Hidden mitochondrial DNA divergence in the Lake Biwa endemic goby Gymnogobius isaza: implications for its evolutionary history

The gobiid Gymnogobius isaza is an endemic species that has adapted remarkably to the pelagic environment in Lake Biwa, Japan, a representative ancient lake in East Asia. To obtain clues that would reveal the origin and evolution of this species, we conducted phylogenetic and population genetic analyses based on partial sequences of the mitochondrial cytochrome b gene. Consistent with previous studies, our Bayesian phylogenetic analysis with a relaxed molecular clock model reconfirmed a sister relationship between G. isaza and Gymnogobius urotaenia?+?Gymnogobius petschiliensis, with a divergence time of about 2.9 million years (Myr), and provided an evolutionary rate of 3.0 %/Myr (pairwise) for their clade. Population genetic analysis revealed two distinct mtDNA groups in G. isaza, which were estimated to have diverged 0.66 million years ago (Mya) at the Lake Katata stage of Paleo-Lake Biwa, preceding the origin of the present Lake Biwa environment with its extensive deep pelagic area (0.3–0.4 Mya). A dumbbell-like haplotype network and bimodal mismatch distribution suggested that the population of G. isaza experienced secondary contact between two genetically differentiated populations. Demographic parameters from mismatch distribution analysis and Bayesian skyline plot analysis suggested that both of the mtDNA groups of G. isaza exhibited a signal of sudden population expansion at approximately the same time (80–90 thousand years ago) during the last glacial period after the development of the present Lake Biwa. These results imply the complex population history of G. isaza, including genetic isolation and secondary contact following differentiation from its relatives in the Pliocene.     

A new lentic form of the “yoshinobori” species complex, Rhinogobius spp. from Lake Biwa, Japan, compared with lake–river migrating Rhinogobius sp. OR

 The various life history strategies seen within the “yoshinobori” species complex of the genus Rhinogobius, which differentiated from an amphidromous ancestor, have been grouped ecologically into amphidromous, fluvial, and lacustrine types. In the Lake Biwa water system, two lacustrine forms exist, a newly discovered, exclusively lentic form and the already well known Rhinogobius sp. OR, which generally undergoes lake–river migration but also includes lentic individuals that share spawning grounds with the former lentic form. Detailed morphological comparisons and allozyme analysis revealed consistently clear differences between the two forms, indicating them to be distinct species. The newly discovered lentic form has many distinctive morphological features that enable it to be distinguished from sympatric Rhinogobius sp. OR: dwarfness, short snout, longitudinally slender pelvic fin, undeveloped frenum with a low lamella, low first dorsal fin in adult males, lesser caudal peduncle depth, scaleless predorsal and ventral areas, and incomplete sensory canals. The lentic form was temporarily named Rhinogobius sp. BW. The life history patterns of the lake-inhabiting populations were separated into two categories: a lake–river migratory lifestyle and an exclusively lentic lifestyle.     

A new species: Gerres microphthalmus (Perciformes: Gerreidae) from Japan with notes on limited distribution, included in the “G. filamentosus complex”

 Gerres microphthalmus sp. nov., described on the basis of the holotype and 38 paratypes, has a limited distribution in Japan, including Tanega Island, southeastern Kyushu, southern Shikoku, and southern Kii Peninsula, central Honshu. It has not been recorded from the Ryukyu Islands. The species is the fourth member of the “G. filamentosus complex,” characterized by an elongated second dorsal fin spine, the others being G. filamentosus, G. infasciatus, and G. macracanthus. Gerres microphthalmus sp. nov. is most similar to G. filamentosus in overall body appearance, but differs from the latter in having smaller eyes (8%–11% of standard length vs. 10%–16% in the latter), a higher orbit diameter ratio (as % of snout length) (93%–143% of snout vs. 71%–104% of snout), and fewer pored lateral line scales (40–43 vs. 43–46). The limited distribution pattern of the new species is discussed with G. equulus and Lates japonicus (Centropomidae) having a limited distribution similar to that of the new species. Received: June 28, 2001 / Revised: November 13, 2001 / Accepted: December 10, 2001     

Stereotyped sequence of mating behavior in the Far Eastern catfish, Silurus asotus, from Lake Biwa

 Mating behavior of the Far Eastern catfish, Silurus asotus (Siluriformes: Siluridae), was observed in a ricefield system facing the shore of Lake Biwa in mid-May to early June in 1990–1997. A set behavioral sequence similar to those of two other silurid fishes, S. biwaensis and S. lithophilus, both endemic to the Lake Biwa system, was observed: “chasing,”“clinging,”“enfolding” while “squeezing” by the male, and “circling” by the spawning pair. This form of mating behavior is quite different from that of S. asotus reported from the Ooi River system in Kyoto Prefecture, which mainly spawns in running water in ditches. Received: April 10, 2001 / Revised: November 5, 2001 / Accetped: November 20, 2001     

The physical factor inducing spawning of the Biwa catfish, Silurus biwaensis

The physical factor inducing spawning of the Biwa catfish, Silurus biwaensis (Siluriformes: Siluridae), an endemic species of Lake Biwa, was investigated on the basis of field observations on 150 nights at the spawning site, the rocky shore of the Seta River, the lake's outlet, and environmental data from April to July in 1989–1994. The catfish gathered at the spawning site when the water level of the river rapidly rose and the rocky shoal became submerged, within a wide range of water temperature (15.0°–30.0°C); their spawning was induced in relation to increases in the submerged portion of the rocky shoal. This observation suggests that water level control operations in Lake Biwa might critically affect the spawning of this and other fish species. Received: December 17, 1999 / Revised: September 13, 2000 / Accepted: January 16, 2001     

Isolation and characterisation of microsatellite loci in Calystegia soldanella (Convolvulaceae), an endangered coastal plant isolated in Lake Biwa,Japan

Eight microsatellite loci of Calystegia soldanella useful for comparisons of the genetic structure of isolated populations in the ancient Lake Biwa and coastal populations in Japan were isolated and characterised. The number of alleles ranged from 2 to 5. The expected (H _E) and observed (H _O) heterozygosities were 0.097–0.583 and 0.000–0.380, respectively, from 100 individuals from Lake Biwa and coastal populations. Seven of the eight loci exhibited significantly fewer heterozygotes than expected based on the Hardy–Weinberg equilibrium (P < 0.05). These primers amplifying microsatellites in C. soldanella may provide a population genetics tool useful in the establishment of a conservation strategy.     

Annual variations in length–weight relationship of Gymnogobius isaza (Tanaka, 1916) from Lake Biwa,Japan

The study describes length–weight relationships (LWRs) of Gymnogobius isaza (Tanaka, 1916) collected from Lake Biwa, Japan, between 1975 and 2002. Annual values of the allometric exponent of LWRs ranged from 2.47 to 3.42. This study is one of the few to report annual variations in LWR.     

A new species of the cardinalfish genus Gymnapogon (Perciformes, Apogonidae) from the Red Sea

 A new cardinalfish species, Gymnapogon melanogaster, is described from two specimens collected at night in the Gulf of Aqaba, Eilat, Israel. This species is characterized by having 9 dorsal and 8 anal fin soft rays; 14–15 pectoral fin rays; 2 + 11 gill rakers; a flat, bifurcated preopercular spine; a naked body without a papillae network; black pelvic fins; and a black stomach. It is similar to Gymnapogon vanderbilti (Fowler, 1938) that is known only from the Line Islands of the Central Pacific Ocean. Received: December 26, 2001 / Revised: June 10, 2002 / Accepted: June 24, 2002 Acknowledgments We thank D. Didier and M. Sabaj of the Academy of Natural Sciences, Philadelphia, for loans of and for taking data from type specimens; T.H. Fraser of the Mote Marine Laboratory, Sarasota, kindly provided data on type specimens. We are grateful to E. Heemstra of the South African Institute for Aquatic Biodiversity, Grahamstown, South Africa, for the artwork presented in this article and to A. Lerner of the Hebrew University, Jerusalem, for his assistance in collecting the specimens. Correspondence to:Ofer Gon     

Genetic variations estimated from PCR-RFLP analysis of two morphs of the freshwater goby <Emphasis Type="Italic">Rhinogobius</Emphasis> in the Lake Biwa water system

The freshwater goby Rhinogobius is the most abundant fish in the shore area of Lake Biwa, Japan. Recently, it has been reported that two morphs of Rhinogobius inhabit this lake. In this study, genetic variations in Rhinogobius sp. OR (Orange-type) and Rhinogobius sp. BW (Biwa-type) in the Lake Biwa water system have been investigated using polymerase chain reaction-based restriction fragment length polymorphism (PCR-RFLP) analysis of mitochondrial DNA, including the variable D-loop region. Samples of Rhinogobius sp. OR were collected from the middle sites of three rivers, two outlets, and two lakeshore sites, whereas samples of Rhinogobius sp. BW were taken from two lakeshore sites. Rhinogobius sp. OR and Rhinogobius sp. BW did not share any haplotypes, suggesting that PCR-RFLP analysis is effective for distinguishing between these species of goby. The haplotype diversity of Rhinogobius sp. OR (0.214–0.543) was lower than that of Rhinogobius sp. BW (0.543–0.682). There were no significant differences in haplotype frequencies between Rhinogobius sp. BW groups from the two localities. In addition, haplotype frequencies in Rhinogobius sp. OR did not differ significantly among samples from the middle sites of rivers, the outlets, and the shores. These results indicate that in Rhinogobius sp. OR there is frequent gene flow among fish inhabiting different sites, and that this species of goby consists of a single population throughout the Lake Biwa water system.     

Disturbance of the indigenous gene pool of the threatened brook lamprey Lethenteron sp. S by intraspecific introgression and habitat fragmentation

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 <0.01), one introgressed population (0.71 and 0.57) and one population almost displaced by exogenous genotypes (0.93 and 0.96). Samples from three tributaries with weirs were genetically differentiated from the others by using pairwise F _ST and Bayesian analyses; the results suggested isolation by the weirs. Reduced mitochondrial DNA diversity was observed in 1 of the 3 samples probably due to reduced population size. These findings indicate that the indigenous lamprey populations in the Jinzu River are seriously affected by introgression with exogenous genotypes via unintentional introduction and habitat fragmentation by weirs.     

Descriptive morphology of the eggs,larvae, and juveniles of two cyprinid fishes belonging to the <Emphasis Type="Italic">Zacco temminckii</Emphasis> species' group

 Embryonic, larval, and juvenile development of two cyprinid species belonging to the Zacco temminckii species' group, Z. temminckii (Temminck and Schlegel) and Zacco sp. (type A), are described and compared with each other from laboratory-reared and wild specimens. The eggs of both species were closely similar except in diameter [1.92–2.20 mm in Z. temminckii vs. 1.60–1.75 mm in Z. sp. (type A)], being demersal, almost spherical in shape, transparent and unpigmented, with a pale yellow yolk, and no oil globule. Hatching occurred 40–53 h after fertilization in Z. temminckii and after 47–60 h in Z. sp. (type A). The newly hatched larvae of both species [4.9–5.3 mm in body length (BL) in Z. temminckii and 3.5–4.8 mm BL in Z. sp. (type A)] also resembled each other, having a large transparent pear-shaped yolk and lacking body pigmentation. Myomere counts of Z. temminckii and Z. sp. (type A) larvae and juveniles were 24–27 + 14–17 = 41–42 and 23–27 + 14–17 = 40–41, respectively. The yolk was completely absorbed at 8.3 mm BL in Z. temminckii and at 6.6 mm BL in Z. sp. (type A). Notochord flexion was initiated and completed at 7.8 mm BL and 8.2 mm BL in Z. temminckii and at 6.3 mm BL and 6.6 mm BL in Z. sp. (type A), respectively. Aggregate numbers of all fin rays were completed at 17 mm BL in Z. temminckii and 13 mm BL in Z. sp. (type A). Although the morphology of larvae and juveniles of both species was very similar, differences in body length of each developmental stage, the duration and process of disappearance of the adipose finfold, the anal fin ray counts, and pigmentation on the lateral body surface were clearly recognized. Received: August 10, 2001 / Revised: March 14, 2002 / Accepted: March 27, 2002     

Behavior and distribution of upstream-migrating juvenilerhinogobius sp. (The orange form)

Upstream-migration of juvenileRhinogobius sp. OR was studied along the Ado River, a tributary of Lake Biwa. Juvenile gobies, mainly 18–21 mm in standard length, migrated from the lake in a belt of about 3 m wide in lower reaches and about 10–20 cm wide in middler reaches. Their upstream-migration was restricted to places shallower than 20 cm with bottom current velocities less than 20 cm/sec. Individual migration speed varied between 4.2–8.9 m/min at places with bottom current velocity of 8.8–20.0 cm/sec, slowing down with increasing current velocity. Most active migration occurred between 14:00 and 16:00, number of upstream-migrating juveniles decreasing with distance from the river mouth. Riffles in the mid-and upper reaches, having few slow current areas, probably present barriers to upstream-migration of the juvenile gobies, although both adults and subadults of the species are distributed in more upper reaches.     

Upeneus australiae, a new goatfish (Mullidae: Perciformes) from Australia

 Upeneus australiae sp. nov. is described on the basis of 14 specimens collected from Australian waters. Although it belongs to the seven-spined group of Upeneus, now comprising five species, U. australiae is distinguished from its congeners by the combination of the following characters: 6–7 + 16–18 (modally 7 + 17) gill rakers, ectopterygoids without teeth, five and six black oblique bars on upper and lower caudal lobes, respectively, and peritoneum transparent with small black spots. Received: July 26, 2001 / Revised: November 2, 2001 / Accepted: December 4, 2001     

Influence of edaphic and climatic factors on dynamics of root colonization and spore density of vesicular-arbuscular mycorrhizal fungi in Acacia farnesiana Willd. and A. planifrons W.et.A.

 A study was conducted to assess the dynamics of vesicular-arbuscular mycorrhizal (VAM) fungi associated with Acacia farnesiana and A. planifrons in moderately fertile alkaline soils. The intensity of root colonization by VAM fungi and the distribution of VAM fungal structures varied with host species over a period of time. The occurrence of vesicles with varied morphology in the mycorrhizal roots indicates infection by different VAM fungal species. This was further confirmed from the presence of spores belonging to different VAM fungal species in the rhizosphere soils. Root colonization and spore number ranged from 56% – 72% and 5 – 14 g^{–  1}soil in A. farnesiana and from 60% – 73% and 5 – 15 g^{–  1} soil in A. planifrons. Per cent root colonization and VAM spore number in the rhizosphere soil were inversely related to each other in both the Acacia species. However, patterns of the occurrence of VAM fungal structures were erratic. Spores of Acaulospora foveata, Gigaspora albida, Glomus fasciculatum, G. geosporum and Sclerocystis sinuosa were isolated from the rhizosphere of A. farnesiana whereas A. scrobiculata, G. pustulatum, G. fasciculatum, G. geosporum and G. microcarpum were isolated from that of A. planifrons. The response of VAM status to fluctuating edaphic factors varied with host species. In A. farnesiana though soil nitrogen (N) was positively correlated with root colonization, soil moisture, potassium and air temperature were negatively correlated to both root colonization and spore number. Per cent root colonization and spore number in A. planifrons were negatively related to each other. Further, in A. planifrons as the soil phosphorus and N were negatively correlated with the density of VAM fungal spores, the same edaphic factors along with soil moisture negatively influenced root colonization. Received: 16 May 1995 / Accepted: 7 February 1996     

The origins of limnetic forms and cryptic divergence in Gnathopogon fishes (Cyprinidae) in Japan

The cyprinid species of the genus Gnathopogon, exhibiting flexible morphological and ecological variation, include limnetic life forms. We examined the origin of the limnetic forms and the population divergence of the Japanese Gnathopogon species, using molecular phylogenetic and phylogeographic analyses. A Bayesian phylogenetic inference approach based on mtDNA cytochrome b sequence data revealed three major lineages in G. elongatus. One of them formed a monophyletic group with the limnetic species G. caerulescens, which is endemic to an ancient lake, Lake Biwa. The divergence of the G. caerulescens lineage was estimated to date back to the early Pleistocene. This precedes the formation of the extensive pelagic environment in the present Lake Biwa. However, the recent genetic divergence of G. caerulescens was inferred to originate in the present Lake Biwa in the late Pleistocene. Another lacustrine population in the Mikata Lakes was shown to belong to a different lineage from G. caerulescens. The majority of the population possessed unique, but non-monophyletic, haplotypes, suggesting a short evolutionary history. One of the cryptic lineages of G. elongatus discovered in the Ina Valley, the lower area of Lake Suwa, might be related to the extinct lacustrine subspecies G. elongatus suwae, which has been replaced by introduced congeners. The previous and ongoing introductions of Gnathopogon fishes would have produced genetic disturbance to the indigenous populations.     

Landmark-based morphometric analysis of the body shape of two sympatric species, <Emphasis Type="Italic">Ctenopharynx pictus</Emphasis> and <Emphasis Type="Italic">Otopharynx </Emphasis>sp. “heterodon nankhumba” (Teleostei: Cichlidae), from Lake Malawi

 Morphological differences in body shape of two sympatric benthophagous cichlid species from Lake Malawi, Ctenopharynx pictus and an undescribed species, Otopharynx sp. “heterodon nankhumba,” were investigated using geometric morphometric methods. From digitized data of landmark points on lateral profiles of fishes, the shape of each species was compared by the thin-plate spline method. Statistical analyses revealed significant variation in both uniform and nonuniform components of shape between the two species. From the splines generated, it was revealed that most of the significant variation between the two species occurs in the head region. Specifically, C. pictus has a longer and deeper head than Otopharynx sp. In addition, the mouth of C. pictus is larger than that of Otopharynx sp. In the trunk region, C. pictus has a shorter abdominal cavity, which may indicate possession of shorter intestines than Otopharynx sp. The variation in gross head morphology and intestinal length may reflect interspecific differences in trophic ecology, possibly facilitating the coexistence of the two species through resource partitioning.     

Nitrogen-stable isotopic signatures of basal food items, primary consumers and omnivores in rivers with different levels of human impact

We examined how nitrogen-stable isotopic signatures of food web components (basal resources, primary and lower consumers, and omnivores) in rivers change with increasing levels of human population density (HPD) in their watersheds. Samples were collected from 22 rivers flowing in the Lake Biwa basin, Japan. Among three potential resources at the base of food webs (epilithon, benthic and suspended particulate organic matter), the mean isotopic values (δ¹⁵N) of the epilithon (4.5–7.8%) were consistently higher than those of other items (1.9–4.2%) and displayed the most pronounced elevation (by 3.3%) with increasing HPD. The mean δ¹⁵N values of the individual taxa of lower consumers (bivalve, snail and caddisfly) tended to increase with increasing HPD, although the pattern and the extent of the elevation were highly variable among the taxa. These results suggest a taxon-specific feature in the N source (or sources) of lower consumers. Our data suggested that human activities (e.g. nutrient loading) potentially induce changes in the N baselines of river food webs. The major N source of bivalves appeared to be shifted from suspended particulate organic matter to other items with increasing HPD. Trophic levels of goby fish (Rhinogobius sp. OR) and shrimp (Palaemon paucidens), being estimated to be at 2.4–3.8 and 2.1–3.4, respectively, did not differ significantly among rivers with different HPD levels. An erratum to this article can be found at