bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.10.29.762307

Sea slugs unplugged: Review of subpopulation sampling in phylogeographic studies of nudibranchs and their allies

Hart, M.·Dennis, M.
View original source ↗Export metadata ↓

Abstract

Nudibranchs and other sea slugs include many cryptic species groups with unknown phenotypic and ecological diversity. How broadly and deeply should researchers sample those cryptic species pairs to capture the genetic variation within each species and potential adaptive differences between species? Fast and inexpensive surveys of genetic diversity that sample a single well-known locus across the geographical range ("phylogeography unplugged") have long been used to identify structured populations and guide choice of sampling localities for subsequent comparative genomic or phenotypic studies of the same species. Results from such studies might also be used to better understand the expected relationships between sampling and population structure in future comparative studies in other species (including many marine gastropods) for which an unplugged phylogeographic survey is not available or impractical. We reviewed analyses of molecular variance that used mitochondrial barcode sequences from marine sea slugs, and we asked whether there are characteristic patterns of subpopulation sampling that are associated with the magnitude and geographical scale of differentiation. We found wide variation in sampling designs: studies with both many and few samples discovered significant population differentiation or broadly similar distribution of haplotypes on both large and small spatial scales, in species from different higher taxonomic groups and oceans. We found two significant associations between sampling variables and population genetic variables, and we suggest using those associations to help guide (or understand the consequences of) sampling design in future studies.

Explore related subjects

zoologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Hart, M., Dennis, M.. 2026-11-02. Sea slugs unplugged: Review of subpopulation sampling in phylogeographic studies of nudibranchs and their allies. https://doi.org/10.64898/2026.10.29.762307

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

A novel methodology for assessing reinforcement choice in primates under human care

Positive Reinforcement Training is a technique commonly employed in zoological collections to elicit a desired behaviour from an animal under human care. Typically, a food item is offered as a reward for performing that behaviour. Three non-human primate species (Mandrillus sphinx, Pan troglodytes, and Hylobates lar) were offered four different foods (banana, grape, apple, and sweet potato) in a series of choice experiments. Latent variable models were employed to investigate which foods were the best selection to use as reinforcement items. Results show that food preference varies between the three primate species. Pan troglodytes and H. lar showed strong preferences for grape and banana, whereas M. sphinx showed a very strong preference for sweet potato. This study indicates that foraging ecology might play an important part in fruit selection and preference in primates. The findings highlight that understanding a species' natural behaviour and dietary preferences is key to informing reinforcement and training decisions.

zoology↗
bioRxiv2026

A comprehensive identification protocol for postcranial bones of Southeast Asian Ruminantia. Part 2: Morphological criteria for small and medium-sized species

The taxonomic identification of postcranial elements from small and medium-sized ruminants represents a significant challenge in zooarchaeological and Late Quaternary paleontological studies, particularly in biodiversity-rich regions such as continental Southeast Asia. This study presents a comprehensive osteological reference framework for the small and medium-sized Ruminantia of this region, based on a comparative sample of 228 specimens representing 14 species across three families (Bovidae, Cervidae, and Moschidae). Osteological characters were first described on a small initial specimen set and subsequently scored across the full sample. Although a small number of character states were found to be unique to specific taxa, most proved highly variable, limiting their individual identification potential. To address this, a Random Forest and a Naive Bayes classifier were applied to assess the discriminatory power of character combinations across four taxonomic ranks (Family, Subfamily, Genus, and Species) on independent bones. Both approaches performed similarly, achieving mean identification accuracies of 87-86% at the family level, 69% at the subfamily level, 50% at the genus level, and 35-33% at the species level. The Naive Bayes models were further deployed as an interactive web application, allowing users to perform bone identification based on any combination of observable character states from a single anatomical element. Our results highlight the limits of morphological identification of postcranial elements in this taxonomic and biogeographic context, while demonstrating that a transparent, reproducible, and statistically grounded approach can still represent a significant step forward for zooarchaeological and Late Quaternary paleontological studies in Southeast Asia and beyond.

zoology↗
bioRxiv2026

A comprehensive identification protocol for postcranial bones of Southeast Asian Ruminantia. Part 3: Morphological criteria for large-sized species

Postcranial remains of large-bodied ruminants are abundant in the Late Quaternary record of continental Southeast Asia, yet their taxonomic attribution remains one of the least resolved problems in the zooarchaeology of this biodiversity-rich region. We address it here with an osteological identification protocol covering the six large ruminant species of the mainland: Bubalus bubalis, Bos javanicus, Bos sauveli, Bos gaurus, Budorcas taxicolor and Rusa unicolor, built from a comparative sample of 109 skeletons. A total of 148 discrete characters over 27 skeletal elements representing 442 states were defined on a restricted set of individuals, then scored across the entire sample. Most proved remarkably stable within taxa with 80.0% of the character/taxon combinations showing a dominant state at a frequency above 95%, and a substantial number of states occurred in a single family, subfamily, genus or species. Character combinations for taxonomic identification were then evaluated by the use of two supervised machine learning methods, a random forest model and a naive Bayes classifier at each of four taxonomic ranks. The two behaved almost identically, with mean accuracies of 95-94% for families, 93% for subfamilies, 89% for genera and 76% for species; only the three closely related and unevenly sampled species of Bos resisted consistent separation. The weighted naive Bayes models are distributed as a standalone web application in which any combination of states observed on a single element returns attribution probabilities for every rank. Together these results offer a transparent and statistically explicit alternative to expert judgement for the identification of Late Quaternary postcranial mammal remains, in Southeast Asia and elsewhere.

zoology↗