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20 results for “Anchored phylogenomics”
Anchored phylogenomics unravels the evolution of spider flies (Diptera, Acroceridae) and reveals discordance between nucleotides and amino acids
<p>Supplementary Material accompanying the manuscript titled "Anchored phylogenomics unravels the evolution of spider flies (Acroceridae) and reveals discordance between nucleotides and amino acids", including Supplementary Figures, Tables and Datasets.</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: Resolving rapid radiations within angiosperm families using anchored phylogenomics
Despite the promise that molecular data would provide a seemingly unlimited source of independent characters, many plant phylogenetic studies are still based on only two regions, the plastid genome and nuclear ribosomal DNA (nrDNA). Their popularity can be explained by high copy numbers and universal PCR primers that make their sequences easily amplified and converted into parallel datasets. Unfortunately, their utility is limited by linked loci and limited characters resulting in low confidence in the accuracy of phylogenetic estimates, especially when rapid radiations occur. In another contribution on anchored phylogenomics in angiosperms, we presented flowering plant-specific anchored enrichment probes for hundreds of conserved nuclear genes and demonstrated their use at the level of all angiosperms. In this contribution, we focus on a common problem in phylogenetic reconstructions below the family level: weak or unresolved backbone due to rapid radiations (≤10 million years) followed by long divergence, using the Cariceae-Dulichieae-Scirpeae clade (CDS, Cyperaceae) as a test case. By comparing our nuclear matrix of 461 genes to a typical Sanger-sequence dataset consisting of a few plastid genes (matK, ndhF) and an nrDNA marker (ETS), we demonstrate that our nuclear data is fully compatible with the Sanger dataset and resolves short backbone internodes with high support in both concatenated and coalescence-based analyses. In addition, we show that nuclear gene tree incongruence is inversely proportional to phylogenetic information content, indicating that incongruence is mostly due to gene tree estimation error. This suggests that large numbers of conserved nuclear loci could produce more accurate trees than sampling rapidly evolving regions prone to saturation and long-branch attraction. The robust phylogenetic estimates obtained here, and high congruence with previous morphological and molecular analyses, are strong evidence for a complete tribal revision of CDS. The anchored hybrid enrichment probes used in this study should be similarly effective in other flowering plant groups.
Anchored phylogenomics and a revised classification of the Planidial Larva Clade of Jewel Wasps (Hymenoptera: Chalcidoidea)
<p>Planidia are free-living, mobile first-instar larvae that are notable in their ability to transition on a single host between different larval stadia, and for completing their development on the host prepupa as ectoparasitoids, effectively acting as larval-pupal external koinobionts. Within Chalcidoidea, a mega-diverse superfamily of parasitoid wasps, taxa with a planidium form a monophyletic group, the Planidial-Larva-Clade (PLC), which has been comprised of three recognized groups: Eutrichosomatinae (Pteromalidae), Perilampidae (Chrysolampinae, Perilampinae, Philomidinae and the unplaced genus Jambiya), and Eucharitidae (Akapalinae, Eucharitinae, Gollumiellinae and Oraseminae). To clarify the classification and better understand the evolution of this clade, we conducted a phylogenomic study of the PLC using anchored hybrid enrichment data. The phylogenetic analyses support the backbone relationship of PLC as: (Eutrichosomatinae, ((Philomidinae, Chrysolampinae), (Perilampinae, Eucharitidae))). Although excluded from the main analyses, the genus Jambiya, based on only 11 loci recovered, was placed as the sister of Chrysolampinae + Philomidinae or Perilampinae + Eucharitidae. Our results support the placement of Eutrichosomatinae at the base of the PLC phylogeny and demonstrate that Perilampidae (Philomidinae, Chrysolampinae and Perilampinae) are paraphyletic. In contrast to other studies, anchored enrichment data fail to recover the Ponerinae- Ectatomminae-Myrmeciinae (PEM) parasitoid clade within Eucharitinae, which may indicate a more complicated evolutionary history of ant-host shifts. Traits explored using Likelihood Ancestral State Reconstruction include the evolution of host associations, direct versus indirect hyperparasitism, ability to attack a host within a cocoon, soft versus hard planidial forms, and mobility of the planidium. Divergence dating based on four calibration fossils suggests that the planidial clade arose approximately 111 Ma and the evolution of ant parasitism at least 64 Ma. A revised higher-level classification of the planidial larva clade is proposed with Eutrichosomatinae elevated to Eutrichosomatidae (Rev. Stat.), Chrysolampinae and Philomidinae placed in Chrysolampidae (Rev. Stat.), Perilampidae (Rev. Stat.) restricted to what was referred to as Perilampinae, and Eucharitidae maintained with four subfamilies, with Akapalinae (unknown biology) as sister group to the core Eucharitidae, all of which are ant parasitoids. Jambiya is treated as an incertae sedis taxon within the planidial clade.</p>
Fig. 2 in A strong backbone for an invertebrate group: anchored phylogenomics improves the resolution of genus-level relationships within the Lumbricidae (Annelida, Crassiclitellata)
Fig. 2 Left. Bayesian inference of the phylogenetic tree based on the concatenated sequences of the nuclear marker 28S rRNA and the mitochondrial 16S rRNA, NADH dehydrogenase (ND1), 12S rRNA, and COI. Right. Phylogenetic tree based on the same analysis but imple-
Data from: Resolving rapid radiations within angiosperm families using anchored phylogenomics
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Data from: Anchored phylogenomics of burrowing mayflies (Ephemeroptera) and the evolution of tusks
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Anchored phylogenomics and a revised classification of the Planidial Larva Clade of Jewel Wasps (Hymenoptera: Chalcidoidea)
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Data from: Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes
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Data from: Allopatric speciation in Asia contributed to the diversity anomaly between eastern Asia and eastern North America: evidence from anchored phylogenomics of Stewartia (Theaceae)
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Data from: Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L.
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A combined approach of mitochondrial DNA and anchored nuclear phylogenomics sheds light on unrecognized diversity, phylogeny, and historical biogeography of the cascade frogs, genus Amolops (Anura: Ranidae)
<p><i>Amolops</i> is one of the most species-rich genera in Ranidae, with 59 recognized species. This genus currently includes six species groups diagnosed mainly by morphology. Several recent molecular studies indicated that the classification of species groups within <i>Amolops</i> remains controversial, and key nodes in the phylogeny have been inadequately resolved. In addition, the diversity of cascade frogs remains poorly understood, especially for those from incompletely sampled regions. Herein, we investigate the species-level diversity within genus <i>Amolops</i> throughout southern China and Southeast Asia, and infer evolutionary relationships among the species using mtDNA data (16S, <i>COI</i>, and <i>ND2</i>). Molecular analyses indicate nine new unnamed species, mostly distributed in the Himalayas. We then utilized anchored hybrid enrichment to generate a dataset representing major mitochondrial lineages to resolve phylogenetic relationships, biogeography, and pattern of species diversification. Our resulting phylogeny strongly supports the monophyly of three previously identified species groups (the <i>A. ricketti</i>, <i>A. daiyunensis</i>,<i> </i>and <i>A. hainanensis</i> groups), the paraphyly of the <i>A. mantzorum</i> and <i>A. marmoratus</i> groups, as previously defined, and monophyly of the <i>A. monticola</i> group. We erect one new species group, the <i>A. viridimaculatus</i> group, and recognize Dubois (1992) 'subgenus' <i>Amo</i> as the <i>A. larutensis</i> species group. Biogeographic analysis suggests that <i>Amolops</i> originated on the Indo-Burma/Tai-Malay Peninsula at the Eocene/Oligocene boundary, and dispersed outward, exemplifying a common pattern observed for the origin of Asia's biodiversity. The early divergence within <i>Amolops</i> coincides with the Himalayas uplift, and the lateral extrusion of Indochina at the Oligocene/Miocene boundary. Our results show that paleoclimatic and geomorphological events have profoundly influenced the pattern of lineage diversification within <i>Amolops</i>.</p>
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.
Data from: The impact of anchored phylogenomics and taxon sampling on phylogenetic inference in narrow-mouthed frogs (Anura, Microhylidae)
Despite considerable progress in unravelling the phylogenetic relationships of microhylid frogs, relationships among subfamilies remain largely unstable and many genera are not demonstrably monophyletic. Here, we used five alternative combinations of DNA sequence data (ranging from seven loci for 48 taxa to up to 73 loci for as many as 142 taxa) generated using the anchored phylogenomics sequencing method (66 loci, derived from conserved genome regions, for 48 taxa) and Sanger sequencing (seven loci for up to 142 taxa) to tackle this problem. We assess the effects of character sampling, taxon sampling, analytical methods and assumptions in phylogenetic inference of microhylid frogs. The phylogeny of microhylids shows high susceptibility to different analytical methods and datasets used for the analyses. Clades inferred from maximum-likelihood are generally more stable across datasets than those inferred from parsimony. Parsimony trees inferred within a tree-alignment framework are generally better resolved and better supported than those inferred within a similarity-alignment framework, even under the same cost matrix (equally weighted) and same treatment of gaps (as a fifth nucleotide state). We discuss potential causes for these differences in resolution and clade stability among discovery operations. We also highlight the problem that commonly used algorithms for model-based analyses do not explicitly model insertion and deletion events (i.e. gaps are treated as missing data). Our results corroborate the monophyly of Microhylidae and most currently recognized subfamilies but fail to provide support for relationships among subfamilies. Several taxonomic updates are provided, including naming of two new subfamilies, both monotypic.
Data from: Anchored phylogenomics illuminates the skipper butterfly tree of life
Butterflies (Papilionoidea) are perhaps the most charismatic insect lineage, yet phylogenetic relationships among them remain incompletely studied and controversial. We sequenced nearly 400 loci using Anchored Hybrid Enrichment and sampled all tribes and more than 120 genera of skippers (Hesperiidae), one of the most species-rich and poorly studied butterfly families. Maximum-likelihood, parsimony and coalescent multi-species methods all converged on a novel, robust phylogenetic hypothesis for skippers. Different optimality criteria and methodologies recovered almost identical phylogenetic trees with strong nodal support at nearly all taxonomic levels. Our results support Coeliadinae as the sister group to the remaining skippers, the monotypic Euschemoninae as sister group to all other subfamilies but Coeliadinae, and the monophyly of Eudaminae plus Pyrginae. Within Pyrginae, Celaenorrhinini and Tagiadini are sister groups, the Neotropical firetips, Pyrrhopygini, are sister to all other tribes but Celaenorrhinini and Tagiadini. Achlyodini is recovered as the sister group to Carcharodini, and Erynnini as sister group to Pyrgini. Within Hesperiinae, there is strong support for the monophyly of Aeromachini plus remaining Hesperiinae. The giant skippers (Agathymus and Megathymus) once classified as a single subfamily, are recovered as monophyletic with strong support, but are deeply nested within grass skippers (Hesperiinae). These results enhance understanding of the evolution of one of the most species-rich butterfly families.
Data from: The impact of anchored phylogenomics and taxon sampling on phylogenetic inference in narrow-mouthed frogs (Anura, Microhylidae)
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Data from: Anchored phylogenomics illuminates the skipper butterfly tree of life
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A combined approach of mitochondrial DNA and anchored nuclear phylogenomics sheds light on unrecognized diversity, phylogeny, and historical biogeography of the cascade frogs, genus Amolops (Anura: Ranidae)
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Data from: Anchored hybrid enrichment for massively high-throughput phylogenomics
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Data from: Resolving relationships among the megadiverse butterflies and moths with a novel pipeline for Anchored Phylogenomics
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