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37 results for “museum genomics”
Figure 4 in Complete mitochondrial genomes from museum specimens clarify millipede evolution in the Eastern Arc Mountains
Figure 4. Maximum likelihood-based phylogeny, with 100 bootstrap replicates and using all the 26 mitochondrial genomes generated in this study. The dataset was supplemented with Thyropygus sp. and Abacion magnum as outgroups, with sequences derived from GenBank. GenBank accession numbers are given in parentheses. Colours represent Tropostreptus sample origins. The upper right inset shows the topology of the Tropostreptus hamatus lineage, enlarged to clarify the branching order. Only support values <100 are shown. *Thyropygus sp. (red font) is very likely to be a species misidentification; for more information, see Discussion text.
Figure 5. Bayesian phylogeny, with species divergence age estimates reconstructed with BEAST using all the 26 in Complete mitochondrial genomes from museum specimens clarify millipede evolution in the Eastern Arc Mountains
Figure 5. Bayesian phylogeny, with species divergence age estimates reconstructed with BEAST using all the 26 mitochondrial genomes generated in this study. The dataset was supplemented with Thyropygus sp. and Abacion magnum as outgroups, derived from GenBank. GenBank accession numbers are provided in parentheses. Blue bars indicate the 95% highest probability density intervals for node ages. Age estimation for lineage divergence was based on a general arthropod mitochondrial DNA substitution rate and should be considered with caution. *Thyropygus sp. (red font) is very likely to be a misidentification; for more information, see the Discussion.
Figure 1 in Complete mitochondrial genomes from museum specimens clarify millipede evolution in the Eastern Arc Mountains
Figure 1. Typical Tropostreptus appearance exemplified by a Tropostreptus hamatus individual from Udzungwa Mountains, Tanzania (photograph credit: Nikolaj Scharff).
Figure 2 in Complete mitochondrial genomes from museum specimens clarify millipede evolution in the Eastern Arc Mountains
Figure 2. Map showing the origin of the millipede specimens used in the study, with the accuracy of location restricted to mountain blocks. Coloured circles all represent Tropostreptus species, whereas grey symbols represent species from other millipede genera. Base map published by permission of the Eastern Arc Mountains Conservation Endowment Fund.
Figure 3 in Complete mitochondrial genomes from museum specimens clarify millipede evolution in the Eastern Arc Mountains
Figure 3. The gene order of mitochondrial coding sequences shared among all analysed millipede species in this study, which include all known species of Tropostreptus (T. droides, T. hamatus, T. kipunji, T. microcephalus, T. severus and T. sigmatospinus), in addition to Archispirostreptus gigas, Chaleponcus netus, Macrolenostreptus orestes, Prionopetalum kraepelini and Pseudotibiozus cerasopus. Colour key: red, ribosomal RNA (rRNA); pink, transfer RNA (tRNA); yellow, protein-coding sequences (CDS). Arrows indicate gene transcription orientation.
Museum genomics reveals the hybrid origin of an extinct crater lake endemic
<p>Crater lake fishes are common evolutionary model systems, with recent studies suggesting a key role for gene flow in promoting rapid adaptation and speciation. However, the study of these young lakes can be complicated by human-mediated extinctions. Museum genomics approaches integrating genetic data from recently extinct species are therefore critical to understanding the complex evolutionary histories of these fragile systems. Here, we examine the evolutionary history of an extinct Southern Hemisphere crater lake endemic, the rainbowfish Melanotaenia eachamensis. We undertook comprehensive sampling of extant rainbowfish populations of the Atherton Tablelands of Australia alongside historical museum material to understand the evolutionary origins of the extinct crater lake population and the dynamics of gene flow across the ecoregion. The extinct crater lake species is genetically distinct from all other nearby populations due to historic introgression between two proximate riverine lineages, similar to other prominent crater lake speciation systems, but this historic gene flow has not been sufficient to induce a species flock. Our results suggest that museum genomics approaches can be successfully combined with extant sampling to unravel complex speciation dynamics involving recently extinct species.</p>
Data and source code for: Recent adaptation in a threatened salmonid revealed by museum genomics
<p>Steelhead/rainbow trout (Oncorhynchus mykiss) is an imperiled salmonid with two main life history strategies: migrate to the ocean or remain in freshwater. Domesticated hatchery forms of this species have been stocked into almost all California waterbodies, possibly resulting in introgression into natural populations and altered population structure. </p> <p>We compared whole-genome sequence data from contemporary populations against a set of museum population samples of steelhead from the same locations that were collected prior to most hatchery stocking. </p> <p>We observed minimal introgression and few steelhead-hatchery trout hybrids despite a century of extensive stocking. Our historical data show signals of introgression with a sister species and indications of an early hatchery facility. Finally, we found that migration-associated haplotypes have become less frequent over time, a likely adaptation to decreased opportunities for migration. Since contemporary migration-associated haplotype frequencies have been used to guide species management, we consider this to be a rare example of shifting baseline syndrome that has been validated with historical data. </p> <p>We suggest cautious optimism that a century of hatchery stocking has had minimal impact on California steelhead population genetic structure, but we note that continued shifts in life history may lead to further declines in the ocean-going form of the species. </p>
Museum genomics reveals the hybrid origin of an extinct crater lake endemic
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Data and source code for: Recent adaptation in a threatened salmonid revealed by museum genomics
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The origins of coca: museum genomics reveals multiple independent domestications from progenitor Erythroxylum gracilipes
<p>Coca is the natural source of cocaine as well as a sacred and medicinal plant farmed by South American Amerindians and mestizos. The coca crop comprises four closely related varieties classified into two species (Amazonian and Huánuco varieties<i> </i>within <i>Erythroxylum coca</i> Lam., and Colombian and Trujillo varieties within<i> E. novogranatense </i>(D.Morris) Hieron.) but our understanding of their wild progenitor(s) and origins remains rudimentary. In this study we use genomic data from natural history collections to estimate the geographic origins and genetic diversity of this economically and culturally important crop in the context of its wild relatives. Our phylogeographic analyses clearly demonstrate the four varieties of coca comprise two or three exclusive groups nested within the diverse lineages of the widespread, wild species <i>E. gracilipes</i>; establishing a new and robust hypothesis of domestication wherein coca originated two or three times from this wild progenitor. The Colombian and Trujillo coca varieties are descended from a single, ancient domestication event in northwestern South America. Huánuco coca was domesticated more recently, possibly in southeastern Peru. Amazonian coca either shares a common domesticated ancestor with Huánuco coca, or it was the product of a third and most recent independent domestication event in the western Amazon basin. This chronology of coca domestication reveals different Holocene peoples in South America were able to independently transform the same natural resource to serve their needs; in this case, a workaday stimulant.</p>
Data from: Climate-mediated hybrid zone movement revealed with genomics, museum collection and simulation modeling
Climate-mediated changes in hybridization will dramatically alter the genetic diversity, adaptive capacity and evolutionary trajectory of interbreeding species. Our ability to predict the consequences of such changes will be key to future conservation and management decisions. Here we tested through simulations how recent warming (over a 32-year period) is affecting the geographic extent of a climate-mediated developmental threshold implicated in maintaining a butterfly hybrid zone (Papilio glaucus and Papilio canadensis; Lepidoptera: Papilionidae). These simulations predict a 68 km shift of this hybrid zone. To empirically test this prediction, we assessed genetic and phenotypic changes using contemporary and museum collections and document a 40 km northward shift of this hybrid zone. Interactions between the two species appear relatively unchanged during hybrid zone movement. We found no change in the frequency of hybridization and regions of the genome that experience little to no introgression moved largely in concert with the shifting hybrid zone. Model predictions based on climate scenarios predict this hybrid zone will continue to move northward, but with substantial spatial heterogeneity in the velocity (55-144 km/1°C), shape, and contiguity of movement. Our findings suggest that the presence of non-climatic barriers (e.g., genetic incompatibilities) and/or non-linear responses to climatic gradients may preserve species boundaries as the species shift. Further, we show that variation in the "geography" of hybrid zone movement could result in evolutionary responses that differ for geographically distinct populations spanning hybrid zones and thus have implications for the conservation and management of genetic diversity.
Museum genomics of reveals temporal genetic stasis and global genetic diversity in Arabidopsis thaliana
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Data from: Climate-mediated hybrid zone movement revealed with genomics, museum collection and simulation modeling
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The origins of coca: museum genomics reveals multiple independent domestications from progenitor Erythroxylum gracilipes
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A snakemake toolkit for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes and ribosomal genes from genome skims of museum collections
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Data from: Moorean and Tahitian Partula tree snail survival after a mass extinction: new genomic insights using museum specimens
Natural history museum collections provide a biodiversity window into the past and are of particular importance to the study of extinction-impacted clades such as the Pacific Island tree snail family Partulidae. Deliberate introduction of the predatory rosy wolf snail Euglandina rosea in the late 20th century led to the extinction/extirpation of 55/61 Society Island Partulidae species. In this study, we phylogenomically investigated the inter-relationships of the three surviving Society Island valley Partula species: P. taeniata (Moorea), P. clara and P. hyalina (Tahiti). All three formed a distinct clade in earlier mitochondrial phylogenies. Using Next Generation Sequencing (NGS) double digested Restriction Associated DNA sequencing (ddRADseq), we found that 46-year-old lyophilized museum specimens produced similar numbers of reads, sequencing depth, and loci as 10-year old ethanol-preserved collections. Phylogenomic trees indicated that Tahitian P. clara and P. hyalina are the result of a single founding lineage from Moorea, contrasting previous mitochondrial results and clarifying the enigmatic taxonomic status of P. c. incrassa. Our study highlights the utility and viability of NGS techniques for museum specimens and their increased resolution of evolutionary patterns. Sampling will be expanded to include the remaining Society Island partulid taxa to further explore the evolutionary history of this radiation.
Fig. 5 in Webs of intrigue: museum genomics elucidate relationships of the marronoid spider clade (Araneae)
Fig. 5. Result of BAMM inference best rate shift configuration for the RTA probe plus Sanger loci maximum likelihood tree with sampling estimates based on species totals from the World Spider Catalog (2023), plotted in BAMMtools. Red indicates significant evolutionary rate shifts. Photo of Agelenopsis sp. uploaded to Flickrby Judy Gallagher, used with permission.
Fig. 3 in Webs of intrigue: museum genomics elucidate relationships of the marronoid spider clade (Araneae)
Fig. 3. Summary tree of marronoid families from maximum likelihood inference in IQ-TREE2 of UCE loci, and UCE locicombined with legacy Sanger loci. Grids at the nodes correspond to support values in various analyses as indicated in the legend to the lower left. Images to the right of the phylogeny are of marronoid spiders observed on iNaturalist, used with permission from contributors. First column, top to bottom: Amaurobius fenestralis by iNaturalist user wp-polzin, Cycloctenus sp. by Dustin LaMont, Badumna longinqua by Andrès Costa, Neoantistea magna by Ruan Booysen, Cicurina cicur by Julien C., Toxopsoides huttoni by Cameron Rodda. Second column, top to bottom: Amaurobius ferox in typical web by Caveman, Stiphidion facetum by Linda Coster, Desis martensi by Marcus F.C. Ng, Cybaeus sp. byTony Iwane, Argyroneta aquatica by Ben Williams, Nigma puella male and female in web by David Gil Pérez.Third column, top to bottom: Agelena labyrinthica by Sabine Gasparitz, Agelena labyrinthica web by Lenni Gottlieb, Stiphidion facetum web by iNaturalist user davidkaipatiki, Malenella nana by Matías Gargiulo, Calymmaria persica in web by CandiceTalbot, Nigma walckenaeri by Ewelina Oszust.
Fig. 4 in Webs of intrigue: museum genomics elucidate relationships of the marronoid spider clade (Araneae)
Fig. 4. Phylogeny of the marronoids from IQ-TREE2 maximum likelihood inference after 10,000 UFboot replicates (support are UFboot values) for 50% gene occupancy matrix of RTA spider probes combined with Sanger loci (COI, H3, 12SrRNA, 16SrRNA, 18SrRNA, 28SrRNA).Tips with data for UCE and Sanger loci in bold, and tips with only legacy Sanger loci not in bold. Families in the marronoid clade are indicated by color. Numbers at nodes correspond to SH-aLRT value/ UFBoot value.
Fig. 2 in Webs of intrigue: museum genomics elucidate relationships of the marronoid spider clade (Araneae)
Fig. 2. Timeline depicting significant rearrangements in the marronoid clade from the inception of each family. Families currently contained in the marronoid clade are indicated by the same colors as in Fig. 1. Solid lines indicate movements by the indicated author, arrows, and colors indicate the destination family. Dotted lines indicate families originally described as subfamilies, or taxonomic suggestions that did not result in a formal taxonomic action. Movements in red indicate taxonomic changes that were not accepted by subsequent authors. Positions are illustrative and not to scale. Any papers referenced in this figure and not in the main text are referenced in Appendix A.
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