Phylogeography infers the demographic history of various species by resolving genetic relationships among populations across a geographic range. Comparison of phylogeographic patterns of multiple ...species with similar geographic distributions, i.e., comparative phylogeography, allows us to assess the roles of regional historical events and species-specific ecological factors in shaping intraspecific genetic diversity, providing model systems for studying the processes and genetic basis of adaptive evolution and speciation. In addition, these patterns can also be compared among species from different regions to infer the impact of global-scale historical and present events, such as Pleistocene glacial cycles, on current biodiversity. In this review, I summarize and integrate recent findings of phylogeographic studies for two geographic lineages, Pacific Ocean (PO) and Sea of Japan (SJ) lineages, of five coastal gobies distributed around the Japanese Archipelago. Using mitochondrial and nuclear DNA markers, these studies revealed genetic divergences of the PO and SJ lineages in the coastal gobies. However, the two types of markers showed discordant patterns for genetic divergences between the two lineages (mitonuclear discordance), suggesting different coalescent processes between these genetic markers. Ecological features that depend on shallow coastal resources may contribute to restricted gene flow and be responsible for the existence of the two lineages that are predominantly found in the coastal gobies. All coastal gobies shared sharp contrasts in genetic diversity between the two lineages, with the SJ lineages rapidly expanding during Pleistocene interglacial periods. Such rapid population expansions can provide alternative ways to obtain recent calibration points to estimate divergence times of the two lineages. A comparison of the geographic distributions between the two lineages indicated that the centers of their secondary contact zones vary, which may appear to represent the continuous transition process of the two lineage distributions. Compared with results of phylogeographic studies from other oceans, multiple divergence times, sharply contrasting demographic histories, and two independent secondary contact zones are unique characteristics of the divergence between the PO and SJ lineages. These characteristics will allow us to test the continuous processes of genomic divergence during geographical isolation with environmental fluctuations and the consequences of hybridization of divergent lineages in independent secondary contact zones with different environmental settings.
While various technologies for high‐throughput genotyping have been developed for ecological studies, simple methods tolerant to low‐quality DNA samples are still limited. In this study, we tested ...the availability of a random PCR‐based genotyping‐by‐sequencing technology, genotyping by random amplicon sequencing, direct (GRAS‐Di). We focused on population genetic analysis of estuarine mangrove fishes, including two resident species, the Amboina cardinalfish (Fibramia amboinensis, Bleeker, 1853) and the Duncker's river garfish (Zenarchopterus dunckeri, Mohr, 1926), and a marine migrant, the blacktail snapper (Lutjanus fulvus, Forster, 1801). Collections were from the Ryukyu Islands, southern Japan. PCR amplicons derived from ~130 individuals were pooled and sequenced in a single lane on a HiSeq2500 platform, and an average of three million reads was obtained per individual. Consensus contigs were assembled for each species and used for genotyping of single nucleotide polymorphisms by mapping trimmed reads onto the contigs. After quality filtering steps, 4,000–9,000 putative single nucleotide polymorphisms were detected for each species. Although DNA fragmentation can diminish genotyping performance when analysed on next‐generation sequencing technology, the effect was small. Genetic differentiation and a clear pattern of isolation‐by‐distance was observed in F. amboinensis and Z. dunckeri by means of principal component analysis, FST and the admixture analysis. By contrast, L. fulvus comprised a genetically homogeneous population with directional recent gene flow. These genetic differentiation patterns reflect patterns of estuary use through life history. These results showed the power of GRAS‐Di for fine‐grained genetic analysis using field samples, including mangrove fishes.
The genetic basis of speciation in free‐spawning marine invertebrates is poorly understood. Although gene copy number variations (GCNVs) and nucleotide variations possibly trigger the speciation of ...these organisms, empirical evidence for such a hypothesis is limited. In this study, we searched for genomic signatures of GCNVs that may contribute to the speciation of Western Pacific abalone species. Whole‐genome sequencing data suggested the existence of significant amounts of GCNVs in closely related abalones, Haliotis discus and H. madaka, in the early phase of speciation. In addition, the degree of interspecies genetic differentiation in the genes where GCNVs were estimated was higher than that in other genes, suggesting that nucleotide divergence also accumulates in the genes with GCNVs. GCNVs in some genes were also detected in other related abalone species, suggesting that these GCNVs are derived from both ancestral and de novo mutations. Our findings suggest that GCNVs have been accumulated in the early phase of free‐spawning abalone speciation.
Although gene copy number variations (GCNVs) and nucleotide variations possibly trigger the speciation of free‐spawning marine invertebrates, empirical evidence for such a hypothesis is limited. Our findings suggest that the accumulation of GCNVs contributes to the speciation of free‐spawning marine invertebrates during the early phase.
Hybrid zones, where two genetic groups come in contact, provide valuable opportunities for testing whether reproductive isolation is complete between the groups. The intertidal goby Chaenogobius ...annularis comprises a group in the Sea of Japan and another group in the Pacific Ocean that exhibit a substantial level of genetic divergence; however, it is unclear whether they are reproductively isolated. In this study, we analyzed six populations sampled around a transition zone (approximately 300km) between the two major groups, i.e., along the Sanriku coast of the northeastern Pacific coastline of the Japanese Archipelago, using mitochondrial DNA sequences of the cytochrome b gene, the allozyme loci of malate dehydrogenase, and eight microsatellite DNA loci. We detected considerable genetic admixture in the Taro population located at the center of the transition zone, where most individuals (98%) appeared to be post-F2 hybrids. Bayesian clustering analysis, mitochondrial DNA phylogenetic tree, and private alleles in the allozyme and microsatellite DNA loci demonstrated that contemporary gene flow has been negligible between the hybrid population and either of the two groups. These findings demonstrate the long-term isolation and self-sustaining nature of this population after ancient hybridization.
•A transition zone between two groups of Chaenogobius annularis was analyzed.•Hybridization was detected in a population at the center of the zone.•Most individuals appeared to be post-F2 hybrids with unique genetic features.•The hybrid population must be associated with ancient hybridization.
Genetic and phenotypic analyses of independent secondary contact zones between certain pairs of divergent populations offer powerful opportunities to assess whether the consequences vary with ...different environmental backgrounds. Populations of the ice goby Leucopsarion petersii are distributed throughout the Japanese archipelago and comprise genetically and phenotypically divergent groups in the Japan Sea and the Pacific Ocean. In particular, populations in the Japan Sea have a larger body size and numbers of vertebrae than those in the Pacific Ocean. Herein, we performed integrated analyses of genotypes and phenotypes of two independent secondary contact zones and investigated their consequences. Population genetic analyses revealed asymmetric introgression of the mitochondrial genome of either lineage relative to little admixture of nuclear genomes in both secondary contact zones. On phenotype analyses, vertebral numbers were clearly explained by nuclear genomic ancestry in both secondary contact zones, whereas body size was not, suggesting that a little introgression of nuclear genes regulates body size. Actually, we observed biased introgression of a candidate gene, neuropeptide Y (NPY), which potentially controls body size in the ice goby. Moreover, the body size changes in the introgressed populations possibly affect the introgression patterns of mitochondrial genomes across these zones. Collectively, our results demonstrated that genomic and phenotypic consequences of secondary contact varied in marine variable environments.
The three large abalone species in the Japanese archipelago (Haliotis discus discus, H. madaka, and H. gigantea) are closely related genetically but exhibit unique ecological characteristics. The ...shells of the three species also exhibit qualitatively unique morphological characteristics; however, only limited studies have quantitatively evaluated these differences. To address this, we quantitatively evaluated the morphological differences among shells of these three abalone species, collected from the Kyushu coast. Our morphological analyses were based on multiple quantitative features, including overall shell length, breadth, and height, respiratory pore height, apex height, and lip breadth. These analyses reveal that the shell specimens of H. gigantea were quantitatively distinct from those of H. discus discus and H. madaka. However, the morphological characteristics of H. discus discus and H. madaka specimens were not quantitatively distinct, and instead showed substantial overlap. These findings suggest that there are individuals with intermediate quantitative traits between H. discus discus and H. madaka, although the shell phenotypes of these species are typically qualitatively distinct.
Paleoenvironmental changes in marginal seas on the coast of the northwestern Pacific during the Quaternary have caused genetic differentiation and subsequent secondary contacts between populations of ...coastal organisms in this region. However, little is known about how geographical isolation and the subsequent connection events associated with these multiple marginal seas have shaped the population structure of coastal organisms in the boundary area. The coastal area of Kyushu Island of the Japanese Archipelago, where the East China Sea (ECS), the Sea of Japan (SJ), and the Pacific Ocean (PO) adjoin within a narrow region, would be a suitable field for elucidating the effect of multiple vicariances. Herein, we conducted phylogeographical analyses of the intertidal goby
Chaenogobius annularis,
focusing on populations around Kyushu Island, using partial mitochondrial (mt) DNA sequences and analysis of 8 microsatellite (ms) DNA loci. We discovered a new lineage distributed along the coast of the ECS distinct from the already-known SJ and PO lineages, which we termed the ECS lineage. This ECS lineage showed remarkable mito-nuclear discordance: mtDNA analyses indicated that the ECS lineage is a highly diverged lineage branched from the PO lineage, whereas msDNA analyses suggested that the ECS lineage is closely related to the SJ lineage. This discordance could have been due to ancient hybridization. In addition, we detected SJ-PO and ECS-SJ hybrid zones on the western Seto Inland Sea and on the northwestern coast of Kyushu, respectively. Such a complex population structure suggests that the secondary contacts after multiple isolation events among marginal seas around Kyushu have a great impact on coastal biodiversity in the area and emphasize the peculiarities of the region.
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•Perkinsus beihaiensis was detected in Mediterranean mussels in Japan.•Infected mussels were found only in Tokyo Bay.•P. beihaiensis in Japan is phylogenetically closest to South ...American isolates.•Invasion of P. beihaiensis into Japan from South America is suggested.
During analyses of the invasive Mediterranean mussel Mytilus galloprovincialis for pathologies in Tokyo Bay, infection by the protozoan parasite Perkinsus beihaiensis was found through histological examination, Ray’s Fluid Thioglycollate Medium assays, and molecular analyses. Specific PCR assays for each Perkinsus species also revealed the presence of an indigenous congeneric species, Perkinsus olseni, but P. beihaiensis was dominant in M. galloprovincialis. Sequences of the ribosomal internal transcribed spacer region I of P. beihaiensis found in Japan were genetically more similar to those found in South American countries (Panama and Brazil) than in Asian countries (China and India). Though Mediterranean mussels have become widespread in Japanese waters since their invasion in the 1930s, epidemiological surveys show that mussels collected outside Tokyo Bay are free of any Perkinsus infections. Based on these results, it was strongly suggested that P. beihaiensis invaded Tokyo Bay by transportation of bivalves originating from South America but has not yet spread to other parts of Japan. The possibility is not ruled out, however, that the parasite is indigenous in Japan but the environment in Tokyo Bay favors its transmission to Mediterranean mussels.
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