Comparison of evolutionary rates in the mitochondrial DNA cytochrome b gene and control region and their implications for phylogeny of the Cobitoidea (Teleostei: Cypriniformes)

Fish diversity and selection of taxa for conservation in the Salween and Irrawaddy Rivers, Southeast Asia

Species diversity indices provide quantitative data for understanding the variations and trends in fish species diversity, as well as information on species richness and evenness. However, these diversity indices do not reflect differences in specific taxa, which can be of importance as key conservation targets, especially during the planning and construction of protected areas. In this study, simultaneously combining our improved traditional fish fauna analysis (TFFA) with the value of fish fauna presence (VFFP) methods, we studied fish diversity in the Salween and Irrawaddy basins. The results of the TFFA reflected the families (subfamilies) and genera that constitute the main body of fish diversity in the river basins. The results of the VFFP assessment showed which families (subfamilies) and genera were representative of certain characteristics in the basins. The VFFP scores of genera could be used as indicator indices and as priority taxa in the planning and construction of fish resource reserves. In this paper, we propose for the first time that the role and status of monotypic genera (genera comprising only a single species) in the conservation of fish diversity should not be ignored, and they should rather be a priority for protection.

Characterization of the Complete Mitochondrial Genome of the Elongate Loach and Its Phylogenetic Implications in Cobitidae

The elongate loach is an endemic fish in China. Previous studies have provided some insights into the mitochondrial genome composition and the phylogenetic relationships of the elongate loach inferred using protein-coding genes (PCGs), yet detailed information about it remains limited. Therefore, in this study we sequenced the complete mitochondrial genome of the elongate loach and analyzed its structural characteristics. The PCGs and mitochondrial genome were used for selective stress analysis and genomic comparative analysis. The complete mitochondrial genome of the elongate loach, together with those of 35 Cyprinidae species, was used to infer the phylogenetic relationships of the Cobitidae family through maximum likelihood (ML) reconstruction. The results showed that the genome sequence has a full length of 16,591 bp, which includes 13 PCGs, 22 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA), and 2 non-coding regions (CR D-loop and light chain sub-chain replication origin OL). Overall, the elongate loach shared the same gene arrangement and composition of the mitochondrial genes with other teleost fishes. The Ka/Ks ratios of all mitochondrial PCGs were less than 1, indicating that all of the PCGs were evolving under purifying selection. Genome comparison analyses showed a significant sequence homology of species of Leptobotia. A significant identity between L. elongata and the other five Leptobotia species was observed in the visualization result, except for L. mantschurica, which lacked the tRNA-Arg gene and had a shorter tRNA-Asp gene. The phylogenetic tree revealed that the Cobitidae species examined here can be grouped into two clades, with the elongate loach forming a sister relationship with L. microphthalma. This study could provide additional inferences for a better understanding of the phylogenetic relationships among Cobitidae species.

Formosaniaimmaculata, a new species of hillstream loach (Teleostei, Cypriniformes, Gastromyzontidae) from the Ou-Jiang River, Southeast China

Formosaniaimmaculata, a new species, is described from the Ou-Jiang basin in Zhejiang Province, Southeast China. It is distinguished from other species of the genus by having a combination of the following characteristics: body without obvious mottling; snout length longer than postorbital length; abdominal scaleless area extending to middle of pectoral-fin base; shorter rostral barbels, the outermost pair length 112.9%-140.0% of eye diameter; and shorter lower lip papillae, length 19.9%-24.4% of eye diameter. Its validity is also affirmed by its distinct Cytb gene sequence divergence from all congeners and its monophyly recovered in a Cytb gene-based phylogenetic analysis.

Significance of two different ranking methods for studying fish fauna: a case study on the fish fauna from upper and middle portions from Mekong River

Studies on fish fauna should not only focus on fish composition and the comparison of fish composition among the study region and adjacent regions, but should also explore the origin and uniqueness of different taxa as well as the substitution of genera and species. In this study, the value of floristic presence method was modified and renamed the value of fish fauna presence (VFFP) method. The specific steps of the VFFP method and the traditional fish fauna analysis (TFFA) method were refined and standardized. Then, the VFFP and TFFA methods were applied to study the fish fauna of the upper and middle portions of the Mekong River basin. The results indicate that the TFFA method reflects the families (subfamilies) and genera that constitute the main body of fish in the studied river basin. The results of the VFFP method show which families (subfamilies) and genera are representative for the basin. Therefore, combining the TFFA and VFFP methods to analyze the composition of fish fauna can reflect the characteristics of fish fauna from different perspectives. The case study shows that the fish fauna of the Mekong River is a part of the fish fauna of Southeast Asia. Although it shows some similarities to the composition of South Asian fish fauna, it does not belong to the South Asian fish fauna as a whole, and is essentially different from the East Asian fish fauna. This study provides an objective, quantitative, and verifiable method for studying fish fauna.

Comparative analyses of the complete mitochondrial genomes of two southern African endemic guitarfish, Acroteriobatus annulatus and A. blochii

Shark-like rays (order Rhinopristiformes) are among the most threatened cartilaginous fish globally. Despite this, unresolved taxonomic issues still exist within the group. To date, no studies have used complete mitochondrial genomes to assess the phylogenetic placement of Acroteriobatus within the non-monophyletic family Rhinobatidae. The current study reports the first complete mitochondrial genomes for Acroteriobatus annulatus and A. blochii. Similar to other rhinopristiforms, the complete sequences of A. annulatus (16,773 bp) and A. blochii (16,771 bp) were circular molecules with gene organisations identical to that of the typical vertebrate mitogenome. The A + T content was higher than the G + C content, with a bias towards A and C nucleotides observed in all complete mitogenomes. The stem-and-loop secondary structures of the putative origin of light-strand replication were found to have highly conserved synthesis and stem regions, with all substitutions and indels restricted to the loop structure. The ratios of non-synonymous to synonymous substitution rates indicated that purifying selection has been the dominant driver of evolution in rhinopristiform mitogenomes. Phylogenetic reconstructions placed Acroteriobatus as a sister-group to Rhinobatos, confirming its affiliation with the family Rhinobatidae. However, based on its apparent polyphyly with the aforementioned genera, the familial assignment of Pseudobatos is not fully resolved and requires further investigation.

Three new species of Homatula (Teleostei: Nemacheilidae) from Yunnan, China, with comments on habitat conservation

Based on the morphological comparisons and molecular results, three new species of Homatula, i.e., H. geminusclathratus sp. nov., H. microcephala sp. nov., and H. longibarbatus sp. nov., have been described and named from the Lancang-jiang (the upper Mekong River) and the Chuan-he (the upper Black River, a tributary of the Red River) basins. The loaches of Homatula from the Lancang-jiang and the Chuan-he can be distinguished via morphology, genetics, and geographic distribution. All of the 10 recorded species distributed in the Nu-jiang (the upper Salween River), the Lancang-jiang, and the upper Black River share the following combination of character states: whole body, except head, densely scaled; lateral line complete; and a short adipose crest along the dorsal midline of the caudal peduncle, anteriorly not reaching vertically through the anal-fin origin. Species with these characters are called the densely-scaled group of Homatula. The three newly described species belong to the densely-scaled group of Homatula. Based on molecular phylogenetics, these Homatula species form a monophyletic group that can be divided into two clades, the densely-scaled group and the non-densely-scaled group. The densely-scaled group of Homatula includes 13 species occurring between the Nu-jiang and the upper Black River. The non-densely-scaled group is non-monophyletic and includes 14 species that are distributed in the Red, Pearl, Yangtze, and Yellow River basins. Species of the non-densely-scaled group are clustered into four sub-clades that are constrained to the four river basins. Homatula exclusively inhabits mountain streams with rapid or gentle currents, vauclusian springs, underground rivers connected to streams, and ditches near villages and farmland. No specimens of Homatula were collected from the main streams of Lixian-jiang, Lancang-jiang, and Nu-jiang as well as their large tributaries. Small environmental changes in the habitat of Homatula, such as water pollution or extensive human use, can lead to species/population extinction. Effective conservation of rare and endemic fishes, like loaches of Homatula, entails systematic observations and more targeted protection.

FishPIE: a universal phylogenetically informative exon markers set for ray-finned fishes

Understanding the evolutionary history of the highly diverse ray-finned fishes has been challenging, and the development of more universal primers for phylogenetic analyses may help overcoming these challenges. We developed FishPIE, a nested PCR primer set of 82 phylogenetically informative exon markers, and tested it on 203 species from 31 orders of Actinopterygii. We combined orthologous sequences of the FishPIE markers obtained from published genomes and transcriptomes and constructed the phylogeny of 710 species belonging to 190 families and 60 orders. The resulting phylogenies had topologies comparable to previous phylogenomic studies. We demonstrated that the FishPIE markers could address phylogenetic questions across broad taxonomic levels. By incorporating the newly sequenced taxa, we were able to shed new light on the phylogeny of the highly diverse Cypriniformes. Thus, FishPIE holds great promise for generating genetic data for broad taxonomic groups and accelerating our understanding of the fish tree of life.

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FishPIE is a nested PCR primer set of 82 markers for fish phylogenetic analysis

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The markers can be broadly applied to all orders of ray-finned fishes

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Their phylogenetic performance is comparable to that of genomic analyses

Using Species Groups to Approach the Large and Taxonomically Unresolved Freshwater Fish Family Nemacheilidae (Teleostei: Cypriniformes)

Large animal families with unresolved taxonomy are notoriously difficult to handle with respect to their biodiversity, systematics, and evolutionary history. We approach a large and taxonomically unresolved family of freshwater fishes (Nemacheilidae, >600 species) by proposing, on the basis of morphologic data, a species group within the family and study its phylogeny with conclusions regarding its diversity, taxonomy, and biogeographic history. Phylogenetic analyses of two mitochondrial and three nuclear genes of 139 specimens, representing about 46 species (17 candidate species from the proposed species-group, plus 29 comparative species), revealed that the proposed species group does not form a distinct monophyletic lineage, but that the candidate and comparative species mixed in three different lineages. However, the results revealed more than 20% of undescribed species within the ingroup and showed that species do not cluster according to the presently recognised genera. At least one of the genetic clades shows signs of an eastward range expansion during the second half of Miocene from north India via Myanmar into Laos, western China, and western Thailand. We conclude that the approach of picking monophyletic lineages to study biodiversity, systematics, and evolutionary history helps to open the door to large animal families.

Genetic diversity and genetic differentiation of Megalobrama populations inferred by mitochondrial markers

BACKGROUND

Megalobrama is economically one of the most important freshwater fish genera in China. However, phylogenetic relationships among M. amblycephala, M. skolkovii, M. hoffmanni and M. pellegrini remain unresolved.

OBJECTIVE

To explore the genetic diversity and phylogenetic relationship of Megalobrama populations belonging to all four species.

METHODS

The concatenated sequences of mitochondrial cytochrome b (Cytb) and control region (CR) were used to analyze the genetic variation, genetic differentiation and population expansion of 15 Megalobrama populations.

RESULTS

The study showed that haplotype diversity and nucleotide diversity of M. hoffmanni and M. skolkovii were high, and that M. hoffmanni was the most genetically divergent of the four species. Haplotype network analysis revealed that M. hoffmanni and M. amblycephala formed a monophyletic group each, while M. skolkovii and M. pellegrini clustered together. There was a high genetic differentiation among the four Megalobrama species, and genetic distance among populations was not affected by geographical distance. Additionally, the results indicated that there was gene flow between the Liangzi Lake (LZL) population and Jinsha River Reservoir (JS) population. Also, Zhaoqing (ZQ) population of M. hoffmanni might have experienced a population expansion.

CONCLUSION

Our study verifies genetic diversity and differentiation of Megalobrama populations, and these findings will represent a significant contribution to the conservation and utilization of germplasm resources of Megalobrama.

A review of the Cypriniform tribe Yunnanilini Prokofiev, 2010 from China, with an emphasis on five genera based on morphologies and complete mitochondrial genomes of some species

The loach tribe Yunnanilini from China is reviewed here using morphological characters and complete mitochondrial genomes of select species. Molecular data suggest that the tribe Yunnanilini is not monophyletic and can be divided into three clades. Species of the Yunnanilus nigromaculatus group form an independent genus and are placed in Eonemachilus. In the phylogenetic tree, Y. jinxiensis clusters with Paranemachilus genilepis, and Y. pulcherrimus clusters with Micronemacheilus cruciatus, indicating that Y. jinxiensis and Y. pulcherrimus belong to Paranemachilus and Micronemacheilus, respectively. Based on morphological data, Y. bailianensis and Y. longibarbatus are placed in Heminoemacheilus, while Y. jinxiensis and Y. pulcherrimus, are placed in Paranemachilus and Micronemacheilus, respectively. Yunnanilus niulanensis and Y. qujinensis are treated as junior synonyms of Eonemachilus caohaiensis. Eonemachilus, Micronemacheilus, and Yunnanilus are show short separation between anterior and posterior nostrils. The genera can be distinguished from each other by mouth structure, lateral line and cephalic lateral-line canals, and papillae on median part of both lips. The anterior and posterior nostrils of Heminoemacheilus and Paranemachilus are closely set. Paranemachilus and Micronemacheilus are distinguished by cheeks covered with scales and lips with papillae, respectively. Our phylogenetic tree and morphological characters support Traccatichthys as a valid genus, which can be distinguished from Micronemacheilus by anterior and posterior nostrils closely set (vs. clearly separated). Four species are placed in Traccatichthys.

Phylogenetic analysis and osteological comparison of the cave-dwelling spined loach, Bibarba parvoculus (Cypriniformes: Cobitidae), and its surface congener

Bibarba parvoculus, a depigmented and small-eyed, spined loach, is endemic to a karst cave in southern China. Both mitochondrial Cytb and nuclear RAG1 gene analyses indicate that B. parvoculus and its only surface congener, B. bibarba, form the basal-most lineage in the so-called Northern Clade of Cobitidae. Genetic divergence for Cytb is 10.3 % between B. parvoculus and B. bibarba. A duplication of the lamina circularis on the second and third pectoral rays occurs in male Bibarba species. The osteology of the two species is illustrated and compared using X-ray microtomography. Bibarba parvoculus has higher vertebral counts, a broader anterior part of the frontal bone at the orbital region and decreased sexual dimorphism when compared with B. bibarba. The coracoid, mesocoracoid and scapula are stouter in males of both species, but the three bones are autogenous in B. parvoculus, while fused with the cleithrum in B. bibarba. Specific differentiation of B. parvoculus is corroborated by both molecular and morphological evidence. The split between the two species is estimated to have occurred in the Early Miocene.

The complete mitochondrial genomes of Parabotia kiangsiensis (Cypriniformes: Botiidae)

Parabotia kiangsiensis is an endemic species of genus Parabotia in China. In this study, we sequenced the complete mito-genome of P. kiangsiensis. The genome is 16,592 base pair (bp) in length, encoding 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one non-coding control region (D-loop). The nucleotide composition is A: 30.66%, T: 25.13%, G: 16.3%, and C: 27.92% (AT content:55.79%). The complete mitogenome of P. kiangsiensis provides basic data for the genetic diversity conservation of this species.

Molecular phylogeny and biogeography of Triplophysa stone loaches in the Central Chinese Mountains

The geological structure and history of mountains often cause highly complex patterns of evolution. The origin and diversity of the genus Triplophysa is considered to be closely associated with the rapid and persistent rise of the Qinghai-Tibet Plateau (QTP). Species of the genus are widely distributed in the QTP and adjacent regions, and are strongly adapted to its extreme environments. However, the Central Chinese Mountains (CCM), which are far apart from the QTP, also have many Triplophysa populations and yet their taxonomy, phylogeny and origin are unknown. We used three mitochondrial genes of 266 individuals from 29 sites in the CCM to shed light on the evolution of these Triplophysa populations. Phylogenetic analyses and species delimitation revealed seven distinct molecular operational taxonomic units (mOTUs) in the CCM, each with low genetic diversity. Molecular clock and biogeographic analyses suggested that vicariance events resulting from the rapid uplifting of the Qinling and Taihang Mountains initialized diversification in the Pliocene. During the early Pleistocene, dispersal events in the central parts of the Yellow River drainage altered genetic diversity and led to the currently observed biogeographic patterns. Our results suggest the presence of at least six species of Triplophysa in the CCM and more are likely to be discovered in the future.

The complete mitochondrial genomes of Parabotia lijiangensis (Cypriniformes: Botiidae)

In this study, we obtained the 16,579 base pair (bp) mitochondrial DNA sequence of Parabotia lijiangensis. The mitogenome encodes 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, a control region, and has a nucleotide composition of A: 30.8%, T: 25.2%, G: 16.1%, and C: 27.9% (AT content: 56.0%). The complete mitogenome of P. lijiangensis provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis of the Botiidae family.

The mitogenome of freshwater loach Homatula laxiclathra (Teleostei: Nemacheilidae) with phylogenetic analysis of Nemacheilidae

The complete mitogenome can provide valuable genetic information to reconstruct relationships between species. In this study, we sequenced a stone loach, Homatula laxiclathra (Teleostei: Nemacheilidae), which is found in the northern region of the Qinling Mountains in China. The size of the H. laxiclathra mitogenome is 16,570 bp, which contains 37 typical mitochondrial genes including 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and a control region (D-loop) with a total AT content of 55.8%. This is similar to other Nemacheilidae sequences published in GenBank. Furthermore, a mito-phylogenomic analysis of 46 Nemacheilidae species places H. laxiclathra in a robust monophyletic Homatula cluster with other Homatula species. Our results contribute toward a better understanding of a true phylogeny of these species based on large-scale taxonomic samplings as well as to help grasp the evolution of fish mitogenomes.

A Chromosome-Scale Reference Assembly of a Tibetan Loach, Triplophysa siluroides

Cobitoidea is one of the two superfamilies in Cypriniformes; however, few genomes have been sequenced for Cobitoidea fishes. Here, we obtained a total of 252.90 Gb of short Illumina reads and 31.60 Gb of long PacBio Sequel reads, representing approximate genome coverage of 256× and 50×, respectively. The final assembled genome is about 583.47 Mb with contig N50 sizes of 2.87 Mb, which accounts for 91.44% of the estimated genome size of 638.07 Mb. Using Hi-C-based chromatin contact maps, 99.31% of the genome assembly was placed into 25 chromosomes, and the N50 is 22.3 Mb. The gene annotation completeness was evaluated by BUSCO, and 2,470 of the 2,586 conserved genes (95.5%) could be found in our assembly. Repetitive elements were calculated to reach 33.08% of the whole genome. Moreover, we identified 25,406 protein-coding genes, of which 92.59% have been functionally annotated. This genome assembly will be a valuable genomic resource to understand the biology of the Tibetan loaches and will also set a stage for comparative analysis of the classification, diversification, and adaptation of fishes in Cobitoidea.

Exploring taxonomic diversity and biogeography of the family Nemacheilinae (Cypriniformes)

Nemacheilidae, in the superfamily Cobitoidea, is comprised of many of morphologically similar fish species that occur in Eurasian water bodies. This large group shows inconsistencies between traditional morphological taxonomy and molecular phylogenetic data. We used mitochondrial genomes, recombinase-activating gene proteins 1 (RAG1) and the mitochondrial cytochrome c oxidase I gene (COI) to study the phylogenetic relationships among Nemacheilidae species using Bayesian inference and maximum likelihood approaches. Phylogenetic analyses based on mitogenomes provided support for two clades (I and II). The mitogenomes, RAG1, and COI results indicated that several species and genera were not consistent with the traditional morphological subdivisions. The two clades inferred from mitogenomes showed clear geographical patterns. The Tibetan Plateau, Hengduan Mountains, and the Iran Plateau may act as a barrier dividing the clades. The estimated timing of clades separation (36.05 million years ago) coincides with the first uplift of the Tibetan Plateau. We conclude that the geological history of the Tibetan Plateau played a role in the diversification and distribution of the Nemacheilidae taxa. These results provided a phylogenetic framework for future studies of this complex group.

Evolution and phylogeography analysis of diploid and polyploid Misgurnus anguillicaudatus populations across China

The origin and evolution of polyploid organisms have been extensively studied in plants, but this topic remains only partially understood in vertebrates, where polyploidy is relatively rare. In this study, we used Misgurnus anguillicaudatus, a fish that comprises five ploidy levels in nature, as a model animal to improve our understanding of biogeographic history and evolution of polyploid vertebrates. After collecting samples from different geographical populations in China, their ploidy levels were determined using flow cytometry. Two mitochondrial markers ( cytochrome b and control region) were then used for phylogeographic analyses to unravel the possible origins of diploids and tetraploids in China. The results showed that diploids have wider geographical distribution than tetraploids and triploids. There was no clear allopatric geographical range or boundary to divide diploid and polyploid populations. Rather, the analysis of mitochondrial DNA sequences indicated that tetraploids were autopolyploids, with lower genetic diversity than diploids. This suggests that tetraploids originated from sympatric diploids via multiple independent polyploidization events. Genetic structure patterns were similar between diploids and tetraploids, whereas complex genetic differentiation was found among different regions. The potential origin of M. anguillicaudatus was deduced to be in the Pearl River basin, which exhibited the highest nucleotide diversity and genetic differentiation. These findings provide insights into the evolution of polyploidy in vertebrates.

Structure, evolution and phylogenetic informativeness of eelpouts (Cottoidei: Zoarcales) mitochondrial control region sequences

Control region (CR) is a major non-coding domain of mitochondrial DNA in vertebrates which contains the promoters for replication and transcription of mitochondrial genome along with the binding sites for metabolic machinery and, hence, is a vital element for the integrity of mitochondrial genome as a biological replicator. The origin and diversity of structural elements within CR have been intensively studied in recent years with the involvement of new diverse taxa. In this paper, we provide new data on the nucleotide and structural patterns of CR evolution and phylogenetic suitability among eelpouts (Cottoidei: Zoarcales). To achieve this, we carried out a comparative phylogenetic and structural analysis of 29 CR sequences belonging to the long shanny Stichaeus grigorjewi together with nine sequences of other eelpouts taxa representing four families in contrast to mitochondrial protein-coding fragments. The CR organization within S. grigorjewi, as well as in all other eelpouts, is consistent with the common three-domain structure known from most vertebrates. We found a hidden CR variation constrains on the landscape level and a lack of nucleotide saturation. Finally, our results demonstrate the advantage of the length variation in CR sequences for phylogenetic reconstructions among eelpouts.

Phylogeographical and Morphological Analyses of Triplophysa stenura (Cypriniformes: Nemacheilidae) from the Three Parallel Rivers Region, China

Qiu Ren, Jun-Xing Yang, and Xiao-Yong Chen (2018) Triplophysa stenura is an indigenous and widely distributed loach in the Qinghai-Tibet plateau and adjacent Three Parallel Rivers region of China. Morphological and phylogenetic analyses were performed in order to explore the genetic and morphological variation in T. stenura populations from different geographic regions and infer the divergence time and relationships between populations from the three rivers (Jinsha River, Nu River and Lancang River). Two mitochondrial genes (Cyt b, D-Loop) and 35 morphological characters were selected for genetic and morphological analyses, respectively. Phylogenetic and network analyses reveal that T. stenura is a single lineage with three well supported clades strictly corresponding to specific river systems. Divergence time analysis suggests that the divergence of T. stenura and formation of the Three Parallel Rivers are closely associated with the Kun-Huang Movement (1.1- 0.6 MYA), which lead to the uplift of the Qinghai-Tibet plateau. AMOVA reveals that there is moderate genetic differentiation among populations. Results from ANOVA suggest that several morphological characters show significant variation among populations and drainages. Descriptive morphological variation (e.g., color pattern) in different populations of T. stenura clarifies a set of characters that can be used to accurately identify members of this group in the future. We conclude that T. stenura has moderate population genetic structure and character variation in this study area and the divergence and evolution of T. stenura is associated with the uplift of the Qinghai-Tibet plateau.

Genetic legacy of tertiary climatic change: a case study of two freshwater loaches, Schistura fasciolata and Pseudogastromyzon myersi, in Hong Kong

The high biodiversity and strong population structure of freshwater fauna has often been attributed to historical geological and climatic alterations. The impact of these historical changes on obligate freshwater species on a small geographical scale has not been well understood due to the lack of fine-scale comparative phylogeographic studies. Strong population structure has been reported in a goby and a caridean shrimp in Hong Kong, a small but highly developed city in South China, but the common drivers of population differentiation in freshwater fauna in this region remain unclear. This study examined the fine-scale phylogeographic patterns of two freshwater loaches, Schistura fasciolata and Pseudogastromyzon myersi in Hong Kong, using sequence data of mitochondrial control region and two nuclear markers (interphotoreceptor retinoid binding protein gene 2 and ribosomal protein S13 gene). Results show that they exhibit pronounced population structure as supported by high and significant Φ_ST. Phylogenetic analyses based on the control region reveal six and three distinct lineages in S. fasciolata and P. myersi, respectively. Phylogeographic structure of both species generally follows the paleodrainage pattern, though P. myersi shows a shallower structure on the Mainland, perhaps due to their higher mobility. Most of these lineages diverged during the Pliocene and Late Pleistocene, a period with marked sea-level fluctuations. In a broader context, this suggests that sea-level fluctuation played an important role in shaping even the fine-scale population structure of freshwater fish in South China, implying that the genetic diversity of this fauna may be higher than expected.

Evolution and phylogenetic application of the MC1R gene in the Cobitoidea (Teleostei: Cypriniformes)

Fish of the superfamily Cobitoidea sensu stricto (namely loaches) exhibit extremely high diversity of color patterns, but so far little is known about their evolutionary mechanism. Melanocortin 1 receptor gene (MC1R) plays an important role during the synthesis of melanin and formation of animal body color patterns. In this study, we amplified and sequenced the partial MC1R gene for 44 loach individuals representing 31 species of four families. Phylogenetic analyses yielded a topology congruent with previous studies using multiple nuclear loci, showing that each of the four families was monophyletic with sister relationships of Botiidae+ (Cobitidae+(Balitoridae+Nemacheilidae)). Gene evolutionary analyses indicated that MC1R in loaches was under purifying selection pressure, with various sites having different dN/dS values. Both Botiidae and Cobitidae had lower dN/dS values than those of background lineages, suggesting their evolution might be strongly affected by purifying selection pressure. For Balitoridae and Nemacheilidae, both had larger dN/dS values than those of background lineages, suggesting they had a faster evolutionary rate under more relaxed selection pressure. Consequently, we inferred that the relatively stable color patterns in Botiidae and Cobitidae might result from the strong purifying selection pressure on the MC1R gene, whereas the complicated and diverse color patterns in Balitoridae and Nemacheilidae might be associated with the relaxed selection pressure. Given the easy experimental procedure for the partial MC1R gene and its excellent performance in reconstructing phylogeny, we suggest this gene could be used as a good molecular marker for the phylogenetic study of fish species.

The Gastric Phenotype in the Cypriniform Loaches: A Case of Reinvention?

The stomach, which is characterized by acid peptic digestion in vertebrates, has been lost secondarily multiple times in the evolution of the teleost fishes. The Cypriniformes are largely seen as an agastric order; however, within the superfamily Cobitoidea, the closely related sister groups Nemacheilidae and Balitoridae have been identified as gastric families. The presence of these most recently diverged gastric families in an otherwise agastric clade indicates that either multiple (>2–3) loss events occurred with the Cyprinidae, Catostomidae and Cobitidae, or that gastric reinvention arose in a recent ancestor of the Nemacheilidae/Balitoridae sister clade. In the present study, the foregut regions of Cobitidae, Nemacheilidae/Balitoridae and the ancestral Botiidae family members were examined for the presence of gastric glands and gastric proton pump (Atp4a) α subunit expression by histology and immunohistochemistry respectively. Atp4a gene expression was assessed by reverse transcriptase-polymerase chain reaction (RT-PCR). Gastric glands expressing apical H⁺/K⁺-ATPase α subunit and isolated partial sequences of atp4a, identified using degenerate primers showing clear orthology to other vertebrate atp4a sequences, were detected in representative species from Nemacheilidae/ Balitoridae and Botiidae, but not Cobitidae (Misgurnus anguillicaudatus). In summary, we provide evidence for an uninterrupted gastric evolutionary lineage in the Cobitoidea, making it highly improbable that the stomach was reinvented in the Nemacheilidae/Balitoridae clade consistent with Dollo’s principle. These results also indicate that the gastric trait may be present elsewhere in the Cobitoidea.

Mitogenomic perspectives on the origin of Tibetan loaches and their adaptation to high altitude

Tibetan loaches are the largest group of Tibetan fishes and are well adapted to the Tibetan Plateau. To investigate the origin of Tibetan loaches and their adaptations to the Tibetan Plateau, we determined 32 complete mitochondrial genomes that included 29 Tibetan loach species, two Barbatula species and Schistura longus. By combining these newly determined sequences with other previously published mitochondrial genomes, we assembled a large mitogenomic data set (11,433 bp) of 96 species in the superfamily Cobitoidea, to investigate the phylogenetic status of the genus Triplophysa. The resulting phylogeny strongly supported that the genus Triplophysa forms a monophyletic group within Nemacheilidae. Our molecular dating time suggests that the lineage leading to the Tibetan loaches and other loaches diverged approximately 23.5 Ma, which falls within the period of recent major uplifts of the Tibetan Plateau in the Early Miocene. Selection analyses revealed that the mitochondrial protein-coding genes of Tibetan loaches have larger ratios of nonsynonymous to synonymous substitutions than do those of non-Tibetan loaches, indicating that Tibetan loaches accumulated more nonsynonymous mutations than non-Tibetan loaches and exhibited rapid evolution. Two positively selected sites were identified in the ATP8 and ND1 genes.

Complete mitochondrial genome of the Pseudogastromyzon jiulongjiangensis Chen (Cypriniformes, Homalopteridae) and phylogenetic analysis of the Cyprinoidei

The Pseudogastromyzon jiulongjiangensis Chen (Cypriniformes, Homalopteridae) is a promising ornamental and commercial candidate in China. In this study, the complete mitochondrial genome of P. jiulongjiangensis was first determined. It is 16,571 bp length and consists of 22 tRNA genes, 13 protein-coding genes, two rRNA genes, and a control region. Except for eight tRNA and ND6 genes, all other mitochondrial genes are encoded on the heavy strand. Phylogenetic analysis revealed that P. jiulongjiangensis, Formosania lacustris, and other seven fish first clustered into the Homalopteridae clade. Then, the Homalopteridae and Cobitidae formed the sister group. The Catostomoidae and Cyprinidae constituted the sister branch, which is inconsistent with the previous phenotypic report. It is suggested that the taxonomic research might lose some significant evolutionary characters. This study will contribute to phylogenetic analysis of the Homalopteridae and the natural resources conservation of P. jiulongjiangensis.

Molecular Evidence for Multiple Origins of the European Spined Loaches (Teleostei, Cobitidae)

We present a phylogenetic investigation of the Northern Clade, the major monophyletic clade within the freshwater fish family Cobitidae, one of the most prominent families of freshwater fishes found in Asian and European waters. Phylogenetic reconstructions based on the cytochrome b and RAG-1 genes show the genera Microcobitis, Sabanejewia, Koreocobitis and Kichulchoia as monophyletic groups. These reconstructions also show a Cobitis sensu lato and a Misgurnus sensu lato group. The Cobitis sensu lato group includes all species of Cobitis, Iksookimia, Niwaella and Kichulchoia, while the Misgurnus sensu lato group includes Misgurnus, Paramisgurnus and Koreocobitis. Although the monophyly of both the Cobitis sensu lato and Misgurnus sensu lato groups is supported, relationships within the groups are incongruent with current generic definitions. The absence of monophyly of most genera included in the Cobitis sensu lato group (Cobitis, Iksookimia and Niwaella) or their low genetic differentiation (Kichuchoia) supports their consideration as synonyms of Cobitis. Molecular phylogenies indicate that the Asian species of Misgurnus experienced a mitochondrial introgression from a lineage of Cobitis. We also find two nuclear haplotypes in the same Cobitis species from the Adriatic area that, in the absence of morphological differentiation, may indicate molecular introgression. Most lineages within the Northern Clade consist of species found in East Asia. However, some lineages also contain species from Europe and Asia Minor. The phylogenetic relationships presented here are consistent with previous studies suggesting an East Asian origin of the Northern Clade. According to the current distributions and phylogenetic relationships of the Misgurnus sensu lato and Cobitis clade lineages, particularly of M. fossilis and C. melanoleuca, the range expansion of East Asian species into Europe was most likely via Siberia into Northern and Central Europe. Phylogenetic analyses also show that the Cobitis sensu lato group consists of two clear subgroups (I and II), each presenting geographical differences. Subgroup I is distributed exclusively in East Asian drainages with an Eastern European offshoot (C. melanoleuca), whereas Subgroup II includes species widespread throughout Europe (including the Mediterranean), Asia Minor, the Black Sea and the Caucasus, with some lineages related to species restricted to East Asia.

Extremely low genetic diversity of mtDNA control region and remarkable population differentiation of Ichthyophis bannanicus (Amphibia: Gymnophiona)

It is widely accepted that the mitochondrial DNA (mtDNA) control region (CR) gene evolves more quickly than protein-encoding genes, such as ND2 and Cyt b, with few exceptions. However, some species have a different evolution pattern. In the present study, we sequenced the mtDNA CR partial sequences (454 base pairs) of 142 individuals from five sampling sites of Ichthyophis bannanicus and compared the genetic diversity and structure with the information from the NADH dehydrogenase subunit 2 (ND2) and Cytochrome b (Cyt b) genes within this species. Extremely low genetic diversity was found in the mtDNA CR compared with those of the ND2 and Cyt b genes. These results showed that the relatively mean clock rate of the CR was broadly lower than those of the ND2 (about 2.55 times) and Cyt b (about 3.14 times) genes. Despite the extremely low genetic diversity of CR, the population structure analysis identified two groups, Xishuangbanna and Northern Vietnam-Yulin-Yangchun-Deqing, which indicated that the Red River systems may have acted as gene-flow barriers for I. bannanicus.

The complete mitochondrial genome of Triplophysa sp. (Teleostei: Cypriniformes: Balitoridae)

The complete mitochondrial genome sequence of balitorid fish, Triplophysa sp., which was from Qinling mountains, central China, has been sequenced by the long polymerase chain with primer walking method. The mitochondrial genome of Triplophysa sp. is similar to those of the typical vertebrates, 16 570 bp in length, including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one control region (D-loop). Most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes which are encoded on the light strand. The overall base composition of the heavy strand of the Triplophysa sp. mitogenome is A: 28.0%, T: 28.0%, C: 25.8%, and G: 18.2%. Combined with the complete mitogenome sequences of other 15 balitorids, the topology demonstrated that Triplophysa sp. has a close relationship with the cluster consisting of Triplophysa yarkandensis, Triplophysa siluroides, and Triplophysa robusta with high support values. The genera Triplophysa and Barbatula formed a sister-group relationship. Further investigations with more Triplophysa species included need to be performed to better understand the evolutionary history of this intriguing genus.

The complete mitochondrial genome of the yellow-browed bunting, Emberiza chrysophrys (Passeriformes: Emberizidae), and phylogenetic relationships within the genus Emberiza

Mitochondrial genomes have proved to be powerful tools in resolving phylogenetic relationships. Emberiza chrysophrys (least concern species: IUCN 2013) is a passerine bird in the bunting family, Emberizidae. The complete mitochondrial genome of E. chrysophrys was sequenced. This circular mitochondrial genome was 16,803 bp in length, with an A+T content of 52.26%, containing 13 protein-coding genes (PCGs), two rRNAs, 22 tRNAs and a putative control region (CR). The CR of E. chrysophrys was divided into three conserved domains. Six conserved sequence boxes in the central conserved domain II were identified as F, E, D, C, b and B. An obvious positive AT-skew and negative GC-skew bias were found for all 28 genes encoded by the H strand, whereas it was the reverse in the remaining nine genes encoded by the L strand. Remarkable rate heterogeneity was present in the mitochondrial genome of E. chrysophrys. Notably, unusual slow rate of evolution in the mitochondrial CR of E. chrysophrys was detected, which is rarely seen in other birds. Phylogenetic analyses were carried out based on 13 PCGs that showed E. pusilla was the sister group of E. rustica, and the monophyly of Emberiza was established.

Characterization of the complete mitochondrial genome sequence of Homatula potanini (Cypriniformes, Nemacheilidae, Nemachilinae)

Homatula potanini is an endemic and one of ornamental fishes in the upper stream of the Yangtze River and its tributaries. However, wild populations of H. potanini declined sharply due to anthropological activity in the Jinsha River during the past decades. In present study, the complete mitochondrial DNA genome sequence of H. potanini was first determined by DNA sequencing based on the PCR fragments. The complete mitochondrial genome sequence is a circular molecule of 16,569 bp in size. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region (D-loop). The gene nucleotide composition of H. potanini is 30.1% A, 26.9% C, 16.7% G, and 26.3% T, with a relatively high A + T content (56.4%). The results could provide useful data for studies on genetic structure and rational resource conservation in H. potanini.

The complete mitochondrial genome of Jinshaia sinensis (Teleostei, Balitoridae, Balitorinae)

Jinshaia sinensis is an endemic and typical fish which is successfully adaptive to mountain torrents in the upper stream of the Yangtze River and its tributaries. In this study, the complete mitogenome sequence of J. sinensis has been first sequenced by DNA sequencing based on the PCR fragments. The mitogenome, consisting of 16,567 base pairs (bp), had typical vertebrate mitochondrial gene arrangement, including 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNA genes and a noncoding control region (CR). The overall base composition of J. sinensis is 30.37% A, 28.82% C, 16.59% G, and 24.22% T, with a relatively a slight AT bias of 54.59%. CR of 903 bp length is located between tRNA(Pro) and tRNA(Phe). The complete mitochondrial genome may provide fundamental informative data not only for unravel the population structure and differentiation, but also for further conservation genetics studies on this balitorid species.

Investigating the effects of Pleistocene events on genetic divergence within Richardsonius balteatus, a widely distributed western North American minnow

Background

Biogeographers seek to understand the influences of global climate shifts and geologic changes to the landscape on the ecology and evolution of organisms. Across both longer and shorter timeframes, the western North American landscape has experienced dynamic transformations related to various geologic processes and climatic oscillations, including events as recently as the Last Glacial Maximum (LGM; ~20 Ka) that have impacted the evolution of the North American biota. Redside shiner is a cyprinid species that is widely distributed throughout western North America. The species’ native range includes several well-documented Pleistocene refugia. Here we use mitochondrial DNA sequence data to assess phylogeography, and to test two biogeographic hypotheses regarding post-glacial colonization by redside shiner: 1) Redside shiner entered the Bonneville Basin at the time of the Bonneville Flood (Late Pleistocene; 14.5 Ka), and 2) redside shiner colonized British Columbia post-glacially from a single refugium in the Upper Columbia River drainage.

Results

Genetic diversification in redside shiner began in the mid to late Pleistocene, but was not associated with LGM. Different clades of redside shiner were distributed in multiple glacial age refugia, and each clade retains a signature of population expansion, with clades having secondary contact in some areas.

Conclusions

Divergence times between redside shiner populations in the Bonneville Basin and the Upper Snake/Columbia River drainage precedes the Bonneville Flood, thus it is unlikely that redside shiner invaded the Bonneville Basin during this flooding event. All but one British Columbia population of redside shiner are associated with the Upper Columbia River drainage with the lone exception being a population near the coast, suggesting that the province as a whole was colonized from multiple refugia, but the inland British Columbia redside shiner populations are affiliated with a refugium in the Upper Columbia River drainage.

New light on the evolutionary history of the common goby (Pomatoschistus microps) with an emphasis on colonization processes in the Mediterranean Sea

Through the study of the phylogeographic structure and demographic history of the common goby, Pomatoschistus microps, the influence of Quaternary climatic changes on the evolutionary history of coastal and marine fishes is investigated. Because of its sedentary life cycle in Mediterranean lagoons, it is also a good model to study more specifically if the formation of lagoons during the Holocene had an impact on population structure and demography. Mitochondrial sequences of Northeastern Atlantic and Western Mediterranean specimens were used for phylogenetic reconstructions as well as divergence time estimates, demographic history and population structure analyses. Pomatoschistus microps was a highly supported monophyletic clade including four lineages. It may have appeared 77,000 yr ago, and the divergence of its lineages likely occured shortly thereafter (between 61,000 and 54,000 yr). Most lineages had polytomic topologies, low nucleotide diversity and demographic analyses providing evidence of population expansion. Each lineage was characterized by a large number of private haplotypes. Most haplotypes found in Mediterranean localities were endemic, and one was dominant. Complex reticulated relationships connecting North European, Atlantic and Mediterranean haplotypes were observed. Moderate to high population structure was underlined. Contrary to previous published studies, no significant differentiation was observed between Atlantic and Mediterranean populations, indicating that the Gibraltar Strait is not a phylogeographic break for P. microps. Indeed, molecular dating combined with the tree topologies, phylogeographic and demographic analyses as well as high haplotype diversity underline a recent and rapid population divergence during the last glacial. However, population structure indicates that differentiation is an ongoing process. From an ancestral population trapped in the Atlantic, this goby colonized first northern Europe and later the Mediterranean Sea. Shared haplotypes could have dispersed in the western Mediterranean basin before the lagoon formation, while most private haplotypes, evidencing a recent isolation, probably diverged in lagoons after their closure.

Comparative analysis of mitochondrial genomes in distinct nuclear ploidy loach Misgurnus anguillicaudatus and its implications for polyploidy evolution

Misgurnus anguillicaudatus has several natural ploidy types. To investigate whether nuclear polyploidy have an impact on mitochondrial DNA (mtDNA), the complete mitochondrial genomes (mitogenomes) of five distinct ploidy M. anguillicaudatus (natural diploid, triploid, tetraploid, pentaploid and hexaploid), which were collected in central China, were sequenced and analyzed. The five mitogenomes share the same gene arrangement and have similar gene size, base composition and codon usage pattern. The most variable regions of the mitogenome were the protein-coding genes, especially the ND4L (5.39% mutation rate). Most variations occurred in tetraploids. The phylogenetic tree showed that the tetraploid M. anguillicaudatus separated early from other ploidy loaches. Meanwhile, the mitogenomes from pentaploids, and hexaploids have the closest phylogenetic relations, but far from that of tetraploids, implying that pentaploids and hexaploids could not be formed from tetraploids, possibly from the diploids and triploids. The genus Misgurnus species were divided into two divergent inter-genus clades, and the five ploidy M. anguillicaudatus were monophyletic, which support the hypotheses about the mitochondrial introgression in loach species.

The complete mitochondrial genome of Cobitis granoei (Cyprinformes: Cobitidae)

Knowledge of animal mitochondrial genomes is very important to understand their molecular evolution and phylogenetic studies. Cobitis granoei (Rendahl, 1935) only had been sequenced D-loop gene and Cytb gene in past research. Here we determined the complete mitochondrial genome of C. granoei. The entire sequence was 16,636 bp in length, including 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes and one control region (D-loop). All the PCGs used ATG as a start codon, except for COI gene, which with GTG as the start codon. Most of the PCGs, including ND1, COI, ATP8, ATP6, ND4L, ND5 and ND6 had TAA as termination codon. While the others were with the incomplete termination codons TA or T. The gene arrangement was in accordance with all known Cyprinformes mitochondrial genomes.

The complete mitochondrial genome of Barbatula nuda (Cypriniformes: Nemacheilidae)

In this study, we cloned and sequenced the complete mitochondrial genome of Barbatula nuda. The genome was found to be 16,619 bp in size with a mostly conserved structural organization when compared with that of other teleost fish. It contained 37 genes (13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes) and 2 main non-coding regions (the control region and the origin of the light-strand replication). All protein-coding genes are initiated with ATG except for COX 1, which begin with GTG instead. However, the termination codons of 13 protein-coding genes varied with TAA, TA, T or TAG. The complete mitochondrial genome sequence is useful for phylogenetic analysis and studies of population genetics of B. nuda.