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91 results for “evolutionary radiation”
Data from: Evolutionary radiation strategy revealed in the Scarabaeidae with evidence of continuous spatiotemporal morphology and phylogenesis
<p>Evolutionary biology faces the important challenge of determining how to interpret the relationship between selection pressures and evolutionary radiation. The lack of morphological evidence on cross-species research adds to difficulty of this challenge.</p> <p>We proposed a new paradigm for evaluating the evolution of branches through changes in characters on continuous spatiotemporal scales, for better interpreting the impact of biotic/abiotic drivers on the evolutionary radiation. It reveals a causal link between morphological changes and selective pressures: consistent deformation signals for all tested characters on timeline, which provided strong support for the evolutionary hypothesis of relationship between scarabs and biotic/abiotic drivers; the evolutionary strategies under niche differentiation, which were manifested in the responsiveness degree of functional morphological characters with different selection pressure.</p> <p>This morphological information-driven integrative approach sheds light on the mechanism of macroevolution under different selection pressures and is applicable to more biodiversity research.</p>
Ecological diversification preceded geographical expansion during the evolutionary radiation of Cataglyphis desert ants
<p>Biological diversity often arises as organisms adapt to new ecological conditions (i.e. ecological opportunities) or colonise suitable areas (i.e. spatial opportunities). Cases of geographical expansion followed by local ecological divergence are well described; they result in clades comprising ecologically heterogeneous subclades. In contrast, nothing is known about evolutionary radiation events in which ecological opportunities preceded spatial spread. Here, we show that the desert ant genus <em>Cataglyphis</em> likely originated in open grassland habitats in the Middle East ~18 million years ago and became a taxon of diverse species specialising in prey of different masses. Around 9 million years ago, southern Europe and northern Africa experienced aridification and were colonised by <em>Cataglyphis</em>, which was preadapted to the harsh environmental conditions. The result was the rapid accumulation of species, and the appearance of local assemblages containing species from different lineages that still displayed ancestral foraging specialties. These findings highlight that, in <em>Cataglyphis</em>, ecological diversification happened before the genus geographically spread into newly arisen suitable habitats, resulting in a clade composed of ecologically homogeneous subclades.</p>
Evolutionary mechanisms of varying chromosome numbers in the radiation of Erebia butterflies
<p>This is the dataset for the study with the same title published at MDPI Genes (please see the paper for all details).</p> <p>To test for a phylogenetic signal of varying chromosome numbers in Erebia butterflies (Lucek submitted), I reconstructed a phylogeny using a subset of Peña et al. Biol J Linn Soc 2016 for which chromosome numbers were available. Data for an additional 5 species was taken from GenBank. Chromosome numbers used are included.<br> The final alignment comprised sequence data for four genes: 620 bp of the mitochondrial cytochrome oxidase subunit I (COI), 598 bp of the nuclear glyceraldehyde-3-phosphate dehydrogenase (GAPDH), 565 bp of the nuclear ribosomal protein S5 (RpS5) and 343 bp of the nuclear wingless gene.</p> <p>I used PartitionFinder 2 (Lanfear et al. Mol Biol Evol 2017) to infer the best partition scheme and associated substitution model for each codon position and gene. The output of PartitionFinder is provided in the data file. The resulting best partitioning scheme for the Bayesian inference is given in each nexus file. For the maximum likelihood (ML) based phylogeny I used the GTR model with invariant sites and gamma correction (GTR+I+G) in RAXML 8.2.8 (Stamatakis, Bioinformatics 2014) with the corresponding partition scheme from PartitionFinder. I further used 1000 bootstrap replicates to assess significance. I ran RAXML for the dataset comprising either all four genes, the mitochondrial COI gene only or the three nuclear genes. In the latter case, data was only available for 35 taxa. I conducted the Bayesian analysis in MrBayes 3.2.2 (Ronquist et al. Syst Biol 2012) for either dataset using in each case, 5’000’000 generations with four chains – three heated and one cold. Trees were sampled every 1’000 generations.<br> Provided are the input and output files of MrBayes and RAXML for all genes combined (subfolder all), the mitochondrial COI gene only (subfolder mtdna) or the three nuclear genes (subfolder nuclear).</p>
Many ways to build an angler: diversity of feeding morphologies in a deep-sea evolutionary radiation
<p>Almost nothing is known about the diets of bathypelagic fishes, but functional morphology can provide useful tools to infer ecological processes. Here we quantify variation in jaw and tooth morphologies across anglerfishes (Lophiiformes), a clade spanning shallow and deep-sea habitats. Deep-sea ceratioid anglerfishes are believed to be dietary generalists due to the presumed necessity of opportunistic feeding in the food-limited bathypelagic zone. However, we found unexpected diversity in the trophic morphologies of ceratioid anglerfishes. Ceratioid jaws span a functional continuum ranging from species with numerous stout teeth, a relatively slow but forceful bite, and high jaw protrusibility at one extreme (characteristics shared with benthic anglerfishes), to species with large fang-like teeth, a fast but weak bite, and low jaw protrusibility at the other (including a unique "wolftrap" phenotype). Our finding of high morphological diversity seems to be at odds with ecological generality, reminiscent of Liem's paradox (morphological specialization allows organisms to have broader niches). Another possible explanation is that diverse ceratioid morphologies may yield similar trophic success (many-to-one mapping of morphology to diet), allowing diversity to arise through neutral evolutionary processes. Our results highlight that there are many ways to be a successful predator in the deep sea.</p>
Data from: Divergent trait and environment relationships among parallel radiations in Pelargonium (Geraniaceae): a role for evolutionary legacy?
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Testing the utility of alternative metrics of branch support to address the ancient evolutionary radiation of tunas, stromateoids, and allies (Teleostei: Pelagiaria)
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Data from: Punctuated versus gradual shifts in the multivariate evolutionary process: a test with paired radiations of scincid lizards
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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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Reduced evolutionary constraint accompanies ongoing radiation in deep-sea anglerfishes
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Data from: Evolutionary radiation strategy revealed in the Scarabaeidae with evidence of continuous spatiotemporal morphology and phylogenesis
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Many ways to build an angler: diversity of feeding morphologies in a deep-sea evolutionary radiation
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Ecological diversification preceded geographical expansion during the evolutionary radiation of Cataglyphis desert ants
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Data from: Functional traits in parallel evolutionary radiations and trait-environment associations in the Cape Floristic region of South Africa
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A hotspot of groundwater amphipod diversity on a crossroad of evolutionary radiations
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Data from: Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L.
PREMISE OF THE STUDY: Estimating phylogenetic relationships in relatively recent evolutionary radiations is challenging, especially if short branches associated with recent divergence result in multiple gene tree histories. We combine anchored enrichment next-generation sequencing with species tree analyses to produce a robust estimate of phylogenetic relationships in the genus Protea (Proteaceae), an iconic radiation in South Africa. METHODS: We sampled multiple individuals within 59 out of 112 species of Protea and 6 outgroup species for a total of 163 individuals, and obtained sequences for 498 low-copy, orthologous nuclear loci using anchored phylogenomics. We compare several approaches for building species trees, and explore gene tree–species tree discrepancies to determine whether poor phylogenetic resolution reflects a lack of informative sites, incomplete lineage sorting, or hybridization. KEY RESULTS: Phylogenetic estimates from species tree approaches are similar to one another and recover previously well-supported clades within Protea, in addition to providing well-supported phylogenetic hypotheses for previously poorly resolved intrageneric relationships. Individual gene trees are markedly different from one another and from species trees. Nonetheless, analyses indicate that differences among gene trees occur primarily concerning clades supported by short branches. CONCLUSIONS: Species tree methods using hundreds of nuclear loci provided strong support for many previously unresolved relationships in the radiation of the genus Protea. In cases where support for particular relationships remains low, these appear to arise from few informative sites and lack of information rather than strongly supported disagreement among gene trees.
Data from: Evidence for past and present hybridization in three Antarctic icefish species provides new perspectives on an evolutionary radiation
Determining the timing, extent, and underlying causes of inter-specific gene exchange during or following speciation is central to understanding species' evolution. Antarctic notothenioid fish, thanks to the acquisition of antifreeze glycoproteins during Oligocene transition to polar conditions, experienced a spectacular radiation to >100 species during Late Miocene cooling events. The impact of recent glacial cycles on this group is poorly known, but alternating warming and cooling periods may have affected species' distributions, promoted ecological divergence into recurrently opening niches, and/or possibly brought allopatric species into contact. Using microsatellite markers and statistical methods including Approximate Bayesian Computation, we investigated genetic differentiation, hybridization and the possible influence of the last glaciation/deglaciation events in three icefish species of the genus Chionodraco. Our results provide strong evidence of contemporary and past introgression by showing that: i) a substantial fraction of contemporary individuals in each species has mixed ancestry; ii) evolutionary scenarios excluding hybridization or including it only in ancient times have small or zero posterior probabilities; iii) the data support a scenario of interspecific gene flow associated with the two most recent interglacial periods. Glacial cycles might therefore have had a profound impact on the genetic composition of Antarctic fauna, as newly available shelf areas during the warmer intervals might have favoured secondary contacts and hybridization between diversified groups. If our findings are confirmed in other notothenioids, they offer new perspectives for understanding evolutionary dynamics of Antarctic fish, and suggest a need for new predictions on the effects of global warming in this group.
Data from: Ecological and evolutionary determinants for the adaptive radiation of the Madagascan vangas
Adaptive radiation is the rapid diversification of a single lineage into many species that inhabit a variety of environments or use a variety of resources and differ in traits required to exploit these. Why some lineages undergo adaptive radiation is not well-understood, but filling unoccupied ecological space appears to be a common feature. We construct a complete, dated, species-level phylogeny of the endemic Vangidae of Madagascar. This passerine bird radiation represents a classic, but poorly known, avian adaptive radiation. Our results reveal an initial rapid increase in evolutionary lineages and diversification in morphospace after colonizing Madagascar in the late Oligocene some 25 Mya. A subsequent key innovation involving unique bill morphology was associated with a second increase in diversification rates about 10 Mya. The volume of morphospace occupied by contemporary Madagascan vangas is in many aspects as large (shape variation)—or even larger (size variation)—as that of other better-known avian adaptive radiations, including the much younger Galapagos Darwin's finches and Hawaiian honeycreepers. Morphological space bears a close relationship to diet, substrate use, and foraging movements, and thus our results demonstrate the great extent of the evolutionary diversification of the Madagascan vangas.
Data from: Evolutionary radiations of Proteaceae are triggered by the interaction between traits and climates in open habitats
Aim: Ecologically driven diversification can create spectacular diversity in both species numbers and form. However, the prediction that the match between intrinsic (e.g. functional trait) and extrinsic (e.g. climatic niche) variables may lead to evolutionary radiation has not been critically tested. Here, we test this hypothesis in the Southern Hemisphere plant family Proteaceae, which shows a spectacular diversity in open mediterranean shrublands in the Southwest Australian Floristic Region (SWAFR) and the Cape Floristic Region (CFR). Species in the Proteaceae family occupy habitats ranging from tropical rain forests to deserts and are remarkably variable in leaf morphology. Location: Southern Hemisphere. Methods: We built a phylogenetic tree for 337 Proteaceae species (21% of the total), representing all main clades, climatic tolerances and morphologies, and collected leaf functional traits (leaf area, sclerophylly, leaf shape) for 261 species and climatic niche data for 1645 species. Phylogenetic generalized least squares regression and quantitative-trait evolutionary model testing were used to investigate the evolutionary pathways of traits and climatic niches, and their effect on diversification rates. Results: We found that divergent selection may have caused lineages in open vegetation types to evolve towards trait and climatic niche optima distinct from those in closed forests. Furthermore, we show that the interaction between open habitats, dry, warm and/or mediterranean climates, and small, sclerophyllous, toothed leaves increases net diversification rates in Proteaceae. Main conclusions: Our results suggest that the evolution of specific leaf adaptations may have allowed Proteaceae to adapt to variable climatic niches and diversify extensively in open ecosystems such as those in the CFR and SWAFR. This match between morphology and environment may therefore more generally lead to evolutionary radiation.
Fig. 2 in The Chalcidoidea bush of life: evolutionary history of a massive radiation of minute wasps
Fig. 2. Overview of the topologies obtained with the different datasets as saturation decreases. Datasets (AHE414 and UCEs) are described in Table 1, and trees are available in Fig. S1 and Appendix S1. Groups that are discussed in text are highlighted. Only IQ-TREE trees are shown. ROTO/BAEO = Rotoitidae (Baeomorphidae); CHAL = Chalcididae; EURY = Eurytomidae; GALL = gall clade (see text); MYMA = Mymaridae; PTERO = group of Pteromalid wasps (Austroterobiinae; part Colotrechninae; Miscogastrinae; part Ormocerinae; Otitesellinae; Pteromalinae; Sycoecinae; Sycoryctinae); "Tiny Wasp clade" (see text).
Fig. 3 in The Chalcidoidea bush of life: evolutionary history of a massive radiation of minute wasps
Fig. 3. Collapsed summary cladograms. Combined AHE (exonsAA) and UCE (UCEs90-25) results for 433 taxa, 2054 loci including 103 395 AA +180 711 nucleotide sites. Results of IQ-TREE concatenated analysis with one partition for each type of data (exonsAA vs. UCEs90-25). SHaLRT/UFBoot/gCF/sCF are indicated at nodes. Clades were collapsed to higher level groups (family, subfamily, tribe). Colours are meant to allow for comparisons between trees. Vertical bars represent similar clade relationships for the analyses of IQ-TREE: UCEs90-25 (UCE407), exonsAA (AHE414), AHE520AA; parsimony: combined (COM433), UCEs90-25 (UCE407), exonsAA (AHE414), AHE520AA; Munro et al. (2011; 720 taxa); Heraty et al. (2013; 300 taxa). Vertical red bars with an X were not recovered as monophyletic in that analysis. Faded colour bars represent that the clade was included but relationships alternated. P indicates paraphyletic lineages. Clades without an X or bar were supported; the lack of a bar indicates the clade was supported but the deeper relationships were not. Higher group names refer to the classification before Burks et al. (2022). Family abbreviations expanded in Table S1.
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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.
Annotated Behaviour and Observability Dataset (ABODe)
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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.