A molecular phylogeny of historical and contemporary specimens of an under‐studied micro‐invertebrate group

Abstract

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Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone

“…Critically, our approaches remove the need for costly and/or unreliable re‐sampling from difficult to access locations, such as Antarctic, alpine or deep‐sea faunas (Orr et al, 2020 ), or of endangered (Geist et al, 2008 ; Hawk & Geller, 2019 ), recently extinct (Geist et al, 2008 ; Sullivan et al, 2021 ) or difficult‐to‐find (Psonis et al, 2022 ) populations and taxa. Use of shell‐derived DNA sequences would, furthermore, enable easier inclusion of topotypic samples and type taxa in data sets, in addition to reducing the need to source fresh samples from many institutions and countries (and the associated cost and time of doing so).…”

“…Mollusc shell‐derived palaeogenetic approaches might form entire data sets or supplement otherwise “conventionally” derived data sets, as reported here. Additionally, these approaches, or parts thereof, might be applied to other carbonate‐structure‐producing invertebrate groups, such as bryozoans (Orr et al, 2020 ), crustaceans, echinoderms, or corals (Gomez Cabrera et al, 2019 ). However, bait generation may be more costly and time consuming for phyla with fewer available reference sequences (Orr et al, 2020 ), as the additional step of Sanger‐sequencing amplicons generated using “universal primers” may be necessary to develop effective taxon‐specific long‐range PCR primers.…”

“…Additionally, these approaches, or parts thereof, might be applied to other carbonate‐structure‐producing invertebrate groups, such as bryozoans (Orr et al, 2020 ), crustaceans, echinoderms, or corals (Gomez Cabrera et al, 2019 ). However, bait generation may be more costly and time consuming for phyla with fewer available reference sequences (Orr et al, 2020 ), as the additional step of Sanger‐sequencing amplicons generated using “universal primers” may be necessary to develop effective taxon‐specific long‐range PCR primers. These enrichment approaches might also be applied to generation of nuclear DNA data (Meyer et al, 2016 ), especially given the low endogenous mitochondrial DNA content in even comparatively modern Haliotis specimens.…”

Paleozoic origins of cheilostome bryozoans and their parental care inferred by a new genome-skimmed phylogeny

“…Two nuclear rRNA operon genes (18S and 28S) were also identified and annotated using RNAmmer (57). A total of 315 published cheilostome sequences (20,(58)(59)(60) and the mitogenomes and rRNA operons of 31 non-cheilostome out-group taxa, both bryozoan and nonbryozoan, were aligned with our sequences to compile a broader out-group taxon sample (table S3).…”

Mining museums for historical DNA: advances and challenges in museomics

“…the first historical specimens to reliably produce hDNA and have since become a frequent sampling target. But recent efforts have obtained DNA from a broader array of museum specimen types and taxonomic groups, including sampling microbial communities from herbarium specimens [18], isolating retroviruses in koala (Phascolarctos cinereus) specimens [19], genetic barcoding of eggshells [20], genotyping century-old insect specimens [21], obtaining mitogenomes from 130 year-old dry Bryozoans [22], and collecting genomic loci from formalinpreserved specimens [23]. Of major significance, the use of museum specimens as a source for DNA greatly increases the scale of genetic resources available for research, and consequently, will accelerate comparative studies by substantially increasing taxonomic inclusion, reducing or eliminating field costs, and saving research time.…”