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1,344 results for “: phylogenomics”
Phylogenomic analyses of the East Asian endemic Abelia (Caprifoliaceae) shed insights into the temporal and spatial diversification history with widespread hybridization
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Mimicry and mitonuclear discordance in nudibranchs: new insights from exon capture phylogenomics
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Nuclear and plastid phylogenomic analyses provide insights into the reticulate evolution, species delimitation and biogeography of the Sino-Japanese disjunctive Diabelia (Caprifoliaceae)
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Phylogenomics resolves the invasion history of Acacia auriculiformis in Florida
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Genomic and GWAS analyses demonstrate phylogenomic relationships of Gossypium barbadense in China and selection for fiber length, lint percentage, and Fusarium wilt resistance
GEO Series GSE184965. Gossypium barbadense. 90 samples. Type: Expression profiling by high throughput sequencing.
Signal, bias, and the role of transcriptome assembly quality in phylogenomic inference
<p>Transcriptome assemblies of liver RNA-seq from 38 craniate taxa. Each taxon has two assemblies from the same read sets, one of high quality and one of low-quality according to overall TransRate score.</p>
Data from: Phylogenomics supports incongruence between ecological specialization and taxonomy in a charismatic clade of buck moths
Local adaptation can be a fundamental component of speciation, but its dynamics in relation to gene flow are not necessarily straightforward. Herbivorous taxa with localized host plant or habitat specialization across their geographic range are ideal models for investigating the patterns and constraints of local adaptation and its impact on diversification. The charismatic, day-flying moths of the Hemileuca maia species complex (Lepidoptera: Saturniidae) are such taxa, as they are geographically-widespread, exhibit considerable ecological and morphological variability and host and habitat specificity, but apparently lack genetic differentiation across their range. Here, we use genome-wide single nucleotide polymorphisms to assess relationships and population structure of this group across North America, and investigate the scales where genomic divergence correlates with adaptive ecological characteristics. In contrast to previous genetic studies of the group, we find broad- and fine-scale genetic differentiation between lineages, which is at odds with various levels of taxonomic description and recognition of conservation units. Furthermore, ecological specialization only explains some fine-scale genetic differentiation, and across much of the group's range, local adaptation is apparently occurring in the face of strong gene flow. These results provide unprecedented insight into drivers of speciation in this group, the relationship between taxonomy and genomics-informed species boundaries, and conservation management of internationally-protected entities. Broadly, this system provides a model for understanding how local adaptation in an herbivore can arise and be maintained in the face of apparently strong gene flow, and the importance of geographic isolation in generating genomic divergence, despite a lack of ecological divergence.
Data from: Chloroplast phylogenomic analysis of chlorophyte green algae identifies a novel lineage sister to the Sphaeropleales (Chlorophyceae)
Background: The class Chlorophyceae (Chlorophyta) includes morphologically and ecologically diverse green algae. Most of the documented species belong to the clade formed by the Chlamydomonadales (also called Volvocales) and Sphaeropleales. Although studies based on the nuclear 18S rRNA gene or a few combined genes have shed light on the diversity and phylogenetic structure of the Chlamydomonadales, the positions of many of the monophyletic groups identified remain uncertain. Here, we used a chloroplast phylogenomic approach to delineate the relationships among these lineages. Results: To generate the analyzed amino acid and nucleotide data sets, we sequenced the chloroplast DNAs (cpDNAs) of 24 chlorophycean taxa; these included representatives from 16 of the 21 primary clades previously recognized in the Chlamydomonadales, two taxa from a coccoid lineage (Jenufa) that was suspected to be sister to the Golenkiniaceae, and two sphaeroplealeans. Using Bayesian and/or maximum likelihood inference methods, we analyzed an amino acid data set that was assembled from 69 cpDNA-encoded proteins of 73 core chlorophyte (including 33 chlorophyceans), as well as two nucleotide data sets that were generated from the 69 genes coding for these proteins and 29 RNA-coding genes. The protein and gene phylogenies were congruent and robustly resolved the branching order of most of the investigated lineages. Within the Chlamydomonadales, 22 taxa formed an assemblage of five major clades/lineages. The earliest-diverging clade displayed Hafniomonas laevis and the Crucicarteria, and was followed by the Radicarteria and then by the Chloromonadinia. The latter lineage was sister to two superclades, one consisting of the Oogamochlamydinia and Reinhardtinia and the other of the Caudivolvoxa and Xenovolvoxa. To our surprise, the Jenufa species and the two spine-bearing green algae belonging to the Golenkinia and Treubaria genera were recovered in a highly supported monophyletic group that also included three taxa representing distinct families of the Sphaeropleales (Bracteacoccaceae, Mychonastaceae, and Scenedesmaceae). Conclusions: Our phylogenomic study advances our knowledge regarding the circumscription and internal structure of the Chlamydomonadales, suggesting that a previously unrecognized lineage is sister to the Sphaeropleales. In addition, it offers new insights into the flagellar structures of the founding members of both the Chlamydomonadales and Sphaeropleales.
Data from: Using phylogenomics to resolve mega-families: an example from Compositae
Next-generation sequencing and phylogenomics hold great promise for elucidating complex relationships among large plant families. Here we performed targeted capture of low copy sequences followed by next-generation sequencing on the Illumina platform in the large and diverse angiosperm family Compositae (Asteraceae). The family is monophyletic based on morphology and molecular data, yet many areas of the phylogeny have unresolved polytomies and interpreting phylogenetic patterns has been historically difficult. In order to outline a method and provide a framework and for future phylogenetic studies in the Compositae, we sequenced 23 taxa from across the family in which the relationships were well established as well as a member of the sister family Calyceraceae. We generated nuclear data from 795 loci and assembled chloroplast genomes from off-target capture reads enabling the comparison of nuclear and chloroplast genomes for phylogenetic analyses. We also analyzed multi-copy nuclear genes in our data set using a clustering method during orthology detection, and we applied a network approach to these clusters—analyzing all related locus copies. Using these data we produced hypotheses of phylogenetic relationships employing both a conservative (restricted to only loci with one copy per targeted locus) and a multigene approach (including all copies per targeted locus). The methods and bioinformatics workflow presented here provide a solid foundation for future work aimed at understanding gene family evolution in the Compositae as well as providing a model for phylogenomic analyses in other plant mega-families.
Data from: Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants
Background: The use of transcriptomic and genomic datasets for phylogenetic reconstruction has become increasingly common as researchers attempt to resolve recalcitrant nodes with increasing amounts of data. The large size and complexity of these datasets introduce significant phylogenetic noise and conflict into subsequent analyses. The sources of conflict may include hybridization, incomplete lineage sorting, or horizontal gene transfer, and may vary across the phylogeny. For phylogenetic analysis, this noise and conflict has been accommodated in one of several ways: by binning gene regions into subsets to isolate consistent phylogenetic signal; by using gene-tree methods for reconstruction, where conflict is presumed to be explained by incomplete lineage sorting (ILS); or through concatenation, where noise is presumed to be the dominant source of conflict. The results provided herein emphasize that analysis of individual homologous gene regions can greatly improve our understanding of the underlying conflict within these datasets. Results: Here we examined two published transcriptomic datasets, the angiosperm group Caryophyllales and the aculeate Hymenoptera, for the presence of conflict, concordance, and gene duplications in individual homologs across the phylogeny. We found significant conflict throughout the phylogeny in both datasets and in particular along the backbone. While some nodes in each phylogeny showed patterns of conflict similar to what might be expected with ILS alone, the backbone nodes also exhibited low levels of phylogenetic signal. In addition, certain nodes, especially in the Caryophyllales, had highly elevated levels of strongly supported conflict that cannot be explained by ILS alone. Conclusion: This study demonstrates that phylogenetic signal is highly variable in phylogenomic data sampled across related species and poses challenges when conducting species tree analyses on large genomic and transcriptomic datasets. Further insight into the conflict and processes underlying these complex datasets is necessary to improve and develop adequate models for sequence analysis and downstream applications. To aid this effort, we developed the open source software phyparts (https://bitbucket.org/blackrim/phyparts), which calculates unique, conflicting, and concordant bipartitions, maps gene duplications, and outputs summary statistics such as internode certainy (ICA) scores and node-specific counts of gene duplications.
Data from: Phylogenomics and historical biogeography of the monocot order Liliales: out of Australia and through Antarctica
We present the first phylogenomic analysis of relationships among all ten families of Liliales, based on 75 plastid genes from 35 species in 29 genera, and 97 additional plastomes stratified across angiosperm lineages. We used a supermatrix approach to extend our analysis to 58 of 64 genera of Liliales, and calibrated the resulting phylogeny against 17 fossil dates to produce a new timeline for monocot evolution. Liliales diverged from other monocots 124 Mya and began splitting into separate families 113 Mya. Our data support an Australian origin for Liliales, with close relationships between three pairs of lineages (Corsiaceae/Campynemataceae, Philesiaceae/Ripogonaceae, tribes Alstroemerieae/Luzuriageae) in South America and Australia or New Zealand reflecting teleconnections of these areas via Antarctica. Long-distance dispersal (LDD) across the Pacific and Tasman Sea led to re-invasion of New Zealand by two lineages (Luzuriaga, Ripogonum); LDD allowed Campynemanthe to colonize New Caledonia after its submergence until 37 Mya. LDD permitted Colchicaceae to invade East Asia and Africa from Australia, and re-invade Africa from Australia. Periodic desert greening permitted Gloriosa and Iphigenia to colonize Southeast Asia overland from Africa, and Androcymbium–Colchicum to invade the Mediterranean from South Africa. Melanthiaceae and Liliaceae crossed the Bering land-bridge several times from the Miocene to the Pleistocene.
Data from: Post K-Pg diversification of the mammalian order Eulipotyphla as suggested by phylogenomic analyses of ultra-conserved elements
The origin of the mammalian order Eulipotyphla has been debated intensively with arguments around whether they began diversifying before or after the Cretaceous-Palaeogene (K-Pg) boundary at 66 Ma. Here, we used an in-solution nucleotide capture method and next generation DNA sequencing to determine the sequence of hundreds of ultra-conserved elements (UCEs), and conducted phylogenomic and molecular dating analyses for the four extant eulipotyphlan lineages—Erinaceidae, Solenodontidae, Soricidae, and Talpidae. Concatenated maximum-likelihood analyses with single or partitioned models and a coalescent species-tree analysis showed that divergences among the four major eulipotyphlan lineages occurred within a short period of evolutionary time, but did not resolve the interrelationships among them. Alternative suboptimal phylogenetic hypotheses received consistently the same amount of support from different UCE loci, and were not significantly different from the maximum likelihood tree topology, suggesting the prevalence of stochastic lineage sorting. Molecular dating analyses that incorporated among-lineage evolutionary rate differences supported a scenario where the four eulipotyphlan families diversified between 57.8 and 63.2 Ma. Given short branch lengths with low support values, traces of rampant genome-wide stochastic lineage sorting, and post K-Pg diversification, we concluded that the crown eulipotyphlan lineages arose through a rapid diversification after the K-Pg boundary when novel niches were created by the mass extinction of species.
Figure 5 from: Du W, Wang Y, Xie D, Li E, Bai Y, Shang C, Zhang Z (2024) Phylogenomics reveal Populus gonggaensis as a hybrid between P. lasiocarpa and P. cathayana (Salicaceae). PhytoKeys 237: 161-177. https://doi.org/10.3897/phytokeys.237.103012
Figure 5 Lectotype of Populus gonggaensis N. Chao & J.R. He.
Figures 28-29 from: Wood TJ, Patiny S, Bossert S (2022) An unexpected new genus of panurgine bees (Hymenoptera, Andrenidae) from Europe discovered after phylogenomic analysis. Journal of Hymenoptera Research 89: 183-210. https://doi.org/10.3897/jhr.89.72083
Figures 28-29 Halopanurgus baldocki comb. nov. profile 28 female 29 male.
Figures 31-32 from: Wood TJ, Patiny S, Bossert S (2022) An unexpected new genus of panurgine bees (Hymenoptera, Andrenidae) from Europe discovered after phylogenomic analysis. Journal of Hymenoptera Research 89: 183-210. https://doi.org/10.3897/jhr.89.72083
Figures 31-32 Flavipanurgus male genitalia 31Flavipanurgus granadensis32Flavipanurgus merceti.
FIGURE 2 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 2. (Continued).
FIGURE 2 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 2. (Continued).
Data from: Phylogenomic analyses reveal novel relationships among snake families
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Data from: Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants
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Data from: Phylogenomics of pike cichlids (Cichlidae: Crenicichla): the rapid evolution and trophic diversification of an incipient species flock
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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
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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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.