Tree of Life Reveals Clock-Like Speciation and Diversification

Molecular Biology and Evolution, Journal Year: 2015, Volume and Issue: 32(4), P. 835 - 845

Published: March 3, 2015

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

Language: Английский

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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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BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees

Methods in Ecology and Evolution, Journal Year: 2014, Volume and Issue: 5(7), P. 701 - 707

Published: April 22, 2014

Summary Understanding the dynamics of speciation, extinction and phenotypic evolution is a central challenge in evolutionary biology. Here, we present BAMM tools, an r package for analysis visualization macroevolutionary on phylogenetic trees. tools companion to , open‐source program reversible‐jump MCMC analyses diversification trait evolution. Functions operate directly output from program. The oriented towards reconstructing visualizing changes rates through time across clades Bayesian statistical framework. enables users extract credible sets shifts identify histories with maximum posteriori probability. Users can compare fit alternative models using Bayes factors by comparing model posterior probabilities. By providing robust framework quantifying uncertainty dynamics, will facilitate inference complex mixture processes that have shaped distribution species phenotypes tree life.

Language: Английский

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An inverse latitudinal gradient in speciation rate for marine fishes

Nature, Journal Year: 2018, Volume and Issue: 559(7714), P. 392 - 395

Published: July 1, 2018

Language: Английский

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The Phylogenetic Study of Adaptive Zones: Has Phytophagy Promoted Insect Diversification?

The American Naturalist, Journal Year: 1988, Volume and Issue: 132(1), P. 107 - 128

Published: July 1, 1988

Simpson's postulate that rapid diversification follows entrance into a new "adaptive zone" is frequently invoked posteriori for groups of unusual diversity. The can be tested more rigorously by defining an adaptive zone according to ecological criteria, independent particular organisms. adaptive-zone hypothesis predicts if multiple lineages have invaded zone, they should consistently diverse than their (equally old) sister groups, when the latter retain primitive way life. Higher-plant feeding among insects independently defined, repeatedly which profound acceleration rate has been attributed. We quantified evidence this comparing and species diversity as many phytophagous insect current taxonomic allows. A sign test showed significant association with adoption phytophagy. possible artifactual bases trend are discussed provisionally rejected. discuss several biological explanations association, including models phylogenesis either dependent on or role.

Language: Английский

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

Proceedings of the National Academy of Sciences, Journal Year: 2017, Volume and Issue: 114(17)

Published: April 3, 2017

Significance Why do so many species occur in mountains? A popular but little-tested hypothesis is that tectonic uplift creates environmental conditions (new habitats, dispersal barriers, etc.) increase the rate at which resident divide and evolve to form new ones. In China’s Hengduan Mountains region, a biodiversity hotspot uplifted over last 8 million years, this does fact show significant during time, relative for adjacent older mountains, of immigration. The flora thus made up disproportionately evolved within region its uplift, supporting original helping explain prevalence mountains as global hotspots.

Language: Английский

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

Systematic Biology, Journal Year: 2016, Volume and Issue: 65(4), P. 583 - 601

Published: March 25, 2016

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

Language: Английский

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Model Inadequacy and Mistaken Inferences of Trait-Dependent Speciation

Systematic Biology, Journal Year: 2015, Volume and Issue: 64(2), P. 340 - 355

Published: Jan. 19, 2015

Species richness varies widely across the tree of life, and there is great interest in identifying ecological, geographic, other factors that affect rates species proliferation. Recent methods for explicitly modeling relationships among character states, speciation rates, extinction on phylogenetic trees— BiSSE, QuaSSE, GeoSSE, related models—have been used to test hypotheses about state-dependent diversification rates. Here, we document disconcerting ease with which neutral traits are inferred have statistically significant associations rate. We first demonstrate this unfortunate effect a known model assumption violation: shifts rate associated not included model. further show many empirical phylogenies, characters simulated absence exhibit an even higher Type I error rate, indicating method susceptible additional, unknown inadequacies. For evolve slowly, root cause appears be statistical framework does require replicated state diversification. However, spurious between arise lack signal, suggesting pseudoreplication alone cannot fully explain problem. The surprising severity phenomenon suggests trait–diversification reported literature may real. More generally, highlight need diagnosing understanding consequences inadequacy comparative methods.

Language: Английский

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Ecological Opportunity and Adaptive Radiation

Annual Review of Ecology Evolution and Systematics, Journal Year: 2016, Volume and Issue: 47(1), P. 507 - 532

Published: Nov. 1, 2016

The process of adaptive radiation—the proliferation species from a single ancestor and diversification into many ecologically different forms—has been great interest to evolutionary biologists since Darwin. Since the middle last century, ecological opportunity has invoked as potential key understanding when how radiation occurs. Interest in topic accelerated research on experienced resurgence, fueled part by advances phylogenetic approaches studying diversification. Nonetheless, what term actually means, much less it mechanistically leads diversification, is currently debated; whether any predictive value or heuristic useful only for post hoc explanation also remains unclear. Recent recognition that change can occur rapidly timescale commensurate with processes suggests time synthesize study community assembly

Language: Английский

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Evolutionary history of Coleoptera revealed by extensive sampling of genes and species

Nature Communications, Journal Year: 2018, Volume and Issue: 9(1)

Published: Jan. 9, 2018

Abstract Beetles (Coleoptera) are the most diverse and species-rich group of insects, a robust, time-calibrated phylogeny is fundamental to understanding macroevolutionary processes that underlie their diversity. Here we infer divergence times all major lineages Coleoptera by analyzing 95 protein-coding genes in 373 beetle species, including ~67% currently recognized families. The subordinal relationships strongly supported as Polyphaga (Adephaga (Archostemata, Myxophaga)). series superfamilies mostly monophyletic. species-poor Nosodendridae robustly recovered novel position sister Staphyliniformia, Bostrichiformia, Cucujiformia. Our time analyses suggest crown extant beetles occurred ~297 million years ago (Mya) ~64% families originated Cretaceous. Most herbivorous experienced significant increase diversification rate during Cretaceous, thus suggesting rise angiosperms Cretaceous may have been an ‘evolutionary impetus’ driving hyperdiversity beetles.

Language: Английский

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