Research Article |
Corresponding author: Jianhong Xia ( snhmichth@hotmail.com ) Corresponding author: Chenhong Li ( chli@shou.edu.cn ) Academic editor: Maria Elina Bichuette
© 2024 Mingwei Zhou, Jianhong Xia, Chenhong Li.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Zhou M, Xia J, Li C (2024) Divergence of the freshwater sleeper, Neodontobutis hainanensis (Chen, 1985) (Teleostei, Odontobutidae), in the Pearl River basin and on Hainan Island of southern China. ZooKeys 1197: 183-196. https://doi.org/10.3897/zookeys.1197.110314
|
Study of divergence of freshwater fish populations between island and adjacent mainland areas can shed light on the phylogeographical relationships of these regions. Neodontobutis hainanensis is a freshwater fish species restricted to Hainan Island and in Guangdong and Guangxi provinces in the southern mainland China. We examine the phylogenetic relationship and population structure of N. hainanensis based on 3,176 nuclear loci using a gene-capture method. STRUCTURE analysis and principal coordinate analyses (PCA) indicate that populations from Guangdong, Guangxi and Hainan are each distinct, except that some individuals of the Guangdong population share minor genetic components with individuals of the Guangxi population. In the concatenated gene tree, the Hainan population is grouped with the Guangdong population, but the coalescent tree groups the Hainan population as the sister to the Guangxi population. Finally, coalescent simulations confirmed the divergence pattern supported by the coalescent tree and revealed a one-way introgression from the Guangxi population to the Guangdong population, which can explain the discordant results supported by the concatenated and coalescent phylogenetic analyses. Due to recent decline of N. hainanensis populations and the genetic patterns in this species, as revealed in this study, the populations in the three areas should be treated as separate conservation units.
Gene flow, phylogeography, population structure, southern China
Hainan Island is the second largest island in China, with an area of 33,920 km2, and is in the northernmost part of the South China Sea (
Although the Qiongzhou Straight is much narrower than the Beibu Gulf, both geographical and biogeographical evidence support the hypothesis that Hainan Island might have originated as part of the northeastern Indo-China Peninsula and adjacent Guangxi, China, but not from southeastern China, and particularly Guangdong (
The genus Neodontobutis (Gobiiformes, Odontobutidae) has three to six species (
We captured and sequenced 4,434 single-copy nuclear coding loci from the individuals of N. hainanensis collected from Hainan Island and Guangdong and Guangxi provinces, applyied a target-gene enrichment method, and performed phylogenetic reconstruction, STRUCTURE analysis, principal coordinate analysis (PCA) and coalescent simulations to infer the relationships of the populations from these three areas and possible historical events shaping the current genetic patterns in this species.
Sixteen individuals of N. hainanensis were collected in total. Five specimens from Haikou, Hainan Island (20.0°N, 110.2°E), 5 specimens from Chongzuo, Zhuang Autonomous Region of Guangxi (22.8°N, 107.2°E), and six specimens from Yangjiang, Guangdong province (21.9°N, 112.1°E) (Table
Voucher number | Sample id | Location | Population id |
---|---|---|---|
SOU1801005-1 | 25461 | Chongzuo, Guangxi | GX |
SOU1801005-2 | 25462 | Chongzuo, Guangxi | GX |
SOU1801005-3 | 25463 | Chongzuo, Guangxi | GX |
SOU1801005-4 | 25464 | Chongzuo, Guangxi | GX |
SOU1801005-5 | 25465 | Chongzuo, Guangxi | GX |
SOU1801010-8 | 20278 | Haikou, Hainan | HN |
SOU1801010-9 | 20279 | Haikou, Hainan | HN |
SOU1801010-10 | 202710 | Haikou, Hainan | HN |
SOU1801010-11 | 202711 | Haikou, Hainan | HN |
SOU1801010-12 | 202712 | Haikou, Hainan | HN |
SOU1801011-2 | CL1227_2 | Yangjiang, Guangdong | GD |
SOU1801011-3 | CL1227_3 | Yangjiang, Guangdong | GD |
SOU1801013 | CL1228 | Yangjiang, Guangdong | GD |
SOU1801014-1 | CL1279_1 | Yangjiang, Guangdong | GD |
SOU1801014-3 | CL1279_3 | Yangjiang, Guangdong | GD |
SOU1801014-4 | CL1279_4 | Yangjiang, Guangdong | GD |
Outgroups | 25913 | Chongzuo, Guangxi | Neodontobutis lani |
CL632_1 | Harbin, Heilongjiang | Perccottus glenii | |
CL1275_4 | Dandong, Liaoning | Odontobutis yaluensis |
Genomic DNA was extracted from tissue samples using an Ezup Column Animal Genomic DNA Purification Kit (Sangon, Shanghai, China). The concentration of extracted DNA was measured using a NanoDropTM 3300 fluorescence spectrophotometer, and the integrity of extracted DNA was visually checked using gel electrophoresis. A cross-species target loci enrichment method was used to enrich 4,434 coding regions of single-copy nuclear loci (
Reads were assembled, aligned, and filtered following the ASSEXON pipeline, which includes a series of Perl scripts for processing target enrichment data (
Aligned sequences were concatenated using a Perl script concat_loci.pl in the ASSEXON package (
To infer the species tree, maximum-likelihood gene trees of all loci were reconstructed by using the Perl script construct_tree.pl in the ASSEXON package, which generated gene trees for each loci using RAxML v. 8.0.0 (
Consensus sequences were generated from the aligned sequences of N. hainanensis using a Perl script consensus.pl in the ASSEXON package (
Principal coordinate analyses (PCA) were conducted on the NEXUS file contained SNP data using TBTOOLS v. 2.03 (
FASTSIMCOAL v. 2.7 (
For each sample, 1,942–2,720 loci from the 4,434 targeted ones were obtained after assembling, aligning, and removing badly aligned sequences. A total of 3,176 loci were used for phylogenetic analysis and in the making of the consensus sequence. The length of the concatenated alignments was 583,539 bp with 29.13% gaps. A total of 3,493 SNP sites were detected through GATK calling and 996 sites were chosen subsequently for PCA, STRUCTURE analysis, and converted to SFS for FASTSIMCOAL 2 simulations.
The concatenated maximum-likelihood tree is shown in Fig.
The PCA result was shown in Fig.
Log-likelihood values estimated by using FASTSIMCOAL v. 2.7 for the three non-migration models are shown in Fig.
Both concatenated tree and species tree show that the three N. hainanensis populations are monophyletic. The PCA and STRUCTURE results show that despite some mixture in the Guangdong population, genetic compositions of the three populations are largely distinct. All results indicate that the three populations of N. hainanensis are highly differentiated. Because N. hainanensis is strictly freshwater fish of small body size, with a benthic habit, and presumably lacks planktonic eggs or a larval stage (
Although the three N. hainanensis populations were found to be monophyletic in both the concatenated tree and the coalescent tree, their phylogenetic relationship shows discordance. In the concatenated tree, the Guangxi population is sister of Guangdong population, but in the coalescent tree the Guangxi population is the sister to Hainan Island population. The results of FASTSIMCOAL v. 2.7 analysis corroborates the divergent history shown by the coalescent tree. Both PCA and STRUCTURE analyses indicate that migration occurred from the Guangxi population to the Guangdong population, which was confirmed by the FASTSIMCOAL v. 2.7 analyses. The migration from the Guangxi population to the Guangdong population might explain the discrepancy between the concatenated tree and the coalescent tree.
According to the results of species tree, PCA, STRUCTURE analysis, and FASTSIMCOAL v. 2.7 simulation, Indo-China Peninsula and the adjacent Guangxi are supposed to be at the center of diversity of the genus Neodontobutis, with two species (N. hainanensis, N. lani) distributed in Guangxi and presumably four species, N. auarmus (Vidthayanon, 1995), N. tonkinensis (Mai, 1978), N. ngheanensis Nguyen & Nguyen, 2011, and N. macropectoralis (Mai, 1978), found on the Indo-China Peninsula (Vietnam, Laos, and Thailand) (
Besides the Qiongzhou Strait and the Beibu Gulf, the Yunkai-Shiwan Mountains may also be a significant barrier that shaped the genetic patterns of N. hainanensis. One-way introgression from the Guangxi population to the Guangdong population was detected from both STRUCTURE and FASTSIMCOAL v. 2.7 analyses. That may have caused by sporadic dispersal events, because the two populations are not in the same river system. Potential river-capture events await further study using species with similar distribution patterns.
Due to the recent population decline in N. hainanensis, we failed to collect more samples from each population. However, by utilizing genome-wide SNPs from thousands of loci in this study, we were able to mitigate the impact of having a limited number of individuals per population and still obtain valuable information. More samples from different populations of N. hainanensis as well as from other species of Neodontobutis from Vietnam would help to investigate the history of divergence in the genus. Excavating a complete fossil of the Odontobutidae also should help to precisely testing relevant geographical timeframe in southern China and on the Indo-China Peninsula. Because the recent decline of N. hainanensis and the distinct genetic patterns of the three populations revealed in this study, we recommend that the populations of N. hainanensis from Guangdong, Guangxi and Hainan should be treated as separate conservation units.
Neodontobutis hainanensis from Hainan Island, upstream and downstream of the Pearl River basin are distinct. The population of upstream Pearl River is sister group to the population of Hainan Island. One-way introgression from the population of upstream Pearl River to the population of downstream was supported by both population structure analysis and coalescent simulation.
The authors sincerely thank Jiahu Lan and Linxi Pan, who helped sampling for this research.
The authors have declared that no competing interests exist.
All animal procedures performed in this research were done in accordance with the “Ethical Standards of the Shanghai Ocean University (2020)”.
This work was supported by the Science and Technology Commission of Shanghai Municipality (19410740500; 19050501900) to CL.
C Li and J Xia conceived the research ideas. M Zhou collected the data and performed the analyses. M Zhou wrote the first draft. J Xia and M Zhou edited the manuscript. All authors revised and approved the final version of the manuscript.
Mingwei Zhou https://orcid.org/0000-0002-1182-8466
Jianhong Xia https://orcid.org/0009-0001-9615-4797
Chenhong Li https://orcid.org/0000-0003-3075-1756
All of the data that support the findings of this study are available in the main text or Supplementary Information.
A text file contains all template files (*.tpl) for FASTSIMCOAL2 simulations in this research
Data type: txt
A text file contains all estimation files (*.est) for FASTSIMCOAL2 simulations in this research
Data type: txt