FLOCK: a method for quick mapping of admixture without source samples

Identifying and estimating individual and/or population admixture is a very common objective in evolution and conservation biology. There are many situations where samples from one or many of the putatively hybridizing entities are not available or easily identified. Here we describe FLOCK, a new method especially designed to provide spatial and/or temporal admixture maps in the absence of one or several source samples. FLOCK is a non-Bayesian method and therefore differs substantially from previous clustering algorithms. Its working principle is repeated re-allocation of all collected specimens (total sample) to the k subsamples, each re-allocation being more effective than the previous one in attracting genetically similar individuals. This snowball effect, more formally referred to as a positive feedback mechanism, makes FLOCK an efficient and quick sorting process. The usage of FLOCK is illustrated with two empirical situations which have been thoroughly analysed previously with other approaches. A number of simulations were run to better assess the power of the FLOCK algorithm. Performance comparisons were made between the FLOCK and Structure algorithms. When non-negligible numbers of pure genotypes were present, the two performed equally well. However, FLOCK proved significantly more powerful in the absence of pure genotypes. Moreover, FLOCK showed more potential for fast processing. Run times were shown to increase linearly with size of total sample and with size of k, the number of reference samples from which admixture mapping is performed.     

Evolutionary impacts of hybridization and interspecific gene flow on an obligately estuarine fish

For free-spawning estuarine taxa, gene flow among estuaries may occur via hybridization with mobile congeners. This phenomenon has rarely been investigated, but is probably susceptible to anthropogenic disturbance. In eastern Australia, the estuarine Black Bream Acanthopagrus butcheri and marine Yellowfin Bream Acanthopagrus australis have overlapping distributions and the potential to hybridize. We used surveys of microsatellite and mtDNA variation in 565 adults from 25 estuaries spanning their distributional range to characterize the species and their putative hybrids. Hybrids were widespread (68% of estuaries) and hybrid frequencies varied greatly among estuaries (0-58%). Most (88%) were classed as advanced generation backcrosses with A. butcheri and displayed A. butcheri mtDNA haplotypes. We found most hybrids in the three estuaries within the zone of sympatry (57%). Our study highlights the underemphasized importance of estuaries as sites of hybridization and suggests that hybridization is driven both by opportunity for contact and human activity.     

Population relationships in the Mediterranean revealed by autosomal genetic data (Alu and Alu/STR compound systems)

The variation of 18 Alu polymorphisms and 3 linked STRs was determined in 1,831 individuals from 15 Mediterranean populations to analyze the relationships between human groups in this geographical region and provide a complementary perspective to information from studies based on uniparental markers. Patterns of population diversity revealed by the two kinds of markers examined were different from one another, likely in relation to their different mutation rates. Therefore, while the Alu biallelic variation underlies general heterogeneity throughout the whole Mediterranean region, the combined use of Alu and STR points to a considerable genetic differentiation between the two Mediterranean shores, presumably strengthened by a considerable sub‐Saharan African genetic contribution in North Africa (around 13% calculated from Alu markers). Gene flow analysis confirms the permeability of the Sahara to human passage along with the existence of trans‐Mediterranean interchanges. Two specific Alu/STR combinations—CD4 110(?) and DM 107(?)—detected in all North African samples, the Iberian Peninsula, Greece, Turkey, and some Mediterranean islands suggest an ancient genetic background of current Mediterranean peoples. Am J Phys Anthropol 2010. © 2009 Wiley‐Liss, Inc.     

The origin and fate of morphological intermediates between wild and cultivated soybeans in their natural habitats in Japan

The spread of transgenes into the genome of wild soybean is a concern when transgenic and wild soybeans are planted sympatrically. The objectives of this study were to investigate the origin and fate of morphological intermediates between wild and cultivated soybeans in their natural habitats in Japan. Twenty nuclear microsatellite and two chloroplast dCAPS markers were used to evaluate genetic variation of 468 wild, 17 intermediate, and 12 cultivated soybean samples collected from six sites between 2003 and 2006. Allelic differentiation of microsatellite markers between wild and cultivated soybeans was sufficient to detect their hybrids. Based on levels of observed heterozygosity, intermediate soybean plants were from two generations: either F₁ or an early segregating generation. Genetic admixture analysis and parentage assignment analysis revealed that the parents of all intermediate soybean plants could be assigned to a particular wild soybean plant and late‐maturing cultivar. The chloroplast DNA haplotypes revealed that all intermediate soybean plants originated from gene flow from cultivated to wild soybeans at all sites. Based on monitoring at both the phenotypic and molecular levels, hybrids quickly disappeared from natural habitats, and secondary gene flow from these plants to wild soybean was not detected. Thus, while gene flow from transgenic soybean into wild soybean can occur, gene introgression appears to be rare in natural habitats in Japan. This is the first report on the detection of gene flow from cultivated to wild soybean at the molecular level.     

Individual assignment using microsatellite DNA reveals unambiguous breed identification in the domestic dog

Modern individual clustering methods utilising hypervariable nuclear microsatellite DNA polymorphisms are being increasingly applied in the field of population genetics. This study explores the efficiency of the clustering methods in identifying the breeds of origin of 250 domestic dog (Canis familiaris) individuals based on 10 microsatellite loci. An allele sharing distance (DAS) matrix and the corresponding neighbour-joining tree of individuals revealed monophyletic assemblages that corresponded perfectly with the breeds of origin of the dogs. Individual assignment tests using a Bayesian statistical approach, an allele frequency based method, and a DCE genetic distance based method were all extremely powerful. Most strikingly, the Bayesian method provided 100% assignment success of individuals into their correct breeds of origin and 100% exclusion success of individuals from all alternate reference populations with a high level of statistical confidence (P < 0.0001). A Bayesian Markov Chain Monte Carlo clustering approach revealed clear distinction of individuals into groups according to their breeds of origin, with a near-zero level of 'genetic admixture' among breeds. The results demonstrate that an FST of 0.18, mean expected gene diversity of 0.6 across 10 loci, and approximately 50 individuals per reference population suffice to provide maximum individual assignment success in C. familiaris. This refutes the traditional view that DNA based dog breed identification is not feasible at the individual level of resolution.     

Estimating the impact of prehistoric admixture on the genome of Europeans

We inferred past admixture processes in the European population from genetic diversity at eight loci, including autosomal, mitochondrial and Y-linked polymorphisms. Admixture coefficients were estimated from multilocus data, assuming that most current populations can be regarded as the result of a hybridization process among four or less potential parental populations. Two main components are apparent in the Europeans' genome, presumably corresponding to the contributions of the first, Paleolithic Europeans, and of the early, Neolithic farmers dispersing from the Near East. In addition, only a small fraction of the European alleles seems to come from North Africa, and a fourth component reflecting gene flow from Northern Asia is largely restricted to the northeast of the continent. The estimated Near Eastern contribution decreases as one moves from east to west, in agreement with the predictions of a model in which (Neolithic) immigrants from the Near East contributed a large share of the alleles in the genome of current Europeans. Several tests suggest that probable departures from the admixture models, due to factors such as choice of the putative parental populations and more complex demographic scenarios, may have affected our main estimates only to a limited extent.     

Native American mtDNA prehistory in the American Southwest

This study examines the mtDNA diversity of the proposed descendants of the multiethnic Hohokam and Anasazi cultural traditions, as well as Uto-Aztecan and Southern-Athapaskan groups, to investigate hypothesized migrations associated with the Southwest region. The mtDNA haplogroups of 117 Native Americans from southwestern North America were determined. The hypervariable segment I (HVSI) portion of the control region of 53 of these individuals was sequenced, and the within-haplogroup diversity of 18 Native American populations from North, Central, and South America was analyzed. Within North America, populations in the West contain higher amounts of diversity than in other regions, probably due to a population expansion and high levels of gene flow among subpopulations in this region throughout prehistory. The distribution of haplogroups in the Southwest is structured more by archaeological tradition than by language. Yumans and Pimans exhibit substantially greater genetic diversity than the Jemez and Zuni, probably due to admixture and genetic isolation, respectively. We find no evidence of a movement of mtDNA lineages northward into the Southwest from Central Mexico, which, in combination with evidence from nuclear markers, suggests that the spread of Uto-Aztecan was facilitated by predominantly male migration. Southern Athapaskans probably experienced a bottleneck followed by extensive admixture during the migration to their current homeland in the Southwest.     

Mitochondrial DNA evidence for admixed origins of central Siberian populations

The Yakuts of northeastern Siberia are a Turkic-speaking population of horse- and cattle-breeders surrounded by Tungusic-speaking reindeer-herders and hunter-gatherers. Archaeological and ethnohistorical data suggest that Yakuts stem from a common ancestral population with the Buryats living near Lake Baikal. To address this hypothesis, we obtained sequences of the first hypervariable segment (HV1) of the mitochondrial DNA control region from Yakuts and Buryats and compared these with sequences from other Eurasian populations. The mtDNA results show that the Buryats have close affinities with both Central Asian Turkic groups and Mongols, while the Yakuts have close affinities with northeastern Siberian, Tungusic-speaking Evenks and south Siberian, Turkic-speaking Tuvans. This different ancestry of the Yakuts and the Tuvans (compared with other Turkic-speaking groups) most likely reflects extensive admixture that occurred between Turkic-speaking steppe groups and Evenks as the former migrated into Siberia. Moreover, the Yakuts are unique among Siberian populations in having a high number of haplotypes shared exclusively with Europeans, suggesting, contrary to the historical record, that occasionally Yakut men took Russian women as wives.     

European Y-chromosomal lineages in Polynesians: a contrast to the population structure revealed by mtDNA.

We have used Y-chromosomal polymorphisms to trace paternal lineages in Polynesians by use of samples previously typed for mtDNA variants. A genealogical approach utilizing hierarchical analysis of eight rare-event biallelic polymorphisms, seven microsatellite loci, and internal structural analysis of the hypervariable minisatellite, MSY1, has been used to define three major paternal-lineage clusters in Polynesians. Two of these clusters, both defined by novel MSY1 modular structures and representing 55% of the Polynesians studied, are also found in coastal Papua New Guinea. Reduced Polynesian diversity, relative to that in Melanesians, is illustrated by the presence of several examples of identical MSY1 codes and microsatellite haplotypes within these lineage clusters in Polynesians. The complete lack of Y chromosomes having the M4 base substitution in Polynesians, despite their prevalence (64%) in Melanesians, may also be a result of the multiple bottleneck events during the colonization of this region of the world. The origin of the M4 mutation has been dated by use of two independent methods based on microsatellite-haplotype and minisatellite-code diversity. Because of the wide confidence limits on the mutation rates of these loci, the M4 mutation cannot be conclusively dated relative to the colonization of Polynesia, 3,000 years ago. The other major lineage cluster found in Polynesians, defined by a base substitution at the 92R7 locus, represents 27% of the Polynesians studied and, most probably, originates in Europe. This is the first Y-chromosomal evidence of major European admixture with indigenous Polynesian populations and contrasts sharply with the picture given by mtDNA evidence.     

Redundancy analysis,genome-wide association studies and the pigmentation of brown trout (Salmo trutta L.)

The association of molecular variants with phenotypic variation is a main issue in biology, often tackled with genome-wide association studies (GWAS). GWAS are challenging, with increasing, but still limited, use in evolutionary biology. We used redundancy analysis (RDA) as a complimentary ordination approach to single- and multitrait GWAS to explore the molecular basis of pigmentation variation in brown trout (Salmo trutta) belonging to wild populations impacted by hatchery fish. Based on 75,684 single nucleotide polymorphic (SNP) markers, RDA, single- and multitrait GWAS allowed the extraction of 337 independent colour patterning loci (CPLs) associated with trout pigmentation traits, such as the number of red and black spots on flanks. Collectively, these CPLs (i) mapped onto 35 out of 40 brown trout linkage groups indicating a polygenic genomic architecture of pigmentation, (ii) were found to be associated with 218 candidate genes, including 197 genes formerly mentioned in the literature associated to skin pigmentation, skin patterning, differentiation or structure notably in a close relative, the rainbow trout (Onchorhynchus mykiss), and (iii) related to functions relevant to pigmentation variation (e.g., calcium- and ion-binding, cell adhesion). Annotated CPLs include genes with well-known pigmentation effects (e.g., PMEL, SLC45A2, SOX10), but also markers associated with genes formerly found expressed in rainbow or brown trout skins. RDA was also shown to be useful to investigate management issues, especially the dynamics of trout pigmentation submitted to several generations of hatchery introgression.