Mining museums for historical DNA: advances and challenges in museomics

Trends in Ecology & Evolution, Journal Year: 2021, Volume and Issue: 36(11), P. 1049 - 1060

Published: Aug. 26, 2021

Historical DNA (hDNA), obtained from museum and herbarium specimens, has yielded spectacular new insights into the history of organisms. This includes documenting historical genetic erosion extinction, discovering species to science, resolving evolutionary relationships, investigating epigenetic effects, determining origins infectious diseases. However, development best-practices in isolating, processing, analyzing hDNA remain under-explored, due substantial diversity specimen preparation types, tissue sources, archival ages, collecting histories. Thus, for reach its full potential, justify destructive sampling rarest more experimental work using time-series collections, improved methods correct data asymmetries biases degradation are required.

Language: Английский

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Enigmas no longer: using ultraconserved elements to place several unusual hawk taxa and address the non-monophyly of the genus Accipiter (Accipitriformes: Accipitridae)

Biological Journal of the Linnean Society, Journal Year: 2024, Volume and Issue: unknown

Published: March 22, 2024

Abstract Hawks, eagles, and their relatives (Accipitriformes: Accipitridae) are a diverse charismatic clade of modern birds, with many members that instantly recognized by the general public. However, surprisingly little is known about relationships among genera within Accipitridae, several studies have suggested some (in particular, megadiverse genus Accipiter) not monophyletic. Here, we combine large new dataset obtained from ultraconserved elements, generated whole genome sequencing 134 species, publicly available legacy markers (i.e. suite commonly sequenced mitochondrial nuclear genes) to infer well-supported, time-calibrated phylogeny 237 extant or recently extinct species. Our densely sampled phylogeny, which includes 90% confirms non-monophyly Accipiter provides sufficient basis revise genus-level taxonomy, such all in Accipitridae represent monophyletic groups.

Language: Английский

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Fourteen New, Endemic Species of Shrew (Genus Crocidura) from Sulawesi Reveal a Spectacular Island Radiation

Bulletin of the American Museum of Natural History, Journal Year: 2021, Volume and Issue: 454(1)

Published: Dec. 14, 2021

After nearly a decade of field inventories in which we preserved voucher specimens the small terrestrial mammals Sulawesi, combined qualitative and quantitative analyses morphological traits with molecular phylogenetics to better understand diversity shrews (Soricidae: Crocidura) on island. We examined morphology 1368 obtained extensive data from many them, including mitochondrial DNA sequences 851 specimens, up five nuclear exons 657 thousands ultraconserved elements 90 specimens. By iteratively testing species limits using distinct character datasets appropriate taxon sampling, found clear, mostly consistent evidence for existence 21 only seven were previously recognized. divide these into morphogroups, provide emended diagnoses named species, describe 14 new species. The Long-Tailed Group contains Crocidura caudipilosa, C. elongata, microelongata, quasielongata, species; Rhoditis rhoditis, pseudorhoditis, australis, pallida, Small-Bodied lea, levicula, baletei, mediocris, parva, tenebrosa, Thick-Tailed brevicauda, caudicrassa, Ordinary musseri, nigripes, normalis, ordinaria, solita, Documenting endemic reveals local radiation (20 are members an clade) elevational gradients played prominent role either promoting speciation, or at minimum, fostering cooccurrence phenotypically similar As now understood, species-level Sulawesi is three times known any other insular shrew fauna. This study highlights fact that if wish true extent biodiversity Earth, large-scale, vouchered organismal followed thorough examinations genetic, morphological, geographic sorely needed montane tropical regions, even purportedly well-studied groups such as mammals.

Language: Английский

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Phylogeny and historical biogeography of the swallow family (Hirundinidae) inferred from comparisons of thousands of UCE loci

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 197, P. 108111 - 108111

Published: May 25, 2024

Language: Английский

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Unlocking inaccessible historical genomes preserved in formalin

Molecular Ecology Resources, Journal Year: 2021, Volume and Issue: 22(6), P. 2130 - 2147

Published: Sept. 22, 2021

Museum specimens represent an unparalleled record of historical genomic data. However, the widespread practice formalin preservation has thus far impeded analysis a large proportion specimens. Limited DNA sequencing from formalin-preserved yielded low coverage with unpredictable success. We set out to refine sample processing methods and identify specimen characteristics predictive With taxonomically diverse collected between 1962 2006 ranging in quality, we compared efficacy several end-to-end whole genome workflows alongside k-mer-based trimming-free read alignment approach maximize mapping endogenous sequence. recovered complete mitochondrial genomes up 3× nuclear tissues. Hot alkaline lysis coupled phenol-chloroform extraction out-performed proteinase K digestion recovering DNA, while library preparation method had little impact on The strongest predictor yield was overall condition, which additively interacts conditions accelerate degradation. Here, demonstrate significant advance capability beyond limited recovery small number loci via PCR or target-capture sequencing. To facilitate strategic selection suitable for sequencing, present decision-making framework that utilizes independent nondestructive assessment criteria. Sequencing will contribute greater understanding temporal trends genetic adaptation, including those associated changing climate. Our work enhances value museum collections worldwide by unlocking have been disregarded as valid molecular resource.

Language: Английский

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A guide to avian museomics: Insights gained from resequencing hundreds of avian study skins

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 22(7), P. 2672 - 2684

Published: June 4, 2022

Biological specimens in natural history collections constitute a massive repository of genetic information. Many have been collected areas which they no longer exist or where present-day collecting is not possible. There are also representing populations species that gone extinct. Furthermore, may sampled throughout an extensive time period, particularly valuable for studies change through time. With the advent high-throughput sequencing, museum resources become accessible genomic research. Consequently, these unique increasingly being used across many fields history. In this paper, we summarize our experiences resequencing hundreds genomes from historical avian specimens. We publish protocols and discuss entire workflow sampling laboratory procedures, to bioinformatic processing specimen data.

Language: Английский

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Genetic Load and Adaptive Potential of a Recovered Avian Species that Narrowly Avoided Extinction

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(12)

Published: Nov. 23, 2023

Abstract High genetic diversity is a good predictor of long-term population viability, yet some species persevere despite having low diversity. Here we study the genomic erosion Seychelles paradise flycatcher (Terpsiphone corvina), that narrowly avoided extinction after declined to 28 individuals in 1960s. The recovered unassisted over 250 1990s and was downlisted from Critically Endangered Vulnerable International Union for Conservation Nature Red List 2020. By comparing historical, prebottleneck (130+ years old) modern genomes, uncovered 10-fold loss Highly deleterious mutations were partly purged during bottleneck, but mildly accumulated. genome shows signs historical inbreeding bottleneck 1960s, levels recent demographic recovery. Computer simulations suggest small Ne reduced masked load made more resilient extinction. However, reduction due chronically severe likely have adaptive potential face environmental change, which together with higher load, compromises its viability. Thus, ancestral offers short-term resilience hampers adaptability shifts. In light rapid global rates decline, our work can continue suffer effect their decline even recovery, highlighting importance considering computer modeling conservation assessments.

Language: Английский

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Historical DNA as a tool to address key questions in avian biology and evolution: A review of methods, challenges, applications, and future directions

Molecular Ecology Resources, Journal Year: 2019, Volume and Issue: 19(5), P. 1115 - 1130

Published: July 23, 2019

Abstract Museum specimens play a crucial role in addressing key questions systematics, evolution, ecology, and conservation. With the advent of high‐throughput sequencing technologies, that have long been foundation important biological discoveries can inform new perspectives as sources genomic data. Despite many possibilities associated with analyzing DNA from historical specimens, several challenges persist. Using avian systems model, we review extraction protocols, capture methods are helping researchers overcome some these difficulties. We highlight empirical examples which used technologies to address fundamental related conservation evolution. Increasing accessibility will provide tools tap into wealth information contained within our valuable natural history collections.

Language: Английский

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Complex histories of gene flow and a mitochondrial capture event in a nonsister pair of birds

Molecular Ecology, Journal Year: 2021, Volume and Issue: 30(9), P. 2087 - 2103

Published: Feb. 22, 2021

Abstract Hybridization, introgression, and reciprocal gene flow during speciation, specifically the generation of mitonuclear discordance, are increasingly observed as parts speciation process. Genomic approaches provide insight into where, when, how adaptation operates after can measure historical modern introgression. Whether adaptive or neutral in origin, hybridization cause discordance by placing mitochondrial genome one species (or population) nuclear background another species. The latter, introgressed may eventually have its own mtDNA replaced “captured” other across entire geographical range. Intermediate stages capture process should be observable. Two nonsister Australasian monarch‐flycatchers, Spectacled Monarch ( Symposiachrus trivirgatus ) mostly Australia Indonesia Spot‐winged S. guttula New Guinea, present an opportunity to observe this We analysed thousands single nucleotide polymorphisms (SNPs) derived from ultraconserved elements all subspecies both Mitochondrial DNA sequences Australian populations form two paraphyletic clades, being sister presumably despite little signal Population genetic analyses (e.g., tests for selection) support at least event between . also uncovered introgression Maluku Islands island population , resulting apparent paraphyly. find that demographic processes, not most likely these complex histories. suggest a Pleistocene extinction mainland resulted range expansion

Language: Английский

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Sequence Capture From Historical Museum Specimens: Maximizing Value for Population and Phylogenomic Studies

Frontiers in Ecology and Evolution, Journal Year: 2022, Volume and Issue: 10

Published: July 22, 2022

The application of high-throughput, short-read sequencing to degraded DNA has greatly increased the feasibility generating genomic data from historical museum specimens. While many published studies report successful results specimens; in reality, success and quality sequence can be highly variable. To examine predictors quality, methodological approaches improving accuracy, we generated analyzed 115 historically collected specimens up 180 years old. Data span both population phylogenomic scales, including 34 four species Australian rock-wallabies (genus Petrogale ) 92 samples 79 Australo-Papuan murine rodents (subfamily Murinae). For rodent specimens, where focus was sampling for phylogenomics, found that regardless specimen age, libraries prepared toe pad or bone subsamples performed significantly better than those taken skin (in terms proportion reads on target, number loci captured, accuracy). In total, 93% resulted reliable phylogenetic inference, compared 63% subsamples. subsamples, target weakly correlated with collection year. Then using rock-wallaby skins as a test case, substantial improvement final by mapping high-quality “closest sister” de novo assembly fresh tissues, sample-specific assembly. Choice approach also affected estimates segregating sites Watterson's θ, important parameters inference. incorporation accurate outcomes evolutionary at scales. By assessing different subsampling, library preparation bioinformatic processing, our provide framework increasing irreplaceable

Language: Английский

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