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Freshwater sculpins, grouped by their common ecological characteristic of freshwater habitats, comprise the species from the genera Cottus, Trachidermus, Mesocottus and Myoxocephalus as well as the Baikal sculpins. These fishes are typically coldwater-adapted, having probably originated polyphyletically from ancestral species of marine sculpins. Gottus, the most speciose taxonomic group, includes at least 64 species and is distributed throughout the fresh waters of the northern part of the Northern Hemisphere. Indinidual species have diverse life histories, such as fluvial, lacustrine, catadromous, and freshwater amphidromous. The second most abundant group, the Baikal sculpins, includes 33 species in 12 genera representing 3 families, and comprises many benthic, and a few bentho-pelagic and pelagic species. The freshwater sculpins belonging to Trachidermus, Mesocottus and Myoxocephalus include only one or two species in each genus. Recent molecular phylogenetic analyses of Cottus species, Baikal sculpins and their relatives have demonstrated mainly that (1) Cottus kazika is a sister taxon to Trachidermus fasciatus (designated lineage A), (2) Cottus species, except for C. kazika, and the Baikal sculpins are monophyletic, (3) on the basis of (1) and (2), Cottus as presently recognized is not monophyletic, and (4) the Major monophyletic lineages include 7 lineages: lineage B from Eurasia, lineages C and D from East Asia, the Cottopsis clade (sensu Copeia 2005:303–311, 2005) from the west coast of North America, the Cottus clade from the Circum-Arctic sea, the monophyletic Baikal sculpins, and the Uranidea clade. These findings suggested that the monophyletic freshwater sculpins that comprise the lineage A and the 7 other lineages may undergone two major radiations, one having occurred in the fresh water Cottus species in the northern part of the Northern Hemisphere, and the other in the Baikal sculpins in the Lake Baikal, the world’s oldest freshwater lake. Through these adaptive radiations, a tremendous diversity of morphological, ecological, physiological and life historical traits now exists in the freshwater sculpins.

To examine how territorial males counter reproductive parasites, we examined the paternity of broods guarded by territorial males using 5 microsatellite loci and factors that determine siring success in a wild population of the Lake Tanganyika cichlid Lamprologus lemairii. Females enter rock holes (nests) and spawn inside, and territorial males release milt over the nest openings. Sneakers attempt to dart into the nests, but territorial males often interrupt the attempt. The body size of territorial males (territorial defense ability) and the size of nest opening (the ability to prevent sneakers from nest intrusions) are predicted to be factors that affect paternity at the premating stage, whereas milt quality traits are factors that affect paternity at the postmating stage. Parentage analyses of 477 offspring revealed that most clutches have few or no cuckolders, and territorial males sired >80% of eggs in 7 of the 10 analyzed clutches. Larger territorial males that spawned in nests with narrower openings had greater siring success. In contrast, none of the milt traits affected the siring success. These suggest that territorial male L. lemairii adopt premating strategies whereby they effectively prevent reproductive parasitism.

Information on migration ecology is important for effective conservation and management of fishery resources, particularly diadromous animals. We investigated the genetic population structure and gene flow pattern of anadromous Arctic lamprey Lethenteron camtschaticum by analyzing polymorphic microsatellite loci. Bayesian population structure analysis was used to estimate the existence of two genetically divergent ancestral sources and latitudinal gradual changes of their frequencies among the present populations. When hypotheses of historical migration models were tested using coalescent-based methods, the best model was found to be an n-island model assuming equal population size and reciprocal migration among all populations. These results suggest that L. camtschaticum has considerable ability to migrate long distances in the sea and has lower homing abilities. For resource management of L. camtschaticum, unconstrained gene flow across all populations should be maintained. The present findings might be beneficial for conservation and contribute the sustainable use of L. camtschaticum resource.

Freshwater sculpin dwelling in Lake Chuzenji, Nikko, Kanto District, Japan, was identified as the lacustrine type of Cottus reinii, Utsusemikajika, by using a combination of pectoral fin ray counts (15–17, mode 16), mitochondrial DNA variations and egg size (1.33 ± 0.06 mm). We suppose that C. reinii in Lake Chuzenji was introduced unintentionally from Lake Biwa along with either Oncorhynchus masou subsp. or Sarcocheilichthys variegatus microoculus during the late nineteenth to early twentieth centuries. This is the first report of an establishment of the lacustrine type of C. reinii outside of Lake Biwa.

Artificial introduction and habitat fragmentation affect the indigenous gene pools of fluvial animals. To investigate the effect of human activities on the genetic population structure of vulnerable brook lamprey Lethenteron sp. S in a single river system, samples from 12 tributaries of the Jinzu River, Japan, were analyzed using mitochondrial and microsatellite DNA markers. Exogenous Lake Biwa (Japan) haplotypes and alleles were detected in lampreys from several Jinzu River tributaries. Since Lake Biwa is the source of the commercial ayu fish Plecoglossus altivelis that is introduced in the Jinzu River, the exogenous Lake Biwa lamprey genotypes in the Jinzu River probably originated from the Lake Biwa lampreys that were unintentionally introduced along with the ayu fish. Bayesian admixture and mitochondrial DNA analyses revealed various genetic disturbance phases of the exogenous genotypes in the Jinzu River, such as the six indigenous populations, four admixed populations with low frequencies (average admixture proportion = 0.02–0.04; exogenous haplotype proportion

The freshwater sculpins, genus Cottus (Teleostei; Cottidae), comprise bottom-dwelling fishes that exhibit various life-history styles, having radiated throughout Northern Hemisphere freshwater habitats. The phylogenetic relationships among Cottus and related taxa were estimated from mitochondrial DNA 12S rRNA and control region (CR) sequences, the freshwater sculpins examined falling into five lineages (A-E). Lineage A consisted of Trachidermus fasciatus and C. kazika, both having a catadromous life-history. The remaining species (lineages B-E) spawn in freshwater habitats regardless of life-history (amphidromous, lacustrine or fluvial), suggesting that the various life-history types post-dated a common ancestor of lineages B-E. Molecular clock estimates suggested a Pliocene-Pleistocene radiation (or Miocene-Pliocene from the alternative clock) of lineages B-E. In eastern Eurasia, speciation with life-history changes to amphidromous or fluvial styles has apparently occurred independently in some lineages, as a general pattern. Mitochondrial DNA CR phylogeny showed the monophyletic Baikalian cottoids (Cottoidei) to be nested within Cottus and Trachidermus, suggesting that the former ecologically and morphologically divergent cottoids may have originated from a single lineage which invaded the ancient lake.

Specimens of the Cottus pollux species' group collected from the upper part of the Honmyo River, Nagasaki Prefecture, Japan, were subjected to morphological and allozyme analyses to place them into one of the recognized valid taxa, viz. small-egg type (SE type), middle-egg type (ME type), or large-egg type (LE type). They were identified as ME type on the basis of specific morphological characteristics, such as laterally depressed cross-sectional shape at posterior half of the body and deep caudal peduncle, and by having a diagnostic allozyme allele (MEP * 54). This ME-type population is the first recorded from Kyushu Island, Japan. An ecological survey of the population revealed that females spawned larger eggs (2.8–3.2 mm in diameter) than those of other amphidromous populations, from which well-developed yolk-sac larvae of about 8.0 mm TL were hatched out. In addition, ME-type specimens collected on 25 and 26 May 2001 included 15 sex-unknown juveniles ranging from 18.8 to 30.2 mm SL, suggesting that they represented larvae hatched out on a nearby spawning ground, with no experience of downstream migration into Isahaya Bay. This observation strongly suggests that the ME-type population in the Honmyo River has a fluvial lifestyle, being different from other amphidromous populations. The former population may have arisen from an amphidromous ancestor through changes in egg size and early ontogenetic development.

The influence of fragmentation on local genetic population structure of the fluvial sculpin Cottus nozawae was studied by comparing populations in two regions: the Tohoku District (the southern margin of the species' native range) and Hokkaido Island (the center of its native range), Japan, based on restriction fragment length polymorphism analysis of mitochondrial DNA amplified by means of the polymerase chain reaction. Relatively high genetic divergences were found among populations from different regions. An analysis of molecular variance showed that ΦSTvalues among samples from the same river system in the Tohoku District were higher than among samples from Hokkaido Island. Heterogeneities in haplotype composition among tributary populations and among distinctive clusters were also found in the Tohoku District river system. Cottus nozawae in the Tohoku District are distributed patchily in headwater streams and may be thermally isolated. As a result, there appears to be little gene flow among tributary populations from different areas that exhibit divergence due to random genetic drift and have small effective population sizes.

The fluvial sculpin, Cottusnozawae, is a coldwater-adapted fish distributed in Hokkaido Island and the northeastern part of Honshu Island (Tohoku District), Japan. Mitochondrial DNA (mtDNA) control region sequencing was used to investigate the geographic distribution of genetic variation and phylogeography of C. nozawae. Most populations possessed unique haplotypes, few being shared across river systems. Phylogenetic analysis of the sequences of the mtDNA control region and adjacent regions of C. nozawae revealed three distinct phylogenetic groups that differed by 3.05% to 3.11%, corresponding to distinct geographic regions, Hokkaido Island, northern Tohoku District, and Yamagata Prefecture (southwestern Tohoku District), respectively. The divergence times of three groups were estimated to be about 1.5 million years ago by applying a general rate for mtDNA, suggesting that the divergence among them might have occurred in the early Pleistocene. Divergence among the haplotypes within the group from the northern Tohoku District was also high (1.84%), no haplotypes being shared by local populations in different river systems in this region. Local populations from a single river system in this region comprise a distinct lineage that differed from other river systems. Such genetically divergent population structures among the different regions and river systems are considered to have resulted mainly from long-term isolation and restricted gene flow among river systems, probably promoted by the fluvial benthic life history and low dispersal ability of this species.

In this study, we examined nucleotide sequences from the first half of the mitochondrial control region gene to test for genetic differentiation in an amphidromous sculpin, Cottus pollux middle-egg type (ME) (Cottidae), obtained from 19 localities across its distribution range. Spatial analysis of molecular variance revealed five divergent groups of related haplotypes among this populations. Analysis with Migrate software revealed that gene flow was quite restricted among the groups, although it occurred practically between neighboring groups. It has previously been reported that the population structure among the amphidromous fishes of the various islands is low or non-existent, and is characterized mainly by the duration of the pelagic larval life. However, the present study demonstrated that the various C. pollux ME populations were different both among the islands, and within the island of the Japanese Archipelago. Our finding indicate that the unique population structure of C. pollux ME may be influenced not only by the extent of the pelagic larval phase of the species but also by the seasonal differentiation of its dispersal phase.

Because freshwater fishes only use freshwater drainages for their colonization, phylogeographic patterns of them have been interpreted in conjunction with physical evidence of historical drainage patterns. The phylogeography of freshwater fishes has an important role in understanding the formation of regional biodiversity. In North America and Europe, numerous studies of phylogeography of freshwater fishes have clarified lineage distributions and colonization histories of them with reference to drastic disturbance during glacial cycles in Pleistocene (reviewed in Bernatchez and Wilson, 1998; Hewitt, 2004). In contrast to North America and Europe, few studies have been on fishes in Siberia and northeastern Asia. Phylogeographic patterns of Siberian fishes were partially discussed in studies of Holarctic fishes, such as of Arctic charr (Brunner et al., 2001), whitefish (Bernatchez and Dodson, 1994) and burbot (Van Houdt et al., 2003). In these studies, populations in Siberia comprise a single lineage (Siberian lineage) that has less diversity among populations. These studies suggest simpler phylogeography of fishes in Siberia despite their geographical width. On the other hand, the Arctic grayling, Thymallus arcticus, is genetically polymorphic in Siberia, suggesting the existence of several refugia in Siberia (Froufe et al., 2003, 2005; Weiss et al., 2006). General patterns of freshwater fish phylogeography in Siberia seem to be far from resolved.

To elucidate the causes of clinal life-history variation in male freshwater amphidromous Cottus hangiongensis found along the river courses, we ex- amined the genetic composition of upstream, mid- stream, and downstream groups using microsatellite DNA markers and different growth patterns among juvenile individuals before and after they ascended a small, steep mountainous river in southern Hokkaido, Japan. Microsatellite allele frequencies indicated that the samples collected from three different habitats appeared to represent a panmictic population and no genetic dif- ferences were found among the three groups. Ecological field surveys showed that juveniles greatly depended on the timing of their ascent into the river from the sea, and that larger juveniles were able to disperse to more up- stream areas and grew larger during the period after they migrated up to the mouth of the river. These results suggested that clinal life-history variations may be in- duced through phenotypic plasticity and that earlier as- cent of juveniles from the mouth of river may be an important source of variation.