Mitochondrial diversity and phylogeography of Acrossocheilus paradoxus (Teleostei: Cyprinidae)

Biogeography of Greater Antillean freshwater fishes, with a review of competing hypotheses

In biogeography, vicariance and long-distance dispersal are often characterised as competing scenarios. However, they are related concepts, both relying on collective geological, ecological, and phylogenetic evidence. This is illustrated by freshwater fishes, which may immigrate to islands either when freshwater connections are temporarily present and later severed (vicariance), or by unusual means when ocean gaps are crossed (long-distance dispersal). Marine barriers have a strong filtering effect on freshwater fishes, limiting immigrants to those most capable of oceanic dispersal. The roles of vicariance and dispersal are debated for freshwater fishes of the Greater Antilles. We review three active hypotheses [Cretaceous vicariance, Greater Antilles-Aves Ridge (GAARlandia), long-distance dispersal] and propose long-distance dispersal to be an appropriate model due to limited support for freshwater fish use of landspans. Greater Antillean freshwater fishes have six potential source bioregions (defined from faunal similarity): Northern Gulf of México, Western Gulf of México, Maya Terrane, Chortís Block, Eastern Panamá, and Northern South America. Faunas of the Greater Antilles are composed of taxa immigrating from many of these bioregions, but there is strong compositional disharmony between island and mainland fish faunas (>90% of Antillean species are cyprinodontiforms, compared to <10% in Northern Gulf of México and Northern South America, and ≤50% elsewhere), consistent with a hypothesis of long-distance dispersal. Ancestral-area reconstruction analysis indicates there were 16 or 17 immigration events over the last 51 million years, 14 or 15 of these by cyprinodontiforms. Published divergence estimates and evidence available for each immigration event suggests they occurred at different times and by different pathways, possibly with rafts of vegetation discharged from rivers or washed to sea during storms. If so, ocean currents likely provide critical pathways for immigration when flowing from one landmass to another. On the other hand, currents create dispersal barriers when flowing perpendicularly between landmasses. In addition to high salinity tolerance, cyprinodontiforms collectively display a variety of adaptations that could enhance their ability to live with rafts (small body size, viviparity, low metabolism, amphibiousness, diapause, self-fertilisation). These adaptations likely also helped immigrants establish island populations after arrival and to persist long term thereafter. Cichlids may have used a pseudo bridge (Nicaragua Rise) to reach the Greater Antilles. Gars (Lepisosteidae) may have crossed the Straits of Florida to Cuba, a relatively short crossing that is not a barrier to gene flow for several cyprinodontiform immigrants. Indeed, widespread distributions of Quaternary migrants (Cyprinodon, Gambusia, Kryptolebias), within the Greater Antilles and among neighbouring bioregions, imply that long-distance dispersal is not necessarily inhibitory for well-adapted species, even though it appears to be virtually impossible for all other freshwater fishes.

Molecular Identification of Acrossocheilus jishouensis (Teleostei: Cyprinidae) and Its Complete Mitochondrial Genome

Molecular identification, such as DNA barcoding, is a useful tool that is widely applied in distinguishing species. To identify the cyprinid Acrossocheilus jishouensis, which was previously known to be restricted to only its type locality, we conducted molecular identification of this species based on 23 samples in five localities. Molecular identification based on the mitochondrial COI gene sequence showed that the morphologically similar samples from the five populations were all A. jishouensis, as the mean genetic distances between populations were very small (0.1-1.6%); thus, the distribution of this species was substantially expanded. The whole mitochondrial genome of one sample was also assembled, which was 16,594 bp in length and consisted of 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and one control region. All PCGs began with ATG except the COI gene, which started with GTG; seven PCGs used the complete stop codon TAA, while four terminated in T(AA) and two ended with TAG. The overall base composition reflected a higher proportion of A+T than G+C and a positive AT-skew and negative GC-skew pattern except for the opposite in ND6. Phylogenetic relationships inferred using BI and ML methods revealed that both Acrossocheilus and Onychostoma were nonmonophyletic, which indicated that the traditional diagnoses between these two genera need to be assessed further. The results of this study not only expanded the known distribution ranges of A. jishouensis, but also provided a valuable data resource for future molecular and evolutionary studies of Acrossocheilus and other cyprinids in Barbinae.

The complete mitochondrial genome of Neolissochilus soroides (Duncker, 1904) (Cypriniformes: Cyprinidae)

In this paper, we first report the complete mitochondrial genome of Neolissochilus soroides. The main purpose of this study was to determine the mitochondrial genome and phylogenetic status of N. soroides. The length mitogenome was 16584 bp, containing 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes, and 3 non-coding control regions. The genome showed a slight A + T bias (A + T = 56.47%). 12 genes (ND1, COX2, ATP6, ND4L, ND5, ND6, ND2, ATP8, ND3, ND4, Cytb, COX3) start with ATG codon, besides one gene (COX1) start with GTG codon. Six genes (ND1, COX1, ATP6, ND4L, ND5, ND6) end with a TAA codon, 3 genes (ND2, ATP8, ND3) end with a TAG codon, and four genes (COX2, ND4, Cytb, COX3) end with the TA or T codon. The phylogenetic analysis showed that N. soroides was closely related to N. hendersoni. The mitogenome could have important implications for phylogeny, population genetics, and conservation of the N. soroides.

Historical Landscape Evolution Shaped the Phylogeography and Population History of the Cyprinid Fishes of Acrossocheilus (Cypriniformes: Cyprinidae) According to Mitochondrial DNA in Zhejiang Province, China

Geological events and landscape features, as well as changes in the climate during the Pliocene period, have shaped the distribution of genetic diversity and demographic history of freshwater fish in mainland China. In this study, we investigated the phylogeny and population genetic structure of Acrossocheilus species (A. fasciatus, A. kreyenbergii and A. wenchowensis) in the Zhejiang region by the mitochondrial cytochrome b (cyt-b) and control (D-loop) region s. Mitochondrial phylogenetic analysis revealed three major lineages (lineages A, B and C), which may represent A. fasciatus, A. wenchowensis and A. kreyenbergii, respectively. Our results revealed that A. fasciatus and A. wenchowensis diverged from A. kreyenbergii in the Zhejiang region. The uplift of the Wuyi Mountains and the Xianxia Mountains served as an important geographic barrier in the diversification of the three Acrossocheilus species. The most recent common ancestors (TMRCAs) of the three lineages and lineages A + B were dated to 1.859 and 1.614 myr, respectively. Our results indicate that the effective population sizes of A. fasciatus and A. wenchowensis remained constant from the past to the present, as supported by ABC analysis. For conservation and protection, a strategy is required because of their genetic uniqueness, and we suggest that the two regions divided by the Xianxia Mountains be regarded as different management units (Mus), conforming to the major zoological regions of the Zhejiang region.

Multilocus Phylogeography and Population Genetic Analyses of Opsariichthys hainanensis Reveal Pleistocene Isolation Followed by High Gene Flow around the Gulf of Tonkin

The ichthyofauna of continental islands is characterized by immigration through a land bridge due to fluctuating sea levels. Hainan Island is adjacent to the southern margin of mainland China and provides opportunities for understanding the origin and diversification of freshwater fishes. The aim of our study was to evaluate the level of genetic variation and phylogeographic structure of Opsariichthys hainanensis on Hainan Island and mainland China, using mtDNA cyt b gene (1140 bp) and D-loop (926 bp), nuclear RAG1 gene (1506 bp), and 12 microsatellite loci. Mitochondrial phylogenetic analysis identified five major lineages according to the geographical distribution from different populations. We suggested that two dispersal events occurred: the population in the Changhua River migrated to the Red River (Lineage B), and the populations in the South Hainan region moved northwards to the North Hainan region. However, populations in Northwest Hainan Island dispersed to the populations around the Gulf of Tonkin (Lineage A1) and populations in Northeast Hainan Island dispersed to the populations in mainland China (Lineage A2). Our results indicated that the populations of O. hainanensis suffered a bottleneck event followed by a recent population expansion supported by the ABC analysis. We suggest that O. hainanensis populations were found mostly in the lowlands and a lack of suitable freshwater habitat in southern mainland China and Hainan during the Last Interglacial period, and then expansion occurred during the Last Glacial Maximum.

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.

Genetic diversity of Rhinogobius delicatus (Perciformes: Gobiidae): origins of the freshwater fish in East Taiwan

Mitochondrial DNA cytochrome b and d-loop sequences (1,984 bp) from 92 specimens of the freshwater goby Rhinogobius delicatus from seven drainages in East Taiwan were identified as two major lineages exhibiting a southern or northern distribution. The existence of low genetic diversity, a pattern of population decline and high population differentiation (F _ST=0.711) support the need for the development of management strategies for the conservation of localized populations. The results of a statistical dispersal-vicariance analysis suggested that the ancestral populations of R. delicatus were widely distributed in East Taiwan. Compared with the phylogeographic patterns of the other endemic eastern Taiwan freshwater fishes, Onychostoma alticorpus, Aphyocypris kikuckii and Hemimyzon taitungensis, our study suggests that the freshwater fishes colonized East Taiwan through northeastern and southwestern Taiwan, although the ancestral populations colonized the island before it reached its present shape.

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.