Maternal Gene Flow Research Articles

Comparative mtDNA analyses of three sympatric macropodids from a conservation area on the Huon Peninsula, Papua New Guinea

Matschie’s tree kangaroo (Dendrolagus matschiei), New Guinea pademelon (Thylogale browni), and small dorcopsis (Dorcopsulus vanheurni) are sympatric macropodid taxa, of conservation concern, that inhabit the Yopno–Urawa–Som (YUS) Conservation Area on the Huon Peninsula, Papua New Guinea. We sequenced three partial mitochondrial DNA (mtDNA) genes from the three taxa to (i) investigate network structure; and (ii) identify conservation units within the YUS Conservation Area. All three taxa displayed a similar pattern in the spatial distribution of their mtDNA haplotypes and the Urawa and Som rivers on the Huon may have acted as a barrier to maternal gene flow. Matschie’s tree kangaroo and New Guinea pademelon within the YUS Conservation Area should be managed as single conservation units because mtDNA nucleotides were not fixed for a given geographic area. However, two distinct conservation units were identified for small dorcopsis from the two different mountain ranges within the YUS Conservation Area.

Exploring the Impact of Habitat Size on Phylogeographic Patterning in the Overberg Velvet Worm Peripatopsis overbergiensis (Onychophora: Peripatopsidae).

Evolutionary relationships in the velvet worm species, Peripatopsis overbergiensis, were examined in 3 forest areas in the Overberg region of South Africa to explore the impact of historical habitat fragmentation on the population genetic structure of the species. We collected 84 P. overbergiensis specimens from Grootvadersbosch, Koppie Alleen, and Marloth Nature Reserves and sequenced all these specimens for the cytochrome c oxidase subunit I (COI) locus, whereas a subset of 13 specimens were also sequenced for the 18S rRNA locus. Phylogenetic analyses of the 20 unique COI haplotypes revealed 4 genetically distinct clades, a result that is corroborated by the haplotype network. A hierarchical analysis of genetic variation was performed on the COI haplotype data within the 2 large forested areas, Grootvadersbosch and Marloth Nature Reserves, and across all 3 of the sample localities. These results revealed low haplotypic and nucleotide diversity within the largest Grootvadersbosch Nature Reserve forest and high haplotypic and nucleotide diversity within the fragmented Marloth Nature Reserve forest, whereas Koppie Alleen had the lowest haplotypic and nucleotide diversity. Across all 3 main localities statistically significant F ST values were found, together with the absence of shared haplotypes indicating the absence of maternal gene flow. Divergence time estimations based on the 20 COI haplotypes calculated in BEAST suggest a Pleistocene/Holocene divergence between the 4 clades as a result of habitat fragmentation and the aridification of the region. Our results indicate that conservation efforts should also prioritize linked, smaller fragmented habitats together with continuous habitats to maximize the genetic diversity of saproxylic fauna.

Stomach Contents of a Cuvier's Beaked Whale (Ziphius cavirostris) Stranded in Monterey Bay, California

From 1942 to 2010 there were 23 reported strandings of Cuvier’s Beaked Whale, Ziphius cavirostris (Odontoceti: Ziphiidae), in the Pacific Northwest (Oregon and Washington), and 25 reported strandings in California between 1982 and 2010 (Moore and Barlow 2013). Although Z. cavirostris appears to be the most cosmopolitan of the beaked whales, occurring in all oceans except in high polar regions (Leatherwood and Reeves 1983; Heyning 1989), global phylogenetic analyses reveal low maternal gene flow among populations confined to isolated ocean basins (Dalebout and others 2005). Extensive surveys throughout the California Current System (CCS) show that Z. cavirostris is distributed offshore over the continental slope, occurring more frequently closer to shore and aggregated in areas of complex bathymetry (for example, Monterey Bay, California and within the Southern California Bight, see Fig. 2 in Moore and Barlow 2013). In the northern CCS, Moore and Barlow (2013) estimated that the Z. cavirostris population likely has decreased by approximately 30% from 10,771 in 1991 to approximately 7550 individuals in 2008, and they suggested that one potential cause could be ecosystem change, thus highlighting the need for additional information on food habits. Heyning (1989) first summarized prey information for Z. cavirostris from around the world, a list that included 10 cephalopod families (16 genera), gadiform and atheriniform fishes, and 2 accounts of crustacean prey. Santos and others (2001) reported prey remains from 3 Z. cavirostris stranded in the eastern Atlantic and provided a review of known prey remains for the species. MacLeod and others (2003) extended the review of Santos and others (2001) to include comparison of Z. cavirostris with 2 additional beaked whales: Mesoplodon spp. and Hyperoodon planifrons. Combining these records with 7 Z. cavirostris stomachs evaluated by Santos and others (2007), the known diet of Z. cavirostris is based on prey remains recovered from only 45 individuals world-wide; diets consisted of 46 cephalopod species (15 families), infrequent crustacean remains, and rare representation among mostly unidentified fishes (MacLeod and others 2003). Compared with records from the Atlantic, food habits of Z. cavirostris off Alaska and in the eastern North Pacific are less well known (n 5 5 individuals, and only 1 from California). Fiscus (1997) identified 6 cephalopod families (11 genera) from a subset of the stomach remains collected and described by Kenyon (1961) from a mature female Z. cavirostris that stranded in March 1959 on Amchitka Island, Aleutian Islands, Alaska. Foster and Hare (1990) identified 3 of the same cephalopod families (4 genera) as reported by Fiscus (1997) from a Z. cavirostris stranded in Kodiak, Alaska. In the Gulf of Mexico, Fertl and others (1997) identified a single beak of Loligo peali from an individual that stranded in Texas. An adult female Z. cavirostris (Moss Landing Marine Laboratory Museum [MLMLM] #499, standard length 600 cm) stranded dead on 15 January 1998 at Marina State Beach, California (UTM: Zone 10S, 607191E, 4062264N, WGS84). During a 2-d field necropsy, to minimize the loss of contents, we tied-off both the esophageal and duodenal ends of the stomach before removing it on 16 January 1998. Prey remains were also collected from the whale’s oral cavity. The stomach contents from 5 pyloric compartments (see Kenyon 1961 for a description of the stomach of an adult female Z. cavirostris) were gently rinsed and sifted through a 500-mm sieve. Cephalopod remains (whole beaks, beak fragments, and eye lenses) and fish remains (bones and eye lenses) were preserved in 50% isopropyl alcohol and fish otoliths were stored dry. Cephalopods were identified to lowest taxon using the GENERAL NOTES

Hybridization and mitochondrial genome introgression betweenRana chensinensisandR. kukunoris

Mitochondrial genome (mito-genome) introgression among metazoans is commonplace, and several biological processes may promote such introgression. We examined two proposed processes for the mito-genome introgression between Rana chensinensis and R. kukunoris: natural hybridization and sex-biased dispersal. We sampled 477 individuals from 28 sites in the potential hybrid zone in the western Tsinling Mountains. Mitochondrial gene (cyt-b) trees were used to examine the introgression events. Microsatellite DNA loci, cyt-b and morphological data were used to identify hybrids and to examine the extent of natural hybridization. We detected rampant bidirectional introgressions, both ancient and recent, between the two species. Furthermore, we found a wide hybrid zone, and frequent and asymmetric hybridization. The hybrid zone cline analysis revealed a clear mitochondrial-nuclear discordance; while most nuclear markers displayed similar and steep clines, cyt-b had a displaced cline centre and a more gradual and wider cline. We also detected strong and asymmetric historical maternal gene flow across the hybrid zone. This widespread hybridization and detected low mito-nuclear conflicts may, at least partially, explain the high frequency of introgression. Lastly, microsatellite data and population genetic methods were used to assess sex-biased dispersal. A weak pattern of female-biased dispersal was detected in both species, suggesting it may not play an important role in the observed introgression. Our data are consistent with the hybridization hypothesis, but support for the sex-biased dispersal hypothesis is weak. We further suggest that selective advantages of the R. kukunoris-type mito-genome in thermal adaptation may also contribute to the introgression between the two species.

Meta-Analysis of Mitochondrial DNA Reveals Several Population Bottlenecks during Worldwide Migrations of Cattle

Several studies have investigated the differentiation of mitochondrial DNA in Eurasian, African and American cattle as well as archaeological bovine material. A global survey of these studies shows that haplogroup distributions are more stable in time than in space. All major migrations of cattle have shifted the haplogroup distributions considerably with a reduction of the number of haplogroups and/or an expansion of haplotypes that are rare or absent in the ancestral populations. The most extreme case is the almost exclusive colonization of Africa by the T1 haplogroup, which is rare in Southwest Asian cattle. In contrast, ancient samples invariably show continuity with present-day cattle from the same location. These findings indicate strong maternal founder effects followed by limited maternal gene flow when new territories are colonized. However, effects of adaptation to new environments may also play a role.

Complete mitochondrial genome sequence of the Eastern gorilla (Gorilla beringei) and implications for african ape biogeography.

The Western and Eastern species of gorillas (Gorilla gorilla and Gorilla beringei) began diverging in the mid-Pleistocene, but in a complex pattern with ongoing gene flow following their initial split. We sequenced the complete mitochondrial genomes of 1 Eastern and 1 Western gorilla to provide the most accurate date for their mitochondrial divergence, and to analyze patterns of nucleotide substitutions. The most recent common ancestor of these genomes existed about 1.9 million years ago, slightly more recent than that of chimpanzee and bonobo. We in turn use this date as a calibration to reanalyze sequences from the Eastern lowland and mountain gorilla subspecies to estimate their mitochondrial divergence at approximately 380000 years ago. These dates help frame a hypothesis whereby populations became isolated nearly 2 million years ago with restricted maternal gene flow, followed by ongoing male migration until the recent past. This process of divergence with prolonged hybridization occurred against the backdrop of the African Pleistocene, characterized by intense fluctuations in temperature and aridity, while at the same time experiencing tectonic uplifting and consequent shifts in the drainage of major river systems. Interestingly, this same pattern of introgression following divergence and discrepancies between mitochondrial and nuclear loci is seen in fossil hominins from Eurasia, suggesting that such processes may be common in hominids and that living gorillas may provide a useful model for understanding isolation and migration in our extinct relatives.

Consecutive five‐year analysis of paternal and maternal gene flow and contributions of gametic heterogeneities to overall genetic composition of dispersed seeds of Pinus densiflora (Pinaceae)

Genetic variability in monoecious woody plant populations results from the assemblage of individuals issued from asymmetrical male and female reproductive functions, produced during spatially and temporarily heterogeneous reproductive and dispersal events. Here we investigated the dispersal patterns and levels of genetic diversity and differentiation of both paternal and maternal gametes in a natural population of Pinus densiflora at the multiple-year scale as long as five consecutive years. • We analyzed the paternity and maternity for 1576 seeds and 454 candidate adult trees using nuclear DNA polymorphisms of diploid biparental embryos and haploid maternal megagametophytes at eight microsatellite loci. • Despite the low levels of genetic differentiation among gamete groups, a two-way AMOVA analysis showed that the parental origin (paternal vs. maternal gametes), the year of gamete production and their interaction had significant effects on the genetic composition of the seeds. While maternal gamete groups showed a significant FST value across the 5 years, this was not true for their paternal counterparts. Within the population, we found that the relative reproductive contributions of the paternal vs. the maternal parent differed among adult trees, the maternal contributions showing a larger year-to-year fluctuation. • The overall genetic variability of dispersed seeds appeared to result from two sources of heterogeneity: the difference between paternal and maternal patterns of reproduction and gamete dispersal and year-to-year heterogeneity of reproduction of adult trees, especially in their maternal reproduction.

Reevaluating a model of gender-biased gene flow among Sub-Saharan Hunter-gatherers and farmers.

In a previous study, we proposed a model for genetic admixture between African hunter-gatherers and food producers, in which we integrated demographic and genetic aspects together with ethnographic knowledge (Destro-Bisol et al. 2004b). In that study it was possible to test the model only using genetic information from widely dispersed and genetically heterogeneous populations. Here we reevaluate the congruence between the model and patterns of genetic variation using an anthropologically and geographically more homogeneous data set that includes Pygmies and farmers from Cameroon, Congo, and the Central African Republic. As implied by the model, the ratios of mtDNA to Y chromosome Nm estimates (effective population size, N, times the migration rate, m; 0.154 in Pygmies and 6.759 in farmers), support an asymmetric gene flow, with a higher Bantu-to-Pygmy gene flow for paternal than for maternal lineages, and vice versa for farmers. Analyses of intra- and interpopulation genetic variation further support the above observation, showing a prevailing effect of genetic drift on maternal lineages and gene flow on paternal lineages among Pygmies, and an opposite pattern among farmers. We also detected differences between patterns for classical and molecular measures of Y chromosome intrapopulation variation, which likely represent signatures of the introgression of Bantu lineages into the gene pool of Pygmy populations. On the whole, our results seem to reflect differences in the demographic history and the degree of patrilocality and polygyny between the two population groups, thus providing further support to our microevolutionary model in an anthropologically coherent framework.

Reevaluating a Model of Gender-Biased Gene Flow among Sub-Saharan Hunter-Gatherers and Farmers

In a previous study, we proposed a model for genetic admixture between African hunter-gatherers and food producers, in which we integrated demographic and genetic aspects together with ethnographic knowledge (). In that study it was possible to test the model only using genetic information from widely dispersed and genetically heterogeneous populations. Here we reevaluate the congruence between the model and patterns of genetic variation using an anthropologically and geographically more homogeneous data set that includes Pygmies and farmers from Cameroon, Congo, and the Central African Republic. As implied by the model, the ratios of mtDNA to Y chromosome Nm estimates (effective population size, N, times the migration rate, m; 0.154 in Pygmies and 6.759 in farmers), support an asymmetric gene flow, with a higher Bantu-to-Pygmy gene flow for paternal than for maternal lineages, and vice versa for farmers. Analyses of intra- and interpopulation genetic variation further support the above observation, showing a prevailing effect of genetic drift on maternal lineages and gene flow on paternal lineages among Pygmies, and an opposite pattern among farmers. We also detected differences between patterns for classical and molecular measures of Y chromosome intrapopulation variation, which likely represent signatures of the introgression of Bantu lineages into the gene pool of Pygmy populations. On the whole, our results seem to reflect differences in the demographic history and the degree of patrilocality and polygyny between the two population groups, thus providing further support to our microevolutionary model in an anthropologically coherent framework.

Editors’ Pick: A real Caucasian and the genetic investigation of Caucasus peoples

Referring to Europeans as Caucasians, as still regularly done in the medical and less frequently in the population genetic literature, most often is not justified according to modern scientific views. This term, first mentioned in 1785 by Christoph Meiners, was picked up by Johann Friedrich Blumenbach in his 1795 suggestion of dividing the human world population into 5 groups (Caucasians, Mongolians, Ethiopians, Americans, and Malays). Nevertheless, a Caucasian classification can still be formally correct if it refers to people who originate from the Caucasus region. One real Caucasian, the molecular anthropologist Dr. Ivan (Vano) Nasidze (Figure ​(Figure1),1), recently passed away, suddenly and unexpectedly. Although this was a huge shock for everybody who knew Vano, in particular his family and his close colleagues, the way he died seemed the preferred one for many of us similarly passionate scientists who seem unable to live without scientific work. If only, however, it would occur several decades later in life than for Vano who unfortunately did not reach his 48 birthday. He died instantly while working at his office computer at the Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology Leipzig, Germany. Figure 1 Ivan (Vano) Nasidze, 1964 – 2012. Max Planck Institute for Evolutionary Anthropology. Ivan Nasidze was a real Caucasian; not only born and raised in Tblisi (Georgia), he dedicated almost all of his professional life to the genetic investigation of human population relationships and history in the Caucasus region. His latest (and now last) in a series of articles on this topic was published in September last year in the European Journal of Human Genetics[1]. Using complete mitochondrial (mt) genomes (whereas traditionally only the mtDNA control region - HV1 - is applied) Nasidze and his colleagues found astonishingly high genetic diversity with 144 different sequences and 97 haplogroups among 147 individuals tested. Strikingly, all of the Georgians, Armenians and Iranians (the latter used for comparison) had different mtDNA sequences, while for the Azeri and the Turks (the latter used for comparison) minor within-group haplotype sharing was observed. These data once again underline the extremely high genetic diversity of the Caucasus people as result of a very complex population history. Nasidze and his coauthors confirmed their previous findings that Indo-European-speaking Armenians and Turkic-speaking Azeri are more closely related genetically to Caucasian-speaking groups in the Caucasus than to other Indo-European-speaking and Turkic-speaking groups. The language shift in the Caucasus, which Nasidze’s previous work already had highlighted, was confirmed with this study. However, in contrast to his previous work using solely HV1, these whole mtDNA genome data now indicate some maternal genetic relationship between Turks and Azeri (both Turkic-speaking groups) suggesting that the language shift in the Azeri probably did involve some maternal gene flow from Turks. Hence, applying current next generation sequencing technology to anthropological questions, Nasidze with this work partly confirmed his earlier findings but also revealed new insights into the human genetic history of the Caucasus. Moreover, this study shows, as may be expected, that individuals with identical HV1 sequence are clearly differentiated based on their whole mtDNA genome data, which has significance for anthropological and also forensic studies. I will miss Vano as a friendly and cooperative colleague who was deeply committed to explore the genetic history of the Caucasus peoples with various molecular approaches (including Y-chromosomal and autosomal DNA variation). I sincerely hope that Dr. Ivan Nasidze will be remembered for his important contributions to the investigative genetics and the molecular anthropology of the Caucasus for a long time to come.

Genetic admixture studies on four in situ evolved, two migrant and twenty-one ethnic populations of Tamil Nadu, south India

We analysed the genetic structure of ≈ 1000 samples representing 27 ethnic groups settled in Tamil Nadu, south India, derived from two linguistic families (Dravidians and Indo-Europeans) representing four religious groups (Hinduism, Islam, Christianity and Jainism) using 11 mtDNA markers. Out of 27 ethnic groups, four are in situ populations (Anglo-Indian, Labbai Muslim, Nadar Christian and south Indian Jain) and two are migrants (Gypsy and north Indian Jain) from north India to Tamil Nadu, and 21 are native ethnic groups. Six of the markers we used were monomorphic (HaeIII663, HpaI3592, AluI5176, AluI7025, AluI13262, 9-bp deletion) and five markers were polymorphic (DdeI10394, AluI10397, HinfI12308, HincII13259 and HaeIII16517). Haplogroup frequencies, genetic affinities and admixture analysis are based on the genotype data of polymorphic markers observed in these populations. Haplogroup frequencies indicate that various ethnic groups entered Tamil Nadu during different time periods. Genetic affinities and admixture estimates revealed that the ethnic groups possessing advanced knowledge of farming cluster in a branch (C), and could be the late arrived settlers as agriculture, was introduced to this region at about 5 to 3 thousand years ago. In situ ethnic groups appear to have arisen at various times as a result of the prevailing dominant socio-cultural forces. Hierarchical Hindu caste system created many ethnic groups in the history of its existence; some of them became isolated for considerable period of time. Over all, among Tamil ethnic groups, in spite of caste systems' rigidity, built in flexibility in the system in the form of hypergamy and hypogamy had allowed maternal gene flow between them.

Cryptic Species? Patterns of Maternal and Paternal Gene Flow in Eight Neotropical Bats

Levels of sequence divergence at mitochondrial loci are frequently used in phylogeographic analysis and species delimitation though single marker systems cannot assess bi-parental gene flow. In this investigation I compare the phylogeographic patterns revealed through the maternally inherited mitochondrial COI region and the paternally inherited 7th intron region of the Dby gene on the Y-chromosome in eight common Neotropical bat species. These species are diverse and include members of two families from the feeding guilds of sanguivores, nectarivores, frugivores, carnivores and insectivores. In each case, the currently recognized taxon is comprised of distinct, substantially divergent intraspecific mitochondrial lineages suggesting cryptic species complexes. In Chrotopterus auritus, and Saccopteryx bilineata I observed congruent patterns of divergence in both genetic regions suggesting a cessation of gene flow between intraspecific groups. This evidence supports the existence of cryptic species complexes which meet the criteria of the genetic species concept. In Glossophaga soricina two intraspecific groups with largely sympatric South American ranges show evidence for incomplete lineage sorting or frequent hybridization while a third group with a Central American distribution appears to diverge congruently at both loci suggesting speciation. Within Desmodus rotundus and Trachops cirrhosus the paternally inherited region was monomorphic and thus does not support or refute the potential for cryptic speciation. In Uroderma bilobatum, Micronycteris megalotis and Platyrrhinus helleri the gene regions show conflicting patterns of divergence and I cannot exclude ongoing gene flow between intraspecific groups. This analysis provides a comprehensive comparison across taxa and employs both maternally and paternally inherited gene regions to validate patterns of gene flow. I present evidence for previously unrecognized species meeting the criteria of the genetic species concept but demonstrate that estimates of mitochondrial diversity alone do not accurately represent gene flow in these species and that contact/hybrid zones must be explored to evaluate reproductive isolation.

Ancient Voyaging and Polynesian Origins

The "Polynesian motif" defines a lineage of human mtDNA that is restricted to Austronesian-speaking populations and is almost fixed in Polynesians. It is widely thought to support a rapid dispersal of maternal lineages from Taiwan ~4000 years ago (4 ka), but the chronological resolution of existing control-region data is poor, and an East Indonesian origin has also been proposed. By analyzing 157 complete mtDNA genomes, we show that the motif itself most likely originated >6 ka in the vicinity of the Bismarck Archipelago, and its immediate ancestor is >8 ka old and virtually restricted to Near Oceania. This indicates that Polynesian maternal lineages from Island Southeast Asia gained a foothold in Near Oceania much earlier than dispersal from either Taiwan or Indonesia 3-4 ka would predict. However, we find evidence in minor lineages for more recent two-way maternal gene flow between Island Southeast Asia and Near Oceania, likely reflecting movements along a "voyaging corridor" between them, as previously proposed on archaeological grounds. Small-scale mid-Holocene movements from Island Southeast Asia likely transmitted Austronesian languages to the long-established Southeast Asian colonies in the Bismarcks carrying the Polynesian motif, perhaps also providing the impetus for the expansion into Polynesia.

Phylogeography and conservation of the bull shark (Carcharhinus leucas) inferred from mitochondrial and microsatellite DNA

The bull shark (Carcharhinus leucas) is a widely distributed, large coastal shark species known to travel long distances. These characteristics, coupled with the species’ long life span and late age of maturity, would lead one to predict significant global genetic exchange among bull shark populations. By contrast, data show localized depletion in some areas of large coastal shark fisheries, indicating some geographic isolation may exist. We examined genetic variation in the control region of mitochondrial DNA and at five nuclear microsatellite loci in bull sharks sampled from the western Atlantic to investigate the degree of population subdivision. The average per sample haplotype and nucleotide diversity in the mtDNA (0.51 ± 0.26 and 0.12% ± 0.12, respectively) and expected heterozygosity (0.84) in the microsatellite loci contrast sharply in having lower and higher values (respectively) relative to many other shark species. Significant structure exists between the Brazilian and all northern populations at the mtDNA control region (pairwise ΦST > 0.8, P < 0.001), but not at the nuclear microsatellite loci. Adjacent northern populations show weak to no genetic differentiation for both markers. These results are congruent with restricted maternal gene flow between populations caused by female site fidelity to nursery areas. We estimate the current effective population size to be around 160,000 and 221,000 individuals for the southern and northern Atlantic populations, respectively. The philopatric habits and the relatively low levels of mtDNA genetic diversity observed in bull sharks must be considered in the conservation of this species. Our results indicate that effective bull shark management strategies will require local, regional, and international attention and cooperation.

Detecting hybridization between willow grouse (Lagopus lagopus) and rock ptarmigan (L. muta) in Central Sweden through Bayesian admixture analyses and mtDNA screening

Willow grouse (L. lagopus) and rock ptarmigan (L. muta) are sibling species with similar phenotypic and life histories that coexist sympatrically in wide areas of their distribution range. These grouse are amongst the most popular game birds in Scandinavia but contrary to other quarry species, no restocking with captive-bred animals has ever been performed. The discovery of two individuals with intermediate plumage features evoked the question of possible hybridization events between both species, an idea that did not seem too unlikely on the basis of habitat overlap. Thus, to assess whether any genetic exchange is occurring, we used different Bayesian-based admixture analyses of multilocus genotypes determined at twelve microsatellite loci. We also obtained mitochondrial COI-sequences from a selected number of individuals to infer the maternal geneflow and potential introgression. The capacity of our panel of microsatellite markers to detect hybridization was verified using assignments of simulated genotypes. We then evaluated the extent of hybridization in an actual sample of 111 individuals collected in a 100-km2 area in the Scandinavian mountain range. An admixed condition was verified in one of the suspected hybrids, that seemed to carry a L. muta genotype with partial L. lagopus introgression. In addition, more than 4% of L. lagopus showed signs of hybridization under the most conservative scenario with respect to discrepancies between population assignment methods. This was unexpected, given that no L. lagopus displayed any apparent intermediate plumage features. Furthermore, interspecific geneflow of mtDNA haplotypes was lower than expected; which suggests that Haldane’s rule might apply for these two grouse species. Hence, plumage identification of hybrid ancestry is not always reliable and might lead to biases in the estimation of hybridization rates. Hybridisation may be expected to increase if the climate gets warmer as the habitat overlap between the species will become more extensive. We discuss whether hybridisation is a threat to the long-term survival of any of the two species.

Genetic diversity and integrity of German wildcat ( Felis silvestris) populations as revealed by microsatellites, allozymes, and mitochondrial DNA sequences

As a consequence of persecution and habitat fragmentation, wildcats ( Felis silvestris silvestris) in Western Europe have experienced a severe reduction in population numbers and sizes. The remaining wildcat populations are considered to be endangered by losses of genetic variability and by hybridisation with free-ranging domestic cats. To investigate genetic diversity within and among wild and domestic cat populations in Germany and to estimate the extent of gene flow between both forms, we analysed a total of 266 individuals. PCR-amplification and sequencing of 322 base pairs of a highly variable part of the mitochondrial control region (HV1) of 244 specimens resulted in 41 haplotypes with 31 polymorphic sites. Additionally, eight microsatellite loci were examined for those 244 cats. Moreover, a total of 46 wildcats and 22 domestic cats could be genotyped for 13 polymorphic out of 31 enzyme loci. Genetic variability in both groups was generally high. Variability in domestic cat populations was higher than in wildcat populations. Almost no differentiation between domestic cat populations could be found (F ST for microsatellites=3%). In contrast, wildcat populations differed significantly from one another (F ST for microsatellites=9.55%) Within the smaller wildcat populations, a reduction of genetic diversity was detectable with regard to the nuclear DNA. Wildcat and domestic cat mitochondrial haplotypes were separated, suggesting a very low level of maternal gene flow between both forms. In microsatellites and to a somewhat lesser extent in allozymes, wildcats and domestic cats showed distinct differentiation, suggesting an only low extent of past hybridisation in certain populations. The microsatellite data set indicated a significantly reduced effective population size (bottleneck) in the recent past for one German wildcat population.

Simultaneous Evaluation of Paternal and Maternal Immigrant Gene Flow and the Implications for the Overall Genetic Composition of Pinus densiflora Dispersed Seeds

When considering the genetic implications of immigrant gene flow, it is important to evaluate both the proportions of immigrant gametes and their genetic composition. We simultaneously investigated paternal and maternal gene flow in dispersed seeds in a natural population of Pinus densiflora located along a ridge. The paternity and maternity of a total of 454 dispersed seeds (in 2004 and 2005) were accurately and separately assigned to 454 candidate adult trees, by analyzing the nuclear DNA of both diploid biparentally derived embryos and haploid maternally derived megagametophytes of the seeds. The relative genetic diversities and differences between within-population and immigrant groups of both paternally and maternally derived gametes (4 groups) that formed the genotypes of the seeds were evaluated. Using 8 microsatellite markers, we found that 64.0-72.6% of paternally derived gametes, and 17.8-20.2% of maternally derived gametes, were from other populations. Principal coordinate analysis showed that the 4 gamete groups tended to be plotted at different locations on the scattergram, indicating that they each have different genetic compositions. Substantial paternal and maternal immigrant gene flow occurred in this population, and therefore, the overall genetic variation of dispersed seeds is enhanced by both paternally and maternally derived immigrant gametes.

Molecular phylogeography and population structure of a mid-elevation montane frog Leptobrachium ailaonicum in a fragmented habitat of southwest China

Leptobrachium ailaonicum is a vulnerable anuran restricted to a patchy distribution associated with small mountain streams surrounded by forested slopes at mid-elevations (approximately 2000-2600m) in the subtropical Mount Wuliang and Mount Ailao ranges in southwest China (Yunnan Province) and northern Vietnam. Given high habitat specificity and lack of suitable habitat in lower elevations between these ranges, we hypothesized limited gene flow between populations throughout its range. We used two mitochondrial genes to construct a phylogeographic pattern within this species in order to test our hypothesis. We also examined whether this phylogeographic pattern is a response to past geological events and/or climatic oscillations. A total of 1989 base pairs were obtained from 81 individuals of nine populations yielding 51 unique haplotypes. Both Bayesian and maximum parsimony phylogenetic analyses revealed four deeply divergent and reciprocally monophyletic mtDNA lineages that approximately correspond to four geographical regions separated by deep river valleys. These results suggest a long history of allopatric separation by vicariance. The distinct geographic distributions of four major clades and the estimated divergence time suggest spatial and temporal separations that coincide with climatic and paleogeographic changes following the orogeny and uplift of Mount Ailao during the late Miocene to mid Pliocene in southwest China. At the southern distribution, the presence of two sympatric yet differentiated clades in two areas are interpreted as a result of secondary contact between previously allopatric populations during cooler Pleistocene glacial cycles. Analysis of molecular variance indicates that most of the observed genetic variation occurs among the four regions implying long-term interruption of maternal gene flow, suggesting that L. ailaonicum may represent more than one distinct species and should at least be separated into four management units corresponding to these four geographic lineages for conservation.

Genetic and Demographic Implications of the Bantu Expansion: Insights from Human Paternal Lineages

The expansion of Bantu languages, which started around 5,000 years before present in west/central Africa and spread all throughout sub-Saharan Africa, may represent one of the major and most rapid demographic movements in the history of the human species. Although the genetic footprints of this expansion have been unmasked through the analyses of the maternally inherited mitochondrial DNA lineages, information on the genetic impact of this massive movement and on the genetic composition of pre-Bantu populations is still scarce. Here, we analyze an extensive collection of Y-chromosome markers--41 single nucleotide polymorphisms and 18 short tandem repeats--in 883 individuals from 22 Bantu-speaking agriculturalist populations and 3 Pygmy hunter-gatherer populations from Gabon and Cameroon. Our data reveal a recent origin for most paternal lineages in west Central African populations most likely resulting from the expansion of Bantu-speaking farmers that erased the more ancient Y-chromosome diversity found in this area. However, some traces of ancient paternal lineages are observed in these populations, mainly among hunter-gatherers. These results are at odds with those obtained from mtDNA analyses, where high frequencies of ancient maternal lineages are observed, and substantial maternal gene flow from hunter-gatherers to Bantu farmers has been suggested. These differences are most likely explained by sociocultural factors such as patrilocality. We also find the intriguing presence of paternal lineages belonging to Eurasian haplogroup R1b1*, which might represent footprints of demographic expansions in central Africa not directly related to the Bantu expansion.

Gene flow is maintained by polyandry and male dispersal in the army antEciton burchellii

AbstractThe combination of haplodiploidy, complementary sex determination and eusociality constrains the effective population size (Ne) of social Hymenoptera far more than in any other insect group. Additional limitations onNeoccur in army ants since they have wingless queens and colony fission, both of which are factors causing restricted maternal gene flow and high population viscosity. Therefore, winged army ant males gain a particular significance to ensure dispersal, facilitate gene flow and avoid inbreeding. Based on population genetic analyses with microsatellite markers, we studied a population of the Neotropical army antEciton burchellii, finding a high level of heterozygosity, weak population differentiation and no evidence for inbreeding. Moreover, by using sibship reconstruction analyses, we quantified the actual number of male contributing colonies represented in a queen's mate sample, demonstrating that, through extreme multiple mating, the queens are able to sample the genes of males from up to ten different colonies, usually located within an approximate radius of 1 km. We finally correlated the individual mating success of each male contributing colony with the relative siring success of individual males and found a significant colony‐dependent male fitness component. Our results imply that the dispersal and mating system of these army ants seem to enhance gene flow and minimise the deleterious effects associated with small effective population size.