Analysis of Applications DNA from Old Scale Samples: Technical Aspects, and Perspectives for Conservation

Molecular based identification and phylogenetic relationship by using cytochrome b gene of Pangasius pangasius

Molecular appraoch for identification of unknown species by using Cytochrome b gene is an effective and reliable as compared with morphological based identification. For DNA barcoding universal molecular genes were used to identify the species. Cytochrome b is a specific gene used for identification purpose. DNA barcoding is a reliable and effective method compared to the different traditional morphological methods of specie identification. So,in the present study which was conducted to identify the species, a total of 50 fish samples were collected from five different sites. DNA was extracted by using the Phenol Chloroform method from muscle tissue. Five sequences were sequenced (one from each site), analyzed, and identified specific species as Pangasius pangasius. Identified sequences were variable in length from 369 bp (Site 1), 364 bp (Site 2), 364 bp (Site 3), 352 bp (Site 4), and 334 bp (Site 5). Identity matches on the NCBI database confirmed the specific specie as P. pangasius. A distancing tree was drawn to show maximum likelihood among the same and different species. Yet, in many cases fishes on diverse development stages are difficult to identify by morphological characters. DNA-based identification methods offer an analytically powerful addition or even an alternative tool for species identification and phylogenetic study. This work intends to provide an updated and extensive overview on the DNA based methods for fish species identification by using Cytochrome b gene as targeted markers for identification purpose.

Is Haemoproteus gabaldoni a valid species? An approach from morphology and molecular tools applied to parasites of Anseriformes

Currently, there are three recognized species of haemoproteids infecting Anseriformes: Haemoproteus nettionis, H. macrovacuolatus, and H. greineri. Unfortunately, genetic information associated with a morphotype is available only for H. macrovacuolatus. We recently found a parasite morphologically compatible with Haemoproteus gabaldoni, a species Bennet (1993) described in a Cairina moschata (Muscovy duck) from Venezuela. This species was synonymized to H. nettionis by Valkiūnas (2005), arguing not enough morphological differentiation between them; it was said that H. greineri could be as well a synonym of H. nettionis. In this study, we aimed to provide evidence to determine if Haemoproteus gabaldoni is a different species of H. nettionis and help to clarify other species status. We first performed morphological and morphometrical analyses and compared this information against the parahapantotypes of H. greineri, H. gabaldoni and material diagnosed as H. nettionis provided by the International Reference center for Avian Haematozoa (IRCAH), and H. macrovacuolatus from the Host-Parasite Relationship Study Group (GERPH, in Spanish Grupo de Estudio Relación Parásito Hospedero) biological collection. We used Principal Component Analysis (PCA) of dimensionless standard morphometrical variables from gametocytes. Furthermore, we amplified a small fragment of cytochrome b (cyt b) to compare the sequence with information in GenBank and Malavi through phylogenetic analyses and haplotype networks. PCA analyses revealed the presence of three distinct groups in the samples studied, supported in the morphological traits of each parasite species analyzed; phylogenetic analyses grouped parasite lineages separately according to the host and continent of provenance. Such results indicate that, H. gabaldoni, is a different species from H. nettionis. One more time, it is demonstrated the importance of linking barcode surveys to morphological studies. Finally, it is highlighted the importance of biological collections as repositories of worldwide biodiversity.

Comparing DNA yield from fish scales following different extraction protocols

Studies on genetic diversity, adaptive potential and fitness of species have become a major tool in conservation biology. These studies require biological material containing a reliable source of DNA which can be extracted and analysed. Recently, non-invasive sampling has become the preferred sampling method of such biological material; particularly when studying endangered species. Elasmoid scales from teleost fish are an example of non-invasive samples from which DNA can successfully be extracted. This study compared different extraction protocols to find an optimal method for extracting DNA from teleost fish scales. This was done with the intent to use the protocol that yielded the highest quantity of DNA on dried, archived scales. The protocols tested in this study included (1) phenol/chloroform with a TNES-urea digestion buffer, (2) phenol/chloroform with an amniocyte digestion buffer and (3) Qiagen DNeasy Blood and Tissue Kit with variations in incubation times and temperatures of each protocol. While the phenol/chloroform with TNES-urea digestion buffer yielded significantly higher concentrations of DNA compared to the other protocols, all protocols followed in this study yielded sufficient quantities of DNA for further downstream applications. Therefore, while there are multiple viable options when selecting a DNA extraction protocol, each research project’s individual needs, requirements and resources need to be carefully considered in order to choose the most effective protocol.

European minnows through time: museum collections aid genetic assessment of species introductions in freshwater fishes (Cyprinidae: Phoxinus species complex)

Massive fish introductions have taken place throughout much of the world, mostly over the last 70 years, and present a major threat to the genetic diversity of native fishes. Introductions have been reported for European Phoxinus, a ubiquitous small cyprinid that populates a wide variety of habitats. Species delineation in European Phoxinus has proven difficult with one reason being ranges of distribution that often traverse drainage boundaries. The present study combines recent samples with museum samples to better understand the current distribution of Phoxinus species and their distributions prior to the massive introductions of fishes in Europe, and to evaluate the use of museum specimens for species distribution studies. For these purposes, genetic lineages from sites collected prior to 1900 (n = 14), and between 1900 and 1950 (n = 8), were analysed using two mitochondrial and nuclear markers. Although possible fish introductions were detected, our results show that the distribution of genetic lineages of museum samples is comparable to that of the extant lineages of European Phoxinus present in those areas. These observations suggest that in the studied ranges the distribution of Phoxinus lineages has been driven by natural processes.

Consideration of sample source for establishing reliable genetic microsatellite data from mammalian carnivore specimens held in natural history collections

Specimens from natural history collections (NHCs) are increasingly being used for genetic studies and can provide information on extinct populations, facilitate comparisons of historical and contemporary populations, produce baseline data before environmental changes, and elucidate patterns of change. Destructive sampling for DNA may be in disagreement with NHC goals of long-term care and maintenance. Differentiating quality among sample sources can direct destructive sampling to the source predicted to yield the highest quality DNA and most reliable data, potentially reducing damage to specimens, laboratory costs, and genotyping errors. We used the kit fox (Vulpes macrotis) as a model species and evaluated the quality and reliability of genetic data obtained from carnivoran specimens via three different sample sources: cranial bones, nasal bones, and toepads. We quantified variation in microsatellite amplification success and genotyping error rates and assessed the reliability of source-specific genic data. Toepads had the highest amplification success rates and lowest genotyping error rates. Shorter loci had higher amplification success and lower allelic dropout rates than longer loci. There were substantial differences in the reliability of resulting multilocus genotypes. Toepads produced the most reliable data, required the fewest replicates, and therefore, had the lowest costs to achieve reliable data. Our results demonstrate that the quality of DNA obtained from specimens varies by sample source and can inform NHCs when evaluating requests for destructive sampling. Our results suggest that prior to large-scale specimen sampling, researchers should conduct pilot studies to differentiate among source-specific data reliability, identify high performing loci, reduce costs of analyses, and minimize destructive sampling.

The genetic relationship between extirpated and contemporary Atlantic salmon Salmo salar L. lines from the southern Baltic Sea

Background

The genetic relationship between original Atlantic salmon populations that are now extinct in the southern Baltic Sea and the present-day populations has long been controversial. To investigate and clarify this issue, we successfully genotyped individuals of the historical populations from the Oder and Vistula Rivers using DNA extracted from dried scales with the Atlantic salmon single nucleotide polymorphism array.

Results

Our results showed a global F_ST of 0.2515 for all pairs of loci, which indicates a high level of genetic differentiation among the groups analyzed in this study. Pairwise F_ST values were significant for all comparisons and the highest values were found between present-day reintroduced Slupia River salmon and extinct Vistula River Atlantic salmon. Bayesian analysis of genetic structure revealed the existence of substructures in the extirpated Polish populations and three main clades among studied stocks.

Conclusions

The historical salmon population from the Oder River was genetically closer to present-day salmon from the Neman River than to the historical salmon from the Vistula River. Vistula salmon clearly separated from all other analyzed salmon stocks. It is likely that the origins of the Atlantic salmon population from the Morrum River and the Polish historical native populations are different.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-016-0208-y) contains supplementary material, which is available to authorized users.

Genetic diversity of upper Lake Constance whitefish Coregonus spp. under the influence of fisheries: a DNA study based on archived scale samples from 1932, 1975 and 2006

This investigation examined changes in the genetic diversity of pelagic upper Lake Constance (ULC) whitefish Coregonus wartmanni population before and after the alteration of fishery methods and management from 1932 to 2006. The study spans a period of pronounced changes in trophic status of the lake and transitions from traditional relatively unselective pelagic seine (Klusgarn) fishing to highly size-selective nylon gillnet techniques. In addition, supportive breeding and stocking became most popular during the phase of eutrophication in the 1970s. The main hypothesis is that size-selective fisheries and breeding lead to an overall decrease in genetic variability over time. A total of 215 archived C. wartmanni scale samples from 1932, 1975 and 2006 were analysed by genotyping 11 microsatellite loci. A comparison of population genetic parameters, including allelic richness, observed and expected heterozygosities, and estimates of effective population sizes, suggests that the genetic diversity of C. wartmanni population has not decreased. The appearance of new alleles in the gene pool in 1975 and 2006 may be indicative of admixture with other forms in the lake or with stocked allochthonous forms. Overall, the fisheries management practice in ULC, including the effects of size-selective fisheries, supportive breeding and stocking, have not significantly altered the genetic diversity of Coregonus spp. over an 80 year period.

Loss of genetic integrity in wild lake trout populations following stocking: insights from an exhaustive study of 72 lakes from Québec, Canada

Stocking represents the most important management tool worldwide to increase and sustain commercial and recreational fisheries in a context of overexploitation. Genetic impacts of this practice have been investigated in many studies, which examined population and individual admixture, but few have investigated determinants of these processes. Here, we addressed these questions from the genotyping at 19 microsatellite loci of 3341 adult lake trout (Salvelinus namaycush) from 72 unstocked and stocked lakes. Results showed an increase in genetic diversity and a twofold decrease in the extent of genetic differentiation among stocked populations when compared to unstocked. Stocked populations were characterized by significant admixture at both population and individual levels. Moreover, levels of admixture in stocked populations were strongly correlated with stocking intensity and a threshold value of total homogenization between source and stocked populations was identified. Our results also suggest that under certain scenarios, the genetic impacts of stocking could be of short duration. Overall, our study emphasizes the important alteration of the genetic integrity of stocked populations and the need to better understand determinants of admixture to optimize stocking strategies and to conserve the genetic integrity of wild populations.

Influence of Holocene environmental change and anthropogenic impact on the diversity and distribution of roe deer

Extant patterns of population structure and levels of diversity are a consequence of factors that vary in both space and time. Our objective in this study is to investigate a species that has responded to both natural and anthropogenic changes in ways that have shaped modern populations and provide insight into the key processes. The roe deer (Capreolus capreolus) is one of the two species of deer native to Britain. During the last glacial maximum (LGM), the British habitat was largely under ice and there was a land bridge to mainland Europe. As the Earth warmed during the early Holocene, the land bridge was lost. Subsequent hunting on the British mainland left the southern region extirpated of roe deer, whereas a refugial population remained in the north. Later reintroductions from Europe led to population expansion, especially in southern United Kingdom. Here, we combine data from ancient and modern DNA to track population dynamics and patterns of connectivity, and test hypotheses about the influence of natural and anthropogenic environmental change. We find that past expansion and divergence events coincided with a warming environment and the subsequent closure of the land bridge between Europe and the United Kingdom. We also find turnover in British roe deer haplotypes between the late-Holocene and modern day that have likely resulted from recent human disturbance activities such as habitat perturbation, overhunting and restocking.

The use of archived tags in retrospective genetic analysis of fish

Collections of historical tissue samples from fish (e.g. scales and otoliths) stored in museums and fisheries institutions are precious sources of DNA for conducting retrospective genetic analysis. However, in some cases, only external tags used for documentation of spatial dynamics of fish populations have been preserved. Here, we test the usefulness of fish tags as a source of DNA for genetic analysis. We extract DNA from historical tags from cod collected in Greenlandic waters between 1950 and 1968. We show that the quantity and quality of DNA recovered from tags is comparable to DNA from archived otoliths from the same individuals. Surprisingly, levels of cross-contamination do not seem to be significantly higher in DNA from external (tag) than internal (otolith) sources. Our study therefore demonstrates that historical tags can be a highly valuable source of DNA for retrospective genetic analysis of fish.

Extracting DNA from museum bird eggs, and whole genome amplification of archive DNA

We present a comprehensive protocol for extracting DNA from egg membranes and other internal debris recovered from the interior of blown museum bird eggs. A variety of commercially available DNA extraction methods were found to be applicable. DNA sequencing of polymerase chain reaction (PCR) products for a 176-bp fragment of mitochondrial DNA was successful for most egg samples (> 78%) even though the amount of DNA extracted (mean = 14.71 ± 4.55 ng/µL) was significantly less than that obtained for bird skin samples (mean = 67.88 ± 4.77 ng/µL). For PCR and sequencing of snipe (Gallinago) DNA, we provide eight new primers for the 'DNA barcode' region of COI mtDNA. In various combinations, the primers target a range of PCR products sized from 72 bp to the full 'barcode' of 751 bp. Not all possible combinations were tested with archive snipe DNA, but we found a significantly better success rate of PCR amplification for a shorter 176-bp target compared with a larger 288-bp fragment (67% vs. 39%). Finally, we explored the feasibility of whole genome amplification (WGA) for extending the use of archive DNA in PCR and sequencing applications. Of two WGA approaches, a PCR-based method was found to be able to amplify whole genomic DNA from archive skins and eggs from museum bird collections. After WGA, significantly more archive egg samples produced visible PCR products on agarose (56.9% before WGA vs. 79.0% after WGA). However, overall sequencing success did not improve significantly (78.8% compared with 83.0%).

Changes in the genetic structure of Atlantic salmon populations over four decades reveal substantial impacts of stocking and potential resiliency

While the stocking of captive-bred fish has been occurring for decades and has had substantial immediate genetic and evolutionary impacts on wild populations, its long-term consequences have only been weakly investigated. Here, we conducted a spatiotemporal analysis of 1428 Atlantic salmon sampled from 1965 to 2006 in 25 populations throughout France to investigate the influence of stocking on the neutral genetic structure in wild Atlantic salmon (Salmo salar) populations. On the basis of the analysis of 11 microsatellite loci, we found that the overall genetic structure among populations dramatically decreased over the period studied. Admixture rates among populations were highly variable, ranging from a nearly undetectable contribution from donor stocks to total replacement of the native gene pool, suggesting extremely variable impacts of stocking. Depending on population, admixture rates either increased, remained stable, or decreased in samples collected between 1998 and 2006 compared to samples from 1965 to 1987, suggesting either rising, long-lasting or short-term impacts of stocking. We discuss the potential mechanisms contributing to this variability, including the reduced fitness of stocked fish and persistence of wild locally adapted individuals.

Resurrecting an extinct salmon evolutionarily significant unit: archived scales, historical DNA and implications for restoration

Archival scales from 603 sockeye salmon (Oncorhynchus nerka), sampled from May to July 1924 in the lower Columbia River, were analysed for genetic variability at 12 microsatellite loci and compared to 17 present-day O. nerka populations-exhibiting either anadromous (sockeye salmon) or nonanadromous (kokanee) life histories-from throughout the Columbia River Basin, including areas upstream of impassable dams built subsequent to 1924. Statistical analyses identified four major genetic assemblages of sockeye salmon in the 1924 samples. Two of these putative historical groupings were found to be genetically similar to extant evolutionarily significant units (ESUs) in the Okanogan and Wenatchee Rivers (pairwise F(ST)  = 0.004 and 0.002, respectively), and assignment tests were able to allocate 77% of the fish in these two historical groupings to the contemporary Okanogan River and Lake Wenatchee ESUs. A third historical genetic grouping was most closely aligned with contemporary sockeye salmon in Redfish Lake, Idaho, although the association was less robust (pairwise F(ST)  = 0.060). However, a fourth genetic grouping did not appear to be related to any contemporary sockeye salmon or kokanee population, assigned poorly to the O. nerka baseline, and had distinctive early return migration timing, suggesting that this group represents a historical ESU originating in headwater lakes in British Columbia that was probably extirpated sometime after 1924. The lack of a contemporary O. nerka population possessing the genetic legacy of this extinct ESU indicates that efforts to reestablish early-migrating sockeye salmon to the headwater lakes region of the Columbia River will be difficult.

Genetic variation over 10,000 years in Ctenomys: comparative phylochronology provides a temporal perspective on rarity, environmental change and demography

An understanding of how ecological traits influence past species response to environmental change can aid our future predictions of species persistence. We used ancient DNA and serial coalescent modelling in a hypothesis-testing framework to reveal differences in temporal genetic variation over 10,000 years for two species of subterranean rodents that currently differ in rarity (abundance, range size and habitat specificity) and mating system, but that reside in the same volcanically active region. Comparative phylochronologic analyses indicated little genetic change and suggest genetic stability in the solitary widespread Ctenomys haigi over thousands of years. In contrast, we found a pattern of haplotypic turnover in the rare and currently endangered Ctenomys sociabilis. Serial coalescent modelling indicated that the best-fit models of microevolutionary change included gene flow between isolated populations for this species. Although C. haigi and C. sociabilis are congeners that share many life history traits, they have behavioural, habitat-preference and population-size differences that may have resulted in contrasting patterns of temporal variation during periods of environmental change.

Multiplex preamplification PCR and microsatellite validation enables accurate single nucleotide polymorphism genotyping of historical fish scales

Incorporating historical tissues into the study of ecological, conservation and management questions can broaden the scope of population genetic research by enhancing our understanding of evolutionary processes and anthropogenic influences on natural populations. Genotyping historical and low-quality samples has been plagued by challenges associated with low amounts of template DNA and the potential for pre-existing DNA contamination among samples. We describe a two-step process designed to (i) accurately genotype large numbers of historical low-quality scale samples in a high-throughput format and (ii) screen samples for pre-existing DNA contamination. First, we describe how an efficient multiplex preamplification PCR of 45 single nucleotide polymorphisms (SNPs) can generate highly accurate genotypes with low failure and error rates in subsequent SNP genotyping reactions of individual historical scales from sockeye salmon (Oncorhynchus nerka). Second, we demonstrate how the method can be modified for the amplification of microsatellite loci to detect pre-existing DNA contamination. A total of 760 individual historical scale and 182 contemporary fin clip samples were genotyped and screened for contamination. Genotyping failure and error rates were exceedingly low and similar for both historical and contemporary samples. Pre-existing contamination in 21% of the historical samples was successfully identified by screening the amplified microsatellite loci. The advantages of automation, low failure and error rates, and ability to multiplex both the preamplification and subsequent genotyping reactions combine to make the protocol ideally suited for efficiently genotyping large numbers of potentially contaminated low-quality sources of DNA.

Genetic stock identification of Atlantic salmon (Salmo salar) populations in the southern part of the European range

BACKGROUND

Anadromous migratory fish species such as Atlantic salmon (Salmo salar) have significant economic, cultural and ecological importance, but present a complex case for management and conservation due to the range of their migration. Atlantic salmon exist in rivers across the North Atlantic, returning to their river of birth with a high degree of accuracy; however, despite continuing efforts and improvements in in-river conservation, they are in steep decline across their range. Salmon from rivers across Europe migrate along similar routes, where they have, historically, been subject to commercial netting. This mixed stock exploitation has the potential to devastate weak and declining populations where they are exploited indiscriminately. Despite various tagging and marking studies, the effect of marine exploitation and the marine element of the salmon lifecycle in general, remain the "black-box" of salmon management. In a number of Pacific salmonid species and in several regions within the range of the Atlantic salmon, genetic stock identification and mixed stock analysis have been used successfully to quantify exploitation rates and identify the natal origins of fish outside their home waters - to date this has not been attempted for Atlantic salmon in the south of their European range.

RESULTS

To facilitate mixed stock analysis (MSA) of Atlantic salmon, we have produced a baseline of genetic data for salmon populations originating from the largest rivers from Spain to northern Scotland, a region in which declines have been particularly marked. Using 12 microsatellites, 3,730 individual fish from 57 river catchments have been genotyped. Detailed patterns of population genetic diversity of Atlantic salmon at a sub-continent-wide level have been evaluated, demonstrating the existence of regional genetic signatures. Critically, these appear to be independent of more commonly recognised terrestrial biogeographical and political boundaries, allowing reporting regions to be defined. The implications of these results on the accuracy of MSA are evaluated and indicate that the success of MSA is not uniform across the range studied; our findings indicate large differences in the relative accuracy of stock composition estimates and MSA apportioning across the geographical range of the study, with a much higher degree of accuracy achieved when assigning and apportioning to populations in the south of the area studied. This result probably reflects the more genetically distinct nature of populations in the database from Spain, northwest France and southern England. Genetic stock identification has been undertaken and validation of the baseline microsatellite dataset with rod-and-line and estuary net fisheries of known origin has produced realistic estimates of stock composition at a regional scale.

CONCLUSIONS

This southern European database and supporting phylogeographic and mixed-stock analyses of net samples provide a unique tool for Atlantic salmon research and management, in both their natal rivers and the marine environment. However, the success of MSA is not uniform across the area studied, with large differences in the relative accuracy of stock composition estimates and MSA apportioning, with a much higher degree of accuracy achieved when assigning and apportioning to populations in the south of the region. More broadly, this study provides a basis for long-term salmon management across the region and confirms the value of this genetic approach for fisheries management of anadromous species.

Identifying footprints of selection in stocked brown trout populations: a spatio-temporal approach

Studies of interactions between farmed and wild salmonid fishes have suggested reduced fitness of farmed strains in the wild, but evidence for selection at the genic level is lacking. We studied three brown trout populations in Denmark which have been significantly admixed with stocked hatchery trout (19-64%), along with two hatchery strains used for stocking. The wild populations were represented by contemporary samples (2000-2006) and two of them by historical samples (1943-1956). We analysed 61 microsatellite loci, nine of which showed putative functional relationships [expressed sequence tag (EST)-linked or quantitative trait loci]. F(ST)-based outlier tests provided support for diversifying selection at chromosome regions marked by three loci, two anonymous and one EST-linked. Patterns of differentiation suggested that the loci were candidates for being under diversifying hitch-hiking selection in hatchery vs. wild environments. Analysis of hatchery strain admixture proportions showed that in one wild population, two of the loci showed significantly lower admixture proportions than the putatively neutral loci, implying contemporary selection against alleles introduced by hatchery strain trout. In the most strongly admixed population, however, there was no evidence for selection, possibly because of immigration by stocked trout overcoming selection against hatchery-derived alleles or supportive breeding practices allowing hatchery strain trout to escape natural selection. To our knowledge, this is the first study demonstrating footprints of selection in wild salmonid populations subject to spawning intrusion by farmed fish.

Long-term changes in the fine-scale population structure of coho salmon populations (Oncorhynchus kisutch) subject to extensive supportive breeding

The long-term viability of a metapopulation depends partly on the gene flow among sub-populations. Management approaches such as translocations and supportive breeding between closely related populations may affect gene flow and overall structure, and therefore viability. Here, we examined temporal changes in the fine-scale population structure of coho salmon (Oncorhynchus kisutch) by comparing archived (1938) and modern (2001-2005) populations in six rivers within a single conservation unit (Puget Sound, Washington) sampled before and after an extended period of between-river transfers and releases of millions of cultured salmon. Genotype frequencies at eight microsatellite loci showed that current populations descended from historical Puget Sound populations, but populations in different rivers that exchanged fish for hatchery propagation share more of their ancestry recently than they did historically. Historically, populations in different rivers were isolated by geographic distance, but that relationship is no longer significant. Allelic richness among all populations declined significantly, suggesting that genetic drift has increased because of a population bottleneck. Populations in different rivers and within the same river have become more diverged, providing further evidence for a widespread bottleneck. Previously, we observed that genetic distance significantly decreased with the number of fish exchanged; however, some populations apparently resisted introgression. Altered gene flow and lost diversity may affect the complexity, and therefore resiliency of sub-populations within a conservation unit. Plans for artificial culture need to maintain existing genetic diversity and avoid disrupting the fine-scale structure by using local populations for parents whenever possible.

Sixty years of anthropogenic pressure: a spatio-temporal genetic analysis of brown trout populations subject to stocking and population declines

Analyses of historical samples can provide invaluable information on changes to the genetic composition of natural populations resulting from human activities. Here, we analyse 21 microsatellite loci in historical (archived scales from 1927 to 1956) and contemporary samples of brown trout (Salmo trutta) from six neighbouring rivers in Denmark, to compare the genetic structure of wild populations before and after population declines and stocking with nonlocal strains of hatchery trout. We show that all populations have been strongly affected by stocking, with admixture proportions ranging from 14 to 64%. Historical population genetic structure was characterized by isolation by distance and by positive correlations between historical effective population sizes and habitat area within river systems. Contemporary population genetic structure still showed isolation by distance, but also reflected differences among populations in hatchery trout admixture proportions. Despite significant changes to the genetic composition within populations over time, dispersal rates among populations were roughly similar before and after stocking. We also assessed whether population declines or introgression by hatchery strain trout should be the most significant conservation concern in this system. Based on theoretical considerations, we argue that population declines have had limited negative effects for the persistence of adaptive variation, but admixture with hatchery trout may have resulted in reduced local adaptation. Collectively, our study demonstrates the usefulness of analysing historical samples for identifying the most important consequences of human activities on the genetic structure of wild populations.

Temporal effective size estimates of a managed walleye Sander vitreus population and implications for genetic-based management

The goal of this research was to use the long-term fishery data set and DNA from archived scales of walleye Sander vitreus in Escanaba Lake, WI, U.S.A., to improve the understanding of the underlying mechanism(s) influencing genetic diversity in naturally recruiting populations. The introduced population of S. vitreus in Escanaba Lake has a low mean effective population size (N(E)) between 124.6 and 185.5 despite a mean census size (N(C)) of 4659 (N(E)/N(C)c. 0.04), suggesting an accelerated rate of genetic drift between 1952 and 2002. These values are smaller than the median N(E) range of several studies suggesting typical N(E)/N(C) ratios of 0.11-0.16 in a wide range of taxa. N(E) increased steadily during the past two sampled decades (1992 and 2002) and was consistent with a lowering of the variance in S. vitreus reproductive success, possibly linked to a large, sustained exploitation (mean 28%) rate. Variance in reproductive success is one of the most important factors influencing N(E) in species, like S. vitreus, which have a potential for large fecundities and large juvenile mortalities (type III survivorship). The N(B) estimates across six sequential cohorts (age classes of S. vitreus, assayed from 1994 to 1999) was consistent with estimates of N(E) reported for 1992-2002. These results, coupled with in-depth census and exploitation data, show that the genetic characteristics of Escanaba Lake S. vitreus have changed substantially and that management activities, such as supplemental stocking and harvest practices, have profoundly influenced the genetic dynamics of S. vitreus in this lake.

Temporally stable genetic structure and low migration in an Atlantic salmon population complex: implications for conservation and management

The evolutionary potential of a population is closely related to two key population genetic parameters, namely the effective population size (N e) and migration rate (m). Furthermore, knowledge of these parameters is required in order to assess potential constraints on local adaptation and for the development of biologically sound management strategies. We addressed these key issues by investigating the temporal and spatial genetic structure of over 2000 adult Atlantic salmon (Salmo salar) collected from 17 sites in the Teno and Näätämö rivers in northernmost Europe with up to five time points spanning temporal intervals up to 24 years (∼4 generations). In all cases except one, local populations were found to be temporally stable within the river system. Estimates of N e were generally a magnitude larger for the mainstem and headwater populations (MS+HW, N e∼340-1200) than for the tributary populations (N e∼35-160), thus explaining the higher genetic diversity and lower divergence of the MS+HW populations compared to tributaries. The overall migration rates to tributaries were low, and in some cases, low enough for local adaptations to potentially evolve, despite their lower N e. Signs of a population bottleneck and natural recruitment from nearby populations were detected in one local population. This highlights a fact which is relevant for the conservation and management of highly substructured population systems in general: that even when the overall census size is large, local populations can be vulnerable to perturbations. To preserve the current and to regain the historical distribution of salmon within the river system, we propose that the status of the total population complex should be evaluated at the local population level rather than from descriptive statistics at the system level.

Back to the future: museum specimens in population genetics

Museums and other natural history collections (NHC) worldwide house millions of specimens. With the advent of molecular genetic approaches these collections have become the source of many fascinating population studies in conservation genetics that contrast historical with present-day genetic diversity. Recent developments in molecular genetics and genomics and the associated statistical tools have opened up the further possibility of studying evolutionary change directly. As we discuss here, we believe that NHC specimens provide a largely underutilized resource for such investigations. However, because DNA extracted from NHC samples is degraded, analyses of such samples are technically demanding and many potential pitfalls exist. Thus, we propose a set of guidelines that outline the steps necessary to begin genetic investigations using specimens from NHC.

Stocking impact and temporal stability of genetic composition in a brackish northern pike population (Esox lucius L.), assessed using microsatellite DNA analysis of historical and contemporary samples

During the last decade, brackish northern pike populations in Denmark have been subject to stocking programmes, using nonindigenous pike from freshwater lakes, in order to compensate for drastic population declines. The present study was designed to investigate the genetic impact of stocking freshwater pike into a brackish pike population in Stege Nor, Denmark. We analysed polymorphism at eight microsatellite loci in samples representing the indigenous Stege Nor population prior to stocking (ie from 1956 to 1957), along with a sample of the contemporary Stege Nor population and samples from the three populations used for stocking. Despite large numbers of stocked fry, the results from both individual and population level admixture analyses demonstrated extremely poor performance and <1% introgression of stocked freshwater pike into the brackish pike population. Furthermore, pairwise F(ST) estimates between samples demonstrated close genetic relationship among temporal samples from Stege Nor, indicating temporal stability over the last 45 years. We also estimated the effective population size (N(e)) of pike in Stege Nor and applied a test for recent population bottlenecks. The harmonic mean of N(e) was relatively high (>250), but there were indications of bottlenecks in all samples and populations. We ascribe this finding to historical rather than recent bottlenecks, possibly dating back to founder events associated with postglacial recolonisation.

Marine landscapes and population genetic structure of herring (Clupea harengus L.) in the Baltic Sea

Numerically small but statistically significant genetic differentiation has been found in many marine fish species despite very large census population sizes and absence of obvious barriers to migrating individuals. Analyses of morphological traits have previously identified local spawning groups of herring (Clupea harengus L.) in the environmentally heterogeneous Baltic Sea, whereas allozyme markers have not revealed differentiation. We analysed variation at nine microsatellite loci in 24 samples of spring-spawning herring collected at 11 spawning locations throughout the Baltic Sea. Significant temporal differentiation was observed at two locations, which we ascribe to sympatrically spawning but genetically divergent 'spawning waves'. Significant differentiation was also present on a geographical scale, though pairwise F(ST) values were generally low, not exceeding 0.027. Partial Mantel tests showed no isolation by geographical distance, but significant associations were observed between genetic differentiation and environmental parameters (salinity and surface temperature) (0.001 < P < or = 0.099), though these outcomes were driven mainly by populations in the southwestern Baltic Sea, which also exhibits the steepest environmental gradients. Application of a novel method for detecting barriers to gene flow by combining geographical coordinates and genetic differentiation allowed us to identify two zones of lowered gene flow. These zones were concordant with the separation of the Baltic Sea into major basins, with environmental gradients and with differences in migration behaviour. We suggest that similar use of landscape genetics approaches may increase the understanding of the biological significance of genetic differentiation in other marine fishes.

Genetic detection of sex-specific dispersal in historical and contemporary populations of anadromous brown trout Salmo trutta

The study of sex-biased dispersal has attracted considerable attention in birds and mammals, but less in other taxa, including fishes. We analysed sex-specific dispersal in historical (1910s and 1950s) and contemporary (1990s) samples of anadromous brown trout Salmo trutta. We tested the hypothesis that dispersal is unbiased using information from microsatellite DNA and applying an assignment index for 11 temporally and spatially separated samples. Our results are most consistent with brown trout dispersal being male biased, and provide no evidence of female bias. We found no evidence that dispersal patterns changed over time, indicating that stocking with hatchery strains did not affect sex-specific dispersal.

Evaluation of methodology for detection of genetic bottlenecks: inferences from temporally replicated lake trout populations

Statistical methods have been proposed to detect recent bottlenecks on the basis of genetic characterizations of natural populations. In the absence of direct estimates of contemporary or historical population numbers, we tested the indirect M-ratio method based on microsatellite motif size frequency profiles using three historical and three contemporary Great Lakes populations of Salvelinus namaysuch for which severe reductions in population numbers are documented. Simulations employing plausible ranges of empirical population parameter values were used to explore bottleneck likelihood surfaces. We show that single values of the M-ratio are not sufficient to unambiguously infer a bottleneck without knowledge of mutation rates and effective population size (i.e., 4Ne mu or [symbol: see text]). Inferences of the degree of population bottleneck would be best supported if analyses were conducted across plausible ranges of [symbol: see text] and by qualitative comparisons among population samples.

Census vs. effective population size in chinook salmon: large- and small-scale environmental perturbation effects

Population viability has often been assessed by census of reproducing adults. Recently this method has been called into question and estimation of the effective population size (Ne) proposed as a complementary method to determine population health. We examined genetic diversity in five populations of chinook salmon (Oncorhynchus tshawytscha) from the upper Fraser River watershed (British Columbia, Canada) at 11 microsatellite loci over 20 years using DNA extracted from archived scale samples. We tested for changes in genetic diversity, calculated the ratio of the number of alleles to the range in allele size to give the statistic M, calculated Ne from the temporal change in allele frequency, used the maximum likelihood method to calculate effective population size (NeM), calculated the harmonic mean of population size, and compared these statistics to annual census estimates. Over the last two decades population size has increased in all five populations of chinook examined; however, Ne calculated for each population was low (81-691) and decreasing over the time interval measured. Values of NeM were low, but substantially higher than Ne calculated using the temporal method. The calculated values for M were generally low (M < 0.70), indicating recent population reductions for all five populations. Large-scale historic barriers to migration and development activities do not appear to account for the low values of Ne; however, available spawning area is positively correlated with Ne. Both Ne and M estimates indicate that these populations are potentially susceptible to inbreeding effects and may lack the ability to respond adaptively to stochastic events. Our findings question the practice of relying exclusively on census estimates for interpreting population health and show the importance of determining genetic diversity within populations.

Non-destructive genetic sampling in fish. An improved method for DNA extraction from fish fins and scales

DNA-based studies have been one of the major interests in conservation biology of endangered species and in population genetics. As species and population genetic assessment requires a source of biological material, the sampling strategy can be overcome by non-destructive procedures for DNA isolation. An improved method for obtaining DNA from fish fins and scales with the use of an extraction buffer containing urea and further DNA purification with phenol-chloroform is described. The methodology combines the benefits of a non-destructive DNA sampling and its high efficiency. In addition, comparisons with other methodologies for isolating DNA from fish demonstrated that the present procedure also becomes a very attractive alternative to obtain large amounts of high-quality DNA for use in different molecular analyses. The DNA samples, isolated from different fish species, have been successfully used on random amplified polymorphic DNA (RAPD) experiments, as well as on amplification of specific ribosomal and mitochondrial DNA sequences. The present DNA extraction procedure represents an alternative for population approaches and genetic studies on rare or endangered taxa.

Patterns of nuclear DNA degeneration over time--a case study in historic teeth samples

The amount of nuclear DNA extracted from teeth of 279 individual red fox Vulpes vulpes collected over a period spanning the last three decades was determined by quantitative polymerase chain reaction (PCR). Although teeth were autoclaved during initial collection, 73.8% of extracts contained sufficient DNA concentration (> 5 pg/ micro L) suitable for reliable microsatellite genotyping but the quantity of nuclear DNA decayed significantly over time in a nonlinear pattern. The success of PCR amplification across four examined canine microsatellites over time was dependent on fragment size. By including data from two different tests for human contamination and from frequencies of allelic dropout and false alleles, the methodological constraints of population genetic studies using microsatellite loci amplified from historic DNA are discussed.

Genetic variation over space and time: analyses of extinct and remnant lake trout populations in the Upper Great Lakes

Lake trout (Salvelinus namaycush) in the upper Laurentian Great Lakes of North America experienced striking reductions in abundance and distribution during the mid-twentieth century. Complete collapse of populations was documented for Lake Michigan, and a few remnant populations remained only in lakes Huron and Superior. Using DNA obtained from historical scale collections, we analysed patterns of genetic diversity at five microsatellite loci from archived historical samples representing 15 populations (range 1940-1959) and from three contemporary remnant populations across lakes Huron and Superior (total n = 893). Demographic declines in abundance and the extirpation of native lake trout populations during the past 40 years have resulted in the loss of genetic diversity between lakes owing to extirpation of Lake Michigan populations and a temporal trend for reduction in allelic richness in the populations of lakes Superior and Huron. Naturally reproducing populations in Lake Superior, which had been considered to be remnants of historical populations, and which were believed to be responsible for the resurgence of lake trout numbers and distribution, have probably been affected by hatchery supplementation.

Long-term effective population sizes, temporal stability of genetic composition and potential for local adaptation in anadromous brown trout (Salmo trutta) populations

We examined the long-term temporal (1910s to 1990s) genetic variation at eight microsatellite DNA loci in brown trout (Salmo trutta L) collected from five anadromous populations in Denmark to assess the long-term stability of genetic composition and to estimate effective population sizes (Ne). Contemporary and historical samples consisted of tissue and archived scales, respectively. Pairwise thetaST estimates, a hierarchical analysis of molecular variance (amova) and multidimensional scaling analysis of pairwise genetic distances between samples revealed much closer genetic relationships among temporal samples from the same populations than among samples from different populations. Estimates of Ne, using a likelihood-based implementation of the temporal method, revealed Ne >or= 500 in two of three populations for which we have historical data. A third population in a small (3 km) river showed Ne >or= 300. Assuming a stepping-stone model of gene flow we considered the relative roles of gene flow, random genetic drift and selection to assess the possibilities for local adaptation. The requirements for local adaptation were fulfilled, but only adaptations resulting from strong selection were expected to occur at the level of individual populations. Adaptations resulting from weak selection were more likely to occur on a regional basis, i.e. encompassing several populations. Ne appears to have declined recently in at least one of the studied populations, and the documented recent declines of many other anadromous brown trout populations may affect the persistence of local adaptation.

Estimating the long-term effects of stocking domesticated trout into wild brown trout (Salmo trutta) populations: an approach using microsatellite DNA analysis of historical and contemporary samples

Indigenous salmonid fish gene pools are affected by domesticated conspecifics, derived from aquaculture escapes and deliberate releases. Variability was examined at nine microsatellite loci in order to assess the long-term impact of stocking domesticated trout in two brown trout populations. The study was based on analysis of two historical samples (1945-56), represented by old scale collections, and seven contemporary samples (1986-2000). In one population historical and contemporary samples were remarkably genetically similar despite more than a decade of intense stocking. Estimation of admixture proportions showed a small genetic contribution from domesticated trout (approximately 6%), and individual admixture analysis demonstrated a majority of nonadmixed individuals. The expected genetic contribution by domesticated trout was 64%, assessed from the number of stocked trout and assuming equal survival and reproductive performance of wild and domesticated trout. This demonstrates poor performance and low fitness of domesticated trout in the wild. In another population there was a strong genetic contribution from domesticated trout (between 57% and 88% in different samples), both in samples from a broodstock thought to represent the indigenous population and in a sample of wild spawners. Survival of domesticated trout and admixture with indigenous fish in the broodstock and subsequent stocking into the river, combined with a low population size of native trout relative to the number of stocked trout, could explain the observed introgression. Few nonadmixed individuals remained in the introgressed population, and I discuss how individual admixture analysis can be used to identify and conserve nonintrogressed remains of the population.

Temporal change in genetic structure and effective population size in steelhead trout (Oncorhynchus mykiss)

There is a wealth of published molecular population genetic studies, however, most do not include historic samples and thus implicitly assume temporal genetic stability. We tested for changes in genetic diversity and structure in three populations of steelhead trout (Oncorhynchus mykiss) from a northern British Columbia watershed using seven microsatellite loci over 40 years. We found little change in genetic diversity (mean allele numbers and observed and expected heterozygosity), despite large variation in the estimated numbers of steelhead returning to the watershed over the same time period. However, the temporal stability in genetic diversity is not reflected in population structure, which appears to be high among populations, yet significantly variable over time. The neighbour-joining tree showed that, overall, two of the populations (Zymoetz and Kispiox) clustered separately from the third (Babine); a finding which was not consistent with their geographical separation. The clustering pattern was also not temporally consistent. We used the temporal method to estimate the effective number of breeders (Nb ) for the three populations; our values (Nb = 17-102) were low for the large and presumed vigorous populations of steelhead trout sampled. The low Nb values were also not consistent with the generally high genetic diversity estimates, suggesting the possibility of intermittent gene flow among the three populations. The use of temporal analyses in population genetic samples should be a priority; first, to verify observed patterns in contemporary data, and second, to build a dataset of temporal analyses to allow generalizations to be made concerning temporal genetic stability and effective population size in natural populations.

Lacustrine spatial distribution of landlocked Atlantic salmon populations assessed across generations by multilocus individual assignment and mixed-stock analyses

The objective of this study was to assess the spatiotemporal distribution of four landlocked Atlantic salmon (Salmo salar) populations during their sympatric feeding phase in lake St-Jean (Québec, Canada). A total of 1100 fish captured over a period of 25 years was genotyped at six microsatellite loci in order to assess the temporal stability of the relative proportion of each population in different lake sectors using both individual-based assignment and mixed-stock analysis. Estimates of relative proportions obtained from both methods were highly correlated. A nonrandom spatial distribution of populations was observed for each period and, despite the fact that the overall proportion of each population varied over time, the pattern of differential distribution remained generally stable over time. Furthermore, there were indications that the extent of horizontal spatial overlap among populations was negatively correlated with that of their genetic differentiation at both microsatellites and a major histocompatibility complex locus, and independent of the geographical distance between the rivers of origin. We discuss the hypothesis that the temporal stability of spatial distribution, the lack of an association between spatial partitioning and geographical distance between rivers of origin, and the apparent negative correlation between spatial overlap and genetic differentiation, reflect the outcome of selective pressures driving behavioural differences for spatial niche partitioning among populations.

Genetic consequences of population decline in the European otter (Lutra lutra): an assessment of microsatellite DNA variation in Danish otters from 1883 to 1993

The European otter (Lutra lutra) was common in Denmark until the 1960s, but its present distribution encompasses only a minor part of the country. The aim of this study was to assess whether the recent population decline has resulted in loss of genetic variability and to gain further insight into the dynamics of the population decline. This was done by analysing microsatellite DNA variation in contemporary and historical samples, the latter encompassing DNA samples extracted from museum specimens covering a time-span from the 1880s to the 1960s. Tests for differences in expected heterozygosity and the numbers of alleles in contemporary versus historical samples and a test for detecting population bottlenecks provided few indications of a recent bottleneck and loss of variability. However, a procedure for detecting population expansions and declines, based on the genealogical history of microsatellite alleles, suggested that a drastic long-term population decline has taken place, which could have started more than 2000 years ago, possibly due to ancient anthropogenic pressure. Finally, assignment tests and pairwise F(ST) values suggested weak but statistically significant genetic differentiation between the extant population and historical samples of otters from other regions in Denmark, more likely reflecting differentiation among original populations rather than recent drift.