Contemporary factors influencing genetic diversity in the Alaska humpback whitefish Coregonus clupeaformis complex

Thirteen microsatellite loci were used to address three hypotheses regarding genetic diversity in the humpback whitefish Coregonus clupeaformis complex in Alaska. The test results provided further insight into the factors influencing C. clupeaformis complex population structure and level of genetic variation. First, the microsatellite data did not provide evidence of two spatially distinct Beringian and Eurasian refugial groups as revealed in previous phylogeographic analyses of mitochondrial DNA variation. Rather, the population structure inferred from the microsatellite variation appears to reveal the influence of factors on a more recent time scale, including gene flow among the refugial groups and isolation of some anadromous and freshwater resident populations. Second, anadromous C. clupeaformis complex collections exhibited higher intra‐population genetic diversity than freshwater resident collections. This outcome is consistent with previous meta analyses suggesting that freshwater resident populations probably have smaller historical effective population sizes and less conspecific gene flow because the habitat tends to be smaller and supports fewer and smaller populations. Finally, the analysis of contemporary immigration rates was consistent with, but did not provide statistical support for, the hypothesis that gene flow among anadromous C. clupeaformis complex populations along coastal Alaska is influenced by the Alaska Coastal Current. Further studies are needed to evaluate gene flow among coastal Alaska C. clupeaformis complex populations.     

Geographic variation in otolith morphology among freshwater populations of Aphanius dispar (Teleostei,Cyprinodontiformes) from the southeastern Arabian Peninsula

Aphanius Nardo is a large genus of teleost fishes in the Old World, with 19 described species. Several of these species have only recently been recognized and additional species can be expected from isolated populations in remote areas. We show here that otolith morphology and statistical analyses of otolith variables can contribute to the detection of genetic differentiation in Aphanius. We studied samples of eight Aphanius dispar populations from the southeastern part of the Arabian Peninsula. Two populations originate from freshwater habitats far inland and probably have been isolated since the late Holocene some 4,000 years ago, three populations come from freshwater habitats with occasional connections to the sea, one population originates from a coastal site, and two were artificially introduced populations. The coastal population is interpreted as possessing the basic otolith type of A. dispar. The basic otolith type also occurs in fishes from the freshwater habitat which is located closest to the coast. Otoliths from the two other freshwater populations with occasional connections to the coast differ slightly from the basic type. However, the two populations from the long‐term isolated freshwater habitats far inland show distinct morphological changes. Our results are consistent with the hypotheses that i) otolith morphology is primarily genetically determined and is little influenced by physical parameters of the habitat, and ii) isolated A. dispar populations may be capable of evolving into new species within short periods of time. J. Morphol., 2009. © 2008 Wiley‐Liss, Inc.     

The effect of migratory behaviour on genetic diversity and population divergence: a comparison of anadromous and freshwater Atlantic salmon Salmo salar

The genetic diversity of anadromous and freshwater Atlantic salmon ( Salmo salar ) populations from north-west Russia and other north European locations was compared using microsatellite variation to evaluate the importance of anadromous migration, population size and population glacial history in determining population genetic diversity and divergence. In anadromous Atlantic salmon populations, the level of genetic diversity was significantly higher and the level of population divergence was significantly lower than among the freshwater Atlantic salmon populations, even after correcting for differences in stock size. The phylogeographic origin of the populations also had a significant effect on the genetic diversity characteristics of populations: anadromous populations from the basins of the Atlantic Ocean, White Sea and Barents Sea possessed higher levels of genetic diversity than anadromous populations from the Baltic Sea basin. Among the freshwater populations, the result was the opposite: the Baltic freshwater populations were more variable. The results of this study imply that differences in the level of long-term gene flow between freshwater populations and anadromous populations have led to different levels of genetic diversity, which was also evidenced by the hierarchical analysis of molecular variance. Furthermore, the results emphasize the importance of taking the life history of a population into consideration when developing conservation strategies: due to the limited possibilities for new genetic diversity to be generated via gene flow, it is expected that freshwater Atlantic salmon populations would be more vulnerable to extinction following a population crash. Hence, high conservation status is warranted in order to ensure the long-term survival of the limited number of European populations with this life-history strategy.     

Anadromy and heterogenous population of a tropical shad Tenualosa ilisha in Malaysia,as revealed by otolith microchemistry and molecular evidence

Tenualosa ilisha was found recently in the Perak River in western Peninsular Malaysia. Molecular phylogenetic and haplotype network analyses suggest that T. ilisha has two genetically distinct populations/groups: (i) Peninsular Malaysia (Malaysia population), and (ii) Peninsular Malaysia, Thailand, India and Bangladesh (Indian Ocean population). The results also suggest that the T ilisha population in Peninsular Malaysia is genetically heterogeneous with a typical anadromous migration pattern.     

Independent evolutionary origins of landlocked alewife populations and rapid parallel evolution of phenotypic traits

Alewife, Alosa pseudoharengus, populations occur in two discrete life-history variants, an anadromous form and a landlocked (freshwater resident) form. Landlocked populations display a consistent pattern of life-history divergence from anadromous populations, including earlier age at maturity, smaller adult body size, and reduced fecundity. In Connecticut (USA), dams constructed on coastal streams separate anadromous spawning runs from lake-resident landlocked populations. Here, we used sequence data from the mtDNA control region and allele frequency data from five microsatellite loci to ask whether coastal Connecticut landlocked alewife populations are independently evolved from anadromous populations or whether they share a common freshwater ancestor. We then used microsatellite data to estimate the timing of the divergence between anadromous and landlocked populations. Finally, we examined anadromous and landlocked populations for divergence in foraging morphology and used divergence time estimates to calculate the rate of evolution for foraging traits. Our results indicate that landlocked populations have evolved multiple times independently. Tests of population divergence and estimates of gene flow show that landlocked populations are genetically isolated, whereas anadromous populations exchange genes. These results support a 'phylogenetic raceme' model of landlocked alewife divergence, with anadromous populations forming an ancestral core from which landlocked populations independently diverged. Divergence time estimates suggest that landlocked populations diverged from a common anadromous ancestor no longer than 5000 years ago and perhaps as recently as 300 years ago, depending on the microsatellite mutation rate assumed. Examination of foraging traits reveals landlocked populations to have significantly narrower gapes and smaller gill raker spacings than anadromous populations, suggesting that they are adapted to foraging on smaller prey items. Estimates of evolutionary rates (in haldanes) indicate rapid evolution of foraging traits, possibly in response to changes in available resources.     

Genetic structure of threespine stickleback,Gasterosteus aculeatus,in Lake Harutori,Japan, with reference to coexisting anadromous and freshwater forms

Both anadromous and freshwater forms of threespine sticklebacks (Gasterosteus aculeatus) inhabit Lake Harutori on the pacific coast of eastern Hokkaido, Japan. Since the two groups of threespine sticklebacks, Pacific Ocean and Japan Sea groups, which showed high genetic differentiation between them, were sympatrically distributed on the Pacific Ocean coast of Hokkaido Island, the genetic structures of the two forms were examined in Lake Harutori. Allozyme analyses of the two forms showed that most specimens from Lake Harutori belonged to the Pacific Ocean group, with a few fish belonging to the Japan Sea group or representing hybrids between the two groups. Both anadromous and freshwater sticklebacks were detected in the Pacific Ocean group. There were no significant differences in allelic frequencies at 17 presumptive loci between the two forms. Analyses of genetic relationships among 5 populations showed that the freshwater population from Lake Harutori was genetically more closely related to the sympatric anadromous population than to the freshwater population from a neighboring river. These results suggested that anadromous and freshwater sticklebacks in Lake Harutori form a single breeding population, and that the two forms might represent a life-history polymorphism within a single population.     

Molecular and morphological divergence in the inland silverside (<Emphasis Type="Italic">Menidia beryllina</Emphasis>) along a freshwater-estuarine interface

Populations that vary across ecological gradients or that have invaded novel habitats are important to elucidate the association between adaptive divergence and gene flow, factors that may play an important role in speciation of silverside fishes. The inland silverside, Menidia beryllina, is an ideal organism for this kind of research, displaying a great diversity in morphology among freshwater and coastal brackish habitats. Using a combination of geometric morphometrics and mitochondrial (mt) DNA, we investigated patterns of variation within and among the nominal freshwater Menidia audens and coastal M. beryllina, spanning the transition from freshwater to tidally influenced semi-brackish waters of the lower Mississippi River to brackish waters of the Lake Pontchartrain estuary. Although we found no evidence for a phylogenetic split between M. audens and M. beryllina, our results indicate that significant genetic divergence corresponds with body shape differences among the two, with a clear distinction at the interface of freshwater and brackish water. Patterns in mtDNA suggest that freshwater populations referred to as M. audens are of recent origin with evidence for habitat-based divergence compared to coastal populations referred to as M. beryllina. Our findings add to a growing body of evidence that ecological shifts, following colonization of novel habitats, may promote rapid adaptive divergence and reduced gene flow among silverside populations in adjacent environmental regimes.     

Rapid ecological speciation in three‐spined stickleback Gasterosteus aculeatus from Middleton Island,Alaska: the roles of selection and geographic isolation

Morphological analysis of three‐spined stickleback Gasterosteus aculeatus collected in Middleton Island, Alaska, was conducted in order to study how gene flow and selection interact during divergence. Middleton Island was uplifted by 3·4 m during the Great Alaska Earthquake in 1964; this event formed a series of new freshwater sites, triggering rapid evolution, and probably rapid speciation, in G. aculeatus populations that colonized them. The level of hybridization between the anadromous and the resident freshwater populations is reflected by the level of morphological variance of the resident freshwater G. aculeatus. Therefore, geographic isolation of the sites from the sea (approximating gene flow) and ionic concentration of the water (reflecting selection pressures) were correlated with morphological variance of the resident freshwater populations. Geographic isolation was negatively correlated with morphological variance in a majority of the analysed traits. Both selection and gene flow surrogates were found to be important influences on variance in morphology, though selection had a larger effect, especially on armour traits. It was concluded that gene flow appeared to constrain ecological speciation, but even in the presence of gene flow the strong selection in the freshwater environment was apparently leading to rapid divergence.     

Population genetics,conservation and evolution in salmonids and other widely cultured fishes: some perspectives over six decades

This paper explores my shifting understandings of interactions primarily between salmonid fish culture and fish conservation during the latter half of the 20th century. The idea that conspecific natural and cultured fish were largely interchangeable among phenotypically similar populations began to change with the advent of molecular genetic markers. With the gradual clarification of major geographic lineages beginning in the 1970s came awareness that translocations among anadromous lineages were generally destined for failure; in contrast, gene flow more readily occurred among non-anadromous lineages and sometimes, species. Within lineages, data concurrently were accumulating that showed adaptations to their respective environments distinguished cultured and wild populations. Reduced obstacles to gene flow at this level often resulted in homogenizations among wild and cultured fish in areas where widespread hatchery releases occurred; conversely, adaptive radiations in vacant habitats sometimes occurred over a few decades from single source hatchery releases. Current ideas relating to salmonid interbreeding, population substructure and culture evolved from these observations. Among lineages, resistance to gene flow is much greater between anadromous than purely freshwater populations or species. Within lineages, ease of gene flow in both anadromous and freshwater populations is problematical with regard to cultured and wild populations because large-scale supplementation programs erode local adaptations and fine-scale population substructures. At this level, a potential ability to regenerate natural substructure upon relaxation of supplementation is offset by uncertainties of time scales and intrinsic capabilities of homogenized populations. However, management that separates harvest and reproduction of wild and cultured subpopulations can minimize these losses. Some generality of this strategy to other fishes is supported by losses of local adaptations and outbreeding depression in black basses following population admixtures that parallel those observed in salmonids.     

Patterns of subspecific anthropogenic introgression in two salmonid genera

Introgressive hybridizations have often been observed between native and introduced trouts of North America (Oncorhynchus spp.) and Europe (Salmo spp.), including some lineages that have been isolated for more than a million years. These observations have suggested that introgression is the expected result between introduced and indigenous conspecific salmonids. However, an examination of published information reveals a high variability in such anticipated gene flow. Many studies have noted the relative ease of translocating freshwater over anadromous salmonids, and this difference has been related to the more complex adaptations of anadromous populations (e.g., freshwater and marine residence, smoltification, juvenile and adult migration) that obstruct their translocation to conspecifically colonized areas. This contrast extends to introgressive capabilities where examples of introgression among freshwater populations predominate. Despite intensive introductions of non-native salmonids, indigenous anadromous populations commonly resist introgression. However, within major lineages, anadromous populations appear to be more susceptible to introgression. Measuring the extent and dynamics of such introgressions remains challenging because subgroups within major lineages lie on or below the threshold for detection by molecular genetic markers. These substructures appear to reflect the more rapid evolution of directional selection promoting, for instance, temporal or microgeographic divergence within a population unit defined by genetic markers. Consequently, management that assumes panmixia within a particular region based on even intensive molecular genetic analysis will inevitably erode and prevent reformation of this substructure to the detriment of the overall genetic variability and productivity.     

Genetic structure of coastal and inland populations of <Emphasis Type="Italic">Spergularia media</Emphasis> (L.) C. Presl (Caryophyllaceae) in Central Europe

In Central Europe, salt-influenced habitats are restricted mainly to the coastlines of the North Sea and the Baltic Sea. The few natural inland salt sites suffer from size reduction and loss in biodiversity, while anthropogenic salt sites around potash mining dumps experienced recent and massive de novo colonization by numerous halophytes. Our study aimed to elucidate the general patterns of gene flow among coastal and inland salt habitats. We used amplified fragment length polymorphisms to assess the genetic diversity and genetic structure of 18 European populations of the halophyte Spergularia media (Caryophyllaceae), sampled from inland and coastal salt sites of Germany, the Netherlands, Denmark, Austria, France and Italy. Estimates of genetic diversity on the population level were generally low, especially within inland salt habitats. Analyses of molecular variance showed comparatively strong differentiation among populations. Multivariate ordination (principal coordinate analysis) and a NeighborNet analysis revealed four distinct groups of populations that showed good correspondence to their geographic origins. A Bayesian analysis performed with the program Structure as well as high pairwise Φ _ST values supported the results of the phenetic analyses. The observed patterns of diversity and differentiation among inland populations of S. media are best explained by the isolated nature of suitable salt habitats, with concomitant reduction of gene flow to and among these sites. Our data support the hypothesis that the colonization of anthropogenic salt sites by S. media originated from natural inland habitats.     

Low Phylogeographic Structure in a Wide Spread Endangered Australian Frog <Emphasis Type="Italic">Litoria aurea</Emphasis> (Anura: Hylidae)

The green and golden bell frog (Litoria aurea) has a widespread distribution along the south-east coast of Australia. The species range, however, is highly fragmented and remaining populations are predominately isolated and restricted to the coastline. Previously, the range extended further inland and the species was considered common. Here we report a study designed to identify the phylogeographic and conservation genetic parameters of L. aurea. Mitochondrial DNA sequences were examined from 263 individuals sampled from 26 locations using both phylogenetic and population analyses. Despite a general consensus that amphibians are highly structured we found no phylogeographic divisions within the species, however, there was significant structure amongst extant populations (F _ST=0.385). Patterns of haplotype relatedness, high haplotypic diversity (mean h=0.547) relative to low nucleotide diversity (mean π=0.003) and mismatch distribution analysis supported a Pleistocene expansion hypothesis with continued restricted dispersal and gene flow. We conclude that the genetic structure of the species may permit ‘well managed’ intervention to mediate gene flow amongst isolated populations and provide some guidelines for the implementation of such conservation strategies.     

Contrasting population genetic structure among freshwater‐resident and anadromous lampreys: the role of demographic history,differential dispersal and anthropogenic barriers to movement

The tendency of many species to abandon migration remains a poorly understood aspect of evolutionary biology that may play an important role in promoting species radiation by both allopatric and sympatric mechanisms. Anadromy inherently offers an opportunity for the colonization of freshwater environments, and the shift from an anadromous to a wholly freshwater life history has occurred in many families of fishes. Freshwater‐resident forms have arisen repeatedly among lampreys (within the Petromyzontidae and Mordaciidae), and there has been much debate as to whether anadromous lampreys, and their derived freshwater‐resident analogues, constitute distinct species or are divergent ecotypes of polymorphic species. Samples of 543 European river lamprey Lampetra fluviatilis (mostly from anadromous populations) and freshwater European brook lamprey Lampetra planeri from across 18 sites, primarily in the British Isles, were investigated for 13 polymorphic microsatellite DNA loci, and 108 samples from six of these sites were sequenced for 829 bp of mitochondrial DNA (mtDNA). We found contrasting patterns of population structure for mtDNA and microsatellite DNA markers, such that low diversity and little structure were seen for all populations for mtDNA (consistent with a recent founder expansion event), while fine‐scale structuring was evident for nuclear markers. Strong differentiation for microsatellite DNA loci was seen among freshwater‐resident L. planeri populations and between L. fluviatilis and L. planeri in most cases, but little structure was evident among anadromous L. fluviatilis populations. We conclude that postglacial colonization founded multiple freshwater‐resident populations with strong habitat fidelity and limited dispersal tendencies that became highly differentiated, a pattern that was likely intensified by anthropogenic barriers.     

Contemporary trait change in a classic ecological experiment: rapid decrease in alewife gill‐raker spacing following introduction to an inland lake

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Gene flow and effective population size in two life-history types of broad whitefish Coregonus nasus from the Canadian Arctic

In this study, the magnitude and direction of gene flow and estimates of effective population sizes (N(e) ) were quantified among two life-history types (lacustrine and anadromous) of broad whitefish Coregonus nasus in the lower Mackenzie River system. The data suggest that dispersal and subsequent gene flow occurs between these groups, with the former appearing to be asymmetrical. Gene flow may potentially be directionally biased as well, a result attributed to source-sink population dynamics and the ongoing process of post-glacial colonization and contemporary range expansion. Additionally, average N(e) estimates were consistently lower for lacustrine populations of C. nasus although confidence intervals for both contemporary and historical estimates broadly overlapped. The lower average estimates of N(e) for lacustrine populations was suggested to be the result of more recent founding events following post-glacial dispersal. This study provides one of the first assessments of gene flow and N(e) in an Arctic coregonine, results that may be relevant to other freshwater and anadromous Arctic species persisting in systems near the periphery of their range.     

Genomic population structure of freshwater‐resident and anadromous ide (Leuciscus idus) in north‐western Europe

Climate change experts largely agree that future climate change and associated rises in oceanic water levels over the upcoming decades, will affect marine salinity levels. The subsequent effects on fish communities in estuarine ecosystems however, are less clear. One species that is likely to become increasingly affected by changes in salinity is the ide (Leuciscus idus). The ide is a stenohaline freshwater fish that primarily inhabits rivers, with frequent anadromous behavior when sea salinity does not exceed 15%. Unlike most other anadromous Baltic Sea fish species, the ide has yet to be subjected to large‐scale stocking programs, and thus provides an excellent opportunity for studying the natural population structure across the current salinity gradient in the Danish Belts. To explore this, we used Genotyping‐by‐Sequencing to determine genomic population structure of both freshwater resident and anadromous ide populations in the western Baltic Sea region, and relate the results to the current salinity gradient and the demographic history of ide in the region. The sample sites separate into four clusters, with all anadromous populations in one cluster and the freshwater resident populations in the remaining three. Results demonstrate high level of differentiation between sites hosting freshwater resident populations, but little differentiation among anadromous populations. Thus ide exhibit the genomic population structure of both a typical freshwater species, and a typical anadromous species. In addition to providing a first insight into the population structure of north‐western European ide, our data also (1) provide indications of a single illegal introduction by man; (2) suggest limited genetic effects of heavy pollution in the past; and (3) indicate possible historical anadromous behavior in a now isolated freshwater population.     

Formation of a fluvial non-parasitic population of Lethenteron camtschaticum as the first step in petromyzontid speciation

To elucidate the petromyzontid speciation process, the genetic independence of the fluvial non-parasitic populations within the anadromous parasitic Lethenteron camtschaticum was estimated by using polymorphic microsatellite loci. Abundant gene flow was revealed in multitemporal scales between potentially sympatric populations, suggesting ongoing gene flow resulting from imperfect size-assortative mating between them and plastic determination of life histories. On the contrary, landlocked fluvial non-parasitic populations in the upper region of dams were genetically divergent from anadromous parasitic populations. The temporal heterogeneity of gene flow, i.e. contemporary little gene flow but significant gene flow over the long-term between the landlocked fluvial non-parasitic and anadromous parasitic populations was elucidated. In addition, the divergence time of isolation of the landlocked populations from the ancestral anadromous parasitic population was estimated to have occurred 17.9-428.2 years ago, which includes the construction times of an initial dam c. 90 years ago. These instances indicate that the landlocked populations should have very recently been established, and subsequent accumulation of divergence and development of reproductive isolation are predicted. The present landlocked fluvial non-parasitic populations should be analogous to the founder populations in terms of petromyzontid speciation. The data also strongly support the hypothesis of multitemporal and multispatial speciation in the petromyzontid stem-satellite species complex.     

Trade‐offs in osmoregulation and parallel shifts in molecular function follow ecological transitions to freshwater in the Alewife

Adaptation to freshwater may be expected to reduce performance in seawater because these environments represent opposing selective regimes. We tested for such a trade‐off in populations of the Alewife (Alosa pseudoharengus). Alewives are ancestrally anadromous, and multiple populations have been independently restricted to freshwater (landlocked). We conducted salinity challenge experiments, whereby juvenile Alewives from one anadromous and multiple landlocked populations were exposed to freshwater and seawater on acute and acclimation timescales. In response to acute salinity challenge trials, independently derived landlocked populations varied in the degree to which seawater tolerance has been lost. In laboratory‐acclimation experiments, landlocked Alewives exhibited improved freshwater tolerance, which was correlated with reductions in seawater tolerance and hypo‐osmotic balance, suggesting that trade‐offs in osmoregulation may be associated with local adaptation to freshwater. We detected differentiation between life‐history forms in the expression of an ion‐uptake gene (NHE3), and in gill Na⁺/K⁺‐ATPase activity. Trade‐offs in osmoregulation, therefore, may be mediated by differentiation in ion‐uptake and salt‐secreting pathways.     

Parallel and nonparallel genome‐wide divergence among replicate population pairs of freshwater and anadromous Atlantic salmon

Little is known about the genetic basis differentiating resident and anadromous forms found in many salmonid species. Using a medium‐density SNP array, we documented genomic diversity and divergence at 2336 genetically mapped loci among three pairs of North American anadromous and freshwater Atlantic salmon populations. Our results show that across the genome, freshwater populations have lower diversity and a smaller proportion of private polymorphism relative to anadromous populations. Moreover, differentiation was more pronounced among freshwater than among anadromous populations at multiple spatial scales, suggesting a large effect of genetic drift in these isolated freshwater populations. Using nonhierarchical and hierarchical genome scans, we identified hundreds of markers spread across the genome that are potentially under divergent selection between anadromous and freshwater populations, but few outlier loci were repeatedly found in all three freshwater–anadromous comparisons. Similarly, a sliding window analysis revealed numerous regions of high divergence that were nonparallel among the three comparisons. These last results show little evidence for the parallel evolution of alleles selected for in freshwater populations, but suggest nonparallel adaptive divergence at many loci of small effects distributed through the genome. Overall, this study emphasizes the important role of genetic drift in driving genome‐wide reduction in diversity and divergence in freshwater Atlantic salmon populations and suggests a complex multigenic basis of adaptation to resident and anadromous strategies with little parallelism.