Gene Flow Events Research Articles

Gene flow and range expansion in a mountain-dwelling passerine with a fragmented distribution

We studied gene flow and bottleneck events in the population history of locally isolated citril finches endemic to European mountains. For the present study, we used two genetic markers with different rates of evolution: a fast evolving mitochondrial marker (ATPase6/8) and a more slowly evolving nuclear marker (02401). Populations north of the Pyrenees showed in general fewer haplotypes and a considerable lower nucleotide and gene diversity than the Iberian populations. Unexpectedly, we found very little genetic variability in the fast evolving mitochondrial marker, arguing for a strong and relatively recent bottleneck event in the species population history. This pattern potentially reflects a sudden decrease of crucial resources during Mid-Holocene (mountain pine, Scots pine, and black pine) and a subsequent breakdown of the population. The bottleneck could also have been caused or coincide with a selective sweep in the mitochondrion. By contrast, the slowly evolving nuclear marker showed a much higher variability. This marker probably reflects major gene flow along a potential expansion pathway from the Eastern Pyrenees, northwards to the populations of Central Europe, and southwards to the more fragmented populations of central and southern Spain. The population of the Western Pyrenees (Navarra) appears to be cut-off from this major gene flow and our data indicate a certain degree of partial isolation, probably reflecting more ancient events (e.g. the separation in distinct refuge sites during the last glacial maximum).

Estimating Parameters of Speciation Models Based on Refined Summaries of the Joint Site-Frequency Spectrum

Understanding the processes and conditions under which populations diverge to give rise to distinct species is a central question in evolutionary biology. Since recently diverged populations have high levels of shared polymorphisms, it is challenging to distinguish between recent divergence with no (or very low) inter-population gene flow and older splitting events with subsequent gene flow. Recently published methods to infer speciation parameters under the isolation-migration framework are based on summarizing polymorphism data at multiple loci in two species using the joint site-frequency spectrum (JSFS). We have developed two improvements of these methods based on a more extensive use of the JSFS classes of polymorphisms for species with high intra-locus recombination rates. First, using a likelihood based method, we demonstrate that taking into account low-frequency polymorphisms shared between species significantly improves the joint estimation of the divergence time and gene flow between species. Second, we introduce a local linear regression algorithm that considerably reduces the computational time and allows for the estimation of unequal rates of gene flow between species. We also investigate which summary statistics from the JSFS allow the greatest estimation accuracy for divergence time and migration rates for low (around 10) and high (around 100) numbers of loci. Focusing on cases with low numbers of loci and high intra-locus recombination rates we show that our methods for the estimation of divergence time and migration rates are more precise than existing approaches.

Inferences on pathogenic fungus population structures from microsatellite data: new insights from spatial genetics approaches

Landscape genetics, which combines population genetics, landscape ecology and spatial statistics, has emerged recently as a new discipline that can be used to assess how landscape features or environmental variables can influence gene flow and spatial genetic variation. We applied this approach to the invasive plant pathogenic fungus Mycosphaerella fijiensis, which causes black leaf streak disease of banana. Around 880 isolates were sampled within a 50 × 50 km area located in a fragmented banana production zone in Cameroon that includes several potential physical barriers to gene flow. Two clustering algorithms and a new F(ST) -based procedure were applied to define the number of genetic entities and their spatial domain without a priori assumptions. Two populations were clearly delineated, and the genetic discontinuity appeared sharp but asymmetric. Interestingly, no landscape features matched this genetic discontinuity, and no isolation by distance (IBD) was found within populations. Our results suggest that the genetic structure observed in this production area reflects the recent history of M. fijiensis expansion in Cameroon rather than resulting from contemporary gene flow. Finally, we discuss the influence of the suspected high effective population size for such an organism on (i) the absence of an IBD signal, (ii) the characterization of contemporary gene-flow events through assignation methods of analysis and (iii) the evolution of the genetic discontinuity detected in this study.

Movement behavior explains genetic differentiation in American black bears

Individual-based landscape genetic analyses provide empirically based models of gene flow. It would be valuable to verify the predictions of these models using independent data of a different type. Analyses using different data sources that produce consistent results provide strong support for the generality of the findings. Mating and dispersal movements are the mechanisms through which gene flow operates in animal populations. The best means to verify landscape genetic predictions would be to use movement data to independently predict landscape resistance. We used path-level, conditional logistic regression to predict landscape resistance for American black bear (Ursus americanus) in a landscape in which previous work predicted population connectivity using individual-based landscape genetics. We found consistent landscape factors influence genetic differentiation and movement path selection, with strong similarities between the predicted landscape resistance surfaces. Genetic differentiation in American black bear is driven by spring movement (mating and dispersal) in relation to residential development, roads, elevation and forest cover. Given the limited periods of the year when gene flow events primarily occur, models of landscape connectivity should carefully consider temporal changes in functional landscape resistance.

An ancient autosomal haplotype bearing a rare achromatopsia-causing founder mutation is shared among Arab Muslims and Oriental Jews

Numerous cultural aspects, mainly based on historical records, suggest a common origin of the Middle-Eastern Arab Muslim and Jewish populations. This is supported, to some extent, by Y-chromosome haplogroup analysis of Middle-Eastern and European samples. Up to date, no genomic regions that are shared among Arab Muslim and Jewish chromosomes and are unique to these populations have been reported. Here, we report of a rare achromatopsia-causing CNGA3 mutation (c.1585G>A) presents in both Arab Muslim and Oriental Jewish patients. A haplotype analysis of c.1585G>A-bearing chromosomes from Middle Eastern and European origins revealed a shared Muslim-Jewish haplotype, which is different from those detected in European patients, indicating a recurrent mutation stratified by a Jewish-Muslim founder effect. Comprehensive whole-genome haplotype analysis using 250 K single nucleotide polymorphism arrays revealed a large homozygous region of ~11 Mbp shared by both Arab Muslim and Oriental Jewish chromosomes. A subsequent microsatellite analysis of a 21.5 cM interval including CNGA3 and the adjacent chromosome 2 centromere revealed a unique and extremely rare haplotype associated with the c.1585G>A mutation. The age of the shared c.1585G>A mutation was calculated using the microsatellite genotyping data to be about 200 generations ago. A similar analysis of mutation age based on the Arab Muslim data alone showed that the mutation was unlikely to be the product of a recent gene flow event. The data present here demonstrate a large (11 Mbp) genomic region that is likely to originate from an ancient common ancestor of Middle-Eastern Arab Muslims and Jews who lived approximately 5,000 years ago.

Updating Phylogeny of Mitochondrial DNA Macrohaplogroup M in India: Dispersal of Modern Human in South Asian Corridor

To construct maternal phylogeny and prehistoric dispersals of modern human being in the Indian sub continent, a diverse subset of 641 complete mitochondrial DNA (mtDNA) genomes belonging to macrohaplogroup M was chosen from a total collection of 2,783 control-region sequences, sampled from 26 selected tribal populations of India. On the basis of complete mtDNA sequencing, we identified 12 new haplogroups - M53 to M64; redefined/ascertained and characterized haplogroups M2, M3, M4, M5, M6, M8′C′Z, M9, M10, M11, M12-G, D, M18, M30, M33, M35, M37, M38, M39, M40, M41, M43, M45 and M49, which were previously described by control and/or coding-region polymorphisms. Our results indicate that the mtDNA lineages reported in the present study (except East Asian lineages M8′C′Z, M9, M10, M11, M12-G, D ) are restricted to Indian region.The deep rooted lineages of macrohaplogroup ‘M’ suggest in-situ origin of these haplogroups in India. Most of these deep rooting lineages are represented by multiple ethnic/linguist groups of India. Hierarchical analysis of molecular variation (AMOVA) shows substantial subdivisions among the tribes of India (Fst = 0.16164). The current Indian mtDNA gene pool was shaped by the initial settlers and was galvanized by minor events of gene flow from the east and west to the restricted zones. Northeast Indian mtDNA pool harbors region specific lineages, other Indian lineages and East Asian lineages. We also suggest the establishment of an East Asian gene in North East India through admixture rather than replacement.

The Complex and Diversified Mitochondrial Gene Pool of Berber Populations

The mitochondrial DNA variation of 295 Berber-speakers from Morocco (Asni, Bouhria and Figuig) and the Egyptian oasis of Siwa was evaluated by sequencing a portion of the control region (including HVS-I and part of HVS-II) and surveying haplogroup-specific coding region markers. Our findings show that the Berber mitochondrial pool is characterized by an overall high frequency of Western Eurasian haplogroups, a somehow lower frequency of sub-Saharan L lineages, and a significant (but differential) presence of North African haplogroups U6 and M1, thus occupying an intermediate position between European and sub-Saharan populations in PCA analysis. A clear and significant genetic differentiation between the Berbers from Maghreb and Egyptian Berbers was also observed. The first are related to European populations as shown by haplogroup H1 and V frequencies, whereas the latter share more affinities with East African and Nile Valley populations as indicated by the high frequency of M1 and the presence of L0a1, L3i, L4*, and L4b2 lineages. Moreover, haplogroup U6 was not observed in Siwa. We conclude that the origins and maternal diversity of Berber populations are old and complex, and these communities bear genetic characteristics resulting from various events of gene flow with surrounding and migrating populations.

Patterns in genetic diversity of Trifolium pallescens populations do not reflect chronosequence on alpine glacier forelands

How does genetic diversity within populations of plants develop during primary succession on alpine glacier forelands? Theory predicts that pioneer populations are characterized by low genetic diversity due to founder effects and that genetic diversity increases within populations as they mature and recurrent gene flow occurs. However, few genetic studies have so far been carried out on plants on glacier forelands. In this study, we analysed the development of genetic diversity with time for populations of Trifolium pallescens along successional series (chronosequences) on three parallel glacier forelands in the European Alps, using neutral amplified fragment length polymorphism. No general trend in the development of genetic diversity was observed with increasing population age: even pioneer populations harboured substantial genetic diversity. Assignment tests showed that the latter consist of a genetic sub-sample from several source areas, and not just from other populations on the glacier forelands. We also detected some long distances-that is, inter-valley gene flow events. However, gene flow was not spatially unrestricted, as shown by a weak isolation by distance pattern within glacier valleys. The actual patterns of genetic diversity along the chronosequences are a result of the combination of factors, such as gene flow and growth rate, influenced by site- and species-specific attributes.

Brief Communication: Human cranial variation fits iterative founder effect model with African origin

Recent studies comparing craniometric and neutral genetic affinity matrices have concluded that, on average, human cranial variation fits a model of neutral expectation. While human craniometric and genetic data fit a model of isolation by geographic distance, it is not yet clear whether this is due to geographically mediated gene flow or human dispersal events. Recently, human genetic data have been shown to fit an iterative founder effect model of dispersal with an African origin, in line with the out-of-Africa replacement model for modern human origins, and Manica et al. (Nature 448 (2007) 346-349) have demonstrated that human craniometric data also fit this model. However, in contrast with the neutral model of cranial evolution suggested by previous studies, Manica et al. (2007) made the a priori assumption that cranial form has been subject to climatically driven natural selection and therefore correct for climate prior to conducting their analyses. Here we employ a modified theoretical and methodological approach to test whether human cranial variability fits the iterative founder effect model. In contrast with Manica et al. (2007) we employ size-adjusted craniometric variables, since climatic factors such as temperature have been shown to correlate with aspects of cranial size. Despite these differences, we obtain similar results to those of Manica et al. (2007), with up to 26% of global within-population craniometric variation being explained by geographic distance from sub-Saharan Africa. Comparative analyses using non-African origins do not yield significant results. The implications of these results are discussed in the light of the modern human origins debate.

Cross-Species Amplification of Coconut Microsatellite Markers in Rattans

Summary Cross-species amplification of microsatellite loci is considered to be a time-saving as well as a cost-effective approach for developing locus specific markers for new species. In an attempt to identify molecular markers to determine gene flow events and genetic differentiation of populations in rattans, microsatellite primer pairs developed for Cocos nucifera (Arecaceae) were examined for cross-species amplification in rattans. Of the six microsatellite primer pairs screened, two (CNZ34 and CN2A5) yielded good cross-species amplification across different rattan genera and species from South and Southeast Asia. Based on microsatellite-specific PCR amplification products, cluster analysis was performed. The dendrogram indicated a clear grouping of rattans based on their genera and species. The coconut locus specific primer pairs could be successfully used to construct molecular differentiation of rattan genera across different geographical locations.

Investigation of rice transgene flow in compass sectors by using male sterile line as a pollen detector

Rice is the most important staple food in the world. The rapid development of transgenic rice and its future commercialization have raised concerns regarding transgene flow and its potential environmental risk. It is known that rice is a self-pollinated crop; the outcrossing rate between common cultivars is generally less than 1%. In order to improve the detection sensitivity of rice transgene flow, a male sterile (ms) line BoA with a high outcrossing rate was used as a pollen detector in this study. A concentric circle design was adopted, in which the transgenic rice B2 containing bar gene as a pollen donor was planted in the center circle and the recipient BoA was planted in eight compass sectors. The frequency of transgene flow in compass sectors was analyzed by continuous sampling to generate cumulative data. The results of two years with sound reproducibility demonstrated that the rice gene flow was closely associated with the wind direction. According to the mean frequency of transgene flow, the eight sectors can be divided into two groups: a higher frequency group downstream of the prevailing wind (DPW) with a mean frequency ranging from 6.47 to 26.24%, and a lower frequency group lateral to or upstream of the prevailing wind (UPW) with a mean frequency of 0.39 to 3.03%. On the basis of the cumulative data, 90-96% of the cumulative gene flow events occurred in the four DPW sectors, while it was 4-10% in the four UPW sectors. By using these systematic data, simulation models and isograms of transgene flow in the eight compass sectors were calculated and drawn, respectively.

Distinguishing Terminal Monophyletic Groups from Reticulate Taxa: Performance of Phenetic, Tree-Based, and Network Procedures

Hybridization is a well-documented, natural phenomenon that is common at low taxonomic levels in the higher plants and other groups. In spite of the obvious potential for gene flow via hybridization to cause reticulation in an evolutionary tree, analytical methods based on a strictly bifurcating model of evolution have frequently been applied to data sets containing taxa known to hybridize in nature. Using simulated data, we evaluated the relative performance of phenetic, tree-based, and network approaches for distinguishing between taxa with known reticulate history and taxa that were true terminal monophyletic groups. In all methods examined, type I error (the erroneous rejection of the null hypothesis that a taxon of interest is not monophyletic) was likely during the early stages of introgressive hybridization. We used the gradual erosion of type I error with continued gene flow as a metric for assessing relative performance. Bifurcating tree-based methods performed poorly, with highly supported, incorrect topologies appearing during some phases of the simulation. Based on our model, we estimate that many thousands of gene flow events may be required in natural systems before reticulate taxa will be reliably detected using tree-based methods of phylogeny reconstruction. We conclude that the use of standard bifurcating tree-based methods to identify terminal monophyletic groups for the purposes of defining or delimiting phylogenetic species, or for prioritizing populations for conservation purposes, is difficult to justify when gene flow between sampled taxa is possible. As an alternative, we explored the use of two network methods. Minimum spanning networks performed worse than most tree-based methods and did not yield topologies that were easily interpretable as phylogenies. The performance of NeighborNet was comparable to parsimony bootstrap analysis. NeighborNet and reverse successive weighting were capable of identifying an ephemeral signature of reticulate evolution during the early stages of introgression by revealing conflicting phylogenetic signal. However, when gene flow was topologically complex, the conflicting phylogenetic signal revealed by these methods resulted in a high probability of type II error (inferring that a monophyletic taxon has a reticulate history). Lastly, we present a novel application of an existing nonparametric clustering procedure that, when used against a density landscape derived from principal coordinate data, showed superior performance to the tree-based and network procedures tested.

Early Pleistocene Homo erectus fossils from Konso, southern Ethiopia

Homo erectus has been broadly defined to include fossils from Africa, Asia, and possibly Europe, or restricted to a supposedly confined Asian clade. Recently discovered fossils of H. erectus are allowing new insights into aspects of its evolution, such as the timing and mode of the species’ emergence in Africa and its relationship to Asian populations. However, the currently available African record predating 1.0 Ma is poor, consisting of the Turkana basin, Olduvai and the more limited South African materials. Here, we describe and compare eight craniodental fossils of ~1.4 Ma recovered from Konso, Ethiopia, that we attribute to H. erectus. These include KGA10-1, one of the better-preserved H. erectus mandibular specimens known from eastern Africa, and other fragmentary dental and cranial remains. The Konso H. erectus fossils show a mosaic of primitive and derived features. These include a large and thick mandibular corpus, a moderately developed lateral prominence, a reduced premolar morphology, and a tendency for smaller relative sizes of the posterior molars compared with earlier Homo. In some dentognathic details, such as the lack of a buccolingually narrow M1 and the presence of double mental foramina, the Konso fossils differ from eastern African H. erectus of ≥1.5 Ma. The fragmentary cranial remains exhibit weak angular and occipital tori, and an apparently weak occipital flexion, as with the eastern African H. erectus examples known from ~1.65 to 1.2 Ma. The available evidence is consistent with the interpretation that African early H. erectus shows morphological continuity within the ~1.65 to 1.0 Ma time period, with relatively little morphological evolution prior to 1.4 Ma and advanced dentognathic gracility occurring sometime thereafter. The Konso evidence corroborates the hypothesis that the African H. erectus populations represent a variable but continuous evolutionary succession that was a likely source of multiple events of gene flow to the Eurasian continent.

Reproductive biology and mating system estimates of two Andean melocacti, Melocactus schatzlii and M. andinus (Cactaceae).

The genus Melocactus comprises 36 species of globose cacti with the most derived traits in the Cereeae tribe. It is the proper study system to examine what are the most derived reproductive strategies within that tribe. This study aims to characterize the reproductive biology and to estimate the mating system parameters of two Andean melocacti, Melocactus schatzlii and M. andinus. The reproductive attributes of the two species were described, including floral morphology, anthesis patterns, floral rewards, floral visitors and visitation patterns. Levels of self-compatibility and autonomous self-pollination were estimated by hand-pollination experiments. Mating system estimates were obtained by conducting progeny array analyses using isozymes. The flowers of the two species present the typical hummingbird-pollination syndrome. Despite their morphological resemblance, the two species differ in flower size, pollen and ovule production and anthesis pattern. Their main pollinator agents are hummingbirds, four species in M. schatzlii and one species in M. andinus. Both cacti are self-compatible and capable of self-pollination without the aid of pollen vectors. Population-level outcrossing rate was higher for M. schatzlii (t(m)=0.9) than for M. andinus (t(m)=0.4). At the family level, outcrossing rates for most mothers of M. schatzlii were higher (t(m)>0.8) than for M. andinus (t(m)<0.5). Although the two cacti are capable of selfing, M. schatzlii is a predominantly outcrossing species, while M. andinus behaves as a mixed-mating cactus. Hummingbirds are the only pollinators responsible for outcrossing and gene flow events in these species. In their absence, both melocacti set seeds by selfing. Based on its low population size, restricted distribution in Venezuela, low rates of floral visits, and high levels of inbreeding, M. andinus is considered to be an endangered species deserving further study to define its conservation status.

Genetic admixture of burbot (Teleostei: Lota lota) in Lake Constance from two European glacial refugia

The burbot, Lota lota, is the only freshwater species of the codfish family and has a Holarctic distribution. Pleistocene glaciations caused significant geographical differentiation in the past, but its life history characterized by winter spawning migrations over large distances is likely to homogenize populations by contemporary gene flow. We investigated the population genetic structure of 541 burbots from Lake Constance and adjacent Rhine and Danube tributaries in Europe using the entire mitochondrial DNA (mtDNA) control region and 11 microsatellites. Microsatellites revealed considerable population divergence (F(ST) = 0.26) and evidenced recent bottlenecks in two Central European rivers. In accordance to previous evidence two main phylogeographic lineages (Atlantic and Danubian) were found co-occurring at similar frequencies in Lake Constance, where they currently undergo random mating as indicated by microsatellites. The Danubian lineage contributed only a small proportion to the lake's mtDNA diversity, and probably expanded within the lake shortly after its formation approximately 10,000-15,000 BP. The larger Atlantic haplotype diversity suggested a population expansion older than the lake itself. Levels of admixture at microsatellite loci were less obvious due to their high variability, and coalescence methods were used to estimate past admixture proportions. Our results reinforce a model of a two-step colonization of Europe by burbot from an ancestral Danubian refuge, and confirm the persistence of a secondary Atlantic refuge, as proposed to exist for other freshwater fish. We conclude that the present-day burbot population in Lake Constance bears the genetic signature of both contemporary gene flow and historical separation events.

Modeling the Influence of Gene Flow and Selection Pressure on the Frequency of a GE Herbicide‐Tolerant Trait in Non‐GE Wheat and Wheat Volunteers

Different types of transgenic wheat (Triticum aestivum L.) will be ready for commercialization within the next decade, including varieties with higher yields, greater tolerance to biotic and abiotic stresses, and resistance to herbicides. The release of genetically engineered (GE) wheat may require segregation of GE and non‐GE wheat to satisfy international markets. Before GE wheat is released, it is important to understand the movement of a GE trait within the agronomic production system. This study evaluated the effects of gene flow and selection pressure on the frequency of a GE trait (herbicide tolerance) in non‐GE wheat and wheat volunteers. Gene flow of GE traits to non‐GE wheat is inevitable through pollen or seed movement. When a GE trait does not confer a selective advantage in the production system, the frequency of the GE trait within non‐GE wheat will be a function of the rate of gene flow. Low rates of gene flow will lead to low levels of the GE trait in the non‐GE crop. With repeated gene flow events, the frequency of the GE trait may slowly increase in the non‐GE crop. When the GE trait has a selective advantage, the frequency of the GE trait will increase rapidly in volunteer populations of the non‐GE crop. Herbicide tolerance is an example of a GE trait that provides a high selective advantage when the herbicide is applied in the production system. Predictive models show that even with very low rates of initial gene flow, frequent applications of a highly effective herbicide will quickly increase the frequency of the herbicide‐tolerant (HT) GE trait in volunteer populations. This has negative implications for control of volunteers and the ability to maintain tolerance levels of GE traits in non‐GE wheat crops.

Fine‐scale genetic structure of life history stages in the food‐deceptive orchid Orchis purpurea

In natural plant populations, fine-scale spatial genetic structure can result from limited gene flow, selection pressures or historical events, but the role of each factor is in general hard to discern. One way to investigate the origination of spatial genetic structure within a plant population consists of comparing spatial genetic structure among different life history stages. In this study, spatial genetic structure of the food-deceptive orchid Orchis purpurea was determined across life history stages in two populations that were regenerating after many years of population decline. Based on demographic analyses (2001-2004), we distinguished between recruits and adult plants. For both sites, there was no difference in the proportion of polymorphic loci and expected heterozygosity between life history stages. However, spatial autocorrelation analyses showed that spatial genetic structure increased in magnitude with life history stage. Weak or no spatial genetic structure was observed for recruits, whereas adult plants showed a pattern that is consistent with that found in other species with a predominantly outcrossing mating system. The observed differences between seedlings and adults are probably a consequence of changes in management of the two study sites and associated demographic changes in both populations. Our results illustrate that recurrent population crashes and recovery may strongly affect genetic diversity and fine-scale spatial genetic structure of plant populations.

The effects of inbreeding, outbreeding and long‐distance gene flow on survivorship in North American populations of Silene vulgaris

Summary Silene vulgaris was introduced from Europe to North America prior to 1800. We evaluated the influence of the resulting population structure on traits related to fitness in a two generation series of glasshouse crosses. Plants were either self‐fertilized, outcrossed within local populations, outcrossed between local populations or outcrossed between three geographical regions separated by &gt; 150 km. Inbreeding depression following self‐fertilization occurred in nearly every maternal lineage studied but its magnitude varied among geographical regions, especially when the fitness component compared was seed germination. The consequences of long‐distance gene flow varied among geographical regions: crosses between some pairs of regions resulted in fitter offspring than within region outcrosses (i.e. heterosis), whereas other pairs of regions showed outbreeding depression (offspring of more distant crosses were less fit). Individuals derived from self‐fertilization of F1 individuals were fitter if the first crosses had been made between populations or regions rather than within populations, both in terms of seed germination and seedling survivorship. The benefits of gene flow therefore persist for at least one generation beyond that created by the gene flow event. The fitness of offspring of crosses between F1 individuals and their maternal population did not depend on the relatedness of the parents of the F1. Thus, there was no evidence of outbreeding depression following recombination within F1 individuals whose creation involved gene flow. Our results imply that alteration of the rate of self‐fertilization or the rate of gene flow between populations of S. vulgaris could affect the demographic characters that influence population establishment and persistence in this species.

Population structure in the Atlantic salmon: insights from 40 years of research into genetic protein variation

Electrophoretic studies of proteins remain a primary source of insight into genetic diversity in many species including the Atlantic salmon Salmo salar, one of the most culturally and economically important fish species of the North Atlantic region. Since 1966, &gt;350 scientific papers on protein variation have been published encompassing 25 000+ salmon from over 400 locations in &gt;200 river systems across the species’ distribution. Variation has been detected at 30% of the 110 protein loci screened, though most studies examine &lt;40. The method has been applied largely to the investigation of population structure and differentiation, but work has also led to the systematic revision of the genus Salmo and remains the primary source of insight into hybridization in the wild with brown trout Salmo trutta. Spatial patterns of differentiation show temporal stability, both within and among river systems, and strongly support structuring of the species into river and tributary specific populations and the designation of European and North American populations as distinct sub‐species. They also show widespread regional differentiation within both continents, beyond the marked subcontinental differences between Baltic Sea and Atlantic Ocean populations in Europe. Most of the differentiation probably reflects gene flow and founder events associated with colonization following the retreat of the glaciers from much of the species’ modern range. However, variation at MEP‐2* shows strong correlations with environmental temperature, both within and among rivers, and associations with phenotypic performance. This suggests selection is acting on the locus and provides compelling evidence for the local adaptation of populations. Protein studies have led to more population centred management of the species and have been exploited in the discrimination of regional stocks in mixed stock analysis in high seas fisheries, particularly in the Baltic Sea, and as markers for the assessment of stocking success. They have also advanced insight into how the genetic character of populations can be changed in cultivation and the potential impact of salmon aquaculture and stocking on wild populations. The method has been largely superseded by DNA based analyses, but the results remain highly relevant to Atlantic salmon management and conservation and are an irreplaceable data set for studying genetic stability of populations over time.

Allelic diversity at the Mhc‐DQA locus of woodmouse populations (Apodemus sylvaticus) present in the islands and mainland of the northern Mediterranean

ABSTRACTAim Polymorphism at neutral markers and at MHC loci in rodent populations living on islands is generally low. The main genetic factors that may contribute to a reduced level of genetic variability are genetic drift, reduced gene flow and founder events. We investigated the pattern of polymorphism at the second exon of the Mhc‐DQA gene in island populations of Apodemus sylvaticus and in their mainland counterparts to investigate the pattern of MHC polymorphism in a phylogeographical context and to assess the impact of insularity on diversity at this locus.Location Eight north Mediterranean populations of Apodemus sylvaticus were studied, including five island populations (Majorca, Minorca, Porquerolles, Port‐Cros and Sicily) and three mainland populations.Methods cDNA sequencing and nucleotide sequences analyses. Synonymous and non‐synonymous substitutions were examined at the PBR and non‐PBR sites. The DQA allelic distribution in populations was compared with the woodmouse phylogeography.Results This study presents novel DQA alleles. High polymorphism of the DQA locus is recorded in natural populations of A. sylvaticus with 13 alleles being widely distributed irrespective of the geographical origin and palaeoclimatic history of populations. The DQA locus does not show the expected pattern for non‐synonymous substitutions at the PBR sites. However, island populations show a weak loss of polymorphism in comparison with their mainland counterparts.Main conclusions The DQA locus in the woodmouse seems to be subject to weak selection and does not allow resolution of phylogeographical relationships among European woodmouse populations. The presence of at least three alleles in island populations and the maintenance of five alleles between the two European lineages over 1.5 Myr suggest that balancing selection may act within populations, and more precisely within island populations, to maintain genetic variability. This study shows that phylogeographical studies are a prerequisite for any genetic investigation of selected genes in natural populations.