Microsatellite DNA Population Structure and Stock Identification of Steelhead Trout (<Emphasis Type="BoldItalic">Oncorhynchus mykiss</Emphasis>) in the Nass and Skeena Rivers in Northern British Columbia

Population structure and the application to genetic stock identification for steelhead (Oncorhynchus mykiss) in the Nass and Skeena Rivers in northern British Columbia was examined using microsatellite markers. Variation at 8 microsatellite loci (Oki200, Omy77, Ots1, Ots3, Ssa85, Ots100, Ots103, and Ots108) was surveyed for approximately 930 steelhead from 7 populations in the Skeena River drainage and 850 steelhead from 10 populations in the Nass River drainage, as well as 1550 steelhead from test fisheries near the mouth of each river. Differentiation among populations within rivers accounted for about 1.9 times the variation observed among years within populations, with differences between drainages less than variation among populations within drainages. In the Nass River, winter-run populations formed a distinct group from the summer-run populations. Winter-run populations were not assessed in the Skeena River watershed. Simulated mixed-stock samples suggested that variation at the 8 microsatellite loci surveyed should provide relatively accurate and precise estimates of stock composition for fishery management applications within drainages. In the Skeena River drainage in 1998, Babine River (27%) and Bulkley drainage populations (31%) comprised the main components of the returns. For the Nass River in 1998 steelhead returning to Bell-Irving River were estimated to have comprised 39% of the fish sampled in the test fishery, with another 27% of the returns estimated to be derived from Cranberry River. The survey of microsatellite variation did not reveal enough differentiation between Nass River and Skeena River populations to be applied confidently in estimation of stock composition in marine fisheries at this time. Received January 14, 2000; accepted July 13, 2000.     

Historical process lead to false genetic signal of current connectivity among populations

Identification of the effects of historical processes on spatial genetic variation is of major importance in landscape genetics, especially in recent systems where the signal of recent isolation is often hardly perceptible. The goal of this study was to assess how differences in colonization patterns could influence spatial genetic variation using two centrarchidae species, the pumpkinseed sunfish (Lepomis gibbosus) and the rock bass (Ambloplites rupestris), from two adjacent drainage systems. The striking difference between the spatial genetic variations of the two species suggests completely opposite patterns of colonization. Rock bass colonized the drainage system from a downstream source, which resulted in a loss of diversity in upstream populations and a strong differentiation between drainage systems. In contrast, the reduction of genetic diversity and increase of differentiation toward downstream populations that were observed among sunfish populations suggest colonization from upstream to downstream. The colonization pattern observed in sunfish, which result in low differentiation between upstream most sites of the two drainages, leads to a false genetic signal of current inter-drainage gene flow. The present study demonstrates through empirical evidence that colonization patterns may impede the capacity to estimate current connectivity.     

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.     

Past and present patterns of connectivity among populations of four cryptic species of freshwater mussels Velesunio spp. (Hyriidae) in central Australia

We examined genetic structure and levels of connectivity among subpopulations within each of four cryptic species belonging to the freshwater mussel genus Velesunio. We used allozymes and a fragment of the mitochondrial cytochrome c oxidase I gene to examine genetic variation in populations from isolated waterholes, belonging to four major inland drainages in eastern Australia. Based on evidence from other invertebrates in the region we predicted that, in each species, we would find evidence of historical connectivity among populations from different drainages. This was clearly not the case, as for the two species that occurred in more than one drainage there was evidence of both current and past restriction to gene flow. Moreover, given the potential for extensive dispersal of these mussels through the river systems during flood times via their fish hosts, we predicted low levels of genetic variation among populations from waterholes in the same drainage. Contrary to our expectations, all four species showed some evidence of restricted gene flow among waterholes within drainages. This suggests that either (a) mussel larvae are not produced during flood times, when their fish hosts would be free to move between waterholes, or (b) mussel larvae are attached to their hosts at these times, but the fish movement is limited between waterholes.     

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.     

Geographic variation in Austrolebias luteoflamulatus Vaz‐Ferreira, Sierra & Scaglia (Cyprinodontiformes, Rivulidae)

The morphological variation in the annual killifish Austrolebias luteoflamulatus was studied using meristic and pigmentation characters analysed with univariate and multivariate analysis, and morphometric characters analysed with a geometric morphometry approach (thin plate spline). The results showed that morphological variation in this species was associated with a geographical pattern. In the case of meristic and pigmentation characters, the strongest distinction occured in males, while females were more similar among different drainages. Males from Rocha (eastern Uruguay) exhibited the greatest differences from the others. The number of dorsal fin rays and bars on the flanks were the characters that contributed most to this segregation. When morphometrics were considered, the three populations analysed could be distinguished well from each other in both sexes. Some of the characters that contributed to this pattern were dorsal fin origin, position of eyes and length of snout. Since pigmentation characteristics and some characters of the dorsal fin in males were involved in the differences observed, sexual selection could have played an important role in the differentiation of populations of this species. Since Austrolebias luteoflamulatus has a restricted geographical distribution, conservation of this species should include consideration of these populations individually since they might represent different evolutionary units.     

Spatial heterogeneity in the parasite communities of creek chub (Semotilus atromaculatus) in southeastern Nebraska

The intestinal helminth communities of creek chub (Semotilus atromaculatus) were studied in the streams of southeastern Nebraska to characterize spatial variation, to determine whether drainages act as regional species pools, and to examine the spatial patterning of individual parasite species within and among drainages. Creek chub were sampled in the summer of 2003 and the spring of 2004 at each of 12 sites distributed evenly among 3 drainages in the Big Nemaha River watershed. Four intestinal helminths were recovered: Allocreadium lobatum, Proteocephalus sp., Rhabdochona canadensis, and Paulisentis missouriensis. Host size had little or no effect on the composition of the parasite communities of creek chub, either among individual fish or among samples. In contrast, drainage and sample date explained 82% of the variation in mean infracommunity species richness among samples, and 62% of the variation in mean infracommunity abundance among samples. Drainage differences were determined by the distributions of P. missouriensis and R. canadensis; whereas, A. lobatum and Proteocephalus sp. were more uniformly distributed among drainages. Each drainage was characterized by a unique pattern of species diversity at infracommunity, component community, and drainage levels of organization.     

Mitochondrial DNA evidence for high levels of gene flow among populations of a widely distributed anadromous lamprey Entosphenus tridentatus (Petromyzontidae)

Mitochondrial DNA variation among 1246 individuals of Pacific lamprey ( Entosphenus tridentatus ) from 81 populations spanning 2600 km from the Skeena River, British Columbia, to the Ventura River, California, was surveyed using five restriction enzymes. A total of 29 composite haplotypes was detected in two gene fragments (ND2 and ND5). The three most common haplotypes, occurring in 91% of all samples, were present at similar frequencies in all regions. Samples were divided into six biogeographic regions based on sample distribution and geographical landmarks to assess geographic genetic structure. Analysis of molecular variance indicated that 99% of the genetic variation was explained by variability within drainages. The lack of geographical population structure is likely related to a life-history pattern that includes a prolonged larval freshwater stage, migration to oceanic feeding and return to fresh water to spawn. The lack of strong natal homing apparently promotes gene flow among drainages and regions.     

Hybridization among divergent stocks of largemouth bass (Micropterus salmoides) results in altered cardiovascular performance: the influence of genetic and geographic distance

Animal populations exhibit wide ranges of divergence associated with both geographic and genetic distances. Here, we examined the role of crossing distance on the cardiovascular response to exhaustive exercise among differentiated stocks of largemouth bass Micropterus salmoides at 10 degrees C and 20 degrees C. Stocks of 2+ fish were produced using adults from three regions in the midwestern United States (southeastern Wisconsin, northwestern Wisconsin, and west central Minnesota) and were crossed with fish from central Illinois. Doppler flow probes were used to quantify cardiac output, heart rate, and stroke volume. Cardiac variables (both resting and maximal) were consistently lowest in pure Illinois fish relative to the F(1) interstock hybrids. Additionally, when exposed to exercise, cardiac variables for F(1) interstock hybrids required approximately 40% longer to return to resting levels compared with the pure Illinois stock. However, the time required to exhaust fish was similar across stocks. Interestingly, all of the stocks (including the interstock hybrids and pure Illinois) maintained cardiac scope. In general, the patterns observed in cardiovascular performance were consistent for both water temperatures. Multiple regression analysis was used to determine which of the divergence metrics contributed to variation in cardiovascular performance in interstock hybrids. Mitochondrial DNA data (genetic distance) were infrequently identified as a significant source of variation in cardiovascular performance. However, genetic distance data for the neutral allozyme markers revealed that these stocks have experienced significant divergence. Latitude (geographic distance) accounted for between 31% and 45% of variation observed in the recovery parameters. This study suggests that the magnitude of stock divergence is an important determinant in the degree to which cardiovascular performance of bass is altered from interstock hybridization and associated breakdown of coadapted gene complexes. Furthermore, these data suggest that translocating bass among even geographically discrete regions or among stocks with reasonable genetic similarity can result in substantial performance alterations at the F(1) generation.     

Differences in morphological growth trajectories between greenside darter Etheostoma blennioides populations from two distinct drainages

The greenside darter Etheostoma blennioides is a small-bodied benthic stream fish that occurs in multiple drainages of the eastern USA. Previous studies have revealed some morphological differentiations among greensides from isolated drainage systems but growth relationships among functional morphological characteristics have not been examined within and between populations. Specifically, we tested for differences in functional morphology and allometric distinctions in morphological growth trajectories between greenside populations from two drainages, the Osage River and White River. Morphological differences between individuals of the two drainages included more dorso-ventrally compressed bodies, longer snouts and larger jaw features in White River darters. Furthermore, body depth, snout length and jaw width grow at significantly different trajectories in individuals of the two drainages. Individuals of the White River drainage (generally a higher gradient stream system) become comparatively more streamlined and develop proportionately larger feeding related traits during growth. These results suggest that individuals of both drainages share a similar morphology during early life but deviate during continued development and this may be partially due to environmentally induced plastic response. This study represents a novel approach for comparing morphological development among fish populations and presents environmental factors (e.g., stream gradient and elevation) that potentially influence functional characteristics.     

Microsatellite DNA markers developed for the Australian bass (Macquaria novemaculeata) and their cross‐amplification in estuary perch (Macquaria colonorum)

The Australian bass is a catadromous species found in drainages of southeastern Australia. As an economically important resource that is declining in number, the Australian bass is currently extensively stocked in New South Wales and Victoria to meet the requirements of fisheries programs. We have developed six microsatellite markers that amplify in both Australian bass and the congeneric estuary perch. These markers are useful for investigating population genetic structure and for identifying hybrids between these two species.     

Unrecognized and imperilled diversity in an endemic barb (Smiliogastrini,Enteromius) from the Fouta Djallon highlands

The Upper Guinean Forests of Guinea, Sierra Leone and Liberia contain high levels of freshwater biodiversity. The Guinean Range and associated Fouta Djallon highlands separate two biogeographical provinces in the region and served as a refugium during past climatic fluctuations. While many species of freshwater fishes are restricted to one biogeographical province or the other, some are reported to occur on both sides of the divide. Here, we examine the molecular and morphological diversity of an endemic small African barb, Enteromius foutensis, reported to occur in both provinces. This integrative analysis revealed unrecognized diversity and suggests recent, or ongoing, events that facilitated geodispersal and subsequent divergence in the region. The molecular analysis revealed three divergent and well‐supported populations within E. foutensis. Accounting for allometric shape variation allowed us to observe diagnostic morphological differences among the populations. Enteromius foutensis sensu stricto is restricted to the Little Scarcies drainage in Guinea and northern Sierra Leone. Our study revealed two candidate species distinct from E. foutensis. One is likely a narrow endemic restricted to a small area in the Konkouré River basin; the other candidate species inhabits the upper Senegal and Gambie River drainages. How these patterns of diversity compare with other freshwater species from the Fouta Djallon highlands and the conservation status of these candidate species are also discussed.     

Modern human cranial diversity in the Late Pleistocene of Africa and Eurasia: Evidence from Nazlet Khater,Peştera cu Oase,and Hofmeyr

The origin and evolutionary history of modern humans is of considerable interest to paleoanthropologists and geneticists alike. Paleontological evidence suggests that recent humans originated and expanded from an African lineage that may have undergone demographic crises in the Late Pleistocene according to archaeological and genetic data. This would suggest that extant human populations derive from, and perhaps sample a restricted part of the genetic and morphological variation that was present in the Late Pleistocene. Crania that date to Marine Isotope Stage 3 should yield information pertaining to the level of Late Pleistocene human phenotypic diversity and its evolution in modern humans. The Nazlet Khater (NK) and Hofmeyr (HOF) crania from Egypt and South Africa, together with penecontemporaneous specimens from the Pe?tera cu Oase in Romania, permit preliminary assessment of variation among modern humans from geographically disparate regions at this time. Morphometric and morphological comparisons with other Late Pleistocene modern human specimens, and with 23 recent human population samples, reveal that elevated levels of variation are present throughout the Late Pleistocene. Comparison of Holocene and Late Pleistocene craniometric variation through resampling analyses supports hypotheses derived from genetic data suggesting that present phenotypic variation may represent only a restricted part of Late Pleistocene human diversity. The Nazlet Khater, Hofmeyr, and Oase specimens provide a unique glimpse of that diversity. Am J Phys Anthropol, 2009. © 2009 Wiley‐Liss, Inc.     

Hierarchical organization of genetic variation in the Costa Rican livebearing fish Brachyrhaphis rhabdophora (Poeciliidae)

I examined the geographic distribution of genetic variation in the livebearing freshwater fish Brachyrhaphis rhabdophora in northwestern Costa Rica as revealed by allozymes and mitochondrial DNA sequences. Allelic variability at 11 enzyme-coding loci surveyed across 12 localities revealed marked genetic differentiation among populations within drainages (0_P= 0.36) and among drainages within regions (0_D=0.17), but not between northern and southern geographic regions (0_R=– 0.02). Allozyme variation was hierarchically organized such that populations found within stream drainages were more similar to each other than to populations found in adjacent drainages, a result confirmed by cluster analysis. In contrast to the allozyme data, there was extremely little DNA sequence variation among populations in the mitochondrial control region (3 variable nucleotide positions out of 444 bp examined). The difference in genetic divergence between allozyme and mtDNA markers was unexpected and is discussed in terms of biogeographical colonization events and a molecular selective swéep on the mitochondrial genome, both processes that could explain the lack of mitochondrial variability in this highly subdivided species.     

Predator-prey interactions in size-structured fish communities: implications of prey growth

Predator-prey interactions among size-structured populations may be strongly influenced by factors which affect growth rates of prey. I examined the importance of prey growth in the interaction between large-mouth bass (Micropterus salmoides) and their prey, bluegill (Lepomis macrochirus), by analyzing diets and growth rates of bass in a set of seven lakes in south-central Wisconsin. Sizes of bluegill consumed by bass changed dramatically across a gradient of bluegill growth, which resulted in differing patterns of bass growth. In lakes with slow bluegill growth, small bass fed on the youngest bluegill cohort, but large bass were capable of feeding on several age classes. Consequently, bass growth rates were strongly size-dependent; small bass ate small prey and had low growth, but growth rates increased substantially with size as bass ate progressively larger prey. When bluegill had high growth rates, they quickly reached a size refuge from predation and bass of all sizes were restricted to feeding on the youngest/smallest prey. In these lakes, bass growth rates were more uniform across bass sizes. Because growth rates influence population size-distributions, variation in bluegill growth can have strong effects on the structure of bass populations. These effects could potentially feed back to further influence the interaction between predator and prey.     

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.     

SNP panel development for genetic management of wild and domesticated white bass (Morone chrysops)

White bass (Morone chrysops), striped bass and their interspecific hybrid are important game fishes, whereas the hybrid striped bass is an important aquaculture species in the US. Numerous state, federal and private hatcheries, therefore, rear these species for stocking purposes as well as for food fish. Although striped bass populations (both wild and domesticated) have been extensively evaluated, relatively little effort has been directed toward the study and improvement of white bass. In this study, we developed SNP resources to examine the genetic relationships among a long‐term domesticated white bass line and five potential founder stocks for selective breeding collected from drainages in Arkansas, Texas and Alabama. Using genotyping‐by‐sequencing, we generated 13 872 genome‐wide SNP loci across the six populations. Stringent filtering of SNP‐calling parameters identified 426 informative SNP loci. Population genetic and structure analyses using these loci revealed only moderate genetic differentiation between populations (global F_st = 0.083) and indicated two major genetic clusters. A final 57‐SNP assay was successfully designed and validated using the MassARRAY system. The developed SNP panel assigned 96 additional genotyped individuals to their population of origin with 100% accuracy. The SNP resources developed in this study should facilitate ongoing efforts in selective breeding and conservation of white bass.     

Phenotypic consequences of genetic variation in a gynogenetic complex of Phoxinus eos-neogaeus clonal fish (Pisces: Cyprinidae) inhabiting a heterogeneous environment

We examined the genetic composition, habitat use, and morphological variation of a Phoxinus eos-neogaeus unisexual hybrid complex and its sexually reproducing progenitor species inhabiting beaver-modified drainages of Voyageurs National Park, Minnesota. In addition to the single diploid P. eos-neogaeus gynogenetic clone, triploid and diploid-triploid mosaic biotypes were present at our study sites. Both P. eos and P. neogaeus, and all three hybrid biotypes were ubiquitous throughout one intensively surveyed drainage, but abundances and relative frequencies of the parental species and hybrids varied considerably within and among successional environments. Data from a large number of additional sites indicated that the proportion of polyploid hybrids within an environment was negatively related to hybrid relative frequency, implying that the genomic constitution of hybrids is an important determinant of clonal fitness among successional environments. Statistical comparisons of variation along size-free multivariate body shape axes indicated that despite its genetic uniformity, the P. eos-neogaeus clone is no less variable than its sexual progenitors, suggesting that a single genotype may actually respond to environmental variation with as much phenotypic variation as a genetically variable sexual population. The incorporation and expression of a third genome in triploid and diploid-triploid mosaic biotypes derived from the gynogenetic clone significantly expanded phenotypic variation of the clone. This additional variation results in greater similarities in habitat use and morphological overlap with the parental species, primarily P. eos, the predominant sperm donor for gynogenetic hybrid females in this complex. Polyploid augmentation of a diploid gynogenetic clone appears to be typical in the P. eos-neogaeus complex, and the additional genetic and phenotypic variation that it generates has potentially significant ecological and evolutionary consequences for the success and persistence of a single genotype in highly variable environments.     

Age, phylogeography and population structure of the microendemic banded spring snail, Mexipyrgus churinceanus

Recent theoretical and empirical studies of phylogeography and population structure indicate that many processes influence intraspecific evolutionary history. The present study represents the first examination of various forces influencing the spatial and temporal patterns of sequence variation in the freshwater Mexican banded spring snail, Mexipyrgus churinceanus. This snail occurs in one of the most critically endangered centres of freshwater endemism, the desert ecosystem of Cuatro Ciénegas. From cytochrome b mtDNA sequence variation, there is strong evidence of long-term isolation of three regions, suggesting that these regions represent evolutionarily distinct lineages. Molecular clock estimates of clade age indicate a time to most recent common ancestor of approximately 2.5 million years ago (Ma). The three regions differ considerably in the historical and demographic forces affecting population structure. The western populations have extremely low mtDNA diversity consistent with a severe bottleneck dating to 50,000 years before present (bp). The nearby Rio Mesquites drainage is characterized by fragmentation events, restricted gene flow with isolation by distance, and higher levels of mtDNA polymorphism. These patterns are consistent with the long-term stability of this drainage along with habitat heterogeneity and brooding contributing to population isolation and restricted gene flow. Southeastern populations show evidence of range expansion and a strong influence of genetic drift. Migration rates between drainages indicate very little gene flow between drainages except for asymmetric migration from the Rio Mesquites into both western and southeastern drainages.     

花鲈群体的遗传变异

采用水平淀粉凝胶电泳技术对花鲈群体的遗传结构进行了研究 ,共检测了中国沿海花鲈 14 6尾和 40尾日本东京湾花鲈。其群体的多态位点比例为 0 2 667— 0 53 3 3 ,观测杂合度和预期杂合度分别为 0 0 2 11— 0 0 515和0 0 3 98— 0 0 797。中日花鲈在LDH ,GPI 1 ,GPI 2 基因位点上的等位基因接近完全置换。中国花鲈各群体之间的根井遗传距离为 0 0 0 0 4— 0 0 0 11,平均值约为 0 0 0 80 ;而中日花鲈间的根井遗传距离为 0 1870— 0 1954,平均值为 0 192 6。以上结果表明中国花鲈群体间遗传变异很小 ,中日花鲈间遗传变异远大于中国花鲈群体间的遗传距离。