Patterns of genetic variation in Native America.

Allele frequencies from seven polymorphic red cell antigen loci (ABO, Rh, MN, S, P, Duffy, and Diego) were examined in 144 Native American populations. Mean genetic distances (Nei's D) and the fixation index FST are approximately equal for the North and South American samples but are reduced in the Central American geographic area. The relationship between genetic distance and geographic distance differs markedly across geographic areas. The correlation between geographic distance and genetic distance for the North and Central American data is twice as large as that observed for the South American samples. This geographic difference is confirmed in spatial autocorrelation analyses; no geographic structure is apparent in the South American data but geographic structure is prominent in North and Central American samples. These results confirm earlier observations regarding differences between North and South American gene frequency patterns.     

Distribution of immunoglobulin allotypes among local populations of Kenya olive baboons

In this paper we report on the distributions of immunoglobulin allotypes among 564 olive baboons collected at six localities in Kenya. The sample localities and sizes are 1) Lake Magadi, N = 107; 2) Nanyuki, N = 77; 3) Lake Baringo, N = 55; 4) Mosiro, N = 132; 5) Isiolo, N = 36; 6) Gilgil, N = 157. Gm allotypes 1, 10, 13, 15, and 17 are polymorphic among these samples. Gm(11) and Km(3) were present in all samples, and Gm(2,3,5,6,14,16,21,24,26) and Km(1) were absent from all samples. The proportions of individuals positive for polymorphic allotypes varied substantially between different local samples, as did the arrays and estimated frequencies of haplotypes. Allotype frequencies in local samples do not appear to be simply related to either geographic location or habitat characteristics of the localities. Our data suggest that much of the geographic variability in Kenya olive baboon populations occurs between populations separated by small geographic distances.     

Pyrosequencing analysis of bacterial community and assembly in activated sludge samples from different geographic regions in China

In order to investigate if there are geographic differences of bacterial community in the activated sludge collected from different geographic regions (eastern, northwestern, and northern parts) of China and to determine the co-occurrence patterns of bacterial community, activated sludge samples were collected from 10 municipal wastewater treatment plants located in 8 cities in China. High-throughput pyrosequencing combined with the bioinformatics analysis were used to examine the bacterial community compositions in the activated sludge samples. The result of taxonomy classifier indicated that a total of 76 genera were commonly shared by more than 7 samples, which accounted for 62 to 96 % of the classified sequences in each sample. Even though some core genera existed in all examined activated sludge samples regardless of the sampling geographic location and treatment process, significant geographic differences of bacterial community compositions among the activated sludge samples were revealed by the nonmetric multidimensional scaling (NMDS) and analyses of similarity (ANOSIM) analysis. A total of 165 pairs of significant and robust correlations (positive and negative) were identified from 61 bacterial genera based on the network analysis. The data obtained in this study could provide useful information to understand the bacterial community composition in geographically distributed wastewater treatment plants and discern the co-occurrence patterns of bacterial community.     

Fungi Identify the Geographic Origin of Dust Samples

There is a long history of archaeologists and forensic scientists using pollen found in a dust sample to identify its geographic origin or history. Such palynological approaches have important limitations as they require time-consuming identification of pollen grains, a priori knowledge of plant species distributions, and a sufficient diversity of pollen types to permit spatial or temporal identification. We demonstrate an alternative approach based on DNA sequencing analyses of the fungal diversity found in dust samples. Using nearly 1,000 dust samples collected from across the continental U.S., our analyses identify up to 40,000 fungal taxa from these samples, many of which exhibit a high degree of geographic endemism. We develop a statistical learning algorithm via discriminant analysis that exploits this geographic endemicity in the fungal diversity to correctly identify samples to within a few hundred kilometers of their geographic origin with high probability. In addition, our statistical approach provides a measure of certainty for each prediction, in contrast with current palynology methods that are almost always based on expert opinion and devoid of statistical inference. Fungal taxa found in dust samples can therefore be used to identify the origin of that dust and, more importantly, we can quantify our degree of certainty that a sample originated in a particular place. This work opens up a new approach to forensic biology that could be used by scientists to identify the origin of dust or soil samples found on objects, clothing, or archaeological artifacts.     

Relationships of Nematodirus species and Nematodirus battus isolates (Nematoda: Trichostrongyloidea) based on nuclear ribosomal DNA sequences

Nuclear ribosomal sequence data from the internal transcribed spacers (ITS-1 and ITS-2), 5.8S subunit, and regions of the 18S and 28S genes were used to investigate sequence diversity among geographic samples of Nematodirus battus, and to infer phylogenetic relationships among Nematodirus species. Phylogenetic analysis of these data yielded strong support for relationships among species, depicting Nematodirus helvetianus and Nematodirus spathiger as sister-taxa and a clade of these 2 species and Nematodirus filicollis. This tree is consistent with caprine bovids as ancestral hosts, with a subsequent host shift to Bovinae in N. helvetianus. Eleven of 14 N. battus sequences were unique, with 19 variable sites among sequences representing 5 geographic samples. The lowest number of variable nucleotide sites was observed in samples representing apparently recent introductions to the United States and Canada, which is consistent with a population bottleneck concomitant with translocation. Comparison of directly sequenced polymerase chain reaction products and clones revealed evidence for intraindividual variation at some of the sequence sites, and this pattern of variation and that within geographic samples indicates incomplete rDNA repeat homogenization within species. This pattern of variation is not conducive for inferring phylogenetic relationships among sequences representing N. battus or addressing the putative history of introduction.     

Mammalian body size changes and Plio-Pleistocene environmental shifts: implications for understanding hominin evolution in eastern and southern Africa

This study examines geographic and temporal variation in three mammalian taxa co-occurring in eastern and southern Africa. The selected taxa-the spotted hyena (Crocuta crocuta), the plains zebra (Equus burchellii), and the impala (Aepyceros melampus)--are geographically widespread in modern times and are abundant in eastern and southern African Plio-Pleistocene fossil sites. Craniodental measurements of modern conspecifics from known geographic locations are compared using multivariate statistical methods to discern patterns of modern geographic variation within taxa. Modern and fossil samples are statistically compared to assess the nature and extent of inferred shifts in body size, both between modern samples and through time in each region. These results indicate that modern spotted hyenas and plains zebras exhibit mainly size variation between regions, with southern African samples possessing statistically larger craniodental metrics than eastern African samples. Comparison of fossil and modern samples reveals that the fossil assemblages do not show the same pattern of geographic variation. Significant temporal changes are more numerous between fossil and modern eastern African samples, and these changes are not mirrored by similar changes in the southern African samples. The changes experienced by taxa in eastern Africa appear to have been more extreme and wide-ranging than those in southern Africa, a presumed refugium. This result accords well with genetic studies of several large mammal species and paleoenvironmental studies suggesting that eastern African localized environments were more affected by tectonism and volcanism than were those in southern Africa. This study suggests that different evolutionary scenarios may have existed within Africa during the Plio-Pleistocene, but that both regions played unique and complementary roles in the evolution of African hominins and the broader faunal community.     

Morphometric variation in the Nearctic collared lemming (Dicrostonyx)

A. H. Macpherson suggested that much of the current geographic diversity in Canadian Arctic mammals resulted from isolation in refugia during the Wisconsin glacial stage. This study evaluates the refugium hypothesis, insofar as it applies to Nearctic Dicrostonyx , by means of a statistical analysis of geographic variation in 13 skull characters. Overall, geographic variation among samples is not significant, although D. hudsonius and D. unalascensis are geographically and morphologically distinct. Some variation in skull shape is correlated with winter temperature. Partitioning tests on other measures of shape variation indicate some discontinuities consistent with the refugial hypothesis. Discrete samples reflect possible refugial populations in northern North America, Eastern Beringia and two southern periglacial refugia, one in eastern North America and at least one in western North America.     

In search of polymorphic Alu insertions with restricted geographic distributions

Alu elements are transposable elements that have reached over one million copies in the human genome. Some Alu elements inserted in the genome so recently that they are still polymorphic for insertion presence or absence in human populations. Recently, there has been an increasing interest in using Alu variation for studies of human population genetic structure and inference of individual geographic origin. Currently, this requires a high number of Alu loci. Here, we used a linker-mediated polymerase chain reaction method to preferentially identify low-frequency Alu elements in various human DNA samples with different geographic origins. The candidate Alu loci were subsequently genotyped in 18 worldwide human populations (approximately 370 individuals), resulting in the identification of two new Alu insertions restricted to populations of African ancestry. Our results suggest that it may ultimately become possible to correctly infer the geographic affiliation of unknown samples with high levels of confidence without having to genotype as many as 100 Alu loci. This is desirable if Alu insertion polymorphisms are to be used for human evolution studies or forensic applications.     

不同地区甜菜夜蛾种群的遗传多样性分析

甜菜夜蛾Spodoptera exigua (Hübner)是一种重要的农业害虫,曾给我国农牧业生产造成过重大的经济损失。为了阐明甜菜夜蛾的种群动态规律,改善和提高其预测、防治水平,我们应用扩增片段长度多态性(AFLP)技术对我国7个甜菜夜蛾种群的42头雄蛾的遗传多样性进行了研究分析。结果表明,不同种群个体间遗传相似性指数分布在0.143～0.824之间,同一种群内不同个体间的遗传相似性指数分布在0.250～0.786之间,同一种群内个体间的遗传相似性指数有许多小于不同种群个体间的。江西种群的多态性条带比例最低,为80.7%; 山东种群的多态性条带比例最高,达88.6%。总体而言,北方种群内的遗传多样性高于南方种群。聚类分析结果表明,同一种群的个体并不总能聚在一起,即种群间不存在明显的遗传分化。这些结果为明确我国甜菜夜蛾的迁飞规律及各发生危害区的虫源关系提供了进一步的实验依据。     

Effect of different sampling strategies for a single geographic region in Yemen on standard genetic analyses of mitochondrial DNA sequence data

Collection of biological samples is the foundation of genetic studies ranging from estimation of genetic diversity to reconstruction of population history. Sample collections are intended to accurately represent the genetic, biological, ecological, cultural, geographic, and/or linguistic diversity of a particular region or population by providing a small, but representative, set of samples. In this study, we analyze human mitochondrial DNA variation in samples collected using four different sampling strategies to represent the same geographic region. Specifically, samples were collected from a village, a rural area, a regional clinic, and a national university in the governorate of Dhamar in Yemen. All samples were assayed for mitochondrial hypervariable region I DNA sequence variation and data were subjected to standard molecular genetic analyses. Our results suggest that analyses in which individual DNA sequences are explicitly compared or evaluated, e.g. phylogenetic and network analyses, may be more sensitive to sample collection design than analyses in which data are averaged across individuals or are analyzed more indirectly, e.g. summary statistics.     

Flavonoid patterns in Fagonia mollis-complex

Twenty samples of Fagonia mollis and F. tristis of different geographic distribution were investigated for their flavonoids. Kaempherol and isorhamnetin 3-rutinosides were the major flavonoids of F. mollis, while F. tristis contained, in addition, 8-O-methylherbacetin. The flavonoid patterns are discussed in correlation with the geographic distribution of both species.     

Population structure and its effects on patterns of nucleotide polymorphism in teosinte (Zea mays ssp. parviglumis)

Surveys of nucleotide diversity in the wild ancestor of maize, Zea mays ssp. parviglumis, have revealed genomewide departures from the standard neutral equilibrium (NE) model. Here we investigate the degree to which population structure may account for the excess of rare polymorphisms frequently observed in species-wide samples. On the basis of sequence data from five nuclear and two chloroplast loci, we found significant population genetic structure among seven subpopulations from two geographic regions. Comparisons of estimates of population genetic parameters from species-wide samples and subpopulation-specific samples showed that population genetic subdivision influenced observed patterns of nucleotide polymorphism. In particular, Tajima's D was significantly higher (closer to zero) in subpopulation-specific samples relative to species-wide samples, and therefore more closely corresponded to NE expectations. In spite of these overall patterns, the extent to which levels and patterns of polymorphism within subpopulations differed from species-wide samples and NE expectations depended strongly on the geographic region (Jalisco vs. Balsas) from which subpopulations were sampled. This may be due to the demographic history of subpopulations in those regions. Overall, these results suggest that explicitly accounting for population structure may be important for studies examining the genetic basis of ecologically and agronomically important traits as well as for identifying loci that have been the targets of selection.     

Geographic variation in the essential oil monoterpenes of Liriodendron tulipifera L

The monoterpene component of Liriodendron tulipifera L. (Magnoliaceae) essential oils was quantitatively analysed in branch samples collected from an Ohio provenance test of 11 geographic seed sources representing the natural range of the species. Mean monoterpene composition of the essential oil is described and significant differences in the monoterpene composition among geographic sources are discussed.     

Evaluation of microsatellites of Catha edulis (qat; Celastraceae) identified using pyrosequencing

The use of Next Generation Sequencing (NGS) techniques to identify microsatellite markers has replaced more time intensive methods such as molecular cloning. The main advantage of NGS over traditional methods of identifying microsatellite markers is the generation of many more sequences with less effort. It is possible to design primers from unenriched DNA, thereby further reducing the workload and also allowing the use of SSRs that are difficult to enrich (e.g., TA/AT and TAA/ATT). We present microsatellite primer pairs that may be used for phylogeographic analysis as well as to infer the geographical origin of traded material of Catha edulis, which contains two amphetamines that are controlled substances in many counties. We used data from two partial 454 pyrosequencing runs that generated about 2000 sequences containing microsatellites (3% of all sequences) as well as flanking regions sufficient for primer design. Using 23 samples of C. edulis we identified 27 single-copy markers that were broadly amplified across the sampled individuals; 18 showed polymorphism information content (PIC) higher than 0.5. The genetic structure in wild individuals is concordant with their geographic origins; wild samples from northern Kenya are more closely related to Ethiopian samples than are other wild samples from Kenya. The geographic differences in allele frequencies indicate that microsatellite analysis can be used to determine the geographic source of cultivated and wild collected material.     

Marine turtle mitogenome phylogenetics and evolution

The sea turtles are a group of cretaceous origin containing seven recognized living species: leatherback, hawksbill, Kemp's ridley, olive ridley, loggerhead, green, and flatback. The leatherback is the single member of the Dermochelidae family, whereas all other sea turtles belong in Cheloniidae. Analyses of partial mitochondrial sequences and some nuclear markers have revealed phylogenetic inconsistencies within Cheloniidae, especially regarding the placement of the flatback. Population genetic studies based on D-Loop sequences have shown considerable structuring in species with broad geographic distributions, shedding light on complex migration patterns and possible geographic or climatic events as driving forces of sea-turtle distribution. We have sequenced complete mitogenomes for all sea-turtle species, including samples from their geographic range extremes, and performed phylogenetic analyses to assess sea-turtle evolution with a large molecular dataset. We found variation in the length of the ATP8 gene and a highly variable site in ND4 near a proton translocation channel in the resulting protein. Complete mitogenomes show strong support and resolution for phylogenetic relationships among all sea turtles, and reveal phylogeographic patterns within globally-distributed species. Although there was clear concordance between phylogenies and geographic origin of samples in most taxa, we found evidence of more recent dispersal events in the loggerhead and olive ridley turtles, suggesting more recent migrations (<1Myr) in these species. Overall, our results demonstrate the complexity of sea-turtle diversity, and indicate the need for further research in phylogeography and molecular evolution.     

Cross-cultural analysis of migration rates: effects of geographic distance and population size.

A model is developed that treats migration rates among populations as a function of the geographic distance between them and the size of both sources and recipient population. Specifically, mij/mjj = a(Ni/Nj)pe-bd, where mij/mjj is the relative migration rate into population j from population i, Ni is the size of the source population, Nj is the size of the recipient population, d is the geographic distance between populations i and j, p is a measure of differential density-dependence, b is a measure of distance decay, and a is an adjustment parameter with little demographic meaning. Methods of parameter estimation and hypothesis testing using maximum likelihood are outlined. These methods are applied to migration matrix data from 13 samples obtained from the literature representing a wide range of ecological settings. All samples show a significant effect of geographic distance on migration, and all but one show a significant effect of differential population size. All but one sample show an overall tendency for migration to be negative density-dependent; that is, the relative migration rate is greater from larger populations to smaller populations than the reverse.     

Geographic/ethnic differences in human herpesvirus-6 antibody patterns.

Serum samples from healthy adults in four geographic/ethnic groups (Ghanaian Blacks, Malaysian Chinese, Malaysian Indians and United States Caucasians) were tested under code for antibodies to human herpesvirus-6 (HHV-6). The prevalence and titer of HHV-6 antibody in the healthy Ghanaians were significantly higher than in the Malaysian Chinese; United States Caucasians and Malaysian Indians had intermediate prevalence and titer of antibodies. Thus far, no specific differences in HHV-6-associated diseases have been noted between geographic/ethnic groups with these marked variations in antibody patterns.     

Clines, clusters, and the effect of study design on the inference of human population structure

Previously, we observed that without using prior information about individual sampling locations, a clustering algorithm applied to multilocus genotypes from worldwide human populations produced genetic clusters largely coincident with major geographic regions. It has been argued, however, that the degree of clustering is diminished by use of samples with greater uniformity in geographic distribution, and that the clusters we identified were a consequence of uneven sampling along genetic clines. Expanding our earlier dataset from 377 to 993 markers, we systematically examine the influence of several study design variables—sample size, number of loci, number of clusters, assumptions about correlations in allele frequencies across populations, and the geographic dispersion of the sample—on the “clusteredness” of individuals. With all other variables held constant, geographic dispersion is seen to have comparatively little effect on the degree of clustering. Examination of the relationship between genetic and geographic distance supports a view in which the clusters arise not as an artifact of the sampling scheme, but from small discontinuous jumps in genetic distance for most population pairs on opposite sides of geographic barriers, in comparison with genetic distance for pairs on the same side. Thus, analysis of the 993-locus dataset corroborates our earlier results: if enough markers are used with a sufficiently large worldwide sample, individuals can be partitioned into genetic clusters that match major geographic subdivisions of the globe, with some individuals from intermediate geographic locations having mixed membership in the clusters that correspond to neighboring regions.     

A survey for Cyclospora spp. in Kenyan primates, with some notes on its biology.

From March 1999 through August 2000, 511 stool samples collected from 11 different primate species in 10 geographically distinct locations in Kenya, East Africa, were screened for the presence of Cyclospora spp. oocysts. Positive samples (43/102, 42%) were identified in vervet monkeys (Cercopithecus aethiops) in 4 of 4 locations; 19/206 (9%) in yellow and olive baboons (Papio cynocephalus, P. anubis, respectively) in 5 of 5 locations; and 19/76 (25%) in black and white colobus monkeys (Colobus angolensis, C. guereza, respectively) from 2 of 3 locations. DNA sequences obtained from 18 S rRNA coding regions from respective subsets of these positive samples were typed as Cyclospora cercopitheci (samples from Cercopithecus aethiops). Cyclospora papionis (samples from Papio cynocephalus and P. anubis), and Cyclospora colobi (samples from Colobus angolensis and C. guereza). Cyclospora oocysts were not detected in samples collected from patas, highland sykes, lowland sykes, blue sykes, DeBrazza, or red-tailed monkeys. A coded map showing the geographic location of the collected samples is given. Stool samples from 1 troop of vervet monkeys were collected over a 12-mo period. Positive samples ranged between 21 and 63%. These results suggest that there is no strongly marked seasonality evident in Cyclospora infection in monkeys as has been noted in human infection. This is further confirmed by the recovery of positive samples collected from vervet monkeys, baboons, and colobus monkeys at all times of the year during this survey. This absence of seasonality in infection is especially notable because of the extreme weather patterns typical of Kenya, where marked rainy and dry seasons occur. A second noteworthy observation is that the striking host specificity of the Cyclospora species initially described was confirmed in this survey. Baboons were only infected with C. papionis, vervet monkeys with C. cercopitheci, and colobus monkeys with C. colobi, despite geographic overlaps of both the monkey and parasite species and wide geographic distribution of each parasite and monkey host.     

Phenotypic variation in calorific value of melaleuca materials from south florida

Phenotypic variation in calorific value among melaleuca samples from natural stands in South Florida is described. One hundred trees were selected from ten 5 m × 5 m test plots distributed evenly in 2 geographic areas—Lee County and Dade County. In general, no geographic changes in calorific value, for either wood and bark, were evident. Differences among the plot averages were significant. Both calorific values of wood and bark fluctuated greatly among trees within plots. The calorific value did not seem to relate with the size of tree. Implications for tree improvement are discussed.