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

Irestedt, Martin; Thörn, Filip; Müller, Ingo A.; Jønsson, Knud A.; Ericson, Per G. P.; Blom, Mozes P. K.

doi:10.1111/1755-0998.13660

Cited by 30 publications

(36 citation statements)

References 75 publications

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“…Genomic DNA was extracted from muscle and gill arch tissue ( n = 7) in special facilities for degraded DNA from museum samples, using QIAamp DNA Micro Kit (Qiagen, Hilden, Germany) following the protocol described in Irestedt et al . (2022). For two extractions, vouchers NRM 70871 and BMNH 1926.5.5:1, that were found to be particularly promising (curves of DNA with concentrations and average fragment lengths of 3.2 nM and 105 bp, and 0.9 nM and 130 bp, respectively, when run on a Bioanalyser), the authors continued with library preparation.…”

Section: Methodsmentioning

confidence: 99%

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Museomics reveals the phylogenetic position of the extinct Moroccan troutSalmo pallaryi

Delling

Thörn

Norén

et al. 2023

Journal of Fish Biology

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The authors used museomics to reconstruct the mitochondrial genome from two individuals of the Moroccan, endemic and extinct trout, Salmo pallaryi. They further obtained partial data from 21 nuclear genes previously used for trout phylogenetic analyses. Phylogenetic analyses, including publicly available data from the mitochondrial control region and the cytochrome b gene, and the 21 nuclear genes, place S. pallaryi among other North African trouts. mtDNA places S. pallaryi close to Salmo macrostigma within a single North African clade. Although the nuclear coverage of the genome was low, both specimens were independently positioned as sisters to one of two distantly related North African clades, viz. the Atlas clade with the Dades trout, Salmo multipunctatus. Phylogenetic discordance between mtDNA and nuclear DNA phylogenies is briefly discussed. As several specimens that were extracted failed to produce DNA of sufficient quality, the authors discuss potential reasons for the failure.They suggest that museum specimens in poor physical condition may be better for DNA extraction compared to better-preserved ones, possibly related to the innovation of formalin as a fixative before ethanol storage in the early 20th century.

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Section: Methodsmentioning

confidence: 99%

“…For detailed descriptions of the laboratory facilities and procedures used for preparing genome libraries see Irestedt et al . (2022). The raw reads have been deposited at the NCBI Sequence Read Archive (SRA), under the BioProject accession number PRJNA868711.…”

Section: Methodsmentioning

confidence: 99%

Museomics reveals the phylogenetic position of the extinct Moroccan troutSalmo pallaryi

Delling

Thörn

Norén

et al. 2023

Journal of Fish Biology

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“…All libraries were pooled at equal ratios and sequenced on Illumina NovaSeq6000. For detailed descriptions of our laboratory procedures to obtain historic DNA (hDNA) from degraded museum specimens, see Irestedt et al (2022). The raw reads have been deposited at the NCBI Sequence Read Archive (SRA), accession no.…”

Section: Methodsmentioning

confidence: 99%

Demographic history, local adaptation and vulnerability to climate change in a tropical mountain bird in New Guinea

Ericson

Irestedt

2022

Diversity and Distributions

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Aim To investigate how and when allopatric populations of a widely spread mountain bird in New Guinea, Amblyornis macgregoriae, have diversified, how they differ genetically, and how they may respond to future climate conditions. Location New Guinea. Methods Using whole‐genome resequencing data for 26 individuals of A. macgregoriae, we studied how geographically separate populations of this species have responded to past environmental change and how this may have shaped their current genomic structure. We estimated genotype–environment associations and variation in genomic offset to predict how the different populations may respond to climate change. Results A. macgregoriae today has six allopatric mountain populations, occupying sky‐islands with limited gene flow between them. We show that these populations fall into three distinct genetic clusters. Through genotype–environment modelling, we identified annual precipitation and seasonal and day‐to‐night temperature fluctuations as the environmental factors that explain most of the genetic variation in A. macgregoriae. By comparing current and predicted future (RCP 8.5 greenhouse gas scenario for year 2070) genomic variation, we found that the populations close to the Strickland Gorge region in Central Range are those most heavily affected by the predicted climate conditions. Main conclusions The A. macgregoriae populations have fluctuated in size as the glacial cycles caused their montane habitats to repeatedly expand and contract. Low gene flow between populations promoted local adaptation and increased genetic divergence, resulting in a considerable variation in their genomic offset to future climate conditions. Understanding populations' differential response to the ongoing global warming is important for conservation strategy planning, not least for the sensitive mountainous biodiversity in New Guinea.

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“…Conservation genetics has moved towards an era where high-quality reference genomes are often required (Lee et al, 2016; Formenti et al, 2022). For threatened large animals, one of major challenges in conservation genomics is to obtain fresh samples for genome sequencing, in particular long-read sequencing (Irestedt et al, 2022). Noninvasive sampling (Pierre Taberlet, Waits, & Luikart, 1999), including collecting hairs, feathers (Higuchi, von Beroldingen, Sensabaugh, & Erlich, 1988; Morin, Wallis, Moore, Chakraborty, & Woodruff, 1993), feces(Hoss, Kohn, Paabo, Knauer, & Schroder, 1992), or museum specimens (Feng et al, 2019) has been widely used in conservation biology, but severe RNA degradation, highly fragmented DNA and heavy contamination limit the performance of high-quality DNA extraction or transcriptome profiling (P. Taberlet, Mattock, Dubois-Paganon, & Bouvet, 1993; Pierre Taberlet & Luikart, 1999).…”

Section: Introductionmentioning

confidence: 99%

“…The degeneration of DNA and RNA is much slower in cold temperatures, therefore sampling animals of a recent death in frigid zones provides an alternative strategy for obtaining well-preserved DNA or RNA. Retrieving well-preserved DNA from wild frozen samples for genome assembly and population genetic analyses has been successful for several mammalian species(S. Liu et al, 2014; Palkopoulou et al, 2015), including the extinct mammoth (Palkopoulou et al, 2015; Rogers & Slatkin, 2017; van der Valk et al, 2021), but such study for avian species has been rare (Irestedt et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Retrieving the near-complete genome of a threatened bird from wild frozen samples

Luo

Jiang

et al. 2022

Preprint

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Conservation genomics often relies on non-invasive methods to obtain DNA fragments which limit the power of multi-omic analyses for threatened species. Collecting samples from frozen dead animals in the wild provides an alternative approach to obtaining high-quality nucleic acids. Here, we report multi-omic analyses based on a well-preserved great bustard individual (Otis tarda, Otidiformes) of a recent death found in the mountainous region in Gansu, China. We generated a near-complete genome assembly (OTswu) having only 18 gaps scattering in 8 out of the 40 assembled chromosomes. Unlikely most other bird genome assemblies, OTswu contains complete chromosome models (2n = 80). We demonstrated that the great bustard genome likely retained the ancestral avian karyotype. We also characterized the DNA methylation landscapes of OTswu which are strongly correlated with GC content and gene expression. Our phylogenomic analysis suggested Otidiformes and Musophagiformes were sister groups that diverged from each other 46.3 million years ago. The genetic diversity of great bustard was found the lowest among the four available Otidiformes genomes, possibly due to population declines during past glacial periods. As one of the heaviest migratory birds, great bustard possesses several expanded gene families related to cardiac contraction, actin contraction, calcium ion signaling transduction, as well as positively selected genes enriching for metabolism. Finally, we identified an extremely young evolutionary stratum on the sex chromosome, a rare case among Neoaves. Together, our study combining long-read sequencing and RNA-seq technology provides a working strategy for conducting multi-omic analyses for threatened species by retrieving high-quality nucleic acids from dead animals frozen in the wild.

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

Cited by 30 publications

References 75 publications

Museomics reveals the phylogenetic position of the extinct Moroccan troutSalmo pallaryi

Museomics reveals the phylogenetic position of the extinct Moroccan troutSalmo pallaryi

Demographic history, local adaptation and vulnerability to climate change in a tropical mountain bird in New Guinea

Retrieving the near-complete genome of a threatened bird from wild frozen samples

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