History of the terrestrial isopod genus Ligidium in Japan based on phylogeographic analysis

被引：5

作者：

Harigai, Wakana ^{[1
,2
]}

Saito, Aya ^{[3
]}

Zemmoto, Chika ^{[3
]}

Karasawa, Shigenori ^{[4
]}

Yokoi, Touta ^{[4
]}

Nagano, Atsushi J. ^{[5
,6
]}

Suzuki, Hitoshi ^{[1
,7
]}

Yamamoto, Masanobu ^{[1
,7
]}

机构：

[1] Hokkaido Univ, Grad Sch Environm Sci, Kita Ku, Sapporo 0600810, Japan

[2] Osaka Univ, United Grad Sch Child Dev, Dept Child Dev & Mol Brain Sci, Suita 5650871, Japan

[3] Hokkaido Univ, Fac Sci, Dept Earth & Planetary Sci, Kita Ku, Sapporo 0600810, Japan

[4] Tottori Univ, Fac Agr, 4-101 Koyama Cho Minami, Tottori 6808553, Japan

[5] Ryukoku Univ, Fac Agr, Otsu, Shiga 5202194, Japan

[6] Keio Univ, Inst Adv Biosci, Tsuruoka, Yamagata 9970017, Japan

[7] Hokkaido Univ, Fac Environm Earth Sci, Kita Ku, Sapporo 0600810, Japan

来源：

BMC ECOLOGY AND EVOLUTION | 2023年 / 23卷 / 01期

基金：

日本学术振兴会;

关键词：

Genome-wide analysis; Geology; Ligidium; Phylogeography; Quaternary glacial cycle; RAD-seq; POPULATION-STRUCTURE; TOOL SET; GENETICS; ASSOCIATION; DIVERSITY; SOFTWARE; PATTERNS; NUMBER;

D O I：

10.1186/s12862-023-02144-8

中图分类号：

Q14 [生态学（生物生态学）];

学科分类号：

071012 ; 0713 ;

摘要：

BackgroundPhylogeographical approaches explain the genetic diversity of local organisms in the context of their geological and geographic environments. Thus, genetic diversity can be a proxy for geological history. Here we propose a genus of woodland isopod, Ligidium, as a marker of geological history in relation to orogeny and the Quaternary glacial cycle.ResultsMitochondrial analysis of 721 individuals from 97 sites across Japan revealed phylogenetic divergence between the northeastern and southwestern Japan arcs. It also showed repeated population expansions in northeastern Japan in response to Quaternary glacial and interglacial cycles. Genome-wide analysis of 83 selected individuals revealed multiple genetic nuclear clusters. The genomic groupings were consistent with the local geographic distribution, indicating that the Ligidium phylogeny reflects its regional history.ConclusionLigidium DNA sequence analysis can provide insight into the geological, geographical, and paleoenvironmental history of the studied region.

引用

页数：25

共 57 条

[1]

Avise J.C., 1999, PHYLOGEOGRAPHY HIST, DOI DOI 10.2307/J.CTV1NZFGJ7

[2] Trimmomatic: a flexible trimmer for Illumina sequence data [J].

Bolger, Anthony M. ;

Lohse, Marc ;

Usadel, Bjoern .

BIOINFORMATICS, 2014, 30 (15) :2114-2120

[3] BEAST 2: A Software Platform for Bayesian Evolutionary Analysis [J].

Bouckaert, Remco ;

Heled, Joseph ;

Kuehnert, Denise ;

Vaughan, Tim ;

Wu, Chieh-Hsi ;

Xie, Dong ;

Suchard, Marc A. ;

Rambaut, Andrew ;

Drummond, Alexei J. .

PLOS COMPUTATIONAL BIOLOGY, 2014, 10 (04)

[4] TASSEL: software for association mapping of complex traits in diverse samples [J].

Bradbury, Peter J. ;

Zhang, Zhiwu ;

Kroon, Dallas E. ;

Casstevens, Terry M. ;

Ramdoss, Yogesh ;

Buckler, Edward S. .

BIOINFORMATICS, 2007, 23 (19) :2633-2635

[5] The origin of terrestrial isopods (Crustacea: Isopoda: Oniscidea) [J].

Broly, Pierre ;

Deville, Pascal ;

Maillet, Sebastien .

EVOLUTIONARY ECOLOGY, 2013, 27 (03) :461-476

[6] Stacks: an analysis tool set for population genomics [J].

Catchen, Julian ;

Hohenlohe, Paul A. ;

Bassham, Susan ;

Amores, Angel ;

Cresko, William A. .

MOLECULAR ECOLOGY, 2013, 22 (11) :3124-3140

[7] Genetic diversity of soil invertebrates corroborates timing estimates for past collapses of the West Antarctic Ice Sheet [J].

Collins, Gemma E. ;

Hogg, Ian D. ;

Convey, Peter ;

Sancho, Leopoldo G. ;

Cowan, Don A. ;

Lyons, W. Berry ;

Adams, Byron J. ;

Wall, Diana H. ;

Green, T. G. Allan .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2020, 117 (36) :22293-22302

[8]

Dent R, 2012, PLOS ONE, V7, DOI [10.1371/journal.pone.0036889, 10.1371/journal.pone.0037135]

[9] Genetic evidence against monophyly of Oniscidea implies a need to revise scenarios for the origin of terrestrial isopods [J].

Dimitriou, Andreas C. ;

Taiti, Stefano ;

Sfenthourakis, Spyros .

SCIENTIFIC REPORTS, 2019, 9 (1)

[10] BEAST: Bayesian evolutionary analysis by sampling trees [J].

Drummond, Alexei J. ;

Rambaut, Andrew .

BMC EVOLUTIONARY BIOLOGY, 2007, 7 (1)

← 1 2 3 4 5 6 →