Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

Green, Edward; Braun, Edward L.; Armstrong, Joel; Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Vandewege, Michael W.; John, John A. St; Capella-Gutierrez, Salvador; Castoe, Todd A.; Kern, Colin; Fujita, Matthew K.; Opazo, Juan C.; Jurka, Jerzy; Kojima, Kenji; Caballero, Juan; Hubley, Robert; Smit, Arian F. A.; Platt, Roy N.; Lavoie, Christine A.; Ramakodi, Meganathan P.; Finger, John W.; Suh, Alexander; Isberg, Sally R.; Miles, Lee G.; Chong, Amanda Y; Jaratlerdsiri, Weerachai; Gongora, Jaime; Moran, C.; Iriarte, Andrés; McCormack, John E.; Burgess, Shane C.; Edwards, Scott V.; Lyons, Eric; Williams, Christina L.; Breen, Matthew; Howard, Jason T.; Gresham, Cathy; Peterson, Daniel G.; Schmitz, Juergen; Pollock, David D.; Haussler, David; Triplett, Eric W.; 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.

doi:10.1126/science.1254449

Cited by 320 publications

(359 citation statements)

References 176 publications

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“…In particular, because PSMC is applied to a single diploid genome, it has been used to infer population size histories in numerous species for which one or more genome sequences are available, in many cases finding support for large changes in population size (Groenen et al 2012;Albert et al 2013;Prado-Martinez et al 2013;Zhan et al 2013;Freedman et al 2014;Green et al 2014;Wallberg et al 2014;Auton et al 2015;Lamichhaney et al 2015). Our findings suggest that natural selection may alter the shape of, and inflate the degree of change in, these inferred histories.…”

Section: Discussionmentioning

confidence: 81%

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

2016

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The availability of large-scale population genomic sequence data has resulted in an explosion in efforts to infer the demographic histories of natural populations across a broad range of organisms. As demographic events alter coalescent genealogies, they leave detectable signatures in patterns of genetic variation within and between populations. Accordingly, a variety of approaches have been designed to leverage population genetic data to uncover the footprints of demographic change in the genome. The vast majority of these methods make the simplifying assumption that the measures of genetic variation used as their input are unaffected by natural selection. However, natural selection can dramatically skew patterns of variation not only at selected sites, but at linked, neutral loci as well. Here we assess the impact of recent positive selection on demographic inference by characterizing the performance of three popular methods through extensive simulation of data sets with varying numbers of linked selective sweeps. In particular, we examined three different demographic models relevant to a number of species, finding that positive selection can bias parameter estimates of each of these models-often severely. We find that selection can lead to incorrect inferences of population size changes when none have occurred. Moreover, we show that linked selection can lead to incorrect demographic model selection, when multiple demographic scenarios are compared. We argue that natural populations may experience the amount of recent positive selection required to skew inferences. These results suggest that demographic studies conducted in many species to date may have exaggerated the extent and frequency of population size changes.KEYWORDS population genetics; positive selection; demographic inference T HE widespread availability of population genomic data has spurred a new generation of studies aimed at understanding the histories of natural populations from a host of model and nonmodel organisms alike. In particular, genomescale variation data allows for inference of demographic factors such as population size changes, the timing and ordering of population splits, migration rates between populations, and the founding of admixed populations (Pool et al. 2010;Pickrell and Pritchard 2012;Sousa and Hey 2013). Such efforts can refine our picture of demographic events inferred from the archaeological record (e.g., Fagundes et al. 2007;Goebel et al. 2008), or reveal such events in species where no archaeological data are available, and can aid conservation efforts by complementing census data (e.g., Hájková et al. 2007;Garrick et al. 2015).Population genomic data sets are well suited for this task simply because demographic changes leave their mark on patterns of genetic variation. Recent population growth, for example, will result in an excess of rare variation compared to equilibrium expectations (Fu 1997), while population contraction will result in an excess of intermediate frequency alleles (Maruyama and Fuerst 198...

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Section: Discussionmentioning

confidence: 81%

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

2016

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“…Our results also support early (pre-genome) inferences that crocodilian and turtle genomes contained minimal microsatellite landscapes (Shedlock et al 2007). Despite deep divergences among lineages sampled, we found that all crocodilian species contain nearly identical microsatellite landscapes, which further emphasizes the relatively slow rates of molecular evolution in crocodilians -thought to be among the slowest of all vertebrate lineages (Green et al 2014). …”

Section: Divergent Patterns Of Microsatellite Composition In Reptiliamentioning

confidence: 89%

Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution

Adams

Blackmon

Reyes-Velasco

et al. 2016

Genome

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Abstract:The evolutionary dynamics of simple sequence repeats (SSRs or microsatellites) across the vertebrate tree of life remain largely undocumented and poorly understood. In this study, we analyzed patterns of genomic microsatellite abundance and evolution across 71 vertebrate genomes. The highest abundances of microsatellites exist in the genomes of ray-finned fishes, squamate reptiles, and mammals, while crocodilian, turtle, and avian genomes exhibit reduced microsatellite landscapes. We used comparative methods to infer evolutionary rates of change in microsatellite abundance across vertebrates and to highlight particular lineages that have experienced unusually high or low rates of change in genomic microsatellite abundance. Overall, most variation in microsatellite content, abundance, and evolutionary rate is observed among major lineages of reptiles, yet we found that several deeply divergent clades (i.e., squamate reptiles and mammals) contained relatively similar genomic microsatellite compositions. Archosauromorph reptiles (turtles, crocodilians, and birds) exhibit reduced genomic microsatellite content and the slowest rates of microsatellite evolution, in contrast to squamate reptile genomes that have among the highest rates of microsatellite evolution. Substantial branch-specific shifts in SSR content in primates, monotremes, rodents, snakes, and fish are also evident. Collectively, our results support multiple major shifts in microsatellite genomic landscapes among vertebrates.Key words: comparative genomics, microsatellite seeding, repeat elements, tandem repeats, simple sequence repeats.Résumé : La dynamique évolutive des séquences simples répétées (SSR ou microsatellites) au sein des vertébrés demeure largement non-documentée et mal connue. Dans ce travail, les auteurs ont analysé l'abondance et l'évolution des microsatellites chez 71 génomes de vertébrés. Les abondances de microsatellites les plus grandes ont été rencontrées au sein des génomes des poissons dotés de nageoires à rayons, des reptiles à écailles et des mammifères, tandis que les génomes des crocodiliens, des tortues et des oiseaux présentaient le moins de microsatellites. Les auteurs ont employé des méthodes comparatives pour inférer les taux de changements évolutifs en matière d'abondance des microsatellites parmi les vertébrés et pour mettre en évidence des lignages qui ont connu des taux exceptionnellement élevés ou faibles. Globalement, la majeure partie de la variation en matière de contenu, d'abondance et de taux d'évolution des microsatellites a été observée au sein des grands groupes de reptiles, et pourtant, les auteurs ont noté que certains clades très distants (p. ex. les reptiles à écailles et les mammifères) présentaient des compositions génomiques semblables en matière de microsatellites. Les reptiles archosauromorphes (tortues, crocodiliens et oiseaux) affichaient une teneur réduite en microsatellites et les plus faibles taux évolutifs au sein des microsatellites, tandis que les génomes des reptiles à écailles avai...

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“…They do not constitute a monophyletic group, since some reptiles are more closely related to birds than they are to other reptiles (Green et al, 2014). There are many groups that are now extinct, in some cases due to mass extinction events: pterosaurs, plesiosaurs, ornithischians, sauropods, many theropods, and squamates (e.g., mosasaurids) are examples (Benton, 2014).…”

Section: Reptiles: Unpopular Players In Ecological Processesmentioning

confidence: 99%

The Plight of Reptiles as Ecological Actors in the Tropics

Miranda

Everton²

2017

Front. Ecol. Evol.

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Earth's tropical ecosystems have witnessed several extinctions and a dramatic reduction of the range and abundance of large reptile species, which is directly related to the rise of early and modern humans. The occurrence of such extinctions, range reduction, species loss, and the consequences for several paramount ecosystem processes are poorly documented compared to other large vertebrate species. Here, I reviewed the literature on the ecological processes performed by large tropical reptile species and their human-induced widespread demise in order to determine knowledge gaps and encourage a paradigm shift in understanding on the interactiveness of such species. The interactions and species involved indicate that large abundant reptiles in the tropics are important in ecological processes, and can consequently have an important role in ecosystem function through gene dispersal, nutrient cycling, trophic action, and ecosystem engineering. These important interactions performed by reptiles are not solely performed by few species, or geographically restricted to islands, but instead present a pattern that repeatedly occurs in large reptiles distributed over tropical ecosystems. The observed tendency of reptiles to be tightly involved in these ecological interactions has important implications for the ecology of tropical ecosystems. Lost and current ecological processes performed by large reptiles may be orders of magnitude higher than what is currently perceived, and the misleading baseline of those processes must be addressed otherwise we risk losing species and services that are dependent of such interactions. To fix this bias I suggest: (a) Increase information spreading about Pleistocene-Holocene reptile extinctions using popular media; (b) Improved exchange between the research field of megafauna effects in ecosystems and herpetologists working with large reptiles; (c) Increase research effort on anthropogenic reptile extinctions and their potential to predict future losses; (d) Address the knowledge gaps, as human-reptile conflict, chelonian seed dispersal and nutrient movement; (e) Increase quantitative research on large reptile population ecology, density, and abundance. (f) address the potentially present or lost ecosystem effects of extant and extinct reptile species. Although the importance of reptiles in most tropical ecosystems has been perceived as negligible, this study shows that this may be a misleading paradigm.

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Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

Cited by 320 publications

References 176 publications

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution

The Plight of Reptiles as Ecological Actors in the Tropics

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