Evidence for hybridization-driven heteroplasmy maintained across generations in a ricefish endemic to a Wallacean ancient lake.

Heteroplasmy, the presence of multiple mitochondrial DNA (mtDNA) haplotypes within cells of an individual, is caused by mutation or paternal leakage. However, heteroplasmy is usually resolved to homoplasmy within a few generations because of germ-line bottlenecks; therefore, instances of heteroplasmy are limited in nature. Here, we report heteroplasmy in the ricefish species , endemic to Lake Matano, an ancient lake in Sulawesi Island, in which one individual was known to have many heterozygous sites in the mitochondrial NADH dehydrogenase subunit 2 (ND2) gene.

Ancient Admixture in Freshwater Halfbeaks of the Genus in Southeast Sulawesi.

Freshwater halfbeaks of the genus (Zenarchopteridae) uniquely diversified on Sulawesi Island, where tectonic movements have been very active since the Pliocene. Most species of this genus have quite limited distributions, which indicates that geographic isolations have contributed to their diversification. In this study, we demonstrated that secondary contacts and resultant admixtures between long-isolated species/populations may have also been important.

Species divergence and repeated ancient hybridization in a Sulawesian lake system.

An increasing volume of empirical studies demonstrated that hybridization between distant lineages may have promoted speciation in various taxa. However, the timing, extent and direction of introgressive hybridization remain unknown in many cases. Here, we report a possible case in which repeated hybridization promoted divergence of Oryzias ricefishes (Adrianichthyidae) on Sulawesi, an island of Wallacea.

Convergent evolution of body color between sympatric freshwater fishes via different visual sensory evolution.

Although there are many examples of color evolution potentially driven by sensory drive, only few studies have examined whether distinct species inhabiting the same environments evolve similar body colors via shared sensory mechanisms. In this study, we tested whether two sympatric freshwater fish taxa, halfbeaks of the genus and ricefishes of the genus in Sulawesi Island, converge in both body color and visual sensitivity. After reconstructing the phylogeny separately for and using transcriptome-wide sequences, we demonstrated positive correlations of body redness between these two taxa across environments, even after phylogenetic corrections, which support convergent evolution.

Association between duplicated maltase genes and the transcriptional regulation for the carbohydrate changes in Drosophila melanogaster.

Gene duplication could promote phenotypic and genetic adaptation to various environments. To understand the effects of gene duplication on transcriptional regulation associated with environmental changes, we focused on the starch hydrolysis pathway, in which amylase enzymes together with maltase enzymes hydrolyze starch into glucose. Drosophila genomes involve ten duplicated Maltase genes.

The element invaded rapidly and caused hybrid dysgenesis in natural populations of in Japan.

Transposable elements not only can change genomic positions and disperse across the gene pool, but also can jump to another species through horizontal transmission. Of late, the element, a DNA transposon in insects, was shown to cross the genetic boundary from to in Europe around 2006. To understand the dynamics of transposable elements, especially in the early stages of invasion, we examined 63 lines of from 11 natural populations in Japan established in 1976-2015.

Discrepancy in the degree of population differentiation between color-morph frequencies and neutral genetic loci in the damselfly Ischnura senegalensis in Okinawa Island, Japan.

Evaluation of relative contribution of natural selection and stochastic processes to population differentiation has been of great interest in evolutionary biology. In a damselfly, Ischnura senegalensis, females show color dimorphism (gynochrome vs. androchrome), and color-morph frequencies are known to greatly vary among local populations within Okinawa Island, a small island of Ryukyu Archipelago, Japan.

Extremely low nucleotide polymorphism in Pinus krempfii Lecomte, a unique flat needle pine endemic to Vietnam.

Pinus krempfii Lecomte is a morphologically and ecologically unique pine, endemic to Vietnam. It is regarded as vulnerable species with distribution limited to just two provinces: Khanh Hoa and Lam Dong. Although a few phylogenetic studies have included this species, almost nothing is known about its genetic features.

High prevalence of non-synonymous substitutions in mtDNA of cichlid fishes from Lake Victoria.

When a population size is reduced, genetic drift may fix slightly deleterious mutations, and an increase in nonsynonymous substitution is expected. It has been suggested that past aridity has seriously affected and decreased the populations of cichlid fishes in Lake Victoria, while geographical studies have shown that the water levels in Lake Tanganyika and Lake Malawi have remained fairly constant. The comparably stable environments in the latter two lakes might have kept the populations of cichlid fishes large enough to remove slightly deleterious mutations.

Inferences of evolutionary history of a widely distributed mangrove species, Bruguiera gymnorrhiza, in the Indo-West Pacific region.

Inference of genetic structure and demographic history is fundamental issue in evolutionary biology. We examined the levels and patterns of genetic variation of a widespread mangrove species in the Indo-West Pacific region, Bruguiera gymnorrhiza, using ten nuclear gene regions. Genetic variation of individual populations covering its distribution range was low, but as the entire species it was comparable to other plant species.

Population structure and demographic history of a tropical lowland rainforest tree species Shorea parvifolia (Dipterocarpaceae) from Southeastern Asia.

Distribution of tropical rainforests in Southeastern Asia has changed over geo-logical time scale, due to movement of tectonic plates and/or global climatic changes. Shorea parvifolia is one of the most common tropical lowland rainforest tree species in Southeastern Asia. To infer population structure and demographic history of S.

Speciation history of three closely related oak gall wasps, Andricus mukaigawae, A. kashiwaphilus, and A. pseudoflos (Hymenoptera: Cynipidae) inferred from nuclear and mitochondrial DNA sequences.

The Andricus mukaigawae complex of oak gall wasps is composed of cyclically parthenogenetic species: A. mukaigawae and Andricus kashiwaphilus, and a parthenogenetic species, Andricus pseudoflos. The component species differ in life history, host plant, karyotype, and asexual gall shape, although little difference is found in the external morphology of asexual adults.

Protein crosslinking by transglutaminase controls cuticle morphogenesis in Drosophila.

Transglutaminase (TG) plays important and diverse roles in mammals, such as blood coagulation and formation of the skin barrier, by catalyzing protein crosslinking. In invertebrates, TG is known to be involved in immobilization of invading pathogens at sites of injury. Here we demonstrate that Drosophila TG is an important enzyme for cuticle morphogenesis.

Levels and patterns of DNA variation in two sympatric mangrove species, Rhizophora apiculata and R. mucronata from Thailand.

In mangrove species the past geomorphic changes in coastal regions and reproductive systems are important factors of their distribution and genetic structure of populations. However, very little is known about the levels of genetic variation of Rhiozophora species in Southeast Asia. In this study, we surveyed levels and patterns of genetic variation as well as population structure of two sympatric mangrove species, Rhizophora apiculata and R.

Seasonal changes in the long-distance linkage disequilibrium in Drosophila melanogaster.

Seasonal environmental changes have the potential to influence the genetic structure of species with a short generation time, such as Drosophila. We previously found the seasonal change in linkage disequilibrium (LD) between the chemoreceptor (Cr) genes in a local Japanese population (Kyoto [KY]). This could be caused by fluctuation in the population size or selection in temporally heterogeneous environments or both.

Genetic variation in populations of Allothrombium pulvinum (Acari: Trombidiidae) from Northern Iran revealed by mitochondrial coxI and nuclear rDNA ITS2 sequences.

Allothrombium pulvinum Ewing is a common natural enemy of aphids and some other arthropods. So far, there are no studies that have addressed genetic variation of this predatory mite. We investigated genetic variation of A.

Phylogeography of Eurasian Larix species inferred from nucleotide variation in two nuclear genes.

Larch (Larix Mill.) is one of the most widely distributed tree genera in Eurasia. To determine population structure and to verify classification of five species and three varieties of the Eurasian Larix species, we investigated levels and patterns of nucleotide variation of two nuclear gene regions: the 4-coumarate coenzyme A ligase (4CL) and the coumarate 3-hydroxylase (C3H).

Short 5'-flanking regions of the Amy gene of Drosophila kikkawai affect amylase gene expression and respond to food environments.

Evolution of the duplicated genes and regulation in gene expression is of great interest, especially in terms of adaptation. Molecular population genetic and evolutionary studies on the duplicated amylase genes of Drosophila species have suggested that their 5'-flanking (cis-regulatory) regions play an important role in evolution of these genes. For better understanding of evolution of the duplicated amylase genes and gene expression, we studied functional significance of the Amy1 gene of Drosophila kikkawai using in vitro deletion mutagenesis followed by P-element-mediated germline transformation.

A new test for detecting ongoing selection.

Much effort has been made to search for signatures of past natural selection in DNA sequences. However, currently acting selection is rarely detected in natural populations because of its rarity, low detection power of available methods, or both. Here, we develop a new test to detect viability selection over a single generation.

Comprehensive molecular phylogeny of the sub-family Dipterocarpoideae (Dipterocarpaceae) based on chloroplast DNA sequences.

Dipterocarpoideae, the largest sub-family of well-known plant family Dipterocarpaceae, dominates in South Asian rain forests. Although several previous studies addressed the phylogeny of the Dipterocarpaceae family, relationships among many of its genera from the Dipterocarpoideae sub-family are still not well understood. In particular, little is known about the relationships of the genera Vateriopsis, Stemonoporus, Vateria and inconsistence remains between phylogenetic results and taxonomic classifications of Shorea and Hopea species.

Interlocus nonrandom association of polymorphisms in Drosophila chemoreceptor genes.

Some forms of multilocus selection with epistasis, such as truncation selection, can effectively reduce the mutation load [Kondrashov, A. S. (1988) Nature 336, 435-440].

A single-amino-acid change of the gustatory receptor gene, Gr5a, has a major effect on trehalose sensitivity in a natural population of Drosophila melanogaster.

Variation in trehalose sensitivity and nucleotide sequence polymorphism of the Gr5a gene encoding the gustatory receptor to sugar trehalose were investigated in 152 male lines of Drosophila melanogaster collected from a natural population. Among the observed 59 segregating sites, some pairs of sites showed significant linkage disequilibrium. A single SNP, which results in the Ala218Thr amino acid change, was significantly associated with trehalose sensitivity, as previously suggested.

Nucleotide variation of seven genes in Drosophila kikkawai.

We examined levels and patterns of nucleotide variation in 21 strains of Drosophila kikkawai from Miyako island, Japan for the partial regions of the following seven nuclear genes: Adh, Ddc, esc, ksr, Pgi, su(f), and Tpi. The nucleotide variation at total sites (pi(t)) ranged from 0.0013 in the ksr, to 0.