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176 results for “Diversification pattern”
Complex patterns of diversification in the gray zone of speciation: Model-based approaches applied to Patagonian liolaemid lizards (Squamata: Liolaemus kingii clade)
<p>In this study, we detangled the evolutionary history of the Patagonian lizard clade <em>Liolaemus kingii</em>, coupling dense geographic sampling and novel computational analytical approaches. We analyzed nuclear and mitochondrial data (restriction DNA sequencing and cytochrome <em>b</em>) to hypothesize and evaluate species limits, phylogenetic relationships, and demographic histories. We also conducted posterior predictive simulations to assess the fit of the genomic data to the multispecies coalescent model. Our results show several instances of mito-nuclear discordance and consistent support for a reticulated history, supporting the view that the complex evolutionary history of the <em>kingii</em> clade is characterized by extensive gene flow and rapid diversification events. We discuss our findings in the contexts of the "gray zone" of speciation, phylogeographic patterns in the Patagonian region, and taxonomic outcomes.</p>
Data for: Global diversity patterns are explained by diversification rates and dispersal at ancient, not shallow, timescales
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Branching patterns in phylogenies cannot distinguish diversity-dependent diversification from time-dependent diversification
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Trait-dependent diversification in angiosperms: Patterns, models and data
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Complex patterns of diversification in the gray zone of speciation: Model-based approaches applied to Patagonian liolaemid lizards (Squamata: Liolaemus kingii clade)
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Data from: Cenozoic colonization and diversification patterns of tropical American palms: evidence from Astrocaryum (Arecaceae)
With 788 species in 67 genera in the Neotropics, Arecaceae are an important ecological and economic component of the region. We review the influence of geological events such as the Pebas system, the Andean uplift and the land connections between South and Central/North America, on the historical assembly of Neotropical palms. We present a case study of the palm genus Astrocaryum (40 species) as a model for evaluating colonization and diversification patterns of lowland Neotropical taxa. We conducted a Bayesian dated phylogenetic analysis based on four low-copy nuclear DNA regions and a biogeographical analysis using the dispersal, extinction and cladogenesis model. Cladogenesis of Western Amazonian Astrocaryum spp. (c. 6 Mya) post-dated the drainage of the aquatic Pebas system, supporting the constraining role of Pebas on in situ diversification and colonization. The ancestral distribution of Astrocaryum spp. in the Guiana Shield supported the hypothesis of an old formation that acted as a source area from which species colonized adjacent regions, but an earliest branching position for Guianan species was not confidently recovered. A twofold increase in diversification rate was found in a clade, the ancestor of which occupied the Guiana Shield (c. 13 Mya, a time of climatic change and Andean uplift).
Evolutionary dynamics of structural variation at a key locus for color pattern diversification in cichlid fishes
<p>Color patterns in African cichlid fishes vary spectacularly. Although phylogenetic analysis showed already 30 years ago that many color patterns evolved repeatedly in these adaptive radiations, only recently have we begun to understand the genomic basis of color variation. Horizontal stripe patterns evolved and were lost several times independently across the adaptive radiations of Lake Victoria, Malawi, and Tanganyika and regulatory evolution of agouti-related peptide 2 (agrp2/asip2b) has been linked to this phenotypically labile trait. Here, we asked whether the agrp2 locus exhibits particular characteristics that facilitate divergence in color patterns. Based on comparative genomic analyses, we discovered several recent duplications, insertions, and deletions. Interestingly, one of these events resulted in a tandem duplication of the last exon of agrp2. The duplication likely precedes the East African radiations that started 8–12 Ma, is not fixed within any of the radiations, and is found to vary even within some species. Moreover, we also observed variation in copy number (two to five copies) and secondary loss of the duplication, illustrating a surprising dynamic at this locus that possibly promoted functional divergence of agrp2. Our work suggests that such instances of exon duplications are a neglected mechanism potentially involved in the repeated evolution and diversification that deserves more attention.</p>
Environmentally driven extinction and opportunistic origination explain fern diversification patterns
<p>Datasets supporting "Contrasting drivers of originations and extinctions explain fern diversification patterns".</p>
Supplementary material from: Alpine extremophytes in evolutionary turmoil: Complex diversification patterns and demographic responses of a Halophilic grass in a Central Asian biodiversity hotspot
<p>Diversification and demographic responses are key processes shaping species evolutionary history. Yet we still lack a full understanding of ecological mechanisms that shape genetic diversity at different spatial scales upon rapid environmental changes. In this study, we examined genetic differentiation in an extremophilic grass <em>Puccinellia pamirica</em> and factors affecting its population dynamics among the occupied hypersaline alpine wetlands on the arid Pamir Plateau in Central Asia. Using genomic data, we found evidence of fine-scale population structure and gene flow among the localities established across the high-elevation plateau as well as fingerprints of historical demographic expansion. We showed that an increase in the effective population size could coincide with the Last Glacial Period, which was followed by the species demographic decline during the Holocene. Geographic distance plays a vital role in shaping the spatial genetic structure of <em>P. pamirica</em> alongside with isolation-by-environment and habitat fragmentation. Our results highlight a complex history of divergence and gene flow in this species-poor alpine region during the Late Quaternary. We demonstrate that regional climate specificity and a shortage of nonclimate data largely impede predictions of future range changes of the alpine extremophile using ecological niche modeling. This study emphasizes the importance of fine-scale environmental heterogeneity for population dynamics and species distribution shifts.</p>
The influence of history, geography and environment on patterns of diversification in the western terrestrial garter snake
<p><b>Aim:</b> A central aim of biogeography is to understand how biodiversity is generated and maintained across landscapes. Here, we establish phylogenetic and population genetic patterns in a widespread reptile to quantify the influence of historical biogeography and current environmental variation on patterns of genetic diversity.</p> <p><b>Location: </b>Western North America.</p> <p><b>Taxon: </b>Western terrestrial garter snake, <i>Thamnophis elegans</i>.</p> <p><b>Methods: </b>We used double-digest RADseq to estimate phylogenetic relationships and characterize population genetic structure across the three widespread subspecies of <em>T. elegans</em>: <em>T. e. vagrans</em> (wandering garter snake), <em>T. e. elegans </em>(mountain garter snake) and <em>T. e. terrestris</em> (coast garter snake). We assessed patterns of dispersal and vicariance across biogeographic regions using ancestral area reconstruction (AAR) and deviations from isolation-by-distance across the landscape using estimated effective migration surfaces (EEMS). We identified environmental variables potentially shaping local adaptation in regional lineages using genetic-environment association (GEA) analyses.</p> <p><b>Results:</b> We recovered three well-differentiated genetic groups that correspond to the three subspecies. AAR analyses inferred the eastern Cascade Range as the ancestral area, with dispersal to both the east and west across western North America. Populations of <em>T. e. elegans</em> displayed a latitudinal gradient in genetic variation across the Sierra Nevada and northern California, while populations of <em>T. e. terrestris</em> show discrete genetic breaks consistent with well-known biogeographic barriers. Lastly, GEA analyses identified allele frequency shifts at loci associated with a common set of environmental variables in both <em>T. e. elegans</em> and <em>T. e. terrestris</em>.</p> <p><b>Main Conclusion: </b><em>T. elegans </em>is composed of distinct evolutionary lineages, each with its own geographic range and history of diversification. <em>T. e. elegans</em> and <em>T. e. terrestris</em> show unique patterns of diversification as populations dispersed from east to west and while adapting to the new environments they colonized. Historical events, landscape features and environmental variation have all contributed to patterns of differentiation in <em>T. elegans</em>.</p> <p> </p>
Phylogenomics of the Scaly-toed geckos and allies (Gekkonidae: Lepidodactylus and Gekko) reveal a continental origin with unidirectional patterns of island arc diversification
<p>Absolute time tree based on 1696 loci (1,923,100bp) estimated in MCMCTree with three secondary calibrations and a conservative root height calibration (Table1). The light green density distributions at the nodes are based on the posterior age distributions estimated in MCMCTree and the numbers represent the mean age at the respective nodes.</p>
Testing the causes of richness patterns in the paleotropics: time and diversification in cycads (Cycadaceae)
<p>The paleotropics harbor many biodiversity hotspots and show many different species richness patterns. However, it remains unclear which factors are the most important in directly shaping richness patterns among regions in the paleotropics (i.e. diversification rates, colonization times, dispersal frequency). Here we used Cycadaceae as a model system to test the causes of regional richness patterns in the paleotropics. Specifically we tested the roles of dispersal frequency, colonization time, diversification rates, and their combined role in explaining richness patterns among regions. We generated a well-sampled, time-calibrated phylogeny and then used this to estimate dispersal events, colonization times, and diversification rates. Richness patterns were significantly associated with the timing of the first colonization of each region, and were best explained by the combined effects of colonization time and diversification rates. The number of dispersal events into each region and the diversification rates of species in each region were not significantly related to richness. Ancestral-area reconstructions showed frequent migrations across Wallace's Line, with a higher diversification rate east of Wallace's Line than west of it. Overall, our study shows that colonization time can be an important factor for explaining regional richness patterns in the paleotropics.</p>
Diversification patterns in Boeckella
<p><b>Aim</b>: We investigated evolutionary relationships and biogeographical patterns within the genus <i>Boeckella</i> to evaluate: 1) whether its current widespread distribution in the Southern Hemisphere is due to recent long-distance dispersal or long-term diversification; and 2) the age and origin of sub-Antarctic and Antarctic <i>Boeckella</i> species, with particular focus on the most widely distributed species: <i>B. poppei.</i></p> <p><b>Location</b>: South America, sub-Antarctic islands, maritime Antarctica, continental Antarctica and Australasia.</p> <p><b>Methods</b>: To reconstruct phylogenetic patterns of <i>Boeckella</i>, we used molecular sequence data collected from 12 regions, and applied Bayesian and Maximum Likelihood analyses using multiple loci. We also estimated divergence times and reconstructed ancestral ranges using two different models of species evolution.</p> <p><b>Results</b>: Phylogenetic analyses and divergence time estimates suggested that <i>Boeckella</i> originated on the Gondwanan supercontinent and initially split into two main clades during the late Cretaceous (ca. 80 Ma). The first clade diversified in Australasia and the second clade is currently distributed in South America, various sub-Antarctic islands and Antarctica. Dispersal from South America to the Kerguelen and Crozet archipelagos occurred during the Eocene/Oligocene (B. vallentini) and in the late Pliocene (<i>B. brevicaudata</i>), while South Georgia and the maritime Antarctic were likely colonized during the late Pleistocene (<i>B. poppei</i>).</p> <p><b>Main conclusions</b>: Boeckella has a Gondwanan origin, with further diversifications after the physical separation of the continental landmasses. Extant populations of <i>Boeckella </i>from the Scotia Arc islands and Antarctic Peninsula originated from South America during the Pleistocene, suggesting that original Antarctic Gondwanan lineages did not survive repeated glacial cycles during the Quaternary ice ages. A continuous decline in the species accumulation rate is apparent within the genus since the early Eocene, suggesting that <i>Boeckella </i>diversification may have decreased due to progressive cooling throughout the Cenozoic era.</p>
Unexpected colour pattern variation in mimetic frogs: implication for the diversification of warning signals in the genus Ranitomeya
<p>Predation is expected to promote uniformity in the warning colouration of defended prey, but also mimicry convergence between aposematic species. Despite selection constraining both colour-pattern and population divergence, many aposematic animals display numerous geographically structured populations with distinct warning signals. Here, we explore the extent of phenotypic variation of sympatric species of <em>Ranitomeya</em> poison frogs and test for theoretical expectations on variation and convergence in mimetic signals. We demonstrate that both warning signal and mimetic convergence are highly variable and are negatively correlated: some localities display high variability and no mimicry while in others the phenotype is fixed and mimicry is perfect. Moreover, variation in warning signals is always present within localities, and in many cases, this variation overlaps between populations, such that variation is continuous. Finally, we show that coloration is consistently the least variable element and is likely of greater importance for predator avoidance compared to patterning. We discuss the implications of our results in the context of warning signal diversification and suggest that, like many other locally adapted traits, a combination of standing genetic variation and founding effect might be sufficient to enable divergence in colour pattern.</p>
Phylogenomics reveals patterns ancient hybridization and differential diversification that contribute to phylogenetic conflict in willows, poplars, and close relatives
<p>Despite the economic, ecological, and scientific importance of the genera <em>Salix</em> L. (willows) and <em>Populus</em> L. (poplars, cottonwoods, and aspens) Salicaceae, we know little about the sources of differences in species diversity between the genera and of the phylogenetic conflict that often confounds estimating phylogenetic trees. <em>Salix</em> subgenera and sections, in particular, have been difficult to classify, with one recent attempt termed a 'spectacular failure' due to a speculated radiation of the subgenera <em>Vetrix</em> and <em>Chamaetia</em>. Here we use targeted sequence capture to understand the evolutionary history of this portion of the Salicaceae plant family. Our phylogenetic hypothesis was based on 787 gene regions and identified extensive phylogenetic conflict among genes. Our analysis supported some previously described subgeneric relationships and confirmed polyphyly of others. Using an f<sub>branch</sub> analysis we identified several cases of hybridization in deep branches of the phylogeny, which likely contributed to discordance among gene trees. In addition, we identified a rapid increase in diversification rate near the origination of the <em>Vetrix</em>-<em>Chamaetia</em> clade in <em>Salix</em>. This region of the tree coincided with several nodes that lacked strong statistical support, indicating a possible increase in incomplete lineage sorting due to rapid diversification. The extraordinary level of both recent and ancient hybridization in both <em>Salix</em> and <em>Populus</em> have played important roles in the diversification and diversity in these two genera.</p>
Evolutionary origins and patterns of diversification in animal brood parasitism
<p>Brood parasitism involves the exploitation of host parental care rather than the extraction of resources directly from hosts. Although often excluded, we show that brood parasitism fits within existing frameworks of parasitic strategies, and formulate defining criteria, including that the parasites be obligate and the hosts non-eusocial (thereby distinguishing them from social parasites). A systematic literature survey revealed 59 independently derived brood parasitic lineages with most origins (49) in insects, particularly among bees and wasps, and other origins in birds (7) and fish (3). Insects account for over 98% of brood parasitic species, with much of that diversity reflecting ancient (100+ million-year-old) brood parasitic lineages. Brood parasites usually, but not always, evolve from forms that show parental care. In insects, brood parasitism often first evolves through exploitation of a closely related species, following Emery's rule, but this is less typical in birds, which we discuss. We conducted lineage-level comparisons between brood parasitic clades and their sister groups, finding mixed results but an overall neutral to negative effect of brood parasitism on species richness and diversification. Our review of brood parasites reveals many unanswered questions requiring new research including further modelling of the co-evolutionary dynamics of brood parasites and their hosts.</p>
Data from: Cenozoic colonization and diversification patterns of tropical American palms: evidence from Astrocaryum (Arecaceae)
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Data from: The evolution of darter color and pattern: Small, rocky streams and riffles enhance the diversification of bright and conspicuous fishes
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Phylogenomics reveals patterns ancient hybridization and differential diversification that contribute to phylogenetic conflict in willows, poplars, and close relatives
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Data for: Phylogenomic and population genomic analyses of ultraconserved elements reveal deep coalescence and introgression shaped diversification patterns in Lamprologine cichlids of the Congo River
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Allen Brain Atlas
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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.