Population structure in the Connecticut Valley: II. A comparison of multidimensional scaling solutions of migration matrices and isonymy

In a previous paper (Swedlund et al., 1984) we have described the population structure of the historical Connecticut River Valley of Massachusetts in terms of matrimonial migration matrices. Using procedures described by Morton (1973), Harpending and Jenkins (1974), Jorde (1980), and others the exchanges between subdivisions which make up the matrices are made column stochastic and analyzed to predict genetic kinship. Subsequently the kinship estimates within and between subdivisions can be interpreted as genetic covariance and compared to the actual geographic distances between the respective subdivisions using a principal components analysis. In the present paper we extend these results by applying nonmetric multidimensional scaling to the migration matrices, and to isonymy matrices based on the same communities. We demonstrate that the multidimensional scaling configurations of marital migration represent the actual geographic relationships between the communities quite effectively for this particular case study from historical Massachusetts. Moreover, we argue that while these migration data may provide good estimates of social and genetic exchange between the subdivisions, surname analysis may also be informative of processes not revealed in the migration matrices alone.     

Genetic distances,geographic distances and migration between four villages of a single region in Slovakia

Genetic microdifferentiation has been studied among four endogamous villages of the Bystrica Valley in the Kysuce region of northwest Slovakia, which arose from a single ancestral population about 15 generations ago. Genetic distances and sample kinship between the villages were estimated from the gene frequencies of seven serum-group and isozyme genetic markers. The genetic distance was found to correlate positively (though insignificantly) with the geographic distance, and negatively with the intensity of migration between villages; the sample kinship correlates negatively with geography as well as with the genetic distance. This pattern of genetic structure within the area indicates that the genetic variation among the villages is attributable to the genetic drift. Thus, drift has brought about a detectable differentiation in the area within a limited period of approximately 300 years, in spite of the fact that the villages were not completely genetically isolated from each other. The finding of a negative correlation between the sample kinship and geographic distance indicates that the recent breakdown of genetic isolates in Slovakia is likely to be accompanied with an overall increase of heterozygosity.     

Genetic differentiation among Sardinian villages.

The present study reports an analysis of genetic differentiation among 14 Sardinian villages located mainly in the center of the island. Chi-square tests show significant genetic heterogeneity among villages, and analyses by F- and R- statistics indicate an essentially random pattern of differentiation for all alleles. Using the kinship methods of Morton, a matrix, R, with elements rij describing the correlations between the gene frequencies of villages i and j is obtained. Use of Malécot's formula relating the rij to the geographic distances between villages shows a rapid decline of kinship with increasing distance but reveals essentially no relationship for distances over 40 km. Rotation of a two-dimensional reduction of the kinship matrix to maximum congruence with the geographic distances indicates that about 25% of the genetic distances can be accounted for by the geographic location of the villages. Isolation due in part to cultural factors, genetic drift, and special local or regional patterns of villages associations appear to be involved in the pattern of genetic variation.     

Disruption of historical patterns of isolation by distance in coastal steelhead

When natural populations exchange migrants at a rate proportional to their geographic distance, population genetics theory leads to the expectation of a pattern of isolation-by-distance (IBD), whereby geographic and genetic distance are correlated. However, the presence or absence of such patterns in modern populations may not fully reflect the historical relationships among those populations. Thus, historical samples, collected prior to modern human impacts, can often provide a critical baseline for comparison with modern populations. Steelhead, the anadromous form of rainbow trout, Oncorhynchus mykiss, are native to western North America and are endangered or threatened throughout most of California, near the southern extent of their native range. Population samples of steelhead collected in 1897 and 1909 in Central California rivers provided the opportunity to evaluate the historical genetic composition and population structure of these threatened fish. Here we show that these steelhead populations had a historically strong correlation between genetic and geographic distance that has been virtually erased in modern populations, suggesting that current relationships among modern steelhead populations are no longer reflective of natural migratory pathways. This demonstrates the critical role of migration in maintaining population relationships of threatened species and highlights the importance of natural history museums in providing historical baseline information.     

Global patterns of isolation by distance based on genetic and morphological data

The isolation-by-distance model predicts that genetic similarity between populations will decrease exponentially as the geographic distance between them increases, because of the limiting effect of geographic distance on rates of gene flow. Many studies of human populations have applied the isolation-by-distance model to genetic variation between local populations in a limited geographic area, but few have done so on a global level, and these few used different models and analytical methods. I assess genetic variation between human populations across the world using data on red blood cell polymorphisms, microsatellite DNA markers, and craniometric traits. The isolation-by-distance model provides an excellent fit to average levels of genetic similarity within geographic distance classes for all three data sets, and the rate of distance decay is the same in all three. These results suggest that a common pattern of global gene flow mediated by geographic distance is detectable in diverse genetic and morphological data. An alternative explanation is that the correspondence between genetic similarity and geographic distance reflects the history of dispersal of the human species out of Africa.     

Migration and genetic structure in Northumberland

To understand the genetic variation that occurs among regions of northern England, we estimated migration from places of birth and residence in the last two generations for a sample of 1367 families in Northumberland. There has been an increase in kinship among regions, compatible with the increased mobility of recent decades, but the kinship patterns suggest that any regional gene frequency differences have remained relatively undiluted. Comparison of kinship and geographic distance between regions indicates that geographic location is an important determinant of genetic structure.     

不同地区棉铃虫种群DNA多态性的RAPD分析

通过对棉铃虫Helicoverpa armigera(Hubner)17个地理种群DNA多态性进行了RAPD分析,结果表明：棉铃虫可以分为四大类群,三亚(SY)、莎车(SC)和哈密(HM)种群各为独立的一类,与内地种群有明显的差异,其中三亚种群差异最大;第四类包含14个地理种群,它们之间相对分化较小,基因相似程度较高,特别是黄河流域和辽河流域南部的种群间遗传距离最小,无基因交流障碍。单个个体的RAPD分析表明,这些种群间的某些个体相互交错,进一步说明这些种群间可能存在着广泛的基因交流。最后还讨论了形成棉铃虫遗传多态性的主要原因,     

Genetic variation and phylogeography of the swordtail fish Xiphophorus cortezi (Cyprinodontiformes, Poeciliidae)

Swordtail fish have been studied extensively in relation to diverse aspects of biology; however, little attention has been paid to the patterns of genetic variation within and among populations of swordtails. In this study, we sequenced the mtDNA control region from 65 individuals and 10 populations of Xiphophorus cortezi to investigate the genetic variation within and among populations, including tests for correlations between genetic and geographic distances and tests for species monophyly. We found low gene and nucleotide diversity within populations and high degrees of genetic differentiation among populations. Significant and positive correlations between genetic distance and both river and straight-line geographic distance indicate that genetic differentiation among X. cortezi populations can be explained, to some extent, by an isolation-by-distance model and provide evidence of stream capture. Phylogenetic analyses suggest that X. cortezi is paraphyletic relative to X. malinche, raising questions concerning the status of these taxa as separate species.     

Isolation by distance, linguistic similarity, and the genetic structure on Bougainville Island

Previous research has revealed extensive genetic variation among villages on Bougainville, in the Solomon Islands. Using previously published gene frequency data for seven loci, the role of isolation by distance in structuring genetic variation on Bougainville was reanalyzed. Newer methods of kinship estimation show that earlier estimates of the isolation by distance parameters were low. The fit of the model is highly significant (R2 = 0.409; P less than 0.001), and the parameter estimates indicate high isolation: a = 0.0538, b = 0.1978, L = -0.0057. Several methods of residual analysis were applied in order to determine factors affecting the fit of the model. Linguistic similarity has a significant effect on genetic variation once the effects of geographic distance are taken into account. Population-specific deviations from the expected model may be explained, in part, in terms of population history. Compared to other human populations, Bougainville Island shows an even greater among-group variation than has been suggested previously.     

Gene flow, historical population dynamics and genetic diversity within French Guianan populations of a rainforest tree species, Vouacapoua americana

Both gene flow and historical events influence the genetic diversity of natural populations. One way to understand their respective impact is to analyze population genetic structure at large spatial scales. We studied the distribution of genetic diversity of 17 populations of Vouacapoua americana (Caesalpiniaceae) in French Guiana, using nine microsatellite loci. Low genetic diversity was observed within populations, with a mean allelic richness and gene diversity of 4.1 and 0.506, respectively, which could be due to low effective population size and/or past bottlenecks. Using the regression between Fst/(1-Fst), estimated between pairs of populations, and the logarithm of the geographical distance, the spatial genetic structure can partly be explained by isolation-by-distance and limited gene flow among populations. This result is in agreement with the species' biology, including seed and pollen dispersal by rodents and insects, respectively. In contrast, no clear genetic signal of historical events was found when examining genetic differentiation among populations in relation to biogeographical hypotheses or by testing for bottlenecks within populations. Our conclusion is that nuclear spatial genetic structure of V. americana, at the geographic scale of French Guiana, is better explained by gene flow rather than by historical events.     

Environmental and geographic correlates of the taxonomic structure of primate communities

Previous research has shown that both environmental and historical factors influence the taxonomic structure of animal communities; yet, the relative importance of these effects is not known for primates. Environmental characteristics shape the possible niches in a community, providing suitable habitats for some species and not others. Therefore, communities found in similar environments should display similar species compositions. Additionally, geography may be viewed as a surrogate for historical processes. For instance, as the geographic distance between communities increases, dispersal between sites is more limited, and the probability of historical vicariance increases. Therefore, communities in close proximity to each other should exhibit similar species compositions. The geographic location, environmental characteristics, and species composition of 168 primate communities were gathered from the literature. Canonical correspondence analyses were conducted to examine the relative effects of geographic distance and environmental variables on the taxonomic structure of communities. In addition, UPGMA cluster analyses were conducted to better visualize the taxonomic similarity of communities. Spatial variables were significant predictors of community structure in all regions. Rainfall patterns explained African, Malagasy, and Neotropical community structure. In addition, maximum temperature was also correlated with community structure in Madagascar and the Neotropics. No climatic variables predicted Asian community structure. These results demonstrate that both historical and environmental factors play a significant role in structuring modern primate communities; yet, the importance of environmental factors depend on the region in question. Am J Phys Anthropol, 2009. © 2008 Wiley‐Liss, Inc.     

PHYLOGEOGRAPHY AND WITHIN-STREAM GENETIC VARIATION OF BATRACHOSPERMUM HELMENTOSUM (RHODOPHYTA) USING INTER-SIMPLE SEQUENCE REPEATS

A relatively new molecular marker technique, inter-simple sequence repeats (ISSR), was used to assess the within-stream reach genetic variation and phylogeography of the freshwater red alga, Batrachospermum helmentosum. The within-stream reach study was undertaken in Southeastern Ohio, where 58 individuals were collected from an approximately 200 m stream length. Individuals appeared to be congregated into three distinct areas, with no plants between areas. Using three primers, 100 polymorphic bands were scored. Although it was hypothesized that genetic variation would reflect physical distance, the results showed six distinct genetic groupings, some of which consisted of physically distant individuals. Overall, genetic diversity was greater among individuals than between geographic and genetic groups. To investigate phylogeography, 11 stream reaches (3 from Ohio and one each from Connecticut, Massachusetts, Rhode Island, North Carolina, Tennessee, Indiana, Michigan and Louisiana) were sampled throughout the alga's known distribution in North America. Approximately 15 individuals were collected per stream for ISSR analysis. Five primers, yielding 243 polymorphic bands, were used to examine variation among all individuals. Neighbor-joining trees generated from the Dice, Jaccard and Excoffier coefficients showed that individuals from the same stream formed a clade. Among streams there was no distinct correlation between geographic distance and genetic similarity. Genetic groupings varied slightly among distance coefficients employed. Michigan and Tennessee, Connecticut and Rhode Island, and Indiana and Massachusetts streams consistently showed the same relationship, but the relationships among the three Ohio streams and Louisiana stream were variably related to each other.     

Genetic structure of the human population in the Po delta

The genetic structure of the population of Ferrara Province in the Po delta in Italy was investigated using chi 2 analysis, kinship analysis, analysis of correspondences, and geographical mapping of principal components of gene frequencies. chi 2 Analysis tests for Hardy-Weinberg equilibrium and for heterogeneity of gene and phenotype frequencies; kinship analysis tests for association between indicators of genetic and geographic proximity; analysis of correspondences relates localities and genetic systems in an eigenvectorial space; and geographic mapping displays the principal components of gene frequencies in the real space. In 1,364 adults in 26 residential units, seven presumably neutral isoenzyme systems were typed; ACP1 ESD, GLO I, GPT, PGD, PGM1 and PGP. It was found that average kinship for these neutral systems is correlated with geographic distance in this small area, but not as strongly as kinship for beta-thalassemia. A north-south gradient was observed for ESD. Analysis of correspondences indicated GPT, PGM1, and GLO I as the systems contributing most to differentiation within the province. The maps obtained from principal components of gene frequencies were consistent with the migrational history of the area.     

A Historical Perspective on Pitch Pine–Scrub Oak Communities in the Connecticut Valley of Massachusetts

We present a regional–historical approach to the interpretation, conservation, and management of pitch pine–scrub oak (PPSO) communities in the Connecticut Valley of Massachusetts. Historical studies, aerial photographs, GIS analyses, and extensive field sampling are used to (a) document changes in the historical distribution, composition, and dynamics of these communities, and (b) evaluate the importance of regional–historical approaches to understanding, conserving, and managing uncommon communities. At the time of European settlement, pine plains dominated by both pitch and white pine were widespread, occurring on 9000 ha or more of the extensive (approximately 32,000 ha) xeric outwash deposits in the Connecticut Valley. Pine plains were harvested for diverse forest products from the 17th to the early 19th centuries. After 1830, most sites were cleared and plowed for agriculture and then abandoned in the late 19th and early 20th centuries, resulting in widespread natural reforestation. Modern PPSO communities differ from historical communities with respect to landscape distribution, composition, and structure. Nearly all modern pitch pine stands in the Connecticut Valley became established on former agricultural fields. Current vegetation on these former fields differs substantially from those few sites that were never plowed. In particular, several species (for example, Gaultheria procumbens, Gaylussacia baccata, Quercus ilicifolia, and Q. prinoides) that are characteristic of unplowed sites have not successfully colonized former fields in the 50 to more than 100 years since agricultural abandonment. Urban, commercial, and residential development have been widespread in the 20th century. By 1985, only 38.6% of the outwash deposits remained forested, and only 1094 ha of pitch pine stands and 74 ha of scrub oak stands occurred, primarily in numerous small patches. Several stands have been destroyed since 1985, and development threatens all remaining sites. The trend towards rapid urban development in the 20th century makes it increasingly urgent that the few, relatively large, undeveloped sites be protected. Our results suggest that (a) land protection efforts should prioritize large, undeveloped sand plains, areas that were not plowed historically, and reestablishment of contiguity between isolated sites to facilitate colonization of former agricultural lands by sand plain species; (b) management of PPSO communities should not be restricted to maintenance of open barrens; “old-growth” pitch and white pine stands occurred historically, and some PPSO communities should be allowed to mature without frequent disturbance; (c) the exclusive use of prescribed fires during the spring months is unlikely to maintain communities similar to modern ones or to restore communities similar to historical ones. Establishment or maintenance of open barrens species and communities may require more varied disturbance regimes, perhaps including mechanical treatment in combination with prescribed fire to simulate severe summer fires; (d) regional–historical perspectives are critical for understanding modern community dynamics and for evaluating conservation objectives and management strategies for uncommon plant communities.     

Alternative bioassays of kinship between loci.

In this study four asymptotically equivalent estimates of kinship are derived, in the general case and for kinship between multiallelic loci. Two estimates based on chi 2 agree closely, with the Shannon estimate giving the smaller variance. The PAH, GH, GM, and HBB systems conform to a recombinational model with an evolutionary size of approximately 4,000 and a ratio of recombination to physical distance of approximately 1.4 X 10(-5) morgans/kb, as predicted on the basis of the genetic and physical lengths of the human genome. The INS and D11S12 systems have a much more rapid decline of kinship with physical distance, suggesting overlapping RFLPs (unrecognized allelism), recombinational hot spots, or selection. Sources of error in predicting kinship over small distances are discussed.     

Multiple Mantel tests and isolation-by-distance, taking into account long-term historical divergence

Mantel tests of matrix correspondence have been widely used in population genetics to examine microevolutionary processes, such as isolation-by-distance (IBD). We used partial and multiple Mantel tests to simultaneously test long-term historical effects and current divergence and equilibrium processes, such as IBD. We used these procedures to calculate genetic divergence among Eugenia dysenterica (Myrtaceae) populations in Central Brazil. The Nei's genetic distances between pairs of local populations were strongly correlated with geographic distances, suggesting an IBD process, but field observations and the geographic distribution of the samples suggest that populations may have been subjected to more complex evolutionary processes of genetic divergence. Partial Mantel regression was used to partition the effects of geographic structure and long-term divergence associated with a possible historical barrier. The R(2) of the model with both effects was 73.3%, and after the partition 21.9% of the variation in the genetic distances could be attributed to long-term historical divergence alone, whereas only 1.5% of the variation in genetic distances could be attributed to IBD. As expected, there was a large overlap between these processes when explaining genetic divergence, so it was not possible to entirely partition divergence between historical and contemporary processes.     

Drivers of genetic differentiation in a generalist insect‐pollinated herb across spatial scales

The isolation‐by‐distance model (IBD) predicts that genetic differentiation among populations increases with geographic distance. Yet, empirical studies show that a variety of ecological, topographic and historical factors may override the effect of geographic distance on genetic variation. This may particularly apply to species with narrow but highly heterogeneous distribution ranges, such as those occurring along elevational gradients. Using nine SSR markers, we study the genetic differentiation of the montane pollination‐generalist herb, Erysimum mediohispanicum. Because the effects of any given factor may depend on the geographic scale considered, we investigate the contribution of different environmental and historical factors at three different spatial scales. We evaluate five competing models that put forward the role of geographic distance, local environmental factors [biotic interactions (IBEb) and climatic variables (IBEa)], landscape resistance (IBR) and phylogeographic patterns (IBP), respectively. We find significant IBD regardless of the spatial scale and the genetic distance estimator considered. However, IBEa and IBP also play a prominent role in shaping genetic differentiation patterns at the larger spatial scales, and IBR is significant at the fine spatial scale. Overall, our results highlight the importance of combining different estimators, statistical approaches and spatial scales to disentangle the relative importance of the various ecological factors contributing to the shaping of genetic divergence patterns in natural populations.     

Surname analysis of the Corsican population reveals an agreement with geographical and linguistic structure

The surname is a cultural trait that is extremely useful for historical and linguistic studies and can effectively be used as a genetic marker. In many human populations the surname is inherited in the paternal lineage, and can therefore be considered a marker for the Y chromosome. In this study, surnames were recorded from the white pages of telephone directories in current use in Corsica in 1993. All surnames present in thirteen villages scattered over the whole island and covering the main historical regions were transcribed. Surname variability was found to be higher in coastal villages, and lower in more isolated communities. The isonymy detected among the thirteen villages allowed the calculation of kinship values, visualized in a tree showing two main clusters, one referring to the northern villages and one encompassing the villages of the south. The pattern reflects the administrative division of the island, with the exception of Vico, which belongs to the southern administrative region but is geographically close to the northern villages, and Ghisoni, which belongs to the northern district but is more similar to the village of Bastelica in the southern district. The data presented here show a structure in the surname distribution that is in substantial agreement with the geographical patterns. The kinship values are consistent with a moderated gene flow among villages producing a surname structure according to the geographic features of the territory.     

Habitat differentiation vs. isolation-by-distance: the genetic population structure of Elymus athericus in European salt marshes

We investigated genetic differentiation among populations of the clonal grass Elymus athericus, a common salt-marsh species occurring along the Wadden Sea coast of Europe. While E. athericus traditionally occurs in the high salt marsh, it recently also invaded lower parts of the marsh. In one of the first analyses of the genetic population structure in salt-marsh species, we were interested in population differentiation through isolation-by-distance, and among strongly divergent habitats (low and high marsh) in this wind- and water-dispersed species. High and low marsh habitats were sampled at six sites throughout the Wadden Sea. Based on reciprocal transplantation experiments conducted earlier revealing lower survival of foreign genotypes we predicted reduced gene flow among habitats. Accordingly, an analysis with polymorphic cross-species microsatellite primers revealed significant genetic differentiation between high and low marsh habitats already on a very small scale (< 100 m), while isolation-by-distance was present only on larger scales (60-443 km). In an analysis of molecular variance we found that 14% of the genetic variance could be explained by the differentiation between habitats, as compared to only 8.9% to geographical (isolation-by-distance) effects among six sites 2.5-443 km distant from each other. This suggests that markedly different selection regimes between these habitats, in particular intraspecific competition and herbivory, result in habitat adaptation and restricted gene flow over distances as small as 80 m. Hence, the genetic population structure of plant species can only be understood when considering geographical and selection-mediated restrictions to gene flow simultaneously.