Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction‐site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small N_e (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome‐wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high F_ST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high F_ST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small N_e in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential.     

Contrasting Levels of Variation in Neutral and Quantitative Genetic Loci on Island Populations of Moor Frogs (<Emphasis Type="Italic">Rana arvalis</Emphasis>)

Reduced levels of genetic variability and a prominent differentiation in both neutral marker genes and phenotypic traits are typical for many island populations as compared to their mainland conspecifics. However, whether genetic diversity in neutral marker genes reflects genetic variability in quantitative traits, and thus, their evolutionary potential, remains typically unclear. Moreover, the phenotypic differentiation on islands could be attributable to phenotypic plasticity, selection or drift; something which seldom has been tested. Using eight polymorphic microsatellite loci and quantitative genetic breeding experiments we conducted a detailed comparison on genetic variability and differentiation between Nordic islands (viz. Gotland, Öland and Læsø) and neighbouring mainland populations of moor frogs (Rana arvalis). As expected, the neutral variation was generally lower in island than in mainland populations. But as opposed to this, higher levels of additive genetic variation (V _A) in body size and tibia length were found on the island of Gotland as compared to the mainland population. When comparing the differentiation seen in neutral marker genes (F _ST) with the differentiation in genes coding quantitative traits (Q _ST) two different evolutionary scenarios were found: while selection might explain a smaller size of moor frogs on Gotland, the differentiation seen in tibia length could be explained by genetic drift. These results highlight the limited utility of microsatellite loci alone in inferring the causes behind an observed phenotypic differentiation, or in predicting the amount of genetic variation in ecologically important quantitative traits.     

GENETIC STRUCTURE OF NORWAY SPRUCE (PICEA ABIES): CONCORDANCE OF MORPHOLOGICAL AND ALLOZYMIC VARIATION

This study describes the population structure of Norway spruce (Picea abies) as revealed by protein polymorphisms and morphological variation. Electrophoretically detectable genetic variability was examined at 22 protein loci in 70 populations from the natural range of the species in Europe. Like other conifers, Norway spruce exhibits a relatively large amount of genetic variability and little differentiation among populations. Sixteen polymorphic loci (73%) segregate for a total of 51 alleles, and average heterozygosity per population is 0.115. Approximately 5% of the total genetic diversity is explained by differences between populations (G_ST = 0.052), and Nei's standard genetic distance is less than 0.04 in all cases. We suggest that the population structure largely reflects relatively recent historical events related to the last glaciation and that Norway spruce is still in a process of adaptation and differentiation. There is a clear geographic pattern in the variation of allele frequencies. A major part of the allelefrequency variation can be accounted for by a few synthetic variables (principal components), and 80% of the variation of the first principal component is “explained” by latitude and longitude. The central European populations are consistently depauperate of genetic variability, most likely as an effect of severe restrictions of population size during the last glaciation. The pattern of differentiation at protein loci is very similar to that observed for seven morphological traits examined. This similarity suggests that the same evolutionary forces have acted upon both sets of characters.     

Genetic diversity in micronesian island populations of the tropical tree campnosperma brevipetiolata (anacardiaceae)

Tropical plant species have been the focus of considerable attention in regard to their potential economic and social importance in the face of rapidly diminishing biodiversity in the tropics. Pacific Island species represent an even more fragile resource because different island populations are widely scattered and overall population sizes are small. We examined the distribution of genetic variation in Campnosperma brevipetiolata (Anacardiaceae), an upland rainforest tree species that is of potential use for both lumber and reforestation efforts in the Federated States of Micronesia (FSM). Seeds were collected from multiple populations on four island groups in the Caroline Islands (Kosrae, Pohnpei, and Yap in the FSM; and the Republic of Palau) and subjected to an electrophoretic analysis involving four polymorphic genetic loci. We hypothesized that variation on these islands would decrease with increasing distance from the presumed Indo-Malayan source of these island floras. Indeed, we found a trend of decreasing variation from west to east indicated by the mean number of alleles per locus (A = 1.50-1.33), effective number of alleles per locus (A_e = 1.14-1.12) and mean genetic diversity (H_e = 0.123-0.107). We also found little genetic differentiation among the islands (F_pt = 0.174) and among subpopulations within islands (F_sp = 0.047), indicating that either there are high levels of gene flow among the islands by seed dispersal or that these populations have not been established long enough for divergence to have occurred. The lack of divergence among islands observed for Campnosperma brevipetiolata suggests that germplasm sampled from any one island population would be a suitable starting point for plant breeding or reforestation efforts.     

Spatial and ecological population genetic structures within two island‐endemic Aeonium species of different niche width

The Crassulacean genus Aeonium is a well‐known example for plant species radiation on oceanic archipelagos. However, while allopatric speciation among islands is documented for this genus, the role of intra‐island speciation due to population divergence by topographical isolation or ecological heterogeneity has not yet been addressed. The aim of this study was to investigate intraspecific genetic structures and to identify spatial and ecological drivers of genetic population differentiation on the island scale. We analyzed inter simple sequence repeat variation within two island‐endemic Aeonium species of La Palma: one widespread generalist that covers a large variety of different habitat types (Ae. davidbramwellii) and one narrow ecological specialist (Ae. nobile), in order to assess evolutionary potentials on this island. Gene pool differentiation and genetic diversity patterns were associated with major landscape structures in both species, with phylogeographic implications. However, overall levels of genetic differentiation were low. For the generalist species, outlier loci detection and loci–environment correlation approaches indicated moderate signatures of divergent selection pressures linked to temperature and precipitation variables, while the specialist species missed such patterns. Our data point to incipient differentiation among populations, emphasizing that ecological heterogeneity and topographical structuring within the small scales of an island can foster evolutionary processes. Very likely, such processes have contributed to the radiation of Aeonium on the Canary Islands. There is also support for different evolutionary mechanisms between generalist and specialist species.     

Differentiation of Alpine marmot populations traced by DNA fingerprinting.

As revealed by allozyme studies, the genetic variation of the Alpine marmot (Marmota m. marmota) has been reduced by a species-wide bottleneck at the end of the last glaciation. Therefore the more variable microsatellite loci were used as a genetic marker system to investigate variablility and differentiation of four autochthonous and four allochthonous populations founded by the release of small numbers of individuals during the last 150 years. The microsatellite loci detected by the DNA-probe (ATCC)₄ were found to be polymorphic in all populations, but the amount of variation was lower than in comparable mammalian species. In spite of founder effects the variation in the allochthonous populations was not significanlty reduced compared to the autochthonous populations. The autochthonous populations from Austria and from the eastern part of Switzerland were genetically similar, only the population from western Switzerland was clearly differentiated from the others. In the allochthonous populations similarities in the microsatellite patterns reveal genetic affinities to putative autochthonous source populations of the founder individuals.     

Genetic structure of island populations of <Emphasis Type="Italic">Prunus lannesiana</Emphasis> var. <Emphasis Type="Italic">speciosa</Emphasis> revealed by chloroplast DNA,AFLP and nuclear SSR loci analyses

The wild flowering cherry Prunus lannesiana var. speciosa is highly geographically restricted, being confined to the Izu Islands and neighboring peninsulas in Japan. In an attempt to elucidate how populations of this species have established we investigated the genetic diversity and differentiation in seven populations (sampling 408 individuals in total), using three kinds of genetic markers: chloroplast DNA (cpDNA), amplified fragment length polymorphisms (AFLPs), and 11 nuclear SSR polymorphic loci. Eight haplotypes were identified based on the cpDNA sequence variations, 64 polymorphic fragments were scored for the AFLP markers, and a total of 154 alleles were detected at the 11 nuclear SSR loci. Analysis of molecular variance showed that among-population variation accounted for 16.55, 15.04 and 7.45% of the total detected variation at the cpDNA, AFLPs, and SSR loci, respectively. Thus, variation within populations accounted for most of the genetic variance for all types of markers, although the genetic differentiation among populations was also highly significant. For cpDNA variation, no clear structure was found among the populations, except that of the most distant island, although an “isolation by distance” pattern was found for each marker. Both neighbor-joining trees and structure analysis indicate that the genetic relationships between populations reflect geological variations between the peninsula and the islands and among the islands. Furthermore, hybridization with related species may have affected the genetic structure, and some genetic introgression is likely to have occurred.     

Genetic Differentiation of Pedunculate Oak Quercus robur L. in the European Part of Russia Based on RAPD Markers

Using randomly amplified polymorphic DNA markers (RAPD), genetic variation and differentiation in four populations of pedunculate oak Quercus robur L. were examined. The populations occupy a large part of the Quercus robur range in the European Russia (Voronezh and Novgorod oblasts; Republics of Mordovia and Bashkortostan). With each of six random primers (A02, A09, A17, B01, B08, B11), 96 DNA samples were analyzed by PCR. In all, 48 putative polymorphic RAPD loci were detected. We failed to reveal population-specific DNA fragments for any primer although the frequencies of 14 fragments were significantly different among populations. The oak populations studied exhibited high variability: 73–90% of genes were polymorphic and the effective allele number was about 1.4. The total genetic variation varied from 0.202 (Vor) to 0.245 (Nov), which corresponded to the estimates for populations of this species from Central and Western Europe. The populations examined showed low among-population differentiation (G _ST = 0.098); gene flow N _e m was 4.61. The proportion of among-population variation of the RAPD loci studied accounted for 7% of the total variability; more than 93% of the total variability was explained by individual and within-population variation.     

Genetic structure of Polytrichum formosum in relation to the breeding system as revealed by microsatellites

Microsatellite variation was determined for three Danish and three Dutch populations of the haploid moss species Polytrichum formosum to gain insight into the relative importance of sexual vs. asexual reproduction for the amount and structure of genetic variation. In general, low levels of microsatellite variation were observed within this species. Even when estimated for polymorphic loci only, the levels of microsatellite variability (P=90.6, A=4.3 and H_S=0.468) within populations were on average lower than those reported for most other plant species. In contrast, genotypic diversity was high within each of the examined populations, indicating that sexual reproduction is a very important determinant of the genetic structure of P. formosum within populations. In agreement with previous findings for allozyme data, no significant genetic differentiation (F_ST=0.028, R_ST=0.015) was observed neither between populations nor between regions approximately 450 km apart (Denmark vs. the Netherlands). These low levels of population differentiation observed for both types of genetic markers are probably best explained by a high level of effective spore dispersal (gene flow) between populations. Therefore, also on a large geographical scale sexual reproduction is the most important determinant of the genetic structure of P. formosum, despite the high potential to reproduce clonally.     

Analysis of F ST outliers at allozyme loci in Pacific salmon: implications for natural selection

Natural selection has been invoked to explain the observed geographic distribution of allozyme allele frequencies for a number of teleost species. The effects of selection on allozyme loci in three species of Pacific salmon were tested. A simulation-based approach to estimate the null distribution of population differentiation (F _ST) and test for F _ST outliers was used. This approach showed that a majority of allozyme loci conform to neutral expectations predicted by the simulation model, with relatively few F _ST outliers found. No consistent F _ST outlier loci were found across species. Analysis of population sub-groups based on geography and genetic identity reduced the number of outlier loci for some species, indicating that large geographic groups may include genetically divergent populations and/or that there is geographic heterogeneity in selection pressure upon allozyme loci. Two outlier allozyme loci found in this analysis, lactate dehydrogenase-B and malic enzyme, have been shown to be influenced by selection in other teleost species. This approach is also useful in identifying allozyme loci (or other genetic markers) that meet assumptions for population genetic study.     

GENETIC DIVERGENCE IN PERIPHERALLY ISOLATED POPULATIONS OF CHAFFINCHES IN THE ATLANTIC ISLANDS

Peripherally isolated populations of common chaffinches (Fringilla coelebs) in the Canaries, Madeira, and Azores were compared genetically with their putative ancestral stock in Iberia and Morocco, and with a population of blue chaffinches (F. teydea) from Tenerife, using protein electrophoresis of 42 loci. The continental populations are only weakly differentiated genetically (F_ST = 0.092), despite distinctive subspecific differences in plumage and morphometrics between Iberia and Morocco populations. Estimated levels of gene flow among continental populations are high enough to account for their relative genetic homogeneity, and it is unlikely that homogenizing selection is operating to mimic the effects of gene flow. In contrast, the Atlantic island populations are well differentiated genetically (F_ST = 0.321), and have diverged considerably from their continental conspecifics. The development of significant genetic differentiation within the Canaries but not the Azores likely results from smaller population sizes, very restricted gene flow, and enhanced random drift in the former populations. There is no convincing evidence in support of stronger directional selection acting on genotypes or phenotypes to reduce within-population variability in Canaries populations as proposed by Grant (1979), although other tenets of his model of island evolution are supported by our analysis. Although genetic variability is reduced in four of the Canaries populations, only the Hierro population appears to have encountered a severe bottleneck. Yet it has not differentiated markedly from the La Palma population to which it is subspecifically allied. We conclude that gradual divergence in isolated populations of small to moderate size is the most plausible explanation for the evolution of intraspecific and interspecific diversity in Atlantic island chaffinches.     

High population differentiation and genetic variation in the endangered Mexican pine Pinus Rzedowskii (Pinaceae)

Pinus rzedowskii is an endangered pine species from Michoaca´n (central Me´xico), which has been previously reported from only three localities. Classified within the subgenus Strobus, it exhibits intermediate morphological characters between subgenera Strobus and Pinus. We analyzed genetic aspects that could shed light on the evolution and conservation of this species. The genetic structure of nine populations was examined using 14 isozyme loci. Pinus rzedowskii has a relatively high level of genetic variation with 46.8% of the loci assayed being polymorphic, a total of 35 alleles, and a mean heterozygosity per population of 0.219. We calculated Wright's F_ST statistic to estimate gene flow indirectly and to evaluate whether or not there was genetic structuring among populations. We found a marked differentiation among populations (F_ST = 0.175) and significant inbreeding (F_IS = 0.247). No pattern of isolation by distance was found. We also constructed a dendrogram based on a genetic distance matrix to obtain an overview of the possible historical relationships among populations. Finally, we found a convex relationship between the genetic distance among populations and the number of ancestral lineages, suggesting that demographically this species has not been at risk recently. Although endangered, with small and fragmented populations, P. rzedowskii shows higher levels of genetic variation than other conifer species with larger populations or similar conservation status.     

Genetic variation of blood proteins within and between local populations of grivet monkey (Cercopithecus aethiops aethiops) in central Ethiopia

A population genetic study by blood protein electrophoresis revealed that populations of wild grivet monkeys in central Ethiopia show a comparatively low level of variability and less differentiation among local populations over broad geographical areas. This is evaluated by comparison with other wild primate studies using the same electrophoretic technique. A total of 196 blood samples, collected from 10 local populations comprising 11 troops distributed along approximately 600 km of the Awash River, were examined for 33 genetic loci. The low level of variability was indicated by the proportion of polymorphic loci (P_poly), which was on average 11% with an average heterozygosity (H) of 3%. A tendency for lower genetic differentiation among local populations was shown by theG _ST value of 0.09, an averageF _ST of 0.08, andNei's genetic distance; ranging from 0.002 to 0.023. Considering paleoclimatological studies of the area and ecological traits of this species, these findings can be explained as a consequence of a comparatively recent and repeated series of rapid habitat expansions following severe climatic conditions.     

Genetic diversity,population structure and sex‐biased dispersal in three co‐evolving species

Genetic diversity and spatial structure of populations are important for antagonistic coevolution. We investigated genetic variation and population structure of three closely related European ant species: the social parasite Harpagoxenus sublaevis and its two host species Leptothorax acervorum and Leptothorax muscorum. We sampled populations in 12 countries and analysed eight microsatellite loci and an mtDNA sequence. We found high levels of genetic variation in all three species, only slightly less variation in the host L. muscorum. Using a newly introduced measure of differentiation (Jost’s D_est ), we detected strong population structuring in all species and less male‐biased dispersal than previously thought. We found no phylogeographic patterns that could give information on post‐glacial colonization routes – northern populations are as variable as more southern populations. We conclude that conditions for Thompson’s geographic mosaic of coevolution are ideal in this system: all three species show ample genetic variation and strong population structure.     

Genetic variation and structure of house sparrow populations: is there an island effect?

Population genetic structure and intrapopulation levels of genetic variation have important implications for population dynamics and evolutionary processes. Habitat fragmentation is one of the major threats to biodiversity. It leads to smaller population sizes and reduced gene flow between populations and will thus also affect genetic structure. We use a natural system of island and mainland populations of house sparrows along the coast of Norway to characterize the different population genetic properties of fragmented populations. We genotyped 636 individuals distributed across 14 populations at 15 microsatellite loci. The level of genetic differentiation was estimated using F‐statistics and specially designed Mantel tests were conducted to study the influence of population type (i.e. mainland or island) and geographic distance on the genetic population structure. Furthermore, the effects of population type, population size and latitude on the level of genetic variation within populations were examined. Our results suggest that genetic processes on islands and mainland differed in two important ways. First, the intrapopulation level of genetic variation tended to be lower and the occurrence of population bottlenecks more frequent on islands than the mainland. Second, although the general level of genetic differentiation was low to moderate, it was higher between island populations than between mainland populations. However, differentiation increased in mainland populations somewhat faster with geographical distance. These results suggest that population bottleneck events and genetic drift have been more important in shaping the genetic composition of island populations compared with populations on the mainland. Such knowledge is relevant for a better understanding of evolutionary processes and conservation of threatened populations.     

Reduced MHC class II diversity in island compared to mainland populations of the black-footed rock-wallaby (<Emphasis Type="Italic">Petrogale lateralis lateralis</Emphasis>)

Many animal populations that are endangered in mainland areas exist in stable island populations, which have the potential to act as an “ark” in case of mainland population declines. Previous studies have found neutral genetic variation in such species to be up to an order of magnitude lower in island compared to mainland populations. If low genetic variation is prevalent across fitness-related loci, this would reduce the effectiveness of island populations as a source of individuals to supplement declining mainland populations or re-establish extinct mainland populations. One such species, the black-footed rock-wallaby (Petrogale lateralis lateralis), exists within fragmented mainland populations and small island populations off Western Australia. We examined sequence variation in this species within a fitness-related locus under positive selection, the MHC class II DAB β1 locus. The mainland populations displayed greater levels of allelic diversity (4–7 alleles) than the island population, despite being small and isolated, and contained at least two DAB gene copies. The island population displayed low allelic diversity (2 alleles) and fewer alleles per individual in comparison to mainland populations, and probably possesses only one DAB gene copy. The patterns of DAB diversity suggested that the island population has a markedly lower level of genetic variation than the mainland populations, in concordance with results from microsatellites (genotyped in a previous study), but preserved unique alleles which were not found in mainland populations. Where possible, conservation actions should pool individuals from multiple populations, not only island populations, for translocation programs, and focus on preventing further declines in mainland populations.     

Pathogen richness and abundance predict patterns of adaptive major histocompatibility complex variation in insular amphibians

The identification of the factors responsible for genetic variation and differentiation at adaptive loci can provide important insights into the evolutionary process and is crucial for the effective management of threatened species. We studied the impact of environmental viral richness and abundance on functional diversity and differentiation of the MHC class Ia locus in populations of the black‐spotted pond frog (Pelophylax nigromaculatus), an IUCN‐listed species, on 24 land‐bridge islands of the Zhoushan Archipelago and three nearby mainland sites. We found a high proportion of private MHC alleles in mainland and insular populations, corresponding to 32 distinct functional supertypes, and strong positive selection on MHC antigen‐binding sites in all populations. Viral pathogen diversity and abundance were reduced at island sites relative to the mainland, and islands housed distinctive viral communities. Standardized MHC diversity at island sites exceeded that found at neutral microsatellites, and the representation of key functional supertypes was positively correlated with the abundance of specific viruses in the environment (Frog virus 3 and Ambystoma tigrinum virus). These results indicate that pathogen‐driven diversifying selection can play an important role in maintaining functionally important MHC variation following island isolation, highlighting the importance of considering functionally important genetic variation and host–pathogen associations in conservation planning and management.     

Genetic structure in insular and mainland populations of house sparrows (Passer domesticus) and their hemosporidian parasites

Small and isolated populations usually exhibit low levels of genetic variability, and thus, they are expected to have a lower capacity to adapt to changes in environmental conditions, such as exposure to pathogens and parasites. Comparing the genetic variability of selectively neutral versus functional loci allows one to assess the evolutionary history of populations and their future evolutionary potential. The genes of the major histocompatibility complex (MHC) control immune recognition of parasites, and their unusually high diversity is genes which is likely driven by parasite‐mediated balancing selection. Here, we examined diversity and differentiation of neutral microsatellite loci and functional MHC class I genes in house sparrows (Passer domesticus), living in six insular and six mainland populations, and we aimed to determine whether their diversity or differentiation correlates with the diversity and the prevalence of infection of hemosporidian parasites. We found that island bird populations tended to have lower neutral genetic variability, whereas MHC variability gene was similar between island and mainland populations. Similarly, island populations tended to show greater genetic differentiation than mainland populations, especially at microsatellite markers. The maintenance of MHC genetic diversity and its less marked structure in the island populations could be attributed to balancing‐selection. The greater MHC differentiation among populations was negatively correlated with similarity in blood parasites (prevalence and diversity of parasite strains) between populations. Even at low prevalence and small geographical scale, haemosporidian parasites might contribute to structure the variability of immune genes among populations of hosts.