Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation

PLoS Biology, Journal Year: 2019, Volume and Issue: 17(12), P. e3000494 - e3000494

Published: Dec. 4, 2019

Big, time-scaled phylogenies are fundamental to connecting evolutionary processes modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility comparative biologists. To establish a robust timescale all approximately 6,000 living mammals, we developed credible sets capture root-to-tip uncertainty in topology and divergence times. Our "backbone-and-patch" approach tree building applies newly assembled 31-gene supermatrix two levels Bayesian inference: (1) backbone relationships ages among major lineages, using fossil node or tip dating, (2) species-level "patch" with nonoverlapping in-groups each correspond one representative lineage the backbone. Species unsampled DNA either excluded ("DNA-only" trees) imputed within taxonomic constraints branch lengths drawn from local birth–death models ("completed" trees). Joining patches backbones results extant Mammalia branches estimated under same modeling framework, thereby facilitating rate comparisons lineages as disparate marsupials placentals. We compare our previous estimates mammal-wide phylogeny times, finding broadly concordant studies, recent (tip-level) rates speciation more accurately study than "supertree" approaches, which unresolved nodes led branch-length artifacts. Credible mammalian history now available download at http://vertlife.org/phylosubsets, enabling investigations long-standing questions biology.

Language: Английский

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Megaevolutionary dynamics and the timing of evolutionary innovation in reptiles

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: July 3, 2020

The origin of phenotypic diversity among higher clades is one the most fundamental topics in evolutionary biology. However, due to methodological challenges, few studies have assessed rates evolution and disparity across broad scales time understand dynamics behind early new clades. Here, we provide a total-evidence dating approach this problem diapsid reptiles. We find major chronological gaps between periods high (phenotypic molecular) expansion reptile evolution. Importantly, many instances accelerated are detected at body plans, but not concurrent with previously proposed adaptive radiation. Furthermore, strongly heterogenic mark acquisition similarly adapted functional types, snakes marked by highest history.

Language: Английский

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Uncovering the mosaic evolution of the carnivoran skeletal system

Biology Letters, Journal Year: 2024, Volume and Issue: 20(1)

Published: Jan. 1, 2024

The diversity of vertebrate skeletons is often attributed to adaptations distinct ecological factors such as diet, locomotion, and sensory environment. Although the adaptive evolution skull, appendicular skeleton, vertebral column well studied in vertebrates, comprehensive investigations all skeletal components simultaneously are rarely performed. Consequently, we know little how modes differ among components. Here, tested if phylogenetic effects led cranial, regions extant carnivoran skeletons. Using multivariate evolutionary models, found mosaic which only mandible, hindlimb posterior (i.e. last thoracic lumbar) vertebrae showed evidence adaptation towards regimes whereas remaining reflect clade-specific shifts. We hypothesize that decoupled individual may have origination zones morphologies families hierarchies. Overall, our work highlights importance examining multiple ecomorphological analyses. Ongoing integrating fossil palaeoenvironmental record will further clarify deep-time drivers govern see today reveal complexity processes multicomponent systems.

Language: Английский

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Feeding ecology has a stronger evolutionary influence on functional morphology than on body mass in mammals

Evolution, Journal Year: 2020, Volume and Issue: 74(3), P. 610 - 628

Published: Jan. 22, 2020

Ecological specialization is a central driver of adaptive evolution. However, selective pressures may uniquely affect different ecomorphological traits (e.g., size and shape), complicating efforts to investigate the role ecology in generating phenotypic diversity. Comparative studies can help remedy this issue by identifying specific relationships between ecologies morphologies, thus elucidating functionally relevant traits. Jaw shape dietary correlate that offers considerable insight on mammalian evolution, but few have examined influence diet jaw morphology across mammals. To end, I apply phylogenetic comparative methods mandibular measurements data for diverse sample Especially powerful predictors are metrics capture either angular process, which increases with greater herbivory, or length posterior portion jaw, decreases herbivory. The process likely reflects sizes attached muscles produce movements needed grind plant material. Further, examine impact feeding body mass, an oft-used ecological surrogate macroevolutionary studies. Although mass commonly evolutionary shifts it outperformed functional as predictor diet. Body influenced numerous factors beyond diet, be evolutionarily labile relative morphologies. This suggests diversification events initially facilitate at smaller taxonomic temporal scales, sustained will subsequently drive trait partitioning

Language: Английский

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A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses

Systematic Biology, Journal Year: 2021, Volume and Issue: 70(5), P. 922 - 939

Published: Jan. 13, 2021

Phylogenetic trees provide a powerful framework for testing macroevolutionary hypotheses, but it is becoming increasingly apparent that inferences derived from extant species alone can be highly misleading. Trees incorporating living and extinct taxa are needed to address fundamental questions about the origins of diversity disparity has proved challenging generate robust, species-rich phylogenies include large numbers fossil taxa. As result, most studies diversification dynamics continue rely on molecular phylogenies. Here, we extend apply recently developed meta-analytic approach synthesizing previously published phylogenetic infer well-resolved set level, time-scaled hypotheses cetaceans (whales, dolphins, allies). Our sampling $\sim 90$ over 500 species, therefore allow more robust inference dynamics. While scenarios, recover broadly concordant with those inferred they differ in critical ways, notably relative contributions extinction speciation rate shifts driving rapid radiations. The metatree provides immediate route generating higher level opens door re-evaluation only taxa.[Extinction; macroevolution; matrix representation parsimony; morphology; supertree.].

Language: Английский

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A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2019, Volume and Issue: 286(1910), P. 20191502 - 20191502

Published: Sept. 11, 2019

The fish clade Pelagiaria, which includes tunas as its most famous members, evolved remarkable morphological and ecological variety in a setting not generally considered conducive to diversification: the open ocean. Relationships within Pelagiaria have proven elusive due short internodes subtending major lineages suggestive of rapid early divergences. Using novel sequence dataset over 1000 ultraconserved DNA elements (UCEs) for 94 286 species (more than 70% genera), we provide time-calibrated phylogeny this widely distributed clade. Some inferred relationships clear precedents (e.g. monophyly 'core' Stromateoidei, comprising 'Gempylidae' Trichiuridae), but others are unexpected despite strong support Chiasmodontidae +

Language: Английский

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Rapid increase in snake dietary diversity and complexity following the end-Cretaceous mass extinction

PLoS Biology, Journal Year: 2021, Volume and Issue: 19(10), P. e3001414 - e3001414

Published: Oct. 14, 2021

The Cenozoic marked a period of dramatic ecological opportunity in Earth history due to the extinction non-avian dinosaurs as well long-term physiographic changes that created new biogeographic theaters and habitats. Snakes underwent massive diversification during this period, repeatedly evolving novel dietary adaptations prey preferences. evolutionary tempo mode these trophic remain virtually unknown, especially compared with co-radiating lineages birds mammals are simultaneously predators snakes. Here, we assemble dataset on snake diets (34,060 observations 882 species) investigate dynamics multidimensional niche global radiation Our results show per-lineage breadths remained remarkably constant even snakes diversified occupy disparate outposts ecospace. Rapid increases diversity complexity occurred early Cenozoic, overall rate ecospace expansion has slowed through time, suggesting potential response wake end-Cretaceous mass extinction. Explosive bursts innovation followed colonization Nearctic Neotropical realms by group today comprises majority living diversity. indicate repeated transformational shifts ecology important drivers adaptive provide framework for analyzing visualizing evolution complex phenotypes phylogenetic trees.

Language: Английский

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Evolvability and Macroevolution: Overview and Synthesis

Evolutionary Biology, Journal Year: 2022, Volume and Issue: 49(3), P. 265 - 291

Published: July 7, 2022

Abstract Evolvability is best addressed from a multi-level, macroevolutionary perspective through comparative approach that tests for among-clade differences in phenotypic diversification response to an opportunity, such as encountered after mass extinction, entering new adaptive zone, or geographic area. Analyzing the dynamics of clades under similar environmental conditions can (partially) factor out shared external drivers recognize intrinsic evolvability, aiming analog common-garden experiment. Analyses will be most powerful when integrating neontological and paleontological data: determining among extant populations hypothesized generate large-scale, long-term contrasts evolvability clades; observing large-scale clade histories by reflect genetics development observed directly populations. However, many analyses informative on their own, explored this overview. Differences clade-level visualized diversity-disparity plots, which quantify positive negative departures productivity stochastic expectations scaled taxonomic diversification. Factors evidently promote include modularity—when selection aligns with modular structure morphological integration patterns; pronounced ontogenetic changes morphology, allometry multiphase life cycles; genome size; variety evolutionary novelties, also evaluated using lags between acquisition trait diversification, dead-clade-walking patterns may signal loss extrinsic factors excluded. High speciation rates indirectly foster vice versa. Mechanisms are controversial, but higher Cambrian, possibly early history at other times; tropics; and, marine organisms, shallow-water disturbed habitats.

Language: Английский

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Decoupled evolution of the cranium and mandible in carnivoran mammals

Evolution, Journal Year: 2022, Volume and Issue: unknown

Published: July 25, 2022

The relationship between skull morphology and diet is a prime example of adaptive evolution. In mammals, the consists cranium mandible. Although mandible expected to evolve more directly in response dietary changes, regimes may have less influence on because additional sensory brain‐protection functions impose constraints its morphological Here, we tested this hypothesis by comparing evolutionary patterns shape size across 100+ species carnivoran mammals with distinct feeding ecologies. Our results show decoupled modes evolution cranial mandibular shape; follows clade‐based shifts, whereas linked broad regimes. These are consistent previous hypotheses regarding hierarchical carnivorans greater lability respect diet. Furthermore, hypercarnivores, both associated relative prey size. This demonstrates that diversity can be loosely structured craniomandibular within some guilds. suggest mammal shaped mechanisms beyond adaptation alone.

Language: Английский

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When Does Form Reflect Function? Acknowledging and Supporting Ecomorphological Assumptions

Integrative and Comparative Biology, Journal Year: 2019, Volume and Issue: 59(2), P. 358 - 370

Published: May 24, 2019

Ecomorphology is the study of relationships between organismal morphology and ecology. As such, it only way to determine if morphometric data can be used as an informative proxy for ecological variables interest. To achieve this goal, ecomorphology often depends on, or directly tests, assumptions about nature among morphology, performance, We discuss three approaches ecomorphology: morphometry-driven, function-driven, ecology-driven design choices inherent each approach. also identify 10 that underlie ecomorphological research: 4 these are central all studies remaining 6 variably applicable some specific described above. how may impact affect interpretation their findings. point out limitations studies, highlight ways by which we strengthen, validate, eliminate systematic assumptions.

Language: Английский

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