Nonlocal male mountain white-crowned sparrows have lower paternity and higher parasite loads than males singing local dialect

Bird song often varies geographically, and when this geographicvariation has distinct boundaries, the shared song types arereferred to as song dialects. We investigated the role of songdialect in male mating success in a wild breeding populationof mountain white-crowned sparrows (Zonotrichia leucophrysoriantha). In 2 of 3 years, males singing unusual songs ("nonlocal"males) had lower total fertilization success (measured by microsatellitepaternity analysis) than did males singing the local dialect ("local" males). Similarly, females produced disproportionately more young with local than with nonlocal males. However, dialectwas not a significant predictor of male mating success whencontrolling for other factors that might affect paternity.Instead, the low mating success of nonlocal males was apparentlydue to an interaction between song dialect and parasite load.Nonlocal males were more severely infected by bloodborne Haemoproteusthan were local males, although they did not differ in anyother measured aspect of quality. Immigrant birds may be immunologically disadvantaged, possibly due to a lack of previous experiencewith the local parasite fauna, resulting in low mating success.     

Genetic analysis of song dialect populations in Puget Sound white-crowned sparrows

The relationship between cultural variation and biological variationamong natural populations has been the subject of both theoreticaland empirical study. Zonotrichia leucophrys pugetensis is oneof three subspecies of white-crowned sparrow known to form geographicalsong dialects. We investigated whether these dialects correspondto genetic differences among Z. l. pugetensis populations. Wecompared allele frequencies at four microsatellite loci in malesfrom 11 sites spanning six dialects over the subspecies' rangein Oregon and Washington. Cluster analysis and genotype assignmenttests indicated no tendency for sample sites within dialectareas to be genetically more similar than are sites from differentdialect areas. AMOVA tests revealed high within-site variationand low but significant cross-site and cross-dialect-area variation.Finally, genetic distance between sites was not correlated withdialect differences when the effect of geographic distance wascontrolled statistically. We compare our finding of low geneticdifferentiation among Z. l. pugetensis dialect populations toresults of previous studies on Z. l. nuttalli and Z. l. oriantha.Because genetic structuring appears weaker than cultural (songdialect) structure in this species, we discuss the behavioralmechanisms underlying dialect maintenance in the presence ofapparent gene flow.     

群体遗传结构中的基因流

群体遗传结构上的差异是遗传多样性的一种重要体现,对群体遗传结构的研究已有较久的历史,而其中的基因流研究近些年来越来越受到重视。它对群体遗传学、进化生物学、保护生物学、生态学有着极其重要的作用。虽然传统的群体遗传学能估测基因流大小,但它的精确性还有很大局限性。随着生物技术的进步,对基因流的研究逐渐向分子水平过渡,应用蛋白质电泳技术、分子标记技术(RAPD、RFLP、VNTR、ISSR、DNA测序等)方法对群体间基因流的流动水平进行了深入细致的研究。通过综述群体遗传结构的几种模式:陆岛模式、海岛模式、阶石模式、距离隔离模式、层次模式,以及在群体遗传结构的几种模式基础上的基因流的研究方法、作用、地位和近些年来研究者的研究成果,并指出了这些方法的局限性。     

Spatial population genetic structure in Trillium grandiflorum: the roles of dispersal, mating, history, and selection

The roles of the various potential ecological and evolutionary causes of spatial population genetic structure (SPGS) cannot in general be inferred from the extant structure alone. However, a stage-specific analysis can provide clues as to the causes of SPGS. We conducted a stage-specific SPGS analysis of a mapped population of about 2000 Trillium grandiflorum (Liliaceae), a long-lived perennial herb. We compared SPGS for juvenile (J), nonreproductive (NR), and reproductive (R) stages. Fisher's exact test showed that genotypes had Hardy-Weinberg frequencies at all loci and stage classes. Allele frequencies did not differ between stages. Bootstrapped 99% confidence intervals (99%CI) indicate that F-statistic values are indistinguishable from zero, (except for a slightly negative FIT for the R stage). Spatial autocorrelation was used to calculate f the average kinship coefficient between individuals within distance intervals. Null hypothesis 99%CIs for f were constructed by repeatedly randomizing genotypic locations. Significant positive fine-scale genetic structure was detected in the R and NR stages, but not in the J stage. This structure was most pronounced in the R stage, and declined by about half in each remaining stage: near-neighbor f = 0.122, 0.065, 0.027, for R, NR, and J, respectively. For R and NR, the near-neighbor f lies outside the null hypothesis 99%CI, indicating kinship at approximately the level of half-sibs and first cousins, respectively. We also simulated the expected SPGS of juveniles post dispersal, based on measured R-stage SPGS, the mating system, and measured pollen and seed dispersal properties. This provides a null hypothesis expectation (as a 99%CI) for the J-stage correlogram, against which to test the likelihood that post-dispersal events have influenced J-stage SPGS. The actual J correlogram lies within the null hypothesis 99%CI for the shortest distance interval and nearly all other distance intervals indicating that the observed low recruitment, random mating and seed dispersal patterns are sufficient to account for the disappearance of SPSG between the R and the J stages. The observed increase in SPGS between J and R stages has two potential explanations: history and local selection. The observed low total allelic diversity is consistent with a past bottleneck: a possible historical explanation. Only a longitudinal stage-specific study of SPGS structure can distinguish between historical events and local selection as causes of increased structure with increasing life history stage.     

Genetic structure of mountain lion (Puma concolor) populations in California

Analysis of 12 microsatellite loci from431 mountain lions (Puma concolor)revealed distinct genetic subdivision that wasassociated with geographic barriers andisolation by distance in California. Levels ofgenetic variation differed among geographicregions, and mountain lions that inhabitedcoastal areas exhibited less heterozygositythan those sampled inland. The San FranciscoBay and Sacramento-San Joaquin River Delta, theCentral Valley, and the Los Angeles Basinappeared to be substantial barriers to geneflow, and allele frequencies of populationsseparated by those features differedsubstantially. A partial barrier to gene flowappeared to exist along the crest of the SierraNevada. Estimated gene flow was high amongmountain lions inhabiting the Modoc Plateau,the western Sierra Nevada, and northern sectionof the eastern Sierra Nevada. SouthernCalifornia mountain lion populations mayfunction as a metapopulation; however, humandevelopments threaten to eliminate habitat andmovement corridors. While north-south geneflow along the western Sierra Nevada wasestimated to be very high, projected loss andfragmentation of foothill habitat may reducegene flow and subdivide populations. Preservation of existing movement corridorsamong regions could prevent population declinesand loss of genetic variation. This studyshows that mountain lion management andconservation efforts should be individualizedaccording to region and incorporatelandscape-level considerations to protecthabitat connectivity.     

Patchy population structure in a short-distance migrant: evidence from genetic and demographic data

Species often occur in subdivided populations as a consequence of spatial heterogeneity of the habitat. To describe the spatial organization of subpopulations, existing theory proposes three main population models: patchy population, metapopulation and isolated populations. These models differ in their predicted levels of connectivity among subpopulations, and in the risk that a subpopulation will go extinct. However, spatially discrete subpopulations are commonly considered to be organized as metapopulations, even though explicit tests of metapopulation assumptions are rare. Here, we test predictions of the three models on the basis of demographic and genetic data, a combined approach so far surprisingly little used in mobile organisms. From 2002 to 2005, we studied nine subpopulations of the wetland-restricted reed bunting ( Emberiza schoeniclus ) in the southeastern part of the Canton Zurich (Switzerland), from which local declines of this species have been reported. Here, wetlands are as small as 2.7 ha and separated through intensively used agricultural landscapes. Demographic data consisted of dispersal of colour-banded individuals among subpopulations, immigration rates and extinction-/recolonization dynamics. Genetic data were based on the distribution of genetic variability and gene flow among subpopulations derived from the analysis of nine microsatellite loci. Both demographic and genetic data revealed that the patchy population model best described the spatial organization of reed bunting subpopulations. High levels of dispersal among subpopulations, high immigration into the patchy population, and genetic admixture suggested little risk of extinction of both subpopulations and the entire patchy population. This study exemplifies the idea that spatially discrete subpopulations may be organized in ways other than a metapopulation, and hence has implications for the conservation of subpopulations and species.     

Stability of genetic structure and effective population size inferred from temporal changes of microsatellite DNA polymorphisms in the land snail Helix aspersa (Gastropoda: Helicidae)

Temporal evolution of genetic variability may have far-reaching consequences for a diverse array of evolutionary processes. Within the polders of the Bay of Mont-Saint-Michel (France), populations of the land snail Helix aspersa are characterized by a metapopulation structure with occasional extinction processes resulting from farming practices. A temporal survey of genetic structure in H . aspersa was carried out using variability at four microsatellite loci, in ten populations sampled two years apart. Levels of within-population genetic variation, as measured by allelic richness, H _e or F _is , did not change over time and similar levels of population differentiation were demonstrated for both sampling years. The extent of genetic differentiation between temporal samples of the same population established (i) a stable structure for six populations, and (ii) substantial genetic changes for four populations. Using classical F -statistics and a maximum likelihood method, estimates of the effective population size ( N _e) illustrated a mixture of stable populations with high N _e, and unstable populations characterized by very small N _e estimates (of 5–11 individuals). Owing to human disturbances, intermittent gene flow and genetic drift are likely to be the predominant evolutionary processes shaping the observed genetic structure. However, the practice of multiple matings and sperm storage is likely to provide a reservoir of variability, minimizing the eroding genetic effects of population size reduction and increasing the effective population size.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 89–102.     

Allozyme variation and population genetic structure of Betula alnoides from Guangxi,China

Allozyme variation and population genetic structure of Betula alnoides Buch. Ham. ex D. Don in 11 natural populations from Guangxi Zhuang Autonomous Region, China, were investigated by starch gel electrophoresis. Variation at 15 loci from 10 enzyme systems was analyzed. Allozyme analysis revealed a high level of genetic variation in this species, with percentage of polymorphic loci (P _p ), the average number of alleles per locus (A _p ), and the expected heterozygosity (H _ep ) being 55.2%, 2.0, and 0.204, respectively, which exceeds the average level among out-crossing wind-pollinated woody species at the population level. At the species level, P _s , A _s , and H _es were 60.0%, 2.67, and 0.206, respectively.The observed heterozygosity (H _op ) was higher than H _ep , indicating the existence of natural selection against homozygotes. The negative fixation index (F = –0.216) implied a significant excess of heterozygosity at the population level. Among-population differentiation (F _ST ) accounted for 4.0% of the total variation. No significant correlation was detected between the genetic distance and geographic distance among populations. Extensive gene flow was inferred, based on the allozyme data )N _m = 6.000 from F _ST , N _m = 5.605 from the private allele method). The results demonstrated that the fragmentation status of B. alnoides had no remarkable effects on the population genetic structure of this species. Some populations are recommended for both in situ genetic conservation and germplasm collection for breeding programs.     

Surnames and dialects in France: population structure and cultural evolution

To study the isonymy structure of France as related to local language variations, the surname distributions of 6.03 million telephone users registered for the year 2002 were analysed in the 21 conterminous regions, their 94 departments and in 809 towns of the Country. For regions and departments the differences among local dialects were quantified according to the dialecto-metrization of the Atlas Linguistique Fran?ais. We found that Lasker's distance between regions was correlated with geographic distance with r=0.692+/-0.040, while Euclidean (r=0.546+/-0.058) and Nei's (r=0.610+/-0.048) distances were less correlated. Slightly lower correlations were observed for departments. Also, dialectometric distance was correlated with geography (r=0.582+/-0.069 for regions and r=0.617+/-0.015 for departments). The correlations between Lasker and dialectometric matrix distances for regions and departments are r=0.625+/-0.046 and 0.544+/-0.014, respectively, indicating that the common cause generating surname and language diversity accounts for about 35% of the differentiation. Both Lasker and dialectometric distances identify very similar boundaries between Poitou, Centre, Bourgogne and Franche Comptée at the North, and Aquitaine, Limousin, Auvergne, Rh?ne-Alpes in the South. Average Fisher's alpha for France was 7877 the highest value observed for the European countries studied to date. The size of alpha in most French towns indicates considerable recent immigration.     

Significant patterns of population genetic structure and limited gene flow in a threatened macropodid marsupial despite continuous habitat in southeast Queensland, Australia

Many endangered species worldwide are found in remnant populations, often within fragmented landscapes. However, when possible, an understanding of the natural extent of population structure and dispersal behaviour of threatened species would assist in their conservation and management. The brush-tailed rock-wallaby (Petrogale penicillata), a once abundant and widespread rock-wallaby species across southeastern Australia, has become nearly extinct across much of the southern part of its range. However, the northern part of the species’ range still sustains many small colonies closely distributed across suitable habitat, providing a rare opportunity to investigate the natural population dynamics of a listed threatened species. We used 12 microsatellite markers to investigate genetic diversity, population structure and gene flow among brush-tailed rock-wallaby colonies within and among two valley regions with continuous habitat in southeast Queensland. We documented high and significant levels of population genetic structure between rock-wallaby colonies embedded in continuous escarpment habitat and forest. We found a strong and significant pattern of isolation-by-distance among colonies indicating restricted gene flow over a small geographic scale ( <10 km) and conclude that gene flow is more likely limited by intrinsic factors rather than environmental factors. In addition, we provide evidence that genetic diversity was significantly lower in colonies located in a more isolated valley region compared to colonies located in a valley region surrounded by continuous habitat. These findings shed light on the processes that have resulted in the endangered status of rock-wallaby species in Australia and they have strong implications for the conservation and management of both the remaining ‘connected’8 brush-tailed rock-wallaby colonies in the northern parts of the species’8 range and the remnant endangered populations in the south.     

Genetic population structure in an equatorial sparrow: roles for culture and geography

Female preference for local cultural traits has been proposed as a barrier to breeding among animal populations. As such, several studies have found correlations between male bird song dialects and population genetics over relatively large distances. To investigate whether female choice for local dialects could act as a barrier to breeding between nearby and contiguous populations, we tested whether variation in male song dialects explains genetic structure among eight populations of rufous‐collared sparrows (Zonotrichia capensis) in Ecuador. Our study sites lay along a transect, and adjacent study sites were separated by approximately 25 km, an order of magnitude less than previously examined for this and most other species. This transect crossed an Andean ridge and through the Quijos River Valley, both of which may be barriers to gene flow. Using a variance partitioning approach, we show that song dialect is important in explaining population genetics, independent of the geographic variables: distance, the river valley and the Andean Ridge. This result is consistent with the hypothesis that song acts as a barrier to breeding among populations in close proximity. In addition, songs of contiguous populations differed by the same degree or more than between two populations previously shown to exhibit female preference for local dialect, suggesting that birds from these populations would also breed preferentially with locals. As expected, all geographic variables (distance, the river valley and the Andean Ridge) also predicted population genetic structure. Our results have important implications for the understanding whether, and at what spatial scale, culture can affect population divergence.     

湖北海棠的等位酶变异和遗传多样性研究

采用超薄平板微型聚丙烯酰胺等电聚焦电泳方法对湖北海棠（Malus hupehensis)的9个野生居群和2个人工栽培居群的等位酶变异和遗传多样性进行了初步研究。通过对12个酶系统29个酶位点的检测,结果表明湖北海棠有25个酶位点的等位基因频率分布差异,,有10个居群发现稀有等位基因,并有11个（37．9％）重复位点;湖北海棠的遗传多样性水平很高,等位基因平均数A＝2．127,多态位点百分率P＝74．927,平均预期杂合度He=0.376;居群间的基因分化系数GST＝0．224。与其他苹果属植物相比,湖北海棠具有中等丰富的遗传变异水平。居群间的基因流仅为Nm=0.866,表明遗传漂变是影响居群遗传变异和遗传结构的一个重要因素。     

Spatial population structure in a patchily distributed beetle

The dynamics and evolution of populations will critically depend on their spatial structure. Hence, a recent emphasis on one particular type of structure--the metapopulation concept of Levins--can only be justified by empirical assessment of spatial population structures in a wide range of organisms. This paper focuses on Aphodius fossor, a dung beetle specialized on cattle pastures. An agricultural database was used to locate nearly 50 000 local populations of A. fossor in Finland. Several independent methods were then used to quantify key processes in this vast population system. Allozyme markers and mitochondrial DNA (mtDNA) sequences were applied to examine genetic differentiation of local populations and to derive indirect estimates of gene flow. These estimates were compared to values expected on the basis of direct observations of dispersing individuals and assessments of local effective population size. Molecular markers revealed striking genetic homogeneity in A. fossor. Differentiation was only evident in mtDNA haplotype frequencies between the isolated Aland islands and the Finnish mainland. Thus, indirect estimates of gene flow agreed with direct observations that local effective population size in A. fossor is large (hundreds of individuals), and that in each generation, a substantial fraction (approximately one-fifth) of the individuals move between populations. Large local population size, extreme haplotype diversity and a high regional incidence of A. fossor all testify against recurrent population turnover. Taken together, these results provide strong evidence that the whole mainland population of A. fossor is better described as one large 'patchy population', with substantial movement between relatively persistent local populations, than as a classical metapopulation.     

Genome-wide genetic diversity,population structure and admixture analysis in African and Asian cattle breeds

Knowledge about genetic diversity and population structure is useful for designing effective strategies to improve the production, management and conservation of farm animal genetic resources. Here, we present a comprehensive genome-wide analysis of genetic diversity, population structure and admixture based on 244 animals sampled from 10 cattle populations in Asia and Africa and genotyped for 69 903 autosomal single-nucleotide polymorphisms (SNPs) mainly derived from the indicine breed. Principal component analysis, STRUCTURE and distance analysis from high-density SNP data clearly revealed that the largest genetic difference occurred between the two domestic lineages (taurine and indicine), whereas Ethiopian cattle populations represent a mosaic of the humped zebu and taurine. Estimation of the genetic influence of zebu and taurine revealed that Ethiopian cattle were characterized by considerable levels of introgression from South Asian zebu, whereas Bangladeshi populations shared very low taurine ancestry. The relationships among Ethiopian cattle populations reflect their history of origin and admixture rather than phenotype-based distinctions. The high within-individual genetic variability observed in Ethiopian cattle represents an untapped opportunity for adaptation to changing environments and for implementation of within-breed genetic improvement schemes. Our results provide a basis for future applications of genome-wide SNP data to exploit the unique genetic makeup of indigenous cattle breeds and to facilitate their improvement and conservation.     

Evaluating methods for estimating local effective population size with and without migration

Effective population size is a fundamental parameter in population genetics, evolutionary biology, and conservation biology, yet its estimation can be fraught with difficulties. Several methods to estimate N_e from genetic data have been developed that take advantage of various approaches for inferring N_e. The ability of these methods to accurately estimate N_e, however, has not been comprehensively examined. In this study, we employ seven of the most cited methods for estimating N_e from genetic data (Colony2, CoNe, Estim, MLNe, ONeSAMP, TMVP, and NeEstimator including LDNe) across simulated datasets with populations experiencing migration or no migration. The simulated population demographies are an isolated population with no immigration, an island model metapopulation with a sink population receiving immigrants, and an isolation by distance stepping stone model of populations. We find considerable variance in performance of these methods, both within and across demographic scenarios, with some methods performing very poorly. The most accurate estimates of N_e can be obtained by using LDNe, MLNe, or TMVP; however each of these approaches is outperformed by another in a differing demographic scenario. Knowledge of the approximate demography of population as well as the availability of temporal data largely improves N_e estimates.     

The effect of geographic range and dichogamy on genetic variability and population genetic structure in Tricyrtis section Flavae

Populations of each of the four species of Tricyrtis sect. Flavae were sampled using enzyme electrophoresis to examine the effect of geographic range and dichogamy on the genetic diversity of the species. The most widespread species, T. nana, had the lowest level of genetic diversity at both the population and the species level. The depauperate genetic diversity at the population level of T. nana appears to result from the high self-fertilization of the species. The low genetic diversity at the species level of T. nana probably resulted from the bottleneck effect during the speciation process in which this species diverged from the progenitor species, T. flava. Genetic differentiation among populations was high in both adichogamous T. nana and protandrous T. flava. High self-fertilization in T. nana and the colonizing nature of T. flava are likely the main factors causing the differentiated population genetic structure. In contrast to a previous study on chloroplast DNA (cpDNA) variation in Tricyrtis sect. Flavae, T. nana was most closely related to T. flava, which corresponds to the morphological resemblance of both species.     

Gene flow and effective population size in Lepanthes (Orchidaceae): a case for genetic drift

Genetic drift can play an important role in population differentiation, particularly when effective population sizes are small and gene flow is limited. Such conditions are suspected to be common in the species-rich Orchidaceae. We investigated the likelihood of genetic drift in natural populations of three endemic species of Lepanthes (Orchidaceae) from Puerto Rico. We estimated effective population size, Ne, using three ecologically based methods. Two of the three estimates were based on variance in reproductive potential and the third was based on coalescence time. All estimates of Ne were usually <40% of the standing population size, resulting in values of <20 individuals per population. Based on starch gel electrophoresis of isozymes, Nm estimates suggest restricted gene flow among populations in the range of one or less successful migrant per generation. Genetic differentiation among populations is expected under such conditions from random genetic drift. Indeed we observed high genetic differentiation among populations (L. rubripetala, F_ST> G_ST, 6; θ.248, 0.266, 0.293; L. rupestris, 0.148, 0.169, 0.138; L. eltoroensis, 0.251, 0.219, 0.218, respectively). Genetic drift is likely to be important for population differentiation in Lepanthes as a result of small effective population sizes and restricted gene flow.     

Genetic diversity and genetic structure of populations of Ranunculus japonicus Thunb. (Ranunculaceae)

Abstract In order to clarify the genetic diversity and population structure of Ranunculus japonicus , allozymic analysis was conducted on 60 populations in southwestern Japan. Considerable genetic variati ons were detected among the populations of R. japonicus . The genetic diversities within species ( H _es = 0.215) and within populations ( H _ep = 0.172) were slightly higher than those of other perennial herbs with widespread distribution and outcrossing plants. Significantly higher values of fixation index were detected in some populations, which might have arisen from restricted mating partners. The majority of genetic variation (approx. 80%) resided within a population and a moderate level of genetic differentiation ( G _ST = 0.203) was observed among populations. The F _ST value (0.203) suggests the existence of a substantial population structure in this species. The highly significant correlation between geographic distance and F _ST values indicates that isolation by distance has played an important role in the construction of the genetic structure of this species.