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Ancestral Populations (ancestral + population)
Selected AbstractsREPLICATED EVOLUTION OF INTEGRATED PLASTIC RESPONSES DURING EARLY ADAPTIVE DIVERGENCEEVOLUTION, Issue 4 2006Kevin J. Parsons Abstract Colonization of a novel environment is expected to result in adaptive divergence from the ancestral population when selection favors a new phenotypic optimum. Local adaptation in the new environment occurs through the accumulation and integration of character states that positively affect fitness. The role played by plastic traits in adaptation to a novel environment has generally been ignored, except for variable environments. We propose that if conditions in a relatively stable but novel environment induce phenotypically plastic responses in many traits, and if genetic variation exists in the form of those responses, then selection may initially favor the accumulation and integration of functionally useful plastic responses. Early divergence between ancestral and colonist forms will then occur with respect to their plastic responses across the gradient bounded by ancestral and novel environmental conditions. To test this, we compared the magnitude, integration, and pattern of plastic character responses in external body form induced by shallow versus open water conditions between two sunfish ecomorphs that coexist in four postglacial lakes. The novel sunfish ecomorph is present in the deeper open water habitat, whereas the ancestral ecomorph inhabits the shallow waters along the lake margin. Plastic responses by open water ecomorphs were more correlated than those of their local shallow water ecomorph in two of the populations, whereas equal levels of correlated plastic character responses occurred between ecomorphs in the other two populations. Small but persistent differences occurred between ecomorph pairs in the pattern of their character responses, suggesting a recent divergence. Open water ecomorphs shared some similarities in the covariance among plastic responses to rearing environment. Replication in the form of correlated plastic responses among populations of open water ecomorphs suggests that plastic character states may evolve under selection. Variation between ecomorphs and among lake populations in the covariance of plastic responses suggests the presence of genetic variation in plastic character responses. In three populations, open water ecomorphs also exhibited larger plastic responses to the environmental gradient than the local shallow water ecomorph. This could account for the greater integration of plastic responses in open water ecomorphs in two of the populations. This suggests that the plastic responses of local sunfish ecomorphs can diverge through changes in the magnitude and coordination of plastic responses. Although these results require further investigation, they suggest that early adaptive evolution in a novel environment can include changes to plastic character states. The genetic assimilation of coordinated plastic responses could result in the further, and possibly rapid, divergence of such populations and could also account for the evolution of genes of major effect that contribute to suites of phenotypic differences between divergent populations. [source] MATHEMATICAL CONSEQUENCES OF THE GENEALOGICAL SPECIES CONCEPTEVOLUTION, Issue 8 2002Richard R. Hudson Abstract A genealogical species is defined as a basal group of organisms whose members are all more closely related to each other than they are to any organisms outside the group ("exclusivity'), and which contains no exclusive group within it. In practice, a pair of species is so defined when phylogenies of alleles from a sample of loci shows them to be reciprocally monophyletic at all or some specified fraction of the loci. We investigate the length of time it takes to attain this status when an ancestral population divides into two descendant populations of equal size with no gene exchange, and when genetic drift and mutation are the only evolutionary forces operating. The number of loci used has a substantial effect on the probability of observing reciprocal monophyly at different times after population separation, with very long times needed to observe complete reciprocal monophyly for a large number of loci. In contrast, the number of alleles sampled per locus has a relatively small effect on the probability of reciprocal monophyly. Because a single mitochondrial or chloroplast locus becomes reciprocally monophyletic much faster than does a single nuclear locus, it is not advisable to use mitochondrial and chloroplast DNA to recognize genealogical species for long periods after population divergence. Using a weaker criterion of assigning genealogical species status when more than 50% of sampled nuclear loci show reciprocal monophyly, genealogical species status depends much less on the number of sampled loci, and is attained at roughly 4,7 N generations after populations are isolated, where N is the historically effective population size of each descendant. If genealogical species status is defined as more than 95% of sampled nuclear loci showing reciprocal monophyly, this status is attained after roughly 9,12 N generations. [source] PERSPECTIVE: GENE DIVERGENCE, POPULATION DIVERGENCE, AND THE VARIANCE IN COALESCENCE TIME IN PHYLOGEOGRAPHIC STUDIESEVOLUTION, Issue 6 2000ScottV. Abstract Molecular methods as applied to the biogeography of single species (phylogeography) or multiple codistributed species (comparative phylogeography) have been productively and extensively used to elucidate common historical features in the diversification of the Earth's biota. However, only recently have methods for estimating population divergence times or their confidence limits while taking into account the critical effects of genetic polymorphism in ancestral species become available, and earlier methods for doing so are underutilized. We review models that address the crucial distinction between the gene divergence, the parameter that is typically recovered in molecular phylogeographic studies, and the population divergence, which is in most cases the parameter of interest and will almost always postdate the gene divergence. Assuming that population sizes of ancestral species are distributed similarly to those of extant species, we show that phylogeographic studies in vertebrates suggest that divergence of alleles in ancestral species can comprise from less than 10% to over 50% of the total divergence between sister species, suggesting that the problem of ancestral polymorphism in dating population divergence can be substantial. The variance in the number of substitutions (among loci for a given species or among species for a given gene) resulting from the stochastic nature of DNA change is generally smaller than the variance due to substitutions along allelic lines whose coalescence times vary due to genetic drift in the ancestral population. Whereas the former variance can be reduced by further DNA sequencing at a single locus, the latter cannot. Contrary to phylogeographic intuition, dating population divergence times when allelic lines have achieved reciprocal monophyly is in some ways more challenging than when allelic lines have not achieved monophyly, because in the former case critical data on ancestral population size provided by residual ancestral polymorphism is lost. In the former case differences in coalescence time between species pairs can in principle be explained entirely by differences in ancestral population size without resorting to explanations involving differences in divergence time. Furthermore, the confidence limits on population divergence times are severely underestimated when those for number of substitutions per site in the DNA sequences examined are used as a proxy. This uncertainty highlights the importance of multilocus data in estimating population divergence times; multilocus data can in principle distinguish differences in coalescence time (T) resulting from differences in population divergence time and differences in T due to differences in ancestral population sizes and will reduce the confidence limits on the estimates. We analyze the contribution of ancestral population size (,) to T and the effect of uncertainty in , on estimates of population divergence (,) for single loci under reciprocal monophyly using a simple Bayesian extension of Takahata and Satta's and Yang's recent coalescent methods. The confidence limits on , decrease when the range over which ancestral population size , is assumed to be distributed decreases and when increases; they generally exclude zero when /(4Ne) > 1. We also apply a maximum-likelihood method to several single and multilocus data sets. With multilocus data, the criterion for excluding = 0 is roughly that l/(4Ne)> 1, where l is the number of loci. Our analyses corroborate recent suggestions that increasing the number of loci is critical to decreasing the uncertainty in estimates of population divergence time. [source] Morphological variation over ontogeny and environments in resource polymorphic arctic charr (Salvelinus alpinus)EVOLUTION AND DEVELOPMENT, Issue 3 2010Kevin J. Parsons SUMMARY Natural selection requires genetically based phenotypic variation to facilitate its action and cause adaptive evolution. It has become increasingly recognized that morphological development can become canalized likely as a result of selection. However, it is largely unknown how selection may influence canalization over ontogeny and differing environments. Changes in environments or colonization of a novel one is expected to result in adaptive divergence from the ancestral population when selection favors a new phenotypic optimum. In turn, a novel environment may also expose variation previously hidden from natural selection. We tested for changes in phenotypic variation over ontogeny and environments among ecomorphs of Arctic charr (Salvelinus alpinus) from two Icelandic lakes. Populations represented varying degrees of ecological specialization, with one lake population possessing highly specialized ecomorphs exhibiting a large degree of phenotypic divergence, whereas the other displayed more subtle divergence with more ecological overlap. Here we show that ecomorphs hypothesized to be the most specialized in each lake possess significant reductions in shape variation over ontogeny regardless of environmental treatment suggesting canalized development. However, environments did change the amount of shape variation expressed in these ecomorphs, with novel environments slowing the rate at which variation was reduced over ontogeny. Thus, environmental conditions may play an important role in determining the type and amount of genetically based phenotypic variation exposed to natural selection. [source] Inter-ocean dispersal is an important mechanism in the zoogeography of hakes (Pisces: Merluccius spp.)JOURNAL OF BIOGEOGRAPHY, Issue 6 2001W. Stewart Grant Aim To present new genetic data and to review available published genetic data that bear on the phylogeny of hakes in the genus Merluccius. To construct a zoogeographical model from a summary phylogenetic tree with dated nodes. To search for an explanation of antitropical distributions in hakes. To assess peripheral isolate, centrifugal and vicariance models of speciation in view of the molecular phylogeny and zoogeography of hakes. Locations Northern and southern Atlantic Ocean, eastern Pacific Ocean, South Pacific Ocean. Methods Electrophoretic analysis of 20 allozyme loci in 10 species of hakes. Phylogenetic tree construction with parsimony and bootstrap methods. Reanalysis of previous genetic data. Analysis of zoogeographical patterns with geographical distributions of molecular genetic markers. Results Phylogenetic analyses of new and previous allozyme data and previous mitochondrial DNA data indicate a deep genetic partition between Old- and New-World hakes with genetic distances corresponding to 10,15 Myr of separation. This time marks a widening rift between Europe and North America and a rapid drop in ocean temperatures that subdivided an ancestral population of North Atlantic hake. Two Old-World clades spanning the equator include pairs of sister taxa separated by tropical waters. Divergence times between these pairs of sister-taxa variously date to the early Pliocene and late Pleistocene. Amongst New-World hakes, pairs of sister taxa are separated by equatorial waters, by the Southern Ocean, and by the Panama Isthmus. These genetic separations reflect isolation by the rise of the Isthmus 3,4 Ma and by Pliocene and Pleistocene dispersals. Pairs of species occurring in sympatry or parapatry in six regions do not reflect sister-species relationships, but appear to reflect allopatric divergence and back dispersals of descendent species. Some geographically isolated regional populations originating within the last few hundreds of thousands of years merit subspecies designations. Conclusions Vicariance from tectonic movement of continental plates or ridge formation cannot account for the disjunct distributions of most hake sister taxa. Molecular genetic divergences place the origin of most hake species diversity in the last 2,3 Myr, a period of negligible tectonic activity. Distributions of many hake species appear to have resulted from dispersals and back dispersals across both warm equatorial waters and cool waters in the Southern Ocean, driven by oscillations in climate and ocean temperatures. Genetic and ecological divergence prevents hybridization and competitive exclusion between sympatric species pairs in six regions. Sister-taxa relationships and estimates of divergence are consistent with the modified peripheral isolate model of speciation in which vicariances, range expansions and contractions, dispersals and founder events lead to isolated populations that subsequently diverge to form new species. [source] Five questions on ecological speciation addressed with individual-based simulationsJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 1 2009X. THIBERT-PLANTE Abstract We use an individual-based simulation model to investigate factors influencing progress toward ecological speciation. We find that environmental differences can quickly lead to the evolution of substantial reproductive barriers between a population colonizing a new environment and the ancestral population in the old environment. Natural selection against immigrants and hybrids was a major contributor to this isolation, but the evolution of sexual preference was also important. Increasing dispersal had both positive and negative effects on population size in the new environment and had positive effects on natural selection against immigrants and hybrids. Genetic divergence at unlinked, neutral genetic markers was low, except when environmental differences were large and sexual preference was present. Our results highlight the importance of divergent selection and adaptive divergence for ecological speciation. At the same time, they reveal several interesting nonlinearities in interactions between environmental differences, sexual preference, dispersal and population size. [source] The genus Adriohydrobia (Hydrobiidae: Gastropoda): polytypic species or polymorphic populations?JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 4 2001T. Wilke In molluscs, the shell characters have historically played an important role in discrimination among species. However, because of the paucity, variability and degree of homoplasy of shell characters, their sole use for taxonomic and systematic studies is controversial in many groups. In the present paper the genus AdriohydrobiaRadoman, 1973 is used as a paradigm to test relationships of taxa that were considered to be species, mainly on the basis of the shell size variations. We tested whether the genus consists of several sympatric and polytypic species or a single species with polymorphic populations and whether the reported shell size differences, on which the description of three putative species is mainly based, are intrinsic or extrinsic. A fragment of the mitochondrial cytochrome oxidase I (COI) gene was used as an independent genetic marker. We found very little genetic variability in 40 specimens from four populations studied. The nucleotide-sequence diversity (,) within populations ranges from 0.0017 to 0.0056 and the nucleotide-sequence divergence (Dxy) between populations from 0.0018 to 0.0051. The phylogenetic network is very compact with two ,groups' of haplotypes that are separated by only two nucleotide positions. A plot of pairwise nucleotide differences against pairwise shell size differences did not reveal any distinct clusters and a Mantel test did not show any significant associations between the two matrices. Based on the very low genetic diversity, the lack of distinct clusters in the phylogenetic network and the lack of concordance between morphological and genetic differentiation it is concluded that only one species is involved, Adriohydrobia gagatinella. The previously reported morphogroups within Adriohydrobia are probably due to a discrete age structure in these population and/or due to the effect of trematode-induced gigantism. The observed genetic patterns in Adriohydrobia indicate a rapid population growth from an ancestral population of small evolutionary-effective size. The present study stresses the importance of testing species-level hypotheses based on shell characters using one or more independent markers. Die Gattung Adriohydrobia (Hydrobiidae: Gastropoda): polytypische Arten oder polymorphe Populationen? Schalenmerkmale spielen historisch eine wichtige Rolle bei der Bestimmung von Molluskenarten. Die alleinige Nutzung von Schalenmerkmalen für systematische und taxonomische Arbeiten ist jedoch in vielen Gruppen umstritten, da die relativ wenigen Schalenmerkmale oft sehr variabel und durch einen hohen Grad von Homoplasie gekennzeichnet sind. In der vorliegenden Arbeit wurde die Gattung AdriohydrobiaRadoman, 1973 als Fallbeispiel genutzt, um Beziehungen von Arten innerhalb einer Gattung zu untersuchen, die hauptsächlich anhand ihrer Schalengröße unterschieden werden. Es wurde getestet, ob die Gattung mehrere sympatrische und polytypische Arten oder nur eine Art mit polymorphen Populationen umfasst. Darüber hinaus wurde untersucht, ob die dokumentierten Unterschiede in der Schalenhöhe, auf welchen die Beschreibung der drei potentiellen Arten der Gattung hauptsächlich beruhte, intrinsisch oder extrinsisch sind. Als unabhängiger genetischer Marker wurde ein Fragment des mitochondrialen Gens für Cytochromoxidase I (COI) verwendet. Die untersuchten 40 Individuen von vier Populationen zeichneten sich durch eine nur sehr geringe genetische Variabilität aus. Die Nukleotidsequenz-Diversität (,) innerhalb der Populationen variiert zwischen 0.0017 und 0.0056; die Nukleotidsequenz-Divergenz (Dxy) zwischen den Populationen reicht von 0.0018 bi 0.0051. Das phylogenetische Netzwerk ist sehr kompakt und umfasst zwei ,Gruppen' von Haplotypen, welche durch nur zwei Nukleotidpositionen getrennt sind. Die graphische Darstellung von paarweisen Nukleotid-Differenzen gegen paarweise Gehäusegröße-Differenzen lässt keine diskreten Gruppen erkennen und ein Mantel-Test zeigt keine signifikanten Beziehungen zwischen den Matrices. Aufgrund der geringen genetischen Differenzierung, des Fehlens von diskreten Gruppen im phylogenetischen Netzwerk und des nicht-signifikanten Zusammenhanges von morphologischer and genetischer Differenzierung wird geschlussfolgert, dass nur eine Art involviert ist, Adriohydrobia gagatinella. Die in der Literatur dokumentierten Morpho-Gruppen beruhen vermutlich auf einer diskreten Altersstruktur in diesen Populationen und/oder auf den Auswirkungen von trematoden-induziertem Gigantismus. Die festgestellten genetischen Muster in Adriohydrobia lassen das schnelle Wachstum einer Stammpopulation von geringer evolutionär-effektiver Größe vermuten. Die vorliegende Studie ist ein Beispiel dafür, wie wichtig es sein kann, auf Schalenmerkmale beruhende Arthypothesen mit unabhängigen Markern zu verifizieren. [source] Mitochondrial DNA and microsatellite variation in the eider duck (Somateria mollissima) indicate stepwise postglacial colonization of Europe and limited current long-distance dispersalMOLECULAR ECOLOGY, Issue 6 2004R. Tiedemann Abstract To unravel the postglacial colonization history and the current intercolony dispersal in the common eider, Somateria mollissima, we analysed genetic variation at a part of the mitochondrial control region and five unlinked autosomal microsatellite loci in 175 eiders from 11 breeding colonies, covering the entire European distribution range of this species. As a result of extreme female philopatry, mitochondrial DNA differentiation is substantial both among local colonies and among distant geographical regions. Our study further corroborates the previous hypothesis of a single Pleistocene refugium for European eiders. A nested clade analysis on mitochondrial haplotypes suggests that (i) the Baltic Sea eider population is genetically closest to a presumably ancestral population and that (ii) the postglacial recolonization progressed in a stepwise fashion via the North Sea region and the Faroe Islands to Iceland. Current long-distance dispersal is limited. Differentiation among colonies is much less pronounced at microsatellite loci. The geographical pattern of this nuclear genetic variation is to a large extent explained by isolation by distance. As female dispersal is very limited, the geographical pattern of nuclear variation is probably explained by male-mediated gene flow among breeding colonies. Our study provides genetic evidence for the assumed prominent postglacial colonization route shaping the present terrestrial fauna of the North Atlantic islands Iceland and the Faroes. It suggests that this colonization had been a stepwise process originating in continental Europe. It is the first molecular study on eider duck populations covering their entire European distribution range. [source] Genetic structure of native circumpolar populations based on autosomal, mitochondrial, and Y chromosome DNA markersAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 1 2010Rohina Rubicz Abstract This study investigates the genetic structure of the present-day inhabitants of Beringia in order to answer questions concerning their origins and evolution. According to recent studies, the ancestors of Native Americans paused for a time in Beringia, during which they differentiated genetically from other Asians before peopling the New World. Furthermore, the Koryaks of Kamchatka share a "ubiquitous" allele (D9S1120) with Native Americans, indicating they may have descended from the same ancestral Beringian population that gave rise to the New World founders. Our results show that a genetic barrier exists between Kamchatkans (Koryaks and Even) and Bering Island inhabitants (Aleuts, mixed Aleuts, and Russians), based on Analysis of Molecular Variance (AMOVA) and structure analysis of nine autosomal short tandem repeats (STRs). This is supported by mitochondrial DNA evidence, but not by analysis of Y chromosome markers, as recent non-native male admixture into the region appears to have partially obscured ancient population relationships. Our study indicates that while Aleuts are descended from the original New World founders, the Koryaks are unlikely to represent a Beringian remnant of the ancestral population that gave rise to Native Americans. They are instead, like the Even, more recent arrivals to Kamchatka from interior Siberia, and the "ubiquitous" allele in Koryaks may result from recent gene flow from Chukotka. Genbank accession numbers for mtDNA sequences: GQ922935-GQ922973. Am J Phys Anthropol 143:62,74, 2010. © 2010 Wiley-Liss, Inc. [source] Coalescent simulations of Yakut mtDNA variation suggest small founding populationAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 4 2009Mark Zlojutro Abstract The Yakuts are a Turkic-speaking population from northeastern Siberia who are believed to have originated from ancient Turkic populations in South Siberia, based on archaeological and ethnohistorical evidence. In order to better understand Yakut origins, we modeled 25 demographic scenarios and tested by coalescent simulation whether any are consistent with the patterns of mtDNA diversity observed in present-day Yakuts. The models consist of either two simulated demes that represent Yakuts and a South Siberian ancestral population, or three demes that also include a regional Northeast Siberian population that served as a source of local gene flow into the Yakut deme. The model that produced the best fit to the observed data defined a founder group with an effective female population size of only 150 individuals that migrated northwards approximately 1,000 years BP and who experienced significant admixture with neighboring populations in Northeastern Siberia. These simulation results indicate a pronounced founder effect that was primarily kin-structured and reconcile reported discrepancies between Yakut mtDNA and Y chromosome diversity levels. Am J Phys Anthropol, 2009. © 2009 Wiley-Liss, Inc. [source] Genetic diversity of growth hormone receptor gene in cattleANIMAL SCIENCE JOURNAL, Issue 5 2009Bang Zhong LIN ABSTRACT Growth hormone receptor (GHR) belongs to a member of the cytokine receptor superfamily. Polymorphism of presence or absence of an approximately 1.2 kbp LINE-1 element is observed in bovine GHR gene. The present study was carried out for estimating the genetic diversity and the origin of the LINE-1 element in 10 European, Southeastern Asian and East Asian cattle breeds or populations. Genotyping of the LINE-1 revealed predominant LINE-1 presence in European breeds (0.917,0.991), absence in the Bos taurus indicus populations (0.000,0.017), and intermediate presence in Northeast Asian cattle (0.417,0.522). From genetic features of LINE families, LINE-1 of GHR could be attributed to the same origin in both European and Asian cattle, and Asian LINE-1 may not be derived from recent introgression. This result suggested that LINE-1 in bovine GHR gene could have arisen in an ancestral population of Bos taurus taurus. [source] First Genetic Insight into Libyan Tuaregs: A Maternal PerspectiveANNALS OF HUMAN GENETICS, Issue 4 2009Claudio Ottoni Summary The Tuaregs are a semi-nomadic pastoralist people of northwest Africa. Their origins are still a matter of debate due to the scarcity of genetic and historical data. Here we report the first data on the mitochondrial DNA (mtDNA) genetic characterization of a Tuareg sample from Fezzan (Libyan Sahara). A total of 129 individuals from two villages in the Acacus region were genetically analysed. Both the hypervariable regions and the coding region of mtDNA were investigated. Phylogeographic investigation was carried out in order to reconstruct human migratory shifts in central Sahara, and to shed light on the origin of the Libyan Tuaregs. Our results clearly show low genetic diversity in the sample, possibly due to genetic drift and founder effect associated with the separation of Libyan Tuaregs from an ancestral population. Furthermore, the maternal genetic pool of the Libyan Tuaregs is characterized by a major ,European" component shared with the Berbers that could be traced to the Iberian Peninsula, as well as a minor ,south Saharan' contribution possibly linked to both Eastern African and Near Eastern populations. [source] Evolutionary ecology, sexual conflict, and behavioral differentiation among baboon populationsEVOLUTIONARY ANTHROPOLOGY, Issue 5 2003Peter Henzi Abstract A central assumption of baboon socio-ecological models is that all populations have the same capacity to react to different environments. The burden of our argument is that this assumption needs to be reconsidered. Data suggest not only that hamadryas, but chacma as well, differ in interesting ways from the stock baboon model that has been derived, in the main, from earlier work on anubis and cynocephalus. Although environmental factors are behind these differences, much of their influence is a consequence of their effect on restricted ancestral populations, where selection for appropriate responses to the social challenges set by local conditions now constrains the nature of individual responses to contemporary environments. Available genetic evidence suggess a southern African origin for Papio at a time when climatic conditions were certainly no better than they are now and when temperatures, if nothing else, were probably lower. In light of this, a reconstruction of how climate has structured the sexual conflict between males and female charcma, which itself hinges on infanticide, can help explain not only the East African pattern, but also how the apparently anomalous hamadryas pattern has been derived. [source] A panel of ancestry informative markers for estimating individual biogeographical ancestry and admixture from four continents: utility and applications,HUMAN MUTATION, Issue 5 2008Indrani Halder Abstract Autosomal ancestry informative markers (AIMs) are useful for inferring individual biogeographical ancestry (I-BGA) and admixture. Ancestry estimates obtained from Y and mtDNA are useful for reconstructing population expansions and migrations in our recent past but individual genomic admixture estimates are useful to test for association of admixture with phenotypes, as covariate in association studies to control for stratification and, in forensics, to estimate certain overt phenotypes from ancestry. We have developed a panel of 176 autosomal AIMs that can effectively distinguish I-BGA and admixture proportions from four continental ancestral populations: Europeans, West Africans, Indigenous Americans, and East Asians. We present allele frequencies for these AIMs in all four ancestral populations and use them to assess the global apportionment of I-BGA and admixture diversity among some extant populations. We observed patterns of apportionment similar to those described previously using sex and autosomal markers, such as European admixture for African Americans (14.3%) and Mexicans (43.2%), European (65.5%) and East Asian affiliation (27%) for South Asians, and low levels of African admixture (2.8,10.8%) mirroring the distribution of Y E3b haplogroups among various Eurasian populations. Using simulation studies and pedigree analysis we show that I-BGA estimates obtained using this panel and a four-population model has a high degree of precision (average root mean square error [RMSE]=0.026). Using ancestry,phenotype associations we demonstrate that a large and informative AIM panel such as this can help reduce false-positive and false-negative associations between phenotypes and admixture proportions, which may result when using a smaller panel of less informative AIMs. Hum Mutat 29(5), 648,658, 2008. © 2008 Wiley-Liss, Inc. [source] Comparison of IL10 and IL2 genotypes of Turkish population with other populationsINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 2 2009A. C. Yaz Summary The human genome has been shaped by evolutionary and historical forces. Therefore, genetic polymorphisms are useful tools not only to understand the susceptibility to disease in modern populations, but the history of ancestral populations as well. For this purpose, data on genetic polymorphisms such as human leucocyte antigen, mitochondrial DNA sequence variability and the frequencies of TAP1 and TAP2 gene variants in Turkey have been reported previously. Here we have used interleukin (IL)-10 (,592C/A, ,819T/C, ,1082G/A) and IL-2 (,330T/G) as genetic markers to study the relationship between Turkish population and other populations. [source] Process in the evolution of bird migration and pattern in avian ecogeographyJOURNAL OF AVIAN BIOLOGY, Issue 2 2000Christopher P. Bell Current ideas about the evolution of bird migration equate its origin with the first appearance of fully migratory populations, and attribute its evolution to a selective advantage generated by increased breeding success, gained through temporary emigration from resident populations to breed in under-exploited seasonal areas. I propose an alternative hypothesis in which migration first appears as a temporary directional shift away from the breeding site outside the reproductive period, in response to seasonal variation in the direction and/or severity of environmental gradients. Fully migratory populations then appear through either extinction of sedentary phenotypes, or colonisation of vacant seasonal areas by migrants. Where colonisation occurs, resident ancestral populations can be driven to extinction by competition from migrants which invade their range outside the breeding season, resulting in fully migratory species. An analogous process drives the evolution of migration between high latitudes and the tropics, since extension of breeding range into higher latitudes may drive low latitude populations to extinction, resulting in an overall shift of breeding range. This process can explain reverse latitudinal gradients in avian diversity in the temperate zone, since the breeding ranges of migratory species concentrate in latitudes where they enjoy the highest breeding success. Near absence of forest-dwelling species among Palaearctic-African migrants is attributable to the lack of forest in northern Africa for much of the Tertiary, which has precluded selection both for southward extension of migration by west Palaearctic forest species, and northward breeding colonisation by African forest species. [source] Genetic diversity and phylogeographic analysis of Pinus leiophylla: a post-glacial range expansionJOURNAL OF BIOGEOGRAPHY, Issue 9 2009Abril Rodríguez-Banderas Abstract Aim, Mexico is a centre of diversity for species of the genus Pinus, most of which have restricted geographical distributions. An exception is Pinus leiophylla Schiede and Deppe, which is widely distributed throughout most of Mexico's mountainous regions. We attempt to reconstruct the phylogeographic history of this species, in order to determine if its current broad distribution is associated with major events of environmental change that occurred during the Quaternary. Location, Coniferous forests in Sierra Madre Occidental, Eje Volcánico Transversal and Sierra Montañosa del Norte de Oaxaca, Mexico. Methods, A total of 323 individuals of both P. leiophylla var. leiophylla and P. leiophylla var. chihuahuana sampled from 22 populations were screened for variation at six paternally inherited chloroplast DNA microsatellite markers (cpSSR). In addition to haplotypic diversity estimates and neutrality tests, the following clustering methods were employed: principal components analysis (PCA), analysis of molecular variance (AMOVA), spatial analysis of molecular variance (SAMOVA), haplotype network and a technique similar to Croizat's panbiogeographical method of individual and generalized tracks. Results, The combination of mutations at the six microsatellites yielded a total of 92 different haplotypes. The percentage of shared haplotypes between varieties (P. leiophylla var. leiophylla and P. leiophylla var. chihuahuana) was only 2.2%. The average haplotypic diversity for the species was H = 0.760. PCA and SAMOVA indicate the presence of four main genetic clusters. The estimated divergence time between the two most frequent haplotypes was between 75,000 and 110,000 years. Significantly large negative Fs values suggest that most of the sampled populations are currently expanding. Individual and generalized tracks identified three potential zones that may have harboured ancestral populations of P. leiophylla and from which the expansion of this species started, as well as two secondary contact zones between the two varieties. Main conclusions, The results indicate that one of the three potential areas hypothesized to have harboured ancestral populations of P. leiophylla may be related to the origin of P. leiophylla var. chihuahuana, while the other two may be related to the origin of P. leiophylla var. leiophylla. The current broad distribution of P. leiophylla is probably associated with its strong colonization ability. [source] Bayesian identification of admixture events using multilocus molecular markersMOLECULAR ECOLOGY, Issue 10 2006JUKKA CORANDER Abstract Bayesian statistical methods for the estimation of hidden genetic structure of populations have gained considerable popularity in the recent years. Utilizing molecular marker data, Bayesian mixture models attempt to identify a hidden population structure by clustering individuals into genetically divergent groups, whereas admixture models target at separating the ancestral sources of the alleles observed in different individuals. We discuss the difficulties involved in the simultaneous estimation of the number of ancestral populations and the levels of admixture in studied individuals' genomes. To resolve this issue, we introduce a computationally efficient method for the identification of admixture events in the population history. Our approach is illustrated by analyses of several challenging real and simulated data sets. The software (baps), implementing the methods introduced here, is freely available at http://www.rni.helsinki.fi/~jic/bapspage.html. [source] DNA barcode discovers two cryptic species and two geographical radiations in the invasive drosophilid Zaprionus indianusMOLECULAR ECOLOGY RESOURCES, Issue 3 2008AMIR YASSIN Abstract Comparing introduced to ancestral populations within a phylogeographical context is crucial in any study aiming to understand the ecological genetics of an invasive species. Zaprionus indianus is a cosmopolitan drosophilid that has recently succeeded to expand its geographical range upon three continents (Africa, Asia and the Americas). We studied the distribution of mitochondrial DNA (mtDNA) haplotypes for two genes (CO-I and CO-II) among 23 geographical populations. mtDNA revealed the presence of two well-supported phylogenetic lineages (phylads), with bootstrap value of 100%. Phylad I included three African populations, reinforcing the African-origin hypothesis of the species. Within phylad II, a distinct phylogeographical pattern was discovered: Atlantic populations (from the Americas and Madeira) were closer to the ancestral African populations than to Eastern ones (from Madagascar, Middle East and India). This means that during its passage from endemism to cosmopolitanism, Z. indianus exhibited two independent radiations, the older (the Eastern) to the East, and the younger (the Atlantic) to the West. Discriminant function analysis using 13 morphometrical characters was also able to discriminate between the two molecular phylads (93.34 ± 1.67%), although detailed morphological analysis of male genitalia using scanning electron microscopy showed no significant differences. Finally, crossing experiments revealed the presence of reproductive barrier between populations from the two phylads, and further between populations within phylad I. Hence, a bona species status was assigned to two new, cryptic species: Zaprionus africanus and Zaprionus gabonicus, and both were encompassed along with Z. indianus and Zaprionus megalorchis into the indianus complex. The ecology of these two species reveals that they are forest dwellers, which explains their restricted endemic distribution, in contrast to their relative cosmopolitan Z. indianus, known to be a human-commensal. Our results reconfirm the great utility of mtDNA at both inter- and intraspecific analyses within the frame of an integrated taxonomical project. [source] Functional significance of genetic variation underlying limb bone diaphyseal structureAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 1 2010Ian J. Wallace Abstract Limb bone diaphyseal structure is frequently used to infer hominin activity levels from skeletal remains, an approach based on the well-documented ability of bone to adjust to its loading environment during life. However, diaphyseal structure is also determined in part by genetic factors. This study investigates the possibility that genetic variation underlying diaphyseal structure is influenced by the activity levels of ancestral populations and might also have functional significance in an evolutionary context. We adopted an experimental evolution approach and tested for differences in femoral diaphyseal structure in 1-week-old mice from a line that had been artificially selected (45 generations) for high voluntary wheel running and non-selected controls. As adults, selected mice are significantly more active on wheels and in home cages, and have thicker diaphyses. Structural differences at 1 week can be assumed to primarily reflect the effects of selective breeding rather than direct mechanical stimuli, given that the onset of locomotion in mice is shortly after Day 7. We hypothesized that if genetically determined diaphyseal structure reflects the activity patterns of members of a lineage, then selected animals will have relatively larger diaphyseal dimensions at 1 week compared to controls. The results provide strong support for this hypothesis and suggest that limb bone cross sections may not always only reflect the activity levels of particular fossil individuals, but also convey an evolutionary signal providing information about hominin activity in the past. Am J Phys Anthropol 143:21,30, 2010. © 2010 Wiley-Liss, Inc. [source] Pre-Hispanic Mesoamerican demography approximates the present-day ancestry of Mestizos throughout the territory of MexicoAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 3 2009Rodrigo Rubi-Castellanos Abstract Over the last 500 years, admixture among Amerindians, Europeans, and Africans, principally, has come to shape the present-day gene pool of Mexicans, particularly Mestizos, who represent about 93% of the total Mexican population. In this work, we analyze the genetic data of 13 combined DNA index system-short tandem repeats (CODIS-STRs) in 1,984 unrelated Mestizos representing 10 population samples from different regions of Mexico, namely North, West, Central, and Southeast. The analysis of molecular variance (AMOVA) test demonstrated low but significant differentiation among Mestizos from different regions (FST = 0.34%; P = 0.0000). Although the spatial analysis of molecular variance (SAMOVA) predicted clustering Mestizo populations into four well-delimited groups, the main differentiation was observed between Northwest when compared with Central and Southeast regions. In addition, we included analysis of individuals of Amerindian (Purepechas), European (Huelva, Spain), and African (Fang) origin. Thus, STRUCTURE analysis was performed identifying three well-differentiated ancestral populations (k = 3). STRUCTURE results and admixture estimations by means of LEADMIX software in Mestizo populations demonstrated genetic heterogeneity or asymmetric admixture throughout Mexico, displaying an increasing North-to-South gradient of Amerindian ancestry, and vice versa regarding the European component. Interestingly, this distribution of Amerindian ancestry roughly reflects pre-Hispanic Native-population density, particularly toward the Mesoamerican area. The forensic, epidemiological, and evolutionary implications of these findings are discussed herein. Am J Phys Anthropol 2009. © 2009 Wiley-Liss, Inc. [source] Biohistorical approaches to "race" in the United States: Biological distances among African Americans, European Americans, and their ancestors,AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 1 2009Heather J.H. Edgar Abstract Folk taxonomies of race are the categorizations used by people in their everyday judgments concerning the persons around them. As cultural traditions, folk taxonomies may shape gene flow so that it is unequal among groups sharing geography. The history of the United States is one of disparate people being brought together from around the globe, and provides a natural experiment for exploring the relationship between culture and gene flow. The biohistories of African Americans and European Americans were compared to examine whether population histories are shaped by culture when geography and language are shared. Dental morphological data were used to indicate phenotypic similarity, allowing diachronic change through United States history to be considered. Samples represented contemporary and historic African Americans and European Americans and their West African and European ancestral populations (N = 1445). Modified Mahalanobis' D2 and Mean Measure of Divergence statistics examined how biological distances change through time among the samples. Results suggest the social acceptance for mating between descendents of Western Europeans and Eastern and Southern European migrants to the United States produced relatively rapid gene flow between the groups. Although African Americans have been in the United States much longer than most Eastern and Southern Europeans, social barriers have been historically stronger between them and European Americans. These results indicate that gene flow is in part shaped by cultural factors such as folk taxonomies of race, and have implications for understanding contemporary human variation, relationships among prehistoric populations, and forensic anthropology. Am J Phys Anthropol 2009. © 2009 Wiley-Liss, Inc. [source] Genetic diversity in farm animals , a reviewANIMAL GENETICS, Issue 2010L. F. Groeneveld Summary Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition, molecular genetic studies allow a comparison of genetic diversity within and across breeds and a reconstruction of the history of breeds and ancestral populations. This has been summarized for cattle, yak, water buffalo, sheep, goats, camelids, pigs, horses, and chickens. Further progress is expected to benefit from advances in molecular technology. [source] The population genetic effects of ancestry and admixture in a subdivided cattle breedANIMAL GENETICS, Issue 4 2009T. C. Bray Summary The genetic structure of the Dexter, a minority cattle breed with complex demographic history, was investigated using microsatellite markers and a range of statistical approaches designed to detect both admixture and genetic drift. Modern representatives of two putative ancestral populations, the Devon and Kerry, together with the different populations of the Dexter, which have experienced different demographic histories, were analysed. Breed units showed comparatively high levels of genetic variability (HE = 0.63,0.68); however, distinct genetic subgroups were detected within the Dexter, which could be attributed to known demographic events. Much lower diversity was identified in three small, isolated Dexter populations (HE = 0.52,0.55) and higher differentiation (FST > 0.13) was found. For one of these populations, where strong selection has taken place, we also found evidence of a demographic bottleneck. Three methods for quantifying breed admixture were applied and substantial method-based variation in estimates for the genetic contribution of the two proposed ancestral populations for each subdivision of the Dexter was found. Results were consistent only in the case of a group consisting of selected Traditional Dexter animals, where the ancestor of the modern Kerry breed was also determined as the greater parental contributor to the Dexter. The inconsistency of estimation of admixture proportions between the methods highlights the potentially confounding role of genetic drift in shaping small population structure, and the consequences of accurately describing population histories from contemporary genetic data. [source] Genetic Admixture in Brazilians Exposed to Infection with Leishmania chagasiANNALS OF HUMAN GENETICS, Issue 3 2009Nicholas A. Ettinger Summary Visceral leishmaniasis (VL) in northeast Brazil is a disease caused by infection with the protozoan Leishmania chagasi. Infection leads to variable clinical outcomes ranging from asymptomatic infection to potentially fatal disease. Prior studies suggest the genetic background of the host contributes to the development of different outcomes after infection, although it is not known if ancestral background itself influences outcomes. VL is endemic in peri-urban areas around the city of Natal in northeast Brazil. The population of northeast Brazil is a mixture of distinct racial and ethnic groups. We hypothesized that some sub-populations may be more susceptible than others to develop different clinical outcomes after L. chagasi infection. Using microsatellite markers, we examined whether admixture of the population as a whole, or markers likely inherited from a distinct ethnic background, differed between individuals with VL, individuals with an asymptomatic infection, or individuals with no infection. There was no apparent significant difference in overall population admixture proportions among the three clinical phenotype groups. However, one marker on Chr. 22 displayed evidence of excess ancestry from putative ancestral populations among different clinical phenotypes, suggesting this region may contain genes determining the course of L. chagasi infection. [source] Varying rates of diversification in the genus Melitaea (Lepidoptera: Nymphalidae) during the past 20 million yearsBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 2 2009JULIEN LENEVEU The influence of Quarternary glacial cycles on the extant diversity of Holarctic species has been intensively studied. It has been hypothesized that palaeoclimatic changes are responsible for divergence events in lineages. A constant improvement in DNA sequencing and modeling methods, as well as palaeoclimatic reconstruction, permit a deeper exploration of general causes of speciation in geological time. In the present study, we sampled, as exhaustively as possible, the butterflies belonging to the genus Melitaea (Lepidoptera: Nymphalidae), which are widely spread in the Palaearctic region. We conducted analyses to assess the phylogeny of the genus and estimated the timing of divergence and the most likely distribution of ancestral populations. The results obtained indicate that the systematics of the genus is in need of revision and that the diversity of the genus has been profoundly shaped by palaeoenvironmental changes during its evolutionary history. The present study also emphasizes that, when employed with caveats, major palaeoenvironmental events could represent very powerful tools for the calibration of the dating of divergences using molecular data. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 346,361. [source] Genotype frequencies and linkage disequilibrium in the CEPH human diversity panel for variants in folate pathway genes MTHFR, MTHFD, MTRR, RFC1, and GCP2BIRTH DEFECTS RESEARCH, Issue 8 2003Min Shi BACKGROUND Genetic variation in enzymes involved in vitamin metabolism is a candidate for analysis in studies of how nutritional covariates may impact a disease state. The role of folate pathway genes in birth defects and cardiovascular disease in humans has been widely studied. Since incidence rates for these disorders vary by geographic origins, it is useful to know which variants are the best candidates for studies based on genotype and allele frequency, as well as linkage disequilibrium (LD) in founder populations. METHODS Six polymorphisms in five folate metabolism-related genes (MTHFR, MTHFD, MTRR, GCP2, and RFC1) were genotyped on a collection of 1064 DNA samples from populations around the world, which were made available by the Centre d'Étude du Polymorphisme Humain (CEPH) consortium for analysis. RESULTS In this study we report the genotype frequencies for variants in the MTHFR, MTHFD, MTRR, GCP2, and RFC1 genes, and the LD for two variants (C677T and A1298C) in MTHFR. CONCLUSIONS The rare allele frequency for each of the five genes studied varied widely. LD is strongest in Pakistani and Brazilian populations (D, = 1.0) and weakest in Mexican populations (D, = 0.45). These findings will allow the selection of variants that will provide the most power in studies of folate pathway genes involving different ancestral populations, and contribute to our knowledge of the population distribution of selected nutritional gene variants. Birth Defects Research (Part A), 2003. © 2003 Wiley-Liss, Inc. [source] CTG repeats at the myotonic protein kinase gene in a healthy Chilean population sampleACTA NEUROLOGICA SCANDINAVICA, Issue 5 2009F. Amenabar Objectives,,, To study the variability at the myotonic dystrophy protein kinase (DMPK) gene in a Chilean sample of healthy people. DM1 is an autosomal dominant disorder caused by an expansion of a (CTG) repeat at the 3,-UTR of the gene DMPK. Healthy individuals have alleles under 35 repeats and diseased individuals have over 50. Methods,,, Genotyping the number of (CTG) repeats at this gene in a sample of healthy Chilean people. Results,,, Allele frequencies were significantly different from those of other populations. The most frequent allele was with five repeats. The frequency of larger alleles (>18 CTG repeats) was 11%, close to the European frequency (12%) and higher than the Japanese (8%) and Aboriginal Pehuenche samples (8%). Conclusions,,, Allelic frequencies in the Chilean sample studied were intermediate between those of the two ancestral populations (European and Pehuenche). [source] | ||||||||||||||||||||||||||||