Phylogenomic analyses reveal incongruences between divergence times and fossil records of freshwater snails in East Asia

Takahiro Hirano; Takumi Saito; Shun Ito; Bin Ye; T Mason Linscott; Van Tu Do; Zhengzhong Dong; Satoshi Chiba

doi:10.1016/j.ympev.2023.107728

Phylogenomic analyses reveal incongruences between divergence times and fossil records of freshwater snails in East Asia

Mol Phylogenet Evol. 2023 May:182:107728. doi: 10.1016/j.ympev.2023.107728. Epub 2023 Feb 16.

Authors

Takahiro Hirano¹, Takumi Saito², Shun Ito³, Bin Ye⁴, T Mason Linscott⁵, Van Tu Do⁶, Zhengzhong Dong⁷, Satoshi Chiba⁸

Affiliations

¹ Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Graduate School of Life Sciences, Tohoku University, Miyagi, Japan; Biology Program, Faculty of Science, University of the Ryukyus, Okinawa, Japan. Electronic address: hirano0223t@gmail.com.
² Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.
³ Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan.
⁴ Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
⁵ Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, USA.
⁶ Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Ha Noi, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Ha Noi, Viet Nam.
⁷ Agricultural Experiment Station, Zhejiang University, Hangzhou, China.
⁸ Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Graduate School of Life Sciences, Tohoku University, Miyagi, Japan.

PMID: 36804427
DOI: 10.1016/j.ympev.2023.107728

Abstract

Fossils provide important insight into our understanding of phylogenetic history by serving as calibration points for divergence time estimation. However, uncertainties in the fossil record due to parallel evolution and convergent evolution can critically affect estimates of node ages. Here, we compare and contrast estimates of phylogenetic divergence with geologic and fossil history for two freshwater snail genera of the family Viviparidae in East Asia (Cipangopaludina and Margarya). Cipangopaludina species are commonly widely distributed species in East Asia, but extant Margarya species are endemic to the ancient lakes in Yunnan, China. According to some previous studies, parallel evolution or convergent evolution of shell morphology has occurred in the family several times which may affect divergence time estimation using fossil records. In this study, we used SNP data derived from ddRAD-seq loci to investigate population demographic history of both genera. Our results show a common pattern of lake endemic lineages diversifying from widely distributed lineages in the Miocene, and multiple colonization to a single ancient lake occurred in the Pleistocene. Our results indicate substantial incongruence among estimated phylogenomic divergence times, some fossil records, and formation ages of ancient lakes. These findings suggest some fossil records may be misidentified in these groups and highlight the need to carefully evaluate geological evidence and fossil records when using these for divergence time estimation.

Keywords: Ancient lakes; Approximate Bayesian computation; Population genetics; Viviparidae.

MeSH terms

Animals
Asia, Eastern
China
Fossils*
Lakes
Phylogeny
Snails*