Mitochondrial genetic diversity of Rhinogobius giurinus (Teleostei: Gobiidae) in East Asia

Genetic diversity and divergence among native and translocated populations of the golden flathead goby Glossogobius aureus (Gobiiformes: Gobiidae) in Philippine lakes

The golden flathead goby Glossogobius aureus is a native species in the Philippines, Australia, Japan, Taiwan, and many other countries in Asia. In the Philippines, it is an important food fish as it is commonly caught in major lakes. In this study, a total of 307 specimens morphologically identified as G. aureus were sampled from nine major lakes in the Philippines and were sequenced for their mitochondrial cytochrome b (cyt b) gene. Two hundred sixty of the 307 cyt b sequences had sequence similarities of ≥ 99% with G. aureus reference sequence in GenBank, while the remaining 47 (all from Lake Lanao) had sequence similarities of only 95% and were thus designated as Glossogobius cf. aureus and treated as a separate population. The sequences were then analyzed to examine the pattern of genetic diversity, relatedness, divergence, and demographic history among native and translocated populations of the species. Twenty-nine haplotypes were recovered, of which four haplotypes were shared among three to seven populations. Only one haplotype each was found in the native population in Lake Buhi and translocated population in Lake Paoay. Low haplotype and low nucleotide diversities were found for the populations in Laguna de Bay, Lanao, Bato, Buhi, Paoay, and Sebu lakes, which indicate founder event for the introduced populations in Lanao, Paoay, and Sebu lakes and recent genetic bottleneck for the native populations in Laguna de Bay, Bato, and Buhi. In contrast, high haplotype but low nucleotide diversities were found for the native populations of Taal, Naujan, and Buluan lakes, signifying a recent bottleneck followed by population expansion. Pairwise FST values showed generally large (FST = 0.168-0.249) to very large (FST = 0.302-1.000) genetic divergence between populations except between Laguna de Bay and Lake Bato, Laguna de Bay and Lake Buhi, and Lake Bato and Lake Buhi populations, which showed nonsignificant genetic differentiation. Lake Buluan and Lake Sebu populations showed moderate genetic differentiation (FST = 0.098). Neutrality tests showed significant negative Tajima's D and Fu's FS values only for the population from Laguna de Bay, which suggests that the population is undergoing expansion. These results are important for establishing scientifically sound strategies for effective conservation and sustainable exploitation of G. aureus in the Philippines.

Phylogenics of the genus Glossogobius in the Mekong Delta based on the mitochondrial cytochrome b (cytb) gene

The Glossogobius species play an essential role in food supply and are distributed widely from the marine to freshwater, especially in the Mekong Delta, Vietnam (VMD). Some of their morphometrics and meristics are observed to vary with species and sampling sites. Therefore, the present study aims to verify if their mitochondrial Cytochrome b (Cytb) gene, one of the popular gene sequences used in fish phylogenic variation assessment, varies with species and sampling sites in the VMD. The Cytb gene size was 1300 bp for GcytbH/GcytbL primer pair and 1045 bp for GluMuq1-F/Mixcyto937-2R. The genetic distances within and among these three fish species groups were 0-11%. The Cytb gene sequences' similarity between this study and the NCBI database was 85.84-100%. The Glossogobius specimens were observed to disperse in small branches of the phylogenetic tree with a low K2P value, suggesting that the Cytb genetic diversity may be low among species.

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.

Population genetic diversity and structure of Rhinogobius candidianus (Gobiidae) in Taiwan: Translocation and release

Rhinogobius candidianus is a freshwater goby distributed in north, northwest, west, and south Taiwan, but this species has been introduced to east Taiwan and became dominant. To investigate its native population genetic diversity and structure and evaluate the sources and diversity of translocated populations, the mitochondrial DNA control region and cytochrome b gene (1981 bp) from 220 specimens were analyzed. These results indicated that (1) the east populations originated from two sources in west Taiwan; (2) translocated populations exist in east Taiwan and south Taiwan; (3) many populations have likely been moved secondarily by human intervention; (4) the effective size of the populations had declined greatly; (5) within the native populations, the ancestral populations colonized Taiwan during the land bridge phase in the Pleistocene through north Taiwan; (6) the landform changes in Taiwan shaped the population structure; and (7) the landforms of the coastline during glaciation also shaped the native range. The low-level genetic diversity, high population differentiation, and population decline greatly suggest the need for resource management and conservation interventions. Four clades (α-δ) should be managed as four distinct evolutionarily significant units, while the translocated populations should be managed as separate management units. Moreover, the translocated populations in east Taiwan should be evaluated and monitored carefully.

A high-resolution genome of an euryhaline and eurythermal rhinogoby (Rhinogobius similis Gill 1895)

Rhinogobius similis is distributed in East and Southeast Asia. It is an amphidromous species found mostly in freshwater and sometimes brackish waters. We have obtained a high-resolution assembly of the R. similis genome using nanopore sequencing, high-throughput chromosome conformation capture (Hi-C), and transcriptomic data. The assembled genome was 890.10 Mb in size and 40.15% in GC content. Including 1373 contigs with contig N50 is 1.54 Mb, and scaffold N50 is 41.51 Mb. All of the 1373 contigs were anchored on 22 pairs of chromosomes. The BUSCO evaluation score was 93.02% indicating high quality of genome assembly. The repeat sequences accounted for 34.92% of the whole genome, with retroelements (30.13%), DNA transposons (1.64%), simple repeats (2.34%), and so forth. A total of 31,089 protein-coding genes were predicted in the genome and functionally annotated using Maker, of those genes, 26,893 (86.50%) were found in InterProScan5. There were 1910 gene families expanded in R. similis, 1171 gene families contracted and 170 gene families rapidly evolving. We have compared one rapidly change gene family (PF05970) commonly found in four species (Boleophthalmus pectinirostris, Neogobius melanostomus, Periophthalmus magnuspinnatus, and R. similis), which was found probably related to the lifespan of those species. During 400-10 Ka, the period of the Guxiang Ice Age, the population of R. similis decreased drastically, and then increased gradually following the last interglacial period. A high-resolution genome of R. similis should be useful to study taxonomy, biogeography, comparative genomics, and adaptive evolution of the most speciose freshwater goby genus, Rhinogobius.

Genetic Structure and Diversity of the Yellowbelly Threadfin Bream Nemipterus bathybius in the Northern South China Sea

The genetic structure and demography of the yellowbelly threadfin bream, Nemipterus bathybius, in the northern South China Sea were examined using the mitochondrial DNA cytochrome b gene (1141 bp). High levels of haplotype and nucleotide diversities (0.98 and 5.26 × 10−3, respectively) showed that all populations exhibited a high level of genetic diversity. Analysis of molecular variance (AMOVA), FST statistics, and haplotype networks suggested the absence of significant genetic differentiation along the coast of the northern South China Sea. Although the results suggested that the lack of differentiation within the population structure of N. bathybius was shaped by ocean currents, our results also showed that the Qiongzhou Strait limited their migration between Beibu Gulf and the northern South China Sea. Neutrality tests and mismatch distributions indicated population expansion, but the Bayesian skyline plots and approximate Bayesian computation approaches suggested that the population sizes recently contracted. The diversification of multiple stocks, which were induced by two ocean current systems, contributed to these discordant results. Although these analyses of demographic history revealed no evidence for recent population bottlenecks, the population demography needs to be evaluated further.

Temporal species-level composition of larvae resources in the lower Pearl River drainage and implications for species' reproductive cycles

Resolving the temporal community composition of a larvae population can not only further our understanding of the regional species composition but also help us to infer the reproductive times of regional fish taxa, which can have implications on the development of effective monitoring and conservation policies for the regional fish stock. Nevertheless, correctly diagnosing the fish larvae is extremely challenging due to the paucity of diagnostic morphological characters at the species level. Based on daily larval samplings during March and October in 2018, this study combined morphological features with a DNA barcode technique to determine the species composition of fish larvae in the lower Pearl River drainage (LPR) and evaluate the spawning periods of identified species. Due to an absence of reference barcodes for LPR fishes, a DNA barcode library of adult fishes in the LPR was built for 384 individuals representing 78 morphological species. Analyses demonstrated the usability of the barcode library and uncovered many undetected mitochondrial lineages in 12 species. Morphological analyses performed on 81 temporal larval samples revealed 25 morphotypes and assigned 9 morphotypes into the species level. A total of 1624 larvae from 96 temporal larval samples were selected for molecular identification, and high quality barcoding sequences were obtained from 1391 larvae. We accurately assigned 1078 larvae to 37 species using our barcode library and published database. Among the identified species, a critically endangered species, namely, Ochetobius elongatus, and several invasive species were examined, providing a new perspective to assess the stock of regional endangered and invasive species. Furthermore, this study found high species diversity occurred primarily between May and September, and clarified the spawning periods of identified species inferred from the temporal occurrences of larvae. Above all, our study highlights the applicability to fish larval ecology to assist conservation and fishery management efforts.

Geographical and temporal origins of Neocaridina species (Decapoda: Caridea: Atyidae) in Taiwan

BACKGROUND

The freshwater species on Taiwan Island have been documented to have originated from mainland China and the Japanese islands from multiple events and by multiple colonization routes. Moreover, the sequences from the mitochondrial DNA cytochrome c oxidase subunit I (COI) have been used for DNA barcoding to identify the species. This study used the COI sequences to identify Neocaridina species in Taiwan and to examine their geographical and temporal origins.

RESULTS

In total, 479 specimens were collected from 35 localities, which covered almost all rivers in Taiwan. In addition, some sequences were downloaded from GenBank. The maximum likelihood (ML) tree displayed that all sequences were sorted into 13 taxa (clades), and all sequences in Taiwan were sorted into four clades. The Bayesian skyline plots revealed that these four Neocaridina species have declined recently in Taiwan.

CONCLUSIONS

All results support that (1) there are four Neocaridina species in Taiwan, which are N. davidi, N. saccam, N. ketagalan and an undescribed Neocaridina species (N. sp.); (2) these four species colonized Taiwan Island in four colonization events; (3) N. sp. colonized Taiwan first; (4) after the island reached its shape, N. ketagalan and N. saccam colonized Taiwan from the Japanese islands and mainland China, respectively; (5) N. davidi colonized northern Taiwan last; and (6) the cyclic glacial and landform changes in East Asia shaped the colonization events and population structures of the Neocaridina species.

Characterization and phylogenetic analysis of the complete mitochondrial genome of Rhinogobius sp. (Perciformes, Gobiidae)

The genus Rhinogobius was widely distributed in East Asia. In the present study, the complete mitochondrial genome of Rhinogobius sp., possible a new species of freshwater goby from Anhui province of China, was sequenced for the first time. Sequence analysis showed that it is 16,511 bp in length with A + T content of 52.3%, consisting of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and a control region (CR). Phylogenetic analyses placed Rhinogobius sp. in a well-supported monophyletic cluster with other Rhinogobius fish and the phylogenetic position of Rhinogobius sp. was closer to Rhinogobius cliffordpopei.

Complete mitochondrial genome of freshwater goby Rhinogobius cliffordpopei (Perciformes, Gobiidae): genome characterization and phylogenetic analysis

Freshwater gobies Rhinogobius cliffordpopei and R. giurinus are invasive species with particular concern because they have become dominant and were fierce competitors in the invaded areas in Yunnan-Guizhou Plateau (southwest of China). Information about genetic characteristics of R. giurinus have been published, but there were still no relevant reports about R. cliffordpopei. In present study, the complete mitochondrial genome of R. cliffordpopei was determined, which was 16,511 bp in length with A + T content of 51.1%, consisting of 13 protein-coding genes, 22 tRNAs, 2 ribosomal RNAs, and a control region. The gene composition and the structural arrangement of the R. cliffordpopei complete mtDNA were identical to most of other teleosts. Phylogenetic analyses placed R. cliffordpopei in a well-supported monophyletic cluster with other Rhinogobius fish. But the phylogenetic relationship between genus Rhinogobius and Tridentiger remained to be resolved.

Genetic variation of the land-locked freshwater shrimp Caridina pseudodenticulata (Decapoda: Atyidae: Caridina) in Taiwan

Caridina pseudodenticulata is a land-locked freshwater shrimp, which is endemic to North and West Taiwan. It is listed as Vulnerable under criteria A1ce in the IUCN Red List. Our study used mitochondrial DNA fragment sequences of the cytochrome oxidase subunit I (COI) gene to examine its genetic structure. In total, 204 sequences were analyzed from 22 populations, and all 39 haplotypes were identified. Our study (1) found that the genetic diversity within population of this species was similar to that of other land-locked freshwater prawn in Taiwan; (2) displayed that during glaciation, the Taiwan Strait was largely above water, an event which created opportunities for colonization Taiwan and dispersal widely; (3) showed that although the phylogenetic analysis showed the lack of a population genetic structure, the AMOVA and haplotypes distribution pattern revealed geographically divided; (4) indicated that C. pseudodenticulata could across to neighbor rivers through the mouths of rivers, which confluent with each other during floods.

New insights on geographical/ecological populations within Coilia nasus (Clupeiformes: Engraulidae) based on mitochondrial DNA and microsatellites

The Coilia nasus is an important fish species, which is of commercial values in China. In order to manage the fisheries resources and the development of sustainable fishing strategies to protect this species, 11 microsatellite loci polymorphisms and mtDNA COI sequences were used to examine the genetic diversity of C. nasus in Japan and China. In total, the 40 COI haplotypes and 93 microsatellite alleles were detected. The mtDNA phylogeny did not support population grouping, but the distribution patterns of mtDNA haplotypes and the results of STRUCTURE analysis based on microsatellite indicated a degree of genetic isolation in this species. Our study suggested that the lack of a population genetic structure might result in its amphidromous life cycle, and the geographical distance and habitat fragments might cause isolated populations. Thus, the sampling populations of C. nasus in Japan and China could be divided as four geographical/ecological populations.