Statistical analysis of the migration component of genetic drift

Statistical methods are introduced for analysis of the migration component of genetic drift, i.e., of the stochastic changes that affect allele frequencies during migration between local groups. Attention focuses on alpha M, a parameter that measures the extent to which this component of drift departs from the ideal of independent random sampling, and which can be interpreted as a measure of the extent to which migration is kin-structured. It is shown that alpha M can be estimated from genetic data, even in the absence of information about the genealogical relationships of migrants, and Monte-Carlo simulations are used to approximate the sampling distribution of the estimator under the null hypothesis of independent random sampling. Application of these methods to data from the Aland Islands, Finland, shows that the migration pattern there is consistent with the hypothesis of independent random sampling.     

Biological affinities between migrant and parental populations of fishermen on the east coast of India.

We examined biological affinities between the migrant groups of fishermen in Puri and their parental counterparts using 3 sets of variables: genetic markers, anthropometric measurements, and quantitative dermatoglyphics. Results of both univariate and multivariate analyses suggest a significant migration effect, diversifying migrants from their parental populations, although the distance configurations based on each set of variables resemble each other. The migration effect is particularly remarkable for the anthropometric measurements. The plot of group centroids based on the discriminant analysis of the 7 populations depicts a clear segregation of migrants from the parental populations. Because of relatively large effective population sizes and short history of these populations in Puri, the role of genetic drift can be safely ruled out. However, a founder effect is a plausible reason for the observed differentiation of the migrants from their parental groups, especially given that certain rare variants that were not observed in the parental populations appear in the migrants. That the founders were a select group of fishermen with respect to body dimensions, not a random group, can be inferred from the occupational differences among the migrant groups, which in turn suggests phenotypic plasticity in the observed differentiation. Regression of mean phenotypic variance and heterozygosity on the distance from the centroid suggests a strong possibility of external gene flow into the migrant populations in Puri.     

A POPULATION MEMETICS APPROACH TO CULTURAL EVOLUTION IN CHAFFINCH SONG: DIFFERENTIATION AMONG POPULATIONS

We investigated cultural evolution in populations of common chaffinches (Fringilla coelebs) in the Atlantic islands (Azores, Madeira, and Canaries) and neighboring continental regions (Morocco and Iberia) by employing a population-memetic approach. To quantify differentiation, we used the concept of a song meme, defined as a single syllable or a series of linked syllables capable of being transmitted. The levels of cultural differentiation are higher among the Canaries populations than among the Azorean ones, even though the islands are on average closer to each other geographically. This is likely the result of reduced levels of migration, lower population sizes, and bottlenecks (possibly during the colonization of these populations) in the Canaries; all these factors produce a smaller effective population size and therefore accentuate the effects of differentiation by random drift. Significant levels of among-population differentiation in the Azores, in spite of substantial levels of migration, attest to the differentiating effects of high mutation rates of memes, which allow the accumulation of new mutants in different populations before migration can disperse them throughout the entire region.     

Nonrandom larval dispersal can steepen marine clines

Sharp and stable clinal variation is enigmatic when found in species with high gene flow. Classical population genetic models treat gene flow as a random homogenizing force countering local adaptation across habitat discontinuities. Under this view, dispersal over large spatial scales will lower the effectiveness of adaptation by natural selection at finer spatial scales. Thus, random gene flow will create a shallow phenotypic cline across an ecotone in response to a steep selection gradient. In sedentary marine species that disperse primarily as larvae, nonrandom dispersal patterns are expected due to coastal hydrodynamics. Surprisingly sharp phenotypic and genotypic clines have been documented in marine species with high gene flow. We are interested in the extent to which nonrandom dispersal could accentuate such clines. We model a linear species range in which populations have stable and uniform densities along a selection gradient; in contrast to random dispersal, convergent advection of larvae can amplify phenotypic differentiation if coupled with a semipermeable dispersal barrier in the convergence zone. The migration load caused by directional dispersal pushes the phenotypic mean away from the local trait optimum in downstream populations, that is, near the convergence zone. A dispersal barrier is possible as a result of colliding currents if the water and larvae are mostly displaced offshore, away from suitable settlement habitat. Disjunctions in a quantitative trait were enlarged in the convergence zone by faster current flows or a more complete dispersal barrier. With advection of larvae per generation one-third as far as the average dispersal distance by diffusion, convergence on a dispersal barrier with 40% permeability generated a trait disjunction across the convergence zone of two phenotypic standard deviations. Without directional dispersal, similar clines also developed across a habitat gap, where population density was low, or across dispersal barriers with less than 1% permeability. These findings suggest that the types of hydrographic phenomena often associated with marine transition zones can strongly affect the balance between gene flow and selection and generate surprisingly steep clines given the large-scale gene flow expected from larvae.     

Clan-structured migration and phenotypic differentiation in the Jirels of Nepal

This paper examines the impact of clan-structured migration on the between-village differentiation of the Jirels, a tribal population of eastern Nepal. The Jirel population is geographically restricted to nine villages, all of which were sampled to some extent for this study. Data on five head measurements, stature, and digital ridge counts are utilized to illustrate the patterns of phenotypic variation. Multivariate statistical techniques are used to assess the extent to which clan membership and associated patterns of marital exchange influence the population structure of the Jirels. The phenotypic characteristics of randomly generated migrant sets are compared to those of the observed clan-structured sets, demonstrating the clan-related phenotypic nonrandomness of migrants. The results indicate that clan-structured migration may significantly influence the amount of between-village variation. Clan structure may be a significant factor in determining patterns of variation and should not be ignored in studies of microdifferentiation in tribal populations.     

The genetic structure of finland.

The Finnish gene pool derives primarily from a relatively homogeneous Finno-Ugric population established during the Iron Age (100 B.C.-800 A.D.) in the southwest and southeast of Finland. Gene flow from Sweden to the southwest coastal areas, dating from prehistoric times, as well as the patterns of settlement and migration throughout Finland during the past 1000 years, appear to have been the major biosocial factors underlying the genetic structure of the contemporary population. Analysis of genetic variation and covariation at nine polymorphic loci in a large random sample of rural Finns, partitioned into either 8 countries or 27 geographic districts, showed that all of the essential features of the genetic structure suggested by the archaeological and historical data could be distinguished. Procedures for obtaining inference on the genetic structure of such a population are reviewed, including coefficients of similarity and (genetic) distance among subpopulations, the relation between linear or planar geographic structure and genetic covariation, and the methods for describing allelic differentiation. Bias resulting from the inappropriate assumption of a simple phylogenetic model can be substantial, expecially for the analysis of isolation by distance; procedures for avoiding misleading inference on the genetic structure are demonstrated.     

Molecular and morphometric variation in chromosomally differentiated populations of the grasshopper Sinipta dalmani (Orthopthera: Acrididae)

Sinipta dalmani is an Argentine grasshopper whose chromosome polymorphisms have been widely studied through cytogenetic, morphometric, and fitness component analyses. The present work analysed molecular and morphometric variation in seven chromosomally differentiated populations from Entre Rios and Buenos Aires provinces to analyse population structure. Molecular studies were performed studying RAPD loci and morphometric analyses were carried out measuring five morphometric traits. Genetic variability was high in all studied populations and was characterized by a decrease in H as a function of latitude and temperature. Both conventional F(ST) analysis and Bayesian approach for dominant marker showed that there were significant genetic differences among all populations, between provinces, and among populations within provinces. Entre Rios populations showed higher mean numbers of migrants per generation as well as low genetic differentiation and high gene flow with almost all populations whereas Buenos Aires populations may be considered as a result of a more recently colonization. There is considerable morphometric variation between populations and this variation correlates with latitude and temperature. Our results suggest that selection contributes to phenotypic differentiation among populations by moulding the differences in trait means whereas genetic drift is responsible for differences in the matrix of variance-covariance. The gene flow detected is insufficient to prevent phenotypic and chromosome divergences.     

The relative importance of plasticity versus genetic differentiation in explaining between population differences; a meta‐analysis

Both plasticity and genetic differentiation can contribute to phenotypic differences between populations. Using data on non‐fitness traits from reciprocal transplant studies, we show that approximately 60% of traits exhibit co‐gradient variation whereby genetic differences and plasticity‐induced differences between populations are the same sign. In these cases, plasticity is about twice as important as genetic differentiation in explaining phenotypic divergence. In contrast to fitness traits, the amount of genotype by environment interaction is small. Of the 40% of traits that exhibit counter‐gradient variation the majority seem to be hyperplastic whereby non‐native individuals express phenotypes that exceed those of native individuals. In about 20% of cases plasticity causes non‐native phenotypes to diverge from the native phenotype to a greater extent than if plasticity was absent, consistent with maladaptive plasticity. The degree to which genetic differentiation versus plasticity can explain phenotypic divergence varies a lot between species, but our proxies for motility and migration explain little of this variation.     

Population structure of an endangered species living in contrasted habitats: Parnassia palustris (Saxifragaceae)

In endangered species, it is critical to analyse the level at which populations interact (i.e. dispersal) as well as the levels of inbreeding and local adaptation to set up conservation policies. These parameters were investigated in the endangered species Parnassia palustris living in contrasted habitats. We analysed population structure in 14 populations of northern France for isozymes, cpDNA markers and phenotypic traits related to fitness. Within population genetic diversity and inbreeding coefficients were not correlated to population size. Populations seem not to have undergone severe recent bottleneck. Conversely to pollen migration, seed migration seems limited at a regional scale, which could prevent colonization of new sites even if suitable habitats appear. Finally, the habitat type affects neither within-population genetic diversity nor genetic and phenotypic differentiation among populations. Thus, even if unnoticed local adaptation to habitats exists, it does not influence gene flow between populations.     

Three components of genetic drift in subdivided populations

Wright's metaphor of sampling is extended to consider three components of genetic drift: those occurring before, during, and after migration. To the extent that drift at each stage behaves like an independent random sample, the order of events does not matter. When sampling is not random, the order does matter, and the effect of population size is confounded with that of mobility. The widely cited result that genetic differentiation of local groups depends only on the product of group size and migration rate holds only when nonrandom sampling does not occur prior to migration in the life cycle.     

Nodal signaling regulates endodermal cell motility and actin dynamics via Rac1 and Prex1

Embryo morphogenesis is driven by dynamic cell behaviors, including migration, that are coordinated with fate specification and differentiation, but how such coordination is achieved remains poorly understood. During zebrafish gastrulation, endodermal cells sequentially exhibit first random, nonpersistent migration followed by oriented, persistent migration and finally collective migration. Using a novel transgenic line that labels the endodermal actin cytoskeleton, we found that these stage-dependent changes in migratory behavior correlated with changes in actin dynamics. The dynamic actin and random motility exhibited during early gastrulation were dependent on both Nodal and Rac1 signaling. We further identified the Rac-specific guanine nucleotide exchange factor Prex1 as a Nodal target and showed that it mediated Nodal-dependent random motility. Reducing Rac1 activity in endodermal cells caused them to bypass the random migration phase and aberrantly contribute to mesodermal tissues. Together, our results reveal a novel role for Nodal signaling in regulating actin dynamics and migration behavior, which are crucial for endodermal morphogenesis and cell fate decisions.     

A model of kin-migration in plants

Summary Migrants between plant populations may represent a random sample of the donor population or may be related, being identical in the extreme. There is considerable potential for kin-structured migration in many plant species through the co-dispersal of seeds from single individuals. Through simulation experiments we have shown that the greater the level of relatedness of migrants, the less a given level of migration counterbalances the effect of genetic drift among populations.     

Upregulation of intermediate-conductance Ca2+-activated K+ channel (IKCa1) mediates phenotypic modulation of coronary smooth muscle

A hallmark of smooth muscle cell (SMC) phenotypic modulation in atherosclerosis and restenosis is suppression of SMC differentiation marker genes, proliferation, and migration. Blockade of intermediate-conductance Ca(2+)-activated K(+) channels (IKCa1) has been shown to inhibit restenosis after carotid balloon injury in the rat; however, whether IKCa1 plays a role in SMC phenotypic modulation is unknown. Our objective was to determine the role of IKCa1 channels in regulating coronary SMC phenotypic modulation and migration. In cultured porcine coronary SMCs, platelet-derived growth factor-BB (PDGF-BB) increased TRAM-34 (a specific IKCa1 inhibitor)-sensitive K(+) current 20-fold; increased IKCa1 promoter histone acetylation and c-jun binding; increased IKCa1 mRNA approximately 4-fold; and potently decreased expression of the smooth muscle differentiation marker genes smooth muscle myosin heavy chain (SMMHC), smooth muscle alpha-actin (SMalphaA), and smoothelin-B, as well as myocardin. Importantly, TRAM-34 completely blocked PDGF-BB-induced suppression of SMMHC, SMalphaA, smoothelin-B, and myocardin and inhibited PDGF-BB-stimulated migration by approximately 50%. Similar to TRAM-34, knockdown of endogenous IKCa1 with siRNA also prevented the PDGF-BB-induced increase in IKCa1 and decrease in SMMHC mRNA. In coronary arteries from high fat/high cholesterol-fed swine demonstrating signs of early atherosclerosis, IKCa1 expression was 22-fold higher and SMMHC, smoothelin-B, and myocardin expression significantly reduced in proliferating vs. nonproliferating medial cells. Our findings demonstrate that functional upregulation of IKCa1 is required for PDGF-BB-induced coronary SMC phenotypic modulation and migration and support a similar role for IKCa1 in coronary SMC during early coronary atherosclerosis.     

Physical variation and history in Melanesia and Australia

Local biological variation is marked in Melanesia. Some of it may result from gene flow from Micronesia, but the essential variation appears to result from isolation due to social fragmentation, and to genetic drift in place. In different regions, the variation may correspond well with language relationships, and probably constitutes differentiation which has been preserved over a considerable period, especially since the arrival of horticulture and development of village farming. However, none of this patterning suggests distinct waves of migration into Melanesia. Variation among Australian aboriginal groups is smaller, though far from absent. It may reflect a hunting culture together with social customs allowing more intertribal marriage than is typical of Melanesia. While phenotypically Australians and Melanesians differ, cranially they are closely allied, as against other major human groups. It is suggested that the genetic and phenotypic variety is old, that it existed in the previous home of the Australo-Melanesians (Old Melanesia, comprising present Indonesia and the Phillipines) at least back to 40,000 years ago, and that much of the variation in Melanesia and Australia, including their differences, results from the sampling process involved when different groups out of the original populations made early crossings of the water barriers from Old Melanesia.     

Neutral genetic differentiation in an island model with cyclical parthenogenesis

Unusually high levels of genetic differentiation are often observed between populations of Daphnia (Crustacea: Cladocera) and other cladocerans. Selection and departure from migration–mutation–drift equilibrium have been invoked to explain this fact. However, the null model of neutral genes at equilibrium has not been explicitly stated. Using a simple island model that takes into account the main characteristics of the cyclical parthenogenetic life‐cycle, we show that a high level of differentiation can be obtained for neutral genes at equilibrium if the migration rate during the asexual phase is low and the effective size over the season is reduced, or if mating within clones is common. Recurrent population bottlenecks have a large effect on differentiation and the time to reach equilibrium. Such fluctuating clonal dynamics could be brought about by limitations in the number of clones that hatch and establish themselves each season, or by random associations between neutral and selected genes, as previously suggested in the literature.     

一类具有随机周期移民扰动的非线性人口发展方程随机周期解的存在唯一性

本文给出了一类具有随机周期移民扰动的非线性m增生人口发展方程随机周期解的存在性和唯一性结论。     

Diversifying selection drives parallel evolution of gill raker number and body size along the speciation continuum of European whitefish

Adaptive radiation is the evolution of ecological and phenotypical diversity. It arises via ecological opportunity that promotes the exploration of underutilized or novel niches mediating specialization and reproductive isolation. The assumed precondition for rapid local adaptation is diversifying natural selection, but random genetic drift could also be a major driver of this process. We used 27 populations of European whitefish (Coregonus lavaretus) from nine lakes distributed in three neighboring subarctic watercourses in northern Fennoscandia as a model to test the importance of random drift versus diversifying natural selection for parallel evolution of adaptive phenotypic traits. We contrasted variation for two key adaptive phenotypic traits correlated with resource utilization of polymorphic fish; the number of gill rakers and the total length of fish, with the posterior distribution of neutral genetic differentiation from 13 microsatellite loci, to test whether the observed phenotypic divergence could be achieved by random genetic drift alone. Our results show that both traits have been under diversifying selection and that the evolution of these morphs has been driven by isolation through habitat adaptations. We conclude that diversifying selection acting on gill raker number and body size has played a significant role in the ongoing adaptive radiation of European whitefish morphs in this region.     

Model‐based demographic inference of introgression history in European whitefish species pairs'

Parallel phenotypic differentiation is generally attributed to parallel adaptive divergence as an evolutionary response to similar environmental contrasts. Such parallelism may actually originate from several evolutionary scenarios ranging from repeated parallel divergence caused by divergent selection to a unique divergence event followed by gene flow. Reconstructing the evolutionary history underlying parallel phenotypic differentiation is thus fundamental to understand the relative contribution of demography and selection on genomic divergence during speciation. In this study, we investigate the divergence history of replicate European whitefish (Coregonus lavaretus), limnetic and benthic species pairs from two lakes in Norway and two lakes in Switzerland. Demographic models accounting for semi‐permeability and linked selection were fitted to the unfolded joint allele frequency spectrum built from genome‐wide SNPs and compared to each other in each species pair. We found strong support for a model of asymmetrical post‐glacial secondary contact between glacial lineages in all four lakes. Moreover, our results suggest that heterogeneous genomic differentiation has been shaped by the joint action of linked selection accelerating lineage sorting during allopatry, and heterogeneous migration eroding divergence at different rates along the genome following secondary contact. Our analyses reveal how the interplay between demography, selection and historical contingency has influenced the levels of diversity observed in previous whitefish phylogeographic studies. This study thus provides new insights into the historical demographic and selective processes that shaped the divergence associated with ecological speciation in European whitefish.     

A comparative analysis of population structure of a forest tree, Eucalyptus globulus (Myrtaceae), using microsatellite markers and quantitative traits

Eucalyptus globulus (Myrtaceae) is a forest tree native to southeastern Australia, but is grown globally for pulpwood and timber. Eight microsatellite loci were used to determine the degree of selectively neutral differentiation between native populations of the geographic races of E. globulus that are used in a national breeding programme. Spatial differentiation was detected among 340 samples from across the species range (F _ST=0.09±0.02). Analysis of molecular variance showed that there was significant variation between the races, and an unweighted pair group method with arithmetic mean analysis of Nei’s genetic distance between races showed that geographically proximal races tended to be more closely related than geographically distant races. This contrasted markedly with analyses based on quantitative genetic data, where some races appeared to be highly divergent from their geographically closest neighbours. Comparison of racial differentiation based on quantitative (Q _ST) and molecular (F _ST) data suggested that at least five of the quantitative traits used for defining races of E. globulus have been influenced by natural selection, resulting in cases of both phenotypic divergence of parapatric races and phenotypic convergence of allopatric races. We conclude that selectively neutral molecular markers are more useful than quantitative genetic data for identifying the evolutionary affinities and lineages within E. globulus. However, both sources of information should be used in defining evolutionarily important units for conservation. The population structure observed in E. globulus has important consequences for future association studies and may also affect breeding strategies if significant genome co-adaptation has occurred.