Comparative phylogeography of Zacco platypus and Opsariichthys bidens (Teleostei, Cyprinidae) in China based on cytochrome b sequences

We compared the phylogenetic relationships and the population structure of the sympatric cyprinids Opsariichthys bidens and Zacco platypus across the Yangzte, Pearl and Hai He drainages in Mainland China. We used the mitochondrial cytochrome b gene to evaluate their phylogeographical structure and to discuss further systematic implications. We sequenced 71 new individuals of Z. platypus to add to a previous study and to construct a geographically comparable data set with O. bidens (Mol. Phylogenet. Evol. 31, 2004, 192; Mol. Phylogenet. Evol. 37, 2005, 920). Phylogeographic analysis of Z. platypus identified two additional mtDNA lineages (Zacco E and F) in addition to the previously recovered lineages (Zacco A–D). The geographical range of the Zacco A was extended across the Pearl drainage, broadening considerably the previous distribution that was circumscribed to the Yangtze drainage. Our results show high molecular divergence between all Zacco A–F mtDNA lineages (mean TrN + I + G distance 17.7%, range 4.4–30.8%), and the population analyses showed that most of the genetic variation was found among major river tributaries (90.2%). Values of θ_ST higher than 0.97 corroborated this interruption of gene flow between Zacco A–F mtDNA lineages. Nested clade analysis results were also concordant with the phylogenetic relationships recovered. We found similar phylogeographic patterns in Z. platypus and O. bidens: they exhibited two widespread and common lineages (Zacco A and Opsariichthys 1) ranging across the Yangtze and Pearl drainages, and both taxa had Northern lineages (Zacco F and Opsariichthys 5) clearly differentiated. Similar phylogeographic patterns suggest that common historical factors have shaped current Zacco and Opsariichthys diversity. High genetic distances and θ_ST values suggested that differentiation of Zacco A–F mtDNA lineages and Opsariichthys 1–5 was not recent and was probably favoured by old geological events. However, population parameters and low genetic differentiation inside Zacco A and Opsariichthys 1 suggest a recent gene flow across river drainages. Mitochondrial‐based phylogenies for the combined data sets of Zacco A–F and Opsariichthys 1–5 mtDNA lineages always recovered both taxa as paraphyletic, highlighting the notion that their current systematics need a revision.     

Comparative phylogeography of the two pink salmon broodlines: an analysis based on a mitochondrial DNA genealogy

Over most of their natural northern Pacific Ocean range, pink salmon (Oncorhynchus gorbuscha) spawn in a habitat that was repeatedly and profoundly affected by Pleistocene glacial advances. A strictly two-year life cycle of pink salmon has resulted in two reproductively isolated broodlines, which spawn in alternating years and evolved as temporal replicates of the same species. To study the influence of historical events on phylogeographical and population genetic structure of the two broodlines, we first reconstructed a fine-scale mtDNA haplotype genealogy from a sample of 80 individuals and then determined the geographical distribution of the major genealogical assemblages for 718 individuals sampled from nine Alaskan and eastern Asian even- and nine odd-year pink salmon populations. Analysis of restriction site states in seven polymerase chain reaction (PCR)-amplified mtDNA regions (comprising 97% of the mitochondrial genome) using 13 endonucleases resolved 38 haplotypes, which clustered into five genealogical lineages that differed from 0.065 to 0.225% in net sequence divergence. The lineage sorting between broodlines was incomplete, which suggests a recent common ancestry. Within each lineage, haplotypes exhibited star-like genealogies indicating recent population growth. The depth of the haplotype genealogy is shallow ( approximately 0.5% of nucleotide sequence divergence) and probably reflects repeated decreases in population size due to Pleistocene glacial advances. Nested clade analysis (NCA) of geographical distances showed that the geographical distribution observed for mitochondrial DNA (mtDNA) haplotypes resulted from alternating influences of historical range expansions and episodes of restricted dispersal. Analyses of molecular variance showed weak geographical structuring of mtDNA variation, except for the strong subdivision between Asian and Alaskan populations within the even-year broodline. The genetic similarities observed among and within geographical regions probably originated from postglacial recolonizations from common sources rather than extensive gene flow. The phylogeographical and population genetic structures differ substantally between broodlines. This can be explained by stochastic lineage sorting in glacial refugia and perhaps different recolonization routes in even- and odd-year broodlines.     

Phylogeny,genetic diversity and phylogeography of the genus Codoma (Teleostei,Cyprinidae)

This study represents a thorough analysis of Codoma, a monotypic genus endemic to north‐western Mexico. A previous morphological analysis of the species concluded that there exists several morphological groups in Codoma ornata, suggesting diversity in Codoma could be underestimated. No studies have examined the genetic diversity in Codoma ornata to test this hypothesis and identify independent lineages. We present a phylogeographic analysis using one mitochondrial and two nuclear genes, and specimens from across nine major drainages in both the Chihuahuan Desert and the Sierra Madre Occidental of western Mexico. All genes and analyses recovered populations of Codoma in a well‐supported clade and sister to Tampichthys, and this clade sister to Cyprinella. Analyses of both mitochondrial and nuclear genes indicated Codoma is not monotypic and recover more diversity in the genus than currently recognized. The four (mitochondrial) and five (nuclear) genetically distinct lineages are consistent with those groups outlined in the prior morphological study of the genus. Composition and distribution of these major lineages is also consistent with prior biogeographic hypothesis for other fishes in the region, supporting an ancestral Rio Grande system extending south towards central Mexico. Fragmentation of this paleosystem was followed by allopatric speciation in the Chihuahuan Desert. These results suggest a scenario of long‐term isolation in four major regions (upper Conchos, lower Conchos, Nazas, upper Mezquital). Resolution of the diversity and biogeography of these lineages has many implications for various biological disciplines, especially for evolutionary and conservation studies.     

FISH-mapping of 18S ribosomal RNA genes and telomeric sequences in the Japanese bitterlings Rhodeus ocellatus kurumeus and Tanakia limbata (Pisces,Cyprinidae) reveals significant cytogenetic differences in morphologically similar karyotypes

The Japanese rose bitterling, Rhodeus ocellatus kurumeus, and the oily bitterling, Tanakia limbata, were cytogenetically studied by silver (Ag)- and chromomycin A₃ (CMA₃)-staining, by C-banding and by mapping of the 18S ribosomal genes and of the (TTAGGG) _n telomeric sequence. These two representative species of related genera of the subfamily Acheilognathinae show very similar chromosome complements. Nevertheless, significant differences in the chromosomal distribution of nucleolus organizer regions (NORs) and interstitial telomeric sequences were observed. Whereas R. ocellatus kurumeus shows a single NOR-bearing chromosome pair, T. limbata is characterized by a higher number of variable NORs. Multiple telomeric sequence sites were found at the pericentromeric regions of several chromosomes in the rose bitterling. No telomeric sequence sites were detected near centromeres, but they were found to be scattered along the NORs in the oily bitterling. Two karyoevolutive trends might have been identified in the subfamily.     

Genetic structure of the killifish Aphanius fasciatus, Nardo 1827 (Teleostei, Cyprinodontidae), results of mitochondrial DNA analysis

Aphanius fasciatus is a cyprinodont distributed in the salty coastal water of the central and eastern Mediterranean Sea and occasionally in internal fresh water. In this work, the authors have investigated the genetic structure of eight populations of the killifish A. fasciatus from Sardinia and Sicily. The comparison of the mtDNA control region of 237 individuals revealed a total of 49 haplotypes. Several unique haplotypes were present in each population, and no common haplotype was found among Sicilian and Sardinian populations. Almost all Sardinian populations shared a common haplotype, and indeed the four Sicilian populations examined did not share any as determined by the parsimony network analysis. The analysis of molecular variance showed that the percentage of variation among populations is much higher than within each population of A. fasciatus . The overall F _ST value is very high (0·78) and supports an extensive genetic structure of the populations. The observed genetic differentiations of A. fasciatus populations were discussed taking into account the palaeogeographic and palaeoclimatic events that interested the Mediterranean area from Miocenic to Pleistocenic age. The results provide new insight into the knowledge of the pattern of genetic structure and of evolutionary processes occurring in this species.     

The origin and divergence of Gobioninae fishes (Teleostei: Cyprinidae) based on complete mitochondrial genome sequences

The gudgeons (subfamily Gobioninae) are a group of cyprinid fishes primarily distributed in East Asia. However, studies on their origins and divergence are scarce. Here the whole mitochondrial genome sequences of 27 gudgeon species (including one newly determined), 22 other cyprinid species, and two non‐cyprinids as outgroups are applied to infer the evolution of the gudgeons. Based on Bayesian and maximum likelihood phylogenetic analyses, the gudgeons were determined to be a monophyletic group which can be further subdivided into four monophyletic clades with strong supports. The divergence times of the gudgeons were estimated using a relaxed molecular clock method; the results indicate that these fishes originated in the early Paleocene (approx. 63.5 Mya) and that the basal Hemibarbus group diverged from the other gudgeon fishes (approx. 58.3 Mya). As an independent group the Coreius began to diverge from the remaining two groups (approx. 54.6 Mya); the most derived two groups diverged from each other (approx. 53.6 Mya). The divergences of the four gudgeon groups were within a relatively short time frame (approx. 58–53 Mya). Based on the reconstruction of evolutionary trends of gudgeon habitat, evidence is provided that supports the origin and differentiation of this fauna as being associated with some special paleo‐environmental events occurring from the early Paleocene to the Pliocene. The study represents comprehensive molecular dating and character evolution analyses of the gudgeons, and providing a valuable framework for future research in the evolution of the Gobioninae fishes.     

Multiple origins of stone loach,Barbatula barbatula (Teleostei: Nemacheilidae), in Sweden based on mitochondrial DNA

Stone loach, Barbatula barbatula, occurs in scattered localities in Sweden. Some of the populations have usually been considered as feral descendants of escaped 18th Century pond stock, but historical documentation is inconclusive. Using the mitochondrial COI gene as a marker, we analyzed specimens from seven Swedish localities. One of the middle Swedish localities, in Stockholm, belongs to a haplotype found also in Poland and Lithuania. Two other samples, from near Nyköping and Lake Hjälmaren, belong to a haplotype found in northeastern Europe (Finland, Estonia, Latvia, Volga basin in Russia). Those two Swedish populations are probably descendants from at least two introductions, probably for pond rearing for human consumption. Samples from Skåne and Halland in southern Sweden belong to the haplotype found in Denmark, northern Germany and Poland; and whereas it remains possible that they also represent feral populations, they may be naturally occurring, having reached Sweden during the Ancylus period, about 8,000–10,000 years ago. A recently discovered population from the central South Swedish Highlands belongs to a mainly southeastern European haplotype. It probably represents a release of imported aquarium specimens or live bait carried by sport fishing tourists.     

Comparative osteology of lotaks, Cyprinion kais and C. macrostomum (Cypriniformes, Cyprinidae), from Godarkhosh River, western Iran

Osteology of two cyprinid fishes, Cyprinion kais and C. macrostomum, from the Tigris-Euphrates basin was described and compared. Eight specimens of C. kais and ten specimens of C. macrostomum from Godarkhosh River (western Iran) were studied. The skeletal elements were prepared using clearing and softening methods and photographed. The differences between the two taxa include a deeper posterior position of the lower jaw with a much narrower labial surface, a longer last dorsal unbranched ray with weaker posterior serration, and a more embowed dentary, maxillary and premaxillary in C. kais. Based on these differences, the examined specimens of these two taxa could be easily distinguished.     

Comparative phylogeography of sympatric sister species,Clevelandia ios and Eucyclogobius newberryi (Teleostei,Gobiidae), across the California Transition Zone

It is paradigmatic in marine species that greater dispersal ability often, but not always, results in greater gene flow and less population structure. Some of the exceptions may be attributable to studies confounded by comparison of species with dissimilar evolutionary histories, i.e. co-occurring species that are not closely related or species that are closely related but allopatric. Investigation of sympatric sister species, in contrast, should allow differences in phylogeographic structure to be attributed reliably to recently derived differences in dispersal ability. Here, using mitochondrial DNA control region sequence, we first confirm that Clevelandia ios and Eucyclogobius newberryi are sympatric sister taxa, then demonstrate considerably shallower phylogeographic structure in C. ios than in E. newberryi. This shallower phylogeographic structure is consistent with the higher dispersal ability of C. ios, which most likely results from the interaction of habitat and life-history differences between the species. We suggest that the paradigm will be investigated most rigorously by similar studies of other sympatric sister species, appended by thorough ecological studies, and by extending this sister-taxon approach to comparative phylogeographic studies of monophyletic clades of sympatric species.     

Phylogeny and biogeography of highly diverged freshwater fish species (Leuciscinae,Cyprinidae, Teleostei) inferred from mitochondrial genome analysis

The distribution of freshwater taxa is a good biogeographic model to study pattern and process of vicariance and dispersal. The subfamily Leuciscinae (Cyprinidae, Teleostei) consists of many species distributed widely in Eurasia and North America. Leuciscinae have been divided into two phyletic groups, leuciscin and phoxinin. The phylogenetic relationships between major clades within the subfamily are poorly understood, largely because of the overwhelming diversity of the group. The origin of the Far Eastern phoxinin is an interesting question regarding the evolutionary history of Leuciscinae. Here we present phylogenetic analysis of 31 species of Leuciscinae and outgroups based on complete mitochondrial genome sequences to clarify the phylogenetic relationships and to infer the evolutionary history of the subfamily.     

Molecular phylogeny and systematics of the Barbinae (Teleostei: Cyprinidae) in China inferred from mitochondrial DNA sequences

The taxonomy and phylogeny of the Chinese species of the Barbinae (Cypriniformes) has a confusing history. In this study, partial sequences of four mitochondrial genes (cyt b, COI, ND4 and 16S rRNA) from 75 Barbinae species and 38 outgroup species were used to investigate the taxonomy and phylogeny within the Barbinae in China. The monophyly of Neolissochilus, Sikukia and Tor are not supported. Neolissochilus benasi might represent a new genus, and Tor hemispinus and Tor qiaojiensis should be moved into Neolissochilus. Sikukia flavicaudata is not Sikukia species. Puntius paucimaculatus might be a synonym of Puntius semifasciolatus. Puntius semifasciolatus does not belong to Puntius. Onychostoma barbatum might consist of more than one species. Our molecular results corroborate that Acrossocheilus stenotaeniatus is a synonym of Acrossocheilus longipinnis. Finally, Barbonymus gonionotus from Menglun, Yunnan should be Poropuntius huangchuchieni.     

Phylogeny and taxonomy of the genus Ilyodon Eigenmann, 1907 (Teleostei: Goodeidae), based on mitochondrial and nuclear DNA sequences

Taxonomy of the live‐bearing fish of the genus Ilyodon Eigenmann, 1907 (Goodeidae), in Mexico, is controversial, with morphology and mitochondrial genetic analyses in disagreement about the number of valid species. The present study accumulated a comprehensive DNA sequences dataset of 98 individuals of all Ilyodon species and mitochondrial and nuclear loci to reconstruct the evolutionary history of the genus. Phylogenetic inference produced five clades, one with two sub‐clades, and one clade including three recognized species. Genetic distances in mitochondrial genes (cytb: 0.5%–2.1%; coxI: 0.5%–1.1% and d‐loop: 2.3%–10.2%) were relatively high among main clades, while, as expected, nuclear genes showed low variation (0.0%–0.2%), with geographic concordance and few shared haplotypes among river basins. High genetic structure was observed among clades and within basins. Our genetic analyses, applying the priority principle, suggest the recognition only of Ilyodon whitei and Ilyodon furcidens, with I. cortesae relegated to an invalid species, the populations of which belong to I. whitei.     

A molecular phylogeny of the Percidae (Teleostei, Perciformes) based on mitochondrial DNA sequence

The family Percidae is among the most speciose families of northern hemisphere fishes with > 178 178 North American species and 14 Eurasian species. Previous phylogenetic studies have been hampered by a lack of informative characters, inadequate taxonomic sampling, and conflicting data. We estimated phylogenetic relationships among 54 percid species (9 of 10 genera and all but one subgenus of darters) and four outgroup taxa using mitochondrial DNA data from the 12S rRNA and cytochrome b genes. Four primary evolutionary lineages were consistently recovered: Etheostomatinae (Ammocrypta, Crystallaria, Etheostoma, and Percina), Perca, Luciopercinae (Romanichthys, Sander, and Zingel), and Gymnocephalus. Except Etheostoma and Zingel, all polytypic genera were monophyletic. The Etheostoma subgenus Nothonotus failed to resolve with other members of the genus resulting in a paraphyletic Etheostoma. The subfamily Percinae (Gymnocephalus and Perca) was not recovered in phylogenetic analyses with Gymnocephalus sister to Luciopercinae. Etheostomatinae and Romanichthyini were never resolved as sister groups supporting convergent evolution as the cause of small, benthic, stream-inhabiting percids in North American and Eurasian waters.     

Comparative phylogeography of four component species of deciduous broad-leaved forests in Japan based on chloroplast DNA variation

A phylogeographic study of four tree species (Padus grayana, Euonymus oxyphyllus, Magnolia hypoleuca, and Carpinus laxiflora) growing in Japanese deciduous broad-leaved forests was conducted based on chloroplast DNA (cpDNA) variations. Using nucleotide sequences of 702–1,059 bp of intergenic spacers of cpDNA, 20, 27, eight, and eight haplotypes were detected among 251, 251, 226, and 262 individuals sampled from 67, 79, 75, and 71 populations of the above species, respectively. The geographical pattern of the cpDNA variations was highly structured in each species, and the following three regional populations were genetically highly differentiated among all four species: (1) the Sea of Japan-side area, (2) the Kanto region, and (3) southwestern Japan. Based on some interspecific similarities among the phylogeographic patterns, the following migration scenario of Japanese deciduous broad-leaved forests was postulated. During the last glacial maximum (LGM), the forests were separately distributed in six regions. After LGM, as the climate warmed, the forests in eastern Japan separately expanded from each of the refugia along the Sea of Japan-side or along the Pacific Ocean-side. In contrast, those in southwestern Japan retreated and moved to high altitudes from each of the continuous forests.     

Comparative cytogenetics and molecular phylogeography in the group astyanax altiparanae--Astyanax aff. bimaculatus (Teleostei, Characidae)

The genus Astyanax comprises small characin fish of the neotropical region. The so-called 'yellow-tailed characins' compose one of the most widely distributed Astyanax groups. A. altiparanae and A. aff. bimaculatus, are evolutionarily closely related and commonly found in several Brazilian hydrographic basins. In the present work, chromosomal data of specimens of A. altiparanae and A. aff. bimaculatus from 4 hydrographic basins in the states of S?o Paulo (Upper Tietê, Paranapanema, Ribeira de Iguape) and Rio de Janeiro (Guapimirim) are shown. All the populations showed 50 chromosomes, with different karyotypic formula. Although only a single Ag-NOR bearing chromosome pair was observed, all populations possess multiple cistrons of 18S rDNA. FISH with the 5S rDNA probe showed single signals at the interstitial position of one metacentric chromosome pair. C-bands are distributed in the terminal and interstitial regions of several chromosomes. However, the As-51 satDNA are frugally located in a few chromosomes of fishes from Upper Tietê, Paranapanema and Guapimirim Rivers, being absent in individuals of A. aff. bimaculatus from Ribeira de Iguape River basin. Beside these 4 populations, molecular phylogeography studies were also performed in individuals from Middle and Lower Tietê River basin and from 2 additional collection sites in the Paranapanema and Ribeira de Iguape River basins. The phylogeographic analysis using 2 mtDNA regions (totalizing 1.314 bp of ND2 and ATPase6/8 genes) of 8 populations of the group of 'yellow-tailed characins' from 3 major hydrographic basins showed structuring of populations, suggesting a correlation between chromosomal (nuclear) and molecular (mitochondrial) data.     

Comparative phylogeography between the ermine Mustela erminea and the least weasel M. nivalis of Palaearctic and Nearctic regions, based on analysis of mitochondrial DNA control region sequences

Phylogeography of the ermine Mustela erminea and the least weasel M. nivalis from Palaearctic and Nearctic regions were investigated based on mitochondrial DNA control region sequences. Mustela erminea exhibited a very low level of genetic variation, and geographic structures among populations were unclear. This may indicate that M. erminea recently reoccupied a wide territory in Eurasia following the last glacial retreat. In comparison with M. erminea, genetic variations within and among populations of M. nivalis were much greater. Molecular phylogenetic relationships showed that two lineages of M. nivalis occurred in the Holarctic region: one spread from the Eurasian region to North America, and the other occurred in south-eastern Europe, the Caucasus and Central Asia. The results suggest either mitochondrial DNA introgression among populations of south-eastern Europe, the Caucasus and Central Asia, or ancestral polymorphisms remaining in those populations. Contrastive phylogeographic patterns between the two mustelid species could reflect differences of their migration histories in Eurasia after the last glacial age.     

Comparative analysis of mitochondrial DNA variation in four species of Far Eastern redfins of the genus Tribolodon (Pisces, Cyprinidae)

The variability of mtDNA in four Far Eastern endemic species of the genus Tribolodon was studied in the significant part of their areas. There was no close relationship between the lifetime and the level of mtDNA variability. The relation between the population genetic structure and the level of amphidromic species was revealed. The presence of mtDNA phylogroup differed in three of the four species shows that there was a long period of independent intraspecific divergent evolution in the history of these species. This period falls on aproximately the same historical age, and, apparently, is caused by one and the same factors. The period was not enough long and ended in the integration of genetically independent units into a single species.     

Population structure and phylogeography of Aphyocypris kikuchii (Oshima) based on mitochondrial DNA variation

Aphyocypris kikuchii is a cyprinid species endemic to northern and eastern Taiwan and is the only primary freshwater fish native east of the Coastal Mountain Range. In total, 92 individuals of A. kikuchii from seven populations in three regions of the island were surveyed for mitochondrial DNA (mtDNA) variation. High haplotype diversity ( h = 0·989) and low nucleotide diversity ( π = 0·009) of mtDNA were detected. Negative values of Tajima's D and unimodal mismatch distributions probably reflect a history of recent demographic expansions from small populations. Three major haplotype clusters displayed geographically non-overlapping distributions, indicating a long-term isolation between regions. Hierarchical analysis of molecular variance showed significant genetic structuring among populations ( Φ _ST= 0·66). Significant haplotype heterogeneity was also detected among populations within regions ( Φ _SC= 0·41, P < 0·001) and among regions ( Φ _CT= 0·43, P < 0·05). Molecular clock estimates of coalescence in the three major mtDNA lineages indicated coalescence in the most recent common ancestor c. 0·11–0·39 million years ago. Haplotypes of cluster B nested as interior nodes in the haplotype network, indicating that migrations from Shueilian (SL) populations to the northern region (cluster A) and to the eastern region (cluster C) may have occurred independently. Lineages A and B + C should be managed as two distinct evolutionarily significant units, while the northern, SL and southern groups should be managed as separate management units.     

Comparative chloroplast DNA phylogeography of two tropical pioneer trees, Macaranga gigantea and Macaranga pearsonii (Euphorbiaceae)

Macaranga (Euphorbiaceae) has received much ecological and evolutionary research attention as a genus that includes some of the most conspicuous pioneer trees of Southeast Asian tropical rainforests and because of its manifold associations with ants, including about 30 species that are obligate ant-plants (myrmecophytes). We used sequence data from three chloroplast DNA loci (ccmp5, ccmp6, atpB-rbcL) to assess phylogeographical patterns in species of Macaranga, section Pruinosae, sampled from various regions of Borneo and the Malay Peninsula. Forty-nine chloroplast DNA haplotypes (HT) were identified among 768 specimens from five species, Macaranga gigantea (N = 329; 23 HT), Macaranga pearsonii (N = 347; 21 HT), Macaranga puberula (N = 24; 4 HT), Macaranga hosei (N = 48; 6 HT), and Macaranga pruinosa (N = 20; 5 HT). Forty-one haplotypes were species-specific, whereas eight haplotypes were shared by two, three, or four species and occupied internal positions in a parsimony network. Population genetic parameters based on haplotype frequencies proved to be in a similar range in the non-myrmecophytic M. gigantea and in the ant-associated M. pearsonii, which have overlapping distributions in northern and eastern Borneo. A comparison of G _ST and N _ST values revealed a strong phylogeographic structure in both species, whereas colonization pathways suggested by the network topology were different. Both species exhibited similar levels of haplotypic diversity and moderate to high levels of population differentiation. There were no obvious indications for an influence of the symbiotic ant partners on the population structure of their host plants.