Magnitude Of Gene Flow Research Articles

The genetic history of Scandinavia from the Roman Iron Age to the present

We investigate a 2,000-year genetic transect through Scandinavia spanning the Iron Age to the present, based on 48 new and 249 published ancient genomes and genotypes from 16,638 modern individuals. We find regional variation in the timing and magnitude of gene flow from three sources: the eastern Baltic, the British-Irish Isles, and southern Europe. British-Irish ancestry was widespread in Scandinavia from the Viking period, whereas eastern Baltic ancestry is more localized to Gotland and central Sweden. In some regions, a drop in current levels of external ancestry suggests that ancient immigrants contributed proportionately less to the modern Scandinavian gene pool than indicated by the ancestry of genomes from the Viking and Medieval periods. Finally, we show that a north-south genetic cline that characterizes modern Scandinavians is mainly due to the differential levels of Uralic ancestry and that this cline existed in the Viking Age and possibly earlier.

The redlegged earth mite draft genome provides new insights into pesticide resistance evolution and demography in its invasive Australian range.

Genomic data provide valuable insights into pest management issues such as resistance evolution, historical patterns of pest invasions and ongoing population dynamics. We assembled the first reference genome for the redlegged earth mite, Halotydeus destructor (Tucker, 1925), to investigate adaptation to pesticide pressures and demography in its invasive Australian range using whole-genome pool-seq data from regionally distributed populations. Our reference genome comprises 132 autosomal contigs, with a total length of 48.90 Mb. We observed a large complex of ace genes, which has presumably evolved from a long history of organophosphate selection in H. destructor and may contribute towards organophosphate resistance through copy number variation, target-site mutations and structural variants. In the putative ancestral H. destructor ace gene, we identified three target-site mutations (G119S, A201S and F331Y) segregating in organophosphate-resistant populations. Additionally, we identified two new para sodium channel gene mutations (L925I and F1020Y) that may contribute to pyrethroid resistance. Regional structuring observed in population genomic analyses indicates that gene flow in H. destructor does not homogenize populations across large geographic distances. However, our demographic analyses were equivocal on the magnitude of gene flow; the short invasion history of H. destructor makes it difficult to distinguish scenarios of complete isolation vs. ongoing migration. Nonetheless, we identified clear signatures of reduced genetic diversity and smaller inferred effective population sizes in eastern vs. western populations, which is consistent with the stepping-stone invasion pathway of this pest in Australia. These new insights will inform development of diagnostic genetic markers of resistance, further investigation into the multifaceted organophosphate resistance mechanism and predictive modelling of resistance evolution and spread.

Acoustic differentiation and behavioral response reveals cryptic species within Buergeria treefrogs (Anura, Rhacophoridae) from Taiwan.

Buergeria japonica is a widely distributed treefrog occurring from Ryukyu Archipelago to Taiwan. Across this wide distributional range, we combined molecular, acoustic, morphological, and behavioral characters to clarify the taxonomic status among these insular populations. Genetic differentiation in mitochondrial sequences indicated an over 16% divergence among two deeply divergent clades: Japanese clade distributes in Ryukyu Archipelago and northwestern drainages of Taiwan, while Taiwanese clade distributes in the remaining drainages on Taiwan. The Taiwanese clade can be distinguished from the nominative species not only by molecular and morphological differences, but also distinguishable by considerable acoustic differentiation, which is extraordinarily noticeable for an additional type of long call that never recorded from Japanese clade. The two clades form a parapatric distribution pattern with narrow contact zones both in western and eastern Taiwan. Playback experiments indicated that male frogs show significantly stronger defensiveness against conspecific calls rather than heterospecific calls, indicating that these signals play a crucial role in species recognition. Here we describe the Taiwanese clade as a new species; the behavioral response and the magnitude of gene flow across their contact zones are especially worth for detailed studies.

Divergence and gene flow between the East Sea and the Southeast Atlantic populations of North Pacific light fish Maurolicus japonicus Ishikawa

In the present study, we examined the divergence time and the magnitude of gene flow between two distantly separated populations of North Pacific light fish Maurolicus japonicus, one in the southern part of the East Sea (off Korea) and the other in the Southeast Atlantic Ocean (off Namibia). The mitochondrial 16SrDNA sequences (524 base pairs) obtained from the two populations were analyzed using the isolation with migration (IM) coalescent method as well as the conventional F ST statistic and a phylogeographic method. A significant nonzero F ST value (0.176, P<0.05) indicated genetic differentiation between the two populations. The low level of nucleotide diversity compared to the moderately high level of haplotype diversity implied that the populations have experienced a bottleneck followed by rapid growth in both populations. IM analysis suggested that these two populations most likely split approximately 500–800 K years ago during the Pleistocene climatic oscillations and that gene flow has occurred unidirectionally from the Southeast Atlantic population to the East Sea population. Nested clade phylogeographic analysis supports restricted gene flow between the two populations.

Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow

Incomplete lineage sorting has been documented across a diverse set of taxa ranging from song birds to conifers. Such patterns are expected theoretically for species characterized by certain life history characteristics (e.g. long generation times) and those influenced by certain historical demographic events (e.g. recent divergences). A number of methods to estimate the underlying species phylogeny from a set of gene trees have been proposed and shown to be effective when incomplete lineage sorting has occurred. The further effects of gene flow on those methods, however, remain to be investigated. Here, we focus on the performance of three methods of species tree inference, ESP-COAL, minimizing deep coalescence (MDC), and concatenation, when incomplete lineage sorting and gene flow jointly confound the relationship between gene and species trees. Performance was investigated using Monte Carlo coalescent simulations under four models ( n-island, stepping stone, parapatric, and allopatric) and three magnitudes of gene flow ( N em = 0.01, 0.10, 1.00). Although results varied by the model and magnitude of gene flow, methods incorporating aspects of the coalescent process (ESP-COAL and MDC) performed well, with probabilities of identifying the correct species tree topology typically increasing to greater than 0.75 when five more loci are sampled. The only exceptions to that pattern included gene flow at moderate to high magnitudes under the n-island and stepping stone models. Concatenation performs poorly relative to the other methods. We extend these results to a discussion of the importance of species and population phylogenies to the fields of molecular systematics and phylogeography using an empirical example from Rhododendron.

Genetic structure and gene flow in French populations of two Ostrinia taxa: host races or sibling species?

Most models of ecological speciation concern phytophagous insects in which speciation is thought to be driven by host shifts and subsequent adaptations of populations. Despite the ever-increasing number of studies, the current evolutionary status of most models remains incompletely resolved, as estimates of gene flow between taxa remain extremely rare. We studied the population genetics of two taxa of the Ostrinia genus--one feeding mainly on maize and the other on mugwort and hop--occurring in sympatry throughout France. The actual level of divergence of these taxa was unknown because the genetic structure of populations had been investigated over a limited geographical area and the magnitude of gene flow between populations had not been estimated. We used 11 microsatellite markers to investigate the genetic structure of populations throughout France and the extent of gene flow between the two Ostrinia taxa at several sites at which they are sympatric. We observed clear genetic differentiation between most populations collected on the typical respective hosts of each taxon. However, populations displaying intermediate allelic frequencies were found on hop plants in southern France. Individual assignments revealed that this result could be accounted for by the presence of both taxa on the same host. Gene flow, estimated by determining the proportion of hybrids detected, was low: probably<1% per generation, regardless of site. This indicates that the two Ostrinia taxa have reached a high level of genetic divergence and should be considered sibling species rather than host races.

Reply from J.L. Bossart and D. Pashley Prowell

We thank Bohonak et al. for the opportunity to expand upon our perspective of gene flow estimates[1xBossart, J.L. and Prowell, D.P. Trends Ecol. Evol. 1998; 13: 202–206Abstract | Full Text PDF | PubMed | Scopus (375)See all References][1]. We are comfortable with our portrayal of the state of this field based on data from Evolution. Evolution was selected because it has a long history as a top journal focusing on empirically based population genetics, has a vast readership and high citation rates. Molecular Ecology, however, is a new, more specialized and less available journal.We agree that most indirect studies of gene flow report data for multiple loci and many use resampling techniques or regression to conduct sensitivity analyses. The issue is whether these are informative comparisons. For example, have estimates averaged over loci advanced our understanding of gene frequency evolution when estimates among loci vary, not uncommonly, by orders of magnitude[2xTempleton, A.R. Mol. Ecol. 1998; 7: 381–398CrossRef | PubMed | Scopus (898)See all References][2]?Our perspective acknowledged problems associated with direct measures of dispersal. Like others[3xSlatkin, M. Annu. Rev. Ecol. Syst. 1985; 16: 393–430CrossRefSee all References][3], however, we emphasized the essential information these estimates provide. Correlational approaches between Fst and life history traits to assess accuracy of genetic methods, as advocated by Bohonak et al., are statistically weak and confounded by evolutionary history—for example, higher Fst values in sessile versus vagile organisms may reflect vicariant events.Application of conventional indirect methods to address ecological questions is inappropriate for two reasons. First, there is no temporal reference point. Do data reveal processes operating over ten years, 100 years, 1000 years or 10 000 years? Second, Nm changes only trivially between Nm=2 and Nm=infinity, so Nm=2 is virtually indistinguishable from Nm=2000 (Ref. [2xTempleton, A.R. Mol. Ecol. 1998; 7: 381–398CrossRef | PubMed | Scopus (898)See all References][2]). Thus, conventional approaches have insufficient power to address relative rates of gene flow among populations impinged upon by human activities, metapopulation dynamics, trophic interactions or relative magnitude of gene flow versus selection.Our overall conclusion that indirect methods `provide a useful starting point'[1xBossart, J.L. and Prowell, D.P. Trends Ecol. Evol. 1998; 13: 202–206Abstract | Full Text PDF | PubMed | Scopus (375)See all References][1]was mirrored by Bohonak et al. in their statement that indirect methods `provide a valuable first approximation'. We part company, however, on the widespread use of new analytical models, as our review validated. As this changes, the field will advance.

Gene Flow and Diversity at Allozyme Loci in the Twospotted Lady Beetle (Coleoptera: Coccinellidae)

High levels of genetic variation in biological control agents are thought to be necessary to ensure their successful establishment and geographical spread. Gene diversity was studied in F2 twospotted lady beetle, Adalia bipunctata (L.), descended from specimens collected in Uzbekistan and from beetles collected in Oregon, Iowa, and Lake Michigan at Chicago, IL. Twenty-four of 39 resolved putative loci were polymorphic and the mean observed heterozygosity was 22.7 ± 4.4% at the polymorphic loci. The average expected heterozygosity was 24.7 ± 4.9% at the polymorphic loci and 15.2 ± 3.3% at all loci. The mean number of alleles at the 39 loci was 1.9 ± 1.0, and the mean effective number of alleles was 1.3 ± 0.5. These are substantial levels of diversity. Significant departures from random mating were detected within ( FIS = 0.068 ± 0.042) and among ( FST = 0.070 ± 0.012) the North American populations but matings were random within populations when problematic loci were excluded. Analysis of gene frequencies at 5 loci in 4 British and a French population showed the same magnitude of gene flow as the 3 North American populations. The fixation index between Iowa and Uzbekistan ladybirds was FST = 0.428 ± 0.128. Our data do not support an Old World origin for North American A. bipunctata in historical times.

EVIDENCE FOR RESTRICTED GENE FLOW IN THE VIVIPAROUS CORAL SERIATOPORA HYSTRIX ON AUSTRALIA'S GREAT BARRIER REEF.

Viviparous, branching corals such as Seriatopora hystrix are expected to generate most recruits through asexual reproduction (fission or fragmentation) but are expected to use sexual reproduction to produce widely dispersed colonists. In this study, allozyme electrophoresis was used to test for variation in the relative contributions of sexual and asexual reproduction to recruitment and to assess the apparent scale of larval dispersal (gene flow) in the central Great Barrier Reef. Fifty-seven collections (within ≤ 25 m2 ) of fragments from sets of approximately 40 colonies were made (where possible) within each of five habitats on each of 12 reefs. These reefs, within the central region of the Great Barrier Reef, were separated by up to 90 km and included one inner-shelf continental island and groups of seven midshelf reefs and four outer-shelf reefs. Most collections contained a high level of multilocus genotypic diversity and hence showed little evidence of recruitment through fragmentation, although the majority of collections displayed large and consistent deficits of heterozygotes. Allele frequencies varied greatly among collections (FST = 0.43), and this variation was sufficient to explain two-thirds of observed deficiencies of heterozygotes via a Wahlund effect. A hierarchical assessment of FST values revealed that 45% of allelic variation occurred among reefs (FST = 0.20), and only 16% of variation within reefs was explained by variation among five major habitat types (FST = 0.05). A relatively small component of the total variation among samples was attributable to across-shelf variation among the groups of middle- and outer-shelf reefs (FST = 0.03); however, the outer-shelf reefs form a single UPGMA cluster separate from all but 4 of the other 43 collections. These data imply that widespread dispersal does occur but that the direction or magnitude of gene flow may be influenced by the along-shelf movement of major ocean currents and weather-dependent currents on or near reefs. Each reef, therefore, forms a partially isolated and highly subdivided population.