Abstract:This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
“…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).…”
Section: Discussionmentioning
confidence: 99%
“…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.…”
Section: Discussionmentioning
confidence: 99%
“…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.…”
Natural history collections worldwide contain a plethora of mollusc shells. Recent studies have detailed the sequencing of DNA extracted from shells up to thousands of years old and from various taphonomic and preservational contexts. However, previous approaches have largely addressed methodological rather than evolutionary research questions. Here, we report the generation of DNA sequence data from mollusc shells using such techniques, applied to Haliotis virginea Gmelin, 1791, a New Zealand abalone, in which morphological variation has led to the recognition of several forms and subspecies. We successfully recovered near‐complete mitogenomes from 22 specimens including 12 dry‐preserved shells up to 60 years old. We used a combination of palaeogenetic techniques that have not previously been applied to shell, including DNA extraction optimized for ultra‐short fragments and hybridization‐capture of single‐stranded DNA libraries. Phylogenetic analyses revealed three major, well‐supported clades comprising samples from: (1) The Three Kings Islands; (2) the Auckland, Chatham and Antipodes Islands; and (3) mainland New Zealand and Campbell Island. This phylogeographic structure does not correspond to the currently recognized forms. Critically, our nonreliance on freshly collected or ethanol‐preserved samples enabled inclusion of topotypes of all recognized subspecies as well as additional difficult‐to‐sample populations. Broader application of these comparatively cost‐effective and reliable methods to modern, historical, archaeological and palaeontological shell samples has the potential to revolutionize invertebrate genetic research.
“…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).…”
Section: Discussionmentioning
confidence: 99%
“…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.…”
Section: Discussionmentioning
confidence: 99%
“…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.…”
Natural history collections worldwide contain a plethora of mollusc shells. Recent studies have detailed the sequencing of DNA extracted from shells up to thousands of years old and from various taphonomic and preservational contexts. However, previous approaches have largely addressed methodological rather than evolutionary research questions. Here, we report the generation of DNA sequence data from mollusc shells using such techniques, applied to Haliotis virginea Gmelin, 1791, a New Zealand abalone, in which morphological variation has led to the recognition of several forms and subspecies. We successfully recovered near‐complete mitogenomes from 22 specimens including 12 dry‐preserved shells up to 60 years old. We used a combination of palaeogenetic techniques that have not previously been applied to shell, including DNA extraction optimized for ultra‐short fragments and hybridization‐capture of single‐stranded DNA libraries. Phylogenetic analyses revealed three major, well‐supported clades comprising samples from: (1) The Three Kings Islands; (2) the Auckland, Chatham and Antipodes Islands; and (3) mainland New Zealand and Campbell Island. This phylogeographic structure does not correspond to the currently recognized forms. Critically, our nonreliance on freshly collected or ethanol‐preserved samples enabled inclusion of topotypes of all recognized subspecies as well as additional difficult‐to‐sample populations. Broader application of these comparatively cost‐effective and reliable methods to modern, historical, archaeological and palaeontological shell samples has the potential to revolutionize invertebrate genetic research.
“…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).…”
Phylogenetic relationships and the timing of evolutionary events are essential for understanding evolution on longer time scales. Cheilostome bryozoans are a group of ubiquitous, species-rich, marine colonial organisms with an excellent fossil record but lack phylogenetic relationships inferred from molecular data. We present genome-skimmed data for 395 cheilostomes and combine these with 315 published sequences to infer relationships and the timing of key events among c. 500 cheilostome species. We find that named cheilostome genera and species are phylogenetically coherent, rendering fossil or contemporary specimens readily delimited using only skeletal morphology. Our phylogeny shows that parental care in the form of brooding evolved several times independently but was never lost in cheilostomes. Our fossil calibration, robust to varied assumptions, indicates that the cheilostome lineage and parental care therein could have Paleozoic origins, much older than the first known fossil record of cheilostomes in the Late Jurassic.
“…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.…”
Section: Box 1 Consistent Naming Of Dna Sources Ancient Versus Historical Versus Modern Versus Archival Dnamentioning
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.