Molecular phylogeography and evolutionary history of Poropuntius huangchuchieni (Cyprinidae) in Southwest China

Taxonomic revision of the Southeast Asian brook barb genus Poropuntius Smith, 1931 (Teleostei, Cyprinidae) with description of a new species from Vietnam

Molecular data from samples encompassing 22 nominal species of Poropuntius indicate that the species-level diversity in the genus has been vastly overestimated, likely due to inadequate taxon and geographic sampling and reliance on morphological characters that vary intra-specifically. The latter includes discrete mouth morphologies related to alternate feeding strategies (ecomorphs) within populations. One new species is described, Poropuntiusanlaoensis Hoàng, Phạm & Trần, sp. nov., and 17 synonyms of six valid species names of Poropuntius, P.krempfi, P.alloiopleurus, P.huangchuchieni, P.laoensis, P.kontumensis, and P.deauratus, are recognised. Additional taxonomic changes in this widespread and generally poorly known genus are likely as more molecular and morphological data become available.

Impacts of Quaternary glaciation, geological history and geography on animal species history in continental East Asia: A phylogeographic review

Continental East Asia has a mild Pleistocene climate and a complex recent geological history. Phylogeographic studies of animals over the last 30 years have produced several distinctive patterns. Glaciation refugia are numerous and are not restricted to any particular regions. Most of them are localized and species-specific, although several large refugia, for example the mountains of SW China, are shared by multiple species and have refugia-within-refugia. Furthermore, postglaciation range expansion events vary greatly in time, scale and direction. Large-scale south-to-north post-LGM expansions are few and mostly occurred in the northern regions. Additionally, several unique geographic features, including the three-step terrain of China and the northern arid belt, have significant impacts on many species histories. Overall, the impacts of Pleistocene glaciations, particularly the LGM, on species history vary drastically from nondetectable to significant. The impacts are the least for species from the southwestern region and are most dominant for species from the north. Geological events play a more significant role in shaping species history than Pleistocene climatic changes. Phylogeographic patterns among animals species are highly consistent with those of plants. Future phylogeographic endeavour in East Asia should be hypothesis-driven and seek processes that underlie common patterns. The wide use of genomic data allow accurate estimates of historical population processes and exploration of older history beyond the Pleistocene.

The role of landscape evolution in the genetic diversification of a stream fish Sarcocheilichthys parvus from Southern China

Sarcocheilichthys parvus (Cypriniformes: Gobionidae) is a stream fish which is endemic to sub-tropical coastal drainages in southern China, thus offering a valuable model for understanding how genetic divergence arises in stream-adapting freshwater fishes in this region. Using the mitochondrial Cyt b gene, integrative analyses of phylogeny, population demography, and ancestral area and paleo-drainage reconstructions are carried out to explicitly explore the role of landscape evolution in genetic diversification of S. parvus. The time-calibrated phylogeny of S. parvus indicates the splitting of two major lineages (A and B) at ∼3.66 Ma. Lineage A inhabits the Poyang Lake sub-drainage of the middle Yangtze River, Han River and Pearl River, and can be split into two sub-lineages (A-I and A-II), where sub-lineage A-II can be further sub-divided into three infra-sub-lineages (A-IIa, A-IIb and A-IIc). Except for the infra-sub-lineage A-IIc, which is restricted to the Han River and Pearl River, the other sub-lineages and infra-sub-lineages live exclusively in the Poyang Lake sub-drainage. Lineage B lives in the lower Yangtze River, Qiantang River, Jiaojiang River and Ou River, displaying close genetic relationships among the drainages. Rapid population expansion has occurred since the Late Pleistocene. Our findings indicate that the splitting of lineages A and B could be attributed to geographic isolation due to the Zhe-Min Uplift, acting as a biogeographic barrier before the late Early Pleistocene. Furthermore, the strong genetic divergence within Lineage A could be explained by the isolation role of the Nanling Mountains and Poyang Lake acting as an ecological barrier; while the lack of phylogenetic structure within Lineage B may have been the result of paleo-drainage connections or episodic freshwater connections during the eustatic low stand of sea level in the late Middle-Late Pleistocene.

Genetic Diversity and Population Structure of Hemiculter leucisculus (Basilesky, 1855) in Xinjiang Tarim River

Hemiculter leucisculus is an invasive fish and widely distributed in the Xinjiang Tarim River. In this study, RAD-seq was used to explore the genetic diversity and population subgroup structure of H. leucisculus in the Tarim River and develop relevant Simple Sequence Repeat (SSR) markers. The study collected 40 samples distributed at four different sites of the Tarim River. A total of 7,291,260 single nucleotide polymorphisms (SNPs) were obtained. The genetic diversity results showed that the population genetic diversity level of H. leucisculus was low. The population pairwise F_ST values ranged from 0.231 to 0.258, indicating that there was moderate genetic differentiation among these populations. AMOVA showed that the genetic variation within populations accounted for 92.31% of the total variation. The principal component analysis (PCA) and neighbor joining (NJ) tree revealed that the four populations could be separated into two clusters (upper-middle and downstream populations) and the individuals from Taitema Lake (TTMH) showed differences and had a bigger geographic distance than the others. There is the probability that the H. leucisculus from Bosten Lake entered Taitema Lake to breed and then expanded into the Tarim River due to the water diversion projects in location. In addition, 147,705 SSRs loci were detected and 22,651 SSR primer pairs were developed. This study will contribute to providing valuable molecular data for the management of wild populations, marker-assisted selection and resource exploitation of H. leucisculus.

Phylogeographical Analysis of the Freshwater Gudgeon Huigobio chenhsienensis (Cypriniformes: Gobionidae) in Southern China

The freshwater gudgeon Huigobio chenhsienensis (Cypriniformes: Gobionidae) is a small fish endemic to southern China. In this study, we used mitochondrial cytochrome b gene (Cytb), from wide-ranging samplings of H. chenhsienensis from the Ou River (the central of southern China) to the Yangtze River Basin (the northernmost part of southern China) to explore genetic variations and the evolutionary history of H. chenhsienensis in southern China. In total, 66 haplotypes were identified from Cytb sequences of 142 H. chenhsienensis individuals, which could be divided into lineages A, B, and C with divergence times of ~4.24 Ma and ~3.03 Ma. Lineage A was distributed in the lower reaches of the Yangtze River, the Oujiang River, and the Jiao River, lineage B was distributed in the Qiantang River and the Cao'e River, whereas lineage C was restricted to the Poyang Lake drainage from the middle reaches of the Yangtze River. Lineage A could be subdivided into sub-lineages A-I, A-II, A-III, and A-IV, with divergence times of 1.30, 0.97, and 0.44 Ma. Lineage C could be subdivided into sub-lineages C-I and C-II, with a divergence time of 0.85 Ma. Our findings indicate that climate change during the Pliocene and Pleistocene eras, as well as the limited dispersal ability of H. chenhsienensis, have been major drivers for shaping the phylogeographical patterns of H. chenhsienensis.

Chromosome-level genome of Poropuntius huangchuchieni provides a diploid progenitor-like reference genome for the allotetraploid Cyprinus carpio

The diploid Poropuntius huangchuchieni in the cyprinid family, which is widely distributed in the Mekong and Red River basins, is one of the most closely related diploid progenitor-like species of allotetraploid common carp, which was generated by merging of two diploid genomes during evolution. Therefore, the P. huangchuchieni genome is essential for polyploid evolution studies in Cyprinidae. Here, we report a high-quality chromosome-level genome assembly of P. huangchuchieni by integrating Oxford Nanopore and Hi-C technologies. The assembled genome size was 1,021.38 Mb, 895.66 Mb of which was anchored onto 25 chromosomes with a N50 of 32.93 Mb. The genome contained 486.28 Mb repetitive elements and 24,099 protein-coding genes. Approximately 95.9% of the complete BUSCOs were detected, suggesting a high completeness of the genome. Evolutionary analysis revealed that P. huangchuchieni diverged from Cyprinus carpio at approximately 12 Mya. Genome comparison between P. huangchuchieni and the B subgenome of C. carpio provided insights into chromosomal rearrangements during the allotetraploid speciation. With the complete gene set, 17,474 orthologous genes were identified between P. huangchuchieni and C. carpio, providing a broad view of the gene component in the allotetraploid genome, which is critical for future genetic analyses. The high-quality genomic data set created for P. huangchuchieni provides a diploid progenitor-like reference for the evolution and adaptation of allotetraploid carps.

The speciation and adaptation of the polyploids: a case study of the Chinese Isoetes L. diploid-polyploid complex

BACKGROUND

The Chinese Isoetes L. are distributed in a stairway pattern: diploids in the high altitude and polyploids in the low altitude. The allopolyploid I. sinensis and its diploid parents I. yunguiensis and I. taiwanensis is an ideal system with which to investigate the relationships between polyploid speciation and the ecological niches preferences.

RESULTS

There were two major clades in the nuclear phylogenetic tree, all of the populations of polyploid were simultaneously located in both clades. The chloroplast phylogenetic tree included two clades with different populations of the polyploid clustered with the diploids separately: I. yunguiensis with partial populations of the I. sinensis and I. taiwanensis with the rest populations of the I. sinensis. The crow node of the I. sinensis allopolyploid system was 4.43 Ma (95% HPD: 2.77-6.97 Ma). The divergence time between I. sinensis and I. taiwanensis was estimated to 0.65 Ma (95% HPD: 0.26-1.91 Ma). The narrower niche breadth in I.sinensis than those of its diploid progenitors and less niche overlap in the pairwise comparisons between the polyploid and its progenitors.

CONCLUSIONS

Our results elucidate that I. yunguinensis and I. taiwanensis contribute to the speciation of I. sinensis, the diploid parents are the female parents of different populations. The change of altitude might have played an important role in allopolyploid speciation and the pattern of distribution of I. sinensis. Additionally, niche novelty of the allopolyploid population of I. sinensis has been detected, in accordance with the hypothesis that niche shift between the polyploids and its diploid progenitors is important for the establishment and persistence of the polyploids.

Mitogenomic Perspectives on the Adaptation to Extreme Alkaline Environment of Amur ide (Leuciscus waleckii)

Amur ide (Leuciscus waleckii, Family Cyprinidae) is widely distributed in Northeast Asia. L. waleckii usually inhabits freshwater environments but can also survive in the Lake Dali Nur, one of the most extreme aquatic environments on the earth, with an alkalinity up to 50 mmol/L (pH 9.6). To investigate mechanisms of mitogenomic evolution underlying adaptation to extreme environments, we determined 30 complete mitogenomes that included Lake Dali Nur (alkaline environment, AL) population and Amur basin (freshwater environment, FW) population. Through phylogenetic and divergence time analysis, we found that AL and FW populations forming distinct two groups which were consistent with geographic divergence (the formation of Lake Dali Nur). In addition, we found that almost of the windows exhibited higher nucleotide diversity in FW population (avg 0.0046) than AL population (avg 0.0012). This result indicated that severe environment selection had remarkably reduced the genetic diversity of mitogenome in AL population and suggested that severe environment selection had remarkably reduced the genetic diversity of mitogenome in the AL population. Compared with the FW population (ω = 0.064), the AL population (ω = 0.092) had a larger mean ω (dN/dS ratios) value for the 13 concatenated mitochondrial protein-coding genes, indicating that the high alkaline tolerated group had accumulated more nonsynonymous mutations. These nonsynonymous mutations had resulted in slightly beneficial amino acid changes that allowed adaption to the severe conditions. This study provides an additional view to decipher the adaptive mitogenome evolution of L. waleckii of the high alkaline environment.

The complete mitochondrial genome of Poropuntius huangchuchieni (Cyprinidae)

We sequenced the mitogenome of Poropuntius huangchuchieni from Yunnan Plateau. The mitogenome was 16,554 bp in length and comprised 13 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs. The base composition included 32.3% for A, 25.8% for T, 15.6% for G, and 26.3% for C, respectively. The gene order was identical to other published Cyprinidae species. The phylogenetic analysis showed that P. huangchuchieni was close to Puntius tetrazona, a Puntigrus fish in Cyprinidae family.

Seed germination schedule and environmental context shaped the population genetic structure of subtropical evergreen oaks on the Yun-Gui Plateau, Southwest China

The evergreen broadleaved forests (EBLFs) of Southwest China have a long-term stable environment and support a diverse flora, thus forming a global biodiversity hotspot. However, the key drivers that have shaped the genetic diversity patterns of species in these EBLFs are not well understood. Quercus delavayi, Q. schottkyana, and Q. kerrii are sympatric oak species with different seed biological traits that are typical for these EBLFs. This study combined multilocus phylogeography and ecological niche modeling to screen 33 Q. delavayi populations. Their population genetic structure was inferred in comparison with previous studies on Q. schottkyana and Q. kerrii. The seed germination traits of all three species were also investigated. cpDNAs showed a significant phylogeographic structure in Q. delavayi, which was not detected in Q. schottkyana or Q. kerrii. Quercus delavayi, Q. kerrii, and Q. schottkyana exhibited different pollen-to-seed migration ratios (r = 219, 117, and 22, respectively), which are linked to the germination schedules of acorns. The distributions of Q. delavayi and Q. schottkyana remained long-term stable since the last glacial maximum (LGM) with a similar nSSR genetic gradient change along latitude. Instead, Q. kerrii experienced a prominent range expansion since the LGM with genetic diversification between the East and the West of the Tanaka line due to environmental heterogeneity. These results identify seed traits and environmental heterogeneity as two key drivers that shape the population genetic structure of EBLF trees in Southwest China. These should be considered in regional forestry conservation and management.

Phylogeographic structure, cryptic speciation and demographic history of the sharpbelly (Hemiculter leucisculus), a freshwater habitat generalist from southern China

BACKGROUND

Species with broad distributions frequently divide into multiple genetic forms and may therefore be viewed as "cryptic species". Here, we used the mitochondrial cytochrome b (Cytb) and 12 nuclear DNA loci to investigate phylogeographic structures of the sharpbelly (Hemiculter leucisculus) in rivers in southern China and explored how the geological and climatic factors have shaped the genetic diversity and evolutionary history of this species.

RESULTS

Our mitochondrial phylogenetic analysis identified three major lineages (lineages A, B, and C). Lineages B and C showed a relatively narrower geographic distribution, whereas lineage A was widely distributed in numerous drainages. Divergence dates suggested that H. leucisculus populations diverged between 1.61-2.38 Ma. Bayesian species delimitation analysis using 12 nuclear DNA loci indicated the three lineages probably represented three valid taxa. Isolation-with-migration (IM) analysis found substantial gene flow has occurred among the three lineages. Demographic analyses showed that lineages B and C have experienced rapid demographic expansion at 0.03 Ma and 0.08 Ma, respectively.

CONCLUSIONS

Hemiculter leucisculus populations in drainages in southern China comprise three mtDNA lineages, and each of which may represent a separate species. Intense uplift of the Qinghai-Tibetan Plateau, evolution of Asian monsoons, changes in paleo-drainages, and poor dispersal ability may have driven the divergence of the three putative species. However, gene flow occurs among the three lineages. Climatic fluctuations have a prominent impact on the populations from the lineages B and C, but exerted little influence on the lineage A.

Phylogeographic investigation and ecological niche modelling of the endemic frog species Nanorana pleskei revealed multiple refugia in the eastern Tibetan Plateau

The largest plateau Tibetan Plateau supplied an excellent opportunity to investigate the influence of the Pleistocene events on the high-elevation species. To test for the alternative hypotheses of Pleistocene glacial refugia, we used partial sequences of two mitochondrial genes and one nuclear gene to examine the phylogeographic patterns of the endemic frog species Nanorana pleskei across its known range in the eastern Tibetan Plateau, and conducted species distribution modelling (SDM) to explore changes of its distribution range through current and paleo periods. In all data sets, the species was divided into lineage north occupying open plateau platform and lineage south colonizing the mountainous plateau. The divergence of two major clades was estimated at the early Pleistocene. In mtDNA, lineage north contained northeastern and northwestern sublineages, and lineage south had two overlapping-distributed sublineages. Different lineages possessed distinct demographic characteristics, i.e., subdivision in the northeastern sublineage, historical bottleneck effects and recent expansions in the northwestern sublineage and the southeastern sublineage. SDMs depicted that stable suitable habitats had existed in the upper-middle streams of the Yellow River, Dadu River, Jinsha River and Yalong River. These regions were also recognized as the ancestral areas of different lineages. In conclusion, Nanorana pleskei lineages have probably experienced long-term separations. Stable suitable habitats existing in upper-middle streams of major rivers on the eastern Tibetan Plateau and distinct demographic dynamics of different lineages indicated that the lineages possessed independent evolutionary processes in multiple glacial refugia. The findings verified the profound effects of Pleistocene climatic fluctuations on the plateau endemic species.

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.

Phylogeny and Evolution of Multiple Common Carp (Cyprinus carpio L.) Populations Clarified by Phylogenetic Analysis Based on Complete Mitochondrial Genomes

Common carp (Cyprinus carpio L.) is one of the oldest, most widely farmed commercially important freshwater fish in the world. However, many undetermined phylogenetic relationships and origins of common carp lineages remain, which are obstacles to conservation and genetic breeding of this species. Phylogenetic analyses based on molecular tools are helpful to distinguish the origin of species, understand and clarify their evolutionary history, and provide a genetic basis for selective breeding. In this study, we demonstrated a method to extract complete mitochondrial genome sequences from whole-genome resequencing data using the Illumina platform. The complete mitochondrial genome sequences of 26 individuals representing nine strains were obtained and subjected to a phylogenetic analysis. We reconstructed the phylogenetic topologies of the nine strains and analyzed the haplotypes. Results from both analyses suggested that the genome sequences belonged to two distinct subspecies from Europe and East Asia. We also estimated the time of divergence of the nine strains, which was up to 100 KYA. The phylogenetic results clarified the breeding history of Songpu mirror carp and suggest that this species may be hybrid of paternal European mirror carp and maternal Xingguo red carp. The results also support a previous hypothesis that koi may have originated from or have close ancestry with Oujiang color carp in China.