Diversity of mtDNA in Southern River Otter (Lontra provocax) from Argentinean Patagonia

Lontra provocax is an endemic species from Patagonia that has been categorized as "endangered" by the International Union for Conservation of Nature. In this study, noninvasive molecular methods were used to investigate the genetic diversity and haplotype distribution of L. provocax in Argentinean Patagonia. We analyzed 150 scat samples collected from 1995 to 2006 and obtained 13 sequences of control region with 1 haplotype and 34 sequences of cytochrome b with 4 haplotypes. The population of the south of Patagonia (Tierra del Fuego and De los Estados Island) showed a relatively high haplotype diversity (h = 0.71) and was statistically different to the population of the north (analysis of molecular variance, F(ST) = 0.15, P = 0.018). We concluded that there are 2 different subpopulations of L. provocax that deserve conservation attention and that the southern population appears not to have suffered a human-induced population bottleneck of the sort typically experienced by various otter species around the world.     

Range expansion and prey use of American mink in Argentinean Patagonia: dilemmas for conservation

Following the establishment of American mink farms outside North America, the species has successfully invaded Europe and South America, and in some places, their presence demonstrably threatens native biodiversity. We surveyed for mink signs along the Andean Patagonian forest in Argentina from 38°52′ S to 54°52′ S, revealing that their range has now expanded to span 800 km of contiguous occupation on the continent including several types of wetlands and has also colonised Tierra del Fuego Island. Rate of expansion was estimated using two methodologies and varied between 5.53 and 9.00 km/year (linear method, large-scale spread) and 4.86 km/year (within a more restricted area, grid method). Diet throughout the region fitted the generalist pattern described for mink elsewhere. Native small mammals were the most frequently consumed category. Crustaceans (patchily distributed in the region) occurred in the diet in proportion to their availability (r _s=0.961, p<0.001), but that of waterfowl did not (r _s=0.178, p=0.713). Diet was evaluated at one lake throughout a year, revealing that consumption of crustaceans fell in the cold months when bird abundance increased. Based on published work on the impact of American mink as an introduced species in Patagonia and elsewhere, together with our own survey, we discuss the implications of this invasion for biodiversity conservation in Argentinean Patagonia and the associated dilemmas for management policy.     

Native South American genetic structure and prehistory inferred from hierarchical modeling of mtDNA

Genetic diversity in Native South Americans forms a complexpattern at both the continental and local levels. In comparingthe West to the East, there is more variation within groupsand smaller genetic distances between groups. From this pattern,researchers have proposed that there is more variation in theWest and that a larger, more genetically diverse, founding populationentered the West than the East. Here, we question this characterizationof South American genetic variation and its interpretation.Our concern arises because others have inferred regional variationfrom the mean variation within local populations without takinginto account the variation among local populations within thesame region. This failure produces a biased view of the actualvariation in the East. In this study, we analyze the mitochondrial DNA sequence betweenpositions 16040 and 16322 of the Cambridge reference sequence.Our sample represents a total of 886 people from 27 indigenouspopulations from South (22), Central (3), and North America(2). The basic unit of our analyses is nucleotide identity bydescent, which is easily modeled and proportional to nucleotidediversity. We use a forward modeling strategy to fit a seriesof nested models to identity by descent within and between allpairs of local populations. This method provides estimates ofidentity by descent at different levels of population hierarchywithout assuming homogeneity within populations, regions, orcontinents. Our main discovery is that Eastern South America harbors moregenetic variation than has been recognized. We find no evidencethat there is increased identity by descent in the East relativeto the total for South America. By contrast, we discovered thatpopulations in the Western region, as a group, harbor more identityby descent than has been previously recognized, despite thefact that average identity by descent within groups is lower.In this light, there is no need to postulate separate foundingpopulations for the East and the West because the variabilityin the East could serve as a source for the Western gene pools.     

Spatial variation in molluscan assemblages from coralline turfs of Argentinean Patagonia

Patterns of spatial variation of molluscan communities associatedwith coralline algal turfs were evaluated over 1,000 kmof the coast of Argentinean Patagonia. A hierarchically-nestedexperimental design was used to determine the relative importanceof molluscan assemblage variation at three different spatialscales (shores, sites and cores). Hypotheses were also testedabout the potential role of habitat variables (frond density,frond length, sediment and epiphytes) for determining molluscancommunity structure. In total, 38 molluscan species were foundcomprising 16, 18 and 4 species of bivalves, gastropods andpolyplacophorans, respectively. Densities of molluscs in corallineturfs reached ca 77,000 individuals per m² and were dominatedby mussels, especially Perumytilus purpuratus. Multivariateand univariate analyses of assemblage structure consistentlyshowed that variation at scales of metres and hundreds of kilometresdominated, with sites 20–50 m apart always contributingless than 24% of the total. Significant associations betweenmolluscan community structure and both frond density and frondlength demonstrated the potential importance of habitat structurein determining community structure at local scales. Variationin molluscan assemblages at the scale of shores, however, didnot appear to correlate with latitudinal, temperature or waveexposure gradients, indicating that other processes must beoperating. The compositions of molluscan assemblages in corallineturfs on the coast of Argentina were similar to those reportedfor central Chile. Comparisons of the richness of these SouthAmerican assemblages to other parts of the world revealed somestriking biogeographical patterns that warrant further investigation.Overall, this work highlights the general importance of small-scalevariation in molluscan assemblages on rocky shores and the consistentinfluence of habitat complexity in determining the structureof diverse molluscan communities associated with mat-like habitats. (Received 10 August 2006; accepted 20 January 2007)     

A covariance structure model for the admixture of binary genetic variation

I derive a covariance structure model for pairwise linkage disequilibrium (LD) between binary markers in a recently admixed population and use a generalized least-squares method to fit the model to two different data sets. Both linked and unlinked marker pairs are incorporated in the model. Under the model, a pairwise LD matrix is decomposed into two component matrices, one containing LD attributable to admixture, and another containing, in an aggregate form, LD specific to the populations forming the mixture. I use population genetics theory to show that the latter matrix has block-diagonal structure. For the data sets considered here, I show that the number of source populations can be determined by statistical inference on the canonical correlations of the sample LD matrix.     

Apicultural pollen from the Andean region of Chubut (Argentinean Patagonia)

An analysis of pollen loads of Apis mellifera was performed in order to identify the pollen sources that support the hives in the Andean region of Chubut. During the apicultural period (from 9 September 2010 to 12 March 2011), pollen loads were collected every fortnight in a selected apiary located in a transition area between the sub-Antarctic forests and the Patagonian steppe. Forty-six pollen types belonging to 26 plant families were found in the pollen spectrum of pollen loads, of which the most diverse were Asteraceae (11 types) and Fabaceae (six types). Families with major biomass contribution were Asteraceae (49%), Fabaceae (10%), Salicaceae (10%), Rhamnaceae (7%), Rosaceae (7%) and Brassicaceae (4%). Thirty-one per cent of the identified pollen belonged to the native flora. The major contribution of indigenous species occurred in late spring. Mutisia spp., Discaria type, Senecio spp., Adesmia spp. and Maytenus spp. were the most collected native taxa. Most plants providing pollen to the beehive are also nectariferous resources in the Andean region of Chubut. The protein content of the collected pollen ranged from 7.78% to 32.48%. The most collected types had protein content between 13.09% and 30.93%.     

Characterization of the genetic diversity, structure and admixture of British chicken breeds

The characterization of livestock genetic diversity can inform breed conservation initiatives. The genetic diversity and genetic structure were assessed in 685 individual genotypes sampled from 24 British chicken breeds. A total of 239 alleles were found across 30 microsatellite loci with a mean number of 7.97 alleles per locus. The breeds were highly differentiated, with an average F(ST) of 0.25, similar to that of European chicken breeds. The genetic diversity in British chicken breeds was comparable to that found in European chicken breeds, with an average number of alleles per locus of 3.59, ranging from 2.00 in Spanish to 4.40 in Maran, and an average expected heterozygosity of 0.49, ranging from 0.20 in Spanish to 0.62 in Araucana. However, the majority of breeds were not in Hardy-Weinberg Equilibrium, as indicated by heterozygote deficiency in the majority of breeds (average F(IS) of 0.20), with an average observed heterozygote frequency of 0.39, ranging from 0.15 in Spanish to 0.49 in Cochin. Individual-based clustering analyses revealed that most individuals clustered to breed origin. However, genetic subdivisions occurred in several breeds, and this was predominantly associated with flock supplier and occasionally by morphological type. The deficit of heterozygotes was likely owing to a Wahlund effect caused by sampling from different flocks, implying structure within breeds. It is proposed that gene flow amongst flocks within breeds should be enhanced to maintain the current levels of genetic diversity. Additionally, certain breeds had low levels of both genetic diversity and uniqueness. Consideration is required for the conservation and preservation of these potentially vulnerable breeds.     

Analyses of genetic structure of Tibeto-Burman populations reveals sex-biased admixture in southern Tibeto-Burmans

An unequal contribution of male and female lineages from parental populations to admixed ones is not uncommon in the American continents, as a consequence of directional gene flow from European men into African and Hispanic Americans in the past several centuries. However, little is known about sex-biased admixture in East Asia, where substantial migrations are recorded. Tibeto-Burman (TB) populations were historically derived from ancient tribes of northwestern China and subsequently moved to the south, where they admixed with the southern natives during the past 2600 years. They are currently extensively distributed in China and Southeast Asia. In this study, we analyze the variations of 965 Y chromosomes and 754 mtDNAs in >20 TB populations from China. By examining the haplotype group distributions of Y-chromosome and mtDNA markers and their principal components, we show that the genetic structure of the extant southern Tibeto-Burman (STB) populations were primarily formed by two parental groups: northern immigrants and native southerners. Furthermore, the admixture has a bias between male and female lineages, with a stronger influence of northern immigrants on the male lineages (approximately 62%) and with the southern natives contributing more extensively to the female lineages (approximately 56%) in the extant STBs. This is the first genetic evidence revealing sex-biased admixture in STB populations, which has genetic, historical, and anthropological implications.     

Genetic admixture, self-reported ethnicity, self-estimated admixture, and skin pigmentation among Hispanics and Native Americans

The relationship between ethnicity and biology is of interest to anthropologists, biomedical scientists, and historians in understanding how human groups are constructed. Ethnic self-identification in recently admixed groups such as Hispanics, African Americans, and Native Americans (NA) is likely to be complex due to the heterogeneity in individual admixture proportions and social environments within these groups. This study examines the relationships between self-identified ethnicity, self-estimated admixture proportions, skin pigmentation, and genetic marker estimated admixture proportions. These measures were assessed using questionnaires, skin color measurements, and genotyping of a panel of 76 ancestry informative markers, among 170 Hispanics and NAs from New Mexico, a state known for its complex history of interactions between people of NA and European (EU) ancestry. Results reveal that NAs underestimate their degree of EU admixture, and that Hispanics underestimate their degree of NA admixture. Within Hispanics, genetic-marker estimated admixture is better predicted by forehead skin pigmentation than by self-estimated admixture. We also find that Hispanic individuals self-identified as "half-White, half Hispanic" and "Spanish" have lower levels of NA admixture than those self-identified as "Mexican" and "Mexican American." Such results highlight the interplay between culture and biology in how individuals identify and view themselves, and have implications for how ethnicity and disease risk are assessed in a medical setting.     

Biogeographically dynamic genetic structure bridging two continents in the monotypic Central American rodent Ototylomys phyllotis

Central America is an ideal region in which to study patterns of historical divergence and population genetic differentiation, because of its extraordinarily dynamic biogeographical, tectonic, and climatic history. The rodent Ototylomys phyllotis is the only extant species of the genus Ototylomys and is distributed within this region from the Isthmus of Tehuantepec, Mexico, to central Costa Rica, offering an excellent opportunity to study spatial and temporal patterns of population structure of the species and to explain the ecological and evolutionary processes responsible for those patterns. We estimated the genetic diversity and structure within and between populations of O. phyllotis, times of divergence, and migration patterns using mitochondrial DNA and a comprehensive combination of phylogenetic and phylogeographical computational analyses. Our results support monophyly of the genus Ototylomys. We identified three major phylogeographical lineages within O. phyllotis that are linked to its diversification and coincide with the main geological features that shaped Middle America. The origin of the genus was before 3.35 Mya, prior to the Great American Biotic Interchange (GABI), and its initial occurrence was near the centre of its current distribution (Honduras/El Salvador), from which it later spread (3.20–2.84 Mya) following a series of GABI pulses. The species showed an initial northward dispersal to the Chiapas and Guatemala highlands (2.27 Mya) followed by diversification. A later dispersal (1.82 Mya) occurred toward both the south (Nicaragua, Costa Rica) and the north (Belize). The Yucatan peninsula was colonized (0.8 Mya) by individuals from Belize. Extremely high radiation and range expansion occurred throughout the entire range, the highest of which was in the Yucatan peninsula (0.125 Mya). © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107 , 593–610.     

Mating system parameters and genetic structure in Argentinean populations of Acacia caven (Leguminosae, Mimosoideae)

Acacia caven (Mol.) Mol. is native to South America. The species is a leguminous, woody small tree that is considered to have certain potential as a managed silvopastoral crop. Six varieties have been described for the species based on both morphological traits and molecular markers. Little information is available on its mating system. The main objectives of this work were to test the hypothesis that A. caven is an outcrosser and to estimate parameters of its mating system and population structure on the basis of isozyme markers. In the four populations studied, a high homozygote excess was found in the progeny population but not in the mother plant genotypes. The estimate for the multi-locus outcrossing rate (t _m) was high (??0.957) in all populations, indicating that Acacia caven is a predominantly outcrosser species. The results of genetic structure analysis within each population indicated that differences in allelic frequencies among families in all of the populations studied are highly significant. The difference in F estimates between progeny and mother plants suggests some selection favouring heterozygotes between the seedling and adult stages. Therefore, a strategy for ex situ conservation might emphasise sampling more populations with a relative large number of trees per site.     

Fine‐scale genetic structure of Tujia and central Han Chinese revealing massive genetic admixture under language borrowing

Archaeological, genetic, and linguistic evidence has supported the idea that northern China is the original center of modern Sino‐Tibetan‐speaking populations. However, the demographic history of subsequent southward migration and genetic admixture of Han Chinese with surrounding indigenous populations remain uncharacterized, and the language shifts and assimilations accompanied by movement of people, or just an adaptation of cultural ideas among populations in central China is still unclear, especially for Tibeto‐Burman‐speaking Tujia and central Han Chinese populations. To resolve this, we genotyped over 60K genome‐wide markers in 505 unrelated individuals from 63 indigenous populations. Our results showed both studied Han and Tujia were at the intermediate position in the modern East Asian North–South genetic cline and there was a correlation between the genetic composition and the latitude. We observed the strong genetic assimilation between Tujia people and central Han Chinese, which suggested massive population movements and genetic admixture under language borrowing. Tujia and central Han Chinese could be modeled as a two‐way admixture deriving primary ancestry from a northern ancestral population closely related to the ancient DevilsCave and present‐day Tibetans and a southern ancestral population closely related to the present‐day Tai‐Kadai and Austronesian‐speaking groups. The ancestral northern population we suspect to be related to the Neolithic millet farming groups in the Yellow River Basin or central China. We showed that the newly genotyped populations in Hubei Province had a higher proportion of DevilsCave or modern Tungusic/Mongolic‐related northern ancestries, while the Hunan populations harbored a higher proportion of Austronesian/Tai‐Kadai‐related southern ancestries.     

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.     

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.     

Population genetic structure of peninsular Malaysia Malay sub-ethnic groups

Patterns of modern human population structure are helpful in understanding the history of human migration and admixture. We conducted a study on genetic structure of the Malay population in Malaysia, using 54,794 genome-wide single nucleotide polymorphism genotype data generated in four Malay sub-ethnic groups in peninsular Malaysia (Melayu Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis). To the best of our knowledge this is the first study conducted on these four Malay sub-ethnic groups and the analysis of genotype data of these four groups were compiled together with 11 other populations' genotype data from Indonesia, China, India, Africa and indigenous populations in Peninsular Malaysia obtained from the Pan-Asian SNP database. The phylogeny of populations showed that all of the four Malay sub-ethnic groups are separated into at least three different clusters. The Melayu Jawa, Melayu Bugis and Melayu Minang have a very close genetic relationship with Indonesian populations indicating a common ancestral history, while the Melayu Kelantan formed a distinct group on the tree indicating that they are genetically different from the other Malay sub-ethnic groups. We have detected genetic structuring among the Malay populations and this could possibly be accounted for by their different historical origins. Our results provide information of the genetic differentiation between these populations and a valuable insight into the origins of the Malay sub-ethnic groups in Peninsular Malaysia.     

A first record of Phlebotominae from Argentinean Patagonia (Diptera: Psychodidae: Phlebotominae)

A species of the Lutzomyia oswaldoi group is recorded from the Valcheta stream basin, Somuncura plateau, Patagonia. It represents the World southermost record of a species of Phlebotominae, apparently supporting the hypothesis about the relictual character of several components of the Somuncura plateau biota, particularly for those species belonging to the Paranaense lineages.