Museomics

Lalueza‐Fox, Carles

doi:10.1016/j.cub.2022.09.019

Cited by 17 publications

(7 citation statements)

References 8 publications

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“…Our study further demonstrates the value of museum insect specimens for estimating temporal changes in genetic diversity at a population scale 26 . Despite being notoriously abundant, insects, and in particular butterflies, are very sensitive to climate fluctuations.…”

Section: Discussionsupporting

confidence: 55%

Whole-genomes from the extinct Xerces Blue butterfly can help identify declining insect species

de-Dios

Fontsere

Renom

et al. 2021

Preprint

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The Xerces Blue (Glaucopsyche xerces) is considered to be the first butterfly to become extinct at global scale in historical times. It was notable for its chalky lavender wings with conspicuous white spots on the ventral wings. The last individuals were collected in their restricted habitat, in the dunes near the Presidio military base in San Francisco, in 1941. To explore the demographic history of this iconic butterfly and to better understand why it went extinct, we sequenced at medium coverage the genomes of four 80 to 100-year-old Xerces Blue specimens and seven historic specimens of its closest relative, the Silvery Blue (G. lygdamus). We compared these to a novel annotated genome of the Green-Underside Blue (G. alexis). Phylogenetic relationships inferred from complete mitochondrial genomes indicate that Xerces Blue was a distinct species that diverged from the Silvery Blue lineage at least 850,000 years ago. Using nuclear genomes, we show that both species experienced population growth during the MIS 7 interglacial period, but the Xerces Blue decreased to a very low effective population size subsequently, a trend opposite to that observed in the Silvery Blue. Runs of homozygosity in the Xerces Blue were significantly greater than in the Silvery Blue, suggesting a higher incidence of inbreeding. In addition, the Xerces Blue carried a higher proportion of derived, putatively deleterious amino acid-changing alleles than the Silvery Blue. These results demonstrate that the Xerces Blue experienced more than 100 thousand years of population decline, prior to its human-induced final extinction.

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Section: Discussionsupporting

confidence: 55%

Whole-genomes from the extinct Xerces Blue butterfly can help identify declining insect species

de-Dios

Fontsere

Renom

et al. 2021

Preprint

Self Cite

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“…Museum collections are, therefore, an invaluable resource not only for rare (endangered or extinct) taxa but also for material from inaccessible geographic areas, and assortments of same species throughout their range (Raxworthy & Smith, 2021). In congruence, the number of studies based on museum specimens has been increasing rapidly in recent years, with new milestones constantly being reached due to evolving methods in the field of historical DNA research (Kjær et al, 2022; Lalueza‐Fox, 2022). The falling costs of sequencing have enabled biodiversity assessments made from museum collections to become a reality.…”

Section: Discussionmentioning

confidence: 99%

“…Nevertheless, there is a growing number of studies that have successfully used whole genome or target‐capture sequencing methods for acquiring complete (mitochondrial) genomes from museum material (e.g., Li et al, 2015; Straube, Lyra, et al, 2021), including of formalin‐preserved specimens (Hahn et al, 2022; Hykin et al, 2015). While target‐capture sequencing can be considered advantageous in some cases (e.g., Agne, Naylor, et al, 2022), whole genome sequencing – especially when coupled with custom‐made bioinformatics analysis (Hahn et al, 2022) – provides a wider set of information for further research (for further reading see, e.g., Lalueza‐Fox (2022) or Raxworthy and Smith (2021)). In molecular taxonomy studies, the necessity of including type specimens as name‐bearing specimens is increasingly being recognized (e.g., Agne, Naylor, et al, 2022; Agne, Preick, et al, 2022; Li et al, 2015; Straube, Preick, et al, 2021; Sullivan et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

From historical expedition diaries to whole genome sequencing: A case study of the likely extinct Red Sea torpedo ray

Palandačić,

Kapun,

Greve

et al. 2023

Zoologica Scripta

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Torpedo rays (Torpedinidae, Torpediniformes) are small to moderately large batoids that produce an electric discharge. They are distributed worldwide in temperate and tropical seas and are, as a result of their bottom‐dwelling behaviour, susceptible to trawl fishing and often end up as victims of bycatch. The distribution ranges of most recognized species seem to be restricted; however, their species‐level systematics is not adequately resolved. In the genus Torpedo, in which many species require revision, there are possibly several undescribed species, while numerous misidentifications add to the complexity of the issue. In the latest lists of living rays, 13 species are accepted in the genus Torpedo, including three of doubtful validity and several recently discovered undescribed species. Among the valid species is the critically endangered, possibly extinct, Torpedo suessii Steindachner, 1898, the Red Sea torpedo, of which only four specimens have been recorded in the literature until now, three of which still exist in the fish collection of the Natural History Museum of Vienna. Museum collections are the most important archive of biodiversity on Earth, and are increasingly being used for various studies, including phylogenetics, population genomics, and biogeography. Nevertheless, molecular analysis of old museum material remains challenging because the genetic material has degraded, is fragmented, and of low quantity. In molecular taxonomy, the necessity of including type specimens as name‐bearing specimens is increasingly recognized. Here, the extended specimen approach was applied to re‐describe the lectotype of T. suessii. The approach included research of historical information and whole genome sequencing, followed by genome assembly and phylogenetic analysis.

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“…Herbarium and museum collections are especially well‐suited for contemporary invasion dynamics of plants and animals (Alves et al., 2019; Holmes et al., 2016; Lalueza‐Fox, 2022; Lang et al., 2019). Unlike archaeological remains, these collections provide ample samples in space and time and abundant opportunities for phenotyping (Heberling, 2022).…”

Section: Types Of Temporal Datamentioning

confidence: 99%

“…Herbarium and museum collections are especially well-suited for contemporary invasion dynamics of plants and animals (Alves et al, 2019;Holmes et al, 2016;Lalueza-Fox, 2022;Lang et al, 2019).…”

Section: T Ype S Of Temp or Al Datamentioning

confidence: 99%

Temporal collections to study invasion biology

Kim,

Kreiner,

Hernández

et al. 2023

Molecular Ecology

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Biological invasions represent an extraordinary opportunity to study evolution. This is because accidental or deliberate species introductions have taken place for centuries across large geographical scales, frequently prompting rapid evolutionary transitions in invasive populations. Until recently, however, the utility of invasions as evolutionary experiments has been hampered by limited information on the makeup of populations that were part of earlier invasion stages. Now, developments in ancient and historical DNA technologies, as well as the quickening pace of digitization for millions of specimens that are housed in herbaria and museums globally, promise to help overcome this obstacle. In this review, we first introduce the types of temporal data that can be used to study invasions, highlighting the timescale captured by each approach and their respective limitations. We then discuss how ancient and historical specimens as well as data available from prior invasion studies can be used to answer questions on mechanisms of (mal)adaptation, rates of evolution, or community‐level changes during invasions. By bridging the gap between contemporary and historical invasive populations, temporal data can help us connect pattern to process in invasion science. These data will become increasingly important if invasions are to achieve their full potential as experiments of evolution in nature.

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Museomics

Cited by 17 publications

References 8 publications

Whole-genomes from the extinct Xerces Blue butterfly can help identify declining insect species

Whole-genomes from the extinct Xerces Blue butterfly can help identify declining insect species

From historical expedition diaries to whole genome sequencing: A case study of the likely extinct Red Sea torpedo ray

Temporal collections to study invasion biology

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