High FST Values Research Articles

Phylogeography of a good Caribbean disperser: Argiope argentata (Araneae, Araneidae) and a new 'cryptic' species from Cuba.

The Caribbean islands harbor rich biodiversity with high levels of single island endemism. Stretches of ocean between islands represent significant barriers to gene-flow. Yet some native species are widespread, indicating dispersal across oceans, even in wingless organisms like spiders. Argiope argentata (Fabricius, 1775) is a large, charismatic, and widespread species of orb-weaving spider ranging from the United States to Argentina and is well known to balloon. Here we explore the phylogeography of Argiope argentata in the Caribbean as a part of the multi-lineage CarBio project, through mtDNA haplotype and multi-locus phylogenetic analyses. The history of the Argiope argentata lineage in the Caribbean goes back 3-5 million years and is characterized by multiple dispersal events and isolation-by-distance. We find a highly genetically distinct lineage on Cuba which we describe as Argiope butchko sp. n. While the argentata lineage seems to readily balloon shorter distances, stretches of ocean still act as filters for among-island gene-flow as evidenced by distinct haplotypes on the more isolated islands, high FST values, and strong correlation between intraspecific (but not interspecific) genetic and geographic distances. The new species described here is clearly genetically diagnosable, but morphologically cryptic, at least with reference to the genitalia that typically diagnose spider species. Our results are consistent with the intermediate dispersal model suggesting that good dispersers, such as our study species, limit the effect of oceanic barriers and thus diversification and endemism.

Genetic Diversity in Apple Fruit Moth Indicate Different Clusters in the Two Most Important Apple Growing Regions of Norway

The apple fruit moth (Argyresthia conjugella (A. conjugella)) in Norway was first identified as a pest in apple production in 1899. We here report the first genetic analysis of A. conjugella using molecular markers. Amplified fragment length polymorphism (AFLP) analysis was applied to 95 individuals from six different locations in the two most important apple-growing regions of Norway. Five AFLP primer combinations gave 410 clear polymorphic bands that distinguished all the individuals. Further genetic analysis using the Dice coefficient, Principal Coordinate analysis (PCO) and Bayesian analyses suggested clustering of the individuals into two main groups showing substantial genetic distance. Analysis of molecular variance (AMOVA) revealed greater variation among populations (77.94%) than within populations (22.06%) and significant and high FST values were determined between the two major regions (Distance = 230 km, FST = 0.780). AFLP analysis revealed low to moderate genetic diversity in our population sample from Norway (Average: 0.31 expected heterozygosity). The positive significant correlation between the geographic and the molecular data (r2 = 0.6700) indicate that genetic differences between the two major regions may be due to geographical barriers such as high mountain plateaus (Hardangervidda) in addition to isolation by distance (IBD).

Balancing selection contributed to domestication of autopolyploid sugarcane (Saccharum officinarum L.)

Sugarcane was domesticated in New Guinea about 10,000 years ago, and the domesticated species Saccharum officinarum is autooctoploid. For diploid domesticated crops, genetic diversity is reduced for those genes controlling favorable traits. However, the domestication traits in sugarcane such as sugar content and biomass yield are controlled by multiple genes with multiple alleles. A genomics approach to identify genes involved in the transition from wild to domesticated may provide useful insight into complex polyploid traits such as sucrose accumulation. Fifteen accessions each of domesticated S. officinarum and the wild species S. robustum and eighteen accessions of S. spontaneum were used for sequencing of leaf and stalk transcriptomes. We found high allelic diversity among genes expressed in the stalk tissues where the domesticated S. officinarum (Fis = 0.69) surprisingly has higher allele diversity than its wild relative S. spontaneum (Fis = 0.41). However, there were no SNP loci with extremely high FST values despite the observed higher average FST among the three species, indicative of the action of balancing selection. This is corroborated by nucleotide diversity and site frequency spectrum (SFS) patterns that show that majority of expressed genes in S. officinarum have comparable per-site heterozygosity to the wild species. These candidate domestication genes, bearing signatures of balancing selection and excess singleton SNPs in S. officinarum, perturbs pathways involved in sucrose and starch metabolism.

Population genetic structure and geographic differentiation in butter catfish, Ompok bimaculatus, from Indian waters inferred by cytochrome b mitochondrial gene

Documentation of genetic differentiation among the populations of a species can provide useful information that has roles in conservation, breeding, and management plans. In the present study, we examined the genetic structure and phylogenetic relationships among the 149 individuals of Ompok bimaculatus belonging to 24 populations, collected from Indian waters, using cytochrome b gene. The combined analyses of data suggested that the Indian O. bimaculatus consist of three distinct mtDNA lineages with star-like haplotypes network, which exhibited high genetic variation and haplotypic diversity. Analysis of molecular variance indicated that most of the observed genetic variation was found among the populations suggesting restricted gene flow. Long-term interruption of gene flow was also evidenced by high overall Fst values (0.82367) that could be favored by the discontinuous distributions of the lineages.

Genetic Population Structure of Macridiscus multifarius (Mollusca: Bivalvia) on the Basis of Mitochondrial Markers: Strong Population Structure in a Species with a Short Planktonic Larval Stage.

The clam Macridiscus multifarius with a planktonic larval stage of about 10 days is an ecologically and economically important species in the coastal regions of China. In this study, 3 mt-DNA markers (COI, 12S rRNA, and ND1) were used to investigate the population structure and demography of wild M. multifarius populations in 3 coastal localities of the East China Sea (ZS and ZP populations) and Beibu Gulf in the South China Sea (BH population). Sequences of 685 bp in COI, 350 bp in 12S rRNA, and 496 bp in ND1 were determined. High level and significant F ST values were obtained among the different localities on the basis of either COI (F ST = 0.100–0.444, p < 0.05) or 12S rRNA (F ST = 0.199–0.742, p < 0.05) gene, indicating a high degree of genetic differentiation among the populations. F ST values were significant but weak for the ND1 gene because it is highly conservative. The median-joining network suggested an obvious genetic differentiation between ZS and BH populations, and the finding is consistent with the results of our demographic analyses using the unweighted pair group method with arithmetic mean. Our study unraveled the extant population genetic structure of M. multifarius and explained the strong population structure of a species with a short planktonic larval stage species; this information could be useful for fishery management measures, including artificial breeding and conservation.

Quantifying polymorphism and divergence from epigenetic data: a framework for inferring the action of selection.

Epigenetic modifications are alterations that regulate gene expression without modifying the underlying DNA sequence. DNA methylation and histone modifications, for example, are capable of spatial and temporal regulation of expression—with several studies demonstrating that these epigenetic marks are heritable. Thus, like DNA sequence, epigenetic marks are capable of storing information and passing it from one generation to the next. Because the epigenome is dynamic and epigenetic modifications can respond to external environmental stimuli, such changes may play an important role in adaptive evolution. While recent studies provide strong evidence for species-specific signatures of epigenetic marks, little is known about the mechanisms by which such modifications evolve. In order to address this question, we analyze the genome wide distribution of an epigenetic histone mark (H3K4me3) in prefrontal cortex neurons of humans, chimps and rhesus macaques. We develop a novel statistical framework to quantify within- and between-species variation in histone methylation patterns, using an ANOVA-based method and defining an FST -like measure for epigenetics (termed epi- FST), in order to develop a deeper understanding of the evolutionary pressures acting on epigenetic variation. Results demonstrate that genes with high epigenetic FST values are indeed significantly overrepresented among genes that are differentially expressed between species, and we observe only a weak correlation with SNP density.

Phylogeographical Structure in Mitochondrial DNA of Legume Pod Borer (Maruca vitrata) Population in Tropical Asia and Sub-Saharan Africa.

This study was undertaken to assess the genetic diversity and host plant races of M. vitrata population in South and Southeast Asia and sub-Saharan Africa. The cytochrome c oxidase subunit 1 (cox1) gene was used to understand the phylogenetic relationship of geographically different M. vitrata population, but previous studies did not include population from Southeast Asia, the probable center of origin for Maruca, and from east Africa. Extensive sampling was done from different host plant species in target countries. Reference populations from Oceania and Latin America were used. An amplicon of 658 bp was produced by polymerase chain reaction, and 64 haplotypes were identified in 686 M. vitrata individuals. Phylogenetic analysis showed no difference among the M. vitrata population from different host plants. However, the results suggested that M. vitrata has formed two putative subspecies (which cannot be differentiated based on morphological characters) in Asia and sub-Saharan Africa, as indicated by the high pairwise FST values (0.44–0.85). The extremely high FST values (≥0.93) of Maruca population in Latin America and Oceania compared to Asian and African population seem to indicate a different species. On the continental or larger geographical region basis, the genetic differentiation is significantly correlated with the geographical distance. In addition, two putative species of Maruca, including M. vitrata occur in Australia, Indonesia and Papua New Guinea. The negative Tajima’s D and Fu’s FS values showed the recent demographic expansion of Maruca population. The haplotype network and Automatic Barcode Gap Discovery analyses confirmed the results of phylogenetic analysis. Thus, this study confirmed the presence of three putative Maruca species, including one in Latin America, one in Oceania (including Indonesia) and M. vitrata in Asia, Africa and Oceania. Hence, the genetic differences in Maruca population should be carefully considered while designing the pest management strategies in different regions.

A genetic analysis of taoyuan pig and its phylogenetic relationship to eurasian pig breeds.

Taoyuan pig is a native Taiwan breed. According to the historical record, the breed was first introduced to Taiwan from Guangdong province, Southern China, around 1877. The breed played an important role in Taiwan’s early swine industry. It was classified as an indigenous breed in 1986. After 1987, a conserved population of Taoyuan pig was collected and reared in isolation. In this study, mitochondrial DNA sequences and 18 microsatellite markers were used to investigate maternal lineage and genetic diversity within the Taoyuan pig population. Population differentiation among Taoyuan, Asian type, and European type pig breeds was also evaluated using differentiation indices. Only one D-loop haplotype of the Taoyuan pig was found. It clustered with Lower Changjiang River Basin and Central China Type pig breeds. Based on the polymorphism of microsatellite markers, a positive fixation index value (FIS) indicates that the conserved Taoyuan population suffers from inbreeding. In addition, high FST values (>0.2105) were obtained, revealing high differentiation among these breeds. Non-metric multi-dimensional scaling showed a clear geometric structure among 7 breeds. Together these results indicate that maternally Taoyuan pig originated in the Lower Changjiang River Basin and Central China; however, since being introduced to Taiwan differentiation has occurred. In addition, Taoyuan pig has lost genetic diversity in both its mitochondrial and nuclear genomes.

The effects of purifying selection on patterns of genetic differentiation between Drosophila melanogaster populations.

Using the data provided by the Drosophila Population Genomics Project, we investigate factors that affect the genetic differentiation between Rwandan and French populations of D. melanogaster. By examining within-population polymorphisms, we show that sites in long introns (especially those >2000 bp) have significantly lower π (nucleotide diversity) and more low-frequency variants (as measured by Tajima's D, minor allele frequencies, and prevalence of variants that are private to one of the two populations) than short introns, suggesting a positive relationship between intron length and selective constraint. A similar analysis of protein-coding polymorphisms shows that 0-fold (degenerate) sites in more conserved genes are under stronger purifying selection than those in less conserved genes. There is limited evidence that selection on codon bias has an effect on differentiation (as measured by FST) at 4-fold (degenerate) sites, and 4-fold sites and sites in 8–30 bp of short introns ⩽65 bp have comparable FST values. Consistent with the expected effect of purifying selection, sites in long introns and 0-fold sites in conserved genes are less differentiated than those in short introns and less conserved genes, respectively. Genes in non-crossover regions (for example, the fourth chromosome) have very high FST values at both 0-fold and 4-fold degenerate sites, which is probably because of the large reduction in within-population diversity caused by tight linkage between many selected sites. Our analyses also reveal subtle statistical properties of FST, which arise when information from multiple single nucleotide polymorphisms is combined and can lead to the masking of important signals of selection.

Cepaea nemoralis (L.) in Göteborg, S.W. Sweden: variation in a recent urban invader

Although present since the mid 19th century, the introduced snail species Cepaea nemoralis has spread extensively in Goteborg, mainly in the last two decades. Early samples show the predominance of yellow-shelled morphs, but in modern populations pink shells predominate. There is great variation in morph frequencies among modern populations with high values of FST, and with no relationships to habitat. The patterns shown resemble those seen in Sheffield (UK), a city also colonised over a similar time period, but differ from those seen in regions where the species has been established for much longer. The combination of early and recent records suggests not only that founder effects play a large part in determining morph frequencies, but that present populations derive from multiple colonisations from different sources. key woRDs: Cepaea nemoralis, polymorphism, invasion, Goteborg

Brazil nuts are subject to infection with B and G aflatoxin-producing fungus, Aspergillus pseudonomius

The exploitation of the Brazil nut is one of the most important activities of the extractive communities of the Amazon rainforest. However, its commercialization can be affected by the presence of aflatoxins produced by fungi, namely Aspergillus section Flavi. In the present study, we investigated a collection of Aspergillus nomius strains isolated from Brazil nuts using different approaches, including morphological characters, RAPD and AFLP profiles, partial β-tubulin and calmodulin nucleotide sequences, aflatoxin patterns, as well as tolerance to low water activity in cultured media. Results showed that most of the isolates do belong to A. nomius species, but a few were re-identified as Aspergillus pseudonomius, a very recently described species. The results of the analyses of molecular variance, as well as the high pairwise FST values between A. nomius and A. pseudonomius suggested the isolation between these two species and the inexistence of gene flow. Fixed interspecific nucleotide polymorphisms at β-tubulin and calmodulin loci are presented. All A. pseudonomius strains analyzed produced aflatoxins AFB1, AFB2, AFG1 and AFG2. This study contains the first-ever report on the occurrence in Brazil nuts of A. pseudonomius. The G-type aflatoxins and the mycotoxin tenuazonic acid are reported here for the first time in A. pseudonomius.

Population genetics of forest type of Trypanosoma congolense circulating in Glossina palpalis palpalis of Fontem in the South-West region of Cameroon.

BackgroundGenetic variation of microsatellite loci is a widely used method for the analysis of population genetic structure of several organisms. To improve our knowledge on the population genetics of trypanosomes, Trypanosoma congolense forest and savannah types were identified in the mid-guts of Glossina palpalis palpalis caught in five villages of Fontem in the South-West region of Cameroon. From the positive samples of Trypanosoma congolense forest, the genetic diversity and the population genetic structure of these parasites were evaluated.MethodFor this study, pyramidal traps were set up during three entomological surveys and 3347 tsetse flies were collected, dissected and 1903 midguts collected. DNA was extracted from midguts and specific primers were used to identify Trypanosoma congolense forest and savannah. All Trypanosoma congolense forest positive samples were characterized with seven microsatellite markers.ResultsMicroscopic examination revealed 25 (1.31%) mid-gut infections with trypanosomes while the PCR method identified 120 (6.3%) infections due to Trypanosoma congolense: 94 (78.33%) Trypanosoma congolense forest and 28 (21.77%) Trypanosoma congolense savannah. The trypanosome infection rates varied significantly between villages and years of capture. Menji recorded the highest infection rate (15.11%); and samples captured in 2009 were more infected (14.33%). The microsatellite markers revealed a genetic variability between Trypanosoma congolense forest populations of Fontem villages and 6.38% of mixed infections due to different genotypes of T. congolense “forest type”.ConclusionOur data on the population genetics play in favor of a clonal reproduction of this parasite. The microsatellite markers used here showed a low genetic differentiation and an absence of sub-structuration (FST ≤ 0.0003) between Trypanosoma congolense forest populations of Fontem villages. However, the high FST value (FST ≥ 0.3911) between samples of the Democratic Republic of Congo and those of Fontem villages indicates low migration rates between trypanosomes of these subpopulations.Electronic supplementary materialThe online version of this article (doi:10.1186/1756-3305-7-385) contains supplementary material, which is available to authorized users.

Genetic diversity of local Yunnan chicken breeds and their relationships with Red Junglefowl.

Yunnan is situated in the Southwest China and encompasses regions having high biodiversity, including habitats for several ancestral species of domestic animals such as chicken. Domestic chickens in Yunnan were kept by peoples of varied ethnic and economic backgrounds living in highly varied geographic environments. To identify the genetic background of Yunnan domestic chickens and their relationships with Red Junglefowl, we applied 28 widely used microsatellite DNA markers to genotype 340 birds from 7 chicken breeds and Red Junglefowl indigenous to Yunnan. Among a total of 342 alleles identified, 121 (35.4%) were breed specific, with Red Junglefowl harboring most microsatellite alleles (23). High levels of heterozygosity were observed within populations indicated by a mean unbiased HE value of 0.663, which was higher than the reported for most populations elsewhere. The FIS value of domestic populations ranged from -0.098-0.005, indicating a lack of inbreeding among these populations. A high proportion of significant departures (89) from the 224 HWE tests for each locus in each population reflected an excess of heterozygosity and population substructure. Individual assignment tests, high FST values (0.1757-0.3015), and Nei's DA genetic distances (0.4232-0.6950) indicated clear differentiation among these populations. These observations, along with the close genetic distance between indigenous domestic populations and Red Junglefowl, were consistent with the primitive and ancestral state of Yunnan indigenous chickens. Protecting the unique variants of these indigenous poultry varieties from contamination with commercial breeds might provide values for improving modern agricultural livestock and breeding programs. Thus, the current study may benefit breeding management and conservation efforts.

Phylogenetic relationships among populations of the Nacobbus aberrans (Nematoda, Pratylenchidae) complex reveal the existence of cryptic species

The plant‐parasitic nematode Nacobbus aberrans sensu lato is an agricultural pest of quarantine importance. Due to the morphometric, physiological and genetic variability observed within the species, there is no agreement on the taxonomy of this nematode. The objective of this study was to analyse the ITS rDNA region and the D2–D3 expansion segments of 28S rDNA in 10 Argentine populations and one from Ecuador and to establish their phylogenetic relationship with other known sequences from South and North America. Phylogenetic trees of the ITS gene showed seven statistically well‐supported clades; the high and significant Fst values obtained among these groups confirmed this partitioning. The Argentine populations here considered were separated into three clades: one comprising a population from the Andean region and two grouping nematodes from lower altitudes. Three other clades were distinguished for South American populations, which included known sequences of individuals from Peru, Bolivia and north of Argentina. The other clade included sequences from Mexico, Ecuador and two Argentine populations of unknown origin. The important degree of genetic divergence observed among Andean populations suggests that the Andes may have played a crucial role in speciation of Nacobbus, which would have originated in this region. Although D2–D3 segments exhibited lower variation, they were useful for establishing phylogenetic relationships among the Argentine populations considered in this work. As there are no other GenBank sequences available for these segments, it was not possible to make comparisons with other populations from South and North America. The considerable genetic differentiation observed in ITS rDNA region among Nacobbus populations showed evidence of cryptic species within the N. aberrans s.l. complex. Integration of morphological and morphometric studies and molecular analyses considering other genes may aid in the identification of species and their phylogenetic relationships within this genus.

Mitochondrial phylogeography of the killifish Aphanius fasciatus (Teleostei, Cyprinodontidae) reveals highly divergent Mediterranean populations

We studied the genetic structure of the Mediterranean killifish Aphanius fasciatus. Analysis of the sequence variation in a 372-bp portion of the mitochondrial control region in 623 fish from 27 sampling sites along the species’ distributional range (Tyrrhenian coast, Sardinia, Sicily, Adriatic coast, Malta, Tunisia, and Greece) yielded 120 distinct haplotypes. Most of the haplotypes are unique, and only 15 % are shared among different populations. The high F ST value (=0.80) suggests a strong population genetic structuring. The phylogenetic analysis based on Bayesian inference, maximum likelihood and maximum parsimony, and the median-joining network show a sharp separation of the Southeastern Sicilian populations (belonging to the Hyblean region) and of the fluvial Tunisian population of Rio Melah from the others. The Adriatic, the Eastern Sicilian, and the Greek populations are well differentiated, while the group of populations from the Central-Western Mediterranean does not show a clear pattern of differentiation. Our findings indicate that the current genetic structuring of A. fasciatus reflects historical geographical patterns occurring within the Mediterranean basin from the Late Miocene to the Pleistocene. The presence of divergent evolutionary entities in the Hyblean region and the Tunisian Rio Melah supports their inclusion as target areas for the conservation of A. fasciatus.

Population Genetic Analysis of the Rice Stem Borer, Chilo suppressalis, in the South China

Genetic variation and patterns of genetic differentiation of the rice stem borer, Chilo suppressalis (Lepidoptera: Pyralidae), from the South China were analyzed using 6 microsatellite markers and two partial mtDNA (cox1 and cox2) regions. All of the 6 microsatellite loci were polymorphic in the studied seven populations. The allelic richness per population ranged between 5.67 and 14.00, and average HE and HO values were 0.6246-0.8329 and 0.2634-0.6061, respectively. As the mitochondrial genome is a single genetic locus, we only present results for the concatenated data set (cox1 plus cox2 gene sequences, 513 bp). The concatenated data showed high level of genetic diversity and there are 23 variable polymorphic sites among the 513 sites in concatenated data. Nearly all of (20 of 21) pairwise FST comparisons among populations showed genetic differentiation with moderate to high pairwise FST values based on microsatellite markers. However, for the mtDNA data, most of the seven populations did not show significant differentiation with other populations. The differences of population differentiation obtained with the two different genetic markers could be mainly attributed to the different mutation rates of microsatellite and mtDNA. There was not genetic structure existed in these studied populations based on microsatellite loci and mtDNA data. The analysis based on network, mismatch distribution, Tajima's D and FS indicated that the studied populations were from the recent same ancestor or the same refuge and followed by a sudden demographic expansion condition.

Analysis of Population Substructure in Two Sympatric Populations of Gran Chaco, Argentina

Sub-population structure and intricate kinship dynamics might introduce biases in molecular anthropology studies and could invalidate the efforts to understand diseases in highly admixed populations. In order to clarify the previously observed distribution pattern and morbidity of Chagas disease in Gran Chaco, Argentina, we studied two populations (Wichí and Criollos) recruited following an innovative bio-cultural model considering their complex cultural interactions. By reconstructing the genetic background and the structure of these two culturally different populations, the pattern of admixture, the correspondence between genealogical and genetic relationships, this integrated perspective had the power to validate data and to link the gap usually relying on a singular discipline. Although Wichí and Criollos share the same area, these sympatric populations are differentiated from the genetic point of view as revealed by Non Recombinant Y Chromosome genotyping resulting in significantly high Fst values and in a lower genetic variability in the Wichí population. Surprisingly, the Amerindian and the European components emerged with comparable amounts (20%) among Criollos and Wichí respectively. The detailed analysis of mitochondrial DNA showed that the two populations have as much as 87% of private haplotypes. Moreover, from the maternal perspective, despite a common Amerindian origin, an Andean and an Amazonian component emerged in Criollos and in Wichí respectively. Our approach allowed us to highlight that quite frequently there is a discrepancy between self-reported and genetic kinship. Indeed, if self-reported identity and kinship are usually utilized in population genetics as a reliable proxy for genetic identity and parental relationship, in our model populations appear to be the result not only and not simply of the genetic background but also of complex cultural determinants. This integrated approach paves the way to a rigorous reconstruction of demographic and cultural history as well as of bioancestry and propensity to diseases of Wichí and Criollos.

Abstract 1330: Genetic variation in the vitamin D pathway and risk for colorectal cancer in African Americans.

Abstract Background: Colorectal cancer (CRC) is the third leading cause of cancer-related deaths in both sexes in the United States. There is a large disparity in both CRC incidence and survival between African Americans (AAs) and all other US racial groups. Differences in serum vitamin D levels could contribute to this disparity because vitamin D is thought to protect against CRC and AAs have lower serum vitamin D levels than whites. We hypothesized that genetic variants in vitamin D-related genes are associated with CRC risk in AAs. Methods: To evaluate association with CRC risk, we genotyped 39 putatively functional single nucleotide polymorphisms (SNPs) in vitamin D-related genes (CYP27A1, GC, CYP3A4, CYP2R1, DHCR7/NADSYN1, VDR, CYP27B1 and CYP24A1, in 961 AA cases (292 right colon, 340 left colon, 113 rectal) and 838 AA controls from the North Carolina Colorectal Cancer Study and the Chicago Colorectal Cancer Consortium. We calculated odds ratios (OR) using logistic regression, assuming an additive genetic model and controlling for age, gender, and West African ancestry. We further evaluated whether the genetic polymorphisms conferred differential risk for right-sided CRC (R-CRC) and left-sided CRC (L-CRC, including rectal). Results: Nominal associations (p&amp;lt;0.05) were detected between CRC and SNPs in the 24-hydroxylase gene CYP24A1, rs73913755 (OR, 0.73; P = 0.0003), which degrades calcidiol, and the 25-hydroxylase gene CYP2R1, rs12794714 (OR, 0.82; P = 0.032), which converts cholecalciferol into calcidiol. When we analyzed R-CRC and L-CRC separately, no SNPs were associated with R-CRC, whereas 4 SNPs were associated with L-CRC. Two SNPs in the vitamin D binding protein gene GC, rs1155563 (OR, 0.77; P = 0.039) and rs16847024 (OR, 1.56; P = 0.003) and two SNPs in the 24-hydroxylase gene CYP24A1, rs6022990 (OR, 1.48; P = 0.006) and rs73913755 (OR, 0.67; P = 0.0002). The P value for rs73913755 was statistically significant after adjustment for multiple testing. Conclusion: Our results indicate that several SNPs in the vitamin D pathway contribute to CRC susceptibility in AAs. The minor allele of rs73913755 was present in at least one dose in 48% of AA controls and only 30% of cases, conferring increased protection against L-CRC. We hypothesize that the minor allele of rs73913755 causes a reduction in the expression levels of CYP24A1. Because rs73913755 is African-specific, showing high Fst value in comparison to ancestrally European populations, its presence could explain in part the lower proportion of L-CRC in AAs compared to whites. Future studies include analysis of vitamin D pathway gene expression levels relative to genotype and analysis of possible gene-vitamin D level interactions in AA CRC. Citation Format: Fabio Pibiri, Nathan Ellis, Rick Kittles, Xavier LLor, Rosa Xicola, Sonia Kupfer, Robert S. Sandler, Temitope Keku. Genetic variation in the vitamin D pathway and risk for colorectal cancer in African Americans. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1330. doi:10.1158/1538-7445.AM2013-1330

Local genetic structure of a montane herb among isolated grassland patches: implications for the preservation of genetic diversity under climate change

AbstractHabitat loss, fragmentation of meadow patches, and global climate change (GCC) threaten plant communities of montane grasslands. We analyzed the genetic structure of the montane herb Geranium sylvaticum L. on a local scale in order to understand the effects of habitat fragmentation and potential GCC impacts on genetic diversity and differentiation. Amplified fragment length polymorphism (AFLP) fingerprinting and cpDNA sequencing was performed for 295 individuals of 15 G. sylvaticum populations spanning the entire distribution range of the species in the Taunus mountain range in Germany. We found patterns of substantial genetic differentiation among populations using 150 polymorphic AFLP markers (mean FST = 0.105), but no variation in 896 bp of plastid DNA sequences. While populations in the center of their local distribution range were genetically diverse and less differentiated, higher FST values and reduced genetic variability was revealed for the populations at the low‐altitudinal distribution margins. Projections of GCC effects on the distribution of G. sylvaticum in 2050 showed that GCC will likely lead to the extinction of most edge populations. To maintain regional genetic diversity, conservation efforts should focus on the diverse high‐altitude populations, although a potential loss of unique variations in genetically differentiated peripheral populations could lower the overall genetic diversity and potentially the long‐term viability in the study region. This study documents the usefulness of fine‐scale assessments of genetic population structure in combination with niche modeling to reveal priority regions for the effective long‐term conservation of populations and their genetic variation under climate change.

Genetic structure of a Japanese brown frog (Rana japonica) population implies severe restriction of gene flow caused by recent urbanization in a satoyama landscape

Rapid urbanization is one of the major pressures on amphibian species. Elucidating changes in genetic structure will be useful in evaluating the effects of urbanization on amphibian populations. Our study focused on Rana japonica, which is common in complex agricultural landscapes known as satoyama, which are also under intense development pressure. We conducted landscape genetic analyses based on mitochondrial DNA haplotype frequencies of 13 breeding sites in a rapidly urbanizing area of Japan. We found several breeding sites had significantly higher Fst values, and we also identified the barriers to gene flow between these sites. Observation of past aerial photographs revealed that these barriers coincided with the construction of man-made structures in the last few decades, suggesting that urbanization has restricted gene flow in R. japonica. Our results show that landscape genetic approaches are useful in conservation planning where rapid habitat degradation has taken place.