Dating the origin of the CCR5-Delta32 AIDS-resistance allele by the coalescence of haplotypes.

The CCR5-Delta32 deletion obliterates the CCR5 chemokine and the human immunodeficiency virus (HIV)-1 coreceptor on lymphoid cells, leading to strong resistance against HIV-1 infection and AIDS. A genotype survey of 4,166 individuals revealed a cline of CCR5-Delta32 allele frequencies of 0%-14% across Eurasia, whereas the variant is absent among native African, American Indian, and East Asian ethnic groups. Haplotype analysis of 192 Caucasian chromosomes revealed strong linkage disequilibrium between CCR5 and two microsatellite loci. By use of coalescence theory to interpret modern haplotype genealogy, we estimate the origin of the CCR5-Delta32-containing ancestral haplotype to be approximately 700 years ago, with an estimated range of 275-1,875 years. The geographic cline of CCR5-Delta32 frequencies and its recent emergence are consistent with a historic strong selective event (e.g. , an epidemic of a pathogen that, like HIV-1, utilizes CCR5), driving its frequency upward in ancestral Caucasian populations.     

Molecular and morphological divergence in a stygobiont gastropod lineage (Truncatelloidea,Moitessieriidae, Paladilhiopsis) within an isolated karstic area in the Mecsek Mountains (Hungary)

Truncatelloid gastropods are one of the most species‐rich subterranean invertebrate groups. Their current taxonomy is based on morphological characters. However, this is not a comprehensive approach and does not take into account the degree of phylogenetic divergence between stygobiont populations inhabiting hydrologically isolated but geographically close caves. We studied two Paladilhiopsis populations of a small and isolated karstic area (Mecsek Mountains, Hungary) with two hydrologically separated cave systems, investigating morphological (shell morphometrics) and genetic (COI, 16S) divergence together. The populations differed both morphologically and genetically: we found strong divergence in the relative width of the shell (best described by the variable “shell angle”) and a 6.4% divergence in COI. This provides strong support for the presence of two distinct taxa; however, it is still doubtful whether they differ at the species or the subspecies level. In one of the caves, we found representatives of both haplotypes (and phenotypes), which can be explained by secondary contact after an allopatric divergence.     

Genetic variations and phylogeography of the swallowtail butterfly Papilio machaon on the Japanese Islands

The swallowtail butterfly Papilio machaon Linnaeus, 1758 is widely distributed in the Holarctic region, including all of the main islands of Japan, as well as Sakhalin, and on other smaller islands south to Yakushima Island. The Japanese population is situated at the margin of the Eurasian distribution range of this species. It is morphologically different from other populations and has been classified as the subspecies hippocrates C. & R. Felder, 1864. The population of the Japanese Islands is considered to be genetically distinct from the continental populations in relation to the geographical history of the Japanese Islands. Therefore, we examined a part of the ND5 gene sequence of the mitochondrial DNA for P. machaon individuals of various localities in Japan and some nearby countries, and found 68 haplotypes in 400 individuals from the Japanese Islands and Sakhalin. A DNA polymorphism analysis revealed that the genetic structure of the Hokkaido population was significantly different from that of the southern populations on the main Japanese islands. These results imply that P. machaon expanded its range from the Amur region of Russia southward through Sakhalin to the Japanese Islands, and that the Tsugaru Strait between Hokkaido and Honshu may have subsequently limited their gene flow as a geographical barrier.     

Novel Y‐chromosome short tandem repeats in Sus scrofa and their variation in European wild boar and domestic pig populations

Y‐chromosome markers are important tools for studying male‐specific gene flow within and between populations, hybridization patterns and kinship. However, their use in non‐human mammals is often hampered by the lack of Y‐specific polymorphic markers. We identified new male‐specific short tandem repeats (STRs) in Sus scrofa using the available genome sequence. We selected four polymorphic loci (5–10 alleles per locus), falling in one duplicated and two single‐copy regions. A total of 32 haplotypes were found by screening 211 individuals from eight wild boar populations across Europe and five domestic pig populations. European wild boar were characterized by significantly higher levels of haplotype diversity compared to European domestic pigs (H_D = 0.904 ± 0.011 and H_D = 0.491 ± 0.077 respectively). Relationships among STR haplotypes were investigated by combining them with single nucleotide polymorphisms at two linked genes (AMELY and UTY) in a network analysis. A differentiation between wild and domestic populations was observed (F_ST = 0.229), with commercial breeds sharing no Y haplotype with the sampled wild boar. Similarly, a certain degree of geographic differentiation was observed across Europe, with a number of local private haplotypes and high diversity in northern populations. The described Y‐chromosome markers can be useful to track male inheritance and gene flow in wild and domestic populations, promising to provide insights into evolutionary and population genetics in Sus scrofa.     

HapStar: automated haplotype network layout and visualization

Haplotype networks are commonly used for representing associations between sequences, yet there is currently no straightforward way to create optimal layouts. Automated optimal layouts are particularly useful not only because of the time-saving element but also because they avoid both human error and human-induced biases in the presentation of figures. HapStar directly uses the network connection output data generated from Arlequin (or a simple user-generated input file) and uses a force-directed algorithm to automatically lay out the network for easy visualization. In addition, this program is able to use the alternative connections generated by Arlequin to create a minimum spanning tree. HapStar provides a straightforward user-friendly interface, and publication-ready figures can be exported simply. HapStar is freely available (under a GPLv3 licence) for download for MacOSX, UNIX and Windows, at http://fo.am/hapstar.     

Locally asymmetric introgressions between subspecies suggest circular range expansion at the Antirrhinum majus global scale

Assessing processes of geographic expansion in contact zones is a crucial step towards an accurate prediction of the evolution of species genetic diversity. The geographic distribution of cytonuclear discordance often reflects genetic introgression patterns across a species geographic range. Antirrhinum majus pseudomajus and A. m. striatum are two interfertile subspecies that occupy nonoverlapping areas but enter in contact in many locations at the margin of their geographic distribution. We found that genetic introgression between both subspecies was asymmetric at the local scale and geographically oriented in opposite directions at both ends of their contact zone perimeter in the Pyrenees. Our results suggest that the geographic expansion of A. majus subspecies was circular around the perimeter of their contact zone and pinpoint the need to integrate different spatial scales to unravel complex patterns of species geographic expansion.     

Elevated genetic diversity of mitochondrial genes in asexual populations of Bark Lice ('Psocoptera': Echmepteryx hageni)

Asexual reproduction is commonly thought to be associated with low genetic diversity in animals. Echmepteryx hageni (Insecta: 'Psocoptera') is one of several psocopteran species that are primarily parthenogenetic, but also exists in small, isolated sexual populations. We used mitochondrial DNA sequences to investigate the population history and genealogical relationships between the sexual and asexual forms of this species. The asexual population of E. hageni exhibits extremely high mitochondrial haplotype diversity (H=0.98), whereas the sexual forms had significantly lower haplotypic diversity (H=0.25, after correcting for sample size). This diversity in asexuals represents one the greatest genetic diversities reported for asexual animals in the literature. Nucleotide diversities were also higher in asexual compared to sexual populations (π=0.0071 vs. 0.00027). Compared to other reported estimates of π in insects, asexual nucleotide diversity is high, but not remarkably elevated. Three hypotheses might explain the elevated genetic diversity of asexual populations: (i) larger effective population size, (ii) greater mutation rate or (iii) possible recent origin of sexuals. In addition, phylogeographic analysis revealed little geographic structure among asexual E. hageni, although specimens from the upper Midwest form a single clade and are genetically differentiated. The mismatch distribution and neutrality tests indicate a historical population size increase, possibly associated with expansion from glacial refugia.     

Distribution of <Emphasis Type="Italic">S</Emphasis> haplotypes and its relationship with restorer–maintainers of self-incompatibility in cultivated <Emphasis Type="Italic">Brassica napus</Emphasis>

Brassica napus (AACC, 2n = 38) is a self-compatible amphidiploid plant that arose from the interspecies hybridization of two self-incompatible species, B. rapa (AA, 2n = 20) and B. oleracea (CC, 2n = 18). Self-incompatibility (S) haplotypes in one self-incompatible line and 124 cultivated B. napus lines were detected using S-locus-specific primers, and their relationships with restorer-maintainers were investigated. Two class I (S-I ( SLG ) a and S-I ( SLG ) b) and four class II (S-II ( SLG ) a, S-II ( SLG ) b, S-II ( SP11 ) a and S-II ( SP11 ) b) S haplotypes were observed, of which S-II ( SP11 ) b was newly identified. The nucleotide sequence of SP11 showed little similarity to the reported SP11 alleles. The lines were found to express a total of eleven S genotypes. The self-incompatible line had a specific genotype consisting of S-II ( SP11 ) a, similar to B. rapa S-60, and S-II ( SLG ) a, similar to B. oleracea S-15. Restorers expressed six genotypes: the most common genotype contained S-I ( SLG ) a, similar to B. rapa S-47, and S-II ( SLG ) b, similar to B. oleracea S-15. Maintainers expressed nine genotypes: the predominant genotype was homozygous for two S haplotypes, S-II ( SLG ) a and S-II ( SP11 ) b. One genotype was specific to restorers and four genotypes were specific to maintainers, whereas five genotypes were expressed in both restorers and maintainers. This suggests that there is no definitive correlation between the distribution of S genotypes and restorer-maintainers of self-incompatibility. The finding that restorers and maintainers express unique genotypes, and share some common genotypes, would be valuable for detecting the interaction of S haplotypes in inter- or intra-genomes as well as for developing markers-assisted selection in self-incompatibility hybrid breeding.     

Development and characterization of chloroplast microsatellite markers for Cryptomeria japonica D. Don

We developed 17 chloroplast microsatellite markers, which consisted of seven mononucleotide microsatellites with a minimum repeat number of 10 and 10 dinucleotide microsatellites with a minimum repeat number of six, from the complete chloroplast genomic sequence of Cryptomeria japonica. A survey of 45 C. japonica individuals showed the number of alleles ranging from two to 11 alleles and a diversity index ranging from 0.085 to 0.895. Consequently, the 45 C. japonica individuals were divided into 39 haplotypes. These markers will be useful genetic markers in the gene flow analysis and population genetics of C. japonica.     

Population genetic structure of Chilo suppressalis (Walker) (Lepidoptera: Crambidae): strong subdivision in China inferred from microsatellite markers and mtDNA gene sequences

Chilo suppressalis (Walker) displays significant geographical differences in ecological preference that may be congruent with patterns of molecular variation. To test this, we collected and analysed 381 individuals of this species from cultivated rice at 18 localities in China during the rice-growing season of 2005–2006. We used four microsatellite DNA markers and four mitochondrial DNA gene fragments. We found that this species is highly differentiated, coupled with an estimated population expansion date of at least 60 000  bp . Phylogenetic analyses, Bayesian clustering, and phylogeographical analyses of statistical parsimony haplotype network consistently divided the populations into three clades: a central China (CC) clade, a northern plus northeastern China (NN) clade and a southwestern China (SW) clade. Analysis of molecular variance indicated a high level of geographical differentiation at different hierarchical levels [ F _ST for microsatellite markers, COI, COII, 16S and ND1 is 0.06004 ( P  < 0.0001), 0.27607 ( P  < 0.0001), 0.22949 ( P  < 0.0001), 0.19485 ( P  < 0.0001) and 0.29285 ( P  < 0.0001), respectively]. Isolation by distance appeared among the samples from within China ( r  = 0.404, P  = 0.0002); N_em values estimated using a coalescent-based method were small (< 2 migrants per generation), suggesting that the observed levels of differentiation are a result of migration–drift equilibrium. Our results imply that the genetic differentiation of this borer, which is approximately in accordance with its observed number of generations per year in different Chinese geographical regions, is probably attributed to climatic and/or geological events (e.g. the last glacial maximum) and subsequently strengthened by the domestication of rice.