Intraspecific variation in nitrogen status and photosynthetic capacity within mountain birch populations

The relative variation in leaf nitrogen concentration and photosynthetic capacity among individuals and sites are compared for mountain birch populations ( Betula pubsecens Ehrh. ssp tortuosa (Ledeb.) Nyman).
Leaf nitrogen concentration and photosynthetic capacity showed significant differences among individuals; 35 and 26% of the total sum of squares respectively, was attributable to differences among individuals. Two measures of leaf morphology also showed differences among individuals (35–58% of total variation). The variation attributable to site differences ranged from 13% (leaf shape, P = 0.11) to 36% (leaf N concentration and photosynthetic capacity, P≤0.01). Of the variation in photosynthetic capacity, 51% was related to leaf nitrogen concentration. Possible causes for and consequences of the differences found are discussed.     

Genetic diversity of wild grapevine populations in Spain and their genetic relationships with cultivated grapevines

The wild grapevine, Vitis vinifera L. ssp. sylvestris (Gmelin) Hegi, considered as the ancestor of the cultivated grapevine, is native from Eurasia. In Spain, natural populations of V. vinifera ssp. sylvestris can still be found along river banks. In this work, we have performed a wide search of wild grapevine populations in Spain and characterized the amount and distribution of their genetic diversity using 25 nuclear SSR loci. We have also analysed the possible coexistence in the natural habitat of wild grapevines with naturalized grapevine cultivars and rootstocks. In this way, phenotypic and genetic analyses identified 19% of the collected samples as derived from cultivated genotypes, being either naturalized cultivars or hybrid genotypes derived from spontaneous crosses between wild and cultivated grapevines. The genetic diversity of wild grapevine populations was similar than that observed in the cultivated group. The molecular analysis showed that cultivated germplasm and wild germplasm are genetically divergent with low level of introgression. Using a model‐based approach implemented in the software structure , we identified four genetic groups, with two of them fundamentally represented among cultivated genotypes and two among wild accessions. The analyses of genetic relationships between wild and cultivated grapevines could suggest a genetic contribution of wild accessions from Spain to current Western cultivars.     

Genetic diversity within and between natural populations of Rattus norvegicus

The levels of gene diversity for 17 polymorphic loci in natural populations of wild rats were examined for three separate locations in North and South America. The level of gene diversity in the total sample for the RT1.A locus, the dominant class I histocompatibility locus in the major histocompatibility (RT1) complex of the rat, was 0.807. The degree of gene diversity for nonalloantigenic loci scattered throughout the rat genome was 0.215, a level comparable to, if not slightly higher than, that for other mammalian species. The large and consistent levels of diversity for individuals within each population suggest that significant deviations from random mating have occurred within each group. Conclusions from analyzing genetic distance and the index of genetic differentiation between the three populations are consistent with these populations' geographic isolation and small effective population size. Assuming that the separation of the North and South American groups has existed for approximately 300 years, the effective size of these populations is estimated to be approximately 1,500 individuals. Apparent differences in the distribution of the number and frequency of alleles in the major histocompatibility complexes of mice and rats and the level of genetic differentiation among separate rat populations may be due to the effects of genetic drift in small populations.     

Low levels of genetic variation within and high levels of genetic differentiation among populations of species of Abies from southern Mexico and Guatemala

Populations of Abies in southern Mexico and Guatemala (A. flinckii, A. guatemalensis, A. hickeli, and A. religiosa) have a patchy distribution. This pattern is particularly clear in A. guatemalensis. Genetic diversity within populations, measured by average heterozygosity at 16 isozyme loci, is lower than the range reported for most conifers (mean H(o) ranging from 0.069 in A. guatemalensis to 0.113 in A. flinckii), while differentiation among populations is higher than that observed in most conifer species studied (θ = F(st) ranging from 0.073 in A. hickeli to 0.271 in A. flinckii). Estimated levels of gene flow are low (ranging from 0.672 in A. flinckii to 3.17 in A. hickeli). Populations in most cases had an excess of homozygosity over that expected under Hardy-Weinberg equilibrium, suggesting some inbreeding (F(is) ranging from 0.074 in A. flinckii to 0.235 in A. guatemalensis). A significant relationship between gene flow and geographic distance was observed in A. religiosa, but not in the other three taxa studied. The patterns of genetic variation appear to have been influenced by the distributions and histories of these species. Paleoclimatic evidence suggests that the ranges of these species retreated upwards during the Pleistocene glaciation and became fragmented during the warming period that followed. The populations could have passed through genetic bottlenecks that reduced genetic variation and led to interpopulation differentiation.     

Genetic variation within and among populations of Arabidopsis thaliana.

We investigated levels of nucleotide polymorphism within and among populations of the highly self-fertilizing Brassicaceous species, Arabidopsis thaliana. Four-cutter RFLP data were collected at one mitochondrial and three nuclear loci from 115 isolines representing 11 worldwide population collections, as well as from seven commonly used ecotypes. The collections include multiple populations from North America and Eurasia, as well as two pairs of collections from locally proximate sites, and thus allow a hierarchical geographic analysis of polymorphism. We found no variation at the mitochondrial locus Nad5 and very low levels of intrapopulation nucleotide diversity at Adh, Dhs1, and Gpa1. Interpopulation nucleotide diversity was also consistently low among the loci, averaging 0.0014. gst, a measure of population differentiation, was estimated to be 0.643. Interestingly, we found no association between geographical distance between populations and genetic distance. Most haplotypes have a worldwide distribution, suggesting a recent expansion of the species or long-distance gene flow. The low level of polymorphism found in this study is consistent with theoretical models of neutral mutations and background selection in highly self-fertilizing species.     

High levels of allozyme variation within populations and low allozyme divergence within and among species of Hemerocallis (Liliaceae)

Thirty populations from five species of Hemerocallis in Korea were analyzed by starch gel electrophoresis to measure genetic diversity and to determine genetic population structure and the amount of genetic divergence within and between species at 12 isozyme loci. In addition, Moran's I spatial autocorrelation statistics were used to examine the spatial distribution of allozyme polymorphisms in populations of H. thunbergii and H. hakuunensis. Populations of five Korean species maintain high levels of genetic variation and little differentiation among populations and species. Mean expected heterozygosities range from 0.165 in H. hongdoensis, an island endemic, to 0.265 in H. taeanensis, and a total of 81 alleles across the 12 loci were detected in the five species. G(ST) values for each of the five species were low, ranging from 0.051 in H. taeanensis to 0.078 in H. hakuunensis. Mean intraspecific Nei's genetic identities (I) between populations of the five species were all above 0.97. However, a considerable level of heterozygote deficiencies within populations was detected, ranging from 0.242 to 0.411 measured as F(IS) statistics. This deficiencies may be due to inbreeding, limited pollen and seed dispersal, or from the pooling of subpopulations that differ in allele frequencies. A small spatial scale population substructuring (<12 m) was found in H. thunbergii and H. hakuunensis. A group of populations from each of the five previously designated Hemerocallis species (based on their morphology, ecology, and phenology) agrees with our allozyme data, though pairwise comparisons among species had high I values (from 0.862, H. middendorffii vs. H. hongdoensis, to 0.969, H. thunbergii vs. H. taeanensis). This is attributed to the presence of the same high-frequency alleles in different species at seven loci. In addition, no "diagnostic allele" that appears in all populations of one species, but is absent in other species, was detected at the 12 isozyme loci. These all suggest that species of Hemerocallis in Korea may have recently derived from an ancestor or progenitor harboring high levels of genetic diversity.     

Factors affecting levels of genetic diversity in natural populations.

Genetic variability is the clay of evolution, providing the base material on which adaptation and speciation depend. It is often assumed that most interspecific differences in variability are due primarily to population size effects, with bottlenecked populations carrying less variability than those of stable size. However, we show that population bottlenecks are unlikely to be the only factor, even in classic case studies such as the northern elephant seal and the cheetah, where genetic polymorphism is virtually absent. Instead, we suggest that the low levels of variability observed in endangered populations are more likely to result from a combination of publication biases, which tend to inflate the level of variability which is considered ''normal'', and inbreeding effects, which may hasten loss of variability due to drift. To account for species with large population sizes but low variability we advance three hypotheses. First, it is known that certain metapopulation structures can result in effective population sizes far below the census size. Second, there is increasing evidence that heterozygous sites mutate more frequently than equivalent homozygous sites, plausibly because mismatch repair between homologous chromosomes during meiosis provides extra opportunities to mutate. Such a mechanism would undermine the simple relationship between heterozygosity and effective population size. Third, the fact that related species that differ greatly in variability implies that large amounts of variability can be gained or lost rapidly. We argue that such cases are best explained by rapid loss through a genome-wide selective sweep, and suggest a mechanism by which this could come about, based on forced changes to a control gene inducing coevolution in the genes it controls. Our model, based on meiotic drive in mammals, but easily extended to other systems, would tend to facilitate population isolation by generating molecular incompatabilities. Circumstances can even be envisioned in which the process could provide intrinsic impetus to speciation.     

Effects of insularity on genetic diversity within and among natural populations

We conducted a quantitative literature review of genetic diversity (GD) within and among populations in relation to categorical population size and isolation (together referred to as “insularity”). Using populations from within the same studies, we were able to control for between‐study variation in methodology, as well as demographic and life histories of focal species. Contrary to typical expectations, insularity had relatively minor effects on GD within and among populations, which points to the more important role of other factors in shaping evolutionary processes. Such effects of insularity were sometimes seen—particularly in study systems where GD was already high overall. That is, insularity influenced GD in a study system when GD was high even in non‐insular populations of the same study system—suggesting an important role for the “scope” of influences on GD. These conclusions were more robust for within population GD versus among population GD, although several biases might underlie this difference. Overall, our findings indicate that population‐level genetic assumptions need to be tested rather than assumed in nature, particularly for topics underlying current conservation management practices.     

Genetic variation within and between populations of Potamogeton pusillus agg.

Patterns of isozyme variation were examined in 17 populations of P. pusillus and P. berchtoldii, together with one population of P. trichoides taken for comparison. Both P. pusillus and P. berchtoldii displayed low levels of variation within populations associated with high levels of interpopulation differentiation. This pattern of partitioning of genetic variation within and between populations is attributed to the founder effect, frequent vegetative propagation by turions, dominant self-fertilization and limited seedling recruitment. The mechanism of pollen transfer was investigated in cultivation. Effective pollination takes place in air above the water surface (autogamy, geitonogamy, anemogamy), on the water surface (epihydrogamy) or below water surface (hydroautogamy). The species are self-compatible. The low level of infra-population variation together with rare occurrence of heterozygotes suggest that selfing is the most frequent mode of pollination, although the protogynous flowers may occasionally permit some cross-pollination. Unique enzyme markers were found for P. pusillus and P. berchtoldii, and also for the single population of P. trichoides. All multienzyme phenotypes were species-specific. Isozyme data support the separate position of P. pusillus and P. berchtoldii. UPGMA dendogram based on enzyme data of 133 plant samples revealed three distinct main enzymatic entities perfectly corresponding to the three morphologically defined species.     

Genetic diversity in Leavenworthia populations with different inbreeding levels.

Levels of neutral genetic diversity within and between populations were compared between outcrossing (self-incompatible) and inbreeding populations in the annual plant genus Leavenworthia. Two taxonomically independent comparisons are possible, since self-incompatibility has been lost twice in the group of species studied. Within inbred populations of L.uniflora and L.crassa, no DNA sequence variants were seen among the alleles sampled, but high diversity was seen in alleles from populations of the outcrosser L. stylosa, and in self-incompatible L. crassa populations. Diversity between populations was seen in all species. Although total diversity values were lower in the sets of inbreeding populations, between-population values were as high or higher, than those in the outcrossing taxa. Possible reasons for these diversity patterns are discussed. As the effect of inbreeding appears to be a greater than twofold reduction in diversity, we argue that some process such as selection for advantageous mutations, or against deleterious mutations, or bottlenecks occurring predominantly in the inbreeders, appears necessary to account for the findings. If selection for advantageous mutations is responsible, it appears that it must be some form of local adaptive selection, rather than substitution of alleles that are advantageous throughout the species. This is consistent with the finding of high between-population diversity in the inbreeding taxa.     

Genetic variation and genotypic diversity in Epipactis helleborine populations from NE Poland

Enzyme electrophoreses were used to estimate genetic variation in five populations of Epipactis helleborine from two National Parks (Biebrza and Wigry) in northeast Poland. It has been proved that populations from these two regions differed in genetic structure, with the populations belonging to the Biebrza group having a higher level of genetic variation than those from Wigry. The number of polymorphic loci (P) ranged from 18.2% to 40.9% and the mean number of alleles per polymorphic locus (Ap) from 2.25 to 2.80. Although the observed heterozygosity (H_o) was lower than the expected one (H_e) in each population, the values of H_o and H_e were 2–3 times lower in the populations from Wigry than in those from Biebrza. Excluding the LUK population with the smallest genotypic diversity, the majority of 345 distinct multilocus genotypes occurred only once, sporadically 2–4 times in each population and their frequency ranged from 0.2% to 3.7%. Moreover, factors shaping genetic structure of E. helleborine and their intensity varied in the populations studied. Reproduction from seeds seems to influence greatly the genetic variation of the populations from the Biebrza National Park, while an assortative mating between related individuals or population size appears to be more important in the case of the populations from the Wigry National Park.     

Genetic diversity within chicken populations from different continents and management histories

Intra-population variation was assessed in 1970 chickens from 64 populations using 29 autosomal microsatellites. On average, 95% of the loci were polymorphic across populations. In 1456 ( c. 83%) of the 1763 combinations of populations and polymorphic loci, no departure from Hardy–Weinberg equilibrium was observed. On average, there were 11.4 alleles per locus and 3.6 alleles per population across loci. Within populations, the average observed heterozygote frequency was 0.46, with a range between 0.20 and 0.64. Dagu, a Chinese population, and the Red Jungle Fowl ( Gallus gallus gallus ) had the highest average heterozygote frequencies at 0.64 and 0.63 respectively. An inbred line used as a reference population for comparison showed the lowest average of observed heterozygote frequency (0.05), followed by the European population Hamburger Lackhuhn, whose average observed heterozygote frequency was 0.20. A total of 32 private alleles (alleles detected in only one population) for 20 loci were found in 18 populations. H'mong chickens, a Vietnamese population, carried the largest number of private alleles at five, followed by the Red Jungle Fowl with four private alleles. Genetic diversity within populations was low in the NW European fancy breeds and high in the non-commercial Asian populations, in agreement with population management history.     

Small population size and extremely low levels of genetic diversity in island populations of the platypus, Ornithorhynchus anatinus

Genetic diversity generally underpins population resilience and persistence. Reductions in population size and absence of gene flow can lead to reductions in genetic diversity, reproductive fitness, and a limited ability to adapt to environmental change increasing the risk of extinction. Island populations are typically small and isolated, and as a result, inbreeding and reduced genetic diversity elevate their extinction risk. Two island populations of the platypus, Ornithorhynchus anatinus, exist; a naturally occurring population on King Island in Bass Strait and a recently introduced population on Kangaroo Island off the coast of South Australia. Here we assessed the genetic diversity within these two island populations and contrasted these patterns with genetic diversity estimates in areas from which the populations are likely to have been founded. On Kangaroo Island, we also modeled live capture data to determine estimates of population size. Levels of genetic diversity in King Island platypuses are perilously low, with eight of 13 microsatellite loci fixed, likely reflecting their small population size and prolonged isolation. Estimates of heterozygosity detected by microsatellites (H(E)= 0.032) are among the lowest level of genetic diversity recorded by this method in a naturally outbreeding vertebrate population. In contrast, estimates of genetic diversity on Kangaroo Island are somewhat higher. However, estimates of small population size and the limited founders combined with genetic isolation are likely to lead to further losses of genetic diversity through time for the Kangaroo Island platypus population. Implications for the future of these and similarly isolated or genetically depauperate populations are discussed.     

High levels of variation despite genetic fragmentation in populations of the endangered mountain pygmy-possum, Burramys parvus, in alpine Australia

In endangered mammals, levels of genetic variation are often low and this is accompanied by genetic divergence among populations. The mountain pygmy-possum (Burramys parvus) is an endangered marsupial restricted to the alpine region of Victoria and New South Wales, Australia. By scoring variation at eight microsatellite loci, we found that B. parvus populations exhibit high levels of genetic divergence and fall into three distinct groups from the northern, central and southern areas of the distribution of this species, consistent with previous assessments of mitochondrial DNA variation. F(ST) values between populations from these regions ranged from 0.19 to 0.54. Within the central area, there was further genetic fragmentation, and a linear association between genetic and geographical distance. This pattern is likely to reflect limited dispersal across barriers despite the fact that individual B. parvus can move several kilometres. Levels of genetic variation within populations were high with the exception of a southern population where there was evidence of inbreeding. From a conservation perspective, all three areas where B. parvus are found should be considered as separate gene pools; management of populations within these areas needs to take into account the low gene flow between populations, as well as threats posed by roads, resorts and other developments in the alpine region. The low genetic variability and inbreeding in the southern population is of particular concern given the high levels of variability in other B. parvus populations.     

Genetic variation within and among populations of Fomitopsis pinicola (Basidiomycetes)

RAPD polymorphisms were used to reveal the genetic population structure of Fomitopsis pinicola from 5 populations in southwestern Sweden with outliers in Finland and Norway. Eleven primers were used on 35 isolates. Using the Analysis of Molecular Variance (AMOVA), the total variance was divided into 3 hierarchical components: 84% within populations, 11% among regions, and 5% among populations within regions. The 3 large Swedish populations contained 95% of the variation within them. The statistical significance of these patterns was supported by permutation tests. The similarity index between all genets ranged from 0.10 to 0.72, with an average of 0.45. Genets from the same population could form more than one cluster in the neighbor-joining analysis. Some of these clusters were also supported by parsimony jack-knifing. This pattern is tentatively explained by establishment of spores from different basidiomata. The result of somatic incompatibility tests and RAPD markers were compared and this comparison indicated that compatible reactions do not necessarily imply genetic identity. Sampling from cut sections of infected trees revealed that multiple infections were present in a single tree and that the fungus probably infects host-trees by basidiospores, arriving via the air. Each somatically incompatible genet characteristically monopolized only part of a resource unit. Spore trapping showed no evidence of long distance spore dispersal, but this is probably due to the limited experiment, since the genetic analysis suggested a high rate of gene flow.     

The first SSR-based assessment of genetic variation and structure among Pinus laricio Poiret populations within their native area

Pinus laricio Poiret is the most widespread conifer occurring in Calabria (Sila and Aspromonte Massifs), Sicily (Mount Etna) and Corsica. Particularly, Calabrian laricio pine forests are strongly related to complex geological history, lithological and climatic characteristics and long human exploitation of the Sila territory, of which they are the most emblematic element. As far as we know, the P. laricio populations from their main range areas have never been thoroughly studied at the molecular level. This article reports on the first deep analysis of the genetic variability and structure of individuals from populations located in Calabria, Sicily and Corsica using both chloroplast and nuclear microsatellite markers. Significant variation within populations and low differentiation among populations were found by means of molecular variance estimates for the both types of markers. Bayesian clustering analyses revealed an unexpected grouping of P. laricio populations with individuals from Sila and, particularly, those from the Natural Reserve of Fallistro, have been identified as genetically distinct. Temporal genetic analysis in three large P. laricio populations also showed that there were no differences in genetic diversity levels over time; however, it allowed to recognize populations that deserve to be considered as a high priority for suitable preservation and management.     

Structuring of genetic variation inHordeum spontaneum (Poaceae): Genotypic variation within populations

Samples from eleven populations of wild barley were examined for metric growth and reproductive traits in a common garden field trial. Descendants of these plants were examined for electrophoretically determined genotypes. In most cases each population had one or more predominant electrophoretically detectable genotypes and many infrequent genotypes. Analysis of variance ofHordeum spontaneum shows that the between-population variance component contributed the bulk of the observed variation in metric traits, with only a small proportion of the total variation contributed by the between-genotype within-population variance component. Nevertheless, a full 20% of the F values for the among genotype analysis were significant at the 5% level. In addition, using discriminant analysis, electrophoretically determined genotypes could be easily distinguished on the basis of trait (i.e., metric) measurements. The joint use of electrophoresis (to identify genotypes) and of trait measurements is a powerful tool for investigating intrapopulation genetic variation.     

Genetic variation within and relatedness among wood and plains bison populations.

There are two recognized subspecies of bison, wood (Bison bison athabascae) and plains (Bison bison bison) bison. The establishment of most bison populations from a small number of individuals has raised concerns about their genetic variation. To this end, 11 bison populations were surveyed with 11 microsatellite loci in order to calculate genetic variation and genetic distances. Mean number of alleles ranged between 3.18 at Antelope Island State Park (Utah) and 6.55 at Wood Buffalo National Park (Alberta and Northwest Territories). Mean heterozygosity ranged from 0.295 at Antelope Island State Park to 0.669 at Custer State Park (South Dakota). The amount of genetic variability present in the bison populations as measured by mean number of alleles and overall probability of identity was found to correlate with the number of founders for all sampled populations. The G-test for heterogeneity revealed some evidence for the existence of subpopulations at Wood Buffalo National Park, however very small genetic distances between these subpopulations suggest that nuclear material from the plains bison introduced into Wood Buffalo National Park has diffused throughout the park. Genetic distances between the sampled populations were generally larger between than within the two bison subspecies.     

Strong founder effects and low genetic diversity in introduced populations of Coqui frogs

The success of non-native species may depend on the genetic resources maintained through the invasion process. The Coqui ( Eleutherodactylus coqui ), a frog endemic to Puerto Rico, was introduced to Hawaii in the late 1980s via the horticulture trade, and has become an aggressive invader. To explore whether genetic diversity and population structure changed with the introduction, we assessed individuals from 15 populations across the Hawaiian Islands and 13 populations across Puerto Rico using six to nine polymorphic microsatellite loci and five dorsolateral colour patterns. Allelic richness ( R _T) and gene diversity were significantly higher in Puerto Rico than in Hawaii populations. Hawaii also had fewer colour patterns (two versus three to five per population) than Puerto Rico. We found no isolation by distance in the introduced range, even though it exists in the native range. Results suggest extensive mixing among frog populations across Hawaii, and that their spread has been facilitated by humans. Like previous research, our results suggest that Hawaiian Coquis were founded by individuals from sites around San Juan, but unlike previous research the colour pattern and molecular genetic data (nuclear and mtDNA) support two separate introductions, one on the island of Hawaii and one on Maui. Coquis are successful invaders in Hawaii despite the loss of genetic variation. Future introductions may increase genetic variation and potentially its range.