Museum genomics reveals the speciation history of Dendrortyx wood-partridges in the Mesoamerican highlands

Sequence capture phylogenomics of historical ethanol‐preserved museum specimens: Unlocking the rest of the vault

“…We recover essentially the full complement of UCE loci from museum specimens collected in the last 10 years, with potential for hundreds of UCEs from specimens collected up to 60 years ago. This result makes it reasonable for more specimens in taxa that are targets of current/ongoing research to be preserved for morphological purposes, as recently collected ethanol-preserved "morphological specimens" are also viable for genetic work with essentially full recovery (Hedin, Derkarabetian, Blair, et al, 2018;Miller et al, 2013;Wood et al, 2018), as also recently suggested for dried bird tissue (Tsai et al, 2019). What remains to be tested is the relative success of sequencing DNA from specimens preserved in 70% ethanol and stored in freezers, something that is not common practice, as only "DNA-grade" specimens preserved in >95% EtOH are typically stored in freezers.…”

“…The ability to incorporate museum specimens into modern molecular systematics offers plenty of research possibilities, as evidenced by the plethora of studies published in recent years. One obvious benefit in systematics is the inclusion of rare, difficult to collect, endangered or extinct taxa in phylogenomic analyses (Hedin et al, ; Hedin, Derkarabetian, Blair, et al, ; Hedin, Derkarabetian, Ramírez, et al, ; Oliveros et al, ; Tsai et al, ; Wood et al, ), or even datasets consisting entirely of museum specimens (Tsai et al, ). One important consideration will be the proportion of specimens in the final dataset that are historical museum specimens.…”

“…Given that there is a decrease in UCE loci sequenced with increasing age, a higher proportion of museum specimens in the final matrix decreases the total number of loci retained for phylogenetic analyses. Given more specific probe sets and better genomic resources, obtaining thousands of loci in a final matrix is certainly possible for datasets composed entirely of museum specimens (Tsai et al, ). In this study we were able to include museum specimens of described and undescribed taxa for which recently collected specimens intended for genetic work are extremely limited or nonexistent.…”

“…Sequence capture methods have great utility at shallow taxonomic levels (Blaimer, LaPolla, Branstetter, Lloyd, & Brady, 2016;Derkarabetian et al, 2019;Hedin, Derkarabetian, Blair, et al, 2018;Smith, Harvey, Faircloth, Glenn, & Brumfield, 2013;Starrett et al, 2017;Tsai et al, 2019;Zarza et al, 2018) including population genomics (Bi et al, 2013), and given the high success in sequencing historical museum specimens, there is great potential for species delimitation. Clear phylogenetic structure and species-level variation are seen across all Vonones samples included in this study, further indicating the potential of incorporating museum specimens into both species-and population-level analyses (Hedin, Derkarabetian, Blair, et al, 2018;Tsai et al, 2019). Including historical type specimens in species delimitation studies is an obvious application, for example in assigning populations and specimens to species listed as federally endangered (Hedin, Derkarabetian, Blair, et al, 2018), or in helping to resolve long-standing taxonomic issues (Kehlmaier et al, 2019;McGuire et al, 2018).…”

“…In this regard, museum specimens can be considered genomic resources (McCormack, Rodríguez-Gómez, Tsai, & Faircloth, 2017) and can be used for diverse types of studies. Examples of such studies are fine-scale population genomics and genotyping (Bi et al, 2013;Lim & Braun, 2016), genome sequencing (Staats et al, 2013), metagenomics (Der Sarkissian et al, 2017), epigenomics (Rubi, Knowles, & Dantzer, 2019), barcoding (Miller, Beentjes, van Helsdingen, & IJland, 2013); Prosser, deWaard, Miller, & Hebert, 2016), species delimitation (Hedin, Derkarabetian, Blair, & Paquin, 2018;Kehlmaier et al, 2019), and phylogenomics (Blaimer, Lloyd, Guillory, & Brady, 2016;Hedin, Derkarabetian, Ramírez, Vink, & Bond, 2018;Ruane & Austin, 2017;Sproul & Maddison, 2017;Starrett et al, 2017;Wood, González, Lloyd, Coddington, & Scharff, 2018), including phylogenomic studies that incorporate genetic data from rare, endangered and/or extinct taxa held in historical collections (Hedin, Derkarabetian, Blair, et al, 2018;Oliveros et al, 2019;Tsai et al, 2019). This was not the case just a few years ago, when historical museum samples were not routinely used for molecular work.…”