Combining demographic, environmental and genetic data to test hypotheses about colonization events in metapopulations

We describe a method for making inferences about the factors that influence colonization processes in natural populations. We consider the general situation where we have genetic data from a newly colonized population and also from I source populations that may have contributed individuals to the founding group that established the new population. The model assumes that p (biotic/abiotic) factors, G(1), ... ,G(p) may have influenced some individuals in some of the source populations to find a new habitat patch where they could establish a new population. The aim of the method is to determine the composition of the founding group and to ascertain if the aforementioned factors have indeed played a role in the colonization event. We investigate the performance of our method using simulated data sets and illustrate its application with data from the grey seal Halichoerus grypus. These applications demonstrate that the method can identify accurately those factors that are most important for the founding of new populations. This is the case even when genetic differentiation among source populations is low. The estimates of the contribution that each source population makes to the founding groups is somewhat sensitive to the degree of genetic differentiation but it is still possible to identify the sources that are the main contributors to the founding group, even when genetic differentiation is low (F(ST) = 0.01).     

MIGRATION AND GENETIC DRIFT IN HUMAN POPULATIONS

In humans and many other species, mortality is concentrated early in the life cycle, and is low during the ages of dispersal and reproduction. Yet precisely the opposite is assumed by classical population-genetics models of migration and genetic drift. We introduce a model in which population regulation occurs before migration. In contrast to the conventional model, our model implies that geographic variation in the allele frequencies of newborns should exceed that of adults. Thus, it is important to distinguish genetic variation of adults from that of newborns in species with human-like life cycles. Classical models deal with the variance of group allele frequencies about the allele frequency of a hypothetical “continent” or “foundation stock.” Empirical studies, however, can only measure “reduced” variance, i.e., variance about the current population mean. Our model deals with reduced variance, and should therefore be more relevant to field studies. We show that reduced variance converges faster, which implies that populations are more likely to be at equilibrium with respect to reduced than unreduced variance. To summarize the effect of migration on genetic population structure, we introduce a new parameter, the effective migration rate. Unlike most population structure statistics, it does not confound the effects of mobility and population size, and it should therefore be useful for comparisons between populations. Finally, we show that the difference between geographic variation of newborn and adult allele frequencies contains information about both effective population size and effective migration rate.     

Serial founder effects during range expansion: a spatial analog of genetic drift

Range expansions cause a series of founder events. We show that, in a one-dimensional habitat, these founder events are the spatial analog of genetic drift in a randomly mating population. The spatial series of allele frequencies created by successive founder events is equivalent to the time series of allele frequencies in a population of effective size ke, the effective number of founders. We derive an expression for ke in a discrete-population model that allows for local population growth and migration among established populations. If there is selection, the net effect is determined approximately by the product of the selection coefficients and the number of generations between successive founding events. We use the model of a single population to compute analytically several quantities for an allele present in the source population: (i) the probability that it survives the series of colonization events, (ii) the probability that it reaches a specified threshold frequency in the last population, and (iii) the mean and variance of the frequencies in each population. We show that the analytic theory provides a good approximation to simulation results. A consequence of our approximation is that the average heterozygosity of neutral alleles decreases by a factor of 1-1/(2ke) in each new population. Therefore, the population genetic consequences of surfing can be predicted approximately by the effective number of founders and the effective selection coefficients, even in the presence of migration among populations. We also show that our analytic results are applicable to a model of range expansion in a continuously distributed population.     

鄂温克族与鄂伦春族的群体遗传学研究(续)

本次调查采印了645名鄂温克族和424名鄂伦春族中、小学生和部分牧民、猎民的指纹和掌纹。观察了各型指纹出现率、指纹总嵴数、atd角和掌褶纹等指标。 1.各型指纹出现率 弓(A)、尺侧箕(L~u)、桡侧箕(L~r)和斗(W)的出现频率见表11。额左旗和陈旗鄂温克人中斗多于箕,与汉族相似。有些指纹型在某个手指上较为多见,在汉族中斗在环指     

Colonization genetics of an animal-dispersed plant (Vaccinium membranaceum) at Mount St Helens, Washington

Population founding and spatial spread may profoundly influence later population genetic structure, but their effects are difficult to quantify when population history is unknown. We examined the genetic effects of founder group formation in a recently founded population of the animal-dispersed Vaccinium membranaceum (black huckleberry) on new volcanic deposits at Mount St Helens (Washington, USA) 24 years post-eruption. Using amplified fragment length polymorphisms and assignment tests, we determined sources of the newly founded population and characterized genetic variation within new and source populations. Our analyses indicate that while founders were derived from many sources, about half originated from a small number of plants that survived the 1980 eruption in pockets of remnant soil embedded within primary successional areas. We found no evidence of a strong founder effect in the new population; indeed genetic diversity in the newly founded population tended to be higher than in some of the source regions. Similarly, formation of the new population did not increase among-population genetic variance, and there was no evidence of kin-structured dispersal in the new population. These results indicate that high gene flow among sources and long-distance dispersal were important processes shaping the genetic diversity in this young V. membranaceum population. Other species with similar dispersal abilities may also be able to colonize new habitats without significant reduction in genetic diversity or increase in differentiation among populations.     

A meta‐analysis of isolation by distance: relic or reference standard for landscape genetics?

Isolation by distance (IBD) has been a common measure of genetic structure among populations and is based on Euclidean distances among populations. Whereas IBD does not incorporate geographic complexity (e.g. dispersal barriers, corridors) that may better predict genetic structure, a new approach (landscape genetics) joins landscape ecology with population genetics to better model genetic structure. Should IBD be set aside or should it persist as the most simple model in landscape genetics? We evaluated the status of IBD by collecting and analyzing results of 240 IBD data sets among diverse taxa and study systems. IBD typically represented a low proportion of variance in genetic structure (mean r²=0.22) in part because many studies included relatively few populations (mean=11). The number of populations studied (N) was asymptotically related to IBD significance; a study with 9 populations has only 50% probability of significance, while one with >23 populations will have 90% probability of significance. Surprisingly, ectothermic animals were significantly (p=0.0018) more likely to have significant IBD than endotherms, which suggests a metabolic basis underlying gene flow rates. We also observed marginally significant effects on IBD significance for a) taxa in general and b) dispersal modes within actively‐dispersing endotherms. Other factors analyzed (genetic markers, genetic distances, habitats, active or passive dispersal, plant growth form) did not significantly affect IBD, likely related to typical N. For multiple reasons we conclude that IBD should continue as the simplest reference standard against which all other, more complex models should be compared in landscape genetics research.     

EXTINCTION AND RECOLONIZATION: THEIR EFFECTS ON THE GENETIC DIFFERENTIATION OF LOCAL POPULATIONS

In this paper, we use a model by Slatkin (1977) to investigate the genetic effects of extinction and recolonization for a species whose population structure consists of an array of local demes with some migration among them. In particular, we consider the conditions under which extinction and recolonization might enhance or diminish gene flow and increase or decrease the rate of genetic differentiation relative to the static case with no extinctions. We explicitly take into account the age-structure that is established within the array of populations by the extinction and colonization process. We also consider two different models of the colonization process, the so-called “migrant pool” and “propagule pool” models. Our theoretical studies indicate that the genetic effects of extinction and colonization depend upon the relative magnitudes of K, the number of individuals founding new colonies, and 2Nm, twice the number of migrants moving into extant populations. We find that these genetic effects are surprisingly insensitive to the extinction rate. We conclude that, in order to assess the genetic effects of the population dynamics, we must first answer an important empirical question that is essentially ecological: is colonization a behavior distinct from migration?     

The influence of multiple inseminations and multiple foundresses on social evolution

The breeding biology of a population determines the way in which individuals are distributed within and between progeny groups and, thus, affects the genetic variation within and between these groups. The breeding biology of any organism can be characterized by the distribution of the numbers of mates of females, the apportionment of paternity among males, the distribution of the numbers of females reproducing in common nests, and the apportionment of total fecundity within a nest among founding females. In addition, the possibility of genetic correlations among mates or among founding females is an important consideration and will be addressed in a later paper. The influence of the breeding biology on social evolution was evaluated by deriving the necessary conditions for the spread of genes for social behaviors and the rate of spread of these genes for populations with different breeding biologies. The first step in this derivation is to demonstrate that selection for genes determining social behavior can be represented as the covariance between gene frequency and relative fitness. Secondly, it is shown that this covariance can be formally partitioned into within and between group components. Thirdly, each covariance component is shown to be equivalent to the product of a genetic variance and a coefficient of linear regression of relative fitness on gene frequency. Lastly, specific models for the genotype fitnesses and breeding biologies are assumed and the necessary conditions for the increase in the frequency of altruistic alleles are obtained. The theory illustrates that variation in the numbers of mates per female has less of an effect on the evolution of social behaviors than does variation in the numbers of reproductive females per nest. In addition, it points out that the harmonic mean number of mates per female or of females per nest is a more useful summary statistic for characterizing populations with respect to the expected degree of evolved sociality than is the arithmetic mean.     

The role of founder effects on the evolution of reproductive isolation

Several theories argue that large changes in allele frequencies through genetic drift after a small founding population becomes allopatrically isolated can lead to significant changes in reproductive isolation and thus trigger the origin of new species. For this reason, founder speciation has been proposed as a potent force in the generation of new species. Nonetheless, the relative importance of such ‘founder effects’ remains largely untested. In this report, I used experimental evolution to create one thousand replicates that underwent an extreme bottleneck and to study whether founder effects can lead to an increase in reproductive isolation in Drosophila yakuba. Even though the most common outcome of inbreeding is extinction, founder effects can lead to increased premating reproductive isolation in a very small proportion of cases. Changes in reproductive isolation after a founding population bottleneck are similar to changes in other phenotypic traits, in which inbreeding might displace the mean phenotypic value and substantially increase the phenotypic variance. This increase in phenotypic variance does not confer an increase in the response to selection for reproductive isolation in artificial selection experiments, indicating that the increased phenotypic variance is not caused by increases in additive genetic variance. These results also demonstrate that, similar to morphological and life‐history traits, behavioural traits can be affected by inbreeding and genetic drift.     

Population structure in the endangered Mauna Loa silversword, Argyroxiphium kauense (Asteraceae), and its bearing on reintroduction

Reintroduction of populations of endangered species is a challenging task, involving a number of environmental, demographic and genetic factors. Genetic parameters of interest include historical patterns of genetic structure and gene flow. Care must be taken during reintroduction to balance the contrasting risks of inbreeding and outbreeding depression. The Mauna Loa silversword, Argyroxiphium kauense, has experienced a severe decline in population size and distribution in the recent past. Currently, three populations with a total of fewer than 1000 individuals remain. We measured genetic variation within and among the remnant populations using seven microsatellite loci. We found significant genetic variation remaining within all populations, probably related to the recent nature of the population impact, the longevity of the plants, and their apparent self-incompatibility. We also found significant genetic differentiation among the populations, reinforcing previous observations of ecological and morphological differentiation. With respect to reintroduction, the results suggest that, in the absence of additional data to the contrary, inbreeding depression may not be a substantial risk as long as propagules for the founding of new populations are adequately sampled from within each source population before additional inbreeding takes place. The results further suggest that if mixing of propagules from different source populations is not required to increase within-population genetic variation in the reintroduced populations, it may best be avoided.     

EPISTASIS AS A SOURCE OF INCREASED ADDITIVE GENETIC VARIANCE AT POPULATION BOTTLENECKS

The role of epistasis in evolution and speciation has remained controversial. We use a new parameterization of physiological epistasis to examine the effects of epistasis on levels of additive genetic variance during a population bottleneck. We found that all forms of epistasis increase average additive genetic variance in finite populations derived from initial populations with intermediate allele frequencies. Average additive variance continues to increase over many generations, especially at larger population sizes (N = 32 to 64). Additive-by-additive epistasis is the most potent source of additive genetic variance in this situation, whereas dominance-by-dominance epistasis contributes smaller amounts of additive genetic variance. With additive-by-dominance epistasis, additive genetic variance decreases at a relatively high rate immediately after a population bottleneck, rebounding to higher levels after several generations. Empirical examples of epistasis for murine adult body weight based on measured genotypes are provided illustrating the varying effects of epistasis on additive genetic variance during population bottlenecks.     

Minimal sharing of Y-chromosome STR haplotypes among five endogamous population groups from western and southwestern India

We attempt to address the issue of genetic variation and the pattern of male gene flow among and between five Indian population groups of two different geographic and linguistic affiliations using Y-chromosome markers. We studied 221 males at three Y-chromosome biallelic loci and 184 males for the five Y-chromosome STRs. We observed 111 Y-chromosome STR haplotypes. An analysis of molecular variance (AMOVA) based on Y-chromosome STRs showed that the variation observed between the population groups belonging to two major regions (western and southwestern India) was 0.17%, which was significantly lower than the level of genetic variance among the five populations (0.59%) considered as a single group. Combined haplotype analysis of the five STRs and the biallelic locus 92R7 revealed minimal sharing of haplotypes among these five ethnic groups, irrespective of the similar origin of the linguistic and geographic affiliations; this minimal sharing indicates restricted male gene flow. As a consequence, most of the haplotypes were population specific. Network analysis showed that the haplotypes, which were shared between the populations, seem to have originated from different mutational pathways at different loci. Biallelic markers showed that all five ethnic groups have a similar ancestral origin despite their geographic and linguistic diversity.     

TEMPORAL PATTERNS IN POPULATION GENETIC DIVERSITY OF PROROCENTRUM MICANS (DINOPHYCEAE)1

We describe temporal changes in the genetic structure of populations of the dinoflagellate Prorocentrum micans Ehrenberg over a period of 2 years at Scripps Pier (La Jolla, CA, USA). We collected 12 water samples over the course of two blooms and analyzed 166 single‐cell isolates using randomly amplified polymorphic DNA analysis. Six PCR primers uncovered 27 polymorphic markers, allowing the identification of 40 unique haplotypes. Analysis of molecular variance demonstrated that >92% of the genetic variance was partitioned within water samples, providing evidence of high levels of genetic diversity and possibly sexual reproduction. Although the level of genetic diversity remained fairly stable over the sampled time interval, several populations (sampled in June 1998 and March 1999) exhibited significantly different genetic composition, demonstrating differences among bloom and nonbloom periods. About 40% of the isolates in each sample were identified as one haplotype, suggesting that a genetically distinct subgroup was a common member of the populations during the sampled periods. The composition of the remaining isolates was genetically diverse and changed over time, indicating rapid responses (days) to changing environmental conditions or extensive genetic spatial patchiness (kilometers). Within the limitations of our sampling, these two genetically distinct groups appear to exhibit different population dynamics (one stable and the other variable), suggesting that genetic diversity may be closely linked to the change in abundance of phytoplankton on ecological time scales.     

Fast evolutionary genetic differentiation during experimental colonizations

Founder effects during colonization of a novel environment are expected to change the genetic composition of populations, leading to differentiation between the colonizer population and its source population. Another expected outcome is differentiation among populations derived from repeated independent colonizations starting from the same source. We have previously detected significant founder effects affecting rate of laboratory adaptation among Drosophila subobscura laboratory populations derived from the wild. We also showed that during the first generations in the laboratory, considerable genetic differentiation occurs between foundations. The present study deepens that analysis, taking into account the natural sampling hierarchy of six foundations, derived from different locations, different years and from two samples in one of the years. We show that striking stochastic effects occur in the first two generations of laboratory culture, effects that produce immediate differentiation between foundations, independent of the source of origin and despite similarity among all founders. This divergence is probably due to powerful genetic sampling effects during the first few generations of culture in the novel laboratory environment, as a result of a significant drop in N _e. Changes in demography as well as high variance in reproductive success in the novel environment may contribute to the low values of N _e. This study shows that estimates of genetic differentiation between natural populations may be accurate when based on the initial samples collected in the wild, though considerable genetic differentiation may occur in the very first generations of evolution in a new, confined environment. Rapid and significant evolutionary changes can thus occur during the early generations of a founding event, both in the wild and under domestication, effects of interest for both scientific and conservation purposes.     

NEUTRAL THEORY OF QUANTITATIVE GENETIC VARIANCE IN AN ISLAND MODEL WITH LOCAL EXTINCTION AND COLONIZATION

Additive genetic variance maintained by mutation in a selectively neutral quantitative character is analyzed for an ideal population distributed on n islands, each with local effective size N, that exchange migrants at a small rate, m. In a stable population structure, the expected genetic variance maintained within islands is identical to that in a panmictic population of the same total size, regardless of the migration rate (m > 0). This result contrasts with Wright's classical conclusion, based on inbreeding coefficients, that at least one immigrant per island every other generation (Nm > ½) is necessary for the genetic variance within local populations to approach that under panmixia. The expected genetic variance maintained among islands is inversely proportional to m and increases with the number of islands, but is independent of N. Local extinction and colonization diminish the genetic variance maintained within islands by reducing the effective size of island populations through the founder effect, although the expected genetic variance within islands is nearly as large as that in a panmictic population of the same total effective size. If the founders of new colonies originate from more than one island, rates of local extinction and colonization larger than about twice the migration rate will substantially reduce the genetic variance maintained among islands. These results indicate the importance of mutation and migration in maintaining quantitative genetic variance within small local populations.     

Genetic variation in a network of natural and reintroduced populations of Griffon vulture (Gyps fulvus) in Europe

It is generally considered that limiting the loss of genetic diversity in reintroduced populations is essential to optimize the chances of success of population restoration. Indeed, to counter founder effect in a reintroduced population we should maximize the genetic variability within the founding group but also take into account networks of natural populations in the choice of the reintroduction area. However, assessment of relevant reintroduction strategies requires long-term post-release genetic monitoring. In this study, we analyzed genetic data from a network of native and reintroduced Griffon vulture (Gyps fulvus) populations successfully restored in Southern Europe. Using microsatellite markers, we characterized the level of genetic diversity and degree of genetic structure within and among three native colonies, four captive founding groups and one long-term monitored reintroduced population. We also used Bayesian assignment analysis to examine recent genetic connections between the reintroduced population and the other populations. We aimed to assess the level of fragmentation among native populations, the effectiveness of random choice of founders to retain genetic variability of the species, the loss of genetic diversity in the reintroduced population and the effect of gene flow on this founder effect. Our results indicate that genetic diversity was similar in all populations but we detected signs of recent isolation for one native population. The reintroduced population showed a high immigration rate that limited loss of genetic diversity. Genetic investigations performed in native populations and post-released genetic monitoring have direct implications for founder choice and release design.     

From nature to the laboratory: the impact of founder effects on adaptation

Most founding events entail a reduction in population size, which in turn leads to genetic drift effects that can deplete alleles. Besides reducing neutral genetic variability, founder effects can in principle shift additive genetic variance for phenotypes that underlie fitness. This could then lead to different rates of adaptation among populations that have undergone a population size bottleneck as well as an environmental change, even when these populations have a common evolutionary history. Thus, theory suggests that there should be an association between observable genetic variability for both neutral markers and phenotypes related to fitness. Here, we test this scenario by monitoring the early evolutionary dynamics of six laboratory foundations derived from founders taken from the same source natural population of Drosophila subobscura. Each foundation was in turn three‐fold replicated. During their first few generations, these six foundations showed an abrupt increase in their genetic differentiation, within and between foundations. The eighteen populations that were monitored also differed in their patterns of phenotypic adaptation according to their immediately ancestral founding sample. Differences in early genetic variability and in effective population size were found to predict differences in the rate of adaptation during the first 21 generations of laboratory evolution. We show that evolution in a novel environment is strongly contingent not only on the initial composition of a newly founded population but also on the stochastic changes that occur during the first generations of colonization. Such effects make laboratory populations poor guides to the evolutionary genetic properties of their ancestral wild populations.     

Conservation genetics of small relic populations of silver fir (Abies alba Mill.) in the northern Apennines

Abstract

Small and isolated silver fir populations from the Emilian Apennines (northern Italy) were studied to assess their level of genetic variation and their relationship with Alpine populations. We investigated the variability of two chloroplast microsatellites to analyse the within‐population genetic variability of four peripheral and fragmented Apennine populations and to determine their phylogenetic relatedness to seven Alpine populations covering the entire distribution of silver fir in the Alps. Haplotypic richness and haplotype diversity as well as the fraction of private haplotypes were lower in Apennine populations, evidencing the genetic impoverishment of these stands. The among‐population genetic variability analysis revealed the genetic peculiarity of Apennine populations. Analysis of molecular variance showed that the highest level of the among‐population variation occurs between Alpine and Apennine regions. A neighbour‐joining dendrogram revealed a distinct Apennine cluster that included the closest Alpine population. Our genetic analysis supports a common origin for Emilian Apennine populations, suggesting that these populations are relicts of past large silver fir populations in the northern Apennines. Our results point to a relevant conservation value for these stands, to be considered in their management.     

ON THE EFFECT OF FOUNDER EVENTS ON EPISTATIC GENETIC VARIANCE

Mayr (1963) proposed that small isolated propagules from a large panmictic population would occasionally undergo a genetic revolution due to loss of genetic variability. More recently Templeton (1980a) has suggested that founder events may be much more important in systems that have strong epistasis. Because of the work of these and other authors it becomes an interesting theoretical problem to study the distribution of epistatic variance in a population following a founder event. In the model presented here measures of coancestry (Cockerham, 1967, 1984; Cockerham and Weir, 1973; Weir and Cockerham, 1973, 1977; Tachida and Cockerham, unpubl.) are used to examine the effect of founder events on additive-by-additive epistasis. Using this approach, the coancestries, or intraclass correlations, within individuals and within demes, together with the genetic variance components in the ancestral population are used to obtain the variance within and among demes following a founder event. Examples are analyzed for single founder events of 1–25 individuals and multiple founder events of two individuals. Following a single founder event, the contribution of the additive variance to the variance within demes relative to the additive variance in the ancestral population is always less than one. However, the contribution of epistatic variance to the variance within demes relative to the epistatic variance in the ancestral population is always greater than one. Thus, while a founder event decreases the contribution of additive variance to the variance within demes, it increases the contribution of epistatic variance to the variance within demes. The contribution of epistatic variance to the variance among demes following a single founder event is not qualitatively different from the contribution of additive variance to the variance among demes. These results indicate that epistatic variance is less likely than additive variance to cause a genetic revolution following a single founder event. When populations undergo multiple founder events the situation changes considerably. Epistatic variance may contribute as much as four times its original value to the variance among demes, while additive variance can contribute maximally twice its original value to the variance among demes. Thus, epistasis, which is relatively unimportant following a single founder event, may have major evolutionary implications if drift is allowed to continue for several generations.     

Genetic analysis of microsatellite polymorphism in the Elliot's Pheasant (Syrmaticus ellioti) in China

In this study, we reported the population genetic analyses in the Elliot's Pheasant(Syrnaticus ellioti) using seven polymorphism microsatellite loci based on 105 individuals from 4 geographical populations. Departures from Hardy-Weinberg equilibrium were found in four geographical populations. The average number of alleles was 8.86, with a total of 62 alleles across 7 loci; observed heterozygosity (HO) was generally low and the average number was 0.504. For the seven microsatellite loci, the polymorphism information content ranged from 0.549 to 0.860, with an average number 0.712. Population bottlenecks of the four geographical populations were tested by infinite allele mutation model, step-wise mutation model and two-phase mutation model, which found that each population had experienced bottleneck effect during the recent period. Fst analysis across all geographical populations indicated that the genetic differentiaton between the Guizhou geographical population and the Hunan geographical population was highly significant (P<0.001), a finding supported by the far genetic relationship showed by the neighbor-joining tree of four geographical populations based on Nei's unbiased genetic distances. Using hierarchical analysis of molecular variance (Guizhou geographical population relative to all others pooled), we found a low level of the genetic variation among geographical populations and that between groups. However, differences among populations relative to the total sample explained most of the genetic variance (92.84%), which was significant.