Genetic variation and divergence of Leuciscus pyrenaicus and L. carolitertii (Pisces, Cyprinidae)

The taxonomy of the genus Leuciscus in the Iberian Peninsula has been presented on the basis of morphological analysis. Two species are believed to occur in Portuguese inland waters, L. carolitertii , the northern basins chub, and L. pyrenaicus , which was described for the Tejo and southern basins. Since only slight differences in the meristic and morphometric characters are observed, the distinction between the two species has been made previously mainly on the basis of osteology. In order to investigate the patterns of genetic differentiation between these species, 24 sites were sampled for both species, and examined electrophoretically for the study of variation at 27 presumptive loci. The results pointed to different levels of population differentiation among drainages and support the recognition of the species level for L. pyrenaicus and L. carolitertii. Our results also suggested that the distribution area of L. pyrenaicus is probably restricted to Tejo and to the small drainages near Tejo, while L. carolitertii seems to have a widespread distribution area, including Lima, Douro, Vouga, Mondego, Guadina and Sado drainages. Moreover, concerning the southern populations, Mira and Arade, the surprisingly high level of differentiation observed at several loci, supports the existence of a further species occurring in these small drainages. The evolutionary aspects related to that differentiation are discussed.     

Assessing inter‐drainage connections: patterns of genetic diversity in an Iberian cyprinid fish

The phylogeography of Iberian freshwater fish species strongly reflects the geomorphological history of Iberian water drainages and formation of mountain ranges. In particular, the Iberian Central Massif limits two ichthyogeographical districts based on fish distribution assemblages: the Northwest district, which comprises all river basins north of the Central massif, and the Central‐west district, which comprises the Tejo and Sado basins. Despite this scenario, the cyprinid Pseudochondrostoma polylepis occurs in both the Tejo and Mondego rivers (one either side of the Estrela Mountains, in the western end of the Central Massif). By analysing the population structure and demographic history of this straight‐mouth nase, based on both mtDNA and microsatellites, we have found evidence of a relatively recent common origin for both Mondego and Tejo populations. Shared haplotypes and lack of divergent lineages for mitochondrial marker, high levels of admixture and common ancestry at the nuclear level, together with signatures of asymmetrical gene flow from Tejo to Mondego suggest a Mondego colonization through a founder event with an origin in Tejo. We suggest that this colonization might have resulted from the occurrence of river connections/captures between Mondego and Tejo headwater tributaries in the recent past. With this study we reinforce that local‐scale geomorphological events and the adaptation/dispersal ability of a species to new environments can have a major impact on its demographic history, colonization processes, and ultimately its distribution. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 656–669.     

Interspecific variations of otolith chemistry in estuarine fish nurseries

Otolith chemical composition differed between juveniles of five fish species ( Solea solea , Solea senegalensis , Platichthys flesus , Diplodus vulgaris and Dicentrarchus labrax ) in nursery areas of six estuaries along the Portuguese coast (Douro, Ria de Aveiro, Mondego, Tejo, Sado and Mira). Spatially consistent patterns in the concentration of some elements were responsible for differences between species. Discrimination of estuaries using data from all species simultaneously averaged 44·7% of correctly classified cases, whilst discrimination of species averaged 76·2%. Moreover, species-related patterns in otolith fingerprints were highlighted when comparing species for each estuarine nursery area, with intra estuarine species discrimination averages ranging from 86·2 to 100·0%. Similarities in the otolith elemental fingerprints were larger between species with close phylogeny and ecology, particularly between flatfish and perciform species. In addition to the differences in physiological regulation of species, specific microhabitat use in a common environment was suggested as a relevant factor for the differentiation of otolith chemistry among species occurring in the same locations. Despite positive results in specific estuaries, variation in otolith composition limited the use of species as proxies to classify others to their system of origin.     

Morphological analysis of geographic variation of sea lamprey ammocoetes in Portuguese river basins

The main objective of this study was to compare the morphological variability of sea lamprey (Petromyzon marinus L.) larvae from the main Portuguese river basins. Samples were collected in rivers Minho, Lima, Cávado, Vouga, Mondego, Tejo and Guadiana. Specimens were analysed in terms of morphometric (linear body measures) and meristic (number of myomeres) characters to investigate the hypothesis of population fragmentation between river basins caused by some degree of homing behaviour. The discriminant analysis showed a morphological segregation of the studied populations based on the characters head, tail and branchial length. The discriminatory power of the meristic characters was comparatively weaker, with the number of trunk myomeres, and to some extent the head myomeres, being responsible for the reduced separation between groups. Both analyses were consistent in identifying the cephalic region as the most important morphological feature to discriminate populations of sea lamprey larvae in the Portuguese territory. The largest cephalic region of the ammocoetes sampled in the northern river basins may be responsible for a better feeding efficiency and, consequently, higher values of condition factor. Guest editors: S. Dufour, E. Prévost, E. Rochard & P. Williot Fish and diadromy in Europe (ecology, management, conservation)     

Species delimitation in a range-restricted group of cascudinhos (Loricariidae: Epactionotus) supports morphological and genetic differentiation across coastal rivers of southern Brazil

Epactionotus species are known for inhabiting the rocky-bottom stretches of fast-flowing rivers in a limited geographic area along the Atlantic coast of southern Brazil. These species are endemic to single coastal river drainages (two neighbouring drainages for Epactionotus bilineatus) isolated from each other by the coastal lacustrine environments or the Atlantic Ocean. E. bilineatus is from the Maquiné and Três Forquilhas River basins, both tributaries of the Tramandaí River system, whereas E. itaimbezinho is endemic to the Mampituba River drainage and Epactionotus gracilis to the Araranguá River drainage. Recent fieldwork in the Atlantic coastal drainages of southern Brazil revealed new populations in the Urussanga, Tubarão, d'Una and Biguaçu River drainages. Iterative species delimitation using molecular data (cytochrome c oxidase subunit I) and morphology (morphometrics and meristics) was applied to evaluate species recognition of isolated populations. With regard to new data, the genus was re-diagnosed, the status of Epactionotus species/populations was re-evaluated, formerly described species were supported and population structure was recognized. As for the newly discovered populations, both morphological and molecular data strongly support the population from the Biguaçu River drainage, in Santa Catarina State, as a new species. Molecular data revealed strong per-basin population structure, which may be related to species habitat specificity and low or no dispersal among drainages.     

Molecular and morphological analysis of endangered species <Emphasis Type="Italic">Gymnodiptychus integrigymnatus</Emphasis> (Teleostei: Cyprinidae)

Gymnodiptychus integrigymnatus is a critically endangered species endemic to the Gaoligongshan Mountains. It was thought to be only distributed in several headwater-streams of the Longchuanjiang River (west slope of the Gaoligongshan Mountains, belonging to the Irrawaddy River drainage). In recent years, dozens of G. integrigymnatus specimens have been collected in some streams on the east slope of the Gaoligongshan Mountains (the Salween drainage). We performed a morphological and genetic analyses (based on cytochrome b and D-loop) of the newly discovered populations of G. integrigymnatus to determine whether the degree of separation of these populations warrants species status. Our analysis from the cytochrome b gene revealed that nine individuals from the Irrawaddy drainage area and seven individuals from the Salween drainage area each have only one unique haplotype. The genetic distance between the two haplotypes is 1.97%. Our phylogenetic analysis revealed that G. integrigymnatus is closely related to highly specialized schizothoracine fishes. Analysis from the mitochondrial control region revealed that G. integrigymnatus has relatively high genetic diversity (π was 0.00891 and h was 0.8714), and individuals from different river drainages do not share the same haplotypes. The AMOVA results indicated 87.27% genetic variability between the Salween and Irrawaddy populations. Phylogenetic trees show two major geographic groups corresponding to the river systems. We recommend that G. integrigymnatus should be considered as a high priority for protected species status in the Gaoligongshan Mountains National Nature Reserve, and that the area of the Gaoligongshan Mountains National Nature Reserve should be expanded to cover the entire distribution of G. integrigymnatus. Populations of G. integrigymnatus from different river systems should be treated as evolutionarily significant units.     

Phylogeography and monophyly of the swordtail fish species Xiphophorus birchmanni (Cyprinodontiformes, Poeciliidae)

We used sequences of the mitochondria control region to assess the distribution of genetic variation within and among populations of the poeciliid fish species Xiphophorus birchmanni . We collected 122 X. birchmanni samples from 11 sites in three drainage systems comprising the distribution of the species. We found low levels of polymorphism among aligned sequences and low levels of genetic variation within populations but high levels of genetic differentiation among populations. Haplotypes are exclusive to three river drainages (Los Hules, Calabozo and San Pedro). Mantel tests revealed correlations between geographical (both straight-line and river distances) and genetic distance, consistent with an isolation by distance scenario, while nested clade analysis suggested allopatric fragmentation between haplotypes from two of the major drainages, and isolation by distance with restricted gene flow within those drainages. Finally, monophyly of X. birchmanni is strongly supported while the previous hypothesis of the evolutionary origin of this species from X. malinche is not.     

Shape variability in topminnows (Fundulus notatus species complex) along the river continuum

We examined intra‐ and interspecific variability in shape of three topminnow species (Funduluidae: Fundulus notatus, F. olivaceus, and F. euryzonus) across ten drainages. Within each drainage, five or more adult male topminnows were digitized at multiple sites (83 total sites) along the river continuum representing a range of stream sizes (cumulative drainage area) and hydrological conditions. Nine of the ten drainages contained two Fundulus species that were longitudinally separated along the river continuum with narrow areas of coexistence. Upstream–downstream distribution patterns were variable by drainage, allowing us to examine patterns repeated across ecologically similar species. More variability in shape was explained by drainage (19.7%) than by species (7.4%) differences. Populations of F. notatus from headwaters (three drainages) converged on a deep‐bodied form similar to F. olivaceus which was typically sampled in headwaters. Fundulus notatus shape was more closely related to stream size than in the other two species. Headwater populations of F. notatus and F. olivaceus had fineness ratios near the hydrodynamic optima of 4.5 whereas downstream populations of F. notatus had shallower bodies. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103 , 612–621.     

Phylogeography of the cyprinid Squalius aradensis and implications for conservation of the endemic freshwater fauna of southern Portugal

The Iberian cyprinid fauna, characterized by the presence of numerous endemic species, has suffered from significant habitat degradation. The critically endangered Squalius aradensis is restricted to small drainages of southern Portugal, habitats that typically exhibit a characteristic Mediterranean-type heterogeneous hydrological system throughout the year, including alternation of flooding events during winter and complete drought in large river sections during summer. To assess the effect of historical and recent processes on genetic diversity in S. aradensis we examined within- and among-population variability in cytochrome b and six polymorphic microsatellite loci. Estimates of genetic diversity in time and space through the combined use of traditional Phi-/F-statistics, phylogenetic trees, ordination methods and nested clade analysis indicated significant and congruent structuring among populations. Data suggest that the Arade drainage represent the evolutionary centre of the species, with subsequent allopatric fragmentation across drainages. Factors other than isolation by distance strongly affected the within-drainage genetic differentiation observed in these Mediterranean-type drainages, including recent population expansion from a bottleneck event and restricted gene flow imposed by a long-term barrier (brackish water area). Significant correlation was found between S. aradensis allelic diversity and upstream drainage area. The relevance of findings for conservation issues is discussed in relation to local intermittent hydrological conditions, the highly restricted distribution and the critically endangered status of the species.     

REPRODUCTIVE ISOLATION AND INTROGRESSION BETWEEN NOTROPIS CORNUTUS AND NOTROPIS CHRYSOCEPHALUS (FAMILY CYPRINIDAE): COMPARISON OF MORPHOLOGY,ALLOZYMES, AND MITOCHONDRIAL DNA

Hybrid zones in fluvial fishes may be heterogeneous from drainage to drainage. The comparison of data from morphology, allozymes, and mitochondrial DNA (mtDNA) indicates variability in the causes and degree of restriction of gene flow between Notropis cornutus and Notropis chrysocephalus. Allozyme marker loci show frequency-dependent introgression; i.e., the rarer species, whichever it is at a particular locality, tends to exhibit a higher proportion of introgressed alleles. Unlike allozymes, introgression of mtDNA haplotypes varies geographically. In westward-flowing Michigan drainages, N. cornutus mtDNA haplotypes are more common in F₁ hybrids and backcrosses, independent of parental frequencies. In eastward-flowing Michigan drainages, N. chrysocephalus mtDNA is more common in F₁ hybrids and backcrosses; this pattern may be due to local ecological effects or frequency-dependent introgression. Morphological data alone are not sufficient to distinguish all classes of hybrids. The lack of concordance of morphological, allozymic, and mtDNA introgression patterns implies operation of one or two factors: 1) geographically variable patterns of selection against different hybrid and backcross combinations or 2) genetic differences between Michigan populations inhabiting eastward- and westward-flowing drainage systems accumulated during historical isolation.     

MATERNAL ANCESTRY OF THE RUTILUS ALBURNOIDES COMPLEX (TELEOSTEI,CYPRINIDAE) AS DETERMINED BY ANALYSIS OF CYTOCHROME b SEQUENCES

Cytochrome b (cyt b) sequences from specimens of the Rutilus alburnoides unisexual complex and five bisexual species were compared to examine hypotheses regarding the origin and maternal ancestry of this complex. Phylogenetic analysis revealed a monophyletic relationship among unisexuals and Leuciscus pyrenaicus, clearly identifying this species as the maternal ancestor. Considerable mtDNA diversity exists among R. alburnoides populations, with many localities exhibiting unique haplotypes. The topology recovered from analysis of cyt b variation among populations suggested that R. alburnoides is polyphyletically derived from their sympatric L. pyrenaicus populations, indicating that unisexual lineages have been generated through multiple hybridization events. Although much less abundant, R. alburnoides is present outside the range of L. pyrenaicus, suggesting that it may have dispersed from the Tejo drainage into the northern basins. In this region, Leuciscus carolitertii is most likely the sexual host for the unisexual complex.     

Patterns of population differentiation in annual killifishes from the Paraná–Uruguay–La Plata Basin: the role of vicariance and dispersal

Aim To elucidate the role of vicariance versus dispersal at the microevolutionary scale in annual killifish populations belonging to the Austrolebias bellottii species complex (Rivulidae). Within this complex, A. bellottii and A. apaii have low vagility and occur widely within the study area, making them excellent models for testing biogeographic hypotheses of differentiation. Location South America, in the Paraná–Uruguay–La Plata river basin. Methods Molecular data and morphometric analyses were used to reconstruct the phylogeographic history and morphological variation of 24 populations of two taxa of the A. bellottii species complex. Phylogenetic analyses using maximum likelihood (ML) and Bayesian inference (BI) model‐based methods, estimates of clade divergence times implemented in beast , non‐metric multidimensional scaling, analysis of molecular variance results, and morphological analyses elucidated the role of vicariance versus dispersal hypotheses in population differentiation in the aforementioned river basin. Results In the A. bellottii species complex from the Paraná–Uruguay–La Plata river basin, past allopatric fragmentation from vicariance events seems to be the most plausible scenario for diversification since the Late Miocene and more recently since the Plio‐Pleistocene. The Plio‐Pleistocene vicariance produced the differentiation of three major clades in A. bellottii populations. One clade from the eastern Uruguay River drainage was separated from another in western Uruguay and the Paraná–La Plata River drainages. A later vicariance event split populations to the south (lower Paraná–La Plata Basin) and north (middle Paraná) of the western Paraná River drainage. However, our results do not exclude the possibility of dispersal events among A. bellottii populations from both the Uruguay and Paraná river drainages, which could occur in these river basins during hypothesized connectivity cycles of the Late Pliocene and Pleistocene. Main conclusions Past allopatric fragmentation caused by different vicariance events seems to be the main driver of diversification in the A. bellottii species complex since the Plio‐Pleistocene. However, the current molecular data suggest that populations from both drainages of the Paraná–Uruguay rivers may have experienced cycles of connectivity during the Pleistocene, perhaps including multiple vicariance or dispersal events from populations located in the western lower Uruguay River drainage, which encompassed climatic and geological changes in the Paraná–Uruguay–La Plata Basin.     

Genetic structure of the Iberian chub,Leuciscus pyrenaicus,in the Tejo drainage

The pattern of genetic variation in 38 samples of Leuciscus pyrenaicus, from seven sites in the Tejo drainage sampled on six occasions (over 19 months), were examined electrophoretically at 12 variable loci. Significant levels of spatial subdivision were observed. In general, the genetic distances in a river, were smaller than those between rivers. The differences observed suggest that isolation-by-distance is one important factor responsible for the spatial genetic differentiation. Moreover, the genetic diversity of this species in the Tejo drainage seems to be influenced by habitat heterogeneity, i.e., upland and lowland rivers. In opposition to other cyprinid species inhabiting the same drainage, the disruption of connectivity between populations above and below dams was not confirmed. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic variation of European grayling (Thymallus thymallus) populations in the Western Balkans

In order to elucidate genetic composition of European grayling (Thymallus thymallus) populations in the Western Balkans, the partial mitochondrial DNA (mtDNA) control region was sequenced and 12 microsatellite loci genotyped in 14 populations originating from tributaries of the Adriatic and Danube drainages. Eleven mtDNA haplotypes were found, one confined to the Adriatic clade, one to the Alpine group and the rest to the ‘Balkan’ grayling phylogenetic clade. Haplotypes from the Balkan clade were confined to the Danube drainage and constituted two groups: northern group with haplotypes found in the Slovenian part of the Danube drainage, and southern group, consisting from Bosnia–Herzegovina and Montenegro. Substantial genetic distance between northern and southern groups of haplotypes (0.75–1.8%) and well supported divisions within the northern group indicate very structured grayling population within the studied Danube basin that most probably did not evolve due to vicariance but rather as a consequence of multiple colonization waves that might have occurred during the Pleistocene. Furthermore, genetic distance of ~4% between Adriatic and Danube populations’ haplotypes, suggest that their separation occurred in mid-Pliocene. These findings imply a complex colonization pattern of the Western Balkans drainages. Microsatellite data also confirm high genetic diversity in Western Balkans populations of grayling (on average 7.5 alleles per microsatellite locus and H _exp 0.58). Limited stocking activities were detected based on microsatellites and mtDNA data. Regarding current knowledge of grayling phylogeography appropriate management strategies were proposed to preserve unique, autochthonous grayling populations in Western Balkan.     

Population genetics of the freshwater mussel, <Emphasis Type="Italic">Amblema plicata</Emphasis> (Say 1817) (Bivalvia: Unionidae): Evidence of high dispersal and post-glacial colonization

Over 70% of North American freshwater mussel species (families Unionidae and Margaritiferidae) are listed as threatened or endangered. Knowledge of the genetic structure of target species is essential for the development of effective conservation plans. Because Ambelma plicata is a common species, its population genetic structure is likely to be relatively intact, making it a logical model species for investigations of freshwater mussel population genetics. Using mtDNA and allozymes, we determined the genotypes of 170+ individuals in each of three distinct drainages: Lake Erie, Ohio River, and the Lower Mississippi River. Overall, within-population variation increased significantly from north to south, with unique haplotypes and allele frequencies in the Kiamichi River (Lower Mississippi River drainage). Genetic diversity was relatively low in the Strawberry River (Lower Mississippi River drainage), and in the Lake Erie drainage. We calculated significant among-population structure using both molecular markers (A.p. Φ_st = 0.15, θ_st = 0.12). Using a hierarchical approach, we found low genetic structure among rivers and drainages separated by large geographic distances, indicating high effective population size and/or highly vagile fish hosts for this species. Genetic structure in the Lake Erie drainage was similar to that in the Ohio River, and indicates that northern populations were founded from at least two glacial refugia following the Pleistocene. Conservation of genetic diversity in Amblema plicata and other mussel species with similar genetic structure should focus on protection of a number of individual populations, especially those in southern rivers.     

Migration patterns counteract seasonal isolation of <Emphasis Type="Italic">Squalius torgalensis</Emphasis>, a critically endangered freshwater fish inhabiting a typical Circum-Mediterranean small drainage

Freshwater species with small distribution ranges are vulnerable to extinction, especially when they exhibit small effective population sizes. Squalius torgalensis, Cyprinidae, is an endemic critically endangered fish species from southwestern Portugal, confined to the intermittent streams of the Mira drainage. Assessment of genetic diversity and population structure levels was conducted through the analysis of both mitochondrial (cytochrome b) and nine nuclear microsatellite markers. Remarkable low levels of genetic diversity for both markers were observed (He < 0.38, π < 0.001). These results may be related with the restricted distribution range and dispersion patterns of the species together with demographic fluctuations associated with the intermittent features of the river system. Population structure analyses suggest the existence of two incipient divergent populations; one comprising the tributaries located upstream and the other comprising downstream tributaries of the Mira River. Data also supports the occurrence of high gene flow mainly from downstream to upstream, failing to reflect isolation of populations due to seasonal drought. Obtained results should be incorporated in future management plans for the species. These should be centred around the current connection between populations and on the maintenance of suitable habitat patches, not only for reproduction, but also for summer refuges.     

Phylogeography of the freshwater fish, Mogurnda adspersa, in streams of northeastern Queensland, Australia: evidence for altered drainage patterns

A phylogeographic survey was used to elucidate the relative roles of historical processes and contemporary gene flow in structuring the genetic pattern observed with Mogurnda adspersa. This species of freshwater fish is found in the rivers and streams of the northeastern highlands of Queensland, Australia. Specifically, this project focused on populations in the Tully and Herbert Rivers in the Atherton Tablelands. Sequence analysis indicated that three distinct clades exist in the headwaters of the Tully River. The population sampled from one of the Tully River streams (Cheetah Creek) contained haplotypes that displayed ≈ 3.4% sequence divergence from other haplotypes detected in this river. Furthermore, these haplotypes formed part of the clade which exists throughout not only the Herbert River but other surrounding drainages in the area. These results support the hypothesis that the current genetic structure is strongly affected by changes in drainage patterns due to geomorphological processes that occurred in the recent past.     

Genetic diversity and population structure of the endangered ripon barbel,Barbus altianalis (Boulenger, 1900) in Lake Victoria catchment,Kenya based on mitochondrial DNA sequences

Approximately 850 bp of the mitochondrial control region was used to assess the genetic diversity, population structure and demographic expansion of the endangered cyprinid Barbus altianalis, a species known to be potamodramous in the Lake Victoria drainage system. The 196 samples taken from the four main rivers draining the Lake Victoria catchment (Nzoia, Yala, Nyando and Sondu–Miriu) yielded 49 mitochondrial DNA haplotypes; 83.7% thereof were private haplotypes restricted to particular rivers. The overall mean haplotype diversity was high (0.93663 ± 0.008) and ranged between 0.566 (Sondu – Miriu) and 0.944 (Nzoia). The overall mean nucleotide diversity was low (0.01322 ± 0.00141), ranging from 0.0342 (Sondu – Miriu) to 0.0267 (Nzoia). Population differentiation tests revealed strong and highly significant (P ≤ 0.001) segregation of populations in the four river basins. F_ST values among the four river‐based populations ranged from 0.05202 to 0.44352. The samples formed two main haplotype networks based on a 95% parsimony criterion, each exhibiting a strong signature of past population expansion. The smaller network was restricted to the River Nzoia, whereas the larger network contained representatives from all four rivers; within this the central haplotypes were found in more than one river, whereas the peripheral haplotypes tended to be river‐specific. The degree of population differentiation and the number of river‐specific haplotypes are too high to be explained by recent anthropogenic impacts alone and suggest that the species has probably existed in the Lake Victoria catchment as two populations: the now ‘extinct’ migratory population and the extant river restricted non‐migratory populations.