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

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.

River fragmentation and barrier impacts on fishes have been greatly underestimated in the upper Mekong River

River barriers reduce river connectivity and lead to fragmentation of fish habitats, which can result in decline or even extinction of aquatic biota, including fish populations. In the Mekong basin, previous studies have mainly focused on the impacts of large dams but ignored the impacts of small-scale barriers, or drew conclusions from incomplete barrier databases, potentially leading to research biases. To test the completeness of existing databases and to evaluate the catchment-scale fragmentation level, a detailed investigation of river barriers for the whole Upper Mekong (Lancang catchment) was performed, by conducting visual interpretation of high-resolution remotely sensed images. Then, a complete catchment-scale barrier database was created for the first time. By comparing our barrier database with existing databases, this study indicates that 93.7% of river barriers were absent from the existing database, including 75% of dams and 99.5% of small barriers. Barrier density and dendritic connectivity index (DCI_D and DCI_P) were used to measure channel fragmentation within the catchment. Overall, 50.5% of sub-catchments contained river barriers. The Middle region is the most fragmented area within the Lancang catchment, with a median [quartiles] barrier density of 5.34 [0.70-9.67] per 100 km, DCI_P value of 49.50 [21.50-90.00] and DCI_D value of 38.50 [9.00-92.25]. Furthermore, since 2010, distribution ranges of two representative fish species Schizothorax lissolabiatus (a rheophilic cyprinid) and Bagarius yarrelli (a large catfish) have reduced by 19.2% and 32.8% respectively, probably due in part to the construction of river barriers. Our findings indicate that small-scale barriers, in particular weirs and also small dams are the main reason for habitat fragmentation in the Lancang and must be considered alongside large dams in water management and biodiversity conservation within the Mekong.

Resolving the phylogenetic relationship of Himalayan snow trout Schizothorax plagiostomus with other species of Schizothoracine using mitochondrial CO-I and Cyt b genes

BACKGROUND

The classification of the sub-family Schizothoracinae has been debatable due to the overlap in morphological characters. There are discrepancies between classical taxonomy and molecular taxonomy, as well. In the present study, mitochondrial genes CO-I and Cyt b were sequenced to elucidate the phylogenetic status of three species of the genus Schizothorax.

METHODS AND RESULTS

In total, 29 samples of three species viz., S. plagiostomus, S. progastus, and S. richardsonii, were collected from rivers of Uttarakhand, India. For phylogenetic analyses, 40 sequences of CO-I and 41 sequences of Cyt b of Schizothoracinae species were downloaded from NCBI. The highest genetic divergence based on CO-I (16.08%) is between S. plagiostomus and Ptychobarbus dipogon, while the lowest divergence (0.00%) is between 10 pairs of species. The highest divergence based on Cyt b (19.43%), is between S. niger and Gymnocypris eckloni, while the lowest divergence (0.00%) is between four pairs of species. The divergence (0.00% for CO-I and 2.38% for Cyt b) between S. chongi and S. kozlovi, seems a case of convergent molecular evolution of the CO-I gene and in this case, CO-I alone cannot be used to differentiate these two species.

CONCLUSION

The simultaneous use of two molecular markers along with morphomeristic data is a better strategy for the classification of the sub-family Schizothoracinae. These results will be a resource dataset for determining the taxonomical status of Schizothoracine species and will help in the conservation and commercial production of these commercially important fish species.

Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- and M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia)

The Unionidae represent an excellent model taxon for unravelling the drivers of freshwater diversity, but, phylogeographic studies on Southeast Asian taxa are hampered by lack of a comprehensive phylogeny and mutation rates for this fauna. We present complete female- (F) and male-type (M) mitogenomes of four genera of the Southeast Asian clade Contradentini+Rectidentini. We calculate substitution rates for the mitogenome, the 13 protein-coding genes, the two ribosomal units and three commonly used fragments (co1, nd1 and 16S) of both F- and M-mtDNA, based on a fossil-calibrated, mitogenomic phylogeny of the Unionidae. Phylogenetic analyses, including an M+F concatenated dataset, consistently recovers a monophyletic Gonideinae. Subfamily-level topology is congruent with that of a previous nuclear genomic study and with patterns in mitochondrial gene order, suggesting Unionidae F-type 2 as a synapomorphy of the Gonideinae. Our phylogeny indicates that the clades Contradentini+Rectidentini and Lamprotulini+Pseudodontini+Gonideini split in the early Cretaceous (~125 Mya), and that the crown group of Contradentini+Rectidentini originated in the late Cretaceous (~79 Mya). Most gonideine tribes originated during the early Palaeogene. Substitution rates were comparable to those previously published for F-type co1 and 16S for certain Unionidae and Margaritiferidae species (pairs).

Phylogeography of Schizopygopsis malacanthus Herzenstein (Cypriniformes, Cyprinidae) in relation to the tectonic events and Quaternary climatic oscillations in the Shaluli Mountains Region

The tectonic events and Quaternary climatic oscillations in the Shaluli Mountains (the margin of the southeastern Tibetan Plateau) had an extensive effect on the genetic structure and distribution patterns of this region's terrestrial fauna and flora. It is not yet clear whether similar mechanisms influence this region's fish fauna. Schizopygopsis malacanthus is limited to high-elevation rivers and lakes, and exhibits distinct adaptations to the mountains of, and near to, the Qinghai-Tibet Plateau (QTP). Therefore, this species is a good candidate for investigating patterns of genetic variation resulting from palaeoenvironmental fluctuations in the Shaluli Mountains (China). Here, we used microsatellite and mitochondrial DNA control region sequences to analyze six populations of S. malacanthus collected from the Jinsha and Yalong River drainages. Genealogical analyses identified four maternal lineages and perhaps even four putative species, of which the Ouqu River lineage played a pivotal role during the course of the species' evolution. Two lineages from the Yalong River drainage did not cluster together, whereas those from different drainages grouped together, suggesting tectonic event impacts that possibly altered regional river drainages have been highly influential in population connectivity and gene flow. Population genetic analysis indicated that the geographic barriers and this species preference for higher elevations both played key roles in the divergence of S. malacanthus populations. Demographic tests suggested large-scale spatial synchrony in population fluctuations of S. malacanthus, accompanying dramatic Pleistocene climatic oscillations. It appears that palaeoenvironmental changes in the Shaluli Mountains influenced the distribution and evolution of studied S. malacanthus populations, which provide important information about the factors that influenced the phylogeographic history of this region's fish fauna. Additionally, our study also has implications for ongoing conservation of this vulnerable fish.

Habitat Selection and Genetic Structure of the Endangered Frog Species Odorrana wuchuanensis (Anura: Ranidae)

Understanding the habitat selection and population genetic structure of an endangered species can play important roles in its protection. The Wuchuan odorous frog (Odorrana wuchuanensis) is endemic to the karst regions of southwest China. This frog is currently listed as "Critically Endangered" by the IUCN, but little is known about its habitat selection and population genetics. In this study, we conducted analyses of habitat selection with occurrence/absence sites and environmental data, and assessed the genetic structure between north and south populations in Guizhou provinces in China using three mitochondrial markers. The results revealed that the probability of this frog occupying cave habitats increased with higher average humidity in July and higher lowest temperature in January, but was negatively related to precipitation in January. Analyses of F statistics combined with analyses of median-joining haplotype networks and the phylogenetic tree showed low genetic differentiation between the two populations of O. wuchuanensis. Considering the small population size and geographic isolation because of the complex karst terrains, we suggest careful management practices are needed to protect this species.

The potential colonization histories of Opsariichthys bidens (Cyprinidae) in China using Bayesian binary MCMC analysis

Vicariance and/or long-distance dispersal shape the distribution patterns of many extant taxa, and orogenesis and/or climate fluctuations are key factors that drive the events of vicariance and/or dispersal. In this study, we yielded biogeographical inferences from Bayesian binary MCMC (BBM) analysis to explore the potential colonization histories of Opsariichthys bidens in China and to identify potential factors responsible for the colonization histories. Many vicariance and dispersal events were identified. The results suggested that O. bidens seemed to have originated from the Yangtze River and/or the Pearl River and experienced a Yangtze River-Pearl River split at 7.04 million years ago (Ma). BBM analysis revealed that the Pearl River populations had undergone expansions to the Hainan drainages, the Lancangjiang River (upper Mekong) and the Nanpanjiang River (upper branch of the Pearl River) at 0.74 Ma. Meanwhile, the Yangtze River populations expanded to the northeastern drainages during the Early Pleistocene. Subsequently, the northeastern drainages dispersed to the Yellow River during the Middle Pleistocene. More recently, the northeastern drainage populations also dispersed to the Huaihe River and back to the Yangtze River. A portion of the Pearl River populations originated from the Yangtze River dispersed to the Jiulongjiang River during the Middle Pleistocene. These time scales fit well with the uplift of the Qinghai-Tibet Plateau and Pleistocene glacial cycles, indicating the two factors played vital roles in shaping the colonization histories of O. bidens.

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.