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101 results for “rapid radiation”
Phylogenomic analyses reveal an allopolyploid origin of core Didymocarpinae (Gesneriaceae) followed by rapid radiation
<p><span>Allopolyploid plants have long been regarded as possessing genetic advantages under certain circumstances due to the combined effects of their hybrid origins and duplicated genomes. However, the evolutionary consequences of allopolyploidy in lineage diversification remain to be fully understood. Here, we investigate the evolutionary consequences of allopolyploidy using 138 transcriptomic sequences of Gesneriaceae, including 124 newly sequenced, focusing particularly on the largest subtribe Didymocarpinae. We estimated the phylogeny of Gesneriaceae using concatenated and coalescent-based methods based on five different nuclear matrices and 27 plastid genes, focusing on relationships among major clades. To better understand the evolutionary affinities in this family, we applied a range of approaches to characterize the extent and cause of phylogenetic incongruence. We found that extensive conflicts between nuclear and chloroplast genomes and among nuclear genes were caused by both incomplete lineage sorting (ILS) and reticulation, and we found evidence of widespread ancient hybridization and introgression. Using the most highly supported phylogenomic framework, we revealed multiple bursts of gene duplication throughout the evolutionary history of Gesneriaceae. By incorporating molecular dating and analyses of diversification dynamics, our study shows that an ancient allopolyploidization event occurred around the Oligocene-Miocene boundary, which may have driven the rapid radiation of core Didymocarpinae.</span></p>
Phylogenomics reveal extensive phylogenetic discordance due to incomplete lineage sorting following the rapid radiation of alpine butterflies (Papilionidae: Parnassius)
<p><span><span>In rapid radiation, the earliest components of evolutionary divergence are often difficult to resolve, which were always driven by the characteristics of taxa and the limitations of alternative analytical methods</span>. </span><span>The origin and radiation of the alpine butterfly <em>Parnassius</em>, a high-altitude mountainous insect group, can be attributed to the uplift of the Qinghai-Tibet Plateau (QTP). Despite detailed phylogenetic analyses of the genus, deep phylogenetic relationships among the major subgenera remain recalcitrant. In this study, 102 individuals from 10 representative <em>Parnassius</em> species were sampled to resolve the phylogenetic relationships among subgenera based on nuclear and mitochondrial genome data sets. Gene-tree/species-tree conflicts were detected by concatenation and multispecies coalescent (MSC) approaches. We recovered a well-supported species tree, despite these conflicts, and detected considerable phylogenetic discordance among genomic regions. The main explanation for the topological discordance among subgenera was extensive incomplete lineage sorting (ILS), whereas introgression events were not prominent. The origin and explosive radiation of <em>Parnassius</em> (i.e., rapid succession of speciation events) in the late Miocene associated with environmental events on the plateau led to short internal branches, thereby increasing ILS and topological conflicts, especially among closely related subgenera. Our results also suggested that MSC approaches (SNAPP and SVDquartets) are accurate and superior to the concatenation approach; in particular, SVDquartets can explicitly accommodate gene-tree/species-tree conflicts caused by high ILS and demonstrate strong robustness. Lastly, we explored the phylogenomic data by testing multiple sources of phylogenomic conflict to clarify the strengths and limitations of different approaches, while considering phylogenetic signal variation in mitochondrial loci. We anticipate that the phylogeny described here will be the backbone of future evolutionary studies of the genus and will provide insight into phylogenetic discordance due to rapid radiation.</span></p>
Supplementary material: Ultraconserved elements improve the resolution of difficult nodes within the rapid radiation of neotropical sigmodontine rodents (Cricetidae: Sigmodontinae)
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Data from: Phylogenomics reveals three sources of adaptive variation during a rapid radiation
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Data from: Rapid radiation in a highly diverse marine environment
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Interrogating discordance resolves relationships in the rapid radiation of Old World fruit bats (Chiroptera: Pteropodidae)
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Phylogenomic analyses reveal an allopolyploid origin of core Didymocarpinae (Gesneriaceae) followed by rapid radiation
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Data from: Whole-genome phylogenetic reconstruction as a powerful tool to reveal homoplasy and ancient rapid radiation in waterflea evolution
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Adaptive radiation of pelagiarian fishes at the K/Pg boundary led to rapid diversification of mandible morphology
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Amino acids (AA) all genes for: Beyond Drosophila: resolving the rapid radiation of schizophoran flies with phylotranscriptomics
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Implementing large genomic SNP datasets in phylogenetic network reconstructions: a case study of particularly rapid radiations of cichlid fish
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Phylogenomics reveal extensive phylogenetic discordance due to incomplete lineage sorting following the rapid radiation of alpine butterflies (Papilionidae: Parnassius)
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Data from: Impacts of inference method and dataset filtering on phylogenomic resolution in a rapid radiation of ground squirrels (Xerinae: Marmotini)
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Rampant Reticulation in a Rapid Radiation of Tropical Trees - Insights from <i>Inga</i> (Fabaceae)
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Data from: Phylogenomic analysis of target enrichment and transcriptome data uncovers rapid radiation and extensive hybridization in slipper orchid genus Cypripedium L.
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Extensive photobiont sharing in a rapidly-radiating cyanolichen clade
<p>Recent studies have uncovered remarkable diversity <i>Dictyonema </i>s.lat. basidiolichens, here recognized as subtribe Dictyonemateae. This group includes five genera and 148 species, but hundreds more await description. The photobionts of these lichens belong to <i>Rhizonema</i>, a recently resurrected cyanobacterial genus known by a single species. To further investigate photobiont diversity within Dictyonemateae, we generated 765 new cyanobacterial sequences from 635 specimens collected from 18 countries. The ITS barcoding locus supported the recognition of 200 mycobiont (fungal) species among these samples, but the photobiont diversity was comparatively low. Our analyses revealed three main divisions of <i>Rhizonema</i>, with two repeatedly recovered as monophyletic (proposed as new species), and the third mostly paraphyletic. The paraphyletic lineage corresponds to <i>R. interruptum</i> and partnered with mycobionts from all five genera in Dictyonemateae. There was no evidence of photobiont-mycobiont co-speciation, but one of the monophyletic lineages of <i>Rhizonema</i> appears to partner predominantly with one of the two major clades of <i>Cora</i> (mycobiont) with samples collected largely from the northern Andes. Molecular clock estimations indicate the <i>Rhizonema</i> species are much older than the fungal species in the Dictyonemateae, suggesting that these basidiolichens obtained their photobionts from older ascolichen lineages and the photobiont variation in extant lineages of Dictyonemateae is the result of multiple photobiont switches. These results support the hypothesis of lichens representing "fungal farmers", in which diverse mycobiont lineages associate with a substantially lower diversity of photobionts by sharing those photobionts best suited for the lichen symbiosis among multiple and often unrelated mycobiont lineages.</p>
Supplementary data for: Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression
<p>Our understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to increased acceptance of once controversial hypotheses regarding phylogenetic relationships, hybridization and introgression, and the biogeographical history of primate groups. Among these findings is a pattern of recent introgression between species within all major primate groups examined to date, though little is known about introgression deeper in time. To address this and other phylogenetic questions, here we present new reference genome assemblies for three Old World Monkey species: <i>Colobus angolensis ssp. palliatus </i>(the black and white colobus), <i>Macaca nemestrina </i>(southern pig-tailed macaque), and <i>Mandrillus leucophaeus </i>(the drill). We combine these data with 23 additional primate genomes to estimate both the species tree and individual gene trees using thousands of loci. While our species tree is largely consistent with previous phylogenetic hypotheses, the gene trees reveal high levels of genealogical discordance associated with multiple primate radiations. We use strongly asymmetric patterns of gene tree discordance around specific branches to identify multiple instances of introgression between ancestral primate lineages. In addition, we exploit recent fossil evidence to perform fossil-calibrated molecular dating analyses across the tree. Taken together, our genome-wide data help to resolve multiple contentious sets of relationships among primates, while also providing insight into the biological processes and technical artifacts that led to the disagreements in the first place.</p>
Data from: Reticulate evolution, ancient chloroplast haplotypes, and rapid radiation of the Australian plant genus Adenanthos (Proteaceae)
<p><span><span><span><span><span><span><span><span><span><span><span>Cytonuclear discordance, commonly detected in phylogenetic studies, is often attributed to hybridisation and/or incomplete lineage sorting (ILS). New sequencing technologies and analytical approaches can provide new insights into the relative importance of these processes. Hybridisation has previously been reported in the Australian endemic plant genus <i>Adenanthos </i>(Proteaceae). Like many Australian genera, <i>Adenanthos</i> is of relatively ancient origin, and provides an opportunity to examine long-term evolutionary consequences of gene flow between lineages. Using a hybrid capture approach, we assembled densely sampled low-copy nuclear and plastid DNA sequences for <i>Adenanthos</i>, inferred its evolutionary history, and used a Bayesian posterior predictive approach and coalescent simulations to assess relative contributions of hybridisation and ILS to cytonuclear discordance. Our analyses indicate that strong incongruence detected between our plastid and nuclear phylogenies is not only the result of ILS, but also result from extensive ancient introgression as well as recent chloroplast capture and introgression between extant <i>Adenanthos </i>species<i>. </i>The deep reticulation was also detected from long-persisting chloroplast haplotypes shared between evolutionarily distant species. These haplotypes may have persisted for over 12 Ma in localised populations across southwest Western Australia, indicating that the region is not only an important area for old endemic lineages and accumulation of species, but is also characterized by persistence of high genetic diversity. Deep introgression in <i>Adenanthos</i> coincided with the rapid radiation of the genus during the Miocene, a time when many Australian temperate plant groups radiated in response to large-scale climatic change. This study suggests that ancient introgression may play an important role in the evolution of the Australian flora more broadly. </span></span></span></span></span></span></span></span></span></span></span></p>
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: The challenges of resolving a rapid, recent radiation: empirical and simulated phylogenomics of Philippine shrews
Phylogenetic relationships in recent, rapid radiations can be difficult to resolve due to incomplete lineage sorting and reliance on genetic markers that evolve slowly relative to the rate of speciation. By incorporating hundreds to thousands of unlinked loci, phylogenomic analyses have the potential to mitigate these difficulties. Here, we attempt to resolve phylogenetic relationships among eight shrew species (genus Crocidura) from the Philippines, a phylogenetic problem that has proven intractable with small (< 10 loci) data sets. We sequenced hundreds of ultraconserved elements and whole mitochondrial genomes in these species and estimated phylogenies using concatenation, summary coalescent, and hierarchical coalescent methods. The concatenated approach recovered a maximally supported and fully resolved tree. In contrast, the coalescent-based approaches produced similar topologies, but each had several poorly supported nodes. Using simulations, we demonstrate that the concatenated tree could be positively misleading. Our simulations also show that the tree shape we tend to infer, which involves a series of short internal branches, is difficult to resolve, even if substitution models are known and multiple individuals per species are sampled. As such, the low support we obtained for backbone relationships in our coalescent-based inferences reflects a real and appropriate lack of certainty. Our results illuminate the challenges of estimating a bifurcating tree in a rapid and recent radiation, providing a rare empirical example of a nearly simultaneous series of speciation events in a terrestrial animal lineage as it spreads across an oceanic archipelago.
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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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.