Genetic differentiation in South Amerindians is related to environmental and cultural diversity: evidence from the Y chromosome

The geographic structure of Y-chromosome variability has been analyzed in native populations of South America, through use of the high-frequency Native American haplogroup defined by the DYS199-T allele and six Y-chromosome-linked microsatellites (DYS19, DYS389A, DYS389B, DYS390, DYS391, and DYS393), analyzed in 236 individuals. The following pattern of within- and among-population variability emerges from the analysis of microsatellite data: (1) the Andean populations exhibit significantly higher levels of within-population variability than do the eastern populations of South America; (2) the spatial-autocorrelation analysis suggests a significant geographic structure of Y-chromosome genetic variability in South America, although a typical evolutionary pattern could not be categorically identified; and (3) genetic-distance analyses and the analysis of molecular variance suggest greater homogeneity between Andean populations than between non-Andean ones. On the basis of these results, we propose a model for the evolution of the male lineages of South Amerindians that involves differential patterns of genetic drift and gene flow. In the western part of the continent, which is associated with the Andean area, populations have relatively large effective sizes and gene-flow levels among them, which has created a trend toward homogenization of the gene pool. On the other hand, eastern populations-settled in the Amazonian region, the central Brazilian plateau, and the Chaco region-have exhibited higher rates of genetic drift and lower levels of gene flow, with a resulting trend toward genetic differentiation. This model is consistent with the linguistic and cultural diversity of South Amerindians, the environmental heterogeneity of the continent, and the available paleoecological data.     

Genetic diversity in maize landraces from indigenous settlements of Northeastern Argentina

In South America, native maize germplasm has been extensively studied particularly for the Andean region. However, relatively few genetic diversity studies include materials from the eastern region of the continent. Herein we present a genetic diversity characterization of four Popcorn maize landraces, maintained in indigenous settlements, from Northeastern Argentina (NEA). In addition, one Popcorn landrace from Northwestern Argentina (NWA) was incorporated for comparison. We characterized these landraces using ten microsatellite markers. For the whole data set, a total of 65 alleles were found, with an average of 7.22 alleles per locus. The average gene diversity was 0.370. Global fit to Hardy–Weinberg proportions was observed in all landraces. Global estimates of F _ST revealed a significant differentiation among the populations. Individual Neighbor-joining clustering and Bayesian analyses allowed the recognition of most populations studied. Two main groups were distinguished by the Neighbor-joining clustering of populations. This grouping pattern would be consistent with a hypothesis of successive introductions of Popcorn in South America. The results presented will be useful to design strategies that maximize the utility of maize genetic resources.     

Hierarchical modeling of genome‐wide Short Tandem Repeat (STR) markers infers native American prehistory

This study examines a genome‐wide dataset of 678 Short Tandem Repeat loci characterized in 444 individuals representing 29 Native American populations as well as the Tundra Netsi and Yakut populations from Siberia. Using these data, the study tests four current hypotheses regarding the hierarchical distribution of neutral genetic variation in native South American populations: (1) the western region of South America harbors more variation than the eastern region of South America, (2) Central American and western South American populations cluster exclusively, (3) populations speaking the Chibchan‐Paezan and Equatorial‐Tucanoan language stock emerge as a group within an otherwise South American clade, (4) Chibchan‐Paezan populations in Central America emerge together at the tips of the Chibchan‐Paezan cluster. This study finds that hierarchical models with the best fit place Central American populations, and populations speaking the Chibchan‐Paezan language stock, at a basal position or separated from the South American group, which is more consistent with a serial founder effect into South America than that previously described. Western (Andean) South America is found to harbor similar levels of variation as eastern (Equatorial‐Tucanoan and Ge‐Pano‐Carib) South America, which is inconsistent with an initial west coast migration into South America. Moreover, in all relevant models, the estimates of genetic diversity within geographic regions suggest a major bottleneck or founder effect occurring within the North American subcontinent, before the peopling of Central and South America. Am J Phys Anthropol 2010. © 2009 Wiley‐Liss, Inc.     

Genetic structuring in a Neotropical palm analyzed through an Andean orogenesis‐scenario

Andean orogenesis has driven the development of very high plant diversity in the Neotropics through its impact on landscape evolution and climate. The analysis of the intraspecific patterns of genetic structure in plants would permit inferring the effects of Andean uplift on the evolution and diversification of Neotropical flora. In this study, using microsatellite markers and Bayesian clustering analyses, we report the presence of four genetic clusters for the palm Oenocarpus bataua var. bataua which are located within four biogeographic regions in northwestern South America: (a) Chocó rain forest, (b) Amotape‐Huancabamba Zone, (c) northwestern Amazonian rain forest, and (d) southwestern Amazonian rain forest. We hypothesize that these clusters developed following three genetic diversification events mainly promoted by Andean orogenic events. Additionally, the distinct current climate dynamics among northwestern and southwestern Amazonia may maintain the genetic diversification detected in the western Amazon basin. Genetic exchange was identified between the clusters, including across the Andes region, discarding the possibility of any cluster to diversify as a distinct intraspecific variety. We identified a hot spot of genetic diversity in the northern Peruvian Amazon around the locality of Iquitos. We also detected a decrease in diversity with distance from this area in westward and southward direction within the Amazon basin and the eastern Andean foothills. Additionally, we confirmed the existence and divergence of O. bataua var. bataua from var. oligocarpus in northern South America, possibly expanding the distributional range of the latter variety beyond eastern Venezuela, to the central and eastern Andean cordilleras of Colombia. Based on our results, we suggest that Andean orogenesis is the main driver of genetic structuring and diversification in O. bataua within northwestern South America.     

The impact of founder effects, gene flow, and European admixture on native American genetic diversity

Recent studies have concluded that the global pattern of neutral genetic diversity in humans reflects a series of founder effects and population movements associated with our recent expansion out of Africa. In contrast, regional studies tend to emphasize the significance of more complex patterns of colonization, gene flow, and secondary population movements in shaping patterns of diversity. Our objective in this study is to examine how founder effects, gene flow, and European admixture have molded patterns of neutral genetic diversity in the Americas. Our strategy is to test the fit of a serial founder effects process to the pattern of neutral autosomal genetic variation and to examine the contribution of gene flow and European admixture to departures from fit. The genetic data consist of 678 autosomal microsatellite loci assayed by Wang and colleagues in 530 individuals in 29 widely distributed Native American populations. We find that previous evidence for serial founder effects in the Americas may be driven in part by high levels of European admixture in northern North America, intermediate levels in Central America, and low levels in eastern South America. Geographically patterned admixture may also account for previously reported genetic differences between Andean and Amazonian groups. Though admixture has obscured the precise details of precontact evolutionary processes, we find that genetic diversity is still largely hierarchically structured and that gene flow between neighboring groups has had surprisingly little impact on macrogeographic patterns of genetic diversity in the Americas.     

Structure and genetic diversity in Colliguaja odorifera Mol. (Euphorbiaceae), a shrub subjected to Pleisto-Holocenic natural perturbations in a mediterranean South American region

Aim Colliguaja odorifera Mol., a Euphorbiaceous shrub of central Chile, inhabits the matorral formation, growing at low altitudes on both Andean and coastal mountain range slopes. In the recent geological past, this region was subjected to climatic changes and geological disturbances that most probably caused population shrinkages on the Andean mountain slopes. This study tested the hypothesis that under such a scenario, existing populations should show lower genetic diversity in the Andean than in the coastal areas; these coastal populations being the potential source populations for recolonization. Location The study was carried out in central Chile by comparing the genetic diversity between the Andean and coastal areas, each represented by five localities distributed from 32°30′ S to 34° S. Methods Genetic diversity was estimated by DNA analysis using 18 dominant multilocus Random Amplified Polymorphic DNA (RAPD) loci, characterizing 73 genetic phenotypes. Results The comparison of the two matorral areas showed that Andean populations of C. odorifera have a subset of the genetic diversity found in the coastal populations. Andean populations also show a consistently lower genetic diversity, lower genetic distances and higher genetic structure, coincident with expectations based on the Pleisto‐Holocenic perturbation regime. Main conclusions This first genetic analysis for South American mediterranean populations confirms the findings of previous floristic and palynological studies that identified refuge zones in the coastal mountain range of central Chile, a situation analogous with that occurring during periods of inter‐glacial northward migration in Southern Europe.     

Recent phylogeographic structure in a widespread ‘weedy’ Neotropical tree species,Cordia alliodora (Boraginaceae)

Aim Although hundreds of tree species have broad geographic ranges in the Neotropics, little is known about how such widespread species attained disjunct distributions around mountain, ocean and xeric barriers. Here, we examine the phylogeographic structure of a widespread and economically important tree, Cordia alliodora, to: (1) test the roles of vicariance and dispersal in establishing major range disjunctions, (2) determine which geographic regions and/or habitats contain the highest levels of genetic diversity, and (3) infer the geographic origin of the species. Location Twenty‐five countries in Central and South America, and the West Indies. Methods Chloroplast simple sequence repeats (cpSSR; eight loci) were assayed in 67 populations (240 individuals) sampled from the full geographic range of C. alliodora. Chloroplast (trnH–psbA) and nuclear (internal transcribed spacer, ITS) DNA sequences were sampled from a geographically representative subset. Genetic structure was determined with samova , structure and haplotype networks. Analysis of molecular variance (AMOVA) and rarefaction analyses were used to compare regional haplotype diversity and differentiation. Results Although the ITS region was polymorphic it revealed limited phylogeographic structure, and trnH–psbA was monomorphic. However, structure analysis of cpSSR variation recovered three broad demes spanning Central America (Deme 1), the Greater Antilles and the Chocó (Deme 2), and the Lesser Antilles and cis‐Andean South America (Deme 3). samova showed two predominant demes (Deme 1 + 2 and Deme 3). The greatest haplotype diversity was detected east of the Andes, while significantly more genetic variation was partitioned among trans‐Andean populations. Populations experiencing high precipitation seasonality (dry ecotype) had greater levels of genetic variation. Main conclusions Cordia alliodora displayed weak cis‐ and trans‐Andean phylogeographic structure based on DNA sequence data, indicative of historical dispersal around this barrier and genetic exchange across its broad range. The cpSSR data revealed phylogeographic structure corresponding to three biogeographic zones. Patterns of genetic diversity are indicative of an origin in the seasonally dry habitats of South America. Therefore, C. alliodora fits the disperser hypothesis for widespread Neotropical species. Dispersal is evident in the West Indies and the northern Andean cordilleras. The dry ecotype harbours genetic variation that is likely to represent the source for the establishment of populations under future warmer and drier climatic scenarios.     

Population Histories and Genomic Diversity of South American Natives

South America is home to one of the most culturally diverse present-day native populations. However, the dispersion pattern, genetic substructure, and demographic complexity within South America are still poorly understood. Based on genome-wide data of 58 native populations, we provide a comprehensive scenario of South American indigenous groups considering the genomic, environmental, and linguistic data. Clear patterns of genetic structure were inferred among the South American natives, presenting at least four primary genetic clusters in the Amazonian and savanna regions and three clusters in the Andes and Pacific coast. We detected a cline of genetic variation along a west-east axis, contradicting a hard Andes-Amazon divide. This longitudinal genetic variation seemed to have been shaped by both serial population bottlenecks and isolation by distance. Results indicated that present-day South American substructures recapitulate ancient macroregional ancestries and western Amazonia groups show genetic evidence of cultural exchanges that led to language replacement in precontact times. Finally, demographic inferences pointed to a higher resilience of the western South American groups regarding population collapses caused by the European invasion and indicated precontact population reductions and demic expansions in South America.     

Analysis of genetic variability of South American wild rice populations (Oryza glumaepatula) with isozymes and RAPD markers

The knowledge of population structure and genetic diversity of wild relatives of rice is needed to investigate their evolutionary history and potential use in breeding programs. Very little is known about the wild rice species ( Oryza spp.), particularly those that are native to South America. A study using isozyme and RAPD markers was conducted to estimate the level of genetic diversity of four South American wild rice populations ( Oryza glumaepatula ) recently collected in the Amazon forest and western Brazil rivers. F -statistics and genetic diversity parameters calculated from isozyme and RAPD markers indicated high values for inbreeding coefficients and differentiation among the four populations. In agreement with this, a pattern of greater variation between than within populations was observed with both types of markers. These findings were corroborated by an AMOVA analysis, which indicated that a large portion of the total genetic variation was attributed to regional divergence. The partition of the AMOVA analysis among populations showed that most of the genetic diversity was due to differences among populations. This distribution pattern of genetic variation of O. glumaepatula populations is in agreement with the expectation for an autogamous species and provides important baseline data for conservation and collection strategies for this species.     

Distribution of Y chromosomes among native North Americans: a study of Athapaskan population history

In this study, 231 Y chromosomes from 12 populations were typed for four diagnostic single nucleotide polymorphisms (SNPs) to determine haplogroup membership and 43 Y chromosomes from three of these populations were typed for eight short tandem repeats (STRs) to determine haplotypes. These data were combined with previously published data, amounting to 724 Y chromosomes from 26 populations in North America, and analyzed to investigate the geographic distribution of Y chromosomes among native North Americans and to test the Southern Athapaskan migration hypothesis. The results suggest that European admixture has significantly altered the distribution of Y chromosomes in North America and because of this caution should be taken when inferring prehistoric population events in North America using Y chromosome data alone. However, consistent with studies of other genetic systems, we are still able to identify close relationships among Y chromosomes in Athapaskans from the Subarctic and the Southwest, suggesting that a small number of proto-Apachean migrants from the Subarctic founded the Southwest Athapaskan populations.     

Dispersal Pathways and Genetic Differentiation among Worldwide Populations of the Invasive Weed Centaurea solstitialis L. (Asteraceae)

The natural history of introduced species is often unclear due to a lack of historical records. Even when historical information is readily available, important factors of the invasions such as genetic bottlenecks, hybridization, historical relationships among populations and adaptive changes are left unknown. In this study, we developed a set of nuclear, simple sequence repeat markers and used these to characterize the genetic diversity and population structure among native (Eurasian) and non-native (North and South American) populations of Centaurea solstitialis L., (yellow starthistle). We used these data to test hypotheses about the invasion pathways of the species that were based on historical and geographical records, and we make inferences about historical relationships among populations and demographic processes following invasion. We confirm that the center of diversity and the native range of the species is likely the eastern Mediterranean region in the vicinity of Turkey. From this region, the species likely proceeded to colonize other parts of Europe and Asia via a slow, stepwise range expansion. Spanish populations were the primary source of seed to invade South America via human-mediated events, as was evident from historical records, but populations from the eastern Mediterranean region were also important. North American populations were largely derived from South America, but had secondary contributors. We suggest that the introduction history of non-native populations from disparate parts of the native range have allowed not just one, but multiple opportunities first in South America then again in North America for the creation of novel genotypes via intraspecific hybridization. We propose that multiple intraspecific hybridization events may have created especially potent conditions for the selection of a noxious invader, and may explain differences in genetic patterns among North and South America populations, inferred differences in demographic processes, as well as morphological differences previously reported from common garden experiments.     

Worldwide translocation of teak—origin of landraces and present genetic base

Teak (Tectona grandis Linn. f.) is one of the major plantation timbers of the world. The species is native to India, Myanmar, Thailand and Laos in South East Asia but was translocated to several countries in Africa and Central and South America during the past century. Today, large areas of plantations are grown outside the species native range. It is speculated that genetic bottlenecks and founder effects combined with new selection pressures under new growing conditions have led to the formation of distinct landraces; this hypothesis is supported by results from international provenance tests. In the present study, we apply genetic markers to identify the likely origin of teak grown outside its native range and examine if the landraces show signs of reduced genetic diversity. We find large variation in the level of diversity among landraces, although not larger than that observed among native populations. We conclude that variation in the studied teak landraces probably reflects their areas of genetic origin rather than severe founder effects created during their introduction. The genetic data suggests that the studied landraces originated from either the semi-moist east coast of India, southern Myanmar or western Thailand. These results indicate that translocation of teak has mainly come from a certain part of the native distribution and that this did not include the widespread natural teak areas of southern, dry interior or western India or northern Myanmar.     

Genetic variation and population structure in native Americans

We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians--signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1) a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2) a relative lack of differentiation between Mesoamerican and Andean populations, (3) a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4) a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas.     

Molecular phylogeography of the Chagas' disease vector Triatoma infestans in Argentina

Triatoma infestans is the main vector of Chagas' disease in South America between latitudes 10°S and 46°S. A multilocus microsatellite data set of 836 individuals from 27 populations of T. infestans, from all its range of distribution in Argentina, was analyzed. Our results favor the hypothesis of two independent migration events of colonization in Argentina and secondary contacts. The majority of the populations of the western provinces of Catamarca, La Rioja, San Juan and the west of Cordoba province, had almost no shared ancestry with the rest of the populations analyzed. Probably those populations, belonging to localities close to the Andean region, could have been established by the dispersal line of T. infestans that would have arrived to Argentina through the Andes, whereas most of the rest of the populations analyzed may have derived from the dispersal line of T. infestans in non-Andean lowlands. Among them, those from the provinces of Formosa, Chaco, Santiago del Estero and Santa Fe shared different percentages of ancestry and presented lower degree of genetic differentiation. The migratory movement linked to regional economies and possibly associated with passive dispersal, would allow a higher genetic exchange among these populations of T. infestans. This study, using microsatellite markers, provides a new approach for evaluating the validity of the different hypotheses concerning the evolutionary history of this species. Two major lineages of T. infestans, an Andean and non-Andean, are suggested.     

Higher genetic diversity in introduced than in native populations of the mussel Mytella charruana: evidence of population admixture at introduction sites

Aim  Levels of genetic diversity can be used to determine haplotype frequency, population size and patterns of invasive species distribution. In this study, we sought to investigate the genetic structure of the invasive marine mussel Mytella charruana and compare variation from invasive populations with variation found within three native populations.
Location  Invaded areas in the USA (Florida, Georgia); native areas in Ecuador, Colombia and Brazil.
Methods  We sequenced 722 bp of the mitochondrial COI gene from 83 M. charruana samples from four invasive populations (USA) and 71 samples from two natural populations (Ecuador, Columbia). In addition, we sequenced 31 individuals of a congeneric species, Mytella guyanensis , from Salvador, Brazil. We constructed the phylogenetic relationship among all haplotypes and compared diversity measures among all populations.
Results  We found significantly higher levels of nucleotide diversity in invasive populations than in native populations, although the number of haplotypes was greater in the native populations. Moreover, mismatch distribution analyses resulted in a pattern indicative of population admixture for the invasive populations. Conversely, mismatch distributions of native populations resulted in a pattern indicative of populations in static equilibrium.
Main conclusion  Our data present compelling evidence that the M. charruana invasion resulted from admixture of at least two populations, which combined to form higher levels of genetic diversity in invasive populations. Moreover, our data suggest that one of these populations originated from the Caribbean coast of South America. Overall, this study provides an analysis of genetic diversity within invasive populations and explores how that diversity may be influenced by the genetic structure of native populations and how mass dispersal may lead to invasion success.     

Continent-Wide Decoupling of Y-Chromosomal Genetic Variation from Language and Geography in Native South Americans

Numerous studies of human populations in Europe and Asia have revealed a concordance between their extant genetic structure and the prevailing regional pattern of geography and language. For native South Americans, however, such evidence has been lacking so far. Therefore, we examined the relationship between Y-chromosomal genotype on the one hand, and male geographic origin and linguistic affiliation on the other, in the largest study of South American natives to date in terms of sampled individuals and populations. A total of 1,011 individuals, representing 50 tribal populations from 81 settlements, were genotyped for up to 17 short tandem repeat (STR) markers and 16 single nucleotide polymorphisms (Y-SNPs), the latter resolving phylogenetic lineages Q and C. Virtually no structure became apparent for the extant Y-chromosomal genetic variation of South American males that could sensibly be related to their inter-tribal geographic and linguistic relationships. This continent-wide decoupling is consistent with a rapid peopling of the continent followed by long periods of isolation in small groups. Furthermore, for the first time, we identified a distinct geographical cluster of Y-SNP lineages C-M217 (C3*) in South America. Such haplotypes are virtually absent from North and Central America, but occur at high frequency in Asia. Together with the locally confined Y-STR autocorrelation observed in our study as a whole, the available data therefore suggest a late introduction of C3* into South America no more than 6,000 years ago, perhaps via coastal or trans-Pacific routes. Extensive simulations revealed that the observed lack of haplogroup C3* among extant North and Central American natives is only compatible with low levels of migration between the ancestor populations of C3* carriers and non-carriers. In summary, our data highlight the fact that a pronounced correlation between genetic and geographic/cultural structure can only be expected under very specific conditions, most of which are likely not to have been met by the ancestors of native South Americans.     

HISTORICAL DIVERSIFICATION OF BIRDS IN NORTHWESTERN SOUTH AMERICA: A MOLECULAR PERSPECTIVE ON THE ROLE OF VICARIANT EVENTS

Studies of South American biodiversity have identified several areas of endemism that may have enhanced historical diversification of South American organisms. Hypotheses concerning the derivation of birds in the Chocó area of endemism in northwestern South America were evaluated using protein electrophoretic data from 14 taxonomically diverse species groups of birds. Nine of these groups demonstrated that the Chocó area of endemism has a closer historical relationship to Central America than to Amazonia, a result that is consistent with phytogeographic evidence. Within species groups, genetic distances between cis-Andean (east of the Andes) and trans-Andean (west of the Andes) taxa are, on average, roughly twice that between Chocó and Central American taxa. The genetic data are consistent with the hypotheses that the divergence of most cis-Andean and trans-Andean taxa was the result of either the Andean uplift fragmenting a once continuous Amazonian-Pacific population (Andean Uplift Hypothesis), the isolation of the two faunas in forest refugia on opposite sides of the Andes during arid climates (Forest Refugia Hypothesis), or dispersal of Amazonian forms directly across the Andes into the trans-Andean region (Across-Andes Dispersal Hypothesis). Disentangling these hypotheses is difficult due to the complexity of the Andean uplift and to the scant geologic and paleoclimatic information that elucidates diversification events in northwestern South America. Regarding the divergence of cis- and trans-Andean taxa, the genetic, geologic, and paleoclimatic data allow weak rejection of the Andean Uplift Hypothesis and weak support for the Forest Refugia and Andean Dispersal Hypotheses. The subsequent diversification of Chocó and Central American taxa was the result of Pleistocene forest refugia, marine transgressions, or parapatric speciation.     

Genetic Diversity of Twelve Switchgrass Populations Using Molecular and Morphological Markers

Switchgrass (Panicum virgatum L.) is a warm season, C₄ perennial grass native to most of North America with numerous applications, including use as a bioenergy feedstock species. To date, no studies on genetic diversity in switchgrass have been conducted that use both molecular and morphological markers. The objectives of this study were to assess genetic diversity and determine differences among and between 12 switchgrass populations grown in New Jersey by examining both morphological and molecular characteristics, and to determine whether morphological, molecular, and/or combined data sets can detect ecotype and/or geographical differences at the population level. Twelve plants from each population were characterized with 16 switchgrass expressed sequence tag-simple sequence repeat markers (EST-SSRs) and seven morphological characters. Data was analyzed using GenAlEx and Unweighted Pair-Group Method of Averages (UPGMA) cluster analysis. Most (64%) of the molecular variation in switchgrass populations exists among individuals within populations, with lesser amounts between populations (36%). Upland and lowland populations were distinguished in all three data sets. Some eastern US and midwestern US populations were distinct in all three data sets. Similarities were observed between all three data sets indicating molecular markers may be useful for identifying morphological differences or other adaptive traits. The combined data set was the most useful in differentiating populations based on geography and found separation between midwestern and eastern upland populations. The results indicate that the combination of morphological and molecular markers may be useful in future applications such as genetic diversity studies, plant variety protection, cultivar identification, and/or identifying geographic origin.     

Molecular population genetics of the malaria vector Anopheles darlingi in Central and South America

To analyze the genetic relatedness and phylogeographic structure of Anopheles darlingi from 19 localities throughout Central and South America, we used a minimum spanning network, diversity measures, differentiation, neutrality tests, and mismatch distribution with mitochondrial cytochrome oxidase subunit I (COI) sequences. All the Central American haplotypes were separated by seven mutational steps from the South American haplotypes and the FST distance-based neighbor-joining tree showed a primary division between Central and South America, evidence for a putative gene pool division. More ancestral and diverse haplotypes were found in Amazonian and southern Brazil populations, suggesting that Central American populations may have originated in South America. The patterns of the mtDNA haplotype diversity and five of six tests for equilibrium implicate demographic expansion in the South American populations as the historical structure, but mismatch distribution depicts populations at mutation drift equilibrium (MDE). In South America, the departure from equilibrium was consistent with an expansion that occurred during the Pleistocene.     

Discovery and characterization of single nucleotide polymorphisms in two anadromous alosine fishes of conservation concern

Freshwater habitat alteration and marine fisheries can affect anadromous fish species, and populations fluctuating in size elicit conservation concern and coordinated management. We describe the development and characterization of two sets of 96 single nucleotide polymorphism (SNP) assays for two species of anadromous alosine fishes, alewife and blueback herring (collectively known as river herring), that are native to the Atlantic coast of North America. We used data from high‐throughput DNA sequencing to discover SNPs and then developed molecular genetic assays for genotyping sets of 96 individual loci in each species. The two sets of assays were validated with multiple populations that encompass both the geographic range and the known regional genetic stocks of both species. The SNP panels developed herein accurately resolved the genetic stock structure for alewife and blueback herring that was previously identified using microsatellites and assigned individuals to regional stock of origin with high accuracy. These genetic markers, which generate data that are easily shared and combined, will greatly facilitate ongoing conservation and management of river herring including genetic assignment of marine caught individuals to stock of origin.