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65 results for “diversification models”
DNA metabarcoding and spatial modelling link diet diversification with distribution homogeneity in European bats
<p>Inferences of the interactions between species’ ecological niches and spatial distribution have been historically based on simple metrics such as low-resolution dietary breadth and range size, which might have impeded the identification of meaningful links between niche features and spatial patterns. We analysed the relationship between dietary niche breadth and spatial distribution features of European bats, by combining continent-wide DNA metabarcoding of faecal samples with species distribution modelling. Our results show that while range size is not correlated with dietary features of bats, the homogeneity of the spatial distribution of species exhibits a strong correlation with dietary breadth. We also found that dietary breadth is correlated with bats’ hunting flexibility. However, these two patterns only stand when the phylogenetic relations between prey are accounted for when measuring dietary breadth. Our results suggest that the capacity to exploit different prey types enables species to thrive in more distinct environments and therefore exhibit more homogeneous distributions within their ranges.</p>
Data from: Exploring rainforest diversification using demographic model testing in the African foam-nest treefrog (Chiromantis rufescens)
Aim: Species with wide distributions spanning the African Guinean and Congolian rainforests are often composed of genetically distinct populations or cryptic species with geographic distributions that mirror the locations of the remaining forest habitats. We used phylogeographic inference and demographic model testing to evaluate diversification models in a widespread rainforest species, the African Foam-nest Treefrog (Chiromantis rufescens). Location: Guinean and Congolian rainforests, West and Central Africa. Taxon: Chiromantis rufescens. Methods: We collected mitochondrial DNA (mtDNA) and single nucleotide polymorphism (SNP) data for 130 samples of Chiromantis rufescens. After estimating population structure and inferring species trees using coalescent methods, we tested demographic models to evaluate alternative population divergence histories that varied with respect to gene flow, population size change, and periods of isolation and secondary contact. Species distribution models were used to identify regions of climatic stability that could have served as forest refugia since the Last Interglacial. Results: Population structure within Chiromantis rufescens resembles the major biogeographic regions of the Guinean and Congolian forests. Coalescent-based phylogenetic analyses provide strong support for an early divergence between the western Upper Guinean forest and the remaining populations. Demographic inferences support diversification models with gene flow and population size changes even in cases where contemporary populations are currently allopatric, which provides support for forest refugia and barrier models. Species distribution models suggest that forest refugia were available for each of the populations throughout the Pleistocene. Main conclusions: Considering historical demography is essential for understanding population diversification, especially in complex landscapes such as those found in the Guineo-Congolian forest. Population demographic inferences help connect patterns of genetic variation to diversification model predictions. The diversification history of Chiromantis rufescens was shaped by a variety of processes, including vicariance from river barriers, forest fragmentation, and adaptive evolution along environmental gradients.
TA B L E 1 Summary of model fit, based on the area under the curve (AUC) of the receiver operating characteristic (ROC) for training data, and the most important bioclimatic variables in past, present, and future (2070) Maxent models of 13 bat species included in this study. in Southern Africa's Great Escarpment as an amphitheater of climate-driven diversification and a buffer against future climate change in bats
TA B L E 1 Summary of model fit, based on the area under the curve (AUC) of the receiver operating characteristic (ROC) for training data, and the most important bioclimatic variables in past, present, and future (2070) Maxent models of 13 bat species included in this study.
figure 5 Lineage through time plot within G. subgutturosa with cytb. The 95 in Unraveling goitered gazelle (Gazella subgutturosa) diversification: insights from phylogeography and species distribution modeling
figure 5 Lineage through time plot within G. subgutturosa with cytb. The 95% highest posterior density interval is shown in blue.
figure 3 Mismatch distributions within the G in Unraveling goitered gazelle (Gazella subgutturosa) diversification: insights from phylogeography and species distribution modeling
figure 3 Mismatch distributions within the G. subgutturosa. The expected line (green color) compared with the observed frequencies under the sudden expansion model using cytb. (A) the mmd diagram for the Asiatic population shows a recent expansion. (B) the mmd diagram for the Middle Eastern population and (C) the mmd diagram for the Central Iranian population.
figure 8 Potential distribution modeling for G. subgutturosa across different time periods, including a in Unraveling goitered gazelle (Gazella subgutturosa) diversification: insights from phylogeography and species distribution modeling
figure 8 Potential distribution modeling for G. subgutturosa across different time periods, including a) the Last Glacial Maximum (lgm; 21 Kya) and b) mid-Holocene (6 kya) as past scenarios, c) the present as a current scenario, and future climatic projections for 2070 are based on specific climate models (d: bcc-csm 1, rcp: 4.5; e: bcc-csm1, rcp: 6; f: ccsm 4, rcp: 4.5; g: ccsm 4, rcp: 6.0). Habitat suitability is visualized using color gradients, with blue representing the highest suitability Downloaded from Brill.com 06/21/2024 06:25:06PM and green representing the via lowestOpensuitability Access..This The is presence an openof access article distributed under the terms G. subgutturosa is denoted by a red dot. of the CC BY 4.0 license. https://creativecommons.org/licenses/by/4.0/
figure 2 The dated phylogenetic trees using the cytb gene for G. subgutturosa. Blue bars show 95 in Unraveling goitered gazelle (Gazella subgutturosa) diversification: insights from phylogeography and species distribution modeling
figure 2 The dated phylogenetic trees using the cytb gene for G. subgutturosa. Blue bars show 95% highest posterior density intervals of the estimated node ages; numbers next to the nodes are mean node ages (Mya). The red and green lines show new haplotypes from this study.
figure 1 in Unraveling goitered gazelle (Gazella subgutturosa) diversification: insights from phylogeography and species distribution modeling
figure 1 Sampling locations of new specimens of G. subgutturosa from four locations in the present study. Parvar Protected Area, Sorkheh-Hesar National Park, Bashgol Protected Area, and Sohrein Protected Area. Hatched areas on the map indicate the provinces where each location is situated.
figure 6 in Unraveling goitered gazelle (Gazella subgutturosa) diversification: insights from phylogeography and species distribution modeling
figure 6 Median-joining haplotype network of G. subgutturosa using the cytb gene. The blue color Haplogroup refers to the Asiatic clade, the pink color Haplogroup is assigned to the Middle Eastern clade and the yellow color Haplogroup demonstrates the Central Iranian clade.
figure 7 in Unraveling goitered gazelle (Gazella subgutturosa) diversification: insights from phylogeography and species distribution modeling
figure 7 The biogeographic analysis of G. subgutturosa using s-diva (1) and bbm (2) based on cytb. For these analyses, three clades were considered: the Asiatic distribution (A), the Middle Eastern distribution (B), and the central Iranian distribution (C). The green and red circles around the nodes show vicariance and dispersal events, respectively.
Trait-dependent diversification in angiosperms: Patterns, models and data
<p>Variation in species richness across the tree of life, accompanied by the incredible variety of ecological and morphological characteristics found in nature, has inspired many studies to link traits with species diversification. Angiosperms are a highly diverse group that has fundamentally shaped life on earth since the Cretaceous and illustrate how species diversification affects ecosystem functioning. Numerous traits and processes have been linked to differences in species richness within this group, but we know little about their relative importance and how they interact. Here, we synthesized data from 152 studies that used state-dependent speciation and extinction (SSE) models on angiosperm clades. Intrinsic traits related to reproduction and morphology were often linked to diversification but a set of universal drivers did not emerge as traits did not have consistent effects across clades. Importantly, SSE model results were correlated to dataset properties – trees that were larger, older, or less well-sampled tended to yield trait-dependent outcomes. We compared these properties to recommendations for SSE model use and provide a set of best practices to follow when designing studies and reporting results. Finally, we argue that SSE model inferences should be considered in a larger context incorporating species' ecology, demography and genetics.</p>
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>
Dataset for: Paleoenvironmental models for Australia and the impact of aridification on blindsnake diversification
<p><strong>Aim</strong>: Shifts in diversification rates of Australian flora and fauna have been associated with aridification, but the relationship between diversification rates and aridity has never been quantified. We employed multiple approaches to accurately reconstruct paleoenvironments of Australia for the first time. We used this information, and phylogenetic-based analyses, to explore how changes in temperature and increasing aridity during the Neogene influenced the diversification of the Australian blindsnakes. We tested whether diversification rates differ between arid-adapted and mesic-adapted lineages.</p> <p><strong>Taxon</strong>: Typhlopidae, <em>Anilios </em>blindsnakes</p> <p><strong>Location</strong>: Australia</p> <p><strong>Materials and Methods</strong>: We estimated the historical biogeography of blindsnakes using BioGeoBEARS. We synthesised multiple approaches to reconstruct paleotemperature and paleoaridity of Australia during the Neogene. We fit several birth-death models and estimate diversification rates under paleoenvironmental conditions using RPANDA. We further compare diversification rates between arid-adapted lineages versus mesic-adapted lineages using ClaDS and GeoHiSSE.</p> <p><strong>Results</strong>: Ancestral area estimation indicated Australian blindsnakes have tropical grassland origins. We found that Australia-specific regional paleotemperature and paleoaridity provided a better explanation for diversification rate variation than global paleotemperature. Specifically, our best-fitting model indicated that speciation rates of blindsnakes decreased with increasing aridity. We found no difference in diversification rates between arid- and mesic-adapted lineages.</p> <p><strong>Main conclusions</strong>: Soon after dispersing to Australia, the common ancestors of Australian blindsnakes diversified rapidly in mesic habitats during the early Miocene. However, as the continent became increasingly arid, diversification rates decreased. We found that shifts in the environment led to the emergence of two major clades: one remaining in primarily mesic habitats and the other adapting to the expanding arid biome. Our results emphasise the importance of both arid and tropical biomes as sources and sinks of diversification.</p>
Trait-dependent diversification in angiosperms: Patterns, models and data
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Data from: Exploring rainforest diversification using demographic model testing in the African foam-nest treefrog (Chiromantis rufescens)
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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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Dataset for: Paleoenvironmental models for Australia and the impact of aridification on blindsnake diversification
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Using demographic model selection to untangle allopatric divergence and diversification mechanisms in the Rheum palmatum complex in the Eastern Asiatic Region
<p>Allopatric divergence is often initiated by geological uplift and restriction to sky-islands, climate oscillations, or river capture. However, it can be difficult to establish which mechanism was the most likely to generate the current phylogeographic structure of a species. Recently, genomic data in conjunction with a model testing framework have been applied to address this issue in animals. To test whether such an approach is also likely to be successful in plants we used population genomic data of the <i>Rheum palmatum</i> complex from the Eastern Asiatic Region, in conjunction with biogeographical reconstruction and demographic model selection to identify the potential mechanism(s) which have led to the current level of divergence. Our results indicate that the <i>R. palmatum</i> complex originated in the central Hengduan Mts. and possibly in regions further to the east, and then dispersed westward and eastward resulting in genetically distinct lineages. Populations are likely to have diverged in refugia during climate oscillations followed by subsequent expansion and secondary contact. However, model simulations within the western lineage of the <i>R. palmatum</i> complex cannot reject a restriction to sky-islands as a possible mechanism of diversification due to the genetically ambiguous position of one population. This highlights that genetically mixed populations might introduce ambiguity regarding the best diversification model in some cases. Although it might be possible to resolve this ambiguity using other data, sometimes this could prove to be difficult in complex biogeographic areas.</p>
Data from: Evaluating mechanisms of diversification in a Guineo-Congolian tropical forest frog using demographic model selection
The accumulation of biodiversity in tropical forests can occur through multiple allopatric and parapatric models of diversification, including forest refugia, riverine barriers and ecological gradients. Considerable debate surrounds the major diversification process, particularly in the West African Lower Guinea forests, which contain a complex geographic arrangement of topographic features and historical refugia. We used genomic data to investigate alternative mechanisms of diversification in the Gaboon forest frog, Scotobleps gabonicus, by first identifying population structure and then performing demographic model selection and spatially explicit analyses. We found that a majority of population divergences are best explained by allopatric models consistent with the forest refugia hypothesis and involve divergence in isolation with subsequent expansion and gene flow. These population divergences occurred simultaneously and conform to predictions based on climatically stable regions inferred through ecological niche modelling. Although forest refugia played a prominent role in the intraspecific diversification of S. gabonicus, we also find evidence for potential interactions between landscape features and historical refugia, including major rivers and elevational barriers such as the Cameroonian Volcanic Line. We outline the advantages of using genomewide variation in a model-testing framework to distinguish between alternative allopatric hypotheses, and the pitfalls of limited geographic and molecular sampling. Although phylogeographic patterns are often species-specific and related to life-history traits, additional comparative studies incorporating genomic data are necessary for separating shared historical processes from idiosyncratic responses to environmental, climatic and geological influences on diversification.
Data from: Early diversification dynamics in a highly successful insular plant taxon are consistent with the general dynamic model of oceanic island biogeography
<p>The general dynamic model (GDM) of oceanic island biogeography views oceanic islands predominantly as sinks rather than sources of dispersing lineages. To test this, we conducted a biogeographic analysis of a highly successful insular plant taxon, <em>Cyrtandra </em>and inferred directionality of dispersal and founder events throughout the four biogeographical units of the Indo-Australian Archipelago (IAA), namely Sunda, Wallacea, Philippines, and Sahul. Sunda was recovered as the major source area, followed by Wallacea, a system of oceanic islands. The relatively high number of events originating from Wallacea is attributed to its central location in the IAA and its complex geological history selecting for increased dispersibility. We also tested if diversification dynamics in <em>Cyrtandra </em>follow predictions of adaptive radiation, which is the dominant process as per the GDM. Diversification dynamics of dispersing lineages of <em>Cyrtandra</em> in the Southeast Asian grade showed early bursts followed by a plateau, which is consistent with adaptive radiation. We did not detect signals of diversity-dependent diversification, and this is attributed to Southeast Asian cyrtandras<em> </em>occupying various niche spaces, evident by their wide morphological range in habit and floral characters. The Pacific clade, which arrived at the immaturity phase of the Pacific Islands, showed diversification dynamics predicted by the Island Immaturity Speciation Pulse (IISP) model, wherein rates increase exponentially, and their morphological range is controlled by the least action effect favoring woodiness and fleshy fruits. Our study provides a first step toward a framework for investigating diversification dynamics as predicted by the GDM in highly successful insular taxa.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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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.