Tempo and Mode of the Evolution of Venom and Poison in Tetrapods.

PubMed

Harris, Richard J; Arbuckle, Kevin

2016-06-23

Toxic weaponry in the form of venom and poison has evolved in most groups of animals, including all four major lineages of tetrapods. Moreover, the evolution of such traits has been linked to several key aspects of the biology of toxic animals including life-history and diversification. Despite this, attempts to investigate the macroevolutionary patterns underlying such weaponry are lacking. In this study we analyse patterns of venom and poison evolution across reptiles, amphibians, mammals, and birds using a suite of phylogenetic comparative methods. We find that each major lineage has a characteristic pattern of trait evolution, but mammals and reptiles evolve under a surprisingly similar regime, whilst that of amphibians appears to be particularly distinct and highly contrasting compared to other groups. Our results also suggest that the mechanism of toxin acquisition may be an important distinction in such evolutionary patterns; the evolution of biosynthesis is far less dynamic than that of sequestration of toxins from the diet. Finally, contrary to the situation in amphibians, other tetrapod groups show an association between the evolution of toxic weaponry and higher diversification rates. Taken together, our study provides the first broad-scale analysis of macroevolutionary patterns of venom and poison throughout tetrapods.

Tempo and Mode of the Evolution of Venom and Poison in Tetrapods

PubMed Central

Harris, Richard J.; Arbuckle, Kevin

2016-01-01

Toxic weaponry in the form of venom and poison has evolved in most groups of animals, including all four major lineages of tetrapods. Moreover, the evolution of such traits has been linked to several key aspects of the biology of toxic animals including life-history and diversification. Despite this, attempts to investigate the macroevolutionary patterns underlying such weaponry are lacking. In this study we analyse patterns of venom and poison evolution across reptiles, amphibians, mammals, and birds using a suite of phylogenetic comparative methods. We find that each major lineage has a characteristic pattern of trait evolution, but mammals and reptiles evolve under a surprisingly similar regime, whilst that of amphibians appears to be particularly distinct and highly contrasting compared to other groups. Our results also suggest that the mechanism of toxin acquisition may be an important distinction in such evolutionary patterns; the evolution of biosynthesis is far less dynamic than that of sequestration of toxins from the diet. Finally, contrary to the situation in amphibians, other tetrapod groups show an association between the evolution of toxic weaponry and higher diversification rates. Taken together, our study provides the first broad-scale analysis of macroevolutionary patterns of venom and poison throughout tetrapods. PMID:27348001

A universal driver of macroevolutionary change in the size of marine phytoplankton over the Cenozoic

PubMed Central

Finkel, Z. V.; Sebbo, J.; Feist-Burkhardt, S.; Irwin, A. J.; Katz, M. E.; Schofield, O. M. E.; Young, J. R.; Falkowski, P. G.

2007-01-01

The size structure of phytoplankton assemblages strongly influences energy transfer through the food web and carbon cycling in the ocean. We determined the macroevolutionary trajectory in the median size of dinoflagellate cysts to compare with the macroevolutionary size change in other plankton groups. We found the median size of the dinoflagellate cysts generally decreases through the Cenozoic. Diatoms exhibit an extremely similar pattern in their median size over time, even though species diversity of the two groups has opposing trends, indicating that the macroevolutionary size change is an active response to selection pressure rather than a passive response to changes in diversity. The changes in the median size of dinoflagellate cysts are highly correlated with both deep ocean temperatures and the thermal gradient between the surface and deep waters, indicating the magnitude and frequency of nutrient availability may have acted as a selective factor in the macroevolution of cell size in the plankton. Our results suggest that climate, because it affects stratification in the ocean, is a universal abiotic driver that has been responsible for macroevolutionary changes in the size structure of marine planktonic communities over the past 65 million years of Earth's history. PMID:18077334

Probabilistic models of eukaryotic evolution: time for integration

PubMed Central

Lartillot, Nicolas

2015-01-01

In spite of substantial work and recent progress, a global and fully resolved picture of the macroevolutionary history of eukaryotes is still under construction. This concerns not only the phylogenetic relations among major groups, but also the general characteristics of the underlying macroevolutionary processes, including the patterns of gene family evolution associated with endosymbioses, as well as their impact on the sequence evolutionary process. All these questions raise formidable methodological challenges, calling for a more powerful statistical paradigm. In this direction, model-based probabilistic approaches have played an increasingly important role. In particular, improved models of sequence evolution accounting for heterogeneities across sites and across lineages have led to significant, although insufficient, improvement in phylogenetic accuracy. More recently, one main trend has been to move away from simple parametric models and stepwise approaches, towards integrative models explicitly considering the intricate interplay between multiple levels of macroevolutionary processes. Such integrative models are in their infancy, and their application to the phylogeny of eukaryotes still requires substantial improvement of the underlying models, as well as additional computational developments. PMID:26323768

Model for macroevolutionary dynamics.

PubMed

Maruvka, Yosef E; Shnerb, Nadav M; Kessler, David A; Ricklefs, Robert E

2013-07-02

The highly skewed distribution of species among genera, although challenging to macroevolutionists, provides an opportunity to understand the dynamics of diversification, including species formation, extinction, and morphological evolution. Early models were based on either the work by Yule [Yule GU (1925) Philos Trans R Soc Lond B Biol Sci 213:21-87], which neglects extinction, or a simple birth-death (speciation-extinction) process. Here, we extend the more recent development of a generic, neutral speciation-extinction (of species)-origination (of genera; SEO) model for macroevolutionary dynamics of taxon diversification. Simulations show that deviations from the homogeneity assumptions in the model can be detected in species-per-genus distributions. The SEO model fits observed species-per-genus distributions well for class-to-kingdom-sized taxonomic groups. The model's predictions for the appearance times (the time of the first existing species) of the taxonomic groups also approximately match estimates based on molecular inference and fossil records. Unlike estimates based on analyses of phylogenetic reconstruction, fitted extinction rates for large clades are close to speciation rates, consistent with high rates of species turnover and the relatively slow change in diversity observed in the fossil record. Finally, the SEO model generally supports the consistency of generic boundaries based on morphological differences between species and provides a comparator for rates of lineage splitting and morphological evolution.

Integration and macroevolutionary patterns in the pollination biology of conifers.

PubMed

Leslie, Andrew B; Beaulieu, Jeremy M; Crane, Peter R; Knopf, Patrick; Donoghue, Michael J

2015-06-01

Integration influences patterns of trait evolution, but the relationship between these patterns and the degree of trait integration is not well understood. To explore this further, we study a specialized pollination mechanism in conifers whose traits are linked through function but not development. This mechanism depends on interactions among three characters: pollen that is buoyant, ovules that face downward at pollination, and the production of a liquid droplet that buoyant grains float through to enter the ovule. We use a well-sampled phylogeny of conifers to test correlated evolution among these characters and specific sequences of character change. Using likelihood models of character evolution, we find that pollen morphology and ovule characters evolve in a concerted manner, where the flotation mechanism breaks down irreversibly following changes in orientation or drop production. The breakdown of this functional constraint, which may be facilitated by the lack of developmental integration among the constituent traits, is associated with increased trait variation and more diverse pollination strategies. Although this functional "release" increases diversity in some ways, the irreversible way in which the flotation mechanism is lost may eventually result in its complete disappearance from seed plant reproductive biology. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Testing for coevolutionary diversification: linking pattern with process.

PubMed

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

2014-02-01

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

Macroevolutionary patterns of glucosinolate defense and tests of defense-escalation and resource availability hypotheses.

PubMed

Cacho, N Ivalú; Kliebenstein, Daniel J; Strauss, Sharon Y

2015-11-01

We explored macroevolutionary patterns of plant chemical defense in Streptanthus (Brassicaceae), tested for evolutionary escalation of defense, as predicted by Ehrlich and Raven's plant-herbivore coevolutionary arms-race hypothesis, and tested whether species inhabiting low-resource or harsh environments invest more in defense, as predicted by the resource availability hypothesis (RAH). We conducted phylogenetically explicit analyses using glucosinolate profiles, soil nutrient analyses, and microhabitat bareness estimates across 30 species of Streptanthus inhabiting varied environments and soils. We found weak to moderate phylogenetic signal in glucosinolate classes and no signal in total glucosinolate production; a trend toward evolutionary de-escalation in the numbers and diversity of glucosinolates, accompanied by an evolutionary increase in the proportion of aliphatic glucosinolates; some support for the RAH relative to soil macronutrients, but not relative to serpentine soil use; and that the number of glucosinolates increases with microhabitat bareness, which is associated with increased herbivory and drought. Weak phylogenetic signal in chemical defense has been observed in other plant systems. A more holistic approach incorporating other forms of defense might be necessary to confidently reject escalation of defense. That defense increases with microhabitat bareness supports the hypothesis that habitat bareness is an underappreciated selective force on plants in harsh environments. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Pacing of Paleozoic macroevolutionary rates by Milankovitch grand cycles.

PubMed

Crampton, James S; Meyers, Stephen R; Cooper, Roger A; Sadler, Peter M; Foote, Michael; Harte, David

2018-05-29

Periodic fluctuations in past biodiversity, speciation, and extinction have been proposed, with extremely long periods ranging from 26 to 62 million years, although forcing mechanisms remain speculative. In contrast, well-understood periodic Milankovitch climate forcing represents a viable driver for macroevolutionary fluctuations, although little evidence for such fluctuation exists except during the Late Cenozoic. The reality, magnitude, and drivers of periodic fluctuations in macroevolutionary rates are of interest given long-standing debate surrounding the relative roles of intrinsic biotic interactions vs. extrinsic environmental factors as drivers of biodiversity change. Here, we show that, over a time span of 60 million years, between 9 and 16% of the variance in biological turnover (i.e., speciation probability plus species extinction probability) in a major Early Paleozoic zooplankton group, the graptoloids, can be explained by long-period astronomical cycles (Milankovitch "grand cycles") associated with Earth's orbital eccentricity (2.6 million years) and obliquity (1.3 million years). These grand cycles modulate climate variability, alternating times of relative stability in the environment with times of maximum volatility. We infer that these cycles influenced graptolite speciation and extinction through climate-driven changes to oceanic circulation and structure. Our results confirm the existence of Milankovitch grand cycles in the Early Paleozoic Era and show that known processes related to the mechanics of the Solar System were shaping marine macroevolutionary rates comparatively early in the history of complex life. We present an application of hidden Markov models to macroevolutionary time series and protocols for the evaluation of statistical significance in spectral analysis.

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.

Trait-specific processes of convergence and conservatism shape ecomorphological evolution in ground-dwelling squirrels.

PubMed

McLean, Bryan S; Helgen, Kristofer M; Goodwin, H Thomas; Cook, Joseph A

2018-03-01

Our understanding of mechanisms operating over deep timescales to shape phenotypic diversity often hinges on linking variation in one or few trait(s) to specific evolutionary processes. When distinct processes are capable of similar phenotypic signatures, however, identifying these drivers is difficult. We explored ecomorphological evolution across a radiation of ground-dwelling squirrels whose history includes convergence and constraint, two processes that can yield similar signatures of standing phenotypic diversity. Using four ecologically relevant trait datasets (body size, cranial, mandibular, and molariform tooth shape), we compared and contrasted variation, covariation, and disparity patterns in a new phylogenetic framework. Strong correlations existed between body size and two skull traits (allometry) and among skull traits themselves (integration). Inferred evolutionary modes were also concordant across traits (Ornstein-Uhlenbeck with two adaptive regimes). However, despite these broad similarities, we found divergent dynamics on the macroevolutionary landscape, with phenotypic disparity being differentially shaped by convergence and conservatism. Such among-trait heterogeneity in process (but not always pattern) reiterates the mosaic nature of morphological evolution, and suggests ground squirrel evolution is poorly captured by single process descriptors. Our results also highlight how use of single traits can bias macroevolutionary inference, affirming the importance of broader trait-bases in understanding phenotypic evolutionary dynamics. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Macroevolutionary developmental biology: Embryos, fossils, and phylogenies.

PubMed

Organ, Chris L; Cooper, Lisa Noelle; Hieronymus, Tobin L

2015-10-01

The field of evolutionary developmental biology is broadly focused on identifying the genetic and developmental mechanisms underlying morphological diversity. Connecting the genotype with the phenotype means that evo-devo research often considers a wide range of evidence, from genetics and morphology to fossils. In this commentary, we provide an overview and framework for integrating fossil ontogenetic data with developmental data using phylogenetic comparative methods to test macroevolutionary hypotheses. We survey the vertebrate fossil record of preserved embryos and discuss how phylogenetic comparative methods can integrate data from developmental genetics and paleontology. Fossil embryos provide limited, yet critical, developmental data from deep time. They help constrain when developmental innovations first appeared during the history of life and also reveal the order in which related morphologies evolved. Phylogenetic comparative methods provide a powerful statistical approach that allows evo-devo researchers to infer the presence of nonpreserved developmental traits in fossil species and to detect discordant evolutionary patterns and processes across levels of biological organization. © 2015 Wiley Periodicals, Inc.

Macroevolutionary patterns of sexual size dimorphism in copepods

PubMed Central

Hirst, Andrew G.; Kiørboe, Thomas

2014-01-01

Major theories compete to explain the macroevolutionary trends observed in sexual size dimorphism (SSD) in animals. Quantitative genetic theory suggests that the sex under historically stronger directional selection will exhibit greater interspecific variance in size, with covariation between allometric slopes (male to female size) and the strength of SSD across clades. Rensch's rule (RR) also suggests a correlation, but one in which males are always the more size variant sex. Examining free-living pelagic and parasitic Copepoda, we test these competing predictions. Females are commonly the larger sex in copepod species. Comparing clades that vary by four orders of magnitude in their degree of dimorphism, we show that isometry is widespread. As such we find no support for either RR or for covariation between allometry and SSD. Our results suggest that selection on both sexes has been equally important. We next test the prediction that variation in the degree of SSD is related to the adult sex ratio. As males become relatively less abundant, it has been hypothesized that this will lead to a reduction in both inter-male competition and male size. However, the lack of such a correlation across diverse free-living pelagic families of copepods provides no support for this hypothesis. By comparison, in sea lice of the family Caligidae, there is some qualitative support of the hypothesis, males may suffer elevated mortality when they leave the host and rove for sedentary females, and their female-biased SSD is greater than in many free-living families. However, other parasitic copepods which do not appear to have obvious differences in sex-based mate searching risks also show similar or even more extreme SSD, therefore suggesting other factors can drive the observed extremes. PMID:25100692

Tempo and mode in the macroevolutionary reconstruction of Darwinism.

PubMed Central

Gould, S J

1994-01-01

Among the several central meanings of Darwinism, his version of Lyellian uniformitarianism--the extrapolationist commitment to viewing causes of small-scale, observable change in modern populations as the complete source, by smooth extension through geological time, of all magnitudes and sequences in evolution--has most contributed to the causal hegemony of microevolution and the assumption that paleontology can document the contingent history of life but cannot act as a domain of novel evolutionary theory. G. G. Simpson tried to combat this view of paleontology as theoretically inert in his classic work, Tempo and Mode in Evolution (1944), with a brilliant argument that the two subjects of his title fall into a unique paleontological domain and that modes (processes and causes) can be inferred from the quantitative study of tempos (pattern). Nonetheless, Simpson did not cash out his insight to paleontology's theoretical benefit because he followed the strict doctrine of the Modern Synthesis. He studied his domain of potential theory and concluded that no actual theory could be found--and that a full account of causes could therefore be located in the microevolutionary realm after all. I argue that Simpson was unduly pessimistic and that modernism's belief in reductionistic unification (the conventional view of Western intellectuals from the 1920s to the 1950s) needs to be supplanted by a postmodernist commitment to pluralism and multiple levels of causation. Macro- and microevolution should not be viewed as opposed, but as truly complementary. I describe the two major domains where a helpful macroevolutionary theory may be sought--unsmooth causal boundaries between levels (as illustrated by punctuated equilibrium and mass extinction) and hierarchical expansion of the theory of natural selection to levels both below (gene and cell-line) and above organisms (demes, species, and clades). Problems remain in operationally defining selection at non-organismic levels

Predator-induced macroevolutionary trends in Mesozoic crinoids

PubMed Central

Gorzelak, Przemysław; Salamon, Mariusz A.; Baumiller, Tomasz K.

2012-01-01

Sea urchins are a major component of recent marine communities where they exert a key role as grazers and benthic predators. However, their impact on past marine organisms, such as crinoids, is hard to infer in the fossil record. Analysis of bite mark frequencies on crinoid columnals and comprehensive genus-level diversity data provide unique insights into the importance of sea urchin predation through geologic time. These data show that over the Mesozoic, predation intensity on crinoids, as measured by bite mark frequencies on columnals, changed in step with diversity of sea urchins. Moreover, Mesozoic diversity changes in the predatory sea urchins show a positive correlation with diversity of motile crinoids and a negative correlation with diversity of sessile crinoids, consistent with a crinoid motility representing an effective escape strategy. We contend that the Mesozoic diversity history of crinoids likely represents a macroevolutionary response to changes in sea urchin predation pressure and that it may have set the stage for the recent pattern of crinoid diversity in which motile forms greatly predominate and sessile forms are restricted to deep-water refugia. PMID:22509040

Body mass evolution and diversification within horses (family Equidae).

PubMed

Shoemaker, Lauren; Clauset, Aaron

2014-02-01

Horses (family Equidae) are a classic example of adaptive radiation, exhibiting a nearly 60-fold increase in maximum body mass and a peak taxonomic diversity of nearly 100 species across four continents. Such patterns are commonly attributed to niche competition, in which increased taxonomic diversity drives increased size disparity. However, neutral processes, such as macroevolutionary 'diffusion', can produce similar increases in disparity without increased diversity. Using a comprehensive database of Equidae species size estimates and a common mathematical framework, we measure the contributions of diversity-driven and diffusion-driven mechanisms for increased disparity during the Equidae radiation. We find that more than 90% of changes in size disparity are attributable to diffusion alone. These results clarify the role of species competition in body size evolution, indicate that morphological disparity and species diversity may be only weakly coupled in general, and demonstrate that large species may evolve from neutral macroevolutionary diffusion processes alone. © 2013 John Wiley & Sons Ltd/CNRS.

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.

Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria).

PubMed

Bapst, D W; Wright, A M; Matzke, N J; Lloyd, G T

2016-07-01

Dated phylogenies of fossil taxa allow palaeobiologists to estimate the timing of major divergences and placement of extinct lineages, and to test macroevolutionary hypotheses. Recently developed Bayesian 'tip-dating' methods simultaneously infer and date the branching relationships among fossil taxa, and infer putative ancestral relationships. Using a previously published dataset for extinct theropod dinosaurs, we contrast the dated relationships inferred by several tip-dating approaches and evaluate potential downstream effects on phylogenetic comparative methods. We also compare tip-dating analyses to maximum-parsimony trees time-scaled via alternative a posteriori approaches including via the probabilistic cal3 method. Among tip-dating analyses, we find opposing but strongly supported relationships, despite similarity in inferred ancestors. Overall, tip-dating methods infer divergence dates often millions (or tens of millions) of years older than the earliest stratigraphic appearance of that clade. Model-comparison analyses of the pattern of body-size evolution found that the support for evolutionary mode can vary across and between tree samples from cal3 and tip-dating approaches. These differences suggest that model and software choice in dating analyses can have a substantial impact on the dated phylogenies obtained and broader evolutionary inferences. © 2016 The Author(s).

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.

Competition and constraint drove Cope's rule in the evolution of giant flying reptiles.

PubMed

Benson, Roger B J; Frigot, Rachel A; Goswami, Anjali; Andres, Brian; Butler, Richard J

2014-04-02

The pterosaurs, Mesozoic flying reptiles, attained wingspans of more than 10 m that greatly exceed the largest birds and challenge our understanding of size limits in flying animals. Pterosaurs have been used to illustrate Cope's rule, the influential generalization that evolutionary lineages trend to increasingly large body sizes. However, unambiguous examples of Cope's rule operating on extended timescales in large clades remain elusive, and the phylogenetic pattern and possible drivers of pterosaur gigantism are uncertain. Here we show 70 million years of highly constrained early evolution, followed by almost 80 million years of sustained, multi-lineage body size increases in pterosaurs. These results are supported by maximum-likelihood modelling of a comprehensive new pterosaur data set. The transition between these macroevolutionary regimes is coincident with the Early Cretaceous adaptive radiation of birds, supporting controversial hypotheses of bird-pterosaur competition, and suggesting that evolutionary competition can act as a macroevolutionary driver on extended geological timescales.

Competition and constraint drove Cope's rule in the evolution of giant flying reptiles

PubMed Central

Benson, Roger B. J.; Frigot, Rachel A.; Goswami, Anjali; Andres, Brian; Butler, Richard J.

2014-01-01

The pterosaurs, Mesozoic flying reptiles, attained wingspans of more than 10 m that greatly exceed the largest birds and challenge our understanding of size limits in flying animals. Pterosaurs have been used to illustrate Cope’s rule, the influential generalization that evolutionary lineages trend to increasingly large body sizes. However, unambiguous examples of Cope’s rule operating on extended timescales in large clades remain elusive, and the phylogenetic pattern and possible drivers of pterosaur gigantism are uncertain. Here we show 70 million years of highly constrained early evolution, followed by almost 80 million years of sustained, multi-lineage body size increases in pterosaurs. These results are supported by maximum-likelihood modelling of a comprehensive new pterosaur data set. The transition between these macroevolutionary regimes is coincident with the Early Cretaceous adaptive radiation of birds, supporting controversial hypotheses of bird–pterosaur competition, and suggesting that evolutionary competition can act as a macroevolutionary driver on extended geological timescales. PMID:24694584

Song evolution, speciation, and vocal learning in passerine birds.

PubMed

Mason, Nicholas A; Burns, Kevin J; Tobias, Joseph A; Claramunt, Santiago; Seddon, Nathalie; Derryberry, Elizabeth P

2017-03-01

Phenotypic divergence can promote reproductive isolation and speciation, suggesting a possible link between rates of phenotypic evolution and the tempo of speciation at multiple evolutionary scales. To date, most macroevolutionary studies of diversification have focused on morphological traits, whereas behavioral traits─including vocal signals─are rarely considered. Thus, although behavioral traits often mediate mate choice and gene flow, we have a limited understanding of how behavioral evolution contributes to diversification. Furthermore, the developmental mode by which behavioral traits are acquired may affect rates of behavioral evolution, although this hypothesis is seldom tested in a phylogenetic framework. Here, we examine evidence for rate shifts in vocal evolution and speciation across two major radiations of codistributed passerines: one oscine clade with learned songs (Thraupidae) and one suboscine clade with innate songs (Furnariidae). We find that evolutionary bursts in rates of speciation and song evolution are coincident in both thraupids and furnariids. Further, overall rates of vocal evolution are higher among taxa with learned rather than innate songs. Taken together, these findings suggest an association between macroevolutionary bursts in speciation and vocal evolution, and that the tempo of behavioral evolution can be influenced by variation in developmental modes among lineages. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Phylogeny suggests nondirectional and isometric evolution of sexual size dimorphism in argiopine spiders.

PubMed

Cheng, Ren-Chung; Kuntner, Matjaž

2014-10-01

Sexual dimorphism describes substantial differences between male and female phenotypes. In spiders, sexual dimorphism research almost exclusively focuses on size, and recent studies have recovered steady evolutionary size increases in females, and independent evolutionary size changes in males. Their discordance is due to negative allometric size patterns caused by different selection pressures on male and female sizes (converse Rensch's rule). Here, we investigated macroevolutionary patterns of sexual size dimorphism (SSD) in Argiopinae, a global lineage of orb-weaving spiders with varying degrees of SSD. We devised a Bayesian and maximum-likelihood molecular species-level phylogeny, and then used it to reconstruct sex-specific size evolution, to examine general hypotheses and different models of size evolution, to test for sexual size coevolution, and to examine allometric patterns of SSD. Our results, revealing ancestral moderate sizes and SSD, failed to reject the Brownian motion model, which suggests a nondirectional size evolution. Contrary to predictions, male and female sizes were phylogenetically correlated, and SSD evolution was isometric. We interpret these results to question the classical explanations of female-biased SSD via fecundity, gravity, and differential mortality. In argiopines, SSD evolution may be driven by these or additional selection mechanisms, but perhaps at different phylogenetic scales. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Identifying heterogeneity in rates of morphological evolution: discrete character change in the evolution of lungfish (Sarcopterygii; Dipnoi).

PubMed

Lloyd, Graeme T; Wang, Steve C; Brusatte, Stephen L

2012-02-01

Quantifying rates of morphological evolution is important in many macroevolutionary studies, and critical when assessing possible adaptive radiations and episodes of punctuated equilibrium in the fossil record. However, studies of morphological rates of change have lagged behind those on taxonomic diversification, and most authors have focused on continuous characters and quantifying patterns of morphological rates over time. Here, we provide a phylogenetic approach, using discrete characters and three statistical tests to determine points on a cladogram (branches or entire clades) that are characterized by significantly high or low rates of change. These methods include a randomization approach that identifies branches with significantly high rates and likelihood ratio tests that pinpoint either branches or clades that have significantly higher or lower rates than the pooled rate of the remainder of the tree. As a test case for these methods, we analyze a discrete character dataset of lungfish, which have long been regarded as "living fossils" due to an apparent slowdown in rates since the Devonian. We find that morphological rates are highly heterogeneous across the phylogeny and recover a general pattern of decreasing rates along the phylogenetic backbone toward living taxa, from the Devonian until the present. Compared with previous work, we are able to report a more nuanced picture of lungfish evolution using these new methods. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Convergence and Divergence in the Evolution of Cat Skulls: Temporal and Spatial Patterns of Morphological Diversity

PubMed Central

Sakamoto, Manabu; Ruta, Marcello

2012-01-01

Background Studies of biological shape evolution are greatly enhanced when framed in a phylogenetic perspective. Inclusion of fossils amplifies the scope of macroevolutionary research, offers a deep-time perspective on tempo and mode of radiations, and elucidates life-trait changes. We explore the evolution of skull shape in felids (cats) through morphometric analyses of linear variables, phylogenetic comparative methods, and a new cladistic study of saber-toothed cats. Methodology/Principal Findings A new phylogenetic analysis supports the monophyly of saber-toothed cats (Machairodontinae) exclusive of Felinae and some basal felids, but does not support the monophyly of various saber-toothed tribes and genera. We quantified skull shape variation in 34 extant and 18 extinct species using size-adjusted linear variables. These distinguish taxonomic group membership with high accuracy. Patterns of morphospace occupation are consistent with previous analyses, for example, in showing a size gradient along the primary axis of shape variation and a separation between large and small-medium cats. By combining the new phylogeny with a molecular tree of extant Felinae, we built a chronophylomorphospace (a phylogeny superimposed onto a two-dimensional morphospace through time). The evolutionary history of cats was characterized by two major episodes of morphological divergence, one marking the separation between saber-toothed and modern cats, the other marking the split between large and small-medium cats. Conclusions/Significance Ancestors of large cats in the ‘Panthera’ lineage tend to occupy, at a much later stage, morphospace regions previously occupied by saber-toothed cats. The latter radiated out into new morphospace regions peripheral to those of extant large cats. The separation between large and small-medium cats was marked by considerable morphologically divergent trajectories early in feline evolution. A chronophylomorphospace has wider applications in

Hydrozoan insights in animal development and evolution.

PubMed

Leclère, Lucas; Copley, Richard R; Momose, Tsuyoshi; Houliston, Evelyn

2016-08-01

The fresh water polyp Hydra provides textbook experimental demonstration of positional information gradients and regeneration processes. Developmental biologists are thus familiar with Hydra, but may not appreciate that it is a relatively simple member of the Hydrozoa, a group of mostly marine cnidarians with complex and diverse life cycles, exhibiting extensive phenotypic plasticity and regenerative capabilities. Hydrozoan species offer extensive opportunities to address many developmental mechanisms relevant across the animal kingdom. Here we review recent work from non-Hydra hydrozoans - hydromedusae, hydroids and siphonophores - shedding light on mechanisms of oogenesis, embryonic patterning, allorecognition, stem cell regulation and regeneration. We also highlight potential research directions in which hydrozoan diversity can illuminate the evolution of developmental processes at micro- and macro-evolutionary time scales. Copyright © 2016 Elsevier Ltd. All rights reserved.

Are the metabolomic responses to folivory of closely related plant species linked to macroevolutionary and plant-folivore coevolutionary processes?

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

Rivas-Ubach, Albert; Hódar, José A.; Sardans, Jordi

The debate whether the coevolution of plants and insects or macroevolutionary processes (phylogeny) is the main driver determining the arsenal of molecular defensive compounds of plants remains unresolved. Attacks by herbivorous insects affect not only the composition of defensive compounds in plants but the entire metabolome (the set of molecular metabolites), including defensive compounds. Metabolomes are the final products of genotypes and are directly affected by macroevolutionary processes, so closely related species should have similar metabolomic compositions and may respond in similar ways to attacks by folivores. We analyzed the elemental compositions and metabolomes of needles from Pinus pinaster, P.more » nigra and P. sylvestris to determine if these closely related Pinus species with different coevolutionary histories with the caterpillars of the processionary moth respond similarly to attacks by this lepidopteran. All pines had different metabolomes and metabolic responses to herbivorous attack. The metabolomic variation among the pine species and the responses to folivory reflected their macroevolutionary relationships, with P. pinaster having the most divergent metabolome. The concentrations of phenolic metabolites were generally not higher in the attacked trees, which had lower concentrations of terpenes, suggesting that herbivores avoid individuals with high concentrations of terpenes. Our results suggest that macroevolutionary history plays important roles in the metabolomic responses of these pine species to folivory, but plant-insect coevolution probably constrains those responses. Combinations of different evolutionary factors and trade-offs are likely responsible for the different responses of each species to folivory, which is not necessarily exclusively linked to plant-insect coevolution.« less

Prolegomenon to patterns in evolution.

PubMed

Kauffman, Stuart A

2014-09-01

Despite Darwin, we remain children of Newton and dream of a grand theory that is epistemologically complete and would allow prediction of the evolution of the biosphere. The main purpose of this article is to show that this dream is false, and bears on studying patterns of evolution. To do so, I must justify the use of the word "function" in biology, when physics has only happenings. The concept of "function" lifts biology irreducibly above physics, for as we shall see, we cannot prestate the ever new biological functions that arise and constitute the very phase space of evolution. Hence, we cannot mathematize the detailed becoming of the biosphere, nor write differential equations for functional variables we do not know ahead of time, nor integrate those equations, so no laws "entail" evolution. The dream of a grand theory fails. In place of entailing laws, I propose a post-entailing law explanatory framework in which Actuals arise in evolution that constitute new boundary conditions that are enabling constraints that create new, typically unprestatable, adjacent possible opportunities for further evolution, in which new Actuals arise, in a persistent becoming. Evolution flows into a typically unprestatable succession of adjacent possibles. Given the concept of function, the concept of functional closure of an organism making a living in its world becomes central. Implications for patterns in evolution include historical reconstruction, and statistical laws such as the distribution of extinction events, or species per genus, and the use of formal cause, not efficient cause, laws. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Wnt signaling underlies evolution and development of the butterfly wing pattern symmetry systems.

PubMed

Martin, Arnaud; Reed, Robert D

2014-11-15

Most butterfly wing patterns are proposed to be derived from a set of conserved pattern elements known as symmetry systems. Symmetry systems are so-named because they are often associated with parallel color stripes mirrored around linear organizing centers that run between the anterior and posterior wing margins. Even though the symmetry systems are the most prominent and diverse wing pattern elements, their study has been confounded by a lack of knowledge regarding the molecular basis of their development, as well as the difficulty of drawing pattern homologies across species with highly derived wing patterns. Here we present the first molecular characterization of symmetry system development by showing that WntA expression is consistently associated with the major basal, discal, central, and external symmetry system patterns of nymphalid butterflies. Pharmacological manipulations of signaling gradients using heparin and dextran sulfate showed that pattern organizing centers correspond precisely with WntA, wingless, Wnt6, and Wnt10 expression patterns, thus suggesting a role for Wnt signaling in color pattern induction. Importantly, this model is supported by recent genetic and population genomic work identifying WntA as the causative locus underlying wing pattern variation within several butterfly species. By comparing the expression of WntA between nymphalid butterflies representing a range of prototypical symmetry systems, slightly deviated symmetry systems, and highly derived wing patterns, we were able to infer symmetry system homologies in several challenging cases. Our work illustrates how highly divergent morphologies can be derived from modifications to a common ground plan across both micro- and macro-evolutionary time scales. Copyright © 2014 Elsevier Inc. All rights reserved.

Extreme Postnatal Scaling in Bat Feeding Performance: A View of Ecomorphology from Ontogenetic and Macroevolutionary Perspectives.

PubMed

Santana, Sharlene E; Miller, Kimberly E

2016-09-01

Ecomorphology studies focus on understanding how anatomical and behavioral diversity result in differences in performance, ecology, and fitness. In mammals, the determinate growth of the skeleton entails that bite performance should change throughout ontogeny until the feeding apparatus attains its adult size and morphology. Then, interspecific differences in adult phenotypes are expected to drive food resource partitioning and patterns of lineage diversification. However, Formal tests of these predictions are lacking for the majority of mammal groups, and thus our understanding of mammalian ecomorphology remains incomplete. By focusing on a fundamental measure of feeding performance, bite force, and capitalizing on the extraordinary morphological and dietary diversity of bats, we discuss how the intersection of ontogenetic and macroevolutionary changes in feeding performance may impact ecological diversity in these mammals. We integrate data on cranial morphology and bite force gathered through longitudinal studies of captive animals and comparative studies of free-ranging individuals. We demonstrate that ontogenetic trajectories and evolutionary changes in bite force are highly dependent on changes in body and head size, and that bats exhibit dramatic, allometric increases in bite force during ontogeny. Interspecific variation in bite force is highly dependent on differences in cranial morphology and function, highlighting selection for ecological specialization. While more research is needed to determine how ontogenetic changes in size and bite force specifically impact food resource use and fitness in bats, interspecific diversity in cranial morphology and bite performance seem to closely match functional differences in diet. Altogether, these results suggest direct ecomorphological relationships at ontogenetic and macroevolutionary scales in bats. © The Author 2016. Published by Oxford University Press on behalf of the Society for Integrative and Comparative

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.

Common functional targets of adaptive micro- and macro-evolutionary divergence in killifish.

PubMed

Whitehead, Andrew; Zhang, Shujun; Roach, Jennifer L; Galvez, Fernando

2013-07-01

Environmental salinity presents a key barrier to dispersal for most aquatic organisms, and adaptation to alternate osmotic environments likely enables species diversification. Little is known of the functional basis for derived tolerance to environmental salinity. We integrate comparative physiology and functional genomics to explore the mechanistic underpinnings of evolved variation in osmotic plasticity within and among two species of killifish; Fundulus majalis harbours the ancestral mainly salt-tolerant phenotype, whereas Fundulus heteroclitus harbours a derived physiology that retains extreme salt tolerance but with expanded osmotic plasticity towards the freshwater end of the osmotic continuum. Common-garden comparative hypo-osmotic challenge experiments show that F. heteroclitus is capable of remodelling gill epithelia more quickly and at more extreme osmotic challenge than F. majalis. We detect an unusual pattern of baseline transcriptome divergence, where neutral evolutionary processes appear to govern expression divergence within species, but patterns of divergence for these genes between species do not follow neutral expectations. During acclimation, genome expression profiling identifies mechanisms of acclimation-associated response that are conserved within the genus including regulation of paracellular permeability. In contrast, several responses vary among species including those putatively associated with cell volume regulation, and these same mechanisms are targets for adaptive physiological divergence along osmotic gradients within F. heteroclitus. As such, the genomic and physiological mechanisms that are associated with adaptive fine-tuning within species also contribute to macro-evolutionary divergence as species diversify across osmotic niches. © 2013 John Wiley & Sons Ltd.

Patterns and Processes of Vertebrate Evolution

NASA Astrophysics Data System (ADS)

Carroll, Robert Lynn

1997-04-01

This new text provides an integrated view of the forces that influence the patterns and rates of vertebrate evolution from the level of living populations and species to those that resulted in the origin of the major vertebrate groups. The evolutionary roles of behavior, development, continental drift, and mass extinctions are compared with the importance of variation and natural selection that were emphasized by Darwin. It is extensively illustrated, showing major transitions between fish and amphibians, dinosaurs and birds, and land mammals to whales. No book since Simpson's Major Features of Evolution has attempted such a broad study of the patterns and forces of evolutionary change. Undergraduate students taking a general or advanced course on evolution, and graduate students and professionals in evolutionary biology and paleontology will find the book of great interest.

Correlated evolution of sex and reproductive mode in corals (Anthozoa: Scleractinia).

PubMed

Kerr, Alexander M; Baird, Andrew H; Hughes, Terry P

2011-01-07

Sexuality and reproductive mode are two fundamental life-history traits that exhibit largely unexplained macroevolutionary patterns among the major groups of multicellular organisms. For example, the cnidarian class Anthozoa (corals and anemones) is mainly comprised of gonochoric (separate sex) brooders or spawners, while one order, Scleractinia (skeleton-forming corals), appears to be mostly hermaphroditic spawners. Here, using the most complete phylogeny of scleractinians, we reconstruct how evolutionary transitions between sexual systems (gonochorism versus hermaphrodism) and reproductive modes (brooding versus spawning) have generated large-scale taxonomic patterns in these characters. Hermaphrodites have independently evolved in three large, distantly related lineages consisting of mostly reef-building species. Reproductive mode in corals has evolved at twice the rate of sexuality, while the evolution of sexuality has been heavily biased: gonochorism is over 100 times more likely to be lost than gained, and can only be acquired by brooders. This circuitous evolutionary pathway accounts for the prevalence of hermaphroditic spawners among reef-forming scleractinians, despite their ancient gonochoric heritage.

Correlated evolution of sex and reproductive mode in corals (Anthozoa: Scleractinia)

PubMed Central

Kerr, Alexander M.; Baird, Andrew H.; Hughes, Terry P.

2011-01-01

Sexuality and reproductive mode are two fundamental life-history traits that exhibit largely unexplained macroevolutionary patterns among the major groups of multicellular organisms. For example, the cnidarian class Anthozoa (corals and anemones) is mainly comprised of gonochoric (separate sex) brooders or spawners, while one order, Scleractinia (skeleton-forming corals), appears to be mostly hermaphroditic spawners. Here, using the most complete phylogeny of scleractinians, we reconstruct how evolutionary transitions between sexual systems (gonochorism versus hermaphrodism) and reproductive modes (brooding versus spawning) have generated large-scale taxonomic patterns in these characters. Hermaphrodites have independently evolved in three large, distantly related lineages consisting of mostly reef-building species. Reproductive mode in corals has evolved at twice the rate of sexuality, while the evolution of sexuality has been heavily biased: gonochorism is over 100 times more likely to be lost than gained, and can only be acquired by brooders. This circuitous evolutionary pathway accounts for the prevalence of hermaphroditic spawners among reef-forming scleractinians, despite their ancient gonochoric heritage. PMID:20659935

Ecological interactions on macroevolutionary time scales: clams and brachiopods are more than ships that pass in the night.

PubMed

Liow, Lee Hsiang; Reitan, Trond; Harnik, Paul G

2015-10-01

Competition among organisms has ecological and evolutionary consequences. However, whether the consequences of competition are manifested and measureable on macroevolutionary time scales is equivocal. Marine bivalves and brachiopods have overlapping niches such that competition for food and space may occur. Moreover, there is a long-standing debate over whether bivalves outcompeted brachiopods evolutionarily, because brachiopod diversity declined through time while bivalve diversity increased. To answer this question, we estimate the origination and extinction dynamics of fossil marine bivalve and brachiopod genera from the Ordovician through to the Recent while simultaneously accounting for incomplete sampling. Then, using stochastic differential equations, we assess statistical relationships among diversification and sampling dynamics of brachiopods and bivalves and five paleoenvironmental proxies. None of these potential environmental drivers had any detectable influence on brachiopod or bivalve diversification. In contrast, elevated bivalve extinction rates causally increased brachiopod origination rates, suggesting that bivalves have suppressed brachiopod evolution. © 2015 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.

Quantifying patterns of research interest evolution

NASA Astrophysics Data System (ADS)

Jia, Tao; Wang, Dashun; Szymanski, Boleslaw

Changing and shifting research interest is an integral part of a scientific career. Despite extensive investigations of various factors that influence a scientist's choice of research topics, quantitative assessments of mechanisms that give rise to macroscopic patterns characterizing research interest evolution of individual scientists remain limited. Here we perform a large-scale analysis of extensive publication records, finding that research interest change follows a reproducible pattern characterized by an exponential distribution. We identify three fundamental features responsible for the observed exponential distribution, which arise from a subtle interplay between exploitation and exploration in research interest evolution. We develop a random walk based model, which adequately reproduces our empirical observations. Our study presents one of the first quantitative analyses of macroscopic patterns governing research interest change, documenting a high degree of regularity underlying scientific research and individual careers.

PSEMA: An Algorithm for Pattern Stimulated Evolution of Music

NASA Astrophysics Data System (ADS)

Mavrogianni, A. N.; Vlachos, D. S.; Harvalias, G.

2008-11-01

An algorithm for pattern stimulating evolution of music is presented in this work (PSEMA). The system combines a pattern with a genetic algorithm for automatic music composition in order to create a musical phrase uniquely characterizing the pattern. As an example a musical portrait is presented. The initialization of the musical phrases is done with a Markov Chain process. The evolution is dominated by an arbitrary correspondence between the pattern (feature extraction of the pattern may be used in this step) and the esthetic result of the musical phrase.

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

PubMed

Papadopoulou, Anna; Knowles, L Lacey

2017-12-01

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

Do arms races punctuate evolutionary stasis? Unified insights from phylogeny, phylogeography and microevolutionary processes.

PubMed

Toju, Hirokazu; Sota, Teiji

2009-09-01

One of the major controversies in evolutionary biology concerns the processes underlying macroevolutionary patterns in which prolonged stasis is disrupted by rapid, short-term evolution that leads species to new adaptive zones. Recent advances in the understanding of contemporary evolution have suggested that such rapid evolution can occur in the wild as a result of environmental changes. Here, we examined a novel hypothesis that evolutionary stasis is punctuated by co-evolutionary arms races, which continuously alter adaptive peaks and landscapes. Based on the phylogeny of long-mouthed weevils in the genus Curculio, likelihood ratio tests showed that the macroevolutionary pattern of the weevils coincides with the punctuational evolution model. A coalescent analysis of a species, Curculio camelliae, the mouthpart of which has diverged considerably among populations because of an arms race with its host plant, further suggested that major evolutionary shifts had occurred within 7000 generations. Through a microevolutionary analysis of the species, we also found that natural selection acting through co-evolutionary interactions is potentially strong enough to drive rapid evolutionary shifts between adaptive zones. Overall, we posit that co-evolution is an important factor driving the history of organismal evolution.

Transcriptomic and macroevolutionary evidence for phenotypic uncoupling between frog life history phases

PubMed Central

Wollenberg Valero, Katharina C.; Garcia-Porta, Joan; Rodríguez, Ariel; Arias, Mónica; Shah, Abhijeet; Randrianiaina, Roger Daniel; Brown, Jason L.; Glaw, Frank; Amat, Felix; Künzel, Sven; Metzler, Dirk; Isokpehi, Raphael D.; Vences, Miguel

2017-01-01

Anuran amphibians undergo major morphological transitions during development, but the contribution of their markedly different life-history phases to macroevolution has rarely been analysed. Here we generate testable predictions for coupling versus uncoupling of phenotypic evolution of tadpole and adult life-history phases, and for the underlying expression of genes related to morphological feature formation. We test these predictions by combining evidence from gene expression in two distantly related frogs, Xenopus laevis and Mantidactylus betsileanus, with patterns of morphological evolution in the entire radiation of Madagascan mantellid frogs. Genes linked to morphological structure formation are expressed in a highly phase-specific pattern, suggesting uncoupling of phenotypic evolution across life-history phases. This gene expression pattern agrees with uncoupled rates of trait evolution among life-history phases in the mantellids, which we show to have undergone an adaptive radiation. Our results validate a prevalence of uncoupling in the evolution of tadpole and adult phenotypes of frogs. PMID:28504275

When should we expect early bursts of trait evolution in comparative data? Predictions from an evolutionary food web model.

PubMed

Ingram, T; Harmon, L J; Shurin, J B

2012-09-01

Conceptual models of adaptive radiation predict that competitive interactions among species will result in an early burst of speciation and trait evolution followed by a slowdown in diversification rates. Empirical studies often show early accumulation of lineages in phylogenetic trees, but usually fail to detect early bursts of phenotypic evolution. We use an evolutionary simulation model to assemble food webs through adaptive radiation, and examine patterns in the resulting phylogenetic trees and species' traits (body size and trophic position). We find that when foraging trade-offs result in food webs where all species occupy integer trophic levels, lineage diversity and trait disparity are concentrated early in the tree, consistent with the early burst model. In contrast, in food webs in which many omnivorous species feed at multiple trophic levels, high levels of turnover of species' identities and traits tend to eliminate the early burst signal. These results suggest testable predictions about how the niche structure of ecological communities may be reflected by macroevolutionary patterns. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Repeated evolution of vertebrate pollination syndromes in a recently diverged Andean plant clade.

PubMed

Lagomarsino, Laura P; Forrestel, Elisabeth J; Muchhala, Nathan; Davis, Charles C

2017-08-01

Although specialized interactions, including those involving plants and their pollinators, are often invoked to explain high species diversity, they are rarely explored at macroevolutionary scales. We investigate the dynamic evolution of hummingbird and bat pollination syndromes in the centropogonid clade (Lobelioideae: Campanulaceae), an Andean-centered group of ∼550 angiosperm species. We demonstrate that flowers hypothesized to be adapted to different pollinators based on flower color fall into distinct regions of morphospace, and this is validated by morphology of species with known pollinators. This supports the existence of pollination syndromes in the centropogonids, an idea corroborated by ecological studies. We further demonstrate that hummingbird pollination is ancestral, and that bat pollination has evolved ∼13 times independently, with ∼11 reversals. This convergence is associated with correlated evolution of floral traits within selective regimes corresponding to pollination syndrome. Collectively, our results suggest that floral morphological diversity is extremely labile, likely resulting from selection imposed by pollinators. Finally, even though this clade's rapid diversification is partially attributed to their association with vertebrate pollinators, we detect no difference in diversification rates between hummingbird- and bat-pollinated lineages. Our study demonstrates the utility of pollination syndromes as a proxy for ecological relationships in macroevolutionary studies of certain species-rich clades. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Do Macrophylogenies Yield Stable Macroevolutionary Inferences? An Example from Squamate Reptiles.

PubMed

Title, Pascal O; Rabosky, Daniel L

2017-09-01

Advances in the generation, retrieval, and analysis of phylogenetic data have enabled researchers to create phylogenies that contain many thousands of taxa. These "macrophylogenies"-large trees that typically derive from megaphylogeny, supermatrix, or supertree approaches-provide researchers with an unprecedented ability to conduct evolutionary analyses across broad phylogenetic scales. Many studies have now used these phylogenies to explore the dynamics of speciation, extinction, and phenotypic evolution across large swaths of the tree of life. These trees are characterized by substantial phylogenetic uncertainty on multiple levels, and the stability of macroevolutionary inferences from these data sets has not been rigorously explored. As a case study, we tested whether five recently published phylogenies for squamate reptiles-each consisting of more than 4000 species-yield congruent inferences about the processes that underlie variation in species richness across replicate evolutionary radiations of Australian snakes and lizards. We find discordance across the five focal phylogenies with respect to clade age and several diversification rate metrics, and in the effects of clade age on species richness. We also find that crown clade ages reported in the literature on these Australian groups are in conflict with all of the large phylogenies examined. Macrophylogenies offer an unprecedented opportunity to address evolutionary and ecological questions at broad phylogenetic scales, but accurately representing the uncertainty that is inherent to such analyses remains a critical challenge to our field. [Australia; macroevolution; macrophylogeny; squamates; time calibration.]. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Correlated evolution of thermal niches and functional physiology in tropical freshwater fishes.

PubMed

Culumber, Zachary W; Tobler, Michael

2018-05-01

The role of ecology in phenotypic and species diversification is widely documented. Nonetheless, numerous nonadaptive processes can shape realized niches and phenotypic variation in natural populations, complicating inferences about adaptive evolution at macroevolutionary scales. We tested for evolved differences in thermal tolerances and their association with the realized thermal niche (including metrics describing diurnal and seasonal patterns of temperature extremes and variability) across a genus of tropical freshwater fishes reared in a standardized environment. There was limited evolution along the thermal niche axis associated with variation in maximum temperature and in upper thermal limits. In contrast, there was considerable diversification along the first major axis of the thermal niche associated with minimum temperatures and in lower thermal limits. Across our adaptive landscape analyses, 70% of species exhibited evidence of divergence in thermal niches. Most importantly, the first two major axes of thermal niche variation were significantly correlated with variation in lower thermal limits. Our results indicate adaptation to divergent thermal niches and adaptive evolution of related functional traits, and highlight the importance of divergence in lower thermal limits for the evolution of tropical biodiversity. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

Short Lesson Plan Associated with Increased Acceptance of Evolutionary Theory and Potential Change in Three Alternate Conceptions of Macroevolution in Undergraduate Students

ERIC Educational Resources Information Center

Abraham, Joel K.; Perez, Kathryn E.; Downey, Nicholas; Herron, Jon C.; Meir, Eli

2012-01-01

Undergraduates commonly harbor alternate conceptions about evolutionary biology; these alternate conceptions often persist, even after intensive instruction, and may influence acceptance of evolution. We interviewed undergraduates to explore their alternate conceptions about macroevolutionary patterns and designed a 2-h lesson plan to present…

Ecology and evolution of mammalian biodiversity

PubMed Central

Jones, Kate E.; Safi, Kamran

2011-01-01

Mammals have incredible biological diversity, showing extreme flexibility in eco-morphology, physiology, life history and behaviour across their evolutionary history. Undoubtedly, mammals play an important role in ecosystems by providing essential services such as regulating insect populations, seed dispersal and pollination and act as indicators of general ecosystem health. However, the macroecological and macroevolutionary processes underpinning past and present biodiversity patterns are only beginning to be explored on a global scale. It is also particularly important, in the face of the global extinction crisis, to understand these processes in order to be able to use this knowledge to prevent future biodiversity loss and loss of ecosystem services. Unfortunately, efforts to understand mammalian biodiversity have been hampered by a lack of data. New data compilations on current species' distributions, ecologies and evolutionary histories now allow an integrated approach to understand this biodiversity. We review and synthesize these new studies, exploring the past and present ecology and evolution of mammalian biodiversity, and use these findings to speculate about the mammals of our future. PMID:21807728

Ecology and evolution of mammalian biodiversity.

PubMed

Jones, Kate E; Safi, Kamran

2011-09-12

Mammals have incredible biological diversity, showing extreme flexibility in eco-morphology, physiology, life history and behaviour across their evolutionary history. Undoubtedly, mammals play an important role in ecosystems by providing essential services such as regulating insect populations, seed dispersal and pollination and act as indicators of general ecosystem health. However, the macroecological and macroevolutionary processes underpinning past and present biodiversity patterns are only beginning to be explored on a global scale. It is also particularly important, in the face of the global extinction crisis, to understand these processes in order to be able to use this knowledge to prevent future biodiversity loss and loss of ecosystem services. Unfortunately, efforts to understand mammalian biodiversity have been hampered by a lack of data. New data compilations on current species' distributions, ecologies and evolutionary histories now allow an integrated approach to understand this biodiversity. We review and synthesize these new studies, exploring the past and present ecology and evolution of mammalian biodiversity, and use these findings to speculate about the mammals of our future.

Clonal Heterogeneity and Tumor Evolution: Past, Present, and the Future.

PubMed

McGranahan, Nicholas; Swanton, Charles

2017-02-09

Intratumor heterogeneity, which fosters tumor evolution, is a key challenge in cancer medicine. Here, we review data and technologies that have revealed intra-tumor heterogeneity across cancer types and the dynamics, constraints, and contingencies inherent to tumor evolution. We emphasize the importance of macro-evolutionary leaps, often involving large-scale chromosomal alterations, in driving tumor evolution and metastasis and consider the role of the tumor microenvironment in engendering heterogeneity and drug resistance. We suggest that bold approaches to drug development, harnessing the adaptive properties of the immune-microenvironment while limiting those of the tumor, combined with advances in clinical trial-design, will improve patient outcome. Crown Copyright © 2017. Published by Elsevier Inc. All rights reserved.

Mosaic patterns of diversification dynamics following the colonization of Melanesian islands.

PubMed

Toussaint, Emmanuel F A; Hendrich, Lars; Shaverdo, Helena; Balke, Michael

2015-11-03

The fate of newly settled dispersers on freshly colonized oceanic islands is a central theme of island biogeography. The emergence of increasingly sophisticated methods of macroevolutionary pattern inference paves the way for a deeper understanding of the mechanisms governing these diversification patterns on lineages following their colonization of oceanic islands. Here we infer a comprehensive molecular phylogeny for Melanesian Exocelina diving beetles. Recent methods in historical biogeography and diversification rate inference were then used to investigate the evolution of these insects in space and time. An Australian origin in the mid-Miocene was followed by independent colonization events towards New Guinea and New Caledonia in the late Miocene. One colonization of New Guinea led to a large radiation of >150 species and 3 independent colonizations of New Caledonia gave rise to about 40 species. The comparably late colonizations of Vanuatu, Hawaii and China left only one or two species in each region. The contrasting diversification trajectories of these insects on Melanesian islands are likely accounted for by island size, age and availability of ecological opportunities during the colonization stage.

Alternate pathways of body shape evolution translate into common patterns of locomotor evolution in two clades of lizards.

PubMed

Bergmann, Philip J; Irschick, Duncan J

2010-06-01

Body shape has a fundamental impact on organismal function, but it is unknown how functional morphology and locomotor performance and kinematics relate across a diverse array of body shapes. We showed that although patterns of body shape evolution differed considerably between lizards of the Phrynosomatinae and Lerista, patterns of locomotor evolution coincided between clades. Specifically, we found that the phrynosomatines evolved a stocky phenotype through body widening and limb shortening, whereas Lerista evolved elongation through body lengthening and limb shortening. In both clades, relative limb length played a key role in locomotor evolution and kinematic strategies, with long-limbed species moving faster and taking longer strides. In Lerista, the body axis also influenced locomotor evolution. Similar patterns of locomotor evolution were likely due to constraints on how the body can move. However, these common patterns of locomotor evolution between the two clades resulted in different kinematic strategies and levels of performance among species because of their morphological differences. Furthermore, we found no evidence that distinct body shapes are adaptations to different substrates, as locomotor kinematics did not change on loose or solid substrates. Our findings illustrate the importance of studying kinematics to understand the mechanisms of locomotor evolution and phenotype-function relationships.

Macroevolutionary assembly of ant/plant symbioses: Pseudomyrmex ants and their ant-housing plants in the Neotropics

PubMed Central

Chomicki, Guillaume; Ward, Philip S.; Renner, Susanne S.

2015-01-01

Symbioses include some of the clearest cases of coevolution, but their origin, loss or reassembly with different partners can rarely be inferred. Here we use ant/plant symbioses involving three plant clades to investigate the evolution of symbioses. We generated phylogenies for the big-eyed arboreal ants (Pseudomyrmecinae), including 72% of their 286 species, as well as for five of their plant host groups, in each case sampling more than 61% of the species. We show that the ant-housing Vachellia (Mimosoideae) clade and its ants co-diversified for the past 5 Ma, with some species additionally colonized by younger plant-nesting ant species, some parasitic. An apparent co-radiation of ants and Tachigali (Caesalpinioideae) was followed by waves of colonization by the same ant clade, and subsequent occupation by a younger ant group. Wide crown and stem age differences between the ant-housing genus Triplaris (Polygonaceae) and its obligate ant inhabitants, and stochastic trait mapping, indicate that its domatium evolved earlier than the ants now occupying it, suggesting previous symbioses that dissolved. Parasitic ant species evolved from generalists, not from mutualists, and are younger than the mutualistic systems they parasitize. Our study illuminates the macroevolutionary assembly of ant/plant symbioses, which has been highly dynamic, even in very specialized systems. PMID:26582029

Color pattern evolution in Vanessa butterflies (Nymphalidae: Nymphalini): non-eyespot characters.

PubMed

Abbasi, Roohollah; Marcus, Jeffrey M

2015-01-01

A phylogenetic approach was used to study color pattern evolution in Vanessa butterflies. Twenty-four color pattern elements from the Nymphalid ground plan were identified on the dorsal and ventral surfaces of the fore- and hind wings. Eyespot characters were excluded and will be examined elsewhere. The evolution of each character was traced over a Bayesian phylogeny of Vanessa reconstructed from 7750 DNA base pairs from 10 genes. Generally, the correspondence between character states on the same surface of the two wings is stronger on the ventral side compared to the dorsal side. The evolution of character states on both sides of a wing correspond with each other in most extant species, but the correspondence between dorsal and ventral character states is much stronger in the forewing than in the hindwing. The dorsal hindwing of many species of Vanessa is covered with an extended Basal Symmetry System and the Discalis I pattern element is highly variable between species, making this wing surface dissimilar to the other wing surfaces. The Basal Symmetry System and Discalis I may contribute to behavioral thermoregulation in Vanessa. Overall, interspecific directional character state evolution of non-eyespot color patterns is relatively rare in Vanessa, with a majority of color pattern elements showing non-variable, non-directional, or ambiguous character state evolution. The ease with which the development of color patterns can be modified, including character state reversals, has likely made important contributions to the production of color pattern diversity in Vanessa and other butterfly groups. © 2014 Wiley Periodicals, Inc.

Evolution of central pattern generators and rhythmic behaviours

PubMed Central

Katz, Paul S.

2016-01-01

Comparisons of rhythmic movements and the central pattern generators (CPGs) that control them uncover principles about the evolution of behaviour and neural circuits. Over the course of evolutionary history, gradual evolution of behaviours and their neural circuitry within any lineage of animals has been a predominant occurrence. Small changes in gene regulation can lead to divergence of circuit organization and corresponding changes in behaviour. However, some behavioural divergence has resulted from large-scale rewiring of the neural network. Divergence of CPG circuits has also occurred without a corresponding change in behaviour. When analogous rhythmic behaviours have evolved independently, it has generally been with different neural mechanisms. Repeated evolution of particular rhythmic behaviours has occurred within some lineages due to parallel evolution or latent CPGs. Particular motor pattern generating mechanisms have also evolved independently in separate lineages. The evolution of CPGs and rhythmic behaviours shows that although most behaviours and neural circuits are highly conserved, the nature of the behaviour does not dictate the neural mechanism and that the presence of homologous neural components does not determine the behaviour. This suggests that although behaviour is generated by neural circuits, natural selection can act separately on these two levels of biological organization. PMID:26598733

Evolution of central pattern generators and rhythmic behaviours.

PubMed

Katz, Paul S

2016-01-05

Comparisons of rhythmic movements and the central pattern generators (CPGs) that control them uncover principles about the evolution of behaviour and neural circuits. Over the course of evolutionary history, gradual evolution of behaviours and their neural circuitry within any lineage of animals has been a predominant occurrence. Small changes in gene regulation can lead to divergence of circuit organization and corresponding changes in behaviour. However, some behavioural divergence has resulted from large-scale rewiring of the neural network. Divergence of CPG circuits has also occurred without a corresponding change in behaviour. When analogous rhythmic behaviours have evolved independently, it has generally been with different neural mechanisms. Repeated evolution of particular rhythmic behaviours has occurred within some lineages due to parallel evolution or latent CPGs. Particular motor pattern generating mechanisms have also evolved independently in separate lineages. The evolution of CPGs and rhythmic behaviours shows that although most behaviours and neural circuits are highly conserved, the nature of the behaviour does not dictate the neural mechanism and that the presence of homologous neural components does not determine the behaviour. This suggests that although behaviour is generated by neural circuits, natural selection can act separately on these two levels of biological organization. © 2015 The Author(s).

Studies of threespine stickleback developmental evolution: progress and promise.

PubMed

Cresko, William A; McGuigan, Katrina L; Phillips, Patrick C; Postlethwait, John H

2007-01-01

A promising route for understanding the origin and diversification of organismal form is through studies at the intersection of evolution and development (evo-devo). While much has been learned over the last two decades concerning macroevolutionary patterns of developmental change, a fundamental gap in the evo-devo synthesis is the integration of mathematical population and quantitative genetics with studies of how genetic variation in natural populations affects developmental processes. This micro-evo-devo synthesis requires model organisms with which to ask empirical questions. Threespine stickleback fish (Gasterosteus aculeatus), long a model for studying behavior, ecology and evolution, is emerging as a prominent model micro-evo-devo system. Research on stickleback over the last decade has begun to address the genetic basis of morphological variation and sex determination, and much of this work has important implications for understanding the genetics of speciation. In this paper we review recent threespine stickleback micro-evo-devo results, and outline the resources that have been developed to make this synthesis possible. The prospects for stickleback research to speed the micro-(and macro-) evo-devo syntheses are great, and this workhorse model system is well situated to continue contributing to our understanding of the generation of diversity in organismal form for many more decades.

A Preliminary Analysis of Correlated Evolution in Mammalian Chewing Motor Patterns

PubMed Central

Williams, Susan H.; Vinyard, Christopher J.; Wall, Christine E.; Doherty, Alison H.; Crompton, Alfred W.; Hylander, William L.

2011-01-01

Descriptive and quantitative analyses of electromyograms (EMG) from the jaw adductors during feeding in mammals have demonstrated both similarities and differences among species in chewing motor patterns. These observations have led to a number of hypotheses of the evolution of motor patterns, the most comprehensive of which was proposed by Weijs in 1994. Since then, new data have been collected and additional hypotheses for the evolution of motor patterns have been proposed. Here, we take advantage of these new data and a well-resolved species-level phylogeny for mammals to test for the correlated evolution of specific components of mammalian chewing motor patterns. We focus on the evolution of the coordination of working-side (WS) and balancing-side (BS) jaw adductors (i.e., Weijs’ Triplets I and II), the evolution of WS and BS muscle recruitment levels, and the evolution of asynchrony between pairs of muscles. We converted existing chewing EMG data into binary traits to incorporate as much data as possible and facilitate robust phylogenetic analyses. We then tested hypotheses of correlated evolution of these traits across our phylogeny using a maximum likelihood method and the Bayesian Markov Chain Monte Carlo method. Both sets of analyses yielded similar results highlighting the evolutionary changes that have occurred across mammals in chewing motor patterns. We find support for the correlated evolution of (1) Triplets I and II, (2) BS deep masseter asynchrony and Triplets I and II, (3) a relative delay in the activity of the BS deep masseter and a decrease in the ratio of WS to BS muscle recruitment levels, and (4) a relative delay in the activity of the BS deep masseter and a delay in the activity of the BS posterior temporalis. In contrast, changes in relative WS and BS activity levels across mammals are not correlated with Triplets I and II. Results from this work can be integrated with dietary and morphological data to better understand how feeding and

A preliminary analysis of correlated evolution in Mammalian chewing motor patterns.

PubMed

Williams, Susan H; Vinyard, Christopher J; Wall, Christine E; Doherty, Alison H; Crompton, Alfred W; Hylander, William L

2011-08-01

Descriptive and quantitative analyses of electromyograms (EMG) from the jaw adductors during feeding in mammals have demonstrated both similarities and differences among species in chewing motor patterns. These observations have led to a number of hypotheses of the evolution of motor patterns, the most comprehensive of which was proposed by Weijs in 1994. Since then, new data have been collected and additional hypotheses for the evolution of motor patterns have been proposed. Here, we take advantage of these new data and a well-resolved species-level phylogeny for mammals to test for the correlated evolution of specific components of mammalian chewing motor patterns. We focus on the evolution of the coordination of working-side (WS) and balancing-side (BS) jaw adductors (i.e., Weijs' Triplets I and II), the evolution of WS and BS muscle recruitment levels, and the evolution of asynchrony between pairs of muscles. We converted existing chewing EMG data into binary traits to incorporate as much data as possible and facilitate robust phylogenetic analyses. We then tested hypotheses of correlated evolution of these traits across our phylogeny using a maximum likelihood method and the Bayesian Markov Chain Monte Carlo method. Both sets of analyses yielded similar results highlighting the evolutionary changes that have occurred across mammals in chewing motor patterns. We find support for the correlated evolution of (1) Triplets I and II, (2) BS deep masseter asynchrony and Triplets I and II, (3) a relative delay in the activity of the BS deep masseter and a decrease in the ratio of WS to BS muscle recruitment levels, and (4) a relative delay in the activity of the BS deep masseter and a delay in the activity of the BS posterior temporalis. In contrast, changes in relative WS and BS activity levels across mammals are not correlated with Triplets I and II. Results from this work can be integrated with dietary and morphological data to better understand how feeding and the

The role of extreme events in evolution

NASA Astrophysics Data System (ADS)

Combes, Claude

2008-09-01

Evolutionists have often had a marked tendency to think that, in the course of time, planetary events were not very different from those occurring during a human life. However, when a 'non-human' timescale is used, the history of our planet appears profoundly and frequently disturbed by extreme events. These events, even not always instantaneous, impose - because of their amplitude - a severe sorting, not between individuals of a species, but between species, or even between phyla. In the face of an extreme event, intraspecific diversity counts little: it is the interspecific diversity that makes the difference. As shown by mass extinctions, extreme events open ecological niches and redistribute the cards of life, giving survivors opportunities to radiate. The capacity to cope with extreme ecological conditions favours certain species in ecosystems, not certain individuals in populations. This is not a macroevolutionary process in terms of acquiring new adaptations, but a macroevolutionary process in terms of sorting entire sections of life. The most important is perhaps that the current 'mediatisation' of a limited number of mass extinctions dissimulates less important extinctions caused by less extreme and more localized events that were possibly responsible for many changes in the composition and structure of communities throughout the evolution. The term of 'pre-adaptation' has been neglected, because it gives an impression of finalism, but it expresses well that, when an unexpected event occurs, a particular species has or has not the 'right genes' to continue to sustain viable populations. The role of extreme events in modifying the course of evolution should not be underestimated.

The evolution of pattern camouflage strategies in waterfowl and game birds.

PubMed

Marshall, Kate L A; Gluckman, Thanh-Lan

2015-05-01

Visual patterns are common in animals. A broad survey of the literature has revealed that different patterns have distinct functions. Irregular patterns (e.g., stipples) typically function in static camouflage, whereas regular patterns (e.g., stripes) have a dual function in both motion camouflage and communication. Moreover, irregular and regular patterns located on different body regions ("bimodal" patterning) can provide an effective compromise between camouflage and communication and/or enhanced concealment via both static and motion camouflage. Here, we compared the frequency of these three pattern types and traced their evolutionary history using Bayesian comparative modeling in aquatic waterfowl (Anseriformes: 118 spp.), which typically escape predators by flight, and terrestrial game birds (Galliformes: 170 spp.), which mainly use a "sit and hide" strategy to avoid predation. Given these life histories, we predicted that selection would favor regular patterning in Anseriformes and irregular or bimodal patterning in Galliformes and that pattern function complexity should increase over the course of evolution. Regular patterns were predominant in Anseriformes whereas regular and bimodal patterns were most frequent in Galliformes, suggesting that patterns with multiple functions are broadly favored by selection over patterns with a single function in static camouflage. We found that the first patterns to evolve were either regular or bimodal in Anseriformes and either irregular or regular in Galliformes. In both orders, irregular patterns could evolve into regular patterns but not the reverse. Our hypothesis of increasing complexity in pattern camouflage function was supported in Galliformes but not in Anseriformes. These results reveal a trajectory of pattern evolution linked to increasing function complexity in Galliformes although not in Anseriformes, suggesting that both ecology and function complexity can have a profound influence on pattern evolution.

The evolution of pattern camouflage strategies in waterfowl and game birds

PubMed Central

Marshall, Kate L A; Gluckman, Thanh-Lan

2015-01-01

Visual patterns are common in animals. A broad survey of the literature has revealed that different patterns have distinct functions. Irregular patterns (e.g., stipples) typically function in static camouflage, whereas regular patterns (e.g., stripes) have a dual function in both motion camouflage and communication. Moreover, irregular and regular patterns located on different body regions (“bimodal” patterning) can provide an effective compromise between camouflage and communication and/or enhanced concealment via both static and motion camouflage. Here, we compared the frequency of these three pattern types and traced their evolutionary history using Bayesian comparative modeling in aquatic waterfowl (Anseriformes: 118 spp.), which typically escape predators by flight, and terrestrial game birds (Galliformes: 170 spp.), which mainly use a “sit and hide” strategy to avoid predation. Given these life histories, we predicted that selection would favor regular patterning in Anseriformes and irregular or bimodal patterning in Galliformes and that pattern function complexity should increase over the course of evolution. Regular patterns were predominant in Anseriformes whereas regular and bimodal patterns were most frequent in Galliformes, suggesting that patterns with multiple functions are broadly favored by selection over patterns with a single function in static camouflage. We found that the first patterns to evolve were either regular or bimodal in Anseriformes and either irregular or regular in Galliformes. In both orders, irregular patterns could evolve into regular patterns but not the reverse. Our hypothesis of increasing complexity in pattern camouflage function was supported in Galliformes but not in Anseriformes. These results reveal a trajectory of pattern evolution linked to increasing function complexity in Galliformes although not in Anseriformes, suggesting that both ecology and function complexity can have a profound influence on pattern

Movement Patterns, Social Dynamics, and the Evolution of Cooperation

PubMed Central

Smaldino, Paul E.; Schank, Jeffrey C.

2012-01-01

The structure of social interactions influences many aspects of social life, including the spread of information and behavior, and the evolution of social phenotypes. After dispersal, organisms move around throughout their lives, and the patterns of their movement influence their social encounters over the course of their lifespan. Though both space and mobility are known to influence social evolution, there is little analysis of the influence of specific movement patterns on evolutionary dynamics. We explored the effects of random movement strategies on the evolution of cooperation using an agent-based prisoner’s dilemma model with mobile agents. This is the first systematic analysis of a model in which cooperators and defectors can use different random movement strategies, which we chose to fall on a spectrum between highly exploratory and highly restricted in their search tendencies. Because limited dispersal and restrictions to local neighborhood size are known to influence the ability of cooperators to effectively assort, we also assessed the robustness of our findings with respect to dispersal and local capacity constraints. We show that differences in patterns of movement can dramatically influence the likelihood of cooperator success, and that the effects of different movement patterns are sensitive to environmental assumptions about offspring dispersal and local space constraints. Since local interactions implicitly generate dynamic social interaction networks, we also measured the average number of unique and total interactions over a lifetime and considered how these emergent network dynamics helped explain the results. This work extends what is known about mobility and the evolution of cooperation, and also has general implications for social models with randomly moving agents. PMID:22838026

The maximum rate of mammal evolution

NASA Astrophysics Data System (ADS)

Evans, Alistair R.; Jones, David; Boyer, Alison G.; Brown, James H.; Costa, Daniel P.; Ernest, S. K. Morgan; Fitzgerald, Erich M. G.; Fortelius, Mikael; Gittleman, John L.; Hamilton, Marcus J.; Harding, Larisa E.; Lintulaakso, Kari; Lyons, S. Kathleen; Okie, Jordan G.; Saarinen, Juha J.; Sibly, Richard M.; Smith, Felisa A.; Stephens, Patrick R.; Theodor, Jessica M.; Uhen, Mark D.

2012-03-01

How fast can a mammal evolve from the size of a mouse to the size of an elephant? Achieving such a large transformation calls for major biological reorganization. Thus, the speed at which this occurs has important implications for extensive faunal changes, including adaptive radiations and recovery from mass extinctions. To quantify the pace of large-scale evolution we developed a metric, clade maximum rate, which represents the maximum evolutionary rate of a trait within a clade. We applied this metric to body mass evolution in mammals over the last 70 million years, during which multiple large evolutionary transitions occurred in oceans and on continents and islands. Our computations suggest that it took a minimum of 1.6, 5.1, and 10 million generations for terrestrial mammal mass to increase 100-, and 1,000-, and 5,000-fold, respectively. Values for whales were down to half the length (i.e., 1.1, 3, and 5 million generations), perhaps due to the reduced mechanical constraints of living in an aquatic environment. When differences in generation time are considered, we find an exponential increase in maximum mammal body mass during the 35 million years following the Cretaceous-Paleogene (K-Pg) extinction event. Our results also indicate a basic asymmetry in macroevolution: very large decreases (such as extreme insular dwarfism) can happen at more than 10 times the rate of increases. Our findings allow more rigorous comparisons of microevolutionary and macroevolutionary patterns and processes.

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

Convergent evolution at the pathway level: predictable regulatory changes during flower color transitions.

PubMed

Larter, Maximilian; Dunbar-Wallis, Amy; Berardi, Andrea E; Smith, Stacey D

2018-06-07

The predictability of evolution, or whether lineages repeatedly follow the same evolutionary trajectories during phenotypic convergence remains an open question of evolutionary biology. In this study, we investigate evolutionary convergence at the biochemical pathway level and test the predictability of evolution using floral anthocyanin pigmentation, a trait with a well-understood genetic and regulatory basis. We reconstructed the evolution of floral anthocyanin content across 28 species of the Andean clade Iochrominae (Solanaceae) and investigated how shifts in pigmentation are related to changes in expression of 7 key anthocyanin pathway genes. We used phylogenetic multivariate analysis of gene expression to test for phenotypic and developmental convergence at a macroevolutionary scale. Our results show that the four independent losses of the ancestral pigment delphinidin involved convergent losses of expression of the three late pathway genes (F3'5'h, Dfr and Ans). Transitions between pigment types affecting floral hue (e.g. blue to red) involve changes to the expression of branching genes F3'h and F3'5'h, while the expression levels of early steps of the pathway are strongly conserved in all species. These patterns support the idea that the macroevolution of floral pigmentation follows predictable evolutionary trajectories to reach convergent phenotype space, repeatedly involving regulatory changes. This is likely driven by constraints at the pathway level, such as pleiotropy and regulatory structure.

Wrinkling pattern evolution of cylindrical biological tissues with differential growth.

PubMed

Jia, Fei; Li, Bo; Cao, Yan-Ping; Xie, Wei-Hua; Feng, Xi-Qiao

2015-01-01

Three-dimensional surface wrinkling of soft cylindrical tissues induced by differential growth is explored. Differential volumetric growth can cause their morphological stability, leading to the formation of hexagonal and labyrinth wrinkles. During postbuckling, multiple bifurcations and morphological transitions may occur as a consequence of continuous growth in the surface layer. The physical mechanisms underpinning the morphological evolution are examined from the viewpoint of energy. Surface curvature is found to play a regulatory role in the pattern evolution. This study may not only help understand the morphogenesis of soft biological tissues, but also inspire novel routes for creating desired surface patterns of soft materials.

Evolution-development congruence in pattern formation dynamics: Bifurcations in gene expression and regulation of networks structures.

PubMed

Kohsokabe, Takahiro; Kaneko, Kunihiko

2016-01-01

Search for possible relationships between phylogeny and ontogeny is important in evolutionary-developmental biology. Here we uncover such relationships by numerical evolution and unveil their origin in terms of dynamical systems theory. By representing developmental dynamics of spatially located cells with gene expression dynamics with cell-to-cell interaction under external morphogen gradient, gene regulation networks are evolved under mutation and selection with the fitness to approach a prescribed spatial pattern of expressed genes. For most numerical evolution experiments, evolution of pattern over generations and development of pattern by an evolved network exhibit remarkable congruence. Both in the evolution and development pattern changes consist of several epochs where stripes are formed in a short time, while for other temporal regimes, pattern hardly changes. In evolution, these quasi-stationary regimes are generations needed to hit relevant mutations, while in development, they are due to some gene expression that varies slowly and controls the pattern change. The morphogenesis is regulated by combinations of feedback or feedforward regulations, where the upstream feedforward network reads the external morphogen gradient, and generates a pattern used as a boundary condition for the later patterns. The ordering from up to downstream is common in evolution and development, while the successive epochal changes in development and evolution are represented as common bifurcations in dynamical-systems theory, which lead to the evolution-development congruence. Mechanism of exceptional violation of the congruence is also unveiled. Our results provide a new look on developmental stages, punctuated equilibrium, developmental bottlenecks, and evolutionary acquisition of novelty in morphogenesis. © 2015 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution Published by Wiley Periodicals, Inc.

Optimized temporal pattern of brain stimulation designed by computational evolution

PubMed Central

Brocker, David T.; Swan, Brandon D.; So, Rosa Q.; Turner, Dennis A.; Gross, Robert E.; Grill, Warren M.

2017-01-01

Brain stimulation is a promising therapy for several neurological disorders, including Parkinson’s disease. Stimulation parameters are selected empirically and are limited to the frequency and intensity of stimulation. We used the temporal pattern of stimulation as a novel parameter of deep brain stimulation to ameliorate symptoms in a parkinsonian animal model and in humans with Parkinson’s disease. We used model-based computational evolution to optimize the stimulation pattern. The optimized pattern produced symptom relief comparable to that from standard high-frequency stimulation (a constant rate of 130 or 185 Hz) and outperformed frequency-matched standard stimulation in the parkinsonian rat and in patients. Both optimized and standard stimulation suppressed abnormal oscillatory activity in the basal ganglia of rats and humans. The results illustrate the utility of model-based computational evolution to design temporal pattern of stimulation to increase the efficiency of brain stimulation in Parkinson’s disease, thereby requiring substantially less energy than traditional brain stimulation. PMID:28053151

Time rescaling and pattern formation in biological evolution.

PubMed

Igamberdiev, Abir U

2014-09-01

Biological evolution is analyzed as a process of continuous measurement in which biosystems interpret themselves in the environment resulting in changes of both. This leads to rescaling of internal time (heterochrony) followed by spatial reconstructions of morphology (heterotopy). The logical precondition of evolution is the incompleteness of biosystem's internal description, while the physical precondition is the uncertainty of quantum measurement. The process of evolution is based on perpetual changes in interpretation of information in the changing world. In this interpretation the external biospheric gradients are used for establishment of new features of organization. It is concluded that biological evolution involves the anticipatory epigenetic changes in the interpretation of genetic symbolism which cannot generally be forecasted but can provide canalization of structural transformations defined by the existing organization and leading to predictable patterns of form generation. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Evolution and convergence of the patterns of international scientific collaboration.

PubMed

Coccia, Mario; Wang, Lili

2016-02-23

International research collaboration plays an important role in the social construction and evolution of science. Studies of science increasingly analyze international collaboration across multiple organizations for its impetus in improving research quality, advancing efficiency of the scientific production, and fostering breakthroughs in a shorter time. However, long-run patterns of international research collaboration across scientific fields and their structural changes over time are hardly known. Here we show the convergence of international scientific collaboration across research fields over time. Our study uses a dataset by the National Science Foundation and computes the fraction of papers that have international institutional coauthorships for various fields of science. We compare our results with pioneering studies carried out in the 1970s and 1990s by applying a standardization method that transforms all fractions of internationally coauthored papers into a comparable framework. We find, over 1973-2012, that the evolution of collaboration patterns across scientific disciplines seems to generate a convergence between applied and basic sciences. We also show that the general architecture of international scientific collaboration, based on the ranking of fractions of international coauthorships for different scientific fields per year, has tended to be unchanged over time, at least until now. Overall, this study shows, to our knowledge for the first time, the evolution of the patterns of international scientific collaboration starting from initial results described by literature in the 1970s and 1990s. We find a convergence of these long-run collaboration patterns between the applied and basic sciences. This convergence might be one of contributing factors that supports the evolution of modern scientific fields.

Spots and stripes: ecology and colour pattern evolution in butterflyfishes

PubMed Central

Kelley, Jennifer L.; Fitzpatrick, John L.; Merilaita, Sami

2013-01-01

The incredible diversity of colour patterns in coral reef fishes has intrigued biologists for centuries. Yet, despite the many proposed explanations for this diversity in coloration, definitive tests of the role of ecological factors in shaping the evolution of particular colour pattern traits are absent. Patterns such as spots and eyespots (spots surrounded by concentric rings of contrasting colour) have often been assumed to function for predator defence by mimicking predators' enemies' eyes, deflecting attacks or intimidating predators, but the evolutionary processes underlying these functions have never been addressed. Striped body patterns have been suggested to serve for both social communication and predator defence, but the impact of ecological constraints remains unclear. We conducted the first comparative analysis of colour pattern diversity in butterflyfishes (Family: Chaetodontidae), fishes with conspicuous spots, eyespots and wide variation in coloration. Using a dated molecular phylogeny of 95 species (approx. 75% of the family), we tested whether spots and eyespots have evolved characteristics that are consistent with their proposed defensive function and whether the presence of spots and body stripes is linked with species' body length, dietary complexity, habitat diversity or social behaviour. Contrary to our expectations, spots and eyespots appeared relatively recently in butterflyfish evolution and are highly evolutionarily labile, suggesting that they are unlikely to have played an important part in the evolutionary history of the group. Striped body patterns showed correlated evolution with a number of ecological factors including habitat type, sociality and dietary complexity. Our findings question the prevailing view that eyespots are an evolutionary response to predation pressure, providing a valuable counter example to the role of these markings as revealed in other taxa. PMID:23427170

Macroevolution of perfume signalling in orchid bees.

PubMed

Weber, Marjorie G; Mitko, Lukasz; Eltz, Thomas; Ramírez, Santiago R

2016-11-01

Theory predicts that both stabilising selection and diversifying selection jointly contribute to the evolution of sexual signalling traits by (1) maintaining the integrity of communication signals within species and (2) promoting the diversification of traits among lineages. However, for many important signalling traits, little is known about whether these dynamics translate into predictable macroevolutionary signatures. Here, we test for macroevolutionary patterns consistent with sexual signalling theory in the perfume signals of neotropical orchid bees, a group well studied for their chemical sexual communication. Our results revealed both high species-specificity and elevated rates of evolution in perfume signals compared to nonsignalling traits. Perfume complexity was correlated with the number of congeners in a species' range, suggesting that perfume evolution may be tied to the remarkably high number of orchid bee species coexisting together in some neotropical communities. Finally, sister-pair comparisons were consistent with both rapid divergence at speciation and character displacement upon secondary contact. Together, our results provide new insight into the macroevolution of sexual signalling in insects. © 2016 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.

The origin and early evolution of whales: macroevolution documented on the Indian subcontinent.

PubMed

Bajpai, S; Thewissen, J G M; Sahni, A

2009-11-01

The origin of whales (order Cetacea) from a four-footed land animal is one of the best understood examples of macroevolutionary change. This evolutionary transition has been substantially elucidated by fossil finds from the Indian subcontinent in the past decade and a half. Here, we review the first steps of whale evolution, i.e. the transition from a land mammal to obligate marine predators, documented by the Eocene cetacean families of the Indian subcontinent: Pakicetidae, Ambulocetidae, Remingtonocetidae, Protocetidae, and Basilosauridae, as well as their artiodactyl sister group, the Raoellidae. We also discuss the influence that the excellent fossil record has on the study of the evolution of organ systems, in particular the locomotor and hearing systems.

Temporal and phylogenetic evolution of the sauropod dinosaur body plan

NASA Astrophysics Data System (ADS)

Bates, Karl T.; Mannion, Philip D.; Falkingham, Peter L.; Brusatte, Stephen L.; Hutchinson, John R.; Otero, Alejandro; Sellers, William I.; Sullivan, Corwin; Stevens, Kent A.; Allen, Vivian

2016-03-01

The colossal size and body plan of sauropod dinosaurs are unparalleled in terrestrial vertebrates. However, to date, there have been only limited attempts to examine temporal and phylogenetic patterns in the sauropod bauplan. Here, we combine three-dimensional computational models with phylogenetic reconstructions to quantify the evolution of whole-body shape and body segment properties across the sauropod radiation. Limitations associated with the absence of soft tissue preservation in fossils result in large error bars about mean absolute body shape predictions. However, applying any consistent skeleton : body volume ratio to all taxa does yield changes in body shape that appear concurrent with major macroevolutionary events in sauropod history. A caudad shift in centre-of-mass (CoM) in Middle Triassic Saurischia, associated with the evolution of bipedalism in various dinosaur lineages, was reversed in Late Triassic sauropodomorphs. A craniad CoM shift coincided with the evolution of quadrupedalism in the Late Triassic, followed by a more striking craniad shift in Late Jurassic-Cretaceous titanosauriforms, which included the largest sauropods. These craniad CoM shifts are strongly correlated with neck enlargement, a key innovation in sauropod evolution and pivotal to their gigantism. By creating a much larger feeding envelope, neck elongation is thought to have increased feeding efficiency and opened up trophic niches that were inaccessible to other herbivores. However, we find that relative neck size and CoM position are not strongly correlated with inferred feeding habits. Instead the craniad CoM positions of titanosauriforms appear closely linked with locomotion and environmental distributions, potentially contributing to the continued success of this group until the end-Cretaceous, with all other sauropods having gone extinct by the early Late Cretaceous.

Evolution of bioconvective patterns in variable gravity

NASA Technical Reports Server (NTRS)

Noever, David A.

1991-01-01

Measurements are reported of the evolution of bioconvective patterns in shallow, dense cultures of microorganisms subjected to varying gravity. Various statistical properties of this random, quasi-two-dimensional structure have been found: Aboav's law is obeyed, the average vertex angles follow predictions for regular polygons, and the area of a pattern varies linearly with its number of sides. As gravity varies between 1 g and 1.8 g, these statistical properties continue to hold despite a tripling of the number of polygons and a reduced average polygon dimension by a third. This work compares with experiments on soap foams, Langmuir monolayer foams, metal grains, and simulations.

Robust regression and posterior predictive simulation increase power to detect early bursts of trait evolution.

PubMed

Slater, Graham J; Pennell, Matthew W

2014-05-01

A central prediction of much theory on adaptive radiations is that traits should evolve rapidly during the early stages of a clade's history and subsequently slowdown in rate as niches become saturated--a so-called "Early Burst." Although a common pattern in the fossil record, evidence for early bursts of trait evolution in phylogenetic comparative data has been equivocal at best. We show here that this may not necessarily be due to the absence of this pattern in nature. Rather, commonly used methods to infer its presence perform poorly when when the strength of the burst--the rate at which phenotypic evolution declines--is small, and when some morphological convergence is present within the clade. We present two modifications to existing comparative methods that allow greater power to detect early bursts in simulated datasets. First, we develop posterior predictive simulation approaches and show that they outperform maximum likelihood approaches at identifying early bursts at moderate strength. Second, we use a robust regression procedure that allows for the identification and down-weighting of convergent taxa, leading to moderate increases in method performance. We demonstrate the utility and power of these approach by investigating the evolution of body size in cetaceans. Model fitting using maximum likelihood is equivocal with regards the mode of cetacean body size evolution. However, posterior predictive simulation combined with a robust node height test return low support for Brownian motion or rate shift models, but not the early burst model. While the jury is still out on whether early bursts are actually common in nature, our approach will hopefully facilitate more robust testing of this hypothesis. We advocate the adoption of similar posterior predictive approaches to improve the fit and to assess the adequacy of macroevolutionary models in general.

The fossil record and macroevolutionary history of the beetles

PubMed Central

Smith, Dena M.; Marcot, Jonathan D.

2015-01-01

Coleoptera (beetles) is the most species-rich metazoan order, with approximately 380 000 species. To understand how they came to be such a diverse group, we compile a database of global fossil beetle occurrences to study their macroevolutionary history. Our database includes 5553 beetle occurrences from 221 fossil localities. Amber and lacustrine deposits preserve most of the beetle diversity and abundance. All four extant suborders are found in the fossil record, with 69% of all beetle families and 63% of extant beetle families preserved. Considerable focus has been placed on beetle diversification overall, however, for much of their evolutionary history it is the clade Polyphaga that is most responsible for their taxonomic richness. Polyphaga had an increase in diversification rate in the Early Cretaceous, but instead of being due to the radiation of the angiosperms, this was probably due to the first occurrences of beetle-bearing amber deposits in the record. Perhaps, most significant is that polyphagan beetles had a family-level extinction rate of zero for most of their evolutionary history, including across the Cretaceous–Palaeogene boundary. Therefore, focusing on the factors that have inhibited beetle extinction, as opposed to solely studying mechanisms that may promote speciation, should be examined as important determinants of their great diversity today. PMID:25788597

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

PubMed Central

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

2016-01-01

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

Discovering significant evolution patterns from satellite image time series.

PubMed

Petitjean, François; Masseglia, Florent; Gançarski, Pierre; Forestier, Germain

2011-12-01

Satellite Image Time Series (SITS) provide us with precious information on land cover evolution. By studying these series of images we can both understand the changes of specific areas and discover global phenomena that spread over larger areas. Changes that can occur throughout the sensing time can spread over very long periods and may have different start time and end time depending on the location, which complicates the mining and the analysis of series of images. This work focuses on frequent sequential pattern mining (FSPM) methods, since this family of methods fits the above-mentioned issues. This family of methods consists of finding the most frequent evolution behaviors, and is actually able to extract long-term changes as well as short term ones, whenever the change may start and end. However, applying FSPM methods to SITS implies confronting two main challenges, related to the characteristics of SITS and the domain's constraints. First, satellite images associate multiple measures with a single pixel (the radiometric levels of different wavelengths corresponding to infra-red, red, etc.), which makes the search space multi-dimensional and thus requires specific mining algorithms. Furthermore, the non evolving regions, which are the vast majority and overwhelm the evolving ones, challenge the discovery of these patterns. We propose a SITS mining framework that enables discovery of these patterns despite these constraints and characteristics. Our proposal is inspired from FSPM and provides a relevant visualization principle. Experiments carried out on 35 images sensed over 20 years show the proposed approach makes it possible to extract relevant evolution behaviors.

Chapter 4. New model systems for the study of developmental evolution in plants.

PubMed

Kramer, Elena M

2009-01-01

The number of genetically tractable plant model systems is rapidly increasing, thanks to the decreasing cost of sequencing and the wide amenability of plants to stable transformation and other functional approaches. In this chapter, I discuss emerging model systems from throughout the land plant phylogeny and consider how their unique attributes are contributing to our understanding of development, evolution, and ecology. These new models are being developed using two distinct strategies: in some cases, they are selected because of their close relationship to the established models, while in others, they are chosen with the explicit intention of exploring distantly related plant lineages. Such complementary approaches are yielding exciting new results that shed light on both micro- and macroevolutionary processes in the context of developmental evolution.

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

Temporal and phylogenetic evolution of the sauropod dinosaur body plan

PubMed Central

Bates, Karl T.; Mannion, Philip D.; Falkingham, Peter L.; Brusatte, Stephen L.; Hutchinson, John R.; Otero, Alejandro; Sellers, William I.; Sullivan, Corwin; Stevens, Kent A.; Allen, Vivian

2016-01-01

The colossal size and body plan of sauropod dinosaurs are unparalleled in terrestrial vertebrates. However, to date, there have been only limited attempts to examine temporal and phylogenetic patterns in the sauropod bauplan. Here, we combine three-dimensional computational models with phylogenetic reconstructions to quantify the evolution of whole-body shape and body segment properties across the sauropod radiation. Limitations associated with the absence of soft tissue preservation in fossils result in large error bars about mean absolute body shape predictions. However, applying any consistent skeleton : body volume ratio to all taxa does yield changes in body shape that appear concurrent with major macroevolutionary events in sauropod history. A caudad shift in centre-of-mass (CoM) in Middle Triassic Saurischia, associated with the evolution of bipedalism in various dinosaur lineages, was reversed in Late Triassic sauropodomorphs. A craniad CoM shift coincided with the evolution of quadrupedalism in the Late Triassic, followed by a more striking craniad shift in Late Jurassic–Cretaceous titanosauriforms, which included the largest sauropods. These craniad CoM shifts are strongly correlated with neck enlargement, a key innovation in sauropod evolution and pivotal to their gigantism. By creating a much larger feeding envelope, neck elongation is thought to have increased feeding efficiency and opened up trophic niches that were inaccessible to other herbivores. However, we find that relative neck size and CoM position are not strongly correlated with inferred feeding habits. Instead the craniad CoM positions of titanosauriforms appear closely linked with locomotion and environmental distributions, potentially contributing to the continued success of this group until the end-Cretaceous, with all other sauropods having gone extinct by the early Late Cretaceous. PMID:27069652

The repeated evolution of large seeds on islands.

PubMed

Kavanagh, Patrick H; Burns, Kevin C

2014-07-07

Several plant traits are known to evolve in predictable ways on islands. For example, herbaceous species often evolve to become woody and species frequently evolve larger leaves, regardless of growth form. However, our understanding of how seed sizes might evolve on islands lags far behind other plant traits. Here, we conduct the first test for macroevolutionary patterns of seed size on islands. We tested for differences in seed size between 40 island-mainland taxonomic pairings from four island groups surrounding New Zealand. Seed size data were collected in the field and then augmented by published seed descriptions to produce a more comprehensive dataset. Seed sizes of insular plants were consistently larger than mainland relatives, even after accounting for differences in growth form, dispersal mode and evolutionary history. Selection may favour seed size increases on islands to reduce dispersibility, as long-distance dispersal may result in propagule mortality at sea. Alternatively, larger seeds tend to generate larger seedlings, which are more likely to establish and outcompete neighbours. Our results indicate there is a general tendency for the evolution of large seeds on islands, but the mechanisms responsible for this evolutionary pathway have yet to be fully resolved. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Bridging Inter- and Intraspecific Trait Evolution with a Hierarchical Bayesian Approach.

PubMed

Kostikova, Anna; Silvestro, Daniele; Pearman, Peter B; Salamin, Nicolas

2016-05-01

The evolution of organisms is crucially dependent on the evolution of intraspecific variation. Its interactions with selective agents in the biotic and abiotic environments underlie many processes, such as intraspecific competition, resource partitioning and, eventually, species formation. Nevertheless, comparative models of trait evolution neither allow explicit testing of hypotheses related to the evolution of intraspecific variation nor do they simultaneously estimate rates of trait evolution by accounting for both trait mean and variance. Here, we present a model of phenotypic trait evolution using a hierarchical Bayesian approach that simultaneously incorporates interspecific and intraspecific variation. We assume that species-specific trait means evolve under a simple Brownian motion process, whereas species-specific trait variances are modeled with Brownian or Ornstein-Uhlenbeck processes. After evaluating the power of the method through simulations, we examine whether life-history traits impact evolution of intraspecific variation in the Eriogonoideae (buckwheat family, Polygonaceae). Our model is readily extendible to more complex scenarios of the evolution of inter- and intraspecific variation and presents a step toward more comprehensive comparative models for macroevolutionary studies. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

The macroevolutionary consequences of phenotypic integration: from development to deep time.

PubMed

Goswami, A; Smaers, J B; Soligo, C; Polly, P D

2014-08-19

Phenotypic integration is a pervasive characteristic of organisms. Numerous analyses have demonstrated that patterns of phenotypic integration are conserved across large clades, but that significant variation also exists. For example, heterochronic shifts related to different mammalian reproductive strategies are reflected in postcranial skeletal integration and in coordination of bone ossification. Phenotypic integration and modularity have been hypothesized to shape morphological evolution, and we extended simulations to confirm that trait integration can influence both the trajectory and magnitude of response to selection. We further demonstrate that phenotypic integration can produce both more and less disparate organisms than would be expected under random walk models by repartitioning variance in preferred directions. This effect can also be expected to favour homoplasy and convergent evolution. New empirical analyses of the carnivoran cranium show that rates of evolution, in contrast, are not strongly influenced by phenotypic integration and show little relationship to morphological disparity, suggesting that phenotypic integration may shape the direction of evolutionary change, but not necessarily the speed of it. Nonetheless, phenotypic integration is problematic for morphological clocks and should be incorporated more widely into models that seek to accurately reconstruct both trait and organismal evolution.

The macroevolutionary consequences of phenotypic integration: from development to deep time

PubMed Central

Goswami, A.; Smaers, J. B.; Soligo, C.; Polly, P. D.

2014-01-01

Phenotypic integration is a pervasive characteristic of organisms. Numerous analyses have demonstrated that patterns of phenotypic integration are conserved across large clades, but that significant variation also exists. For example, heterochronic shifts related to different mammalian reproductive strategies are reflected in postcranial skeletal integration and in coordination of bone ossification. Phenotypic integration and modularity have been hypothesized to shape morphological evolution, and we extended simulations to confirm that trait integration can influence both the trajectory and magnitude of response to selection. We further demonstrate that phenotypic integration can produce both more and less disparate organisms than would be expected under random walk models by repartitioning variance in preferred directions. This effect can also be expected to favour homoplasy and convergent evolution. New empirical analyses of the carnivoran cranium show that rates of evolution, in contrast, are not strongly influenced by phenotypic integration and show little relationship to morphological disparity, suggesting that phenotypic integration may shape the direction of evolutionary change, but not necessarily the speed of it. Nonetheless, phenotypic integration is problematic for morphological clocks and should be incorporated more widely into models that seek to accurately reconstruct both trait and organismal evolution. PMID:25002699

The evolution of dorsal-ventral patterning mechanisms in insects.

PubMed

Lynch, Jeremy A; Roth, Siegfried

2011-01-15

The gene regulatory network (GRN) underpinning dorsal-ventral (DV) patterning of the Drosophila embryo is among the most thoroughly understood GRNs, making it an ideal system for comparative studies seeking to understand the evolution of development. With the emergence of widely applicable techniques for testing gene function, species with sequenced genomes, and multiple tractable species with diverse developmental modes, a phylogenetically broad and molecularly deep understanding of the evolution of DV axis formation in insects is feasible. Here, we review recent progress made in this field, compare our emerging molecular understanding to classical embryological experiments, and suggest future directions of inquiry.

Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix

PubMed Central

Springer, Mark S.; Meredith, Robert W.; Gatesy, John; Emerling, Christopher A.; Park, Jong; Rabosky, Daniel L.; Stadler, Tanja; Steiner, Cynthia; Ryder, Oliver A.; Janečka, Jan E.; Fisher, Colleen A.; Murphy, William J.

2012-01-01

Phylogenetic relationships, divergence times, and patterns of biogeographic descent among primate species are both complex and contentious. Here, we generate a robust molecular phylogeny for 70 primate genera and 367 primate species based on a concatenation of 69 nuclear gene segments and ten mitochondrial gene sequences, most of which were extracted from GenBank. Relaxed clock analyses of divergence times with 14 fossil-calibrated nodes suggest that living Primates last shared a common ancestor 71–63 Ma, and that divergences within both Strepsirrhini and Haplorhini are entirely post-Cretaceous. These results are consistent with the hypothesis that the Cretaceous-Paleogene mass extinction of non-avian dinosaurs played an important role in the diversification of placental mammals. Previous queries into primate historical biogeography have suggested Africa, Asia, Europe, or North America as the ancestral area of crown primates, but were based on methods that were coopted from phylogeny reconstruction. By contrast, we analyzed our molecular phylogeny with two methods that were developed explicitly for ancestral area reconstruction, and find support for the hypothesis that the most recent common ancestor of living Primates resided in Asia. Analyses of primate macroevolutionary dynamics provide support for a diversification rate increase in the late Miocene, possibly in response to elevated global mean temperatures, and are consistent with the fossil record. By contrast, diversification analyses failed to detect evidence for rate-shift changes near the Eocene-Oligocene boundary even though the fossil record provides clear evidence for a major turnover event (“Grande Coupure”) at this time. Our results highlight the power and limitations of inferring diversification dynamics from molecular phylogenies, as well as the sensitivity of diversification analyses to different species concepts. PMID:23166696

Contrasting patterns of nonneutral evolution in proteins encoded in nuclear and mitochondrial genomes.

PubMed Central

Weinreich, D M; Rand, D M

2000-01-01

We report that patterns of nonneutral DNA sequence evolution among published nuclear and mitochondrially encoded protein-coding loci differ significantly in animals. Whereas an apparent excess of amino acid polymorphism is seen in most (25/31) mitochondrial genes, this pattern is seen in fewer than half (15/36) of the nuclear data sets. This differentiation is even greater among data sets with significant departures from neutrality (14/15 vs. 1/6). Using forward simulations, we examined patterns of nonneutral evolution using parameters chosen to mimic the differences between mitochondrial and nuclear genetics (we varied recombination rate, population size, mutation rate, selective dominance, and intensity of germ line bottleneck). Patterns of evolution were correlated only with effective population size and strength of selection, and no single genetic factor explains the empirical contrast in patterns. We further report that in Arabidopsis thaliana, a highly self-fertilizing plant with effectively low recombination, five of six published nuclear data sets also exhibit an excess of amino acid polymorphism. We suggest that the contrast between nuclear and mitochondrial nonneutrality in animals stems from differences in rates of recombination in conjunction with a distribution of selective effects. If the majority of mutations segregating in populations are deleterious, high linkage may hinder the spread of the occasional beneficial mutation. PMID:10978302

Causal evidence between monsoon and evolution of rhizomyine rodents

PubMed Central

López-Antoñanzas, Raquel; Knoll, Fabien; Wan, Shiming; Flynn, Lawrence J.

2015-01-01

The modern Asian monsoonal systems are currently believed to have originated around the end of the Oligocene following a crucial step of uplift of the Tibetan-Himalayan highlands. Although monsoon possibly drove the evolution of many mammal lineages during the Neogene, no evidence thereof has been provided so far. We examined the evolutionary history of a clade of rodents, the Rhizomyinae, in conjunction with our current knowledge of monsoon fluctuations over time. The macroevolutionary dynamics of rhizomyines were analyzed within a well-constrained phylogenetic framework coupled with biogeographic and evolutionary rate studies. The evolutionary novelties developed by these rodents were surveyed in parallel with the fluctuations of the Indian monsoon so as to evaluate synchroneity and postulate causal relationships. We showed the existence of three drops in biodiversity during the evolution of rhizomyines, all of which reflected elevated extinction rates. Our results demonstrated linkage of monsoon variations with the evolution and biogeography of rhizomyines. Paradoxically, the evolution of rhizomyines was accelerated during the phases of weakening of the monsoons, not of strengthening, most probably because at those intervals forest habitats declined, which triggered extinction and progressive specialization toward a burrowing existence. PMID:25759260

Causal evidence between monsoon and evolution of rhizomyine rodents.

PubMed

López-Antoñanzas, Raquel; Knoll, Fabien; Wan, Shiming; Flynn, Lawrence J

2015-03-11

The modern Asian monsoonal systems are currently believed to have originated around the end of the Oligocene following a crucial step of uplift of the Tibetan-Himalayan highlands. Although monsoon possibly drove the evolution of many mammal lineages during the Neogene, no evidence thereof has been provided so far. We examined the evolutionary history of a clade of rodents, the Rhizomyinae, in conjunction with our current knowledge of monsoon fluctuations over time. The macroevolutionary dynamics of rhizomyines were analyzed within a well-constrained phylogenetic framework coupled with biogeographic and evolutionary rate studies. The evolutionary novelties developed by these rodents were surveyed in parallel with the fluctuations of the Indian monsoon so as to evaluate synchroneity and postulate causal relationships. We showed the existence of three drops in biodiversity during the evolution of rhizomyines, all of which reflected elevated extinction rates. Our results demonstrated linkage of monsoon variations with the evolution and biogeography of rhizomyines. Paradoxically, the evolution of rhizomyines was accelerated during the phases of weakening of the monsoons, not of strengthening, most probably because at those intervals forest habitats declined, which triggered extinction and progressive specialization toward a burrowing existence.

Phylogeny and biogeography of Primula sect. Armerina: implications for plant evolution under climate change and the uplift of the Qinghai-Tibet Plateau.

PubMed

Ren, Guangpeng; Conti, Elena; Salamin, Nicolas

2015-08-16

The historical orogenesis and associated climatic changes of mountain areas have been suggested to partly account for the occurrence of high levels of biodiversity and endemism. However, their effects on dispersal, differentiation and evolution of many groups of plants are still unknown. In this study, we examined the detailed diversification history of Primula sect. Armerina, and used biogeographic analysis and macro-evolutionary modeling to investigate a series of different questions concerning the evolution of the geographical and ecological distribution of the species in this section. We sequenced five chloroplast and one nuclear genes for species of Primula sect. Armerina. Neither chloroplast nor nuclear trees support the monophyly of the section. The major incongruences between the two trees occur among closely related species and may be explained by hybridization. Our dating analyses based on the chloroplast dataset suggest that this section began to diverge from its relatives around 3.55 million years ago, largely coinciding with the last major uplift of the Qinghai-Tibet Plateau (QTP). Biogeographic analysis supports the origin of the section in the Himalayan Mountains and dispersal from the Himalayas to Northeastern QTP, Western QTP and Hengduan Mountains. Furthermore, evolutionary models of ecological niches show that the two P. fasciculata clades have significantly different climatic niche optima and rates of niche evolution, indicating niche evolution under climatic changes and further providing evidence for explaining their biogeographic patterns. Our results support the hypothesis that geologic and climatic events play important roles in driving biological diversification of organisms in the QTP area. The Pliocene uplift of the QTP and following climatic changes most likely promoted both the inter- and intraspecific divergence of Primula sect. Armerina. This study also illustrates how niche evolution under climatic changes influences biogeographic

Pigment cell interactions and differential xanthophore recruitment underlying zebrafish stripe reiteration and Danio pattern evolution

PubMed Central

Patterson, Larissa B.; Bain, Emily J.; Parichy, David M.

2014-01-01

Fishes have diverse pigment patterns, yet mechanisms of pattern evolution remain poorly understood. In zebrafish, Danio rerio, pigment-cell autonomous interactions generate dark stripes of melanophores that alternate with light interstripes of xanthophores and iridophores. Here, we identify mechanisms underlying the evolution of a uniform pattern in D. albolineatus in which all three pigment cell classes are intermingled. We show that in this species xanthophores differentiate precociously over a wider area, and that cis regulatory evolution has increased expression of xanthogenic Colony Stimulating Factor-1 (Csf1). Expressing Csf1 similarly in D. rerio has cascading effects, driving the intermingling of all three pigment cell classes and resulting in the loss of stripes, as in D. albolineatus. Our results identify novel mechanisms of pattern development and illustrate how pattern diversity can be generated when a core network of pigment-cell autonomous interactions is coupled with changes in pigment cell differentiation. PMID:25374113

Evolution at the tips: Asclepias phylogenomics and new perspectives on leaf surfaces.

PubMed

Fishbein, Mark; Straub, Shannon C K; Boutte, Julien; Hansen, Kimberly; Cronn, Richard C; Liston, Aaron

2018-03-01

Leaf surface traits, such as trichome density and wax production, mediate important ecological processes such as anti-herbivory defense and water-use efficiency. We present a phylogenetic analysis of Asclepias plastomes as a framework for analyzing the evolution of trichome density and presence of epicuticular waxes. We produced a maximum-likelihood phylogeny using plastomes of 103 species of Asclepias. We reconstructed ancestral states and used model comparisons in a likelihood framework to analyze character evolution across Asclepias. We resolved the backbone of Asclepias, placing the Sonoran Desert clade and Incarnatae clade as successive sisters to the remaining species. We present novel findings about leaf surface evolution of Asclepias-the ancestor is reconstructed as waxless and sparsely hairy, a macroevolutionary optimal trichome density is supported, and the rate of evolution of trichome density has accelerated. Increased sampling and selection of best-fitting models of evolution provide more resolved and robust estimates of phylogeny and character evolution than obtained in previous studies. Evolutionary inferences are more sensitive to character coding than model selection. © 2018 The Authors. American Journal of Botany is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America.

Left Right Patterning, Evolution and Cardiac Development

PubMed Central

Dykes, Iain M.

2018-01-01

Many aspects of heart development are determined by the left right axis and as a result several congenital diseases have their origins in aberrant left-right patterning. Establishment of this axis occurs early in embryogenesis before formation of the linear heart tube yet impacts upon much later morphogenetic events. In this review I discuss the differing mechanisms by which left-right polarity is achieved in the mouse and chick embryos and comment on the evolution of this system. I then discus three major classes of cardiovascular defect associated with aberrant left-right patterning seen in mouse mutants and human disease. I describe phenotypes associated with the determination of atrial identity and venous connections, looping morphogenesis of the heart tube and finally the asymmetric remodelling of the embryonic branchial arch arterial system to form the leftward looped arch of aorta and associated great arteries. Where appropriate, I consider left right patterning defects from an evolutionary perspective, demonstrating how developmental processes have been modified in species over time and illustrating how comparative embryology can aide in our understanding of congenital heart disease. PMID:29755990

Sexual selection on male size drives the evolution of male-biased sexual size dimorphism via the prolongation of male development.

PubMed

Rohner, Patrick T; Blanckenhorn, Wolf U; Puniamoorthy, Nalini

2016-06-01

Sexual size dimorphism (SSD) arises when the net effects of natural and sexual selection on body size differ between the sexes. Quantitative SSD variation between taxa is common, but directional intraspecific SSD reversals are rare. We combined micro- and macroevolutionary approaches to study geographic SSD variation in closely related black scavenger flies. Common garden experiments revealed stark intra- and interspecific variation: Sepsis biflexuosa is monomorphic across the Holarctic, while S. cynipsea (only in Europe) consistently exhibits female-biased SSD. Interestingly, S. neocynipsea displays contrasting SSD in Europe (females larger) and North America (males larger), a pattern opposite to the geographic reversal in SSD of S. punctum documented in a previous study. In accordance with the differential equilibrium model for the evolution of SSD, the intensity of sexual selection on male size varied between continents (weaker in Europe), whereas fecundity selection on female body size did not. Subsequent comparative analyses of 49 taxa documented at least six independent origins of male-biased SSD in Sepsidae, which is likely caused by sexual selection on male size and mediated by bimaturism. Therefore, reversals in SSD and the associated changes in larval development might be much more common and rapid and less constrained than currently assumed. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Between a Pod and a Hard Test: The Deep Evolution of Amoebae.

PubMed

Kang, Seungho; Tice, Alexander K; Spiegel, Frederick W; Silberman, Jeffrey D; Pánek, Tomáš; Cepicka, Ivan; Kostka, Martin; Kosakyan, Anush; Alcântara, Daniel M C; Roger, Andrew J; Shadwick, Lora L; Smirnov, Alexey; Kudryavtsev, Alexander; Lahr, Daniel J G; Brown, Matthew W

2017-09-01

Amoebozoa is the eukaryotic supergroup sister to Obazoa, the lineage that contains the animals and Fungi, as well as their protistan relatives, and the breviate and apusomonad flagellates. Amoebozoa is extraordinarily diverse, encompassing important model organisms and significant pathogens. Although amoebozoans are integral to global nutrient cycles and present in nearly all environments, they remain vastly understudied. We present a robust phylogeny of Amoebozoa based on broad representative set of taxa in a phylogenomic framework (325 genes). By sampling 61 taxa using culture-based and single-cell transcriptomics, our analyses show two major clades of Amoebozoa, Discosea, and Tevosa. This phylogeny refutes previous studies in major respects. Our results support the hypothesis that the last common ancestor of Amoebozoa was sexual and flagellated, it also may have had the ability to disperse propagules from a sporocarp-type fruiting body. Overall, the main macroevolutionary patterns in Amoebozoa appear to result from the parallel losses of homologous characters of a multiphase life cycle that included flagella, sex, and sporocarps rather than independent acquisition of convergent features. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

A general patterning approach by manipulating the evolution of two-dimensional liquid foams

NASA Astrophysics Data System (ADS)

Huang, Zhandong; Su, Meng; Yang, Qiang; Li, Zheng; Chen, Shuoran; Li, Yifan; Zhou, Xue; Li, Fengyu; Song, Yanlin

2017-01-01

The evolution of gas-liquid foams has been an attractive topic for more than half a century. However, it remains a challenge to manipulate the evolution of foams, which restricts the development of porous materials with excellent mechanical, thermal, catalytic, electrical or acoustic properties. Here we report a strategy to manipulate the evolution of two-dimensional (2D) liquid foams with a micropatterned surface. We demonstrate that 2D liquid foams can evolve beyond Ostwald ripening (large bubbles always consuming smaller ones). By varying the arrangement of pillars on the surface, we have prepared various patterns of foams in which the size, shape and position of the bubbles can be precisely controlled. Furthermore, these patterned bubbles can serve as a template for the assembly of functional materials, such as nanoparticles and conductive polymers, into desired 2D networks with nanoscale resolution. This methodology provides new insights in controlling curvature-driven evolution and opens a general route for the assembly of functional materials.

Evolution patterns and parameter regimes in edge localized modes on the National Spherical Torus Experiment

DOE Data Explorer

Smith, D. R. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Bell, R. E. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Podesta, M. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Smith, D. R. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Fonck, R. J. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); McKee, G. R. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Diallo, A. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Kaye, S. M. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); LeBlanc, B. P. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Sabbagh, S. A. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States)

2015-09-01

We implement unsupervised machine learning techniques to identify characteristic evolution patterns and associated parameter regimes in edge localized mode (ELM) events observed on the National Spherical Torus Experiment. Multi-channel, localized measurements spanning the pedestal region capture the complex evolution patterns of ELM events on Alfven timescales. Some ELM events are active for less than 100~microsec, but others persist for up to 1~ms. Also, some ELM events exhibit a single dominant perturbation, but others are oscillatory. Clustering calculations with time-series similarity metrics indicate the ELM database contains at least two and possibly three groups of ELMs with similar evolution patterns. The identified ELM groups trigger similar stored energy loss, but the groups occupy distinct parameter regimes for ELM-relevant quantities like plasma current, triangularity, and pedestal height. Notably, the pedestal electron pressure gradient is not an effective parameter for distinguishing the ELM groups, but the ELM groups segregate in terms of electron density gradient and electron temperature gradient. The ELM evolution patterns and corresponding parameter regimes can shape the formulation or validation of nonlinear ELM models. Finally, the techniques and results demonstrate an application of unsupervised machine learning at a data-rich fusion facility.

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

The influence of habitat on the evolution of plants: a case study across Saxifragales

PubMed Central

de Casas, Rafael Rubio; Mort, Mark E.; Soltis, Douglas E.

2016-01-01

Background and Aims Organismal evolution tends to be closely associated with ecological conditions. However, the extent to which this association constrains adaptation or diversification into new habitats remains unclear. We studied habitat evolution in the hyper-diverse angiosperm clade Saxifragales. Methods We used species-level phylogenies for approx. 950 species to analyse the evolution of habitat shifts as well as their influence on plant diversification. We combined habitat characterization based on floristic assignments and state-of-the art phylogenetic comparative methods to estimate within- and across-habitat diversification patterns. Key Results Our analyses showed that Saxifragales diversified into multiple habitats from a forest-inhabiting ancestor and that this diversification is governed by relatively rare habitat shifts. Lineages are likely to stay within inferred ancestral ecological conditions. Adaptation to some habitat types (e.g. aquatic, desert) may be canalizing events that lineages do not escape. Although associations between increased diversification rates and shifts in habitat preferences are occasionally observed, extreme macroevolutionary rates are closely associated with specific habitats. Lineages occurring in shrubland, and especially tundra and rock cliffs, exhibit comparatively high diversification, whereas forest, grassland, desert and aquatic habitats are associated with low diversification. Conclusions The likelihood of occupation of new habitats appears to be asymmetric. Shifts to aquatic and desert habitats may be canalizing events. Other habitats, such as tundra, might act as evolutionary sources, while forests provide the only habitat seemingly colonized easily by lineages originating elsewhere. However, habitat shifts are very rare, and any major environmental alteration is expected to have dramatic evolutionary consequences. PMID:27551029

Convergent evolution as natural experiment: the tape of life reconsidered.

PubMed

Powell, Russell; Mariscal, Carlos

2015-12-06

Stephen Jay Gould argued that replaying the 'tape of life' would result in radically different evolutionary outcomes. Recently, biologists and philosophers of science have paid increasing attention to the theoretical importance of convergent evolution-the independent origination of similar biological forms and functions-which many interpret as evidence against Gould's thesis. In this paper, we examine the evidentiary relevance of convergent evolution for the radical contingency debate. We show that under the right conditions, episodes of convergent evolution can constitute valid natural experiments that support inferences regarding the deep counterfactual stability of macroevolutionary outcomes. However, we argue that proponents of convergence have problematically lumped causally heterogeneous phenomena into a single evidentiary basket, in effect treating all convergent events as if they are of equivalent theoretical import. As a result, the 'critique from convergent evolution' fails to engage with key claims of the radical contingency thesis. To remedy this, we develop ways to break down the heterogeneous set of convergent events based on the nature of the generalizations they support. Adopting this more nuanced approach to convergent evolution allows us to differentiate iterated evolutionary outcomes that are probably common among alternative evolutionary histories and subject to law-like generalizations, from those that do little to undermine and may even support, the Gouldian view of life.

Temporal patterns of glacial lake evolution in high-mountain environments

NASA Astrophysics Data System (ADS)

Mergili, Martin; Emmer, Adam; Viani, Cristina; Huggel, Christian

2017-04-01

Lakes forming at the front of retreating glaciers are characteristic features of high-mountain areas in a warming climate. Typically, lakes shift from the proglacial phase (lake is in direct contact with glacier) to a glacier-detached (no direct contact) and finally to a non-glacial phase (lake catchment is completely deglaciated) of lake evolution. Apart from changing glacier-lake interactions, each stage is characterized by particular features of lake growth, and by the lake's susceptibility to sudden drainage (lake outburst flood). While this concept appears to be valid globally, some mountain areas are rich in dynamically evolving proglacial lakes, while in others most lakes have already shifted to the glacier-detached or even non-glacial phase. In the present contribution we (i) explore and quantify the history of glacial lake formation and evolution over the past up to 70 years; (ii) assess the current situation of selected contrasting mountain areas (eastern and western European Alps, southern and northern Pamir, Cordillera Blanca); and (iii) link the patterns of lake evolution to the prevailing topographic and glaciological characteristics in order to improve the understanding of high-mountain geoenvironmental change. In the eastern Alps we identify only very few lakes in the proglacial stage. While many lakes appeared and dynamically evolved until the 1980s between 2550 m and 2800 m asl, most of them have lost glacier contact until the 2000s, whereas very few new proglacial lakes appeared at the same time. Even though a similar trend is observed in the higher western Alps, a more dynamic glacial lake evolution is observed there. The arid southern Pamir is characterized by a high number of proglacial lakes, mainly around 4500 m asl. There is strong evidence that glacial lake evolution is, after a highly dynamic phase between the 1970s and approx. 2000, decelerating. Few proglacial lakes exist in the higher and more humid, heavily glacierized northern Pamir

Not just black and white: pigment pattern development and evolution in vertebrates

PubMed Central

Mills, Margaret G.; Patterson, Larissa B.

2009-01-01

Animals display diverse colors and patterns that vary within and between species. Similar phenotypes appear in both closely related and widely divergent taxa. Pigment patterns thus provide an opportunity to explore how development is altered to produce differences in form and whether similar phenotypes share a common genetic basis. Understanding the development and evolution of pigment patterns requires knowledge of the cellular interactions and signaling pathways that produce those patterns. These complex traits provide unparalleled opportunities for integrating studies from ecology and behavior to molecular biology and biophysics. PMID:19073271

Social contact patterns can buffer costs of forgetting in the evolution of cooperation.

PubMed

Stevens, Jeffrey R; Woike, Jan K; Schooler, Lael J; Lindner, Stefan; Pachur, Thorsten

2018-06-13

Analyses of the evolution of cooperation often rely on two simplifying assumptions: (i) individuals interact equally frequently with all social network members and (ii) they accurately remember each partner's past cooperation or defection. Here, we examine how more realistic, skewed patterns of contact-in which individuals interact primarily with only a subset of their network's members-influence cooperation. In addition, we test whether skewed contact patterns can counteract the decrease in cooperation caused by memory errors (i.e. forgetting). Finally, we compare two types of memory error that vary in whether forgotten interactions are replaced with random actions or with actions from previous encounters. We use evolutionary simulations of repeated prisoner's dilemma games that vary agents' contact patterns, forgetting rates and types of memory error. We find that highly skewed contact patterns foster cooperation and also buffer the detrimental effects of forgetting. The type of memory error used also influences cooperation rates. Our findings reveal previously neglected but important roles of contact pattern, type of memory error and the interaction of contact pattern and memory on cooperation. Although cognitive limitations may constrain the evolution of cooperation, social contact patterns can counteract some of these constraints. © 2018 The Author(s).

Evolution of antero‐posterior patterning of the limb: Insights from the chick

PubMed Central

2017-01-01

Summary The developing limbs of chicken embryos have served as pioneering models for understanding pattern formation for over a century. The ease with which chick wing and leg buds can be experimentally manipulated, while the embryo is still in the egg, has resulted in the discovery of important developmental organisers, and subsequently, the signals that they produce. Sonic hedgehog (Shh) is produced by mesenchyme cells of the polarizing region at the posterior margin of the limb bud and specifies positional values across the antero‐posterior axis (the axis running from the thumb to the little finger). Detailed experimental embryology has revealed the fundamental parameters required to specify antero‐posterior positional values in response to Shh signaling in chick wing and leg buds. In this review, the evolution of the avian wing and leg will be discussed in the broad context of tetrapod paleontology, and more specifically, ancestral theropod dinosaur paleontology. How the parameters that dictate antero‐posterior patterning could have been modulated to produce the avian wing and leg digit patterns will be considered. Finally, broader speculations will be made regarding what the antero‐posterior patterning of chick limbs can tell us about the evolution of other digit patterns, including those that were found in the limbs of the earliest tetrapods. PMID:28734068

Evolution and inheritance of early embryonic patterning in Drosophila simulans and D. sechellia.

PubMed

Lott, Susan E; Ludwig, Michael Z; Kreitman, Martin

2011-05-01

Pattern formation in Drosophila is a widely studied example of a robust developmental system. Such robust systems pose a challenge to adaptive evolution, as they mask variation that selection may otherwise act upon. Yet we find variation in the localization of expression domains (henceforth "stripe allometry") in the pattern formation pathway. Specifically, we characterize differences in the gap genes giant and Kruppel, and the pair-rule gene even-skipped, which differ between the sibling species Drosophila simulans and D. sechellia. In a double-backcross experiment, stripe allometry is consistent with maternal inheritance of stripe positioning and multiple genetic factors, with a distinct genetic basis from embryo length. Embryos produced by F1 and F2 backcross mothers exhibit novel spatial patterns of gene expression relative to the parental species, with no measurable increase in positional variance among individuals. Buffering of novel spatial patterns in the backcross genotypes suggests that robustness need not be disrupted in order for the trait to evolve, and perhaps the system is incapable of evolving to prevent the expression of all genetic variation. This limitation, and the ability of natural selection to act on minute genetic differences that are within the "margin of error" for the buffering mechanism, indicates that developmentally buffered traits can evolve without disruption of robustness. © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.

Darwin's missing link - a novel paradigm for evolution education

NASA Astrophysics Data System (ADS)

Catley, Kefyn M.

2006-09-01

Microevolutionary mechanisms are taught almost exclusively in our schools, to the detriment of those mechanisms that allow us to understand the larger picture - macroevolution. The results are demonstrable; as a result of the strong emphasis on micro processes in evolution education, students and teachers still have poor understanding of the processes which operate at the macro level, and virtually no understanding at all of the history of life on our planet. Natural selection has become synonymous with the suite of processes we call evolution. This paper makes the case for a paradigm shift in evolution education, so that both perspectives - micro and macro - are given equal weight. Increasingly, issues of bioethics, human origins, cloning, etc., are being cast in a light that requires an understanding of macroevolution. To deny our students access to this debate is to deny the call for universal science literacy. A methodology from professional practice is proposed that could achieve this goal, and discussed in light of its utility, theoretical underpinnings, and historical legacy. A mandate for research is proposed that focuses on learners' understanding of several challenging macroevolutionary concepts, including species, the formation of higher groups, deep time, and hierarchical thinking.

Antigenic Patterns and Evolution of the Human Influenza A (H1N1) Virus.

PubMed

Liu, Mi; Zhao, Xiang; Hua, Sha; Du, Xiangjun; Peng, Yousong; Li, Xiyan; Lan, Yu; Wang, Dayan; Wu, Aiping; Shu, Yuelong; Jiang, Taijiao

2015-09-28

The influenza A (H1N1) virus causes seasonal epidemics that result in severe illnesses and deaths almost every year. A deep understanding of the antigenic patterns and evolution of human influenza A (H1N1) virus is extremely important for its effective surveillance and prevention. Through development of antigenicity inference method for human influenza A (H1N1), named PREDAC-H1, we systematically mapped the antigenic patterns and evolution of the human influenza A (H1N1) virus. Eight dominant antigenic clusters have been inferred for seasonal H1N1 viruses since 1977, which demonstrated sequential replacements over time with a similar pattern in Asia, Europe and North America. Among them, six clusters emerged first in Asia. As for China, three of the eight antigenic clusters were detected in South China earlier than in North China, indicating the leading role of South China in H1N1 transmission. The comprehensive view of the antigenic evolution of human influenza A (H1N1) virus can help formulate better strategy for its prevention and control.

The natural history of achalasia: Evidence of a continuum-"The evolutive pattern theory".

PubMed

Salvador, Renato; Voltarel, Guerrino; Savarino, Edoardo; Capovilla, Giovanni; Pesenti, Elisa; Perazzolo, Anna; Nicoletti, Loredana; Costantini, Andrea; Merigliano, Stefano; Costantini, Mario

2018-04-01

It is currently unclear if the three manometric patterns of esophageal achalasia represent distinct entities or part of a disease continuum. The study's aims were: a) to test the hypothesis that the three patterns represent different stages in the evolution of achalasia; b) to investigate whether manometric patterns change after Laparoscopic-Heller-Dor (LHD). We assessed the patients diagnosed with achalasia who underwent LHD as their first treatment from 1992 to 2016. Their symptoms were scored using a detailed questionnaire for dysphagia, food-regurgitation, and chest pain. Barium-swallow, endoscopy, and esophageal-manometry were performed before and 6 months after surgery. The study population consisted of 511 patients (M:F=283:228). Patients' demographic and clinical data showed that those with pattern III had a shorter history of symptoms, a higher incidence of chest pain, and a less dilated gullet (p<0.001). All patients with a sigmoid-shaped mega-esophagus had pattern I achalasia. One patient with a diagnosis of pattern III achalasia developed pattern II at a follow-up manometry before surgery. At a median follow-up of 30 months (IQR 12-56), the outcome of surgery was positive in 479 patients (91.7%). All patients with pattern I preoperatively had the same pattern after LHD, whereas more than 50% of patients with pattern III before treatment showed pattern I or II after surgery. This study supports the hypothesis/theory that the different manometric patterns represent different stages in the evolution of the disease-where pattern III is the earliest stage, pattern II an intermediate stage, and pattern I the final stage. Copyright © 2017 Editrice Gastroenterologica Italiana S.r.l. Published by Elsevier Ltd. All rights reserved.

Elastic, not plastic species: frozen plasticity theory and the origin of adaptive evolution in sexually reproducing organisms.

PubMed

Flegr, Jaroslav

2010-01-13

Darwin's evolutionary theory could easily explain the evolution of adaptive traits (organs and behavioral patterns) in asexual but not in sexual organisms. Two models, the selfish gene theory and frozen plasticity theory were suggested to explain evolution of adaptive traits in sexual organisms in past 30 years. The frozen plasticity theory suggests that sexual species can evolve new adaptations only when their members are genetically uniform, i.e. only after a portion of the population of the original species had split off, balanced on the edge of extinction for several generations, and then undergone rapid expansion. After a short period of time, estimated on the basis of paleontological data to correspond to 1-2% of the duration of the species, polymorphism accumulates in the gene pool due to frequency-dependent selection; and thus, in each generation, new mutations occur in the presence of different alleles and therefore change their selection coefficients from generation to generation. The species ceases to behave in an evolutionarily plastic manner and becomes evolutionarily elastic on a microevolutionary time-scale and evolutionarily frozen on a macroevolutionary time-scale. It then exists in this state until such changes accumulate in the environment that the species becomes extinct. Frozen plasticity theory, which includes the Darwinian model of evolution as a special case--the evolution of species in a plastic state, not only offers plenty of new predictions to be tested, but also provides explanations for a much broader spectrum of known biological phenomena than classic evolutionary theories. This article was reviewed by Rob Knight, Fyodor Kondrashov and Massimo Di Giulio (nominated by David H. Ardell).

Bony cranial ornamentation linked to rapid evolution of gigantic theropod dinosaurs

NASA Astrophysics Data System (ADS)

Gates, Terry A.; Organ, Chris; Zanno, Lindsay E.

2016-09-01

Exaggerated cranial structures such as crests and horns, hereafter referred to collectively as ornaments, are pervasive across animal species. These structures perform vital roles in visual communication and physical interactions within and between species. Yet the origin and influence of ornamentation on speciation and ecology across macroevolutionary time scales remains poorly understood for virtually all animals. Here, we explore correlative evolution of osseous cranial ornaments with large body size in theropod dinosaurs using a phylogenetic comparative framework. We find that body size evolved directionally toward phyletic giantism an order of magnitude faster in theropod species possessing ornaments compared with unadorned lineages. In addition, we find a body mass threshold below which bony cranial ornaments do not originate. Maniraptoriform dinosaurs generally lack osseous cranial ornaments despite repeatedly crossing this body size threshold. Our study provides novel, quantitative support for a shift in selective pressures on socio-sexual display mechanisms in theropods coincident with the evolution of pennaceous feathers.

Bony cranial ornamentation linked to rapid evolution of gigantic theropod dinosaurs

PubMed Central

Gates, Terry A.; Organ, Chris; Zanno, Lindsay E.

2016-01-01

Exaggerated cranial structures such as crests and horns, hereafter referred to collectively as ornaments, are pervasive across animal species. These structures perform vital roles in visual communication and physical interactions within and between species. Yet the origin and influence of ornamentation on speciation and ecology across macroevolutionary time scales remains poorly understood for virtually all animals. Here, we explore correlative evolution of osseous cranial ornaments with large body size in theropod dinosaurs using a phylogenetic comparative framework. We find that body size evolved directionally toward phyletic giantism an order of magnitude faster in theropod species possessing ornaments compared with unadorned lineages. In addition, we find a body mass threshold below which bony cranial ornaments do not originate. Maniraptoriform dinosaurs generally lack osseous cranial ornaments despite repeatedly crossing this body size threshold. Our study provides novel, quantitative support for a shift in selective pressures on socio-sexual display mechanisms in theropods coincident with the evolution of pennaceous feathers. PMID:27676310

Eocene evolution of whale hearing.

PubMed

Nummela, Sirpa; Thewissen, J G M; Bajpai, Sunil; Hussain, S Taseer; Kumar, Kishor

2004-08-12

The origin of whales (order Cetacea) is one of the best-documented examples of macroevolutionary change in vertebrates. As the earliest whales became obligately marine, all of their organ systems adapted to the new environment. The fossil record indicates that this evolutionary transition took less than 15 million years, and that different organ systems followed different evolutionary trajectories. Here we document the evolutionary changes that took place in the sound transmission mechanism of the outer and middle ear in early whales. Sound transmission mechanisms change early on in whale evolution and pass through a stage (in pakicetids) in which hearing in both air and water is unsophisticated. This intermediate stage is soon abandoned and is replaced (in remingtonocetids and protocetids) by a sound transmission mechanism similar to that in modern toothed whales. The mechanism of these fossil whales lacks sophistication, and still retains some of the key elements that land mammals use to hear airborne sound.

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

The influence of habitat on the evolution of plants: a case study across Saxifragales.

PubMed

de Casas, Rafael Rubio; Mort, Mark E; Soltis, Douglas E

2016-12-01

Organismal evolution tends to be closely associated with ecological conditions. However, the extent to which this association constrains adaptation or diversification into new habitats remains unclear. We studied habitat evolution in the hyper-diverse angiosperm clade Saxifragales. We used species-level phylogenies for approx. 950 species to analyse the evolution of habitat shifts as well as their influence on plant diversification. We combined habitat characterization based on floristic assignments and state-of-the art phylogenetic comparative methods to estimate within- and across-habitat diversification patterns. Our analyses showed that Saxifragales diversified into multiple habitats from a forest-inhabiting ancestor and that this diversification is governed by relatively rare habitat shifts. Lineages are likely to stay within inferred ancestral ecological conditions. Adaptation to some habitat types (e.g. aquatic, desert) may be canalizing events that lineages do not escape. Although associations between increased diversification rates and shifts in habitat preferences are occasionally observed, extreme macroevolutionary rates are closely associated with specific habitats. Lineages occurring in shrubland, and especially tundra and rock cliffs, exhibit comparatively high diversification, whereas forest, grassland, desert and aquatic habitats are associated with low diversification. The likelihood of occupation of new habitats appears to be asymmetric. Shifts to aquatic and desert habitats may be canalizing events. Other habitats, such as tundra, might act as evolutionary sources, while forests provide the only habitat seemingly colonized easily by lineages originating elsewhere. However, habitat shifts are very rare, and any major environmental alteration is expected to have dramatic evolutionary consequences. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company.

Contrasting impacts of competition on ecological and social trait evolution in songbirds

PubMed Central

Tobias, Joseph A.; Burns, Kevin J.; Mason, Nicholas A.; Shultz, Allison J.; Morlon, Hélène

2018-01-01

Competition between closely related species has long been viewed as a powerful selective force that drives trait diversification, thereby generating phenotypic diversity over macroevolutionary timescales. However, although the impact of interspecific competition has been documented in a handful of iconic insular radiations, most previous studies have focused on traits involved in resource use, and few have examined the role of competition across large, continental radiations. Thus, the extent to which broad-scale patterns of phenotypic diversity are shaped by competition remain largely unclear, particularly for social traits. Here, we estimate the effect of competition between interacting lineages by applying new phylogenetic models that account for such interactions to an exceptionally complete dataset of resource-use traits and social signaling traits for the entire radiation of tanagers (Aves, Thraupidae), the largest family of songbirds. We find that interspecific competition strongly influences the evolution of traits involved in resource use, with a weaker effect on plumage signals, and very little effect on song. Our results provide compelling evidence that interspecific exploitative competition contributes to ecological trait diversification among coexisting species, even in a large continental radiation. In comparison, signal traits mediating mate choice and social competition seem to diversify under different evolutionary models, including rapid diversification in the allopatric stage of speciation. PMID:29385141

Contrasting impacts of competition on ecological and social trait evolution in songbirds.

PubMed

Drury, Jonathan P; Tobias, Joseph A; Burns, Kevin J; Mason, Nicholas A; Shultz, Allison J; Morlon, Hélène

2018-01-01

Competition between closely related species has long been viewed as a powerful selective force that drives trait diversification, thereby generating phenotypic diversity over macroevolutionary timescales. However, although the impact of interspecific competition has been documented in a handful of iconic insular radiations, most previous studies have focused on traits involved in resource use, and few have examined the role of competition across large, continental radiations. Thus, the extent to which broad-scale patterns of phenotypic diversity are shaped by competition remain largely unclear, particularly for social traits. Here, we estimate the effect of competition between interacting lineages by applying new phylogenetic models that account for such interactions to an exceptionally complete dataset of resource-use traits and social signaling traits for the entire radiation of tanagers (Aves, Thraupidae), the largest family of songbirds. We find that interspecific competition strongly influences the evolution of traits involved in resource use, with a weaker effect on plumage signals, and very little effect on song. Our results provide compelling evidence that interspecific exploitative competition contributes to ecological trait diversification among coexisting species, even in a large continental radiation. In comparison, signal traits mediating mate choice and social competition seem to diversify under different evolutionary models, including rapid diversification in the allopatric stage of speciation.

Fitting models of continuous trait evolution to incompletely sampled comparative data using approximate Bayesian computation.

PubMed

Slater, Graham J; Harmon, Luke J; Wegmann, Daniel; Joyce, Paul; Revell, Liam J; Alfaro, Michael E

2012-03-01

In recent years, a suite of methods has been developed to fit multiple rate models to phylogenetic comparative data. However, most methods have limited utility at broad phylogenetic scales because they typically require complete sampling of both the tree and the associated phenotypic data. Here, we develop and implement a new, tree-based method called MECCA (Modeling Evolution of Continuous Characters using ABC) that uses a hybrid likelihood/approximate Bayesian computation (ABC)-Markov-Chain Monte Carlo approach to simultaneously infer rates of diversification and trait evolution from incompletely sampled phylogenies and trait data. We demonstrate via simulation that MECCA has considerable power to choose among single versus multiple evolutionary rate models, and thus can be used to test hypotheses about changes in the rate of trait evolution across an incomplete tree of life. We finally apply MECCA to an empirical example of body size evolution in carnivores, and show that there is no evidence for an elevated rate of body size evolution in the pinnipeds relative to terrestrial carnivores. ABC approaches can provide a useful alternative set of tools for future macroevolutionary studies where likelihood-dependent approaches are lacking. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

An integrative method for testing form–function linkages and reconstructed evolutionary pathways of masticatory specialization

PubMed Central

Tseng, Z. Jack; Flynn, John J.

2015-01-01

Morphology serves as a ubiquitous proxy in macroevolutionary studies to identify potential adaptive processes and patterns. Inferences of functional significance of phenotypes or their evolution are overwhelmingly based on data from living taxa. Yet, correspondence between form and function has been tested in only a few model species, and those linkages are highly complex. The lack of explicit methodologies to integrate form and function analyses within a deep-time and phylogenetic context weakens inferences of adaptive morphological evolution, by invoking but not testing form–function linkages. Here, we provide a novel approach to test mechanical properties at reconstructed ancestral nodes/taxa and the strength and direction of evolutionary pathways in feeding biomechanics, in a case study of carnivorous mammals. Using biomechanical profile comparisons that provide functional signals for the separation of feeding morphologies, we demonstrate, using experimental optimization criteria on estimation of strength and direction of functional changes on a phylogeny, that convergence in mechanical properties and degree of evolutionary optimization can be decoupled. This integrative approach is broadly applicable to other clades, by using quantitative data and model-based tests to evaluate interpretations of function from morphology and functional explanations for observed macroevolutionary pathways. PMID:25994295

Antigenic Patterns and Evolution of the Human Influenza A (H1N1) Virus

PubMed Central

Liu, Mi; Zhao, Xiang; Hua, Sha; Du, Xiangjun; Peng, Yousong; Li, Xiyan; Lan, Yu; Wang, Dayan; Wu, Aiping; Shu, Yuelong; Jiang, Taijiao

2015-01-01

The influenza A (H1N1) virus causes seasonal epidemics that result in severe illnesses and deaths almost every year. A deep understanding of the antigenic patterns and evolution of human influenza A (H1N1) virus is extremely important for its effective surveillance and prevention. Through development of antigenicity inference method for human influenza A (H1N1), named PREDAC-H1, we systematically mapped the antigenic patterns and evolution of the human influenza A (H1N1) virus. Eight dominant antigenic clusters have been inferred for seasonal H1N1 viruses since 1977, which demonstrated sequential replacements over time with a similar pattern in Asia, Europe and North America. Among them, six clusters emerged first in Asia. As for China, three of the eight antigenic clusters were detected in South China earlier than in North China, indicating the leading role of South China in H1N1 transmission. The comprehensive view of the antigenic evolution of human influenza A (H1N1) virus can help formulate better strategy for its prevention and control. PMID:26412348

Rates of molecular evolution in tree ferns are associated with body size, environmental temperature, and biological productivity.

PubMed

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

2018-05-01

Variation in rates of molecular evolution (heterotachy) is a common phenomenon among plants. Although multiple theoretical models have been proposed, fundamental questions remain regarding the combined effects of ecological and morphological traits on rate heterogeneity. Here, we used tree ferns to explore the correlation between rates of molecular evolution in chloroplast DNA sequences and several morphological and environmental factors within a Bayesian framework. We revealed direct and indirect effects of body size, biological productivity, and temperature on substitution rates, where smaller tree ferns living in warmer and less productive environments tend to have faster rates of molecular evolution. In addition, we found that variation in the ratio of nonsynonymous to synonymous substitution rates (dN/dS) in the chloroplast rbcL gene was significantly correlated with ecological and morphological variables. Heterotachy in tree ferns may be influenced by effective population size associated with variation in body size and productivity. Macroevolutionary hypotheses should go beyond explaining heterotachy in terms of mutation rates and instead, should integrate population-level factors to better understand the processes affecting the tempo of evolution at the molecular level. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Sorted bedform pattern evolution: Persistence, destruction and self-organized intermittency

NASA Astrophysics Data System (ADS)

Goldstein, Evan B.; Murray, A. Brad; Coco, Giovanni

2011-12-01

We investigate the long-term evolution of inner continental shelf sorted bedform patterns. Numerical modeling suggests that a range of behaviors are possible, from pattern persistence to spatial-temporal intermittency. Sorted bedform persistence results from a robust sorting feedback that operates when the seabed features a sufficient concentration of coarse material. In the absence of storm events, pattern maturation processes such as defect dynamics and pattern migration tend to cause the burial of coarse material and excavation of fine material, leading to the fining of the active layer. Vertical sorting occurs until a critical state of active layer coarseness is reached. This critical state results in the local cessation of the sorting feedback, leading to a self-organized spatially intermittent pattern, a hallmark of observed sorted bedforms. Bedforms in shallow conditions and those subject to high wave climates may be temporally intermittent features as a result of increased wave orbital velocity during storms. Erosion, or deposition of bimodal sediment, similarly leads to a spatially intermittent pattern, with individual coarse domains exhibiting temporal intermittence. Recurring storm events cause coarsening of the seabed (strengthening the sorting feedback) and the development of large wavelength patterns. Cessation of storm events leads to the superposition of storm (large wavelength) and inter-storm (small wavelength) patterns and spatial heterogeneity of pattern modes.

Stratal stacking patterns and tectono-sedimentary evolution of hyperextended magma-poor rifted margins

NASA Astrophysics Data System (ADS)

Ribes, C.; Gillard, M.; Epin, M. E.; Ghienne, J. F.; Manatschal, G.; Karner, G. D.; Johnson, C. A.

2016-12-01

Research on the formation and evolution of deep-water rifted margins has undergone a major paradigm shift in recent years. An increasing number of studies of present-day and fossil rifted margins allow us to identify and characterize the structural architecture of the most distal parts of rifted margins, the so-called hyperextended, magma-poor rifted margins. However, at present, little is known about the depositional environments, sedimentary facies, stacking patterns, subsidence and thermal history within these domains. In this context, characterizing the stratal stacking patterns and understanding their spatial and temporal evolution is a new challenge. The major difficulty comes from the fact that the observed stratigraphic geometries and facies relationships are a result of the complex interplay between sediment supply and available accommodation, which is controlled by not only the regional generation of accommodation, but also by local tectono-magmatic processes. These parameters are poorly constrained or even sufficiently known in these tectonic settings. Indeed, the complex structural evolution of hyperextended magma-poor rifted margins, including the development of poly-phase in-sequence and out of sequence extensional detachment faults and associated mantle exhumation and magmatic activity, can generate complex accommodation patterns over a highly structured top basement. The presentation summarizes early results concerning the controlling parameters on ultra-deep water stratigraphic stacking patterns and to provide a conceptual framework. This observation-driven approach combines fieldwork from fossil Alpine Tethys margins exposed in the Alps and the analysis of seismic reflection data from present-day deep water rifted margins such as the Australian-Antarctic, East India and Iberia-Newfoundland margins.

Oxygen and evolutionary patterns in the sea: onshore/offshore trends and recent recruitment of deep-sea faunas

NASA Technical Reports Server (NTRS)

Jacobs, D. K.; Lindberg, D. R.

1998-01-01

Over the last 15 years a striking pattern of diversification has been documented in the fossil record of benthic marine invertebrates. Higher taxa (orders) tend to originate onshore, diversify offshore, and retreat into deep-water environments. Previous studies attribute this macroevolutionary pattern to a variety of causes, foremost among them the role of nearshore disturbance in providing opportunities for the evolution of novel forms accorded ordinal rank. Our analysis of the post-Paleozoic record of ordinal first appearances indicates that the onshore preference of ordinal origination occurred only in the Mesozoic prior to the Turonian stage of the Cretaceous, a period characterized by relatively frequent anoxic/dysoxic bottom conditions in deeper marine environments. Later, in the Cretaceous and Cenozoic, ordinal origination of benthic organisms did not occur exclusively, or even preferentially, in onshore environments. This change in environmental pattern of ordinal origination roughly correlates with Late Cretaceous: (i) decline in anoxia/dysoxia in offshore benthic environments; (ii) extinction of faunas associated with dysoxic conditions; (iii) increase in bioturbation with the expansion of deep burrowing forms into offshore environments; and (iv) offshore expansion of bryozoan diversity. We also advance a separate argument that the Cenomanian/Turonian and latest Paleocene global events eliminated much of the deep-water benthos. This requires a more recent origin of modern vent and deep-sea faunas, from shallower water refugia, than the Paleozoic or early Mesozoic origin of these faunas suggested by other workers.

Evolution of increased phenotypic diversity enhances population performance by reducing sexual harassment in damselflies.

PubMed

Takahashi, Yuma; Kagawa, Kotaro; Svensson, Erik I; Kawata, Masakado

2014-07-18

The effect of evolutionary changes in traits and phenotypic/genetic diversity on ecological dynamics has received much theoretical attention; however, the mechanisms and ecological consequences are usually unknown. Female-limited colour polymorphism in damselflies is a counter-adaptation to male mating harassment, and thus, is expected to alter population dynamics through relaxing sexual conflict. Here we show the side effect of the evolution of female morph diversity on population performance (for example, population productivity and sustainability) in damselflies. Our theoretical model incorporating key features of the sexual interaction predicts that the evolution of increased phenotypic diversity will reduce overall fitness costs to females from sexual conflict, which in turn will increase productivity, density and stability of a population. Field data and mesocosm experiments support these model predictions. Our study suggests that increased phenotypic diversity can enhance population performance that can potentially reduce extinction rates and thereby influence macroevolutionary processes.

The critical role of fossils in inferring deep-node phylogenetic relationships and macroevolutionary patterns in Cornales.

PubMed

Atkinson, Brian A

2018-05-24

The basal asterid order, Cornales, experienced a rapid radiation during the Cretaceous, which has made it difficult to elucidate the early evolution of the order using extant taxa only. Recent paleobotanical studies, however, have begun to shed light on the early diversification of Cornales. Herein, fossils are directly incorporated in phylogenetic and quantitative morphological analyses to reconstruct early cornalean evolution. A morphological matrix of 77 fruit characters and 58 taxa (24 extinct) was assembled. Parsimony analyses including and excluding fossils were conducted. A fossil inclusive tree was time-scaled to visualize the timing of the initial cornalean radiation. Disparity analyses were utilized to infer the morphological evolution of cornaleans with drupaceous fruits. Fossil inclusive and exclusive parsimony analyses resulted in well-resolved deep-node relationships within Cornales. Resolution in the fossil inclusive analysis is substantially higher, revealing a basal grade including Loasaceae, Hydrangeaceae, Hydrostachyaceae, Grubbiaceae, a Hironoia+Amersinia clade, and Curtisiaceae, respectively, that leads to a "core" group containing a clade comprising a Cretaceous grade leading to clade of Nyssaceae, Mastixiaceae, and Davidiaceae that is sister to a Cornaceae+Alangiaceae clade. The time-scaled tree indicates that the initial cornalean diversification occurred before 89.8 Ma. Disparity analyses suggest the morphological diversity of Cornales peaked during the Paleogene. Phylogenetic analyses clearly demonstrate that novel character mosaics of Cretaceous cornaleans play a critical role in resolving deep-node relationships within Cornales. The post-Cretaceous increase of cornalean disparity is associated with a shift in morphospace occupation, which can be explained from ecological and developmental perspectives. © 2018 Botanical Society of America.

A novel marsupial hepatitis A virus corroborates complex evolutionary patterns shaping the genus Hepatovirus.

PubMed

de Oliveira Carneiro, Ianei; Sander, Anna-Lena; Silva, Namá; Moreira-Soto, Andres; Normann, Andrea; Flehmig, Bertram; Lukashev, Alexander N; Dotzauer, Andreas; Wieseke, Nicolas; Franke, Carlos Roberto; Drexler, Jan Felix

2018-04-25

The discovery of nonprimate hepatoviruses illuminated the evolutionary origins of hepatitis A virus (HAV) in small mammals. Marsupials are ancient mammals that diverged during the Jurassic from other Eutheria. Viruses from marsupials may thus provide important insight into virus evolution. To investigate Hepatovirus macroevolutionary patterns, we sampled 112 opossums in northeastern Brazil. A novel marsupial HAV (MHAV) was detected in a Brazilian Common Opossum ( Didelphis aurita ) by nested RT-PCR. MHAV concentration in liver was high at 2.5x10 9 RNA copies/gram and about 1000-fold higher than in other solid organs, suggesting hepatotropism. Hepatovirus seroprevalence in D. aurita was 26.6% using an ELISA. End-point titers in confirmatory immunofluorescence assays were high and marsupial antibodies co-localized with anti-HAV control sera, suggesting specificity of serological detection. MHAV showed all genomic hallmarks defining hepatoviruses, including late domain motifs likely involved in quasi-envelope acquisition, a predicted C-terminal pX extension of VP1, strong avoidance of CpG dinucleotides and a type 3 internal ribosomal entry site. Translated polyprotein gene sequence distances of at least 23.7% to other hepatoviruses suggested MHAV represents a novel Hepatovirus species. Conserved predicted cleavage sites suggested similarities in polyprotein processing between HAV and MHAV. MHAV was nested within rodent hepatoviruses in phylogenetic reconstructions, suggesting an ancestral hepatovirus host switch from rodents into marsupials. Co-phylogenetic reconciliations of host and hepatovirus phylogenies confirmed that host-independent macroevolutionary patterns shaped the phylogenetic relationships of extant hepatoviruses. Although Marsupials are synanthropic and consumed as wild game in Brazil, HAV community protective immunity may limit the zoonotic potential of MHAV. IMPORTANCE The hepatitis A virus (HAV) is an ubiquitous cause of acute hepatitis in humans

The evolution of nervous system patterning: insights from sea urchin development

PubMed Central

Angerer, Lynne M.; Yaguchi, Shunsuke; Angerer, Robert C.; Burke, Robert D.

2011-01-01

Recent studies of the sea urchin embryo have elucidated the mechanisms that localize and pattern its nervous system. These studies have revealed the presence of two overlapping regions of neurogenic potential at the beginning of embryogenesis, each of which becomes progressively restricted by separate, yet linked, signals, including Wnt and subsequently Nodal and BMP. These signals act to specify and localize the embryonic neural fields – the anterior neuroectoderm and the more posterior ciliary band neuroectoderm – during development. Here, we review these conserved nervous system patterning signals and consider how the relationships between them might have changed during deuterostome evolution. PMID:21828090

The Evolution of Energetic Scaling across the Vertebrate Tree of Life.

PubMed

Uyeda, Josef C; Pennell, Matthew W; Miller, Eliot T; Maia, Rafael; McClain, Craig R

2017-08-01

Metabolism is the link between ecology and physiology-it dictates the flow of energy through individuals and across trophic levels. Much of the predictive power of metabolic theories of ecology derives from the scaling relationship between organismal size and metabolic rate. There is growing evidence that this scaling relationship is not universal, but we have little knowledge of how it has evolved over macroevolutionary time. Here we develop a novel phylogenetic comparative method to investigate how often and in which clades the macroevolutionary dynamics of the metabolic scaling have changed. We find strong evidence that the metabolic scaling relationship has shifted multiple times across the vertebrate phylogeny. However, shifts are rare and otherwise strongly constrained. Importantly, both the estimated slope and intercept values vary widely across regimes, with slopes that spanned across theoretically predicted values such as 2/3 or 3/4. We further tested whether traits such as ecto-/endothermy, genome size, and quadratic curvature with body mass (i.e., energetic constraints at extreme body sizes) could explain the observed pattern of shifts. Though these factors help explain some of the variation in scaling parameters, much of the remaining variation remains elusive. Our results lay the groundwork for further exploration of the evolutionary and ecological drivers of major transitions in metabolic strategy and for harnessing this information to improve macroecological predictions.

Biophysical models of protein evolution: Understanding the patterns of evolutionary sequence divergence

PubMed Central

Echave, Julian; Wilke, Claus O.

2018-01-01

For decades, rates of protein evolution have been interpreted in terms of the vague concept of “functional importance”. Slowly evolving proteins or sites within proteins were assumed to be more functionally important and thus subject to stronger selection pressure. More recently, biophysical models of protein evolution, which combine evolutionary theory with protein biophysics, have completely revolutionized our view of the forces that shape sequence divergence. Slowly evolving proteins have been found to evolve slowly because of selection against toxic misfolding and misinteractions, linking their rate of evolution primarily to their abundance. Similarly, most slowly evolving sites in proteins are not directly involved in function, but mutating them has large impacts on protein structure and stability. Here, we review the studies of the emergent field of biophysical protein evolution that have shaped our current understanding of sequence divergence patterns. We also propose future research directions to develop this nascent field. PMID:28301766

Colour pattern homology and evolution in Vanessa butterflies (Nymphalidae: Nymphalini): eyespot characters.

PubMed

Abbasi, R; Marcus, J M

2015-11-01

Ocelli are serially repeated colour patterns on the wings of many butterflies. Eyespots are elaborate ocelli that function in predator avoidance and deterrence as well as in mate choice. A phylogenetic approach was used to study ocelli and eyespot evolution in Vanessa butterflies, a genus exhibiting diverse phenotypes among these serial homologs. Forty-four morphological characters based on eyespot number, arrangement, shape and the number of elements in each eyespot were defined and scored. Ocelli from eight wing cells on the dorsal and ventral surfaces of the forewing and hindwing were evaluated. The evolution of these characters was traced over a phylogeny of Vanessa based on 7750 DNA base pairs from 10 genes. Our reconstruction predicts that the ancestral Vanessa had 5 serially arranged ocelli on all four wing surfaces. The ancestral state on the dorsal forewing and ventral hindwing was ocelli arranged in two heterogeneous groups. On the dorsal hindwing, the ancestral state was either homogenous or ocelli arranged in two heterogeneous groups. On the ventral forewing, we determined that the ancestral state was organized into three heterogeneous groups. In Vanessa, almost all ocelli are individuated and capable of independent evolution relative to other colour patterns except for the ocelli in cells -1 and 0 on the dorsal and ventral forewings, which appear to be constrained to evolve in parallel. The genus Vanessa is a good model system for the study of serial homology and the interaction of selective forces with developmental architecture to produce diversity in butterfly colour patterns. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Pollinator-driven ecological speciation in plants: new evidence and future perspectives

PubMed Central

Van der Niet, Timotheüs; Peakall, Rod; Johnson, Steven D.

2014-01-01

Background The hypothesis that pollinators have been important drivers of angiosperm diversity dates back to Darwin, and remains an important research topic today. Mounting evidence indicates that pollinators have the potential to drive diversification at several different stages of the evolutionary process. Microevolutionary studies have provided evidence for pollinator-mediated floral adaptation, while macroevolutionary evidence supports a general pattern of pollinator-driven diversification of angiosperms. However, the overarching issue of whether, and how, shifts in pollination system drive plant speciation represents a critical gap in knowledge. Bridging this gap is crucial to fully understand whether pollinator-driven microevolution accounts for the observed macroevolutionary patterns. Testable predictions about pollinator-driven speciation can be derived from the theory of ecological speciation, according to which adaptation (microevolution) and speciation (macroevolution) are directly linked. This theory is a particularly suitable framework for evaluating evidence for the processes underlying shifts in pollination systems and their potential consequences for the evolution of reproductive isolation and speciation. Scope This Viewpoint paper focuses on evidence for the four components of ecological speciation in the context of plant-pollinator interactions, namely (1) the role of pollinators as selective agents, (2) floral trait divergence, including the evolution of ‘pollination ecotypes‘, (3) the geographical context of selection on floral traits, and (4) the role of pollinators in the evolution of reproductive isolation. This Viewpoint also serves as the introduction to a Special Issue on Pollinator-Driven Speciation in Plants. The 13 papers in this Special Issue range from microevolutionary studies of ecotypes to macroevolutionary studies of historical ecological shifts, and span a wide range of geographical areas and plant families. These studies

Building the backbone: the development and evolution of vertebral patterning.

PubMed

Fleming, Angeleen; Kishida, Marcia G; Kimmel, Charles B; Keynes, Roger J

2015-05-15

The segmented vertebral column comprises a repeat series of vertebrae, each consisting of two key components: the vertebral body (or centrum) and the vertebral arches. Despite being a defining feature of the vertebrates, much remains to be understood about vertebral development and evolution. Particular controversy surrounds whether vertebral component structures are homologous across vertebrates, how somite and vertebral patterning are connected, and the developmental origin of vertebral bone-mineralizing cells. Here, we assemble evidence from ichthyologists, palaeontologists and developmental biologists to consider these issues. Vertebral arch elements were present in early stem vertebrates, whereas centra arose later. We argue that centra are homologous among jawed vertebrates, and review evidence in teleosts that the notochord plays an instructive role in segmental patterning, alongside the somites, and contributes to mineralization. By clarifying the evolutionary relationship between centra and arches, and their varying modes of skeletal mineralization, we can better appreciate the detailed mechanisms that regulate and diversify vertebral patterning. © 2015. Published by The Company of Biologists Ltd.

Morphological evolution of thin polymer film on chemically patterned substrates

NASA Astrophysics Data System (ADS)

Singh, Satya Pal

2018-05-01

In this paper work, pattern formation in ultra thin polymer film, adsorbed on chemically patterned substrates, is reported under strong confinement. The observations indicate for the strong influence of the surface attraction over evolution of spindoal waves, leading to the flattening of the film. But, the film appears to be torn apart in strip or nano fiber like structures, because of coalescences of the monomers at the free ends of the chains. The beads at the free ends of the chain are relatively more mobile. The chain diffusion towards attractive part of the chemically patterned surfaces is clearly seen. Prewetting or crystallization like phenomena seems to appear resulting into formation of strips with coexistence of molten phase drops at the top of the ruptured film. The investigation mimics spindoal dewetting because of the fact that the rupturing occurs in case of strong attractive surface. The investigation is of technical importance as it highlights the formation of nano scale strips and fibers though in a quasi equilibrium case.

Conserved patterns of integrated developmental plasticity in a group of polyphenic tropical butterflies.

PubMed

van Bergen, Erik; Osbaldeston, Dave; Kodandaramaiah, Ullasa; Brattström, Oskar; Aduse-Poku, Kwaku; Brakefield, Paul M

2017-02-27

Developmental plasticity is thought to have profound macro-evolutionary effects, for example, by increasing the probability of establishment in new environments and subsequent divergence into independently evolving lineages. In contrast to plasticity optimized for individual traits, phenotypic integration, which enables a concerted response of plastic traits to environmental variability, may affect the rate of local adaptation by constraining independent responses of traits to selection. Using a comparative framework, this study explores the evolution of reaction norms for a variety of life history and morphological traits across five related species of mycalesine butterflies from the Old World tropics. Our data indicate that an integrated response of a suite of key traits is shared amongst these species. Interestingly, the traits that make up the functional suite are all known to be regulated by ecdysteroid signalling in Bicyclus anynana, one of the species included in this study, suggesting the same underlying hormonal regulator may be conserved within this group of polyphenic butterflies. We also detect developmental thresholds for the expression of alternative morphs. The phenotypic plasticity of a broad suite of morphological and life history traits is integrated and shared among species from three geographically independent lineages of mycalesine butterflies, despite considerable periods of independent evolution and exposure to disparate environments. At the same time, we have detected examples of evolutionary change where independent traits show different patterns of reaction norms. We argue that the expression of more robust phenotypes may occur by shifting developmental thresholds beyond the boundaries of the typical environmental variation.

Decoupled temporal patterns of evolution and ecology in two post-Paleozoic clades

NASA Technical Reports Server (NTRS)

McKinney, F. K.; Lidgard, S.; Sepkoski, J. J. Jr; Taylor, P. D.

1998-01-01

Counts of taxonomic diversity are the prevailing standards for documenting large-scale patterns of evolution in the fossil record. However, the secular pattern of relative ecological importance between the bryozoan clades Cyclostomata and Cheilostomata is not reflected fully in compilations of generic diversity or within-fauna species richness, and the delayed ecological recovery of the Cheilostomata after the mass extinction at the Cretaceous-Tertiary boundary is missed entirely. These observations demonstrate that evolutionary success and ecological dominance can be decoupled and profoundly different, even over tens of millions of years.

A simple model for research interest evolution patterns

NASA Astrophysics Data System (ADS)

Jia, Tao; Wang, Dashun; Szymanski, Boleslaw

Sir Isaac Newton supposedly remarked that in his scientific career he was like ``...a boy playing on the sea-shore ...finding a smoother pebble or a prettier shell than ordinary''. His remarkable modesty and famous understatement motivate us to seek regularities in how scientists shift their research focus as the career develops. Indeed, despite intensive investigations on how microscopic factors, such as incentives and risks, would influence a scientist's choice of research agenda, little is known on the macroscopic patterns in the research interest change undertaken by individual scientists throughout their careers. Here we make use of over 14,000 authors' publication records in physics. By quantifying statistical characteristics in the interest evolution, we model scientific research as a random walk, which reproduces patterns in individuals' careers observed empirically. Despite myriad of factors that shape and influence individual choices of research subjects, we identified regularities in this dynamical process that are well captured by a simple statistical model. The results advance our understanding of scientists' behaviors during their careers and open up avenues for future studies in the science of science.

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

PubMed

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

2017-04-01

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

The evolution of genital complexity and mating rates in sexually size dimorphic spiders.

PubMed

Kuntner, Matjaž; Cheng, Ren-Chung; Kralj-Fišer, Simona; Liao, Chen-Pan; Schneider, Jutta M; Elgar, Mark A

2016-11-09

Genital diversity may arise through sexual conflict over polyandry, where male genital features function to manipulate female mating frequency against her interest. Correlated genital evolution across animal groups is consistent with this view, but a link between genital complexity and mating rates remains to be established. In sexually size dimorphic spiders, golden orbweaving spiders (Nephilidae) males mutilate their genitals to form genital plugs, but these plugs do not always prevent female polyandry. In a comparative framework, we test whether male and female genital complexity coevolve, and how these morphologies, as well as sexual cannibalism, relate to the evolution of mating systems. Using a combination of comparative tests, we show that male genital complexity negatively correlates with female mating rates, and that levels of sexual cannibalism negatively correlate with male mating rates. We also confirm a positive correlation between male and female genital complexity. The macroevolutionary trajectory is consistent with a repeated evolution from polyandry to monandry coinciding with the evolution towards more complex male genitals. These results are consistent with the predictions from sexual conflict theory, although sexual conflict may not be the only mechanism responsible for the evolution of genital complexity and mating systems. Nevertheless, our comparative evidence suggests that in golden orbweavers, male genital complexity limits female mating rates, and sexual cannibalism by females coincides with monogyny.

Environmental and scale-dependent evolutionary trends in the body size of crustaceans

PubMed Central

Klompmaker, Adiël A.; Schweitzer, Carrie E.; Feldmann, Rodney M.; Kowalewski, Michał

2015-01-01

The ecological and physiological significance of body size is well recognized. However, key macroevolutionary questions regarding the dependency of body size trends on the taxonomic scale of analysis and the role of environment in controlling long-term evolution of body size are largely unknown. Here, we evaluate these issues for decapod crustaceans, a group that diversified in the Mesozoic. A compilation of body size data for 792 brachyuran crab and lobster species reveals that their maximum, mean and median body size increased, but no increase in minimum size was observed. This increase is not expressed within lineages, but is rather a product of the appearance and/or diversification of new clades of larger, primarily burrowing to shelter-seeking decapods. This argues against directional selective pressures within lineages. Rather, the trend is a macroevolutionary consequence of species sorting: preferential origination of new decapod clades with intrinsically larger body sizes. Furthermore, body size evolution appears to have been habitat-controlled. In the Cretaceous, reef-associated crabs became markedly smaller than those in other habitats, a pattern that persists today. The long-term increase in body size of crabs and lobsters, coupled with their increased diversity and abundance, suggests that their ecological impact may have increased over evolutionary time. PMID:26156761

Differential scaling patterns of vertebrae and the evolution of neck length in mammals.

PubMed

Arnold, Patrick; Amson, Eli; Fischer, Martin S

2017-06-01

Almost all mammals have seven vertebrae in their cervical spines. This consistency represents one of the most prominent examples of morphological stasis in vertebrae evolution. Hence, the requirements associated with evolutionary modifications of neck length have to be met with a fixed number of vertebrae. It has not been clear whether body size influences the overall length of the cervical spine and its inner organization (i.e., if the mammalian neck is subject to allometry). Here, we provide the first large-scale analysis of the scaling patterns of the cervical spine and its constituting cervical vertebrae. Our findings reveal that the opposite allometric scaling of C1 and C2-C7 accommodate the increase of neck bending moment with body size. The internal organization of the neck skeleton exhibits surprisingly uniformity in the vast majority of mammals. Deviations from this general pattern only occur under extreme loading regimes associated with particular functional and allometric demands. Our results indicate that the main source of variation in the mammalian neck stems from the disparity of overall cervical spine length. The mammalian neck reveals how evolutionary disparity manifests itself in a structure that is otherwise highly restricted by meristic constraints. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

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.

Independent evolution of baleen whale gigantism linked to Plio-Pleistocene ocean dynamics.

PubMed

Slater, Graham J; Goldbogen, Jeremy A; Pyenson, Nicholas D

2017-05-31

Vertebrates have evolved to gigantic sizes repeatedly over the past 250 Myr, reaching their extreme in today's baleen whales (Mysticeti). Hypotheses for the evolution of exceptionally large size in mysticetes range from niche partitioning to predator avoidance, but there has been no quantitative examination of body size evolutionary dynamics in this clade and it remains unclear when, why or how gigantism evolved. By fitting phylogenetic macroevolutionary models to a dataset consisting of living and extinct species, we show that mysticetes underwent a clade-wide shift in their mode of body size evolution during the Plio-Pleistocene. This transition, from Brownian motion-like dynamics to a trended random walk towards larger size, is temporally linked to the onset of seasonally intensified upwelling along coastal ecosystems. High prey densities resulting from wind-driven upwelling, rather than abundant resources alone, are the primary determinant of efficient foraging in extant mysticetes and Late Pliocene changes in ocean dynamics may have provided an ecological pathway to gigantism in multiple independent lineages. © 2017 The Author(s).

Independent evolution of baleen whale gigantism linked to Plio-Pleistocene ocean dynamics

PubMed Central

Goldbogen, Jeremy A.

2017-01-01

Vertebrates have evolved to gigantic sizes repeatedly over the past 250 Myr, reaching their extreme in today's baleen whales (Mysticeti). Hypotheses for the evolution of exceptionally large size in mysticetes range from niche partitioning to predator avoidance, but there has been no quantitative examination of body size evolutionary dynamics in this clade and it remains unclear when, why or how gigantism evolved. By fitting phylogenetic macroevolutionary models to a dataset consisting of living and extinct species, we show that mysticetes underwent a clade-wide shift in their mode of body size evolution during the Plio-Pleistocene. This transition, from Brownian motion-like dynamics to a trended random walk towards larger size, is temporally linked to the onset of seasonally intensified upwelling along coastal ecosystems. High prey densities resulting from wind-driven upwelling, rather than abundant resources alone, are the primary determinant of efficient foraging in extant mysticetes and Late Pliocene changes in ocean dynamics may have provided an ecological pathway to gigantism in multiple independent lineages. PMID:28539520

Inferring individual-level processes from population-level patterns in cultural evolution.

PubMed

Kandler, Anne; Wilder, Bryan; Fortunato, Laura

2017-09-01

Our species is characterized by a great degree of cultural variation, both within and between populations. Understanding how group-level patterns of culture emerge from individual-level behaviour is a long-standing question in the biological and social sciences. We develop a simulation model capturing demographic and cultural dynamics relevant to human cultural evolution, focusing on the interface between population-level patterns and individual-level processes. The model tracks the distribution of variants of cultural traits across individuals in a population over time, conditioned on different pathways for the transmission of information between individuals. From these data, we obtain theoretical expectations for a range of statistics commonly used to capture population-level characteristics (e.g. the degree of cultural diversity). Consistent with previous theoretical work, our results show that the patterns observed at the level of groups are rooted in the interplay between the transmission pathways and the age structure of the population. We also explore whether, and under what conditions, the different pathways can be distinguished based on their group-level signatures, in an effort to establish theoretical limits to inference. Our results show that the temporal dynamic of cultural change over time retains a stronger signature than the cultural composition of the population at a specific point in time. Overall, the results suggest a shift in focus from identifying the one individual-level process that likely produced the observed data to excluding those that likely did not. We conclude by discussing the implications for empirical studies of human cultural evolution.

Inferring individual-level processes from population-level patterns in cultural evolution

PubMed Central

Wilder, Bryan

2017-01-01

Our species is characterized by a great degree of cultural variation, both within and between populations. Understanding how group-level patterns of culture emerge from individual-level behaviour is a long-standing question in the biological and social sciences. We develop a simulation model capturing demographic and cultural dynamics relevant to human cultural evolution, focusing on the interface between population-level patterns and individual-level processes. The model tracks the distribution of variants of cultural traits across individuals in a population over time, conditioned on different pathways for the transmission of information between individuals. From these data, we obtain theoretical expectations for a range of statistics commonly used to capture population-level characteristics (e.g. the degree of cultural diversity). Consistent with previous theoretical work, our results show that the patterns observed at the level of groups are rooted in the interplay between the transmission pathways and the age structure of the population. We also explore whether, and under what conditions, the different pathways can be distinguished based on their group-level signatures, in an effort to establish theoretical limits to inference. Our results show that the temporal dynamic of cultural change over time retains a stronger signature than the cultural composition of the population at a specific point in time. Overall, the results suggest a shift in focus from identifying the one individual-level process that likely produced the observed data to excluding those that likely did not. We conclude by discussing the implications for empirical studies of human cultural evolution. PMID:28989786

The evolution of phenotypic plasticity in fish swimming

PubMed Central

Oufiero, Christopher E.; Whitlow, Katrina R.

2016-01-01

Abstract Fish have a remarkable amount of variation in their swimming performance, from within species differences to diversity among major taxonomic groups. Fish swimming is a complex, integrative phenotype and has the ability to plastically respond to a myriad of environmental changes. The plasticity of fish swimming has been observed on whole-organismal traits such as burst speed or critical swimming speed, as well as underlying phenotypes such as muscle fiber types, kinematics, cardiovascular system, and neuronal processes. Whether the plastic responses of fish swimming are beneficial seems to depend on the environmental variable that is changing. For example, because of the effects of temperature on biochemical processes, alterations of fish swimming in response to temperature do not seem to be beneficial. In contrast, changes in fish swimming in response to variation in flow may benefit the fish to maintain position in the water column. In this paper, we examine how this plasticity in fish swimming might evolve, focusing on environmental variables that have received the most attention: temperature, habitat, dissolved oxygen, and carbon dioxide variation. Using examples from previous research, we highlight many of the ways fish swimming can plastically respond to environmental variation and discuss potential avenues of future research aimed at understanding how plasticity of fish swimming might evolve. We consider the direct and indirect effects of environmental variation on swimming performance, including changes in swimming kinematics and suborganismal traits thought to predict swimming performance. We also discuss the role of the evolution of plasticity in shaping macroevolutionary patterns of diversity in fish swimming. PMID:29491937

Bioclimatic niches are conserved and unrelated to pollination syndromes in Antillean Gesneriaceae

PubMed Central

Faure, Julie; Ginzbarg, Steven; Clark, John; Joly, Simon

2017-01-01

The study of the evolution of abiotic niches can be informative regarding the speciation drivers in a given group. Yet, two factors that could potentially affect niche evolution have seldom been addressed concomitantly, which are biotic interactions and geographical isolation. In this study, we used as a model group the Antillean plant genera Gesneria and Rhytidophyllum (Gesneriaceae) to evaluate the effect of pollinators and geographical isolation on the bioclimatic niche. These genera possess species characterized by interspecific geographical isolation in different islands and are pollinated by different pollinators. Some species are pollinated by hummingbirds, other by bats, while some are more generalists and are pollinated by pollinators from both functional groups. After describing the bioclimatic niches of plant species, we measured niche overlap for species pairs and we fitted Brownian motion and Ornstein–Uhlenbeck (OU) evolution models with multiple evolutionary regimes to test for an effect of pollination strategy or geographical isolation on bioclimatic niche evolution of these plants. The analysis of niche overlap between plant species, which could not be corrected for phylogenetic relationships, showed that it was significantly influenced by pollination mode and island distribution. By contrast, the best fitting evolutionary model on niche optima and tolerance was always an OU model with a unique selective regime, suggesting that neither pollination strategy nor island isolation had an important effect on bioclimatic niches at a macroevolutionary scale. Instead, we conclude that bioclimatic niches of Antillean Gesneriaceae evolved under phylogenetic conservatism and hypothesize that this macroevolutionary pattern could result from adaptation to temporally variable climates in the Antilles. PMID:29291050

Phylomemetic patterns in science evolution--the rise and fall of scientific fields.

PubMed

Chavalarias, David; Cointet, Jean-Philippe

2013-01-01

We introduce an automated method for the bottom-up reconstruction of the cognitive evolution of science, based on big-data issued from digital libraries, and modeled as lineage relationships between scientific fields. We refer to these dynamic structures as phylomemetic networks or phylomemies, by analogy with biological evolution; and we show that they exhibit strong regularities, with clearly identifiable phylomemetic patterns. Some structural properties of the scientific fields - in particular their density -, which are defined independently of the phylomemy reconstruction, are clearly correlated with their status and their fate in the phylomemy (like their age or their short term survival). Within the framework of a quantitative epistemology, this approach raises the question of predictibility for science evolution, and sketches a prototypical life cycle of the scientific fields: an increase of their cohesion after their emergence, the renewal of their conceptual background through branching or merging events, before decaying when their density is getting too low.

Developing a Learning Progression for Three-Dimensional Learning of the Patterns of Evolution

ERIC Educational Resources Information Center

Wyner, Yael; Doherty, Jennifer H.

2017-01-01

This paper examines how students make progress toward three-dimensional (3D) understanding of the patterns of evolution. Specifically, it proposes a learning progression that explains how scientific practices, crosscutting concepts, and disciplinary core ideas come together in naming and grouping, length of change over time, and the role of common…

Convergent evolution as natural experiment: the tape of life reconsidered

PubMed Central

Powell, Russell; Mariscal, Carlos

2015-01-01

Stephen Jay Gould argued that replaying the ‘tape of life’ would result in radically different evolutionary outcomes. Recently, biologists and philosophers of science have paid increasing attention to the theoretical importance of convergent evolution—the independent origination of similar biological forms and functions—which many interpret as evidence against Gould's thesis. In this paper, we examine the evidentiary relevance of convergent evolution for the radical contingency debate. We show that under the right conditions, episodes of convergent evolution can constitute valid natural experiments that support inferences regarding the deep counterfactual stability of macroevolutionary outcomes. However, we argue that proponents of convergence have problematically lumped causally heterogeneous phenomena into a single evidentiary basket, in effect treating all convergent events as if they are of equivalent theoretical import. As a result, the ‘critique from convergent evolution’ fails to engage with key claims of the radical contingency thesis. To remedy this, we develop ways to break down the heterogeneous set of convergent events based on the nature of the generalizations they support. Adopting this more nuanced approach to convergent evolution allows us to differentiate iterated evolutionary outcomes that are probably common among alternative evolutionary histories and subject to law-like generalizations, from those that do little to undermine and may even support, the Gouldian view of life. PMID:26640647

The importance of offshore origination revealed through ophiuroid phylogenomics.

PubMed

Bribiesca-Contreras, Guadalupe; Verbruggen, Heroen; Hugall, Andrew F; O'Hara, Timothy D

2017-07-12

Our knowledge of macro-evolutionary processes in the deep sea is poor, leading to much speculation about whether the deep sea is a source or sink of evolutionary adaptation. Here, we use a phylogenetic approach, on large molecular (688 species, 275 kbp) and distributional datasets (104 513 records) across an entire class of marine invertebrates (Ophiuroidea), to infer rates of bathymetric range shift over time between shallow and deep water biomes. Biome conservation is evident through the phylogeny, with the majority of species in most clades distributed within the same bathome. Despite this, bathymetric shifts have occurred. We inferred from ancestral reconstructions that eurybathic or intermediate distributions across both biomes were a transitional state and direct changes between shallow and deep sea did not occur. The macro-evolutionary pattern of bathome shift appeared to reflect micro-evolutionary processes of bathymetric speciation. Results suggest that most of the oldest clades have a deep-sea origin, but multiple colonization events indicate that the evolution of this group conforms neither to a simple onshore-offshore hypothesis, nor the opposite pattern. Both shallow and deep bathomes have played an important role in generating the current diversity of this major benthic class. © 2017 The Author(s).

The eunuch phenomenon: adaptive evolution of genital emasculation in sexually dimorphic spiders.

PubMed

Kuntner, Matjaž; Agnarsson, Ingi; Li, Daiqin

2015-02-01

Under natural and sexual selection traits often evolve that secure paternity or maternity through self-sacrifice to predators, rivals, offspring, or partners. Emasculation-males removing their genitals-is an unusual example of such behaviours. Known only in insects and spiders, the phenomenon's adaptiveness is difficult to explain, yet its repeated origins and association with sexual size dimorphism (SSD) and sexual cannibalism suggest an adaptive significance. In spiders, emasculation of paired male sperm-transferring organs - secondary genitals - (hereafter, palps), results in 'eunuchs'. This behaviour has been hypothesized to be adaptive because (i) males plug female genitals with their severed palps (plugging hypothesis), (ii) males remove their palps to become better fighters in male-male contests (better-fighter hypothesis), perhaps reaching higher agility due to reduced total body mass (gloves-off hypothesis), and (iii) males achieve prolonged sperm transfer through severed genitals (remote-copulation hypothesis). Prior research has provided evidence in support of these hypotheses in some orb-weaving spiders but these explanations are far from general. Seeking broad macroevolutionary patterns of spider emasculation, we review the known occurrences, weigh the evidence in support of the hypotheses in each known case, and redefine more precisely the particular cases of emasculation depending on its timing in relation to maturation and mating: 'pre-maturation', 'mating', and 'post-mating'. We use a genus-level spider phylogeny to explore emasculation evolution and to investigate potential evolutionary linkage between emasculation, SSD, lesser genital damage (embolic breakage), and sexual cannibalism (females consuming their mates). We find a complex pattern of spider emasculation evolution, all cases confined to Araneoidea: emasculation evolved at least five and up to 11 times, was lost at least four times, and became further modified at least once. We also find

Genetics and evolution of colour patterns in reptiles.

PubMed

Olsson, Mats; Stuart-Fox, Devi; Ballen, Cissy

2013-01-01

The study of coloration in the polyphyletic reptilians has flourished in the last two decades, in particular with respect to the underlying genetics of colour traits, the function of colours in social interactions, and ongoing selection on these traits in the wild. The taxonomic bias, however, is profound: at this level of resolution almost all available information is for diurnal lizards. Therefore, we focus on case studies, for which there are as complete causal sequences of colour evolution as possible, from phenotypic expression of variation in colour, to ongoing selection in the wild. For work prior to 1992 and for a broader coverage of reptilian coloration we refer the readers to Cooper and Greenburg's (Biology of the Reptilia, 1992) review. There are seven major conclusions we would like to emphasise: (a) visual systems in diurnal lizards are broadly conserved but among the wider range of reptiles in general, there is functionally important variation in the number and type of photoreceptors, spectral tuning of photopigments and optical properties of the eye; (b) coloration in reptiles is a function of complex interactions between structural and pigmentary components, with implications for both proximate control and condition dependence of colour expression; (c) studies of colour-variable species have enabled estimates of heritability of colour and colour patterns, which often show a simple Mendelian pattern of inheritance; (d) colour-polymorphic lizard species sometimes, but not always, show striking differences in genetically encoded reproductive tactics and provide useful models for studying the evolution and maintenance of polymorphism; (e) both male and female colours are sometimes, but not always, a significant component of socio-sexual signalling, often based on multiple traits; (f) evidence for effects of hormones and condition on colour expression, and trade-offs with immunocompetence and parasite load, is variable; (g) lizards show fading of colours

Characteristics of pattern formation and evolution in approximations of Physarum transport networks.

PubMed

Jones, Jeff

2010-01-01

Most studies of pattern formation place particular emphasis on its role in the development of complex multicellular body plans. In simpler organisms, however, pattern formation is intrinsic to growth and behavior. Inspired by one such organism, the true slime mold Physarum polycephalum, we present examples of complex emergent pattern formation and evolution formed by a population of simple particle-like agents. Using simple local behaviors based on chemotaxis, the mobile agent population spontaneously forms complex and dynamic transport networks. By adjusting simple model parameters, maps of characteristic patterning are obtained. Certain areas of the parameter mapping yield particularly complex long term behaviors, including the circular contraction of network lacunae and bifurcation of network paths to maintain network connectivity. We demonstrate the formation of irregular spots and labyrinthine and reticulated patterns by chemoattraction. Other Turing-like patterning schemes were obtained by using chemorepulsion behaviors, including the self-organization of regular periodic arrays of spots, and striped patterns. We show that complex pattern types can be produced without resorting to the hierarchical coupling of reaction-diffusion mechanisms. We also present network behaviors arising from simple pre-patterning cues, giving simple examples of how the emergent pattern formation processes evolve into networks with functional and quasi-physical properties including tensionlike effects, network minimization behavior, and repair to network damage. The results are interpreted in relation to classical theories of biological pattern formation in natural systems, and we suggest mechanisms by which emergent pattern formation processes may be used as a method for spatially represented unconventional computation.

Using experimental evolution to explore natural patterns between bacterial motility and resistance to bacteriophages

PubMed Central

Koskella, Britt; Taylor, Tiffany B; Bates, Jennifer; Buckling, Angus

2011-01-01

Resistance of bacteria to phages may be gained by alteration of surface proteins to which phages bind, a mechanism that is likely to be costly as these molecules typically have critical functions such as movement or nutrient uptake. To address this potential trade-off, we combine a systematic study of natural bacteria and phage populations with an experimental evolution approach. We compare motility, growth rate and susceptibility to local phages for 80 bacteria isolated from horse chestnut leaves and, contrary to expectation, find no negative association between resistance to phages and bacterial motility or growth rate. However, because correlational patterns (and their absence) are open to numerous interpretations, we test for any causal association between resistance to phages and bacterial motility using experimental evolution of a subset of bacteria in both the presence and absence of naturally associated phages. Again, we find no clear link between the acquisition of resistance and bacterial motility, suggesting that for these natural bacterial populations, phage-mediated selection is unlikely to shape bacterial motility, a key fitness trait for many bacteria in the phyllosphere. The agreement between the observed natural pattern and the experimental evolution results presented here demonstrates the power of this combined approach for testing evolutionary trade-offs. PMID:21509046

Clades reach highest morphological disparity early in their evolution

PubMed Central

Hughes, Martin; Gerber, Sylvain; Wills, Matthew Albion

2013-01-01

There are few putative macroevolutionary trends or rules that withstand scrutiny. Here, we test and verify the purported tendency for animal clades to reach their maximum morphological variety relatively early in their evolutionary histories (early high disparity). We present a meta-analysis of 98 metazoan clades radiating throughout the Phanerozoic. The disparity profiles of groups through time are summarized in terms of their center of gravity (CG), with values above and below 0.50 indicating top- and bottom-heaviness, respectively. Clades that terminate at one of the “big five” mass extinction events tend to have truncated trajectories, with a significantly top-heavy CG distribution overall. The remaining 63 clades show the opposite tendency, with a significantly bottom-heavy mean CG (relatively early high disparity). Resampling tests are used to identify groups with a CG significantly above or below 0.50; clades not terminating at a mass extinction are three times more likely to be significantly bottom-heavy than top-heavy. Overall, there is no clear temporal trend in disparity profile shapes from the Cambrian to the Recent, and early high disparity is the predominant pattern throughout the Phanerozoic. Our results do not allow us to distinguish between ecological and developmental explanations for this phenomenon. To the extent that ecology has a role, however, the paucity of bottom-heavy clades radiating in the immediate wake of mass extinctions suggests that early high disparity more probably results from the evolution of key apomorphies at the base of clades rather than from physical drivers or catastrophic ecospace clearing. PMID:23884651

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

Parallel evolution of facial stripe patterns in the Neolamprologus brichardi/pulcher species complex endemic to Lake Tanganyika.

PubMed

Duftner, Nina; Sefc, Kristina M; Koblmüller, Stephan; Salzburger, Walter; Taborsky, Michael; Sturmbauer, Christian

2007-11-01

Colour pattern diversity can be due to random processes or to natural or sexual selection. Consequently, similarities in colour patterns are not always correlated with common ancestry, but may result from convergent evolution under shared selection pressures or drift. Neolamprologus brichardi and Neolamprologus pulcher have been described as two distinct species based on differences in the arrangement of two dark bars on the operculum. Our study uses DNA sequences of the mitochondrial control region to show that relatedness of haplotypes disagrees with species assignment based on head colour pattern. This suggests repeated parallel evolution of particular stripe patterns. The complete lack of shared haplotypes between populations of the same or different phenotypes reflects strong philopatric behaviour, possibly induced by the cooperative breeding mode in which offspring remain in their natal territory and serve as helpers until they disperse to nearby territories or take over a breeding position. Concordant phylogeographic patterns between N. brichardi/N. pulcher populations and other rock-dwelling cichlids suggest that the same colonization routes have been taken by sympatric species and that these routes were affected by lake level fluctuations in the past.

Spatial pattern of reference evapotranspiration change and its temporal evolution over Southwest China

NASA Astrophysics Data System (ADS)

Sun, Shanlei; Wang, Guojie; Huang, Jin; Mu, Mengyuan; Yan, Guixia; Liu, Chunwei; Gao, Chujie; Li, Xing; Yin, Yixing; Zhang, Fangmin; Zhu, Siguang; Hua, Wenjian

2017-11-01

Due to the close relationship of climate change with reference evapotranspiration (ETo), detecting changes in ETo spatial distribution and its temporal evolution at local and regional levels is favorable to comprehensively understand climate change-induced impacts on hydrology and agriculture. In this study, the objective is to identify whether climate change has caused variation of ETo spatial distribution in different analysis periods [i.e., long- (20-year), medium- (10-year), and short-term (5-year)] and to investigate its temporal evolution (namely, when these changes happened) at annual and monthly scales in Southwest China (SWC). First, we estimated ETo values using the United Nations Food and Agriculture Organization (FAO) Penman-Monteith equation, based on historical climate data measured at 269 weather sites during 1973-2012. The analysis of variance (ANOVA) results indicated that the spatial pattern of annual ETo had significantly changed during the past 40 years, particularly in west SWC for the long-term analysis period, and west and southeast SWC in both medium- and short-term periods, which corresponded to the percent area of significant differences which were 21.9, 58.0, and 48.2 %, respectively. For investigating temporal evolution of spatial patterns of annual ETo, Duncan's multiple range test was used, and we found that the most significant changes appeared during 1988-2002 with the significant area of higher than 25.0 %. In addition, for long-, medium-, and short-term analysis periods, the spatial distribution has significantly changed during March, September, November, and December, especially in the corresponding periods of 1988-1997, 1983-1992, 1973-1977, and 1988-2002. All in all, climate change has resulted in significant ETo changes in SWC since the 1970s. Knowledge of climate change-induced spatial distribution of ETo and its temporal evolution would aid in formulating strategies for water resources and agricultural managements.

Cenozoic Icehouse Forcing Mechanisms on Coccolithophorid Evolution

NASA Astrophysics Data System (ADS)

Henderiks, J.

2007-12-01

An overall macroevolutionary size decrease in marine unicellular calcifying algae, the coccolithophores, is punctuated by distinct size responses that correlate to major climatic and paleoceanographic events during the Cenozoic. Notably, major size decreases in the ancestors of the modern blooming species Emiliania huxleyi and Gephyrocapsa oceanica are recorded at the Eocene-Oligocene transition (34 Ma) and in the late Miocene (9 Ma). Coccolithophorid cell size (as reconstructed from individual coccolith biometry) is likely influenced by a variety of passive and active evolutionary selection pressures, with specific factors, such as resource availability and climatic change, determining trends in specific intervals of time. This study presents biometric data of the Noelaerhabdacaea, Calcidiscaceae and Coccolithaceae families, which together represent the bulk of coccolith-carbonate buried in Cenozoic deep-sea sediments, from multiple Deep Sea Drilling Project and Ocean Drilling Project sites covering temperate to tropical regions in the Atlantic, Indian and Pacific oceans. Despite distinct regional ecologic responses at each site, striking correspondences within the global data set call for global forcing mechanisms on the size evolution and ecological success of coccolithophores in an 'icehouse' world.

Evolutionary transitions in controls reconcile adaptation with continuity of evolution.

PubMed

Badyaev, Alexander V

2018-05-19

Evolution proceeds by accumulating functional solutions, necessarily forming an uninterrupted lineage from past solutions of ancestors to the current design of extant forms. At the population level, this process requires an organismal architecture in which the maintenance of local adaptation does not preclude the ability to innovate in the same traits and their continuous evolution. Representing complex traits as networks enables us to visualize a fundamental principle that resolves tension between adaptation and continuous evolution: phenotypic states encompassing adaptations traverse the continuous multi-layered landscape of past physical, developmental and functional associations among traits. The key concept that captures such traversing is network controllability - the ability to move a network from one state into another while maintaining its functionality (reflecting evolvability) and to efficiently propagate information or products through the network within a phenotypic state (maintaining its robustness). Here I suggest that transitions in network controllability - specifically in the topology of controls - help to explain how robustness and evolvability are balanced during evolution. I will focus on evolutionary transitions in degeneracy of metabolic networks - a ubiquitous property of phenotypic robustness where distinct pathways achieve the same end product - to suggest that associated changes in network controls is a common rule underlying phenomena as distinct as phenotypic plasticity, organismal accommodation of novelties, genetic assimilation, and macroevolutionary diversification. Capitalizing on well understood principles by which network structure translates into function of control nodes, I show that accumulating redundancy in one type of network controls inevitably leads to the emergence of another type of controls, forming evolutionary cycles of network controllability that, ultimately, reconcile local adaptation with continuity of evolution

Reconstructing the Phylogenetic History of Long-Term Effective Population Size and Life-History Traits Using Patterns of Amino Acid Replacement in Mitochondrial Genomes of Mammals and Birds

PubMed Central

Nabholz, Benoit; Lartillot, Nicolas

2013-01-01

The nearly neutral theory, which proposes that most mutations are deleterious or close to neutral, predicts that the ratio of nonsynonymous over synonymous substitution rates (dN/dS), and potentially also the ratio of radical over conservative amino acid replacement rates (Kr/Kc), are negatively correlated with effective population size. Previous empirical tests, using life-history traits (LHT) such as body-size or generation-time as proxies for population size, have been consistent with these predictions. This suggests that large-scale phylogenetic reconstructions of dN/dS or Kr/Kc might reveal interesting macroevolutionary patterns in the variation in effective population size among lineages. In this work, we further develop an integrative probabilistic framework for phylogenetic covariance analysis introduced previously, so as to estimate the correlation patterns between dN/dS, Kr/Kc, and three LHT, in mitochondrial genomes of birds and mammals. Kr/Kc displays stronger and more stable correlations with LHT than does dN/dS, which we interpret as a greater robustness of Kr/Kc, compared with dN/dS, the latter being confounded by the high saturation of the synonymous substitution rate in mitochondrial genomes. The correlation of Kr/Kc with LHT was robust when controlling for the potentially confounding effects of nucleotide compositional variation between taxa. The positive correlation of the mitochondrial Kr/Kc with LHT is compatible with previous reports, and with a nearly neutral interpretation, although alternative explanations are also possible. The Kr/Kc model was finally used for reconstructing life-history evolution in birds and mammals. This analysis suggests a fairly large-bodied ancestor in both groups. In birds, life-history evolution seems to have occurred mainly through size reduction in Neoavian birds, whereas in placental mammals, body mass evolution shows disparate trends across subclades. Altogether, our work represents a further step toward a more

Influence of continental history on the ecological specialization and macroevolutionary processes in the mammalian assemblage of South America: differences between small and large mammals.

PubMed

Bofarull, Ana Moreno; Royo, Antón Arias; Fernández, Manuel Hernández; Ortiz-Jaureguizar, Edgardo; Morales, Jorge

2008-03-26

, deviations from the expectations indicate the importance of differences in reproductive traits and paleobiogeographic history for the macroevolutionary processes involved. In the case of South American mammals, the Pliocene Great American Biotic Interchange strongly influences the ecological characteristics of this assemblage. Furthermore, the Andes have acted as a fertile ground for speciation in environments prone to vicariance. Finally, the micromammals appear as more prone to biomic specialization than larger species. These factors are responsible for some of the differences found between South America and Africa in the studied pattern. For example, the extensive South American mountain ranges favour a higher number of combinations of inhabited biomes in comparison with Africa.

Competition promotes the evolution of host generalists in obligate parasites

PubMed Central

Johnson, Kevin P.; Malenke, Jael R.; Clayton, Dale H.

2009-01-01

Ecological theory traditionally predicts that interspecific competition selects for an increase in ecological specialization. Specialization, in turn, is often thought to be an evolutionary ‘dead end,’ with specialist lineages unlikely to evolve into generalist lineages. In host–parasite systems, this specialization can take the form of host specificity, with more specialized parasites using fewer hosts. We tested the hypothesis that specialists are evolutionarily more derived, and whether competition favours specialization, using the ectoparasitic feather lice of doves. Phylogenetic analyses revealed that complete host specificity is actually the ancestral condition, with generalists repeatedly evolving from specialist ancestors. These multiple origins of generalists are correlated with the presence of potentially competing species of the same genus. A competition experiment with captive doves and lice confirmed that congeneric species of lice do, in fact, have the potential to compete in ecological time. Taken together, these results suggest that interspecific competition can favour the evolution of host generalists, not specialists, over macroevolutionary time. PMID:19710056

Periodic Pattern of Genetic and Fitness Diversity during Evolution of an Artificial Cell-Like System.

PubMed

Ichihashi, Norikazu; Aita, Takuyo; Motooka, Daisuke; Nakamura, Shota; Yomo, Tetsuya

2015-12-01

Genetic and phenotypic diversity are the basis of evolution. Despite their importance, however, little is known about how they change over the course of evolution. In this study, we analyzed the dynamics of the adaptive evolution of a simple evolvable artificial cell-like system using single-molecule real-time sequencing technology that reads an entire single artificial genome. We found that the genomic RNA population increases in fitness intermittently, correlating with a periodic pattern of genetic and fitness diversity produced by repeated diversification and domination. In the diversification phase, a genomic RNA population spreads within a genetic space by accumulating mutations until mutants with higher fitness are generated, resulting in an increase in fitness diversity. In the domination phase, the mutants with higher fitness dominate, decreasing both the fitness and genetic diversity. This study reveals the dynamic nature of genetic and fitness diversity during adaptive evolution and demonstrates the utility of a simplified artificial cell-like system to study evolution at an unprecedented resolution. © The Author 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.

Ancient homology underlies adaptive mimetic diversity across butterflies

PubMed Central

Gallant, Jason R.; Imhoff, Vance E.; Martin, Arnaud; Savage, Wesley K.; Chamberlain, Nicola L.; Pote, Ben L.; Peterson, Chelsea; Smith, Gabriella E.; Evans, Benjamin; Reed, Robert D.; Kronforst, Marcus R.; Mullen, Sean P.

2014-01-01

Convergent evolution provides a rare, natural experiment with which to test the predictability of adaptation at the molecular level. Little is known about the molecular basis of convergence over macro-evolutionary timescales. Here we use a combination of positional cloning, population genomic resequencing, association mapping and developmental data to demonstrate that positionally orthologous nucleotide variants in the upstream region of the same gene, WntA, are responsible for parallel mimetic variation in two butterfly lineages that diverged >65 million years ago. Furthermore, characterization of spatial patterns of WntA expression during development suggests that alternative regulatory mechanisms underlie wing pattern variation in each system. Taken together, our results reveal a strikingly predictable molecular basis for phenotypic convergence over deep evolutionary time. PMID:25198507

New Perspectives on Pharyngeal Dorsoventral Patterning in Development and Evolution of the Vertebrate Jaw

PubMed Central

Medeiros, Daniel Meulemans; Crump, J. Gage

2012-01-01

Patterning of the vertebrate facial skeleton involves the progressive partitioning of neural-crest-derived skeletal precursors into distinct subpopulations along the anteroposterior (AP) and dorsoventral (DV) axes. Recent evidence suggests that complex interactions between multiple signaling pathways, in particular Endothelin-1 (Edn1), Bone Morphogenetic Protein (BMP), and Jagged-Notch, are needed to pattern skeletal precursors along the DV axis. Rather than directly determining the morphology of individual skeletal elements, these signals appear to act through several families of transcription factors, including Dlx, Msx, and Hand, to establish dynamic zones of skeletal differentiation. Provocatively, this patterning mechanism is largely conserved from mouse and zebrafish to the jawless vertebrate, lamprey. This implies that the diversification of the vertebrate facial skeleton, including the evolution of the jaw, was driven largely by modifications downstream of a conversed pharyngeal DV patterning program. PMID:22960284

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

Unpacking boxes: Integration of molecular, morphological and ecological approaches reveals extensive patterns of reticulate evolution in box eucalypts.

PubMed

Flores-Rentería, Lluvia; Rymer, Paul D; Riegler, Markus

2017-03-01

Reticulate evolution by hybridization is considered a common process shaping the evolution of many plant species, however, reticulation could also be due to incomplete lineage sorting in biodiverse systems. For our study we selected a group of closely related plant taxa with contrasting yet partially overlapping geographic distributions and different population sizes, to distinguish between reticulated patterns due to hybridization and incomplete lineage sorting. We predicted that sympatric or proximal populations of different species are more likely to have gene flow than geographically distant populations of the same widespread species. Furthermore, for species with restricted distributions, and therefore, small effective population sizes, we predicted complete lineage sorting. Eastern grey box eucalypt species (Eucalyptus supraspecies Moluccanae) provide an ideal system to explore patterns of reticulate evolution. They form a diverse, recently evolved and phylogenetically undefined group within Eucalyptus, with overlapping morphological features and hybridization in nature. We used a multi-faceted approach, combining analyses of chloroplast and nuclear DNA, as well as seedling morphology, flowering time and ecological spatial differentiation in order to test for species delimitation and reticulate evolution in this group. The multiple layers of results were consistent and suggested a lack of monophyly at different hierarchical levels due to multidirectional gene flow among several species, challenging species delimitation. Chloroplast and nuclear haplotypes were shared among different species in geographic proximity, consistent with hybridization zones. Furthermore, species with restricted distributions appeared better resolved due to lineage sorting in the absence of hybridization. We conclude that a combination of molecular, morphological and ecological approaches is required to disentangle patterns of reticulate evolution in the box eucalypts. Published by

Repeated evolution and reversibility of self-fertilization in the volvocine green algae.

PubMed

Hanschen, Erik R; Herron, Matthew D; Wiens, John J; Nozaki, Hisayoshi; Michod, Richard E

2018-02-01

Outcrossing and self-fertilization are fundamental strategies of sexual reproduction, each with different evolutionary costs and benefits. Self-fertilization is thought to be an evolutionary "dead-end" strategy, beneficial in the short term but costly in the long term, resulting in self-fertilizing species that occupy only the tips of phylogenetic trees. Here, we use volvocine green algae to investigate the evolution of self-fertilization. We use ancestral-state reconstructions to show that self-fertilization has repeatedly evolved from outcrossing ancestors and that multiple reversals from selfing to outcrossing have occurred. We use three phylogenetic metrics to show that self-fertilization is not restricted to the tips of the phylogenetic tree, a finding inconsistent with the view of self-fertilization as a dead-end strategy. We also find no evidence for higher extinction rates or lower speciation rates in selfing lineages. We find that self-fertilizing species have significantly larger colonies than outcrossing species, suggesting the benefits of selfing may counteract the costs of increased size. We speculate that our macroevolutionary results on self-fertilization (i.e., non-tippy distribution, no decreased diversification rates) may be explained by the haploid-dominant life cycle that occurs in volvocine algae, which may alter the costs and benefits of selfing. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

The evolution of egg colour and patterning in birds.

PubMed

Kilner, R M

2006-08-01

Avian eggs differ so much in their colour and patterning from species to species that any attempt to account for this diversity might initially seem doomed to failure. Here I present a critical review of the literature which, when combined with the results of some comparative analyses, suggests that just a few selective agents can explain much of the variation in egg appearance. Ancestrally, bird eggs were probably white and immaculate. Ancient diversification in nest location, and hence in the clutch's vulnerability to attack by predators, can explain basic differences between bird families in egg appearance. The ancestral white egg has been retained by species whose nests are safe from attack by predators, while those that have moved to a more vulnerable nest site are now more likely to lay brown eggs, covered in speckles, just as Wallace hypothesized more than a century ago. Even blue eggs might be cryptic in a subset of nests built in vegetation. It is possible that some species have subsequently turned these ancient adaptations to new functions, for example to signal female quality, to protect eggs from damaging solar radiation, or to add structural strength to shells when calcium is in short supply. The threat of predation, together with the use of varying nest sites, appears to have increased the diversity of egg colouring seen among species within families, and among clutches within species. Brood parasites and their hosts have probably secondarily influenced the diversity of egg appearance. Each drives the evolution of the other's egg colour and patterning, as hosts attempt to avoid exploitation by rejecting odd-looking eggs from their nests, and parasites attempt to outwit their hosts by laying eggs that will escape detection. This co-evolutionary arms race has increased variation in egg appearance both within and between species, in parasites and in hosts, sometimes resulting in the evolution of egg colour polymorphisms. It has also reduced variation in

Selection towards different adaptive optima drove the early diversification of locomotor phenotypes in the radiation of Neotropical geophagine cichlids.

PubMed

Astudillo-Clavijo, Viviana; Arbour, Jessica H; López-Fernández, Hernán

2015-05-01

Simpson envisaged a conceptual model of adaptive radiation in which lineages diversify into "adaptive zones" within a macroevolutionary adaptive landscape. However, only a handful of studies have empirically investigated this adaptive landscape and its consequences for our interpretation of the underlying mechanisms of phenotypic evolution. In fish radiations the evolution of locomotor phenotypes may represent an important dimension of ecomorphological diversification given the implications of locomotion for feeding and habitat use. Neotropical geophagine cichlids represent a newly identified adaptive radiation and provide a useful system for studying patterns of locomotor diversification and the implications of selective constraints on phenotypic divergence in general. We use multivariate ordination, models of phenotypic evolution and posterior predictive approaches to investigate the macroevolutionary adaptive landscape and test for evidence of early divergence of locomotor phenotypes in Geophagini. The evolution of locomotor phenotypes was characterized by selection towards at least two distinct adaptive peaks and the early divergence of modern morphological disparity. One adaptive peak included the benthic and epibenthic invertivores and was characterized by fishes with deep, laterally compressed bodies that optimize precise, slow-swimming manoeuvres. The second adaptive peak resulted from a shift in adaptive optima in the species-rich ram-feeding/rheophilic Crenicichla-Teleocichla clade and was characterized by species with streamlined bodies that optimize fast starts and rapid manoeuvres. Evolutionary models and posterior predictive approaches favoured an early shift to a new adaptive peak over decreasing rates of evolution as the underlying process driving the early divergence of locomotor phenotypes. The influence of multiple adaptive peaks on the divergence of locomotor phenotypes in Geophagini is compatible with the expectations of an ecologically driven

The fundamental units, processes and patterns of evolution, and the Tree of Life conundrum

PubMed Central

Koonin, Eugene V; Wolf, Yuri I

2009-01-01

Background The elucidation of the dominant role of horizontal gene transfer (HGT) in the evolution of prokaryotes led to a severe crisis of the Tree of Life (TOL) concept and intense debates on this subject. Concept Prompted by the crisis of the TOL, we attempt to define the primary units and the fundamental patterns and processes of evolution. We posit that replication of the genetic material is the singular fundamental biological process and that replication with an error rate below a certain threshold both enables and necessitates evolution by drift and selection. Starting from this proposition, we outline a general concept of evolution that consists of three major precepts. 1. The primary agency of evolution consists of Fundamental Units of Evolution (FUEs), that is, units of genetic material that possess a substantial degree of evolutionary independence. The FUEs include both bona fide selfish elements such as viruses, viroids, transposons, and plasmids, which encode some of the information required for their own replication, and regular genes that possess quasi-independence owing to their distinct selective value that provides for their transfer between ensembles of FUEs (genomes) and preferential replication along with the rest of the recipient genome. 2. The history of replication of a genetic element without recombination is isomorphously represented by a directed tree graph (an arborescence, in the graph theory language). Recombination within a FUE is common between very closely related sequences where homologous recombination is feasible but becomes negligible for longer evolutionary distances. In contrast, shuffling of FUEs occurs at all evolutionary distances. Thus, a tree is a natural representation of the evolution of an individual FUE on the macro scale, but not of an ensemble of FUEs such as a genome. 3. The history of life is properly represented by the "forest" of evolutionary trees for individual FUEs (Forest of Life, or FOL). Search for trends

Ancient Wings: animating the evolution of butterfly wing patterns.

PubMed

Arbesman, Samuel; Enthoven, Leo; Monteiro, Antónia

2003-10-01

Character optimization methods can be used to reconstruct ancestral states at the internal nodes of phylogenetic trees. However, seldom are these ancestral states visualized collectively. Ancient Wings is a computer program that provides a novel method of visualizing the evolution of several morphological traits simultaneously. It allows users to visualize how the ventral hindwing pattern of 54 butterflies in the genus Bicyclus may have changed over time. By clicking on each of the nodes within the evolutionary tree, the user can see an animation of how wing size, eyespot size, and eyespot position relative the wing margin, have putatively evolved as a collective whole. Ancient Wings may be used as a pedagogical device as well as a research tool for hypothesis-generation in the fields of evolutionary, ecological, and developmental biology.

Dispersal capacity predicts both population genetic structure and species richness in reef fishes.

PubMed

Riginos, Cynthia; Buckley, Yvonne M; Blomberg, Simon P; Treml, Eric A

2014-07-01

Dispersal is a fundamental species characteristic that should directly affect both rates of gene flow among spatially distributed populations and opportunities for speciation. Yet no single trait associated with dispersal has been demonstrated to affect both micro- and macroevolutionary patterns of diversity across a diverse biological assemblage. Here, we examine patterns of genetic differentiation and species richness in reef fishes, an assemblage of over 7,000 species comprising approximately one-third of the extant bony fishes and over one-tenth of living vertebrates. In reef fishes, dispersal occurs primarily during a planktonic larval stage. There are two major reproductive and parental investment syndromes among reef fishes, and the differences between them have implications for dispersal: (1) benthic guarding fishes lay negatively buoyant eggs, typically guarded by the male parent, and from these eggs hatch large, strongly swimming larvae; in contrast, (2) pelagic spawning fishes release small floating eggs directly into the water column, which drift unprotected before small weakly swimming larvae hatch. Using phylogenetic comparative methods, we show that benthic guarders have significantly greater population structure than pelagic spawners and additionally that taxonomic families of benthic guarders are more species rich than families of pelagic spawners. Our findings provide a compelling case for the continuity between micro- and macroevolutionary processes of biological diversification and underscore the importance of dispersal-related traits in influencing the mode and tempo of evolution.

The effects of a deleterious mutation load on patterns of influenza A/H3N2's antigenic evolution in humans

PubMed Central

Koelle, Katia; Rasmussen, David A

2015-01-01

Recent phylogenetic analyses indicate that RNA virus populations carry a significant deleterious mutation load. This mutation load has the potential to shape patterns of adaptive evolution via genetic linkage to beneficial mutations. Here, we examine the effect of deleterious mutations on patterns of influenza A subtype H3N2's antigenic evolution in humans. By first analyzing simple models of influenza that incorporate a mutation load, we show that deleterious mutations, as expected, act to slow the virus's rate of antigenic evolution, while making it more punctuated in nature. These models further predict three distinct molecular pathways by which antigenic cluster transitions occur, and we find phylogenetic patterns consistent with each of these pathways in influenza virus sequences. Simulations of a more complex phylodynamic model further indicate that antigenic mutations act in concert with deleterious mutations to reproduce influenza's spindly hemagglutinin phylogeny, co-circulation of antigenic variants, and high annual attack rates. DOI: http://dx.doi.org/10.7554/eLife.07361.001 PMID:26371556

Phylogenetic patterns and the adaptive evolution of osmoregulation in fiddler crabs (Brachyura, Uca)

PubMed Central

Faria, Samuel Coelho; Provete, Diogo Borges; Thurman, Carl Leo

2017-01-01

Salinity is the primary driver of osmoregulatory evolution in decapods, and may have influenced their diversification into different osmotic niches. In semi-terrestrial crabs, hyper-osmoregulatory ability favors sojourns into burrows and dilute media, and provides a safeguard against hemolymph dilution; hypo-osmoregulatory ability underlies emersion capability and a life more removed from water sources. However, most comparative studies have neglected the roles of the phylogenetic and environmental components of inter-specific physiological variation, hindering evaluation of phylogenetic patterns and the adaptive nature of osmoregulatory evolution. Semi-terrestrial fiddler crabs (Uca) inhabit fresh to hyper-saline waters, with species from the Americas occupying higher intertidal habitats than Indo-west Pacific species mainly found in the low intertidal zone. Here, we characterize numerous osmoregulatory traits in all ten fiddler crabs found along the Atlantic coast of Brazil, and we employ phylogenetic comparative methods using 24 species to test for: (i) similarities of osmoregulatory ability among closely related species; (ii) salinity as a driver of osmoregulatory evolution; (iii) correlation between salt uptake and secretion; and (iv) adaptive peaks in osmoregulatory ability in the high intertidal American lineages. Our findings reveal that osmoregulation in Uca exhibits strong phylogenetic patterns in salt uptake traits. Salinity does not correlate with hyper/hypo-regulatory abilities, but drives hemolymph osmolality at ambient salinities. Osmoregulatory traits have evolved towards three adaptive peaks, revealing a significant contribution of hyper/hypo-regulatory ability in the American clades. Thus, during the evolutionary history of fiddler crabs, salinity has driven some of the osmoregulatory transformations that underpin habitat diversification, although others are apparently constrained phylogenetically. PMID:28182764

Ten years in the library: new data confirm paleontological patterns

NASA Technical Reports Server (NTRS)

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

1993-01-01

A comparison is made between compilations of times of origination and extinction of fossil marine animal families published in 1982 and 1992. As a result of ten years of library research, half of the information in the compendia has changed: families have been added and deleted, low-resolution stratigraphic data been improved, and intervals of origination and extinction have been altered. Despite these changes, apparent macroevolutionary patterns for the entire marine fauna have remained constant. Diversity curves compiled from the two data bases are very similar, with a goodness-of-fit of 99%; the principal difference is that the 1992 curve averages 13% higher than the older curve. Both numbers and percentages of origination and extinction also match well, with fits ranging from 83% to 95%. All major events of radiation and extinction are identical. Therefore, errors in large paleontological data bases and arbitrariness of included taxa are not necessarily impediments to the analysis of pattern in the fossil record, so long as the data are sufficiently numerous.

Time: The Biggest Pattern in Natural History Research

NASA Astrophysics Data System (ADS)

Gontier, Nathalie

2016-10-01

We distinguish between four cosmological transitions in the history of Western intellectual thought, and focus on how these cosmologies differentially define matter, space and time. We demonstrate that how time is conceptualized significantly impacts a cosmology's notion on causality, and hone in on how time is conceptualized differentially in modern physics and evolutionary biology. The former conflates time with space into a single space-time continuum and focuses instead on the movement of matter, while the evolutionary sciences have a tradition to understand time as a given when they cartography how organisms change across generations over or in time, thereby proving the phenomenon of evolution. The gap becomes more fundamental when we take into account that phenomena studied by chrono-biologists demonstrate that numerous organisms, including humans, have evolved a "sense" of time. And micro-evolutionary/genetic, meso-evolutionary/developmental and macro-evolutionary phenomena including speciation and extinction not only occur by different evolutionary modes and at different rates, they are also timely phenomena that follow different periodicities. This article focusses on delineating the problem by finding its historical roots. We conclude that though time might be an obsolete concept for the physical sciences, it is crucial for the evolutionary sciences where evolution is defined as the change that biological individuals undergo in/over or through time.

Sex-specific patterns of morphological diversification: evolution of reaction norms and static allometries in neriid flies.

PubMed

Cassidy, Elizabeth J; Bath, Eleanor; Chenoweth, Stephen F; Bonduriansky, Russell

2014-02-01

The consequences of sex-specific selection for patterns of diversification remain poorly known. Because male secondary sexual traits are typically costly to express, and both costs and benefits are likely to depend on ambient environment and individual condition, such traits may be expected to diversify via changes in reaction norms as well as the scaling of trait size with body size (static allometry). We investigated morphological diversification within two species of Australian neriid flies (Telostylinus angusticollis, Telostylinus lineolatus) by rearing larvae from several populations on larval diets varying sixfold in nutrient concentration. Mean body size varied among populations of T. angusticollis, but body size reaction norms did not vary within either species. However, we detected diversification of reaction norms for body shape in males and females within both species. Moreover, unlike females, males also diversified in static allometry slope and reaction norms for static allometry slope of sexual and nonsexual traits. Our findings reveal qualitative sex differences in patterns of morphological diversification, whereby shape-size relationships diversify extensively in males, but remain conserved in females despite extensive evolution of trait means. Our results highlight the importance of incorporating plasticity and allometry in studies of adaptation and diversification. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Complex and changing patterns of natural selection explain the evolution of the human hip.

PubMed

Grabowski, Mark; Roseman, Charles C

2015-08-01

Causal explanations for the dramatic changes that occurred during the evolution of the human hip focus largely on selection for bipedal function and locomotor efficiency. These hypotheses rest on two critical assumptions. The first-that these anatomical changes served functional roles in bipedalism-has been supported in numerous analyses showing how postcranial changes likely affected locomotion. The second-that morphological changes that did play functional roles in bipedalism were the result of selection for that behavior-has not been previously explored and represents a major gap in our understanding of hominin hip evolution. Here we use evolutionary quantitative genetic models to test the hypothesis that strong directional selection on many individual aspects of morphology was responsible for the large differences observed across a sample of fossil hominin hips spanning the Plio-Pleistocene. Our approach uses covariance among traits and the differences between relatively complete fossils to estimate the net selection pressures that drove the major transitions in hominin hip evolution. Our findings show a complex and changing pattern of natural selection drove hominin hip evolution, and that many, but not all, traits hypothesized to play functional roles in bipedalism evolved as a direct result of natural selection. While the rate of evolutionary change for all transitions explored here does not exceed the amount expected if evolution was occurring solely through neutral processes, it was far above rates of evolution for morphological traits in other mammalian groups. Given that stasis is the norm in the mammalian fossil record, our results suggest that large shifts in the adaptive landscape drove hominin evolution. Copyright © 2015 Elsevier Ltd. All rights reserved.

Microevolutionary dynamics of a macroevolutionary key innovation in a Lepidopteran herbivore

PubMed Central

2010-01-01

Background A molecular population genetics understanding is central to the study of ecological and evolutionary functional genomics. Population genetics identifies genetic variation and its distribution within and among populations, it reveals the demographic history of the populations studied, and can provide indirect insights into historical selection dynamics. Here we use this approach to examine the demographic and selective dynamics acting of a candidate gene involved in plant-insect interactions. Previous work documents the macroevolutionary and historical ecological importance of the nitrile-specifier protein (Nsp), which facilitated the host shift of Pieridae butterflies onto Brassicales host plants ~80 Myr ago. Results Here we assess the microevolutionary dynamics of the Nsp gene by studying the within and among-population variation at Nsp and reference genes in the butterfly Pieris rapae (Small Cabbage White). Nsp exhibits unexpectedly high amounts of amino acid polymorphism, unequally distributed across the gene. The vast majority of genetic variation exists within populations, with little to no genetic differentiation among four populations on two continents. A comparison of synonymous and nonsynonymous substitutions in 70 randomly chosen genes among P. rapae and its close relative Pieris brassicae (Large Cabbage White) finds Nsp to have a significantly relaxed functional constraint compared to housekeeping genes. We find strong evidence for a recent population expansion and no role for strong purifying or directional selection upon the Nsp gene. Conclusions The microevolutionary dynamics of the Nsp gene in P. rapae are dominated by recent population expansion and variation in functional constraint across the repeated domains of the Nsp gene. While the high amounts of amino acid diversity suggest there may be significant functional differences among allelic variants segregating within populations, indirect tests of selection could not conclusively

[Prediction method of rural landscape pattern evolution based on life cycle: a case study of Jinjing Town, Hunan Province, China].

PubMed

Ji, Xiang; Liu, Li-Ming; Li, Hong-Qing

2014-11-01

Taking Jinjing Town in Dongting Lake area as a case, this paper analyzed the evolution of rural landscape patterns by means of life cycle theory, simulated the evolution cycle curve, and calculated its evolution period, then combining CA-Markov model, a complete prediction model was built based on the rule of rural landscape change. The results showed that rural settlement and paddy landscapes of Jinjing Town would change most in 2020, with the rural settlement landscape increased to 1194.01 hm2 and paddy landscape greatly reduced to 3090.24 hm2. The quantitative and spatial prediction accuracies of the model were up to 99.3% and 96.4%, respectively, being more explicit than single CA-Markov model. The prediction model of rural landscape patterns change proposed in this paper would be helpful for rural landscape planning in future.

Evolution of extreme ontogenetic allometric diversity and heterochrony in pythons, a clade of giant and dwarf snakes.

PubMed

Esquerré, Damien; Sherratt, Emma; Keogh, J Scott

2017-12-01

Ontogenetic allometry, how species change with size through their lives, and heterochony, a decoupling between shape, size, and age, are major contributors to biological diversity. However, macroevolutionary allometric and heterochronic trends remain poorly understood because previous studies have focused on small groups of closely related species. Here, we focus on testing hypotheses about the evolution of allometry and how allometry and heterochrony drive morphological diversification at the level of an entire species-rich and diverse clade. Pythons are a useful system due to their remarkably diverse and well-adapted phenotypes and extreme size disparity. We collected detailed phenotype data on 40 of the 44 species of python from 1191 specimens. We used a suite of analyses to test for shifts in allometric trajectories that modify morphological diversity. Heterochrony is the main driver of initial divergence within python clades, and shifts in the slopes of allometric trajectories make exploration of novel phenotypes possible later in divergence history. We found that allometric coefficients are highly evolvable and there is an association between ontogenetic allometry and ecology, suggesting that allometry is both labile and adaptive rather than a constraint on possible phenotypes. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Herbivorous ecomorphology and specialization patterns in theropod dinosaur evolution.

PubMed

Zanno, Lindsay E; Makovicky, Peter J

2011-01-04

Interpreting key ecological parameters, such as diet, of extinct organisms without the benefit of direct observation or explicit fossil evidence poses a formidable challenge for paleobiological studies. To date, dietary categorizations of extinct taxa are largely generated by means of modern analogs; however, for many species the method is subject to considerable ambiguity. Here we present a refined approach for assessing trophic habits in fossil taxa and apply the method to coelurosaurian dinosaurs--a clade for which diet is particularly controversial. Our findings detect 21 morphological features that exhibit statistically significant correlations with extrinsic fossil evidence of coelurosaurian herbivory, such as stomach contents and a gastric mill. These traits represent quantitative, extrinsically founded proxies for identifying herbivorous ecomorphology in fossils and are robust despite uncertainty in phylogenetic relationships among major coelurosaurian subclades. The distribution of these features suggests that herbivory was widespread among coelurosaurians, with six major subclades displaying morphological evidence of the diet, and that contrary to previous thought, hypercarnivory was relatively rare and potentially secondarily derived. Given the potential for repeated, independent evolution of herbivory in Coelurosauria, we also test for repetitive patterns in the appearance of herbivorous traits within sublineages using rank concordance analysis. We find evidence for a common succession of increasing specialization to herbivory in the subclades Ornithomimosauria and Oviraptorosauria, perhaps underlain by intrinsic functional and/or developmental constraints, as well as evidence indicating that the early evolution of a beak in coelurosaurians correlates with an herbivorous diet.

Herbivorous ecomorphology and specialization patterns in theropod dinosaur evolution

PubMed Central

Zanno, Lindsay E.; Makovicky, Peter J.

2011-01-01

Interpreting key ecological parameters, such as diet, of extinct organisms without the benefit of direct observation or explicit fossil evidence poses a formidable challenge for paleobiological studies. To date, dietary categorizations of extinct taxa are largely generated by means of modern analogs; however, for many species the method is subject to considerable ambiguity. Here we present a refined approach for assessing trophic habits in fossil taxa and apply the method to coelurosaurian dinosaurs—a clade for which diet is particularly controversial. Our findings detect 21 morphological features that exhibit statistically significant correlations with extrinsic fossil evidence of coelurosaurian herbivory, such as stomach contents and a gastric mill. These traits represent quantitative, extrinsically founded proxies for identifying herbivorous ecomorphology in fossils and are robust despite uncertainty in phylogenetic relationships among major coelurosaurian subclades. The distribution of these features suggests that herbivory was widespread among coelurosaurians, with six major subclades displaying morphological evidence of the diet, and that contrary to previous thought, hypercarnivory was relatively rare and potentially secondarily derived. Given the potential for repeated, independent evolution of herbivory in Coelurosauria, we also test for repetitive patterns in the appearance of herbivorous traits within sublineages using rank concordance analysis. We find evidence for a common succession of increasing specialization to herbivory in the subclades Ornithomimosauria and Oviraptorosauria, perhaps underlain by intrinsic functional and/or developmental constraints, as well as evidence indicating that the early evolution of a beak in coelurosaurians correlates with an herbivorous diet. PMID:21173263

Using long-term experimental evolution to uncover the patterns and determinants of molecular evolution of an Escherichia coli natural isolate in the streptomycin treated mouse gut

PubMed Central

Ghalayini, Mohamed; Magnan, Mélanie; Glodt, Jérémy; Pintard, Coralie; Dion, Sara; Denamur, Erick; Tenaillon, Olivier

2017-01-01

Though microbial ecology of the gut is now a major focus of interest, little is known about the molecular determinants of microbial adaptation in the gut. Experimental evolution coupled with whole genome sequencing can provide insights of the adaptive process. In vitro experiments have revealed some conserved patterns: intermediate convergence, epistatic interactions between beneficial mutations and mutations in global regulators. To test the relevance of these patterns and to identify the selective pressures acting in vivo, we have performed a long-term adaptation of an E. coli natural isolate, the streptomycin resistant strain 536, in the digestive tract of streptomycin treated mice. After a year of evolution, a clone from 15 replicates was sequenced. Consistently with in vitro observations, the identified mutations revealed a strong pattern of convergence at the mutation, gene, operon and functional levels. Yet, the rate of molecular evolution was lower than in in vitro and no mutations in global regulators were recovered. More specific targets were observed: the dgo operon, involved in the galactonate pathway that improved growth on D-galactonate, and rluD and gidB, implicated in the maturation of the ribosomes, which mutations improved growth only in the presence of streptomycin. As in vitro, the non-random associations of mutations within the same pathways suggested a role of epistasis in shaping the adaptive landscape. Overall, we show that “evolve and sequence” approach coupled to an analysis of convergence, when applied to a natural isolate, can be used to study adaptation in vivo and uncover the specific selective pressures of that environment. PMID:27661780

Adaptive Patterns of Mitogenome Evolution Are Associated with the Loss of Shell Scutes in Turtles.

PubMed

Escalona, Tibisay; Weadick, Cameron J; Antunes, Agostinho

2017-10-01

The mitochondrial genome encodes several protein components of the oxidative phosphorylation (OXPHOS) pathway and is critical for aerobic respiration. These proteins have evolved adaptively in many taxa, but linking molecular-level patterns with higher-level attributes (e.g., morphology, physiology) remains a challenge. Turtles are a promising system for exploring mitochondrial genome evolution as different species face distinct respiratory challenges and employ multiple strategies for ensuring efficient respiration. One prominent adaptation to a highly aquatic lifestyle in turtles is the secondary loss of keratenized shell scutes (i.e., soft-shells), which is associated with enhanced swimming ability and, in some species, cutaneous respiration. We used codon models to examine patterns of selection on mitochondrial protein-coding genes along the three turtle lineages that independently evolved soft-shells. We found strong evidence for positive selection along the branches leading to the pig-nosed turtle (Carettochelys insculpta) and the softshells clade (Trionychidae), but only weak evidence for the leatherback (Dermochelys coriacea) branch. Positively selected sites were found to be particularly prevalent in OXPHOS Complex I proteins, especially subunit ND2, along both positively selected lineages, consistent with convergent adaptive evolution. Structural analysis showed that many of the identified sites are within key regions or near residues involved in proton transport, indicating that positive selection may have precipitated substantial changes in mitochondrial function. Overall, our study provides evidence that physiological challenges associated with adaptation to a highly aquatic lifestyle have shaped the evolution of the turtle mitochondrial genome in a lineage-specific manner. © The Author 2017. 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.

Influence of continental history on the ecological specialization and macroevolutionary processes in the mammalian assemblage of South America: Differences between small and large mammals

PubMed Central

2008-01-01

mammalian evolution. Nevertheless, deviations from the expectations indicate the importance of differences in reproductive traits and paleobiogeographic history for the macroevolutionary processes involved. In the case of South American mammals, the Pliocene Great American Biotic Interchange strongly influences the ecological characteristics of this assemblage. Furthermore, the Andes have acted as a fertile ground for speciation in environments prone to vicariance. Finally, the micromammals appear as more prone to biomic specialization than larger species. These factors are responsible for some of the differences found between South America and Africa in the studied pattern. For example, the extensive South American mountain ranges favour a higher number of combinations of inhabited biomes in comparison with Africa. PMID:18366786

Forelimb kinematics and motor patterns of swimming loggerhead sea turtles (Caretta caretta): are motor patterns conserved in the evolution of new locomotor strategies?

PubMed

Rivera, Angela R V; Wyneken, Jeanette; Blob, Richard W

2011-10-01

Novel functions in animals may evolve through changes in morphology, muscle activity or a combination of both. The idea that new functions or behavior can arise solely through changes in structure, without concurrent changes in the patterns of muscle activity that control movement of those structures, has been formalized as the neuromotor conservation hypothesis. In vertebrate locomotor systems, evidence for neuromotor conservation is found across evolutionary transitions in the behavior of terrestrial species, and in evolutionary transitions from terrestrial species to flying species. However, evolutionary transitions in the locomotion of aquatic species have received little comparable study to determine whether changes in morphology and muscle function were coordinated through the evolution of new locomotor behavior. To evaluate the potential for neuromotor conservation in an ancient aquatic system, we quantified forelimb kinematics and muscle activity during swimming in the loggerhead sea turtle, Caretta caretta. Loggerhead forelimbs are hypertrophied into wing-like flippers that produce thrust via dorsoventral forelimb flapping. We compared kinematic and motor patterns from loggerheads with previous data from the red-eared slider, Trachemys scripta, a generalized freshwater species exhibiting unspecialized forelimb morphology and anteroposterior rowing motions during swimming. For some forelimb muscles, comparisons between C. caretta and T. scripta support neuromotor conservation; for example, the coracobrachialis and the latissimus dorsi show similar activation patterns. However, other muscles (deltoideus, pectoralis and triceps) do not show neuromotor conservation; for example, the deltoideus changes dramatically from a limb protractor/elevator in sliders to a joint stabilizer in loggerheads. Thus, during the evolution of flapping in sea turtles, drastic restructuring of the forelimb was accompanied by both conservation and evolutionary novelty in limb motor

Riparian vegetation patterns in relation to fluvial landforms and channel evolution along selected rivers of Tuscany (Central Italy)

USGS Publications Warehouse

Hupp, C.R.; Rinaldi, M.

2007-01-01

Riparian vegetation distribution patterns and diversity relative to various fluvial geomorphic channel patterns, landforms, and processes are described and interpreted for selected rivers of Tuscany, Central Italy; with emphasis on channel evolution following human impacts. Field surveys were conducted along thirteen gauged reaches for species presence, fluvial landforms, and the type and amount of channel/riparian zone change. Inundation frequency of different geomorphic surfaces was determined, and vegetation data were analyzed using BDA (binary discriminate analysis) and DCA (detrended correspondence analysis) and related to hydrogeomorphology. Multivariate analyses revealed distinct quantitative vegetation patterns relative to six major fluvial geomorphic surfaces. DCA of the vegetation data also showed distinct associations of plants to processes of adjustment that are related to stage of channel evolution, and clearly separated plants along disturbance/landform/soil moisture gradients. Species richness increases from the channel bed to the terrace and on heterogeneous riparian areas, whereas species richness decreases from moderate to intense incision and from low to intense narrowing. ?? 2007 by Association of American Geographers.

Age-Related Evolution Patterns in Online Handwriting

PubMed Central

2016-01-01

Characterizing age from handwriting (HW) has important applications, as it is key to distinguishing normal HW evolution with age from abnormal HW change, potentially triggered by neurodegenerative decline. We propose, in this work, an original approach for online HW style characterization based on a two-level clustering scheme. The first level generates writer-independent word clusters from raw spatial-dynamic HW information. At the second level, each writer's words are converted into a Bag of Prototype Words that is augmented by an interword stability measure. This two-level HW style representation is input to an unsupervised learning technique, aiming at uncovering HW style categories and their correlation with age. To assess the effectiveness of our approach, we propose information theoretic measures to quantify the gain on age information from each clustering layer. We have carried out extensive experiments on a large public online HW database, augmented by HW samples acquired at Broca Hospital in Paris from people mostly between 60 and 85 years old. Unlike previous works claiming that there is only one pattern of HW change with age, our study reveals three major aging HW styles, one specific to aged people and the two others shared by other age groups. PMID:27752277

Evolution of Daily Gene Co-expression Patterns from Algae to Plants

PubMed Central

de los Reyes, Pedro; Romero-Campero, Francisco J.; Ruiz, M. Teresa; Romero, José M.; Valverde, Federico

2017-01-01

Daily rhythms play a key role in transcriptome regulation in plants and microalgae orchestrating responses that, among other processes, anticipate light transitions that are essential for their metabolism and development. The recent accumulation of genome-wide transcriptomic data generated under alternating light:dark periods from plants and microalgae has made possible integrative and comparative analysis that could contribute to shed light on the evolution of daily rhythms in the green lineage. In this work, RNA-seq and microarray data generated over 24 h periods in different light regimes from the eudicot Arabidopsis thaliana and the microalgae Chlamydomonas reinhardtii and Ostreococcus tauri have been integrated and analyzed using gene co-expression networks. This analysis revealed a reduction in the size of the daily rhythmic transcriptome from around 90% in Ostreococcus, being heavily influenced by light transitions, to around 40% in Arabidopsis, where a certain independence from light transitions can be observed. A novel Multiple Bidirectional Best Hit (MBBH) algorithm was applied to associate single genes with a family of potential orthologues from evolutionary distant species. Gene duplication, amplification and divergence of rhythmic expression profiles seems to have played a central role in the evolution of gene families in the green lineage such as Pseudo Response Regulators (PRRs), CONSTANS-Likes (COLs), and DNA-binding with One Finger (DOFs). Gene clustering and functional enrichment have been used to identify groups of genes with similar rhythmic gene expression patterns. The comparison of gene clusters between species based on potential orthologous relationships has unveiled a low to moderate level of conservation of daily rhythmic expression patterns. However, a strikingly high conservation was found for the gene clusters exhibiting their highest and/or lowest expression value during the light transitions. PMID:28751903

How do geological sampling biases affect studies of morphological evolution in deep time? A case study of pterosaur (Reptilia: Archosauria) disparity.

PubMed

Butler, Richard J; Brusatte, Stephen L; Andres, Brian; Benson, Roger B J

2012-01-01

A fundamental contribution of paleobiology to macroevolutionary theory has been the illumination of deep time patterns of diversification. However, recent work has suggested that taxonomic diversity counts taken from the fossil record may be strongly biased by uneven spatiotemporal sampling. Although morphological diversity (disparity) is also frequently used to examine evolutionary radiations, no empirical work has yet addressed how disparity might be affected by uneven fossil record sampling. Here, we use pterosaurs (Mesozoic flying reptiles) as an exemplar group to address this problem. We calculate multiple disparity metrics based upon a comprehensive anatomical dataset including a novel phylogenetic correction for missing data, statistically compare these metrics to four geological sampling proxies, and use multiple regression modeling to assess the importance of uneven sampling and exceptional fossil deposits (Lagerstätten). We find that range-based disparity metrics are strongly affected by uneven fossil record sampling, and should therefore be interpreted cautiously. The robustness of variance-based metrics to sample size and geological sampling suggests that they can be more confidently interpreted as reflecting true biological signals. In addition, our results highlight the problem of high levels of missing data for disparity analyses, indicating a pressing need for more theoretical and empirical work. © 2011 The Author(s). Evolution © 2011 The Society for the Study of Evolution.

Phylo-Allometric Analyses Showcase the Interplay between Life-History Patterns and Phenotypic Convergence in Cleaner Wrasses.

PubMed

Baliga, Vikram B; Mehta, Rita S

2018-05-01

Phenotypic convergence is a macroevolutionary pattern that need not be consistent across life history. Ontogenetic transitions in dietary specialization clearly illustrate the dynamics of ecological selection as organisms grow. The extent of phenotypic convergence among taxa that share a similar ecological niche may therefore vary ontogenetically. Because ontogenetic processes have been shown to evolve, phylogenetic comparative methods can be useful in examining how the scaling of traits relates to ecology. Cleaning, a behavior in which taxa consume ectoparasites off clientele, is well represented among wrasses (Labridae). Nearly three-fourths of labrids that clean do so predominately as juveniles, transitioning away as adults. We examine the scaling patterns of 33 labrid species to understand how life-history patterns of cleaning relate to ontogenetic patterns of phenotypic convergence. We find that as juveniles, cleaners exhibit convergence in body and cranial traits that enhance ectoparasitivory. We then find that taxa that transition away from cleaning exhibit ontogenetic trajectories that are distinct from those of other wrasses. Obligate and facultative species that continue to clean over ontogeny, however, maintain characteristics that are conducive to cleaning. Collectively, we find that life-history patterns of cleaning behavior are concordant with ontogenetic patterns in phenotype in wrasses.

Morphological Evolution of Pit-Patterned Si(001) Substrates Driven by Surface-Energy Reduction

NASA Astrophysics Data System (ADS)

Salvalaglio, Marco; Backofen, Rainer; Voigt, Axel; Montalenti, Francesco

2017-09-01

Lateral ordering of heteroepitaxial islands can be conveniently achieved by suitable pit-patterning of the substrate prior to deposition. Controlling shape, orientation, and size of the pits is not trivial as, being metastable, they can significantly evolve during deposition/annealing. In this paper, we exploit a continuum model to explore the typical metastable pit morphologies that can be expected on Si(001), depending on the initial depth/shape. Evolution is predicted using a surface-diffusion model, formulated in a phase-field framework, and tackling surface-energy anisotropy. Results are shown to nicely reproduce typical metastable shapes reported in the literature. Moreover, long time scale evolutions of pit profiles with different depths are found to follow a similar kinetic pathway. The model is also exploited to treat the case of heteroepitaxial growth involving two materials characterized by different facets in their equilibrium Wulff's shape. This can lead to significant changes in morphologies, such as a rotation of the pit during deposition as evidenced in Ge/Si experiments.

Morphological Evolution of Pit-Patterned Si(001) Substrates Driven by Surface-Energy Reduction.

PubMed

Salvalaglio, Marco; Backofen, Rainer; Voigt, Axel; Montalenti, Francesco

2017-09-29

Lateral ordering of heteroepitaxial islands can be conveniently achieved by suitable pit-patterning of the substrate prior to deposition. Controlling shape, orientation, and size of the pits is not trivial as, being metastable, they can significantly evolve during deposition/annealing. In this paper, we exploit a continuum model to explore the typical metastable pit morphologies that can be expected on Si(001), depending on the initial depth/shape. Evolution is predicted using a surface-diffusion model, formulated in a phase-field framework, and tackling surface-energy anisotropy. Results are shown to nicely reproduce typical metastable shapes reported in the literature. Moreover, long time scale evolutions of pit profiles with different depths are found to follow a similar kinetic pathway. The model is also exploited to treat the case of heteroepitaxial growth involving two materials characterized by different facets in their equilibrium Wulff's shape. This can lead to significant changes in morphologies, such as a rotation of the pit during deposition as evidenced in Ge/Si experiments.

Phylogenetic escalation and decline of plant defense strategies

PubMed Central

Agrawal, Anurag A.; Fishbein, Mark

2008-01-01

As the basal resource in most food webs, plants have evolved myriad strategies to battle consumption by herbivores. Over the past 50 years, plant defense theories have been formulated to explain the remarkable variation in abundance, distribution, and diversity of secondary chemistry and other defensive traits. For example, classic theories of enemy-driven evolutionary dynamics have hypothesized that defensive traits escalate through the diversification process. Despite the fact that macroevolutionary patterns are an explicit part of defense theories, phylogenetic analyses have not been previously attempted to disentangle specific predictions concerning (i) investment in resistance traits, (ii) recovery after damage, and (iii) plant growth rate. We constructed a molecular phylogeny of 38 species of milkweed and tested four major predictions of defense theory using maximum-likelihood methods. We did not find support for the growth-rate hypothesis. Our key finding was a pattern of phyletic decline in the three most potent resistance traits (cardenolides, latex, and trichomes) and an escalation of regrowth ability. Our neontological approach complements more common paleontological approaches to discover directional trends in the evolution of life and points to the importance of natural enemies in the macroevolution of species. The finding of macroevolutionary escalating regowth ability and declining resistance provides a window into the ongoing coevolutionary dynamics between plants and herbivores and suggests a revision of classic plant defense theory. Where plants are primarily consumed by specialist herbivores, regrowth (or tolerance) may be favored over resistance traits during the diversification process. PMID:18645183

Patterns of evolution of MHC class II genes of crows (Corvus) suggest trans-species polymorphism

PubMed Central

Townsend, Andrea K.; Sepil, Irem; Nishiumi, Isao; Satta, Yoko

2015-01-01

A distinguishing characteristic of genes that code for the major histocompatibility complex (MHC) is that alleles often share more similarity between, rather than within species. There are two likely mechanisms that can explain this pattern: convergent evolution and trans-species polymorphism (TSP), in which ancient allelic lineages are maintained by balancing selection and retained by descendant species. Distinguishing between these two mechanisms has major implications in how we view adaptation of immune genes. In this study we analyzed exon 2 of the MHC class IIB in three passerine bird species in the genus Corvus: jungle crows (Corvus macrorhynchos japonensis) American crows (C. brachyrhynchos) and carrion crows (C. corone orientalis). Carrion crows and American crows are recently diverged, but allopatric, sister species, whereas carrion crows and jungle crows are more distantly related but sympatric species, and possibly share pathogens linked to MHC IIB polymorphisms. These patterns of evolutionary divergence and current geographic ranges enabled us to test for trans-species polymorphism and convergent evolution of the MHC IIB in crows. Phylogenetic reconstructions of MHC IIB sequences revealed several well supported interspecific clusters containing all three species, and there was no biased clustering of variants among the sympatric carrion crows and jungle crows. The topologies of phylogenetic trees constructed from putatively selected sites were remarkably different than those constructed from putatively neutral sites. In addition, trees constructed using non-synonymous substitutions from a continuous fragment of exon 2 had more, and generally more inclusive, supported interspecific MHC IIB variant clusters than those constructed from the same fragment using synonymous substitutions. These phylogenetic patterns suggest that recombination, especially gene conversion, has partially erased the signal of allelic ancestry in these species. While clustering of

Breath Figures under Electrowetting: Electrically Controlled Evolution of Drop Condensation Patterns

NASA Astrophysics Data System (ADS)

Baratian, Davood; Dey, Ranabir; Hoek, Harmen; van den Ende, Dirk; Mugele, Frieder

2018-05-01

We show that electrowetting (EW) with structured electrodes significantly modifies the distribution of drops condensing onto flat hydrophobic surfaces by aligning the drops and by enhancing coalescence. Numerical calculations demonstrate that drop alignment and coalescence are governed by the drop-size-dependent electrostatic energy landscape that is imposed by the electrode pattern and the applied voltage. Such EW-controlled migration and coalescence of condensate drops significantly alter the statistical characteristics of the ensemble of droplets. The evolution of the drop size distribution displays self-similar characteristics that significantly deviate from classical breath figures on homogeneous surfaces once the electrically induced coalescence cascades set in beyond a certain critical drop size. The resulting reduced surface coverage, coupled with earlier drop shedding under EW, enhances the net heat transfer.

Identification of tumor evolution patterns by means of inductive logic programming.

PubMed

Bevilacqua, Vitoantonio; Chiarappa, Patrizia; Mastronardi, Giuseppe; Menolascina, Filippo; Paradiso, Angelo; Tommasi, Stefania

2008-06-01

In considering key events of genomic disorders in the development and progression of cancer, the correlation between genomic instability and carcinogenesis is currently under investigation. In this work, we propose an inductive logic programming approach to the problem of modeling evolution patterns for breast cancer. Using this approach, it is possible to extract fingerprints of stages of the disease that can be used in order to develop and deliver the most adequate therapies to patients. Furthermore, such a model can help physicians and biologists in the elucidation of molecular dynamics underlying the aberrations-waterfall model behind carcinogenesis. By showing results obtained on a real-world dataset, we try to give some hints about further approach to the knowledge-driven validations of such hypotheses.

Evolution of vocal patterns: tuning hindbrain circuits during species divergence.

PubMed

Barkan, Charlotte L; Zornik, Erik; Kelley, Darcy B

2017-03-01

The neural circuits underlying divergent courtship behaviors of closely related species provide a framework for insight into the evolution of motor patterns. In frogs, male advertisement calls serve as unique species identifiers and females prefer conspecific to heterospecific calls. Advertisement calls of three relatively recently (∼8.5 Mya) diverged species - Xenopus laevis , X. petersii and X. victorianus - include rapid trains of sound pulses (fast trills). We show that while fast trills are similar in pulse rate (∼60 pulses s -1 ) across the three species, they differ in call duration and period (time from the onset of one call to the onset of the following call). Previous studies of call production in X. laevis used an isolated brain preparation in which the laryngeal nerve produces compound action potentials that correspond to the advertisement call pattern (fictive calling). Here, we show that serotonin evokes fictive calling in X. petersii and X. victorianus as it does in X. laevis As in X. laevis , fictive fast trill in X. petersii and X. victorianus is accompanied by an N -methyl-d-aspartate receptor-dependent local field potential wave in a rostral hindbrain nucleus, DTAM. Across the three species, wave duration and period are strongly correlated with species-specific fast trill duration and period, respectively. When DTAM is isolated from the more rostral forebrain and midbrain and/or more caudal laryngeal motor nucleus, the wave persists at species-typical durations and periods. Thus, intrinsic differences within DTAM could be responsible for the evolutionary divergence of call patterns across these related species. © 2017. Published by The Company of Biologists Ltd.

Generic patterns in the evolution of urban water networks: Evidence from a large Asian city

NASA Astrophysics Data System (ADS)

Krueger, Elisabeth; Klinkhamer, Christopher; Urich, Christian; Zhan, Xianyuan; Rao, P. Suresh C.

2017-03-01

We examine high-resolution urban infrastructure data using every pipe for the water distribution network (WDN) and sanitary sewer network (SSN) in a large Asian city (≈4 million residents) to explore the structure as well as the spatial and temporal evolution of these infrastructure networks. Network data were spatially disaggregated into multiple subnets to examine intracity topological differences for functional zones of the WDN and SSN, and time-stamped SSN data were examined to understand network evolution over several decades as the city expanded. Graphs were generated using a dual-mapping technique (Hierarchical Intersection Continuity Negotiation), which emphasizes the functional attributes of these networks. Network graphs for WDNs and SSNs are characterized by several network topological metrics, and a double Pareto (power-law) model approximates the node-degree distributions of both water infrastructure networks (WDN and SSN), across spatial and hierarchical scales relevant to urban settings, and throughout their temporal evolution over several decades. These results indicate that generic mechanisms govern the networks' evolution, similar to those of scale-free networks found in nature. Deviations from the general topological patterns are indicative of (1) incomplete establishment of network hierarchies and functional network evolution, (2) capacity for growth (expansion) or densification (e.g., in-fill), and (3) likely network vulnerabilities. We discuss the implications of our findings for the (re-)design of urban infrastructure networks to enhance their resilience to external and internal threats.

Out of the dark: 350 million years of conservatism and evolution in diel activity patterns in vertebrates.

PubMed

Anderson, Samantha R; Wiens, John J

2017-08-01

Many animals are active only during a particular time (e.g., day vs. night), a partitioning that may have important consequences for species coexistence. An open question is the extent to which this diel activity niche is evolutionarily conserved or labile. Here, we analyze diel activity data across a phylogeny of 1914 tetrapod species. We find strong phylogenetic signal, showing that closely related species tend to share similar activity patterns. Ancestral reconstructions show that nocturnality was the most likely ancestral diel activity pattern for tetrapods and many major clades within it (e.g., amphibians, mammals). Remarkably, nocturnal activity appears to have been maintained continuously in some lineages for ∼350 million years. Thus, we show that traits involved in local-scale resource partitioning can be conserved over strikingly deep evolutionary time scales. We also demonstrate a potentially important (but often overlooked) metric of niche conservatism. Finally, we show that diurnal lineages appear to have faster speciation and diversification rates than nocturnal lineages, which may explain why there are presently more diurnal tetrapod species even though diurnality appears to have evolved more recently. Overall, our results may have implications for studies of community ecology, species richness, and the evolution of diet and communication systems. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Protein change in plant evolution: tracing one thread connecting molecular and phenotypic diversity

PubMed Central

Bartlett, Madelaine E.; Whipple, Clinton J.

2013-01-01

Proteins change over the course of evolutionary time. New protein-coding genes and gene families emerge and diversify, ultimately affecting an organism’s phenotype and interactions with its environment. Here we survey the range of structural protein change observed in plants and review the role these changes have had in the evolution of plant form and function. Verified examples tying evolutionary change in protein structure to phenotypic change remain scarce. We will review the existing examples, as well as draw from investigations into domestication, and quantitative trait locus (QTL) cloning studies searching for the molecular underpinnings of natural variation. The evolutionary significance of many cloned QTL has not been assessed, but all the examples identified so far have begun to reveal the extent of protein structural diversity tolerated in natural systems. This molecular (and phenotypic) diversity could come to represent part of natural selection’s source material in the adaptive evolution of novel traits. Protein structure and function can change in many distinct ways, but the changes we identified in studies of natural diversity and protein evolution were predicted to fall primarily into one of six categories: altered active and binding sites; altered protein–protein interactions; altered domain content; altered activity as an activator or repressor; altered protein stability; and hypomorphic and hypermorphic alleles. There was also variability in the evolutionary scale at which particular changes were observed. Some changes were detected at both micro- and macroevolutionary timescales, while others were observed primarily at deep or shallow phylogenetic levels. This variation might be used to determine the trajectory of future investigations in structural molecular evolution. PMID:24124420

Biophysical modeling of the temporal niche: from first principles to the evolution of activity patterns.

PubMed

Levy, Ofir; Dayan, Tamar; Kronfeld-Schor, Noga; Porter, Warren P

2012-06-01

Most mammals can be characterized as nocturnal or diurnal. However infrequently, species may overcome evolutionary constraints and alter their activity patterns. We modeled the fundamental temporal niche of a diurnal desert rodent, the golden spiny mouse, Acomys russatus. This species can shift into nocturnal activity in the absence of its congener, the common spiny mouse, Acomys cahirinus, suggesting that it was competitively driven into diurnality and that this shift in a small desert rodent may involve physiological costs. Therefore, we compared metabolic costs of diurnal versus nocturnal activity using a biophysical model to evaluate the preferred temporal niche of this species. The model predicted that energy expenditure during foraging is almost always lower during the day except during midday in summer at the less sheltered microhabitat. We also found that a shift in summer to foraging in less sheltered microhabitats in response to predation pressure and food availability involves a significant physiological cost moderated by midday reduction in activity. Thus, adaptation to diurnality may reflect the "ghost of competition past"; climate-driven diurnality is an alternative but less likely hypothesis. While climate is considered to play a major role in the physiology and evolution of mammals, this is the first study to model its potential to affect the evolution of activity patterns of mammals.

Evolution and inheritance of early embryonic patterning in D. simulans and D. sechellia

PubMed Central

Lott, Susan E.; Ludwig, Michael Z.; Kreitman, Martin

2010-01-01

Pattern formation in Drosophila is a widely studied example of a robust developmental system. Such robust systems pose a challenge to adaptive evolution, as they mask variation which selection may otherwise act upon. Yet we find variation in the localization of expression domains (henceforth ‘stripe allometry’) in the pattern formation pathway. Specifically, we characterize differences in the gap genes giant and Kruppel, and the pair-rule gene even-skipped, which differ between the sibling species D. simulans and D. sechellia. In a double-backcross experiment, stripe allometry is consistent with maternal inheritance of stripe positioning and multiple genetic factors, with a distinct genetic basis from embryo length. Embryos produced by F1 and F2 backcross mothers exhibit novel spatial patterns of gene expression relative to the parental species, with no measurable increase in positional variance among individuals. Buffering of novel spatial patterns in the backcross genotypes suggests that robustness need not be disrupted in order for the trait to evolve, and perhaps the system is incapable of evolving to prevent the expression of all genetic variation. This limitation, and the ability of natural selection to act on minute genetic differences that are within the “margin of error” for the buffering mechanism, indicates that developmentally buffered traits can evolve without disruption of robustness PMID:21121913

The impact of shifts in marine biodiversity hotspots on patterns of range evolution: Evidence from the Holocentridae (squirrelfishes and soldierfishes).

PubMed

Dornburg, Alex; Moore, Jon; Beaulieu, Jeremy M; Eytan, Ron I; Near, Thomas J

2015-01-01

One of the most striking biodiversity patterns is the uneven distribution of marine species richness, with species diversity in the Indo-Australian Archipelago (IAA) exceeding all other areas. However, the IAA formed fairly recently, and marine biodiversity hotspots have shifted across nearly half the globe since the Paleogene. Understanding how lineages have responded to shifting biodiversity hotspots represents a necessary historic perspective on the formation and maintenance of global marine biodiversity. Such evolutionary inferences are often challenged by a lack of fossil evidence that provide insights into historic patterns of abundance and diversity. The greatest diversity of squirrelfishes and soldierfishes (Holocentridae) is in the IAA, yet these fishes also represent some of the most numerous fossil taxa in deposits of the former West Tethyan biodiversity hotspot. We reconstruct the pattern of holocentrid range evolution using time-calibrated phylogenies that include most living species and several fossil lineages, demonstrating the importance of including fossil species as terminal taxa in ancestral area reconstructions. Holocentrids exhibit increased range fragmentation following the West Tethyan hotspot collapse. However, rather than originating within the emerging IAA hotspot, the IAA has acted as a reservoir for holocentrid diversity that originated in adjacent regions over deep evolutionary time scales. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Lineage tracing reveals multipotent stem cells maintain human adenomas and the pattern of clonal expansion in tumor evolution

PubMed Central

Humphries, Adam; Cereser, Biancastella; Gay, Laura J.; Miller, Daniel S. J.; Das, Bibek; Gutteridge, Alice; Elia, George; Nye, Emma; Jeffery, Rosemary; Poulsom, Richard; Novelli, Marco R.; Rodriguez-Justo, Manuel; McDonald, Stuart A. C.; Wright, Nicholas A.; Graham, Trevor A.

2013-01-01

The genetic and morphological development of colorectal cancer is a paradigm for tumorigenesis. However, the dynamics of clonal evolution underpinning carcinogenesis remain poorly understood. Here we identify multipotential stem cells within human colorectal adenomas and use methylation patterns of nonexpressed genes to characterize clonal evolution. Numerous individual crypts from six colonic adenomas and a hyperplastic polyp were microdissected and characterized for genetic lesions. Clones deficient in cytochrome c oxidase (CCO−) were identified by histochemical staining followed by mtDNA sequencing. Topographical maps of clone locations were constructed using a combination of these data. Multilineage differentiation within clones was demonstrated by immunofluorescence. Methylation patterns of adenomatous crypts were determined by clonal bisulphite sequencing; methylation pattern diversity was compared with a mathematical model to infer to clonal dynamics. Individual adenomatous crypts were clonal for mtDNA mutations and contained both mucin-secreting and neuroendocrine cells, demonstrating that the crypt contained a multipotent stem cell. The intracrypt methylation pattern was consistent with the crypts containing multiple competing stem cells. Adenomas were epigenetically diverse populations, suggesting that they were relatively mitotically old populations. Intratumor clones typically showed less diversity in methylation pattern than the tumor as a whole. Mathematical modeling suggested that recent clonal sweeps encompassing the whole adenoma had not occurred. Adenomatous crypts within human tumors contain actively dividing stem cells. Adenomas appeared to be relatively mitotically old populations, pocketed with occasional newly generated subclones that were the result of recent rapid clonal expansion. Relative stasis and occasional rapid subclone growth may characterize colorectal tumorigenesis. PMID:23766371

Lineage tracing reveals multipotent stem cells maintain human adenomas and the pattern of clonal expansion in tumor evolution.

PubMed

Humphries, Adam; Cereser, Biancastella; Gay, Laura J; Miller, Daniel S J; Das, Bibek; Gutteridge, Alice; Elia, George; Nye, Emma; Jeffery, Rosemary; Poulsom, Richard; Novelli, Marco R; Rodriguez-Justo, Manuel; McDonald, Stuart A C; Wright, Nicholas A; Graham, Trevor A

2013-07-02

The genetic and morphological development of colorectal cancer is a paradigm for tumorigenesis. However, the dynamics of clonal evolution underpinning carcinogenesis remain poorly understood. Here we identify multipotential stem cells within human colorectal adenomas and use methylation patterns of nonexpressed genes to characterize clonal evolution. Numerous individual crypts from six colonic adenomas and a hyperplastic polyp were microdissected and characterized for genetic lesions. Clones deficient in cytochrome c oxidase (CCO(-)) were identified by histochemical staining followed by mtDNA sequencing. Topographical maps of clone locations were constructed using a combination of these data. Multilineage differentiation within clones was demonstrated by immunofluorescence. Methylation patterns of adenomatous crypts were determined by clonal bisulphite sequencing; methylation pattern diversity was compared with a mathematical model to infer to clonal dynamics. Individual adenomatous crypts were clonal for mtDNA mutations and contained both mucin-secreting and neuroendocrine cells, demonstrating that the crypt contained a multipotent stem cell. The intracrypt methylation pattern was consistent with the crypts containing multiple competing stem cells. Adenomas were epigenetically diverse populations, suggesting that they were relatively mitotically old populations. Intratumor clones typically showed less diversity in methylation pattern than the tumor as a whole. Mathematical modeling suggested that recent clonal sweeps encompassing the whole adenoma had not occurred. Adenomatous crypts within human tumors contain actively dividing stem cells. Adenomas appeared to be relatively mitotically old populations, pocketed with occasional newly generated subclones that were the result of recent rapid clonal expansion. Relative stasis and occasional rapid subclone growth may characterize colorectal tumorigenesis.

Patterns and processes of drainage network evolution on Mars

NASA Astrophysics Data System (ADS)

Stucky de Quay, G.; Roberts, G. G.

2017-12-01

Large, complex drainage networks exist on the surface of Mars. These drainage patterns suggest that base level change, fluvial erosion, and deposition of sedimentary rock have played important roles in determining the shape of Martian topography. On Earth, base-level change plays the most important role in determining shapes of river profiles at wavelengths greater than a few kilometers. Wavelet transforms of Martian drainage patterns indicate that the same is true for most Martian drainage. For example, rivers in the Warrego Valles system have large convex-upward elevation profiles, with broad knickzones spanning more than 100 kilometers in length and few kilometers in height. More than 90% of the spectra power of rivers in this system resides at wavelengths greater than 10 kilometers. We examine the source of this long wavelength spectra power by jointly inverting suites of Martian river profiles for damped spatio-temporal histories of base-level change. Drainage networks were extracted from the High Resolution Stereo Camera (HRSC) topographic dataset using flow-routing algorithms. Calculated uplift rate histories indicate that regional uplift at wavelengths greater than 100 kilometers play an important role in determining the history of landscape evolution in Warrego Valles. In other regions (e.g. Holden and Eberswalde craters) joint inversion of families of rivers draining craters helps to constrain values of erosional parameters in a simplified version of the stream power erosional model. Integration of calculated incision rates suggest that we can perform a simple mass balance between eroded and deposited rock in regions where both depositional and erosional landforms exist.

Geography and major host evolutionary transitions shape the resource use of plant parasites

PubMed Central

Calatayud, Joaquín; Hórreo, José Luis; Madrigal-González, Jaime; Migeon, Alain; Rodríguez, Miguel Á.; Magalhães, Sara; Hortal, Joaquín

2016-01-01

The evolution of resource use in herbivores has been conceptualized as an analog of the theory of island biogeography, assuming that plant species are islands separated by phylogenetic distances. Despite its usefulness, this analogy has paradoxically led to neglecting real biogeographical processes in the study of macroevolutionary patterns of herbivore–plant interactions. Here we show that host use is mostly determined by the geographical cooccurrence of hosts and parasites in spider mites (Tetranychidae), a globally distributed group of plant parasites. Strikingly, geography accounts for most of the phylogenetic signal in host use by these parasites. Beyond geography, only evolutionary transitions among major plant lineages (i.e., gymnosperms, commelinids, and eudicots) shape resource use patterns in these herbivores. Still, even these barriers have been repeatedly overcome in evolutionary time, resulting in phylogenetically diverse parasite communities feeding on similar hosts. Therefore, our results imply that patterns of apparent evolutionary conservatism may largely be a byproduct of the geographic cooccurrence of hosts and parasites. PMID:27535932

Geography and major host evolutionary transitions shape the resource use of plant parasites.

PubMed

Calatayud, Joaquín; Hórreo, José Luis; Madrigal-González, Jaime; Migeon, Alain; Rodríguez, Miguel Á; Magalhães, Sara; Hortal, Joaquín

2016-08-30

The evolution of resource use in herbivores has been conceptualized as an analog of the theory of island biogeography, assuming that plant species are islands separated by phylogenetic distances. Despite its usefulness, this analogy has paradoxically led to neglecting real biogeographical processes in the study of macroevolutionary patterns of herbivore-plant interactions. Here we show that host use is mostly determined by the geographical cooccurrence of hosts and parasites in spider mites (Tetranychidae), a globally distributed group of plant parasites. Strikingly, geography accounts for most of the phylogenetic signal in host use by these parasites. Beyond geography, only evolutionary transitions among major plant lineages (i.e., gymnosperms, commelinids, and eudicots) shape resource use patterns in these herbivores. Still, even these barriers have been repeatedly overcome in evolutionary time, resulting in phylogenetically diverse parasite communities feeding on similar hosts. Therefore, our results imply that patterns of apparent evolutionary conservatism may largely be a byproduct of the geographic cooccurrence of hosts and parasites.

Continental faunal exchange and the asymmetrical radiation of carnivores.

PubMed

Pires, Mathias M; Silvestro, Daniele; Quental, Tiago B

2015-10-22

Lineages arriving on islands may undergo explosive evolutionary radiations owing to the wealth of ecological opportunities. Although studies on insular taxa have improved our understanding of macroevolutionary phenomena, we know little about the macroevolutionary dynamics of continental exchanges. Here we study the evolution of eight Carnivora families that have migrated across the Northern Hemisphere to investigate if continental invasions also result in explosive diversification dynamics. We used a Bayesian approach to estimate speciation and extinction rates from a substantial dataset of fossil occurrences while accounting for the incompleteness of the fossil record. Our analyses revealed a strongly asymmetrical pattern in which North American lineages invading Eurasia underwent explosive radiations, whereas lineages invading North America maintained uniform diversification dynamics. These invasions into Eurasia were characterized by high rates of speciation and extinction. The radiation of the arriving lineages in Eurasia coincide with the decline of established lineages or phases of climate change, suggesting differences in the ecological settings between the continents may be responsible for the disparity in diversification dynamics. These results reveal long-term outcomes of biological invasions and show that the importance of explosive radiations in shaping diversity extends beyond insular systems and have significant impact at continental scales. © 2015 The Author(s).

Continental faunal exchange and the asymmetrical radiation of carnivores

PubMed Central

Pires, Mathias M.; Silvestro, Daniele; Quental, Tiago B.

2015-01-01

Lineages arriving on islands may undergo explosive evolutionary radiations owing to the wealth of ecological opportunities. Although studies on insular taxa have improved our understanding of macroevolutionary phenomena, we know little about the macroevolutionary dynamics of continental exchanges. Here we study the evolution of eight Carnivora families that have migrated across the Northern Hemisphere to investigate if continental invasions also result in explosive diversification dynamics. We used a Bayesian approach to estimate speciation and extinction rates from a substantial dataset of fossil occurrences while accounting for the incompleteness of the fossil record. Our analyses revealed a strongly asymmetrical pattern in which North American lineages invading Eurasia underwent explosive radiations, whereas lineages invading North America maintained uniform diversification dynamics. These invasions into Eurasia were characterized by high rates of speciation and extinction. The radiation of the arriving lineages in Eurasia coincide with the decline of established lineages or phases of climate change, suggesting differences in the ecological settings between the continents may be responsible for the disparity in diversification dynamics. These results reveal long-term outcomes of biological invasions and show that the importance of explosive radiations in shaping diversity extends beyond insular systems and have significant impact at continental scales. PMID:26490792

The dorsoventral patterning of Musca domestica embryos: insights into BMP/Dpp evolution from the base of the lower cyclorraphan flies.

PubMed

Hodar, Christian; Cambiazo, Verónica

2018-01-01

In the last few years, accumulated information has indicated that the evolution of an extra-embryonic membrane in dipterans was accompanied by changes in the gene regulatory network controlled by the BMP/Dpp pathway, which is responsible for dorsal patterning in these insects. However, only comparative analysis of gene expression levels between distant species with two extra-embryonic membranes, like A. gambiae or C. albipunctata , and D. melanogaster, has been conducted. Analysis of gene expression in ancestral species, which evolved closer to the amnioserosa origin, could provide new insights into the evolution of dorsoventral patterning in dipterans. Here we describe the spatial expression of several key and downstream elements of the Dpp pathway and show the compared patterns of expression between Musca and Drosophila embryos, both dipterans with amnioserosa. Most of the analyzed gene showed a high degree of expression conservation, however, we found several differences in the gene expression pattern of M. domestica orthologs for sog and tolloid . Bioinformatics analysis of the promoter of both genes indicated that the variations could be related to the gain of several binding sites for the transcriptional factor Dorsal in the Md.tld promoter and Snail in the Md.sog enhancer . These altered expressions could explain the unclear formation of the pMad gradient in the M. domestica embryo, compared to the formation of the gradient in D. melanogaster. Gene expression changes during the dorsal-ventral patterning in insects contribute to the differentiation of extra-embryonic tissues as a consequence of changes in the gene regulatory network controlled by BMP/Dpp. In this work, in early M. domestica embryos, we identified the expression pattern of several genes members involved in the dorsoventral specification of the embryo. We believe that these data can contribute to understanding the evolution of the BMP/Dpp pathway, the regulation of BMP ligands, and the

Deciphering the evolution of birdwing butterflies 150 years after Alfred Russel Wallace.

PubMed

Condamine, Fabien L; Toussaint, Emmanuel F A; Clamens, Anne-Laure; Genson, Gwenaelle; Sperling, Felix A H; Kergoat, Gael J

2015-07-02

One hundred and fifty years after Alfred Wallace studied the geographical variation and species diversity of butterflies in the Indomalayan-Australasian Archipelago, the processes responsible for their biogeographical pattern remain equivocal. We analysed the macroevolutionary mechanisms accounting for the temporal and geographical diversification of the charismatic birdwing butterflies (Papilionidae), a major focus of Wallace's pioneering work. Bayesian phylogenetics and dating analyses of the birdwings were conducted using mitochondrial and nuclear genes. The combination of maximum likelihood analyses to estimate biogeographical history and diversification rates reveals that diversity-dependence processes drove the radiation of birdwings, and that speciation was often associated with founder-events colonizing new islands, especially in Wallacea. Palaeo-environment diversification models also suggest that high extinction rates occurred during periods of elevated sea level and global warming. We demonstrated a pattern of spatio-temporal habitat dynamics that continuously created or erased habitats suitable for birdwing biodiversity. Since birdwings were extinction-prone during the Miocene (warmer temperatures and elevated sea levels), the cooling period after the mid-Miocene climatic optimum fostered birdwing diversification due to the release of extinction. This also suggests that current global changes may represent a serious conservation threat to this flagship group.

Long-term patterns of body mass and stature evolution within the hominin lineage.

PubMed

Will, Manuel; Pablos, Adrián; Stock, Jay T

2017-11-01

Body size is a central determinant of a species' biology and adaptive strategy, but the number of reliable estimates of hominin body mass and stature have been insufficient to determine long-term patterns and subtle interactions in these size components within our lineage. Here, we analyse 254 body mass and 204 stature estimates from a total of 311 hominin specimens dating from 4.4 Ma to the Holocene using multi-level chronological and taxonomic analytical categories. The results demonstrate complex temporal patterns of body size variation with phases of relative stasis intermitted by periods of rapid increases. The observed trajectories could result from punctuated increases at speciation events, but also differential proliferation of large-bodied taxa or the extinction of small-bodied populations. Combined taxonomic and temporal analyses show that in relation to australopithecines, early Homo is characterized by significantly larger average body mass and stature but retains considerable diversity, including small body sizes. Within later Homo , stature and body mass evolution follow different trajectories: average modern stature is maintained from ca 1.6 Ma, while consistently higher body masses are not established until the Middle Pleistocene at ca 0.5-0.4 Ma, likely caused by directional selection related to colonizing higher latitudes. Selection against small-bodied individuals (less than 40 kg; less than 140 cm) after 1.4 Ma is associated with a decrease in relative size variability in later Homo species compared with earlier Homo and australopithecines. The isolated small-bodied individuals of Homo naledi ( ca 0.3 Ma) and Homo floresiensis ( ca 100-60 ka) constitute important exceptions to these general patterns, adding further layers of complexity to the evolution of body size within the genus Homo . At the end of the Late Pleistocene and Holocene, body size in Homo sapiens declines on average, but also extends to lower limits not seen in

Long-term patterns of body mass and stature evolution within the hominin lineage

PubMed Central

Pablos, Adrián; Stock, Jay T.

2017-01-01

Body size is a central determinant of a species' biology and adaptive strategy, but the number of reliable estimates of hominin body mass and stature have been insufficient to determine long-term patterns and subtle interactions in these size components within our lineage. Here, we analyse 254 body mass and 204 stature estimates from a total of 311 hominin specimens dating from 4.4 Ma to the Holocene using multi-level chronological and taxonomic analytical categories. The results demonstrate complex temporal patterns of body size variation with phases of relative stasis intermitted by periods of rapid increases. The observed trajectories could result from punctuated increases at speciation events, but also differential proliferation of large-bodied taxa or the extinction of small-bodied populations. Combined taxonomic and temporal analyses show that in relation to australopithecines, early Homo is characterized by significantly larger average body mass and stature but retains considerable diversity, including small body sizes. Within later Homo, stature and body mass evolution follow different trajectories: average modern stature is maintained from ca 1.6 Ma, while consistently higher body masses are not established until the Middle Pleistocene at ca 0.5–0.4 Ma, likely caused by directional selection related to colonizing higher latitudes. Selection against small-bodied individuals (less than 40 kg; less than 140 cm) after 1.4 Ma is associated with a decrease in relative size variability in later Homo species compared with earlier Homo and australopithecines. The isolated small-bodied individuals of Homo naledi (ca 0.3 Ma) and Homo floresiensis (ca 100–60 ka) constitute important exceptions to these general patterns, adding further layers of complexity to the evolution of body size within the genus Homo. At the end of the Late Pleistocene and Holocene, body size in Homo sapiens declines on average, but also extends to lower limits not seen in

Body size reductions in nonmammalian eutheriodont therapsids (Synapsida) during the end-Permian mass extinction.

PubMed

Huttenlocker, Adam K

2014-01-01

The extent to which mass extinctions influence body size evolution in major tetrapod clades is inadequately understood. For example, the 'Lilliput effect,' a common feature of mass extinctions, describes a temporary decrease in body sizes of survivor taxa in post-extinction faunas. However, its signature on existing patterns of body size evolution in tetrapods and the persistence of its impacts during post-extinction recoveries are virtually unknown, and rarely compared in both geologic and phylogenetic contexts. Here, I evaluate temporal and phylogenetic distributions of body size in Permo-Triassic therocephalian and cynodont therapsids (eutheriodonts) using a museum collections-based approach and time series model fitting on a regional stratigraphic sequence from the Karoo Basin, South Africa. I further employed rank order correlation tests on global age and clade rank data from an expanded phylogenetic dataset, and performed evolutionary model testing using Brownian (passive diffusion) models. Results support significant size reductions in the immediate aftermath of the end-Permian mass extinction (ca. 252.3 Ma) consistent with some definitions of Lilliput effects. However, this temporal succession reflects a pattern that was underscored largely by Brownian processes and constructive selectivity. Results also support two recent contentions about body size evolution and mass extinctions: 1) active, directional evolution in size traits is rare over macroevolutionary time scales and 2) geologically brief size reductions may be accomplished by the ecological removal of large-bodied species without rapid originations of new small-bodied clades or shifts from long-term evolutionary patterns.

Exploring the patterns and evolution of self-organized urban street networks through modeling

NASA Astrophysics Data System (ADS)

Rui, Yikang; Ban, Yifang; Wang, Jiechen; Haas, Jan

2013-03-01

As one of the most important subsystems in cities, urban street networks have recently been well studied by using the approach of complex networks. This paper proposes a growing model for self-organized urban street networks. The model involves a competition among new centers with different values of attraction radius and a local optimal principle of both geometrical and topological factors. We find that with the model growth, the local optimization in the connection process and appropriate probability for the loop construction well reflect the evolution strategy in real-world cities. Moreover, different values of attraction radius in centers competition process lead to morphological change in patterns including urban network, polycentric and monocentric structures. The model succeeds in reproducing a large diversity of road network patterns by varying parameters. The similarity between the properties of our model and empirical results implies that a simple universal growth mechanism exists in self-organized cities.

The evolution of test size in the Planktic Foraminifera

NASA Astrophysics Data System (ADS)

Fraass, A.; Huber, B. T.; Kelly, D. C.

2017-12-01

Planktic foraminifera are vital tools for understanding paleoceanography, paleoclimate, and evolution. A dataset of measurements from all planktic foraminiferal species is used here to investigate how their size changes through the late Jurassic to Recent. The mean test size of planktic foraminifera increases in the Cretaceous and the Cenozoic, with substantial drops at the Aptian/Albian boundary, in the Coniacian and Santonian, with the end-Cretaceous extinction, and across the Paleocene/Eocene boundary. The Oligocene contains only a small drop in mean size, which is surprising given the substantial extinction of planktic foraminifera at that boundary. There is a qualitative connection between mean and median size and paleoceanographic events, but several key issues remain before rigorous quantitative interrogation of the dataset can be undertaken. In general, species that originate early in a family's range are smaller than those evolving later, though this is a weak relationship. Individual families do not always conform to that finding, however, and have both increasing and decreasing family age-size relationships. The 'three faunas' concept for foraminiferal evolution fails with respect to mean and median size; each diversification has a unique rate of increase and character. Lastly, through comparison with the Schmidt et al. (2004) population-level test size dataset, the size response to climate in the low-latitudes is at the species-level. In the high-latitude regions, however, the response to climate is at the population level. Thus, methods for uncovering climate responses in planktic foraminifera must be specific to the region. Taxonomic or macroevolutionary responses dominate the tropics and global signals, while the polar regions appear to have a unique, and more microevolutionary response.Schmidt, D., Thierstein, H., Bollmann, J., & Schiebel, R. (2004). Abiotic Forcing of Plankton Evolution in the Cenozoic. Science, 303(5655), 207-210.

Geologic drivers of late ordovician faunal change in laurentia: investigating links between tectonics, speciation, and biotic invasions.

PubMed

Wright, David F; Stigall, Alycia L

2013-01-01

Geologic process, including tectonics and global climate change, profoundly impact the evolution of life because they have the propensity to facilitate episodes of biogeographic differentiation and influence patterns of speciation. We investigate causal links between a dramatic faunal turnover and two dominant geologic processes operating within Laurentia during the Late Ordovician: the Taconian Orogeny and GICE related global cooling. We utilize a novel approach for elucidating the relationship between biotic and geologic changes using a time-stratigraphic, species-level evolutionary framework for articulated brachiopods from North America. Phylogenetic biogeographic analyses indicate a fundamental shift in speciation mode-from a vicariance to dispersal dominated macroevolutionary regime-across the boundary between the Sandbian to Katian Stages. This boundary also corresponds to the onset of renewed intensification of tectonic activity and mountain building, the development of an upwelling zone that introduced cool, nutrient-rich waters into the epieric seas of eastern Laurentia, and the GICE isotopic excursion. The synchronicity of these dramatic geologic, oceanographic, and macroevolutionary changes supports the influence of geologic events on biological evolution. Together, the renewed tectonic activity and oceanographic changes facilitated fundamental changes in habitat structure in eastern North America that reduced opportunities for isolation and vicariance. They also facilitated regional biotic dispersal of taxa that led to the subsequent establishment of extrabasinal (=invasive) species and may have led to a suppression of speciation within Laurentian faunas. Phylogenetic biogeographic analysis further indicates that the Richmondian Invasion was a multidirectional regional invasion event that involved taxa immigrating into the Cincinnati region from basins located near the continental margins and within the continental interior.

Evolution of roughness during the pattern transfer of high-chi, 10nm half-pitch, silicon-containing block copolymer structures

NASA Astrophysics Data System (ADS)

Blachut, Gregory; Sirard, Stephen M.; Liang, Andrew; Mack, Chris A.; Maher, Michael J.; Rincon-Delgadillo, Paulina A.; Chan, Boon Teik; Mannaert, Geert; Vandenberghe, Geert; Willson, C. Grant; Ellison, Christopher J.; Hymes, Diane

2018-03-01

A pattern transfer study was conducted to monitor the evolution of roughness in sub-10 nm half-pitch lines generated by the directed self-assembly (DSA) of a high-chi, silicon-containing block copolymer, poly(4-trimethylsilylstyrene)-block-poly(4-methoxystyrene). Unbiased roughness measurements were used to characterize the roughness of the structures before and after pattern transfer into silicon nitride. Parameters of the reactive ion etch process used as a dry development were systematically modified to minimize undesired line walking created by the DSA pre-pattern and to determine their impacts on roughness. The results of this study indicate that an optimized dry development can mitigate the effects of pre-pattern inhomogeneity, and that both dry development and pattern transfer steps effect the roughness of the final structures.

Formation and Evolution of Target Patterns in Cahn-Hilliard Flows: An Extension of the Flux Expulsion Studies in MHD

NASA Astrophysics Data System (ADS)

Fan, Xiang; P H Diamond Collaboration; Luis Chacon Collaboration

2017-10-01

Spinodal decomposition is a second order phase transition for a binary liquid mixture to evolve from a miscible phase (e.g., water + alcohol) to two co-existing phases (e.g., water + oil). The Cahn-Hilliard model for spinodal decomposition is analogous to 2D MHD. We study the evolution of the concentration field in a single eddy in the 2D Cahn-Hilliard system to better understand scalar mixing processes in that system. This study extends investigations of the classic studies of flux expulsion in 2D MHD and homogenization of potential vorticity in 2D fluids. Simulation results show that there are three stages in the evolution: (A) formation of a ``jelly roll'' pattern, for which the concentration field is constant along spirals; (B) a change in isoconcentration contour topology; and (C) formation of a target pattern, for which the isoconcentration contours follow concentric annuli. In the final target pattern stage, the isoconcentration bands align with stream lines. The results indicate that the target pattern is a metastable state. Band merger process continues on a time scale exponentially long relative to the eddy turnover time. The band merger process resembles step merger in drift-ZF staircases. This material is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Fusion Energy Sciences, under Award Number DE-FG02-04ER54738.

Dual spinal lesion paradigm in the cat: evolution of the kinematic locomotor pattern.

PubMed

Barrière, Grégory; Frigon, Alain; Leblond, Hugues; Provencher, Janyne; Rossignol, Serge

2010-08-01

The recovery of voluntary quadrupedal locomotion after an incomplete spinal cord injury can involve different levels of the CNS, including the spinal locomotor circuitry. The latter conclusion was reached using a dual spinal lesion paradigm in which a low thoracic partial spinal lesion is followed, several weeks later, by a complete spinal transection (i.e., spinalization). In this dual spinal lesion paradigm, cats can express hindlimb walking 1 day after spinalization, a process that normally takes several weeks, suggesting that the locomotor circuitry within the lumbosacral spinal cord had been modified after the partial lesion. Here we detail the evolution of the kinematic locomotor pattern throughout the dual spinal lesion paradigm in five cats to gain further insight into putative neurophysiological mechanisms involved in locomotor recovery after a partial spinal lesion. All cats recovered voluntary quadrupedal locomotion with treadmill training (3-5 days/wk) over several weeks. After the partial lesion, the locomotor pattern was characterized by several left/right asymmetries in various kinematic parameters, such as homolateral and homologous interlimb coupling, cycle duration, and swing/stance durations. When no further locomotor improvement was observed, cats were spinalized. After spinalization, the hindlimb locomotor pattern rapidly reappeared, but left/right asymmetries in swing/stance durations observed after the partial lesion could disappear or reverse. It is concluded that, after a partial spinal lesion, the hindlimb locomotor pattern was actively maintained by new dynamic interactions between spinal and supraspinal levels but also by intrinsic changes within the spinal cord.

Major transitions in human evolution.

PubMed

Foley, Robert A; Martin, Lawrence; Mirazón Lahr, Marta; Stringer, Chris

2016-07-05

Evolutionary problems are often considered in terms of 'origins', and research in human evolution seen as a search for human origins. However, evolution, including human evolution, is a process of transitions from one state to another, and so questions are best put in terms of understanding the nature of those transitions. This paper discusses how the contributions to the themed issue 'Major transitions in human evolution' throw light on the pattern of change in hominin evolution. Four questions are addressed: (1) Is there a major divide between early (australopithecine) and later (Homo) evolution? (2) Does the pattern of change fit a model of short transformations, or gradual evolution? (3) Why is the role of Africa so prominent? (4) How are different aspects of adaptation-genes, phenotypes and behaviour-integrated across the transitions? The importance of developing technologies and approaches and the enduring role of fieldwork are emphasized.This article is part of the themed issue 'Major transitions in human evolution'. © 2016 The Author(s).

Rapid evolution of binding specificities and expression patterns of inhibitory CD33-related Siglecs in primates

PubMed Central

Padler-Karavani, Vered; Hurtado-Ziola, Nancy; Chang, Yung-Chi; Sonnenburg, Justin L.; Ronaghy, Arash; Yu, Hai; Verhagen, Andrea; Nizet, Victor; Chen, Xi; Varki, Nissi; Varki, Ajit; Angata, Takashi

2014-01-01

Siglecs are sialic acid-binding Ig-like lectins that recognize sialoglycans via amino-terminal V-set domains. CD33-related Siglecs (CD33rSiglecs) on innate immune cells recognize endogenous sialoglycans as “self-associated molecular patterns” (SAMPs), dampening immune responses via cytosolic immunoreceptor tyrosine-based inhibition motifs that recruit tyrosine phosphatases. However, sialic acid-expressing pathogens subvert this mechanism through molecular mimicry. Meanwhile, endogenous host SAMPs must continually evolve to evade other pathogens that exploit sialic acids as invasion targets. We hypothesized that these opposing selection forces have accelerated CD33rSiglec evolution. We address this by comparative analysis of major CD33rSiglec (Siglec-3, Siglec-5, and Siglec-9) orthologs in humans, chimpanzees, and baboons. Recombinant soluble molecules displaying ligand-binding domains show marked quantitative and qualitative interspecies differences in interactions with strains of the sialylated pathogen, group B Streptococcus, and with sialoglycans presented as gangliosides or in the form of sialoglycan microarrays, including variations such as N-glycolyl and O-acetyl groups. Primate Siglecs also show quantitative and qualitative intra- and interspecies variations in expression patterns on leukocytes, both in circulation and in tissues. Taken together our data explain why the CD33rSiglec-encoding gene cluster is undergoing rapid evolution via multiple mechanisms, driven by the need to maintain self-recognition by innate immune cells, while escaping 2 distinct mechanisms of pathogen subversion.—Padler-Karavani, V., Hurtado-Ziola, N., Chang, Y.-C., Sonnenburg, J. L., Ronaghy, A., Yu, H., Verhagen, A., Nizet, V., Chen, X., Varki, N., Varki, A., Angata, T. Rapid evolution of binding specificities and expression patterns of inhibitory CD33-related Siglecs in primates. PMID:24308974

Does ecological specialization transcend scale? Habitat partitioning among individuals and species of Anolis lizards.

PubMed

Kamath, Ambika; Losos, Jonathan B

2017-03-01

Ecological specialization is common across all levels of biological organization, raising the question of whether the evolution of specialization at one scale in a taxon is linked to specialization at other scales. Anolis lizards have diversified repeatedly along axes of habitat use, but it remains unknown if this diversification into habitat use specialists is underlain by individual specialization. From repeated observations of individuals in a population of Anolis sagrei in Florida, we show that the extent of habitat use specialization among individuals is comparable to the extent of specialization in the same traits among ten sympatric Anolis habitat specialist species in Cuba. However, the adaptive correlations between habitat use and morphology commonly seen across species of Anolis were not observed across individuals in the sampled population. Our results therefore suggest that while patterns of ecological specialization can transcend scale, these parallels are the consequence of distinct ecological processes acting at microevolutionary and macroevolutionary scales. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Mountain uplift explains differences in Palaeogene patterns of mammalian evolution and extinction between North America and Europe

PubMed Central

Eronen, Jussi T.; Janis, Christine M.; Chamberlain, C. Page; Mulch, Andreas

2015-01-01

Patterns of late Palaeogene mammalian evolution appear to be very different between Eurasia and North America. Around the Eocene–Oligocene (EO) transition global temperatures in the Northern Hemisphere plummet: following this, European mammal faunas undergo a profound extinction event (the Grande Coupure), while in North America they appear to pass through this temperature event unscathed. Here, we investigate the role of surface uplift to environmental change and mammalian evolution through the Palaeogene (66–23 Ma). Palaeogene regional surface uplift in North America caused large-scale reorganization of precipitation patterns, particularly in the continental interior, in accord with our combined stable isotope and ecometric data. Changes in mammalian faunas reflect that these were dry and high-elevation palaeoenvironments. The scenario of Middle to Late Eocene (50–37 Ma) surface uplift, together with decreasing precipitation in higher-altitude regions of western North America, explains the enigma of the apparent lack of the large-scale mammal faunal change around the EO transition that characterized western Europe. We suggest that North American mammalian faunas were already pre-adapted to cooler and drier conditions preceding the EO boundary, resulting from the effects of a protracted history of surface uplift. PMID:26041349

Speciation in parasites: a population genetics approach.

PubMed

Huyse, Tine; Poulin, Robert; Théron, André

2005-10-01

Parasite speciation and host-parasite coevolution should be studied at both macroevolutionary and microevolutionary levels. Studies on a macroevolutionary scale provide an essential framework for understanding the origins of parasite lineages and the patterns of diversification. However, because coevolutionary interactions can be highly divergent across time and space, it is important to quantify and compare the phylogeographic variation in both the host and the parasite throughout their geographical range. Furthermore, to evaluate demographic parameters that are relevant to population genetics structure, such as effective population size and parasite transmission, parasite populations must be studied using neutral genetic markers. Previous emphasis on larger-scale studies means that the connection between microevolutionary and macroevolutionary events is poorly explored. In this article, we focus on the spatial fragmentation of parasites and the population genetics processes behind their diversification in an effort to bridge the micro- and macro-scales.

An end to endless forms: epistasis, phenotype distribution bias, and nonuniform evolution.

PubMed

Borenstein, Elhanan; Krakauer, David C

2008-10-01

Studies of the evolution of development characterize the way in which gene regulatory dynamics during ontogeny constructs and channels phenotypic variation. These studies have identified a number of evolutionary regularities: (1) phenotypes occupy only a small subspace of possible phenotypes, (2) the influence of mutation is not uniform and is often canalized, and (3) a great deal of morphological variation evolved early in the history of multicellular life. An important implication of these studies is that diversity is largely the outcome of the evolution of gene regulation rather than the emergence of new, structural genes. Using a simple model that considers a generic property of developmental maps-the interaction between multiple genetic elements and the nonlinearity of gene interaction in shaping phenotypic traits-we are able to recover many of these empirical regularities. We show that visible phenotypes represent only a small fraction of possibilities. Epistasis ensures that phenotypes are highly clustered in morphospace and that the most frequent phenotypes are the most similar. We perform phylogenetic analyses on an evolving, developmental model and find that species become more alike through time, whereas higher-level grades have a tendency to diverge. Ancestral phenotypes, produced by early developmental programs with a low level of gene interaction, are found to span a significantly greater volume of the total phenotypic space than derived taxa. We suggest that early and late evolution have a different character that we classify into micro- and macroevolutionary configurations. These findings complement the view of development as a key component in the production of endless forms and highlight the crucial role of development in constraining biotic diversity and evolutionary trajectories.

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

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

PubMed

Esquerré, Damien; Scott Keogh, J

2016-07-01

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

Global Pattern of The Evolutions of the Sub-Auroral Polarization Streams

NASA Astrophysics Data System (ADS)

He, F.; Zhang, X.; Wang, W.; Wan, W.

2017-12-01

Due to the spatial and temporal limitations of the in-situ measurements from the low altitude polar orbiting satellites or the ionospheric scan by incoherent scatter radars, the global configuration and evolution of SAPS are still not very clear. Here, we present multi-satellite observations of the evolution of subauroral polarization streams (SAPS) during the main phase of a server geomagnetic storm occurred on 31 March 2001. DMSP F12 to F15 observations indicate that the SAPS were first generated in the dusk sector at the beginning of the main phase. Then the SAPS channel expanded towards the midnight and moved to lower latitudes as the main phase went on. The peak velocity, latitudinal width, latitudinal alignment, and longitudinal span of the SAPS channels were highly dynamic during the storm main phase. The global evolution of the SAPS corresponds well with that of the region-2 field-aligned currents, which are mainly determined by the azimuthal pressure gradient of the ring current. Further studies on 37 storms and 30 isolated substorms indicate that the lifetime of the SAPS channel was proportional to the period of time for southward interplanetary magnetic field (IMF). The SAPS channel disappeared after northward turning of the IMF. During the recovery phase, if the IMF kept northward, no SAPS channel was generated, if the IMF turned to southward again, however, SAPS channel will be generated again with lifetime proportional to the duration of the southward IMF. During isolated substorms, the SAPS channel was also controlled by IMF. The SAPS channel was generated after substorm onset and the peak drift velocity of the SAPS channel achieved its maximum during the recovery phase of the substorm. It is suggested that, SAPS channel were mainly controlled by IMF, more works should be done with observations or simulations of investigate the global patterns of the SAPS and the magnetosphere-ionosphere couplings.

Inhibition of Shh signalling in the chick wing gives insights into digit patterning and evolution.

PubMed

Pickering, Joseph; Towers, Matthew

2016-10-01

In an influential model of pattern formation, a gradient of Sonic hedgehog (Shh) signalling in the chick wing bud specifies cells with three antero-posterior positional values, which give rise to three morphologically different digits by a self-organizing mechanism with Turing-like properties. However, as four of the five digits of the mouse limb are morphologically similar in terms of phalangeal pattern, it has been suggested that self-organization alone could be sufficient. Here, we show that inhibition of Shh signalling at a specific stage of chick wing development results in a pattern of four digits, three of which can have the same number of phalanges. These patterning changes are dependent on a posterior extension of the apical ectodermal ridge, and this also allows the additional digit to arise from the Shh-producing cells of the polarizing region - an ability lost in ancestral theropod dinosaurs. Our analyses reveal that, if the specification of antero-posterior positional values is curtailed, self-organization can then produce several digits with the same number of phalanges. We present a model that may give important insights into how the number of digits and phalanges has diverged during the evolution of avian and mammalian limbs. © 2016. Published by The Company of Biologists Ltd.

Spatial-temporal evolution of self-organized loop-patterns on a water surface and a diffuse discharge in the gap

NASA Astrophysics Data System (ADS)

Li, Xuechen; Geng, Jinling; Jia, Pengying; Zhang, Panpan; Zhang, Qi; Li, Yaru

2017-11-01

Excited by an alternating current voltage, a patterned discharge and a diffuse discharge are generated in a needle to liquid configuration. Using an intensified charge-coupled device (ICCD), temporal evolution of the discharge between the two electrodes is investigated for the diffuse mode and the patterned mode, respectively. For the diffuse mode, the positive discharge is in a glow regime, and the negative discharge is in a Townsend discharge regime. For the patterned mode, the discharge always belongs to the Townsend discharge regime. Moreover, in the patterned mode, various patterns including the single loop, single loop with the surrounding corona, triple loops, and concentric loops with a central spot are observed on the water surface with the increasing positive peak-value of the applied voltage (Upp). Temporally resolved images of the loop-patterns are captured on the water surface. From the electrical measurements and the ICCD imaging, it is found that the loop pattern emerges after the discharge bridges the two electrodes. Then, it begins to evolve and finally degenerates with the decrease in the discharge current. The pattern does not disappear until the discharge quenches. Formation of the loop-patterns is attributed to the role of negative ions.

An eco-epidemiological study of Morbilli-related paramyxovirus infection in Madagascar bats reveals host-switching as the dominant macro-evolutionary mechanism.

PubMed

Mélade, Julien; Wieseke, Nicolas; Ramasindrazana, Beza; Flores, Olivier; Lagadec, Erwan; Gomard, Yann; Goodman, Steven M; Dellagi, Koussay; Pascalis, Hervé

2016-04-12

An eco-epidemiological investigation was carried out on Madagascar bat communities to better understand the evolutionary mechanisms and environmental factors that affect virus transmission among bat species in closely related members of the genus Morbillivirus, currently referred to as Unclassified Morbilli-related paramyxoviruses (UMRVs). A total of 947 bats were investigated originating from 52 capture sites (22 caves, 18 buildings, and 12 outdoor sites) distributed over different bioclimatic zones of the island. Using RT-PCR targeting the L-polymerase gene of the Paramyxoviridae family, we found that 10.5% of sampled bats were infected, representing six out of seven families and 15 out of 31 species analyzed. Univariate analysis indicates that both abiotic and biotic factors may promote viral infection. Using generalized linear modeling of UMRV infection overlaid on biotic and abiotic variables, we demonstrate that sympatric occurrence of bats is a major factor for virus transmission. Phylogenetic analyses revealed that all paramyxoviruses infecting Malagasy bats are UMRVs and showed little host specificity. Analyses using the maximum parsimony reconciliation tool CoRe-PA, indicate that host-switching, rather than co-speciation, is the dominant macro-evolutionary mechanism of UMRVs among Malagasy bats.

Dynamical patterning modules: physico-genetic determinants of morphological development and evolution

NASA Astrophysics Data System (ADS)

Newman, Stuart A.; Bhat, Ramray

2008-03-01

The shapes and forms of multicellular organisms arise by the generation of new cell states and types and changes in the numbers and rearrangements of the various kinds of cells. While morphogenesis and pattern formation in all animal species are widely recognized to be mediated by the gene products of an evolutionarily conserved 'developmental-genetic toolkit', the link between these molecular players and the physics underlying these processes has been generally ignored. This paper introduces the concept of 'dynamical patterning modules' (DPMs), units consisting of one or more products of the 'toolkit' genes that mobilize physical processes characteristic of chemically and mechanically excitable meso- to macroscopic systems such as cell aggregates: cohesion, viscoelasticity, diffusion, spatiotemporal heterogeneity based on lateral inhibition and multistable and oscillatory dynamics. We suggest that ancient toolkit gene products, most predating the emergence of multicellularity, assumed novel morphogenetic functions due to change in the scale and context inherent to multicellularity. We show that DPMs, acting individually and in concert with each other, constitute a 'pattern language' capable of generating all metazoan body plans and organ forms. The physical dimension of developmental causation implies that multicellular forms during the explosive radiation of animal body plans in the middle Cambrian, approximately 530 million years ago, could have explored an extensive morphospace without concomitant genotypic change or selection for adaptation. The morphologically plastic body plans and organ forms generated by DPMs, and their ontogenetic trajectories, would subsequently have been stabilized and consolidated by natural selection and genetic drift. This perspective also solves the apparent 'molecular homology-analogy paradox', whereby widely divergent modern animal types utilize the same molecular toolkit during development by proposing, in contrast to the Neo

Deciphering the evolution of birdwing butterflies 150 years after Alfred Russel Wallace

PubMed Central

Condamine, Fabien L.; Toussaint, Emmanuel F. A.; Clamens, Anne-Laure; Genson, Gwenaelle; Sperling, Felix A. H.; Kergoat, Gael J.

2015-01-01

One hundred and fifty years after Alfred Wallace studied the geographical variation and species diversity of butterflies in the Indomalayan-Australasian Archipelago, the processes responsible for their biogeographical pattern remain equivocal. We analysed the macroevolutionary mechanisms accounting for the temporal and geographical diversification of the charismatic birdwing butterflies (Papilionidae), a major focus of Wallace’s pioneering work. Bayesian phylogenetics and dating analyses of the birdwings were conducted using mitochondrial and nuclear genes. The combination of maximum likelihood analyses to estimate biogeographical history and diversification rates reveals that diversity-dependence processes drove the radiation of birdwings, and that speciation was often associated with founder-events colonizing new islands, especially in Wallacea. Palaeo-environment diversification models also suggest that high extinction rates occurred during periods of elevated sea level and global warming. We demonstrated a pattern of spatio-temporal habitat dynamics that continuously created or erased habitats suitable for birdwing biodiversity. Since birdwings were extinction-prone during the Miocene (warmer temperatures and elevated sea levels), the cooling period after the mid-Miocene climatic optimum fostered birdwing diversification due to the release of extinction. This also suggests that current global changes may represent a serious conservation threat to this flagship group. PMID:26133078

Body Size Reductions in Nonmammalian Eutheriodont Therapsids (Synapsida) during the End-Permian Mass Extinction

PubMed Central

Huttenlocker, Adam K.

2014-01-01

The extent to which mass extinctions influence body size evolution in major tetrapod clades is inadequately understood. For example, the ‘Lilliput effect,’ a common feature of mass extinctions, describes a temporary decrease in body sizes of survivor taxa in post-extinction faunas. However, its signature on existing patterns of body size evolution in tetrapods and the persistence of its impacts during post-extinction recoveries are virtually unknown, and rarely compared in both geologic and phylogenetic contexts. Here, I evaluate temporal and phylogenetic distributions of body size in Permo-Triassic therocephalian and cynodont therapsids (eutheriodonts) using a museum collections-based approach and time series model fitting on a regional stratigraphic sequence from the Karoo Basin, South Africa. I further employed rank order correlation tests on global age and clade rank data from an expanded phylogenetic dataset, and performed evolutionary model testing using Brownian (passive diffusion) models. Results support significant size reductions in the immediate aftermath of the end-Permian mass extinction (ca. 252.3 Ma) consistent with some definitions of Lilliput effects. However, this temporal succession reflects a pattern that was underscored largely by Brownian processes and constructive selectivity. Results also support two recent contentions about body size evolution and mass extinctions: 1) active, directional evolution in size traits is rare over macroevolutionary time scales and 2) geologically brief size reductions may be accomplished by the ecological removal of large-bodied species without rapid originations of new small-bodied clades or shifts from long-term evolutionary patterns. PMID:24498335

Tectonic evolution of the Mexico flat slab and patterns of intraslab seismicity.

NASA Astrophysics Data System (ADS)

Moresi, L. N.; Sandiford, D.

2017-12-01

The Cocos plate slab is horizontal for about 250 km beneath the Guerrero region of southern Mexico. Analogous morphologies can spontaneously develop in subduction models, through the presence of a low-viscosity mantle wedge. The Mw 7.1 Puebla earthquake appears to have ruptured the inboard corner of the Mexican flat slab; likely in close proximity to the mantle wedge corner. In addition to the historical seismic record, the Puebla earthquake provides a valuable constraint through which to assess geodynamic models for flat slab evolution. Slab deformation predicted by the "weak wedge" model is consistent with past seismicity in the both the upper plate and slab. Below the flat section, the slab is anomalously warm relative to its depth; the lack of seismicity in the deeper part of the slab fits the global pattern of temperature-controlled slab seismicity. This has implications for understanding the deeper structure of the slab, including the seismic hazard from source regions downdip of the Puebla rupture (epicenters closer to Mexico City). While historical seismicity provides a deformation pattern consistent with the weak wedge model , the Puebla earthquake is somewhat anomalous. The earthquake source mechanism is consistent with stress orientations in our models, however it maps to a region of relatively low deviatoric stress.

Major transitions in human evolution

PubMed Central

Foley, Robert A.; Martin, Lawrence; Mirazón Lahr, Marta; Stringer, Chris

2016-01-01

Evolutionary problems are often considered in terms of ‘origins', and research in human evolution seen as a search for human origins. However, evolution, including human evolution, is a process of transitions from one state to another, and so questions are best put in terms of understanding the nature of those transitions. This paper discusses how the contributions to the themed issue ‘Major transitions in human evolution’ throw light on the pattern of change in hominin evolution. Four questions are addressed: (1) Is there a major divide between early (australopithecine) and later (Homo) evolution? (2) Does the pattern of change fit a model of short transformations, or gradual evolution? (3) Why is the role of Africa so prominent? (4) How are different aspects of adaptation—genes, phenotypes and behaviour—integrated across the transitions? The importance of developing technologies and approaches and the enduring role of fieldwork are emphasized. This article is part of the themed issue ‘Major transitions in human evolution’. PMID:27298461

Extraterrestrial civilizations: Problems of their evolution

NASA Technical Reports Server (NTRS)

Leskov, L. V.

1987-01-01

The problem of finding extraterrestrial civilizations and establishing contact with them is directly related to the problem of their evolution. Possible patterns in this evolution and the stages in the evolution of extraterrestrial civilizations are examined.

Mountain uplift explains differences in Palaeogene patterns of mammalian evolution and extinction between North America and Europe.

PubMed

Eronen, Jussi T; Janis, Christine M; Chamberlain, C Page; Mulch, Andreas

2015-06-22

Patterns of late Palaeogene mammalian evolution appear to be very different between Eurasia and North America. Around the Eocene-Oligocene (EO) transition global temperatures in the Northern Hemisphere plummet: following this, European mammal faunas undergo a profound extinction event (the Grande Coupure), while in North America they appear to pass through this temperature event unscathed. Here, we investigate the role of surface uplift to environmental change and mammalian evolution through the Palaeogene (66-23 Ma). Palaeogene regional surface uplift in North America caused large-scale reorganization of precipitation patterns, particularly in the continental interior, in accord with our combined stable isotope and ecometric data. Changes in mammalian faunas reflect that these were dry and high-elevation palaeoenvironments. The scenario of Middle to Late Eocene (50-37 Ma) surface uplift, together with decreasing precipitation in higher-altitude regions of western North America, explains the enigma of the apparent lack of the large-scale mammal faunal change around the EO transition that characterized western Europe. We suggest that North American mammalian faunas were already pre-adapted to cooler and drier conditions preceding the EO boundary, resulting from the effects of a protracted history of surface uplift. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Geologic Drivers of Late Ordovician Faunal Change in Laurentia: Investigating Links between Tectonics, Speciation, and Biotic Invasions

PubMed Central

Wright, David F.; Stigall, Alycia L.

2013-01-01

Geologic process, including tectonics and global climate change, profoundly impact the evolution of life because they have the propensity to facilitate episodes of biogeographic differentiation and influence patterns of speciation. We investigate causal links between a dramatic faunal turnover and two dominant geologic processes operating within Laurentia during the Late Ordovician: the Taconian Orogeny and GICE related global cooling. We utilize a novel approach for elucidating the relationship between biotic and geologic changes using a time-stratigraphic, species-level evolutionary framework for articulated brachiopods from North America. Phylogenetic biogeographic analyses indicate a fundamental shift in speciation mode—from a vicariance to dispersal dominated macroevolutionary regime—across the boundary between the Sandbian to Katian Stages. This boundary also corresponds to the onset of renewed intensification of tectonic activity and mountain building, the development of an upwelling zone that introduced cool, nutrient-rich waters into the epieric seas of eastern Laurentia, and the GICE isotopic excursion. The synchronicity of these dramatic geologic, oceanographic, and macroevolutionary changes supports the influence of geologic events on biological evolution. Together, the renewed tectonic activity and oceanographic changes facilitated fundamental changes in habitat structure in eastern North America that reduced opportunities for isolation and vicariance. They also facilitated regional biotic dispersal of taxa that led to the subsequent establishment of extrabasinal (=invasive) species and may have led to a suppression of speciation within Laurentian faunas. Phylogenetic biogeographic analysis further indicates that the Richmondian Invasion was a multidirectional regional invasion event that involved taxa immigrating into the Cincinnati region from basins located near the continental margins and within the continental interior. PMID:23869215

Disentangling geographical, biotic, and abiotic drivers of plant diversity in neotropical Ruellia (Acanthaceae).

PubMed

Tripp, Erin A; Tsai, Yi-Hsin Erica

2017-01-01

It has long been hypothesized that biotic interactions are important drivers of biodiversity evolution, yet such interactions have been relatively less studied than abiotic factors owing to the inherent complexity in and the number of types of such interactions. Amongst the most prominent of biotic interactions worldwide are those between plants and pollinators. In the Neotropics, the most biodiverse region on Earth, hummingbird and bee pollination have contributed substantially to plant fitness. Using comparative methods, we test the macroevolutionary consequences of bird and bee pollination within a species rich lineage of flowering plants: Ruellia. We additionally explore impacts of species occupancy of ever-wet rainforests vs. dry ecosystems including cerrado and seasonally dry tropical forests. We compared outcomes based on two different methods of model selection: a traditional approach that utilizes a series of transitive likelihood ratio tests as well as a weighted model averaging approach. Analyses yield evidence for increased net diversification rates among Neotropical Ruellia (compared to Paleotropical lineages) as well as among hummingbird-adapted species. In contrast, we recovered no evidence of higher diversification rates among either bee- or non-bee-adapted lineages and no evidence for higher rates among wet or dry habitat lineages. Understanding fully the factors that have contributed to biases in biodiversity across the planet will ultimately depend upon incorporating knowledge of biotic interactions as well as connecting microevolutionary processes to macroevolutionary patterns.

Evolution in the lineament patterns associated to strong earthquakes revealed by satellite observations

NASA Astrophysics Data System (ADS)

Soto-Pinto, C. A.; Arellano-Baeza, A. A.; Ouzounov, D. P.

2011-12-01

We study the temporal evolution of the stress patterns in the crust by using high-resolution (10-300 m) satellite images from MODIS and ASTER satellite sensors. We are able to detect some changes in density and orientation of lineaments preceding earthquake events. A lineament is generally defined as a straight or a somewhat curved feature in the landscape visible in a satellite image as an aligned sequence of pixels of a contrasting intensity compared to the background. The system of lineaments extracted from the satellite images is not identical to the geological lineaments; nevertheless, it generally reflects the structure of the faults and fractures in the Earth's crust. Our analysis has shown that the system of lineaments is very dynamical, and the significant number of lineaments appeared approximately one month before an earthquake, while one month after the earthquake the lineament configuration returned to its initial state. These features were not observed in the test areas that are free of any seismic activity in that period (null hypothesis). We have designed a computational prototype capable to detect lineament evolution and to utilize both ASTER and MODIS satellite L1/L2. We will demonstrate the first successful test results for several Mw> 5 earthquakes in Chile, Peru, China, and California (USA).

Inferring directions of evolution from patterns of variation: The legacy of Sergei Meyen

PubMed Central

Sharov, Alexei A.; Igamberdiev, Abir U.

2014-01-01

In the era of the Extended Evolutionary Synthesis, which no longer considers natural selection as the only leading factor of evolution, it is meaningful to revisit the legacy of biologists who discussed the role of alternative factors. Here we analyze the evolutionary views of Sergei Meyen (1935-1987), a paleobotanist who argued that the theory of evolution should incorporate a “nomothetical” approach which infers the laws of morphogenesis (i.e., form generation) from the observed patterns of variation in living organisms and in the fossil records. Meyen developed a theory of “repeated polymorphic sets” (RPSs), which he applied consistently to describe inter-organism variation in populations, intra-organism variation of metameric organs, variation of abnormalities, heterotopy, changes during embryo development, and inter-species variation within evolutionary lineages. The notion of RPS assumes the active nature of organisms that possess hidden morphogenic and behavioural capacities. Meyen's theory is compatible with Darwin's natural selection; however Meyen emphasized the importance of other forms of selection (e.g., selection of developmental trajectories, habitats, and behaviours) in choosing specific elements from the RPS. Finally, Meyen developed a new typological concept of time, where time represents variability (i.e., change) of real objects such as living organisms or geological formations. PMID:25072709

What does convergent evolution mean? The interpretation of convergence and its implications in the search for limits to evolution

PubMed Central

Stayton, C. Tristan

2015-01-01

Convergent evolution is central to the study of life's evolutionary history. Researchers have documented the ubiquity of convergence and have used this ubiquity to make inferences about the nature of limits on evolution. However, these inferences are compromised by unrecognized inconsistencies in the definitions, measures, significance tests and inferred causes of convergent evolution. I review these inconsistencies and provide recommendations for standardizing studies of convergence. A fundamental dichotomy exists between definitions that describe convergence as a pattern and those that describe it as a pattern caused by a particular process. When this distinction is not acknowledged it becomes easy to assume that a pattern of convergence indicates that a particular process has been active, leading researchers away from alternative explanations. Convergence is not necessarily caused by limits to evolution, either adaptation or constraint; even substantial amounts of convergent evolution can be generated by a purely stochastic process. In the absence of null models, long lists of examples of convergent events do not necessarily indicate that convergence or any evolutionary process is ubiquitous throughout the history of life. Pattern-based definitions of convergence, coupled with quantitative measures and null models, must be applied before drawing inferences regarding large-scale limits to evolution. PMID:26640646

The Relation between Recombination Rate and Patterns of Molecular Evolution and Variation in Drosophila melanogaster

PubMed Central

Campos, José L.; Halligan, Daniel L.; Haddrill, Penelope R.; Charlesworth, Brian

2014-01-01

Genetic recombination associated with sexual reproduction increases the efficiency of natural selection by reducing the strength of Hill–Robertson interference. Such interference can be caused either by selective sweeps of positively selected alleles or by background selection (BGS) against deleterious mutations. Its consequences can be studied by comparing patterns of molecular evolution and variation in genomic regions with different rates of crossing over. We carried out a comprehensive study of the benefits of recombination in Drosophila melanogaster, both by contrasting five independent genomic regions that lack crossing over with the rest of the genome and by comparing regions with different rates of crossing over, using data on DNA sequence polymorphisms from an African population that is geographically close to the putatively ancestral population for the species, and on sequence divergence from a related species. We observed reductions in sequence diversity in noncrossover (NC) regions that are inconsistent with the effects of hard selective sweeps in the absence of recombination. Overall, the observed patterns suggest that the recombination rate experienced by a gene is positively related to an increase in the efficiency of both positive and purifying selection. The results are consistent with a BGS model with interference among selected sites in NC regions, and joint effects of BGS, selective sweeps, and a past population expansion on variability in regions of the genome that experience crossing over. In such crossover regions, the X chromosome exhibits a higher rate of adaptive protein sequence evolution than the autosomes, implying a Faster-X effect. PMID:24489114

Macroecological and macroevolutionary patterns of leaf herbivory across vascular plants.

PubMed

Turcotte, Martin M; Davies, T Jonathan; Thomsen, Christina J M; Johnson, Marc T J

2014-07-22

The consumption of plants by animals underlies important evolutionary and ecological processes in nature. Arthropod herbivory evolved approximately 415 Ma and the ensuing coevolution between plants and herbivores is credited with generating much of the macroscopic diversity on the Earth. In contemporary ecosystems, herbivory provides the major conduit of energy from primary producers to consumers. Here, we show that when averaged across all major lineages of vascular plants, herbivores consume 5.3% of the leaf tissue produced annually by plants, whereas previous estimates are up to 3.8× higher. This result suggests that for many plant species, leaf herbivory may play a smaller role in energy and nutrient flow than currently thought. Comparative analyses of a diverse global sample of 1058 species across 2085 populations reveal that models of stabilizing selection best describe rates of leaf consumption, and that rates vary substantially within and among major plant lineages. A key determinant of this variation is plant growth form, where woody plant species experience 64% higher leaf herbivory than non-woody plants. Higher leaf herbivory in woody species supports a key prediction of the plant apparency theory. Our study provides insight into how a long history of coevolution has shaped the ecological and evolutionary relationships between plants and herbivores. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Heterochrony, cannibalism, and the evolution of viviparity in Salamandra salamandra.

PubMed

Buckley, David; Alcobendas, Marina; García-París, Mario; Wake, Marvalee H

2007-01-01

The way in which novelties that lead to macroevolutionary events originate is a major question in evolutionary biology, and one that can be addressed using the fire salamander (Salamandra salamandra) as a model system. It is exceptional among amphibians in displaying intraspecific diversity of reproductive strategies. In S. salamandra, two distinct modes of reproduction co-occur: the common mode, ovoviviparity (females giving birth to many small larvae), and a phylogenetically derived reproductive strategy, viviparity (females producing only a few large, fully metamorphosed juveniles, which are nourished maternally). We examine the relationship between heterochronic modifications of the ontogeny and the evolution of the new reproductive mode in the fire salamander. The in vitro development of embryos of ovoviviparous and viviparous salamanders from fertilization to metamorphosis is compared, highlighting the key events that distinguish the two modes of reproduction. We identify the heterochronic events that, together with the intrauterine cannibalistic behavior, characterize the derived viviparous reproductive strategy. The ways in which evolutionary novelties can arise by modification of developmental programs can be studied in S. salamandra. Moreover, the variation in reproductive modes and the associated variation of sequences of development occur in neighboring, conspecific populations. Thus, S. salamandra is a unique biological system in which evolutionary developmental research questions can be addressed at the level of populations.

Machine Learning Biogeographic Processes from Biotic Patterns: A New Trait-Dependent Dispersal and Diversification Model with Model Choice By Simulation-Trained Discriminant Analysis.

PubMed

Sukumaran, Jeet; Economo, Evan P; Lacey Knowles, L

2016-05-01

Current statistical biogeographical analysis methods are limited in the ways ecology can be related to the processes of diversification and geographical range evolution, requiring conflation of geography and ecology, and/or assuming ecologies that are uniform across all lineages and invariant in time. This precludes the possibility of studying a broad class of macroevolutionary biogeographical theories that relate geographical and species histories through lineage-specific ecological and evolutionary dynamics, such as taxon cycle theory. Here we present a new model that generates phylogenies under a complex of superpositioned geographical range evolution, trait evolution, and diversification processes that can communicate with each other. We present a likelihood-free method of inference under our model using discriminant analysis of principal components of summary statistics calculated on phylogenies, with the discriminant functions trained on data generated by simulations under our model. This approach of model selection by classification of empirical data with respect to data generated under training models is shown to be efficient, robust, and performs well over a broad range of parameter space defined by the relative rates of dispersal, trait evolution, and diversification processes. We apply our method to a case study of the taxon cycle, that is testing for habitat and trophic level constraints in the dispersal regimes of the Wallacean avifaunal radiation. ©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.

Evolution in the block: common elements of 5S rDNA organization and evolutionary patterns in distant fish genera.

PubMed

Campo, Daniel; García-Vázquez, Eva

2012-01-01

The 5S rDNA is organized in the genome as tandemly repeated copies of a structural unit composed of a coding sequence plus a nontranscribed spacer (NTS). The coding region is highly conserved in the evolution, whereas the NTS vary in both length and sequence. It has been proposed that 5S rRNA genes are members of a gene family that have arisen through concerted evolution. In this study, we describe the molecular organization and evolution of the 5S rDNA in the genera Lepidorhombus and Scophthalmus (Scophthalmidae) and compared it with already known 5S rDNA of the very different genera Merluccius (Merluccidae) and Salmo (Salmoninae), to identify common structural elements or patterns for understanding 5S rDNA evolution in fish. High intra- and interspecific diversity within the 5S rDNA family in all the genera can be explained by a combination of duplications, deletions, and transposition events. Sequence blocks with high similarity in all the 5S rDNA members across species were identified for the four studied genera, with evidences of intense gene conversion within noncoding regions. We propose a model to explain the evolution of the 5S rDNA, in which the evolutionary units are blocks of nucleotides rather than the entire sequences or single nucleotides. This model implies a "two-speed" evolution: slow within blocks (homogenized by recombination) and fast within the gene family (diversified by duplications and deletions).

Study on relationship between pollen exine ornamentation pattern and germplasm evolution in flowering crabapple

PubMed Central

Zhang, Wang-Xiang; Zhao, Ming-Ming; Fan, Jun-Jun; Zhou, Ting; Chen, Yong-Xia; Cao, Fu-Liang

2017-01-01

Pollen ornamentation patterns are important in the study of plant genetic evolution and systematic taxonomy. However, they are normally difficult to quantify. Based on observations of pollen exine ornamentation characteristics of 128 flowering crabapple germplasms (44 natural species and 84 varieties), three qualitative variables with binary properties (Xi: regularity of pollen exine ornamentation; Yi: scope of ornamentation arrangement regularity; Zi: ornamentation arrangement patterns) were extracted to establish a binary three-dimensional data matrix (Xi Yi Zi) and the matrix data were converted to decimal data through weight assignment, which facilitated the unification of qualitative analysis and quantitative analysis. The result indicates that from species population to variety population and from parent population to variety population, the exine ornamentation of all three dimensions present the evolutionary trend of regular → irregular, wholly regular → partially regular, and single pattern → multiple patterns. Regarding the evolutionary degree, the regularity of ornamentation was significantly lower in both the variety population and progeny population, with a degree of decrease 0.82–1.27 times that of the regularity range of R-type ornamentation. In addition, the evolutionary degree significantly increased along Xi  → Yi → Zi. The result also has certain reference values for defining the taxonomic status of Malus species. PMID:28059122

Between a Pod and a Hard Test: The Deep Evolution of Amoebae

PubMed Central

Kang, Seungho; Tice, Alexander K.; Spiegel, Frederick W.; Silberman, Jeffrey D.; Pánek, Tomáš; Čepička, Ivan; Kostka, Martin; Kosakyan, Anush; Alcântara, Daniel M.C.; Roger, Andrew J.; Shadwick, Lora L.; Smirnov, Alexey; Kudryavtsev, Alexander; Lahr, Daniel J.G.; Brown, Matthew W.

2017-01-01

Abstract Amoebozoa is the eukaryotic supergroup sister to Obazoa, the lineage that contains the animals and Fungi, as well as their protistan relatives, and the breviate and apusomonad flagellates. Amoebozoa is extraordinarily diverse, encompassing important model organisms and significant pathogens. Although amoebozoans are integral to global nutrient cycles and present in nearly all environments, they remain vastly understudied. We present a robust phylogeny of Amoebozoa based on broad representative set of taxa in a phylogenomic framework (325 genes). By sampling 61 taxa using culture-based and single-cell transcriptomics, our analyses show two major clades of Amoebozoa, Discosea, and Tevosa. This phylogeny refutes previous studies in major respects. Our results support the hypothesis that the last common ancestor of Amoebozoa was sexual and flagellated, it also may have had the ability to disperse propagules from a sporocarp-type fruiting body. Overall, the main macroevolutionary patterns in Amoebozoa appear to result from the parallel losses of homologous characters of a multiphase life cycle that included flagella, sex, and sporocarps rather than independent acquisition of convergent features. PMID:28505375

Time scales of pattern evolution from cross-spectrum analysis of advanced very high resolution radiometer and coastal zone color scanner imagery

NASA Technical Reports Server (NTRS)

Denman, Kenneth L.; Abbott, Mark R.

1994-01-01

We have selected square subareas (110 km on a side) from coastal zone color scanner (CZCS) and advanced very high resolution radiometer (AVHRR) images for 1981 in the California Current region off northern California for which we could identify sequences of cloud-free data over periods of days to weeks. We applied a two-dimensional fast Fourier transformation to images after median filtering, (x, y) plane removal, and cosine tapering. We formed autospectra and coherence spectra as functions of a scalar wavenumber. Coherence estimates between pairs of images were plotted against time separation between images for several wide wavenumber bands to provide a temporal lagged coherence function. The temporal rate of loss of correlation (decorrelation time scale) in surface patterns provides a measure of the rate of pattern change or evolution as a function of spatial dimension. We found that patterns evolved (or lost correlation) approximately twice as rapidly in upwelling jets as in the 'quieter' regions between jets. The rapid evolution of pigment patterns (lifetime of about 1 week or less for scales of 50-100 km) ought to hinder biomass transfer to zooplankton predators compared with phytoplankton patches that persist for longer times. We found no significant differences between the statistics of CZCS and AVHRR images (spectral shape or rate of decorrelation). In addition, in two of the three areas studied, the peak correlation between AVHRR and CZCS images from the same area occurred at zero lag, indicating that the patterns evolved simutaneously. In the third area, maximum coherence between thermal and pigment patterns occurred when pigment images lagged thermal images by 1-2 days, mirroring the expected lag of high pigment behind low temperatures (and high nutrients) in recently upwelled water. We conclude that in dynamic areas such as coastal upwelling systems, the phytoplankton cells (identified by pigment color patterns) behave largely as passive scalars at the

Embodied cognitive evolution and the cerebellum.

PubMed

Barton, Robert A

2012-08-05

Much attention has focused on the dramatic expansion of the forebrain, particularly the neocortex, as the neural substrate of cognitive evolution. However, though relatively small, the cerebellum contains about four times more neurons than the neocortex. I show that commonly used comparative measures such as neocortex ratio underestimate the contribution of the cerebellum to brain evolution. Once differences in the scaling of connectivity in neocortex and cerebellum are accounted for, a marked and general pattern of correlated evolution of the two structures is apparent. One deviation from this general pattern is a relative expansion of the cerebellum in apes and other extractive foragers. The confluence of these comparative patterns, studies of ape foraging skills and social learning, and recent evidence on the cognitive neuroscience of the cerebellum, suggest an important role for the cerebellum in the evolution of the capacity for planning, execution and understanding of complex behavioural sequences--including tool use and language. There is no clear separation between sensory-motor and cognitive specializations underpinning such skills, undermining the notion of executive control as a distinct process. Instead, I argue that cognitive evolution is most effectively understood as the elaboration of specialized systems for embodied adaptive control.

Diversification of Angraecum (Orchidaceae, Vandeae) in Madagascar: Revised Phylogeny Reveals Species Accumulation through Time Rather than Rapid Radiation

PubMed Central

2016-01-01

Angraecum is the largest genus of subtribe Angraecinae (Orchidaceae) with about 221 species. Madagascar is the center of the diversity for the genus with ca. 142 species, of which 90% are endemic. The great morphological diversity associated with species diversification in the genus on the island of Madagascar offers valuable insights for macroevolutionary studies. Phylogenies of the Angraecinae have been published but a lack of taxon and character sampling and their limited taxonomic resolution limit their uses for macroevolutionary studies. We present a new phylogeny of Angraecum based on chloroplast sequence data (matk, rps16, trnL), nuclear ribosomal (ITS2) and 39 morphological characters from 194 Angraecinae species of which 69 were newly sampled. Using this phylogeny, we evaluated the monophyly of the sections of Angraecum as defined by Garay and investigated the patterns of species diversification within the genus. We used maximum parsimony and bayesian analyses to generate phylogenetic trees and dated divergence times of the phylogeny. We analyzed diversification patterns within Angraecinae and Angraecum with an emphasis on four floral characters (flower color, flower size, labellum position, spur length) using macroevolutionary models to evaluate which characters or character states are associated with speciation rates, and inferred ancestral states of these characters. The phylogenetic analysis showed the polyphyly of Angraecum sensu lato and of all Angraecum sections except sect. Hadrangis, and that morphology can be consistent with the phylogeny. It appeared that the characters (flower color, flower size, spur length) formerly used by many authors to delineate Angraecum groups were insufficient to do so. However, the newly described character, position of the labellum (uppermost and lowermost), was the main character delimiting clades within a monophyletic Angraecum sensu stricto. This character also appeared to be associated with speciation rates in

Diversification of Angraecum (Orchidaceae, Vandeae) in Madagascar: Revised Phylogeny Reveals Species Accumulation through Time Rather than Rapid Radiation.

PubMed

Andriananjamanantsoa, Herinandrianina N; Engberg, Shannon; Louis, Edward E; Brouillet, Luc

Angraecum is the largest genus of subtribe Angraecinae (Orchidaceae) with about 221 species. Madagascar is the center of the diversity for the genus with ca. 142 species, of which 90% are endemic. The great morphological diversity associated with species diversification in the genus on the island of Madagascar offers valuable insights for macroevolutionary studies. Phylogenies of the Angraecinae have been published but a lack of taxon and character sampling and their limited taxonomic resolution limit their uses for macroevolutionary studies. We present a new phylogeny of Angraecum based on chloroplast sequence data (matk, rps16, trnL), nuclear ribosomal (ITS2) and 39 morphological characters from 194 Angraecinae species of which 69 were newly sampled. Using this phylogeny, we evaluated the monophyly of the sections of Angraecum as defined by Garay and investigated the patterns of species diversification within the genus. We used maximum parsimony and bayesian analyses to generate phylogenetic trees and dated divergence times of the phylogeny. We analyzed diversification patterns within Angraecinae and Angraecum with an emphasis on four floral characters (flower color, flower size, labellum position, spur length) using macroevolutionary models to evaluate which characters or character states are associated with speciation rates, and inferred ancestral states of these characters. The phylogenetic analysis showed the polyphyly of Angraecum sensu lato and of all Angraecum sections except sect. Hadrangis, and that morphology can be consistent with the phylogeny. It appeared that the characters (flower color, flower size, spur length) formerly used by many authors to delineate Angraecum groups were insufficient to do so. However, the newly described character, position of the labellum (uppermost and lowermost), was the main character delimiting clades within a monophyletic Angraecum sensu stricto. This character also appeared to be associated with speciation rates in

Rates and patterns of molecular evolution in freshwater versus terrestrial insects.

PubMed

Mitterboeck, T Fatima; Fu, Jinzhong; Adamowicz, Sarah J

2016-11-01

Insect lineages have crossed between terrestrial and aquatic habitats many times, for both immature and adult life stages. We explore patterns in molecular evolutionary rates between 42 sister pairs of related terrestrial and freshwater insect clades using publicly available protein-coding DNA sequence data from the orders Coleoptera, Diptera, Lepidoptera, Hemiptera, Mecoptera, Trichoptera, and Neuroptera. We furthermore test for habitat-associated convergent molecular evolution in the cytochrome c oxidase subunit I (COI) gene in general and at a particular amino acid site previously reported to exhibit habitat-linked convergence within an aquatic beetle group. While ratios of nonsynonymous-to-synonymous substitutions across available loci were higher in terrestrial than freshwater-associated taxa in 26 of 42 lineage pairs, a stronger trend was observed (20 of 31, p binomial = 0.15, p Wilcoxon = 0.017) when examining only terrestrial-aquatic pairs including fully aquatic taxa. We did not observe any widespread changes at particular amino acid sites in COI associated with habitat shifts, although there may be general differences in selection regime linked to habitat.

Evolution of aging: individual life history trade-offs and population heterogeneity account for mortality patterns across species.

PubMed

Le Cunff, Y; Baudisch, A; Pakdaman, K

2014-08-01

A broad range of mortality patterns has been documented across species, some even including decreasing mortality over age. Whether there exist a common denominator to explain both similarities and differences in these mortality patterns remains an open question. The disposable soma theory, an evolutionary theory of aging, proposes that universal intracellular trade-offs between maintenance/lifespan and reproduction would drive aging across species. The disposable soma theory has provided numerous insights concerning aging processes in single individuals. Yet, which specific population mortality patterns it can lead to is still largely unexplored. In this article, we propose a model exploring the mortality patterns which emerge from an evolutionary process including only the disposable soma theory core principles. We adapt a well-known model of genomic evolution to show that mortality curves producing a kink or mid-life plateaus derive from a common minimal evolutionary framework. These mortality shapes qualitatively correspond to those of Drosophila melanogaster, Caenorhabditis elegans, medflies, yeasts and humans. Species evolved in silico especially differ in their population diversity of maintenance strategies, which itself emerges as an adaptation to the environment over generations. Based on this integrative framework, we also derive predictions and interpretations concerning the effects of diet changes and heat-shock treatments on mortality patterns. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Amphioxus and lamprey AP-2 genes: implications for neural crest evolution and migration patterns

NASA Technical Reports Server (NTRS)

Meulemans, Daniel; Bronner-Fraser, Marianne

2002-01-01

The neural crest is a uniquely vertebrate cell type present in the most basal vertebrates, but not in cephalochordates. We have studied differences in regulation of the neural crest marker AP-2 across two evolutionary transitions: invertebrate to vertebrate, and agnathan to gnathostome. Isolation and comparison of amphioxus, lamprey and axolotl AP-2 reveals its extensive expansion in the vertebrate dorsal neural tube and pharyngeal arches, implying co-option of AP-2 genes by neural crest cells early in vertebrate evolution. Expression in non-neural ectoderm is a conserved feature in amphioxus and vertebrates, suggesting an ancient role for AP-2 genes in this tissue. There is also common expression in subsets of ventrolateral neurons in the anterior neural tube, consistent with a primitive role in brain development. Comparison of AP-2 expression in axolotl and lamprey suggests an elaboration of cranial neural crest patterning in gnathostomes. However, migration of AP-2-expressing neural crest cells medial to the pharyngeal arch mesoderm appears to be a primitive feature retained in all vertebrates. Because AP-2 has essential roles in cranial neural crest differentiation and proliferation, the co-option of AP-2 by neural crest cells in the vertebrate lineage was a potentially crucial event in vertebrate evolution.

Punctuated evolution and robustness in morphogenesis

PubMed Central

Grigoriev, D.; Reinitz, J.; Vakulenko, S.; Weber, A.

2014-01-01

This paper presents an analytic approach to the pattern stability and evolution problem in morphogenesis. The approach used here is based on the ideas from the gene and neural network theory. We assume that gene networks contain a number of small groups of genes (called hubs) controlling morphogenesis process. Hub genes represent an important element of gene network architecture and their existence is empirically confirmed. We show that hubs can stabilize morphogenetic pattern and accelerate the morphogenesis. The hub activity exhibits an abrupt change depending on the mutation frequency. When the mutation frequency is small, these hubs suppress all mutations and gene product concentrations do not change, thus, the pattern is stable. When the environmental pressure increases and the population needs new genotypes, the genetic drift and other effects increase the mutation frequency. For the frequencies that are larger than a critical amount the hubs turn off; and as a result, many mutations can affect phenotype. This effect can serve as an engine for evolution. We show that this engine is very effective: the evolution acceleration is an exponential function of gene redundancy. Finally, we show that the Eldredge-Gould concept of punctuated evolution results from the network architecture, which provides fast evolution, control of evolvability, and pattern robustness. To describe analytically the effect of exponential acceleration, we use mathematical methods developed recently for hard combinatorial problems, in particular, for so-called k-SAT problem, and numerical simulations. PMID:24996115

Biological and genetic evolution of HIV type 1 in two siblings with different patterns of disease progression.

PubMed

Ripamonti, Chiara; Leitner, Thomas; Laurén, Anna; Karlsson, Ingrid; Pastore, Angela; Cavarelli, Mariangela; Antonsson, Liselotte; Plebani, Anna; Fenyö, Eva Maria; Scarlatti, Gabriella

2007-12-01

To investigate the immunological and virological factors that may lead to different patterns of disease progression characteristic of HIV-1-infected children, two HIV-1-infected siblings, a slow and a fast progressor, were followed prospectively before the onset of highly active antiretroviral therapy. Viral coreceptor usage, including the use of CCR5/CXCR4 chimeric receptors, macrophage tropism, and sensitivity to the CC-chemokine RANTES, has been studied. An autologous and heterologous neutralizing antibody response has been documented using peripheral blood mononuclear cells- and GHOST(3) cell line-based assays. Viral evolution was investigated by env C2-V3 region sequence analysis. Although both siblings were infected with HIV-1 of the R5 phenotype, their viruses showed important biological differences. In the fast progressor there was a higher RANTES sensitivity of the early virus, an increased trend to change the mode of CCR5 receptor use, and a larger genetic evolution. Both children developed an autologous neutralizing antibody response starting from the second year with evidence of the continuous emergence of resistant variants. A marked viral genetic and phenotypic evolution was documented in the fast progressor sibling, which is accompanied by a high viral RANTES sensitivity and persistent neutralizing antibodies.

Streamflow droughts in major watershed regions of the conterminous U.S.: Understanding evolution of historic patterns

NASA Astrophysics Data System (ADS)

Pournasiri Poshtiri, M.; Pal, I.

2015-12-01

Climate non-stationarity affects regional hydrological extremes. This research looks into historic patterns of streamflow drought indicators and their evolution for major watershed regions in the conterminous U.S. (CONUS). The results indicate general linear and non-linear drying trends, particularly in the last four decades, as opposed to wetting trends reported in previous studies. Regional differences in the trends are notable, and echo the local climatic changes documented in the recent National Climate Assessment (NCA). A reversal of linear trends is seen for some northern regions after 1980s. Patterns in return periods and corresponding return values of the indicators are also examined, which suggests changing risk conditions that are important for water-resources decision-making. Persistent or flash drought conditions in a river can lead to chronic or short-term water scarcity—a main driver of societal and cross-boundary conflicts. Thus, this research identifies "hotspot" locations where suitable adaptive management measures are most needed.

Clinicopathogenomic analysis of mismatch repair proficient colorectal adenocarcinoma uncovers novel prognostic subgroups with differing patterns of genetic evolution.

PubMed

Braxton, David R; Zhang, Ray; Morrissette, Jennifer D; Loaiza-Bonilla, Arturo; Furth, Emma E

2016-10-01

Cancer somatic genetic evolution is a direct contributor to heterogeneity at the clonal and molecular level in colorectal adenocarcinoma (COAD). We sought to determine the extent to which genetic evolution may be detected in COAD in routinely obtained single clinical specimens and establish clinical significance with regard to clinicopathologic and outcome data. One hundred and twenty three cases of routinely collected mismatch repair proficient COAD were sequenced on the Illumina Truseq Amplicon assay. Measures of intratumoral heterogeneity and the preferential timing of mutational events were assessed and compared to clinicopathologic data. Survival subanalysis was performed on 55 patients. Patient age (p = 0.013) and specimen percent tumor (p = 0.033) was associated with clonal diversity, and biopsy (p = 0.044) and metastasis (p = 0.044) returned fewer mutations per case. APC and TP53 mutations preferentially occurred early while alterations in FBXW7, FLT3, SMAD4, GNAS and PTEN preferentially occurred as late events. Temporal heterogeneity was evident in KRAS and PIK3CA mutations. Hierarchical clustering revealed a TP53 mutant subtype and a MAPK-PIK3CA subtype with differing patterns of late mutational events. Survival subanalysis showed a decreased median progression free survival for the MAPK-PIK3CA subtype (8 months vs. 13 months; univariate logrank p = 0.0380, cox model p= 0.018). Neoadjuvant therapy associated mutations were found for ERBB2 (p = 0.0481) and FBXW7 (p = 0.015). Our data indicate novel molecular subtypes of mismatch repair proficient COAD display differing patterns of genetic evolution which correlate with clinical outcomes. Furthermore, we report treatment acquired and/or selected mutations in ERBB2 and FBXW7. © 2016 UICC.

Temporal evolution of age data under transient pumping conditions

NASA Astrophysics Data System (ADS)

Leray, S.; De Dreuzy, J.; Aquilina, L.; Vergnaud, V.; Labasque, T.; Bour, O.; Le Borgne, T.

2013-12-01

While most age data derived from tracers have been analyzed in steady-state flow conditions, we determine their temporal evolution under transient pumping conditions. Starting pumping in a well modifies the natural flow patterns induced by the topographical gradient to a mainly convergent flow to the well. Our study is based on a set of models made up of a shallowly dipping aquifer overlain by a less permeable aquitard. These settings are characteristic of the crystalline aquifer of Plœmeur (Brittany, France) located in a highly fractured zone at the contact between a granite and micaschists. Under a pseudo steady-state flow assumption (instantaneous shift between two steady-state flow fields), we solve the transport equation with a backward particle-tracking method and determine the temporal evolution of the concentrations at the pumping well of the four atmospheric tracers CFC 11, CFC 12, CFC 113 and SF6. We show that apparent ages deduced from these concentrations evolve both because of the flow patterns modifications and because of the non-linear evolution of the atmospheric tracer concentrations. Flow patterns modifications only intervene just after the start of pumping, when the initially piston-like residence time distribution is transformed to a broader distribution mixing residence times from a wide variety of flow lines. Later, while flow patterns and the supplying volume of the pumping well still evolve, the residence time distributions are hardly modified and apparent ages are solely altered by the non-linear atmospheric tracer concentrations that progressively modifies the weighting of the residence time distribution. These results are confirmed by the observations at the site of Plœmeur in the pumping area. First, long term chloride observations confirm the quick evolution of the flow patterns after the start of pumping. Second, posterior and more recent evolutions of apparent ages derived from CFCs are consistent with the modeling results revealing

Patterns and rates of viral evolution in HIV-1 subtype B infected females and males.

PubMed

Dapp, Michael J; Kober, Kord M; Chen, Lennie; Westfall, Dylan H; Wong, Kim; Zhao, Hong; Hall, Breana M; Deng, Wenjie; Sibley, Thomas; Ghorai, Suvankar; Kim, Katie; Chen, Natalie; McHugh, Sarah; Au, Lily; Cohen, Mardge; Anastos, Kathryn; Mullins, James I

2017-01-01

Biological sex differences affect the course of HIV infection, with untreated women having lower viral loads compared to their male counterparts but, for a given viral load, women have a higher rate of progression to AIDS. However, the vast majority of data on viral evolution, a process that is clearly impacted by host immunity and could be impacted by sex differences, has been derived from men. We conducted an intensive analysis of HIV-1 gag and env-gp120 evolution taken over the first 6-11 years of infection from 8 Women's Interagency HIV Study (WIHS) participants who had not received combination antiretroviral therapy (ART). This was compared to similar data previously collected from men, with both groups infected with HIV-1 subtype B. Early virus populations in men and women were generally homogenous with no differences in diversity between sexes. No differences in ensuing nucleotide substitution rates were found between the female and male cohorts studied herein. As previously reported for men, time to peak diversity in env-gp120 in women was positively associated with time to CD4+ cell count below 200 (P = 0.017), and the number of predicted N-linked glycosylation sites generally increased over time, followed by a plateau or decline, with the majority of changes localized to the V1-V2 region. These findings strongly suggest that the sex differences in HIV-1 disease progression attributed to immune system composition and sensitivities are not revealed by, nor do they impact, global patterns of viral evolution, the latter of which proceeds similarly in women and men.

Tracking interspecies transmission and long-term evolution of an ancient retrovirus using the genomes of modern mammals

PubMed Central

Diehl, William E; Patel, Nirali; Halm, Kate; Johnson, Welkin E

2016-01-01

Mammalian genomes typically contain hundreds of thousands of endogenous retroviruses (ERVs), derived from ancient retroviral infections. Using this molecular 'fossil' record, we reconstructed the natural history of a specific retrovirus lineage (ERV-Fc) that disseminated widely between ~33 and ~15 million years ago, corresponding to the Oligocene and early Miocene epochs. Intercontinental viral spread, numerous instances of interspecies transmission and emergence in hosts representing at least 11 mammalian orders, and a significant role for recombination in diversification of this viral lineage were also revealed. By reconstructing the canonical retroviral genes, we identified patterns of adaptation consistent with selection to maintain essential viral protein functions. Our results demonstrate the unique potential of the ERV fossil record for studying the processes of viral spread and emergence as they play out across macro-evolutionary timescales, such that looking back in time may prove insightful for predicting the long-term consequences of newly emerging viral infections. DOI: http://dx.doi.org/10.7554/eLife.12704.001 PMID:26952212

Tracking interspecies transmission and long-term evolution of an ancient retrovirus using the genomes of modern mammals.

PubMed

Diehl, William E; Patel, Nirali; Halm, Kate; Johnson, Welkin E

2016-03-08

Mammalian genomes typically contain hundreds of thousands of endogenous retroviruses (ERVs), derived from ancient retroviral infections. Using this molecular 'fossil' record, we reconstructed the natural history of a specific retrovirus lineage (ERV-Fc) that disseminated widely between ~33 and ~15 million years ago, corresponding to the Oligocene and early Miocene epochs. Intercontinental viral spread, numerous instances of interspecies transmission and emergence in hosts representing at least 11 mammalian orders, and a significant role for recombination in diversification of this viral lineage were also revealed. By reconstructing the canonical retroviral genes, we identified patterns of adaptation consistent with selection to maintain essential viral protein functions. Our results demonstrate the unique potential of the ERV fossil record for studying the processes of viral spread and emergence as they play out across macro-evolutionary timescales, such that looking back in time may prove insightful for predicting the long-term consequences of newly emerging viral infections.

Covariance structure in the skull of Catarrhini: a case of pattern stasis and magnitude evolution.

PubMed

de Oliveira, Felipe Bandoni; Porto, Arthur; Marroig, Gabriel

2009-04-01

The study of the genetic variance/covariance matrix (G-matrix) is a recent and fruitful approach in evolutionary biology, providing a window of investigating for the evolution of complex characters. Although G-matrix studies were originally conducted for microevolutionary timescales, they could be extrapolated to macroevolution as long as the G-matrix remains relatively constant, or proportional, along the period of interest. A promising approach to investigating the constancy of G-matrices is to compare their phenotypic counterparts (P-matrices) in a large group of related species; if significant similarity is found among several taxa, it is very likely that the underlying G-matrices are also equivalent. Here we study the similarity of covariance and correlation structure in a broad sample of Old World monkeys and apes (Catarrhini). We made phylogenetically structured comparisons of correlation and covariance matrices derived from 39 skull traits, ranging from between species to the superfamily level. We also compared the overall magnitude of integration between skull traits (r2) for all Catarrhini genera. Our results show that P-matrices were not strictly constant among catarrhines, but the amount of divergence observed among taxa was generally low. There was significant and positive correlation between the amount of divergence in correlation and covariance patterns among the 30 genera and their phylogenetic distances derived from a recently proposed phylogenetic hypothesis. Our data demonstrate that the P-matrices remained relatively similar along the evolutionary history of catarrhines, and comparisons with the G-matrix available for a New World monkey genus (Saguinus) suggests that the same holds for all anthropoids. The magnitude of integration, in contrast, varied considerably among genera, indicating that evolution of the magnitude, rather than the pattern of inter-trait correlations, might have played an important role in the diversification of the

Evolution: Understanding Life on Earth.

ERIC Educational Resources Information Center

Dybas, Cheryl Lyn

2002-01-01

Reports on presentations representing evolution at the 53rd annual meeting of the American Institute of Biological Sciences (AIBS) which was held March 22-24, 2002. Explains evolutionary patterns, phylogenetic pageantry, molecular clocks, speciation and biogeography, speciation and macroevolution, and human-induced evolution of drugs-resistant…

The role of biotic forces in driving macroevolution: beyond the Red Queen

PubMed Central

Voje, Kjetil L.; Holen, Øistein H.; Liow, Lee Hsiang; Stenseth, Nils Chr.

2015-01-01

A multitude of hypotheses claim that abiotic factors are the main drivers of macroevolutionary change. By contrast, Van Valen's Red Queen hypothesis is often put forward as the sole representative of the view that biotic forcing is the main evolutionary driver. This imbalance of hypotheses does not reflect our current knowledge: theoretical work demonstrates the plausibility of biotically driven long-term evolution, whereas empirical work suggests a central role for biotic forcing in macroevolution. We call for a more pluralistic view of how biotic forces may drive long-term evolution that is compatible with both phenotypic stasis in the fossil record and with non-constant extinction rates. Promising avenues of research include contrasting predictions from relevant theories within ecology and macroevolution, as well as embracing both abiotic and biotic proxies while modelling long-term evolutionary data. By fitting models describing hypotheses of biotically driven macroevolution to data, we could dissect their predictions and transcend beyond pattern description, possibly narrowing the divide between our current understanding of micro- and macroevolution. PMID:25948685

Constraints in cancer evolution.

PubMed

Venkatesan, Subramanian; Birkbak, Nicolai J; Swanton, Charles

2017-02-08

Next-generation deep genome sequencing has only recently allowed us to quantitatively dissect the extent of heterogeneity within a tumour, resolving patterns of cancer evolution. Intratumour heterogeneity and natural selection contribute to resistance to anticancer therapies in the advanced setting. Recent evidence has also revealed that cancer evolution might be constrained. In this review, we discuss the origins of intratumour heterogeneity and subsequently focus on constraints imposed upon cancer evolution. The presence of (1) parallel evolution, (2) convergent evolution and (3) the biological impact of acquiring mutations in specific orders suggest that cancer evolution may be exploitable. These constraints on cancer evolution may help us identify cancer evolutionary rule books, which could eventually inform both diagnostic and therapeutic approaches to improve survival outcomes. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

PubMed

Green, Richard E; Braun, Edward L; Armstrong, Joel; Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Vandewege, Michael W; St John, John A; Capella-Gutiérrez, Salvador; Castoe, Todd A; Kern, Colin; Fujita, Matthew K; Opazo, Juan C; Jurka, Jerzy; Kojima, Kenji K; Caballero, Juan; Hubley, Robert M; Smit, Arian F; Platt, Roy N; Lavoie, Christine A; Ramakodi, Meganathan P; Finger, John W; Suh, Alexander; Isberg, Sally R; Miles, Lee; Chong, Amanda Y; Jaratlerdsiri, Weerachai; Gongora, Jaime; Moran, Christopher; Iriarte, Andrés; McCormack, John; Burgess, Shane C; Edwards, Scott V; Lyons, Eric; Williams, Christina; Breen, Matthew; Howard, Jason T; Gresham, Cathy R; Peterson, Daniel G; Schmitz, Jürgen; Pollock, David D; Haussler, David; Triplett, Eric W; Zhang, Guojie; Irie, Naoki; Jarvis, Erich D; Brochu, Christopher A; Schmidt, Carl J; McCarthy, Fiona M; Faircloth, Brant C; Hoffmann, Federico G; Glenn, Travis C; Gabaldón, Toni; Paten, Benedict; Ray, David A

2014-12-12

To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs. Copyright © 2014, American Association for the Advancement of Science.

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

PubMed Central

Green, Richard E; Braun, Edward L; Armstrong, Joel; Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Vandewege, Michael W; St John, John A; Capella-Gutiérrez, Salvador; Castoe, Todd A; Kern, Colin; Fujita, Matthew K; Opazo, Juan C; Jurka, Jerzy; Kojima, Kenji K; Caballero, Juan; Hubley, Robert M; Smit, Arian F; Platt, Roy N; Lavoie, Christine A; Ramakodi, Meganathan P; Finger, John W; Suh, Alexander; Isberg, Sally R; Miles, Lee; Chong, Amanda Y; Jaratlerdsiri, Weerachai; Gongora, Jaime; Moran, Christopher; Iriarte, Andrés; McCormack, John; Burgess, Shane C; Edwards, Scott V; Lyons, Eric; Williams, Christina; Breen, Matthew; Howard, Jason T; Gresham, Cathy R; Peterson, Daniel G; Schmitz, Jürgen; Pollock, David D; Haussler, David; Triplett, Eric W; Zhang, Guojie; Irie, Naoki; Jarvis, Erich D; Brochu, Christopher A; Schmidt, Carl J; McCarthy, Fiona M; Faircloth, Brant C; Hoffmann, Federico G; Glenn, Travis C; Gabaldón, Toni; Paten, Benedict; Ray, David A

2015-01-01

To provide context for the diversifications of archosaurs, the group that includes crocodilians, dinosaurs and birds, we generated draft genomes of three crocodilians, Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the relatively rapid evolution of bird genomes represents an autapomorphy within that clade. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these new data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs. PMID:25504731

Disentangling geographical, biotic, and abiotic drivers of plant diversity in neotropical Ruellia (Acanthaceae)

PubMed Central

Tsai, Yi-Hsin Erica

2017-01-01

It has long been hypothesized that biotic interactions are important drivers of biodiversity evolution, yet such interactions have been relatively less studied than abiotic factors owing to the inherent complexity in and the number of types of such interactions. Amongst the most prominent of biotic interactions worldwide are those between plants and pollinators. In the Neotropics, the most biodiverse region on Earth, hummingbird and bee pollination have contributed substantially to plant fitness. Using comparative methods, we test the macroevolutionary consequences of bird and bee pollination within a species rich lineage of flowering plants: Ruellia. We additionally explore impacts of species occupancy of ever-wet rainforests vs. dry ecosystems including cerrado and seasonally dry tropical forests. We compared outcomes based on two different methods of model selection: a traditional approach that utilizes a series of transitive likelihood ratio tests as well as a weighted model averaging approach. Analyses yield evidence for increased net diversification rates among Neotropical Ruellia (compared to Paleotropical lineages) as well as among hummingbird-adapted species. In contrast, we recovered no evidence of higher diversification rates among either bee- or non-bee-adapted lineages and no evidence for higher rates among wet or dry habitat lineages. Understanding fully the factors that have contributed to biases in biodiversity across the planet will ultimately depend upon incorporating knowledge of biotic interactions as well as connecting microevolutionary processes to macroevolutionary patterns. PMID:28472046

Pattern and process in the evolution of the sole dioecious member of Brassicaceae.

PubMed

Soza, Valerie L; Le Huynh, Vietnam; Di Stilio, Verónica S

2014-01-01

Lepidium sisymbrioides, a polyploid New Zealand endemic, is the sole dioecious species in Brassicaceae and therefore the closest dioecious relative of the model plant Arabidopsis thaliana. The attractiveness of developing this system for future studies on the genetics of sex determination prompted us to investigate historical and developmental factors surrounding the evolution of its unisexual flowers. Our goal was to determine the evolutionary pattern of polyploidization of L. sisymbrioides and the timing and process of flower reproductive organ abortion. To that end, we used a combination of phylogenetics to place this species within the complex history of polyploidization events in Lepidium and histology to compare its floral ontogeny to that of its closest hermaphroditic relatives and to A. thaliana. Using a nuclear locus (PISTILLATA), we reconstructed the gene tree among Lepidium taxa and applied a phylogenetic network analysis to identify ancestral genomes that contributed to the evolution of L. sisymbrioides. Combining this phylogenetic framework with cytological and genome size data, we estimated L. sisymbrioides as an allo-octoploid resulting from three hybridization events. Our investigations of flower development showed that unisexual flowers appear to abort reproductive organs by programmed cell death in female flowers and by developmental arrest in male flowers. This selective abortion occurs at the same floral developmental stage in both males and females, corresponding to Arabidopsis stage nine. Dioecy in Brassicaceae evolved once in L. sisymbrioides following several allopolyploidization events, by a process of selective abortion of reproductive organs at intermediate stages of flower development. Different developmental processes, but similar timing of abortions, affect male versus female flower development. An increased understanding of how and when reproductive organs abort in this species, combined with our estimates of ancestral genome

Emerging principles of regulatory evolution.

PubMed

Prud'homme, Benjamin; Gompel, Nicolas; Carroll, Sean B

2007-05-15

Understanding the genetic and molecular mechanisms governing the evolution of morphology is a major challenge in biology. Because most animals share a conserved repertoire of body-building and -patterning genes, morphological diversity appears to evolve primarily through changes in the deployment of these genes during development. The complex expression patterns of developmentally regulated genes are typically controlled by numerous independent cis-regulatory elements (CREs). It has been proposed that morphological evolution relies predominantly on changes in the architecture of gene regulatory networks and in particular on functional changes within CREs. Here, we discuss recent experimental studies that support this hypothesis and reveal some unanticipated features of how regulatory evolution occurs. From this growing body of evidence, we identify three key operating principles underlying regulatory evolution, that is, how regulatory evolution: (i) uses available genetic components in the form of preexisting and active transcription factors and CREs to generate novelty; (ii) minimizes the penalty to overall fitness by introducing discrete changes in gene expression; and (iii) allows interactions to arise among any transcription factor and downstream CRE. These principles endow regulatory evolution with a vast creative potential that accounts for both relatively modest morphological differences among closely related species and more profound anatomical divergences among groups at higher taxonomical levels.

The evolution of colour pattern complexity: selection for conspicuousness favours contrasting within-body colour combinations in lizards.

PubMed

Pérez I de Lanuza, G; Font, E

2016-05-01

Many animals display complex colour patterns that comprise several adjacent, often contrasting colour patches. Combining patches of complementary colours increases the overall conspicuousness of the complex pattern, enhancing signal detection. Therefore, selection for conspicuousness may act not only on the design of single colour patches, but also on their combination. Contrasting long- and short-wavelength colour patches are located on the ventral and lateral surfaces of many lacertid lizards. As the combination of long- and short-wavelength-based colours generates local chromatic contrast, we hypothesized that selection may favour the co-occurrence of lateral and ventral contrasting patches, resulting in complex colour patterns that maximize the overall conspicuousness of the signal. To test this hypothesis, we performed a comparative phylogenetic study using a categorical colour classification based on spectral data and descriptive information on lacertid coloration collected from the literature. Our results demonstrate that conspicuous ventral (long-wavelength-based) and lateral (short-wavelength-based) colour patches co-occur throughout the lacertid phylogeny more often than expected by chance, especially in the subfamily Lacertini. These results suggest that selection promotes the evolution of the complex pattern rather than the acquisition of a single conspicuous colour patch, possibly due to the increased conspicuousness caused by the combination of colours with contrasting spectral properties. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Aging and fertility patterns in wild chimpanzees provide insights into the evolution of menopause

PubMed Central

Thompson, Melissa Emery; Jones, James H.; Pusey, Anne E.; Brewer-Marsden, Stella; Goodall, Jane; Marsden, David; Matsuzawa, Tetsuro; Nishida, Toshisada; Reynolds, Vernon; Sugiyama, Yukimaru; Wrangham, Richard W.

2008-01-01

Summary Human menopause is remarkable in that reproductive senescence is markedly accelerated relative to somatic aging, leaving an extended post-reproductive period for a large proportion of women [1, 2]. Functional explanations for this are debated [4-11], in part because comparative data from closely-related species are inadequate. Existing studies of chimpanzees are based on very small samples and have not provided clear conclusions about the reproductive function of aging females [12-19]. These studies have not examined whether reproductive senescence in chimpanzees exceeds the pace of general aging, as in humans, or occurs in parallel with declines in overall health, as in many other animals [20, 21]. In order to remedy these problems, we examined fertility and mortality patterns in 6 free-living chimpanzee populations. Chimpanzee and human birth rates show similar patterns of decline beginning in the 4th decade, suggesting that the physiology of reproductive senescence was relatively conserved in human evolution. However, in contrast to humans, chimpanzee fertility declines are consistent with declines in survivorship, and healthy females maintain high birth rates late into life. Thus, in contrast to recent claims [16], we find no evidence that menopause is a typical characteristic of chimpanzee life histories. PMID:18083515

[Dynamic evolution of landscape spatial pattern in Taihu Lake basin, China].

PubMed

Wang, Fang; Xie, Xiao Ping; Chen, Zhi Cong

2017-11-01

Based on the land-use satellite image datasets of 2000, 2010 and 2015, the landscape index, dynamic change model, landscape transfer matrix and CLUE-S model were integrated to analyze the dynamic evolution of the landscape spatial pattern of Taihu Lake basin. The results showed that the landscape type of the basin was dominated by cultivated land and construction land, and the degree of landscape fragmentation was strengthened from 2000 to 2015, and the distribution showed a uniform trend. From the point of transfer dynamic change, the cultivated land and construction land changed significantly, which was reduced by 6761 km 2 (2.1%) and increased by 6615.33 km 2 (8.4%), respectively. From the landscape transfer, it could be seen that the main change direction of the cultivated land reduction was the construction land, and the cultivated land with 7866.30 km 2 was converted into construction land, accounting for 91.6% of the cultivated land change, and the contribution to the construction land was 96.5%. The trend of dynamic changes of cultivated and construction land in the counties and cities was the same as that of the whole Taihu Lake basin. For Shanghai Central Urban, as well as Pudong District, Lin'an City, Baoshan District, Minhang District, Jiading District and Changzhou City, the area of the cultivated land and construction land changed more prominently. However, compared with the CLUE-S model for the landscape pattern change in 2030, the change of cultivated and construction lands would be the largest in the natural development scenario. Under the ecological protection scenario, the area of grassland would increase and the dynamic degree would reach 54.5%. Under the situation of cultivated land protection, the conversion of cultivated land to construction land would be decreased.

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

PubMed

Kozak, Kenneth H; Wiens, John J

2016-11-01

Understanding which traits drive species diversification is essential for macroevolutionary studies and to understand patterns of species richness among clades. An important tool for testing if traits influence diversification is to estimate rates of net diversification for each clade, and then test for a relationship between traits and diversification rates among clades. However, this general approach has become very controversial. Numerous papers have now stated that it is inappropriate to analyze net diversification rates in groups in which clade richness is not positively correlated with clade age. Similarly, some have stated that variation in net diversification rates does not explain variation in species richness patterns among clades across the Tree of Life. Some authors have also suggested that strong correlations between richness and diversification rates are a statistical artifact and effectively inevitable. If this latter point is true, then correlations between richness and diversification rates would be uninformative (or even misleading) for identifying how much variation in species richness among clades is explained by variation in net diversification rates. Here, we use simulations (based on empirical data for plethodontid salamanders) to address three main questions. First, how is variation in net diversification rates among clades related to the relationship between clade age and species richness? Second, how accurate are these net diversification rate estimators, and does the age-richness relationship have any relevance to their accuracy? Third, is a relationship between species richness and diversification rates an inevitable, statistical artifact? Our simulations show that strong, positive age-richness relationships arise when diversification rates are invariant among clades, whereas realistic variation in diversification rates among clades frequently disrupts this relationship. Thus, a significant age-richness relationship should not be a

Genetic drift and rapid evolution of viviparity in insular fire salamanders (Salamandra salamandra)

PubMed Central

Velo-Antón, G; Zamudio, K R; Cordero-Rivera, A

2012-01-01

Continental islands offer an excellent opportunity to investigate adaptive processes and to time microevolutionary changes that precede macroevolutionary events. We performed a population genetic study of the fire salamander (Salamandra salamandra), a species that displays unique intraspecific diversity of reproductive strategies, to address the microevolutionary processes leading to phenotypic and genetic differentiation of island, coastal and interior populations. We used eight microsatellite markers to estimate genetic diversity, population structure and demographic parameters in viviparous insular populations and ovoviviparous coastal and interior populations. Our results show considerable genetic differentiation (FST range: 0.06–0.27), and no clear signs of gene flow among populations, except between the large and admixed interior populations. We find no support for island colonization by rafting or intentional/accidental anthropogenic introductions, indicating that rising sea levels were responsible for isolation of the island populations approximately 9000 years ago. Our study provides evidence of rapid genetic differentiation between island and coastal populations, and rapid evolution of viviparity driven by climatic selective pressures on island populations, geographic isolation with genetic drift, or a combination of these factors. Studies of these viviparous island populations in early stages of divergence help us better understand the microevolutionary processes involved in rapid phenotypic shifts. PMID:22086081

Genetic drift and rapid evolution of viviparity in insular fire salamanders (Salamandra salamandra).

PubMed

Velo-Antón, G; Zamudio, K R; Cordero-Rivera, A

2012-04-01

Continental islands offer an excellent opportunity to investigate adaptive processes and to time microevolutionary changes that precede macroevolutionary events. We performed a population genetic study of the fire salamander (Salamandra salamandra), a species that displays unique intraspecific diversity of reproductive strategies, to address the microevolutionary processes leading to phenotypic and genetic differentiation of island, coastal and interior populations. We used eight microsatellite markers to estimate genetic diversity, population structure and demographic parameters in viviparous insular populations and ovoviviparous coastal and interior populations. Our results show considerable genetic differentiation (F(ST) range: 0.06-0.27), and no clear signs of gene flow among populations, except between the large and admixed interior populations. We find no support for island colonization by rafting or intentional/accidental anthropogenic introductions, indicating that rising sea levels were responsible for isolation of the island populations approximately 9000 years ago. Our study provides evidence of rapid genetic differentiation between island and coastal populations, and rapid evolution of viviparity driven by climatic selective pressures on island populations, geographic isolation with genetic drift, or a combination of these factors. Studies of these viviparous island populations in early stages of divergence help us better understand the microevolutionary processes involved in rapid phenotypic shifts.

The tree balance signature of mass extinction is erased by continued evolution in clades of constrained size with trait-dependent speciation

PubMed Central

Yang, Guan-Dong; Agapow, Paul-Michael

2017-01-01

The kind and duration of phylogenetic topological “signatures” left in the wake of macroevolutionary events remain poorly understood. To this end, we examined a broad range of simulated phylogenies generated using trait-biased, heritable speciation probabilities and mass extinction that could be either random or selective on trait value, but also using background extinction and diversity-dependence to constrain clade sizes. In keeping with prior results, random mass extinction increased imbalance of clades that recovered to pre-extinction size, but was a relatively weak effect. Mass extinction that was selective on trait values tended to produce clades of similar or greater balance compared to random extinction or controls. Allowing evolution to continue past the point of clade-size recovery resulted in erosion and eventual erasure of this signal, with all treatments converging on similar values of imbalance, except for very intense extinction regimes targeted at taxa with high speciation rates. Return to a more balanced state with extended post-extinction evolution was also associated with loss of the previous phylogenetic root in most treatments. These results further demonstrate that while a mass extinction event can produce a recognizable phylogenetic signal, its effects become increasingly obscured the further an evolving clade gets from that event, with any sharp imbalance due to unrelated evolutionary factors. PMID:28644846

Evolution of meiotic recombination genes in maize and teosinte.

PubMed

Sidhu, Gaganpreet K; Warzecha, Tomasz; Pawlowski, Wojciech P

2017-01-25

Meiotic recombination is a major source of genetic variation in eukaryotes. The role of recombination in evolution is recognized but little is known about how evolutionary forces affect the recombination pathway itself. Although the recombination pathway is fundamentally conserved across different species, genetic variation in recombination components and outcomes has been observed. Theoretical predictions and empirical studies suggest that changes in the recombination pathway are likely to provide adaptive abilities to populations experiencing directional or strong selection pressures, such as those occurring during species domestication. We hypothesized that adaptive changes in recombination may be associated with adaptive evolution patterns of genes involved in meiotic recombination. To examine how maize evolution and domestication affected meiotic recombination genes, we studied patterns of sequence polymorphism and divergence in eleven genes controlling key steps in the meiotic recombination pathway in a diverse set of maize inbred lines and several accessions of teosinte, the wild ancestor of maize. We discovered that, even though the recombination genes generally exhibited high sequence conservation expected in a pathway controlling a key cellular process, they showed substantial levels and diverse patterns of sequence polymorphism. Among others, we found differences in sequence polymorphism patterns between tropical and temperate maize germplasms. Several recombination genes displayed patterns of polymorphism indicative of adaptive evolution. Despite their ancient origin and overall sequence conservation, meiotic recombination genes can exhibit extensive and complex patterns of molecular evolution. Changes in these genes could affect the functioning of the recombination pathway, and may have contributed to the successful domestication of maize and its expansion to new cultivation areas.

Mass extinction in tetraodontiform fishes linked to the Palaeocene-Eocene thermal maximum.

PubMed

Arcila, Dahiana; Tyler, James C

2017-11-15

Integrative evolutionary analyses based upon fossil and extant species provide a powerful approach for understanding past diversification events and for assessing the tempo of evolution across the Tree of Life. Herein, we demonstrate the importance of integrating fossil and extant species for inferring patterns of lineage diversification that would otherwise be masked in analyses that examine only one source of evidence. We infer the phylogeny and macroevolutionary history of the Tetraodontiformes (triggerfishes, pufferfishes and allies), a group with one of the most extensive fossil records among fishes. Our analyses combine molecular and morphological data, based on an expanded matrix that adds newly coded fossil species and character states. Beyond confidently resolving the relationships and divergence times of tetraodontiforms, our diversification analyses detect a major mass-extinction event during the Palaeocene-Eocene Thermal Maximum (PETM), followed by a marked increase in speciation rates. This pattern is consistently obtained when fossil and extant species are integrated, whereas examination of the fossil occurrences alone failed to detect major diversification changes during the PETM. When taking into account non-homogeneous models, our analyses also detect a rapid lineage diversification increase in one of the groups (tetraodontoids) during the middle Miocene, which is considered a key period in the evolution of reef fishes associated with trophic changes and ecological opportunity. In summary, our analyses show distinct diversification dynamics estimated from phylogenies and the fossil record, suggesting that different episodes shaped the evolution of tetraodontiforms during the Cenozoic. © 2017 The Author(s).

Evolution of Muscle Activity Patterns Driving Motions of the Jaw and Hyoid during Chewing in Gnathostomes

PubMed Central

Konow, Nicolai; Herrel, Anthony; Ross, Callum F.; Williams, Susan H.; German, Rebecca Z.; Sanford, Christopher P. J.; Gintof, Chris

2011-01-01

Although chewing has been suggested to be a basal gnathostome trait retained in most major vertebrate lineages, it has not been studied broadly and comparatively across vertebrates. To redress this imbalance, we recorded EMG from muscles powering anteroposterior movement of the hyoid, and dorsoventral movement of the mandibular jaw during chewing. We compared muscle activity patterns (MAP) during chewing in jawed vertebrate taxa belonging to unrelated groups of basal bony fishes and artiodactyl mammals. Our aim was to outline the evolution of coordination in MAP. Comparisons of activity in muscles of the jaw and hyoid that power chewing in closely related artiodactyls using cross-correlation analyses identified reorganizations of jaw and hyoid MAP between herbivores and omnivores. EMG data from basal bony fishes revealed a tighter coordination of jaw and hyoid MAP during chewing than seen in artiodactyls. Across this broad phylogenetic range, there have been major structural reorganizations, including a reduction of the bony hyoid suspension, which is robust in fishes, to the acquisition in a mammalian ancestor of a muscle sling suspending the hyoid. These changes appear to be reflected in a shift in chewing MAP that occurred in an unidentified anamniote stem-lineage. This shift matches observations that, when compared with fishes, the pattern of hyoid motion in tetrapods is reversed and also time-shifted relative to the pattern of jaw movement. PMID:21705368

Design of Spiking Central Pattern Generators for Multiple Locomotion Gaits in Hexapod Robots by Christiansen Grammar Evolution

PubMed Central

Espinal, Andres; Rostro-Gonzalez, Horacio; Carpio, Martin; Guerra-Hernandez, Erick I.; Ornelas-Rodriguez, Manuel; Sotelo-Figueroa, Marco

2016-01-01

This paper presents a method to design Spiking Central Pattern Generators (SCPGs) to achieve locomotion at different frequencies on legged robots. It is validated through embedding its designs into a Field-Programmable Gate Array (FPGA) and implemented on a real hexapod robot. The SCPGs are automatically designed by means of a Christiansen Grammar Evolution (CGE)-based methodology. The CGE performs a solution for the configuration (synaptic weights and connections) for each neuron in the SCPG. This is carried out through the indirect representation of candidate solutions that evolve to replicate a specific spike train according to a locomotion pattern (gait) by measuring the similarity between the spike trains and the SPIKE distance to lead the search to a correct configuration. By using this evolutionary approach, several SCPG design specifications can be explicitly added into the SPIKE distance-based fitness function, such as looking for Spiking Neural Networks (SNNs) with minimal connectivity or a Central Pattern Generator (CPG) able to generate different locomotion gaits only by changing the initial input stimuli. The SCPG designs have been successfully implemented on a Spartan 6 FPGA board and a real time validation on a 12 Degrees Of Freedom (DOFs) hexapod robot is presented. PMID:27516737

ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation

PubMed Central

Kristensen, David M.; Wolf, Yuri I.; Koonin, Eugene V.

2017-01-01

The Alignable Tight Genomic Clusters (ATGCs) database is a collection of closely related bacterial and archaeal genomes that provides several tools to aid research into evolutionary processes in the microbial world. Each ATGC is a taxonomy-independent cluster of 2 or more completely sequenced genomes that meet the objective criteria of a high degree of local gene order (synteny) and a small number of synonymous substitutions in the protein-coding genes. As such, each ATGC is suited for analysis of microevolutionary variations within a cohesive group of organisms (e.g. species), whereas the entire collection of ATGCs is useful for macroevolutionary studies. The ATGC database includes many forms of pre-computed data, in particular ATGC-COGs (Clusters of Orthologous Genes), multiple sequence alignments, a set of ‘index’ orthologs representing the most well-conserved members of each ATGC-COG, the phylogenetic tree of the organisms within each ATGC, etc. Although the ATGC database contains several million proteins from thousands of genomes organized into hundreds of clusters (roughly a 4-fold increase since the last version of the ATGC database), it is now built with completely automated methods and will be regularly updated following new releases of the NCBI RefSeq database. The ATGC database is hosted jointly at the University of Iowa at dmk-brain.ecn.uiowa.edu/ATGC/ and the NCBI at ftp.ncbi.nlm.nih.gov/pub/kristensen/ATGC/atgc_home.html. PMID:28053163

Conservative and compensatory evolution in oxidative phosphorylation complexes of angiosperms with highly divergent rates of mitochondrial genome evolution.

PubMed

Havird, Justin C; Whitehill, Nicholas S; Snow, Christopher D; Sloan, Daniel B

2015-12-01

Interactions between nuclear and mitochondrial gene products are critical for eukaryotic cell function. Nuclear genes encoding mitochondrial-targeted proteins (N-mt genes) experience elevated rates of evolution, which has often been interpreted as evidence of nuclear compensation in response to elevated mitochondrial mutation rates. However, N-mt genes may be under relaxed functional constraints, which could also explain observed increases in their evolutionary rate. To disentangle these hypotheses, we examined patterns of sequence and structural evolution in nuclear- and mitochondrial-encoded oxidative phosphorylation proteins from species in the angiosperm genus Silene with vastly different mitochondrial mutation rates. We found correlated increases in N-mt gene evolution in species with fast-evolving mitochondrial DNA. Structural modeling revealed an overrepresentation of N-mt substitutions at positions that directly contact mutated residues in mitochondrial-encoded proteins, despite overall patterns of conservative structural evolution. These findings support the hypothesis that selection for compensatory changes in response to mitochondrial mutations contributes to the elevated rate of evolution in N-mt genes. We discuss these results in light of theories implicating mitochondrial mutation rates and mitonuclear coevolution as drivers of speciation and suggest comparative and experimental approaches that could take advantage of heterogeneity in rates of mtDNA evolution across eukaryotes to evaluate such theories. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Nondegenerative Evolution in Ancient Heritable Bacterial Endosymbionts of Fungi.

PubMed

Mondo, Stephen J; Salvioli, Alessandra; Bonfante, Paola; Morton, Joseph B; Pawlowska, Teresa E

2016-09-01

Bacterial endosymbionts are critical to the existence of many eukaryotes. Among them, vertically transmitted endobacteria are uniquely typified by reduced genomes and molecular evolution rate acceleration relative to free-living taxa. These patterns are attributable to genetic drift-dominated degenerative processes associated with reproductive dependence on the host. The degenerative evolution scenario is well supported in endobacteria with strict vertical transmission, such as essential mutualists of insects. In contrast, heritable endosymbionts that are nonessential to their hosts and engage occasionally in horizontal transmission are expected to display deviations from the degenerative evolution model. To explore evolution patterns in such nonessential endobacteria, we focused on Candidatus Glomeribacter gigasporarum ancient heritable mutualists of fungi. Using a collection of genomes, we estimated in Glomeribacter mutation rate at 2.03 × 10(-9) substitutions per site per year and effective population size at 1.44 × 10(8) Both fall within the range of values observed in free-living bacteria. To assess the ability of Glomeribacter to purge slightly deleterious mutations, we examined genome-wide dN/dS values and distribution patterns. We found that these dN/dS profiles cluster Glomeribacter with free-living bacteria as well as with other nonessential endosymbionts, while distinguishing it from essential heritable mutualists of insects. Finally, our evolutionary simulations revealed that the molecular evolution rate acceleration in Glomeribacter is caused by limited recombination in a largely clonal population rather than by increased fixation of slightly deleterious mutations. Based on these patterns, we propose that genome evolution in Glomeribacter is nondegenerative and exemplifies a departure from the model of degenerative evolution in heritable endosymbionts. © The Author 2016. Published by Oxford University Press on behalf of the Society for

VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma.

PubMed

Jiang, Yanwen; Nie, Kui; Redmond, David; Melnick, Ari M; Tam, Wayne; Elemento, Olivier

2015-12-28

Understanding tumor clonality is critical to understanding the mechanisms involved in tumorigenesis and disease progression. In addition, understanding the clonal composition changes that occur within a tumor in response to certain micro-environment or treatments may lead to the design of more sophisticated and effective approaches to eradicate tumor cells. However, tracking tumor clonal sub-populations has been challenging due to the lack of distinguishable markers. To address this problem, a VDJ-seq protocol was created to trace the clonal evolution patterns of diffuse large B cell lymphoma (DLBCL) relapse by exploiting VDJ recombination and somatic hypermutation (SHM), two unique features of B cell lymphomas. In this protocol, Next-Generation sequencing (NGS) libraries with indexing potential were constructed from amplified rearranged immunoglobulin heavy chain (IgH) VDJ region from pairs of primary diagnosis and relapse DLBCL samples. On average more than half million VDJ sequences per sample were obtained after sequencing, which contain both VDJ rearrangement and SHM information. In addition, customized bioinformatics pipelines were developed to fully utilize sequence information for the characterization of IgH-VDJ repertoire within these samples. Furthermore, the pipeline allows the reconstruction and comparison of the clonal architecture of individual tumors, which enables the examination of the clonal heterogeneity within the diagnosis tumors and deduction of clonal evolution patterns between diagnosis and relapse tumor pairs. When applying this analysis to several diagnosis-relapse pairs, we uncovered key evidence that multiple distinctive tumor evolutionary patterns could lead to DLBCL relapse. Additionally, this approach can be expanded into other clinical aspects, such as identification of minimal residual disease, monitoring relapse progress and treatment response, and investigation of immune repertoires in non-lymphoma contexts.

Temporal and spatial evolution characteristics of gas-liquid two-phase flow pattern based on image texture spectrum descriptor

NASA Astrophysics Data System (ADS)

Zhou, Xi-Guo; Jin, Ning-De; Wang, Zhen-Ya; Zhang, Wen-Yin

2009-11-01

The dynamic image information of typical gas-liquid two-phase flow patterns in vertical upward pipe is captured by a highspeed dynamic camera. The texture spectrum descriptor is used to describe the texture characteristics of the processed images whose content is represented in the form of texture spectrum histogram, and four time-varying characteristic parameter indexes which represent image texture structure of different flow patterns are extracted. The study results show that the amplitude fluctuation of texture characteristic parameter indexes of bubble flow is lowest and shows very random complex dynamic behavior; the amplitude fluctuation of slug flow is higher and shows intermittent motion behavior between gas slug and liquid slug, and the amplitude fluctuation of churn flow is the highest and shows better periodicity; the amplitude fluctuation of bubble-slug flow is from low to high and oscillating frequence is higher than that of slug flow, and includes the features of both slug flow and bubble flow; the slug-churn flow loses the periodicity of slug flow and churn flow, and the amplitude fluctuation is high. The results indicate that the image texture characteristic parameter indexes of different flow pattern can reflect the flow characteristics of gas-liquid two-phase flow, which provides a new approach to understand the temporal and spatial evolution of flow pattern dynamics.

Distinct biological subtypes and patterns of genome evolution in lymphoma revealed by circulating tumor DNA.

PubMed

Scherer, Florian; Kurtz, David M; Newman, Aaron M; Stehr, Henning; Craig, Alexander F M; Esfahani, Mohammad Shahrokh; Lovejoy, Alexander F; Chabon, Jacob J; Klass, Daniel M; Liu, Chih Long; Zhou, Li; Glover, Cynthia; Visser, Brendan C; Poultsides, George A; Advani, Ranjana H; Maeda, Lauren S; Gupta, Neel K; Levy, Ronald; Ohgami, Robert S; Kunder, Christian A; Diehn, Maximilian; Alizadeh, Ash A

2016-11-09

Patients with diffuse large B cell lymphoma (DLBCL) exhibit marked diversity in tumor behavior and outcomes, yet the identification of poor-risk groups remains challenging. In addition, the biology underlying these differences is incompletely understood. We hypothesized that characterization of mutational heterogeneity and genomic evolution using circulating tumor DNA (ctDNA) profiling could reveal molecular determinants of adverse outcomes. To address this hypothesis, we applied cancer personalized profiling by deep sequencing (CAPP-Seq) analysis to tumor biopsies and cell-free DNA samples from 92 lymphoma patients and 24 healthy subjects. At diagnosis, the amount of ctDNA was found to strongly correlate with clinical indices and was independently predictive of patient outcomes. We demonstrate that ctDNA genotyping can classify transcriptionally defined tumor subtypes, including DLBCL cell of origin, directly from plasma. By simultaneously tracking multiple somatic mutations in ctDNA, our approach outperformed immunoglobulin sequencing and radiographic imaging for the detection of minimal residual disease and facilitated noninvasive identification of emergent resistance mutations to targeted therapies. In addition, we identified distinct patterns of clonal evolution distinguishing indolent follicular lymphomas from those that transformed into DLBCL, allowing for potential noninvasive prediction of histological transformation. Collectively, our results demonstrate that ctDNA analysis reveals biological factors that underlie lymphoma clinical outcomes and could facilitate individualized therapy. Copyright © 2016, American Association for the Advancement of Science.

The Evolution and Expression Pattern of Human Overlapping lncRNA and Protein-coding Gene Pairs.

PubMed

Ning, Qianqian; Li, Yixue; Wang, Zhen; Zhou, Songwen; Sun, Hong; Yu, Guangjun

2017-03-27

Long non-coding RNA overlapping with protein-coding gene (lncRNA-coding pair) is a special type of overlapping genes. Protein-coding overlapping genes have been well studied and increasing attention has been paid to lncRNAs. By studying lncRNA-coding pairs in human genome, we showed that lncRNA-coding pairs were more likely to be generated by overprinting and retaining genes in lncRNA-coding pairs were given higher priority than non-overlapping genes. Besides, the preference of overlapping configurations preserved during evolution was based on the origin of lncRNA-coding pairs. Further investigations showed that lncRNAs promoting the splicing of their embedded protein-coding partners was a unilateral interaction, but the existence of overlapping partners improving the gene expression was bidirectional and the effect was decreased with the increased evolutionary age of genes. Additionally, the expression of lncRNA-coding pairs showed an overall positive correlation and the expression correlation was associated with their overlapping configurations, local genomic environment and evolutionary age of genes. Comparison of the expression correlation of lncRNA-coding pairs between normal and cancer samples found that the lineage-specific pairs including old protein-coding genes may play an important role in tumorigenesis. This work presents a systematically comprehensive understanding of the evolution and the expression pattern of human lncRNA-coding pairs.

Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution.

PubMed

Kendall, Michelle; Colijn, Caroline

2016-10-01

Evolutionary relationships are frequently described by phylogenetic trees, but a central barrier in many fields is the difficulty of interpreting data containing conflicting phylogenetic signals. We present a metric-based method for comparing trees which extracts distinct alternative evolutionary relationships embedded in data. We demonstrate detection and resolution of phylogenetic uncertainty in a recent study of anole lizards, leading to alternate hypotheses about their evolutionary relationships. We use our approach to compare trees derived from different genes of Ebolavirus and find that the VP30 gene has a distinct phylogenetic signature composed of three alternatives that differ in the deep branching structure. phylogenetics, evolution, tree metrics, genetics, sequencing. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Variation in the Intensity of Selection on Codon Bias over Time Causes Contrasting Patterns of Base Composition Evolution in Drosophila

PubMed Central

Jackson, Benjamin C.; Campos, José L.; Haddrill, Penelope R.; Charlesworth, Brian

2017-01-01

Four-fold degenerate coding sites form a major component of the genome, and are often used to make inferences about selection and demography, so that understanding their evolution is important. Despite previous efforts, many questions regarding the causes of base composition changes at these sites in Drosophila remain unanswered. To shed further light on this issue, we obtained a new whole-genome polymorphism data set from D. simulans. We analyzed samples from the putatively ancestral range of D. simulans, as well as an existing polymorphism data set from an African population of D. melanogaster. By using D. yakuba as an outgroup, we found clear evidence for selection on 4-fold sites along both lineages over a substantial period, with the intensity of selection increasing with GC content. Based on an explicit model of base composition evolution, we suggest that the observed AT-biased substitution pattern in both lineages is probably due to an ancestral reduction in selection intensity, and is unlikely to be the result of an increase in mutational bias towards AT alone. By using two polymorphism-based methods for estimating selection coefficients over different timescales, we show that the selection intensity on codon usage has been rather stable in D. simulans in the recent past, but the long-term estimates in D. melanogaster are much higher than the short-term ones, indicating a continuing decline in selection intensity, to such an extent that the short-term estimates suggest that selection is only active in the most GC-rich parts of the genome. Finally, we provide evidence for complex evolutionary patterns in the putatively neutral short introns, which cannot be explained by the standard GC-biased gene conversion model. These results reveal a dynamic picture of base composition evolution. PMID:28082609

Adaptive processes drive ecomorphological convergent evolution in antwrens (Thamnophilidae).

PubMed

Bravo, Gustavo A; Remsen, J V; Brumfield, Robb T

2014-10-01

Phylogenetic niche conservatism (PNC) and convergence are contrasting evolutionary patterns that describe phenotypic similarity across independent lineages. Assessing whether and how adaptive processes give origin to these patterns represent a fundamental step toward understanding phenotypic evolution. Phylogenetic model-based approaches offer the opportunity not only to distinguish between PNC and convergence, but also to determine the extent that adaptive processes explain phenotypic similarity. The Myrmotherula complex in the Neotropical family Thamnophilidae is a polyphyletic group of sexually dimorphic small insectivorous forest birds that are relatively homogeneous in size and shape. Here, we integrate a comprehensive species-level molecular phylogeny of the Myrmotherula complex with morphometric and ecological data within a comparative framework to test whether phenotypic similarity is described by a pattern of PNC or convergence, and to identify evolutionary mechanisms underlying body size and shape evolution. We show that antwrens in the Myrmotherula complex represent distantly related clades that exhibit adaptive convergent evolution in body size and divergent evolution in body shape. Phenotypic similarity in the group is primarily driven by their tendency to converge toward smaller body sizes. Differences in body size and shape across lineages are associated to ecological and behavioral factors. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Evolution of reproductive proteins from animals and plants.

PubMed

Clark, Nathaniel L; Aagaard, Jan E; Swanson, Willie J

2006-01-01

Sexual reproduction is a fundamental biological process common among eukaryotes. Because of the significance of reproductive proteins to fitness, the diversity and rapid divergence of proteins acting at many stages of reproduction is surprising and suggests a role of adaptive diversification in reproductive protein evolution. Here we review the evolution of reproductive proteins acting at different stages of reproduction among animals and plants, emphasizing common patterns. Although we are just beginning to understand these patterns, by making comparisons among stages of reproduction for diverse organisms we can begin to understand the selective forces driving reproductive protein diversity and the functional consequences of reproductive protein evolution.

Potential pitfalls of reconstructing deep time evolutionary history with only extant data, a case study using the canidae (mammalia, carnivora).

PubMed

Finarelli, John A; Goswami, Anjali

2013-12-01

Reconstructing evolutionary patterns and their underlying processes is a central goal in biology. Yet many analyses of deep evolutionary histories assume that data from the fossil record is too incomplete to include, and rely solely on databases of extant taxa. Excluding fossil taxa assumes that character state distributions across living taxa are faithful representations of a clade's entire evolutionary history. Many factors can make this assumption problematic. Fossil taxa do not simply lead-up to extant taxa; they represent now-extinct lineages that can substantially impact interpretations of character evolution for extant groups. Here, we analyze body mass data for extant and fossil canids (dogs, foxes, and relatives) for changes in mean and variance through time. AIC-based model selection recovered distinct models for each of eight canid subgroups. We compared model fit of parameter estimates for (1) extant data alone and (2) extant and fossil data, demonstrating that the latter performs significantly better. Moreover, extant-only analyses result in unrealistically low estimates of ancestral mass. Although fossil data are not always available, reconstructions of deep-time organismal evolution in the absence of deep-time data can be highly inaccurate, and we argue that every effort should be made to include fossil data in macroevolutionary studies. © 2013 The Authors. Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Diversity patterns amongst herbivorous dinosaurs and plants during the Cretaceous: implications for hypotheses of dinosaur/angiosperm co-evolution.

PubMed

Butler, R J; Barrett, P M; Kenrick, P; Penn, M G

2009-03-01

Palaeobiologists frequently attempt to identify examples of co-evolutionary interactions over extended geological timescales. These hypotheses are often intuitively appealing, as co-evolution is so prevalent in extant ecosystems, and are easy to formulate; however, they are much more difficult to test than their modern analogues. Among the more intriguing deep time co-evolutionary scenarios are those that relate changes in Cretaceous dinosaur faunas to the primary radiation of flowering plants. Demonstration of temporal congruence between the diversifications of co-evolving groups is necessary to establish whether co-evolution could have occurred in such cases, but is insufficient to prove whether it actually did take place. Diversity patterns do, however, provide a means for falsifying such hypotheses. We have compiled a new database of Cretaceous dinosaur and plant distributions from information in the primary literature. This is used as the basis for plotting taxonomic diversity and occurrence curves for herbivorous dinosaurs (Sauropodomorpha, Stegosauria, Ankylosauria, Ornithopoda, Ceratopsia, Pachycephalosauria and herbivorous theropods) and major groups of plants (angiosperms, Bennettitales, cycads, cycadophytes, conifers, Filicales and Ginkgoales) that co-occur in dinosaur-bearing formations. Pairwise statistical comparisons were made between various floral and faunal groups to test for any significant similarities in the shapes of their diversity curves through time. We show that, with one possible exception, diversity patterns for major groups of herbivorous dinosaurs are not positively correlated with angiosperm diversity. In other words, at the level of major clades, there is no support for any diffuse co-evolutionary relationship between herbivorous dinosaurs and flowering plants. The diversification of Late Cretaceous pachycephalosaurs (excluding the problematic taxon Stenopelix) shows a positive correlation, but this might be spuriously related to

Carbon source utilization patterns of Bacillus simplex ecotypes do not reflect their adaptation to ecologically divergent slopes in 'Evolution Canyon', Israel.

PubMed

Sikorski, Johannes; Pukall, Rüdiger; Stackebrandt, Erko

2008-10-01

The 'Evolution Canyons' I and II in Israel are model habitats to study adaptation and speciation of bacteria in the environment. These canyons represent similar ecological replicates, separated by 40 km, with a strongly sun-exposed and hot 'African' south-facing slope (SFS) vs. a cooler and mesic-lush 'European' north-facing slope (NFS). Previously, among 131 Bacillus simplex isolates, distinct genetic lineages (ecotypes), each specific for either SFS or NFS, were identified, suggesting a temperature-driven slope-specific adaptation. Here, we asked whether the ecological heterogeneity of SFS vs. NFS also affected carbon utilization abilities, as determined using the Biolog assay. Contrary to expectation, a correlation between substrate utilization patterns and the ecological origin of strains was not found. Rather, the patterns split according to the two major phylogenetic lineages each of which contain SFS and NFS ecotypes. We conclude that traits related to the general energy metabolism, as far as assessed here, are neither shaped by the major abiotic features of 'Evolution Canyon', namely solar radiation, temperature, and drought, nor by the soil characteristics. We further conclude that some traits diverge rather neutrally from each other, whereas other, more environmentally related traits are shaped by natural selection and show evolutionary convergence.

SWS2 visual pigment evolution as a test of historically contingent patterns of plumage color evolution in warblers.

PubMed

Bloch, Natasha I; Morrow, James M; Chang, Belinda S W; Price, Trevor D

2015-02-01

Distantly related clades that occupy similar environments may differ due to the lasting imprint of their ancestors-historical contingency. The New World warblers (Parulidae) and Old World warblers (Phylloscopidae) are ecologically similar clades that differ strikingly in plumage coloration. We studied genetic and functional evolution of the short-wavelength-sensitive visual pigments (SWS2 and SWS1) to ask if altered color perception could contribute to the plumage color differences between clades. We show SWS2 is short-wavelength shifted in birds that occupy open environments, such as finches, compared to those in closed environments, including warblers. Phylogenetic reconstructions indicate New World warblers were derived from a finch-like form that colonized from the Old World 15-20 Ma. During this process, the SWS2 gene accumulated six substitutions in branches leading to New World warblers, inviting the hypothesis that passage through a finch-like ancestor resulted in SWS2 evolution. In fact, we show spectral tuning remained similar across warblers as well as the finch ancestor. Results reject the hypothesis of historical contingency based on opsin spectral tuning, but point to evolution of other aspects of visual pigment function. Using the approach outlined here, historical contingency becomes a generally testable theory in systems where genotype and phenotype can be connected. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Item Feature Effects in Evolution Assessment

ERIC Educational Resources Information Center

Nehm, Ross H.; Ha, Minsu

2011-01-01

Despite concerted efforts by science educators to understand patterns of evolutionary reasoning in science students and teachers, the vast majority of evolution education studies have failed to carefully consider or control for item feature effects in knowledge measurement. Our study explores whether robust contextualization patterns emerge within…

Mutation—The Engine of Evolution: Studying Mutation and Its Role in the Evolution of Bacteria

PubMed Central

Hershberg, Ruth

2015-01-01

Mutation is the engine of evolution in that it generates the genetic variation on which the evolutionary process depends. To understand the evolutionary process we must therefore characterize the rates and patterns of mutation. Starting with the seminal Luria and Delbruck fluctuation experiments in 1943, studies utilizing a variety of approaches have revealed much about mutation rates and patterns and about how these may vary between different bacterial strains and species along the chromosome and between different growth conditions. This work provides a critical overview of the results and conclusions drawn from these studies, of the debate surrounding some of these conclusions, and of the challenges faced when studying mutation and its role in bacterial evolution. PMID:26330518

Trends and patterns of anthropogenic evolution of chernozems in lands of agricultural afforestation within the territory of forest-steppe in the center of eastern Europe

USDA-ARS?s Scientific Manuscript database

The anthropogenic evolution of chernozems as a result of plowing and the creation of forest shelterbelts on three meadow-steppe areas of forest-steppe were studied. It was established, that in all areas there are similar patterns, caused by the transformation of virgin soils into arable soils and vi...

Global ecological pattern of ammonia-oxidizing archaea.

PubMed

Cao, Huiluo; Auguet, Jean-Christophe; Gu, Ji-Dong

2013-01-01

The global distribution of ammonia-oxidizing archaea (AOA), which play a pivotal role in the nitrification process, has been confirmed through numerous ecological studies. Though newly available amoA (ammonia monooxygenase subunit A) gene sequences from new environments are accumulating rapidly in public repositories, a lack of information on the ecological and evolutionary factors shaping community assembly of AOA on the global scale is apparent. We conducted a meta-analysis on uncultured AOA using over ca. 6,200 archaeal amoA gene sequences, so as to reveal their community distribution patterns along a wide spectrum of physicochemical conditions and habitat types. The sequences were dereplicated at 95% identity level resulting in a dataset containing 1,476 archaeal amoA gene sequences from eight habitat types: namely soil, freshwater, freshwater sediment, estuarine sediment, marine water, marine sediment, geothermal system, and symbiosis. The updated comprehensive amoA phylogeny was composed of three major monophyletic clusters (i.e. Nitrosopumilus, Nitrosotalea, Nitrosocaldus) and a non-monophyletic cluster constituted mostly by soil and sediment sequences that we named Nitrososphaera. Diversity measurements indicated that marine and estuarine sediments as well as symbionts might be the largest reservoirs of AOA diversity. Phylogenetic analyses were further carried out using macroevolutionary analyses to explore the diversification pattern and rates of nitrifying archaea. In contrast to other habitats that displayed constant diversification rates, marine planktonic AOA interestingly exhibit a very recent and accelerating diversification rate congruent with the lowest phylogenetic diversity observed in their habitats. This result suggested the existence of AOA communities with different evolutionary history in the different habitats. Based on an up-to-date amoA phylogeny, this analysis provided insights into the possible evolutionary mechanisms and environmental

How predation shaped fish: the impact of fin spines on body form evolution across teleosts.

PubMed

Price, S A; Friedman, S T; Wainwright, P C

2015-11-22

It is well known that predators can induce morphological changes in some fish: individuals exposed to predation cues increase body depth and the length of spines. We hypothesize that these structures may evolve synergistically, as together, these traits will further enlarge the body dimensions of the fish that gape-limited predators must overcome. We therefore expect that the orientation of the spines will predict which body dimension increases in the presence of predators. Using phylogenetic comparative methods, we tested this prediction on the macroevolutionary scale across 347 teleost families, which display considerable variation in fin spines, body depth and width. Consistent with our predictions, we demonstrate that fin spines on the vertical plane (dorsal and anal fins) are associated with a deeper-bodied optimum. Lineages with spines on the horizontal plane (pectoral fins) are associated with a wider-bodied optimum. Optimal body dimensions across lineages without spines paralleling the body dimension match the allometric expectation. Additionally, lineages with longer spines have deeper and wider body dimensions. This evolutionary relationship between fin spines and body dimensions across teleosts reveals functional synergy between these two traits and a potential macroevolutionary signature of predation on the evolutionary dynamics of body shape. © 2015 The Author(s).

Latitudinal patterns in plant defense: evolution of cardenolides, their toxicity and induction following herbivory.

PubMed

Rasmann, Sergio; Agrawal, Anurag A

2011-05-01

Attempts over the past 50 years to explain variation in the abundance, distribution and diversity of plant secondary compounds gave rise to theories of plant defense. Remarkably, few phylogenetically robust tests of these long-standing theories have been conducted. Using >50 species of milkweed (Asclepias spp.), we show that variation among plant species in the induction of toxic cardenolides is explained by latitude, with higher inducibility evolving more frequently at lower latitudes. We also found that: (1) the production of cardenolides showed positive-correlated evolution with the diversity of cardenolides, (2) greater cardenolide investment by a species is accompanied by an increase in an estimate of toxicity (measured as chemical polarity) and (3) instead of trading off, constitutive and induced cardenolides were positively correlated. Analyses of root and shoot cardenolides showed concordant patterns. Thus, milkweed species from lower latitudes are better defended with higher inducibility, greater diversity and added toxicity of cardenolides. © 2011 Blackwell Publishing Ltd/CNRS.

Patterns of microsatellite evolution inferred from the Helianthus annuus (Asteraceae) transcriptome.

PubMed

Pramod, Sreepriya; Perkins, Andy D; Welch, Mark E

2014-08-01

The distribution of microsatellites in exons, and their association with gene ontology (GO) terms is explored to elucidate patterns of microsatellite evolution in the common sunflower, Helianthus annuus. The relative position, motif, size and level of impurity were estimated for each microsatellite in the unigene database available from the Compositae Genome Project (CGP), and statistical analyses were performed to determine if differences in microsatellite distributions and enrichment within certain GO terms were significant. There are more translated than untranslated microsatellites, implying that many bring about structural changes in proteins. However, the greatest density is observed within the UTRs, particularly 5'UTRs. Further, UTR microsatellites are purer and longer than coding region microsatellites. This suggests that UTR microsatellites are either younger and under more relaxed constraints, or that purifying selection limits impurities, and directional selection favours their expansion. GOs associated with response to various environmental stimuli including water deprivation and salt stress were significantly enriched with microsatellites. This may suggest that these GOs are more labile in plant genomes, or that selection has favoured the maintenance of microsatellites in these genes over others. This study shows that the distribution of transcribed microsatellites in H. annuus is nonrandom, the coding region microsatellites are under greater constraint compared to the UTR microsatellites, and that these sequences are enriched within genes that regulate plant responses to environmental stress and stimuli.

From Teeth to Baleen and Raptorial to Bulk Filter Feeding in Mysticete Cetaceans: The Role of Paleontological, Genetic, and Geochemical Data in Feeding Evolution and Ecology.

PubMed

Berta, Annalisa; Lanzetti, Agnese; Ekdale, Eric G; Deméré, Thomas A

2016-12-01

The origin of baleen and filter feeding in mysticete cetaceans occurred sometime between approximately 34 and 24 million years ago and represents a major macroevolutionary shift in cetacean morphology (teeth to baleen) and ecology (raptorial to filter feeding). We explore this dramatic change in feeding strategy by employing a diversity of tools and approaches: morphology, molecules, development, and stable isotopes from the geological record. Adaptations for raptorial feeding in extinct toothed mysticetes provide the phylogenetic context for evaluating morphological apomorphies preserved in the skeletons of stem and crown edentulous mysticetes. In this light, the presence of novel vascular structures on the palates of certain Oligocene toothed mysticetes is interpreted as the earliest evidence of baleen and points to an intermediate condition between an ancestral condition with teeth only and a derived condition with baleen only. Supporting this step-wise evolutionary hypothesis, evidence from stable isotopes show how changes in dental chemistry in early toothed mysticetes tracked the changes in diet and environment. Recent discoveries also demonstrate how this transition was made possible by radical changes in cranial ontogeny. In addition, genetic mutations and the possession of dental pseudogenes in extant baleen whales support a toothed ancestry for mysticetes. Molecular and morphological data also document the dramatic developmental shifts that take place in extant fetal baleen whales, in skull development, resorption of a fetal dentition and growth of baleen. The mechanisms involved in this complex evolutionary transition that entails multiple, integrated aspects of anatomy and ecology are only beginning to be understood, and future work will further clarify the processes underlying this macroevolutionary pattern. © The Author 2016. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved

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

PubMed

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

2016-01-18

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

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

PubMed Central

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

2016-01-01

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

Distinct genetic evolution patterns of relapsing diffuse large B-cell lymphoma revealed by genome-wide copy number aberration and targeted sequencing analysis.

PubMed

Juskevicius, D; Lorber, T; Gsponer, J; Perrina, V; Ruiz, C; Stenner-Liewen, F; Dirnhofer, S; Tzankov, A

2016-12-01

Recurrences of diffuse large B-cell lymphomas (DLBCL) result in significant morbidity and mortality, but their underlying genetic and biological mechanisms are unclear. Clonal relationship in DLBCL relapses so far is mostly addressed by the investigation of immunoglobulin (IG) rearrangements, therefore, lacking deeper insights into genome-wide lymphoma evolution. We studied mutations and copy number aberrations in 20 paired relapsing and 20 non-relapsing DLBCL cases aiming to test the clonal relationship between primaries and relapses to track tumors' genetic evolution and to investigate the genetic background of DLBCL recurrence. Three clonally unrelated DLBCL relapses were identified (15%). Also, two distinct patterns of genetic evolution in clonally related relapses were detected as follows: (1) early-divergent/branching evolution from a common progenitor in 6 patients (30%), and (2) late-divergent/linear progression of relapses in 11 patients (65%). Analysis of recurrent genetic events identified potential early drivers of lymphomagenesis (KMT2D, MYD88, CD79B and PIM1). The most frequent relapse-specific events were additional mutations in KMT2D and alterations of MEF2B. SOCS1 mutations were exclusive to non-relapsing DLBCL, whereas primaries of relapsing DLBCL more commonly displayed gains of 10p15.3-p12.1 containing the potential oncogenes PRKCQ, GATA3, MLLT10 and ABI1. Altogether, our study expands the knowledge on clonal relationship, genetic evolution and mutational basis of DLBCL relapses.

Climatic niche evolution is faster in sympatric than allopatric lineages of the butterfly genus Pyrgus

PubMed Central

Pitteloud, Camille; Arrigo, Nils; Suchan, Tomasz; Mastretta-Yanes, Alicia; Dincă, Vlad; Hernández-Roldán, Juan; Brockmann, Ernst; Chittaro, Yannick; Kleckova, Irena; Fumagalli, Luca; Buerki, Sven; Pellissier, Loïc

2017-01-01

Understanding how speciation relates to ecological divergence has long fascinated biologists. It is assumed that ecological divergence is essential to sympatric speciation, as a mechanism to avoid competition and eventually lead to reproductive isolation, while divergence in allopatry is not necessarily associated with niche differentiation. The impact of the spatial context of divergence on the evolutionary rates of abiotic dimensions of the ecological niche has rarely been explored for an entire clade. Here, we compare the magnitude of climatic niche shifts between sympatric versus allopatric divergence of lineages in butterflies. By combining next-generation sequencing, parametric biogeography and ecological niche analyses applied to a genus-wide phylogeny of Palaearctic Pyrgus butterflies, we compare evolutionary rates along eight climatic dimensions across sister lineages that diverged in large-scale sympatry versus allopatry. In order to examine the possible effects of the spatial scale at which sympatry is defined, we considered three sets of biogeographic assignments, ranging from narrow to broad definition. Our findings suggest higher rates of niche evolution along all climatic dimensions for sister lineages that diverge in sympatry, when using a narrow delineation of biogeographic areas. This result contrasts with significantly lower rates of climatic niche evolution found in cases of allopatric speciation, despite the biogeographic regions defined here being characterized by significantly different climates. Higher rates in allopatry are retrieved when biogeographic areas are too widely defined—in such a case allopatric events may be recorded as sympatric. Our results reveal the macro-evolutionary significance of abiotic niche differentiation involved in speciation processes within biogeographic regions, and illustrate the importance of the spatial scale chosen to define areas when applying parametric biogeographic analyses. PMID:28404781

Evolution of DNA Methylation across Insects.

PubMed

Bewick, Adam J; Vogel, Kevin J; Moore, Allen J; Schmitz, Robert J

2017-03-01

DNA methylation contributes to gene and transcriptional regulation in eukaryotes, and therefore has been hypothesized to facilitate the evolution of plastic traits such as sociality in insects. However, DNA methylation is sparsely studied in insects. Therefore, we documented patterns of DNA methylation across a wide diversity of insects. We predicted that underlying enzymatic machinery is concordant with patterns of DNA methylation. Finally, given the suggestion that DNA methylation facilitated social evolution in Hymenoptera, we tested the hypothesis that the DNA methylation system will be associated with presence/absence of sociality among other insect orders. We found DNA methylation to be widespread, detected in all orders examined except Diptera (flies). Whole genome bisulfite sequencing showed that orders differed in levels of DNA methylation. Hymenopteran (ants, bees, wasps and sawflies) had some of the lowest levels, including several potential losses. Blattodea (cockroaches and termites) show all possible patterns, including a potential loss of DNA methylation in a eusocial species whereas solitary species had the highest levels. Species with DNA methylation do not always possess the typical enzymatic machinery. We identified a gene duplication event in the maintenance DNA methyltransferase 1 (DNMT1) that is shared by some Hymenoptera, and paralogs have experienced divergent, nonneutral evolution. This diversity and nonneutral evolution of underlying machinery suggests alternative DNA methylation pathways may exist. Phylogenetically corrected comparisons revealed no evidence that supports evolutionary association between sociality and DNA methylation. Future functional studies will be required to advance our understanding of DNA methylation in insects. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Genetic Regulatory Networks in Embryogenesis and Evolution

NASA Technical Reports Server (NTRS)

1998-01-01

The article introduces a series of papers that were originally presented at a workshop titled Genetic Regulatory Network in Embryogenesis and Evaluation. Contents include the following: evolution of cleavage programs in relationship to axial specification and body plan evolution, changes in cell lineage specification elucidate evolutionary relations in spiralia, axial patterning in the leech: developmental mechanisms and evolutionary implications, hox genes in arthropod development and evolution, heterochronic genes in development and evolution, a common theme for LIM homeobox gene function across phylogeny, and mechanisms of specification in ascidian embryos.

The evolution within us

PubMed Central

Cobey, Sarah; Wilson, Patrick; Matsen, Frederick A.

2015-01-01

The B-cell immune response is a remarkable evolutionary system found in jawed vertebrates. B-cell receptors, the membrane-bound form of antibodies, are capable of evolving high affinity to almost any foreign protein. High germline diversity and rapid evolution upon encounter with antigen explain the general adaptability of B-cell populations, but the dynamics of repertoires are less well understood. These dynamics are scientifically and clinically important. After highlighting the remarkable characteristics of naive and experienced B-cell repertoires, especially biased usage of genes encoding the B-cell receptors, we contrast methods of sequence analysis and their attempts to explain patterns of B-cell evolution. These phylogenetic approaches are currently unlinked to explicit models of B-cell competition, which analyse repertoire evolution at the level of phenotype, the affinities and specificities to particular antigenic sites. The models, in turn, suggest how chance, infection history and other factors contribute to different patterns of immunodominance and protection between people. Challenges in rational vaccine design, specifically vaccines to induce broadly neutralizing antibodies to HIV, underscore critical gaps in our understanding of B cells' evolutionary and ecological dynamics. PMID:26194749

Self-organized criticality in forest-landscape evolution

Treesearch

J.C. Sprott; Janine Bolliger; David J. Mladenoff

2002-01-01

A simple cellular automaton replicates the fractal pattern of a natural forest landscape and predicts its evolution. Spatial distributions and temporal fluctuations in global quantities show power-law spectra, implying scale-invariance, characteristic of self-organized criticality. The evolution toward the SOC state and the robustness of that state to perturbations...

Tyrannosauroid integument reveals conflicting patterns of gigantism and feather evolution.

PubMed

Bell, Phil R; Campione, Nicolás E; Persons, W Scott; Currie, Philip J; Larson, Peter L; Tanke, Darren H; Bakker, Robert T

2017-06-01

Recent evidence for feathers in theropods has led to speculations that the largest tyrannosaurids, including Tyrannosaurus rex , were extensively feathered. We describe fossil integument from Tyrannosaurus and other tyrannosaurids ( Albertosaurus, Daspletosaurus, Gorgosaurus and Tarbosaurus ), confirming that these large-bodied forms possessed scaly, reptilian-like skin. Body size evolution in tyrannosauroids reveals two independent occurrences of gigantism; specifically, the large sizes in Yutyrannus and tyrannosaurids were independently derived. These new findings demonstrate that extensive feather coverings observed in some early tyrannosauroids were lost by the Albian, basal to Tyrannosauridae. This loss is unrelated to palaeoclimate but possibly tied to the evolution of gigantism, although other mechanisms exist. © 2017 The Author(s).

Molecular evolution and patterns of duplication in the SEP/AGL6-like lineage of the Zingiberales: a proposed mechanism for floral diversification.

PubMed

Yockteng, Roxana; Almeida, Ana M R; Morioka, Kelsie; Alvarez-Buylla, Elena R; Specht, Chelsea D

2013-11-01

The diversity of floral forms in the plant order Zingiberales has evolved through alterations in floral organ morphology. One striking alteration is the shift from fertile, filamentous stamens to sterile, laminar (petaloid) organs in the stamen whorls, attributed to specific pollination syndromes. Here, we examine the role of the SEPALLATA (SEP) genes, known to be important in regulatory networks underlying floral development and organ identity, in the evolution of development of the diverse floral organs phenotypes in the Zingiberales. Phylogenetic analyses show that the SEP-like genes have undergone several duplication events giving rise to multiple copies. Selection tests on the SEP-like genes indicate that the two copies of SEP3 have mostly evolved under balancing selection, probably due to strong functional restrictions as a result of their critical role in floral organ specification. In contrast, the two LOFSEP copies have undergone differential positive selection, indicating neofunctionalization. Reverse transcriptase-polymerase chain reaction, gene expression from RNA-seq data, and in situ hybridization analyses show that the recovered genes have differential expression patterns across the various whorls and organ types found in the Zingiberales. Our data also suggest that AGL6, sister to the SEP-like genes, may play an important role in stamen morphology in the Zingiberales. Thus, the SEP-like genes are likely to be involved in some of the unique morphogenetic patterns of floral organ development found among this diverse order of tropical monocots. This work contributes to a growing body of knowledge focused on understanding the role of gene duplications and the evolution of entire gene networks in the evolution of flower development.

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

Dislocation evolution in 316 L stainless steel during multiaxial ratchetting deformation

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

Dong Yawei; Kang Guozheng, E-mail: guozhengkang@yahoo.com.cn; Liu Yujie

2012-03-15

Dislocation patterns and their evolutions in 316 L stainless steel during the multiaxial ratchetting deformation were observed by transmission electron microscopy (TEM). The microscopic observations indicate that the dislocation evolution presented during the multiaxial ratchetting with four kinds of multiaxial loading paths is similar to that in the uniaxial case [G. Z. Kang et al., Mater Sci Eng A 527 (2010) 5952]. That is, dislocation networks and dislocation tangles are formed quickly by the multiple-slip and cross-slip of dislocation activated by applied multiaxial stress; and then polarized patterns such as dislocation walls and elongated incipient dislocation cells are formed atmore » the last stage of multiaxial ratchetting. The dislocation patterns evolve more quickly from the modes at low dislocation density to the ones at high density during the multiaxial ratchetting than that in the uniaxial case, and some traces of multiple-slip are observed in the multiaxial ones. The dislocation evolution during the multiaxial ratchetting deformation is summarized by comparing the observed dislocation patterns with those presented in the multiaxial strain-controlled and symmetrical stress-controlled cyclic tests. The multiaxial ratchetting of 316 L stainless steel can be microscopically and qualitatively explained by the observed evolution of dislocation patterns. - Highlights: Black-Right-Pointing-Pointer Dislocation patterns change from lines and nets to tangles, walls and cells. Black-Right-Pointing-Pointer Dislocation patterns evolve quicker in the multiaxial case. Black-Right-Pointing-Pointer Aligned dislocation arrays and some traces of multiple slips are observed. Black-Right-Pointing-Pointer Heterogeneous dislocation patterns result in the multiaxial ratchetting.« less

[Hyperbolic growth of marine and continental biodiversity through the phanerozoic and community evolution].

PubMed

Markov, A V; Korotaev, A V

2008-01-01

models, the hyperbolic pattern of the world population growth arises from a non-linear second-order positive feedback between the demographic growth and technological development (more people - more potential inventors - faster technological growth - the carrying capacity of the Earth grows faster - faster population growth - more people - more potential inventors, and so on). Based on the analogy with macrosociological models and diverse paleontological data, we suggest that the hyperbolic character of biodiversity growth can be similarly accounted for by a non-linear second-order positive feedback between the diversity growth and community structure complexity. The feedback can work via two parallel mechanisms: 1) decreasing extinction rate (more taxa- higher alpha diversity, or mean number of taxa in a community - communities become more complex and stable - extinction rate decreases - more taxa, and so on) and 2) increasing origination rate (new taxa facilitate niche construction; newly formed niches can be occupied by the next "generation" of taxa). The latter possibility makes the mechanisms underlying the hyperbolic growth of biodiversity and human population even more similar, because the total ecospace of the biota is analogous to the "carrying capacity of the Earth" in demography. As far as new species can increase ecospace and facilitate opportunities for additional species entering the community, they are analogous to the "inventors" of the demographic models whose inventions increase the carrying capacity of the Earth. The hyperbolic growth of the Phanerozoic biodiverstiy suggests that "cooperative" interactions between taxa can play an important role in evolution, along with generally accepted competitive interactions. Due to this "cooperation", the evolution of biodiversity acquires some features of a self-accelerating process. Macroevolutionary "cooperation" reveals itself in: 1) increasing stability of communities that arises from alpha diversity growth

Barrier Displacement on a Neutral Landscape: Toward a Theory of Continental Biogeography.

PubMed

Albert, James S; Schoolmaster, Donald R; Tagliacollo, Victor; Duke-Sylvester, Scott M

2017-03-01

Macroevolutionary theory posits three processes leading to lineage diversification and the formation of regional biotas: dispersal (species geographic range expansion), speciation (species lineage splitting), and extinction (species lineage termination). The Theory of Island Biogeography (TIB) predicts species richness values using just two of these processes; dispersal and extinction. Yet most species on Earth live on continents or continental shelves, and the dynamics of evolutionary diversification at regional and continental scales are qualitatively different from those that govern the formation of species richness on biogeographic islands. Certain geomorphological processes operating perennially on continental platforms displace barriers to gene flow and organismal dispersal, and affect all three terms of macroevolutionary diversification. For example, uplift of a dissected landscape and river capture both merge and separate portions of adjacent areas, allowing dispersal and larger geographic ranges, vicariant speciation and smaller geographic ranges, and extinction when range sizes are subdivided below a minimum persistence threshold. The TIB also does not predict many biogeographic and phylogenetic patterns widely observed in continentally distributed taxa, including: (i) power function-like species-area relationships; (ii) log-normal distribution of species geographic range sizes, in which most species have restricted ranges (are endemic) and few species have broad ranges (are cosmopolitan); (iii) mid-domain effects with more species toward the geographic center, and more early-branching, species-poor clades toward the geographic periphery; (iv) exponential rates of net diversification with log-linear accumulation of lineages through geological time; and (v) power function-like relationships between species-richness and clade diversity, in which most clades are species-poor and few clades are species-rich. Current theory does not provide a robust

Linking micro- and macro-evolution at the cell type level: a view from the lophotrochozoan Platynereis dumerilii.

PubMed

Simakov, Oleg; Larsson, Tomas A; Arendt, Detlev

2013-09-01

Ever since the origin of the first metazoans over 600 million years ago, cell type diversification has been driven by micro-evolutionary processes at population level, leading to macro-evolution changes above species level. In this review, we introduce the marine annelid Platynereis dumerilii, a member of the lophotrochozoan clade (a key yet most understudied superphylum of bilaterians), as a suitable model system for the simultaneous study, at cellular resolution, of macro-evolutionary processes across phyla and of micro-evolutionary processes across highly polymorphic populations collected worldwide. Recent advances in molecular and experimental techniques, easy maintenance and breeding, and the fast, synchronous and stereotypical development have facilitated the establishment of Platynereis as one of the leading model species in the eco-evo-devo field. Most importantly, Platynereis allows the combination of expression profiling, morphological and physiological characterization at the single cell level. Here, we discuss recent advances in the collection of -omics data for the lab strain and for natural populations collected world-wide that can be integrated with population-specific cellular analyses to result in a cellular atlas integrating genetic, phenotypic and ecological variation. This makes Platynereis a tractable system to begin understanding the interplay between macro- and micro-evolutionary processes and cell type diversity.

The grass was greener: Repeated evolution of specialized morphologies and habitat shifts in ghost spiders following grassland expansion in South America.

PubMed

Ceccarelli, F Sara; Mongiardino Koch, Nicolás; Soto, Eduardo M; Barone, Mariana L; Arnedo, Miquel A; Ramírez, Martín J

2018-04-14

While grasslands, one of Earth's major biomes, are known for their close evolutionary ties with ungulate grazers, these habitats are also paramount to the origins and diversification of other animals. Within the primarily South American spider subfamily Amaurobioidinae (Anyphaenidae), several species are found living in the continent's grasslands, with some displaying putative morphological adaptations to dwelling unnoticed in the grass blades. Here, a dated molecular phylogeny provides the backbone for analyses revealing the ecological and morphological processes behind these spiders' grassland adaptations. The multiple switches from Patagonian forests to open habitats coincide with the expansion of South America's grasslands during the Miocene, while the specialized morphology of several grass-dwelling spiders originated at least three independent times and is best described as the result of different selective regimes operating on macroevolutionary timescales. Although grass-adapted lineages evolved towards different peaks in adaptive landscape, they all share one characteristic: an anterior narrowing of the prosoma allowing spiders to extend the first two pairs of legs, thus maintaining a slender resting posture in the grass blade. By combining phylogenetic, morphological, and biogeographic perspectives we disentangle multiple factors determining the evolution of a clade of terrestrial invertebrate predators alongside their biomes.

Contrasting Patterns of Nucleotide Substitution Rates Provide Insight into Dynamic Evolution of Plastid and Mitochondrial Genomes of Geranium.

PubMed

Park, Seongjun; Ruhlman, Tracey A; Weng, Mao-Lun; Hajrah, Nahid H; Sabir, Jamal S M; Jansen, Robert K

2017-06-01

Geraniaceae have emerged as a model system for investigating the causes and consequences of variation in plastid and mitochondrial genomes. Incredible structural variation in plastid genomes (plastomes) and highly accelerated evolutionary rates have been reported in selected lineages and functional groups of genes in both plastomes and mitochondrial genomes (mitogenomes), and these phenomena have been implicated in cytonuclear incompatibility. Previous organelle genome studies have included limited sampling of Geranium, the largest genus in the family with over 400 species. This study reports on rates and patterns of nucleotide substitutions in plastomes and mitogenomes of 17 species of Geranium and representatives of other Geraniaceae. As detected across other angiosperms, substitution rates in the plastome are 3.5 times higher than the mitogenome in most Geranium. However, in the branch leading to Geranium brycei/Geranium incanum mitochondrial genes experienced significantly higher dN and dS than plastid genes, a pattern that has only been detected in one other angiosperm. Furthermore, rate accelerations differ in the two organelle genomes with plastomes having increased dN and mitogenomes with increased dS. In the Geranium phaeum/Geranium reflexum clade, duplicate copies of clpP and rpoA genes that experienced asymmetric rate divergence were detected in the single copy region of the plastome. In the case of rpoA, the branch leading to G. phaeum/G. reflexum experienced positive selection or relaxation of purifying selection. Finally, the evolution of acetyl-CoA carboxylase is unusual in Geraniaceae because it is only the second angiosperm family where both prokaryotic and eukaryotic ACCases functionally coexist in the plastid. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Trends in the sand: Directional evolution in the shell shape of recessing scallops (Bivalvia: Pectinidae).

PubMed

Sherratt, Emma; Alejandrino, Alvin; Kraemer, Andrew C; Serb, Jeanne M; Adams, Dean C

2016-09-01

Directional evolution is one of the most compelling evolutionary patterns observed in macroevolution. Yet, despite its importance, detecting such trends in multivariate data remains a challenge. In this study, we evaluate multivariate evolution of shell shape in 93 bivalved scallop species, combining geometric morphometrics and phylogenetic comparative methods. Phylomorphospace visualization described the history of morphological diversification in the group; revealing that taxa with a recessing life habit were the most distinctive in shell shape, and appeared to display a directional trend. To evaluate this hypothesis empirically, we extended existing methods by characterizing the mean directional evolution in phylomorphospace for recessing scallops. We then compared this pattern to what was expected under several alternative evolutionary scenarios using phylogenetic simulations. The observed pattern did not fall within the distribution obtained under multivariate Brownian motion, enabling us to reject this evolutionary scenario. By contrast, the observed pattern was more similar to, and fell within, the distribution obtained from simulations using Brownian motion combined with a directional trend. Thus, the observed data are consistent with a pattern of directional evolution for this lineage of recessing scallops. We discuss this putative directional evolutionary trend in terms of its potential adaptive role in exploiting novel habitats. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Tropics accelerate the evolution of hybrid male sterility in Drosophila.

PubMed

Yukilevich, Roman

2013-06-01

Understanding the evolutionary mechanisms that facilitate speciation and explain global patterns of species diversity has remained a challenge for decades. The most general pattern of species biodiversity is the latitudinal gradient, whereby species richness increases toward the tropics. Although such a global pattern probably has a multitude of causes, recent attention has focused on the hypothesis that speciation and the evolution of reproductive isolation occur faster in the tropics. Here, I tested this prediction using a dataset on premating and postzygotic isolation between recently diverged Drosophila species. Results showed that while the evolution of premating isolation was not greater between tropical Drosophila relative to nontropical species, postzygotic isolation evolved faster in the tropics. In particular, hybrid male sterility was much greater among tropical Drosophila compared to nontropical species pairs of similar genetic age. Several testable explanations for the novel pattern are discussed, including greater role for sterility-inducing bacterial endosymbionts in the tropics and more intense sperm-sperm competition or sperm-egg sexual conflict in the tropics. The results imply that processes of speciation in the tropics may evolve at different rates or may even be somewhat different from those at higher latitudes. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Patterns of covariation in the masticatory apparatus of hystricognathous rodents: implications for evolution and diversification.

PubMed

Hautier, Lionel; Lebrun, Renaud; Cox, Philip G

2012-12-01

The mammalian masticatory apparatus is a highly plastic region of the skull. In this study, a quantification of shape variation, the separation of phylogeny from ecology in the genesis of shape brings new insights on the relationships between morphological changes in the cranium, mandible, and muscle architecture. Our study focuses on the Ctenohystrica, a clade that is remarkably diverse and exemplifies a rich evolutionary history in the Old and New World. Current and past rodent diversity brings out the limitations of the qualitative descriptive approach and highlights the need for using integrative quantitative methods. We present here the first descriptive comparison of the whole masticatory apparatus within the Ctenohystrica, by combining geometric morphometric approaches with a noninvasive method of dissection in 3D, iodine-enhanced microcomputed tomography. We used these methods to explore the patterns of covariation between the cranium and the mandible, and the interspecific morphological variation of the skull with regard to several factors such as phylogeny, activity period, type of habitat, and diet. Our study revealed strong phylogenetic and ecological imprints on the morphological traits associated with masticatory mechanics. We showed that, despite a high diversification of lineages, the evolutionary history of Ctenohystrica comprises only a small number of morphotypes for the skull and mandible. The position of the eye was suggested as a key factor determining morphological evolution of the masticatory apparatus by limiting the number of possible pathways and promoting convergent evolution toward new habitats and diets between different clades. Copyright © 2012 Wiley Periodicals, Inc.

Evolution Analysis of Simple Sequence Repeats in Plant Genome.

PubMed

Qin, Zhen; Wang, Yanping; Wang, Qingmei; Li, Aixian; Hou, Fuyun; Zhang, Liming

2015-01-01

Simple sequence repeats (SSRs) are widespread units on genome sequences, and play many important roles in plants. In order to reveal the evolution of plant genomes, we investigated the evolutionary regularities of SSRs during the evolution of plant species and the plant kingdom by analysis of twelve sequenced plant genome sequences. First, in the twelve studied plant genomes, the main SSRs were those which contain repeats of 1-3 nucleotides combination. Second, in mononucleotide SSRs, the A/T percentage gradually increased along with the evolution of plants (except for P. patens). With the increase of SSRs repeat number the percentage of A/T in C. reinhardtii had no significant change, while the percentage of A/T in terrestrial plants species gradually declined. Third, in dinucleotide SSRs, the percentage of AT/TA increased along with the evolution of plant kingdom and the repeat number increased in terrestrial plants species. This trend was more obvious in dicotyledon than monocotyledon. The percentage of CG/GC showed the opposite pattern to the AT/TA. Forth, in trinucleotide SSRs, the percentages of combinations including two or three A/T were in a rising trend along with the evolution of plant kingdom; meanwhile with the increase of SSRs repeat number in plants species, different species chose different combinations as dominant SSRs. SSRs in C. reinhardtii, P. patens, Z. mays and A. thaliana showed their specific patterns related to evolutionary position or specific changes of genome sequences. The results showed that, SSRs not only had the general pattern in the evolution of plant kingdom, but also were associated with the evolution of the specific genome sequence. The study of the evolutionary regularities of SSRs provided new insights for the analysis of the plant genome evolution.

Consequences of elastic anisotropy in patterned substrate heteroepitaxy.

PubMed

Dixit, Gopal Krishna; Ranganathan, Madhav

2018-06-13

The role of elastic anisotropy on quantum dot formation and evolution on a pre-patterned substrate is evaluated within the framework of a continuum model. We first extend the formulation for surface evolution to take elastic anisotropy into account. Using a small slope approximation, we derive the evolution equation and show how it can be numerically implemented up to linear and second order for stripe and egg-carton patterned substrates using an accurate and efficient procedure. The semi--infinite nature of the substrate is used to solve the elasticity problem subject to other boundary conditions at the free surface and at the film--substrate interface. The positioning of the quantum dots with respect to the peaks and valleys of the pattern is explained by a competition between the length scale of the pattern and the wavelength of the Asaro--Tiller--Grinfeld instability, which is also affected by the elastic anisotropy. The alignment of dots is affected by a competition between the elastic anisotropy of the film and the pattern orientation. A domain of pattern inversion, wherein the quantum dots form exclusively in the valleys of the patterns is identified as a function of the average film thickness and the elastic anisotropy, and the time--scale for this inversion as function of height is analyzed. © 2018 IOP Publishing Ltd.

Evolution of DNA Methylation across Insects

PubMed Central

Vogel, Kevin J.; Moore, Allen J.; Schmitz, Robert J.

2017-01-01

DNA methylation contributes to gene and transcriptional regulation in eukaryotes, and therefore has been hypothesized to facilitate the evolution of plastic traits such as sociality in insects. However, DNA methylation is sparsely studied in insects. Therefore, we documented patterns of DNA methylation across a wide diversity of insects. We predicted that underlying enzymatic machinery is concordant with patterns of DNA methylation. Finally, given the suggestion that DNA methylation facilitated social evolution in Hymenoptera, we tested the hypothesis that the DNA methylation system will be associated with presence/absence of sociality among other insect orders. We found DNA methylation to be widespread, detected in all orders examined except Diptera (flies). Whole genome bisulfite sequencing showed that orders differed in levels of DNA methylation. Hymenopteran (ants, bees, wasps and sawflies) had some of the lowest levels, including several potential losses. Blattodea (cockroaches and termites) show all possible patterns, including a potential loss of DNA methylation in a eusocial species whereas solitary species had the highest levels. Species with DNA methylation do not always possess the typical enzymatic machinery. We identified a gene duplication event in the maintenance DNA methyltransferase 1 (DNMT1) that is shared by some Hymenoptera, and paralogs have experienced divergent, nonneutral evolution. This diversity and nonneutral evolution of underlying machinery suggests alternative DNA methylation pathways may exist. Phylogenetically corrected comparisons revealed no evidence that supports evolutionary association between sociality and DNA methylation. Future functional studies will be required to advance our understanding of DNA methylation in insects. PMID:28025279

Pan-vertebrate comparative genomics unmasks retrovirus macroevolution.

PubMed

Hayward, Alexander; Cornwallis, Charlie K; Jern, Patric

2015-01-13

Although extensive research has demonstrated host-retrovirus microevolutionary dynamics, it has been difficult to gain a deeper understanding of the macroevolutionary patterns of host-retrovirus interactions. Here we use recent technological advances to infer broad patterns in retroviral diversity, evolution, and host-virus relationships by using a large-scale phylogenomic approach using endogenous retroviruses (ERVs). Retroviruses insert a proviral DNA copy into the host cell genome to produce new viruses. ERVs are provirus insertions in germline cells that are inherited down the host lineage and consequently present a record of past host-viral associations. By mining ERVs from 65 host genomes sampled across vertebrate diversity, we uncover a great diversity of ERVs, indicating that retroviral sequences are much more prevalent and widespread across vertebrates than previously appreciated. The majority of ERV clades that we recover do not contain known retroviruses, implying either that retroviral lineages are highly transient over evolutionary time or that a considerable number of retroviruses remain to be identified. By characterizing the distribution of ERVs, we show that no major vertebrate lineage has escaped retroviral activity and that retroviruses are extreme host generalists, having an unprecedented ability for rampant host switching among distantly related vertebrates. In addition, we examine whether the distribution of ERVs can be explained by host factors predicted to influence viral transmission and find that internal fertilization has a pronounced effect on retroviral colonization of host genomes. By capturing the mode and pattern of retroviral evolution and contrasting ERV diversity with known retroviral diversity, our study provides a cohesive framework to understand host-virus coevolution better.

Bone microstructure and the evolution of growth patterns in Permo-Triassic therocephalians (Amniota, Therapsida) of South Africa

PubMed Central

Botha-Brink, Jennifer

2014-01-01

Therocephalians were a speciose clade of nonmammalian therapsids whose ecological diversity and survivorship of the end-Permian mass extinction offer the potential to investigate the evolution of growth patterns across the clade and their underlying influences on post-extinction body size reductions, or ‘Lilliput effects’. We present a phylogenetic survey of limb bone histology and growth patterns in therocephalians from the Middle Permian through Middle Triassic of the Karoo Basin, South Africa. Histologic sections were prepared from 80 limb bones representing 11 genera of therocephalians. Histologic indicators of skeletal growth, including cortical vascularity (%CV) and mean primary osteon diameters (POD), were evaluated in a phylogenetic framework and assessed for correlations with other biologically significant variables (e.g., size and robusticity). Changes in %CV and POD correlated strongly with evolutionary changes in body size (i.e., smaller-bodied descendants tended to have lower %CV than their larger-bodied ancestors across the tree). Bone wall thickness tended to be high in early therocephalians and lower in the gracile-limbed baurioids, but showed no general correlation with cross-sectional area or degree of vascularity (and, thus, growth). Clade-level patterns, however, deviated from previously studied within-lineage patterns. For example, Moschorhinus, one of few therapsid genera to have survived the extinction boundary, demonstrated higher %CV in the Triassic than in the Permian despite its smaller size in the extinction aftermath. Results support a synergistic model of size reductions for Triassic therocephalians, influenced both by within-lineage heterochronic shifts in survivor taxa (as reported in Moschorhinus and the dicynodont Lystrosaurus) and phylogenetically inferred survival of small-bodied taxa that had evolved short growth durations (e.g., baurioids). These findings mirror the multi-causal Lilliput patterns described in marine faunas

A new paradigma on the plant evolution: from a natural evolution to an artificial evolution?

PubMed

Bennici, Andrea

2005-01-01

After evidencing the great importance of plants for animals and humans in consequence of the photosynthesis, several considerations on plant evolution are made. One of the peculiar characteristics of the plant is the sessile property, due especially to the cell wall. This factor, principally, strengthened by the photosynthetic process, determined the particular developmental pattern of the plant, which is characterized by the continuous formation of new organs. The plant immobility, although negative for its survival, has been, in great part, overcome by the acquisition of the capacity of adaptation (plasticity) to the environmental stresses and changes, and the establishment of more adapted genotypes. This capacity to react to the external signals induced Trewavas to speak of "plant intelligence". The plant movement incapacity and the evolution of the sexual reproduction system were strongly correlated. In this context, the evolution of the flower in the Angiosperms has been particularly important to allow the male gamete to fertilize the immobile female gamete. Moreover, the formation of fruit and seed greatly improved the dispersal and conservation of the progeny in the environment. With the flower, mechanisms to favour the outcrossing among different individuals appeared, which are essential to increase the genetic variability and, then, the plant evolution itself. Although the Angiosperms seem highly evolved, the plant evolution is not surely finished, because many reported morpho-physiological processes may be still considered susceptible of further improvement. In the last years the relationships among humans, plants and environment are becoming closer and closer. This is due to the use of the DNA recombinant techniques with the aim to modify artificially plant characters. Therefore, the risk of a plant evolution strongly directed towards practical or commercial objectives, or "an artificial evolution", may be hypothesized.

ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation.

PubMed

Kristensen, David M; Wolf, Yuri I; Koonin, Eugene V

2017-01-04

The Alignable Tight Genomic Clusters (ATGCs) database is a collection of closely related bacterial and archaeal genomes that provides several tools to aid research into evolutionary processes in the microbial world. Each ATGC is a taxonomy-independent cluster of 2 or more completely sequenced genomes that meet the objective criteria of a high degree of local gene order (synteny) and a small number of synonymous substitutions in the protein-coding genes. As such, each ATGC is suited for analysis of microevolutionary variations within a cohesive group of organisms (e.g. species), whereas the entire collection of ATGCs is useful for macroevolutionary studies. The ATGC database includes many forms of pre-computed data, in particular ATGC-COGs (Clusters of Orthologous Genes), multiple sequence alignments, a set of 'index' orthologs representing the most well-conserved members of each ATGC-COG, the phylogenetic tree of the organisms within each ATGC, etc. Although the ATGC database contains several million proteins from thousands of genomes organized into hundreds of clusters (roughly a 4-fold increase since the last version of the ATGC database), it is now built with completely automated methods and will be regularly updated following new releases of the NCBI RefSeq database. The ATGC database is hosted jointly at the University of Iowa at dmk-brain.ecn.uiowa.edu/ATGC/ and the NCBI at ftp.ncbi.nlm.nih.gov/pub/kristensen/ATGC/atgc_home.html. Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

The building of a biodiversity hotspot across a land-bridge in the Mediterranean.

PubMed

Molina-Venegas, Rafael; Aparicio, Abelardo; Lavergne, Sébastien; Arroyo, Juan

2015-08-22

Many of the macroevolutionary processes that have shaped present-day phylogenetic patterns were caused by geological events such as plate tectonics and temporary land-bridges. The study of spatial patterns of phylogenetic diversity can provide insights into these past events. Here we focus on a western Mediterranean biodiversity hotspot located in the southern Iberian Peninsula and northwest Africa, two regions that are separated by the Strait of Gibraltar. We explore the spatial structure of the phylogenetic relationships within and across large-scale plant assemblages. Significant turnover in terminal lineages tends to occur between landmasses, whereas turnover in deep lineages tends to occur within landmasses. Plant assemblages in the western ecoregions of this hotspot tend to be phylogenetically overdispersed but are phylogenetically clustered on its eastern margins. We discuss our results in the light of potential scenarios of niche evolution (or conservatism) and lineage diversification. The significant turnover between landmasses suggests a common scenario of allopatric speciation that could have been facilitated by the intermittent joining of the two continents. This may have constituted an important stimulus for diversification and the emergence of this western Mediterranean biodiversity hotspot. © 2015 The Author(s).

The building of a biodiversity hotspot across a land-bridge in the Mediterranean

PubMed Central

Molina-Venegas, Rafael; Aparicio, Abelardo; Lavergne, Sébastien; Arroyo, Juan

2015-01-01

Many of the macroevolutionary processes that have shaped present-day phylogenetic patterns were caused by geological events such as plate tectonics and temporary land-bridges. The study of spatial patterns of phylogenetic diversity can provide insights into these past events. Here we focus on a western Mediterranean biodiversity hotspot located in the southern Iberian Peninsula and northwest Africa, two regions that are separated by the Strait of Gibraltar. We explore the spatial structure of the phylogenetic relationships within and across large-scale plant assemblages. Significant turnover in terminal lineages tends to occur between landmasses, whereas turnover in deep lineages tends to occur within landmasses. Plant assemblages in the western ecoregions of this hotspot tend to be phylogenetically overdispersed but are phylogenetically clustered on its eastern margins. We discuss our results in the light of potential scenarios of niche evolution (or conservatism) and lineage diversification. The significant turnover between landmasses suggests a common scenario of allopatric speciation that could have been facilitated by the intermittent joining of the two continents. This may have constituted an important stimulus for diversification and the emergence of this western Mediterranean biodiversity hotspot. PMID:26246551

Rate of evolutionary change in cranial morphology of the marsupial genus Monodelphis is constrained by the availability of additive genetic variation

PubMed Central

Porto, Arthur; Sebastião, Harley; Pavan, Silvia Eliza; VandeBerg, John L.; Marroig, Gabriel; Cheverud, James M.

2015-01-01

We tested the hypothesis that the rate of marsupial cranial evolution is dependent on the distribution of genetic variation in multivariate space. To do so, we carried out a genetic analysis of cranial morphological variation in laboratory strains of Monodelphis domestica and used estimates of genetic covariation to analyze the morphological diversification of the Monodelphis brevicaudata species group. We found that within-species genetic variation is concentrated in only a few axes of the morphospace and that this strong genetic covariation influenced the rate of morphological diversification of the brevicaudata group, with between-species divergence occurring fastest when occurring along the genetic line of least resistance. Accounting for the geometric distribution of genetic variation also increased our ability to detect the selective regimen underlying species diversification, with several instances of selection only being detected when genetic covariances were taken into account. Therefore, this work directly links patterns of genetic covariation among traits to macroevolutionary patterns of morphological divergence. Our findings also suggest that the limited distribution of Monodelphis species in morphospace is the result of a complex interplay between the limited dimensionality of available genetic variation and strong stabilizing selection along two major axes of genetic variation. PMID:25818173

Fracture patterns of the drainage basin of Wadi Dahab in relation to tectonic-landscape evolution of the Gulf of Aqaba - Dead Sea transform fault

NASA Astrophysics Data System (ADS)

Shalaby, Ahmed

2017-10-01

Crustal rifting of the Arabian-Nubian Shield and formation of the Afro-Arabian rifts since the Miocene resulted in uplifting and subsequent terrain evolution of Sinai landscapes; including drainage systems and fault scarps. Geomorphic evolution of these landscapes in relation to tectonic evolution of the Afro-Arabian rifts is the prime target of this study. The fracture patterns and landscape evolution of the Wadi Dahab drainage basin (WDDB), in which its landscape is modeled by the tectonic evolution of the Gulf of Aqaba-Dead Sea transform fault, are investigated as a case study of landscape modifications of tectonically-controlled drainage systems. The early developed drainage system of the WDDB was achieved when the Sinai terrain subaerially emerged in post Eocene and initiation of the Afro-Arabian rifts in the Oligo-Miocene. Conjugate shear fractures, parallel to trends of the Afro-Arabian rifts, are synthesized with tensional fracture arrays to adapt some of inland basins, which represent the early destination of the Sinai drainage systems as paleolakes trapping alluvial sediments. Once the Gulf of Aqaba rift basin attains its deeps through sinistral movements on the Gulf of Aqaba-Dead Sea transform fault in the Pleistocene and the consequent rise of the Southern Sinai mountainous peaks, relief potential energy is significantly maintained through time so that it forced the Pleistocene runoffs to flow via drainage systems externally into the Gulf of Aqaba. Hence the older alluvial sediments are (1) carved within the paleolakes by a new generation of drainage systems; followed up through an erosional surface by sandy- to silty-based younger alluvium; and (2) brought on footslopes of fault scarps reviving the early developed scarps and inselbergs. These features argue for crustal uplifting of Sinai landscapes syn-rifting of the Gulf of Aqaba rift basin. Oblique orientation of the Red Sea-Gulf of Suez rift relative to the WNW-trending Precambrian Najd faults; and

Evolution‐development congruence in pattern formation dynamics: Bifurcations in gene expression and regulation of networks structures

PubMed Central

Kohsokabe, Takahiro

2016-01-01

ABSTRACT Search for possible relationships between phylogeny and ontogeny is important in evolutionary‐developmental biology. Here we uncover such relationships by numerical evolution and unveil their origin in terms of dynamical systems theory. By representing developmental dynamics of spatially located cells with gene expression dynamics with cell‐to‐cell interaction under external morphogen gradient, gene regulation networks are evolved under mutation and selection with the fitness to approach a prescribed spatial pattern of expressed genes. For most numerical evolution experiments, evolution of pattern over generations and development of pattern by an evolved network exhibit remarkable congruence. Both in the evolution and development pattern changes consist of several epochs where stripes are formed in a short time, while for other temporal regimes, pattern hardly changes. In evolution, these quasi‐stationary regimes are generations needed to hit relevant mutations, while in development, they are due to some gene expression that varies slowly and controls the pattern change. The morphogenesis is regulated by combinations of feedback or feedforward regulations, where the upstream feedforward network reads the external morphogen gradient, and generates a pattern used as a boundary condition for the later patterns. The ordering from up to downstream is common in evolution and development, while the successive epochal changes in development and evolution are represented as common bifurcations in dynamical‐systems theory, which lead to the evolution‐development congruence. Mechanism of exceptional violation of the congruence is also unveiled. Our results provide a new look on developmental stages, punctuated equilibrium, developmental bottlenecks, and evolutionary acquisition of novelty in morphogenesis. J. Exp. Zool. (Mol. Dev. Evol.) 326B:61–84, 2016. © 2015 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution

The Evolution of Tropical Precipitation Patterns During ENSO Events Using 21+ Years of GPCP Merged Data

NASA Technical Reports Server (NTRS)

Curtis, Scott; Adler, Robert

2000-01-01

The ENSO phenomenon is characterized by fluctuations in the climate system of the tropical Pacific. Quantifying changes in the precipitation component of this system is important in understanding the distribution of heating in the atmosphere which drives the large-scale circulation and affects the weather patterns in the mid-latitudes. Monitoring precipitation anomalies in the Pacific is also an important component for tracking the evolution of ENSO. The most timely and complete observations of the earth come from satellite instruments. In this study, the state of the art satellite-gauge merged monthly precipitation data set from the Global Precipitation Climatology Project (GPCP) is used to depict tropical rainfall patterns during ENSO events over the past two decades and quantify these patterns using indices. This analysis will be complemented by daily precipitation data which can resolve the Madden-Julian Oscillation and westerly wind burst events. The 1997-98 El Nino and 1998-2000 La Nina were the best observed ENSO cycle in the historic record. Prior to the El Nino (in terms of anomalous warming of the east Pacific) dry anomalies over the Maritime Continent were observed in February 1997 as a westerly wind burst advected convection to the east. The largest SST anomalies occurred around November-December 1997, which were followed by the largest precipitation anomalies in the beginning of 1998. The largest precipitation departures from normal were not colocated with the SST anomalies, but were further west, In the spring of 1998 negative precipitation anomalies to the north of the equator intensified, signaling the mature phase of the El Nino. A rapid increase in the precipitation-based La Nina index from December-January 1998 to March-April 1998 signaled the coming La Nina. The 1982-1983 El Nino was comparable in strength (according to several indices) and the precipitation patterns evolved in a similar fashion. For the 1998-2000 La Nina, the coldest anomalies

Temporal evolution of age data under transient pumping conditions

NASA Astrophysics Data System (ADS)

Leray, S.; de Dreuzy, J.-R.; Aquilina, L.; Vergnaud-Ayraud, V.; Labasque, T.; Bour, O.; Le Borgne, T.

2014-04-01

While most age data derived from tracers have been analyzed in steady-state flow conditions, we determine their temporal evolution when starting a pumping. Our study is based on a model made up of a shallowly dipping aquifer overlain by a less permeable aquitard characteristic of the crystalline aquifer of Plœmeur (Brittany, France). Under a pseudo transient flow assumption (instantaneous shift between two steady-state flow fields), we solve the transport equation with a backward particle-tracking method and determine the temporal evolution of the concentrations at the pumping well of CFC-11, CFC-12, CFC-113 and SF6. Apparent ages evolve because of the modifications of the flow pattern and because of the non-linear evolution of the tracer atmospheric concentrations. To identify the respective role of these two causes, we propose two successive analyses. We first convolute residence time distributions initially arising at different times at the same sampling time. We secondly convolute one residence time distribution at various sampling times. We show that flow pattern modifications control the apparent ages evolution in the first pumping year when the residence time distribution is modified from a piston-like distribution to a much broader distribution. In the first pumping year, the apparent age evolution contains transient information that can be used to better constrain hydrogeological systems and slightly compensate for the small number of tracers. Later, the residence time distribution hardly evolves and apparent ages only evolve because of the tracer atmospheric concentrations. In this phase, apparent age time-series do not reflect any evolution in the flow pattern.

Solar radiation and landscape evolution: co-evolution of topography, vegetation, and erosion rates in a semi-arid ecosystem

NASA Astrophysics Data System (ADS)

Istanbulluoglu, Erkan; Yetemen, Omer

2016-04-01

In this study CHILD landscape evolution model (LEM) is used to study the role of solar radiation on the co-evolution of landscape morphology, vegetation patterns, and erosion rates in a central New Mexico catchment. In the study site north facing slopes (NFS) are characterized by steep diffusion-dominated planar hillslopes covered by co-exiting juniper pine and grass vegetation. South facing slopes (SFS) are characterized by shallow slopes and covered by sparse shrub vegetation. Measured short-term and Holocene-averaged erosion rates show higher soil loss on SFS than NFS. In this study CHILD LEM is first confirmed with ecohydrologic field data and used to systematically examine the co-evolution of topography, vegetation pattern, and erosion rates. Aspect- and network-control are identified as the two main topographic drivers of soil moisture and vegetation organization on the landscape. Landscape-scale and long-term implications of solar radiation driven ecohdrologic patterns emerged in modeled landscape: NFS supported denser vegetation cover and became steeper and planar, while on SFS vegetation grew sparser and slopes declined with more fluvial activity. At the landscape scale, these differential erosion processes led to asymmetric development of catchment forms, consistent with regional observations. While the general patterns of vegetation and topography were reproduced by the model using a stationary representation of the current climate, the observed differential Holocene erosion rates were captured by the model only when cyclic climate is used. This suggests sensitivity of Holocene erosion rates to long-term climate fluctuations.

Within-host evolution of bacterial pathogens

PubMed Central

Didelot, Xavier; Walker, A. Sarah; Peto, Tim E.; Crook, Derrick W.; Wilson, Daniel J.

2016-01-01

Whole genome sequencing has opened the way to investigating the dynamics and genomic evolution of bacterial pathogens during colonization and infection of humans. The application of this technology to the longitudinal study of adaptation in the infected host — in particular, the evolution of drug resistance and host adaptation in patients chronically infected with opportunistic pathogens — has revealed remarkable patterns of convergent evolution, pointing to an inherent repeatability of evolution. In this Review, we describe how these studies have advanced our understanding of the mechanisms and principles of within-host genome evolution, and we consider the consequences of findings such as a potent adaptive potential for pathogenicity. Finally, we discuss the possibility that genomics may be used in the future to predict the clinical progression of bacterial infections, and to suggest the best treatment option. PMID:26806595

Within-host evolution of bacterial pathogens.

PubMed

Didelot, Xavier; Walker, A Sarah; Peto, Tim E; Crook, Derrick W; Wilson, Daniel J

2016-03-01

Whole-genome sequencing has opened the way for investigating the dynamics and genomic evolution of bacterial pathogens during the colonization and infection of humans. The application of this technology to the longitudinal study of adaptation in an infected host--in particular, the evolution of drug resistance and host adaptation in patients who are chronically infected with opportunistic pathogens--has revealed remarkable patterns of convergent evolution, suggestive of an inherent repeatability of evolution. In this Review, we describe how these studies have advanced our understanding of the mechanisms and principles of within-host genome evolution, and we consider the consequences of findings such as a potent adaptive potential for pathogenicity. Finally, we discuss the possibility that genomics may be used in the future to predict the clinical progression of bacterial infections and to suggest the best option for treatment.

Measuring the Complexity of Seismicity Pattern Evolution

NASA Astrophysics Data System (ADS)

Goltz, C.

2004-12-01

``Complexity'' has become an ubiquitous term in science. However, there is, much as with ``fractality'', no clear definition of what complexity actually means. Yet, it is important to distinguish between what is merely complicated and what is complex in the sense that simple rules can give rise to very rich behaviour. Seismicity is certainly a complicated phenomenon (difficult to understand) but simple models such as cellular automata indicate that earthquakes are truly complex. From the observational point of view, there exists the problem of quantification of complexity in real world seismicity patterns (in the absence of even a rigid definition of complexity). Such a measurement is desirable, however, not only for fundamental understanding but also for monitoring and possibly for prediction purposes. Maybe the most workable definitions of complexity exist in informatics, summarised under the topic of algorithmic complexity. Here, after introducing the concepts, I apply such measures of complexity to temporally evolving seismicity patterns from different geographic regions. Finally, I discuss the usefulness of the approach and discuss results in view of the occurrence of large earthquakes.

Methylome evolution in plants.

PubMed

Vidalis, Amaryllis; Živković, Daniel; Wardenaar, René; Roquis, David; Tellier, Aurélien; Johannes, Frank

2016-12-20

Despite major progress in dissecting the molecular pathways that control DNA methylation patterns in plants, little is known about the mechanisms that shape plant methylomes over evolutionary time. Drawing on recent intra- and interspecific epigenomic studies, we show that methylome evolution over long timescales is largely a byproduct of genomic changes. By contrast, methylome evolution over short timescales appears to be driven mainly by spontaneous epimutational events. We argue that novel methods based on analyses of the methylation site frequency spectrum (mSFS) of natural populations can provide deeper insights into the evolutionary forces that act at each timescale.

Evolution of the Mauthner axon cap.

PubMed

Bierman, Hilary S; Zottoli, Steven J; Hale, Melina E

2009-01-01

Studies of vertebrate brain evolution have focused primarily on patterns of gene expression or changes in size and organization of major brain regions. The Mauthner cell, an important reticulospinal neuron that functions in the startle response of many species, provides an opportunity for evolutionary comparisons at the cellular level. Despite broad interspecific similarities in Mauthner cell morphology, the motor patterns and startle behaviors it initiates vary markedly. Response diversity has been hypothesized to result, in part, from differences in the structure and function of the Mauthner cell-associated axon cap. We used light microscopy techniques to compare axon cap morphology across a wide range of species, including all four extant basal actinopterygian orders, representatives of a variety of teleost lineages and lungfishes, and we combined our data with published descriptions of axon cap structure. The 'composite' axon cap, observed in teleosts, is an organized conglomeration of glia and fibers of inhibitory and excitatory interneurons. Lungfish, amphibian tadpoles and several basal actinopterygian fishes have 'simple' axon caps that appear to lack glia and include few fibers. Several other basal actinopterygian fishes have 'simple-dense' caps that include greater numbers of fibers than simple caps, but lack the additional elements and organization of composite caps. Phylogenetic mapping shows that through evolution there are discrete transitions in axon cap morphology occurring at the base of gnathostomes, within basal actinopterygians, and at the base of the teleost radiation. Comparing axon cap evolution to the evolution of startle behavior and motor pattern provides insight into the relationship between Mauthner cell-associated structures and their functions in behavior. Copyright 2009 S. Karger AG, Basel.

Food web structure and the evolution of ecological communities

NASA Astrophysics Data System (ADS)

Quince, Christopher; Higgs, Paul G.; McKane, Alan J.

Simulations of the coevolution of many interacting species are performed using the Webworld model. The model has a realistic set of predator-prey equations that describe the population dynamics of the species for any structure of the food web. The equations account for competition between species for the same resources, and for the diet choice of predators between alternative prey according to an evolutionarily stable strategy. The set of species present undergoes long-term evolution d ue to speciation and extinction events. We summarize results obtained on the macro-evolutionary dynamics of speciations and extinctions, and on the statistical properties of the food webs that are generated by the model. Simulations begin from small numbers of species and build up to larger webs with relatively constant species number on average. The rate of origination and extinction of species are relatively high, but remain roughly balanced throughout the simulations. When a 'parent' species undergoes sp eciation, the 'child' species usually adds to the same trophic level as the parent. The chance of the child species surviving is significantly higher if the parent is on the second or third trophic level than if it is on the first level, most likely due to a wider choice of possible prey for species on higher levels. Addition of a new species sometimes causes extinction of existing species. The parent species has a high probability of extinction because it has strong competition with the new species. Non-pa rental competitors of the new species also have a significantly higher extinction probability than average, as do prey of the new species. Predators of the new species are less likely than average to become extinct.

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.

Unstable genomes elevate transcriptome dynamics

PubMed Central

Stevens, Joshua B.; Liu, Guo; Abdallah, Batoul Y.; Horne, Steven D.; Ye, Karen J.; Bremer, Steven W.; Ye, Christine J.; Krawetz, Stephen A.; Heng, Henry H.

2015-01-01

The challenge of identifying common expression signatures in cancer is well known, however the reason behind this is largely unclear. Traditionally variation in expression signatures has been attributed to technological problems, however recent evidence suggests that chromosome instability (CIN) and resultant karyotypic heterogeneity may be a large contributing factor. Using a well-defined model of immortalization, we systematically compared the pattern of genome alteration and expression dynamics during somatic evolution. Co-measurement of global gene expression and karyotypic alteration throughout the immortalization process reveals that karyotype changes influence gene expression as major structural and numerical karyotypic alterations result in large gene expression deviation. Replicate samples from stages with stable genomes are more similar to each other than are replicate samples with karyotypic heterogeneity. Karyotypic and gene expression change during immortalization is dynamic as each stage of progression has a unique expression pattern. This was further verified by comparing global expression in two replicates grown in one flask with known karyotypes. Replicates with higher karyotypic instability were found to be less similar than replicates with stable karyotypes. This data illustrates the karyotype, transcriptome, and transcriptome determined pathways are in constant flux during somatic cellular evolution (particularly during the macroevolutionary phase) and this flux is an inextricable feature of CIN and essential for cancer formation. The findings presented here underscore the importance of understanding the evolutionary process of cancer in order to design improved treatment modalities. PMID:24122714

Patterns in shrinking gels

NASA Astrophysics Data System (ADS)

Matsuo, Eriko Sato; Tanaka, Toyoichi

1992-08-01

POLYMER gels can undergo a volume phase transition (either continuous or discontinuous) when an external condition, such as temperature or solvent composition, is altered1-3. During this transition, the volume may change by a factor of several thousand, and various patterns develop in the gel. The patterns arising from swelling and shrinking differ in both their appearance and their physical mechanisms. The mechanism for the formation and evolution of patterns on swelling gels has been established as being due to a single kind of mechanical instability4-7 in contrast, the shrinking patterns seem to be sensitive to both the initial and final states of the transition. Here we classify the various shrinking patterns in the form of a phase diagram, and explain the poly-morphism in terms of macroscopic phase separation.

Genes involved in convergent evolution of eusociality in bees

PubMed Central

Woodard, S. Hollis; Fischman, Brielle J.; Venkat, Aarti; Hudson, Matt E.; Varala, Kranthi; Cameron, Sydney A.; Clark, Andrew G.; Robinson, Gene E.

2011-01-01

Eusociality has arisen independently at least 11 times in insects. Despite this convergence, there are striking differences among eusocial lifestyles, ranging from species living in small colonies with overt conflict over reproduction to species in which colonies contain hundreds of thousands of highly specialized sterile workers produced by one or a few queens. Although the evolution of eusociality has been intensively studied, the genetic changes involved in the evolution of eusociality are relatively unknown. We examined patterns of molecular evolution across three independent origins of eusociality by sequencing transcriptomes of nine socially diverse bee species and combining these data with genome sequence from the honey bee Apis mellifera to generate orthologous sequence alignments for 3,647 genes. We found a shared set of 212 genes with a molecular signature of accelerated evolution across all eusocial lineages studied, as well as unique sets of 173 and 218 genes with a signature of accelerated evolution specific to either highly or primitively eusocial lineages, respectively. These results demonstrate that convergent evolution can involve a mosaic pattern of molecular changes in both shared and lineage-specific sets of genes. Genes involved in signal transduction, gland development, and carbohydrate metabolism are among the most prominent rapidly evolving genes in eusocial lineages. These findings provide a starting point for linking specific genetic changes to the evolution of eusociality. PMID:21482769

A comparison of phenotypic variation and covariation patterns and the role of phylogeny, ecology, and ontogeny during cranial evolution of new world monkeys.

PubMed

Marroig, G; Cheverud, J M

2001-12-01

Similarity of genetic and phenotypic variation patterns among populations is important for making quantitative inferences about past evolutionary forces acting to differentiate populations and for evaluating the evolution of relationships among traits in response to new functional and developmental relationships. Here, phenotypic co variance and correlation structure is compared among Platyrrhine Neotropical primates. Comparisons range from among species within a genus to the superfamily level. Matrix correlation followed by Mantel's test and vector correlation among responses to random natural selection vectors (random skewers) were used to compare correlation and variance/covariance matrices of 39 skull traits. Sampling errors involved in matrix estimates were taken into account in comparisons using matrix repeatability to set upper limits for each pairwise comparison. Results indicate that covariance structure is not strictly constant but that the amount of variance pattern divergence observed among taxa is generally low and not associated with taxonomic distance. Specific instances of divergence are identified. There is no correlation between the amount of divergence in covariance patterns among the 16 genera and their phylogenetic distance derived from a conjoint analysis of four already published nuclear gene datasets. In contrast, there is a significant correlation between phylogenetic distance and morphological distance (Mahalanobis distance among genus centroids). This result indicates that while the phenotypic means were evolving during the last 30 millions years of New World monkey evolution, phenotypic covariance structures of Neotropical primate skulls have remained relatively consistent. Neotropical primates can be divided into four major groups based on their feeding habits (fruit-leaves, seed-fruits, insect-fruits, and gum-insect-fruits). Differences in phenotypic covariance structure are correlated with differences in feeding habits, indicating

A comparative physical map reveals the pattern of chromosomal evolution between the turkey (Meleagris gallopavo) and chicken (Gallus gallus) genomes

PubMed Central

2011-01-01

Background A robust bacterial artificial chromosome (BAC)-based physical map is essential for many aspects of genomics research, including an understanding of chromosome evolution, high-resolution genome mapping, marker-assisted breeding, positional cloning of genes, and quantitative trait analysis. To facilitate turkey genetics research and better understand avian genome evolution, a BAC-based integrated physical, genetic, and comparative map was developed for this important agricultural species. Results The turkey genome physical map was constructed based on 74,013 BAC fingerprints (11.9 × coverage) from two independent libraries, and it was integrated with the turkey genetic map and chicken genome sequence using over 41,400 BAC assignments identified by 3,499 overgo hybridization probes along with > 43,000 BAC end sequences. The physical-comparative map consists of 74 BAC contigs, with an average contig size of 13.6 Mb. All but four of the turkey chromosomes were spanned on this map by three or fewer contigs, with 14 chromosomes spanned by a single contig and nine chromosomes spanned by two contigs. This map predicts 20 to 27 major rearrangements distinguishing turkey and chicken chromosomes, despite up to 40 million years of separate evolution between the two species. These data elucidate the chromosomal evolutionary pattern within the Phasianidae that led to the modern turkey and chicken karyotypes. The predominant rearrangement mode involves intra-chromosomal inversions, and there is a clear bias for these to result in centromere locations at or near telomeres in turkey chromosomes, in comparison to interstitial centromeres in the orthologous chicken chromosomes. Conclusion The BAC-based turkey-chicken comparative map provides novel insights into the evolution of avian genomes, a framework for assembly of turkey whole genome shotgun sequencing data, and tools for enhanced genetic improvement of these important agricultural and model species. PMID:21906286

Chromosome Evolution in Connection with Repetitive Sequences and Epigenetics in Plants

PubMed Central

Li, Shu-Fen; Su, Ting; Cheng, Guang-Qian; Wang, Bing-Xiao; Li, Xu; Deng, Chuan-Liang; Gao, Wu-Jun

2017-01-01

Chromosome evolution is a fundamental aspect of evolutionary biology. The evolution of chromosome size, structure and shape, number, and the change in DNA composition suggest the high plasticity of nuclear genomes at the chromosomal level. Repetitive DNA sequences, which represent a conspicuous fraction of every eukaryotic genome, particularly in plants, are found to be tightly linked with plant chromosome evolution. Different classes of repetitive sequences have distinct distribution patterns on the chromosomes. Mounting evidence shows that repetitive sequences may play multiple generative roles in shaping the chromosome karyotypes in plants. Furthermore, recent development in our understanding of the repetitive sequences and plant chromosome evolution has elucidated the involvement of a spectrum of epigenetic modification. In this review, we focused on the recent evidence relating to the distribution pattern of repetitive sequences in plant chromosomes and highlighted their potential relevance to chromosome evolution in plants. We also discussed the possible connections between evolution and epigenetic alterations in chromosome structure and repatterning, such as heterochromatin formation, centromere function, and epigenetic-associated transposable element inactivation. PMID:29064432

Chromosome Evolution in Connection with Repetitive Sequences and Epigenetics in Plants.

PubMed

Li, Shu-Fen; Su, Ting; Cheng, Guang-Qian; Wang, Bing-Xiao; Li, Xu; Deng, Chuan-Liang; Gao, Wu-Jun

2017-10-24

Chromosome evolution is a fundamental aspect of evolutionary biology. The evolution of chromosome size, structure and shape, number, and the change in DNA composition suggest the high plasticity of nuclear genomes at the chromosomal level. Repetitive DNA sequences, which represent a conspicuous fraction of every eukaryotic genome, particularly in plants, are found to be tightly linked with plant chromosome evolution. Different classes of repetitive sequences have distinct distribution patterns on the chromosomes. Mounting evidence shows that repetitive sequences may play multiple generative roles in shaping the chromosome karyotypes in plants. Furthermore, recent development in our understanding of the repetitive sequences and plant chromosome evolution has elucidated the involvement of a spectrum of epigenetic modification. In this review, we focused on the recent evidence relating to the distribution pattern of repetitive sequences in plant chromosomes and highlighted their potential relevance to chromosome evolution in plants. We also discussed the possible connections between evolution and epigenetic alterations in chromosome structure and repatterning, such as heterochromatin formation, centromere function, and epigenetic-associated transposable element inactivation.

Neutral null models for diversity in serial transfer evolution experiments.

PubMed

Harpak, Arbel; Sella, Guy

2014-09-01

Evolution experiments with microorganisms coupled with genome-wide sequencing now allow for the systematic study of population genetic processes under a wide range of conditions. In learning about these processes in natural, sexual populations, neutral models that describe the behavior of diversity and divergence summaries have played a pivotal role. It is therefore natural to ask whether neutral models, suitably modified, could be useful in the context of evolution experiments. Here, we introduce coalescent models for polymorphism and divergence under the most common experimental evolution assay, a serial transfer experiment. This relatively simple setting allows us to address several issues that could affect diversity patterns in evolution experiments, whether selection is operating or not: the transient behavior of neutral polymorphism in an experiment beginning from a single clone, the effects of randomness in the timing of cell division and noisiness in population size in the dilution stage. In our analyses and discussion, we emphasize the implications for experiments aimed at measuring diversity patterns and making inferences about population genetic processes based on these measurements. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Social, moral, and temporal qualities: Pre-service teachers' considerations of evolution and creation

NASA Astrophysics Data System (ADS)

Hahn, Deirdre

The introduction of the theories of evolution into public education has created a history of misinterpretation and uncertainty about its application to understanding deep time and human origins. Conceptions about negative social and moral outcomes of evolution itself along with cognitive temporal constraints may be difficult for many individuals to uncouple from the scientific theory, serving to provoke the ongoing debate about the treatment of evolution in science education. This debate about teaching evolution is strongly influenced by groups who strive to add creationism to the science curriculum for a balanced treatment of human origins and to mediate implied negative social and moral outcomes of evolution. Individual conceptualization of evolution and creation may influence the choice of college students to teach science. This study is designed to examine if pre-service teachers' conceptualize an evolutionary and creationist process of human development using certain social, moral or temporal patterns; and if the patterns follow a negative conceptual theme. The pilot study explored 21 pre-service teachers' conceptual representation of an evolutionary process through personal narratives. Participants tended to link evolutionary changes with negative social and moral consequences and seemed to have difficulty envisioning change over time. The pilot study was expanded to include a quantitative examination of attribute patterns of an evolutionary and creationist developmental process. Seventy-three pre-service teachers participated in the second experiment and tended to fall evenly along a continuum of creationist and evolutionist beliefs about life. Using a chi-square and principle components analysis, participants were found to map concepts of evolution and creation onto each other using troubling attributes of development to distinguish negative change over time. A strong negative social and moral pattern of human development was found in the creation condition

A multidimensional approach for detecting species patterns in Malagasy vertebrates

PubMed Central

Yoder, Anne D.; Olson, Link E.; Hanley, Carol; Heckman, Kellie L.; Rasoloarison, Rodin; Russell, Amy L.; Ranivo, Julie; Soarimalala, Voahangy; Karanth, K. Praveen; Raselimanana, Achille P.; Goodman, Steven M.

2005-01-01

The biodiversity of Madagascar is extraordinarily distinctive, diverse, and endangered. It is therefore urgent that steps be taken to document, describe, interpret, and protect this exceptional biota. As a collaborative group of field and laboratory biologists, we employ a suite of methodological and analytical tools to investigate the vertebrate portion of Madagascar's fauna. Given that species are the fundamental unit of evolution, where micro- and macroevolutionary forces converge to generate biological diversity, a thorough understanding of species distribution and abundance is critical for understanding the evolutionary, ecological, and biogeographic forces that have shaped Malagasy vertebrate diversity. We illustrate the means by which we apply Mayr's “three basic tasks” of the systematist [Mayr, E. (1942) Systematics and the Origin of Species from the Viewpoint of a Zoologist (Harvard Univ. Press, Cambridge, MA)] to identify, classify, and study the organisms that together constitute Madagascar's vertebrate community. Using field inventory methods, specimen-based studies, and morphological and molecular analyses, we formulate hypotheses of species identity that then serve as the foundation for subsequent studies of biology and history. Our experience, as well as that of other investigators, has shown that much of the vertebrate species diversity in Madagascar is “cryptic” for both biological and practical reasons. Beyond issues of cryptic biological diversity, the resolution of species identity in Madagascar has been hampered because of a lack of vouchered comparative material at the population level. Through our activities, we are attempting to remedy these limitations while simultaneously enhancing research capacity in Madagascar. PMID:15851666

Amber fossils demonstrate deep-time stability of Caribbean lizard communities.

PubMed

Sherratt, Emma; del Rosario Castañeda, María; Garwood, Russell J; Mahler, D Luke; Sanger, Thomas J; Herrel, Anthony; de Queiroz, Kevin; Losos, Jonathan B

2015-08-11

Whether the structure of ecological communities can exhibit stability over macroevolutionary timescales has long been debated. The similarity of independently evolved Anolis lizard communities on environmentally similar Greater Antillean islands supports the notion that community evolution is deterministic. However, a dearth of Caribbean Anolis fossils--only three have been described to date--has precluded direct investigation of the stability of anole communities through time. Here we report on an additional 17 fossil anoles in Dominican amber dating to 15-20 My before the present. Using data collected primarily by X-ray microcomputed tomography (X-ray micro-CT), we demonstrate that the main elements of Hispaniolan anole ecomorphological diversity were in place in the Miocene. Phylogenetic analysis yields results consistent with the hypothesis that the ecomorphs that evolved in the Miocene are members of the same ecomorph clades extant today. The primary axes of ecomorphological diversity in the Hispaniolan anole fauna appear to have changed little between the Miocene and the present, providing evidence for the stability of ecological communities over macroevolutionary timescales.

Amber fossils demonstrate deep-time stability of Caribbean lizard communities

PubMed Central

Sherratt, Emma; del Rosario Castañeda, María; Garwood, Russell J.; Mahler, D. Luke; Sanger, Thomas J.; Herrel, Anthony; de Queiroz, Kevin; Losos, Jonathan B.

2015-01-01

Whether the structure of ecological communities can exhibit stability over macroevolutionary timescales has long been debated. The similarity of independently evolved Anolis lizard communities on environmentally similar Greater Antillean islands supports the notion that community evolution is deterministic. However, a dearth of Caribbean Anolis fossils—only three have been described to date—has precluded direct investigation of the stability of anole communities through time. Here we report on an additional 17 fossil anoles in Dominican amber dating to 15–20 My before the present. Using data collected primarily by X-ray microcomputed tomography (X-ray micro-CT), we demonstrate that the main elements of Hispaniolan anole ecomorphological diversity were in place in the Miocene. Phylogenetic analysis yields results consistent with the hypothesis that the ecomorphs that evolved in the Miocene are members of the same ecomorph clades extant today. The primary axes of ecomorphological diversity in the Hispaniolan anole fauna appear to have changed little between the Miocene and the present, providing evidence for the stability of ecological communities over macroevolutionary timescales. PMID:26216976

Integrating Competition for Food, Hosts, or Mates via Experimental Evolution.

PubMed

Rodrigues, Leonor R; Duncan, Alison B; Clemente, Salomé H; Moya-Laraño, Jordi; Magalhães, Sara

2016-02-01

Competitive interactions shape the evolution of organisms. However, often it is not clear whether competition is the driving force behind the patterns observed. The recent use of experimental evolution in competitive environments can help establish such causality. Unfortunately, this literature is scattered, as competition for food, mates, and hosts are subject areas that belong to different research fields. Here, we group these bodies of literature, extract common processes and patterns concerning the role of competition in shaping evolutionary trajectories, and suggest perspectives stemming from an integrative view of competition across these research fields. This review reinstates the power of experimental evolution in addressing the evolutionary consequences of competition, but highlights potential pitfalls in the design of such experiments. Copyright © 2015 Elsevier Ltd. All rights reserved.

Evolution of neurotransmitter receptor systems.

PubMed

Venter, J C; di Porzio, U; Robinson, D A; Shreeve, S M; Lai, J; Kerlavage, A R; Fracek, S P; Lentes, K U; Fraser, C M

1988-01-01

The presence of hormones, neurotransmitters, their receptors and biosynthetic and degradative enzymes is clearly not only associated with the present and the recent past but with the past several hundred million years. Evidence is mounting which indicates substantial conservation of protein structure and function of these receptors and enzymes over these tremendous periods of time. These findings indicate that the evolution and development of the nervous system was not dependent upon the formation of new or better transmitter substances, receptor proteins, transducers and effector proteins but involved better utilization of these highly developed elements in creating advanced and refined circuitry. This is not a new concept; it is one that is now substantiated by increasingly sophisticated studies. In a 1953 article discussing chemical aspects of evolution (Danielli, 1953) Danielli quotes Medawar, "... endocrine evolution is not an evolution of hormones but an evolution of the uses to which they are put; an evolution not, to put it crudely, of chemical formulae but of reactivities, reaction patterns and tissue competences." To also quote Danielli, "In terms of comparative biochemistry, one must ask to what extent the evolution of these reactivities, reaction patterns and competences is conditional upon the evolution of methods of synthesis of new proteins, etc., and to what extent the proteins, etc., are always within the synthetic competence of an organism. In the latter case evolution is the history of changing uses of molecules, and not of changing synthetic abilities." (Danielli, 1953). Figure 4 outlines a phylogenetic tree together with an indication of where evidence exists for both the enzymes that determine the biosynthesis and metabolism of the cholinergic and adrenergic transmitters and their specific cholinergic and adrenergic receptors. This figure illustrates a number of important points. For example, the evidence appears to show that the transmitters

Early cellular evolution.

NASA Technical Reports Server (NTRS)

Margulis, L.

1972-01-01

Study of the evolutionary developments that occurred subsequent to the origin of ancestral cells. Microbial physiology and ecology are potential sharp tools for shaping concepts of microbial evolution. Some popular unjustified assumptions are discussed. It is considered that certain principles derived mainly from the advances of molecular biology can be used to order the natural groups (genera) of extant prokaryotes and their patterns phylogenetically.

Adaptive evolution of Mediterranean pines.

PubMed

Grivet, Delphine; Climent, José; Zabal-Aguirre, Mario; Neale, David B; Vendramin, Giovanni G; González-Martínez, Santiago C

2013-09-01

Mediterranean pines represent an extremely heterogeneous assembly. Although they have evolved under similar environmental conditions, they diversified long ago, ca. 10 Mya, and present distinct biogeographic and demographic histories. Therefore, it is of special interest to understand whether and to what extent they have developed specific strategies of adaptive evolution through time and space. To explore evolutionary patterns, the Mediterranean pines' phylogeny was first reconstructed analyzing a new set of 21 low-copy nuclear genes with multilocus Bayesian tree reconstruction methods. Secondly, a phylogenetic approach was used to search for footprints of natural selection and to examine the evolution of multiple phenotypic traits. We identified two genes (involved in pines' defense and stress responses) that have likely played a role in the adaptation of Mediterranean pines to their environment. Moreover, few life-history traits showed historical or evolutionary adaptive convergence in Mediterranean lineages, while patterns of character evolution revealed various evolutionary trade-offs linking growth-development, reproduction and fire-related traits. Assessing the evolutionary path of important life-history traits, as well as the genomic basis of adaptive variation is central to understanding the past evolutionary success of Mediterranean pines and their future response to environmental changes. Copyright © 2013 Elsevier Inc. All rights reserved.

Cognition and the evolution of camouflage.

PubMed

Skelhorn, John; Rowe, Candy

2016-02-24

Camouflage is one of the most widespread forms of anti-predator defence and prevents prey individuals from being detected or correctly recognized by would-be predators. Over the past decade, there has been a resurgence of interest in both the evolution of prey camouflage patterns, and in understanding animal cognition in a more ecological context. However, these fields rarely collide, and the role of cognition in the evolution of camouflage is poorly understood. Here, we review what we currently know about the role of both predator and prey cognition in the evolution of prey camouflage, outline why cognition may be an important selective pressure driving the evolution of camouflage and consider how studying the cognitive processes of animals may prove to be a useful tool to study the evolution of camouflage, and vice versa. In doing so, we highlight that we still have a lot to learn about the role of cognition in the evolution of camouflage and identify a number of avenues for future research. © 2016 The Author(s).

Cognition and the evolution of camouflage

PubMed Central

2016-01-01

Camouflage is one of the most widespread forms of anti-predator defence and prevents prey individuals from being detected or correctly recognized by would-be predators. Over the past decade, there has been a resurgence of interest in both the evolution of prey camouflage patterns, and in understanding animal cognition in a more ecological context. However, these fields rarely collide, and the role of cognition in the evolution of camouflage is poorly understood. Here, we review what we currently know about the role of both predator and prey cognition in the evolution of prey camouflage, outline why cognition may be an important selective pressure driving the evolution of camouflage and consider how studying the cognitive processes of animals may prove to be a useful tool to study the evolution of camouflage, and vice versa. In doing so, we highlight that we still have a lot to learn about the role of cognition in the evolution of camouflage and identify a number of avenues for future research. PMID:26911959

In silico evolution of biochemical networks

NASA Astrophysics Data System (ADS)

Francois, Paul

2010-03-01

We use computational evolution to select models of genetic networks that can be built from a predefined set of parts to achieve a certain behavior. Selection is made with the help of a fitness defining biological functions in a quantitative way. This fitness has to be specific to a process, but general enough to find processes common to many species. Computational evolution favors models that can be built by incremental improvements in fitness rather than via multiple neutral steps or transitions through less fit intermediates. With the help of these simulations, we propose a kinetic view of evolution, where networks are rapidly selected along a fitness gradient. This mathematics recapitulates Darwin's original insight that small changes in fitness can rapidly lead to the evolution of complex structures such as the eye, and explain the phenomenon of convergent/parallel evolution of similar structures in independent lineages. We will illustrate these ideas with networks implicated in embryonic development and patterning of vertebrates and primitive insects.

Testing the link between population genetic differentiation and clade diversification in Costa Rican orchids.

PubMed

Kisel, Yael; Moreno-Letelier, Alejandra C; Bogarín, Diego; Powell, Martyn P; Chase, Mark W; Barraclough, Timothy G

2012-10-01

Species population genetics could be an important factor explaining variation in clade species richness. Here, we use newly generated amplified fragment length polymorphism (AFLP) data to test whether five pairs of sister clades of Costa Rican orchids that differ greatly in species richness also differ in average neutral genetic differentiation within species, expecting that if the strength of processes promoting differentiation within species is phylogenetically heritable, then clades with greater genetic differentiation should diversify more. Contrary to expectation, neutral genetic differentiation does not correlate directly with total diversification in the clades studied. Neutral genetic differentiation varies greatly among species and shows no heritability within clades. Half of the variation in neutral genetic differentiation among populations can be explained by ecological variables, and species-level traits explain the most variation. Unexpectedly, we find no isolation by distance in any species, but genetic differentiation is greater between populations occupying different niches. This pattern corresponds with those observed for microscopic eukaryotes and could reflect effective widespread dispersal of tiny and numerous orchid seeds. Although not providing a definitive answer to whether population genetics processes affect clade diversification, this work highlights the potential for addressing new macroevolutionary questions using a comparative population genetic approach. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Pattern and Process in the Comparative Study of Convergent Evolution.

PubMed

Mahler, D Luke; Weber, Marjorie G; Wagner, Catherine E; Ingram, Travis

2017-08-01

Understanding processes that have shaped broad-scale biodiversity patterns is a fundamental goal in evolutionary biology. The development of phylogenetic comparative methods has yielded a tool kit for analyzing contemporary patterns by explicitly modeling processes of change in the past, providing neontologists tools for asking questions previously accessible only for select taxa via the fossil record or laboratory experimentation. The comparative approach, however, differs operationally from alternative approaches to studying convergence in that, for studies of only extant species, convergence must be inferred using evolutionary process models rather than being directly measured. As a result, investigation of evolutionary pattern and process cannot be decoupled in comparative studies of convergence, even though such a decoupling could in theory guard against adaptationist bias. Assumptions about evolutionary process underlying comparative tools can shape the inference of convergent pattern in sometimes profound ways and can color interpretation of such patterns. We discuss these issues and other limitations common to most phylogenetic comparative approaches and suggest ways that they can be avoided in practice. We conclude by promoting a multipronged approach to studying convergence that integrates comparative methods with complementary tests of evolutionary mechanisms and includes ecological and biogeographical perspectives. Carefully employed, the comparative method remains a powerful tool for enriching our understanding of convergence in macroevolution, especially for investigation of why convergence occurs in some settings but not others.

SWS2 visual pigment evolution as a test of historically contingent patterns of plumage color evolution in Warblers

PubMed Central

Bloch, Natasha I.; Morrow, James M.; Chang, Belinda S.W.; Price, Trevor D.

2014-01-01

Distantly related clades that occupy similar environments may differ due to the lasting imprint of their ancestors – historical contingency. The New World warblers (Parulidae) and Old World warblers (Phylloscopidae) are ecologically similar clades that differ strikingly in plumage coloration. We studied genetic and functional evolution of the short-wavelength sensitive visual pigments (SWS2 and SWS1) to ask if altered color perception could contribute to the plumage color differences between clades. We show SWS2 is short-wavelength shifted in birds that occupy open environments, such as finches, compared to those in closed environments, including warblers. Phylogenetic reconstructions indicate New World warblers were derived from a finch-like form that colonized from the Old World 15-20Ma. During this process the SWS2 gene accumulated 6 substitutions in branches leading to New World warblers, inviting the hypothesis that passage through a finch-like ancestor resulted in SWS2 evolution. In fact, we show spectral tuning remained similar across warblers as well as the finch ancestor. Results reject the hypothesis of historical contingency based on opsin spectral tuning, but point to evolution of other aspects of visual pigment function. Using the approach outlined here, historical contingency becomes a generally testable theory in systems where genotype and phenotype can be connected. PMID:25496318

Pattern Formation

NASA Astrophysics Data System (ADS)

Hoyle, Rebecca

2006-03-01

From the stripes of a zebra and the spots on a leopard's back to the ripples on a sandy beach or desert dune, regular patterns arise everywhere in nature. The appearance and evolution of these phenomena has been a focus of recent research activity across several disciplines. This book provides an introduction to the range of mathematical theory and methods used to analyse and explain these often intricate and beautiful patterns. Bringing together several different approaches, from group theoretic methods to envelope equations and theory of patterns in large-aspect ratio-systems, the book also provides insight behind the selection of one pattern over another. Suitable as an upper-undergraduate textbook for mathematics students or as a fascinating, engaging, and fully illustrated resource for readers in physics and biology, Rebecca Hoyle's book, using a non-partisan approach, unifies a range of techniques used by active researchers in this growing field. Accessible description of the mathematical theory behind fascinating pattern formation in areas such as biology, physics and materials science Collects recent research for the first time in an upper level textbook Features a number of exercises - with solutions online - and worked examples

Integrating influenza antigenic dynamics with molecular evolution

PubMed Central

Bedford, Trevor; Suchard, Marc A; Lemey, Philippe; Dudas, Gytis; Gregory, Victoria; Hay, Alan J; McCauley, John W; Russell, Colin A; Smith, Derek J; Rambaut, Andrew

2014-01-01

Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed through pairwise measurement of cross-reactivity between influenza strains using the hemagglutination inhibition (HI) assay. Here, we extend previous approaches to antigenic cartography, and simultaneously characterize antigenic and genetic evolution by modeling the diffusion of antigenic phenotype over a shared virus phylogeny. Using HI data from influenza lineages A/H3N2, A/H1N1, B/Victoria and B/Yamagata, we determine patterns of antigenic drift across viral lineages, showing that A/H3N2 evolves faster and in a more punctuated fashion than other influenza lineages. We also show that year-to-year antigenic drift appears to drive incidence patterns within each influenza lineage. This work makes possible substantial future advances in investigating the dynamics of influenza and other antigenically-variable pathogens by providing a model that intimately combines molecular and antigenic evolution. DOI: http://dx.doi.org/10.7554/eLife.01914.001 PMID:24497547

Involvement of Hedgehog and FGF signalling in the lamprey telencephalon: evolution of regionalization and dorsoventral patterning of the vertebrate forebrain.

PubMed

Sugahara, Fumiaki; Aota, Shin-ichi; Kuraku, Shigehiro; Murakami, Yasunori; Takio-Ogawa, Yoko; Hirano, Shigeki; Kuratani, Shigeru

2011-03-01

Dorsoventral (DV) specification is a crucial step for the development of the vertebrate telencephalon. Clarifying the origin of this mechanism will lead to a better understanding of vertebrate central nervous system (CNS) evolution. Based on the lamprey, a sister group of the gnathostomes (jawed vertebrates), we identified three lamprey Hedgehog (Hh) homologues, which are thought to play central signalling roles in telencephalon patterning. However, unlike in gnathostomes, none of these genes, nor Lhx6/7/8, a marker for the migrating interneuron subtype, was expressed in the ventral telencephalon, consistent with the reported absence of the medial ganglionic eminence (MGE) in this animal. Homologues of Gsh2, Isl1/2 and Sp8, which are involved in the patterning of the lateral ganglionic eminence (LGE) of gnathostomes, were expressed in the lamprey subpallium, as in gnathostomes. Hh signalling is necessary for induction of the subpallium identity in the gnathostome telencephalon. When Hh signalling was inhibited, the ventral identity was disrupted in the lamprey, suggesting that prechordal mesoderm-derived Hh signalling might be involved in the DV patterning of the telencephalon. By blocking fibroblast growth factor (FGF) signalling, the ventral telencephalon was suppressed in the lamprey, as in gnathostomes. We conclude that Hh- and FGF-dependent DV patterning, together with the resultant LGE identity, are likely to have been established in a common ancestor before the divergence of cyclostomes and gnathostomes. Later, gnathostomes would have acquired a novel Hh expression domain corresponding to the MGE, leading to the obtainment of cortical interneurons.

Transition Characteristic Analysis of Traffic Evolution Process for Urban Traffic Network

PubMed Central

Chen, Hong; Li, Yang

2014-01-01

The characterization of the dynamics of traffic states remains fundamental to seeking for the solutions of diverse traffic problems. To gain more insights into traffic dynamics in the temporal domain, this paper explored temporal characteristics and distinct regularity in the traffic evolution process of urban traffic network. We defined traffic state pattern through clustering multidimensional traffic time series using self-organizing maps and construct a pattern transition network model that is appropriate for representing and analyzing the evolution progress. The methodology is illustrated by an application to data flow rate of multiple road sections from Network of Shenzhen's Nanshan District, China. Analysis and numerical results demonstrated that the methodology permits extracting many useful traffic transition characteristics including stability, preference, activity, and attractiveness. In addition, more information about the relationships between these characteristics was extracted, which should be helpful in understanding the complex behavior of the temporal evolution features of traffic patterns. PMID:24982969

Biostratigraphy, taxonomic diversity and patterns of morphological evolution of Ordovician acritarchs (organic-walled microphytoplankton) from the northern Gondwana margin in relation to palaeoclimatic and palaeogeographic changes

NASA Astrophysics Data System (ADS)

Vecoli, Marco; Le Hérissé, Alain

2004-10-01

Acritarchs, the fossilizable, resting cysts of phytoplanktonic algal protists, are the dominant component of marine organic-walled microfossils in the Palaeozoic. The majority of acritarchs show strong similarities with dinoflagellate cysts in morphological and biogeochemical features, as well as distributional patterns in the sediments. The production of these organic-walled microfossils and their distribution and survivorship in the sediments were controlled by differences in ecological tolerances and life cycle (autecology) of the planktonic parent organisms. Calculation of evolutionary rates and development of a detailed diversity curve at specific level, form the basis for discussing the influence of global palaeoenvironmental perturbations on the evolution of organic-walled microphytoplankton in northern Gondwana during latest Cambrian through Ordovician times. The potential of acritarchs for biostratigraphic correlation at the regional scale (northern Gondwana domain) is much improved by our detailed revision of distributional patterns of 245 acritarch taxa. The most important Cambro-Ordovician acritarch bio-events are short periods of diversification, which also correspond to introduction of morphological innovations, observed in latest Cambrian and earliest Tremadoc, late Tremadoc, early Arenig, basal Llanvirn, and latest Ashgill, and an important extinction phase in the early Caradoc. Overall, acritarch diversity increased from the basal Ordovician up to the middle Llanvirn, then declined in the early and middle Caradoc. During Ashgill times, the assemblages are poorly diversified at the generic level as a result of a combined effect of sea level drawdown and onset of glacial conditions, but no major extinction event is observed in connection with the end-Ordovician biotic crisis. The peak in acritarch diversity during Middle Ordovician times appears to be correlated to maximum spread of palaeogeographical assembly. Acritarch dynamics appear largely

Formal Definitions of Unbounded Evolution and Innovation Reveal Universal Mechanisms for Open-Ended Evolution in Dynamical Systems.

PubMed

Adams, Alyssa; Zenil, Hector; Davies, Paul C W; Walker, Sara Imari

2017-04-20

Open-ended evolution (OEE) is relevant to a variety of biological, artificial and technological systems, but has been challenging to reproduce in silico. Most theoretical efforts focus on key aspects of open-ended evolution as it appears in biology. We recast the problem as a more general one in dynamical systems theory, providing simple criteria for open-ended evolution based on two hallmark features: unbounded evolution and innovation. We define unbounded evolution as patterns that are non-repeating within the expected Poincare recurrence time of an isolated system, and innovation as trajectories not observed in isolated systems. As a case study, we implement novel variants of cellular automata (CA) where the update rules are allowed to vary with time in three alternative ways. Each is capable of generating conditions for open-ended evolution, but vary in their ability to do so. We find that state-dependent dynamics, regarded as a hallmark of life, statistically out-performs other candidate mechanisms, and is the only mechanism to produce open-ended evolution in a scalable manner, essential to the notion of ongoing evolution. This analysis suggests a new framework for unifying mechanisms for generating OEE with features distinctive to life and its artifacts, with broad applicability to biological and artificial systems.

Biogeographic patterns in ocean microbes emerge in a neutral agent-based model.

PubMed

Hellweger, Ferdi L; van Sebille, Erik; Fredrick, Neil D

2014-09-12

A key question in ecology and evolution is the relative role of natural selection and neutral evolution in producing biogeographic patterns. We quantify the role of neutral processes by simulating division, mutation, and death of 100,000 individual marine bacteria cells with full 1 million-base-pair genomes in a global surface ocean circulation model. The model is run for up to 100,000 years and output is analyzed using BLAST (Basic Local Alignment Search Tool) alignment and metagenomics fragment recruitment. Simulations show the production and maintenance of biogeographic patterns, characterized by distinct provinces subject to mixing and periodic takeovers by neighbors (coalescence), after which neutral evolution reestablishes the province and the patterns reorganize. The emergent patterns are substantial (e.g., down to 99.5% DNA identity between North and Central Pacific provinces) and suggest that microbes evolve faster than ocean currents can disperse them. This approach can also be used to explore environmental selection. Copyright © 2014, American Association for the Advancement of Science.

Does Gene Tree Discordance Explain the Mismatch between Macroevolutionary Models and Empirical Patterns of Tree Shape and Branching Times?

PubMed Central

Stadler, Tanja; Degnan, James H.; Rosenberg, Noah A.

2016-01-01

Classic null models for speciation and extinction give rise to phylogenies that differ in distribution from empirical phylogenies. In particular, empirical phylogenies are less balanced and have branching times closer to the root compared to phylogenies predicted by common null models. This difference might be due to null models of the speciation and extinction process being too simplistic, or due to the empirical datasets not being representative of random phylogenies. A third possibility arises because phylogenetic reconstruction methods often infer gene trees rather than species trees, producing an incongruity between models that predict species tree patterns and empirical analyses that consider gene trees. We investigate the extent to which the difference between gene trees and species trees under a combined birth–death and multispecies coalescent model can explain the difference in empirical trees and birth–death species trees. We simulate gene trees embedded in simulated species trees and investigate their difference with respect to tree balance and branching times. We observe that the gene trees are less balanced and typically have branching times closer to the root than the species trees. Empirical trees from TreeBase are also less balanced than our simulated species trees, and model gene trees can explain an imbalance increase of up to 8% compared to species trees. However, we see a much larger imbalance increase in empirical trees, about 100%, meaning that additional features must also be causing imbalance in empirical trees. This simulation study highlights the necessity of revisiting the assumptions made in phylogenetic analyses, as these assumptions, such as equating the gene tree with the species tree, might lead to a biased conclusion. PMID:26968785

The beta-diversity of species interactions: Untangling the drivers of geographic variation in plant-pollinator diversity and function across scales.

PubMed

Burkle, Laura A; Myers, Jonathan A; Belote, R Travis

2016-01-01

Geographic patterns of biodiversity have long inspired interest in processes that shape the assembly, diversity, and dynamics of communities at different spatial scales. To study mechanisms of community assembly, ecologists often compare spatial variation in community composition (beta-diversity) across environmental and spatial gradients. These same patterns inspired evolutionary biologists to investigate how micro- and macro-evolutionary processes create gradients in biodiversity. Central to these perspectives are species interactions, which contribute to community assembly and geographic variation in evolutionary processes. However, studies of beta-diversity have predominantly focused on single trophic levels, resulting in gaps in our understanding of variation in species-interaction networks (interaction beta-diversity), especially at scales most relevant to evolutionary studies of geographic variation. We outline two challenges and their consequences in scaling-up studies of interaction beta-diversity from local to biogeographic scales using plant-pollinator interactions as a model system in ecology, evolution, and conservation. First, we highlight how variation in regional species pools may contribute to variation in interaction beta-diversity among biogeographic regions with dissimilar evolutionary history. Second, we highlight how pollinator behavior (host-switching) links ecological networks to geographic patterns of plant-pollinator interactions and evolutionary processes. Third, we outline key unanswered questions regarding the role of geographic variation in plant-pollinator interactions for conservation and ecosystem services (pollination) in changing environments. We conclude that the largest advances in the burgeoning field of interaction beta-diversity will come from studies that integrate frameworks in ecology, evolution, and conservation to understand the causes and consequences of interaction beta-diversity across scales. © 2016 Botanical

Pan-vertebrate comparative genomics unmasks retrovirus macroevolution

PubMed Central

Hayward, Alexander; Cornwallis, Charlie K.; Jern, Patric

2015-01-01

Although extensive research has demonstrated host-retrovirus microevolutionary dynamics, it has been difficult to gain a deeper understanding of the macroevolutionary patterns of host–retrovirus interactions. Here we use recent technological advances to infer broad patterns in retroviral diversity, evolution, and host–virus relationships by using a large-scale phylogenomic approach using endogenous retroviruses (ERVs). Retroviruses insert a proviral DNA copy into the host cell genome to produce new viruses. ERVs are provirus insertions in germline cells that are inherited down the host lineage and consequently present a record of past host–viral associations. By mining ERVs from 65 host genomes sampled across vertebrate diversity, we uncover a great diversity of ERVs, indicating that retroviral sequences are much more prevalent and widespread across vertebrates than previously appreciated. The majority of ERV clades that we recover do not contain known retroviruses, implying either that retroviral lineages are highly transient over evolutionary time or that a considerable number of retroviruses remain to be identified. By characterizing the distribution of ERVs, we show that no major vertebrate lineage has escaped retroviral activity and that retroviruses are extreme host generalists, having an unprecedented ability for rampant host switching among distantly related vertebrates. In addition, we examine whether the distribution of ERVs can be explained by host factors predicted to influence viral transmission and find that internal fertilization has a pronounced effect on retroviral colonization of host genomes. By capturing the mode and pattern of retroviral evolution and contrasting ERV diversity with known retroviral diversity, our study provides a cohesive framework to understand host–virus coevolution better. PMID:25535393

Playing evolution in the laboratory: From the first major evolutionary transition to global warming

NASA Astrophysics Data System (ADS)

Fragata, Inês; Simões, Pedro; Matos, Margarida; Szathmáry, Eörs; Santos, Mauro

2018-05-01

Experimental evolution allows testing hypotheses derived from theory or from observed patterns in nature. We have designed a droplet-based microfluidic “evolution machine” to test how transient compartmentalization (“trait-groups”) of independent molecular replicators (likely a critical step in the origin of life) could have prevented the spread of parasitic mutants; that is, inactive RNAs that have been reported to spoil a system of free replicators. In remarkable agreement with the theory, we show that this simple population structure was sufficient to prevent takeover by inactive RNAs. A more complex scenario arises when we use experimental evolution to test field-derived hypotheses; for instance, the idea that temperature is driving genetic spatiotemporal patterns of climate change. In the fly Drosophila subobscura, latitudinal clines in gene arrangement frequencies occur worldwide, and more equatorial gene arrangements are becoming more frequent at higher latitudes as a correlated response to climate change. However, the evolution at different constant temperatures in the laboratory was not consistent with patterns in nature, suggesting some limitations of experimental evolution. Finally, also in D. subobscura, we show that repeatability in experimental evolution is staggeringly consistent for life history traits, making evolution quite predictable and suggesting that laboratory selection can quickly erase differences between populations. Yet, the genetic paths used to attain the same adaptive phenotypes are complex and unpredictable. Contribution to the Focus Issue Evolutionary Modeling and Experimental Evolution edited by José Cuesta, Joachim Krug and Susanna Manrubia.

Extinction in Phylogenetics and Biogeography: From Timetrees to Patterns of Biotic Assemblage

PubMed Central

Meseguer, Andrea S.

2016-01-01

Global climate change and its impact on biodiversity levels have made extinction a relevant topic in biological research. Yet, until recently, extinction has received less attention in macroevolutionary studies than speciation; the reason is the difficulty to infer an event that actually eliminates rather than creates new taxa. For example, in biogeography, extinction has often been seen as noise, introducing homoplasy in biogeographic relationships, rather than a pattern-generating process. The molecular revolution and the possibility to integrate time into phylogenetic reconstructions have allowed studying extinction under different perspectives. Here, we review phylogenetic (temporal) and biogeographic (spatial) approaches to the inference of extinction and the challenges this process poses for reconstructing evolutionary history. Specifically, we focus on the problem of discriminating between alternative high extinction scenarios using time trees with only extant taxa, and on the confounding effect introduced by asymmetric spatial extinction – different rates of extinction across areas – in biogeographic inference. Finally, we identify the most promising avenues of research in both fields, which include the integration of additional sources of evidence such as the fossil record or environmental information in birth–death models and biogeographic reconstructions, the development of new models that tie extinction rates to phenotypic or environmental variation, or the implementation within a Bayesian framework of parametric non-stationary biogeographic models. PMID:27047538

Ecological divergence and conservatism: spatiotemporal patterns of niche evolution in a genus of livebearing fishes (Poeciliidae: Xiphophorus).

PubMed

Culumber, Zachary W; Tobler, Michael

2016-02-19

Ecological factors often have a strong impact on spatiotemporal patterns of biodiversity. The integration of spatial ecology and phylogenetics allows for rigorous tests of whether speciation is associated with niche conservatism (constraints on ecological divergence) or niche divergence. We address this question in a genus of livebearing fishes for which the role of sexual selection in speciation has long been studied, but in which the potential role of ecological divergence during speciation has not been tested. By combining reconstruction of ancestral climate tolerances and disparity indices, we show that the earliest evolutionary split in Xiphophorus was associated with significant divergence for temperature variables. Niche evolution and present day niches were most closely associated with each species' geographic distribution relative to a biogeographic barrier, the Trans-Mexican Volcanic Belt. Tests for similarity of the environmental backgrounds of closely related species suggested that the relative importance of niche conservatism and divergence during speciation varied among the primary clades of Xiphophorus. Closely related species in the two swordtail clades exhibited higher levels of niche overlap than expected given environmental background similarity indicative of niche conservatism. In contrast, almost all species of platyfish had significantly divergent niches compared to environmental backgrounds, which is indicative of niche divergence. The results suggest that the relative importance of niche conservatism and divergence differed among the clades of Xiphophorus and that traits associated with niche evolution may be more evolutionarily labile in the platyfishes. Our results ultimately suggest that the taxonomic scale of tests for conservatism and divergence could greatly influence inferences of their relative importance in the speciation process.

Spatial-pattern-induced evolution of a self-replicating loop network.

PubMed

Suzuki, Keisuke; Ikegami, Takashi

2006-01-01

We study a system of self-replicating loops in which interaction rules between individuals allow competition that leads to the formation of a hypercycle-like network. The main feature of the model is the multiple layers of interaction between loops, which lead to both global spatial patterns and local replication. The network of loops manifests itself as a spiral structure from which new kinds of self-replicating loops emerge at the boundaries between different species. In these regions, larger and more complex self-replicating loops live for longer periods of time, managing to self-replicate in spite of their slower replication. Of particular interest is how micro-scale interactions between replicators lead to macro-scale spatial pattern formation, and how these macro-scale patterns in turn perturb the micro-scale replication dynamics.

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.

Predicting Key Events in the Popularity Evolution of Online Information.

PubMed

Hu, Ying; Hu, Changjun; Fu, Shushen; Fang, Mingzhe; Xu, Wenwen

2017-01-01

The popularity of online information generally experiences a rising and falling evolution. This paper considers the "burst", "peak", and "fade" key events together as a representative summary of popularity evolution. We propose a novel prediction task-predicting when popularity undergoes these key events. It is of great importance to know when these three key events occur, because doing so helps recommendation systems, online marketing, and containment of rumors. However, it is very challenging to solve this new prediction task due to two issues. First, popularity evolution has high variation and can follow various patterns, so how can we identify "burst", "peak", and "fade" in different patterns of popularity evolution? Second, these events usually occur in a very short time, so how can we accurately yet promptly predict them? In this paper we address these two issues. To handle the first one, we use a simple moving average to smooth variation, and then a universal method is presented for different patterns to identify the key events in popularity evolution. To deal with the second one, we extract different types of features that may have an impact on the key events, and then a correlation analysis is conducted in the feature selection step to remove irrelevant and redundant features. The remaining features are used to train a machine learning model. The feature selection step improves prediction accuracy, and in order to emphasize prediction promptness, we design a new evaluation metric which considers both accuracy and promptness to evaluate our prediction task. Experimental and comparative results show the superiority of our prediction solution.

On the role of sparseness in the evolution of modularity in gene regulatory networks

PubMed Central

2018-01-01

Modularity is a widespread property in biological systems. It implies that interactions occur mainly within groups of system elements. A modular arrangement facilitates adjustment of one module without perturbing the rest of the system. Therefore, modularity of developmental mechanisms is a major factor for evolvability, the potential to produce beneficial variation from random genetic change. Understanding how modularity evolves in gene regulatory networks, that create the distinct gene activity patterns that characterize different parts of an organism, is key to developmental and evolutionary biology. One hypothesis for the evolution of modules suggests that interactions between some sets of genes become maladaptive when selection favours additional gene activity patterns. The removal of such interactions by selection would result in the formation of modules. A second hypothesis suggests that modularity evolves in response to sparseness, the scarcity of interactions within a system. Here I simulate the evolution of gene regulatory networks and analyse diverse experimentally sustained networks to study the relationship between sparseness and modularity. My results suggest that sparseness alone is neither sufficient nor necessary to explain modularity in gene regulatory networks. However, sparseness amplifies the effects of forms of selection that, like selection for additional gene activity patterns, already produce an increase in modularity. That evolution of new gene activity patterns is frequent across evolution also supports that it is a major factor in the evolution of modularity. That sparseness is widespread across gene regulatory networks indicates that it may have facilitated the evolution of modules in a wide variety of cases. PMID:29775459

On the role of sparseness in the evolution of modularity in gene regulatory networks.

PubMed

Espinosa-Soto, Carlos

2018-05-01

Modularity is a widespread property in biological systems. It implies that interactions occur mainly within groups of system elements. A modular arrangement facilitates adjustment of one module without perturbing the rest of the system. Therefore, modularity of developmental mechanisms is a major factor for evolvability, the potential to produce beneficial variation from random genetic change. Understanding how modularity evolves in gene regulatory networks, that create the distinct gene activity patterns that characterize different parts of an organism, is key to developmental and evolutionary biology. One hypothesis for the evolution of modules suggests that interactions between some sets of genes become maladaptive when selection favours additional gene activity patterns. The removal of such interactions by selection would result in the formation of modules. A second hypothesis suggests that modularity evolves in response to sparseness, the scarcity of interactions within a system. Here I simulate the evolution of gene regulatory networks and analyse diverse experimentally sustained networks to study the relationship between sparseness and modularity. My results suggest that sparseness alone is neither sufficient nor necessary to explain modularity in gene regulatory networks. However, sparseness amplifies the effects of forms of selection that, like selection for additional gene activity patterns, already produce an increase in modularity. That evolution of new gene activity patterns is frequent across evolution also supports that it is a major factor in the evolution of modularity. That sparseness is widespread across gene regulatory networks indicates that it may have facilitated the evolution of modules in a wide variety of cases.

Patterns of craniofacial integration in extant Homo, Pan, and Gorilla.

PubMed

Polanski, Joshua M; Franciscus, Robert G

2006-09-01

Brain size increased greatly during Pleistocene human evolution, while overall facial and dentognathic size decreased markedly. This mosaic pattern is due to either selective forces that acted uniquely on each functional unit in a modularized, developmentally uncoupled craniofacial complex, or alternatively, selection that acted primarily on one unit, with the other responding passively as part of a coevolved set of ontogenetically and evolutionarily integrated structures. Using conditional independence modeling on homologous linear measurements of the height, breadth, and depth of the cranium in Pan (n = 95), Gorilla (n = 102), and recent Homo (n = 120), we reject the null hypothesis of equal levels of overall cranial integration. While all three groups share the pattern of greater neurocranial integration with distinct separation between the face and neurocranium (modularization), family differences do exist. The apes are more integrated in their entire crania, but display a particularly strong pattern of integration within the facial complex related to prognathism. Modern humans display virtually no facial integration, a pattern which is likely related to their markedly decreased facial projection. Modern humans also differ from their great ape counterparts in being more integrated within the breadth dimension of the cranial vault, likely tied to the increase in brain size and eventual globularity seen in human evolution. That the modern human integration pattern differs from the ancestral African great ape pattern along the inverse neurocranial-facial trend seen in human evolution indicates that this shift in the pattern of integration is evolutionarily significant, and may help to clarify aspects of the current debate over defining modern humans. 2006 Wiley-Liss, Inc.

Three tiers of genome evolution in reptiles

PubMed Central

Organ, Chris L.; Moreno, Ricardo Godínez; Edwards, Scott V.

2008-01-01

Characterization of reptilian genomes is essential for understanding the overall diversity and evolution of amniote genomes, because reptiles, which include birds, constitute a major fraction of the amniote evolutionary tree. To better understand the evolution and diversity of genomic characteristics in Reptilia, we conducted comparative analyses of online sequence data from Alligator mississippiensis (alligator) and Sphenodon punctatus (tuatara) as well as genome size and karyological data from a wide range of reptilian species. At the whole-genome and chromosomal tiers of organization, we find that reptilian genome size distribution is consistent with a model of continuous gradual evolution while genomic compartmentalization, as manifested in the number of microchromosomes and macrochromosomes, appears to have undergone early rapid change. At the sequence level, the third genomic tier, we find that exon size in Alligator is distributed in a pattern matching that of exons in Gallus (chicken), especially in the 101—200 bp size class. A small spike in the fraction of exons in the 301 bp—1 kb size class is also observed for Alligator, but more so for Sphenodon. For introns, we find that members of Reptilia have a larger fraction of introns within the 101 bp–2 kb size class and a lower fraction of introns within the 5–30 kb size class than do mammals. These findings suggest that the mode of reptilian genome evolution varies across three hierarchical levels of the genome, a pattern consistent with a mosaic model of genomic evolution. PMID:21669810

Natural selection and the predictability of evolution in Timema stick insects.

PubMed

Nosil, Patrik; Villoutreix, Romain; de Carvalho, Clarissa F; Farkas, Timothy E; Soria-Carrasco, Víctor; Feder, Jeffrey L; Crespi, Bernard J; Gompert, Zach

2018-02-16

Predicting evolution remains difficult. We studied the evolution of cryptic body coloration and pattern in a stick insect using 25 years of field data, experiments, and genomics. We found that evolution is more difficult to predict when it involves a balance between multiple selective factors and uncertainty in environmental conditions than when it involves feedback loops that cause consistent back-and-forth fluctuations. Specifically, changes in color-morph frequencies are modestly predictable through time ( r 2 = 0.14) and driven by complex selective regimes and yearly fluctuations in climate. In contrast, temporal changes in pattern-morph frequencies are highly predictable due to negative frequency-dependent selection ( r 2 = 0.86). For both traits, however, natural selection drives evolution around a dynamic equilibrium, providing some predictability to the process. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

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.

How is the rate of climatic-niche evolution related to climatic-niche breadth?

PubMed

Fisher-Reid, M Caitlin; Kozak, Kenneth H; Wiens, John J

2012-12-01

The rate of climatic-niche evolution is important to many research areas in ecology, evolution, and conservation biology, including responses of species to global climate change, spread of invasive species, speciation, biogeography, and patterns of species richness. Previous studies have implied that clades with higher rates of climatic-niche evolution among species should have species with narrower niche breadths, but there is also evidence suggesting the opposite pattern. However, the relationships between rate and breadth have not been explicitly analyzed. Here, we examine the relationships between the rate of climatic-niche evolution and climatic-niche breadth using phylogenetic and climatic data for 250 species in the salamander family Plethodontidae, a group showing considerable variation in both rates of climatic-niche evolution and climatic-niche breadths. Contrary to some expectations, we find no general relationship between climatic-niche breadth and the rate of climatic-niche evolution. Climatic-niche breadths for some ecologically important climatic variables considered separately (temperature seasonality and annual precipitation) do show significant relationships with the rate of climatic-niche evolution, but rates are faster in clades in which species have broader (not narrower) niche breadths. In summary, our results show that narrower niche breadths are not necessarily associated with faster rates of niche evolution. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Analyzing endocrine system conservation and evolution.

PubMed

Bonett, Ronald M

2016-08-01

Analyzing variation in rates of evolution can provide important insights into the factors that constrain trait evolution, as well as those that promote diversification. Metazoan endocrine systems exhibit apparent variation in evolutionary rates of their constituent components at multiple levels, yet relatively few studies have quantified these patterns and analyzed them in a phylogenetic context. This may be in part due to historical and current data limitations for many endocrine components and taxonomic groups. However, recent technological advancements such as high-throughput sequencing provide the opportunity to collect large-scale comparative data sets for even non-model species. Such ventures will produce a fertile data landscape for evolutionary analyses of nucleic acid and amino acid based endocrine components. Here I summarize evolutionary rate analyses that can be applied to categorical and continuous endocrine traits, and also those for nucleic acid and protein-based components. I emphasize analyses that could be used to test whether other variables (e.g., ecology, ontogenetic timing of expression, etc.) are related to patterns of rate variation and endocrine component diversification. The application of phylogenetic-based rate analyses to comparative endocrine data will greatly enhance our understanding of the factors that have shaped endocrine system evolution. Copyright © 2016 Elsevier Inc. All rights reserved.

Disparity changes in 370 Ma Devonian fossils: the signature of ecological dynamics?

PubMed

Girard, Catherine; Renaud, Sabrina

2012-01-01

Early periods in Earth's history have seen a progressive increase in complexity of the ecosystems, but also dramatic crises decimating the biosphere. Such patterns are usually considered as large-scale changes among supra-specific groups, including morphological novelties, radiation, and extinctions. Nevertheless, in the same time, each species evolved by the way of micro-evolutionary processes, extended over millions of years into the evolution of lineages. How these two evolutionary scales interacted is a challenging issue because this requires bridging a gap between scales of observation and processes. The present study aims at transferring a typical macro-evolutionary approach, namely disparity analysis, to the study of fine-scale evolutionary variations in order to decipher what processes actually drove the dynamics of diversity at a micro-evolutionary level. The Late Frasnian to Late Famennian period was selected because it is punctuated by two major macro-evolutionary crises, as well as a progressive diversification of marine ecosystem. Disparity was estimated through this period on conodonts, tooth-like fossil remains of small eel-like predators that were part of the nektonic fauna. The study was focused on the emblematic genus of the period, Palmatolepis. Strikingly, both crises affected an already impoverished Palmatolepis disparity, increasing risks of random extinction. The major disparity signal rather emerged as a cycle of increase and decrease in disparity during the inter-crises period. The diversification shortly followed the first crisis and might correspond to an opportunistic occupation of empty ecological niche. The subsequent oriented shrinking in the morphospace occupation suggests that the ecological space available to Palmatolepis decreased through time, due to a combination of factors: deteriorating climate, expansion of competitors and predators. Disparity changes of Palmatolepis thus reflect changes in the structure of the ecological

Disparity Changes in 370 Ma Devonian Fossils: The Signature of Ecological Dynamics?

PubMed Central

Girard, Catherine; Renaud, Sabrina

2012-01-01

Early periods in Earth's history have seen a progressive increase in complexity of the ecosystems, but also dramatic crises decimating the biosphere. Such patterns are usually considered as large-scale changes among supra-specific groups, including morphological novelties, radiation, and extinctions. Nevertheless, in the same time, each species evolved by the way of micro-evolutionary processes, extended over millions of years into the evolution of lineages. How these two evolutionary scales interacted is a challenging issue because this requires bridging a gap between scales of observation and processes. The present study aims at transferring a typical macro-evolutionary approach, namely disparity analysis, to the study of fine-scale evolutionary variations in order to decipher what processes actually drove the dynamics of diversity at a micro-evolutionary level. The Late Frasnian to Late Famennian period was selected because it is punctuated by two major macro-evolutionary crises, as well as a progressive diversification of marine ecosystem. Disparity was estimated through this period on conodonts, tooth-like fossil remains of small eel-like predators that were part of the nektonic fauna. The study was focused on the emblematic genus of the period, Palmatolepis. Strikingly, both crises affected an already impoverished Palmatolepis disparity, increasing risks of random extinction. The major disparity signal rather emerged as a cycle of increase and decrease in disparity during the inter-crises period. The diversification shortly followed the first crisis and might correspond to an opportunistic occupation of empty ecological niche. The subsequent oriented shrinking in the morphospace occupation suggests that the ecological space available to Palmatolepis decreased through time, due to a combination of factors: deteriorating climate, expansion of competitors and predators. Disparity changes of Palmatolepis thus reflect changes in the structure of the ecological

Patterns of host-plant choice in bees of the genus Chelostoma: the constraint hypothesis of host-range evolution in bees.

PubMed

Sedivy, Claudio; Praz, Christophe J; Müller, Andreas; Widmer, Alex; Dorn, Silvia

2008-10-01

To trace the evolution of host-plant choice in bees of the genus Chelostoma (Megachilidae), we assessed the host plants of 35 Palearctic, North American and Indomalayan species by microscopically analyzing the pollen loads of 634 females and reconstructed their phylogenetic history based on four genes and a morphological dataset, applying both parsimony and Bayesian methods. All species except two were found to be strict pollen specialists at the level of plant family or genus. These oligolectic species together exploit the flowers of eight different plant orders that are distributed among all major angiosperm lineages. Based on ancestral state reconstruction, we found that oligolecty is the ancestral state in Chelostoma and that the two pollen generalists evolved from oligolectic ancestors. The distinct pattern of host broadening in these two polylectic species, the highly conserved floral specializations within the different clades, the exploitation of unrelated hosts with a striking floral similarity as well as a recent report on larval performance on nonhost pollen in two Chelostoma species clearly suggest that floral host choice is physiologically or neurologically constrained in bees of the genus Chelostoma. Based on this finding, we propose a new hypothesis on the evolution of host range in bees.

Biological adaptations for functional features of language in the face of cultural evolution.

PubMed

Christiansen, Morten H; Reali, Florencia; Chater, Nick

2011-04-01

Although there may be no true language universals, it is nonetheless possible to discern several family resemblance patterns across the languages of the world. Recent work on the cultural evolution of language indicates the source of these patterns is unlikely to be an innate universal grammar evolved through biological adaptations for arbitrary linguistic features. Instead, it has been suggested that the patterns of resemblance emerge because language has been shaped by the brain, with individual languages representing different but partially overlapping solutions to the same set of nonlinguistic constraints. Here, we use computational simulations to investigate whether biological adaptation for functional features of language, deriving from cognitive and communicative constraints, may nonetheless be possible alongside rapid cultural evolution. Specifically, we focus on the Baldwin effect as an evolutionary mechanism by which previously learned linguistic features might become innate through natural selection across many generations of language users. The results indicate that cultural evolution of language does not necessarily prevent functional features of language from becoming genetically fixed, thus potentially providing a particularly informative source of constraints on cross-linguistic resemblance patterns.

Incorporating evolutionary insights to improve ecotoxicology for freshwater species

USGS Publications Warehouse

Brady, Steven P.; Richardson, Jonathan L.; Kunz, Bethany K.

2017-01-01

Ecotoxicological studies have provided extensive insights into the lethal and sublethal effects of environmental contaminants. These insights are critical for environmental regulatory frameworks, which rely on knowledge of toxicity for developing policies to manage contaminants. While varied approaches have been applied to ecotoxicological questions, perspectives related to the evolutionary history of focal species or populations have received little consideration. Here, we evaluate chloride toxicity from the perspectives of both macroevolution and contemporary evolution. First, by mapping chloride toxicity values derived from the literature onto a phylogeny of macroinvertebrates, fish, and amphibians, we tested whether macroevolutionary relationships across species and taxa are predictive of chloride tolerance. Next, we conducted chloride exposure tests for two amphibian species to assess whether potential contemporary evolutionary change associated with environmental chloride contamination influences chloride tolerance across local populations. We show that explicitly evaluating both macroevolution and contemporary evolution can provide important and even qualitatively different insights from those obtained via traditional ecotoxicological studies. While macroevolutionary perspectives can help forecast toxicological end points for species with untested sensitivities, contemporary evolutionary perspectives demonstrate the need to consider the environmental context of exposed populations when measuring toxicity. Accounting for divergence among populations of interest can provide more accurate and relevant information related to the sensitivity of populations that may be evolving in response to selection from contaminant exposure. Our data show that approaches accounting for and specifically examining variation among natural populations should become standard practice in ecotoxicology.

Major histocompatibility complex class I evolution in songbirds: universal primers, rapid evolution and base compositional shifts in exon 3

PubMed Central

Alcaide, Miguel; Liu, Mark

2013-01-01

Genes of the Major Histocompatibility Complex (MHC) have become an important marker for the investigation of adaptive genetic variation in vertebrates because of their critical role in pathogen resistance. However, despite significant advances in the last few years the characterization of MHC variation in non-model species still remains a challenging task due to the redundancy and high variation of this gene complex. Here we report the utility of a single pair of primers for the cross-amplification of the third exon of MHC class I genes, which encodes the more polymorphic half of the peptide-binding region (PBR), in oscine passerines (songbirds; Aves: Passeriformes), a group especially challenging for MHC characterization due to the presence of large and complex MHC multigene families. In our survey, although the primers failed to amplify exon 3 from two suboscine passerine birds, they amplified exon 3 of multiple MHC class I genes in all 16 species of oscine songbirds tested, yielding a total of 120 sequences. The 16 songbird species belong to 14 different families, primarily within the Passerida, but also in the Corvida. Using a conservative approach based on the analysis of cloned amplicons (n = 16) from each species, we found between 3 and 10 MHC sequences per individual. Each allele repertoire was highly divergent, with the overall number of polymorphic sites per species ranging from 33 to 108 (out of 264 sites) and the average number of nucleotide differences between alleles ranging from 14.67 to 43.67. Our survey in songbirds allowed us to compare macroevolutionary dynamics of exon 3 between songbirds and non-passerine birds. We found compelling evidence of positive selection acting specifically upon peptide-binding codons across birds, and we estimate the strength of diversifying selection in songbirds to be about twice that in non-passerines. Analysis using comparative methods suggest weaker evidence for a higher GC content in the 3rd codon position of

The rule of declining adaptability in microbial evolution experiments

PubMed Central

Couce, Alejandro; Tenaillon, Olivier A.

2015-01-01

One of the most recurrent observations after two decades of microbial evolution experiments regards the dynamics of fitness change. In a given environment, low-fitness genotypes are recurrently observed to adapt faster than their more fit counterparts. Since adaptation is the main macroscopic outcome of Darwinian evolution, studying its patterns of change could potentially provide insight into key issues of evolutionary theory, from fixation dynamics to the genetic architecture of organisms. Here, we re-analyze several published datasets from experimental evolution with microbes and show that, despite large differences in the origin of the data, a pattern of inverse dependence of adaptability with fitness clearly emerges. In quantitative terms, it is remarkable to observe little if any degree of idiosyncrasy across systems as diverse as virus, bacteria and yeast. The universality of this phenomenon suggests that its emergence might be understood from general principles, giving rise to the exciting prospect that evolution might be statistically predictable at the macroscopic level. We discuss these possibilities in the light of the various theories of adaptation that have been proposed and delineate future directions of research. PMID:25815007

The evolution of vertebral formulae in Hominoidea.

PubMed

Thompson, Nathan E; Almécija, Sergio

2017-09-01

Primate vertebral formulae have long been investigated because of their link to locomotor behavior and overall body plan. Knowledge of the ancestral vertebral formulae in the hominoid tree of life is necessary to interpret the pattern of evolution among apes, and to critically evaluate the morphological adaptations involved in the transition to hominin bipedalism. Though many evolutionary hypotheses have been proposed based on living and fossil species, the application of quantitative phylogenetic methods for thoroughly reconstructing ancestral vertebral formulae and formally testing patterns of vertebral evolution is lacking. To estimate the most probable scenarios of hominoid vertebral evolution, we utilized an iterative ancestral state reconstruction approach to determine likely ancestral vertebral counts in apes, humans, and other anthropoid out-groups. All available ape and hominin fossil taxa with an inferred regional vertebral count were included in the analysis. Sensitivity iterations were performed both by changing the phylogenetic position of fossil taxa with a contentious placement, and by changing the inferred number of vertebrae in taxa with uncertain morphology. Our ancestral state reconstruction results generally support a short-backed hypothesis of human evolution, with a Pan-Homo last common ancestor possessing a vertebral formulae of 7:13:4:6 (cervical:thoracic:lumbar:sacral). Our results indicate that an initial reduction in lumbar vertebral count and increase in sacral count is a synapomorphy of crown hominoids (supporting an intermediate-backed hypothesis for the origins of the great ape-human clade). Further reduction in lumbar count occurs independently in orangutans and African apes. Our results highlight the complexity and homoplastic nature of vertebral count evolution, and give little support to the long-backed hypothesis of human evolution. Copyright © 2017 Elsevier Ltd. All rights reserved.

Mitochondrial genome evolution in the Saccharomyces sensu stricto complex.

PubMed

Ruan, Jiangxing; Cheng, Jian; Zhang, Tongcun; Jiang, Huifeng

2017-01-01

Exploring the evolutionary patterns of mitochondrial genomes is important for our understanding of the Saccharomyces sensu stricto (SSS) group, which is a model system for genomic evolution and ecological analysis. In this study, we first obtained the complete mitochondrial sequences of two important species, Saccharomyces mikatae and Saccharomyces kudriavzevii. We then compared the mitochondrial genomes in the SSS group with those of close relatives, and found that the non-coding regions evolved rapidly, including dramatic expansion of intergenic regions, fast evolution of introns and almost 20-fold higher rearrangement rates than those of the nuclear genomes. However, the coding regions, and especially the protein-coding genes, are more conserved than those in the nuclear genomes of the SSS group. The different evolutionary patterns of coding and non-coding regions in the mitochondrial and nuclear genomes may be related to the origin of the aerobic fermentation lifestyle in this group. Our analysis thus provides novel insights into the evolution of mitochondrial genomes.

Evolution under monogamy feminizes gene expression in Drosophila melanogaster.

PubMed

Hollis, Brian; Houle, David; Yan, Zheng; Kawecki, Tadeusz J; Keller, Laurent

2014-03-18

Many genes have evolved sexually dimorphic expression as a consequence of divergent selection on males and females. However, because the sexes share a genome, the extent to which evolution can shape gene expression independently in each sex is controversial. Here, we use experimental evolution to reveal suboptimal sex-specific expression for much of the genome. By enforcing a monogamous mating system in populations of Drosophila melanogaster for over 100 generations, we eliminated major components of selection on males: female choice and male-male competition. If gene expression is subject to sexually antagonistic selection, relaxed selection on males should cause evolution towards female optima. Monogamous males and females show this pattern of feminization in both the whole-body and head transcriptomes. Genes with male-biased expression patterns evolved decreased expression under monogamy, while genes with female-biased expression evolved increased expression, relative to polygamous populations. Our results demonstrate persistent and widespread evolutionary tension between male and female adaptation.

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

PubMed

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

2018-08-01

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

Geography, environment and organismal traits in the diversification of a major tropical herbaceous angiosperm radiation

PubMed Central

2018-01-01

Abstract The generation of plant diversity involves complex interactions between geography, environment and organismal traits. Many macroevolutionary processes and emergent patterns have been identified in different plant groups through the study of spatial data, but rarely in the context of a large radiation of tropical herbaceous angiosperms. A powerful system for testing interrelated biogeographical hypotheses is provided by the terrestrial bromeliads, a Neotropical group of extensive ecological diversity and importance. In this investigation, distributional data for 564 species of terrestrial bromeliads were used to estimate variation in the position and width of species-level hydrological habitat occupancy and test six core hypotheses linking geography, environment and organismal traits. Taxonomic groups and functional types differed in hydrological habitat occupancy, modulated by convergent and divergent trait evolution, and with contrasting interactions with precipitation abundance and seasonality. Plant traits in the Bromeliaceae are intimately associated with bioclimatic differentiation, which is in turn strongly associated with variation in geographical range size and species richness. These results emphasize the ecological relevance of structural-functional innovation in a major plant radiation. PMID:29479409

Early archosauromorph remains from the Permo-Triassic Buena Vista Formation of north-eastern Uruguay

PubMed Central

Velozo, Pablo; Meneghel, Melitta; Piñeiro, Graciela

2015-01-01

The Permo-Triassic archosauromorph record is crucial to understand the impact of the Permo-Triassic mass extinction on the early evolution of the group and its subsequent dominance in Mesozoic terrestrial ecosystems. However, the Permo-Triassic archosauromorph record is still very poor in most continents and hampers the identification of global macroevolutionary patterns. Here we describe cranial and postcranial bones from the Permo-Triassic Buena Vista Formation of northeastern Uruguay that contribute to increase the meagre early archosauromorph record from South America. A basioccipital fused to both partial exoccipitals and three cervical vertebrae are assigned to Archosauromorpha based on apomorphies or a unique combination of characters. The archosauromorph remains of the Buena Vista Formation probably represent a multi-taxonomic assemblage composed of non-archosauriform archosauromorphs and a ‘proterosuchid-grade’ animal. This assemblage does not contribute in the discussion of a Late Permian or Early Triassic age for the Buena Vista Formation, but reinforces the broad palaeobiogeographic distribution of ‘proterosuchid grade’ diapsids in Permo-Triassic beds worldwide. PMID:25737816

Tempo and mode in human evolution.

PubMed Central

McHenry, H M

1994-01-01

The quickening pace of paleontological discovery is matched by rapid developments in geochronology. These new data show that the pattern of morphological change in the hominid lineage was mosaic. Adaptations essential to bipedalism appeared early, but some locomotor features changed much later. Relative to the highly derived postcrania of the earliest hominids, the craniodental complex was quite primitive (i.e., like the reconstructed last common ancestor with the African great apes). The pattern of craniodental change among successively younger species of Hominidae implies extensive parallel evolution between at least two lineages in features related to mastication. Relative brain size increased slightly among successively younger species of Australopithecus, expanded significantly with the appearance of Homo, but within early Homo remained at about half the size of Homo sapiens for almost a million years. Many apparent trends in human evolution may actually be due to the accumulation of relatively rapid shifts in successive species. PMID:8041697

HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC.

PubMed

Wood, Natasha; Bhattacharya, Tanmoy; Keele, Brandon F; Giorgi, Elena; Liu, Michael; Gaschen, Brian; Daniels, Marcus; Ferrari, Guido; Haynes, Barton F; McMichael, Andrew; Shaw, George M; Hahn, Beatrice H; Korber, Bette; Seoighe, Cathal

2009-05-01

The pattern of viral diversification in newly infected individuals provides information about the host environment and immune responses typically experienced by the newly transmitted virus. For example, sites that tend to evolve rapidly across multiple early-infection patients could be involved in enabling escape from common early immune responses, could represent adaptation for rapid growth in a newly infected host, or could represent reversion from less fit forms of the virus that were selected for immune escape in previous hosts. Here we investigated the diversification of HIV-1 env coding sequences in 81 very early B subtype infections previously shown to have resulted from transmission or expansion of single viruses (n = 78) or two closely related viruses (n = 3). In these cases, the sequence of the infecting virus can be estimated accurately, enabling inference of both the direction of substitutions as well as distinction between insertion and deletion events. By integrating information across multiple acutely infected hosts, we find evidence of adaptive evolution of HIV-1 env and identify a subset of codon sites that diversified more rapidly than can be explained by a model of neutral evolution. Of 24 such rapidly diversifying sites, 14 were either i) clustered and embedded in CTL epitopes that were verified experimentally or predicted based on the individual's HLA or ii) in a nucleotide context indicative of APOBEC-mediated G-to-A substitutions, despite having excluded heavily hypermutated sequences prior to the analysis. In several cases, a rapidly evolving site was embedded both in an APOBEC motif and in a CTL epitope, suggesting that APOBEC may facilitate early immune escape. Ten rapidly diversifying sites could not be explained by CTL escape or APOBEC hypermutation, including the most frequently mutated site, in the fusion peptide of gp41. We also examined the distribution, extent, and sequence context of insertions and deletions, and we provide

HIV Evolution in Early Infection: Selection Pressures, Patterns of Insertion and Deletion, and the Impact of APOBEC

PubMed Central

Wood, Natasha; Bhattacharya, Tanmoy; Keele, Brandon F.; Giorgi, Elena; Liu, Michael; Gaschen, Brian; Daniels, Marcus; Ferrari, Guido; Haynes, Barton F.; McMichael, Andrew; Shaw, George M.; Hahn, Beatrice H.; Korber, Bette; Seoighe, Cathal

2009-01-01

The pattern of viral diversification in newly infected individuals provides information about the host environment and immune responses typically experienced by the newly transmitted virus. For example, sites that tend to evolve rapidly across multiple early-infection patients could be involved in enabling escape from common early immune responses, could represent adaptation for rapid growth in a newly infected host, or could represent reversion from less fit forms of the virus that were selected for immune escape in previous hosts. Here we investigated the diversification of HIV-1 env coding sequences in 81 very early B subtype infections previously shown to have resulted from transmission or expansion of single viruses (n = 78) or two closely related viruses (n = 3). In these cases, the sequence of the infecting virus can be estimated accurately, enabling inference of both the direction of substitutions as well as distinction between insertion and deletion events. By integrating information across multiple acutely infected hosts, we find evidence of adaptive evolution of HIV-1 env and identify a subset of codon sites that diversified more rapidly than can be explained by a model of neutral evolution. Of 24 such rapidly diversifying sites, 14 were either i) clustered and embedded in CTL epitopes that were verified experimentally or predicted based on the individual's HLA or ii) in a nucleotide context indicative of APOBEC-mediated G-to-A substitutions, despite having excluded heavily hypermutated sequences prior to the analysis. In several cases, a rapidly evolving site was embedded both in an APOBEC motif and in a CTL epitope, suggesting that APOBEC may facilitate early immune escape. Ten rapidly diversifying sites could not be explained by CTL escape or APOBEC hypermutation, including the most frequently mutated site, in the fusion peptide of gp41. We also examined the distribution, extent, and sequence context of insertions and deletions, and we provide

Correlated evolution between male ejaculate allocation and female remating behaviour in seed beetles (Bruchidae).

PubMed

Katvala, M; Rönn, J L; Arnqvist, G

2008-03-01

Sperm competition theory suggests that female remating rate determines the selective regime that dictates the evolution of male ejaculate allocation. To test for correlated evolution between female remating behaviour and male ejaculate traits, we subjected detailed experimental data on female and male reproductive traits in seven-seed beetle species to phylogenetic comparative analyses. The evolution of a larger first ejaculate was positively correlated with the evolution of a more rapid decline in ejaculate size over successive matings. Further, as predicted by theory, an increase in female remating rate correlated with the evolution of larger male testes but smaller ejaculates. However, an increase in female remating was associated with the evolution of a less even allocation of ejaculate resources over successive matings, contrary to classic sperm competition theory. We failed to find any evidence for coevolution between the pattern of male ejaculate allocation and variation in female quality and we conclude that some patterns of correlated evolution are congruent with current theory, whereas some are not. We suggest that this may reflect the fact that much sperm competition theory does not fully incorporate other factors that may affect the evolution of male and female traits, such as trade-offs between ejaculate expenditure and other competing demands and the evolution of resource acquisition.

Within-Host Evolution of Simian Arteriviruses in Crab-Eating Macaques

PubMed Central

Moncla, Louise H.; Weiler, Andrea M.; Barry, Gabrielle; Weinfurter, Jason T.; Dinis, Jorge M.; Charlier, Olivia; Lauck, Michael; Bailey, Adam L.; Wahl-Jensen, Victoria; Nelson, Chase W.; Johnson, Joshua C.; Caì, Yíngyún; Goldberg, Tony L.; O'Connor, David H.; Jahrling, Peter B.

2016-01-01

ABSTRACT Simian arteriviruses are a diverse clade of viruses infecting captive and wild nonhuman primates. We recently reported that Kibale red colobus virus 1 (KRCV-1) causes a mild and self-limiting disease in experimentally infected crab-eating macaques, while simian hemorrhagic fever virus (SHFV) causes lethal viral hemorrhagic fever. Here we characterize how these viruses evolved during replication in cell culture and in experimentally infected macaques. During passage in cell culture, 68 substitutions that were localized in open reading frames (ORFs) likely associated with host cell entry and exit became fixed in the KRCV-1 genome. However, we did not detect any strong signatures of selection during replication in macaques. We uncovered patterns of evolution that were distinct from those observed in surveys of wild red colobus monkeys, suggesting that these species may exert different adaptive challenges for KRCV-1. During SHFV infection, we detected signatures of selection on ORF 5a and on a small subset of sites in the genome. Overall, our data suggest that patterns of evolution differ markedly among simian arteriviruses and among host species. IMPORTANCE Certain RNA viruses can cross species barriers and cause disease in new hosts. Simian arteriviruses are a diverse group of related viruses that infect captive and wild nonhuman primates, with associated disease severity ranging from apparently asymptomatic infections to severe, viral hemorrhagic fevers. We infected nonhuman primate cell cultures and then crab-eating macaques with either simian hemorrhagic fever virus (SHFV) or Kibale red colobus virus 1 (KRCV-1) and assessed within-host viral evolution. We found that KRCV-1 quickly acquired a large number of substitutions in its genome during replication in cell culture but that evolution in macaques was limited. In contrast, we detected selection focused on SHFV ORFs 5a and 5, which encode putative membrane proteins. These patterns suggest that in

Host and Parasite Evolution in a Tangled Bank.

PubMed

Betts, Alex; Rafaluk, Charlotte; King, Kayla C

2016-11-01

Most hosts and parasites exist in diverse communities wherein they interact with other species, spanning the parasite-mutualist continuum. These additional interactions have the potential to impose selection on hosts and parasites and influence the patterns and processes of their evolution. Yet, host-parasite interactions are almost exclusively studied in species pairs. A wave of new research has incorporated a multispecies community context, showing that additional ecological interactions can alter components of host and parasite fitness, as well as interaction specificity and virulence. Here, we synthesize these findings to assess the effects of increased species diversity on the patterns and processes of host and parasite evolution. We argue that our understanding of host-parasite interactions would benefit from a richer biotic perspective. Copyright © 2016 Elsevier Ltd. All rights reserved.

The evolution of embryonic patterning mechanisms in animals

NASA Technical Reports Server (NTRS)

Wray, G. A.

2000-01-01

Animals exhibit an enormous diversity of life cycles and larval morphologies. The developmental basis for this diversity is not well understood. It is clear, however, that mechanisms of pattern formation in early embryos differ significantly among and within groups of animals. These differences show surprisingly little correlation with phylogenetic relationships; instead, many are correlated with ecological factors, such as changes in life histories. Copyright 2000 Academic Press.

Predicting Key Events in the Popularity Evolution of Online Information

PubMed Central

Fu, Shushen; Fang, Mingzhe; Xu, Wenwen

2017-01-01

The popularity of online information generally experiences a rising and falling evolution. This paper considers the “burst”, “peak”, and “fade” key events together as a representative summary of popularity evolution. We propose a novel prediction task—predicting when popularity undergoes these key events. It is of great importance to know when these three key events occur, because doing so helps recommendation systems, online marketing, and containment of rumors. However, it is very challenging to solve this new prediction task due to two issues. First, popularity evolution has high variation and can follow various patterns, so how can we identify “burst”, “peak”, and “fade” in different patterns of popularity evolution? Second, these events usually occur in a very short time, so how can we accurately yet promptly predict them? In this paper we address these two issues. To handle the first one, we use a simple moving average to smooth variation, and then a universal method is presented for different patterns to identify the key events in popularity evolution. To deal with the second one, we extract different types of features that may have an impact on the key events, and then a correlation analysis is conducted in the feature selection step to remove irrelevant and redundant features. The remaining features are used to train a machine learning model. The feature selection step improves prediction accuracy, and in order to emphasize prediction promptness, we design a new evaluation metric which considers both accuracy and promptness to evaluate our prediction task. Experimental and comparative results show the superiority of our prediction solution. PMID:28046121

Evolution of Courtship Songs in Xenopus : Vocal Pattern Generation and Sound Production.

PubMed

Leininger, Elizabeth C; Kelley, Darcy B

2015-01-01

The extant species of African clawed frogs (Xenopus and Silurana) provide an opportunity to link the evolution of vocal characters to changes in the responsible cellular and molecular mechanisms. In this review, we integrate several robust lines of research: evolutionary trajectories of Xenopus vocalizations, cellular and circuit-level mechanisms of vocalization in selected Xenopus model species, and Xenopus evolutionary history and speciation mechanisms. Integrating recent findings allows us to generate and test specific hypotheses about the evolution of Xenopus vocal circuits. We propose that reduced vocal sex differences in some Xenopus species result from species-specific losses of sexually differentiated neural and neuromuscular features. Modification of sex-hormone-regulated developmental mechanisms is a strong candidate mechanism for reduced vocal sex differences.

Modularity of a leaf moth-wing pattern and a versatile characteristic of the wing-pattern ground plan

PubMed Central

2013-01-01

Background One of the most intriguing questions in evolutionary developmental biology is how an insect acquires a mimicry pattern within its body parts. A striking example of pattern mimicry is found in the pattern diversity of moth and butterfly wings, which is thought to evolve from preexisting elements illustrated by the nymphalid ground plan (NGP). Previous studies demonstrated that individuality of the NGP facilitates the decoupling of associated common elements, leading to divergence. In contrast, recent studies on the concept of modularity have argued the importance of a combination of coupling and decoupling of the constituent elements. Here, we examine the modularity of a mimicry wing pattern in a moth and explore an evolvable characteristic of the NGP. Results This study examined the wings of the noctuid moth Oraesia excavata, which closely resemble leaves with a leaf venation pattern. Based on a comparative morphological procedure, we found that this leaf pattern was formed by the NGP common elements. Using geometric morphometrics combined with network analysis, we found that each of the modules in the leaf pattern integrates the constituent components of the leaf venation pattern (i.e., the main and lateral veins). Moreover, the detected modules were established by coupling different common elements and decoupling even a single element into different modules. The modules of the O. excavata wing pattern were associated with leaf mimicry, not with the individuality of the NGP common elements. For comparison, we also investigated the modularity of a nonmimetic pattern in the noctuid moth Thyas juno. Quantitative analysis demonstrated that the modules of the T. juno wing pattern regularly corresponded to the individuality of the NGP common elements, unlike those in the O. excavata wing pattern. Conclusions This study provides the first evidence for modularity in a leaf mimicry pattern. The results suggest that the evolution of this pattern involves coupling

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.

Convergent and divergent evolution in carnivorous pitcher plant traps.

PubMed

Thorogood, Chris J; Bauer, Ulrike; Hiscock, Simon J

2018-02-01

Contents Summary 1035 I. Introduction 1035 II. Evolution of the pitcher 1036 III. Convergent evolution 1036 IV. Divergent evolution 1038 V. Adaptive radiation and speciation 1040 VI. Conclusions and perspectives 1040 Acknowledgements 1040 References 1040 SUMMARY: The pitcher trap is a striking example of convergent evolution across unrelated carnivorous plant lineages. Convergent traits that have evolved across pitcher plant lineages are essential for trap function, suggesting that key selective pressures are in action. Recent studies have also revealed patterns of divergent evolution in functional pitcher morphology within genera. Adaptations to differences in local prey assemblages may drive such divergence and, ultimately, speciation. Here, we review recent research on convergent and divergent evolution in pitcher plant traps, with a focus on the genus Nepenthes, which we propose as a new model for research into adaptive radiation and speciation. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Convergent evolution of sexual shape dimorphism in Diptera.

PubMed

Bonduriansky, Russell

2006-05-01

Several patterns of sexual shape dimorphism, such as male body elongation, eye stalks, or extensions of the exoskeleton, have evolved repeatedly in the true flies (Diptera). Although these dimorphisms may have evolved in response to sexual selection on male body shape, conserved genetic factors may have contributed to this convergent evolution, resulting in stronger phenotypic convergence than might be expected from functional requirements alone. I compared phenotypic variation in body shape in two distantly related species exhibiting sexually dimorphic body elongation: Prochyliza xanthostoma (Piophilidae) and Telostylinus angusticollis (Neriidae). Although sexual selection appears to act differently on male body shape in these species, they exhibited strikingly similar patterns of sexual dimorphism. Likewise, patterns of within-sex shape variation were similar in the two species, particularly in males: relative elongation of the male head capsule, antenna, and legs was associated with reduced head capsule width and wing length, but was nearly independent of variation in thorax length. However, the two species presented contrasting patterns of static allometry: male sexual traits exhibited elevated allometric slopes in T. angusticollis, but not in P. xanthostoma. These results suggest that a shared pattern of covariation among traits may have channeled the evolution of sexually dimorphic body elongation in these species. Nonetheless, static allometries may have been shaped by species-specific selection pressures or genetic architectures. Copyright 2006 Wiley-Liss, Inc.

Banding patterns and chromosomal evolution in five species of neotropical Teiinae lizards (Squamata: Teiidae).

PubMed

dos Santos, Rodrigo Marques Lima; Pellegrino, Katia Cristina Machado; Rodrigues, Miguel Trefaut; Yonenaga-Yassuda, Yatiyo

2007-11-01

Karyotypes of five species of South American teiid lizards from subfamily Teiinae: Ameiva ameiva, Kentropyx calcarata, K. paulensis, K. vanzoi (2n = 50, all acrocentric), and Cnemidophorus ocellifer (2n = 50, all biarmed), are herein described and compared on the basis of conventional and silver staining, and CBG and RBG banding patterns. Meiotic data are also included. Karyotypes of K. paulensis, K. vanzoi, and C. ocellifer are reported here for the first time. Inter-generic variability in Ag-NORs location was detected with NORs occurring at the end of long arm of pair 1 in K. calcarata, K. paulensis, and K. vanzoi; pair 5 in C. ocellifer and pair 7 in A. ameiva. The location of NORs, along with the karyological differences between A. ameiva and the Central American species (A. auberi), corroboretes the molecular-based hypothesis that the genus Ameiva is paraphyletic. Inter-populational heteromorphism in Ag-NORs size was detected between populations of C. ocellifer. RBG and CBG banding data demonstrated that the biarmed condition of the C. ocellifer chromosomes is due to multiple pericentric inversion events instead of addition of constitutive heterochromatin. Differential-staining techniques used here revealed valuable information about Teiinae karyotypic diversity and made it possible to compare these species, contributing to both the better comprehension of their chromosomal evolution and issues on taxa systematics.