Research Article |
Corresponding author: Zhengwang Zhang ( zzw@bnu.edu.cn ) Academic editor: George Sangster
© 2016 De Chen, Qiong Liu, Jiang Chang, Aiwu Jiang, Fang Zhou, Yanyun Zhang, Zhengwang Zhang.
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:
Chen D, Liu Q, Chang J, Jiang A, Zhou F, Zhang Y, Zhang Z (2016) Multi-locus analysis supports the taxonomic validity of Arborophila gingica guangxiensis Fang Zhou & Aiwu Jiang, 2008. ZooKeys 555: 125-136. https://doi.org/10.3897/zookeys.555.6814
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The taxonomic status of subspecies has long been debated, especially in conservation biology. Some proposed subspecies must be evolutionarily distinct to be considered conservation units. White-necklaced Partridge (Arborophila gingica) comprises two subspecies, A. g. gingica and A. g. guangxiensis. A. g. guangxiensis, restricted to three isolated small areas in Guangxi, China, with limited population sizes, is a newly discovered subspecies based on recently identified geographic and phenotypic differences between A. g. gingica; however, evidence is lacking that can effectively identify whether the subspecies is evolutionarily distinct. Here, three mitochondrial DNA segments and four nuclear introns were used to test whether the two subspecies are reciprocally monophyletic, which has been proposed as an objective method to evaluate evolutionary distinctiveness. The results indicate that the two subspecies are genetically divergent and form reciprocal monophyletic groups. Therefore, this study further supports the taxonomic validity and distinctiveness of A. g. guangxiensis and suggests that this subspecies be considered as a conservation unit.
Conservation unit, evolutionary distinctiveness, hill partridge, mitochondrial DNA, nuclear introns, monophyletic groups
The taxonomic status of subspecies has long been debated (
The near threatened (NT) White-necklaced Partridge (Arborophila gingica) (
Map of southeast China showing the distribution area of A. gingica. The purple area represents the distribution of the nominate subspecies A. g. gingica according to
Recently, molecular systematics has become one of the most vigorous disciplines to assist in avian taxonomy (
Here, three mtDNA segments and four nuclear introns of White-necklaced Partridge were combined to conduct a series of phylogenetic analyses and test whether A. g. guangxiensis and A. g. gingica form reciprocally monophyletic groups. Furthermore, times of divergence within A. gingica, between A. gingica and its closest relative, were investigated, and attempts to identify possible drivers of the diversification process were made.
Seven individuals of A. g. guangxiensis were sampled from Jiuwanshan National Nature Reserve, Guangxi, and three individuals of A. g. gingica from Wuyishan National Nature Reserve, Jiangxi (Fig.
We amplified three mtDNA segments, cytochrome oxidase subunit 1 (COI), cytochrome
The best-fitting nucleotide substitution model for each partition was selected using the Akaike Information Criterion with JMODELTEST v2.1.7 (
First, we performed molecular clock tests in MEGA v6 (
The complete matrix was 4750 base pairs (bp) in length, including 2861 bp of mtDNA sequence data, and 1889 bp of nuclear intron sequence data. Exclude outgroup, there were 18 variable and 13 informative sites in mtDNA, and 24 variable and 19 informative sites in nuDNA (after phasing). The genetic distance between the two subspecies was higher in mtDNA (0.0038) than in nuDNA (0.0028), and in nuclear introns the genetic distance within subspecies partially overlapped with that between subspecies (Table
Phylogenetic analyses of the complete matrix and mtDNA matrix showed that A. g. guangxiensis and A. g. gingica formed monophyletic groups, with relatively high support (Fig.
Divergence time estimates from the species tree showed that the two subspecies A. g. guangxiensis and A. g. gingica diverged approximately 0.11 (0.05–0.19) mya (million years ago), whereas the divergence between A. gingica and A. rufogularis occurred 2.02 (0.91–2.91) mya (Fig.
Phylogenetic consensus trees from the mtDNA matrix and complete data matrix. Node values above the branches represented the BI posterior probability and ML bootstrap support. Values below the branches represent the divergence times (median) and 95% highest posterior density (HPD) between lineage groups, note that the divergence times in the multi-locus tree were estimated by species tree analysis. The last number in tip labels in the multi-locus tree represent the two haplotypes phased from diploid nuclear sequences.
Mean distance | mtDNA | ALDOB | FGB | G3PDH | OVOG | nuDNA |
---|---|---|---|---|---|---|
Within guangxiensis | 0.0013 ±0.0005 |
0.0017 ±0.0009 |
0.0032 ±0.0012 |
0.0037 ±0.0017 |
0.0032 ±0.0015 |
0.0029 ±0.0007 |
Within gingica | 0.0012 ±0.0005 |
0.0013 ±0.0012 |
0.0021 ±0.0012 |
0.0009 ±0.0009 |
0.0019 ±0.0013 |
0.0016 ±0.0007 |
Between subspecies | 0.0038 ±0.0009 |
0.0017 ±0.0011 |
0.0033 ±0.0012 |
0.0024 ±0.0011 |
0.0038 ±0.0018 |
0.0028 ±0.0007 |
This study documents genetic differentiation between A. g. guangxiensis and A. g. gingica. The phylogenetic analyses based on mtDNA indicate that A. g. guangxiensis and A. g. gingica form reciprocal monophyletic groups (Fig.
However, although the A. g. guangxiensis clade received high support in the mtDNA tree (Fig.
In general, molecular phylogenetic study often reveals non-monophyly of avian subspecies (
The divergence between A. gingica and A. rufogularis in southwest China (
Our results suggest that the divergence between A. g. guangxiensis and A. g. gingica occurred 0.11 (0.05–0.19) mya, during or after the penultimate glaciation (0.13–0.42 mya). We speculate that A. g. guangxiensis and A. g. gingica might have had separate refugia during the glaciation, inducing population differentiation. This Pleistocene refugia scenario has been proposed for several bird species in southeast China, including Tragopan caboti (
In any case, geographical isolation has likely played a role in population differentiation. A. g. guangxiensis and A. g. gingica are currently separated by the karst basin in central Guangxi. This area also represents unfavorable habitat for some montane species, including Gorsachius magnificus (
The estimated temporal diversification and historical biogeography of A. gingica proposed here is based on a small dataset and thus should ideally be substantiated with additional data. To better explore the underlying diversification process (e.g. speciation-with-gene-flow,
Our study demonstrates that the newly found subspecies A. g. guangxiensis and nominate A. g. gingica formed reciprocal monophyletic groups in a multi-locus molecular phylogenetic analyses. The allopatric distribution of A. g. guangxiensis and A. g. gingica and a single diagnostic morphological difference underscore the distinctiveness of these two taxa (
This study was funded by the National Natural Science Foundation of China (No. 31272296), the National Basic Research Program of China (2011BAZ03186) and the China Postdoctoral Science Foundation (2015M580060). We thank Dr Lu Dong and Dr Yue Sun for their help with the collection of samples, Mr Yinong Liu for his help with figure preparation, and Prof. Shou-Hsien Li for his help with manuscript’s revision. We also thank Dr Geoffrey Davison and another anonymous reviewer for their comments on the manuscript, and especially thanks to the editor Dr George Sangster for his comments, edits, and patience.
Table S1
Data type: molecular data
Explanation note: Primers used for PCR amplification and sequencing in this study.
Figure S1
Data type: molecular data
Explanation note: Phylogenetic trees from the nuDNA matrix and each of the nuclear introns.