Genetic divergence between Cyprinus carpio carpio and Cyprinus carpio haematopterus as assessed by mitochondrial DNA analysis,with emphasis on origin of European domestic carp

Although common carp is the major fish species in Asian and European aquaculture and many domestic varieties have occurred, there is a controversy about the origination of European domestic common carp. Some scientists affirmed that the ancestor of European domestic common carp was Danube River wild common carp, but others considered it might be Asian common carp. For elucidating origination of European domestic common carp, we chose two representative European domestic common carp strains (German mirror carp and Russian scattered scaled mirror carp) and one wild common carp strain of Cyprinus carpio carpio subspecies (Volga River wild common carp) and two Asian common carp strains, the Yangtze River wild common carp (Cyprinus carpio haematopterus) and traditionally domestic Xingguo red common carp, as experimental materials. ND5–ND6 and D-loop segments of mitochondrial DNA were amplified by polymerase chain reaction and analyzed through restriction fragment length polymorphism (RFLP) and sequencing respectively. The results revealed that HaeIII and DdeI digestion patterns of ND5–ND6 segment and sequences of control region were different between European subspecies C. carpio carpio and Asian subspecies C. carpio haematopterus. Phylogenetic analysis showed that German mirror carp and Russian scattered scaled mirror carp belonged to two subspecies, C. carpio carpio and C. carpio haematopterus, respectively. Therefore, there were different ancestors for domestic carp in Europe: German mirror carp was domesticated from European subspecies C. carpio carpio and Russian scattered scaled mirror carp originated from Asian subspecies C. carpio haematopterus.     

Molecular phylogeny of three subspecies of common carp Cyprinus carpio, based on sequence analysis of cytochrome b and control region of mtDNA

The complete cytochrome b and the control region of mtDNA (about 2070 bp in total) of 10 strains belonging to three subspecies of the common carp, including three wild subspecies (the Yangtze River wild common carp – Cyprinus carpio haematopterus , Yuanjiang River wild common carp – Cyprinus carpio rubrofuscus and Volga River wild common carp – Cyprinus carpio carpio ) and seven domestic strains (Xingguo red carp, Russian scattered scaled mirror carp, Qingtian carp, Japanese Koi carp, purse red carp, Big-belly carp, German mirror carp) were sequenced. Phylogenetic analysis indicated that the 10 strains form three distinct clades, corresponding to C. c. haematopterus , C. c. rubrofuscus and C. c. carpio respectively. Purse red carp, an endemic domestic strain in Jiangxi province of China, showed a higher evolution rate in comparison with the other strains of C. c. haematopterus , most probably because of intensive selection and a long history of domestication. Base variation ratios among the three subspecies varied from 0.78% (between C. c. haematopterus and C. c. rubrofuscus ) to 1.47%(between C. c. carpio and C. c. rubrofuscus ). The topography of the phylogenetic tree and the geographic distribution of three subspecies closely resemble each other. The divergence time between C. c. carpio and the other two subspecies was estimated to be about 0.9 Myr and about 0.5 Myr between C. c. haematopterus and C. c. rubrofuscus . Based on phylogenetic analysis, C. c. rubrofuscus might have diverged from C. c. haematopterus .     

Genetic evolution and diversity of common carp Cyprinus carpio L.

Knowledge of genetic variation and population structure of existing strains of both farmed and wild common carp Cyprinus carpio L. is absolutely necessary for any efficient fish management and/or conservation program. To assess genetic diversity in common carp populations, a variety of molecular markers were analyzed. Of those, microsatellites and mitochondrial DNA were most frequently used in the analysis of genetic diversity and genome evolution of common carp. Using microsatellites showed that the genome evolution in common carp exhibited two waves of rearrangements: one whole-genome duplication (12–16 million years ago) and a more recent wave of segmental duplications occurring between 2.3 and 6.8 million years ago. The genome duplication event has resulted in tetraploidy since the common carp currently harbors a substantial portion of duplicated loci in its genome and twice the number of chromosomes (n = 100–104) of most other cyprinid fishes. The variation in domesticated carp populations is significantly less than that in wild populations, which probably arises from the loss of variation due to founder effects and genetic drift. Genetic differentiation between the European carp C.c. carpio and Asian carp C.c. haematopterus is clearly evident. In Asia, two carp subspecies, C.c. haematopterus and C.c. varidivlaceus, seem to be also genetically distinct.     

Polymorphism of the cytochrome oxidase b gene (<Emphasis Type="Italic">cyt b</Emphasis>) in Russian populations of common carp and wild common carp (<Emphasis Type="Italic">Cyprinus carpio</Emphasis> L.)

Polymorphism of the mitochondrial cyt b gene was examined in 35 individuals of common carp and wild common carp (Cyprinus carpio L.). The fish examined represented two natural populations from Khabarovsk krai (Ac and Am), Volga wild common carp, Don wild common carp, and two common carp breeds, Ropsha (strains BB and MM) common carp and Hungarian common carp. The highest level of nucleotide (π) and haplotype (h) diversity was detected in two strains of Ropsha common carp (MM, π = 0.67%, h = 0.7; and BB, π = 0.21%, h = 0.9) and in one population (Am) of Amur wild common carp (π = 0.26%; h = 0.6). The second population of Amur wild common carp (Ac) and Hungarian common carp were characterized by lower variation estimates (π = 0.035%, h = 0.4; and π = 0.09%, h = 0.7, respectively). Genetic homogeneity was demonstrated for the populations of Volga and Don wild common carp (π = 0, h = 0). In the sample of the cyt b sequences examined, three lineages were identified. Lineages I and II united all haplotypes of the Am Amur wild common carp along with two haplotypes of Ropsha common carp, strain MM. The third lineage (III) was formed by the haplotypes of three individuals of Ropsha common carp strain MM, all representatives of Ropsha common carp strain BB, Hungarian common carp, Ac Amur wild common carp, and Don and Volga wild common carps. Statistically significant amino acid differences were observed only for the sequences, corresponding to haplotypes of lineage III, and the sum of sequences of lineages I and II. Effectiveness of different types of markers to differentiate the two subspecies of European and Amur wild common carp (C. c. carpio and C. c. haematopterus) is discussed, as well as the issues of the origin and dispersal of Russian common carp and wild common carp breeds.     

Genetic characterization of common carp (Cyprinus carpio) populations from Greece using mitochondrial DNA sequences

Wild common carp from two lakes and two rivers in Greece were genetically characterized with sequencing analysis of two mitochondrial DNA segments: cytochrome b (1119 bp) and D-loop (646 bp). A total of 9 variable singleton sites and 7 unique haplotypes were detected. A common haplotype was found in three out of the four populations examined, which seems to be the ancestral one and represents the European origin of common carp from Greece. This haplotype could be also justified by the introductions reported with individuals belonging to the Central European race, into many natural habitats in Greece. Limited genetic variation — in Evros and Aliakmonas populations — could be due to bottleneck effects and small effective population sizes, whereas the different haplotypes found in Lake Volvi could represent different common carp stocks. Values of sequence divergence among Greek haplotypes ranged from 0.0006 to 0.0023. The Neighbour-Joining (NJ) phylogenetic tree constructed based on the combined sequences, reveals that the populations of common carp from Greece belong to the European group of populations — which is highly divergent from the South East-Asia cluster — and to the subspecies Cyprinus carpio carpio.     

Polymorphism of microsatellite markers in Russian common carp (<Emphasis Type="Italic">Cyprinus carpio</Emphasis> L.) breeds

Using five microsatellite loci, genotyping and genetic diversity estimates were obtained for nine samples representing seven common carp breeds most widespread in Russia. For comparison, the samples of Amur wild common carp (Cyprinus carpio haematopterus) and a sample of European Hungarian carp were used. In the samples examined (n = 148) a total of 78 alleles were revealed. The highest mean allele number per locus (7.3) was identified in Amur wild common carp, while the lowest number was found in Cherepets carps (4.0). In different breeds, the observed heterozygosities varied from 0.819 (Altai carp) to 0.651 (Cherepets scaly carp). Three out of five microsatellite loci (MFW-24, MFW-28, and MFW-19) revealed a high level of population differentiation. In the dendrogram of genetic differences, all breeds clustered into two groups. One of these groups was composed of the two strains of Ropsha carp, Stavropol carp, Amur wild common carp, and the two samples of Cherepets carp. The second cluster included Altai carp (Priobskii and Chumysh populations), two Angelinskii carp breeds (mirror and scaly), and Hungarian carp. The pairs of breeds/populations/strains, having common origin, were differentiated. Specifically, these were two populations of Altai carp, two strains of Ropsha carp, as well as the breeds of Angelinskii and Cherepets carps. The reasons for genetic differentiation of Russian common carp breeds, as well as the concordance of the evolutionary histories of these breeds, some of which originated from the European breeds, while the others contain substantial admixture of the Amur wild common carp, are discussed.     

Population genetics of invasive common carp Cyprinus carpio L. in coastal drainages in eastern Australia

The common carp Cyprinus carpio introduced in two drainages in eastern Australia are largely descended from European common carp, and in a third drainage they descend largely from East Asian common carp. The partial genetic differentiation among the species in those drainages is consistent with their origins.     

Population structure and genetic management of Rio Grande cutthroat trout (Oncorhynchus clarkii virginalis)

The Rio Grande cutthroat trout, Oncorhynchus clarkii virginalis, has declined precipitously over the past century, and currently exhibits a highly fragmented distribution within the Canadian, Pecos and Rio Grande river systems of the western United States. The relationships between populations in the three river drainages, and between O. c. virginalis and the closely related taxa O. c. pleuriticus and O. c. stomias, are not well understood. In order to guide management decisions for the subspecies, we investigated the distribution of variation at 12 microsatellite loci and two regions of the mitochondrial genome. We observed a high level of genetic differentiation between O. c. virginalis populations occupying different headwater streams (global F_st = 0.41). However, we found evidence for previous gene flow within the Rio Grande drainage, indicating that inter-population differentiation may have been exacerbated by the recent effects of population fragmentation. Despite large-scale anthropogenic movement of individuals from the Rio Grande into the Canadian and Pecos, the genetic signature of long-term evolutionary independence between the three drainages has been retained.     

Systematics and evolution of the libyan jird based on molecular and morphometric data

The libyan jird is one of the most widely distributed species among wild rodents, with its range extending from Morocco to China. Fifteen subspecies were described but their validity and the phylogenetic relationships among them are uncertain. Based on a comprehensive sampling, this study aims to define subspecies limits within Meriones libycus and to discuss the factors driving subspecific diversification. We used an integrative approach combining molecular (Cytochrome b and Cytochrome Oxidase Subunit 1 genes) and geometric morphometric data. Genetic data allowed us to identify three allopatric lineages within M. libycus: Western lineage in North Africa, Central lineage in Saudi Arabia, Jordan, and Syria, and Eastern lineage in Iran, Afghanistan, and China. These three lineages can also be differentiated based on skull morphology. Our results support the existence of at least three subspecies within the libyan jird: Meriones libycus libycus, M. l. syrius, and Meriones libycus erythrourus. Based on our divergence time estimates, all divergence events within M. libycus probably occurred during the Pleistocene, after 1.597 Ma. Quaternary climate fluctuations in the Sinai Peninsula explain the differentiation between the African M. l. libycus and the Levant-Arabian M. l. syrius. The differentiation of M. l. syrius with respect to the eastern M. l. erythrourus is putatively linked to the climatic fluctuations and tectonic activity of the Zagros Mountains and/or the Mesopotamia Plain of Iraq during the Pleistocene.     

Evolutionary history of the Persian Jird,Meriones persicus,based on genetics,species distribution modelling and morphometric data

The Persian Jird, Meriones persicus, is distributed from Eastern Anatolia to Afghanistan and western Pakistan. Six subspecies were described based on skull features and coat colours, but the validity of these subspecies is uncertain, and no molecular work has ever been conducted on this species. Iran appears to be a key geographical region in which to revise the systematic and evolutionary history of this species, because five of the six subspecies are present in this country. To evaluate the phylogeographical history and taxonomy of this species in Iran, we used a combination of genetic (cytochrome b gene sequences of 70 specimens) and geometric morphometric (2D landmarks on the ventral side of skull of 258 specimens) analyses. We also used ecological niche modelling to make inferences about the evolutionary history of these lineages. Our molecular data highlight the existence of four genetic lineages, but they only partly correspond to the previously described subspecies. Our molecular and morphometric data confirm the validity of M. p. rossicus and show that it has a wider geographical range than previously thought. M. p. gurganensis and M. p. baptistae are genetically very close. The skull of M. p. gurganensis is morphologically distinguishable from other subspecies. The subspecies M. p. persicus and M. p. baptistae are genetically distinct, but morphologically close. Meriones p. ambrosius is genetically close to M. p. persicus, and additional analyses with more specimens are needed to validate its subspecific status. The genetic structure observed in Iran seems to fit the topography and biogeography of the country and emphasize the role of the Abarkooh, Central and Lut deserts as barriers to gene flow. All intraspecific divergent events within the Persian Jird occurred during the last 1.4 My, suggesting that climatic changes probably trigger diversification within this species. Our genetic and species niche modelling results suggest that potential refugial areas persisted during glacial periods for this species in north‐western Zagros Mountains, north‐eastern Alborz Mountains and Kohrud Mountains.     

Ichthyofauna of the Lena River (Laptev Sea Basin): Modern composition and historical formation

The modern ichthyofauna of the Lena River includes 46 species and subspecies: 45 bony fishes and one lamprey. In the upper reaches, 24 species have been recorded, 38 in the middle reaches, 36 in the lower reaches, and 24 in the delta. Four of the seven species intentionally introduced into water bodies of the Lena River basin have successfully naturalized; the presence of the others is unconfirmed. All areas of the river are dominated by fishes of the orders Salmoniformes and Cypriniformes. The ranges of the Amur carp Cyprinus rubrofuscus, common bream Abramis brama, ide Leuciscus idus, roach Rutilus rutilus, pike Esox lucius, and perch Perca fluviatilis have expanded over the last few years. The causes and possible ways of the historical formation of the Lena River fish population are discussed in the light of data on the Pleistocene paleogeographical events and patterns of the distribution of species in the river and in adjacent basins.     

Genetic Diversity in Crucian Carp (Carassius auratus)

A survey of restriction fragment polymorphism in mitochondrial DNA of three subspecies of Carassius auratus throughout four provinces in China was undertaken using 17 restriction enzymes. Two carp, Cyprinus carpio rubbrofuscus and Cyprinus carpio carpio, were included as the outgroup. A total of 16 haplotypes was observed: 5 in tetraploids of C. auratus auratus; 8 in hexaploids of C. auratus auratus; and 2 in C. auratus gibelio and C. auratus cuvieri, respectively. The tetraploids and hexaploids share three common haplotypes as I, V, and VI. C. a. Cuvieri may have diverged first among the three subspecies. Interestingly, C. a. auratus and C. a. cuvieri did not form monophyletic clades, which indicated that the classification of Carassius auratus required further studies. The current hypothesis, that hexaploids originated from tetraploids by a polyploidy event, is less favorable, based on the distribution of haplotypes and the lower diversity in tetraploids than in hexaploids. Our data also indicate that divergence of hexaploids and tetraploids might be recent and mtDNA polymorphism existed before the divergence. Meanwhile, genetic isolation exists between the hexaploids and the tetraploids.     

Length-weight relationships of eight fish from seagrass meadows in Wenchang,China

The length-weight relationships (LWRs) were studied for eight seagrass fish from Wenchang, China, using gill nets (150*1 m, mesh size 0.5 cm), including Gerres oblongus, Ambassis kopsii, Halichoeres nigrescens, Sillago aeolus, Yongeichthys criniger, Oxyurichthys tentacularis, Lethrinus haematopterus and Hypoatherina tsurugae, in November 2017, March and August 2018. Results suggest that mean LWR parameters b for these eight seagrass fish varied from 2.801 for L. haematopterus to 3.640 for A. kopsii, and r² valued from .950 for L. haematopterus to 0.993 for H. nigrescens. This study will help us to better understand the ecological parameters these seagrass fish.     

Length–weight relationships of nine fish species from Xingkai (Khanka) Lake,Heilongjiang, China

In this study the length–weight relationships of nine fish species from Xingkai (Khanka) Lake in China belonging to three families and eight genera were analyzed. A total of 273 specimens were used to estimate the relationship parameters. Four of these species (Chanodichthys dabryi, Hemibarbus maculatus, Tachysurus fulvidraco and Cyprinus carpio haematopterus) had no previous estimations and one maximum length is new to science for inclusion in FishBase.     

从江及周边地区稻田鲤的遗传结构及系统发育关系

为探究贵州从江及邻近的榕江、黎平和锦屏以及广西三江、湖南的通道和靖州等地稻田鲤Cyprinus carpio Linnaeus的遗传结构及系统关系, 研究基于mtDNA Cyt b基因测序技术对6个地理群体进行了分析。447尾稻田鲤中共界定出29种Cyt b基因序列单倍型, 结合NCBI中鲤同源序列的系统发育和序列比对分析表明, 从江及邻近苗侗族地区稻田鲤是一个含欧亚2大谱系、3个鲤亚种和多个母系血统成分的混合群体, 主体类群是华南鲤C. carpio rubrofuscus, 同时混有欧洲鲤C. carpio carpio和远东鲤C. carpio haematopterus, 遭受国内外鲤养殖品种的遗传渗析。遗传多样性分析显示, 欧洲鲤亚种群体为低H_d低π, 遗传多样性贫乏, 远东鲤和华南鲤2个亚种群体呈高H_d低π特点。华南鲤6个稻田群体除锦屏为低H_d低π外, 其余都为高H_d低π, 从江的H_d最高, 黎平的π最高。遗传分化和分子方差(AMOVA)分析显示, 谱系间和亚种间存在显著的遗传分化(P<0.001), 锦屏和三江与其他群体存在中等-高度的分化等级, 其余群体间分化较弱, 群体间变异贡献率为16.69%, 群体内为81.14%。综合分析表明, 从江及邻近地区稻田鲤群体间存在有限的遗传交流, 群体内和群体间有不同的遗传结构。研究丰富了该地区稻田鲤遗传背景资料, 可为湘黔桂交界苗侗族地区稻田鲤的种质资源鉴定与保护提供理论依据。     

Phenotypic evolution in high‐elevation populations of western fence lizards (Sceloporus occidentalis) in the Sierra Nevada Mountains

Adaptive divergence in response to variable habitats, climates, and altitude is often accentuated along elevation gradients. We investigate phenotypic evolution in body size and coloration in the western fence lizard (Sceloporus occidentalis Baird & Girard, 1852) across elevation gradients in Yosemite National Park, California, situated in the Sierra Nevada mountains of Western North America. High‐elevation populations occurring above 2100 m a.s.l. are recognized as a separate subspecies (Sceloporus occidentalis taylori Camp, 1916), with a distinctive phenotype characterized by a large body size and extensive blue ventral pigmentation. We sampled S. occidentalis from across elevation gradients in Yosemite National Park, California, and collected phenotypic data (body size and ventral coloration measurements; 410 specimens) and mitochondrial DNA sequence data (complete NADH1 gene; 969 bp, 181 specimens) to infer phylogenetic relationships, and examine the genetic and phenotypic diversity among populations. Populations of S. occidentalis in Yosemite National Park follow Bergmann's rule and exhibit larger body sizes in colder, high‐elevation environments. The high‐elevation subspecies S. o. taylori is not monophyletic, and the mitochondrial DNA genealogy supports a model of convergent phenotypic evolution among high‐elevation populations belonging to different river drainages. The hypothesis that separate populations of S. occidentalis expanded up river drainages after the recession of glaciers is supported by population demographic analyses, and suggest that Bergmann's clines can evolve rapidly along elevation gradients. The distinctive high‐elevation phenotype that is attributable to S. o. taylori has evolved independently several times, and includes adaptive phenotypic changes associated with increases in body size and ventral coloration. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 630–641.     

Cloning of the koi herpesvirus (KHV) gene encoding thymidine kinase and its use for a highly sensitive PCR based diagnosis

Background  

Outbreaks with mass mortality among common carp Cyprinus carpio carpio and koi Cyprinus carpio koi have occurred worldwide since 1998. The herpes-like virus isolated from diseased fish is different from Herpesvirus cyprini and channel catfish virus and was accordingly designated koi herpesvirus (KHV). Diagnosis of KHV infection based on viral isolation and current PCR assays has a limited sensitivity and therefore new tools for the diagnosis of KHV infections are necessary.     

Effects of sustained predation by fast‐growing transgenic common carp (Cyprinus carpio Linnaeus, 1758) on gastropods in artificial environments

The present study addressed the effects of growth hormone‐transgenic and non‐transgenic common carp (Cyprinus carpio L.) predation on the community and populations of four gastropod species cultured in artificial environments. After a 110‐day population‐based predation experiment (three replicate pools [16 m²] for each genotype with one fish [total length 45.0~51.4 cm] and 150 Bellamya aeruginosa (Reeve 1863) per pool), there were no significant effects of predation by either transgenic or non‐transgenic carp on the biomass, number, or size selectivity of the population. Following a 10‐day community‐based predation experiment (three replicate pools [16 m²] for each genotype with one fish [total length 45.0~50.5 cm] and 150 Alocinma longicornis (Benson 1842), 100 Parafossarulus sinensis (Neunayr 1883), 55 B. aeruginosa, and 33 Radix auricularia L. per pool), the consumption rate and the number of gastropods predated by transgenic carp were 2.60 times and 2.85 times higher, respectively, than those of non‐transgenic carp. Furthermore, the biomass of A. longicornis, P. sinensis and B. aeruginosa consumed by transgenic carp was significantly (p < .05) higher than that by non‐transgenic carp. There was a significant difference in the type selection of the four gastropods by the transgenic and non‐transgenic carp, but both predators preferred R. auricularia and avoided B. aeruginosa. Compared with the non‐transgenic carp, predation by transgenic carp resulted in a significant decrease in A. longicornis (p < .05) and an increase in B. aeruginosa (p < .05). These results indicate that the effects of predation by both transgenic and non‐transgenic carp on the B. aeruginosa population tend to be similar, but their effects on the community composed of the four gastropods were significant different. This information may be useful for assessing the environmental risk of transgenic carp.     

Historical museum collections clarify the evolutionary history of cryptic species radiation in the world's largest amphibians

Inaccurate taxonomic assessment of threatened populations can hinder conservation prioritization and management, with human‐mediated population movements obscuring biogeographic patterns and confounding reconstructions of evolutionary history. Giant salamanders were formerly distributed widely across China, and are interpreted as a single species, Andrias davidianus. Previous phylogenetic studies have identified distinct Chinese giant salamander lineages but were unable to associate these consistently with different landscapes, probably because population structure has been modified by human‐mediated translocations for recent commercial farming. We investigated the evolutionary history and relationships of allopatric Chinese giant salamander populations with Next‐Generation Sequencing methods, using historical museum specimens and late 20th‐century samples, and retrieved partial or near‐complete mitogenomes for 17 individuals. Samples from populations unlikely to have been affected by translocations form three clades from separate regions of China, spatially congruent with isolation by either major river drainages or mountain ranges. Pliocene–Pleistocene divergences for these clades are consistent with topographic modification of southern China associated with uplift of the Qinghai‐Tibet Plateau. General Mixed Yule Coalescent model analysis indicates that these clades represent separate species: Andrias davidianus (Blanchard, 1871) (northern Yangtze/Sichuan), Andrias sligoi (Boulenger, 1924) (Pearl/Nanling), and an undescribed species (Huangshan). Andrias sligoi is possibly the world's largest amphibian. Inclusion of additional reportedly wild samples from areas of known giant salamander exploitation and movement leads to increasing loss of biogeographic signal. Wild Chinese giant salamander populations are now critically depleted or extirpated, and conservation actions should be updated to recognize the existence of multiple species.     

Molecular and morphological evidences reveal a cryptic species in the Vinaceous Rosefinch Carpodacus vinaceus (Fringillidae; Aves)

Wu, H.‐C., Lin, R.‐C., Hung, H.‐Y., Yeh, C.‐F., Chu, J.‐H., Yang, X.‐J., Yao, C.‐J., Zou, F.‐S., Yao, C.‐T., Li, S.‐H. & Lei, F.‐M. (2011). Molecular and morphological evidences reveal a cryptic species in the Vinaceous Rosefinch Carpodacus vinaceus (Fringillidae; Aves). —Zoologica Scripta, 40, 468–478. The Vinaceous Rosefinch (Carpodacus vinaceus) is endemic in East Asia with two recognized subspecies –C. v. vinaceus, distributed along the eastern edge of the Tibetan Plateau and the Himalayas, and C. v. formosanus, restricted to Taiwan’s Central Mountain Range. As reflected in a controversial taxonomic history, this vastly disjunctive distribution pattern suggests that the subspecies, having been isolated from each other for a long time, might have diverged, challenging the current taxonomic treatment and calling for possible species delimitation. Sequences of two mitochondrial fragments (mtDNA) and two Z‐linked nuclear loci (zDNA) were used to reconstruct the intraspecific phylogeny of C. vinaceous. The mtDNA tree shows that the two subspecies of the vinaceous rosefinch form two exclusively monophyletic clades. All but one zDNA sequences from the nominate subspecies and C. v. formosanus also formed exclusively monophyletic clades (the exceptional zDNA sequence from C. v. vinaceous formed a weakly supported clade with two outgroup species). Moreover, by conducting quantitative comparisons of morphometric traits and male plumage coloration, we found that the two subspecies exhibit distinguishable morphological differences. All the evidence therefore suggests that C. v. formosanus is a cryptic species and that its taxonomic status should be restored to full species. Molecular dating suggests that the two sibling rosefinches split 1.7 ± 0.2 million years ago, providing a point estimate for the historical connectivity of biota between eastern Tibet‐Himalayas and montane Taiwan.