2025 Hyper Recent •CC0 1.0 Universal

This work is dedicated to the public domain. No rights reserved.

Access Preprint From Server
March 7th, 2025
Version: 1
Setsunan University
evolutionary biology
biorxiv

Genetic population structure of Japanese freshwater crab, Geothelphusa dehaani species complex (Decapoda: Potamidae) using genome-wide SNP

Kunishima, T.Open in Google Scholar•Takata, K.Open in Google Scholar•Nishikawa, K.Open in Google Scholar•Gibu, K.Open in Google Scholar•Nishijima, M.Open in Google Scholar•Iguchi, A.Open in Google Scholar

The Japanese freshwater crab Geothelphusa dehaani species complex is distributed widely across the Japanese Archipelago. Despite its suggested high genetic and morphological diversity, key aspects such as nuclear DNA (nuDNA) population structure and relationship between body color patterns and genetic populations remain unclear. To address these gaps, this study analyzed genome-wide single nucleotide polymorphisms (SNPs) in nuDNA and mitochondrial DNA (mtDNA) cytochrome oxidase subunit 1 (COI) markers in samples from Hokkaido to the Tokara Islands, Japan. Admixture analysis identified five distinct populations with significant geographic boundaries. These populations exhibited unique geographical patterns, spanning across islands and enclave distribution, indicating that G. dehaani populations have been shaped by complex factors, including sea level changes and volcanic activity. Regional body color variations partially aligned with SNP clades. Further, combining body color with collection locality data could help identify the specimen populations. Contrasting patterns between mtDNA and nuDNA suggest historical gene flow and adaptive introgression, emphasizing the need for caution when interpreting earlier phylogenetic studies based on combined mtDNA and nuDNA sequences. Our findings provide a foundational baseline for future research into the taxonomy, phylogeny, and population dynamics of the G. dehaani species complex, advancing our understanding of its evolutionary history.

Similar Papers

biorxiv
Fri Mar 07 2025
Conserved strategies underpin the replicated evolution of aridity tolerance in trees
Predicting forest responses to climate change requires a detailed understanding of trait-environment coordination. Adaptation to environment comprises both conserved and labile components of trait variation. However, few studies explore the decomposition of trait-environment relationships in a rigorous phylogenetic framework. Combining trait, climate and soil data for an unprecedented number of sp...
Halliwell, B.
•
Blackman, C. J.
•
Gallagher, R. V.
•
Yates, L. A.
...•
Brodribb, T. J.
biorxiv
Fri Mar 07 2025
Jointly representing long-range genetic similarity and spatially heterogeneous isolation-by-distance
Isolation-by-distance patterns in genetic variation are a widespread feature of the geographic structure of genetic variation in many species, and many methods have been developed to illuminate such patterns in genetic data. However, long-range genetic similarities also exist, often as a result of rare or episodic long-range gene flow. Jointly characterizing patterns of isolation-by-distance and l...
Shastry, V.
•
Musiani, M.
•
Novembre, J.
biorxiv
Fri Mar 07 2025
Surviving on limited resources: effects of caloric restriction on growth, gene expression and gut microbiota in a species with male pregnancy (Hippocampus erectus).
Caloric restriction (CR) studies have traditionally focused on species with conventional reproductive roles, emphasizing female's greater investment in costly gametes and parental care. While the divergent impact of CR on males and females is evident across species, the factors driving this variation, i.e., resource allocation to reproductive elements as part of distinct life history strategies, r...
Pappert, F. A.
•
Wuest, V. A.
•
Fontanes-Eguiguren, C.
•
Roth, O.
biorxiv
Fri Mar 07 2025
Recombination peaks and fast evolution
Genetic recombination can speed up or slow down evolution toward the global optimum. For analyzing mutational trajectories to the optimum it is conventional to study peaks in the fitness landscapes. However, such mutational peaks cannot provide a complete picture of the interplay between mutations, recombination and selection. Here we use recombination peaks as an additional tool. Informally, a re...
Crona, K.
biorxiv
Fri Mar 07 2025
Estimating allele frequencies, ancestry proportions and genotype likelihoods in the presence of mapping bias
Population genomic analyses rely on an accurate and unbiased characterization of the genetic setup of the studied population. For short-read, high-throughput sequencing data, mapping sequencing reads to a linear reference genome can bias population genetic inference due to mismatches in reads carrying non-reference alleles. In this study, we investigate the impact of mapping bias on allele frequen...
Günther, T.
•
Goldberg, A.
•
Schraiber, J. G.
biorxiv
Fri Mar 07 2025
The complex evolutionary history of Capparis L. (Capparaceae Juss.) in Australia, and the description of five new species and two new subspecies
Capparis L. (Capparaceae) is a genus of approximately 145 species, many of which have an ancient history of human use. Australia harbours 21 accepted species of Capparis, including the widespread and taxonomically complex Capparis spinosa L., two phrase-named species, and two putative new species; however, the relationships of these species and their taxonomic status remains to be tested. Here, we...
Cooper, W. E.
•
Crayn, D. M.
•
Zich, F. A.
•
Joyce, E. M.
biorxiv
Fri Mar 07 2025
Incorporating continuous characters in joint estimation of dicynodont phylogeny
Continuous characters have received comparatively little attention in Bayesian phylogenetic estima- tion. This is predominantly because they cannot be modeled by a standard phylogenetic Q-matrix approach due to their non-discrete nature. In this manuscript, we explore the use of continuous traits under two Brownian Motion models to estimate a phylogenetic tree for Dicynodontia, a well-studied grou...
Wynd, B. M.
•
Khakurel, B.
•
Kammerer, C. F.
•
Wagner, P. J.
•
Wright, A.
biorxiv
Fri Mar 07 2025
Untangling a History of Hybridization: A Comparison of Phylogenetic Network Methods in Reconstructing Reticulate Evolution in New Zealand Cicadas
Rapid species radiations make hybridization among species more likely. Detecting and reconstructing hybridization is therefore critical for understanding species relationships in many cases. We explored the relative performace of two phylogenetic network methods, SNaQ and PhyNEST, in evaluating the likelihood of proposed past hybridization hypotheses. We used a phylogenomic dataset of over 500 nuc...
Stukel, M.
•
Simon, C.
biorxiv
Fri Mar 07 2025
Environmental drivers of genetic adaptation in two corals from the Florida Keys
Increasingly frequent marine heatwaves devastate coral reefs around the world, so there is great interest in finding warm-adapted coral populations that could be used as sources for assisted gene flow and restoration. Here, we evaluated the relative power of various environmental factors to explain coral genetic variation, suggestive of differential local adaptation to these factors, across the Fl...
Black, K. L.
•
Rippe, J. P.
•
Matz, M. V.