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3,761 results for “phylogenetic relationships”
Data from: Phylogenetic relationships, breeding implications, and cultivation history of Hawaiian taro (Colocasia esculenta) through genome-wide SNP genotyping
Taro, Colocasia esculenta, is one of the world's oldest root crops and of particular economic and cultural significance in Hawai'i, where historically more than 150 different landraces were grown. We developed a genome-wide set of more than 2400 high-quality single nucleotide polymorphism (SNP) markers from 70 taro accessions of Hawaiian, South Pacific, Palauan, and mainland Asian origins, with several objectives: (a) uncover the phylogenetic relationships between Hawaiian and other Pacific landraces, (b) shed light on the history of taro cultivation in Hawai'i, and (c) develop a tool to discriminate among Hawaiian and other taros. We found that almost all existing Hawaiian landraces fall into five monophyletic groups that are largely consistent with the traditional Hawaiian classification based on morphological characters, e.g., leaf shape and petiole color. Genetic diversity was low within these clades but considerably higher between them. Population structure analyses further indicated that the diversification of taro in Hawai'i most likely occurred by a combination of frequent somatic mutation and occasional hybridization. Unexpectedly, the South Pacific accessions were found nested within the clades mainly composed of Hawaiian accessions, rather than paraphyletic to them. This suggests that the origin of clades identified here preceded the colonization of Hawai'i, and that early Polynesian settlers brought taro landraces from different clades with them. In the absence of a sequenced genome, this marker set provides a valuable resource towards obtaining a genetic linkage map, and to study the genetic basis of phenotypic traits of interest to taro breeding such as disease resistance.
Data from: Phylogenetic relationships among Old World Ruellia L.: a new classification and reinstatement of the genus Dinteracanthus Schinz
The genus Ruellia (Acanthaceae) consists of some ca. 350 species that are concentrated in tropical and subtropical regions of the world. Old World Ruellia have never been the focus of explicit phylogenetic study, yet comprise the earliest diverging lineages in the genus and contain upwards of 100 species. We sampled 52 accessions representing 29 OW species of Ruellia for phylogenetic analysis. Results yielded five clades that were strongly supported and marked by morphological synapomorphies. Analyses additionally recovered a newly recognized lineage within the tribe Ruellieae, a small radiation of plants in the deserts of Namibia and Angola, and the name Dinteracanthus is available for reinstatement. Divergence time analysis using a primary fossil calibration revealed relatively young estimates for crown ages of all five clades of OW Ruellia (2.5 Ma ‐ 630,000 ypb) as well as for Dinteracanthus (2.0 Ma). Ancestral state reconstruction of pollination systems among OW Ruellia suggest a minimum of two transitions from short-tongued insect pollination to nocturnal moth pollination, one from short-tongued insect to bird pollination, and one reversal from nocturnal moth pollination back to short-tongued insect pollination. We formally delimit the five clades of OW Ruellia as sections and present a key to aid in their identification: sect. Eusiphon, sect. Dipteracanthus, sect. Madagasikara, sect. Pseudoruellia, and sect. Discifolia. We provisionally treat 77 of 97 species of OW Ruellia among these five sections, with the remaining names considered to be unresolved.
Data from: Cryptic diversity in the Mexican highlands: thousands of UCE loci help illuminate phylogenetic relationships, species limits and divergence times of montane rattlesnakes (Viperidae: Crotalus)
With the continued adoption of genome-scale data in evolutionary biology comes the challenge of adequately harnessing the information to make accurate phylogenetic inferences. Coalescent-based methods of species tree inference have become common, and concatenation has been shown in simulation to perform well, particularly when levels of incomplete lineage sorting are low. However, simulation conditions are often overly simplistic, leaving empiricists with uncertainty regarding analytical tools. We use a large ultraconserved element (UCE) data set (>3000 loci) from rattlesnakes of the Crotalus triseriatus group to delimit lineages and estimate species trees using concatenation and several coalescent-based methods. Unpartitioned and partitioned maximum-likelihood and Bayesian analysis of the concatenated matrix yield a topology identical to coalescent analysis of a subset of the data in bpp. ASTRAL analysis on a subset of the more variable loci also result in a tree consistent with concatenation and bpp, whereas the SVDquartets phylogeny differs at additional nodes. The size of the concatenated matrix has a strong effect on species-tree inference using SVDquartets, warranting additional investigation on optimal data characteristics for this method. Species-delimitation analyses suggest up to 16 unique lineages may be present within the C. triseriatus group, with divergences occurring during the Neogene and Quaternary. Network analyses suggest hybridization within the group is relatively rare. Altogether, our results reaffirm the Mexican highlands as a biodiversity hotspot and suggest that coalescent-based species-tree inference on data subsets can provide a strongly supported species tree consistent with concatenation of all loci with a large amount of missing data.
FIGURE 1 in Crozetia Davies (Diptera: Simuliidae): redescription of Cr. crozetensis, Cr. seguyi, number of larval instars, phylogenetic relationships and historical biogeography
FIGURE 1. Geographic position of the Crozet Archipelago. (Adapted from Carroll 2001)
Figure 2. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using COI sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.
Figure 2. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using COI sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.
Figure 4. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using COI and 16S rRNA sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.
Figure 4. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using COI and 16S rRNA sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.
Figure 3. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using 16S rRNA sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.
Figure 3. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using 16S rRNA sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.
Fig. 1 in The Taxonomy And Phylogenetic Relationships Of Species In The Bactrocera Musae Complex Of Fruit Flies (Diptera: Tephritidae: Dacinae) In Papua New Guinea
Fig. 1. Bactrocera (Bactrocera) balagawii, new species.
Fig. 2 in The Taxonomy And Phylogenetic Relationships Of Species In The Bactrocera Musae Complex Of Fruit Flies (Diptera: Tephritidae: Dacinae) In Papua New Guinea
Fig. 2. Bactrocera (Bactrocera) parabancroftii, new species.
Fig. 4 in The Taxonomy And Phylogenetic Relationships Of Species In The Bactrocera Musae Complex Of Fruit Flies (Diptera: Tephritidae: Dacinae) In Papua New Guinea
Fig. 4. Bactrocera (Bactrocera) rufivitta, new species.
Fig. 5 in The Taxonomy And Phylogenetic Relationships Of Species In The Bactrocera Musae Complex Of Fruit Flies (Diptera: Tephritidae: Dacinae) In Papua New Guinea
Fig. 5. Bactrocera (Bactrocera) uvariae, new species.
Fig. 3 in The Taxonomy And Phylogenetic Relationships Of Species In The Bactrocera Musae Complex Of Fruit Flies (Diptera: Tephritidae: Dacinae) In Papua New Guinea
Fig. 3. Bactrocera (Bactrocera) ramuensis, new species.
FIG. 9 in New ctenodactyloid rodents from the Erlian Basin, Nei Mongol, China, and the phylogenetic relationships of Eocene Asian ctenodactyloids
FIG. 9. Occlusal view of a maxillary fragment of Tamquammys fractus with P4–M2.
Shared single copy genes are generally reliable for inferring phylogenetic relationships among polyploid taxa
<p>Polyploidy, or whole-genome duplication, is expected to confound the inference of species trees with phylogenetic methods for two reasons. First, the presence of retained duplicated genes requires the reconciliation of the inferred gene trees to a proposed species tree. Second, even if the analyses are restricted to shared single copy genes, the occurrence of reciprocal gene loss, where the surviving genes in different species are paralogs from the polyploidy rather than orthologs, will mean that such genes will not have evolved under the corresponding species tree and may not have gene trees that allow inference of the species tree. Here we analyze three different ancient polyploidy events, using synteny-based inferences of orthology and paralogy to infer gene trees from more than 17,000 sets of homologous genes. We find that the simple use of single copy genes from polyploid organisms provides reasonably robust phylogenetic signals, despite the presence of reciprocal gene losses. Such gene trees are also most often in accord with the inferred species relationships inferred from maximum likelihood models of gene loss after polyploidy: a completely distinct phylogenetic signal present in these genomes. As seen in other studies, however, we find that methods for inferring phylogenetic confidence yield high support values even in cases where the underlying data suggest meaningful conflict in the phylogenetic signals.</p>
A target enrichment probe set for resolving phylogenetic relationships in the coffee family, Rubiaceae
<p><em>Rubiaceae </em>is among the most species-rich, morphologically and geographically diverse plant families. Phylogenies have been inferred for many different groups across the family, however these have mostly relied on few genomic and plastid loci, as opposed to large-scale genomic data. Target enrichment provides the ability to generate sequence data for hundreds to thousands of phylogenetically informative, single-copy loci, which often leads to improved phylogenetic resolution at both shallow and deep taxonomic scales; however, a publicly accessible <em>Rubiaceae</em>-specific probe set that allows for comparable phylogenetic inference across clades is lacking. Here, we use publicly accessible genomic resources to identify putatively single copy nuclear loci for target enrichment in two <em>Rubiaceae </em>tribes: Hillieae (<em>Cinchonoideae</em>) and Palicoureeae+Psychotrieae (<em>Rubioideae</em>). We sequenced 2270 exons corresponding to 1059 supercontigs in our target clades, and generated in silico target enrichment sequences for other <em>Rubiaceae </em>taxa using our designed probe set. Our probe set, which we call <em>Rubiaceae </em>2270, was effective for targeting loci in species across and even outside of <em>Rubiaceae</em>. This probe set will facilitate phylogenomic studies in <em>Rubiaceae </em>and advance systematics and macroevolutionary studies in the family.</p>
Alignments and tree files from: Phylogenetic relationships within tribe Hibisceae (Malvaceae) reveal complex patterns of polyphyly in Hibiscus and Pavonia
<p>The diverse and spectacular Hibisceae tribe comprises over 750 species. No studies, however, have broadly sampled across the dozens of genera in the tribe, leading to uncertainty in the relationships among genera. The non-monophyly of the genus <em>Hibiscus </em>is infamous and challenging, whereas the monophyly of most other genera in the tribe has yet to be assessed, including the large genus <em>Pavonia</em>. Here we significantly increase taxon sampling in the most complete phylogenetic study of the tribe to date. We assess monophyly of most currently recognized genera in the tribe and include three and thirteen newly sampled sections of <em>Hibiscus </em>and <em>Pavonia</em>, respectively. We also include five rarely sampled genera and 137 species previously unsampled. Our phylogenetic trees demonstrate that <em>Hibiscus</em>, as traditionally defined, encompasses at least 20 additional genera. The status of <em>Pavonia </em>emerges as comparable in complexity to <em>Hibiscus</em>. We offer clarity in the phylogenetic placement of several taxa of uncertain affinity (e.g., <em>Helicteropsis, Hibiscadelphus, Jumelleanthus, and Wercklea)</em>. We also identify two new clades and elevate them to the generic rank with the recognition of two, new monotypic genera: 1) <em>Blanchardia </em>M.M.Hanes & R.L.Barrett is a surprising Caribbean lineage that is sister to the entire tribe, and 2) <em>Astrohibiscus </em>McLay & R.L.Barrett represents former members of <em>Hibiscus caesius</em> s.l. <em>Cravenia </em>McLay & R.L.Barrett is also described as a new genus for the <em>Hibiscus panduriformis</em> clade which is allied to <em>Abelmoschus</em>. Finally, we introduce a new classification for the tribe and clarify the boundaries of <em>Hibiscus </em>and <em>Pavonia</em>.</p>
Data from: Phylogenetic relationships of genera Cladocolea and Struthanthus (Loranthaceae) with emphasis on the Mexican species
<p><em>Cladocolea</em> (Loranthaceae) is a neotropical genus currently containing 24 species. Its taxonomic history included changes in its circumscription as the transfers of some of its species to other genera of the family. Several phylogenetic studies of Loranthaceae have recognized a close relationship between <em>Cladocolea</em> and <em>Struthanthus</em>. However, both genera were poorly represented in these studies, so here we generate a phylogeny of Mexican species of <em>Cladocolea</em>, <em>Struthanthus</em>, and other genera of Psittacanthinae, using nuclear DNA sequences of the ITS region, as well as the chloroplast regions <em>matK</em> and <em>trnL-F</em>. One hundred twelve individuals were sampled and 12 GenBank sequences were included. We included 23 taxa of <em>Cladocolea</em> and 30 species of nine other genera of Loranthaceae. In order to estimate ancestral states and character evolution, 13 morphological characters were mapped, both vegetative and reproductive. Bayesian Inference and Maximum Likelihood analyses were performed using independent matrices and a concatenated matrix of 2842 characters. Our results show that <em>Cladocolea</em> and <em>Struthanthus</em> are both polyphyletic genera. However, the Mexican species of <em>Cladocolea</em> and <em>Struthanthus</em> with convolute or sigmoid styles form a monophyletic group. Finally, the analysis of ancestral character states indicates a trend towards a reduction of inflorescences in the <em>Cladocolea</em>-<em>Struthanthus</em> complex. New combinations and synonymies are proposed.</p>
Fig. 13 in The mostly cavernicolous millipede genus Stygiiulus Verhoeff, 1929, stat. nov.: taxonomy, distribution and phylogenetic relationships (Diplopoda, Julida, Julidae)
Fig. 13. General distribution of the species of the genus Stygiiulus stat. nov.
Resolving the phylogenetic relationship among recently diverged members of the rockfish subgenus Sebastosomus
<p>Rapid speciation is an important aspect of adaptive radiations, but can obfuscate phylogenetic relationships among taxa. For recent radiations, there are challenges to reconstructing the relationships among the species due to often shorter branch lengths. Resolution of these relationships is further confounded when studies only use a few genetic markers. Double digest restriction-site associated DNA sequencing (ddRADseq) is a method of next generation sequencing that identifies many single nucleotide polymorphisms (SNPs) throughout the genome. This increases statistical power to resolve close phylogenetic relationships like those found within an adaptive radiation. We used this approach to understand the evolutionary history of the rockfishes of the genus <em>Sebastes</em>, which experienced an adaptive radiation between 3 to 5 mya. Here, we reconstructed the phylogenetic relationships among six species of rockfish within the subgenus <em>Sebastosomus</em> using over 11,600 SNPs. This reconstruction includes the two recently diverged species, <em>Sebastes</em> mystinus and <em>S. diaconus</em>, that were first described genetically in 2008 using mtDNA control region sequence data and six microsatellite loci. We confirmed the relationship of these cryptic species as sister-taxa and found evidence that <em>S. melanops</em> and <em>S. flavidus</em> were also sister-taxa. The latter contradicts prior studies but is supported by our reconstruction using nuclear DNA and measures of genetic differentiation tests and a discriminant analysis of principal components. The relationships between the species of <em>Sebastosomus</em> are further supported by morphological, biological, and ecological justifications.</p>
The Community Coevolution Model with application to the study of evolutionary relationships between genes based on phylogenetic profiles
<p>Organismal traits can evolve in a coordinated way, with correlated patterns of gains and losses reflecting important evolutionary associations. Discovering these associations can reveal important information about the functional and ecological linkages among traits. Phylogenetic profiles treat individual genes as traits distributed across sets of genomes and can provide a fine-grained view of the genetic underpinnings of evolutionary processes in a set of genomes. Phylogenetic profiling has been used to identify genes that are functionally linked, and to identify common patterns of lateral gene transfer in microorganisms. However, comparative analysis of phylogenetic profiles and other trait distributions should take into account the phylogenetic relationships among the organisms under consideration.</p> <p>Here we propose the Community Coevolution Model (CCM), a new coevolutionary model to analyze the evolutionary associations among traits, with a focus on phylogenetic profiles. In the CCM, traits are considered to evolve as a community with interactions, and the transition rate for each trait depends on the current states of other traits. Surpassing other comparative methods for pairwise trait analysis, CCM has the additional advantage of being able to examine multiple traits as a community to reveal more dependency relationships. We also develop a simulation procedure to generate phylogenetic profiles with correlated evolutionary patterns that can be used as benchmark data for evaluation purposes.</p> <p>A simulation study demonstrates that CCM is more accurate than other methods including the Jaccard Index and three tree-aware methods. The parameterization of CCM makes the interpretation of the relations between genes more direct, which leads to Darwin's scenario being identified easily based on the estimated parameters. We show that CCM is more efficient and fits real data better than other methods resulting in higher likelihood scores with fewer parameters. An examination of 3786 phylogenetic profiles across a set of 659 bacterial genomes highlights linkages between genes with common functions, including many patterns that would not have been identified under a non-phylogenetic model of common distribution. We also applied the CCM to 44 proteins in the well-studied Mitochondrial Respiratory Complex I and recovered associations that mapped well onto the structural associations that exist in the complex.</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.
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.