American diversity in global databases of human variation. Here, we present genome data from four modern populations from Central Southern Chile and Patagonia ( n = 61) and four ancient maritime individuals from Patagonia (∼1,000 y old). Both the modern and ancient individuals studied in this work have a greater genetic affinity with other modern Native Americans than to any non-American population, showing within South America a clear structure between major geographical regions. Native Patagonian Kawéskar and Yámana showed the highest genetic affinity with the ancient individuals, indicating genetic continuity in the region during the past 1,000 y before present, together with an important agreement between the ethnic affiliation and historical distribution of both groups. Lastly, the ancient maritime individuals were genetically equidistant to a ∼200-y-old terrestrial hunter-gatherer from Tierra del Fuego, which supports a model with an initial separation of a common ancestral group to both maritime populations from a terrestrial population, with a later diversification of the maritime groups.

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.

Rapid evolutionary change of common bean (Phaseolus vulgaris L) plastome, and the genomic diversification of legume chloroplasts

PubMed Central

Guo, Xianwu; Castillo-Ramírez, Santiago; González, Víctor; Bustos, Patricia; Luís Fernández-Vázquez, José; Santamaría, Rosa Isela; Arellano, Jesús; Cevallos, Miguel A; Dávila, Guillermo

2007-01-01

Background Fabaceae (legumes) is one of the largest families of flowering plants, and some members are important crops. In contrast to what we know about their great diversity or economic importance, our knowledge at the genomic level of chloroplast genomes (cpDNAs or plastomes) for these crops is limited. Results We sequenced the complete genome of the common bean (Phaseolus vulgaris cv. Negro Jamapa) chloroplast. The plastome of P. vulgaris is a 150,285 bp circular molecule. It has gene content similar to that of other legume plastomes, but contains two pseudogenes, rpl33 and rps16. A distinct inversion occurred at the junction points of trnH-GUG/rpl14 and rps19/rps8, as in adzuki bean [1]. These two pseudogenes and the inversion were confirmed in 10 varieties representing the two domestication centers of the bean. Genomic comparative analysis indicated that inversions generally occur in legume plastomes and the magnitude and localization of insertions/deletions (indels) also vary. The analysis of repeat sequences demonstrated that patterns and sequences of tandem repeats had an important impact on sequence diversification between legume plastomes and tandem repeats did not belong to dispersed repeats. Interestingly, P. vulgaris plastome had higher evolutionary rates of change on both genomic and gene levels than G. max, which could be the consequence of pressure from both mutation and natural selection. Conclusion Legume chloroplast genomes are widely diversified in gene content, gene order, indel structure, abundance and localization of repetitive sequences, intracellular sequence exchange and evolutionary rates. The P. vulgaris plastome is a rapidly evolving genome. PMID:17623083

Freshwater biodiversity and aquatic insect diversification.

PubMed

Dijkstra, Klaas-Douwe B; Monaghan, Michael T; Pauls, Steffen U

2014-01-01

Inland waters cover less than 1% of Earth's surface but harbor more than 6% of all insect species: Nearly 100,000 species from 12 orders spend one or more life stages in freshwater. Little is known about how this remarkable diversity arose, although allopatric speciation and ecological adaptation are thought to be primary mechanisms. Freshwater habitats are highly susceptible to environmental change and exhibit marked ecological gradients. Standing waters appear to harbor more dispersive species than running waters, but there is little understanding of how this fundamental ecological difference has affected diversification. In contrast to the lack of evolutionary studies, the ecology and habitat preferences of aquatic insects have been intensively studied, in part because of their widespread use as bioindicators. The combination of phylogenetics with the extensive ecological data provides a promising avenue for future research, making aquatic insects highly suitable models for the study of ecological diversification.

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.

Multiple Origins and Nested Cycles of Hybridization Result in High Tetraploid Diversity in the Monocot Prospero.

PubMed

Jang, Tae-Soo; Parker, John S; Emadzade, Khatere; Temsch, Eva M; Leitch, Andrew R; Weiss-Schneeweiss, Hanna

2018-01-01

Polyploidy is a major driving force in angiosperm evolution, but our understanding of establishment and early diversification processes following allo- vs. auto-polyploidy is limited. An excellent system to address such questions is the monocot plant Prospero autumnale , as it comprises several genomically and chromosomally distinct diploid cytotypes and their auto- and allotetraploid derivatives. To infer origins and evolutionary trajectories of the tetraploids, we use genome size data, in situ hybridization with parental genomic DNAs and specific probes (satDNA, rDNAs), as well as molecular-phylogenetic analyses. Thus, we demonstrate that an astounding range of allotetraploid lineages has been formed recurrently by chromosomal re-patterning, interactions of chromosomally variable parental genomes and nested cycles of extensive hybridization, whereas autotetraploids have originated at least twice and are cytologically stable. During the recurrent formation and establishment across wide geographic areas hybridization in some populations could have inhibited lineage diversification and nascent speciation of such a hybrid swarm. However, cytotypes that became fixed in populations enhanced the potential for species diversification, possibly exploiting the extended allelic base, and fixed heterozygosity that polyploidy confers. The time required for polyploid cytotype fixation may in part reflect the lag phase reported for polyploids between their formation and species diversification.

Dual origin of tribosphenic mammals.

PubMed

Luo, Z X; Cifelli, R L; Kielan-Jaworowska, Z

2001-01-04

Marsupials, placentals and their close therian relatives possess complex (tribosphenic) molars that are capable of versatile occlusal functions. This functional complex is widely thought to be a key to the early diversification and evolutionary success of extant therians and their close relatives (tribosphenidans). Long thought to have arisen on northern continents, tribosphenic mammals have recently been reported from southern landmasses. The great age and advanced morphology of these new mammals has led to the alternative suggestion of a Gondwanan origin for the group. Implicit in both biogeographic hypotheses is the assumption that tribosphenic molars evolved only once in mammalian evolutionary history. Phylogenetic and morphometric analyses including these newly discovered taxa suggest a different interpretation: that mammals with tribosphenic molars are not monophyletic. Tribosphenic molars evolved independently in two ancient (holotherian) mammalian groups with different geographic distributions during the Jurassic/Early Cretaceous: an australosphenidan clade endemic to Gondwanan landmasses, survived by extant monotremes; and a boreosphenidan clade of Laurasian continents, including extant marsupials, placentals and their relatives.

Divergent Evolutionary Patterns of NAC Transcription Factors Are Associated with Diversification and Gene Duplications in Angiosperm

PubMed Central

Jin, Xiaoli; Ren, Jing; Nevo, Eviatar; Yin, Xuegui; Sun, Dongfa; Peng, Junhua

2017-01-01

NAC (NAM/ATAF/CUC) proteins constitute one of the biggest plant-specific transcription factor (TF) families and have crucial roles in diverse developmental programs during plant growth. Phylogenetic analyses have revealed both conserved and lineage-specific NAC subfamilies, among which various origins and distinct features were observed. It is reasonable to hypothesize that there should be divergent evolutionary patterns of NAC TFs both between dicots and monocots, and among NAC subfamilies. In this study, we compared the gene duplication and loss, evolutionary rate, and selective pattern among non-lineage specific NAC subfamilies, as well as those between dicots and monocots, through genome-wide analyses of sequence and functional data in six dicot and five grass lineages. The number of genes gained in the dicot lineages was much larger than that in the grass lineages, while fewer gene losses were observed in the grass than that in the dicots. We revealed (1) uneven constitution of Clusters of Orthologous Groups (COGs) and contrasting birth/death rates among subfamilies, and (2) two distinct evolutionary scenarios of NAC TFs between dicots and grasses. Our results demonstrated that relaxed selection, resulting from concerted gene duplications, may have permitted substitutions responsible for functional divergence of NAC genes into new lineages. The underlying mechanism of distinct evolutionary fates of NAC TFs shed lights on how evolutionary divergence contributes to differences in establishing NAC gene subfamilies and thus impacts the distinct features between dicots and grasses. PMID:28713414

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

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.

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

An ant genus-group (Prenolepis) illuminates the biogeography and drivers of insect diversification in the Indo-Pacific.

PubMed

Matos-Maraví, Pável; Clouse, Ronald M; Sarnat, Eli M; Economo, Evan P; LaPolla, John S; Borovanska, Michaela; Rabeling, Christian; Czekanski-Moir, Jesse; Latumahina, Fransina; Wilson, Edward O; Janda, Milan

2018-06-01

The Malay Archipelago and the tropical South Pacific (hereafter the Indo-Pacific region) are considered biodiversity hotspots, yet a general understanding of the origins and diversification of species-rich groups in the region remains elusive. We aimed to test hypotheses for the evolutionary processes driving insect species diversity in the Indo-Pacific using a higher-level and comprehensive phylogenetic hypothesis for an ant clade consisting of seven genera. We estimated divergence times and reconstructed the biogeographical history of ant species in the Prenolepis genus-group (Formicidae: Formicinae: Lasiini). We used a fossil-calibrated phylogeny to infer ancestral geographical ranges utilizing a biogeographic model that includes founder-event speciation. Ancestral state reconstructions of the ants' ecological preferences, and diversification rates were estimated for selected Indo-Pacific clades. Overall, we report that faunal interchange between Asia and Australia has occurred since at least 20-25 Ma, and early dispersal to the Fijian Basin happened during the early and mid-Miocene (ca. 10-20 Ma). Differences in diversification rates across Indo-Pacific clades may be related to ecological preference breadth, which in turn may have facilitated geographical range expansions. Ancient dispersal routes suggested by our results agree with the palaeogeography of the region. For this particular group of ants, the rapid orogenesis in New Guinea and possibly subsequent ecological shifts may have promoted their rapid diversification and widespread distribution across the Indo-Pacific. Copyright © 2018 Elsevier Inc. All rights reserved.

Probing the evolutionary origins of music perception.

PubMed

McDermott, Josh; Hauser, Marc D

2005-12-01

Empirical data have recently begun to inform debates on the evolutionary origins of music. In this paper we discuss some of our recent findings and related theoretical issues. We claim that theories of the origins of music will be usefully constrained if we can determine which aspects of music perception are innate, and, of those, which are uniquely human and specific to music. Comparative research in nonhuman animals, particularly nonhuman primates, is thus critical to the debate. In this paper we focus on the preferences that characterize most humans' experience of music, testing whether similar preferences exist in nonhuman primates. Our research suggests that many rudimentary acoustic preferences, such as those for consonant over dissonant intervals, may be unique to humans. If these preferences prove to be innate in humans, they may be candidates for music-specific adaptations. To establish whether such preferences are innate in humans, one important avenue for future research will be the collection of data from different cultures. This may be facilitated by studies conducted over the internet.

Origin and Reticulate Evolutionary Process of Wheatgrass Elymus trachycaulus (Triticeae: Poaceae)

PubMed Central

Zuo, Hongwei; Wu, Panpan; Wu, Dexiang; Sun, Genlou

2015-01-01

To study origin and evolutionary dynamics of tetraploid Elymus trachycaulus that has been cytologically defined as containing StH genomes, thirteen accessions of E. trachycaulus were analyzed using two low-copy nuclear gene Pepc (phosphoenolpyruvate carboxylase) and Rpb2 (the second largest subunit of RNA polymerase II), and one chloroplast region trnL–trnF (spacer between the tRNA Leu (UAA) gene and the tRNA-Phe (GAA) gene). Our chloroplast data indicated that Pseudoroegneria (St genome) was the maternal donor of E. trachycaulus. Rpb2 data indicated that the St genome in E. trachycaulus was originated from either P. strigosa, P. stipifolia, P. spicata or P. geniculate. The Hordeum (H genome)-like sequences of E. trachycaulus are polyphyletic in the Pepc tree, suggesting that the H genome in E. trachycaulus was contributed by multiple sources, whether due to multiple origins or introgression resulting from subsequent hybridization. Failure to recovering St copy of Pepc sequence in most accessions of E. trachycaulus might be caused by genome convergent evolution in allopolyploids. Multiple copies of H-like Pepc sequence from each accession with relative large deletions and insertions might be caused by either instability of Pepc sequence in H- genome or incomplete concerted evolution. Our results highlighted complex evolutionary history of E. trachycaulus. PMID:25946188

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.

Reconciling the evolutionary origin of bread wheat (Triticum aestivum).

PubMed

El Baidouri, Moaine; Murat, Florent; Veyssiere, Maeva; Molinier, Mélanie; Flores, Raphael; Burlot, Laura; Alaux, Michael; Quesneville, Hadi; Pont, Caroline; Salse, Jérôme

2017-02-01

The origin of bread wheat (Triticum aestivum; AABBDD) has been a subject of controversy and of intense debate in the scientific community over the last few decades. In 2015, three articles published in New Phytologist discussed the origin of hexaploid bread wheat (AABBDD) from the diploid progenitors Triticum urartu (AA), a relative of Aegilops speltoides (BB) and Triticum tauschii (DD). Access to new genomic resources since 2013 has offered the opportunity to gain novel insights into the paleohistory of modern bread wheat, allowing characterization of its origin from its diploid progenitors at unprecedented resolution. We propose a reconciled evolutionary scenario for the modern bread wheat genome based on the complementary investigation of transposable element and mutation dynamics between diploid, tetraploid and hexaploid wheat. In this scenario, the structural asymmetry observed between the A, B and D subgenomes in hexaploid bread wheat derives from the cumulative effect of diploid progenitor divergence, the hybrid origin of the D subgenome, and subgenome partitioning following the polyploidization events. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

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.

Phylogenetic relationships, diversification and expansion of chili peppers (Capsicum, Solanaceae).

PubMed

Carrizo García, Carolina; Barfuss, Michael H J; Sehr, Eva M; Barboza, Gloria E; Samuel, Rosabelle; Moscone, Eduardo A; Ehrendorfer, Friedrich

2016-07-01

Capsicum (Solanaceae), native to the tropical and temperate Americas, comprises the well-known sweet and hot chili peppers and several wild species. So far, only partial taxonomic and phylogenetic analyses have been done for the genus. Here, the phylogenetic relationships between nearly all taxa of Capsicum were explored to test the monophyly of the genus and to obtain a better knowledge of species relationships, diversification and expansion. Thirty-four of approximately 35 Capsicum species were sampled. Maximum parsimony and Bayesian inference analyses were performed using two plastid markers (matK and psbA-trnH) and one single-copy nuclear gene (waxy). The evolutionary changes of nine key features were reconstructed following the parsimony ancestral states method. Ancestral areas were reconstructed through a Bayesian Markov chain Monte Carlo analysis. Capsicum forms a monophyletic clade, with Lycianthes as a sister group, following both phylogenetic approaches. Eleven well-supported clades (four of them monotypic) can be recognized within Capsicum, although some interspecific relationships need further analysis. A few features are useful to characterize different clades (e.g. fruit anatomy, chromosome base number), whereas some others are highly homoplastic (e.g. seed colour). The origin of Capsicum is postulated in an area along the Andes of western to north-western South America. The expansion of the genus has followed a clockwise direction around the Amazon basin, towards central and south-eastern Brazil, then back to western South America, and finally northwards to Central America. New insights are provided regarding interspecific relationships, character evolution, and geographical origin and expansion of Capsicum A clearly distinct early-diverging clade can be distinguished, centred in western-north-western South America. Subsequent rapid speciation has led to the origin of the remaining clades. The diversification of Capsicum has culminated in the origin

Phylogenetic relationships, diversification and expansion of chili peppers (Capsicum, Solanaceae)

PubMed Central

Carrizo García, Carolina; Barfuss, Michael H. J.; Sehr, Eva M.; Barboza, Gloria E.; Samuel, Rosabelle; Moscone, Eduardo A.; Ehrendorfer, Friedrich

2016-01-01

Background and Aims Capsicum (Solanaceae), native to the tropical and temperate Americas, comprises the well-known sweet and hot chili peppers and several wild species. So far, only partial taxonomic and phylogenetic analyses have been done for the genus. Here, the phylogenetic relationships between nearly all taxa of Capsicum were explored to test the monophyly of the genus and to obtain a better knowledge of species relationships, diversification and expansion. Methods Thirty-four of approximately 35 Capsicum species were sampled. Maximum parsimony and Bayesian inference analyses were performed using two plastid markers (matK and psbA-trnH) and one single-copy nuclear gene (waxy). The evolutionary changes of nine key features were reconstructed following the parsimony ancestral states method. Ancestral areas were reconstructed through a Bayesian Markov chain Monte Carlo analysis. Key Results Capsicum forms a monophyletic clade, with Lycianthes as a sister group, following both phylogenetic approaches. Eleven well-supported clades (four of them monotypic) can be recognized within Capsicum, although some interspecific relationships need further analysis. A few features are useful to characterize different clades (e.g. fruit anatomy, chromosome base number), whereas some others are highly homoplastic (e.g. seed colour). The origin of Capsicum is postulated in an area along the Andes of western to north-western South America. The expansion of the genus has followed a clockwise direction around the Amazon basin, towards central and south-eastern Brazil, then back to western South America, and finally northwards to Central America. Conclusions New insights are provided regarding interspecific relationships, character evolution, and geographical origin and expansion of Capsicum. A clearly distinct early-diverging clade can be distinguished, centred in western–north-western South America. Subsequent rapid speciation has led to the origin of the remaining clades. The

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.

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

Euryhalinity in an evolutionary context

USGS Publications Warehouse

Schultz, Eric T.; McCormick, Stephen D.; McCormick, Stephen D.; Farrell, Anthony Peter; Brauner, Colin J.

2013-01-01

This chapter focuses on the evolutionary importance and taxonomic distribution of euryhalinity. Euryhalinity refers to broad halotolerance and broad halohabitat distribution. Salinity exposure experiments have demonstrated that species vary tenfold in their range of tolerable salinity levels, primarily because of differences in upper limits. Halotolerance breadth varies with the species’ evolutionary history, as represented by its ordinal classification, and with the species’ halohabitat. Freshwater and seawater species tolerate brackish water; their empirically-determined fundamental haloniche is broader than their realized haloniche, as revealed by the halohabitats they occupy. With respect to halohabitat distribution, a minority of species (<10%) are euryhaline. Habitat-euryhalinity is prevalent among basal actinopterygian fishes, is largely absent from orders arising from intermediate nodes, and reappears in the most derived taxa. There is pronounced family-level variability in the tendency to be halohabitat-euryhaline, which may have arisen during a burst of diversification following the Cretaceous-Palaeogene extinction. Low prevalence notwithstanding, euryhaline species are potent sources of evolutionary diversity. Euryhalinity is regarded as a key innovation trait whose evolution enables exploitation of new adaptive zone, triggering cladogenesis. We review phylogenetically-informed studies that demonstrate freshwater species diversifying from euryhaline ancestors through processes such as landlocking. These studies indicate that some euryhaline taxa are particularly susceptible to changes in halohabitat and subsequent diversification, and some geographic regions have been hotspots for transitions to freshwater. Comparative studies on mechanisms among multiple taxa and at multiple levels of biological integration are needed to clarify evolutionary pathways to, and from, euryhalinity.

The Radiata and the evolutionary origins of the bilaterian body plan

NASA Technical Reports Server (NTRS)

Martindale, Mark Q.; Finnerty, John R.; Henry, Jonathan Q.

2002-01-01

The apparent conservation of cellular and molecular developmental mechanisms observed in a handful of bilaterian metazoans has spawned a "race" to reconstruct the bilaterian ancestor. Knowledge of this ancestor would permit us to reconstruct the evolutionary changes that have occurred along specific bilaterian lineages. However, comparisons among extant bilaterians provide an unnecessarily limited view of the ancestral bilaterian. Since the original bilaterians are believed by many to be derived from a radially symmetrical ancestor, additional evidence might be obtained by examining present-day radially symmetrical animals. We briefly review pertinent features of the body plans of the extant radial eumetazoan phyla, the Cnidaria, and Ctenophora, in the context of revealing potential evolutionary links to the bilaterians.

What explains high plant richness in East Asia? Time and diversification in the tribe Lysimachieae (Primulaceae).

PubMed

Yan, Hai-Fei; Zhang, Cai-Yun; Anderberg, Arne A; Hao, Gang; Ge, Xue-Jun; Wiens, John J

2018-04-17

What causes the disparity in biodiversity among regions is a fundamental question in biogeography, ecology, and evolutionary biology. Evolutionary and biogeographic processes (speciation, extinction, dispersal) directly determine species richness patterns, and can be studied using integrative phylogenetic approaches. However, the strikingly high richness of East Asia relative to other Northern Hemisphere regions remains poorly understood from this perspective. Here, for the first time, we test two general hypotheses (older colonization time, faster diversification rate) to explain this pattern, using the plant tribe Lysimachieae (Primulaceae) as a model system. We generated a new time-calibrated phylogeny for Lysimachieae (13 genes, 126 species), to estimate colonization times and diversification rates for each region and to test the relative importance of these two factors for explaining regional richness patterns. We find that neither time nor diversification rates alone explain richness patterns among regions in Lysimachieae. Instead, a new index that combines both factors explains global richness patterns in the group and their high East Asian biodiversity. Based on our results from Lysimachieae, we suggest that the high richness of plants in East Asia may be explained by a combination of older colonization times and faster diversification rates in this region. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Evolution of ectomycorrhizas as a driver of diversification and biogeographic patterns in the model mycorrhizal mushroom genus Laccaria.

PubMed

Wilson, Andrew W; Hosaka, Kentaro; Mueller, Gregory M

2017-03-01

A systematic and evolutionary ecology study of the model ectomycorrhizal (ECM) genus Laccaria was performed using herbarium material and field collections from over 30 countries covering its known geographic range. A four-gene (nrITS, 28S, RPB2, EF1α) nucleotide sequence dataset consisting of 232 Laccaria specimens was analyzed phylogenetically. The resulting Global Laccaria dataset was used for molecular dating and estimating diversification rates in the genus. Stable isotope analysis of carbon and nitrogen was used to evaluate the origin of Laccaria's ECM ecology. In all, 116 Laccaria molecular species were identified, resulting in a near 50% increase in its known diversity, including the new species described herein: Laccaria ambigua. Molecular dating indicates that the most recent common ancestor to Laccaria existed in the early Paleocene (56-66 million yr ago), probably in Australasia. At this time, Laccaria split into two lineages: one represented by the new species L. ambigua, and the other reflecting a large shift in diversification that resulted in the remainder of Laccaria. L. ambigua shows a different isotopic profile than all other Laccaria species. Isotopes and diversification results suggest that the evolution of the ECM ecology was a key innovation in the evolution of Laccaria. Diversification shifts associated with Laccaria's dispersal to the northern hemisphere are attributed to adaptations to new ecological niches. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Evolutionary bottlenecks in brackish water habitats drive the colonization of fresh water by stingrays.

PubMed

Kirchhoff, K N; Hauffe, T; Stelbrink, B; Albrecht, C; Wilke, T

2017-08-01

Species richness in freshwater bony fishes depends on two main processes: the transition into and the diversification within freshwater habitats. In contrast to bony fishes, only few cartilaginous fishes, mostly stingrays (Myliobatoidei), were able to colonize fresh water. Respective transition processes have been mainly assessed from a physiological and morphological perspective, indicating that the freshwater lifestyle is strongly limited by the ability to perform osmoregulatory adaptations. However, the transition history and the effect of physiological constraints on the diversification in stingrays remain poorly understood. Herein, we estimated the geographic pathways of freshwater colonization and inferred the mode of habitat transitions. Further, we assessed habitat-related speciation rates in a time-calibrated phylogenetic framework to understand factors driving the transition of stingrays into and the diversification within fresh water. Using South American and Southeast Asian freshwater taxa as model organisms, we found one independent freshwater colonization event by stingrays in South America and at least three in Southeast Asia. We revealed that vicariant processes most likely caused freshwater transition during the time of major marine incursions. The habitat transition rates indicate that brackish water species switch preferably back into marine than forth into freshwater habitats. Moreover, our results showed significantly lower diversification rates in brackish water lineages, whereas freshwater and marine lineages exhibit similar rates. Thus, brackish water habitats may have functioned as evolutionary bottlenecks for the colonization of fresh water by stingrays, probably because of the higher variability of environmental conditions in brackish water. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Combining fossil and molecular data to date the diversification of New World Primates.

PubMed

Schrago, C G; Mello, B; Soares, A E R

2013-11-01

Recent methodological advances in molecular dating associated with the growing availability of sequence data have prompted the study of the evolution of New World Anthropoidea in recent years. Motivated by questions regarding historical biogeography or the mode of evolution, these works aimed to obtain a clearer scenario of Platyrrhini origins and diversification. Although some consensus was found, disputed issues, especially those relating to the evolutionary affinities of fossil taxa, remain. The use of fossil taxa for divergence time analysis is traditionally restricted to the provision of calibration priors. However, new analytical approaches have been developed that incorporate fossils as terminals and, thus, directly assign ages to the fossil tips. In this study, we conducted a combined analysis of molecular and morphological data, including fossils, to derive the timescale of New World anthropoids. Differently from previous studies that conducted total-evidence analysis of molecules and morphology, our approach investigated the morphological clock alone. Our results corroborate the hypothesis that living platyrrhines diversified in the last 20 Ma and that Miocene Patagonian fossils compose an independent evolutionary radiation that diversified in the late Oligocene. When compared to the node ages inferred from the molecular timescale, the inclusion of fossils augmented the precision of the estimates for nodes constrained by the fossil tips. We show that morphological data can be analysed using the same methodological framework applied in relaxed molecular clock studies. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

Theories about evolutionary origins of human hepatitis B virus in primates and humans.

PubMed

Souza, Breno Frederico de Carvalho Dominguez; Drexler, Jan Felix; Lima, Renato Santos de; Rosário, Mila de Oliveira Hughes Veiga do; Netto, Eduardo Martins

2014-01-01

The human hepatitis B virus causes acute and chronic hepatitis and is considered one of the most serious human health issues by the World Health Organization, causing thousands of deaths per year. There are similar viruses belonging to the Hepadnaviridae family that infect non-human primates and other mammals as well as some birds. The majority of non-human primate virus isolates were phylogenetically close to the human hepatitis B virus, but like the human genotypes, the origins of these viruses remain controversial. However, there is a possibility that human hepatitis B virus originated in primates. Knowing whether these viruses might be common to humans and primates is crucial in order to reduce the risk to humans. To review the existing knowledge about the evolutionary origins of viruses of the Hepadnaviridae family in primates. This review was done by reading several articles that provide information about the Hepadnaviridae virus family in non-human primates and humans and the possible origins and evolution of these viruses. The evolutionary origin of viruses of the Hepadnaviridae family in primates has been dated back to several thousand years; however, recent analyses of genomic fossils of avihepadnaviruses integrated into the genomes of several avian species have suggested a much older origin of this genus. Some hypotheses about the evolutionary origins of human hepatitis B virus have been debated since the '90s. One theory suggested a New World origin because of the phylogenetic co-segregation between some New World human hepatitis B virus genotypes F and H and woolly monkey human hepatitis B virus in basal sister-relationship to the Old World non-human primates and human hepatitis B virus variants. Another theory suggests an Old World origin of human hepatitis B virus, and that it would have been spread following prehistoric human migrations over 100,000 years ago. A third theory suggests a co-speciation of human hepatitis B virus in non-human primate

Tempo of trophic evolution and its impact on mammalian diversification

PubMed Central

Price, Samantha A.; Hopkins, Samantha S. B.; Smith, Kathleen K.; Roth, V. Louise

2012-01-01

Mammals are characterized by the complex adaptations of their dentition, which are an indication that diet has played a critical role in their evolutionary history. Although much attention has focused on diet and the adaptations of specific taxa, the role of diet in large-scale diversification patterns remains unresolved. Contradictory hypotheses have been proposed, making prediction of the expected relationship difficult. We show that net diversification rate (the cumulative effect of speciation and extinction), differs significantly among living mammals, depending upon trophic strategy. Herbivores diversify fastest, carnivores are intermediate, and omnivores are slowest. The tempo of transitions between the trophic strategies is also highly biased: the fastest rates occur into omnivory from herbivory and carnivory and the lowest transition rates are between herbivory and carnivory. Extant herbivore and carnivore diversity arose primarily through diversification within lineages, whereas omnivore diversity evolved by transitions into the strategy. The ability to specialize and subdivide the trophic niche allowed herbivores and carnivores to evolve greater diversity than omnivores. PMID:22509033

Tempo of trophic evolution and its impact on mammalian diversification.

PubMed

Price, Samantha A; Hopkins, Samantha S B; Smith, Kathleen K; Roth, V Louise

2012-05-01

Mammals are characterized by the complex adaptations of their dentition, which are an indication that diet has played a critical role in their evolutionary history. Although much attention has focused on diet and the adaptations of specific taxa, the role of diet in large-scale diversification patterns remains unresolved. Contradictory hypotheses have been proposed, making prediction of the expected relationship difficult. We show that net diversification rate (the cumulative effect of speciation and extinction), differs significantly among living mammals, depending upon trophic strategy. Herbivores diversify fastest, carnivores are intermediate, and omnivores are slowest. The tempo of transitions between the trophic strategies is also highly biased: the fastest rates occur into omnivory from herbivory and carnivory and the lowest transition rates are between herbivory and carnivory. Extant herbivore and carnivore diversity arose primarily through diversification within lineages, whereas omnivore diversity evolved by transitions into the strategy. The ability to specialize and subdivide the trophic niche allowed herbivores and carnivores to evolve greater diversity than omnivores.

Lineage diversification and morphological evolution in a large-scale continental radiation: The neotropical ovenbirds and woodcreepers (Aves: Furnariidae)

USGS Publications Warehouse

Derryberry, Elizabeth P.; Claramunt, Santiago; Derryberry, Graham; Chesser, R. Terry; Cracraft, Joel; Aleixo, Alexandre; Pérez-Emán, Jorge; Remsen, J.V.; Brumfield, Robb T.

2011-01-01

Patterns of diversification in species-rich clades provide insight into the processes that generate biological diversity. We tested different models of lineage and phenotypic diversification in an exceptional continental radiation, the ovenbird family Furnariidae, using the most complete species-level phylogenetic hypothesis produced to date for a major avian clade (97% of 293 species). We found that the Furnariidae exhibit nearly constant rates of lineage accumulation but show evidence of constrained morphological evolution. This pattern of sustained high rates of speciation despite limitations on phenotypic evolution contrasts with the results of most previous studies of evolutionary radiations, which have found a pattern of decelerating diversity-dependent lineage accumulation coupled with decelerating or constrained phenotypic evolution. Our results suggest that lineage accumulation in tropical continental radiations may not be as limited by ecological opportunities as in temperate or island radiations. More studies examining patterns of both lineage and phenotypic diversification are needed to understand the often complex tempo and mode of evolutionary radiations on continents.

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.

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

Evolutionary Origins of Rhizarian Parasites.

PubMed

Sierra, Roberto; Cañas-Duarte, Silvia J; Burki, Fabien; Schwelm, Arne; Fogelqvist, Johan; Dixelius, Christina; González-García, Laura N; Gile, Gillian H; Slamovits, Claudio H; Klopp, Christophe; Restrepo, Silvia; Arzul, Isabelle; Pawlowski, Jan

2016-04-01

The SAR group (Stramenopila, Alveolata, Rhizaria) is one of the largest clades in the tree of eukaryotes and includes a great number of parasitic lineages. Rhizarian parasites are obligate and have devastating effects on commercially important plants and animals but despite this fact, our knowledge of their biology and evolution is limited. Here, we present rhizarian transcriptomes from all major parasitic lineages in order to elucidate their evolutionary relationships using a phylogenomic approach. Our results suggest that Ascetosporea, parasites of marine invertebrates, are sister to the novel clade Apofilosa. The phytomyxean plant parasites branch sister to the vampyrellid algal ectoparasites in the novel clade Phytorhiza. They also show that Ascetosporea + Apofilosa + Retaria + Filosa + Phytorhiza form a monophyletic clade, although the branching pattern within this clade is difficult to resolve and appears to be model-dependent. Our study does not support the monophyly of the rhizarian parasitic lineages (Endomyxa), suggesting independent origins for rhizarian animal and plant parasites. © The Author(s) 2015. 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.

Genome-wide characterization of GRAS family genes in Medicago truncatula reveals their evolutionary dynamics and functional diversification

PubMed Central

Zhang, Hailing; Cao, Yingping; Shang, Chen; Li, Jikai; Wang, Jianli; Wu, Zhenying; Ma, Lichao; Qi, Tianxiong; Fu, Chunxiang; Hu, Baozhong

2017-01-01

The GRAS gene family is a large plant-specific family of transcription factors that are involved in diverse processes during plant development. Medicago truncatula is an ideal model plant for genetic research in legumes, and specifically for studying nodulation, which is crucial for nitrogen fixation. In this study, 59 MtGRAS genes were identified and classified into eight distinct subgroups based on phylogenetic relationships. Motifs located in the C-termini were conserved across the subgroups, while motifs in the N-termini were subfamily specific. Gene duplication was the main evolutionary force for MtGRAS expansion, especially proliferation of the LISCL subgroup. Seventeen duplicated genes showed strong effects of purifying selection and diverse expression patterns, highlighting their functional importance and diversification after duplication. Thirty MtGRAS genes, including NSP1 and NSP2, were preferentially expressed in nodules, indicating possible roles in the process of nodulation. A transcriptome study, combined with gene expression analysis under different stress conditions, suggested potential functions of MtGRAS genes in various biological pathways and stress responses. Taken together, these comprehensive analyses provide basic information for understanding the potential functions of GRAS genes, and will facilitate further discovery of MtGRAS gene functions. PMID:28945786

[Genetic mechanism and evolutionary significance of the origin of parthenogenetic insects].

PubMed

Wang, Cheng-Ye

2011-12-01

There is a high proportion of parthenogenesis in insecta, and the parthenogenetic potential of insects is an important but often ignored threaten factor for the agricultural and forestry production. The maintenance of parthenogenetic species is a puzzling issue in evolutionary biology. In recent years, although the cellular mechanisms during parthenogenesis in some species have been well studied, the underlying genetic mechanisms that cause the switch from sexual reproduction to parthenogenesis have not been defined. While, understanding the genetic mechanism and evolutionary significance of the origin of parthenogenetic insects is crucial for preventing the pests in agricultural and forestry production. Here we summarized recent studies aimed at identifying the underlying genetic mechanism of parthenogenesis in insects, and briefly discussed its potential application in this filed.

Old Lineages in a New Ecosystem: Diversification of Arcellinid Amoebae (Amoebozoa) and Peatland Mosses

PubMed Central

Leander, Brian S.

2014-01-01

Arcellinid testate amoebae (Amoebozoa) form a group of free-living microbial eukaryotes with one of the oldest fossil records known, yet several aspects of their evolutionary history remain poorly understood. Arcellinids occur in a range of terrestrial, freshwater and even brackish habitats; however, many arcellinid morphospecies such as Hyalosphenia papilio are particularly abundant in Sphagnum-dominated peatlands, a relatively new ecosystem that appeared during the diversification of Sphagnum species in the Miocene (5–20 Myr ago). Here, we reconstruct divergence times in arcellinid testate amoebae after selecting several fossils for clock calibrations and then infer whether or not arcellinids followed a pattern of diversification that parallels the pattern described for Sphagnum. We found that the diversification of core arcellinids occurred during the Phanerozoic, which is congruent with most arcellinid fossils but not with the oldest known amoebozoan fossil (i.e. at ca. 662 or ca. 750 Myr). Overall, Sphagnum and the Hyalospheniidae exhibit different patterns of diversification. However, an extensive molecular phylogenetic analysis of distinct clades within H. papilio species complex demonstrated a correlation between the recent diversification of H. papilio, the recent diversification of Sphagnum mosses, and the establishment of peatlands. PMID:24762929

Evolutionary history of a vanishing radiation: isolation-dependent persistence and diversification in Pacific Island partulid tree snails.

PubMed

Lee, Taehwan; Li, Jingchun; Churchill, Celia K C; Foighil, Diarmaid Ó

2014-09-24

Partulid tree snails are endemic to Pacific high islands and have experienced extraordinary rates of extinction in recent decades. Although they collectively range across a 10,000 km swath of Oceania, half of the family's total species diversity is endemic to a single Eastern Pacific hot spot archipelago (the Society Islands) and all three partulid genera display highly distinctive distributions. Our goal was to investigate broad scale (range wide) and fine scale (within-Society Islands) molecular phylogenetic relationships of the two widespread genera, Partula and Samoana. What can such data tell us regarding the genesis of such divergent generic distribution patterns, and nominal species diversity levels across Oceania? Museum, captive (zoo) and contemporary field specimens enabled us to genotype 54 of the ~120 recognized species, including many extinct or extirpated taxa, from 14 archipelagoes. The genera Partula and Samoana are products of very distinct diversification processes. Originating at the western edge of the familial range, the derived genus Samoana is a relatively recent arrival in the far eastern archipelagoes (Society, Austral, Marquesas) where it exhibits a stepping-stone phylogenetic pattern and has proven adept at both intra-and inter- archipelago colonization. The pronounced east-west geographic disjunction exhibited by the genus Partula stems from a much older long-distance dispersal event and its high taxonomic diversity in the Society Islands is a product of a long history of within-archipelago diversification. The central importance of isolation for partulid lineage persistence and diversification is evident in time-calibrated phylogenetic trees that show that remote archipelagoes least impacted by continental biotas bear the oldest clades and/or the most speciose radiations. In contemporary Oceania, that isolation is being progressively undermined and these tree snails are now directly exposed to introduced continental predators

Evolutionary origins of a novel host plant detoxification gene in butterflies.

PubMed

Fischer, Hanna M; Wheat, Christopher W; Heckel, David G; Vogel, Heiko

2008-05-01

Chemical interactions between plants and their insect herbivores provide an excellent opportunity to study the evolution of species interactions on a molecular level. Here, we investigate the molecular evolutionary events that gave rise to a novel detoxifying enzyme (nitrile-specifier protein [NSP]) in the butterfly family Pieridae, previously identified as a coevolutionary key innovation. By generating and sequencing expressed sequence tags, genomic libraries, and screening databases we found NSP to be a member of an insect-specific gene family, which we characterized and named the NSP-like gene family. Members consist of variable tandem repeats, are gut expressed, and are found across Insecta evolving in a dynamic, ongoing birth-death process. In the Lepidoptera, multiple copies of single-domain major allergen genes are present and originate via tandem duplications. Multiple domain genes are found solely within the brassicaceous-feeding Pieridae butterflies, one of them being NSP and another called major allergen (MA). Analyses suggest that NSP and its paralog MA have a unique single-domain evolutionary origin, being formed by intragenic domain duplication followed by tandem whole-gene duplication. Duplicates subsequently experienced a period of relaxed constraint followed by an increase in constraint, perhaps after neofunctionalization. NSP and its ortholog MA are still experiencing high rates of change, reflecting a dynamic evolution consistent with the known role of NSP in plant-insect interactions. Our results provide direct evidence to the hypothesis that gene duplication is one of the driving forces for speciation and adaptation, showing that both within- and whole-gene tandem duplications are a powerful force underlying evolutionary adaptation.

Biological mechanisms underlying evolutionary origins of psychotic and mood disorders.

PubMed

Goto, Yukiori; Lee, Young-A; Yamaguchi, Yoshie; Jas, Emanuel

2016-10-01

Psychotic and mood disorders are brain dysfunctions that are caused by gene environment interactions. Although these disorders are disadvantageous and involve behavioral phenotypes that decrease the reproductive success of afflicted individuals in the modern human society, the prevalence of these disorders have remained constant in the population. Here, we propose several biological mechanisms by which the genes associated with psychotic and mood disorders could be selected for in specific environmental conditions that provide evolutionary bases for explanations of when, why, and where these disorders emerged and have been maintained in humans. We discuss the evolutionary origins of psychotic and mood disorders with specific focuses on the roles of dopamine and serotonin in the conditions of social competitiveness/hierarchy and maternal care and other potential mechanisms, such as social network homophily and symbiosis. Copyright © 2016 Elsevier Ireland Ltd and Japan Neuroscience Society. All rights reserved.

A molecular signaling approach to linking intraspecific variation and macro-evolutionary patterns.

PubMed

Swanson, Eli M; Snell-Rood, Emilie C

2014-11-01

Macro-evolutionary comparisons are a valued tool in evolutionary biology. Nevertheless, our understanding of how systems involved in molecular signaling change in concert with phenotypic diversification has lagged. We argue that integrating our understanding of the evolution of molecular signaling systems with phylogenetic comparative methods is an important step toward understanding the processes linking variation among individuals with variation among species. Focusing mostly on the endocrine system, we discuss how the complexity and mechanistic nature of molecular signaling systems may influence the application and interpretation of macro-evolutionary comparisons. We also detail five hypotheses concerning the role that physiological mechanisms can play in shaping macro-evolutionary patterns, and discuss ways in which these hypotheses could influence phenotypic diversification. Finally, we review a series of tools able to analyze the complexity of physiological systems and the way they change in concert with the phenotypes for which they coordinate development. © The Author 2014. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Tropical forests are both evolutionary cradles and museums of leaf beetle diversity.

PubMed

McKenna, Duane D; Farrell, Brian D

2006-07-18

The high extant species diversity of tropical lineages of organisms is usually portrayed as a relatively recent and rapid development or as a consequence of the gradual accumulation or preservation of species over time. These explanations have led to alternative views of tropical forests as evolutionary "cradles" or "museums" of diversity, depending on the organisms under study. However, biogeographic and fossil evidence implies that the evolutionary histories of diversification among tropical organisms may be expected to exhibit characteristics of both cradle and museum models. This possibility has not been explored in detail for any group of terrestrial tropical organisms. From an extensively sampled molecular phylogeny of herbivorous Neotropical leaf beetles in the genus Cephaloleia, we present evidence for (i) comparatively ancient Paleocene-Eocene adaptive radiation associated with global warming and Cenozoic maximum global temperatures, (ii) moderately ancient lineage-specific diversification coincident with the Oligocene adaptive radiation of Cephaloleia host plants in the genus Heliconia, and (iii) relatively recent Miocene-Pliocene diversification coincident with the collision of the Panama arc with South America and subsequent bridging of the Isthmus of Panama. These results demonstrate that, for Cephaloleia and perhaps other lineages of organisms, tropical forests are at the same time both evolutionary cradles and museums of diversity.

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

Charles Darwin and the Origins of Plant Evolutionary Developmental Biology

PubMed Central

Friedman, William E.; Diggle, Pamela K.

2011-01-01

Much has been written of the early history of comparative embryology and its influence on the emergence of an evolutionary developmental perspective. However, this literature, which dates back nearly a century, has been focused on metazoans, without acknowledgment of the contributions of comparative plant morphologists to the creation of a developmental view of biodiversity. We trace the origin of comparative plant developmental morphology from its inception in the eighteenth century works of Wolff and Goethe, through the mid nineteenth century discoveries of the general principles of leaf and floral organ morphogenesis. Much like the stimulus that von Baer provided as a nonevolutionary comparative embryologist to the creation of an evolutionary developmental view of animals, the comparative developmental studies of plant morphologists were the basis for the first articulation of the concept that plant (namely floral) evolution results from successive modifications of ontogeny. Perhaps most surprisingly, we show that the first person to carefully read and internalize the remarkable advances in the understanding of plant morphogenesis in the 1840s and 1850s is none other than Charles Darwin, whose notebooks, correspondence, and (then) unpublished manuscripts clearly demonstrate that he had discovered the developmental basis for the evolutionary transformation of plant form. PMID:21515816

Charles Darwin and the origins of plant evolutionary developmental biology.

PubMed

Friedman, William E; Diggle, Pamela K

2011-04-01

Much has been written of the early history of comparative embryology and its influence on the emergence of an evolutionary developmental perspective. However, this literature, which dates back nearly a century, has been focused on metazoans, without acknowledgment of the contributions of comparative plant morphologists to the creation of a developmental view of biodiversity. We trace the origin of comparative plant developmental morphology from its inception in the eighteenth century works of Wolff and Goethe, through the mid nineteenth century discoveries of the general principles of leaf and floral organ morphogenesis. Much like the stimulus that von Baer provided as a nonevolutionary comparative embryologist to the creation of an evolutionary developmental view of animals, the comparative developmental studies of plant morphologists were the basis for the first articulation of the concept that plant (namely floral) evolution results from successive modifications of ontogeny. Perhaps most surprisingly, we show that the first person to carefully read and internalize the remarkable advances in the understanding of plant morphogenesis in the 1840s and 1850s is none other than Charles Darwin, whose notebooks, correspondence, and (then) unpublished manuscripts clearly demonstrate that he had discovered the developmental basis for the evolutionary transformation of plant form.

Phylogenetic analysis shows the general diversification pattern of deep-sea notacanthiforms (Teleostei: Elopomorpha).

PubMed

Barros-García, David; Froufe, Elsa; Bañón, Rafael; Carlos Arronte, Juan; de Carlos, Alejandro

2018-07-01

The Notacanthiformes is an ancient group of deep-sea ray-finned fishes comprising 27 species in two families; Halosauridae and Notacanthidae. Although many studies have tried to reconstruct the phylogenetic relationships among the major clades of Elopomorpha, little is known about the evolutionary history of notacanthiforms. Molecular and morphological data were used to test previous hypotheses regarding the phylogenetic relationships among notacanthiform taxa, and to unravel the origin and evolution of this group. The molecular analyses of notacanthids showed similar results to those previously obtained employing osteological data, which proposed the existence of the Lipogenyinae (Lipogenys) and Notacanthinae (Notacanthus + Polyacanthonotus) subfamilies. Nevertheless, when the external morphology data is considered Lipogenys is more related to Notacanthus than Polyacanthonotus. The analyses could not fully resolve the inner relationships of the halosaurids. The time-calibrated tree of the order Notacanthiformes shows a long process of diversification spanning from the upper Cretaceous, to 50 million years after the K-Pg extinction, with the gradual emergence of all the modern families and genera of the group. This is the first specific phylogeny of the order Notacanthiformes, combining different analyses and data in order to obtain a wider perspective of the evolution and diversification of this group of fishes. Copyright © 2018 Elsevier Inc. All rights reserved.

Corolla morphology influences diversification rates in bifid toadflaxes (Linaria sect. Versicolores)

PubMed Central

Fernández-Mazuecos, Mario; Blanco-Pastor, José Luis; Gómez, José M.; Vargas, Pablo

2013-01-01

Background and Aims The role of flower specialization in plant speciation and evolution remains controversial. In this study the evolution of flower traits restricting access to pollinators was analysed in the bifid toadflaxes (Linaria sect. Versicolores), a monophyletic group of ∼30 species and subspecies with highly specialized corollas. Methods A time-calibrated phylogeny based on both nuclear and plastid DNA sequences was obtained using a coalescent-based method, and flower morphology was characterized by means of morphometric analyses. Directional trends in flower shape evolution and trait-dependent diversification rates were jointly analysed using recently developed methods, and morphological shifts were reconstructed along the phylogeny. Pollinator surveys were conducted for a representative sample of species. Key Results A restrictive character state (narrow corolla tube) was reconstructed in the most recent common ancestor of Linaria sect. Versicolores. After its early loss in the most species-rich clade, this character state has been convergently reacquired in multiple lineages of this clade in recent times, yet it seems to have exerted a negative influence on diversification rates. Comparative analyses and pollinator surveys suggest that the narrow- and broad-tubed flowers are evolutionary optima representing divergent strategies of pollen placement on nectar-feeding insects. Conclusions The results confirm that different forms of floral specialization can lead to dissimilar evolutionary success in terms of diversification. It is additionally suggested that opposing individual-level and species-level selection pressures may have driven the evolution of pollinator-restrictive traits in bifid toadflaxes. PMID:24142920

Origin and functional diversification of an amphibian defense peptide arsenal.

PubMed

Roelants, Kim; Fry, Bryan G; Ye, Lumeng; Stijlemans, Benoit; Brys, Lea; Kok, Philippe; Clynen, Elke; Schoofs, Liliane; Cornelis, Pierre; Bossuyt, Franky

2013-01-01

The skin secretion of many amphibians contains an arsenal of bioactive molecules, including hormone-like peptides (HLPs) acting as defense toxins against predators, and antimicrobial peptides (AMPs) providing protection against infectious microorganisms. Several amphibian taxa seem to have independently acquired the genes to produce skin-secreted peptide arsenals, but it remains unknown how these originated from a non-defensive ancestral gene and evolved diverse defense functions against predators and pathogens. We conducted transcriptome, genome, peptidome and phylogenetic analyses to chart the full gene repertoire underlying the defense peptide arsenal of the frog Silurana tropicalis and reconstruct its evolutionary history. Our study uncovers a cluster of 13 transcriptionally active genes, together encoding up to 19 peptides, including diverse HLP homologues and AMPs. This gene cluster arose from a duplicated gastrointestinal hormone gene that attained a HLP-like defense function after major remodeling of its promoter region. Instead, new defense functions, including antimicrobial activity, arose by mutation of the precursor proteins, resulting in the proteolytic processing of secondary peptides alongside the original ones. Although gene duplication did not trigger functional innovation, it may have subsequently facilitated the convergent loss of the original function in multiple gene lineages (subfunctionalization), completing their transformation from HLP gene to AMP gene. The processing of multiple peptides from a single precursor entails a mechanism through which peptide-encoding genes may establish new functions without the need for gene duplication to avoid adaptive conflicts with older ones.

Origin and Functional Diversification of an Amphibian Defense Peptide Arsenal

PubMed Central

Roelants, Kim; Fry, Bryan G.; Ye, Lumeng; Stijlemans, Benoit; Brys, Lea; Kok, Philippe; Clynen, Elke; Schoofs, Liliane; Cornelis, Pierre; Bossuyt, Franky

2013-01-01

The skin secretion of many amphibians contains an arsenal of bioactive molecules, including hormone-like peptides (HLPs) acting as defense toxins against predators, and antimicrobial peptides (AMPs) providing protection against infectious microorganisms. Several amphibian taxa seem to have independently acquired the genes to produce skin-secreted peptide arsenals, but it remains unknown how these originated from a non-defensive ancestral gene and evolved diverse defense functions against predators and pathogens. We conducted transcriptome, genome, peptidome and phylogenetic analyses to chart the full gene repertoire underlying the defense peptide arsenal of the frog Silurana tropicalis and reconstruct its evolutionary history. Our study uncovers a cluster of 13 transcriptionally active genes, together encoding up to 19 peptides, including diverse HLP homologues and AMPs. This gene cluster arose from a duplicated gastrointestinal hormone gene that attained a HLP-like defense function after major remodeling of its promoter region. Instead, new defense functions, including antimicrobial activity, arose by mutation of the precursor proteins, resulting in the proteolytic processing of secondary peptides alongside the original ones. Although gene duplication did not trigger functional innovation, it may have subsequently facilitated the convergent loss of the original function in multiple gene lineages (subfunctionalization), completing their transformation from HLP gene to AMP gene. The processing of multiple peptides from a single precursor entails a mechanism through which peptide-encoding genes may establish new functions without the need for gene duplication to avoid adaptive conflicts with older ones. PMID:23935531

Evolutionary history of a keystone pollinator parallels the biome occupancy of angiosperms in the Greater Cape Floristic Region.

PubMed

de Jager, Marinus L; Ellis, Allan G

2017-02-01

The Greater Cape Floristic Region (GCFR) in South Africa has been extensively investigated for its phenomenal angiosperm diversity. A key emergent pattern is the occurrence of older plant lineages in the southern Fynbos biome and younger lineages in the northern Succulent Karoo biome. We know practically nothing, however, about the evolutionary history of the animals that pollinate this often highly-specialized flora. In this study, we explore the evolutionary history of an important GCFR fly pollinator, Megapalpus capensis, and ask whether it exhibits broadly congruent genetic structuring and timing of diversification to flowering plants within these biomes. We find that the oldest M. capensis lineages originated in Fynbos during the Miocene, while younger Succulent Karoo lineages diverged in the Pliocene and correspond to the proposed age of this recent biome. A strong signature of population expansion is also recovered for flies in this arid biome, consistent with recent colonization. Our first investigation into the evolutionary history of GCFR pollinators thus supports a recent origin of the SK biome, as inferred from angiosperm phylogenies, and suggests that plants and pollinators may have co-diverged within this remarkable area. Copyright © 2016 Elsevier Inc. All rights reserved.

A comprehensive and integrative reconstruction of evolutionary history for Anomura (Crustacea: Decapoda)

PubMed Central

2013-01-01

Background The infraorder Anomura has long captivated the attention of evolutionary biologists due to its impressive morphological diversity and ecological adaptations. To date, 2500 extant species have been described but phylogenetic relationships at high taxonomic levels remain unresolved. Here, we reconstruct the evolutionary history—phylogeny, divergence times, character evolution and diversification—of this speciose clade. For this purpose, we sequenced two mitochondrial (16S and 12S) and three nuclear (H3, 18S and 28S) markers for 19 of the 20 extant families, using traditional Sanger and next-generation 454 sequencing methods. Molecular data were combined with 156 morphological characters in order to estimate the largest anomuran phylogeny to date. The anomuran fossil record allowed us to incorporate 31 fossils for divergence time analyses. Results Our best phylogenetic hypothesis (morphological + molecular data) supports most anomuran superfamilies and families as monophyletic. However, three families and eleven genera are recovered as para- and polyphyletic. Divergence time analysis dates the origin of Anomura to the Late Permian ~259 (224–296) MYA with many of the present day families radiating during the Jurassic and Early Cretaceous. Ancestral state reconstruction suggests that carcinization occurred independently 3 times within the group. The invasion of freshwater and terrestrial environments both occurred between the Late Cretaceous and Tertiary. Diversification analyses found the speciation rate to be low across Anomura, and we identify 2 major changes in the tempo of diversification; the most significant at the base of a clade that includes the squat-lobster family Chirostylidae. Conclusions Our findings are compared against current classifications and previous hypotheses of anomuran relationships. Many families and genera appear to be poly- or paraphyletic suggesting a need for further taxonomic revisions at these levels. A divergence

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.

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.

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.

Mega-evolutionary dynamics of the adaptive radiation of birds.

PubMed

Cooney, Christopher R; Bright, Jen A; Capp, Elliot J R; Chira, Angela M; Hughes, Emma C; Moody, Christopher J A; Nouri, Lara O; Varley, Zoë K; Thomas, Gavin H

2017-02-16

The origin and expansion of biological diversity is regulated by both developmental trajectories and limits on available ecological niches. As lineages diversify, an early and often rapid phase of species and trait proliferation gives way to evolutionary slow-downs as new species pack into ever more densely occupied regions of ecological niche space. Small clades such as Darwin's finches demonstrate that natural selection is the driving force of adaptive radiations, but how microevolutionary processes scale up to shape the expansion of phenotypic diversity over much longer evolutionary timescales is unclear. Here we address this problem on a global scale by analysing a crowdsourced dataset of three-dimensional scanned bill morphology from more than 2,000 species. We find that bill diversity expanded early in extant avian evolutionary history, before transitioning to a phase dominated by packing of morphological space. However, this early phenotypic diversification is decoupled from temporal variation in evolutionary rate: rates of bill evolution vary among lineages but are comparatively stable through time. We find that rare, but major, discontinuities in phenotype emerge from rapid increases in rate along single branches, sometimes leading to depauperate clades with unusual bill morphologies. Despite these jumps between groups, the major axes of within-group bill-shape evolution are remarkably consistent across birds. We reveal that macroevolutionary processes underlying global-scale adaptive radiations support Darwinian and Simpsonian ideas of microevolution within adaptive zones and accelerated evolution between distinct adaptive peaks.

Mega-evolutionary dynamics of the adaptive radiation of birds

PubMed Central

Capp, Elliot J. R.; Chira, Angela M.; Hughes, Emma C.; Moody, Christopher J. A.; Nouri, Lara O.; Varley, Zoë K.; Thomas, Gavin H.

2017-01-01

The origin and expansion of biological diversity is regulated by both developmental trajectories1,2 and limits on available ecological niches3–7. As lineages diversify an early, often rapid, phase of species and trait proliferation gives way to evolutionary slowdowns as new species pack into ever more densely occupied regions of ecological niche space6,8. Small clades such as Darwin’s finches demonstrate that natural selection is the driving force of adaptive radiations, but how microevolutionary processes scale up to shape the expansion of phenotypic diversity over much longer evolutionary timescales is unclear9. Here we address this problem on a global scale by analysing a novel crowd-sourced dataset of 3D-scanned bill morphology from >2000 species. We find that bill diversity expanded early in extant avian evolutionary history before transitioning to a phase dominated by morphospace packing. However, this early phenotypic diversification is decoupled from temporal variation in evolutionary rate: rates of bill evolution vary among lineages but are comparatively stable through time. We find that rare but major discontinuities in phenotype emerge from rapid increases in rate along single branches, sometimes leading to depauperate clades with unusual bill morphologies. Despite these jumps between groups, the major axes of within-group bill shape evolution are remarkably consistent across birds. We reveal that macroevolutionary processes underlying global-scale adaptive radiations support Darwinian9 and Simpsonian4 ideas of microevolution within adaptive zones and accelerated evolution between distinct adaptive peaks. PMID:28146475

Djebelemur, a Tiny Pre-Tooth-Combed Primate from the Eocene of Tunisia: A Glimpse into the Origin of Crown Strepsirhines

PubMed Central

Marivaux, Laurent; Ramdarshan, Anusha; Essid, El Mabrouk; Marzougui, Wissem; Ammar, Hayet Khayati; Lebrun, Renaud; Marandat, Bernard; Merzeraud, Gilles; Tabuce, Rodolphe; Vianey-Liaud, Monique

2013-01-01

Background Molecular clock estimates of crown strepsirhine origins generally advocate an ancient antiquity for Malagasy lemuriforms and Afro-Asian lorisiforms, near the onset of the Tertiary but most often extending back to the Late Cretaceous. Despite their inferred early origin, the subsequent evolutionary histories of both groups (except for the Malagasy aye-aye lineage) exhibit a vacuum of lineage diversification during most part of the Eocene, followed by a relative acceleration in diversification from the late Middle Eocene. This early evolutionary stasis was tentatively explained by the possibility of unrecorded lineage extinctions during the early Tertiary. However, this prevailing molecular view regarding the ancient origin and early diversification of crown strepsirhines must be viewed with skepticism due to the new but still scarce paleontological evidence gathered in recent years. Methodological/Principal Findings Here, we describe new fossils attributable to Djebelemur martinezi, a≈50 Ma primate from Tunisia (Djebel Chambi). This taxon was originally interpreted as a cercamoniine adapiform based on limited information from its lower dentition. The new fossils provide anatomical evidence demonstrating that Djebelemur was not an adapiform but clearly a distant relative of lemurs, lorises and galagos. Cranial, dental and postcranial remains indicate that this diminutive primate was likely nocturnal, predatory (primarily insectivorous), and engaged in a form of generalized arboreal quadrupedalism with frequent horizontal leaping. Djebelemur did not have an anterior lower dentition as specialized as that characterizing most crown strepsirhines (i.e., tooth-comb), but it clearly exhibited a transformed antemolar pattern representing an early stage of a crown strepsirhine-like adaptation (“pre-tooth-comb”). Conclusions/Significance These new fossil data suggest that the differentiation of the tooth-comb must postdate the djebelemurid divergence, a view

Deep evolutionary origins of neurobiology

PubMed Central

Mancuso, Stefano

2009-01-01

It is generally assumed, both in common-sense argumentations and scientific concepts, that brains and neurons represent late evolutionary achievements which are present only in more advanced animals. Here we overview recently published data clearly revealing that our understanding of bacteria, unicellular eukaryotic organisms, plants, brains and neurons, rooted in the Aristotelian philosophy is flawed. Neural aspects of biological systems are obvious already in bacteria and unicellular biological units such as sexual gametes and diverse unicellular eukaryotic organisms. Altogether, processes and activities thought to represent evolutionary ‘recent’ specializations of the nervous system emerge rather to represent ancient and fundamental cell survival processes. PMID:19513267

Lineage diversification and morphological evolution in a large-scale continental radiation: the neotropical ovenbirds and woodcreepers (aves: Furnariidae).

PubMed

Derryberry, Elizabeth P; Claramunt, Santiago; Derryberry, Graham; Chesser, R Terry; Cracraft, Joel; Aleixo, Alexandre; Pérez-Emán, Jorge; Remsen, J V; Brumfield, Robb T

2011-10-01

Patterns of diversification in species-rich clades provide insight into the processes that generate biological diversity. We tested different models of lineage and phenotypic diversification in an exceptional continental radiation, the ovenbird family Furnariidae, using the most complete species-level phylogenetic hypothesis produced to date for a major avian clade (97% of 293 species). We found that the Furnariidae exhibit nearly constant rates of lineage accumulation but show evidence of constrained morphological evolution. This pattern of sustained high rates of speciation despite limitations on phenotypic evolution contrasts with the results of most previous studies of evolutionary radiations, which have found a pattern of decelerating diversity-dependent lineage accumulation coupled with decelerating or constrained phenotypic evolution. Our results suggest that lineage accumulation in tropical continental radiations may not be as limited by ecological opportunities as in temperate or island radiations. More studies examining patterns of both lineage and phenotypic diversification are needed to understand the often complex tempo and mode of evolutionary radiations on continents. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

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.

The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms

PubMed Central

2012-01-01

Background The entire evolutionary history of life can be studied using myriad sequences generated by genomic research. This includes the appearance of the first cells and of superkingdoms Archaea, Bacteria, and Eukarya. However, the use of molecular sequence information for deep phylogenetic analyses is limited by mutational saturation, differential evolutionary rates, lack of sequence site independence, and other biological and technical constraints. In contrast, protein structures are evolutionary modules that are highly conserved and diverse enough to enable deep historical exploration. Results Here we build phylogenies that describe the evolution of proteins and proteomes. These phylogenetic trees are derived from a genomic census of protein domains defined at the fold family (FF) level of structural classification. Phylogenomic trees of FF structures were reconstructed from genomic abundance levels of 2,397 FFs in 420 proteomes of free-living organisms. These trees defined timelines of domain appearance, with time spanning from the origin of proteins to the present. Timelines are divided into five different evolutionary phases according to patterns of sharing of FFs among superkingdoms: (1) a primordial protein world, (2) reductive evolution and the rise of Archaea, (3) the rise of Bacteria from the common ancestor of Bacteria and Eukarya and early development of the three superkingdoms, (4) the rise of Eukarya and widespread organismal diversification, and (5) eukaryal diversification. The relative ancestry of the FFs shows that reductive evolution by domain loss is dominant in the first three phases and is responsible for both the diversification of life from a universal cellular ancestor and the appearance of superkingdoms. On the other hand, domain gains are predominant in the last two phases and are responsible for organismal diversification, especially in Bacteria and Eukarya. Conclusions The evolution of functions that are associated with corresponding

Using Paleogenomics to Study the Evolution of Gene Families: Origin and Duplication History of the Relaxin Family Hormones and Their Receptors

PubMed Central

Yegorov, Sergey; Good, Sara

2012-01-01

Recent progress in the analysis of whole genome sequencing data has resulted in the emergence of paleogenomics, a field devoted to the reconstruction of ancestral genomes. Ancestral karyotype reconstructions have been used primarily to illustrate the dynamic nature of genome evolution. In this paper, we demonstrate how they can also be used to study individual gene families by examining the evolutionary history of relaxin hormones (RLN/INSL) and relaxin family peptide receptors (RXFP). Relaxin family hormones are members of the insulin superfamily, and are implicated in the regulation of a variety of primarily reproductive and neuroendocrine processes. Their receptors are G-protein coupled receptors (GPCR's) and include members of two distinct evolutionary groups, an unusual characteristic. Although several studies have tried to elucidate the origins of the relaxin peptide family, the evolutionary origin of their receptors and the mechanisms driving the diversification of the RLN/INSL-RXFP signaling systems in non-placental vertebrates has remained elusive. Here we show that the numerous vertebrate RLN/INSL and RXFP genes are products of an ancestral receptor-ligand system that originally consisted of three genes, two of which apparently trace their origins to invertebrates. Subsequently, diversification of the system was driven primarily by whole genome duplications (WGD, 2R and 3R) followed by almost complete retention of the ligand duplicates in most vertebrates but massive loss of receptor genes in tetrapods. Interestingly, the majority of 3R duplicates retained in teleosts are potentially involved in neuroendocrine regulation. Furthermore, we infer that the ancestral AncRxfp3/4 receptor may have been syntenically linked to the AncRln-like ligand in the pre-2R genome, and show that syntenic linkages among ligands and receptors have changed dynamically in different lineages. This study ultimately shows the broad utility, with some caveats, of incorporating

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.

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

Spatially heterogeneous stochasticity and the adaptive diversification of dormancy.

PubMed

Rajon, E; Venner, S; Menu, F

2009-10-01

Diversified bet-hedging, a strategy that leads several individuals with the same genotype to express distinct phenotypes in a given generation, is now well established as a common evolutionary response to environmental stochasticity. Life-history traits defined as diversified bet-hedging (e.g. germination or diapause strategies) display marked differences between populations in spatial proximity. In order to find out whether such differences can be explained by local adaptations to spatially heterogeneous environmental stochasticity, we explored the evolution of bet-hedging dormancy strategies in a metapopulation using a two-patch model with patch differences in stochastic juvenile survival. We found that spatial differences in the level of environmental stochasticity, restricted dispersal, increased fragmentation and intermediate survival during dormancy all favour the adaptive diversification of bet-hedging dormancy strategies. Density dependency also plays a major role in the diversification of dormancy strategies because: (i) it may interact locally with environmental stochasticity and amplify its effects; however, (ii) it can also generate chaotic population dynamics that may impede diversification. Our work proposes new hypotheses to explain the spatial patterns of bet-hedging strategies that we hope will encourage new empirical studies of this topic.

Testing the museum versus cradle tropical biological diversity hypothesis: phylogeny, diversification, and ancestral biogeographic range evolution of the ants.

PubMed

Moreau, Corrie S; Bell, Charles D

2013-08-01

Ants are one of the most ecologically and numerically dominant group of terrestrial organisms with most species diversity currently found in tropical climates. Several explanations for the disparity of biological diversity in the tropics compared to temperate regions have been proposed including that the tropics may act as a "museum" where older lineages persist through evolutionary time or as a "cradle" where new species continue to be generated. We infer the molecular phylogenetic relationships of 295 ant specimens including members of all 21 extant subfamilies to explore the evolutionary diversification and biogeography of the ants. By constraining the topology and age of the root node while using 45 fossils as minimum constraints, we converge on an age of 139-158 Mya for the modern ants. Further diversification analyses identified 10 periods with a significant change in the tempo of diversification of the ants, although these shifts did not appear to correspond to ancestral biogeographic range shifts. Likelihood-based historical biogeographic reconstructions suggest that the Neotropics were important in early ant diversification (e.g., Cretaceous). This finding coupled with the extremely high-current species diversity suggests that the Neotropics have acted as both a museum and cradle for ant diversity. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

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

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.

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.

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.

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).

Assessing elements of an extended evolutionary synthesis for plant domestication and agricultural origin research

PubMed Central

Piperno, Dolores R.

2017-01-01

The development of agricultural societies, one of the most transformative events in human and ecological history, was made possible by plant and animal domestication. Plant domestication began 12,000–10,000 y ago in a number of major world areas, including the New World tropics, Southwest Asia, and China, during a period of profound global environmental perturbations as the Pleistocene epoch ended and transitioned into the Holocene. Domestication is at its heart an evolutionary process, and for many prehistorians evolutionary theory has been foundational in investigating agricultural origins. Similarly, geneticists working largely with modern crops and their living wild progenitors have documented some of the mechanisms that underwrote phenotypic transformations from wild to domesticated species. Ever-improving analytic methods for retrieval of empirical data from archaeological sites, together with advances in genetic, genomic, epigenetic, and experimental research on living crop plants and wild progenitors, suggest that three fields of study currently little applied to plant domestication processes may be necessary to understand these transformations across a range of species important in early prehistoric agriculture. These fields are phenotypic (developmental) plasticity, niche construction theory, and epigenetics with transgenerational epigenetic inheritance. All are central in a controversy about whether an Extended Evolutionary Synthesis is needed to reconceptualize how evolutionary change occurs. An exploration of their present and potential utility in domestication study shows that all three fields have considerable promise in elucidating important issues in plant domestication and in agricultural origin and dispersal research and should be increasingly applied to these issues. PMID:28576881

Evolutionary origin of insect–Wolbachia nutritional mutualism

PubMed Central

Nikoh, Naruo; Hosokawa, Takahiro; Moriyama, Minoru; Oshima, Kenshiro; Hattori, Masahira; Fukatsu, Takema

2014-01-01

Obligate insect–bacterium nutritional mutualism is among the most sophisticated forms of symbiosis, wherein the host and the symbiont are integrated into a coherent biological entity and unable to survive without the partnership. Originally, however, such obligate symbiotic bacteria must have been derived from free-living bacteria. How highly specialized obligate mutualisms have arisen from less specialized associations is of interest. Here we address this evolutionary issue by focusing on an exceptional insect–Wolbachia nutritional mutualism. Although Wolbachia endosymbionts are ubiquitously found in diverse insects and generally regarded as facultative/parasitic associates for their insect hosts, a Wolbachia strain associated with the bedbug Cimex lectularius, designated as wCle, was shown to be essential for host’s growth and reproduction via provisioning of B vitamins. We determined the 1,250,060-bp genome of wCle, which was generally similar to the genomes of insect-associated facultative Wolbachia strains, except for the presence of an operon encoding the complete biotin synthetic pathway that was acquired via lateral gene transfer presumably from a coinfecting endosymbiont Cardinium or Rickettsia. Nutritional and physiological experiments, in which wCle-infected and wCle-cured bedbugs of the same genetic background were fed on B-vitamin–manipulated blood meals via an artificial feeding system, demonstrated that wCle certainly synthesizes biotin, and the wCle-provisioned biotin significantly contributes to the host fitness. These findings strongly suggest that acquisition of a single gene cluster consisting of biotin synthesis genes underlies the bedbug–Wolbachia nutritional mutualism, uncovering an evolutionary transition from facultative symbiosis to obligate mutualism facilitated by lateral gene transfer in an endosymbiont lineage. PMID:24982177

Diversification and biogeography of Juniperus (Cupressaceae): variable diversification rates and multiple intercontinental dispersals.

PubMed

Mao, Kangshan; Hao, Gang; Liu, Jianquan; Adams, Robert P; Milne, Richard I

2010-10-01

• A central aim of biogeography is to understand when and how modern patterns of species diversity and distribution developed. Many plant groups have disjunct distributions within the Northern Hemisphere, but among these very few have been studied that prefer warm semi-arid habitats. • Here we examine the biogeography and diversification history of Juniperus, which occurs in semi-arid habitats through much of the Northern Hemisphere. A phylogeny was generated based on > 10,000 bp of cpDNA for 51 Juniperus species plus many outgroups. Phylogenies based on fewer species were also constructed based on nuclear internal transcribed spacer (nrITS) and combined nrITS/cpDNA data sets to check for congruence. Divergence time-scales and ancestral distributions were further inferred. • Both long dispersal and migration across land bridges probably contributed to the modern range of Juniperus, while long-term climatic changes and the uplift of the Qinghai-Tibetan plateau probably drove its diversification. Diversification apparently slowed down during climate-stable period of the Oligocene, and then speeded up from the Miocene onwards. • Juniperus probably originated in Eurasia, and was a part of the south Eurasian Tethyan vegetation of the Eocene to Oligocene. It reached America once at this time, once in the Miocene and once more recently.

Antipredator behavior promotes diversification of feeding strategies.

PubMed

Ledón-Rettig, Cris C; Pfennig, David W

2012-07-01

Animals often facultatively engage in less risky behavior when predators are present. Few studies, however, have investigated whether, or how, such predator-mediated behavior promotes diversification. Here, we ask whether tadpoles of the spadefoot toad Scaphiopus couchii have a diminished ability to utilize a potentially valuable resource--anostracan fairy shrimp--because of behavioral responses to predation risk imposed by carnivorous tadpoles of the genus Spea. Observations of a congener of Sc. couchii that occurs in allopatry with Spea, coupled with an ancestral character state reconstruction, revealed that Sc. couchii's ancestors likely consumed shrimp. By experimentally manipulating the presence of Spea carnivore-morph tadpoles in microcosms, we found that Sc. couchii reduce feeding and avoid areas where both Spea carnivores and shrimp occur. We hypothesize that the recurrent expression of such behaviors in sympatric populations of Sc. couchii led to the evolutionary fixation of a detritivorous feeding strategy, which is associated with a reduced risk of predation from Spea carnivores. Generally, predator-mediated behavior might play a key role in promoting diversification of feeding strategies.

The Evolutionary Origin of a Terrestrial Flora.

PubMed

Delwiche, Charles Francis; Cooper, Endymion Dante

2015-10-05

Life on Earth as we know it would not be possible without the evolution of plants, and without the transition of plants to live on land. Land plants (also known as embryophytes) are a monophyletic lineage embedded within the green algae. Green algae as a whole are among the oldest eukaryotic lineages documented in the fossil record, and are well over a billion years old, while land plants are about 450-500 million years old. Much of green algal diversification took place before the origin of land plants, and the land plants are unambiguously members of a strictly freshwater lineage, the charophyte green algae. Contrary to single-gene and morphological analyses, genome-scale phylogenetic analyses indicate the sister taxon of land plants to be the Zygnematophyceae, a group of mostly unbranched filamentous or single-celled organisms. Indeed, several charophyte green algae have historically been used as model systems for certain problems, but often without a recognition of the specific phylogenetic relationships among land plants and (other) charophyte green algae. Insight into the phylogenetic and genomic properties of charophyte green algae opens up new opportunities to study key properties of land plants in closely related model. This review will outline the transition from single-celled algae to modern-day land plants, and will highlight the bright promise studying the charophyte green algae holds for better understanding plant evolution. Copyright © 2015 Elsevier Ltd. All rights reserved.

Evidence of Adaptive Evolutionary Divergence during Biological Invasion

PubMed Central

Lucek, Kay; Sivasundar, Arjun; Seehausen, Ole

2012-01-01

Rapid phenotypic diversification during biological invasions can either arise by adaptation to alternative environments or by adaptive phenotypic plasticity. Where experimental evidence for adaptive plasticity is common, support for evolutionary diversification is rare. Here, we performed a controlled laboratory experiment using full-sib crosses between ecologically divergent threespine stickleback populations to test for a genetic basis of adaptation. Our populations are from two very different habitats, lake and stream, of a recently invaded range in Switzerland and differ in ecologically relevant morphological traits. We found that in a lake-like food treatment lake fish grow faster than stream fish, resembling the difference among wild type individuals. In contrast, in a stream-like food treatment individuals from both populations grow similarly. Our experimental data suggest that genetically determined diversification has occurred within less than 140 years after the arrival of stickleback in our studied region. PMID:23152900

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

PubMed Central

Kapusta, Aurélie; Zhuo, Xiaoyu; Ramsay, LeeAnn; Bourque, Guillaume; Yandell, Mark; Feschotte, Cédric

2013-01-01

Advances in vertebrate genomics have uncovered thousands of loci encoding long noncoding RNAs (lncRNAs). While progress has been made in elucidating the regulatory functions of lncRNAs, little is known about their origins and evolution. Here we explore the contribution of transposable elements (TEs) to the makeup and regulation of lncRNAs in human, mouse, and zebrafish. Surprisingly, TEs occur in more than two thirds of mature lncRNA transcripts and account for a substantial portion of total lncRNA sequence (∼30% in human), whereas they seldom occur in protein-coding transcripts. While TEs contribute less to lncRNA exons than expected, several TE families are strongly enriched in lncRNAs. There is also substantial interspecific variation in the coverage and types of TEs embedded in lncRNAs, partially reflecting differences in the TE landscapes of the genomes surveyed. In human, TE sequences in lncRNAs evolve under greater evolutionary constraint than their non–TE sequences, than their intronic TEs, or than random DNA. Consistent with functional constraint, we found that TEs contribute signals essential for the biogenesis of many lncRNAs, including ∼30,000 unique sites for transcription initiation, splicing, or polyadenylation in human. In addition, we identified ∼35,000 TEs marked as open chromatin located within 10 kb upstream of lncRNA genes. The density of these marks in one cell type correlate with elevated expression of the downstream lncRNA in the same cell type, suggesting that these TEs contribute to cis-regulation. These global trends are recapitulated in several lncRNAs with established functions. Finally a subset of TEs embedded in lncRNAs are subject to RNA editing and predicted to form secondary structures likely important for function. In conclusion, TEs are nearly ubiquitous in lncRNAs and have played an important role in the lineage-specific diversification of vertebrate lncRNA repertoires. PMID:23637635

Molecules and fossils reveal punctuated diversification in Caribbean “faviid” corals

PubMed Central

2012-01-01

Background Even with well-known sampling biases, the fossil record is key to understanding macro-evolutionary patterns. During the Miocene to Pleistocene in the Caribbean Sea, the fossil record of scleractinian corals shows a remarkable period of rapid diversification followed by massive extinction. Here we combine a time-calibrated molecular phylogeny based on three nuclear introns with an updated fossil stratigraphy to examine patterns of radiation and extinction in Caribbean corals within the traditional family Faviidae. Results Concatenated phylogenetic analysis showed most species of Caribbean faviids were monophyletic, with the exception of two Manicina species. The time-calibrated tree revealed the stem group originated around the closure of the Tethys Sea (17.0 Ma), while the genus Manicina diversified during the Late Miocene (8.20 Ma), when increased sedimentation and productivity may have favored free-living, heterotrophic species. Reef and shallow water specialists, represented by Diploria and Favia, originate at the beginning of the Pliocene (5 – 6 Ma) as the Isthmus of Panama shoaled and regional productivity declined. Conclusions Later origination of the stem group than predicted from the fossil record corroborates the hypothesis of morphological convergence in Diploria and Favia genera. Our data support the rapid evolution of morphological and life-history traits among faviid corals that can be linked to Mio-Pliocene environmental changes. PMID:22831179

On the evolutionary origins of the egalitarian syndrome

PubMed Central

Gavrilets, Sergey

2012-01-01

The evolutionary emergence of the egalitarian syndrome is one of the most intriguing unsolved puzzles related to the origins of modern humans. Standard explanations and models for cooperation and altruism—reciprocity, kin and group selection, and punishment—are not directly applicable to the emergence of egalitarian behavior in hierarchically organized groups that characterized the social life of our ancestors. Here I study an evolutionary model of group-living individuals competing for resources and reproductive success. In the model, the differences in fighting abilities lead to the emergence of hierarchies where stronger individuals take away resources from weaker individuals and, as a result, have higher reproductive success. First, I show that the logic of within-group competition implies under rather general conditions that each individual benefits if the transfer of the resource from a weaker group member to a stronger one is prevented. This effect is especially strong in small groups. Then I demonstrate that this effect can result in the evolution of a particular, genetically controlled psychology causing individuals to interfere in a bully–victim conflict on the side of the victim. A necessary condition is a high efficiency of coalitions in conflicts against the bullies. The egalitarian drive leads to a dramatic reduction in within-group inequality. Simultaneously it creates the conditions for the emergence of inequity aversion, empathy, compassion, and egalitarian moral values via the internalization of behavioral rules imposed by natural selection. It also promotes widespread cooperation via coalition formation. PMID:22891349

Tempo and mode of performance evolution across multiple independent origins of adhesive toe pads in lizards.

PubMed

Hagey, Travis J; Uyeda, Josef C; Crandell, Kristen E; Cheney, Jorn A; Autumn, Kellar; Harmon, Luke J

2017-10-01

Understanding macroevolutionary dynamics of trait evolution is an important endeavor in evolutionary biology. Ecological opportunity can liberate a trait as it diversifies through trait space, while genetic and selective constraints can limit diversification. While many studies have examined the dynamics of morphological traits, diverse morphological traits may yield the same or similar performance and as performance is often more proximately the target of selection, examining only morphology may give an incomplete understanding of evolutionary dynamics. Here, we ask whether convergent evolution of pad-bearing lizards has followed similar evolutionary dynamics, or whether independent origins are accompanied by unique constraints and selective pressures over macroevolutionary time. We hypothesized that geckos and anoles each have unique evolutionary tempos and modes. Using performance data from 59 species, we modified Brownian motion (BM) and Ornstein-Uhlenbeck (OU) models to account for repeated origins estimated using Bayesian ancestral state reconstructions. We discovered that adhesive performance in geckos evolved in a fashion consistent with Brownian motion with a trend, whereas anoles evolved in bounded performance space consistent with more constrained evolution (an Ornstein-Uhlenbeck model). Our results suggest that convergent phenotypes can have quite distinctive evolutionary patterns, likely as a result of idiosyncratic constraints or ecological opportunities. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Evolutionary and preservational constraints on origins of biologic groups: divergence times of eutherian mammals

NASA Technical Reports Server (NTRS)

Foote, M.; Hunter, J. P.; Janis, C. M.; Sepkoski, J. J. Jr

1999-01-01

Some molecular clock estimates of divergence times of taxonomic groups undergoing evolutionary radiation are much older than the groups' first observed fossil record. Mathematical models of branching evolution are used to estimate the maximal rate of fossil preservation consistent with a postulated missing history, given the sum of species durations implied by early origins under a range of species origination and extinction rates. The plausibility of postulated divergence times depends on origination, extinction, and preservation rates estimated from the fossil record. For eutherian mammals, this approach suggests that it is unlikely that many modern orders arose much earlier than their oldest fossil records.

Key processes for Cheirolophus (Asteraceae) diversification on oceanic islands inferred from AFLP data.

PubMed

Vitales, Daniel; García-Fernández, Alfredo; Pellicer, Jaume; Vallès, Joan; Santos-Guerra, Arnoldo; Cowan, Robyn S; Fay, Michael F; Hidalgo, Oriane; Garnatje, Teresa

2014-01-01

The radiation of the genus Cheirolophus (Asteraceae) in Macaronesia constitutes a spectacular case of rapid diversification on oceanic islands. Twenty species - nine of them included in the IUCN Red List of Threatened Species - have been described to date inhabiting the Madeiran and Canarian archipelagos. A previous phylogenetic study revealed that the diversification of Cheirolophus in Macaronesia started less than 2 Ma. As a result of such an explosive speciation process, limited phylogenetic resolution was reported, mainly due to the low variability of the employed molecular markers. In the present study, we used highly polymorphic AFLP markers to i) evaluate species' boundaries, ii) infer their evolutionary relationships and iii) investigate the patterns of genetic diversity in relation to the potential processes likely involved in the radiation of Cheirolophus. One hundred and seventy-two individuals representing all Macaronesian Cheirolophus species were analysed using 249 AFLP loci. Our results suggest that geographic isolation played an important role in this radiation process. This was likely driven by the combination of poor gene flow capacity and a good ability for sporadic long-distance colonisations. In addition, we also found some traces of introgression and incipient ecological adaptation, which could have further enhanced the extraordinary diversification of Cheirolophus in Macaronesia. Last, we hypothesize that current threat categories assigned to Macaronesian Cheirolophus species do not reflect their respective evolutionary relevance, so future evaluations of their conservation status should take into account the results presented here.

Key Processes for Cheirolophus (Asteraceae) Diversification on Oceanic Islands Inferred from AFLP Data

PubMed Central

Vitales, Daniel; García-Fernández, Alfredo; Pellicer, Jaume; Vallès, Joan; Santos-Guerra, Arnoldo; Cowan, Robyn S.; Fay, Michael F.; Hidalgo, Oriane; Garnatje, Teresa

2014-01-01

The radiation of the genus Cheirolophus (Asteraceae) in Macaronesia constitutes a spectacular case of rapid diversification on oceanic islands. Twenty species – nine of them included in the IUCN Red List of Threatened Species – have been described to date inhabiting the Madeiran and Canarian archipelagos. A previous phylogenetic study revealed that the diversification of Cheirolophus in Macaronesia started less than 2 Ma. As a result of such an explosive speciation process, limited phylogenetic resolution was reported, mainly due to the low variability of the employed molecular markers. In the present study, we used highly polymorphic AFLP markers to i) evaluate species' boundaries, ii) infer their evolutionary relationships and iii) investigate the patterns of genetic diversity in relation to the potential processes likely involved in the radiation of Cheirolophus. One hundred and seventy-two individuals representing all Macaronesian Cheirolophus species were analysed using 249 AFLP loci. Our results suggest that geographic isolation played an important role in this radiation process. This was likely driven by the combination of poor gene flow capacity and a good ability for sporadic long-distance colonisations. In addition, we also found some traces of introgression and incipient ecological adaptation, which could have further enhanced the extraordinary diversification of Cheirolophus in Macaronesia. Last, we hypothesize that current threat categories assigned to Macaronesian Cheirolophus species do not reflect their respective evolutionary relevance, so future evaluations of their conservation status should take into account the results presented here. PMID:25412495

The Early Origin of the Antarctic Marine Fauna and Its Evolutionary Implications.

PubMed

Crame, J Alistair; Beu, Alan G; Ineson, Jon R; Francis, Jane E; Whittle, Rowan J; Bowman, Vanessa C

2014-01-01

The extensive Late Cretaceous - Early Paleogene sedimentary succession of Seymour Island, N.E. Antarctic Peninsula offers an unparalleled opportunity to examine the evolutionary origins of a modern polar marine fauna. Some 38 modern Southern Ocean molluscan genera (26 gastropods and 12 bivalves), representing approximately 18% of the total modern benthic molluscan fauna, can now be traced back through at least part of this sequence. As noted elsewhere in the world, the balance of the molluscan fauna changes sharply across the Cretaceous - Paleogene (K/Pg) boundary, with gastropods subsequently becoming more diverse than bivalves. A major reason for this is a significant radiation of the Neogastropoda, which today forms one of the most diverse clades in the sea. Buccinoidea is the dominant neogastropod superfamily in both the Paleocene Sobral Formation (SF) (56% of neogastropod genera) and Early - Middle Eocene La Meseta Formation (LMF) (47%), with the Conoidea (25%) being prominent for the first time in the latter. This radiation of Neogastropoda is linked to a significant pulse of global warming that reached at least 65°S, and terminates abruptly in the upper LMF in an extinction event that most likely heralds the onset of global cooling. It is also possible that the marked Early Paleogene expansion of neogastropods in Antarctica is in part due to a global increase in rates of origination following the K/Pg mass extinction event. The radiation of this and other clades at ∼65°S indicates that Antarctica was not necessarily an evolutionary refugium, or sink, in the Early - Middle Eocene. Evolutionary source - sink dynamics may have been significantly different between the Paleogene greenhouse and Neogene icehouse worlds.

Global diversification of a tropical plant growth form: environmental correlates and historical contingencies in climbing palms

PubMed Central

Couvreur, Thomas L. P.; Kissling, W. Daniel; Condamine, Fabien L.; Svenning, Jens-Christian; Rowe, Nick P.; Baker, William J.

2015-01-01

Tropical rain forests (TRF) are the most diverse terrestrial biome on Earth, but the diversification dynamics of their constituent growth forms remain largely unexplored. Climbing plants contribute significantly to species diversity and ecosystem processes in TRF. We investigate the broad-scale patterns and drivers of species richness as well as the diversification history of climbing and non-climbing palms (Arecaceae). We quantify to what extent macroecological diversity patterns are related to contemporary climate, forest canopy height, and paleoclimatic changes. We test whether diversification rates are higher for climbing than non-climbing palms and estimate the origin of the climbing habit. Climbers account for 22% of global palm species diversity, mostly concentrated in Southeast Asia. Global variation in climbing palm species richness can be partly explained by past and present-day climate and rain forest canopy height, but regional differences in residual species richness after accounting for current and past differences in environment suggest a strong role of historical contingencies in climbing palm diversification. Climbing palms show a higher net diversification rate than non-climbers. Diversification analyses of palms detected a diversification rate increase along the branches leading to the most species-rich clade of climbers. Ancestral character reconstructions revealed that the climbing habit originated between early Eocene and Miocene. These results imply that changes from non-climbing to climbing habits may have played an important role in palm diversification, resulting in the origin of one fifth of all palm species. We suggest that, in addition to current climate and paleoclimatic changes after the late Neogene, present-day diversity of climbing palms can be explained by morpho-anatomical innovations, the biogeographic history of Southeast Asia, and/or ecological opportunities due to the diversification of high-stature dipterocarps in Asian TRFs

Global diversification of a tropical plant growth form: environmental correlates and historical contingencies in climbing palms.

PubMed

Couvreur, Thomas L P; Kissling, W Daniel; Condamine, Fabien L; Svenning, Jens-Christian; Rowe, Nick P; Baker, William J

2014-01-01

Tropical rain forests (TRF) are the most diverse terrestrial biome on Earth, but the diversification dynamics of their constituent growth forms remain largely unexplored. Climbing plants contribute significantly to species diversity and ecosystem processes in TRF. We investigate the broad-scale patterns and drivers of species richness as well as the diversification history of climbing and non-climbing palms (Arecaceae). We quantify to what extent macroecological diversity patterns are related to contemporary climate, forest canopy height, and paleoclimatic changes. We test whether diversification rates are higher for climbing than non-climbing palms and estimate the origin of the climbing habit. Climbers account for 22% of global palm species diversity, mostly concentrated in Southeast Asia. Global variation in climbing palm species richness can be partly explained by past and present-day climate and rain forest canopy height, but regional differences in residual species richness after accounting for current and past differences in environment suggest a strong role of historical contingencies in climbing palm diversification. Climbing palms show a higher net diversification rate than non-climbers. Diversification analyses of palms detected a diversification rate increase along the branches leading to the most species-rich clade of climbers. Ancestral character reconstructions revealed that the climbing habit originated between early Eocene and Miocene. These results imply that changes from non-climbing to climbing habits may have played an important role in palm diversification, resulting in the origin of one fifth of all palm species. We suggest that, in addition to current climate and paleoclimatic changes after the late Neogene, present-day diversity of climbing palms can be explained by morpho-anatomical innovations, the biogeographic history of Southeast Asia, and/or ecological opportunities due to the diversification of high-stature dipterocarps in Asian TRFs.

Insights on the evolutionary origin of Detarioideae, a clade of ecologically dominant tropical African trees.

PubMed

de la Estrella, Manuel; Forest, Félix; Wieringa, Jan J; Fougère-Danezan, Marie; Bruneau, Anne

2017-06-01

African tropical forests are generally considered less diverse than their Neotropical and Asian counterparts. By contrast, the Detarioideae is much more diverse in Africa than in South America and Asia. To better understand the evolution of this contrasting diversity pattern, we investigated the biogeographical and ecological origin of this subfamily, testing whether they originated in dry biomes surrounding the Tethys Seaway as currently hypothesized for many groups of Leguminosae. We constructed the largest time-calibrated phylogeny for the subfamily to date, reconstructed ancestral states for geography and biome/habitat, estimated diversification and extinction rates, and evaluated biome/habitat and geographic shifts in Detarioideae. The ancestral habitat of Detarioideae is postulated to be a primary forest (terra firme) originated in Africa-South America, in the early Palaeocene, after which several biome/habitat and geographic shifts occurred. The origin of Detarioideae is older than previous estimates, which postulated a dry (succulent) biome origin according to the Tethys Seaway hypothesis, and instead we reveal a post Gondwana and terra firme origin for this early branching clade of legumes. Detarioideae include some of the most dominant trees in evergreen forests and have likely played a pivotal role in shaping continental African forest diversity. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

EvolQG - An R package for evolutionary quantitative genetics

PubMed Central

Melo, Diogo; Garcia, Guilherme; Hubbe, Alex; Assis, Ana Paula; Marroig, Gabriel

2016-01-01

We present an open source package for performing evolutionary quantitative genetics analyses in the R environment for statistical computing. Evolutionary theory shows that evolution depends critically on the available variation in a given population. When dealing with many quantitative traits this variation is expressed in the form of a covariance matrix, particularly the additive genetic covariance matrix or sometimes the phenotypic matrix, when the genetic matrix is unavailable and there is evidence the phenotypic matrix is sufficiently similar to the genetic matrix. Given this mathematical representation of available variation, the \\textbf{EvolQG} package provides functions for calculation of relevant evolutionary statistics; estimation of sampling error; corrections for this error; matrix comparison via correlations, distances and matrix decomposition; analysis of modularity patterns; and functions for testing evolutionary hypotheses on taxa diversification. PMID:27785352

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.

Evolutionary diversification of secondary mechanoreceptor cells in tunicata.

PubMed

Rigon, Francesca; Stach, Thomas; Caicci, Federico; Gasparini, Fabio; Burighel, Paolo; Manni, Lucia

2013-06-04

Hair cells are vertebrate secondary sensory cells located in the ear and in the lateral line organ. Until recently, these cells were considered to be mechanoreceptors exclusively found in vertebrates that evolved within this group. Evidence of secondary mechanoreceptors in some tunicates, the proposed sister group of vertebrates, has recently led to the hypothesis that vertebrate and tunicate secondary sensory cells share a common origin. Secondary sensory cells were described in detail in two tunicate groups, ascidians and thaliaceans, in which they constitute an oral sensory structure called the coronal organ. Among thaliaceans, the organ is absent in salps and it has been hypothesised that this condition is due to a different feeding system adopted by this group of animals. No information is available as to whether a comparable structure exists in the third group of tunicates, the appendicularians, although different sensory structures are known to be present in these animals. We studied the detailed morphology of appendicularian oral mechanoreceptors. Using light and electron microscopy we could demonstrate that the mechanosensory organ called the circumoral ring is composed of secondary sensory cells. We described the ultrastructure of the circumoral organ in two appendicularian species, Oikopleura dioica and Oikopleura albicans, and thus taxonomically completed the data collection of tunicate secondary sensory cells. To understand the evolution of secondary sensory cells in tunicates, we performed a cladistic analysis using morphological data. We constructed a matrix consisting of 19 characters derived from detailed ultrastructural studies in 16 tunicate species and used a cephalochordate and three vertebrate species as outgroups. Our study clearly shows that the circumoral ring is the appendicularian homologue of the coronal organ of other tunicate taxa. The cladistic analysis enabled us to reconstruct the features of the putative ancestral hair cell in

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.

The single evolutionary origin of chlorinated auxin provides a phylogenetically informative trait in the Fabaceae.

PubMed

Lam, Hong Kiat; Ross, John J; McAdam, Erin L; McAdam, Scott A M

2016-07-02

Chlorinated auxin (4-chloroindole-3-acetic acid, 4-Cl-IAA), a highly potent plant hormone, was once thought to be restricted to species of the tribe Fabeae within the Fabaceae, until we recently detected this hormone in the seeds of Medicago, Melilotus and Trifolium species. The absence of 4-Cl-IAA in the seeds of the cultivated species Cicer aeritinum from the Cicerae tribe, immediately basal to the Fabeae and Trifolieae tribes, suggested a single evolutionary origin of 4-Cl-IAA. Here, we provide a more robust phylogenetic placement of the ability to produce chlorinated auxin by screening key species spanning this evolutionary transition. We report no detectable level of 4-Cl-IAA in Cicer echinospermum (a wild relative of C. aeritinum) and 4 species (Galega officinalis, Parochetus communis, Astragalus propinquus and A. sinicus) from tribes or clades more basal or sister to the Cicerae tribe. We did detect 4-Cl-IAA in the dry seeds of 4 species from the genus Ononis that are either basal to the genera Medicago, Melilotus and Trigonella or basal to, but still within, the Fabeae and Trifolieae (ex. Parochetus) clades. We conclude that the single evolutionary origin of this hormone in seeds can be used as a phylogenetically informative trait within the Fabaceae.

The single evolutionary origin of chlorinated auxin provides a phylogenetically informative trait in the Fabaceae

PubMed Central

Lam, Hong Kiat; Ross, John J.; McAdam, Erin L.; McAdam, Scott A. M.

2016-01-01

ABSTRACT Chlorinated auxin (4-chloroindole-3-acetic acid, 4-Cl-IAA), a highly potent plant hormone, was once thought to be restricted to species of the tribe Fabeae within the Fabaceae, until we recently detected this hormone in the seeds of Medicago, Melilotus and Trifolium species. The absence of 4-Cl-IAA in the seeds of the cultivated species Cicer aeritinum from the Cicerae tribe, immediately basal to the Fabeae and Trifolieae tribes, suggested a single evolutionary origin of 4-Cl-IAA. Here, we provide a more robust phylogenetic placement of the ability to produce chlorinated auxin by screening key species spanning this evolutionary transition. We report no detectable level of 4-Cl-IAA in Cicer echinospermum (a wild relative of C. aeritinum) and 4 species (Galega officinalis, Parochetus communis, Astragalus propinquus and A. sinicus) from tribes or clades more basal or sister to the Cicerae tribe. We did detect 4-Cl-IAA in the dry seeds of 4 species from the genus Ononis that are either basal to the genera Medicago, Melilotus and Trigonella or basal to, but still within, the Fabeae and Trifolieae (ex. Parochetus) clades. We conclude that the single evolutionary origin of this hormone in seeds can be used as a phylogenetically informative trait within the Fabaceae. PMID:27302610

The Genomic Diversification of the Whole Acinetobacter Genus: Origins, Mechanisms, and Consequences

PubMed Central

Touchon, Marie; Cury, Jean; Yoon, Eun-Jeong; Krizova, Lenka; Cerqueira, Gustavo C.; Murphy, Cheryl; Feldgarden, Michael; Wortman, Jennifer; Clermont, Dominique; Lambert, Thierry; Grillot-Courvalin, Catherine; Nemec, Alexandr; Courvalin, Patrice; Rocha, Eduardo P.C.

2014-01-01

Bacterial genomics has greatly expanded our understanding of microdiversification patterns within a species, but analyses at higher taxonomical levels are necessary to understand and predict the independent rise of pathogens in a genus. We have sampled, sequenced, and assessed the diversity of genomes of validly named and tentative species of the Acinetobacter genus, a clade including major nosocomial pathogens and biotechnologically important species. We inferred a robust global phylogeny and delimited several new putative species. The genus is very ancient and extremely diverse: Genomes of highly divergent species share more orthologs than certain strains within a species. We systematically characterized elements and mechanisms driving genome diversification, such as conjugative elements, insertion sequences, and natural transformation. We found many error-prone polymerases that may play a role in resistance to toxins, antibiotics, and in the generation of genetic variation. Surprisingly, temperate phages, poorly studied in Acinetobacter, were found to account for a significant fraction of most genomes. Accordingly, many genomes encode clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems with some of the largest CRISPR-arrays found so far in bacteria. Integrons are strongly overrepresented in Acinetobacter baumannii, which correlates with its frequent resistance to antibiotics. Our data suggest that A. baumannii arose from an ancient population bottleneck followed by population expansion under strong purifying selection. The outstanding diversification of the species occurred largely by horizontal transfer, including some allelic recombination, at specific hotspots preferentially located close to the replication terminus. Our work sets a quantitative basis to understand the diversification of Acinetobacter into emerging resistant and versatile pathogens. PMID:25313016

Molecular phylogeny and timing of diversification in Alpine Rhithrogena (Ephemeroptera: Heptageniidae).

PubMed

Vuataz, Laurent; Rutschmann, Sereina; Monaghan, Michael T; Sartori, Michel

2016-09-21

Larvae of the Holarctic mayfly genus Rhithrogena Eaton, 1881 (Ephemeroptera, Heptageniidae) are a diverse and abundant member of stream and river communities and are routinely used as bio-indicators of water quality. Rhithrogena is well diversified in the European Alps, with a number of locally endemic species, and several cryptic species have been recently detected. While several informal species groups are morphologically well defined, a lack of reliable characters for species identification considerably hampers their study. Their relationships, origin, timing of speciation and mechanisms promoting their diversification in the Alps are unknown. Here we present a species-level phylogeny of Rhithrogena in Europe using two mitochondrial and three nuclear gene regions. To improve sampling in a genus with many cryptic species, individuals were selected for analysis according to a recent DNA-based taxonomy rather than traditional nomenclature. A coalescent-based species tree and a reconstruction based on a supermatrix approach supported five of the species groups as monophyletic. A molecular clock, mapped on the most resolved phylogeny and calibrated using published mitochondrial evolution rates for insects, suggested an origin of Alpine Rhithrogena in the Oligocene/Miocene boundary. A diversification analysis that included simulation of missing species indicated a constant speciation rate over time, rather than any pronounced periods of rapid speciation. Ancestral state reconstructions provided evidence for downstream diversification in at least two species groups. Our species-level analyses of five gene regions provide clearer definitions of species groups within European Rhithrogena. A constant speciation rate over time suggests that the paleoclimatic fluctuations, including the Pleistocene glaciations, did not significantly influence the tempo of diversification of Alpine species. A downstream diversification trend in the hybrida and alpestris species groups

The Early Origin of the Antarctic Marine Fauna and Its Evolutionary Implications

PubMed Central

Crame, J. Alistair; Beu, Alan G.; Ineson, Jon R.; Francis, Jane E.; Whittle, Rowan J.; Bowman, Vanessa C.

2014-01-01

The extensive Late Cretaceous – Early Paleogene sedimentary succession of Seymour Island, N.E. Antarctic Peninsula offers an unparalleled opportunity to examine the evolutionary origins of a modern polar marine fauna. Some 38 modern Southern Ocean molluscan genera (26 gastropods and 12 bivalves), representing approximately 18% of the total modern benthic molluscan fauna, can now be traced back through at least part of this sequence. As noted elsewhere in the world, the balance of the molluscan fauna changes sharply across the Cretaceous – Paleogene (K/Pg) boundary, with gastropods subsequently becoming more diverse than bivalves. A major reason for this is a significant radiation of the Neogastropoda, which today forms one of the most diverse clades in the sea. Buccinoidea is the dominant neogastropod superfamily in both the Paleocene Sobral Formation (SF) (56% of neogastropod genera) and Early - Middle Eocene La Meseta Formation (LMF) (47%), with the Conoidea (25%) being prominent for the first time in the latter. This radiation of Neogastropoda is linked to a significant pulse of global warming that reached at least 65°S, and terminates abruptly in the upper LMF in an extinction event that most likely heralds the onset of global cooling. It is also possible that the marked Early Paleogene expansion of neogastropods in Antarctica is in part due to a global increase in rates of origination following the K/Pg mass extinction event. The radiation of this and other clades at ∼65°S indicates that Antarctica was not necessarily an evolutionary refugium, or sink, in the Early – Middle Eocene. Evolutionary source – sink dynamics may have been significantly different between the Paleogene greenhouse and Neogene icehouse worlds. PMID:25493546

Diversification of African tree frogs (genus Leptopelis) in the highlands of Ethiopia.

PubMed

Reyes-Velasco, Jacobo; Manthey, Joseph D; Freilich, Xenia; Boissinot, Stéphane

2018-05-01

The frog genus Leptopelis is composed of ~50 species that occur across sub-Saharan Africa. The majority of these frogs are typically arboreal; however, a few species have evolved a fossorial lifestyle. Most species inhabit lowland forests, but a few species have adapted to high elevations. Five species of Leptopelis occupy the Ethiopian highlands and provide a good opportunity to study the evolutionary transition from an arboreal to a fossorial lifestyle, as well as the diversification in this biodiversity hot spot. We sequenced 14 nuclear and three mitochondrial genes, and generated thousands of SNPs from ddRAD sequencing to study the evolutionary relationships of Ethiopian Leptopelis. The five species of highland Leptopelis form a monophyletic group, which diversified during the late Miocene and Pliocene. We found strong population structure in the fossorial species L. gramineus, with levels of genetic differentiation between populations similar to those found between arboreal species. This could indicate that L. gramineus is a complex of cryptic species. We propose that after the original colonization of the Ethiopian highlands by the ancestor of the L. gramineus group, episodes of vicariance fragmented the ancestral populations of this group. We also report the re-evolution of arboreality in L. susanae, which evolved from a fossorial ancestor, a rare ecological switch in frogs that had previously been reported only once. © 2018 John Wiley & Sons Ltd.

Origin, acquisition and diversification of heritable bacterial endosymbionts in louse flies and bat flies.

PubMed

Duron, Olivier; Schneppat, Ulrich E; Berthomieu, Arnaud; Goodman, Steven M; Droz, Boris; Paupy, Christophe; Nkoghe, Judicaël Obame; Rahola, Nil; Tortosa, Pablo

2014-04-01

The γ-proteobacterium Arsenophonus and its close relatives (Arsenophonus and like organisms, ALOs) are emerging as a novel clade of endosymbionts, which are exceptionally widespread in insects. The biology of ALOs is, however, in most cases entirely unknown, and it is unclear how these endosymbionts spread across insect populations. Here, we investigate this aspect through the examination of the presence, the diversity and the evolutionary history of ALOs in 25 related species of blood-feeding flies: tsetse flies (Glossinidae), louse flies (Hippoboscidae) and bat flies (Nycteribiidae and Streblidae). While these endosymbionts were not found in tsetse flies, we identify louse flies and bat flies as harbouring the highest diversity of ALO strains reported to date, including a novel ALO clade, as well as Arsenophonus and the recently described Candidatus Aschnera chinzeii. We further show that the origin of ALO endosymbioses extends deep into the evolutionary past of louse flies and bat flies, and that it probably played a major role in the ecological specialization of their hosts. The evolutionary history of ALOs is notably complex and was shaped by both vertical transmission and horizontal transfers with frequent host turnover and apparent symbiont replacement in host lineages. In particular, ALOs have evolved repeatedly and independently close relationships with diverse groups of louse flies and bat flies, as well as phylogenetically more distant insect families, suggesting that ALO endosymbioses are exceptionally dynamic systems. © 2014 John Wiley & Sons Ltd.

Evolutionary origins of hepatitis A virus in small mammals.

PubMed

Drexler, Jan Felix; Corman, Victor M; Lukashev, Alexander N; van den Brand, Judith M A; Gmyl, Anatoly P; Brünink, Sebastian; Rasche, Andrea; Seggewiβ, Nicole; Feng, Hui; Leijten, Lonneke M; Vallo, Peter; Kuiken, Thijs; Dotzauer, Andreas; Ulrich, Rainer G; Lemon, Stanley M; Drosten, Christian

2015-12-08

Hepatitis A virus (HAV) is an ancient and ubiquitous human pathogen recovered previously only from primates. The sole species of the genus Hepatovirus, existing in both enveloped and nonenveloped forms, and with a capsid structure intermediate between that of insect viruses and mammalian picornaviruses, HAV is enigmatic in its origins. We conducted a targeted search for hepatoviruses in 15,987 specimens collected from 209 small mammal species globally and discovered highly diversified viruses in bats, rodents, hedgehogs, and shrews, which by pairwise sequence distance comprise 13 novel Hepatovirus species. Near-complete genomes from nine of these species show conservation of unique hepatovirus features, including predicted internal ribosome entry site structure, a truncated VP4 capsid protein lacking N-terminal myristoylation, a carboxyl-terminal pX extension of VP1, VP2 late domains involved in membrane envelopment, and a cis-acting replication element within the 3D(pol) sequence. Antibodies in some bat sera immunoprecipitated and neutralized human HAV, suggesting conservation of critical antigenic determinants. Limited phylogenetic cosegregation among hepatoviruses and their hosts and recombination patterns are indicative of major hepatovirus host shifts in the past. Ancestral state reconstructions suggest a Hepatovirus origin in small insectivorous mammals and a rodent origin of human HAV. Patterns of infection in small mammals mimicked those of human HAV in hepatotropism, fecal shedding, acute nature, and extinction of the virus in a closed host population. The evolutionary conservation of hepatovirus structure and pathogenesis provide novel insight into the origins of HAV and highlight the utility of analyzing animal reservoirs for risk assessment of emerging viruses.

Evolutionary origins of hepatitis A virus in small mammals

PubMed Central

Drexler, Jan Felix; Corman, Victor M.; Lukashev, Alexander N.; van den Brand, Judith M. A.; Gmyl, Anatoly P.; Brünink, Sebastian; Rasche, Andrea; Seggewiβ, Nicole; Feng, Hui; Leijten, Lonneke M.; Vallo, Peter; Kuiken, Thijs; Dotzauer, Andreas; Ulrich, Rainer G.; Lemon, Stanley M.; Drosten, Christian

2015-01-01

Hepatitis A virus (HAV) is an ancient and ubiquitous human pathogen recovered previously only from primates. The sole species of the genus Hepatovirus, existing in both enveloped and nonenveloped forms, and with a capsid structure intermediate between that of insect viruses and mammalian picornaviruses, HAV is enigmatic in its origins. We conducted a targeted search for hepatoviruses in 15,987 specimens collected from 209 small mammal species globally and discovered highly diversified viruses in bats, rodents, hedgehogs, and shrews, which by pairwise sequence distance comprise 13 novel Hepatovirus species. Near-complete genomes from nine of these species show conservation of unique hepatovirus features, including predicted internal ribosome entry site structure, a truncated VP4 capsid protein lacking N-terminal myristoylation, a carboxyl-terminal pX extension of VP1, VP2 late domains involved in membrane envelopment, and a cis-acting replication element within the 3Dpol sequence. Antibodies in some bat sera immunoprecipitated and neutralized human HAV, suggesting conservation of critical antigenic determinants. Limited phylogenetic cosegregation among hepatoviruses and their hosts and recombination patterns are indicative of major hepatovirus host shifts in the past. Ancestral state reconstructions suggest a Hepatovirus origin in small insectivorous mammals and a rodent origin of human HAV. Patterns of infection in small mammals mimicked those of human HAV in hepatotropism, fecal shedding, acute nature, and extinction of the virus in a closed host population. The evolutionary conservation of hepatovirus structure and pathogenesis provide novel insight into the origins of HAV and highlight the utility of analyzing animal reservoirs for risk assessment of emerging viruses. PMID:26575627

The origins and evolutionary history of human non-coding RNA regulatory networks.

PubMed

Sherafatian, Masih; Mowla, Seyed Javad

2017-04-01

The evolutionary history and origin of the regulatory function of animal non-coding RNAs are not well understood. Lack of conservation of long non-coding RNAs and small sizes of microRNAs has been major obstacles in their phylogenetic analysis. In this study, we tried to shed more light on the evolution of ncRNA regulatory networks by changing our phylogenetic strategy to focus on the evolutionary pattern of their protein coding targets. We used available target databases of miRNAs and lncRNAs to find their protein coding targets in human. We were able to recognize evolutionary hallmarks of ncRNA targets by phylostratigraphic analysis. We found the conventional 3'-UTR and lesser known 5'-UTR targets of miRNAs to be enriched at three consecutive phylostrata. Firstly, in eukaryata phylostratum corresponding to the emergence of miRNAs, our study revealed that miRNA targets function primarily in cell cycle processes. Moreover, the same overrepresentation of the targets observed in the next two consecutive phylostrata, opisthokonta and eumetazoa, corresponded to the expansion periods of miRNAs in animals evolution. Coding sequence targets of miRNAs showed a delayed rise at opisthokonta phylostratum, compared to the 3' and 5' UTR targets of miRNAs. LncRNA regulatory network was the latest to evolve at eumetazoa.

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

Evidence of constant diversification punctuated by a mass extinction in the African cycads

PubMed Central

Yessoufou, Kowiyou; Bamigboye, Samuel O; Daru, Barnabas H; van der Bank, Michelle

2014-01-01

The recent evidence that extant cycads are not living fossils triggered a renewed search for a better understanding of their evolutionary history. In this study, we investigated the evolutionary diversification history of the genus Encephalartos, a monophyletic cycad endemic to Africa. We found an antisigmoidal pattern with a plateau and punctual explosive radiation. This pattern is typical of a constant radiation with mass extinction. The rate shift that we found may therefore be a result of a rapid recolonization of niches that have been emptied owing to mass extinction. Because the explosive radiation occurred during the transition Pliocene–Pleistocene, we argued that the processes might have been climatically mediated. PMID:24455160

The developmental basis of an evolutionary diversification of female gametophyte structure in Piper and Piperaceae

PubMed Central

Madrid, Eric N.; Friedman, William E.

2009-01-01

Background and Aims Fritillaria-type female gametophyte development is a complex, yet homoplasious developmental pattern that is interesting from both evolutionary and developmental perspectives. Piper (Piperaceae) was chosen for this study of Fritillaria-type female gametophyte development because Piperales represent a ‘hotspot’ of female gametophyte developmental evolution and have been the subject of several recent molecular phylogenetic analyses. This wealth of phylogenetic and descriptive data make Piper an excellent candidate for inferring the evolutionary developmental basis for the origin of Fritillaria-type female gametophytes. Methods Developing ovules of Piper peltatum were taken from greenhouse collections, embedded in glycol methacrylate, and serially sectioned. Light microscopy and laser scanning confocal microscopy were combined to produce three-dimensional computer reconstructions of developing female gametophytes. The ploidies of the developing embryos and endosperms were calculated using microspectrofluorometry. Key Results The data describe female gametophyte development in Piper with highly detailed three-dimensional models, and document two previously unknown arrangements of megaspore nuclei during early development. Also collected were microspectrofluorometric data that indicate that Fritillaria-type female gametophyte development in Piper results in pentaploid endosperm. Conclusions The three-dimensional models resolve previous ambiguities in developmental interpretations of Fritillaria-type female gametophytes in Piper. The newly discovered arrangements of megaspore nuclei that are described allow for the construction of explicit hypotheses of female gametophyte developmental evolution within Piperaceae, and more broadly throughout Piperales. These detailed hypotheses indicate that the common ancestor of Piperaceae minus Verhuellia had a Drusa-type female gametophyte, and that evolutionary transitions to derived tetrasporic female

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.

Conservation and diversification of the miR166 family in soybean and potential roles of newly identified miR166s.

PubMed

Li, Xuyan; Xie, Xin; Li, Ji; Cui, Yuhai; Hou, Yanming; Zhai, Lulu; Wang, Xiao; Fu, Yanli; Liu, Ranran; Bian, Shaomin

2017-02-01

microRNA166 (miR166) is a highly conserved family of miRNAs implicated in a wide range of cellular and physiological processes in plants. miR166 family generally comprises multiple miR166 members in plants, which might exhibit functional redundancy and specificity. The soybean miR166 family consists of 21 members according to the miRBase database. However, the evolutionary conservation and functional diversification of miR166 family members in soybean remain poorly understood. We identified five novel miR166s in soybean by data mining approach, thus enlarging the size of miR166 family from 21 to 26 members. Phylogenetic analyses of the 26 miR166s and their precursors indicated that soybean miR166 family exhibited both evolutionary conservation and diversification, and ten pairs of miR166 precursors with high sequence identity were individually grouped into a discrete clade in the phylogenetic tree. The analysis of genomic organization and evolution of MIR166 gene family revealed that eight segmental duplications and four tandem duplications might occur during evolution of the miR166 family in soybean. The cis-elements in promoters of MIR166 family genes and their putative targets pointed to their possible contributions to the functional conservation and diversification. The targets of soybean miR166s were predicted, and the cleavage of ATHB14-LIKE transcript was experimentally validated by RACE PCR. Further, the expression patterns of the five newly identified MIR166s and 12 target genes were examined during seed development and in response to abiotic stresses, which provided important clues for dissecting their functions and isoform specificity. This study enlarged the size of soybean miR166 family from 21 to 26 members, and the 26 soybean miR166s exhibited evolutionary conservation and diversification. These findings have laid a foundation for elucidating functional conservation and diversification of miR166 family members, especially during seed development or

Functional innovations and morphological diversification in parrotfish.

PubMed

Price, Samantha A; Wainwright, Peter C; Bellwood, David R; Kazancioglu, Erem; Collar, David C; Near, Thomas J

2010-10-01

The association between diversification and evolutionary innovations has been well documented and tested in studies of taxonomic richness but the impact that such innovations have on the diversity of form and function is less well understood. Using phylogenetically rigorous techniques, we investigated the association between morphological diversity and two design breakthroughs within the jaws of parrotfish. Similar intramandibular joints and other modifications of the pharyngeal jaws have evolved repeatedly in teleost fish and are frequently hypothesized to promote diversity. We quantified morphological diversity within six functionally important oral jaw traits using the Brownian motion rate of evolution to correct for phylogenetic and time-related biases and compared these rates across clades that did and did not possess the intramandibular joint and the parrotfish pharyngeal jaw. No change in morphological diversity was associated with the pharyngeal jaw modification alone but rates of oral jaw diversification were up to 8× faster in parrotfish species that possessed both innovations. Interestingly, this morphological diversity may not have led to differential resource uses as available data suggest that members of this clade show remarkable homogeneity of diet. © 2010 The Author(s). Journal compilation © 2010 The Society for the Study of Evolution.

Evolution of the Fusarium–Euwallacea ambrosia beetle mutualism

USDA-ARS?s Scientific Manuscript database

The Euwallacea – Fusarium mutualistic symbiosis represents one of the independent evolutionary origins of fungus-farming. Diversification time estimates place the evolutionary origin of this mutualism in the early Miocene approximately 21 million years ago. Fusarium is best known as one of the most ...

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

The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences.

PubMed

Touchon, Marie; Cury, Jean; Yoon, Eun-Jeong; Krizova, Lenka; Cerqueira, Gustavo C; Murphy, Cheryl; Feldgarden, Michael; Wortman, Jennifer; Clermont, Dominique; Lambert, Thierry; Grillot-Courvalin, Catherine; Nemec, Alexandr; Courvalin, Patrice; Rocha, Eduardo P C

2014-10-13

Bacterial genomics has greatly expanded our understanding of microdiversification patterns within a species, but analyses at higher taxonomical levels are necessary to understand and predict the independent rise of pathogens in a genus. We have sampled, sequenced, and assessed the diversity of genomes of validly named and tentative species of the Acinetobacter genus, a clade including major nosocomial pathogens and biotechnologically important species. We inferred a robust global phylogeny and delimited several new putative species. The genus is very ancient and extremely diverse: Genomes of highly divergent species share more orthologs than certain strains within a species. We systematically characterized elements and mechanisms driving genome diversification, such as conjugative elements, insertion sequences, and natural transformation. We found many error-prone polymerases that may play a role in resistance to toxins, antibiotics, and in the generation of genetic variation. Surprisingly, temperate phages, poorly studied in Acinetobacter, were found to account for a significant fraction of most genomes. Accordingly, many genomes encode clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems with some of the largest CRISPR-arrays found so far in bacteria. Integrons are strongly overrepresented in Acinetobacter baumannii, which correlates with its frequent resistance to antibiotics. Our data suggest that A. baumannii arose from an ancient population bottleneck followed by population expansion under strong purifying selection. The outstanding diversification of the species occurred largely by horizontal transfer, including some allelic recombination, at specific hotspots preferentially located close to the replication terminus. Our work sets a quantitative basis to understand the diversification of Acinetobacter into emerging resistant and versatile pathogens. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society

Neoendemism in Madagascan scaly tree ferns results from recent, coincident diversification bursts.

PubMed

Janssen, Thomas; Bystriakova, Nadia; Rakotondrainibe, France; Coomes, David; Labat, Jean-Noël; Schneider, Harald

2008-08-01

More than 80% of Madagascar's 12,000 plant species are endemic with the degree of endemism reaching as much as 95% in the scaly tree ferns, an important species rich component of Madagascar's evergreen rainforests. Predominantly African or Asian ancestry and divergence times usually postdating the separation of Madagascar from the Gondwanan landmasses have been demonstrated for several Madagascan animal and angiosperm groups. However, evolutionary studies of rainforest-specific lineages are scarce and the ecological context of radiation events has rarely been investigated. Here, we examine the evolution of Madagascan tree ferns as a rainforest-specific model family, integrate results from bioclimatic niche analysis with a dated phylogenetic framework, and propose an evolutionary scenario casting new light on our knowledge of the evolution of large island endemic clades. We show that Madagascar's extant tree fern diversity springs from three distinct ancestors independently colonizing Madagascar in the Miocene and that these three monophyletic clades diversified in three coincident radiation bursts during the Pliocene, reaching exceptionally high diversification rates and most likely responding to a common climatic trigger. Recent diversification bursts may thus have played a major role in the evolution of the extant Madagascan rainforest biome, which hence contains a significant number of young, neoendemic taxa.

Horizontal Gene Transfer of Pectinases from Bacteria Preceded the Diversification of Stick and Leaf Insects

PubMed Central

Shelomi, Matan; Danchin, Etienne G. J.; Heckel, David; Wipfler, Benjamin; Bradler, Sven; Zhou, Xin; Pauchet, Yannick

2016-01-01

Genes acquired by horizontal transfer are increasingly being found in animal genomes. Understanding their origin and evolution requires knowledge about the phylogenetic relationships from both source and recipient organisms. We used RNASeq data and respective assembled transcript libraries to trace the evolutionary history of polygalacturonase (pectinase) genes in stick insects (Phasmatodea). By mapping the distribution of pectinase genes on a Polyneoptera phylogeny, we identified the transfer of pectinase genes from known phasmatodean gut microbes into the genome of an early euphasmatodean ancestor that took place between 60 and 100 million years ago. This transfer preceded the rapid diversification of the suborder, enabling symbiont-free pectinase production that would increase the insects’ digestive efficiency and reduce dependence on microbes. Bacteria-to-insect gene transfer was thought to be uncommon, however the increasing availability of large-scale genomic data may change this prevailing notion. PMID:27210832

Protein and DNA Modifications: Evolutionary Imprints of Bacterial Biochemical Diversification and Geochemistry on the Provenance of Eukaryotic Epigenetics

PubMed Central

Aravind, L.; Burroughs, A. Maxwell; Zhang, Dapeng; Iyer, Lakshminarayan M.

2014-01-01

Epigenetic information, which plays a major role in eukaryotic biology, is transmitted by covalent modifications of nuclear proteins (e.g., histones) and DNA, along with poorly understood processes involving cytoplasmic/secreted proteins and RNAs. The origin of eukaryotes was accompanied by emergence of a highly developed biochemical apparatus for encoding, resetting, and reading covalent epigenetic marks in proteins such as histones and tubulins. The provenance of this apparatus remained unclear until recently. Developments in comparative genomics show that key components of eukaryotic epigenetics emerged as part of the extensive biochemical innovation of secondary metabolism and intergenomic/interorganismal conflict systems in prokaryotes, particularly bacteria. These supplied not only enzymatic components for encoding and removing epigenetic modifications, but also readers of some of these marks. Diversification of these prokaryotic systems and subsequently eukaryotic epigenetics appear to have been considerably influenced by the great oxygenation event in the Earth’s history. PMID:24984775

Ecological specialization and morphological diversification in Greater Antillean boas.

PubMed

Reynolds, R Graham; Collar, David C; Pasachnik, Stesha A; Niemiller, Matthew L; Puente-Rolón, Alberto R; Revell, Liam J

2016-08-01

Colonization of islands can dramatically influence the evolutionary trajectories of organisms, with both deterministic and stochastic processes driving adaptation and diversification. Some island colonists evolve extremely large or small body sizes, presumably in response to unique ecological circumstances present on islands. One example of this phenomenon, the Greater Antillean boas, includes both small (<90 cm) and large (4 m) species occurring on the Greater Antilles and Bahamas, with some islands supporting pairs or trios of body-size divergent species. These boas have been shown to comprise a monophyletic radiation arising from a Miocene dispersal event to the Greater Antilles, though it is not known whether co-occurrence of small and large species is a result of dispersal or in situ evolution. Here, we provide the first comprehensive species phylogeny for this clade combined with morphometric and ecological data to show that small body size evolved repeatedly on separate islands in association with specialization in substrate use. Our results further suggest that microhabitat specialization is linked to increased rates of head shape diversification among specialists. Our findings show that ecological specialization following island colonization promotes morphological diversity through deterministic body size evolution and cranial morphological diversification that is contingent on island- and species-specific factors. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

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

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.

The diversification of Heliconius butterflies: what have we learned in 150 years?

PubMed

Merrill, R M; Dasmahapatra, K K; Davey, J W; Dell'Aglio, D D; Hanly, J J; Huber, B; Jiggins, C D; Joron, M; Kozak, K M; Llaurens, V; Martin, S H; Montgomery, S H; Morris, J; Nadeau, N J; Pinharanda, A L; Rosser, N; Thompson, M J; Vanjari, S; Wallbank, R W R; Yu, Q

2015-08-01

Research into Heliconius butterflies has made a significant contribution to evolutionary biology. Here, we review our understanding of the diversification of these butterflies, covering recent advances and a vast foundation of earlier work. Whereas no single group of organisms can be sufficient for understanding life's diversity, after years of intensive study, research into Heliconius has addressed a wide variety of evolutionary questions. We first discuss evidence for widespread gene flow between Heliconius species and what this reveals about the nature of species. We then address the evolution and diversity of warning patterns, both as the target of selection and with respect to their underlying genetic basis. The identification of major genes involved in mimetic shifts, and homology at these loci between distantly related taxa, has revealed a surprising predictability in the genetic basis of evolution. In the final sections, we consider the evolution of warning patterns, and Heliconius diversity more generally, within a broader context of ecological and sexual selection. We consider how different traits and modes of selection can interact and influence the evolution of reproductive isolation. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Decoupling of body-plan diversification and ecological structuring during the Ediacaran-Cambrian transition: evolutionary and geobiological feedbacks.

PubMed

Mángano, M Gabriela; Buatois, Luis A

2014-04-07

The rapid appearance of bilaterian clades at the beginning of the Phanerozoic is one of the most intriguing topics in macroevolution. However, the complex feedbacks between diversification and ecological interactions are still poorly understood. Here, we show that a systematic and comprehensive analysis of the trace-fossil record of the Ediacaran-Cambrian transition indicates that body-plan diversification and ecological structuring were decoupled. The appearance of a wide repertoire of behavioural strategies and body plans occurred by the Fortunian. However, a major shift in benthic ecological structure, recording the establishment of a suspension-feeder infauna, increased complexity of the trophic web, and coupling of benthos and plankton took place during Cambrian Stage 2. Both phases were accompanied by different styles of ecosystem engineering, but only the second one resulted in the establishment of the Phanerozoic-style ecology. In turn, the suspension-feeding infauna may have been the ecological drivers of a further diversification of deposit-feeding strategies by Cambrian Stage 3, favouring an ecological spillover scenario. Trace-fossil information strongly supports the Cambrian explosion, but allows for a short time of phylogenetic fuse during the terminal Ediacaran-Fortunian.

Decoupling of body-plan diversification and ecological structuring during the Ediacaran–Cambrian transition: evolutionary and geobiological feedbacks

PubMed Central

Mángano, M. Gabriela; Buatois, Luis A.

2014-01-01

The rapid appearance of bilaterian clades at the beginning of the Phanerozoic is one of the most intriguing topics in macroevolution. However, the complex feedbacks between diversification and ecological interactions are still poorly understood. Here, we show that a systematic and comprehensive analysis of the trace-fossil record of the Ediacaran–Cambrian transition indicates that body-plan diversification and ecological structuring were decoupled. The appearance of a wide repertoire of behavioural strategies and body plans occurred by the Fortunian. However, a major shift in benthic ecological structure, recording the establishment of a suspension-feeder infauna, increased complexity of the trophic web, and coupling of benthos and plankton took place during Cambrian Stage 2. Both phases were accompanied by different styles of ecosystem engineering, but only the second one resulted in the establishment of the Phanerozoic-style ecology. In turn, the suspension-feeding infauna may have been the ecological drivers of a further diversification of deposit-feeding strategies by Cambrian Stage 3, favouring an ecological spillover scenario. Trace-fossil information strongly supports the Cambrian explosion, but allows for a short time of phylogenetic fuse during the terminal Ediacaran–Fortunian. PMID:24523279

Himalayan fossils of the oldest known pantherine establish ancient origin of big cats

PubMed Central

Tseng, Z. Jack; Wang, Xiaoming; Slater, Graham J.; Takeuchi, Gary T.; Li, Qiang; Liu, Juan; Xie, Guangpu

2014-01-01

Pantherine felids (‘big cats’) include the largest living cats, apex predators in their respective ecosystems. They are also the earliest diverging living cat lineage, and thus are important for understanding the evolution of all subsequent felid groups. Although the oldest pantherine fossils occur in Africa, molecular phylogenies point to Asia as their region of origin. This paradox cannot be reconciled using current knowledge, mainly because early big cat fossils are exceedingly rare and fragmentary. Here, we report the discovery of a fossil pantherine from the Tibetan Himalaya, with an age of Late Miocene–Early Pliocene, replacing African records as the oldest pantherine. A ‘total evidence’ phylogenetic analysis of pantherines indicates that the new cat is closely related to the snow leopard and exhibits intermediate characteristics on the evolutionary line to the largest cats. Historical biogeographic models provide robust support for the Asian origin of pantherines. The combined analyses indicate that 75% of the divergence events in the pantherine lineage extended back to the Miocene, up to 7 Myr earlier than previously estimated. The deeper evolutionary origin of big cats revealed by the new fossils and analyses indicate a close association between Tibetan Plateau uplift and diversification of the earliest living cats. PMID:24225466

Himalayan fossils of the oldest known pantherine establish ancient origin of big cats.

PubMed

Tseng, Z Jack; Wang, Xiaoming; Slater, Graham J; Takeuchi, Gary T; Li, Qiang; Liu, Juan; Xie, Guangpu

2014-01-07

Pantherine felids ('big cats') include the largest living cats, apex predators in their respective ecosystems. They are also the earliest diverging living cat lineage, and thus are important for understanding the evolution of all subsequent felid groups. Although the oldest pantherine fossils occur in Africa, molecular phylogenies point to Asia as their region of origin. This paradox cannot be reconciled using current knowledge, mainly because early big cat fossils are exceedingly rare and fragmentary. Here, we report the discovery of a fossil pantherine from the Tibetan Himalaya, with an age of Late Miocene-Early Pliocene, replacing African records as the oldest pantherine. A 'total evidence' phylogenetic analysis of pantherines indicates that the new cat is closely related to the snow leopard and exhibits intermediate characteristics on the evolutionary line to the largest cats. Historical biogeographic models provide robust support for the Asian origin of pantherines. The combined analyses indicate that 75% of the divergence events in the pantherine lineage extended back to the Miocene, up to 7 Myr earlier than previously estimated. The deeper evolutionary origin of big cats revealed by the new fossils and analyses indicate a close association between Tibetan Plateau uplift and diversification of the earliest living cats.

Erasmus Darwin, Herbert Spencer, and the origins of the evolutionary worldview in British provincial scientific culture, 1770-1850.

PubMed

Elliott, Paul

2003-03-01

The significance of Herbert Spencer's evolutionary philosophy has been generally recognized for over a century, as the familiarity of his phrase "survival of the fittest" indicates, yet accounts of the origins of his system still tend to follow too closely his own description, written many decades later. This essay argues that Spencer's own interpretation of his intellectual development gives an inadequate impression of the debt he owed to provincial scientific culture and its institutions. Most important, it shows that his evolutionism was originally stimulated by his association with the Derby philosophical community, for it was through this group--of which his father, who also appears to have espoused a deistic evolutionary theory, was a member--that he was first exposed to progressive Englightenment social and educational philosophies and to the evolutionary worldview of Erasmus Darwin, the first president of the Derby Philosophical Society. Darwin's scheme was the first to incorporate biological evolution, associationist psychology, evolutionary geology, and cosmological developmentalism. Spencer's own implicit denials of the link with Darwin are shown to be implausible in the face of Darwin's continuing influence on the Derby savants, the product of insecurity in his later years when he feared for his reputation as Lamarckism became increasingly untenable.

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.

Diversification and spatial structuring in the mutualism between Ficus septica and its pollinating wasps in insular South East Asia.

PubMed

Rodriguez, Lillian Jennifer; Bain, Anthony; Chou, Lien-Siang; Conchou, Lucie; Cruaud, Astrid; Gonzales, Regielene; Hossaert-McKey, Martine; Rasplus, Jean-Yves; Tzeng, Hsy-Yu; Kjellberg, Finn

2017-08-29

Interspecific interactions have long been assumed to play an important role in diversification. Mutualistic interactions, such as nursery pollination mutualisms, have been proposed as good candidates for diversification through co-speciation because of their intricate nature. However, little is known about how speciation and diversification proceeds in emblematic nursery pollination systems such as figs and fig wasps. Here, we analyse diversification in connection with spatial structuring in the obligate mutualistic association between Ficus septica and its pollinating wasps throughout the Philippines and Taiwan. Ceratosolen wasps pollinating F. septica are structured into a set of three vicariant black coloured species, and a fourth yellow coloured species whose distribution overlaps with those of the black species. However, two black pollinator species were found to co-occur on Lanyu island. Microsatellite data on F. septica indicates the presence of three gene pools that broadly mirrors the distribution of the three black clades. Moreover, receptive fig odours, the specific message used by pollinating wasps to locate their host tree, varied among locations. F. septica and its black pollinator clades exhibited similar geographic structuring. This could be due originally to geographic barriers leading to isolation, local adaptation, and finally co-structuring. Nevertheless, the co-occurrence of two black pollinator species on Lanyu island suggests that the parapatric distribution of the black clades is now maintained by the inability of migrating individuals of black pollinators to establish populations outside their range. On the other hand, the distribution of the yellow clade strongly suggests an initial case of character displacement followed by subsequent range extension: in our study system, phenotypic or microevolutionary plasticity has allowed the yellow clade to colonise hosts presenting distinct odours. Hence, while variation in receptive fig odours

On The Evolutionary Origin of Symbolic Communication

NASA Astrophysics Data System (ADS)

Grouchy, Paul; D'Eleuterio, Gabriele M. T.; Christiansen, Morten H.; Lipson, Hod

2016-10-01

The emergence of symbolic communication is often cited as a critical step in the evolution of Homo sapiens, language, and human-level cognition. It is a widely held assumption that humans are the only species that possess natural symbolic communication schemes, although a variety of other species can be taught to use symbols. The origin of symbolic communication remains a controversial open problem, obfuscated by the lack of a fossil record. Here we demonstrate an unbroken evolutionary pathway from a population of initially noncommunicating robots to the spontaneous emergence of symbolic communication. Robots evolve in a simulated world and are supplied with only a single channel of communication. When their ability to reproduce is motivated by the need to find a mate, robots evolve indexical communication schemes from initially noncommunicating populations in 99% of all experiments. Furthermore, 9% of the populations evolve a symbolic communication scheme allowing pairs of robots to exchange information about two independent spatial dimensions over a one-dimensional channel, thereby increasing their chance of reproduction. These results suggest that the ability for symbolic communication could have emerged spontaneously under natural selection, without requiring cognitive preadaptations or preexisting iconic communication schemes as previously conjectured.

Evolutionary genomics of dog domestication.

PubMed

Wayne, Robert K; vonHoldt, Bridgett M

2012-02-01

We review the underlying principles and tools used in genomic studies of domestic dogs aimed at understanding the genetic changes that have occurred during domestication. We show that there are two principle modes of evolution within dogs. One primary mode that accounts for much of the remarkable diversity of dog breeds is the fixation of discrete mutations of large effect in individual lineages that are then crossed to various breed groupings. This transfer of mutations across the dog evolutionary tree leads to the appearance of high phenotypic diversity that in actuality reflects a small number of major genes. A second mechanism causing diversification involves the selective breeding of dogs within distinct phenotypic or functional groups, which enhances specific group attributes such as heading or tracking. Such progressive selection leads to a distinct genetic structure in evolutionary trees such that functional and phenotypic groups cluster genetically. We trace the origin of the nuclear genome in dogs based on haplotype-sharing analyses between dogs and gray wolves and show that contrary to previous mtDNA analyses, the nuclear genome of dogs derives primarily from Middle Eastern or European wolves, a result more consistent with the archeological record. Sequencing analysis of the IGF1 gene, which has been the target of size selection in small breeds, further supports this conclusion. Finally, we discuss how a black coat color mutation that evolved in dogs has transformed North American gray wolf populations, providing a first example of a mutation that appeared under domestication and selectively swept through a wild relative.

[Human origin and evolution. A review of advances in paleoanthropology, comparative genetics, and evolutionary psychology].

PubMed

Markov, A V

2009-01-01

In his main work, "On the origin of species", Darwin has refrained from discusion of the origin of man; be only mentioned that his theory would "throw light" on this problem. This famous Darwin's phrase turned out to be one of the most succesful scientific predictions. In the present paper some of the most important recent adavnces in paleoanthroplogy, comparative genetics and evolutionary psychology are reviewed. These three disciplines currently contribute most to our knowledge of anthropogenesis. The review demonstrates that Darwin's ideas not only "threw light" on human origin and evolution; they provided a comprehensive framework for a great variety of studies concerning different aspects of anthropogenesis.

Tradeoff between robustness and elaboration in carotenoid networks produces cycles of avian color diversification.

PubMed

Badyaev, Alexander V; Morrison, Erin S; Belloni, Virginia; Sanderson, Michael J

2015-08-20

Resolution of the link between micro- and macroevolution calls for comparing both processes on the same deterministic landscape, such as genomic, metabolic or fitness networks. We apply this perspective to the evolution of carotenoid pigmentation that produces spectacular diversity in avian colors and show that basic structural properties of the underlying carotenoid metabolic network are reflected in global patterns of elaboration and diversification in color displays. Birds color themselves by consuming and metabolizing several dietary carotenoids from the environment. Such fundamental dependency on the most upstream external compounds should intrinsically constrain sustained evolutionary elongation of multi-step metabolic pathways needed for color elaboration unless the metabolic network gains robustness - the ability to synthesize the same carotenoid from an additional dietary starting point. We found that gains and losses of metabolic robustness were associated with evolutionary cycles of elaboration and stasis in expressed carotenoids in birds. Lack of metabolic robustness constrained lineage's metabolic explorations to the immediate biochemical vicinity of their ecologically distinct dietary carotenoids, whereas gains of robustness repeatedly resulted in sustained elongation of metabolic pathways on evolutionary time scales and corresponding color elaboration. The structural link between length and robustness in metabolic pathways may explain periodic convergence of phylogenetically distant and ecologically distinct species in expressed carotenoid pigmentation; account for stasis in carotenoid colors in some ecological lineages; and show how the connectivity of the underlying metabolic network provides a mechanistic link between microevolutionary elaboration and macroevolutionary diversification.

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.

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).

Charles Darwin's Origin of Species, directional selection, and the evolutionary sciences today.

PubMed

Kutschera, Ulrich

2009-11-01

The book On the Origin of Species, published in November 1859, is an "abstract" without references, compiled by Charles Darwin from a much longer manuscript entitled "Natural Selection." Here, I summarize the five theories that can be extracted from Darwin's monograph, explain the true meaning of the phrase "struggle for life" (i.e., competition and cooperation), and outline Darwin's original concept of natural selection in populations of animals and plants. Since neither Darwin nor Alfred R. Wallace distinguished between stabilizing and directional natural selection, the popular argument that "selection only eliminates but is not creative" is still alive today. However, I document that August Weismann (Die Bedeutung der sexuellen Fortpflanzung für die Selektions-Theorie. Gustav Fischer-Verlag, Jena, 1886) and Ivan Schmalhausen (Factors of evolution. The theory of stabilizing selection. The Blackiston Company, Philadelphia, 1949) provided precise definitions for directional (dynamic) selection in nature and illustrate this "Weismann-Schmalhausen principle" with respect to the evolutionary development of novel phenotypes. Then, the modern (synthetic) theory of biological evolution that is based on the work of Theodosius Dobzhansky (Genetics and the origin of species. Columbia University Press, New York, 1937) and others, and the expanded version of this system of theories, are outlined. Finally, I document that symbiogenesis (i.e., primary endosymbiosis, a process that gave rise to the first eukaryotic cells), ongoing directional natural selection, and the dynamic Earth (plate tectonics, i.e., geological events that both created and destroyed terrestrial and aquatic habitats) were the key processes responsible for the documented macroevolutionary patterns in all five kingdoms of life. Since the evolutionary development of the earliest archaic bacteria more than 3,500 mya, the biosphere of our dynamic planet has been dominated by prokaryotic microbes. Eubacteria

Phenotypes in phylogeography: Species’ traits, environmental variation, and vertebrate diversification

PubMed Central

Bell, Rayna C.; Mason, Nicholas A.

2016-01-01

Almost 30 y ago, the field of intraspecific phylogeography laid the foundation for spatially explicit and genealogically informed studies of population divergence. With new methods and markers, the focus in phylogeography shifted to previously unrecognized geographic genetic variation, thus reducing the attention paid to phenotypic variation in those same diverging lineages. Although phenotypic differences among lineages once provided the main data for studies of evolutionary change, the mechanisms shaping phenotypic differentiation and their integration with intraspecific genetic structure have been underexplored in phylogeographic studies. However, phenotypes are targets of selection and play important roles in species performance, recognition, and diversification. Here, we focus on three questions. First, how can phenotypes elucidate mechanisms underlying concordant or idiosyncratic responses of vertebrate species evolving in shared landscapes? Second, what mechanisms underlie the concordance or discordance of phenotypic and phylogeographic differentiation? Third, how can phylogeography contribute to our understanding of functional phenotypic evolution? We demonstrate that the integration of phenotypic data extends the reach of phylogeography to explain the origin and maintenance of biodiversity. Finally, we stress the importance of natural history collections as sources of high-quality phenotypic data that span temporal and spatial axes. PMID:27432983

An emerging synthesis between community ecology and evolutionary biology.

PubMed

Johnson, Marc T J; Stinchcombe, John R

2007-05-01

A synthesis between community ecology and evolutionary biology is emerging that identifies how genetic variation and evolution within one species can shape the ecological properties of entire communities and, in turn, how community context can govern evolutionary processes and patterns. This synthesis incorporates research on the ecology and evolution within communities over short timescales (community genetics and diffuse coevolution), as well as macroevolutionary timescales (community phylogenetics and co-diversification of communities). As we discuss here, preliminary evidence supports the hypothesis that there is a dynamic interplay between ecology and evolution within communities, yet researchers have not yet demonstrated convincingly whether, and under what circumstances, it is important for biologists to bridge community ecology and evolutionary biology. Answering this question will have important implications for both basic and applied problems in biology.

Protein and DNA modifications: evolutionary imprints of bacterial biochemical diversification and geochemistry on the provenance of eukaryotic epigenetics.

PubMed

Aravind, L; Burroughs, A Maxwell; Zhang, Dapeng; Iyer, Lakshminarayan M

2014-07-01

Epigenetic information, which plays a major role in eukaryotic biology, is transmitted by covalent modifications of nuclear proteins (e.g., histones) and DNA, along with poorly understood processes involving cytoplasmic/secreted proteins and RNAs. The origin of eukaryotes was accompanied by emergence of a highly developed biochemical apparatus for encoding, resetting, and reading covalent epigenetic marks in proteins such as histones and tubulins. The provenance of this apparatus remained unclear until recently. Developments in comparative genomics show that key components of eukaryotic epigenetics emerged as part of the extensive biochemical innovation of secondary metabolism and intergenomic/interorganismal conflict systems in prokaryotes, particularly bacteria. These supplied not only enzymatic components for encoding and removing epigenetic modifications, but also readers of some of these marks. Diversification of these prokaryotic systems and subsequently eukaryotic epigenetics appear to have been considerably influenced by the great oxygenation event in the Earth's history. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

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.

Contrasting evolutionary processes during Quaternary climatic changes and historical orogenies: a case study of the Japanese endemic primroses Primula sect. Reinii.

PubMed

Yamamoto, Masaya; Ohtani, Masato; Kurata, Kaoruko; Setoguchi, Hiroaki

2017-11-28

Recent biogeographic studies have illustrated that Quaternary climatic changes and historical orogenies have driven the development of high levels of biodiversity. In this context, phylogenetic niche conservatism may play a role as a major precursor of allopatric speciation. However, the effects of niche evolution on the diversification patterns of plant species under rapid habitat changes are still unknown. Here, Primula section Reinii, one of the few primroses endemic to the Japanese Archipelago, was investigated. This study aimed to clarify the phylogenetic position and relationships of section Reinii, interpret the biogeographic and diversification patterns of this group and gain a better understanding of the role of climatic niche evolution in the Japanese endemic primroses. Dated phylogeny for Primula section Reinii is presented based on the sequences of six chloroplast genes and one nuclear gene. Biogeographic history was reconstructed using statistical dispersal-vicariance analysis. Macro-evolutionary modelling of the climatic niche was combined with biogeographic inferences. Section Reinii was shown to be monophyletic based on chloroplast and nuclear sequences. Fossil-calibrated dating analysis estimated that this section diverged from its sister taxon, sect. Cortusoides, around 1.82 million years ago, and intraspecific diversification occurred within the last million years. This time frame was characterized by Quaternary climatic oscillations and uplift of high mountains in Japan. Biogeographic inference suggested that this section originated at the northern end of the Japanese Archipelago and then dispersed southward to other islands. Models of climatic niche evolution indicated that the closely related species P. reinii and P. tosanensis have contrasting niche optima and rates of niche evolution. Our results highlight that spatiotemporal heterogeneity in the Japanese islands may play a significant role in the biogeographic history of Japanese endemic

Rapid diversification and not clade age explains high diversity in neotropical Adelpha butterflies

PubMed Central

Mullen, Sean P.; Savage, Wesley K.; Wahlberg, Niklas; Willmott, Keith R.

2011-01-01

Latitudinal gradients in species richness are among the most well-known biogeographic patterns in nature, and yet there remains much debate and little consensus over the ecological and evolutionary causes of these gradients. Here, we evaluated whether two prominent alternative hypotheses (namely differences in diversification rate or clade age) could account for the latitudinal diversity gradient in one of the most speciose neotropical butterfly genera (Adelpha) and its close relatives. We generated a multilocus phylogeny of a diverse group of butterflies in the containing tribe Limenitidini, which has both temperate and tropical representatives. Our results suggest there is no relationship between clade age and species richness that could account for the diversity gradient, but that instead it could be explained by a significantly higher diversification rate within the predominantly tropical genus Adelpha. An apparent early larval host-plant shift to Rubiaceae and other plant families suggests that the availability of new potential host plants probably contributed to an increase in diversification of Adelpha in the lowland Neotropics. Collectively, our results support the hypothesis that the equatorial peak in species richness observed within Adelpha is the result of increased diversification rate in the last 10–15 Myr rather than a function of clade age, perhaps reflecting adaptive divergence in response to the dramatic host-plant diversity found within neotropical ecosystems. PMID:21106589

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

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.

Changes in Diversification Patterns and Signatures of Selection during the Evolution of Murinae-Associated Hantaviruses

PubMed Central

Castel, Guillaume; Razzauti, Maria; Jousselin, Emmanuelle; Kergoat, Gael J.; Cosson, Jean-François

2014-01-01

In the last 50 years, hantaviruses have significantly affected public health worldwide, but the exact extent of the distribution of hantavirus diseases, species and lineages and the risk of their emergence into new geographic areas are still poorly known. In particular, the determinants of molecular evolution of hantaviruses circulating in different geographical areas or different host species are poorly documented. Yet, this understanding is essential for the establishment of more accurate scenarios of hantavirus emergence under different climatic and environmental constraints. In this study, we focused on Murinae-associated hantaviruses (mainly Seoul Dobrava and Hantaan virus) using sequences available in GenBank and conducted several complementary phylogenetic inferences. We sought for signatures of selection and changes in patterns and rates of diversification in order to characterize hantaviruses’ molecular evolution at different geographical scales (global and local). We then investigated whether these events were localized in particular geographic areas. Our phylogenetic analyses supported the assumption that RNA virus molecular variations were under strong evolutionary constraints and revealed changes in patterns of diversification during the evolutionary history of hantaviruses. These analyses provide new knowledge on the molecular evolution of hantaviruses at different scales of time and space. PMID:24618811

The origin and genetic differentiation of the socially parasitic aphid Tamalia inquilinus.

PubMed

Miller, Donald G; Lawson, Sarah P; Rinker, David C; Estby, Heather; Abbot, Patrick

2015-11-01

Social and brood parasitisms are nonconsumptive forms of parasitism involving the exploitation of the colonies or nests of a host. Such parasites are often related to their hosts and may evolve in various ecological contexts, causing evolutionary constraints and opportunities for both parasites and their hosts. In extreme cases, patterns of diversification between social parasites and their hosts can be coupled, such that diversity of one is correlated with or even shapes the diversity of the other. Aphids in the genus Tamalia induce galls on North American manzanita (Arctostaphylos) and related shrubs (Arbutoideae) and are parasitized by nongalling social parasites or inquilines in the same genus. We used RNA sequencing to identify and generate new gene sequences for Tamalia and performed maximum-likelihood, Bayesian and phylogeographic analyses to reconstruct the origins and patterns of diversity and host-associated differentiation in the genus. Our results indicate that the Tamalia inquilines are monophyletic and closely related to their gall-forming hosts on Arctostaphylos, supporting a previously proposed scenario for origins of these parasitic aphids. Unexpectedly, population structure and host-plant-associated differentiation were greater in the non-gall-inducing parasites than in their gall-inducing hosts. RNA-seq indicated contrasting patterns of gene expression between host aphids and parasites, and perhaps functional differences in host-plant relationships. Our results suggest a mode of speciation in which host plants drive within-guild diversification in insect hosts and their parasites. Shared host plants may be sufficient to promote the ecological diversification of a network of phytophagous insects and their parasites, as exemplified by Tamalia aphids. © 2015 John Wiley & Sons Ltd.

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.

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

Evolutionary origins of the endocannabinoid system.

PubMed

McPartland, John M; Matias, Isabel; Di Marzo, Vincenzo; Glass, Michelle

2006-03-29

Endocannabinoid system evolution was estimated by searching for functional orthologs in the genomes of twelve phylogenetically diverse organisms: Homo sapiens, Mus musculus, Takifugu rubripes, Ciona intestinalis, Caenorhabditis elegans, Drosophila melanogaster, Saccharomyces cerevisiae, Arabidopsis thaliana, Plasmodium falciparum, Tetrahymena thermophila, Archaeoglobus fulgidus, and Mycobacterium tuberculosis. Sequences similar to human endocannabinoid exon sequences were derived from filtered BLAST searches, and subjected to phylogenetic testing with ClustalX and tree building programs. Monophyletic clades that agreed with broader phylogenetic evidence (i.e., gene trees displaying topographical congruence with species trees) were considered orthologs. The capacity of orthologs to function as endocannabinoid proteins was predicted with pattern profilers (Pfam, Prosite, TMHMM, and pSORT), and by examining queried sequences for amino acid motifs known to serve critical roles in endocannabinoid protein function (obtained from a database of site-directed mutagenesis studies). This novel transfer of functional information onto gene trees enabled us to better predict the functional origins of the endocannabinoid system. Within this limited number of twelve organisms, the endocannabinoid genes exhibited heterogeneous evolutionary trajectories, with functional orthologs limited to mammals (TRPV1 and GPR55), or vertebrates (CB2 and DAGLbeta), or chordates (MAGL and COX2), or animals (DAGLalpha and CB1-like receptors), or opisthokonta (animals and fungi, NAPE-PLD), or eukaryotes (FAAH). Our methods identified fewer orthologs than did automated annotation systems, such as HomoloGene. Phylogenetic profiles, nonorthologous gene displacement, functional convergence, and coevolution are discussed.

Molecular evolution and expression of archosaurian β-keratins: diversification and expansion of archosaurian β-keratins and the origin of feather β-keratins.

PubMed

Greenwold, Matthew J; Sawyer, Roger H

2013-09-01

The archosauria consist of two living groups, crocodilians, and birds. Here we compare the structure, expression, and phylogeny of the beta (β)-keratins in two crocodilian genomes and two avian genomes to gain a better understanding of the evolutionary origin of the feather β-keratins. Unlike squamates such as the green anole with 40 β-keratins in its genome, the chicken and zebra finch genomes have over 100 β-keratin genes in their genomes, while the American alligator has 20 β-keratin genes, and the saltwater crocodile has 21 β-keratin genes. The crocodilian β-keratins are similar to those of birds and these structural proteins have a central filament domain and N- and C-termini, which contribute to the matrix material between the twisted β-sheets, which form the 2-3 nm filament. Overall the expression of alligator β-keratin genes in the integument increases during development. Phylogenetic analysis demonstrates that a crocodilian β-keratin clade forms a monophyletic group with the avian scale and feather β-keratins, suggesting that avian scale and feather β-keratins along with a subset of crocodilian β-keratins evolved from a common ancestral gene/s. Overall, our analyses support the view that the epidermal appendages of basal archosaurs used a diverse array of β-keratins, which evolved into crocodilian and avian specific clades. In birds, the scale and feather subfamilies appear to have evolved independently in the avian lineage from a subset of archosaurian claw β-keratins. The expansion of the avian specific feather β-keratin genes accompanied the diversification of birds and the evolution of feathers. Copyright © 2013 Wiley Periodicals, Inc.

Progenitors of the protochordate ocellus as an evolutionary origin of the neural crest

PubMed Central

2013-01-01

The neural crest represents a highly multipotent population of embryonic stem cells found only in vertebrate embryos. Acquisition of the neural crest during the evolution of vertebrates was a great advantage, providing Chordata animals with the first cellular cartilage, bone, dentition, advanced nervous system and other innovations. Today not much is known about the evolutionary origin of neural crest cells. Here we propose a novel scenario in which the neural crest originates from neuroectodermal progenitors of the pigmented ocelli in Amphioxus-like animals. We suggest that because of changes in photoreception needs, these multipotent progenitors of photoreceptors gained the ability to migrate outside of the central nervous system and subsequently started to give rise to neural, glial and pigmented progeny at the periphery. PMID:23575111

Footprints pull origin and diversification of dinosaur stem lineage deep into Early Triassic.

PubMed

Brusatte, Stephen L; Niedźwiedzki, Grzegorz; Butler, Richard J

2011-04-07

The ascent of dinosaurs in the Triassic is an exemplary evolutionary radiation, but the earliest phase of dinosaur history remains poorly understood. Body fossils of close dinosaur relatives are rare, but indicate that the dinosaur stem lineage (Dinosauromorpha) originated by the latest Anisian (ca 242-244 Ma). Here, we report footprints from the Early-Middle Triassic of Poland, stratigraphically well constrained and identified using a conservative synapomorphy-based approach, which shifts the origin of the dinosaur stem lineage back to the Early Olenekian (ca 249-251 Ma), approximately 5-9 Myr earlier than indicated by body fossils, earlier than demonstrated by previous footprint records, and just a few million years after the Permian/Triassic mass extinction (252.3 Ma). Dinosauromorph tracks are rare in all Polish assemblages, suggesting that these animals were minor faunal components. The oldest tracks are quadrupedal, a morphology uncommon among the earliest dinosauromorph body fossils, but bipedality and moderately large body size had arisen by the Early Anisian (ca 246 Ma). Integrating trace fossils and body fossils demonstrates that the rise of dinosaurs was a drawn-out affair, perhaps initiated during recovery from the Permo-Triassic extinction.

The evolutionary origin of jaw yaw in mammals

PubMed Central

Grossnickle, David M.

2017-01-01

Theria comprises all but three living mammalian genera and is one of the most ecologically pervasive clades on Earth. Yet, the origin and early history of therians and their close relatives (i.e., cladotherians) remains surprisingly enigmatic. A critical biological function that can be compared among early mammal groups is mastication. Morphometrics and modeling analyses of the jaws of Mesozoic mammals indicate that cladotherians evolved musculoskeletal anatomies that increase mechanical advantage during jaw rotation around a dorsoventrally-oriented axis (i.e., yaw) while decreasing the mechanical advantage of jaw rotation around a mediolaterally-oriented axis (i.e., pitch). These changes parallel molar transformations in early cladotherians that indicate their chewing cycles included significant transverse movement, likely produced via yaw rotation. Thus, I hypothesize that cladotherian molar morphologies and musculoskeletal jaw anatomies evolved concurrently with increased yaw rotation of the jaw during chewing cycles. The increased transverse movement resulting from yaw rotation may have been a crucial evolutionary prerequisite for the functionally versatile tribosphenic molar morphology, which underlies the molars of all therians and is retained by many extant clades. PMID:28322334

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.

Evolution and the eye: the Darwin bicentennial and the sesquicentennial of the origin of species.

PubMed

Fishman, Ronald S

2008-11-01

Evolution is an essential concept for anyone who considers science to be the best way to understand the natural world. It is as fully established as any scientific principle can be and is the great unifying theme in all of biology, as integral to understanding life-forms as gravity is to understanding the cosmos. On the bicentennial of the birth of Charles Darwin in 1809, and 150 years after the publication of On the Origin of Species by Means of Natural Selection in 1859, we should remember the main features of eye evolution and the prominent place the eye holds in the development and refinement of evolutionary theory. A few highlights include the antiquity of rhodopsin, the ready capacity of an eye to evolve, the effect of eyes on the diversification of life-forms, and the promising influence of genetics on developmental and evolutionary biology.

Phylotranscriptomic analysis of the origin and early diversification of land plants

PubMed Central

Wickett, Norman J.; Mirarab, Siavash; Nguyen, Nam; Warnow, Tandy; Carpenter, Eric; Matasci, Naim; Ayyampalayam, Saravanaraj; Barker, Michael S.; Burleigh, J. Gordon; Gitzendanner, Matthew A.; Ruhfel, Brad R.; Wafula, Eric; Graham, Sean W.; Mathews, Sarah; Melkonian, Michael; Soltis, Douglas E.; Soltis, Pamela S.; Miles, Nicholas W.; Rothfels, Carl J.; Pokorny, Lisa; Shaw, A. Jonathan; DeGironimo, Lisa; Stevenson, Dennis W.; Surek, Barbara; Villarreal, Juan Carlos; Roure, Béatrice; Philippe, Hervé; dePamphilis, Claude W.; Chen, Tao; Deyholos, Michael K.; Baucom, Regina S.; Kutchan, Toni M.; Augustin, Megan M.; Wang, Jun; Zhang, Yong; Tian, Zhijian; Yan, Zhixiang; Wu, Xiaolei; Sun, Xiao; Wong, Gane Ka-Shu; Leebens-Mack, James

2014-01-01

Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated. PMID:25355905

The oldest parareptile and the early diversification of reptiles

PubMed Central

Modesto, Sean P.; Scott, Diane M.; MacDougall, Mark J.; Sues, Hans-Dieter; Evans, David C.; Reisz, Robert R.

2015-01-01

Amniotes, tetrapods that evolved the cleidoic egg and thus independence from aquatic larval stages, appeared ca 314 Ma during the Coal Age. The rapid diversification of amniotes and other tetrapods over the course of the Late Carboniferous period was recently attributed to the fragmentation of coal-swamp rainforests ca 307 Ma. However, the amniote fossil record during the Carboniferous is relatively sparse, with ca 33% of the diversity represented by single specimens for each species. We describe here a new species of reptilian amniote that was collected from uppermost Carboniferous rocks of Prince Edward Island, Canada. Erpetonyx arsenaultorum gen. et sp. nov. is a new parareptile distinguished by 29 presacral vertebrae and autapomorphies of the carpus. Phylogenetic analyses of parareptiles reveal E. arsenaultorum as the closest relative of bolosaurids. Stratigraphic calibration of our results indicates that parareptiles began their evolutionary radiation before the close of the Carboniferous Period, and that the diversity of end-Carboniferous reptiles is 80% greater than suggested by previous work. Latest Carboniferous reptiles were still half as diverse as synapsid amniotes, a disparity that may be attributable to preservational biases, to collecting biases, to the origin of herbivory in tetrapods or any combination of these factors. PMID:25589601

The oldest parareptile and the early diversification of reptiles.

PubMed

Modesto, Sean P; Scott, Diane M; MacDougall, Mark J; Sues, Hans-Dieter; Evans, David C; Reisz, Robert R

2015-02-22

Amniotes, tetrapods that evolved the cleidoic egg and thus independence from aquatic larval stages, appeared ca 314 Ma during the Coal Age. The rapid diversification of amniotes and other tetrapods over the course of the Late Carboniferous period was recently attributed to the fragmentation of coal-swamp rainforests ca 307 Ma. However, the amniote fossil record during the Carboniferous is relatively sparse, with ca 33% of the diversity represented by single specimens for each species. We describe here a new species of reptilian amniote that was collected from uppermost Carboniferous rocks of Prince Edward Island, Canada. Erpetonyx arsenaultorum gen. et sp. nov. is a new parareptile distinguished by 29 presacral vertebrae and autapomorphies of the carpus. Phylogenetic analyses of parareptiles reveal E. arsenaultorum as the closest relative of bolosaurids. Stratigraphic calibration of our results indicates that parareptiles began their evolutionary radiation before the close of the Carboniferous Period, and that the diversity of end-Carboniferous reptiles is 80% greater than suggested by previous work. Latest Carboniferous reptiles were still half as diverse as synapsid amniotes, a disparity that may be attributable to preservational biases, to collecting biases, to the origin of herbivory in tetrapods or any combination of these factors. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

The ecological origins of snakes as revealed by skull evolution.

PubMed

Da Silva, Filipe O; Fabre, Anne-Claire; Savriama, Yoland; Ollonen, Joni; Mahlow, Kristin; Herrel, Anthony; Müller, Johannes; Di-Poï, Nicolas

2018-01-25

The ecological origin of snakes remains amongst the most controversial topics in evolution, with three competing hypotheses: fossorial; marine; or terrestrial. Here we use a geometric morphometric approach integrating ecological, phylogenetic, paleontological, and developmental data for building models of skull shape and size evolution and developmental rate changes in squamates. Our large-scale data reveal that whereas the most recent common ancestor of crown snakes had a small skull with a shape undeniably adapted for fossoriality, all snakes plus their sister group derive from a surface-terrestrial form with non-fossorial behavior, thus redirecting the debate toward an underexplored evolutionary scenario. Our comprehensive heterochrony analyses further indicate that snakes later evolved novel craniofacial specializations through global acceleration of skull development. These results highlight the importance of the interplay between natural selection and developmental processes in snake origin and diversification, leading first to invasion of a new habitat and then to subsequent ecological radiations.

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.

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.

Revisiting the diffusion approximation to estimate evolutionary rates of gene family diversification.

PubMed

Gjini, Erida; Haydon, Daniel T; David Barry, J; Cobbold, Christina A

2014-01-21

Genetic diversity in multigene families is shaped by multiple processes, including gene conversion and point mutation. Because multi-gene families are involved in crucial traits of organisms, quantifying the rates of their genetic diversification is important. With increasing availability of genomic data, there is a growing need for quantitative approaches that integrate the molecular evolution of gene families with their higher-scale function. In this study, we integrate a stochastic simulation framework with population genetics theory, namely the diffusion approximation, to investigate the dynamics of genetic diversification in a gene family. Duplicated genes can diverge and encode new functions as a result of point mutation, and become more similar through gene conversion. To model the evolution of pairwise identity in a multigene family, we first consider all conversion and mutation events in a discrete manner, keeping track of their details and times of occurrence; second we consider only the infinitesimal effect of these processes on pairwise identity accounting for random sampling of genes and positions. The purely stochastic approach is closer to biological reality and is based on many explicit parameters, such as conversion tract length and family size, but is more challenging analytically. The population genetics approach is an approximation accounting implicitly for point mutation and gene conversion, only in terms of per-site average probabilities. Comparison of these two approaches across a range of parameter combinations reveals that they are not entirely equivalent, but that for certain relevant regimes they do match. As an application of this modelling framework, we consider the distribution of nucleotide identity among VSG genes of African trypanosomes, representing the most prominent example of a multi-gene family mediating parasite antigenic variation and within-host immune evasion. © 2013 Published by Elsevier Ltd. All rights reserved.

Contrasting patterns of evolutionary constraint and novelty revealed by comparative sperm proteomic analysis in Lepidoptera.

PubMed

Whittington, Emma; Forsythe, Desiree; Borziak, Kirill; Karr, Timothy L; Walters, James R; Dorus, Steve

2017-12-02

Rapid evolution is a hallmark of reproductive genetic systems and arises through the combined processes of sequence divergence, gene gain and loss, and changes in gene and protein expression. While studies aiming to disentangle the molecular ramifications of these processes are progressing, we still know little about the genetic basis of evolutionary transitions in reproductive systems. Here we conduct the first comparative analysis of sperm proteomes in Lepidoptera, a group that exhibits dichotomous spermatogenesis, in which males produce a functional fertilization-competent sperm (eupyrene) and an incompetent sperm morph lacking nuclear DNA (apyrene). Through the integrated application of evolutionary proteomics and genomics, we characterize the genomic patterns potentially associated with the origination and evolution of this unique spermatogenic process and assess the importance of genetic novelty in Lepidopteran sperm biology. Comparison of the newly characterized Monarch butterfly (Danaus plexippus) sperm proteome to those of the Carolina sphinx moth (Manduca sexta) and the fruit fly (Drosophila melanogaster) demonstrated conservation at the level of protein abundance and post-translational modification within Lepidoptera. In contrast, comparative genomic analyses across insects reveals significant divergence at two levels that differentiate the genetic architecture of sperm in Lepidoptera from other insects. First, a significant reduction in orthology among Monarch sperm genes relative to the remainder of the genome in non-Lepidopteran insect species was observed. Second, a substantial number of sperm proteins were found to be specific to Lepidoptera, in that they lack detectable homology to the genomes of more distantly related insects. Lastly, the functional importance of Lepidoptera specific sperm proteins is broadly supported by their increased abundance relative to proteins conserved across insects. Our results identify a burst of genetic novelty

Contemporary morphological diversification of passerine birds introduced to the Hawaiian archipelago.

PubMed

Mathys, Blake A; Lockwood, Julie L

2011-08-07

Species that have been introduced to islands experience novel and strong selection pressures after establishment. There is evidence that exotic species diverge from their native source populations; further, a few studies have demonstrated adaptive divergence across multiple exotic populations of a single species. Exotic birds provide a good study system, as they have been introduced to many locations worldwide, and we often know details concerning the propagule origin, time of introduction, and dynamics of establishment and dispersal within the introduced range. These data make them especially conducive to the examination of contemporary evolution. Island faunas have received intense scrutiny, therefore we have expectations concerning the patterns of diversification for exotic species. We examine six passerine bird species that were introduced to the Hawaiian archipelago less than 150 years ago. We find that five of these show morphological divergence among islands from the time since they were established. We demonstrate that some of this divergence cannot be accounted for by genetic drift, and therefore we must consider adaptive evolution to explain it. We also evaluate evolutionary divergence rates and find that these species are diverging at similar rates to those found in published studies of contemporary evolution in native species.

Origins and Evolutionary Dynamics of H3N2 Canine Influenza Virus.

PubMed

Zhu, Henan; Hughes, Joseph; Murcia, Pablo R

2015-05-01

Influenza A viruses (IAVs) are maintained mainly in wild birds, and despite frequent spillover infections of avian IAVs into mammals, only a small number of viruses have become established in mammalian hosts. A new H3N2 canine influenza virus (CIV) of avian origin emerged in Asia in the mid-2000s and is now circulating in dog populations of China and South Korea, and possibly in Thailand. The emergence of CIV provides new opportunities for zoonotic infections and interspecies transmission. We examined 14,764 complete IAV genomes together with all CIV genomes publicly available since its first isolation until 2013. We show that CIV may have originated as early as 1999 as a result of segment reassortment among Eurasian and North American avian IAV lineages. We also identified amino acid changes that might have played a role in CIV emergence, some of which have not been previously identified in other cross-species jumps. CIV evolves at a lower rate than H3N2 human influenza viruses do, and viral phylogenies exhibit geographical structure compatible with high levels of local transmission. We detected multiple intrasubtypic and heterosubtypic reassortment events, including the acquisition of the NS segment of an H5N1 avian influenza virus that had previously been overlooked. In sum, our results provide insight into the adaptive changes required by avian viruses to establish themselves in mammals and also highlight the potential role of dogs to act as intermediate hosts in which viruses with zoonotic and/or pandemic potential could originate, particularly with an estimated dog population of ∼ 700 million. Influenza A viruses circulate in humans and animals. This multihost ecology has important implications, as past pandemics were caused by IAVs carrying gene segments of both human and animal origin. Adaptive evolution is central to cross-species jumps, and this is why understanding the evolutionary processes that shape influenza A virus genomes is key to elucidating

Diversification of the phaseoloid legumes: effects of climate change, range expansion and habit shift

PubMed Central

Li, Honglei; Wang, Wei; Lin, Li; Zhu, Xiangyun; Li, Jianhua; Zhu, Xinyu; Chen, Zhiduan

2013-01-01

Understanding which factors have driven the evolutionary success of a group is a fundamental question in biology. Angiosperms are the most successful group in plants and have radiated and adapted to various habitats. Among angiosperms, legumes are a good example for such successful radiation and adaptation. We here investigated how the interplay of past climate changes, geographical expansion and habit shifts has promoted diversification of the phaseoloid legumes, one of the largest clades in the Leguminosae. Using a comprehensive genus-level phylogeny from three plastid markers, we estimate divergence times, infer habit shifts, test the phylogenetic and temporal diversification heterogeneity, and reconstruct ancestral biogeographical ranges. We found that the phaseoloid lineages underwent twice dramatic accumulation. During the Late Oligocene, at least six woody clades rapidly diverged, perhaps in response to the Late Oligocene warming and aridity, and a result of rapidly exploiting new ecological opportunities in Asia, Africa and Australia. The most speciose lineage is herbaceous and began to rapidly diversify since the Early Miocene, which was likely ascribed to arid climates, along with the expansion of seasonally dry tropical forests in Africa, Asia, and America. The phaseoloid group provides an excellent case supporting the idea that the interplay of ecological opportunities and key innovations drives the evolutionary success. PMID:24130564

Diversification of the phaseoloid legumes: effects of climate change, range expansion and habit shift.

PubMed

Li, Honglei; Wang, Wei; Lin, Li; Zhu, Xiangyun; Li, Jianhua; Zhu, Xinyu; Chen, Zhiduan

2013-01-01

Understanding which factors have driven the evolutionary success of a group is a fundamental question in biology. Angiosperms are the most successful group in plants and have radiated and adapted to various habitats. Among angiosperms, legumes are a good example for such successful radiation and adaptation. We here investigated how the interplay of past climate changes, geographical expansion and habit shifts has promoted diversification of the phaseoloid legumes, one of the largest clades in the Leguminosae. Using a comprehensive genus-level phylogeny from three plastid markers, we estimate divergence times, infer habit shifts, test the phylogenetic and temporal diversification heterogeneity, and reconstruct ancestral biogeographical ranges. We found that the phaseoloid lineages underwent twice dramatic accumulation. During the Late Oligocene, at least six woody clades rapidly diverged, perhaps in response to the Late Oligocene warming and aridity, and a result of rapidly exploiting new ecological opportunities in Asia, Africa and Australia. The most speciose lineage is herbaceous and began to rapidly diversify since the Early Miocene, which was likely ascribed to arid climates, along with the expansion of seasonally dry tropical forests in Africa, Asia, and America. The phaseoloid group provides an excellent case supporting the idea that the interplay of ecological opportunities and key innovations drives the evolutionary success.

Differential Infection Patterns and Recent Evolutionary Origins of Equine Hepaciviruses in Donkeys.

PubMed

Walter, Stephanie; Rasche, Andrea; Moreira-Soto, Andrés; Pfaender, Stephanie; Bletsa, Magda; Corman, Victor Max; Aguilar-Setien, Alvaro; García-Lacy, Fernando; Hans, Aymeric; Todt, Daniel; Schuler, Gerhard; Shnaiderman-Torban, Anat; Steinman, Amir; Roncoroni, Cristina; Veneziano, Vincenzo; Rusenova, Nikolina; Sandev, Nikolay; Rusenov, Anton; Zapryanova, Dimitrinka; García-Bocanegra, Ignacio; Jores, Joerg; Carluccio, Augusto; Veronesi, Maria Cristina; Cavalleri, Jessika M V; Drosten, Christian; Lemey, Philippe; Steinmann, Eike; Drexler, Jan Felix

2017-01-01

The hepatitis C virus (HCV) is a major human pathogen. Genetically related viruses in animals suggest a zoonotic origin of HCV. The closest relative of HCV is found in horses (termed equine hepacivirus [EqHV]). However, low EqHV genetic diversity implies relatively recent acquisition of EqHV by horses, making a derivation of HCV from EqHV unlikely. To unravel the EqHV evolutionary history within equid sister species, we analyzed 829 donkeys and 53 mules sampled in nine European, Asian, African, and American countries by molecular and serologic tools for EqHV infection. Antibodies were found in 278 animals (31.5%), and viral RNA was found in 3 animals (0.3%), all of which were simultaneously seropositive. A low RNA prevalence in spite of high seroprevalence suggests a predominance of acute infection, a possible difference from the mostly chronic hepacivirus infection pattern seen in horses and humans. Limitation of transmission due to short courses of infection may explain the existence of entirely seronegative groups of animals. Donkey and horse EqHV strains were paraphyletic and 97.5 to 98.2% identical in their translated polyprotein sequences, making virus/host cospeciation unlikely. Evolutionary reconstructions supported host switches of EqHV between horses and donkeys without the involvement of adaptive evolution. Global admixture of donkey and horse hepaciviruses was compatible with anthropogenic alterations of EqHV ecology. In summary, our findings do not support EqHV as the origin of the significantly more diversified HCV. Identification of a host system with predominantly acute hepacivirus infection may enable new insights into the chronic infection pattern associated with HCV. The evolutionary origins of the human hepatitis C virus (HCV) are unclear. The closest animal-associated relative of HCV occurs in horses (equine hepacivirus [EqHV]). The low EqHV genetic diversity implies a relatively recent acquisition of EqHV by horses, limiting the time span for

Differential Infection Patterns and Recent Evolutionary Origins of Equine Hepaciviruses in Donkeys

PubMed Central

Walter, Stephanie; Rasche, Andrea; Moreira-Soto, Andrés; Pfaender, Stephanie; Bletsa, Magda; Corman, Victor Max; Aguilar-Setien, Alvaro; García-Lacy, Fernando; Hans, Aymeric; Todt, Daniel; Schuler, Gerhard; Shnaiderman-Torban, Anat; Steinman, Amir; Roncoroni, Cristina; Veneziano, Vincenzo; Rusenova, Nikolina; Sandev, Nikolay; Rusenov, Anton; Zapryanova, Dimitrinka; García-Bocanegra, Ignacio; Jores, Joerg; Carluccio, Augusto; Veronesi, Maria Cristina; Cavalleri, Jessika M. V.; Drosten, Christian; Lemey, Philippe

2016-01-01

ABSTRACT The hepatitis C virus (HCV) is a major human pathogen. Genetically related viruses in animals suggest a zoonotic origin of HCV. The closest relative of HCV is found in horses (termed equine hepacivirus [EqHV]). However, low EqHV genetic diversity implies relatively recent acquisition of EqHV by horses, making a derivation of HCV from EqHV unlikely. To unravel the EqHV evolutionary history within equid sister species, we analyzed 829 donkeys and 53 mules sampled in nine European, Asian, African, and American countries by molecular and serologic tools for EqHV infection. Antibodies were found in 278 animals (31.5%), and viral RNA was found in 3 animals (0.3%), all of which were simultaneously seropositive. A low RNA prevalence in spite of high seroprevalence suggests a predominance of acute infection, a possible difference from the mostly chronic hepacivirus infection pattern seen in horses and humans. Limitation of transmission due to short courses of infection may explain the existence of entirely seronegative groups of animals. Donkey and horse EqHV strains were paraphyletic and 97.5 to 98.2% identical in their translated polyprotein sequences, making virus/host cospeciation unlikely. Evolutionary reconstructions supported host switches of EqHV between horses and donkeys without the involvement of adaptive evolution. Global admixture of donkey and horse hepaciviruses was compatible with anthropogenic alterations of EqHV ecology. In summary, our findings do not support EqHV as the origin of the significantly more diversified HCV. Identification of a host system with predominantly acute hepacivirus infection may enable new insights into the chronic infection pattern associated with HCV. IMPORTANCE The evolutionary origins of the human hepatitis C virus (HCV) are unclear. The closest animal-associated relative of HCV occurs in horses (equine hepacivirus [EqHV]). The low EqHV genetic diversity implies a relatively recent acquisition of EqHV by horses

Characterization of the avian Trojan gene family reveals contrasting evolutionary constraints.

PubMed

Petrov, Petar; Syrjänen, Riikka; Smith, Jacqueline; Gutowska, Maria Weronika; Uchida, Tatsuya; Vainio, Olli; Burt, David W

2015-01-01

"Trojan" is a leukocyte-specific, cell surface protein originally identified in the chicken. Its molecular function has been hypothesized to be related to anti-apoptosis and the proliferation of immune cells. The Trojan gene has been localized onto the Z sex chromosome. The adjacent two genes also show significant homology to Trojan, suggesting the existence of a novel gene/protein family. Here, we characterize this Trojan family, identify homologues in other species and predict evolutionary constraints on these genes. The two Trojan-related proteins in chicken were predicted as a receptor-type tyrosine phosphatase and a transmembrane protein, bearing a cytoplasmic immuno-receptor tyrosine-based activation motif. We identified the Trojan gene family in ten other bird species and found related genes in three reptiles and a fish species. The phylogenetic analysis of the homologues revealed a gradual diversification among the family members. Evolutionary analyzes of the avian genes predicted that the extracellular regions of the proteins have been subjected to positive selection. Such selection was possibly a response to evolving interacting partners or to pathogen challenges. We also observed an almost complete lack of intracellular positively selected sites, suggesting a conserved signaling mechanism of the molecules. Therefore, the contrasting patterns of selection likely correlate with the interaction and signaling potential of the molecules.

Evolution of the Plant Reproduction Master Regulators LFY and the MADS Transcription Factors: The Role of Protein Structure in the Evolutionary Development of the Flower.

PubMed

Silva, Catarina S; Puranik, Sriharsha; Round, Adam; Brennich, Martha; Jourdain, Agnès; Parcy, François; Hugouvieux, Veronique; Zubieta, Chloe

2015-01-01

Understanding the evolutionary leap from non-flowering (gymnosperms) to flowering (angiosperms) plants and the origin and vast diversification of the floral form has been one of the focuses of plant evolutionary developmental biology. The evolving diversity and increasing complexity of organisms is often due to relatively small changes in genes that direct development. These "developmental control genes" and the transcription factors (TFs) they encode, are at the origin of most morphological changes. TFs such as LEAFY (LFY) and the MADS-domain TFs act as central regulators in key developmental processes of plant reproduction including the floral transition in angiosperms and the specification of the male and female organs in both gymnosperms and angiosperms. In addition to advances in genome wide profiling and forward and reverse genetic screening, structural techniques are becoming important tools in unraveling TF function by providing atomic and molecular level information that was lacking in purely genetic approaches. Here, we summarize previous structural work and present additional biophysical and biochemical studies of the key master regulators of plant reproduction - LEAFY and the MADS-domain TFs SEPALLATA3 and AGAMOUS. We discuss the impact of structural biology on our understanding of the complex evolutionary process leading to the development of the bisexual flower.

Evolution of the Plant Reproduction Master Regulators LFY and the MADS Transcription Factors: The Role of Protein Structure in the Evolutionary Development of the Flower

PubMed Central

Silva, Catarina S.; Puranik, Sriharsha; Round, Adam; Brennich, Martha; Jourdain, Agnès; Parcy, François; Hugouvieux, Veronique; Zubieta, Chloe

2016-01-01

Understanding the evolutionary leap from non-flowering (gymnosperms) to flowering (angiosperms) plants and the origin and vast diversification of the floral form has been one of the focuses of plant evolutionary developmental biology. The evolving diversity and increasing complexity of organisms is often due to relatively small changes in genes that direct development. These “developmental control genes” and the transcription factors (TFs) they encode, are at the origin of most morphological changes. TFs such as LEAFY (LFY) and the MADS-domain TFs act as central regulators in key developmental processes of plant reproduction including the floral transition in angiosperms and the specification of the male and female organs in both gymnosperms and angiosperms. In addition to advances in genome wide profiling and forward and reverse genetic screening, structural techniques are becoming important tools in unraveling TF function by providing atomic and molecular level information that was lacking in purely genetic approaches. Here, we summarize previous structural work and present additional biophysical and biochemical studies of the key master regulators of plant reproduction – LEAFY and the MADS-domain TFs SEPALLATA3 and AGAMOUS. We discuss the impact of structural biology on our understanding of the complex evolutionary process leading to the development of the bisexual flower. PMID:26779227

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.

Testing the island effect on phenotypic diversification: insights from the Hemidactylus geckos of the Socotra Archipelago

PubMed Central

Garcia-Porta, Joan; Šmíd, Jiří; Sol, Daniel; Fasola, Mauro; Carranza, Salvador

2016-01-01

Island colonization is often assumed to trigger extreme levels of phenotypic diversification. Yet, empirical evidence suggests that it does not always so. In this study we test this hypothesis using a completely sampled mainland-island system, the arid clade of Hemidactylus, a group of geckos mainly distributed across Africa, Arabia and the Socotra Archipelago. To such purpose, we generated a new molecular phylogeny of the group on which we mapped body size and head proportions. We then explored whether island and continental taxa shared the same morphospace and differed in their disparities and tempos of evolution. Insular species produced the most extreme sizes of the radiation, involving accelerated rates of evolution and higher disparities compared with most (but not all) of the continental groups. In contrast, head proportions exhibited constant evolutionary rates across the radiation and similar disparities in islands compared with the continent. These results, although generally consistent with the notion that islands promote high morphological disparity, reveal at the same time a complex scenario in which different traits may experience different evolutionary patterns in the same mainland-island system and continental groups do not always present low levels of morphological diversification compared to insular groups. PMID:27071837

Testing the island effect on phenotypic diversification: insights from the Hemidactylus geckos of the Socotra Archipelago

NASA Astrophysics Data System (ADS)

Garcia-Porta, Joan; Šmíd, Jiří; Sol, Daniel; Fasola, Mauro; Carranza, Salvador

2016-04-01

Island colonization is often assumed to trigger extreme levels of phenotypic diversification. Yet, empirical evidence suggests that it does not always so. In this study we test this hypothesis using a completely sampled mainland-island system, the arid clade of Hemidactylus, a group of geckos mainly distributed across Africa, Arabia and the Socotra Archipelago. To such purpose, we generated a new molecular phylogeny of the group on which we mapped body size and head proportions. We then explored whether island and continental taxa shared the same morphospace and differed in their disparities and tempos of evolution. Insular species produced the most extreme sizes of the radiation, involving accelerated rates of evolution and higher disparities compared with most (but not all) of the continental groups. In contrast, head proportions exhibited constant evolutionary rates across the radiation and similar disparities in islands compared with the continent. These results, although generally consistent with the notion that islands promote high morphological disparity, reveal at the same time a complex scenario in which different traits may experience different evolutionary patterns in the same mainland-island system and continental groups do not always present low levels of morphological diversification compared to insular groups.

The evolutionary origin of bilaterian smooth and striated myocytes

PubMed Central

Brunet, Thibaut; Fischer, Antje HL; Steinmetz, Patrick RH; Lauri, Antonella; Bertucci, Paola; Arendt, Detlev

2016-01-01

The dichotomy between smooth and striated myocytes is fundamental for bilaterian musculature, but its evolutionary origin is unsolved. In particular, interrelationships of visceral smooth muscles remain unclear. Absent in fly and nematode, they have not yet been characterized molecularly outside vertebrates. Here, we characterize expression profile, ultrastructure, contractility and innervation of the musculature in the marine annelid Platynereis dumerilii and identify smooth muscles around the midgut, hindgut and heart that resemble their vertebrate counterparts in molecular fingerprint, contraction speed and nervous control. Our data suggest that both visceral smooth and somatic striated myocytes were present in the protostome-deuterostome ancestor and that smooth myocytes later co-opted the striated contractile module repeatedly – for example, in vertebrate heart evolution. During these smooth-to-striated myocyte conversions, the core regulatory complex of transcription factors conveying myocyte identity remained unchanged, reflecting a general principle in cell type evolution. DOI: http://dx.doi.org/10.7554/eLife.19607.001 PMID:27906129

Loss of sexual recombination and segregation is associated with increased diversification in evening primroses.

PubMed

Johnson, Marc T J; Fitzjohn, Richard G; Smith, Stacey D; Rausher, Mark D; Otto, Sarah P

2011-11-01

The loss of sexual recombination and segregation in asexual organisms has been portrayed as an irreversible process that commits asexually reproducing lineages to reduced diversification. We test this hypothesis by estimating rates of speciation, extinction, and transition between sexuality and functional asexuality in the evening primroses. Specifically, we estimate these rates using the recently developed BiSSE (Binary State Speciation and Extinction) phylogenetic comparative method, which employs maximum likelihood and Bayesian techniques. We infer that net diversification rates (speciation minus extinction) in functionally asexual evening primrose lineages are roughly eight times faster than diversification rates in sexual lineages, largely due to higher speciation rates in asexual lineages. We further reject the hypothesis that a loss of recombination and segregation is irreversible because the transition rate from functional asexuality to sexuality is significantly greater than zero and in fact exceeded the reverse rate. These results provide the first empirical evidence in support of the alternative theoretical prediction that asexual populations should instead diversify more rapidly than sexual populations because they are free from the homogenizing effects of sexual recombination and segregation. Although asexual reproduction may often constrain adaptive evolution, our results show that the loss of recombination and segregation need not be an evolutionary dead end in terms of diversification of lineages. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

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.

The endosymbiotic origin, diversification and fate of plastids.

PubMed

Keeling, Patrick J

2010-03-12

Plastids and mitochondria each arose from a single endosymbiotic event and share many similarities in how they were reduced and integrated with their host. However, the subsequent evolution of the two organelles could hardly be more different: mitochondria are a stable fixture of eukaryotic cells that are neither lost nor shuffled between lineages, whereas plastid evolution has been a complex mix of movement, loss and replacement. Molecular data from the past decade have substantially untangled this complex history, and we now know that plastids are derived from a single endosymbiotic event in the ancestor of glaucophytes, red algae and green algae (including plants). The plastids of both red algae and green algae were subsequently transferred to other lineages by secondary endosymbiosis. Green algal plastids were taken up by euglenids and chlorarachniophytes, as well as one small group of dinoflagellates. Red algae appear to have been taken up only once, giving rise to a diverse group called chromalveolates. Additional layers of complexity come from plastid loss, which has happened at least once and probably many times, and replacement. Plastid loss is difficult to prove, and cryptic, non-photosynthetic plastids are being found in many non-photosynthetic lineages. In other cases, photosynthetic lineages are now understood to have evolved from ancestors with a plastid of different origin, so an ancestral plastid has been replaced with a new one. Such replacement has taken place in several dinoflagellates (by tertiary endosymbiosis with other chromalveolates or serial secondary endosymbiosis with a green alga), and apparently also in two rhizarian lineages: chlorarachniophytes and Paulinella (which appear to have evolved from chromalveolate ancestors). The many twists and turns of plastid evolution each represent major evolutionary transitions, and each offers a glimpse into how genomes evolve and how cells integrate through gene transfers and protein trafficking.

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)

Charles Darwin's Origin of Species, directional selection, and the evolutionary sciences today

NASA Astrophysics Data System (ADS)

Kutschera, Ulrich

2009-11-01

The book On the Origin of Species, published in November 1859, is an “abstract” without references, compiled by Charles Darwin from a much longer manuscript entitled “Natural Selection.” Here, I summarize the five theories that can be extracted from Darwin’s monograph, explain the true meaning of the phrase “struggle for life” (i.e., competition and cooperation), and outline Darwin’s original concept of natural selection in populations of animals and plants. Since neither Darwin nor Alfred R. Wallace distinguished between stabilizing and directional natural selection, the popular argument that “selection only eliminates but is not creative” is still alive today. However, I document that August Weismann ( Die Bedeutung der sexuellen Fortpflanzung für die Selektions-Theorie. Gustav Fischer-Verlag, Jena, 1886) and Ivan Schmalhausen ( Factors of evolution. The theory of stabilizing selection. The Blackiston Company, Philadelphia, 1949) provided precise definitions for directional (dynamic) selection in nature and illustrate this “Weismann-Schmalhausen principle” with respect to the evolutionary development of novel phenotypes. Then, the modern (synthetic) theory of biological evolution that is based on the work of Theodosius Dobzhansky ( Genetics and the origin of species. Columbia University Press, New York, 1937) and others, and the expanded version of this system of theories, are outlined. Finally, I document that symbiogenesis (i.e., primary endosymbiosis, a process that gave rise to the first eukaryotic cells), ongoing directional natural selection, and the dynamic Earth (plate tectonics, i.e., geological events that both created and destroyed terrestrial and aquatic habitats) were the key processes responsible for the documented macroevolutionary patterns in all five kingdoms of life. Since the evolutionary development of the earliest archaic bacteria more than 3,500 mya, the biosphere of our dynamic planet has been dominated by

Evolutionary patterns and processes in the radiation of phyllostomid bats

PubMed Central

2011-01-01

Background The phyllostomid bats present the most extensive ecological and phenotypic radiation known among mammal families. This group is an important model system for studies of cranial ecomorphology and functional optimisation because of the constraints imposed by the requirements of flight. A number of studies supporting phyllostomid adaptation have focused on qualitative descriptions or correlating functional variables and diet, but explicit tests of possible evolutionary mechanisms and scenarios for phenotypic diversification have not been performed. We used a combination of morphometric and comparative methods to test hypotheses regarding the evolutionary processes behind the diversification of phenotype (mandible shape and size) and diet during the phyllostomid radiation. Results The different phyllostomid lineages radiate in mandible shape space, with each feeding specialisation evolving towards different axes. Size and shape evolve quite independently, as the main directions of shape variation are associated with mandible elongation (nectarivores) or the relative size of tooth rows and mandibular processes (sanguivores and frugivores), which are not associated with size changes in the mandible. The early period of phyllostomid diversification is marked by a burst of shape, size, and diet disparity (before 20 Mya), larger than expected by neutral evolution models, settling later to a period of relative phenotypic and ecological stasis. The best fitting evolutionary model for both mandible shape and size divergence was an Ornstein-Uhlenbeck process with five adaptive peaks (insectivory, carnivory, sanguivory, nectarivory and frugivory). Conclusions The radiation of phyllostomid bats presented adaptive and non-adaptive components nested together through the time frame of the family's evolution. The first 10 My of the radiation were marked by strong phenotypic and ecological divergence among ancestors of modern lineages, whereas the remaining 20 My were

Evolutionary patterns and processes in the radiation of phyllostomid bats.

PubMed

Monteiro, Leandro R; Nogueira, Marcelo R

2011-05-23

The phyllostomid bats present the most extensive ecological and phenotypic radiation known among mammal families. This group is an important model system for studies of cranial ecomorphology and functional optimisation because of the constraints imposed by the requirements of flight. A number of studies supporting phyllostomid adaptation have focused on qualitative descriptions or correlating functional variables and diet, but explicit tests of possible evolutionary mechanisms and scenarios for phenotypic diversification have not been performed. We used a combination of morphometric and comparative methods to test hypotheses regarding the evolutionary processes behind the diversification of phenotype (mandible shape and size) and diet during the phyllostomid radiation. The different phyllostomid lineages radiate in mandible shape space, with each feeding specialisation evolving towards different axes. Size and shape evolve quite independently, as the main directions of shape variation are associated with mandible elongation (nectarivores) or the relative size of tooth rows and mandibular processes (sanguivores and frugivores), which are not associated with size changes in the mandible. The early period of phyllostomid diversification is marked by a burst of shape, size, and diet disparity (before 20 Mya), larger than expected by neutral evolution models, settling later to a period of relative phenotypic and ecological stasis. The best fitting evolutionary model for both mandible shape and size divergence was an Ornstein-Uhlenbeck process with five adaptive peaks (insectivory, carnivory, sanguivory, nectarivory and frugivory). The radiation of phyllostomid bats presented adaptive and non-adaptive components nested together through the time frame of the family's evolution. The first 10 My of the radiation were marked by strong phenotypic and ecological divergence among ancestors of modern lineages, whereas the remaining 20 My were marked by stasis around a number of

Whole Genome and Tandem Duplicate Retention Facilitated Glucosinolate Pathway Diversification in the Mustard Family

PubMed Central

Hofberger, Johannes A.; Lyons, Eric; Edger, Patrick P.; Chris Pires, J.; Eric Schranz, M.

2013-01-01

Plants share a common history of successive whole-genome duplication (WGD) events retaining genomic patterns of duplicate gene copies (ohnologs) organized in conserved syntenic blocks. Duplication was often proposed to affect the origin of novel traits during evolution. However, genetic evidence linking WGD to pathway diversification is scarce. We show that WGD and tandem duplication (TD) accelerated genetic versatility of plant secondary metabolism, exemplified with the glucosinolate (GS) pathway in the mustard family. GS biosynthesis is a well-studied trait, employing at least 52 biosynthetic and regulatory genes in the model plant Arabidopsis. In a phylogenomics approach, we identified 67 GS loci in Aethionema arabicum of the tribe Aethionemae, sister group to all mustard family members. All but one of the Arabidopsis GS gene families evolved orthologs in Aethionema and all but one of the orthologous sequence pairs exhibit synteny. The 45% fraction of duplicates among all protein-coding genes in Arabidopsis was increased to 95% and 97% for Arabidopsis and Aethionema GS pathway inventory, respectively. Compared with the 22% average for all protein-coding genes in Arabidopsis, 52% and 56% of Aethionema and Arabidopsis GS loci align to ohnolog copies dating back to the last common WGD event. Although 15% of all Arabidopsis genes are organized in tandem arrays, 45% and 48% of GS loci in Arabidopsis and Aethionema descend from TD, respectively. We describe a sequential combination of TD and WGD events driving gene family extension, thereby expanding the evolutionary playground for functional diversification and thus potential novelty and success. PMID:24171911

Phylogeography and biogeography of the lower Central American Neotropics: diversification between two continents and between two seas.

PubMed

Bagley, Justin C; Johnson, Jerald B

2014-11-01

Lower Central America (LCA) provides a geologically complex and dynamic, richly biodiverse model for studying the recent assembly and diversification of a Neotropical biota. Here, we review the growing literature of LCA phylogeography studies and their contribution to understanding the origins, assembly, and diversification of the LCA biota against the backdrop of regional geologic and climatic history, and previous biogeographical inquiry. Studies to date reveal that phylogeographical signal within taxa of differing distributions reflects a diversity of patterns and processes rivalling the complexities of LCA landscapes themselves. Even so, phylogeography is providing novel insights into regional diversification (e.g. cryptic lineage divergences), and general evolutionary patterns are emerging. Congruent multi-taxon phylogeographic breaks are found across the Nicaraguan depression, Chorotega volcanic front, western and central Panama, and the Darién isthmus, indicating that a potentially shared history of responses to regional-scale (e.g. geological) processes has shaped the genetic diversity of LCA communities. By contrast, other species show unique demographic histories in response to overriding historical events, including no phylogeographic structure at all. These low-structure or incongruent patterns provide some evidence for a role of local, ecological factors (e.g. long-distance dispersal and gene flow in plants and bats) in shaping LCA communities. Temporally, comparative phylogeographical structuring reflects Pliocene-Pleistocene dispersal and vicariance events consistent with the timeline of emergence of the LCA isthmus and its major physiographic features, e.g. cordilleras. We emphasise the need to improve biogeographic inferences in LCA through in-depth comparative phylogeography projects capitalising on the latest statistical phylogeographical methods. While meeting the challenges of reconstructing the biogeographical history of this complex region

Evolutionary Diversification of Insect Innexins

PubMed Central

Hughes, Austin L.

2014-01-01

Abstract Phylogenetic analysis of insect innexins supported the hypothesis that six major clades of insect innexins arose by gene duplication prior to the origin of the endopterygote insects. Within one of the six clades (the Zpg Clade), two independent gene duplication events were inferred to have occurred in the lineage of Drosophila , after the most recent common ancestor of the dipteran families Culicidae and Drosophilidae. The relationships among this clades were poorly resolved, except for a sister relationship between ShakB and Ogre. Gene expression data from FlyAtlas supported the hypothesis that the latter gene duplication events gave rise to functional differentiation, with Zpg showing a high level of expression in ovary, and Inx5 and Inx6 showing a high level of expression in testis. Because unduplicated members of this clade in Bombyx mori and Anopheles gambiae showed high levels of expression in both ovary and tests, the expression patterns of the Drosophila members of this clade provide evidence of subdivision of an ancestral gene function after gene duplication. PMID:25502029

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.

Glaciations, gradients, and geography: multiple drivers of diversification of bush frogs in the Western Ghats Escarpment

PubMed Central

Menezes, Riya C.; Jayarajan, Aditi; Shanker, Kartik

2016-01-01

The historical processes underlying high diversity in tropical biodiversity hotspots like the Western Ghats of Peninsular India remain poorly understood. We sampled bush frogs on 13 massifs across the Western Ghats Escarpment and examined the relative influence of Quaternary glaciations, ecological gradients and geological processes on the spatial patterns of lineage and clade diversification. The results reveal a large in situ radiation (more than 60 lineages), exhibiting geographical structure and clade-level endemism, with two deeply divergent sister clades, North and South, highlighting the biogeographic significance of an ancient valley, the Palghat Gap. A majority of the bush frog sister lineages were isolated on adjacent massifs, and signatures of range stasis provide support for the dominance of geological processes in allopatric speciation. In situ diversification events within the montane zones (more than 1800 m) of the two highest massifs suggest a role for climate-mediated forest-grassland persistence. Independent transitions along elevational gradients among sub-clades during the Miocene point to diversification along the elevational gradient. The study highlights the evolutionary significance of massifs in the Western Ghats with the high elevations acting as centres of lineage diversification and the low- and mid-elevations of the southern regions, with deeply divergent lineages, serving as museums. PMID:27534957

Glaciations, gradients, and geography: multiple drivers of diversification of bush frogs in the Western Ghats Escarpment.

PubMed

Vijayakumar, S P; Menezes, Riya C; Jayarajan, Aditi; Shanker, Kartik

2016-08-17

The historical processes underlying high diversity in tropical biodiversity hotspots like the Western Ghats of Peninsular India remain poorly understood. We sampled bush frogs on 13 massifs across the Western Ghats Escarpment and examined the relative influence of Quaternary glaciations, ecological gradients and geological processes on the spatial patterns of lineage and clade diversification. The results reveal a large in situ radiation (more than 60 lineages), exhibiting geographical structure and clade-level endemism, with two deeply divergent sister clades, North and South, highlighting the biogeographic significance of an ancient valley, the Palghat Gap. A majority of the bush frog sister lineages were isolated on adjacent massifs, and signatures of range stasis provide support for the dominance of geological processes in allopatric speciation. In situ diversification events within the montane zones (more than 1800 m) of the two highest massifs suggest a role for climate-mediated forest-grassland persistence. Independent transitions along elevational gradients among sub-clades during the Miocene point to diversification along the elevational gradient. The study highlights the evolutionary significance of massifs in the Western Ghats with the high elevations acting as centres of lineage diversification and the low- and mid-elevations of the southern regions, with deeply divergent lineages, serving as museums. © 2016 The Author(s).

Phylogenetic analyses suggest that diversification and body size evolution are independent in insects.

PubMed

Rainford, James L; Hofreiter, Michael; Mayhew, Peter J

2016-01-08

Skewed body size distributions and the high relative richness of small-bodied taxa are a fundamental property of a wide range of animal clades. The evolutionary processes responsible for generating these distributions are well described in vertebrate model systems but have yet to be explored in detail for other major terrestrial clades. In this study, we explore the macro-evolutionary patterns of body size variation across families of Hexapoda (insects and their close relatives), using recent advances in phylogenetic understanding, with an aim to investigate the link between size and diversity within this ancient and highly diverse lineage. The maximum, minimum and mean-log body lengths of hexapod families are all approximately log-normally distributed, consistent with previous studies at lower taxonomic levels, and contrasting with skewed distributions typical of vertebrate groups. After taking phylogeny and within-tip variation into account, we find no evidence for a negative relationship between diversification rate and body size, suggesting decoupling of the forces controlling these two traits. Likelihood-based modeling of the log-mean body size identifies distinct processes operating within Holometabola and Diptera compared with other hexapod groups, consistent with accelerating rates of size evolution within these clades, while as a whole, hexapod body size evolution is found to be dominated by neutral processes including significant phylogenetic conservatism. Based on our findings we suggest that the use of models derived from well-studied but atypical clades, such as vertebrates may lead to misleading conclusions when applied to other major terrestrial lineages. Our results indicate that within hexapods, and within the limits of current systematic and phylogenetic knowledge, insect diversification is generally unfettered by size-biased macro-evolutionary processes, and that these processes over large timescales tend to converge on apparently neutral

Body size as a primary determinant of ecomorphological diversification and the evolution of mimicry in the lampropeltinine snakes (Serpentes: Colubridae).

PubMed

Pyron, R Alexander; Burbrink, F T

2009-10-01

Evolutionary correlations between functionally related character suites are expected as a consequence of coadaptation due to physiological relationships between traits. However, significant correlations may also exist between putatively unrelated characters due to shared relationships between those traits and underlying variables, such as body size. Although such patterns are often dismissed as simple body size scaling, this presumption may overlook important evolutionary patterns of diversification. If body size is the primary determinant of potential diversity in multiple unrelated characters, the observed differentiation of species may be governed by variability in body size, and any biotic or abiotic constraints on the diversification thereof. Here, we demonstrate that traits related to both predatory specialization (gape and diet preference) and predatory avoidance (the development of Batesian mimicry) are phylogenetically correlated in the North American snake tribe Lampropeltini. This is apparently due to shared relationships between those traits and adult body size, suggesting that size is the primary determinant of ecomorphological differentiation in the lampropeltinines. Diversification in body size is apparently not linked to climatic or environmental factors, and may have been driven by interspecific interactions such as competition. Additionally, we find the presence of a 'key zone' for the development of both rattle- and coral snake mimicry; only small snakes feeding primarily on ectothermic prey develop mimetic colour patterns, in or near the range of venomous model species.

Asynchronous origins of ectomycorrhizal clades of Agaricales.

PubMed

Ryberg, Martin; Matheny, P Brandon

2012-05-22

The ectomycorrhizal (ECM) symbiosis is the most widespread biotrophic nutritional mode in mushroom-forming fungi. ECM fungi include, though are not limited to, about 5000 described species of Agaricales from numerous, independently evolved lineages. Two central hypotheses suggest different explanations for the origin of ECM fungal diversity: (i) dual origins, initially with the Pinaceae in the Jurassic and later with angiosperms during the Late Cretaceous, and (ii) a simultaneous and convergent radiation of ECM lineages in response to cooling climate during the Palaeogene and advancing temperate ECM plant communities. Neither of these hypotheses is supported here. While we demonstrate support for asynchronous origins of ECM Agaricales, the timing of such events appears to have occurred more recently than suggested by the first hypothesis, first during the Cretaceous and later during the Palaeogene. We are also unable to reject models of rate constancy, which suggests that the diversity of ECM Agaricales is not a consequence of convergent rapid radiations following evolutionary transitions from saprotrophic to ECM habits. ECM lineages of Agaricales differ not only in age, but also in rates of diversification and rate of substitution at nuclear ribosomal RNA loci. These results question the biological uniformity of the ECM guild.

Asynchronous origins of ectomycorrhizal clades of Agaricales

PubMed Central

Ryberg, Martin; Matheny, P. Brandon

2012-01-01

The ectomycorrhizal (ECM) symbiosis is the most widespread biotrophic nutritional mode in mushroom-forming fungi. ECM fungi include, though are not limited to, about 5000 described species of Agaricales from numerous, independently evolved lineages. Two central hypotheses suggest different explanations for the origin of ECM fungal diversity: (i) dual origins, initially with the Pinaceae in the Jurassic and later with angiosperms during the Late Cretaceous, and (ii) a simultaneous and convergent radiation of ECM lineages in response to cooling climate during the Palaeogene and advancing temperate ECM plant communities. Neither of these hypotheses is supported here. While we demonstrate support for asynchronous origins of ECM Agaricales, the timing of such events appears to have occurred more recently than suggested by the first hypothesis, first during the Cretaceous and later during the Palaeogene. We are also unable to reject models of rate constancy, which suggests that the diversity of ECM Agaricales is not a consequence of convergent rapid radiations following evolutionary transitions from saprotrophic to ECM habits. ECM lineages of Agaricales differ not only in age, but also in rates of diversification and rate of substitution at nuclear ribosomal RNA loci. These results question the biological uniformity of the ECM guild. PMID:22171078

Biogeographic barriers drive co-diversification within associated eukaryotes of the Sarracenia alata pitcher plant system.

PubMed

Satler, Jordan D; Zellmer, Amanda J; Carstens, Bryan C

2016-01-01

Understanding if the members of an ecological community have co-diversified is a central concern of evolutionary biology, as co-diversification suggests prolonged association and possible coevolution. By sampling associated species from an ecosystem, researchers can better understand how abiotic and biotic factors influence diversification in a region. In particular, studies of co-distributed species that interact ecologically can allow us to disentangle the effect of how historical processes have helped shape community level structure and interactions. Here we investigate the Sarracenia alata pitcher plant system, an ecological community where many species from disparate taxonomic groups live inside the fluid-filled pitcher leaves. Direct sequencing of the eukaryotes present in the pitcher plant fluid enables us to better understand how a host plant can shape and contribute to the genetic structure of its associated inquilines, and to ask whether genetic variation in the taxa are structured in a similar manner to the host plant. We used 454 amplicon-based metagenomics to demonstrate that the pattern of genetic diversity in many, but not all, of the eukaryotic community is similar to that of S. alata, providing evidence that associated eukaryotes share an evolutionary history with the host pitcher plant. Our work provides further evidence that a host plant can influence the evolution of its associated commensals.

Parallel evolutionary trajectories underlie the origin of giant suspension-feeding whales and bony fishes

PubMed Central

Friedman, Matt

2012-01-01

Giant suspension feeders such as mysticete whales, basking and whale sharks, and the extinct (indicated by ‘†’) †pachycormiform teleosts are conspicuous members of modern and fossil marine vertebrate faunas. Whether convergent anatomical features common to these clades arose along similar evolutionary pathways has remained unclear because of a lack of information surrounding the origins of all groups of large-bodied suspension feeders apart from baleen whales. New investigation reveals that the enigmatic ray-finned fish †Ohmdenia, from the Lower Jurassic (Toarcian, 183.0–175.6 Ma) Posidonia Shale Lagerstätte, represents the immediate sister group of edentulous †pachycormiforms, the longest lived radiation of large vertebrate suspension feeders. †Ohmdenia bisects the long morphological branch leading to suspension-feeding †pachycormiforms, providing information on the sequence of anatomical transformations preceding this major ecological shift that can be compared to changes associated with the origin of modern mysticetes. Similarities include initial modifications to jaw geometry associated with the reduction of dentition, followed by the loss of teeth. The evolution of largest body sizes within both radiations occurs only after the apparent onset of microphagy. Comparing the fit of contrasting evolutionary models to functionally relevant morphological measurements for whales and †pachycormiform fishes reveals strong support for a common adaptive peak shared by suspension-feeding members of both clades. PMID:21849314

Adaptive introgression from distant Caribbean islands contributed to the diversification of a microendemic adaptive radiation of trophic specialist pupfishes

PubMed Central

2017-01-01

Rapid diversification often involves complex histories of gene flow that leave variable and conflicting signatures of evolutionary relatedness across the genome. Identifying the extent and source of variation in these evolutionary relationships can provide insight into the evolutionary mechanisms involved in rapid radiations. Here we compare the discordant evolutionary relationships associated with species phenotypes across 42 whole genomes from a sympatric adaptive radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas and several outgroup pupfish species in order to understand the rarity of these trophic specialists within the larger radiation of Cyprinodon. 82% of the genome depicts close evolutionary relationships among the San Salvador Island species reflecting their geographic proximity, but the vast majority of variants fixed between specialist species lie in regions with discordant topologies. Top candidate adaptive introgression regions include signatures of selective sweeps and adaptive introgression of genetic variation from a single population in the northwestern Bahamas into each of the specialist species. Hard selective sweeps of genetic variation on San Salvador Island contributed 5 times more to speciation of trophic specialists than adaptive introgression of Caribbean genetic variation; however, four of the 11 introgressed regions came from a single distant island and were associated with the primary axis of oral jaw divergence within the radiation. For example, standing variation in a proto-oncogene (ski) known to have effects on jaw size introgressed into one San Salvador Island specialist from an island 300 km away approximately 10 kya. The complex emerging picture of the origins of adaptive radiation on San Salvador Island indicates that multiple sources of genetic variation contributed to the adaptive phenotypes of novel trophic specialists on the island. Our findings suggest that a suite of factors, including rare adaptive

Evolution of Modern Birds Revealed by Mitogenomics: Timing the Radiation and Origin of Major Orders

PubMed Central

Pacheco, M. Andreína; Battistuzzi, Fabia U.; Lentino, Miguel; Aguilar, Roberto F.; Kumar, Sudhir; Escalante, Ananias A.

2011-01-01

Mitochondrial (mt) genes and genomes are among the major sources of data for evolutionary studies in birds. This places mitogenomic studies in birds at the core of intense debates in avian evolutionary biology. Indeed, complete mt genomes are actively been used to unveil the phylogenetic relationships among major orders, whereas single genes (e.g., cytochrome c oxidase I [COX1]) are considered standard for species identification and defining species boundaries (DNA barcoding). In this investigation, we study the time of origin and evolutionary relationships among Neoaves orders using complete mt genomes. First, we were able to solve polytomies previously observed at the deep nodes of the Neoaves phylogeny by analyzing 80 mt genomes, including 17 new sequences reported in this investigation. As an example, we found evidence indicating that columbiforms and charadriforms are sister groups. Overall, our analyses indicate that by improving the taxonomic sampling, complete mt genomes can solve the evolutionary relationships among major bird groups. Second, we used our phylogenetic hypotheses to estimate the time of origin of major avian orders as a way to test if their diversification took place prior to the Cretaceous/Tertiary (K/T) boundary. Such timetrees were estimated using several molecular dating approaches and conservative calibration points. Whereas we found time estimates slightly younger than those reported by others, most of the major orders originated prior to the K/T boundary. Finally, we used our timetrees to estimate the rate of evolution of each mt gene. We found great variation on the mutation rates among mt genes and within different bird groups. COX1 was the gene with less variation among Neoaves orders and the one with the least amount of rate heterogeneity across lineages. Such findings support the choice of COX 1 among mt genes as target for developing DNA barcoding approaches in birds. PMID:21242529

Evolutionary Diversification of Prey and Predator Species Facilitated by Asymmetric Interactions.

PubMed

Zu, Jian; Wang, Jinliang; Huang, Gang

We investigate the influence of asymmetric interactions on coevolutionary dynamics of a predator-prey system by using the theory of adaptive dynamics. We assume that the defense ability of prey and the attack ability of predators all can adaptively evolve, either caused by phenotypic plasticity or by behavioral choice, but there are certain costs in terms of their growth rate or death rate. The coevolutionary model is constructed from a deterministic approximation of random mutation-selection process. To sum up, if prey's trade-off curve is globally weakly concave, then five outcomes of coevolution are demonstrated, which depend on the intensity and shape of asymmetric predator-prey interactions and predator's trade-off shape. Firstly, we find that if there is a weakly decelerating cost and a weakly accelerating benefit for predator species, then evolutionary branching in the predator species may occur, but after branching further coevolution may lead to extinction of the predator species with a larger trait value. However, if there is a weakly accelerating cost and a weakly accelerating benefit for predator species, then evolutionary branching in the predator species is also possible and after branching the dimorphic predator can evolutionarily stably coexist with a monomorphic prey species. Secondly, if the asymmetric interactions become a little strong, then prey and predators will evolve to an evolutionarily stable equilibrium, at which they can stably coexist on a long-term timescale of evolution. Thirdly, if there is a weakly accelerating cost and a relatively strongly accelerating benefit for prey species, then evolutionary branching in the prey species is possible and the finally coevolutionary outcome contains a dimorphic prey and a monomorphic predator species. Fourthly, if the asymmetric interactions become more stronger, then predator-prey coevolution may lead to cycles in both traits and equilibrium population densities. The Red Queen dynamic is a

Are lowland rainforests really evolutionary museums? Phylogeography of the green hylia (Hylia prasina) in the Afrotropics.

PubMed

Marks, Ben D

2010-04-01

A recent trend in the literature highlights the special role that tropical montane regions and habitat transitions peripheral to large blocks of lowland rainforest play in the diversification process. The emerging view is one of lowland rainforests as evolutionary 'museums'; where biotic diversity is maintained over evolutionary time, and additional diversity is accrued from peripheral areas, but where there has been little recent diversification. This leads to the prediction of genetic diversity without geographic structure in widespread taxa. Here, I assess the notion of the lowland rainforest 'museum' with a phylogeographic study of the green hylia (Aves: Sylviidae: Hylia prasina) using 1132 bp of mtDNA sequence data. The distribution of genetic diversity within the mainland subspecies of Hylia reveals five highly divergent haplotype groups distributed in accordance with broad-scale areas of endemism in the Afrotropics. This pattern of genetic diversity within a currently described subspecies refutes the characterization of lowland forests as evolutionary museums. If the pattern of geographic variation in Hylia occurs broadly in widespread rainforest species, conservation policy makers may need to rethink their priorities for conservation in the Afrotropics. (c) 2009 Elsevier Inc. All rights reserved.

Reconciling extreme branch length differences: decoupling time and rate through the evolutionary history of filmy ferns.

PubMed

Schuettpelz, Eric; Pryer, Kathleen M

2006-06-01

The rate of molecular evolution is not constant across the Tree of Life. Characterizing rate discrepancies and evaluating the relative roles of time and rate along branches through the past are both critical to a full understanding of evolutionary history. In this study, we explore the interactions of time and rate in filmy ferns (Hymenophyllaceae), a lineage with extreme branch length differences between the two major clades. We test for the presence of significant rate discrepancies within and between these clades, and we separate time and rate across the filmy fern phylogeny to simultaneously yield an evolutionary time scale of filmy fern diversification and reconstructions of ancestral rates of molecular evolution. Our results indicate that the branch length disparity observed between the major lineages of filmy ferns is indeed due to a significant difference in molecular evolutionary rate. The estimation of divergence times reveals that the timing of crown group diversification was not concurrent for the two lineages, and the reconstruction of ancestral rates of molecular evolution points to a substantial rate deceleration in one of the clades. Further analysis suggests that this may be due to a genome-wide deceleration in the rate of nucleotide substitution.

Explosive radiation or uninformative genes? Origin and early diversification of tachinid flies (Diptera: Tachinidae).

PubMed

Winkler, Isaac S; Blaschke, Jeremy D; Davis, Daniel J; Stireman, John O; O'Hara, James E; Cerretti, Pierfilippo; Moulton, John K

2015-07-01

Molecular phylogenetic studies at all taxonomic levels often infer rapid radiation events based on short, poorly resolved internodes. While such rapid episodes of diversification are an important and widespread evolutionary phenomenon, much of this poor phylogenetic resolution may be attributed to the continuing widespread use of "traditional" markers (mitochondrial, ribosomal, and some nuclear protein-coding genes) that are often poorly suited to resolve difficult, higher-level phylogenetic problems. Here we reconstruct phylogenetic relationships among a representative set of taxa of the parasitoid fly family Tachinidae and related outgroups of the superfamily Oestroidea. The Tachinidae are one of the most species rich, yet evolutionarily recent families of Diptera, providing an ideal case study for examining the differential performance of loci in resolving phylogenetic relationships and the benefits of adding more loci to phylogenetic analyses. We assess the phylogenetic utility of nine genes including both traditional genes (e.g., CO1 mtDNA, 28S rDNA) and nuclear protein-coding genes newly developed for phylogenetic analysis. Our phylogenetic findings, based on a limited set of taxa, include: a close relationship between Tachinidae and the calliphorid subfamily Polleninae, monophyly of Tachinidae and the subfamilies Exoristinae and Dexiinae, subfamily groupings of Dexiinae+Phasiinae and Tachininae+Exoristinae, and robust phylogenetic placement of the somewhat enigmatic genera Strongygaster, Euthera, and Ceracia. In contrast to poor resolution and phylogenetic incongruence of "traditional genes," we find that a more selective set of highly informative genes is able to more precisely identify regions of the phylogeny that experienced rapid radiation of lineages, while more accurately depicting their phylogenetic context. Although much expanded taxon sampling is necessary to effectively assess the monophyly of and relationships among major tachinid lineages and

Evolutionary History of Assassin Bugs (Insecta: Hemiptera: Reduviidae): Insights from Divergence Dating and Ancestral State Reconstruction

PubMed Central

Hwang, Wei Song; Weirauch, Christiane

2012-01-01

Assassin bugs are one of the most successful clades of predatory animals based on their species numbers (∼6,800 spp.) and wide distribution in terrestrial ecosystems. Various novel prey capture strategies and remarkable prey specializations contribute to their appeal as a model to study evolutionary pathways involved in predation. Here, we reconstruct the most comprehensive reduviid phylogeny (178 taxa, 18 subfamilies) to date based on molecular data (5 markers). This phylogeny tests current hypotheses on reduviid relationships emphasizing the polyphyletic Reduviinae and the blood-feeding, disease-vectoring Triatominae, and allows us, for the first time in assassin bugs, to reconstruct ancestral states of prey associations and microhabitats. Using a fossil-calibrated molecular tree, we estimated divergence times for key events in the evolutionary history of Reduviidae. Our results indicate that the polyphyletic Reduviinae fall into 11–14 separate clades. Triatominae are paraphyletic with respect to the reduviine genus Opisthacidius in the maximum likelihood analyses; this result is in contrast to prior hypotheses that found Triatominae to be monophyletic or polyphyletic and may be due to the more comprehensive taxon and character sampling in this study. The evolution of blood-feeding may thus have occurred once or twice independently among predatory assassin bugs. All prey specialists evolved from generalist ancestors, with multiple evolutionary origins of termite and ant specializations. A bark-associated life style on tree trunks is ancestral for most of the lineages of Higher Reduviidae; living on foliage has evolved at least six times independently. Reduviidae originated in the Middle Jurassic (178 Ma), but significant lineage diversification only began in the Late Cretaceous (97 Ma). The integration of molecular phylogenetics with fossil and life history data as presented in this paper provides insights into the evolutionary history of reduviids and clears

Heritable symbiosis: The advantages and perils of an evolutionary rabbit hole

PubMed Central

Bennett, Gordon M.; Moran, Nancy A.

2015-01-01

Many eukaryotes have obligate associations with microorganisms that are transmitted directly between generations. A model for heritable symbiosis is the association of aphids, a clade of sap-feeding insects, and Buchnera aphidicola, a gammaproteobacterium that colonized an aphid ancestor 150 million years ago and persists in almost all 5,000 aphid species. Symbiont acquisition enables evolutionary and ecological expansion; aphids are one of many insect groups that would not exist without heritable symbiosis. Receiving less attention are potential negative ramifications of symbiotic alliances. In the short run, symbionts impose metabolic costs. Over evolutionary time, hosts evolve dependence beyond the original benefits of the symbiosis. Symbiotic partners enter into an evolutionary spiral that leads to irreversible codependence and associated risks. Host adaptations to symbiosis (e.g., immune-system modification) may impose vulnerabilities. Symbiont genomes also continuously accumulate deleterious mutations, limiting their beneficial contributions and environmental tolerance. Finally, the fitness interests of obligate heritable symbionts are distinct from those of their hosts, leading to selfish tendencies. Thus, genes underlying the host–symbiont interface are predicted to follow a coevolutionary arms race, as observed for genes governing host–pathogen interactions. On the macroevolutionary scale, the rapid evolution of interacting symbiont and host genes is predicted to accelerate host speciation rates by generating genetic incompatibilities. However, degeneration of symbiont genomes may ultimately limit the ecological range of host species, potentially increasing extinction risk. Recent results for the aphid–Buchnera symbiosis and related systems illustrate that, whereas heritable symbiosis can expand ecological range and spur diversification, it also presents potential perils. PMID:25713367

Heritable symbiosis: The advantages and perils of an evolutionary rabbit hole.

PubMed

Bennett, Gordon M; Moran, Nancy A

2015-08-18

Many eukaryotes have obligate associations with microorganisms that are transmitted directly between generations. A model for heritable symbiosis is the association of aphids, a clade of sap-feeding insects, and Buchnera aphidicola, a gammaproteobacterium that colonized an aphid ancestor 150 million years ago and persists in almost all 5,000 aphid species. Symbiont acquisition enables evolutionary and ecological expansion; aphids are one of many insect groups that would not exist without heritable symbiosis. Receiving less attention are potential negative ramifications of symbiotic alliances. In the short run, symbionts impose metabolic costs. Over evolutionary time, hosts evolve dependence beyond the original benefits of the symbiosis. Symbiotic partners enter into an evolutionary spiral that leads to irreversible codependence and associated risks. Host adaptations to symbiosis (e.g., immune-system modification) may impose vulnerabilities. Symbiont genomes also continuously accumulate deleterious mutations, limiting their beneficial contributions and environmental tolerance. Finally, the fitness interests of obligate heritable symbionts are distinct from those of their hosts, leading to selfish tendencies. Thus, genes underlying the host-symbiont interface are predicted to follow a coevolutionary arms race, as observed for genes governing host-pathogen interactions. On the macroevolutionary scale, the rapid evolution of interacting symbiont and host genes is predicted to accelerate host speciation rates by generating genetic incompatibilities. However, degeneration of symbiont genomes may ultimately limit the ecological range of host species, potentially increasing extinction risk. Recent results for the aphid-Buchnera symbiosis and related systems illustrate that, whereas heritable symbiosis can expand ecological range and spur diversification, it also presents potential perils.

Genomic insights into the evolutionary origin of Myxozoa within Cnidaria

PubMed Central

Chang, E. Sally; Neuhof, Moran; Rubinstein, Nimrod D.; Diamant, Arik; Philippe, Hervé; Huchon, Dorothée; Cartwright, Paulyn

2015-01-01

The Myxozoa comprise over 2,000 species of microscopic obligate parasites that use both invertebrate and vertebrate hosts as part of their life cycle. Although the evolutionary origin of myxozoans has been elusive, a close relationship with cnidarians, a group that includes corals, sea anemones, jellyfish, and hydroids, is supported by some phylogenetic studies and the observation that the distinctive myxozoan structure, the polar capsule, is remarkably similar to the stinging structures (nematocysts) in cnidarians. To gain insight into the extreme evolutionary transition from a free-living cnidarian to a microscopic endoparasite, we analyzed genomic and transcriptomic assemblies from two distantly related myxozoan species, Kudoa iwatai and Myxobolus cerebralis, and compared these to the transcriptome and genome of the less reduced cnidarian parasite, Polypodium hydriforme. A phylogenomic analysis, using for the first time to our knowledge, a taxonomic sampling that represents the breadth of myxozoan diversity, including four newly generated myxozoan assemblies, confirms that myxozoans are cnidarians and are a sister taxon to P. hydriforme. Estimations of genome size reveal that myxozoans have one of the smallest reported animal genomes. Gene enrichment analyses show depletion of expressed genes in categories related to development, cell differentiation, and cell–cell communication. In addition, a search for candidate genes indicates that myxozoans lack key elements of signaling pathways and transcriptional factors important for multicellular development. Our results suggest that the degeneration of the myxozoan body plan from a free-living cnidarian to a microscopic parasitic cnidarian was accompanied by extreme reduction in genome size and gene content. PMID:26627241

Genomic insights into the evolutionary origin of Myxozoa within Cnidaria.

PubMed

Chang, E Sally; Neuhof, Moran; Rubinstein, Nimrod D; Diamant, Arik; Philippe, Hervé; Huchon, Dorothée; Cartwright, Paulyn

2015-12-01

The Myxozoa comprise over 2,000 species of microscopic obligate parasites that use both invertebrate and vertebrate hosts as part of their life cycle. Although the evolutionary origin of myxozoans has been elusive, a close relationship with cnidarians, a group that includes corals, sea anemones, jellyfish, and hydroids, is supported by some phylogenetic studies and the observation that the distinctive myxozoan structure, the polar capsule, is remarkably similar to the stinging structures (nematocysts) in cnidarians. To gain insight into the extreme evolutionary transition from a free-living cnidarian to a microscopic endoparasite, we analyzed genomic and transcriptomic assemblies from two distantly related myxozoan species, Kudoa iwatai and Myxobolus cerebralis, and compared these to the transcriptome and genome of the less reduced cnidarian parasite, Polypodium hydriforme. A phylogenomic analysis, using for the first time to our knowledge, a taxonomic sampling that represents the breadth of myxozoan diversity, including four newly generated myxozoan assemblies, confirms that myxozoans are cnidarians and are a sister taxon to P. hydriforme. Estimations of genome size reveal that myxozoans have one of the smallest reported animal genomes. Gene enrichment analyses show depletion of expressed genes in categories related to development, cell differentiation, and cell-cell communication. In addition, a search for candidate genes indicates that myxozoans lack key elements of signaling pathways and transcriptional factors important for multicellular development. Our results suggest that the degeneration of the myxozoan body plan from a free-living cnidarian to a microscopic parasitic cnidarian was accompanied by extreme reduction in genome size and gene content.

Evolutionary Trade-Off between Secondary Sexual Traits and Ejaculates.

PubMed

Simmons, Leigh W; Lüpold, Stefan; Fitzpatrick, John L

2017-12-01

Recent theoretical models predict that the evolutionary diversification of the weapons and ornaments of pre-mating sexual selection should be influenced by trade-offs with male expenditure on ejaculates. However, the patterns of association between secondary sexual traits and ejaculate expenditure are frequently inconsistent in their support of this prediction. We show why consideration of additional life-history, ecological, and mating-system variables is crucial for the interpretation of associations between secondary sexual traits and ejaculate production. Incorporation of these 'missing variables' provides evidence that interactions between pre- and post-mating sexual selection can underlie broad patterns of diversification in male weapons and ornaments. We call for more experimental and genetic approaches to uncover trade-offs, as well as for studies that consider the costs of mate-searching. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

Montane and coastal species diversification in the economically important Mexican grasshopper genus Sphenarium (Orthoptera: Pyrgomorphidae).

PubMed

Pedraza-Lara, Carlos; Barrientos-Lozano, Ludivina; Rocha-Sánchez, Aurora Y; Zaldívar-Riverón, Alejandro

2015-03-01

The genus Sphenarium (Pyrgomorphidae) is a small group of grasshoppers endemic to México and Guatemala that are economically and culturally important both as a food source and as agricultural pests. However, its taxonomy has been largely neglected mainly due to its conserved interspecific external morphology and the considerable intraspecific variation in colour pattern of some taxa. Here we examined morphological as well as mitochondrial and nuclear DNA sequence data to assess the species boundaries and evolutionary history in Sphenarium. Our morphological identification and DNA sequence-based species delimitation, carried out with three different approaches (DNA barcoding, general mixed Yule-coalescent model, Bayesian species delimitation), all recovered a higher number of putative species of Sphenarium than previously recognised. We unambiguously delimit seven species, and between five and ten additional species depending on the data/method analysed. Phylogenetic relationships within the genus strongly support two main clades, one exclusively montane, the other coastal. Divergence time estimates suggest late Miocene to Pliocene ages for the origin and most of the early diversification events in the genus, which were probably influenced by the formation of the Trans-Mexican Volcanic Belt. A series of Pleistocene events could have led to the current species diversification in both montane and coastal regions. This study not only reveals an overlooked species richness for the most popular edible insect in Mexico, but also highlights the influence of the dynamic geological and climatic history of the region in shaping its current diversity. Copyright © 2015 Elsevier Inc. All rights reserved.

Evolutionary Diversification of New Caledonian Araucaria

PubMed Central

Kranitz, Mai Lan; Biffin, Edward; Clark, Alexandra; Hollingsworth, Michelle L.; Ruhsam, Markus; Gardner, Martin F.; Thomas, Philip; Mill, Robert R.; Ennos, Richard A.; Gaudeul, Myriam; Lowe, Andrew J.; Hollingsworth, Peter M.

2014-01-01

New Caledonia is a global biodiversity hotspot. Hypotheses for its biotic richness suggest either that the island is a ‘museum’ for an old Gondwana biota or alternatively it has developed following relatively recent long distance dispersal and in situ radiation. The conifer genus Araucaria (Araucariaceae) comprises 19 species globally with 13 endemic to this island. With a typically Gondwanan distribution, Araucaria is particularly well suited to testing alternative biogeographic hypotheses concerning the origins of New Caledonian biota. We derived phylogenetic estimates using 11 plastid and rDNA ITS2 sequence data for a complete sampling of Araucaria (including multiple accessions of each of the 13 New Caledonian Araucaria species). In addition, we developed a dataset comprising 4 plastid regions for a wider taxon sample to facilitate fossil based molecular dating. Following statistical analyses to identify a credible and internally consistent set of fossil constraints, divergence times estimated using a Bayesian relaxed clock approach were contrasted with geological scenarios to explore the biogeographic history of Araucaria. The phylogenetic data resolve relationships within Araucariaceae and among the main lineages in Araucaria, but provide limited resolution within the monophyletic New Caledonian species group. Divergence time estimates suggest a Late Cretaceous-Cenozoic radiation of extant Araucaria and a Neogene radiation of the New Caledonian lineage. A molecular timescale for the evolution of Araucariaceae supports a relatively recent radiation, and suggests that earlier (pre-Cenozoic) fossil types assigned to Araucaria may have affinities elsewhere in Araucariaceae. While additional data will be required to adequately resolve relationships among the New Caledonian species, their recent origin is consistent with overwater dispersal following Eocene emersion of New Caledonia but is too old to support a single dispersal from Australia to Norfolk Island

Evolutionary origins of mechanosensitive ion channels.

PubMed

Martinac, Boris; Kloda, Anna

2003-01-01

According to the recent revision, the universal phylogenetic tree is composed of three domains: Eukarya (eukaryotes), Bacteria (eubacteria) and Archaea (archaebacteria). Mechanosensitive (MS) ion channels have been documented in cells belonging to all three domains suggesting their very early appearance during evolution of life on Earth. The channels show great diversity in conductance, selectivity and voltage dependence, while sharing the property of being gated by mechanical stimuli exerted on cell membranes. In prokaryotes, MS channels were first documented in Bacteria followed by their discovery in Archaea. The finding of MS channels in archaeal cells helped to recognize and establish the evolutionary relationship between bacterial and archaeal MS channels and to show that this relationship extends to eukaryotic Fungi (Schizosaccharomyces pombe) and Plants (Arabidopsis thaliana). Similar to their bacterial and archaeal homologues, MS channels in eukaryotic cell-walled Fungi and Plants may serve in protecting the cellular plasma membrane from excessive dilation and rupture that may occur during osmotic stress. This review summarizes briefly some of the recent developments in the MS channel research field that may ultimately lead to elucidation of the biophysical and evolutionary principles underlying the mechanosensory transduction in living cells.

Complex longitudinal diversification across South China and Vietnam in Stejneger's pit viper, Viridovipera stejnegeri (Schmidt, 1925) (Reptilia: Serpentes: Viperidae).

PubMed

Guo, Peng; Liu, Qin; Zhu, Fei; Zhong, Guang H; Chen, Xin; Myers, Edward A; Che, Jing; Zhang, Liang; Ziegler, Thomas; Nguyen, Truong Q; Burbrink, Frank T

2016-06-01

Viridovipera stejnegeri is one of the most common pit vipers in Asia, with a wide distribution in southern China and Vietnam. We investigated historical demography and explored how the environment and climatic factors have shaped genetic diversity and the evolutionary history of this venomous snake. A total of 171 samples from 47 localities were sequenced and analysed for two mitochondrial gene fragments and three nuclear genes. Gene trees reveal the existence of two well-supported clades (Southwest China and Southeast China) with seven distinct and strongly supported, geographically structured subclades within V. stejnegeri. Estimation of divergence time and ancestral area suggests that V. stejnegeri originated at ~6.0 Ma in the late Miocene on the Yunnan-Guizhou Plateau. The estimated date of origin and divergence of the island populations of Taiwan and Hainan closely matches the geological origin of the both islands. The mtDNA gene tree reveals the presence of west-east diversification in V. stejnegeri populations. Complex orogenesis and heterogeneous habitats, as well as climate-mediated habitat differentiation including glacial cycles, all have influenced population structure and the distribution of this taxon. The validity of V. stejnegeri chenbihuii is questionable, and this subspecies most probably represents an invalid taxon. © 2016 John Wiley & Sons Ltd.

Interspecific geographic range size-body size relationship and the diversification dynamics of Neotropical furnariid birds.

PubMed

Inostroza-Michael, Oscar; Hernández, Cristián E; Rodríguez-Serrano, Enrique; Avaria-Llautureo, Jorge; Rivadeneira, Marcelo M

2018-05-01

Among the earliest macroecological patterns documented, is the range and body size relationship, characterized by a minimum geographic range size imposed by the species' body size. This boundary for the geographic range size increases linearly with body size and has been proposed to have implications in lineages evolution and conservation. Nevertheless, the macroevolutionary processes involved in the origin of this boundary and its consequences on lineage diversification have been poorly explored. We evaluate the macroevolutionary consequences of the difference (hereafter the distance) between the observed and the minimum range sizes required by the species' body size, to untangle its role on the diversification of a Neotropical species-rich bird clade using trait-dependent diversification models. We show that speciation rate is a positive hump-shaped function of the distance to the lower boundary. The species with highest and lowest distances to minimum range size had lower speciation rates, while species close to medium distances values had the highest speciation rates. Further, our results suggest that the distance to the minimum range size is a macroevolutionary constraint that affects the diversification process responsible for the origin of this macroecological pattern in a more complex way than previously envisioned. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Ceftazidime Is the Key Diversification and Selection Driver of VIM-Type Carbapenemases.

PubMed

Martínez-García, Laura; González-Alba, José M; Baquero, Fernando; Cantón, Rafael; Galán, Juan Carlos

2018-05-08

In recent decades, carbapenems have been considered the last line of antibiotic therapy for Gram-negative bacterial infections. Unfortunately, strains carrying a high diversity of β-lactamases able to hydrolyze carbapenems have emerged in the clinical setting. Among them, VIM β-lactamases have diversified in a bloom of variants. The evolutionary reconstructions performed in this work revealed that, at the end of the 1980s, two independent events involving diversification from VIM-2 and VIM-4 produced at least 25 VIM variants. Later, a third event involving diversification from VIM-1 occurred in the mid-1990s. In a second approach to understanding the emergence of VIM carbapenemases, 44 mutants derived from VIM-2 and VIM-4 were obtained by site-directed mutagenesis based on those positions predicted to be under positive selection. These variants were expressed in an isogenic context. The more-evolved variants yielded increased levels of hydrolytic efficiency toward ceftazidime to a higher degree than toward carbapenems. In fact, an antagonist effect was frequently observed. These results led us to develop an experimental-evolution step. When Escherichia coli strains carrying VIM-2 or VIM-4 were submitted to serial passages at increasing concentrations of carbapenems or ceftazidime, more-efficient new variants (such as VIM-11 and VIM-1, with N165S [bearing a change from N to S at position 165] and R228S mutations, respectively) were only obtained when ceftazidime was present. Therefore, the observed effect of ceftazidime in the diversification and selection of VIM variants might help to explain the recent bloom of carbapenemase diversity, and it also represents another example of the potential universal effect exerted by ceftazidime in the selection of more-efficient β-lactamase variants, as in TEM, CTX-M, or KPC enzymes. IMPORTANCE One of the objectives recently proposed by the World Health Organization (WHO) Assembly in the global plan on antimicrobial

Hostplant change and paleoclimatic events explain diversification shifts in skipper butterflies (Family: Hesperiidae).

PubMed

Sahoo, Ranjit Kumar; Warren, Andrew D; Collins, Steve C; Kodandaramaiah, Ullasa

2017-08-02

Skippers (Family: Hesperiidae) are a large group of butterflies with ca. 4000 species under 567 genera. The lack of a time-calibrated higher-level phylogeny of the group has precluded understanding of its evolutionary past. We here use a 10-gene dataset to reconstruct the most comprehensive time-calibrated phylogeny of the group, and explore factors that affected the diversification of these butterflies. Ancestral state reconstructions show that the early hesperiid lineages utilized dicots as larval hostplants. The ability to feed on monocots evolved once at the K-Pg boundary (ca. 65 million years ago (Mya)), and allowed monocot-feeders to diversify much faster on average than dicot-feeders. The increased diversification rate of the monocot-feeding clade is specifically attributed to rate shifts in two of its descendant lineages. The first rate shift, a four-fold increase compared to background rates, happened ca. 50 Mya, soon after the Paleocene-Eocene thermal maximum, in a lineage of the subfamily Hesperiinae that mostly fed on forest monocots. The second rate shift happened ca. 40 Mya in a grass-feeding lineage of Hesperiinae when open-habitat grasslands appeared in the Neotropics owing to gradual cooling of the atmospheric temperature. The evolution of monocot feeding strongly influenced diversification of skippers. We hypothesize that although monocot feeding was an intrinsic trait that allowed exploration of novel niches, the lack of extensive availability of monocots comprised an extrinsic limitation for niche exploration. The shifts in diversification rate coincided with paleoclimatic events during which grasses and forest monocots were diversified.