Microsatellite analysis of genetic variation among and within Alpine marmot populations in the French Alps

The genetic structure of the Alpine marmot, Marmota marmota, was studied by an analysis of five polymorphic microsatellite loci. Eight locations were sampled in the French Alps, one from Les Ecrins valley (n = 160), another from La Sassière valley (n = 289) and the six others from the Maurienne valley (n = 139). Information on social group structure was available for both Les Ecrins and La Sassière but not for the other samples. The high levels of genetic diversity observed are at odds with the results obtained using microsatellites, minisatellites and allozymes on Alpine marmots from Germany, Austria and Switzerland. Strong deficits in heterozygotes were found in Les Ecrins and La Sassière. They are caused by a Wahlund effect due to the family structure (i.e. differentiation between the family groups). The family groups exhibit excess of heterozygotes rather than deficits. This may be caused by outbreeding and this is compatible with recent results from the genetics of related social species when information on the social structure is taken into account. The observed outbreeding could be the result of females mating with transient males or males coming from neighbouring colonies. Both indicate that the species may not be as monogamous as is usually believed. The results are also compatible with a male-biased dispersal but do not allow us to exclude some female migration. We also found a significant correlation between geographical and genetic distance indicating that isolation by distance could be an issue in marmots. This study is the first that analysed populations of marmots taking into account the social structure within populations and assessing inbreeding at different levels (region, valley, population, and family groups). Our study clearly demonstrated that the sampling strategy and behavioural information can have dramatic effects on both the results and interpretation of the genetic data.     

Factor 13 B (FSF) polymorphism in the Swiss population, with reference to European frequency gradients]

Phenotype and allele frequencies of the coagulation factor 13 B (FSF B) of three Swiss populations (Northern Switzerland, upper Rhone valley and valley of Safien) have been determined after electrophoresis and passive immunoblotting and are discussed with respect to the geographical distribution and to the history of these populations. The populations of the upper Rhone valley and the valley of Safien reveal a closer genetical relationship obviously due to the migration of the antecedents of the recent Safier from the Rhone valley to the Safien valley from the 13th to 14th century. The allele frequencies of the Swiss German population fit rather well the North-South genetical cline which has to be considered in the light of the early settlement of Central Europe and of the numerous migrations thereafter.     

Odontometric microdifferentiation of transplanted Mexican Indian populations: Cuanalan and Saltillo

This study documents odontometric variation in four populations of related genetic background. It is found that the transplanted populations of Cuanalan and Saltillo have undergone significant microdifferentiation in tooth size relative to the two home valley populations. The extent and direction of this microdifferentiation is seen as reflecting differential amounts of admixture from African and European sources in demographic subunits of the two transplanted populations. The dental variables found to discriminate significantly between populations are the same variables predicted to be evolutionarily labile by Butler's Field Theory. Principal component analysis confirms the presence of morphological fields in these data and supports the position that each class has a stable tooth, with stability decreasing with increasing distance from the key tooth. The importance of hybridization in determining which variables significantly discriminate between populations is confounded by the effects of development of the dentition in morphogenetic fields. These data suggest the odontometric data provide an adequate, if somewhat conservative, base from which to evaluate microdifferentiation of human populations.     

Spanish colonial effects on Native American mating structure and genetic variability in northern and central Florida: Evidence from Apalachee and western Timucua

Standard population genetic analyses are implemented for a series of precontact and contact period samples from central and northern Florida to investigate changes in genetic variability and population affinity coincident with the establishment of Spanish missions during the 17th century. Estimates of F(ST) based on odontometric data indicate limited heterogeneity for the Apalachee samples, suggestive of some degree of within-group endogamy for this ethnic group prior to contact. This corresponds well with ethnohistoric reconstructions indicating that Apalachee were populous, partially linguistically isolated from its neighbors, and involved in persistent cycles of warfare with neighboring groups. Estimates of extralocal gene flow for the Apalachee samples indicate limited initial changes in the mating structure of these populations. After 1650, however, extralocal gene flow increases, consistent with evidence for dramatic population movements throughout northern Florida and increased Spanish presence in the province, particularly at the mission of San Luis. Inclusion of non-Apalachee outgroups does not increase estimates of genetic heterogeneity, as was expected based on ethnohistoric data. The pattern of genetic distances suggests a biological division between north and south Florida population groups, consistent with archaeological and ethnohistoric data, and similarly indicates some distinction between precontact and postcontact local groups. Differential extralocal gene flow experienced by pre-1650 Apalachee and Timucua populations suggests localized mission experience. The Apalachee, with large, dense populations, experienced limited initial changes in genetic diversity or mating structure. However, after 1650 they were apparently involved in a much more expansive mating network that may have included Spaniards and immigrant Native American groups to the region. These results are in contrast to the mission experience of the Guale Indians of the Georgia coast.     

Rapid evolutionary escape by large populations from local fitness peaks is likely in nature

Fitness interactions between loci in the genome, or epistasis, can result in mutations that are individually deleterious but jointly beneficial. Such epistasis gives rise to multiple peaks on the genotypic fitness landscape. The problem of evolutionary escape from such local peaks has been a central problem of evolutionary genetics for at least 75 years. Much attention has focused on models of small populations, in which the sequential fixation of valley genotypes carrying individually deleterious mutations operates most quickly owing to genetic drift. However, valley genotypes can also be subject to mutation while transiently segregating, giving rise to copies of the high fitness escape genotype carrying the jointly beneficial mutations. In the absence of genetic recombination, these mutations may then fix simultaneously. The time for this process declines sharply with increasing population size, and it eventually comes to dominate evolutionary behavior. Here we develop an analytic expression for N(crit), the critical population size that defines the boundary between these regimes, which shows that both are likely to operate in nature. Frequent recombination may disrupt high-fitness escape genotypes produced in populations larger than N(crit) before they reach fixation, defining a third regime whose rate again slows with increasing population size. We develop a novel expression for this critical recombination rate, which shows that in large populations the simultaneous fixation of mutations that are beneficial only jointly is unlikely to be disrupted by genetic recombination if their map distance is on the order of the size of single genes. Thus, counterintuitively, mass selection alone offers a biologically realistic resolution to the problem of evolutionary escape from local fitness peaks in natural populations.     

Genetic diversity and structure of managed and semi-natural populations of cocoa (Theobroma cacao) in the Huallaga and Ucayali Valleys of Peru

BACKGROUND AND AIMS: Cocoa (Theobroma cacao) is indigenous to the Amazon region of South America, and it is well known that the Peruvian Amazon harbours a large number of diverse cocoa populations. A small fraction of the diversity has been collected and maintained as an ex-situ germplasm repository in Peru. However, incorrect labelling of accessions and lack of information on genetic diversity have hindered efficient conservation and use of this germplasm. This study targeted assessment of genetic diversity and population structure in a managed and a semi-natural population. METHODS: Using a capillary electrophoresis genotyping system, 105 cocoa accessions collected from the Huallaga and Ucayali valleys of Peru were fingerprinted. Based on 15 loci SSR profiles, genetic identity was examined for each accession and duplicates identified, population structure assessed and genetic diversity analysed in these two populations. KEY RESULTS: Ten synonymous mislabelled groups were identified among the 105 accessions. The germplasm group in the Huallaga valley was clearly separated from the group in Ucayali valley by the Bayesian assignment test. The Huallaga group has lower genetic diversity, both in terms of allelic richness and of gene diversity, than the Ucayali group. Analysis of molecular variance suggested genetic substructure in the Ucayali group. Significant spatial correlation between genetic distance and geographical distances was detected in the Ucayali group by Mantel tests. CONCLUSIONS: These results substantiate the hypothesis that the Peruvian Amazon hosts a high level of cocoa genetic diversity, and the diversity has a spatial structure. The introduction of exotic seed populations into the Peruvian Amazon is changing the cocoa germplasm spectrum in this region. The spatial structure of cocoa diversity recorded here highlights the need for additional collecting and conservation measures for natural and semi-natural cocoa populations.     

The phylogeographical history of the Iberian steppe plant Ferula loscosii (Apiaceae): a test of the abundant-centre hypothesis

The geology and climate of the western Mediterranean area were strongly modified during the Late Tertiary and the Quaternary. These geological and climatic events are thought to have induced changes in the population histories of plants in the Iberian Peninsula. However, fine-scale genetic spatial architecture across western Mediterranean steppe plant refugia has rarely been investigated. A population genetic analysis of amplified fragment length polymorphism variation was conducted on present-day, relict populations of Ferula loscosii (Apiaceae). This species exhibits high individual/population numbers in the middle Ebro river valley and, according to the hypothesis of an abundant-centre distribution, these northern populations might represent a long-standing/ancestral distribution centre. However, our results suggest that the decimated southern and central Iberian populations are more variable and structured than the northeastern ones, representing the likely vestiges of an ancestral distribution centre of the species. Phylogeographical analysis suggests that F. loscosii likely originated in southern Spain and then migrated towards the central and northeastern ranges, further supporting a Late Miocene southern-bound Mediterranean migratory way for its oriental steppe ancestors. In addition, different glacial-induced conditions affected the southern and northern steppe Iberian refugia during the Quaternary. The contrasting genetic homogeneity of the Ebro valley range populations compared to the southern Iberian ones possibly reflects more severe bottlenecks and subsequent genetic drift experienced by populations of the northern Iberia refugium during the Pleistocene, followed by successful postglacial expansion from only a few founder plants.     

Population structure of brush-tailed rock-wallaby (Petrogale penicillata) colonies inferred from analysis of faecal DNA

Genetic data obtained using faecal DNA were used to elucidate the population structure of four brush-tailed rock-wallaby (Petrogale penicillata) colonies located in Wollemi National Park, New South Wales. The results suggested that the four sampled colonies are genetically differentiated and do not form a panmictic unit. Based on assignment tests, approximately 5% of sampled individuals were inferred to be dispersers and both male and female migrants were detected. Multilocus spatial autocorrelation analyses provided evidence for increased philopatry among females compared to males within the largest colony in the valley. Females in close spatial proximity were more genetically similar than expected under a random distribution of females, and females separated by more than 400 m were less genetically similar than expected. In contrast, there was no evidence of a significant clustering of related males. This suggests that within-colony dispersal is male biased. We also investigated the best strategies for conserving genetic diversity in this population. All of the four sampled colonies were found to contain distinct components of the genetic diversity of the Wolgan Valley P. penicillata population and loss of any colony is likely to result in the loss of unique alleles. Conservation and management plans should take into account that these colonies represent genetically differentiated discrete subpopulations. This approach is also the best strategy for maintaining the genetic diversity of the populations in this valley.     

Invasive tall annual willowherb (<Emphasis Type="Italic">Epilobium brachycarpum</Emphasis> C. Presl) in Central Europe originates from high mountain areas of western North America

Identification of the source population of biological invasions has important consequences for the effective control and management of the invader. Tall annual willowherb (Epilobium brachycarpum) is a relatively recent and rapidly spreading neophyte in Europe that was first detected in 1978. Populations of tall annual willowherb from Germany and northern France were analysed by AFLP fingerprinting together with samples from five different localities in its native range in western North America. Three genetically different groups were found corresponding to different altitude zones in the native range. The F_ST is high among all samples indicating a strong genetical separation of the three groups. Invasive populations showed much lower genetic diversity than the native population. Additionally invasive populations revealed genetic affinities to North American specimens originating particularly from high mountain areas. The two large German populations and the population from northern France are genetically distinct while the individuals within the populations are genetically uniform. This suggests multiple introduction events rather than one introduction with consequent spreading across Europe. A third small German population from Treis-Karden in the Mosel valley clusters with North American lowland populations but suffers from frost damage and its permanent establishment is doubtful.     

Conservation genetics of the endangered Iberian steppe plant Ferula loscosii (Apiaceae)

Ferula loscosii (Lange) Willk (Apiaceae) is a threatened endemic species native to the Iberian Peninsula. The plant has a narrow and disjunct distribution in three regions, NE, C and SE Spain. Genetic variability within and among 11 populations from its natural distribution was assessed using allozymes. Intermediate levels of genetic diversity were detected in F. loscosii (P(99%) = 36.83; H(E) = 0.125; H(T) = 0.152). However, the highest genetic diversity (58%) corresponded to the threatened populations from SE and C Spain (H(T) = 0.169) rather than the more abundant and larger populations from NE Spain (Ebro valley) (H(T) = 0.122). Low to moderate levels of genetic structure were found among regional ranges (G(ST) = 0.134), and several statistical spatial correlation analyses corroborated substantial genetic differentiation among the three main regional ranges. However, no significant genetic differentiation was found among the NE Spain populations, except for a northernmost population that is geographically isolated. Outcrossing mating and other biological traits of the species could account for the maintenance of the present values of genetic diversity within populations. The existence of an ancestral late Tertiary wider distribution of the species in SE and C Spain, followed by the maintenance of different Quaternary refugia in these warmer areas, together with a more recent and rapid post-glacial expansion towards NE Spain, are arguments that could explain the low genetic variability and structure found in the Ebro valley and the higher levels of diversity in the southern Iberian populations.     

Population genetics suggests effectiveness of habitat connectivity measures for the European tree frog in Switzerland

1.  Governmental authorities in many countries financially support the implementation of habitat connectivity measures to enhance the exchange of individuals among fragmented populations. The evaluation of the effectiveness of such measures is crucial for future management directions and can be accomplished by using genetic methods.
2.  We retraced the population history of the European tree frog in two Swiss river valleys (Reuss and Thur), performed comprehensive population sampling to infer the genetic structure at 11 microsatellite markers, and used first-generation migrant assignment tests to evaluate the contemporary exchange of individuals.
3.  Compared with the Thur valley, the Reuss valley has lost almost double the number of breeding sites and exhibited a more pronounced genetic grouping. However, similar numbers of contemporary migrants were detected in both valleys. In the Reuss valley, 81% of the migration events occurred within the identified genetic groups, whereas in the Thur valley migration patterns were diffuse.
4.  Our results show that the connectivity measures implemented in the Reuss valley facilitated effective tree frog migration among breeding sites within distances up to 4 km. Nevertheless, the Reuss valley exhibited high genetic differentiation, which reflected the impact of barriers to tree frog movement such as the River Reuss. By contrast in the Thur valley, a larger number of breeding sites have been preserved and high admixture indicated exchange of individuals at distances up to 16 km.
5.   Synthesis and applications . We show that genetic methods can substantiate the effectiveness of connectivity measures taken in conservation management at the landscape scale. We urge responsible authorities from both river valleys to continue implementing connectivity measures and to create a dense network of breeding sites, as spatial gaps of 8 km are rarely traversed by tree frogs.     

Population genetic structure of peninsular Malaysia Malay sub-ethnic groups

Patterns of modern human population structure are helpful in understanding the history of human migration and admixture. We conducted a study on genetic structure of the Malay population in Malaysia, using 54,794 genome-wide single nucleotide polymorphism genotype data generated in four Malay sub-ethnic groups in peninsular Malaysia (Melayu Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis). To the best of our knowledge this is the first study conducted on these four Malay sub-ethnic groups and the analysis of genotype data of these four groups were compiled together with 11 other populations' genotype data from Indonesia, China, India, Africa and indigenous populations in Peninsular Malaysia obtained from the Pan-Asian SNP database. The phylogeny of populations showed that all of the four Malay sub-ethnic groups are separated into at least three different clusters. The Melayu Jawa, Melayu Bugis and Melayu Minang have a very close genetic relationship with Indonesian populations indicating a common ancestral history, while the Melayu Kelantan formed a distinct group on the tree indicating that they are genetically different from the other Malay sub-ethnic groups. We have detected genetic structuring among the Malay populations and this could possibly be accounted for by their different historical origins. Our results provide information of the genetic differentiation between these populations and a valuable insight into the origins of the Malay sub-ethnic groups in Peninsular Malaysia.     

Effects of landscape features on gene flow of valley oaks (<Emphasis Type="Italic">Quercus lobata</Emphasis>)

Landscape features affect habitat connectivity and patterns of gene flow and hence influence genetic structure among populations. We studied valley oak (Quercus lobata), a threatened species of California (USA) savannas and oak woodlands, with a distribution forming a ring around the Central Valley grasslands. Our main goal was to determine the role of topography and land cover on patterns of gene flow and to test whether elevation or land cover forms stronger barriers to gene flow among valley oak populations. We sampled valley oaks in 12 populations across the range of this species, genotyped each tree at eight nuclear microsatellite loci, and created a series of resistance surfaces by assigning different resistance values to land cover type and elevation. We also estimated recent migration rates and evaluated them with regard to landscape features. There was a significant but weak relationship between Euclidian distance and genetic distance. There was no relationship between genetic distances and land cover, but a significant relationship between genetic distances and elevation resistance. We conclude that gene flow is restricted by high elevations in the northern part of the valley oak range and by high elevations and the Central Valley further south. Migration rate analysis indicated some gene flow occurring east–west but we suggest that the high connectivity in the northern Central Valley is facilitating the formation of these links. We predict that southern populations may become more differentiated in the future through genetic isolation and local adaptation taking place in the face of climate change.     

Genetic differentiation of the marbled white butterfly, Melanargia galathea, accounts for glacial distribution patterns and postglacial range expansion in southeastern Europe

Isolation of Mediterranean species in the southern European peninsulas during the cold glacial phases often resulted in differentiation of several genetic lineages confined to the respective peninsulas. However, whilst there is good genetic evidence for multiple refugia in Iberia, there are only limited data available for the Balkans. Therefore, we wish to examine the hypothesis of a strong genetic structuring within southeastern Europe for the existence of multiple Balkan differentiation centres and/or several leading edges. As a model we use the marbled white butterfly, Melanargia galathea. We studied 18 allozyme loci of 564 individuals from 16 populations distributed over a large part of southeastern Europe. The single populations showed moderately high genetic diversity and no northward decline of genetic diversity was detected. The overall genetic differentiation between populations was considerable (F(ST) 7.0%). Cluster analysis discriminated three genetic groups: (i) a western flank in the former Yugoslavia, parts of eastern Austria and Hungary; (ii) an eastern flank with populations from Bulgaria and Romania (south of the southern Carpathians and eastern Carpathians); and (iii) the eastern Carpathian Basin. Hierarchical variance analysis distributed 53% of the variance among populations between these three groups. One sample from the Greek-Bulgarian border clustered within the eastern flank, but showed some tendency towards the eastern Carpathian Basin populations. Two populations from Carinthia clustered together with the eastern Carpathian Basin ones and a population from Styria showed an intermediate genetic composition between the three groups. Most probably, the eastern and the western flank groups are due to postglacial range expansion from the northeastern and the northwestern edges of the glacial differentiation centre (so-called leading edges). The eastern Carpathian Basin group may have resulted from postglacial expansion from northern Greece through valley systems of the central Balkan peninsula, maybe even expanding westwards north of the Balkan mountains reaching some parts of eastern Austria (e.g. Carinthia). Therefore, the Balkanic refugium of M. galathea may or may not have been continuous along the coastal areas of the Mediterranean, but must have been strongly genetically structured.     

Genetic evidence for the phylogenetic relationship between Na-Dene and Yeniseian speakers

Ruhlen's hypothesis, based on linguistic evidence, for a common phylogenetic origin of Na-Dene and Yeniseian speakers is tested using genetic data. Gene frequency data for the Kets, the only surviving Yeniseian speakers, were collected during a field study in 1993. Data for several Na-Dene groups, as well as other New World and Siberian populations, were compiled from the literature. These data were analyzed using R-matrix, principal components analysis, and Mantel tests. In a comparison of 10 New World and Siberian populations using eight alleles, 55.8% of the variation was accounted for by the first principal component, and 22.1% of the variation was subsumed by the second principal component. Contrary to Ruhlen's interpretation of the linguistic data, analysis of the genetic data shows that the Na-Dene cluster with other Native American populations, while the Kets genetically resemble the surrounding Siberian groups. This conclusion is further supported by correlations that are higher when the Kets are considered unrelated to Na-Dene speakers, and an insignificant partial correlation between genes and language when geography is held constant, indicating that spatial patterning accounts for most of the variation present in these populations.     

Phylogenetic information in polymorphic L1 and Alu insertions from East Asians and Native American populations

This study attempts to ascertain genetic affinities between Native American and East Asian populations by analyzing four polymorphic Alu insertions (PAIs) and three L1 polymorphic loci. These two genetic systems demonstrated strong congruence when levels of diversity and genetic distances were considered. Overall, genetic relatedness within Native American groups does not correlate with geographical and linguistic structure, although strong grouping for Native Americans with East Asians was demonstrated, with clear discrimination from African and European groups. Most of the variation was assigned to differences occurring within groups, but the interpopulation variation found for South Amerindians was recognizably higher in comparison to the other sampled groups of populations. Our data suggest that bottleneck events followed by strong influence of genetic drift in the process of the peopling of the Americas may have been determinant factors in delineating the genetic background of present-day South Amerindians. Since no clear subgroups were detected within Native Americans and East Asians, there is no indication of multiple waves in the early colonization of the New World.     

On the genetic interrelationships of South African Negroes

This study addresses the comparative genetic interrelationships between South African Negro groups. For this the genetic distances between seven ethnically defined Negro subsamples (total of 998 individuals) based on 24 genetic loci/polymorphisms are calculated by applying standard distance formulae. These computations offer an opportunity to evaluate the different polymorphisms in terms of their effects on the genetic distances. The genetic interrelationships thus computed are illustrated by way of dendrograms and are discussed in terms of their comparative significance. It follows from the findings that the Ndebele, Northern Sotho (Pedi), and Tswana form a closely related subcluster and that the Zulu and Swazi as well as the Venda and Shangana-Tsonga form two additional, more distant, subclusters. These results are discussed and tentatively interpreted against the background of the reported Khoisan admixture of the populations concerned as well as their ethnological history. The data are also compared to those derived from metric and dermatoglyphic studies. It is concluded that whereas there is some agreement between these categories of variation (genetic, metric, and dermatoglyphic) as far as the comparative evaluation of South African Negro groups is concerned, there also are discrepancies. These conclusions need to be explained in terms of evolutionary mechanisms (such as historic origins, hybridization, natural selection, and genetic drift) in order to obtain a more consistent and comprehensive comparative picture of the physical anthropology of southern African populations.     

Multiple differentiation centres of a non-Mediterranean butterfly species in south-eastern Europe

Aim  The analysis of the phylogeographical structures of many European species reveals the importance of Mediterranean glacial refugia for many thermophilic species, but also underlines the relevance of extra-Mediterranean glacial differentiation centres for a number of temperate species. In this context, phylogeographical analyses of species from south-eastern Europe are highly important for a comprehensive understanding of Europe as a whole.
Location  Romania and Bulgaria.
Methods  We analysed 19 allozyme loci for 615 individuals of the temperate butterfly species Erebia medusa from 28 populations.
Results  These populations had an intermediate genetic diversity, but the Bulgarian populations were significantly more diverse than the ones north of the Danube in Romania. The differentiation among populations was strong, and 52.1% of the genetic variance among populations was distributed between these two countries. The genetic differentiation was considerably stronger in Romania than in Bulgaria, but several sublineages were distinguished within each of these countries.
Main conclusions  The observed genetic structure is so strong that it is most probably the result of glacial differentiation processes in south-eastern Europe and not a post-glacial structure. The strong differentiation into the two groups north and south of the Danube suggests a separating effect by this river valley. The strong differentiation accompanied with genetic impoverishment in Romania suggests the existence of several differentiation centres: at least two small ones on the southern slopes of the southern Carpathians and one in the eastern Carpathian Basin. The considerably weaker differentiation among the Bulgarian samples and their significantly higher genetic diversity imply that gene flow occurred among different regions of Bulgaria during the last ice age.