Population Differentiation Tests Research Articles

Worldwide absence of canonical benzimidazole resistance-associated mutations within β-tubulin genes from Ascaris.

The giant roundworm Ascaris is an intestinal nematode, causing ascariasis by infecting humans and pigs worldwide. Recent estimates suggest that Ascaris infects over half a billion people, with chronic infections leading to reduced growth and cognitive ability. Ascariasis affects innumerable pigs worldwide and is known to reduce production yields via decreased growth and condemnation of livers. The predominant anthelminthic drugs used to treat ascariasis are the benzimidazoles. Benzimidazoles interact with β-tubulins and block their function, and several benzimidazole resistance-associated mutations have been described in the β-tubulins of ruminant nematodes. Recent research on ascarids has shown that these canonical benzimidazole resistance-associated mutations are likely not present in the β-tubulins of Ascaris, Ascaridia or Parascaris, even in phenotypically resistant populations. To further determine the putative absence of key β-tubulin polymorphisms, we screened two β-tubulin isotypes of Ascaris, highly expressed in adult worms. Using adult and egg samples of Ascaris obtained from pigs and humans worldwide, we performed deep amplicon sequencing to look for canonical resistance-associated mutations in Ascaris β-tubulins. Subsequently, we examined these data in closer detail to study the population dynamics of Ascaris and genetic diversity within the two isotypes and tested whether genotypes appeared to partition across human and pig hosts. In the 187 isolates, 69 genotypes were found, made up of eight haplotypes of β-tubulin isotype A and 20 haplotypes of isotype B. Single nucleotide polymorphisms were seen at 14 and 37 positions for β-tubulin isotype A and isotype B, respectively. No evidence of any canonical benzimidazole resistance-associated mutations was found in either human- or pig-derived Ascaris isolates. There was, however, a difference in the genetic diversity of each isotype and distribution of β-tubulin genotypes between human- and pig-derived Ascaris. Statistical tests of population differentiation show significant differences (p < 0.001) between pig- and human-derived worms; however, more diversity was seen between worms from different populations than worms from different hosts. Our work suggests an absence of canonical β-tubulin mutations within Ascaris, but alternative modes of anthelminthic resistance may emerge necessitating continued genetic scrutiny alongside monitoring of drug efficacy.

Genetic diversity and population structure of humpback whales (Megaptera novaeangliae) from Ecuador based on mitochondrial DNA analyses

Information on the genetic characterisation of humpback whales (Megaptera novaeangliae) wintering off Ecuador (Breeding Stock G) is presented. Mitochondrial DNA was extracted and sequenced from 230 skin samples collected between 2002 and 2008 to establish the genetic diversity of this population. From 182 usable samples, 41 different haplotypes were found, eight of which were new and unique. Haplotype diversity (h ± SD) was estimated to be 0.922 ± 0.012 and the nucleotide diversity (π ± SD) 0.019 ± 0.009. A comparison with other areas within the Southeast Pacific (Colombia and Magellan Strait) and the Antarctic Peninsula suggested panmixia within Breeding Stock G, even though significant differentiation was found with Magellan Strait (p &lt; 0.0001 in both FST and ΦST). An additional analysis with the exact test of population differentiation showed significant differences in haplotype frequencies between breeding areas in Ecuador and southern Colombia (p &lt; 0.01), suggesting some level of stratification at breeding grounds as supported by photo-identification studies. The Ecuadorian dataset included haplotypes reported in all three Southern Hemisphere ocean basins indicating recent gene flow within the Southern Hemisphere. The population showed a male-biased sex ratio in adult animals of 2.16:1. Further research and a larger number of samples from breeding areas in the north (Panama and Costa Rica) are required to appropriately assess the extent of structure in this population.

Evaluating population histories in Patagonia and Tierra del Fuego, Chile, using ancient mitochondrial and Y-chromosomal DNA.

This study aims to characterize the genetic histories of ancient hunter-gatherer groups in Fuego-Patagonia (Chile) with distinct Marine, Terrestrial, and Mixed Economy subsistence strategies. Mitochondrial (mtDNA) and Y-chromosome data were generated to test three hypotheses. H0: All individuals were drawn from the same panmictic population; H1: Terrestrial groups first populated the region and gave rise to highly specialized Marine groups by ~7,500 cal BP; or H2: Marine and Terrestrial groups represent distinct ancestral lineages who migrated independently into the region. Ancient DNA was extracted from the teeth of 50 Fuegian-Patagonian individuals dating from 6,895 cal BP to after European arrival, and analyzed alongside other individuals from previous studies. Individuals were assigned to Marine, Terrestrial, and Mixed Economy groups based on archeological context and stable isotope diet inferences, and mtDNA (HVR1/2) and Y-chromosome variation was analyzed. Endogenous aDNA was obtained from 49/50 (98%) individuals. Haplotype diversities, FST comparisons, and exact tests of population differentiation showed that Marine groups were significantly different from Terrestrial groups based on mtDNA (p < 0.05). No statistically significant differences were found between Terrestrial and Mixed Economy groups. Demographic simulations support models in which Marine groups diverged from the others by ~14,000 cal BP. Y-chromosome results showed similar patterns but were not statistically significant due to small sample sizes and allelic dropout. These results support the hypothesis that Marine and Terrestrial economic groups represent distinct ancestral lineages who diverged during the time populations were expanding in the Americas, and may represent independent migrations into Fuego-Patagonia.

Genetic data of 22 autosomal STR loci in Khyber-Pakhtunkhwa, Balochistan and Gilgit Baltistan population of Pakistan using PowerPlex® fusion system

In this study we have provided forensic genetic data of 22 autosomal STRs for Pakhtun, Balochi and Balti population of Pakistan in total of 601 samples. Among these loci, Penta E was found the most discriminatory in all groups and allele 15 was observed most frequent at D22S1045 in Balti whereas in other two populations allele 8 was more common at TPOX. The combined power of discrimination, combined power of exclusion and the combined matching probability was calculated as 0.999999999999999999999999998385, 0.999999988089728 and 1.615 × 10-27 respectively. Based on population differentiation test, significant differences were observed when compared with other populations however, phylogenetic analysis revealed close genetic associations among Pakistani Populations.

Genetic polymorphism and forensic application of 23 autosomal STR loci in the Han population of Panjin City, Liaoning Province, Northeastern China

Background Short tandem repeats (STRs) are consecutive repetition of a repeat motif and widely used in forensic medicine and human genetics because of their high polymorphism. Subjects and methods In the current study, 23 autosomal STR loci were genotyped from 1263 unrelated healthy individuals living in Panjin City, Liaoning Province, Northeastern China using the VeriFilerTM Express PCR Amplification Kit. The population comparison was performed between the Panjin Han population and the other relevant groups to further explore the structure of Panjin Han and its relationship with the other groups. Results The results found 316 alleles across the 23 STRs and the corresponding allelic frequencies ranged from 0.5198 to 0.0004. Except for D3S1358, TPOX, TH01, and D3S1358, all STR loci were highly polymorphic (PIC > 0.7), with the Penta E locus having the highest degree of polymorphism (0.9147). For population comparison, the exact test of population differentiation found that no significant difference was observed between the Panjin Han and the other Han populations, except for Guangdong Han and Jiangxi Han. Conclusion The Panjin Han population showed significant differences with the other ethnic groups in China (Bouyei, Dong, Hui, Miao, Tibetan, and Uygur) and the foreign ethnic groups.

Molecular characterization and forensic relevance of the autosomal STRs for the population of North Indian geographical province Himachal Pradesh, India

Keeping in view the diverse demography of India, present study was undertaken to explore the molecular characterization and forensic relevance of 20 autosomal STRs for the highly diverse population of north Indian state Himachal Pradesh. 724 unrelated individuals from the admixed population of Himachal Pradesh were undertaken for present study and 20 autosomal STRs used to explore genomic diversity of studied population. A total of 270 different alleles along with 13.5 alleles per locus were observed. The allele 8 of the locus TPOX was observed as the most frequent allele. Observed heterozygosity ranged from 0.677 to 0.898, which supported wide range of selection of the unrelated individuals for this study. Combined power of discrimination, power of exclusion, matching probability and paternity index were observed as 1, 0.9999999958, 3.9×10-26 and 2.3×108 respectively, across the studied loci. In the population differentiation test, studied population showed genetic relatedness with Indian population rather than the populations of West, North and North east countries. Present study deciphered the novel autosomal STR data, which could be useful for the forensic application and population genetic studies.

Unrestricted gene flow between two subspecies of translocated brushtail possums (Trichosurus vulpecula) in Aotearoa New Zealand

Two lineages of brushtail possums (Trichosurus vulpecula) were historically introduced to Aotearoa New Zealand, and these two subspecies have different phenotypic forms. Despite over 100 years of potential interbreeding, they appear to retain morphological differences, which may indicate reproductive isolation. We examined this using population samples from a confined landscape and scored each specimen for phenotype using a number of fur colour traits. This resulted in a bimodal trait distribution expected for segregated grey and black lineages. We also sought evidence for genetic partitioning based on spatial and temporal effects. Genetic structure and rates of genetic mixing were determined using seven neutral, species-specific nuclear microsatellite markers and mitochondrial DNA control region sequence. Genotype analyses indicated high levels of variation and mtDNA sequences formed two major haplogroups. Pairwise tests for population differentiation of these markers found no evidence of subdivision, indicating that these brushtail possums behave as a single randomly mating unit. Despite maintenance of two main colour phenotypes with relatively few intermediates, previous inference of assortative mating and anecdotes of distinct races, our data indicate that New Zealand brushtail possums can freely interbreed, and that in some locations they have formed completely mixed populations where neutral genetic markers are unrelated to phenotype. This has implications for effective pest management towards eradication.

Allele frequency data of 15 autosomal STRs in Arain population of Pakistan.

Fifteen autosomal STRs were evaluated using Identifiler plus kit in 121 Arain samples of Pakistan. The highly discriminatory locus was D2S1338 with value of 0.968. Allele 8 at TPOX was the most frequent with value of 0.467. No significant deviations from Hardy-Weinberg equilibrium were seen except D3S1358 and D18S51. Combined power of discrimination, combined power of exclusion, and combined matching probability were obtained as 0.9999999999999999925, 0.99999815, and 7.4897 × -18, respectively. Population differentiation test demonstrated significant differences between Arain and geographically distinct populations.

&lt;strong&gt;&lt;em&gt;Ceratozamia sanchezae&lt;/em&gt; (Zamiaceae): a new cycad species from Chiapas Highlands (Mexico)&lt;/strong&gt;

The taxonomic classification within the Neotropical cycad genus Ceratozamia (Zamiaceae) has been a challenging task because cohorts of morphological variation in association with conspicuous geographic discontinuities that delimit species are not always easy to observe. Ceratozamia robusta is one example. Although previous studies have suggested that C. robusta presents an unusually high morphological variation across populations, this variation remains unquantified. In particular, we noticed that herbarium specimens from populations in the region Los Altos de Chiapas (Chiapas Highlands) that have been considered as C. robusta notably differ from the rest of the typical C. robusta forms by having narrower leaflets and fewer prickles on the petioles. Thus, we asked whether the populations in the Chiapas Highlands correspond to C. robusta as currently circumscribed. We examined the variation of ten leaf and trunk traits of 97 adult plants from six populations of C. robusta. Variation among the ten traits was significantly differentiated across populations, and such variation is correlated with elevation. Pairwise population differentiation tests and linear discriminant analyses clearly separated three groups: 1) populations similar to the neotype of C. robusta occur at mid-elevations in Chiapas, 2) a large C. robusta form occurs at low elevations in Belize, and 3) populations in the Chiapas Highlands that differ from both. The latter have fewer leaves and leaflets, shorter rachis, arched leaves in mature plants, petioles sparsely armed with thin prickles, smaller male cones, and juvenile forms more similar to those of the C. miqueliana species complex. These results suggest that the populations from the Chiapas Highlands represent a new taxon, here described as Ceratozamia sanchezae. This study highlights the importance of quantifying morphological variation across cycad populations to identify the species delimitation in complex groups.

Population genetic data for 21 autosomal STR loci in the Azerbaijani population using the Globalfiler™ kit.

The Republic of Azerbaijan is located in the southern Caucasus mountains, a region which is linguistically and ethnically diverse. We report allele frequency data for 21 autosomal loci from the Globalfiler™ kit in the Azerbaijani population using 467 individuals from Baku. Exact tests for Hardy Weinberg Equilibrium and Linkage Equilibrium were conducted, and all forensic parameters were estimated. High levels of Expected Heterozygosity HE were seen, with a minimum of 0.637 for TPOX and a maximum of 0.949 for SE33. Polymorphism Information Content (PIC) values for all STR loci were high, ranging from 0.587 for TPOX to 0.947 for SE33. Matching probability (MP) estimates ranged from 0.006 for SE33 to 0.178 for TPOX. Power of Discrimination (PD) values for most of the tested loci (17/21) were ≥ 0.9. The Combined Matching Probability (CMP) and the Combined Power of Discrimination (CPD) for all 21 loci were 7.84 × 10-27 and 1.0 respectively. Exact tests for population differentiation using all available Globalfiler™ datasets from across Europe and Asia reveal a general trend of higher differentiation with increasing geographical separation, but there is a need for additional population data from neighboring regions of Azerbaijan.

Genomic diversity at 22 STR loci (extended CODIS STR) in the population of Rajasthan, India

This study presents genetic diversity at 22 autosomal STR loci (extended CODIS STR) in the population of Rajasthan. It provides an allelic database of this population for the purpose of forensic inference. 595 unrelated healthy individuals residing in the state were randomly selected from the routine casework of the laboratory. Compliance of ethical standards was ensured during the collection of blood samples. The allele 15 of locus D22S1045 was found to be the most frequent allele among all the studied genetic markers. The matching probability was found to be 1.80 × 10−26 at all the studied markers. The loci Penta E and TPOX were found to be highest and least forensic importance respectively, among all the studied loci. The heterozygosity ranged from 0.711 for locus TPOX to 0.926 for the locus Penta E. The discrimination and exclusion power were found as 1 and 0.999999998292 respectively at all the studied loci. Overall, the highest polymorphism was observed 0.907 for locus Penta E among the studied markers in the population of Rajasthan. In population differentiation test, the population of Rajasthan showed a greater genetic affinity with north-western and central Indian populations than southern and eastern Indian, as well as East Asian populations.

LEA 3: Factor models in population genetics and ecological genomics with R.

A major objective of evolutionary biology is to understand the processes by which organisms have adapted to various environments, and to predict the response of organisms to new or future conditions. The availability of large genomic and environmental data sets provides an opportunity to address those questions, and the R package LEA has been introduced to facilitate population and ecological genomic analyses in this context. By using latent factor models, the program computes ancestry coefficients from population genetic data and performs genotype-environment association analyses with correction for unobserved confounding variables. In this study, we present new functionalities of LEA, which include imputation of missing genotypes, fast algorithms for latent factor mixed models using multivariate predictors for genotype-environment association studies, population differentiation tests for admixed or continuous populations, and estimation of genetic offset based on climate models. The new functionalities are implemented in version 3.1 and higher releases of the package. Using simulated and real data sets, our study provides evaluations and examples of applications, outlining important practical considerations when analysing ecological genomic data in R.

Genetic Diversity of South African Indigenous Goat Population from Four Provinces Using Genome-Wide SNP Data

Genome-wide assessments of the genetic landscape of Farm Animal Genetic Resources (FAnGR) are key to developing sustainable breed improvements. Understanding the FAnGR adaptation to different environments and supporting their conservation programs from community initiative to national policymakers is very important. The objective of the study was to investigate the genetic diversity and population structure of communal indigenous goat populations from four provinces of South Africa. Communal indigenous goat populations from the Free State (FS) (n = 24), Gauteng (GP) (n = 28), Limpopo (LP) (n = 30), and North West (NW) (n = 35) provinces were genotyped using the Illumina Goats SNP50 BeadChip. An Illumina Goats SNP50 BeadChip data from commercial meat-type breeds: Boer (n = 33), Kalahari Red (n = 40), and Savanna (n = 31) was used in this study as reference populations. The Ho revealed that the genetic diversity of a population ranged between 0.39 ± 0.11 Ho in LP to 0.42 ± 0.09 Ho in NW. Analysis of molecular variance revealed variations of 3.39% (p &lt; 0.0001) and 90.64% among and within populations, respectively. The first two Principal Component Analyses (PCAs) revealed a unique Limpopo population separated from GP, FS, and NW communal indigenous goat populations with high levels of admixture with commercial goat populations. There were unique populations of Kalahari and Savanna that were observed and admixed individuals. Marker FST (Limpopo versus commercial goat populations) revealed 442 outlier single nucleotide polymorphisms (SNPs) across all chromosomes, and the SNP with the highest FST value (FST = 0.72; chromosome 8) was located on the UHRF2 gene. Population differentiation tests (PCAdapt) revealed PC2 as optimal and five outlier SNPs were detected on chromosomes 10, 15, 20, and 21. The study revealed that the SNPs identified by the first two principal components show high FST values in LP communal goat populations and allowed us to identify candidate genes which can be used in the development of breed selection programs to improve this unique LP population and other communal goat population of FS, GP, and NW, and find genetic factors contributing to the adaptation to harsh environments. Effective management and utilization of South African communal indigenous goat populations is important, and effort should be made to maintain unique genetic resources for conservation.

Extended blood group profiles for Malays, Chinese, and Indians in Peninsular Malaysia

BackgroundBlood group antigens are immunogenic polymorphic molecules presented on the surface of RBCs. This study aimed to determine extended blood group profiles (ABO, Rhesus, Kell, Kidd, Duffy, MNS, Cartwright, Dombrock, Colton, Lutheran, and Vel) in Malays, Chinese, and Indians in Peninsular Malaysia.ResultsHere, ABO Type O, DCCee, MNs, and Fy (a+b−) were the most frequent major blood group phenotypes in all three ethnic groups. Other minor blood group systems distributed differently across these ethnic groups, except for the Kell, Lutheran, Cartwright, and Vel blood group systems, where only K−k+, Lu (8+14), Yt (a+b−), and Vel (+) phenotypes were observed. Exact tests of population differentiation generally showed no significant differences between Malays included in the present study vs. other ethnically similar datasets from previous surveys. However, many significant differences were recorded in comparison between blood group datasets from ethnically unrelated populations (Malays vs. Chinese vs. Indians) especially for Rhesus, Kidd, and Duffy blood group systems. A Principal component analysis (PCA) plot showed that population groups from the Peninsular Malaysia map closely together as compared with population groups from other geographical regions.ConclusionsOverall, our present study has successfully provided an extended blood group profiles for Malays, Chinese, and Indians in Peninsular Malaysia. These new blood group datasets can be used as guidelines for donor recruitment and as reference standards for studying diseases associated with blood group systems.

A paleogenetic perspective of the Sabana de Bogotá (Northern South America) population history over the Holocene (9000–550 cal BP)

On the basis of distinct lines of evidence, detailed reconstructions of the Holocene population history of the Sabana de Bogotá (SB) region, Northern South America, have been performed. Currently, there exist two competing models that support temporal continuity or, alternatively, divergence. Despite recent bioarchaeological and isotopic research that lends support to the population discontinuity model, several discrepancies remain, calling for other kinds of evidences to be explored for a more detailed picture of Holocene biocultural evolution. In this study, 15 new complete mitochondrial genomes obtained from 30 individuals recovered from several archaeological sites spanning from the late Pleistocene (11,950–11,262 cal BP) until the initial late Holocene (2941–2752 cal BP) along with published data (n = 20) from the region dating ~9000–540 cal BP were used to investigate diachronic genetic change. Genetic diversity and distance indices were calculated, and demographic models tested in an approximate Bayesian computation (ABC) framework to evaluate whether patterns of genetic affinities of the SB prehispanic populations support genetic continuity or discontinuity. The results show that mitochondrial genomes of the complete dataset fall within the Native American haplogroups A2, B2, C1b, D1 and D4h3a. Haplotype and nucleotide diversity declined over time with further evidence of genetic drift and remarkable reduction of genetic diversity during the final late Holocene. Inter-population distances and the exact test of population differentiation, as well as demographic simulations show no population differentiation and population continuity over time. Consequently, based on the analyzed data, we cannot reject the genetic continuity in the SB region as a plausible population history scenario. However, the restriction of the analyses to the Hyper Variable Region 1 of the mitochondrial genome, and the very low sample size both constitute significant limitations to infer evolutionary history.

Population-genetic and comparative interpopulation studies of Azerbaijan population based on the 15 autosomal STR markers.

We have investigated 765 unrelated individuals from Azerbaijan using AmpFlSTR® Identifiler® Plus PCR Amplification Kit. For each STR locus basic population-genetic and forensic parameters were determined. The calculated P-values (PHWE) for the accuracy of the Hardy-Weinberg equilibrium (HWE) tests, showed that this parameter had a statistically significant value (PHWE=0.0000) only for the THO1, D18S51 and FGA loci. The values of parameters for the set of 15 STR loci such as CPE, CPD, CTPI and the PP showed that the given set of loci can be confidently used to solve identification problems for the studied population. Multiple population differentiation tests performed between Azerbaijan and other 17 world populations revealed that between Azerbaijan and Iraqi, Iranian, Turkish populations there were no significant differences on all STR loci. Additionally, comparisons of Fischer genetic distance indices (FST) P-values did not reveal any statistically significant difference between Azerbaijan and Iranian populations at P<0.05. However, with South African black population differences at all STR loci were detected. Both tests did not reveal a locus by which our population would differ from all the other compared populations. PCA and PCoA analyzes showed that the Azerbaijani population was grouped with different populations in different quarters, showing a negative and zero correlation, respectively. Regarding the location of the Azerbaijan population, there are some differences between NJ and UPGMA phylogenetic trees. For example, in the NJ tree, Azerbaijan population was grouped with Iranian, but in the UPGMA tree, it was grouped with the Turkish population. Based on Nei's genetic distance between populations the second tree has a more realistic outcome.

An analysis of subspecific variation of the honeybee, Apis mellifera L., in parts of West and Central Africa using microsatellite polymorphism

The variation of two (humid and semiarid) populations of the honeybee, Apis mellifera L., from western Africa, was analysed, using microsatellite polymorphism of nuclear DNA. One worker was sampled from each of 133 colonies collected from 38 localities in Nigeria, Niger, Cameroon and Chad and analysed for 15 loci. A total of 292 different alleles were recorded for the 15 microsatellite loci. All loci were polymorphic and the number of different alleles per locus ranged between 10, in locus At163, and 31, in locus A029, while allelic frequencies ranged from 0.007 to 0.569. The mean number of different alleles per locus was 19.5 ± S.E 1.1. The unbiased expected heterozygosity was 0.861 ± S.E. 0.017 for the combined populations and 0.859 ± S.E. 0.023 and 0.864 ± S.E. 0.026 for the humid and semiarid populations, respectively. The overall FST value, which is a good estimate of genetic differentiation of populations, was very low: 0.007 ± S.E. 0.001 (0.001 - 0.014) and AMOVA revealed that the two populations were not significantly different from each other (p > 0.05). Similarly, Raymond and Rousset’s exact test of population differentiation revealed that the two populations were not significantly differentiated at p = 0.05. Furthermore a Bayesian assignment test did not produce clear grouping of the populations. In a nutshell, according to microsatellite analysis, the honeybees of the area of study belonged to a genetically undifferentiated population.

Genetic Differentiation and Origin of Naturalized Rainbow Trout Populations From Southern Chile, Revealed by the mtDNA Control Region Marker.

Numerous self-sustaining naturalized or introduced populations of rainbow trout (Oncorhynchus mykiss) are widely distributed throughout the freshwaters of southern Chile. In this study, analysis of the mitochondrial DNA control region (CR) marker was conducted to investigate the level of genetic divergence among populations and their phylogenetic relationships with respect to native lineages. This information provided a framework to interpret the genetic structure and origin that was shaped during historical trout introduction efforts. To this end, we analyzed eleven naturalized populations of lakes and rivers from five basins. The CR marker revealed five haplotypes. The overall haplotype (H) and nucleotide (Π) diversities were 0.684 ± 0.030 and 0.00460 ± 0.00012, respectively. Global F ST was 0.169, with several pairwise F ST estimates showing significant differences (P < 0.05). The exact test of population differentiation corroborated this result (P < 0.001). Significant geographic structure was found (P < 0.05), with variations explained primarily by differences within populations (61.65%) and among group basins (20.82%). Maximum likelihood phylogenetic analysis resolved two distinct clades with medium bootstrap support when naturalized populations were aligned in conjunction with reference native lineages. The haplotype network revealed a close association between naturalized populations and four main haplotypes representative of three native ecotypes or lineages from western North America (rainbow trout, steelhead trout and redband trout). These results indicate a genetic population structuring for naturalized rainbow trout from southern Chile and an origin probably represented by multiple lineages sources. Thus, mitochondrial DNA data strongly suggest that stocking of rainbow trout from different origins may have occurred during or after the initial introduction efforts.

Phylogeography of higher Diptera in glacial and postglacial grasslands in western North America

BackgroundPleistocene glaciations have had an important impact on the species distribution and community composition of the North American biota. Species survived these glacial cycles south of the ice sheets and/or in other refugia, such as Beringia. In this study, we assessed, using mitochondrial DNA from three Diptera species, whether flies currently found in Beringian grasslands (1) survived glaciation as disjunct populations in Beringia and in the southern refugium; (2) dispersed northward postglacially from the southern refugium; or (3) arose by a combination of the two. Samples were collected in grasslands in western Canada: Prairies in Alberta and Manitoba; the Peace River region (Alberta); and the southern Yukon Territory. We sequenced two gene regions (658 bp of cytochrome c oxidase subunit I, 510 bp of cytochrome b) from three species of higher Diptera: one with a continuous distribution across grassland regions, and two with disjunct populations between the regions. We used a Bayesian approach to determine population groupings without a priori assumptions and performed analysis of molecular variance (AMOVA) and exact tests of population differentiation (ETPD) to examine their validity. Molecular dating was used to establish divergence times.ResultsTwo geographically structured populations were found for all species: a southern Prairie and Peace River population, and a Yukon population. Although AMOVA did not show significant differentiation between populations, ETPD did. Divergence time between Yukon and southern populations predated the Holocene for two species; the species with an ambiguous divergence time had high haplotype diversity, which could suggest survival in a Beringian refugium.ConclusionsPopulations of Diptera in Yukon grasslands could have persisted in steppe habitats in Beringia through Pleistocene glaciations. Current populations in the region appear to be a mix of Beringian relict populations and, to a lesser extent, postglacial dispersal northward from southern prairie grasslands.

Population Structure of the Red Macroalga Botryocladia occidentalis (Børgesen) Kylin (Rhodymeniaceae, Rhodymeniales) in the Gulf of Mexico Before the Deepwater Horizon Oil Spill

Studies on the population structure of common widespread macroalgae in the Gulf of Mexico (GoMx) are scarce, and this knowledge gap limits our understanding on how disturbances affect the genetic diversity of macroalgae in this basin. The latter is due to the lack of a baseline that can be compared with allele frequency surveys conducted after a major disturbance such as the 2010 Deepwater Horizon oil spill (DWH), which leaked 780,000 m3 of crude oil in the vicinity of highly diverse macroalgal communities. Fortunately, quantitative assessments of the population structure pre-DWH can be accomplished for several macroalgae with dried specimens collected from research cruises conducted before 2010 in the offshore GoMx. Based on three markers (cytochrome c oxidase subunit I, COX II-III intergenic spacer, and the RuBisCO large subunit), this study reconstructed the allele frequencies pre-DWH for a GoMx-widespread macroalga, Botryocladia occidentalis, and revealed the existence of distinct populations in each of three distant regions of the GoMx: Florida Middle Grounds (FL), Campeche Banks (CB), and offshore Louisiana (LA). Population structure was assessed with exact tests of population differentiation and Analyses of Molecular Variance. FL harbored the most differentiated and genetically diverse population due to the presence and abundance of unique haplotypes. Interestingly, FL haplotypes were not closely phylogenetically related to each other and included the most divergent lineages of the entire GoMx; this phylogeographic pattern suggests a strong influence of migrants from the Caribbean on the FL population. Additionally, likelihood ratio tests with a small sample collected post-DWH indicated that the LA population underwent strong changes, showing statistically significant differences before (LA) vs. after (L2) the disaster. Whereas the LA population had affinity to CB, L2 showed a FL haplotype that, before the disaster, had never been reported in LA or CB. Such changes may not be permanent but rather a temporary response to disturbance; also, they may not necessarily be caused by the spilled oil but by other factors associated with the DWH.