The youngest split in sympatric schizothoracine fish (Cyprinidae) is shaped by ecological adaptations in a Tibetan Plateau glacier lake

Population Genetic Assessment Model Reveals Conservation Priorities for Gymnocypris Species Resources on the Qinghai-Tibetan Plateau

The Qinghai-Tibetan Plateau (QTP) has nurtured a rich diversity of species because of its unique geographical and environmental conditions. Gymnocypris species (subfamily Schizopygopsinae) are primitive fishes that live in the special environment of the plateau, and their evolution and distribution are inseparable from the historical changes of the QTP. Recently, the resources of Gymnocypris species have been decreasing due to habit deterioration and the intensification of human activities. Therefore, the scientific conservation of the genetic resources of Gymnocypris species is urgently required. In this study, we established two models for the priority conservation assessment of germplasm resources of Gymnocypris species on the basis of the genetic diversity and phylogenetic relationships of 674 individuals from eight Gymnocypris species populations. The results show that the Gymnocypris potanini (GPO), Gymnocypris eckloni (GE), and Gymnocypris przewalskii (GPR) populations are the most genetically diverse in terms of combined genetic diversity values and should be prioritized for conservation. In terms of genetic contribution, the GPO, GE, and GPR populations have a positive impact on maintaining the distinctiveness and diversity of the entire Gymnocypris species population and should be prioritized for conservation. However, in terms of different evolutionary clades, the Gymnocypris namensis, Gymnocypris waddellii, Gymnocypris dobula, and GE populations in clade A should be given priority for protection, the GE population in clade B should be given priority, and the GPR population in clade C should be given priority. In conclusion, the two models and assessment of conservation priorities will provide a scientific basis for the conservation of Gymnocypris species.

Spatially explicit estimation of freshwater fish stock biomass with limited data: A case study of an endangered endemic fish on the Tibetan Plateau, China

Accurate evaluation of fish stock biomass is essential for effective conservation management and targeted species enhancement efforts. However, this remains challenging owing to limited data availability. Therefore, we present an integrated modeling framework combining catch per unit effort with ensemble species distribution modeling called CPUESDM, which explicitly assesses and validates the spatial distribution of stock biomass for freshwater fish species with limited data, applied to Herzensteinia microcephalus. The core algorithm incorporates the Leslie regression model, ensemble species distribution modeling, and exploratory spatial interpolation techniques. We found that H. microcephalus biomass in the Yangtze River source area yielded an initial estimate of 113.52 tons. Our validation results demonstrate high accuracy with a Cohen's kappa coefficient of 0.78 and root mean square error of 0.05. Furthermore, our spatially-explicit, global, absolute biomass density map effectively identified areas with high and low concentrations of biomass distribution centers. Additionally, this study offers access to the source code, example raw data, and a step-by-step instruction manual for other researchers using field data to explore the application of this model. Our findings can help inform for future conservation efforts around fish stock biomass estimation, especially for endangered species.

The Himalayan uplift and evolution of aquatic biodiversity across Asia: Snowtrout (Cyprininae: Schizothorax) as a test case

Global biodiversity hotspots are often remote, tectonically active areas undergoing climatic fluctuations, such as the Himalaya Mountains and neighboring Qinghai-Tibetan Plateau (QTP). They provide biogeographic templates upon which endemic biodiversity can be mapped to infer diversification scenarios. Yet, this process can be somewhat opaque for the Himalaya, given substantial data gaps separating eastern and western regions. To help clarify, we evaluated phylogeographic and phylogenetic hypotheses for a widespread fish (Snowtrout: Cyprininae; Schizothorax) by sequencing 1,140 base pair of mtDNA cytochrome-b (cytb) from Central Himalaya samples (Nepal: N = 53; Bhutan: N = 19), augmented with 68 GenBank sequences (N = 60 Schizothorax/N = 8 outgroups). Genealogical relationships (N = 132) were analyzed via maximum likelihood (ML), Bayesian (BA), and haplotype network clustering, with clade divergence estimated via TimeTree. Snowtrout seemingly originated in Central Asia, dispersed across the QTP, then into Bhutan via southward-flowing tributaries of the east-flowing Yarlung-Tsangpo River (YLTR). Headwaters of five large Asian rivers provided dispersal corridors from Central into eastern/southeastern Asia. South of the Himalaya, the YLTR transitions into the Brahmaputra River, facilitating successive westward colonization of Himalayan drainages first in Bhutan, then Nepal, followed by far-western drainages subsequently captured by the (now) westward-flowing Indus River. Two distinct Bhutanese phylogenetic groups were recovered: Bhutan-1 (with three subclades) seemingly represents southward dispersal from the QTP; Bhutan-2 apparently illustrates northward colonization from the Lower Brahmaputra. The close phylogenetic/phylogeographic relationships between the Indus River (Pakistan) and western tributaries of the Upper Ganges (India/Nepal) potentially implicate an historic, now disjunct connection. Greater species-divergences occurred across rather than within-basins, suggesting vicariance as a driver. The Himalaya is a component of the Earth's largest glacial reservoir (i.e., the "third-pole") separate from the Arctic/Antarctic. Its unique aquatic biodiversity must be defined and conserved through broad, trans-national collaborations. Our study provides an initial baseline for this process.

Sympatric or micro-allopatric speciation in a glacial lake? Genomic islands support neither

Apparent cases of sympatric speciation may actually be due to micro-allopatric or micro-parapatric speciation. One way to distinguish between these models is to examine the existence and nature of genomic islands of divergence, wherein divergent DNA segments are interspersed with low-divergence segments. Such islands should be rare or absent under micro-allopatric speciation but common in cases of speciation with gene flow. Sympatric divergence of endemic fishes is known from isolated saline, crater, postglacial, and ancient lakes. Two morphologically distinct cyprinid fishes, Gymnocypris eckloni scoliostomus (GS) and G. eckloni eckloni (GE), in a small glacial lake on the Qinghai-Tibet Plateau, Lake Sunmcuo, match the biogeographic criteria of sympatric speciation. In this study, we examined genome-wide variation in 46 individuals from these two groups. The divergence time between the GS and GE lineages was estimated to be 20-60 Kya. We identified 54 large genomic islands (≥100 kb) of speciation, which accounted for 89.4% of the total length of all genomic islands. These islands harboured divergent genes related to olfactory receptors and olfaction signals that may play important roles in food selection and assortative mating in fishes. Although the genomic islands clearly indicated speciation with gene flow and rejected micro-allopatric speciation, they were too large to support the hypothesis of sympatric speciation. Theoretical and recent empirical studies suggested that continual gene flow in sympatry should give rise to many small genomic islands (as small as a few kilobases in size). Thus, the observed pattern is consistent with the extensive evidence on parapatric speciation, in which adjacent habitats facilitate divergent selection but also permit gene flow during speciation. We suggest that many, if not most, of the reported cases of sympatric speciation are likely to be micro-parapatric speciation.

Phylogenetic relationship and taxonomic status of Gymnocypris eckloni (Schizothoracinae) based on specific locus amplified fragments sequencing

Accurately delimiting phylogenetic relationships and taxonomic status is important for understanding species diversity and distributions and devising effective strategies for biodiversity conservation. However, species delimitation is controversial in Gymnocypris eckloni, a schizothoracine fish endemic to the Qinghai–Tibetan Plateau. The aim of this study is robustly identifying the phylogeny of G. eckloni in the Yellow River (YR) population and Qaidam basin (QB) population. The specific-locus amplified fragments sequencing (SLAF-seq) is employed with comprehensively sampling of schizothoracine fishes. In total, 350,181,802 clean reads and 5,114,096 SNPs are identified from SLAF-seq. Phylogenetic analysis recovers a non-monophyletic population of G. eckloni between YR and QB populations, representing an independent phylogenetic relationship between the two populations. Species delimitation analyses by SNAPPER and GMYC methods using the genome-wide SNP data confirm that their taxonomic statuses are separated. This study highlights the importance of further reconsidering clearer taxonomy, which would improve the genetic diversity conservation of Tibetan highland fishes.

Morphometric and population genomic evidence for species divergence in the Chimarrichthys fish complex of the Tibetan Plateau

The uplift of the Tibetan Plateau altered the environmental conditions of the local area substantially. Here, we conducted a comprehensive investigation based on morphometrics, population genomics, and climatic factors to evaluate phenotypic and genome-level variations in a radiation of Chimarrichthys catfish endemic to the Plateau. Discriminant function analysis showed phenotypic differences of Chimarrichthys between rivers with respect to elevation. Genetic structure analysis based on 6606 single nucleotide polymorphisms (SNPs) deduced genetic differences between rivers, and species delimitation indicated that the Chimarrichthys fish complex could be divided into three species. Restriction site-associated DNA tags were mapped to the gene sets of Glyptosternon maculatum, and matches were searched against databases for Gene Ontology annotation. Genomic regions exhibiting marked differences among localities represented a range of biological functions, including growth (gdf11), bone development (bmp8a), cellular response to light stimulus (opn3), regulation of the rhodopsin-mediated signalling pathway (grk1), immune response (rag1 and ung), reproductive process (antxr2), and regulation of intracellular iron levels (ireb2). The tag44126, where gene gdf11 is located, was identified as an outlier exhibiting divergence between rivers with altitude differences, and the SNP is thymine (T) in Dadu and Yalong River (~2700 m), but guanine (G) in Jinsha and Qingyi rivers (~2200 and ~ 684 m), suggesting a possible effect of altitude on its differentiation.

Glacier Ice Thickness Estimation and Future Lake Formation in Swiss Southwestern Alps—The Upper Rhône Catchment: A VOLTA Application

Glacial lake formations are currently being observed in the majority of glacierized mountains in the world. Given the ongoing climate change and population increase, studying glacier ice thickness and bed topography is a necessity for understanding the erosive power of glacier activity in the past and lake formation in the future. This study uses the available information to predict potential sites for future lake formation in the Upper Rhône catchment located in the Southwestern Swiss Alps. The study integrates the latest available glacier outlines and high-quality digital elevation models (DEMs) into the Volume and Topography Automation (VOLTA) model to estimate ice thickness within the extent of the glaciers. Unlike the previous ice thickness models, VOLTA calculates ice thickness distribution based on automatically-derived centerlines, while optimizing the model by including the valley side drag parameter in the force equation. In this study, a total ice volume of 37.17 ± 12.26 km3 (1σ) was estimated for the Upper Rhône catchment. The comparison of VOLTA performance indicates a stronger relationship between measured and predicted bedrock, confirming the less variability in VOLTA’s results (r2 ≈ 0.92) than Glacier Bed Topography (GlabTop) (r2 ≈ 0.82). Overall, the mean percentage of ice thickness error for all measured profiles in the Upper Rhône catchment is around ±22%, of which 28 out of 42 glaciers are underestimated. By incorporating the vertical accuracy of free-ice DEM, we could identify 171 overdeepenings. Among them, 100 sites have a high potential for future lake formation based on four morphological criteria. The visual evaluation of deglaciated areas also supports the robustness of the presented methodology, as 11 water bodies were already formed within the predicted overdeepenings. In the wake of changing global climate, such results highlight the importance of combined datasets and parameters for projecting the future glacial landscapes. The timely information on future glacial lake formation can equip planners with essential knowledge, not only for managing water resources and hazards, but also for understanding glacier dynamics, catchment ecology, and landscape evolution of high-mountain regions.

Prevalence and genetic diversity of Echinorhynchus gymnocyprii (Acanthocephala: Echinorhynchidae) in schizothoracine fishes (Cyprinidae: Schizothoracinae) in Qinghai-Tibetan Plateau, China

Background

The schizothoracine fishes, an excellent model for several studies, is a dominant fish group of the Qinghai-Tibet Plateau (QTP). However, species populations have rapidly declined due to various factors, and infection with Echinorhynchus gymnocyprii is cited as a possible factor. In the present study, the molecular characteristics of E. gymnocyprii in four species of schizothoracine fishes from the QTP were explored.

Methods

We investigated the infection status of E. gymnocyprii in 156 schizothoracine fishes from the upper Yangtze River, upper Yellow River, and Qinghai Lake in Qinghai Province, China. The complete internal transcribed spacer (ITS) of the ribosomal RNA (rRNA) gene and part of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene of 35 E. gymnocyprii isolates from these fishes were sequenced and their characteristics analyzed. In addition, we inferred phylogenetic relationships of the E. gymnocyprii populations based on the rRNA-ITS and cox1 sequences.

Results

The total prevalence of E. gymnocyprii in schizothoracine fishes was 57.69% (90/156). However, the prevalence among different species as well as that across the geographical locations of the schizothoracine fishes was significantly different. The results of sequence analysis showed that the four E. gymnocyprii populations from different hosts and regions of Qinghai Province were conspecific, exhibiting rich genetic diversity. Phylogenetic analysis based on rRNA-ITS and cox1 sequences supported the coalescence of branches within E. gymnocyprii; the cox1 gene of E. gymnocyprii populations inferred some geographical associations with water systems. In addition, three species of schizothoracine fishes were recorded as new definitive hosts for E. gymnocyprii.

Conclusions

To the best of our knowledge, this is the first molecular description of E. gymnocyprii populations in schizothoracine fishes from the Qinghai-Tibet Plateau that provides basic data for epidemiological surveillance and control of acanthocephaliasis to protect endemic fish stocks.

Pelagic-benthic resource polymorphism in Schizopygopsis thermalis Herzenstein 1891 (Pisces, Cyprinidae) in a headwater lake in the Salween River system on the Tibetan Plateau

Resource polymorphism is a ubiquitous phenomenon in vertebrates and may represent a critical intermediate stage in speciation. Freshwater lakes in high-altitude areas represent a natural system for understanding resource polymorphism in fishes benefiting from diverse lacustrine environments and species-poor fish assemblages. We report resource polymorphism in a cyprinid fish, Schizopygopsis thermalis, in Lake Amdo Tsonak Co, a headwater lake in the upper Salween River system. Two discrete intraspecific morphs, planktivorous and benthivorous, were identified according to geometric morphometrics and traditional univariate linear measures. The planktivorous morph exhibits a longer head, longer upper and lower jaw, larger asymptotic standard length (L∞ ), lower growth rate (k), and higher growth performance index (φ) than the benthivorous morph. With respect to descriptive traits, the planktivorous morph possesses a large, terminal mouth and obvious mucus pores on the cheek and chin, while the benthivorous morph is characterized by a more inferior mouth with a sharpen horny edge on the lower jaw and unconspicuous mucus pores. The discrete pelagic-benthic resources and low interspecific competition in the lake system might drive the initial differentiation of the two morphs, and partial spatial reproductive isolation in breeding further maintains and reinforces the differences between them.

Transcriptome-Wide Patterns of the Genetic and Expression Variations in Two Sympatric Schizothoracine Fishes in a Tibetan Plateau Glacier Lake

Sympatric speciation remains a central focus of evolutionary biology. Although some evidence shows speciation occurring in this way, little is known about the gene expression evolution and the characteristics of population genetics as species diverge. Two closely related Gymnocypris fish (Gymnocypris chui and Gymnocypris scleracanthus), which come from a small glacier lake in the Tibetan Plateau, Lake Langcuo, exist a possible incipient sympatric adaptive ecological speciation. We generated large amounts of RNA-Seq data from multiple individuals and tissues from each of the two species and compared gene expression patterns and genetic polymorphisms between them. Ordination analysis separated samples by organ rather than by species. The degree of expression difference between organs within and between species was different. Phylogenetic analyses indicated that the two closely related taxa formed a monophyletic complex. Population structure analysis displayed two distinctly divergent clusters of G. chui and G. scleracanthus populations. By contrast, G. scleracanthus population genetic diversity is higher than that of G. chui. Considerable sites of the two populations were differentiated with a coefficient of F_ST = 0.25–0.50, implying that a small proportion of loci nevertheless exhibited deep divergence in two comparisons. Concomitantly, putatively selected genes during speciation revealed functional categories are enriched in bone morphogenesis, cell growth, neurogenetics, enzyme activity, and binding activity in G. chui population. In contrast, nutrition and localization were highlighted in G. scleracanthus. Collectively, morphological traits and dietary preference combine with genetic variation and expression variation, probably contributed to the incipient speciation of two sympatric populations.

Convergent evolution misled taxonomy in schizothoracine fishes (Cypriniformes: Cyprinidae)

Highly specialized grade (HSG; genera Gymnocypris, Oxygymnocypris, Schizopygopsis, Platypharodon and Chuanchia) of the Schizothoracinae (Cypriniformes: Cyprinidae) are endemic to the Qinghai-Tibet Plateau (QTP). Previously, two distinct ecomorphs were recognized according to trophic traits. One was a limnetic omnivore with normal lower jaw morphology, terminal mouth, and moderate or dense gill rakers, mostly inhabiting in open water of lakes, including Gymnocypris and Oxygymnocypris. Another was a benthic feeder with inferior mouth, sparse gill rakers and sharp horny sheath on the lower jaw for scraping of attached prey off hard substrates, including Schizopygopsis, Platypharodon and Chuanchia. However, traditional taxonomy of HSG based on these trophic traits presented extensive conflicts with the molecular studies in recent years. The possible cause could be convergent evolution in morphology, retention of ancestral polymorphisms or mitochondrial introgression, but these hypotheses could not be assessed due to incomplete taxon sampling and only mitochondrial data employed in previous works. Here, we conducted the most comprehensive molecular analysis on HSG fishes to date, using four mitochondrial loci and 152,464 genome-wide SNPs, and including 21 of 24 putative species and one undescribed Schizopygopsis species. Both SNP and mtDNA trees confirmed extensive paraphyly of genera Gymnocypris and Schizopygopsis, where species often were clustered together by watershed instead of by genus. Basal split into the north clade B and the south clade C (ca. 3.03 Ma) approximately by the Tanggula-Tanitawen Mountains in SLAF tree coincided with a violent uplift of the QTP during the phase A of 'Qingzang movement' (ca. 3.6 Ma). Ancestral state reconstruction of the trophic ecomorph showed that the limnetic omnivore ecomorph had evolved repeatedly in clade B and C. Furthermore, we presented a striking case of convergent evolution between two 'subspecies' Gymnocypris chui chui and G. chui longimandibularis, which had diverged as early as two million years ago (ca. 2.42 Ma). Ecological analyses revealed that similar food utilization, particularly in zooplankton, was the main underlying driving force. This work showed an example of taxonomy with the most extensive errors at the genus/species levels due to convergent evolution and suggested that trophic traits could be misleading in fish taxonomy. Therefore, we propose a major generic revision for HSG species.

Adaptive Evolution of the Eda Gene and Scales Loss in Schizothoracine Fishes in Response to Uplift of the Tibetan Plateau

Schizothoracine is the predominant wild fish subfamily of the Tibetan plateau (TP). Their scales, pharyngeal teeth and barbels have gradually regressed with increasing altitude. Schizothoracine have been divided into three groups: primitive, specialized and highly specialized. Ectodysplasin-A (Eda) has been considered as a major gene that contributes to the development of skin appendages. The present study cloned the Eda genes of 51 Schizothoracine fish species which represent the three groups and five Barbinae species. Phylogenetic analyses indicated that Eda may have acted as the genetic trigger for scale loss in the Schizothoracine. Furthermore, 14 single nucleotide polymorphisms (SNPs) and two deletions (18 bp and 6 bp in size), were also detected in the Eda coding sequence of the highly specialized group compared to the primitive group. The same SNPs and two indels result in four non-synonymous and two G-X-Y and 1 XY motif indels, which possibly contribute to significant structure changes in the Eda gene. The domain including (G-X-Y)_n motif in the Eda gene is relatively conserved amongst teleosts. Based on the above results, we hypothesize that the evolution of Eda gene might be associated with the scale loss in Schizothoracine fishes in response to the phased uplift of the TP.

Genomic signature of highland adaptation in fish: a case study in Tibetan Schizothoracinae species

Background

Genome-wide studies on highland adaptation mechanism in terrestrial animal have been widely reported with few available for aquatic animals. Tibetan Schizothoracinae species are ideal model systems to study speciation and adaptation of fish. The Schizothoracine fish, Gymnocypris przewalskii ganzihonensis had underwent the ecological niche shift from salt water to freshwater, and also experienced a recent split from Gymnocypris przewalskii przewalskii. In addition, G. p. ganzihonensis inhabited harsh aquatic environment including low temperature and hypoxia as well as other Schizothoracinae species, its genetic mechanism of highland adaptation have yet to be determined.

Results

Our study used comparative genomic analysis based on the transcriptomic data of G. p. ganzihonensis and other four fish genome datasets to investigate the genetic basis of highland adaptation in Schizothoracine fish. We found that Schizothoracine fish lineage on the terminal branch had an elevated dN/dS ratio than its ancestral branch. A total of 202 gene ontology (GO) categories involved into transport, energy metabolism and immune response had accelerated evolutionary rates than zebrafish. Interestingly, we also identified 162 genes showing signature of positive selection (PSG) involved into energy metabolism, transport and immune response in G. p. ganzihonesis. While, we failed to find any PSG related to hypoxia response as previous studies.

Conclusions

Comparative genomic analysis based on G. p. ganzihonensis transcriptome data revealed significant genomic signature of accelerated evolution ongoing within Tibetan Schizothoracinae species lineage. Molecular evolution analysis suggested that genes involved in energy metabolism, transport and immune response functions in Schizothoracine fish underwent positive selection, especially in innate immunity including toll-like receptor signaling pathway genes. Taken together, our result as a case study in Schizothoracinae species provides novel insights in understanding the aquatic animal adaptation to extreme environment on the Tibetan Plateau, and also provides valuable genomic resource for further functional verification studies.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4352-8) contains supplementary material, which is available to authorized users.

Genetic differentiation of the Schizothorax species complex (Cyprinidae) in the Nujiang River (upper Salween)

Phenotypically diverse species from recently evolved groups always share allele/haplotype due to insufficient differentiation in the early process. In this study, we performed population genetics analyses using sequences from the mitochondrial cytochrome b gene, and two nuclear genes to investigate the genetic differentiation of the closely related Schizothorax species complex, comprising a group of alpine fish living in the Nujiang River. The results from both mtDNA and nDNA markers revealed relatively low but pronounced genetic differentiation among the three Schizothorax species, i.e., Schizothorax gongshanensis, S. lissolabiatus, and S. nukiangensis. However, haplotype sharing was frequently occurred among the three species. Divergence time estimation suggested the last glaciation on the Tibetan Plateau (0.075–0.01 Ma) might drive the divergence of the species complex. Gene flow might contribute to the haplotype sharing between S. gongshanensis and S. lissolabiatus, and between S. gongshanensis and S. nukiangensis, whereas retention of ancestral polymorphisms seemed to be a better explanation of the haplotype sharing between S. lissolabiatus and S. nukiangensis. In addition, S. lissolabiatus populations should obtain more protection in the future because of their low genetic diversity and habitat fragmentation. In summary, our study assesses genetic differentiation among the three closely related Schizothorax species and explores the possible driving forces for their differentiation.

Population genetics analysis of the Nujiang catfish Creteuchiloglanis macropterus through a genome-wide single nucleotide polymorphisms resource generated by RAD-seq

Advances in genome scanning using high-throughput sequencing technologies has led to a revolution in studies of non-model organisms. The glyptosternoid fish Creteuchiloglanis macropterus, is widely distributed in the main stem and tributaries of the Nujiang River basin. Here, we analyzed IIB restriction-site-associated DNA (2b-RAD) sequences and mitochondrial DNA sequences, to assess the genomic signature of adaptation by detecting and estimating the degree of genetic differentiation among ten Creteuchiloglanis macropterus populations from the Nujiang River. The analyses revealed significant population differentiation among the up-tributaries, main stem, mid-tributary and low-tributary. Annotation of contigs containing outlier SNPs revealed that the candidate genes showed significant enrichment in several important biological process terms between up-tributaries and low-tributary, and exhibited prominent enrichment in the term macromolecular metabolic process between all tributaries and the main stem. Population dynamics analyses indicated that the Late Pleistocene glaciations strongly influenced the demographic history of C. macropterus. Our results provide strong evidence for the utility of RAD-seq in population genetics studies, and our generated SNP resource should provide a valuable tool for population genomics studies of C. macropterus in the future.

Phylogeography of Diptychus maculatus (Cyprinidae) endemic to the northern margin of the QTP and Tien Shan region

Background

Phylogeography and historical demography of the cyprinid fish Diptychus maculatus (subfamily Schizothoracinae) are evaluated across three river systems in the Northern Qinghai-Tibetan Plateau (QTP) and Tien Shan range: the Indus River, Tarim River and Ili River.

Results

Results from both mtDNA (16S rRNA, Cyt b and D-loop) and nucDNA (RAG-2) resolved four reciprocally monophyletic clades, representing populations from Indus River, South Tarim River, North Tarim River and Ili River, respectively. The divergence times was estimated to be 1.5–2.5 Mya. It is consistent with the hypothesis that the split of four clades is the consequence of vicariance resulting from both the intensive uplift of QTP and Tien Shan as well as the resultant expansion of the Taklimakan Desert. Several lines of evidences indicate dynamic demographic histories for the populations, with late Pleistocene and Holocene population bottlenecks and expansions except the Indus River.

Conclusions

Our results clearly depicted the phylogenetic relationship of D. maculatus from Indus River, Tarim River and Ili River. The analyses implicated the relationship among the distribution of D. maculatus, paleo-drainages and geographic events, and implied the existence of the South Tarim River in history.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0756-3) contains supplementary material, which is available to authorized users.

Genetic diversity and evolutionary history of the Schizothorax species complex in the Lancang River (upper Mekong)

The genus Schizothorax (Cyprinidae), one of the most diverse genera of ichthyofauna of the Qinghai‐Tibetan Plateau (QTP), is a good candidate for investigating patterns of genetic variation and evolutionary mechanisms. In this study, sequences from the mitochondrial control region, the cytochrome b gene, and two nuclear genes were used to re‐examine the genetic diversity and investigate the evolutionary history of the Schizothorax species complex inhabiting the Lancang River. Three maternal clades were detected in the Schizothorax species complex, but frequent nuclear allele sharing also occurred among the three maternal clades. A discrepancy between topologies of mitochondrial and nuclear loci might result from introgression or/and incomplete lineage sorting. The divergence of the clades of the Schizothorax species complex was closely related to the Late Pliocene and Early Pleistocene orogenesis of the QTP and Southwest Mountains of China. Demographic analyses indicated that the species complex subsequently persisted in situ with stable populations during Pleistocene glacial cycling, which suggested that Pleistocene climate changes did not exert a remarkable influence on the species complex. Our study provides a comprehensive analysis of the genetic diversity and evolutionary history of the Schizothorax species complex in the Lancang River.

Phylogeography and population genetics of Schizothorax o'connori: strong subdivision in the Yarlung Tsangpo River inferred from mtDNA and microsatellite markers

The Qinghai-Tibet Plateau (QTP) is a biodiversity hotspot, resulting from its geological history, contemporary environment and isolation. Uplift of the QTP and Quaternary climatic oscillations are hypothesised to have influenced the genetic diversity, population structure and dynamics of all QTP endemic species. In this study, we tested this hypothesis by assaying variation at two mitochondrial DNA regions (cytochrome b and control region) and at 12 microsatellite loci of seven populations of the endemic fish, Schizothorax o'connori from the Yarlung Tsangpo River (YLTR) on the QTP. Analyses revealed one group of six populations to the west, above the Yarlung Tsangpo Grand Canyon (YTGC), and a second group to the east below the YTGC. Estimates of the timing of this east-west split indicate that these groups represent evolutionarily significant units that have evolved separately and rapidly in the middle Pleistocene, at the time of the Kunlun-Huanghe Movement A Phase and the Naynayxungla glaciation. Population dynamic analyses indicate that S. o'connori experienced a pronounced late Pleistocene expansion during the last interglacial period. The results of this study support the hypotheses that the QTP uplift and Quaternary climatic oscillations have played important roles in shaping the population genetics and dynamics of this endemic fish.

The fish diversity in the upper reaches of the Salween River, Nujiang River, revealed by DNA barcoding

Nujiang River (NR), an essential component of the biodiversity hotspot of the Mountains of Southwest China, possesses a characteristic fish fauna and contains endemic species. Although previous studies on fish diversity in the NR have primarily consisted of listings of the fish species observed during field collections, in our study, we DNA-barcoded 1139 specimens belonging to 46 morphologically distinct fish species distributed throughout the NR basin by employing multiple analytical approaches. According to our analyses, DNA barcoding is an efficient method for the identification of fish by the presence of barcode gaps. However, three invasive species are characterized by deep conspecific divergences, generating multiple lineages and Operational Taxonomic Units (OTUs), implying the possibility of cryptic species. At the other end of the spectrum, ten species (from three genera) that are characterized by an overlap between their intra- and interspecific genetic distances form a single genetic cluster and share haplotypes. The neighbor-joining phenogram, Barcode Index Numbers (BINs) and Automatic Barcode Gap Discovery (ABGD) identified 43 putative species, while the General Mixed Yule-coalescence (GMYC) identified five more OTUs. Thus, our study established a reliable DNA barcode reference library for the fish in the NR and sheds new light on the local fish diversity.

Genetic structure and historical demography of Schizothorax nukiangensis (Cyprinidae) in continuous habitat

Geographic distance, different living habitats or Pleistocene climatic oscillations have frequently been found to shape population genetic structure in many species. The genetic structure of Schizothorax nukiangensis, a high altitude, valuable fish species, which is distributed throughout the Nujiang River, was investigated by mitochondrial DNA sequence analysis. The cytochrome c oxidase subunit I (COI), cytochrome b (cytb), and the mitochondrial control region (MCR) of S. nukiangensis were concatenated for examination of population structure and demographic history. The concatenated data set (2405 bp) implied a pronounced genetic population structure (overall F_ST = 0.149) and defined two population units. Strong differentiation was detected between the Sanjiangkou (SJK) population and other populations due to environmental heterogeneity, dispersal ability, and/or glacial cycles. Additional DNA sequencing of the nuclear RAG2 gene also examined significant differentiation between two units and between SJK and the upstream populations (U-unit). Recent expansion events suggest that S. nukiangensis may have undergone a rapid increase during warm interglacial periods. Surprisingly, S. nukiangensis appears to have undergone an obvious expansion during the last glaciations (LG) for cold hardiness and a sharp contraction from 1.5 ka to the present. However, two population units exhibited different reflections during the LG, which might be closely related to their living habitats and cold hardiness. A clear pattern of isolation by distance was detected in S. nukiangensis due to feeding habits, limited dispersal ability, and/or philopatry. It is vitally important that more attention be given to S. nukiangensis due to low genetic diversity, lack of gene flow, and recent population contraction.

Ongoing speciation in the Tibetan plateau Gymnocypris species complex

Local adaptation towards divergent ecological conditions often results in genetic differentiation and adaptive phenotypic divergence. To illuminate the ecological distinctiveness of the schizothoracine fish, we studied a Gymnocypris species complex consisting of three morphs distributed across four bodies of water (the Yellow River, Lake Qinghai, the Ganzi River and Lake Keluke) in the Northeast Tibetan Plateau. We used a combination of mitochondrial (16S rRNA and Cyt b) and nuclear (RAG-2) genetic sequences to investigate the phylogeography of these morphs based on a sample of 277 specimens. Analysis of gill rakers allowed for mapping of phenotypic trajectories along the phylogeny. The phylogenetic and morphological analyses showed that the three sparsely rakered morphs were present at two extremes of the phylogenetic tree: the Yellow River morphs were located at the basal phylogenetic split, and the Lake Keluke and Ganzi River morphs at the peak, with the densely rakered Lake Qinghai morphs located between these two extremes. Age estimation further indicated that the sparsely rakered morphs constituted the oldest and youngest lineages, whereas the densely rakered morph was assigned to an intermediate-age lineage. These results are most compatible with the process of evolutionary convergence or reversal. Disruptive natural selection due to divergent habitats and dietary preferences is likely the driving force behind the formation of new morphs, and the similarities between their phenotypes may be attributable to the similarities between their forms of niche tracking associated with food acquisition. This study provides the first genetic evidence for the occurrence of convergence or reversal in the schizothoracine fish of the Tibetan Plateau at small temporal scales.

Determination and comparison of two complete mitochondrial genomes of golden Chinese loach, Sinibotia superciliaris (Teleostei, Cypriniformes)

The golden Chinese loach, Sinibotia superciliaris (Günther, 1892) is an endemic fish in China, which is only distributed in the main river and tributaries of the upper and middle Yangtze River. In this study, we sequenced two mitochondrial genomes simultaneously from two samples of S. superciliaris collected from two different locations. Both mitogenomes were 16,572 bp in length, showing a typical vertebrate mitogenome feature with 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and 1 major non-coding control region (CR). Alignment and comparative analyses showed that the two mitogenome sequences possessed 22 mutation sites, all of which were transitions and mainly occurred in protein-coding genes (13/22) and CR (7/22). Among the 13 mutation sites that occurred in protein-coding genes, three mutation sites occurred in the first codon position and the remaining 10 sites occurred in the third codon position. However, only one mutation that occurred in the first codon position resulted in non-synonymous substitution in COI gene. The molecular data presented in this study will contribute to further phylogenetic analyses for this group of fishes.

Freshwater biogeography and limnological evolution of the Tibetan Plateau--insights from a plateau-wide distributed gastropod taxon (Radix spp.)

Background

The Tibetan Plateau is not only the highest and largest plateau on earth; it is also home to numerous freshwater lakes potentially harbouring endemic faunal elements. As it remains largely unknown whether these lakes have continuously existed during the Last Glacial Maximum (LGM), questions arise as to whether taxa have been able to exist on the plateau since before the latest Pleistocene, from where and how often the plateau was colonized, and by which mechanisms organisms conquered remote high altitude lentic freshwater systems. In this study, species of the plateau-wide distributed freshwater gastropod genus Radix are used to answer these biogeographical questions.

Methodology/Principal Findings

Based on a broad spatial sampling of Radix spp. on the Tibetan Plateau, and phylogenetic analyses of mtDNA sequence data, three probably endemic and one widespread major Radix clade could be identified on the plateau. Two of the endemic clades show a remarkably high genetic diversity, indicating a relatively great phylogenetic age. Phylogeographical analyses of individuals belonging to the most widely distributed clade indicate that intra-plateau distribution cannot be explained by drainage-related dispersal alone.

Conclusions/Significance

Our study reveals that Radix spp. persisted throughout the LGM on the Tibetan Plateau. Therefore, we assume the continuous existence of suitable water bodies during that time. The extant Radix diversity on the plateau might have been caused by multiple colonization events combined with a relatively long intra-plateau evolution. At least one colonization event has a Palaearctic origin. In contrast to freshwater fishes, passive dispersal, probably by water birds, might be an important mechanism for conquering remote areas on the plateau. Patterns found in Radix spp. are shared with some terrestrial plateau taxa, indicating that Radix may be a suitable model taxon for inferring general patterns of biotic origin, dispersal and survival on the Tibetan Plateau.

Phylogeography of the endemic Gymnocypris chilianensis (Cyprinidae): sequential westward colonization followed by allopatric evolution in response to cyclical Pleistocene glaciations on the Tibetan Plateau

The schizothoracine Gymnocypris chilianensis is restricted to the Shiyang, Ruoshui and Shule Rivers, listed from east to west, along the northeast edge of the Tibetan Plateau. This distribution provides a valuable system to test hypotheses about postglacial colonization. We used mitochondrial DNA sequence data (a control region and the cytochrome b gene; 1894 bp) to assess the phylogeographic structure of this species based on 278 specimens sampled from throughout the species' entire geographical range. We found three lineages corresponding geographically to the three rivers, suggesting three independent glacial differentiation centers within the northeast edge of the Tibetan Plateau. The phylogenetic analysis suggested that the Shiyang River population forms a lineage that separated from the other populations of G. chilianensis at the basal phylogenetic split within this species. The molecular data further demonstrated a clear pattern of decreasing genetic diversity from the eastern Shiyang River towards the central Ruoshui River and western Shule River lineages, a pattern consistent with sequential western colonization. We therefore propose a phylogeographic scenario for G. chilianensis of a gradual westerly expansion from the Shiyang River population along the northeast edge of the Tibetan Plateau, with subsequent allopatric evolution at approximately 0.37 and 0.05 million years ago (Ma), through at least two glacial maxima. Together with the genetic evidence reported in other species, our findings suggest that this common biogeographic pattern emphasizes the importance of the northeastern edge region of the Tibetan Plateau as a hotspot of genetic diversity for some taxa.