Landscape genetic analysis of the tropical freshwater fish Mogurnda mogurnda (Eleotridae) in a monsoonal river basin: importance of hydrographic factors and population history

1. We performed spatial genetic analyses, incorporating landscape genetic methods using microsatellite data and phylogeographic analyses using mtDNA data, to identify the principal factors that determine population heterogeneity of the tropical freshwater fish, Mogurnda mogurnda, in the Daly River, northern Australia. We tested the individual and interactive effects of several environmental variables on spatial genetic patterns, including metrics relating to connectivity (i.e. stream distance, maximum stream gradient and elevation), habitat size (i.e. mean annual discharge) and a categorical variable relating to population history, as determined by mtDNA phylogeographic analyses. The Daly River is geomorphologically and hydrologically complex, and M. mogurnda has life history traits that limit its dispersal potential at river basin scales. Thus, we predicted that variables relating to connectivity would be the most important landscape factors driving population structure of the species. 2. Tree‐based phylogeographic analyses indicated four divergent mtDNA lineages within M. mogurnda in the Daly River, although three of the lineages were sympatric in various combinations and did not correspond with microsatellite groups identified by assignment tests. The allopatric mtDNA lineage detected in the uppermost part of the catchment was also identified as being highly differentiated by the microsatellite data, strongly suggesting that it may be a cryptic species. This site was therefore excluded from subsequent landscape genetic analyses. 3. Analyses of Molecular Variance indicated that M. mogurnda has a hierarchical population structure in the Daly River, thus supporting theoretical expectations that hierarchically arranged river habitats in dendritic systems impose hierarchal population structures on lotic species. 4. All landscape genetic analyses rejected stream distance, and supported stream gradient, as the major determinant of spatial genetic variation in M. mogurnda in the Daly River. Support for elevation as a determinant of spatial genetic patterns differed among the landscape genetic methods. Several of the landscape genetic methods also indicate that population history, including secondary contact between divergent and formerly allopatric genetic lineages, has a strong influence on spatial genetic patterns within M. mogurnda in the Daly River. 5. This study demonstrates the need to consider multiple environmental factors, especially factors relating to connectivity, and their interactions in spatial genetic analysis, rather than just geographic distance. Importantly, it demonstrates the need to account for population history and evolutionary divergences in landscape genetic analyses.     

Phylogeography of the freshwater fish, Mogurnda adspersa, in streams of northeastern Queensland, Australia: evidence for altered drainage patterns

A phylogeographic survey was used to elucidate the relative roles of historical processes and contemporary gene flow in structuring the genetic pattern observed with Mogurnda adspersa. This species of freshwater fish is found in the rivers and streams of the northeastern highlands of Queensland, Australia. Specifically, this project focused on populations in the Tully and Herbert Rivers in the Atherton Tablelands. Sequence analysis indicated that three distinct clades exist in the headwaters of the Tully River. The population sampled from one of the Tully River streams (Cheetah Creek) contained haplotypes that displayed ≈ 3.4% sequence divergence from other haplotypes detected in this river. Furthermore, these haplotypes formed part of the clade which exists throughout not only the Herbert River but other surrounding drainages in the area. These results support the hypothesis that the current genetic structure is strongly affected by changes in drainage patterns due to geomorphological processes that occurred in the recent past.     

Larval ontogeny and morphology of the fire-tailed gudgeon, Hypseleotris galii (Eleotridae)

The larval ontogeny of Hypseleotris galii is described and illustrated. 'Premature' yolk sac larvae hatch with unpigmented eyes and no mouth. 'Late' yolk sac larvae hatch with pigmented eyes and a functional mouth. Hatching glands are distributed on the head and ventral surface of the body. The yolk is absorbed and the larvae begin feeding 6 days after hatching. Larval development is completed 74 days after hatching. Hypseleotris galii larvae have six pairs of naked neuromasts: two pairs on the head and four pairs on the body. The significance of these results to developmental strategies in Hypseleotris species is discussed.     

Sound production by the gudgeon, Gobio gobio L., a common European freshwater fish (Cyprinidae, Teleostei)

Acoustic signals emitted by the gudgeon are described and the context of sound production is considered.
In aquaria, gudgeons produce creaking sounds of differing duration, which are always built up of single bursts. Each burst is composed of a series of rapidly repeated short pulses. Vocalization is correlated with the level of activity: it increases at higher temperatures and decreases when fish are disturbed. After acclimatization to the aquarium, fish which formerly showed a diurnal pattern of activity became active at all times of the day and night. Gudgeon called as a reaction to digging by other members of the group and a variety of disturbances, the latter including being touched or hindered by a conspecific or being frightened by the sudden movement of another fish. The fact that only certain interactions in a gudgeon shoal are accompanied by sound production is discussed.     

Cytonuclear evidence for hybridogenetic reproduction in natural populations of the Australian carp gudgeon (Hypseleotris: Eleotridae)

Although most vertebrates reproduce sexually, a small number of fishes, amphibians and reptiles are known in which reproduction is asexual, i.e. without meiotic recombination. In fishes, these so-called unisexual lineages usually comprise only females and utilize co-occurring males of a related sexual species to reproduce via gynogenesis or hybridogenesis. Here, we examine patterns of microsatellite and mitochondrial DNA (mtDNA) variation in a widespread group of freshwater fishes (carp gudgeons; Hypseleotris spp.) to investigate a long-standing proposal that this group includes unisexual forms. We show that the mtDNA genome of most carp gudgeons in tributaries of the Goulburn River belongs to one of two deeply divided clades (～10% cyt b divergence) and that nuclear variation divides the same individuals into four distinct groups. Group 1 exhibits the genotypic proportions of a random mating population and has a 1:1 sex ratio. Two other groups are extremely sex-biased (98% male, 96% female), exhibit excess heterozygosity at most loci and share at least one allele per locus with group 1. We propose that these two groups represent 'unisexual' hybridogenetic lineages and that both utilize co-occurring group 1 as sexual host. Interestingly, the fourth distinct group appears to represent hybrid offspring of the two putative hybridogenetic lineages. The propagation of clonal haploid genomes by both males and females and the ability of these clones to unite and form sexually mature diploid hybrid offspring may represent a novel mechanism that contributes to the dynamics of coexistence between hybridogenetic lineages and their sexual hosts.     

Diel abundance, migration and feeding of fish larvae (Eleotridae) in a floodplain billabong

Eleotrid larvae (2.1–16 mm) were collected from surface waters of a billabong in south-eastern Australia. Estimates of larval density in plankton net samples at night averaged 148.3 larvae per m³ and 16.6 larvae per m³ during the day. In contrast, pump samples provided density estimates of 8.3 larvae per m³ at night and 0.9 larvae per m³ during the day. Larval densities did not differ between open water, snag (fallen tree) and Typha habitats, but Typha habitats yielded larger larvae than other habitats. 32.9% of larvae in pump samples were damaged and unmeasurable, creating a bias favouring larger larvae. The modal length of larvae in net samples at night was 5–6 mm, compared with 3–4 mm during the day, reflecting both greater net avoidance by larger larvae during the daytime and dispersal of smaller larvae from the surface at night. Dispersion patterns of larvae suggest that classes of larvae smaller than, and larger than 5.0 mm exhibit reciprocal diel vertical migration behaviour linked to ontogenetic changes in diet. Larvae less than 5 mm fed only during the day and preyed exclusively on rotifers, whereas larger larvae continued to feed at night and consumed mostly planktonic crustaceans.     

Population genetics of a widely distributed small freshwater fish with varying conservation concerns: the southern purple-spotted gudgeon, <Emphasis Type="Italic">Mogurnda adspersa</Emphasis>

Genetic variation plays a pivotal role in species viability and the maintenance of population genetic variation is a main focus of conservation biology. Threatened species often show reduced genetic variation compared to non-threatened species, and this is considered indicative of lowered evolutionary potential, compromised reproductive fitness, and elevated extinction risk. The southern purple-spotted gudgeon, Mogurnda adspersa, is a small freshwater fish with poor dispersal potential that was once common throughout the Murray–Darling Basin (MDB) and along the central east coast of Australia. Its numbers and distribution have shrunk dramatically in the MDB due to flow alteration, degradation of habitat, decreasing water quality, and introduction of alien species. We used microsatellite DNA markers to assess population structure and genetic variation at both large (i.e. across basin) and fine (i.e. within river catchments) spatial scales using a substantial sampling effort across the species range (n = 579 individuals; 35 localities). The results consistently indicated very low levels of genetic variation throughout, including along the east coast where the species is relatively common. At the broader scale, three highly differentiated groups of populations were found, concordant with previously reported genealogical distinctiveness. Hence we propose each group as a distinct Evolutionarily Significant Unit. We also inferred a minimum of 12 management units in M. adspersa, with no appreciable gene flow between them. Our study discloses findings relevant for both long- and short-term management, as it informs on the geographic context in which conservation priorities should be defined and specifies biological units for population monitoring and translocations.     

Society, demography and genetic structure in the spotted hyena

Spotted hyenas (Crocuta crocuta) are large mammalian carnivores, but their societies, called 'clans', resemble those of such cercopithecine primates as baboons and macaques with respect to their size, hierarchical structure, and frequency of social interaction among both kin and unrelated group-mates. However, in contrast to cercopithecine primates, spotted hyenas regularly hunt antelope and compete with group-mates for access to kills, which are extremely rich food sources, but also rare and ephemeral. This unique occurrence of baboon-like sociality among top-level predators has favoured the evolution of many unusual traits in this species. We briefly review the relevant socio-ecology of spotted hyenas, document great demographic variation but little variation in social structure across the species' range, and describe the long-term fitness consequences of rank-related variation in resource access among clan-mates. We then summarize patterns of genetic relatedness within and between clans, including some from a population that had recently gone through a population bottleneck, and consider the roles of sexually dimorphic dispersal and female mate choice in the generation of these patterns. Finally, we apply social network theory under varying regimes of resource availability to analyse the effects of kinship on the stability of social relationships among members of one large hyena clan in Kenya. Although social bonds among both kin and non-kin are weakest when resource competition is most intense, hyenas sustain strong social relationships with kin year-round, despite constraints imposed by resource limitation. Our analyses suggest that selection might act on both individuals and matrilineal kin groups within clans containing multiple matrilines.     

Helminths from the fish Dormitator maculatus (Osteichthyes: Eleotridae) from Alvarado, Veracruz, Mexico

Dormirator maculatus (n=184) was collected in the Alvarado Lagoon, Mexico during a year period (Oct. 1993-1994). In the helminthologic review, the presence of Clinostomum complanatum (82.3%), Neoechinorhynchus golvani (76.1%), Spiroxys sp. (21.3 %), and Camallanus sp. (6.2%) was registered. Reduction of the hematocrit caused by such infection is significant (t, a= 0.05).     

River drying influences genetic variation and population structure in an Arctic freshwater fish

Conserving biodiversity in an era of rapid climate change requires understanding the mechanisms that influence dispersal, gene flow and, ultimately, species persistence. This information is becoming critical for conserving key species in rapidly warming places such as the Arctic. Arctic freshwater fish not only face warmer conditions, but also the drying of tundra streams due to climate change. Here, we examined population structure, gene flow, and the influence of landscape features on the neutral genetic variation of the Arctic grayling on Alaska’s North Slope. We estimated the number of genetically distinct clusters and determined effective population sizes for and patterns of gene flow among geographic regions. We predicted that river distance, river drying, distance to the coast, and elevational gradient would influence genetic differentiation for Arctic grayling. Bayesian clustering and discriminant analysis of principal components found support for five or six genetic clusters roughly corresponding to downstream and headwater subwatersheds. Estimates of gene flow revealed asymmetric downstream bias. River distance and river dry zones were significantly associated with increasing genetic differentiation among sampling locations despite this species' high dispersal capability and the temporary nature of dry zones. Isolation and downstream-biased dispersal could contribute to high levels of inter-population genetic variation among the headwaters of the North Slope Arctic grayling metapopulation, which might be particularly important for species conservation during rapid climate change. More generally, small, isolated populations might drive particular alleles to higher frequencies due to selection or drift, thus promoting the genetic potential for rapid evolutionary changes under future climate change.

     

Subspecific relationships and genetic structure in the spotted owl

Hierarchical genetic structure was examined in the three geographically-defined subspecies of spotted owl (Strix occidentalis) to define relationships among subspecies and quantify variation within and among regional and local populations. Sequences (522 bp) from domains I and II of the mitochondrial control region were analyzed for 213 individuals from 30 local breeding areas. Results confirmed significant differences between northern spotted owls and the other traditional geographically defined subspecies but did not provide support for subspecific level differences between California and Mexican spotted owls. Divergence times among subspecies estimated with a 936 bp portion of the cytochrome b gene dated Northern and California/Mexican spotted owl divergence time to 115,000–125,000 years ago, whereas California/Mexican spotted owl divergence was estimated at 15,000 years ago. Nested clade analyses indicated an association between California spotted owl and Mexican spotted owl haplotypes, implying historical contact between the two groups. Results also identified a number of individuals geographically classified as northern spotted owls (S. o. caurina) that contained haplotypes identified as California spotted owls (S. o. caurina). Among all northern spotted owls sampled (n=131), 12.9% contained California spotted owl haplotypes. In the Klamath region, which is the contact zone between the two subspecies, 20.3% (n=59) of owls were classified as California spotted owls. The Klamath region is a zone of hybridization and speciation for many other taxa as well. Analyses of population structure indicated gene flow among regions within geographically defined subspecies although there was significant differentiation among northern and southern regions of Mexican spotted owls. Among all areas examined, genetic diversity was not significantly reduced except in California spotted owls where the southern region consists of one haplotype. Our results indicate a stable contact zone between northern and California spotted owls, maintaining distinct subspecific haplotypes within their traditional ranges. This supports recovery efforts based on the traditional subspecies designation for the northern spotted owl. Further, although little variation was found between California and Mexican spotted owls, we suggest they should be managed separately because of current isolation between groups.     

The genetic structure of fish: differences in the intraspecific distribution of biochemical genetic variation between marine, anadromous, and freshwater species

Biochemical genetic markers have been increasingly used for inferences on the population genetic structure of various fish, but little attention has been paid to relative differences in the distribution of variability within species in different groups of fish. Nested gene diversity analyses of multiple locus electrophoretic data from the literature for 19 species (6 marine species, 4 anadromous salmonids, and 9 freshwater species (5 salmonids)), mainly from Scandinavia and North America, show that (i) average heterozygosity is higher in marine species than in freshwater species, (ii) the average fraction of the total gene diversity allocated between localities increases in the order marine (1.6%), anadromous (3.7%), and freshwater species (29.4%), and (iii) the fraction of the total gene diversity associated with differences between geographic clusters of localities is generally smaller than that between localities within clusters. This finding is consistent with that the differentiation observed in most species is of postglacial origin, and that the timespan available since deglaciation has been too short to result in the accumulation of substantial differences between clusters.     

Population genetic structure of Earth's largest fish, the whale shark (Rhincodon typus)

Large pelagic vertebrates pose special conservation challenges because their movements generally exceed the boundaries of any single jurisdiction. To assess the population structure of whale sharks (Rhincodon typus), we sequenced complete mitochondrial DNA control regions from individuals collected across a global distribution. We observed 51 single site polymorphisms and 8 regions with indels comprising 44 haplotypes in 70 individuals, with high haplotype (h = 0.974 +/- 0.008) and nucleotide diversity (pi = 0.011 +/- 0.006). The control region has the largest length variation yet reported for an elasmobranch (1143-1332 bp). Phylogenetic analyses reveal no geographical clustering of lineages and the most common haplotype was distributed globally. The absence of population structure across the Indian and Pacific basins indicates that oceanic expanses and land barriers in Southeast Asia are not impediments to whale shark dispersal. We did, however, find significant haplotype frequency differences (AMOVA, Phi(ST) = 0.107, P < 0.001) principally between the Atlantic and Indo-Pacific populations. In contrast to other recent surveys of globally distributed sharks, we find much less population subdivision and no evidence for cryptic evolutionary partitions. Discovery of the mating and pupping areas of whale sharks is key to further population genetic studies. The global pattern of shared haplotypes in whale sharks provides a compelling argument for development of broad international approaches for management and conservation of Earth's largest fish.     

Isolation and characterization of polymorphic microsatellites in a Yangtze River fish,brass gudgeon (Coreius heterodon Bleeker)

The brass gudgeon (Coreius heterodon) is a fish of economic importance in the Yangtze River. From a (GATA)_n‐enriched genomic library, 25 microsatellites were developed by employing the fast isolation by AFLP of sequences containing repeats (FIASCO) protocol. Nine loci exhibited polymorphism with two to 12 alleles (mean 3.9 alleles/locus) in a test population, and observed heterozygosity ranged from 0.1111 to 0.9630 (mean 0.4426). Three of the nine loci showed polymorphism in a congeneric species, the largemouth bronze gudgeon Coreius guichenoti. These loci should provide sufficient level of genetic diversity to evaluate the fine‐scale population structure of C. heterodon.     

Geography and host specificity: two forces behind the genetic structure of the freshwater fish parasite Ligula intestinalis (Cestoda: Diphyllobothriidae)

Parasite species with global distributions and complex life cycles offer a rare opportunity to study alternative mechanisms of speciation and evolution in a single model. Here, genealogy and genetic structure, with respect to geography and fish host preference, have been analyzed for Ligula intestinalis, a tapeworm affecting freshwater fish. The data analyzed consisted of 109 tapeworms sampled from 13 fish host species in 18 different localities on a macrogeographic scale. Two mitochondrial genes, cytochrome oxidase subunit I and cytochrome B, and the nuclear sequence of intergenic transcribed spacer 2 (ITS2) were used for the genetic reconstruction. Different evolutionary patterns were found at the local and at the global geographic scales. On a local scale, the flat genetic structure was mainly attributed to contiguous range expansion. Migrating birds are the most likely cause of the homogenisation of the whole population, preventing the creation of significant genetic barriers. By contrast, on a global scale, genetically distant and well-separated clusters are present in different geographic areas. Reproductive isolation was found even between clades living in sympatry and infecting the same definitive host, suggesting the existence of efficient biologically determined genetic barriers, and thus possibly separate species. Although the ITS2 sequences were found to display considerable intragenomic variability, their relationships were generally in good agreement with the topology derived from mitochondrial genes.     

Fine-scale spatial genetic structure and dispersal among spotted salamander (Ambystoma maculatum) breeding populations

We examined fine-scale genetic variation among breeding aggregations of the spotted salamander (Ambystoma maculatum) to quantify dispersal, interpopulation connectivity and population genetic structure. Spotted salamanders rely on temporary ponds or wetlands for aggregate breeding. Adequate breeding sites are relatively isolated from one another and field studies suggest considerable adult site fidelity; therefore, we expected to find population structure and differentiation at small spatial scales. We used microsatellites to estimate population structure and dispersal among 29 breeding aggregations in Tompkins County, New York, USA, an area encompassing 1272 km(2). Bayesian and frequency-based analyses revealed fine-scale genetic structure with two genetically defined demes: the North deme included seven breeding ponds, and the South deme included 13 ponds. Nine ponds showed evidence of admixture between these two genetic pools. Bayesian assignment tests for detection of interpopulation dispersal indicate that immigration among ponds is common within demes, and that certain populations serve as sources of immigrants to neighbouring ponds. Likewise, spatial genetic correlation analyses showed that populations < or = 4.8 km distant from each other show significant genetic correlation that is not evident at higher scales. Within-population levels of relatedness are consistently larger than expected if mating were completely random across ponds, and in the case of a few ponds, within-population processes such as inbreeding or reproductive skew contribute significantly to differentiation from neighbouring ponds. Our data underscore the importance of these within-population processes as a source of genetic diversity across the landscape, despite considerable population connectivity. Our data further suggest that spotted salamander breeding groups behave as metapopulations, with population clusters as functional units, but sufficient migration among demes to allow for potential rescue and recolonization. Amphibian habitats are becoming increasingly fragmented and a clear understanding of dispersal and patterns of population connectivity for taxa with different ecologies and life histories is crucial for their conservation.     

Phosphoethanolamine in brain of the euritherm lake fish Perccottus glehni (Eleotridae, Perciformes, Dyb. 1877) as a phenomenon depending on temperature factor

The present work studied effect of a seasonal decrease of environmental temperature and cold shock on pools of free amino acids (FA) in brain of the euritherm lake fish P. glehni. For the first time, non-protein amino acid, phosphoethanolamine (PEA), revealed in the great amounts under conditions of near-zero temperatures was found in brain of ectothermic animals. An intensive rise of the PEA pool from 0.3% during the summer period to 33.6% at winter was shown to occur in the brain of P. glehni as a result of a seasonal temperature decrease. In contrast, the level of taurine showing the greatest pool in comparison with other FA (29.0% of the total pool) in summer decreases to 8.9% in the beginning of winter period. Similar negative correlation between the taurine and PEA content was found under effect of acute cold shock (1°C): the taurine level decreased for 4 days from 32.2 to 14.5% of the total pool, whereas the PEA level sharply increased (from 2.1 to 15.3%). Both types of the low-temperature actions have revealed, besides PEA, an intensive rise in the pool of serine and accumulation of phosphoserine. The role of PEA in biochemical evolution and adaptation of the brain to low temperatures is discussed. It is supposed that accumulation of PEA, phosphoserine, and serine is associated with changes in the status of membrane phospholipids at low temperatures.     

Bathymetric barriers promoting genetic structure in the deepwater demersal fish tusk (Brosme brosme)

Population structuring in the North Atlantic deepwater demersal fish tusk ( Brosme brosme ) was studied with microsatellite DNA analyses. Screening eight samples from across the range of the species for seven loci revealed low but significant genetic heterogeneity ( F _ST = 0.0014). Spatial genetic variability was only weakly related to geographical (Euclidean) distance between study sites or separation of study sites along the path of major ocean currents. Instead, we found a significant effect of habitat, indicated by significant differentiation between relatively closely spaced sites: Rockall, which is surrounded by very deep water (>1000 m), and the Mid-Atlantic Ridge, which is separated from the European slope by a deep ocean basin, were differentiated from relatively homogeneous sites across the Nordic Seas. Limited adult migration across bathymetric barriers in combination with limited intersite exchange of pelagic eggs and larvae due to site-specific circulatory retention or poor survival during drift phases across deep basins may be reducing gene flow. We regard these limitations to gene flow as the most likely mechanisms for the observed population structure in this demersal species. The results underscore the importance of habitat boundaries in marine species.