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120 results for “diversification rate”
Data from: Lizard richness in mainland China is more strongly correlated with energy and climatic stability than with diversification rates
<p><strong><span>Aim</span></strong><span>: Contemporary environmental, historical, and evolutionary factors are increasingly used to decipher the drivers of spatial patterns of species richness. Evidence of such correlations for Chinese reptiles is scarce and poorly understood. We therefore explored the validity of the environmental capacity, historical climatic stability, and diversification rates hypotheses on Chinese lizard richness.</span></p> <p><span><strong>Location</strong>:</span><span> Mainland China</span></p> <p><span><strong>Taxon</strong>:</span><span> Squamata: Sauria</span></p> <p><strong><span>Methods</span></strong><span>: We mapped the distribution ranges of all 237 lizards in mainland China using a combination of different datasets. We used current environmental conditions (ambient energy, environmental productivity, and habitat heterogeneity), historical climate stability indices (long-term: since ~3.3 Ma and short-term: since the Last Glacial Maximum), and mean tip diversification rates to test whether current environmental conditions, historical climate change, and diversification rates drive contemporary richness patterns of lizards in China. We applied piecewise structural equation models (pSEM) to jointly evaluate our hypotheses, considering direct and indirect effects.</span></p> <p><strong><span>Results</span></strong><span>: Chinese lizards showed latitudinal diversity gradients. We found consistent support for contemporary climatic and environmental factors' relationships with richness. Richness was also positively correlated with short-term climatic stability, but less so with long-term stability. Diversification rates were only seldom found to be positively correlated with lizard richness.</span></p> <p><span><strong>Main conclusions</strong>:</span><span> Our results support the</span> <span>environmental capacity and historical climate hypotheses, which link high richness to highly productive warm and stable regions (and low richness to cold and unstable regions). We conclude that post-speciation dispersal and short-term climatic oscillations quickly swamp the long-term signal of diversification rates and climatic fluctuations, creating strong current climate-richness associations.</span></p>
Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates
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Supplementary materials for: Phylogenomics, lineage diversification rates, and the evolution of diadromy in clupeiformes (anchovies, herrings, sardines, and relatives)
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Data from: Estimating diversification rates on incompletely-sampled phylogenies: theoretical concerns and practical solutions
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Data from: Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives
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The role of evolutionary time, diversification rates and dispersal in determining the global diversity of a large radiation of passerine birds
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Data from: Lizard richness in mainland China is more strongly correlated with energy and climatic stability than with diversification rates
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Data from: Rates of niche and phenotype evolution lag behind diversification in a temperate radiation
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Dispersal modes affect Rhamnaceae diversification rates in a differentiated manner
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Shaded habitats drive higher rates of fern diversification
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Wallacean and Melanesian islands promote higher rates of diversification within the global passerine radiation Corvides: Supplementary information
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The departure between constant-rate birth-death and empirically inferred diversification processes
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Comparing diversification rates in lakes, rivers, and the sea
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Anther modes influence diversification rates in the animal-pollinated species-rich Didymocarpoideae
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Commonly used Bayesian diversification methods lead to biologically meaningful differences in branch-specific rates on empirical phylogenies
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Data from: Rapid diversification rates in Amazonian Chrysobalanaceae inferred from plastid genome phylogenetics
<p>We studied the evolutionary history of Chrysobalanaceae with phylogenetic analyses of complete plastid genomes from 156 species to assess the tempo of diversification in the Neotropics and help to unravel the causes of Amazonian plant diversification. These plastid genomes had a mean length of 162,204 base pairs, and the nearly complete DNA sequence matrix, with reliable fossils, was used to estimate a phylogenetic tree. Chrysobalanaceae diversified from 38.9 Mya (95% highest posterior density, 95%HPD: 34.2-43.9 Mya). A single clade containing almost all Neotropical species arose after a single dispersal event from the Palaeotropics into the Amazonian biome <i>c.</i> 29.1 Mya (95%HPD: 25.5-32.6 Mya), with subsequent dispersals into other Neotropical biomes. All Neotropical genera diversified from 10 to 14 Mya, lending clear support to the role of Andean orogeny as a major cause of diversification in Chrysobalanaceae. In particular, the understory genus <i>Hirtella</i> diversified extremely rapidly, producing > 100 species in the last 6 My (95% HPD: 4.9-7.4 My). Our study suggests that a large fraction of the Amazonian tree flora has been assembled <i>in situ</i> within the last 15 My. </p>
Empirical and methodological challenges to the model-based inference of diversification rates in extinct clades
<p>Changes in speciation and extinction rates are key to the dynamics of clade diversification, but attempts to infer them from phylogenies of extant species face challenges. Methods capable of synthesizing information from extant and fossil species have yielded novel insights into diversification rate variation through time, but little is known about their behavior when analyzing entirely extinct clades. Here, we use empirical and simulated data to assess how two popular methods, PyRate and Fossil BAMM, perform in this setting. We inferred the first tip-dated trees for ornithischian dinosaurs, and combined them with fossil occurrence data to test whether the clade underwent an end-Cretaceous decline. We then simulated phylogenies and fossil records under empirical constraints to determine whether macroevolutionary and preservation rates can be teased apart under paleobiologically realistic conditions. We obtained discordant inferences about ornithischian macroevolution including a long-term speciation rate decline (BAMM), mostly flat rates with (PyRate) or without (BAMM) a steep diversification drop, and episodes of implausibly accelerated speciation and extinction (PyRate). Simulations revealed little to no conflation between speciation and preservation, but yielded spuriously correlated speciation and extinction estimates while time-smearing tree-wide shifts (BAMM) or overestimating their number (PyRate). Our results indicate that the small phylogenetic datasets available to vertebrate paleontologists and the assumptions made by current model-based methods combine to hinder inferences about the diversification of extinct clades. We provide guidelines for interpreting the results of the existing approaches in light of their limitations, and suggest how the latter may be mitigated.</p>
Fast and accurate estimation of species-specific diversification rates using data augmentation
Diversification rates vary across species as a response to various factors, including environmental conditions and species-specific features. Phylogenetic models that allow accounting for and quantifying this heterogeneity in diversification rates have proven particularly useful for understanding clades diversification. Recently, we introduced the cladogenetic diversification rate shift model (ClaDS), which allows inferring subtle rate variations across lineages. Here we present a new inference technique for this model that considerably reduces computation time through the use of data augmentation and provide an implementation of this method in Julia. In addition to drastically reducing computation time, this new inference approach provides a posterior distribution of the augmented data, that is the tree with extinct and unsampled lineages as well as associated diversification rates. In particular, this allows extracting the distribution through time of both the mean rate and the number of lineages. We assess the statistical performances of our approach using simulations and illustrate its application on the entire bird radiation.
Data from: Diversification rates and phenotypic evolution in venomous snakes (Elapidae)
The relationship between rates of diversification and of body size change (a common proxy for phenotypic evolution) was investigated across Elapidae, the largest radiation of highly venomous snakes. Time-calibrated phylogenetic trees for 175 species of elapids (more than 50% of known taxa) were constructed using seven mitochondrial and nuclear genes. Analyses using these trees revealed no evidence for a link between speciation rates and changes in body size. Two clades (Hydrophis, Micrurus) show anomalously high rates of diversification within Elapidae, yet exhibit rates of body size evolution almost identical to the general elapid 'background' rate. Although correlations between speciation rates and rates of body size change exist in certain groups (e.g. ray-finned fishes, passerine birds), the two processes appear to be uncoupled in elapid snakes. There is also no detectable shift in diversification dynamics associated with the colonization of Australasia, which is surprising given that elapids appear to be the first clade of venomous snakes to reach the continent.
Data from: Inflation of molecular clock rates and dates: molecular phylogenetics, biogeography, and diversification of a global cicada radiation from Australasia (Hemiptera: Cicadidae: Cicadettini)
Dated phylogenetic trees are important for studying mechanisms of diversification, and molecular clocks are important tools for studies of organisms lacking good fossil records. However, studies have begun to identify problems in molecular clock dates caused by uncertainty of the modeled molecular substitution process. Here we explore Bayesian relaxed-clock molecular dating while studying the biogeography of ca. 200 species from the global cicada tribe Cicadettini. Because the available fossils are few and uninformative, we calibrate our trees in part with a cytochrome oxidase I (COI) clock prior encompassing a range of literature estimates for arthropods. We show that tribe-level analyses calibrated solely with the COI clock recover extremely old dates that conflict with published estimates for two well-studied New Zealand subclades within Cicadettini. Additional subclade analyses suggest that COI relaxed-clock rates and maximum-likelihood branch lengths become inflated relative to EF-1α intron and exon rates and branch lengths as clade age increases. We present corrected estimates derived from (1) an extrapolated EF-1α exon clock derived from COI-calibrated analysis within the largest New Zealand subclade, (2) post-hoc scaling of the tribe-level chronogram using results from subclade analyses, and (3) exploitation of a geological calibration point associated with New Caledonia. We caution that considerable uncertainty is generated due to dependence of substitution estimates on both the taxon sample and the choice of model, including gamma category number and the choice of empirical versus estimated base frequencies. Our results suggest that diversification of the tribe Cicadettini commenced in the early- to mid-Cenozoic and continued with the development of open, arid habitats in Australia and worldwide. We find that Cicadettini is a rare example of a global terrestrial animal group with an Australasian origin, with all non-Australasian genera belonging to two distal clades. Within Australia, we show that Cicadettini is more widely distributed than any other cicada tribe, diverse in temperate, arid and monsoonal habitats, and nearly absent from rainforests. We comment on the taxonomic implications of our findings for thirteen cicada genera.
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Allen Brain Atlas
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OpenNeuro
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