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42 results for “hybrid enrichment”
Investigating the utility of Anchored Hybrid Enrichment data to resolve the relationships among the Killifishes (Actinopterygii: Cyprinodontiformes), a globally distributed group of fishes
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Data from: Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life
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Data from: Phylogeny of a cosmopolitan family of morphologically conserved trapdoor spiders (Mygalomorphae, Ctenizidae) using Anchored Hybrid Enrichment, with a description of the family, Halonoproctidae Pocock 1901
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Data from: Tracking temporal shifts in area, biomes, and pollinators in the radiation of Salvia (sages) across continents: leveraging anchored hybrid enrichment and targeted sequence data
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Data from: Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment
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Data from: Anchored hybrid enrichment provides new insights into the phylogeny and evolution of longhorned beetles (Cerambycidae)
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A rodent anchored hybrid enrichment probe set for a range of phylogenetic utility – from order to species
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FIG. 11 in Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment
FIG. 11. Time calibrated tree from BEAST.
Data from: Anchored hybrid enrichment for massively high-throughput phylogenomics
The field of phylogenetics is on the cusp of a major revolution, enabled by new methods of data collection that leverage both genomic resources and recent advances in DNA sequencing. Previous phylogenetic work has required labor-intensive marker development coupled with single-locus PCR and DNA sequencing on a clade-by-clade and marker-by-marker basis. Here, we present a new, cost-efficient, and rapid approach to obtaining data from hundreds of genes for potentially hundreds of individuals for deep and shallow phylogenetic studies. Specifically, we designed probes for target enrichment of >500 loci in highly-conserved anchor regions of vertebrate genomes (flanked by less conserved regions) from five model species and tested enrichment efficiency in non-model species up to 254 million years divergent from the nearest model. We found that hybrid enrichment using conserved probes (anchored enrichment) can recover a large number of unlinked loci that are useful at a diversity of phylogenetic timescales. This new approach has the potential to not only expedite resolution of deep-scale portions of the Tree of Life but also to greatly accelerate resolution of the large number of shallow clades that remain unresolved. The combination of low cost (~1% of the cost of traditional Sanger sequencing and ~3.5% of the cost of high-throughput amplicon sequencing for projects on the scale of 500 loci x 100 individuals) and rapid data collection (~2 weeks of laboratory time) are expected to make this approach tractable even for researchers working on systems with limited or non-existent genomic resources.
Figure 1 from: Maddison WP, Evans SC, Hamilton CA, Bond JE, Lemmon AR, Lemmon EM (2017) A genome-wide phylogeny of jumping spiders (Araneae, Salticidae), using anchored hybrid enrichment. ZooKeys 695: 89-101. https://doi.org/10.3897/zookeys.695.13852
Figure 1 - Maximum likelihood phylogeny from the partitioned concatenated matrix of 447 loci captured by Anchored Hybrid Enrichment. Numbers indicate percentage of likelihood bootstrap replicates showing the clade. Half circle indicates clades supported also in the results of Maddison et al. (2014) or, for the Amycoida, of Ruiz and Maddison (2015). Letters u, p, a, and s indicate clades that fail to appear in the analyses by unpartitioned likelihood, parsimony, ASTRAL and SVDQuartets respectively.
Data from: Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment
Background: The past decade has witnessed remarkable progress towards resolution of the Tree of Life. However, despite the increased use of genomic scale datasets, some phylogenetic relationships remain difficult to resolve. Here we employ anchored phylogenomics to capture 107 nuclear loci in 29 species of acanthomorph teleost fishes, with 25 of these species sampled from the recently delimited clade Ovalentaria. Previous studies employing multilocus nuclear exon datasets have not been able to resolve the nodes at the base of the Ovalentaria tree with confidence. Here we test whether a phylogenomic approach will provide better support for these nodes, and if not, why this may be. Results: After using a novel method to account for paralogous loci, we estimated phylogenies with maximum likelihood and species tree methods using DNA sequence alignments of over 80,000 base pairs. Several key relationships within Ovalentaria are well resolved, including 1) the sister taxon relationship between Cichlidae and Pholidichthys, 2) a clade containing blennies, grammas, clingfishes, and jawfishes, and 3) monophyly of Atherinomorpha (topminnows, flyingfishes, and silversides). However, many nodes in the phylogeny associated with the early diversification of Ovalentaria are poorly resolved in several analyses. Through the use of rarefaction curves we show that limited phylogenetic resolution among the earliest nodes in the Ovalentaria phylogeny does not appear to be due to a deficiency of data, as average global node support ceases to increase when only 1/3rd of the sampled loci are used in analyses. Instead this lack of resolution may be driven by model misspecification as a Bayesian mixed model analysis of the amino acid dataset provided good support for parts of the base of the Ovalentaria tree.Conclusions: Although it does not appear that the limited phylogenetic resolution among the earliest nodes in the Ovalentaria phylogeny is due to a deficiency of data, it may be that both stochastic and systematic error resulting from model misspecification play a role in the poor resolution at the base of the Ovalentaria tree as a Bayesian approach was able to resolve some of the deeper nodes, where the other methods failed.
Data from: Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards
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Data from: In-solution hybridization for mammalian mitogenome enrichment: pros, cons and challenges associated with multiplexing degraded DNA
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Data from: A genome-wide phylogeny of jumping spiders (Araneae, Salticidae), using anchored hybrid enrichment
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Data from: Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment
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Data from: Anchored hybrid enrichment for massively high-throughput phylogenomics
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Data from: Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies
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FIG. 12 in Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment
FIG. 12. Our current hypothesis of species relationships among the named Gryllus species as well as the candidate lineages (denoted with an *) of putative species based on the RAxML analysis of concatenated data. Color coding indicates levels of bootstrap support from 50% (red) – 100% (bright green); branches with <50% bootstrap support collapsed.
FIG. 10 in Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment
FIG. 10. Phylogeny of Gryllus panel 4 of 4. RAxML tree (left) with taxon names; Astral tree (right) with thin lines connecting tips to taxon names. Support value color codes:> 90% = bright green;> 80% and <90% = green;> 70% and <80% = olive;> 60% and <70% = orange/brown;> 50% and <60% = red; <50% = black
FIG. 8 in Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment
FIG. 8. Phylogeny of Gryllus panel 2 of 4. RAxML tree (left) with taxon names; Astral tree (right) with thin lines connecting tips to taxon names. Support value color codes:> 90% = bright green;> 80% and <90% = green;> 70% and <80% = olive;> 60% and <70% = orange/brown;> 50% and <60% = red; <50% = black.
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International Brain Laboratory public data
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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.