Apolipoprotein E variation at the sequence haplotype level: implications for the origin and maintenance of a major human polymorphism

Three common protein isoforms of apolipoprotein E (apoE), encoded by the epsilon2, epsilon3, and epsilon4 alleles of the APOE gene, differ in their association with cardiovascular and Alzheimer's disease risk. To gain a better understanding of the genetic variation underlying this important polymorphism, we identified sequence haplotype variation in 5.5 kb of genomic DNA encompassing the whole of the APOE locus and adjoining flanking regions in 96 individuals from four populations: blacks from Jackson, MS (n=48 chromosomes), Mayans from Campeche, Mexico (n=48), Finns from North Karelia, Finland (n=48), and non-Hispanic whites from Rochester, MN (n=48). In the region sequenced, 23 sites varied (21 single nucleotide polymorphisms, or SNPs, 1 diallelic indel, and 1 multiallelic indel). The 22 diallelic sites defined 31 distinct haplotypes in the sample. The estimate of nucleotide diversity (site-specific heterozygosity) for the locus was 0.0005+/-0.0003. Sequence analysis of the chimpanzee APOE gene showed that it was most closely related to human epsilon4-type haplotypes, differing from the human consensus sequence at 67 synonymous (54 substitutions and 13 indels) and 9 nonsynonymous fixed positions. The evolutionary history of allelic divergence within humans was inferred from the pattern of haplotype relationships. This analysis suggests that haplotypes defining the epsilon3 and epsilon2 alleles are derived from the ancestral epsilon4s and that the epsilon3 group of haplotypes have increased in frequency, relative to epsilon4s, in the past 200,000 years. Substantial heterogeneity exists within all three classes of sequence haplotypes, and there are important interpopulation differences in the sequence variation underlying the protein isoforms that may be relevant to interpreting conflicting reports of phenotypic associations with variation in the common protein isoforms.     

Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history

Since the 1920s, population geneticists have had measures that describe how genetic variation is distributed spatially within a species' geographical range. Modern genetic survey techniques frequently yield information on the evolutionary relationships among the alleles or haplotypes as well as information on allele frequencies and their spatial distributions. This evolutionary information is often expressed in the form of an estimated haplotype or allele tree. Traditional statistics of population structure, such as F statistics, do not make use of evolutionary genealogical information, so it is necessary to develop new statistical estimators and tests that explicitly incorporate information from the haplotype tree. One such technique is to use the haplotype tree to define a nested series of branches (clades), thereby allowing an evolutionary nested analysis of the spatial distribution of genetic variation. Such a nested analysis can be performed regarding the geographical sampling locations either as categorical or continuous variables (i.e. some measure of spatial distance). It is shown that such nested phylogeographical analyses have more power to detect geographical associations than traditional, nonhistorical analyses and, as a consequence, allow a broader range of gene-flow parameters to be estimated in a precise fashion. More importantly, such nested analyses can discriminate between phylogeographical associations due to recurrent but restricted gene flow vs. historical events operating at the population level (e.g. past fragmentation, colonization, or range expansion events). Restricted gene flow and historical events can be intertwined, and the cladistic analyses can reconstruct their temporal juxtapositions, thereby yielding great insight into both the evolutionary history and population structure of the species. Examples are given that illustrate these properties, concentrating on the detection of range expansion events.     

Using Haplotype Trees for Phylogeographic and Species Inference in Fish Populations

Genetic variation is now routinely screened at the DNA sequence level in many studies. If the DNA region being screened has not experienced excessive amounts of recombination, it is often possible to reconstruct the evolutionary history of the genetic variation in the form of a haplotype tree. This tree estimates the evolutionary pathway that interconnects all the different haplotypes (sequence variants) observed in the sample. This haplotype tree can be used to define a series of nested branches (clades) that reflects the relative temporal history of the haplotypes and groups of haplotypes. Geographical information can then be overlaid upon this temporal series to test for significant associations between geography and temporal position in the haplotype tree. This allows a reconstruction of how the genetic variation arose and spread in both space and time. Such reconstructions can yield many insights into the joint roles of recurrent events such as gene flow and of historical events such as fragmentation or range expansion. These points are illustrated with studies on the chub, Leuciscus cephalus. There is also a need to extend such nested phylogeographic analyses to a phylo/reticulate geographic analysis that incorporates both assortment and recombination between and within DNA regions. A preliminary phylo/reticulate geographic analysis is presented of the transferrin locus in the brown trout, Salmo trutta, species complex that reveals the importance of hybridization in the recent evolutionary history of this group. This example shows the inadequacy of a strictly phylogenetic approach and illustrates the need to incorporate reticulate evolution. The results of nested clade phylogeographic analysis and the new phylo/reticulate geographic analysis are then used for inferring species status of the marbled trout. The results indicate that an old hybridization event may have played a role in the origin of the marbled trout. Currently the marbled trout is primarily endangered by hybridization with introduced brown trout. These results show both the positive and negative impacts of hybridization upon biodiversity. Such phylo/reticulate geographic studies will challenge both our concepts of species and our conservation management strategies.     

A Cladistic Analysis of Phenotype Associations with Haplotypes Inferred from Restriction Endonuclease Mapping. II. the Analysis of Natural Populations

Genes that code for products involved in the physiology of a phenotype are logical candidates for explaining interindividual variation in that phenotype. We present a methodology for discovering associations between genetic variation at such candidate loci (assayed through restriction endonuclease mapping) with phenotypic variation at the population level. We confine our analyses to DNA regions in which recombination is very rare. In this case, the genetic variation at the candiate locus can be organized into a cladogram that represents the evolutionary relationships between the observed haplotypes. Any mutation causing a significant phenotypic effect should be imbedded within the same historical structure defined by the cladogram. We showed, in the first paper of this series, how to use the cladogram to define a nested analysis of variance (NANOVA) that was very efficient at detecting and localizing phenotypically important mutations. However, the NANOVA of haplotype effects could only be applied to populations of homozygous genotypes. In this paper, we apply the quantitative genetic concept of average excess to evaluate the phenotypic effect of a haplotype or group of haplotypes stratified and contrasted according to the nested design defined by the cladogram. We also show how a permutational procedure can be used to make statistical inferences about the nested average excess values in populations containing heterozygous as well as homozygous genotypes. We provide two worked examples that investigate associations between genetic variation at or near the Alcohol dehydrogenase (Adh) locus and Adh activity in Drosophila melanogaster, and associations between genetic variation at or near some apolipoprotein loci and various lipid phenotypes in a human population.     

A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. I. Basic theory and an analysis of alcohol dehydrogenase activity in Drosophila

Because some genes have been cloned that have a known biochemical or physiological function, genetic variation can be measured in a population at loci that may directly influence a phenotype of interest. With this measured genotype approach, specific alleles or haplotypes in the probed DNA region can be assigned phenotypic effects. In this paper we address several problems encountered in implementing the measured genotype approach with restriction site data. A number of analytical problems arise in part as a consequence of the linkage disequilibrium that is commonly encountered when dealing with small DNA regions: 1) different restriction site polymorphisms are not statistically independent, 2) the sites being measured are not likely to be the direct cause of the associated phenotypic effects, 3) haplotype classes may be phenotypically heterogeneous, and 4) the sites that are most strongly associated with phenotypic effects are not necessarily the most closely linked to the actual genetic cause of the effects. When recombination and gene conversion are rare, the primary cause of linkage disequilibrium is history (mutational origin, genetic drift, hitchhiking, etc.). We deal with historical association directly by producing a cladogram that partially reconstructs the evolutionary history of the present-day haplotype variability. The cladogram defines a nested analysis of variance that simultaneously detects phenotypic effects, localizes the effects within the cladogram, and identifies haplotypes that are potentially heterogeneous in their phenotypic associations. The power of this approach is illustrated by an analysis of the associations between alcohol dehydrogenase (ADH) activity and restriction site variability in a 13-kb fragment surrounding the ADH locus in Drosophila melanogaster.     

Phylogeography of the Qinghai-Tibetan Plateau endemic Juniperus przewalskii (Cupressaceae) inferred from chloroplast DNA sequence variation

The vegetation of the northeast Qinghai-Tibetan Plateau is dominated by alpine meadow and desert-steppe with sparse forests scattered within it. To obtain a better understanding of the phylogeography of one constituent species of the forests in this region, we examined chloroplast trnT-trnF and trnS-trnG sequence variation within Juniperus przewalskii, a key endemic tree species. Sequence data were obtained from 392 trees in 20 populations covering the entire distribution range of the species. Six cpDNA haplotypes were identified. Significant population subdivision was detected (G(ST) = 0.772, N(ST) = 0.834), suggesting low levels of recurrent gene flow among populations and significant phylogeographic structure (N(ST) > G(ST), P < 0.05). Eight of the nine disjunct populations surveyed on the high-elevation northeast plateau were fixed for a single haplotype (A), while the remaining, more westerly population, contained the same haplotype at high frequency together with two low frequency haplotypes (C and F). In contrast, most populations that occurred at lower altitudes at the plateau edge were fixed or nearly fixed for one of two haplotypes, A or E. However, two plateau edge populations had haplotype compositions different from the rest. In one, four haplotypes (A, B, D and E) were present at approximately equivalent frequencies, which might reflect a larger refugium in the area of this population during the last glacial period. Phylogenetic analysis indicated that the most widely distributed haplotype A is not ancestral to other haplotypes. The contrasting phylogeographic structures of the haplotype-rich plateau edge area and the almost haplotype-uniform plateau platform region indicate that the plateau platform was recolonized by J. przewalskii during the most recent postglacial period. This is supported by the findings of a nested clade analysis, which inferred that postglacial range expansion from the plateau edge followed by recent fragmentation is largely responsible for the present-day spatial distribution of cpDNA haplotypes within the species.     

Glacial history of the alpine herb Rumex Nivalis (Polygonaceae): a comparison of common phylogeographic methods with nested clade analysis

The glacial history of the alpine herb Rumex nivalis was investigated using amplified fragment length polymorphisms (AFLPs) and restriction fragment length polymorphisms with polymerase chain reaction (PCR-RFLPs) of cpDNA. Both traditional statistical methods widely applied in phylogeographic research and nested clade analysis were used. The AFLPs indicated little geographic structure probably due to the wind-pollinated reproductive system of the dioecious R. nivalis. Because cpDNA haplotypes exhibited distinct distributional patterns, correlation between AFLPs and PCR-RFLPs was low. The results of common statistical methods and of nested clade analysis were largely congruent. Both supported in situ survival of one group of common haplotypes in the Central Alps. For another group of common haplotypes, classical phylogeographic analyses gave strong evidence for survival in peripheral refugia at the northern alpine border, whereas this conclusion was not as clearly supported in the nested clade analysis. Nested clade analysis provided several detailed insights on past and ongoing populational demographic processes. Thus, it is a valuable tool in the phylogeographical analysis of haplotype data, but it should preferably be combined with other statistical analyses. In situations with low genetic variation in cpDNA, classical phylogeographic analytical tools on nuclear DNA will still be the methods of choice.     

Phylogeography of the Vosges mountains populations of Gonioctena pallida (Coleoptera: Chrysomelidae): a nested clade analysis of mitochondrial DNA haplotypes

The pattern of genetic variation in the leaf beetle Gonioctena pallida was investigated inside the Vosges mountains using a highly variable 363 bp DNA fragment of the mitochondrial control region. Sequencing of 242 individuals, sampled in a geographical area of 100 x 40 km, identified 61 haplotypes whose genealogy was inferred. The resulting haplotype network exhibits four star-like phylogenies, two of which may be indicative of a population having recently expanded in size from a small number of founders. Nested clade analysis suggested multiple past expansion events, but also isolation by distance and possibly past fragmentation events, as the causes of the detected geographical associations of haplotypes. These results indicate the existence of effective barriers to gene flow inside the investigated area. Because the oldest demographic events inferred in the nested clade analysis were identified as expansion events, we hypothesize that a small population of founders have expanded not only in size, but also in geographical range from the south towards the north and east of the Vosges.     

Northern and Southern expansions of Atlantic brown trout (Salmo trutta) populations during the Pleistocene

The phylogeography of Atlantic brown trout ( Salmo trutta ) was analysed using mitochondrial DNA control region complete sequences of 774 individuals from 57 locations. Additionally, the available haplotype information from 100 published populations was incorporated in the analysis. Combined information from nested clade analysis, haplotype trees, mismatch distributions, and coalescent simulations was used to characterize population groups in the Atlantic basin. A major clade involved haplotypes assigned to the Atlantic (AT) lineage, but another major clade should be considered as a distinct endemic lineage restricted to the Iberian Peninsula. The phylogeography of the Atlantic populations showed the mixed distribution of several Atlantic clades in glaciated areas of Northern Europe, whereas diverged haplotypes dominated the coastal Iberian rivers. Populations inhabiting the Atlantic rivers of southern France apparently contributed to postglacial colonization of northern basins, but also comprised the source of southern expansions during the Pleistocene.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 904–917.     

中国沿海日本囊对虾线粒体16S rRNA基因序列变异及遗传分化

对中国东南沿海4个日本囊对虾地理群体16S rRNA基因片段进行了序列测定和分析.在获得的467bp 序列中,共检测到45个变异位点,多态位点比例为9.64%.具有10种单倍型,三亚群体单倍型多样性最高(0.900±0.161).各群体的核苷酸多样性(π)为0.0007～0.0082,其中三亚群体核苷酸多样性最为丰富,远高于湛江、北海和海口群体.群体间遗传分化指数(F_(st))为0.000～0.945.结合已报道的16S rRNA基因序列,构建了NJ分子系统树,中国海域日本囊对虾可分为3支.香港至台湾沿岸所有单倍型聚集为一分支,湛江、海口和北海群体内的所有单倍型聚集成另一分支,两分支分别属于已报道的变种Ⅰ和变种Ⅱ,但三亚群体内的4个单倍型单独聚集成一分支,与前两分支的核苷酸序列差异大(7.95%～8.35%),遗传分化明显,可能为一亲缘关系很远的新种(或变种).研究结果可为日本囊对虾的资源管理和遗传选育提供参考.     

Patterns of intraspecific diversification in the Piriqueta caroliniana complex in southeastern North America and the Bahamas

Abstract.— We use chloroplast DNA (cpDNA) variation and nested clade phylogeographic analyses to infer the historical processes that have contributed to the high level of morphological and ecological diversification present in a group of herbaceous perennials (the Piriqueta caroliniana complex) in North America and the Bahamas. The presence of morphologically distinct and intercompatible varieties (morphotypes) that can be distinguished based on suites of taxonomic characters (e.g., leaf shape, pubescence type, stature) and contrasting habitat affinities (from marshes to dry pinelands and sand scrub) makes this group particularly appropriate for studies of intraspecific diversification. To examine the distribution of haplotypes among populations, we sampled 467 individuals from 55 locations in Florida, Georgia, and the northern Bahamas (Grand Bahama and Abaco) and screened each individual for cpDNA variation using restriction fragment length polymorphism (RFLP) and heteroduplex analyses. We develop a one-step haplotype phylogeny for this group and use the geographic distributions of haplotypes and clades to test specific phylogeographic hypotheses using the methods developed by Templeton and his colleagues (Templeton 1998). In general, the distribution of haplotypes was strongly influenced by limited dispersal distances, with the more recently derived haplotypes having much lower levels of dispersion and lower frequencies in populations than the ancestral haplotypes. The patterns of clade and haplotype dispersion and displacement and the distribution of morphotypes imply at least three cases of long-distance dispersal and one case of historical fragmentation. The historical patterns inferred for populations of Piriqueta are consistent with known biogeographical events, historical vegetation change, and the concordant patterns of multiple Pleistocene refugia that have been observed for a number of other taxa in southeastern North America.     

Variation of haplotype distributions of two genomic regions of Citrus tristeza virus populations from eastern Spain

Genetic variation in natural populations of Citrus tristeza virus (CTV) was studied using haplotypes detected by single-strand conformation polymorphism (SSCP) analysis of two genomic regions (p20 gene and segment A, located in ORF1a). Analysis of 254 samples from 125 trees, collected at 12 different sites, yielded 8 different haplotypes for p20 and 5 for segment A. The most frequent haplotype of p20 was predominant at all sites, but several sites differed in the predominance of segment A haplotypes. At most sites, the homozygosity observed for the p20 gene tended to be higher than expected in a neutral evolution, whereas the opposite was true for segment A. Comparison of the populations at different sites showed that 44 of the 66 possible population pairs were genetically distinct for segment A, but only six pairs differed for the p20 gene. Analysis of molecular variance grouping trees by site, scion variety, rootstock or age, showed that variation in segment A was significantly affected by site, tree age and rootstock, and that variation between trees in each group and within trees was even more important. In contrast, variation in p20 was affected only by site and rootstock, each factor contributing to < 2% of the variation. The data suggest that sequence variations in segment A must be functionally less important and that it has less evolutionary constraints than p20. Detection of different haplotypes in neighbour trees or in samples from the same tree may help explain part of the variability observed in CTV symptom expression.     

Phylogeography of Mabuya maculilabris (Reptilia) from São Tomé Island (Gulf of Guinea) inferred from mtDNA sequences

The pattern of genetic variation of the lizard Mabuya maculilabris from S?o Tomé Island (Gulf of Guinea) was investigated using a combination of three mitochondrial DNA gene fragments. Forty-eight haplotypes were recovered among 66 individuals covering the whole island. The genealogy inferred from the most parsimonious network of haplotypes allows us to detect two main and long branches departing from the putative group of oldest haplotypes. The tips of these branches exhibit star-like phylogenies, which may indicate of recently expanded populations, most probably from a small number of founders. A nested clade analysis suggests a complex pattern of past events that gave rise to the extant geographical pattern found in the haplotype distribution: past and allopatric fragmentation, range expansion, restricted gene flow and long-distance dispersal. These results are consistent with the complex geological history of the island where important volcanic activity with extensive lava flows has occurred during several periods. Mismatch-distribution analysis and AMOVA also support these conclusions. Substantial genetic structuring among these lizards was detected as well as high levels of differentiation between the southern edge populations (particularly those from the Rolas Islet) and the remaining ones. However, variation is low relative to the geological age of the island. Our results indicate that patterns of variation observed in reptiles in other oceanic islands are not indicative of those observed in the islands of the Gulf of Guinea.     

Relations of APOE promoter polymorphisms to LDL cholesterol and markers of subclinical atherosclerosis in young adults

The common apolipoprotein E (apoE) gene (APOE) epsilon2/epsilon3/epsilon4 polymorphism explains part of serum lipid variation, and polymorphisms in the APOE promoter region have been proposed to participate in the regulation of serum lipid levels within the most common APOE epsilon3/epsilon3 genotype group. We determined APOE -219G/T and +113G/C promoter genotypes and estimated APOE haplotypes in 525 participants of the Cardiovascular Risk in Young Finns Study. We studied the associations of the APOE promoter polymorphisms and their haplotypes with cross-sectional and longitudinal serum lipid and apolipoprotein concentrations as well as with flow-mediated dilatation (FMD), carotid artery compliance (CAC), and intima-media thickness (IMT) within the APOE epsilon3/epsilon3 carriers. We found no significant association between the APOE promoter genotypes and serum lipids [low density lipoprotein-cholesterol (LDL-C), HDL-C, and triglycerides], apolipoproteins (apoA-I and apoB), or brachial artery FMD, CAC, or carotid IMT in either men or women. In longitudinal analyses in males, the carriers of heterozygous genotypes (-219G/T or +113G/C) and, furthermore, carriers of the -219T/+113C/epsilon3 haplotype had significantly higher LDL-C and total cholesterol concentrations throughout the 21 year follow-up period compared with homozygous G allele carriers or noncarriers of the -219T/+113C/epsilon3 haplotype. Such associations were not found in females. In summary, the APOE promoter polymorphisms -219G/T and +113G/C as well as their haplotype are associated with longitudinal changes in LDL-C and total cholesterol concentrations in young Finnish males but do not seem to be major determinants for FMD, CAC, or carotid IMT in males or females.     

Glacial-induced altitudinal migrations in Armeria (Plumbaginaceae) inferred from patterns of chloroplast DNA haplotype sharing

In contrast to northern European areas where large-scale migrations occurred to recolonize territories after glacial periods, species in southern regions survived and diverged without large geographical displacements. As a result of the importance of orography in much of the southern areas, such displacements must have involved populations ascending or descending mountains. The present study provides support for glacial-induced altitudinal migrations from chloroplast phylogeographic patterns in Armeria (Plumbaginaceae) in southeast Spain. One hundred and five sequences of the trnL-F spacer were obtained from seven species. Fifteen different haplotypes were recognized, their genealogy was inferred, and associations with geography were explored using nested clade analysis. Seven instances were detected in which the same haplotype is shared by two or three species within a particular massif. In all the cases, at least one of the species involved displayed different haplotypes in other areas; in most, the haplotype shared is predominant either in one of the species involved or in the massif. These patterns of haplotype sharing strongly suggest horizontal transfer between species. In one of the massifs (Sierra Nevada) the three species involved in haplotype sharing (A. splendens, A. filicaulis ssp. nevadensis, A. villosa ssp. bernisii) occur at markedly different altitudinal belts. It is argued that altitudinal migrations within the contraction-expansion model provide the best explanation for the current pattern, and that at least in one case it resulted in the formation of a new hybrid taxon, A. filicaulis ssp. nevadensis.     

Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history

The major histocompatibility complex (MHC) is recognised as one of the most important genetic regions in relation to common human disease. Advancement in identification of MHC genes that confer susceptibility to disease requires greater knowledge of sequence variation across the complex. Highly duplicated and polymorphic regions of the human genome such as the MHC are, however, somewhat refractory to some whole-genome analysis methods. To address this issue, we are employing a bacterial artificial chromosome (BAC) cloning strategy to sequence entire MHC haplotypes from consanguineous cell lines as part of the MHC Haplotype Project. Here we present 4.25 Mb of the human haplotype QBL (HLA-A26-B18-Cw5-DR3-DQ2) and compare it with the MHC reference haplotype and with a second haplotype, COX (HLA-A1-B8-Cw7-DR3-DQ2), that shares the same HLA-DRB1, -DQA1, and -DQB1 alleles. We have defined the complete gene, splice variant, and sequence variation contents of all three haplotypes, comprising over 259 annotated loci and over 20,000 single nucleotide polymorphisms (SNPs). Certain coding sequences vary significantly between different haplotypes, making them candidates for functional and disease-association studies. Analysis of the two DR3 haplotypes allowed delineation of the shared sequence between two HLA class II-related haplotypes differing in disease associations and the identification of at least one of the sites that mediated the original recombination event. The levels of variation across the MHC were similar to those seen for other HLA-disparate haplotypes, except for a 158-kb segment that contained the HLA-DRB1, -DQA1, and -DQB1 genes and showed very limited polymorphism compatible with identity-by-descent and relatively recent common ancestry (<3,400 generations). These results indicate that the differential disease associations of these two DR3 haplotypes are due to sequence variation outside this central 158-kb segment, and that shuffling of ancestral blocks via recombination is a potential mechanism whereby certain DR-DQ allelic combinations, which presumably have favoured immunological functions, can spread across haplotypes and populations.     

The Wilhelmine W. Key 2002 Invitational Lecture. Phylogeography,haplotype trees,and invasive plant species

The distribution of genetic variants in plant populations is strongly affected both by current patterns of microevolutionary forces, such as gene flow and selection, and by the phylogenetic history of populations and species. Understanding the interplay of shared history and current evolutionary events is particularly confounding in plants due to the reticulating nature of gene exchange between diverging lineages. Certain gene sequences provide historically ordered neutral molecular variation that can be converted to gene genealogies which trace the evolutionary relationships among haplotypes (alleles). Gene genealogies can be used to understand the evolution of specific DNA sequences and relate sequence variation to plant phenotype. For example, in a study of the RPS2 gene in Arabidopsis thaliana, resistant phenotypes clustered in one portion of the gene tree. The field of phylogeography examines the distribution of allele genealogies in an explicit geographical context and, when coupled with a nested clade analysis, can provide insight into historical processes such as range expansion, gene flow, and genetic drift. A phylogeographical approach offers insight into practical issues as well. Here we show how haplotype trees can address the origins of invasive plants, one of the greatest global threats to biodiversity. A study of the geographical diversity of haplotypes in invasive Phragmites populations in the United States indicates that invasiveness is due to the colonization and spread of distinct genotypes from Europe ( Saltonstall 2002). Likewise, a phylogeographical analysis of Tamarix populations indicates that hybridization events between formerly isolated species of Eurasia have produced the most common genotype of the second-worst invasive plant species in the United States.     

Phylogeographic structure suggests multiple glacial refugia in northern Victoria Land for the endemic Antarctic springtail Desoria klovstadi (Collembola, Isotomidae)

We carried out a phylogeographic study using mtDNA (COII) for the endemic springtail Desoria klovstadi (formerly Isotoma klovstadi ) from northern Victoria Land, Antarctica. Low levels of sequence divergence (≤ 1.6%) across 26 unique haplotypes (from 69 individuals) were distributed according to geographic location. Cape Hallett and Daniell Peninsula contained the highest nucleotide (both > 0.004) and haplotype (both > 0.9) diversity with 10 (of 16) and 8 (of 12) unique haplotypes, respectively. All other populations (Football Saddle, Crater Cirque, Cape Jones) had lower diversity with 2–4 unique haplotypes. Across the 69 individuals from five populations there was only a single haplotype shared between two populations (Daniell Peninsula and Football Saddle). Furthermore, nested clade analyses revealed that some of the Daniell Peninsula haplotypes were more closely related to Football Saddle haplotypes than to any other population. Such discrete haplotype groupings suggest historical (rare) dispersal across the Pleistocene (1.8 mya−11 kya) and Holocene (11 kya–present), coupled with repeated extinction, range contraction and expansion events, and/or incomplete sampling across the species range. The nested clade analyses reveal that a common pattern of climatic and geological history over long-term glacial habitat fragmentation has determined the geographic and haplotype distributions found for D. klovstadi .     

A trend of central versus peripheral structuring in mitochondrial and nuclear gene sequences of the Japanese wood mouse, Apodemus speciosus

A phylogeographic analysis was performed on Japanese endemic wood mice (Apodemus speciosus) using nuclear interphotoreceptor retinol binding protein (IRBP) gene sequences (1,152 bp), together with previously published mitochondrial cytochrome b (cyt b) data. In the IRBP analysis, 40 haplotypes were recovered from 84 individuals by statistical and subcloning methods. Substantial sequence variation was determined from the IRBP data (pi=0.0047), and no significant evidence of recombination was detected. From the phylogenetic analysis, the 40 haplotypes fell into two major groups with geographic associations, irrespective of the karyotype groups (2n=46 and 2n=48), yielding a trend of central (Hokkaido, Honshu, Shikoku, Kyushu, and Sado) and peripheral (Izu, Oki, Tsushima, and Satsunan Is.) groupings. This geographic pattern is similar to that observed in the cyt b data, with a different insular grouping of Sado, Hokkaido, Izu, and Satsunan islands, and also to that of morphological features. In both gene data sets, nested clade analyses revealed allopatric fragmentation in the "peripheral island clades" and range expansion in the "central island clades." A mismatch analysis using cyt b data also suggested expansion of the central islands clade. Thus, the trend of central vs. peripheral structuring may be attributable to past demographic dynamics in the two distinct haplotype clades, such as range expansion of one clade in the central area of the Japanese Islands, leaving the other clade in the periphery.     

Further resolution of porcine phylogeny in Southeast Asia by Thai mtDNA haplotypes

The mtDNA control region of 72 Thai native pigs and 11 Thai wild boars indigenous to Northern Thailand was comparatively sequenced. In total, 36 nucleotide variations that accounted for 24 haplotypes have been described (TNH01 to TNH20 and TWH01 to TWH04). These haplotypes and further publicly available mtDNA haplotypes were used to assess phylogenetic relationships. Twenty-three of the 24 haplotypes became integrated into the Asian clade of the phylogenetic tree and eight of them recapitulated another major cluster of haplotypes within this clade (Thai haplogroup, THG). Only haplotype TNH01 fit in with the European clade of the phylogenetic tree. An additional analysis using 510 bp of the mtDNA incorporated the THG haplotypes in to clade MTSEA (mountainous and Southeast Asian distribution) to form haplogroup MTSEA-THG. Recently, MTSEA was renamed in MC3. MC3 contains only signatures of pigs scattered across the Indo-Burma Biodiversity Hotspot (IBBH), a region including Thailand to the Kra Isthmus. Here we propose a putative independent porcine domestication event in South-east Asia (SEA). All haplotypes of haplogroup MTSEA-THG have revealed unique and previously unknown nucleotide signatures at positions 24 (nucleotide A) and at positions 183 (nucleotide C) that differentiate them from all other porcine mtDNA haplotypes.