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42 results for “hybrid enrichment”
Profiling, monitoring and conserving caterpillar fungus in the Himalayan region using anchored hybrid enrichment markers
<p>The collection of caterpillar fungus accounts for 50-70% of the household income of thousands of Himalayan communities and has an estimated market value of $5-11 billion across Asia. However, Himalayan collectors are at multiple economic disadvantages compared with collectors on the Tibetan plateau because their product is not legally recognized. Using a customized hybrid-enrichment probe set and market-grade caterpillar fungus (with samples up to 30 years old) from 94 production zones across Asia, we uncovered clear geography-based signatures of historical dispersal and significant isolation-by-distance among caterpillar fungus hosts. This high-throughput approach can readily distinguish samples from major production zones with definitive geographical resolution, especially for samples from the Himalayan region that form monophyletic clades in our analysis. Based on these results, we propose a two-step procedure to help local communities authenticate their produce and improve this multi-national trade route without creating opportunities for illegal exports and other forms of economic exploitation. We argue that policy makers and conservation practitioners must encourage the fair trade of caterpillar fungus in addition to sustainable harvesting to support a transboundary conservation effort that is much needed for this natural commodity in the Himalayan region.</p>
Data from: Hybrid enrichment of adaptive variation revealed by genotype-environment associations in montane sedges
<p>The role of hybridization in diversification is complex and may result in many possible outcomes. Not only can hybridization produce new lineages, but those lineages may contain unique combinations of adaptive genetic variation derived from parental taxa that allow hybrid-origin lineages to occupy unique environmental space relative to one (or both) parents. We document such a case of hybridization between two sedge species, <em>Carex</em> <em>nova</em> and <em>Carex</em> <em>nelsonii</em> (Cyperaceae), that occupy partially overlapping environmental space in the southern Rocky Mountains, USA. In the region hypothesized to be the origin of the hybrid lineage, one parental taxon (<em>C. nelsonii</em>) is at the edge of its environmental tolerance. Hybrid-origin individuals display mixed ancestry between the parental taxa – of nearly 7,000 unlinked loci sampled, almost 30% showed evidence of excess ancestry from one parental lineage – approximately half displayed a genomic background skewed towards one parent, and half skewed towards the other. To test whether excess ancestry loci may have conferred an adaptive advantage to the hybrid-origin lineage, we conducted genotype-environment association analyses on different combinations of loci – with and without excess ancestry – and with multiple contrasts between the hybrids and parental taxa. Loci with skewed ancestry showed significant environmental associations distinguishing the hybrid lineage from one parent (<em>C. nelsonii</em>), whereas loci with relatively equal representation of parental ancestries showed no such environmental associations. Moreover, the overwhelming majority of candidate adaptive loci with respect to environmental gradients also had excess ancestry from a parental lineage, implying these loci have facilitated the persistence of the hybrid lineage in an environment unsuitable to at least one parent<em>.</em></p>
Making andesite through shallow hybridization of magmas derived from variably enriched lithospheric mantle
<p>We integrate textural and in situ compositional information from plagioclase and clinopyroxene (Cpx) phenocrysts together with groundmass compositions in early Cretaceous andesite dykes within the Sulu belt of China to propose a new petrogenetic model for andesite. Plagioclase phenocrysts are mostly andesine; they are depleted in high field strength elements (HFSE). However, clinopyroxene (Cpx) phenocrysts are either reversely-zoned (type I) or homogeneous (type II), with the zoned Cpx divided into subtypes IA and IB. All Cpx has high Mg#, low Na<sub>2</sub>O and generally low Al<sub>2</sub>O<sub>3</sub>, with depletions in HFSE and variably high <sup>87</sup>Sr/<sup>86</sup>Sr ratios, suggesting crystallization above the Moho from magmas derived from enriched lithospheric mantle. The cores of type IA/IB and type II Cpx have normal major- and trace-element compositional variations and similar <sup>87</sup>Sr/<sup>86</sup>Sr ratios to each other and to plagioclase, consistent with fractional crystallization from a common magma (magma 1). The rims of type IA and IB Cpx also have normal major- and trace-element compositional variations, but these are not as evolved as the cores, and the rims have lower <sup>87</sup>Sr/<sup>86</sup>Sr ratios, demonstrating crystallization from an isotopically-distinct magma (magma 2). Based on modelled major and rare earth element compositions of magmas inferred to have been in equilibrium with different Cpx (± plagioclase) domains, the measured groundmass compositions can be reproduced by variable mixing between the two magmas. Our study demonstrates for the first time that andesite magma can be made through fractionation and shallow hybridization of magmas derived from variably enriched lithospheric mantle.</p>
Profiling, monitoring and conserving caterpillar fungus in the Himalayan region using anchored hybrid enrichment markers
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Data from: Hybrid enrichment of adaptive variation revealed by genotype-environment associations in montane sedges
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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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FIG. 4 in Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment
FIG. 4. Monophyly of North American Gryllus is strongly supported by (A) RAxML analysis of concatenated data (492,531 bp) with bootstrap values, and by (B) Astral analysis of gene trees (563 loci) with quadripartition branch support values.
FIG. 7 in Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment
FIG. 7. Phylogeny of Gryllus panel 1 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. 2 in Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment
FIG. 2. Alexander's first phylogeny of US Gryllus principally based on life-cycle considerations. Redrawn from Alexander (1968). * Note: G. texensis was labeled as G. integer in Alexander's original figure, see Cade & Otte (2000).
FIG. 3 in Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment
FIG. 3. Two mtDNA phylogenies of US Gryllus. (A) Strict consensus of two shortest trees from maximum parsimony analysis of mtDNA restriction sites (redrawn from Harrison & Bogdanowicz 1995). (B) Minimum evolution tree for ~1500 bp of combined Cytochrome b and 16S mtDNA sequence data (redrawn from Huang et al. 2000, with 'G. assimilis CA' renamed G. multipulsator following Weissman et al. 2009)
Fig. 1. Top 10 in Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment
Fig. 1. Top 10 categories of publications involving Gryllus field crickets; data are from the Web of Science and represent 2914 records from 1903 – 2019.
FIG. 6 in Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment
FIG. 6. Overview of in-group taxa relationships based on Astral gene-tree analysis, with quadripartition branch support values. The named Groups correspond to Weissman & Gray (2019).
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
The mygalomorph family Ctenizidae has a world-wide distribution and currently contains nine genera and 135 species. However, the monophyly of this group has long been questioned on both morphological and molecular grounds. Here, we use Anchored Hybrid Enrichment (AHE) to gather hundreds of loci from across the genome for reconstructing the phylogenetic relationships among the nine genera and test the monophyly of the family. We also reconstruct the possible ancestral ranges of the most inclusive clade recovered. Using AHE, we generate a supermatrix of 565 loci and 115,209 bp for 27 individuals. For the first time, analyses using all nine genera produce results definitively establishing the non-monophyly of Ctenizidae. A lineage formed exclusively by representatives of South African Stasimopus was placed as the sister group to the remaining taxa in the tree, and the Mediterranean Cteniza and Cyrtocarenum were recovered with high support as sister to exemplars of Euctenizidae, Migidae, and Idiopidae. All the remaining genera—Bothriocyrtum, Conothele, Cyclocosmia, Hebestatis, Latouchia, and Ummidia—share a common ancestor. Based on these results, we formally elevate this clade to the level of family. Our results definitively establish both the non-monophyly of the Ctenizidae and non-validity of the subfamilies Ummidiinae and Ctenizinae. In order to establish the placement of the remaining three ctenizid genera, Cteniza, Cyrtocarenum, and Stasimopus, thorough analyses within the context of a complete mygalomorph phylogenetic framework are needed. We formally describe the family Halonoproctidae Pocock 1901 and infer that the family's most recent common ancestor was likely distributed in western North America and Asia.
Data from: Hierarchical Hybrid Enrichment: multi-tiered genomic data collection across evolutionary scales, with application to chorus frogs (Pseudacris)
Determining the optimal targets of genomic sub-sampling for phylogenomics, phylogeography, and population genomics remains a challenge for evolutionary biologists. Of the available methods for sub-sampling the genome, hybrid enrichment (sequence capture) has become one of the primary means of data collection for systematics, due to the flexibility and cost efficiency of this approach. Despite the utility of this method, information is lacking as to what genomic targets are most appropriate for addressing questions at different evolutionary scales. In this study, first we compare the benefits of target loci developed for deep- and shallow-scales by comparing these loci at each of three taxonomic levels: within a genus (phylogenetics), within a species (phylogeography) and within a hybrid zone (population genomics). Specifically, we target evolutionary conserved loci that are appropriate for deep phylogenetic scales and more rapidly evolving loci that are informative for phylogeographic and population genomic scales. Second, we assess the efficacy of targeting multiple locus sets for different taxonomic levels in the same hybrid enrichment reaction, an approach we term hierarchical hybrid enrichment. Third, we apply this approach to the North American chorus frog genus Pseudacris to answer longstanding evolutionary questions across taxonomic and temporal scales. We demonstrate that in this system the type of genomic target that produces the most resolved gene trees differs depending on the taxonomic level, although the potential for error is substantially lower for the deep-scale loci at all levels. We successfully recover data for the two different locus sets with high efficiency. Using hierarchical data targeting deep and shallow levels, we (a) resolve the phylogeny of the genus Pseudacris and introduce a novel visual and hypothesis-testing method that uses nodal heat maps to examine the robustness of branch support values to the removal of sites and loci; (b) estimate the phylogeographic history of P. feriarum, which reveals five independent invasions of sympatry by this species to form replicated reinforcement contact zones with P. nigrita with ongoing gene flow into sympatry; and (c) quantify with high confidence the frequency of hybridization in one of these zones between P. feriarum and P. nigrita, which is much lower than previously found by microsatellite-based studies. We find that the hierarchical hybrid enrichment approach offers an efficient, multi-tiered data collection method for simultaneously addressing questions spanning multiple evolutionary scales.
Data from: Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life
Background: Despite considerable effort, progress in spider molecular systematics has lagged behind many other comparable arthropod groups, thereby hindering family-level resolution, classification, and testing of important macroevolutionary hypotheses. Recently, alternative targeted sequence capture techniques have provided molecular systematics a powerful tool for resolving relationships across the Tree of Life. One of these approaches, Anchored Hybrid Enrichment (AHE), is designed to recover hundreds of unique orthologous loci from across the genome, for resolving both shallow and deep-scale evolutionary relationships within non-model systems. Herein we present a modification of the AHE approach that expands its use for application in spiders, with a particular emphasis on the infraorder Mygalomorphae. Results: Our aim was to design a set of probes that effectively capture loci informative at a diversity of phylogenetic timescales. Following identification of putative arthropod-wide loci, we utilized homologous transcriptome sequences from 17 species across all spiders to identify exon boundaries. Conserved regions with variable flanking regions were then sought across the tick genome, three published araneomorph spider genomes, and raw genomic reads of two mygalomorph taxa. Following development of the 585 target loci in the Spider Probe Kit, we applied AHE across three taxonomic depths to evaluate performance: deep-level spider family relationships (33 taxa, 327 loci); family and generic relationships within the mygalomorph family Euctenizidae (25 taxa, 403 loci); and species relationships in the North American tarantula genus Aphonopelma (83 taxa, 581 loci). At the deepest level, all three major spider lineages (the Mesothelae, Mygalomorphae, and Araneomorphae) were supported with high bootstrap support. Strong support was also found throughout the Euctenizidae, including generic relationships within the family and species relationships within the genus Aptostichus. As in the Euctenizidae, virtually identical topologies were inferred with high support throughout Aphonopelma. Conclusions: The Spider Probe Kit, the first implementation of AHE methodology in Class Arachnida, holds great promise for gathering the types and quantities of molecular data needed to accelerate an understanding of the spider Tree of Life by providing a mechanism whereby different researchers can confidently and effectively use the same loci for independent projects, yet allowing synthesis of data across independent research groups.
Investigating the utility of Anchored Hybrid Enrichment data to resolve the relationships among the Killifishes (Actinopterygii: Cyprinodontiformes), a globally distributed group of fishes
<p>The Killifishes (Blenniiformes: Cyprinodontoidea) are a diverse and well-known group of fishes that contains sixteen families inclusive of Anablepidae, Aphaniidae Aplocheilidae, Cubanichthyidae, Cyprinodontidae, Fluviphylacidae, Fundulidae, Goodeidae, Nothobranchiidae, Orestiidae, Pantanodontidae, Poeciliidae, Procatopodidae, Profundulidae, Rivulidae, and Valenciidae and more than 1,200 species that are globally distributed in tropical and temperate, freshwater and estuarine habitats. The evolutionary relationships among the families within the group, based on different molecular and morphological data sets, have remained uncertain. Therefore, the objective of this study was to use a targeted approach, anchored hybrid enrichment, to resolve the phylogenetic relationships among the families within the Superfamily Cyprinodontoidea (formerly the Cyprindontiformes). This study included more than 100 individuals, representing all sixteen families within Cyprinodontoidea, including many recently diagnosed families. We recovered an average of 244 loci per individual. These data were submitted to phylogenetic analyses (RaxML and ASTRAL) and although we recovered many of the same relationships as in previous studies of the group, several novel sets of relationships for other families also were recovered. In addition, two well-established clades were recovered as monophyletic and are in agreement with most previous studies. We also assessed the degree of gene tree discordance in our dataset to evaluate support for alternative topological hypotheses for interfamilial relationships within the Cyprinodontoidea using a variety of different analyses. The results from this study will provide a robust, historical framework needed to investigate a plethora of biogeographic, taxonomic, ecological, and physiological questions for this group of fishes.</p>
A rodent anchored hybrid enrichment probe set for a range of phylogenetic utility – from order to species
<p>Rodents are the largest order of mammals and contain several model organisms important to scientific research in a variety of fields, yet no large set of genomic markers have been designed for this group to date, hindering evolutionary studies into relationships of the group as a whole. Here we present a genomic probe set designed and optimized for rodents with a protocol easy to replicate with little laboratory investment. This design utilizes an anchored hybrid enrichment approach specifically targeting rodents to generate longer loci with a higher mutation rate than existing vertebrate probes to provide utility at various taxonomic levels. Using a test set of rodents from all five suborders we successfully obtained alignments for 416 of the 418 target loci with an average of 1,379 base pairs per locus and a total alignment of more than half a million base pairs. This genomic dataset performed well in all phylogenetic analyses, especially in recent phylogenetic splits, with ample parsimoniously-informative sites within genera and even within species, showing more than four times as many single nucleotide polymorphisms per locus than a recent vertebrate ultra-conserved elements study. Additional support is provided in resolving basal clades in Rodentia. By providing this probe design, we hope that more labs can easily generate data for answering questions in rodents from species delimitation to understanding relationships among families in rapid radiations.</p>
Supplementary material 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
Supplementary table of assembly statistics : Explanation note: Statistics describing raw reads, loci, sequence lengths, and other aspects of sequencing assembly for each of the 34 salticid taxa and 12 outgroup taxa.
Data from: Anchored hybrid enrichment provides new insights into the phylogeny and evolution of longhorned beetles (Cerambycidae)
Cerambycidae is a species-rich family of mostly wood-feeding (xylophagous) beetles containing nearly 35 000 known species. The higher-level phylogeny of Cerambycidae has never been robustly reconstructed using molecular phylogenetic data or a comprehensive sample of higher taxa, and its internal relationships and evolutionary history remain the subjects of ongoing debate. We reconstructed the higher-level phylogeny of Cerambycidae using phylogenomic data from 522 single copy nuclear genes, generated via anchored hybrid enrichment. Our taxon sample (31 Chrysomeloidea, four outgroup taxa: two Curculionoidea and two Cucujoidea) included exemplars of all families and 23 of 30 subfamilies of Chrysomeloidea (18 of 19 non-chrysomelid Chrysomeloidea), with a focus on the large family Cerambycidae. Our results reveal a monophyletic Cerambycidae s.s. in all but one analysis, and a polyphyletic Cerambycidae s.l. When monophyletic, Cerambycidae s.s. was sister to the family Disteniidae. Relationships among the subfamilies of Cerambycidae s.s. were also recovered with strong statistical support except for Cerambycinae being made paraphyletic by Dorcasomus Audinet-Serville (Dorcasominae) in the nucleotide (but not amino acid) trees. Most other chrysomeloid families represented by more than one terminal taxon – Chrysomelidae, Disteniidae, Vesperidae and Orsodacnidae – were monophyletic, but Megalopodidae was rendered paraphyletic by Cheloderus Gray (Oxypeltidae). Our study corroborates some relationships within Chrysomeloidea that were previously inferred from morphological data, while also reporting several novel relationships. The present work thus provides a robust framework for future, more deeply taxon-sampled, phylogenetic and evolutionary studies of the families and subfamilies of Cerambycidae s.l. and other Chrysomeloidea.
Data from: Hierarchical Hybrid Enrichment: multi-tiered genomic data collection across evolutionary scales, with application to chorus frogs (Pseudacris)
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