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120 results for “diversification rate”
Data from: Diversification rates have no effect on the convergent evolution of foraging strategies in the most speciose genus of bats, Myotis
<p>Adaptive radiations are defined as rapid diversification with phenotypic innovation led by colonization to new environments. Notably, adaptive radiations can occur in parallel when habitats with similar selective pressures are accessible promoting convergent adaptions. While convergent evolution appears to be a common process, it is unclear what are the main drivers leading the reappearance of morphologies or ecological roles. We explore this question in <i>Myotis</i> bats, the only Chiropteran genus with a worldwide distribution. Three foraging strategies –gleaning, trawling, and aerial netting– repeatedly evolved in several regions of the world, each linked to characteristic morphologies recognized as ecomorphs. Phylogenomic, morphometric, and comparative approaches were adopted to investigate convergence of such foraging strategies and skull morphology as well as factors that explain diversification rates. Genomic and morphometric data were analyzed from ~80% extant taxa. Results confirm that the ecomorphs evolved multiple times, with trawling evolving more often and foliage gleaning most recently. Skull morphology does not reflect common ancestry, evolves convergently with foraging strategy. While diversification rates have been roughly constant across the genus, speciation rates are area-dependent in taxa with temperate distributions. Results suggest that in this species-rich group of bats, first, stochastic processes have led divergence into multiple lineages. Then, natural selection in similar niches has promoted repeated adaptation of phenotypes and foraging strategies. <i>Myotis</i> bats are thus a remarkable case of ecomorphological convergence and an emerging model system for investigating the genomic basis of parallel adaptive radiation.</p>
Data from Evidence for elevated diversification rate associated with the evolution of active motility in diatoms
<p>These are data files for Evidence for elevated diversification rate associated with the evolution of active motility in diatoms</p>
Rapid in situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales
<p>The macroevolutionary processes that have shaped biodiversity across the temperate realm remain poorly understood and may have resulted from evolutionary dynamics related to diversification rates, dispersal rates, and colonization times, closely coupled with Cenozoic climate change.</p> <p>We integrated phylogenomic, environmental ordination, and macroevolutionary analyses for the cosmopolitan angiosperm family Rhamnaceae to disentangle the evolutionary processes that have contributed to high species diversity within and across temperate biomes.</p> <p>Our results show independent colonization of environmentally similar but geographically separated temperate regions mainly during the Oligocene, consistent with the global expansion of temperate biomes. High global, regional, and local temperate diversity was the result of high <em>in</em> <em>situ</em> diversification rates, rather than high immigration rates or accumulation time, except for Southern China, which was colonized much earlier than other regions. The relatively common lineage dispersals out of temperate hotspots highlights strong source-sink dynamics across the cosmopolitan distribution of Rhamnaceae.</p> <p>The proliferation of temperate environments since the Oligocene may have provided the ecological opportunity for rapid <em>in</em> <em>situ</em> diversification of Rhamnaceae across the temperate realm. Our study illustrates the importance of high <em>in</em> <em>situ</em><strong> </strong>diversification rates for the establishment of modern temperate biomes and biodiversity hotspots across spatial scales.</p>
Exceptions to the rule: Relative roles of time, diversification rates and regional energy in shaping the inverse latitudinal diversity gradient
<p><strong>Aim</strong>: Inverse latitudinal diversity gradients (i-LDG), whereby regional richness peaks outside the tropics, have rarely been investigated and their causes remain unclear. Here, we investigate three prominent explanations, postulating that species-rich regions have had (1) longer time to accumulate species, (2) faster diversification, and (3) more energy to support more diverse communities. These mechanisms have been shown to explain the tropical megadiversity, and we examine whether they can also explain i-LDG.</p> <p><strong>Location</strong>: Global</p> <p><strong>Time period</strong>: Contemporary</p> <p><strong>Major taxa studied</strong>: Amphibians, birds, mammals </p> <p><strong>Methods</strong>: We estimated the time for species accumulation, regional diversification rates, and regional energy for six tetrapod taxa (≈ 800 species). Then, we quantified the relative effects and interactions among these three classes of variables, using variance partitioning, and confirmed the results across alternative metrics for time (community phylometrics and BioGeoBEARS), diversification rates (BAMM and DR), and regional energy (past and current temperature, productivity).</p> <p><strong>Results</strong>: While regional richness across each of the six taxa peaked in the temperate region, it varied markedly across hemispheres and continents. The effects of time, diversification rates, and regional energy varied greatly from one taxon to another, but high diversification rates generally emerged as the best predictor of high regional richness. The effects of time and regional energy were limited, with the exception of salamanders and cetaceans. </p> <p><strong>Main conclusions</strong>: Together, our results indicate that the causes of i-LDG are highly taxon-specific. Consequently, large-scale richness gradients might not have a universal explanation and different causal pathways might converge on similar gradients. Moreover, regional diversification rates might vary dramatically between similar environments and, depending on the taxon, regional richness might or might not depend on the time for species accumulation. Together, these results underscore the complexity behind the formation of richness gradients, which might involve a symphony of variations on the interplay of time, diversification rates, and regional energy.</p>
Fig. 3 in Diversification rates in Tardigrada indicate a decreasing tempo of lineage splitting regardless of reproductive mode
Fig. 3 The negative relation between values of γ statistics and the number of entities based on which they were calculated. Circles indicate Tardigrada; triangles indicate Rotifera; black indicates asexual reproduction; white indicates sexual reproduction
Fig. 2 in Diversification rates in Tardigrada indicate a decreasing tempo of lineage splitting regardless of reproductive mode
Fig. 2 Bayesian phylogenetic reconstructions for three distinct evolutionary lineages of Tardigrada with respective lineage-through-time plots. The trees were calculated based on the reduced datasets with singular sequence representing a given species/entity delimited in this study with multiple DNA taxonomy approaches (see the "Mate-
Data for: Global diversity patterns are explained by diversification rates and dispersal at ancient, not shallow, timescales
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Data from: Diversification rates have no effect on the convergent evolution of foraging strategies in the most speciose genus of bats, Myotis
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Rapid in situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales
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Exceptions to the rule: Relative roles of time, diversification rates and regional energy in shaping the inverse latitudinal diversity gradient
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Female dewlap ornaments are evolutionarily labile and associated with increased influence diversification rates in Anolis lizards
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Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates
<p>As species richness varies along the tree of life, there is a great interest in identifying factors that affect the rates by which lineages speciate or go extinct. To this end, theoretical biologists have developed a suit of phylogenetic comparative methods that aim to identify where shifts in diversification rates had occurred along a phylogeny and whether they are associated with some traits. Using these methods, numerous studies have predicted that speciation and extinction rates vary across the tree of life. In this study we show that asymmetric rates of sequence evolution rates lead to systematic biases in the inferred phylogeny, which in turn lead to erroneous inferences regarding lineage diversification patterns. The results demonstrate that as the asymmetry in sequence evolution rates increases, so does the tendency to select more complicated models that include the possibility of diversification rate shifts. These results thus suggest that any inference regarding shifts in diversification pattern should be treated with great caution, at least until any biases regarding the molecular substitution rate have been ruled out.</p>
The role of evolutionary time, diversification rates and dispersal in determining the global diversity of a large radiation of passerine birds
<p><span><span><span><span><span><span><span><span><span><span><span><b>Aim</b>: Variation in species diversity among different geographic areas may result from differences in speciation and extinction rates, immigration and time for diversification. An area with high species diversity may be the result of a high net diversification rate, multiple immigration events from adjacent regions,anda long time available for the accumulation of species (know as the "time-for-speciation effect"). Here, we examine the relative importance of the three aforementionedprocesses in shaping the geographic diversity patterns of a large radiation of passerine birds.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Location</b>: Global</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Time period</b>: Early Miocene to present</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Major taxa studied</b>: Babblers (Aves: Passeriformes)</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Methods</b>: Using a comprehensive phylogeny of extant species (~90% sampled) and distributions of the world's babblers, we reconstructed their biogeographic history and analysed the diversification dynamics. We examined how species richness correlates with the timing of regional colonization, the number of immigration events and the rate of speciation within all 13 geographic distribution regions.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Results</b>: We found thatbabblers likely originated in the Sino-Himalayan Mountains (SHM) in the early Miocene, suggesting a long time for diversification and species accumulation within the SHM. Regression analyses showed the regional diversity of babblers can be well explained by the timing of the first colonization within of these areas, while differences in rates of speciation or immigration have far weaker effects. Nonetheless, the rapid speciation of <i>Zosterops</i>during the Pleistocene has accounted for the increased diversification and accumulation of species in the oceanic islands.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Main conclusions</b>: Our results suggest that the global diversity patterns of babblers have predominantly been shaped by the time-for-speciation effect. Our findings also support an origin centred in tropical and subtropical parts of the SHM, with a cradle of recent diversification in the oceanic islands of the Indo-Pacific region, which provides new insights into the generation of global biodiversity hotspots.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Estimating diversification rates on incompletely-sampled phylogenies: theoretical concerns and practical solutions
<p>Molecular phylogenies are a key source of information about the tempo and mode of species diversification. However, most empirical phylogenies do not contain representatives of all species, such that diversification rates are typically estimated from incompletely sampled data. Most researchers recognize that incomplete sampling can lead to biased rate estimates, but the statistical properties of methods for accommodating incomplete sampling remain poorly known. In this point of view, we demonstrate theoretical concerns with the widespread use of analytical sampling corrections for sparsely sampled phylogenies of higher taxonomic groups. In particular, corrections based on "sampling fractions" can lead to low statistical power to infer rate variation when it is present, depending on the likelihood function used for inference. In the extreme, the sampling fraction correction can lead to spurious patterns of diversification that are driven solely by unbalanced sampling across the tree in concert with low overall power to infer shifts. Stochastic polytomy resolution provides an alternative to sampling fraction approaches that avoids some of these biases. We show that stochastic polytomy resolvers can greatly improve the power of common analyses to estimate shifts in diversification rates. We introduce a new stochastic polytomy resolution method (TACT: Taxonomic Addition for Complete Trees) that uses birth-death-sampling estimators across an ultrametric phylogeny to estimate branching times for unsampled taxa, with taxonomic information to compatibly place new taxa onto a backbone phylogeny. We close with practical recommendations for diversification inference under several common scenarios of incomplete sampling.</p>
Data from: Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives
Background: Silkmoths and their relatives constitute the ecologically and taxonomically diverse superfamily Bombycoidea, which includes some of the most charismatic species of Lepidoptera. Despite displaying spectacular forms and diverse ecological traits, relatively little attention has been given to understanding their evolution and drivers of their diversity. To begin to address this problem, we created a new Bombycoidea-specific Anchored Hybrid Enrichment (AHE) probe set and sampled up to 571 loci for 117 taxa across all major lineages of the Bombycoidea, with a newly developed DNA extraction protocol that allows Lepidoptera specimens to be readily sequenced from pinned natural history collections.Results The well-supported tree was overall consistent with prior morphological and molecular studies, although some taxa (e.g., the bombycid, Arotros Schaus) were misplaced and here formally transferred to Apatelodidae. We identified important evolutionary patterns (e.g., morphology, biogeography, and differences in speciation and extinction), and our analysis of diversification rates highlights the stark increases that exist within the Sphingidae (hawkmoths) and Saturniidae (wild silkmoths).Conclusions Our study establishes a backbone for future evolutionary, comparative, and taxonomic studies of Bombycoidea. We postulate that the rate shifts identified are due to the well-documented bat-moth "arms race". Our research highlights the flexibility of AHE to generate genomic data from a wide range of museum specimens, both age and preservation method, and will allow researchers to tap into the wealth of biological data residing in natural history collections around the globe.
Dispersal modes affect Rhamnaceae diversification rates in a differentiated manner
<p><span>The evolution of dispersal modes has been proposed to promote the diversification of angiosperms. However, little is known about the relative impact of different dispersal modes on plant diversification. We test the association between dispersal modes and diversification rates using Rhamnaceae, the cosmopolitan buckthorn family, as a model. </span><span>We found that species with diplochory have the highest diversification rates followed by those with myrmecochory and ballistic dispersal, while lineages dispersed by vertebrates and wind have relatively low diversification rates. The difference in diversification rates may be closely linked to the difference in dispersal distance and ecological interactions implied by each dispersal mode. Species that disperse over larger geographic distances may have much higher speciation rates due to the increased chance of establishing isolated populations due to geological barriers or habitat fragmentation. However, long-distance dispersal may also increase the chance of extinction. In contrast, species with short-distance dispersal modes may have low speciation rates. Complex interactions with the surrounding environment may, however, impact diversification rates positively by increasing plant survival and reproductive success. </span></p>
Wallacean and Melanesian islands promote higher rates of diversification within the global passerine radiation Corvides: Supplementary information
<p class="MsoNormal"><span>The complex island archipelagoes of Wallacea and Melanesia have provided empirical data behind integral theories in evolutionary biology, including allopatric speciation and island biogeography. Yet, questions regarding the relative impact of the layered biogeographic barriers, such as deep-water trenches and isolated island systems, on faunal diversification remain underexplored. One such barrier is Wallace's Line, a significant biogeographic boundary that largely separates Australian and Asian biodiversity. To assess the relative roles of biogeographic barriers—specifically isolated island systems and Wallace's Line—we investigated the tempo and mode of diversification in a diverse avian radiation, Corvides (Crows and Jays, Birds-of-paradise, Vangas, and allies). We combined a genus-level dataset of thousands of ultraconserved elements (UCEs) and a species-level, 12-gene Sanger sequence matrix to produce a well-resolved supermatrix tree that we leveraged to explore the group's historical biogeography and effects of biogeographic barriers on their macroevolutionary dynamics. The tree is well-resolved and differs substantially from what has been used extensively for past comparative analyses within this group. We confirmed that Corvides, and its major constituent clades, arose in Australia and a burst of dispersal west across Wallace's Line occurred after the uplift of Wallacea during the mid-Miocene. We found that dispersal across this biogeographic barrier were generally rare, though westward dispersals were two times more frequent than eastward dispersals. Wallacea's central position between Sundaland and Sahul no doubt acted as a bridge for island-hopping dispersal out of Australia, across Wallace's Line, to colonize the rest of Earth. In addition, we found that the complex island archipelagos east of Wallace's Line harbor the highest rates of net diversification and are a substantial source of colonists to continental systems on both sides of this biogeographic barrier. Our results support emerging evidence that island systems, particularly the geologically complex archipelagoes of the Indo-pacific, are drivers of species diversification.<br></span></p>
Data from: Rates of niche and phenotype evolution lag behind diversification in a temperate radiation
Environmental change can create opportunities for increased rates of lineage diversification, but continued species accumulation has been hypothesized to lead to slowdowns via competitive exclusion and niche partitioning. Such density-dependent models imply tight linkages between diversification and trait evolution, but there are plausible alternative models. Little is known about the association between diversification and key ecological and phenotypic traits at broad phylogenetic and spatial scales. Do trait evolutionary rates coincide with rates of diversification, are there lags among these rates, or is diversification niche-neutral? To address these questions, we combine a deeply sampled phylogeny for a major flowering plant clade-Saxifragales-with phenotype and niche data to examine temporal patterns of evolutionary rates. The considerable phenotypic and habitat diversity of Saxifragales is greatest in temperate biomes. Global expansion of these habitats since the mid-Miocene provided ecological opportunities that, with density-dependent adaptive radiation, should result in simultaneous rate increases for diversification, niche, and phenotype, followed by decreases with habitat saturation. Instead, these rates have significantly different timings, with increases in diversification occurring at the mid-Miocene Climatic Optimum (~15 mya), followed by increases in niche and phenotypic evolutionary rates by ~5 mya; all rates increase exponentially to the present. We attribute this surprising lack of temporal coincidence to initial niche-neutral diversification followed by ecological and phenotypic divergence coincident with more extreme cold and dry habitats that proliferated into the Pleistocene. A lack of density-dependence contrasts with investigations of other cosmopolitan lineages, suggesting alternative patterns may be common in the diversification of temperate lineages.
Supplementary Materials for: Phylogenomics, lineage diversification rates, and the evolution of diadromy in Clupeiformes (anchovies, herrings, sardines, and relatives)
<p>Migration independently evolved numerous times in animals, with a myriad of ecological and evolutionary implications. In fishes, perhaps the most extreme form of migration is diadromy, the migration between marine and freshwater environments. A key and longstanding question is how does diadromy influence lineage diversification rates? Many diadromous species travel long distances during migration, have large geographic ranges, and use isolated freshwater habitats, which may increase the likelihood of speciation. Alternatively, diadromy may reduce lineage diversification rates if migration facilitates gene flow, homogenizing populations and stymieing speciation. Clupeiformes (herrings, sardines, shads and anchovies) is a model clade for testing hypotheses about the evolution of diadromy because it includes an exceptionally high proportion of diadromous species and several independent evolutionary origins of diadromy. However, relationships among major clupeiform lineages remain unresolved with sparse (<50%) sampling of diadromous species, limiting the resolution of phylogenetically-informed statistical analyses. We assembled a phylogenomic dataset and used multi-species coalescent and concatenation approaches to generate the most comprehensive, highly-resolved clupeiform phylogeny to date, clarifying relationships among major clades of Clupeiformes, revealing taxa requiring revision, and identifying recalcitrant relationships needing further examination. Using this phylogeny as the evolutionary framework for downstream comparative analyses, we tested the hypothesis that diadromous lineages diversified faster than lineages restricted to either marine or freshwater habitats. We found that transitions to diadromy were more common than transitions from diadromy to non-diadromy. The largest lineage diversification rate increase in clupeiforms is associated with a transition to diadromy, but we uncovered little statistical support for categorically faster lineage diversification rates in diadromous versus non-diadromous fishes. We propose that diadromy may increase the potential for accelerated lineage diversification, particularly in species that migrate long distances, but this potential may only be realized in certain biogeographic contexts.</p>
The departure between constant-rate birth-death and empirically inferred diversification processes
<p>Birth-death models (BDMs) are stochastic processes describing the processes of speciation and extinction through time and across taxa and are widely used in biology for inference of evolutionary timescales. Previous research has highlighted how the expected trees under BDMs tend to differ from empirical trees with respect to indices such as the amount of phylogenetic imbalance. However, our understanding of how trees differ between BDMs and empirical inferences remains incomplete. In this study, we demonstrate how four different constant-rate BDM scenarios influence tree shape and branch-length characteristics of phylogenetic trees, using a wide range of topology and branch-length indices. Comparison of BDM expectations against a comprehensive empirical dataset of 1,189 empirical trees shows that the dominant form of model inadequacy in BDMs is in failing to accommodate large amounts of phylogenetic imbalance in empirical processes. We also find that empirical trees tend to have significantly greater depth, lower stemminess, and longer shortest pendant edge lengths than BD-simulated trees. The results also indicate that accounting for the sampling fraction is the single most important parameter for accommodating empirical stemminess and branch lengths. Overall, our findings demonstrate the limitations of BDM priors when inferring the shape and structural characteristics of phylogenetic trees, highlighting the importance of novel methods that account for a broader tree space and secondarily reduce any possible bias in branch length estimation.</p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.