Host plant diversity of Sesamia calamistis: cytochrome b gene sequences reveal local genetic differentiation

Sesamia calamistis Hampson (Lepidoptera: Noctuidae) is one of the indigenous stem borer pests associated with maize ( Zea mays L.) and sorghum [ Sorghum bicolor (L.) Moench] (both Poaceae) in Africa. Its pest status varies across the continent and this has been attributed to variation in diet breadth and ecological preferences among populations. Its larvae were found on 12 plant species during a study initiated at four sites (Muhaka, Mtito Andei, Kakamega, and Suam) in Kenya to estimate its diet breadth and genetic population structure. Ten of the infested plant species belonged to the family Poaceae [ Echinochloa haploclada (Stapf) Stapf, Eleusine corocana L., Eleusine jaegeri Pilg., Panicum deustum Thunb, Panicum maximum Jacquin, Pennisetum purpureum Schumacher, Setaria verticillata (L.) P. Beauv., Sorghum arundinaceum (Desvaux) Stapf, S. bicolor , and Z. mays ]; the other two were Cyperaceae: Cyperus distans L. and Cyperus dives Delile. Combined with collections from other African countries (Uganda, South Africa, Benin, Ghana, Nigeria, and Togo), comparisons of partial cytochrome b sequences revealed the presence of 68 haplotypes that differentiated into clades I and II. In Kenya, the two clades colonized different regions, except in Mtito Andei where they co-existed. Individuals from Mtito Andei could be separated based on their host plants: clade I with 14 haplotypes was found mainly on maize (78.6%), whereas clade II with 10 haplotypes was found mainly among wild host plants (63.6%). Detection of divergence among these clades with cytochrome b suggests that their evolutionary separation may have taken place about one million years ago. This article discusses the potential implication of this differentiation for the management of S .  calamistis as a pest of maize and sorghum in Africa.     

No evidence of contemporary interploidy gene flow between the closely related European woodland violets Viola reichenbachiana and V. riviniana (sect. Viola,Violaceae)

• Viola reichenbachiana (2n = 4x = 20) and V. riviniana (2n = 8x = 40) are closely related species widely distributed in Europe, often sharing the same habitat throughout their overlapping ranges. It has been suggested in numerous studies that their high intraspecific morphological variability and plasticity might have been further increased by interspecific hybridisation in contact zones, given the sympatry of the species and the incomplete sterility of their hybrid. The aims of this study were to: (i) confirm that V. reichenbachiana and V. riviniana have one 4x genome in common, and (ii) determine the impact of hybridisation and introgression on genetic variation of these two species in selected European populations.
• For our study, we used 31 Viola populations from four European countries, which were analysed using AFLP and sequencing of a variable plastid intergenic spacer, trnH‐psbA.
• Our analysis revealed that V. reichenbachiana exhibited larger haplotype diversity, having three species‐specific haplotypes versus one in V. riviniana. The relationships among haplotypes suggest transfer of common haplotypes into V. riviniana from both V. reichenbachiana and hypothetically the other, now extinct, parental species. AFLP analysis showed low overall genetic diversity of both species, with V. riviniana showing higher among‐population diversity. None of the morphologically designated hybrid populations had additive AFLP polymorphisms that would have indicated recent hybridisation. Also, kinship coefficients between both species did not indicate gene flow. V. riviniana showed significant population subdivision and significant isolation by distance, in contrast to V. reichenbachiana.
• The results indicate lack of gene flow between species, high influence of selfing on genetic variability, as well as probably only localised introgression toward V. riviniana.

     

Y-STR diversity and sex-biased gene flow among Caribbean populations

In the present study, we report, for the first time, the allele and haplotype frequencies of 17 Y-STR (Y-filer) loci in the populations of Haiti, Jamaica and the Bahamas (Abaco, Eleuthera, Exuma, Grand Bahama, Long Island and New Providence). This investigation was undertaken to assess the paternal genetic structure of the abovementioned Caribbean islands. A total of 607 different haplotypes were identified among the 691 males examined, of which 537 (88.5%) were unique. Haplotype diversities (HD) ranged from 0.989 in Long Island to 1.000 in Grand Bahama, with limited haplotype sharing observed among these Caribbean collections. Discriminatory capacity (DC) values were also high, ranging from 79.1% to 100% in Long Island and Grand Bahama, respectively, illustrating the capacity of this set of markers to differentiate between patrilineal related individuals within each population. Phylogenetic comparison of the Bahamian, Haitian and Jamaican groups with available African, European, East Asian and Native American populations reveals strong genetic ties with the continental African collections, a finding that corroborates our earlier work using autosomal STR and Y-chromosome binary markers. In addition, various degrees of sex-biased gene flow exhibiting disproportionately higher European paternal (as compared to autosomal) influences were detected in all Caribbean islands genotyped except for Abaco and Eleuthera. We attribute the presence or absence of asymmetric gene flow to unique, island specific demographic events and family structures.     

Cytochrome b sequences of ancient cattle and wild ox support phylogenetic complexity in the ancient and modern bovine populations

Mitochondrial DNA has been the traditional marker for the study of animal domestication, as its high mutation rate allows for the accumulation of molecular diversity within the time frame of domestic history. Additionally, it is exclusively maternally inherited and haplotypes become part of the domestic gene pool via actual capture of a female animal rather than by interbreeding with wild populations. Initial studies of British aurochs identified a haplogroup, designated P, which was found to be highly divergent from all known domestic haplotypes over the most variable portion of the D-loop. Additional analysis of a large and geographically representative sample of aurochs from northern and central Europe found an additional, separate aurochs haplotype, E. Until recently, the European aurochs appeared to have no matrilinear descendants among the publicly available modern cattle control regions sequenced; if aurochs mtDNA was incorporated into the domestic population, aurochs either formed a very small proportion of modern diversity or had been subsequently lost. However, a haplogroup P sequence has recently been found in a modern sample, along with a new divergent haplogroup called Q. Here we confirm the outlying status of the novel Q and E haplogroups and the modern P haplogroup sequence as a descendent of European aurochs, by retrieval and analysis of cytochrome b sequence data from twenty ancient wild and domesticated cattle archaeological samples.     

Divergence and Remarkable Diversity of the Y Chromosome in Guppies

The guppy sex chromosomes show an extraordinary diversity in divergence across populations and closely related species. In order to understand the dynamics of the guppy Y chromosome, we used linked-read sequencing to assess Y chromosome evolution and diversity across upstream and downstream population pairs that vary in predator and food abundance in three replicate watersheds. Based on our population-specific genome assemblies, we first confirmed and extended earlier reports of two strata on the guppy sex chromosomes. Stratum I shows significant accumulation of male-specific sequence, consistent with Y divergence, and predates the colonization of Trinidad. In contrast, Stratum II shows divergence from the X, but no Y-specific sequence, and this divergence is greater in three replicate upstream populations compared with their downstream pair. Despite longstanding assumptions that sex chromosome recombination suppression is achieved through inversions, we find no evidence of inversions associated with either Stratum I or Stratum II. Instead, we observe a remarkable diversity in Y chromosome haplotypes within each population, even in the ancestral Stratum I. This diversity is likely due to gradual mechanisms of recombination suppression, which, unlike an inversion, allow for the maintenance of multiple haplotypes. In addition, we show that this Y diversity is dominated by low-frequency haplotypes segregating in the population, suggesting a link between haplotype diversity and female preference for rare Y-linked color variation. Our results reveal the complex interplay between recombination suppression and Y chromosome divergence at the earliest stages of sex chromosome divergence.     

Bovine casein haplotypes: number, frequencies and applicability as genetic markers

Three casein loci, tightly linked on bovine chromosome 6, have been studied as haplotypes within families of bulls. The polymorphisms included in the study were CASAS1 (B, C), CASB (A1, A, A5, B), CASK (A, B, E) and a microsatellite in intron III of CASK. A new A5 variant of CASB, caused by a silent mutation in the triplet coding for amino acid 110, was detected by direct polymerase chain reaction sequencing. Our analysis of 306 sons and 15 sires revealed 10 different casein haplotypes with a cumulative polymorphic information content (PIC) of 0.78.     

Characterization of microsatellites in the fungal plant pathogen,Sclerotinia sclerotiorum

Twenty‐five primers produced unambiguous amplification products of 23 microsatellite‐containing loci and two microsatellite‐like polymorphic loci, with 2–10 alleles at each locus in the plant pathogenic fungus, Sclerotinia sclerotiorum. Haplotypes are polymorphic among individuals sharing the same DNA fingerprint and DNA sequence haplotype, facilitating epidemiological monitoring worldwide. Fourteen of these primers also successfully amplified the closely related S. trifoliorum and S. minor.     

Allozyme and chloroplast DNA variation in island and mainland populations of the rare Spanish endemic, Silene hifacensis (Caryophyllaceae)

Silene hifacensis is a narrowly endemicplant, restricted to a few small populations onlimestone cliffs in the Spanish province ofAlicante and on the Balearic island of Ibiza.The species was collected to extinction in itsoriginal mainland location by the early 20thcentury. Attempts have been made to reintroduceS. hifacensis to this area butconservation efforts are limited by a lack ofinformation on the geographic structure ofgenetic variation in the species. We usednuclear (allozyme) and chloroplast DNA (cpDNA)PCR/RFLP markers to investigate the structureof genetic variation in 2 mainland and 6 Ibizanpopulations. Levels of allozyme variation werelow, with a mean of 2 alleles per polymorphiclocus. Mean (over polymorphic loci) totalallozyme diversity (H_tot) was 0.203 and meanwithin-population diversity (H_pop) was 0.085. Mostdiversity was explained by thebetween-population diversity component (G_pop.reg =57%). Both mainland populations showedallozyme fixation. Three composite cpDNAhaplotypes were identified. The first is uniqueto a mainland population that is alsoallozymically distinct from all the otherpopulations. The second haplotype is found inthe other mainland population and one Ibizanpopulation: these two populations areallozymically identical. The remaining Ibizanpopulations contain the third haplotype. Thegeographic distribution of allozymes and cpDNAhaplotypes is discussed in terms of populationhistory, dispersal and, speculatively, in termsof the possibility that there has beenundocumented translocation of material betweenpopulations.     

Genetic and phenotypic variation of Phytophthora crassamura isolates from California nurseries and restoration sites

Phenotypic and sequence data were used to characterize 28 isolates resembling Phytophthora megasperma from 14 host species in 2 plant production facilities and 10 restoration sites across the San Francisco Bay Area (California; USA). Size of the oogonia and DNA sequences (nuclear internal transcribed spacer (ITS) and mitochondrial cytochrome c oxidase subunit 1 (COX 1)) were compared, and sensitivity to mefenoxam and pathogenicity were measured. Based on ITS 61 % of isolates matched ex-type sequences of Phytophthora crassamura from Italy, and the remainder matched or were close to the P. megasperma ex-type. However, all California P. crassamura genotypes belonged to four unique COX 1 haplotype lineages isolated from both nurseries and restoration sites. Although lineages were sensitive to mefenoxam, a significant difference in sensitivity was identified, and all continued growth in-vitro. These results suggested previous mefenoxam exposure in plant production facilities resulting in tolerance. In conclusion, all evidence pointed to a nursery origin of novel P. crassamura lineages found in California restoration sites. In this study, COX 1 sequences and oogonia size provided information relevant to identify geographic and evolutionary intraspecific variation within P. crassamura, and was additionally used to track the spread of this species from nurseries into wildlands.