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72 results for “speciation rates”
Data from: Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation
Several evolutionary theories predict that rates of morphological change should be positively associated with the rate at which new species arise. For example, the theory of punctuated equilibrium proposes that phenotypic change typically occurs in rapid bursts associated with speciation events. However, recent phylogenetic studies have found little evidence linking these processes in nature. Here we demonstrate that rates of species diversification are highly correlated with the rate of body size evolution across the 30,000+ living species of ray-finned fish that comprise the majority of vertebrate biological diversity. This coupling is a general feature of fish evolution and transcends vast differences in ecology and body-plan organization. Our results may reflect a widespread speciational mode of character change in living fishes. Alternatively, these findings are consistent with the hypothesis that phenotypic 'evolvability' – the capacity of organisms to evolve – shapes the dynamics of speciation through time at the largest phylogenetic scales.
Data from: Does population structure predict the rate of speciation? A comparative test across Australia's most diverse vertebrate radiation
Population divergence is the first step in allopatric speciation, as has long been recognized in both theoretical models of speciation and empirical explorations of natural systems. All else being equal, lineages with substantial population differentiation should form new species more quickly than lineages that maintain range-wide genetic cohesion through high levels of gene flow. However, there have been few direct tests of the extent to which population differentiation predicts speciation rates as measured on phylogenetic trees. Here, we explicitly test the links between organismal traits, population-level processes, and phylogenetic speciation rates across a diverse clade of Australian lizards that shows remarkable variation in speciation rate. Using genome-wide ddRAD data from 892 individuals, we generated a comparative dataset on isolation-by-distance and population differentiation across 104 putative species-level lineages (OTUs). We find that species show substantial variation in the extent of population differentiation, and this variation is predicted by organismal traits that are thought to be proxies for dispersal and deme size. However, variation in population structure does not predict variation in speciation rate. Our results suggest that population differentiation is not the rate-limiting step in species formation and that other ecological and historical factors are primary determinants of speciation rates at macroevolutionary scales.
Data from: Geography of speciation affects rate of trait divergence in haemulid fishes
Speciation and the interactions between recently diverged species are thought to be major causes of ecological and morphological divergence in evolutionary radiations. We explored the role of these factors in the diversification of New World haemulid fishes, a major radiation of shore fishes in the tropical West Atlantic and East Pacific that are key members of coral reef ecosystems in this region. A time calibrated molecular phylogeny of this group reveals 21 sister species pairs, of which 8 are fully sympatric and 13 are allopatric. We find no difference between sympatric and allopatric pairs in the rate of divergence in color pattern, overall body shape or functional morphological traits associated with locomotion or feeding. However, sympatric pairs show a significant decrease in the rate of divergence in all of these traits with increasing time since their divergence, consistent with an elevated rate of divergence at the time of speciation, the effect of which attenuates as divergence time increases. Our results are consistent with an important role for speciation driving phenotypic divergence of haemulids, but the lack of difference in divergence between sympatric and allopatric pairs indicates that the interactions between closely related species are not dominant drivers of this divergence.
Data, scripts and supplementary materials for "Color polymorphism and conspicuousness do not increase speciation rates in Lacertids" (de Solan et al. 2023)
<p>This data_and_script file contain the phylogeny and coloration data, as well as the R script used in the article "Color polymorphism and conspicuousness do not increase speciation rates in Lacertids".</p><p>The other file contain the supplementary materials for the publication.</p>
Nucleotide substitutions during speciation may explain substitution rate variation
<p><span>Although molecular mechanisms associated with the generation of mutations are highly conserved across taxa, there is widespread variation in mutation rates between evolutionary lineages. When phylogenies are reconstructed based on nucleotide sequences, such variation is typically accounted for by the assumption of a relaxed molecular clock, which is just a statistical distribution of mutation rates without much underlying biological mechanism. Here, we propose that variation in accumulated mutations may be partly explained by an elevated mutation rate during speciation. Using simulations, we show how shifting mutations from branches to speciation events impacts inference of branching times in phylogenetic reconstruction. Furthermore, the resulting nucleotide alignments are better described by a relaxed than by a strict molecular clock. Thus, elevated mutation rates during speciation potentially explain part of the variation in substitution rates that is observed across the tree of life. </span></p>
A flexible method for estimating tip diversification rates across a range of speciation and extinction scenarios
<p>Estimates of diversification rates at the tips of a phylogeny provide a flexible approach for correlation analyses with multiple traits and to map diversification rates in space, while also avoiding the uncertainty of deep time rate reconstructions. Available methods for tip rate estimation make different assumptions, and thus their accuracy usually depends on characteristics of the underlying model generating the tree. Here we introduce MiSSE, a trait-free, state-dependent speciation and extinction approach that can be used to estimate varying speciation, extinction, net-diversification, turnover rates, and extinction fraction at the tips of the tree. We compare the accuracy of tip rates inferred by MiSSE against similar methods and demonstrate that, due to certain characteristics of the model, the error is generally low across a broad range of speciation and extinction scenarios. MiSSE can be used alongside regular phylogenetic comparative methods in trait related diversification hypotheses, and we also describe a simple correction to avoid pseudoreplication from sister tips in analyses of independent contrasts. Finally, we demonstrate the capabilities of MiSSE, with a renewed focus on classic comparative methods, to examine correlation between plant height and turnover rates in eucalypts, a species-rich lineage of flowering plants.</p>
Historical warming consistently decreased size, dispersal and speciation rate of fish
<p>There is ongoing debate as to whether fish body size will decrease with global warming and how these changes may impact dispersal ability and speciation rate. Theory predicts that, under warmer temperatures, fish grow to a smaller size, undergo a reduction in dispersal ability and increase speciation rates. However, evaluations of such predictions are hampered owing to the lack of empirical data spanning both wide temporal and geographical scales. Here, using phylogenetic methods, we show that smaller clupeiform fish (anchovies and herrings) occurred historically in warmer waters, moved the shortest distances at low speed and displayed the lowest speciation rates. Furthermore, fish moved faster and evolved rapidly under higher rates of temperature change but these historical rates are far lower than current warming rates. Our results predict a future where smaller clupeiform fish that have reduced ability to move will be more prevalent; this, in turn, may reduce future speciation.</p>
Data from: Evolution of the immune system influences speciation rates in teleost fishes
Teleost fishes constitute the most species-rich vertebrate clade and exhibit extensive genetic and phenotypic variation, including diverse immune defense strategies. The genomic basis of a particularly aberrant strategy is exemplified by Atlantic cod, in which a loss of major histocompatibility complex (MHC) II functionality coincides with a marked expansion of MHC I genes. Through low-coverage genome sequencing (9–39×), assembly and comparative analyses for 66 teleost species, we show here that MHC II is missing in the entire Gadiformes lineage and thus was lost once in their common ancestor. In contrast, we find that MHC I gene expansions have occurred multiple times, both inside and outside this clade. Moreover, we identify an association between high MHC I copy number and elevated speciation rates using trait-dependent diversification models. Our results extend current understanding of the plasticity of the adaptive immune system and suggest an important role for immune-related genes in animal diversification.
Figure 4 in Reproductive isolation and the causes of speciation rate variation in nature
Figure 4. Some possible relationships between the rate at which lineages evolve reproductive isolation and their rate of speciation. A, direct correspondence, where the evolution of reproductive evolution shows a one-to-one relationship with the macroevolutionary rate of speciation. In this scenario, the evolution of reproductive isolation is the exclusive determinant of macroevolutionary speciation dynamics. B, offset/dampened relationship, where the rate of evolution of reproductive isolation is the dominant control on speciation rates, although speciation rates are lower than predicted by the rate of evolution of reproductive isolation alone. This relationship implies that many populations evolving reproductive isolation fail to persist through deep time. C, decoupled, such that reproductive isolation shows no predictive relationship with macroevolutionary speciation rates. This scenario suggests that reproductive isolation is not the rate-limiting control on the rate of speciation. Adapted from Rabosky (2013).
Figure 3 in Reproductive isolation and the causes of speciation rate variation in nature
Figure 3. Pairwise postzygotic isolation from interspecific crosses of birds as a function of the pairwise genetic distance between them. Results are shown for two major clades (pheasants, Phasianidae; parrots, Psittacidae). For a given level of genetic divergence, pheasants show greater levels of postzygotic isolation than the parrots, indicating that this sort of reproductive isolation accumulates more quickly in pheasants than in parrots. If intrinsic postzygotic isolation (hybrid inviability and sterility) is the dominant control on speciation rates, pheasants should have faster rates of speciation than parrots. Note that relationships are bounded at 0 (all hybrid offspring fully viable and fertile) and 1 (no offspring produced, or all offspring sterile). Lines show fitted linear relationships between reproductive isolation and genetic distance for each clade. Data are from Price & Bouvier (2002) and Gray (1958); analyses are from Rabosky and Matute (2013). For this pair of clades, speciation rates are faster in the clade with faster rates of evolution of reproductive isolation (pheasants: speciation = 0.26 lineages Myr–1; parrots: speciation = 0.22 lineages Myr–1). However, across all birds, these quantities appear to be unrelated.
Figure 1. A in Reproductive isolation and the causes of speciation rate variation in nature
Figure 1. A, per-lineage rates of speciation across a time-calibrated phylogenetic tree of 6670 species of extant birds (67% of the total diversity) as inferred using a statistical model that simultaneously estimates the magnitude of rate variation through time and across lineages. Colours correspond to the instantaneous rate of speciation at each point in the tree. The fastest 5% of rates exceed 0.4 species Myr –1 (dark red). Analysis of evolutionary rates explicitly accounts for extinction, although only speciation rates are shown. B, estimated present-day speciation rates for all 6670 species; these are simply the best estimate of the instantaneous rate of speciation for each tip in the phylogeny. Inset images depict representative birds with fast (western gull, Larus occidentalis) and slow (go-away-bird, Corythaixoides leucogaster) rates of speciation. The phylogenetic dataset is from Jetz et al. (2012) and speciation rate analysis is described in Rabosky & Matute (2013).
Data from: Testing for differences in rates of speciation, extinction, and morphological evolution in four tribes of cichlids endemic to Lake Tanganyika, East Africa
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Data from: Interaction between digestive strategy and niche specialization predicts speciation rates across herbivorous mammals
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Data from: Evolution of the immune system influences speciation rates in teleost fishes
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Data from: Oligocene niche shift, Miocene diversification - cold tolerance and accelerated speciation rates in the St. John's Worts (Hypericum, Hypericaceae)
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Data from: Geography of speciation affects rate of trait divergence in haemulid fishes
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Data from: Minimal effects of latitude on present-day speciation rates in New World birds
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Data from: Multiple loci and complete taxonomic sampling resolve the phylogeny and biogeographic history of tenrecs (Mammalia: Tenrecidae) and reveal higher speciation rates in Madagascar’s humid forests
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Data from: Historical climatic instability predicts the inverse latitudinal pattern in speciation rate of modern mammalian biota
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A flexible method for estimating tip diversification rates across a range of speciation and extinction scenarios
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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
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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.