Genetic characteristics of the amphidromous fish Ayu Plecoglossus altivelis altivelis (Osmeriformes: Plecoglossidae) on Yaku-shima Island in Japan, the southernmost population of the subspecies.

The Ayu (Plecoglossus altivelis altivelis) population on Yaku-shima Island, Kagoshima Prefecture, Japan represents the southernmost population of the subspecies and is considered to be facing extinction. We investigated the genetic characteristics of Ayu in the Miyanoura River (MYU) in the northeast of the island and the Kurio River (KRO) in the southwest of the island, using partial sequences of mitochondrial (mt) control region and polymorphic microsatellite (simple sequence repeat: SSR) loci. The mtDNA analysis revealed that the Yaku-shima Island population was significantly differentiated from other Ayu populations; additionally, the MYU and KRO populations were significantly different from each other in terms of mtDNA (pairwise ΦST = 0.5826, P < 0.01) and SSR (pairwise ΦST = 0.1598, P < 0.01) analyses, indicating very little or no gene flow between them. The mtDNA haplotype diversity values were minimal for KRO and somewhat lower for MYU (h = 0.8176) than for each population from the mainland of Japan (Honshu-Kyushu) and the Korean Peninsula (h = 0.9905-1.0000). The mean values of expected heterozygosity (He) of SSRs were also lower in KRO (mean He = 0.555) than in MYU (mean He = 0.649). A considerably small effective population size (Ne = 100.1 for MYU, 151.2 for KRO) and a bottleneck effect for Yaku-shima Island population were suggested by SSR analysis. These findings underscore the importance of monitoring the genetic diversity of Ayu on Yaku-shima Island and the necessity of designing conservation policies for each river's population.

Phenotypic and genetic differentiation between diadromous and landlocked puyen Galaxias maculatus.

This study reports the phenotypic and genetic differences between individuals of puyen Galaxias maculatus from two sites in the same river basin in Tierra del Fuego National Park, southern South America. Individuals from the two sampling sites presented morphometric and genetic differences. The morphometric differences indicated that individuals from Laguna Negra (LN) were short and more robust and had large eyes, whereas those from Arroyo Negro (AN) were thin and elongated and had small eyes. Genetic differences showed that AN individuals had a greater genetic structuration and an older demographic history than LN individuals. The results of this study affirmed that the individuals from the two sampling sites belong to different populations with a high degree of isolation. The demographic history could indicate that the individuals of G. maculatus which migrated to northern areas during the last glaciation settled in the Beagle Channel after its formation. The LN population could have originated after the retreat of the glaciers, migrating from AN.

The host defense peptide ß-defensin confers protection against Vibrio anguillarum in ayu, Plecoglossus altivelis.

ß-defensin is a cationic host defense peptide actively participating in host innate immune response against pathogens. In teleost fish, ß-defensin exhibits a diversity in genotypes and functions. Herein, a ß-defensin homolog (PaBD) was identified from ayu, Plecoglossus altivelis, showing multiple tissues' upregulation against Vibrio anguillarum challenge. In vivo experiments revealed that intraperitoneal injection of chemically synthesized mature PaBD (mPaBD) increased the survival rate of V. anguillarum-infected ayu, accompanied by reduced bacterial load and decreased tissue mRNA levels of tumor necrosis factor α (PaTNF-α) and interleukin 1ß (PaIL-1ß). However, in vitro, mPaBD showed weak bactericidal activity against V. anguillarum. Interestingly, mPaBD enhanced phagocytosis, intracellular bacterial killing, and respiratory burst of ayu monocytes/macrophages (MO/MΦ). Moreover, it inhibited mRNA levels of PaIL-1ß and PaTNF-α in MO/MФ upon V. anguillarum infection. In conclusion, PaBD protects ayu against V. anguillarum challenge not only through its direct antibacterial ability, but also through its immunomodulation in MO/MΦ.

Environmental DNA facilitates accurate, inexpensive, and multiyear population estimates of millions of anadromous fish.

Although environmental DNA shed from an organism is now widely used for species detection in a wide variety of contexts, mobilizing environmental DNA for management requires estimation of population size and trends in addition to assessing presence or absence. However, the efficacy of environmental-DNA-based indices of abundance for long-term population monitoring have not yet been assessed. Here we report on the relationship between six years of mark-recapture population estimates for eulachon (Thaleichthys pacificus) and "eDNA rates" which are calculated from the product of stream flow and DNA concentration. Eulachon are a culturally and biologically important anadromous fish that have significantly declined in the southern part of their range but were historically rendered into oil and traded. Both the peak eDNA rate and the area under the curve of the daily eDNA rate were highly predictive of the mark-recapture population estimate, explaining 84.96% and 92.53% of the deviance, respectively. Even in the absence of flow correction, the peak of the daily eDNA concentration explained an astonishing 89.53% while the area under the curve explained 90.74% of the deviance. These results support the use of eDNA to monitor eulachon population trends and represent a >80% cost savings over mark-recapture, which could be further increased with automated water sampling, reduced replication, and focused temporal sampling. Due to its logistical ease and affordability, eDNA sampling can facilitate monitoring a larger number of rivers and in remote locations where mark-recapture is infeasible.

Complex life histories discovered in a critically endangered fish.

Effective conservation of endangered species requires knowledge of the full range of life-history strategies used to maximize population resilience within a stochastic and ever-changing environment. California's endemic Delta Smelt (Hypomesus transpacificus) is rapidly approaching extinction in the San Francisco Estuary, placing it in the crossfire between human and environmental uses of limited freshwater resources. Though managed as a semi-anadromous species, recent studies have challenged this lifecycle model for Delta Smelt, suggesting the species is an estuarine resident with several localized "hot-spots" of abundance. Using laser-ablation otolith strontium isotope microchemistry, we discovered three distinct life-history phenotypes including freshwater resident (FWR), brackish-water resident (BWR), and semi-anadromous (SA) fish. We further refined life-history phenotypes using an unsupervised algorithm and hierarchical clustering and found that in the last resilient year-class, the FWR (12%) and BWR (7%) comprised a small portion of the population, while the majority of fish were SA (81%). Furthermore, the semi-anadromous fish could be clustered into at least four additional life-history phenotypes that varied by natal origin, dispersal age and adult salinity history. These diverse life-history strategies should be incorporated into future conservation and management efforts aimed at preventing the extinction of Delta Smelt in the wild.

Whole genome sequencing of Chinese clearhead icefish, Protosalanx hyalocranius.

Background: Chinese clearhead icefish, Protosalanx hyalocranius , is a representative icefish species with economic importance and special appearance. Due to its great economic value in China, the fish was introduced into Lake Dianchi and several other lakes from the Lake Taihu half a century ago. Similar to the Sinocyclocheilus cavefish, the clearhead icefish has certain cavefish-like traits, such as transparent body and nearly scaleless skin. Here, we provide the whole genome sequence of this surface-dwelling fish and generated a draft genome assembly, aiming at exploring molecular mechanisms for the biological interests. A total of 252.1 Gb of raw reads were sequenced. Subsequently, a novel draft genome assembly was generated, with the scaffold N50 reaching 1.163 Mb. The genome completeness was estimated to be 98.39 % by using the CEGMA evaluation. Finally, we annotated 19 884 protein-coding genes and observed that repeat sequences account for 24.43 % of the genome assembly. We report the first draft genome of the Chinese clearhead icefish. The genome assembly will provide a solid foundation for further molecular breeding and germplasm resource protection in Chinese clearhead icefish, as well as other icefishes. It is also a valuable genetic resource for revealing the molecular mechanisms for the cavefish-like characters.

A new species of Leptoderma Vaillant, 1886 (Osmeriformes: Alepocephalidae) from the Pacific coast of Central America.

A new species of Leptoderma Vaillant, 1886 is described from a single specimen trawled at 1368-1406 m depth off El Salvador, Central America, tropical eastern Pacific. Leptoderma ospesca n. sp. can be readily distinguished from its congeners by the following combination of characters: dermal papillae absent along the lateral line, pectoral-fin rays 6, pelvic-fin rays 5, pre-dorsal length 54.9% of SL, both dorsal and anal fins separated from the caudal fin, dorsal- and anal-fin rays long, procurrent caudal-fin rays numerous and extending far forward on caudal peduncle, caudal-fin rays 16, and total pre-ural vertebrae 60. A key to the species of the genus is presented.

A new species of pencil smelt Nansenia boreacrassicauda (Microstomatidae, Argentiniformes) from the North Atlantic Ocean.

A new microstomatid oceanic species, Nansenia boreacrassicauda spec. nov., is described from the temperate and subarctic Atlantic Ocean. The new species is part of the "stubby caudal peduncle" group and includes the northernmost record of any Nansenia species close to the Arctic Circle. The new species is putatively most similar to the Mediterranean Nansenia iberica, distinguished by a smaller caudal peduncle length/depth ratio, a smaller predorsal distance, more gill rakers, a different lateral line scale type and distribution. Extended Nansenia species distributions and specimens that show extralimital characters in relation to previous works are presented, addressing the current problematic taxonomic issues prevalent in pencil smelts and closely related genera. The new species is described due to increased collecting and taxonomic efforts off Greenland and is not necessarily related to ocean temperature changes.

A review of Galaxiella pusilla (Mack) (Teleostei: Galaxiidae) in south-eastern Australia with a description of a new species.

The dwarf galaxias, Galaxiella pusilla (Mack), is a small, threatened freshwater fish from coastal south-eastern Australia. Recent genetic studies, using multiple nuclear and mitochondrial DNA markers, found substantial differences between populations in western Victoria and south Australia ('west region') compared to eastern Victoria, Flinders Island, and Tasmania ('east region') that suggest the presence of a cryptic species. Morphological measurements and meristic counts from multiple populations within each region were undertaken to investigate potential differences between regions. Several characters, found to discriminate between individuals in the regions and to be diagnostic for two taxa, were used to describe a new species, Galaxiella toourtkoourt, for the west region. This is only the second species in the Galaxiidae to exhibit sexual dimorphism. The original description of Galaxiella pusilla, based on five specimens, is revised following examination of a large number of individuals. Both species are considered nationally threatened and are categorised as 'endangered'; the revised distribution of G. pusilla s.s. is reduced by approximately 60%. A number of inconsistencies in the most recent revision of the genus Galaxiella are also corrected.

Phylogeography in Galaxias maculatus (Jenyns, 1848) along Two Biogeographical Provinces in the Chilean Coast.

Major geologic and climatic changes during the Quaternary exerted a major role in shaping past and contemporary distribution of genetic diversity and structure of aquatic organisms in southern South America. In fact, the northern glacial limit along the Pacific coast, an area of major environmental changes in terms of topography, currents, and water salinity, represents a major biogeographic transition for marine and freshwater species. We used mitochondrial DNA sequences (D-loop) to investigate the consequences of Quaternary glacial cycles over the pattern of genetic diversity and structure of G. maculatus (Pisces: Galaxiidae) along two biogeographical provinces in the Chilean coast. Extreme levels of genetic diversity and strong phylogeographic structure characterize the species suggesting a low amount of influence of the last glacial cycle over its demography. However, we recognized contrasting patterns of genetic diversity and structure between main biogeographical areas here analyzed. Along the Intermediate Area (38°-41° S) each estuarine population constitutes a different unit. In contrast, Magellanic populations (43°-53° S) exhibited low levels of genetic differentiation. Contrasting patterns of genetic diversity and structure recorded in the species between the analyzed biogeographic areas are consistent with the marked differences in abiotic factors (i.e., different coastal configurations, Quaternary glacial histories, and oceanographic regimes) and to inherent characteristics of the species (i.e., salt-tolerance, physiology, and reproductive behavior).

Molecular characterization of a transmembrane C-type lectin receptor gene from ayu (Plecoglossus altivelis) and its effect on the recognition of different bacteria by monocytes/macrophages.

C-type lectin receptors (CTLRs) play vital roles in immune responses as pattern-recognition receptors (PRRs). In this study, we identified a novel C-type lectin receptor (PaCTLRC) gene from ayu, Plecoglossus altivelis. Predicted PaCTLRC is a single transmembrane receptor with a typical carbohydrate recognition domain (CRD) at its C-terminus. Sequence comparison and phylogenetic tree analysis showed that PaCTLRC was most closely related to Atlantic salmon (Salmo salar) CLRC, but was significantly different from two other ayu CTLRs, aCLR and PaCD209L. PaCTLRC transcript was detected in all tested tissues and cells, with high levels in the liver; and its expression was significantly altered upon Vibrio anguillarum infection. Refolded recombinant PaCTLRC (rPaCTLRC) agglutinated three types of Gram-positive bacteria (Listeria monocytogenes, Staphylococcus aureus and Streptococcus iniae) and four types of Gram-negative bacteria (Aeromonas hydrophila, Escherichia coli, V. anguillarum and Vibrio parahaemolyticus) in a Ca(2+)-dependent manner in vitro, and Gram-positive bacteria were shown to be biologically relevant ligands for PaCTLRC. rPaCTLRC bound to d-mannose, d-galactose, l-fucose, N-acetyl-d-glucosamine (GlcNAc), lipopolysaccharide (LPS) and peptidoglycan (PGN), exhibiting a relative binding strength to d-mannose and PGN. d-Mannose, l-fucose, GlcNAc, LPS and PGN could inhibit the agglutinating activity of rPaCTLRC, while d-galactose did not functioned. PaCTLRC neutralization using anti-PaCTLRC IgG resulted in the inhibition of phagocytosis by ayu monocytes/macrophages (MO/MΦ) of S. aureus but not of E. coli, and produced a consistently higher survival rate of S. aureus than that of E. coli. d-Mannose, LPS and PGN treatment had no significant influence on the phagocytosis of ayu MO/MΦ. These results suggest that PaCTLRC may serve as a Gram-positive bacteria-preferred PRR which is involved in pathogen recognition and signal transduction in ayu MO/MΦ.

Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (Thaleichthys pacificus, Osmeridae), an anadromous Pacific smelt.

Twelve eulachon (Thaleichthys pacificus, Osmeridae) populations ranging from Cook Inlet, Alaska and along the west coast of North America to the Columbia River were examined by restriction-site-associated DNA (RAD) sequencing to elucidate patterns of neutral and adaptive variation in this high geneflow species. A total of 4104 single-nucleotide polymorphisms (SNPs) were discovered across the genome, with 193 putatively adaptive SNPs as determined by F(ST) outlier tests. Estimates of population structure in eulachon with the putatively adaptive SNPs were similar, but provided greater resolution of stocks compared with a putatively neutral panel of 3911 SNPs or previous estimates with 14 microsatellites. A cline of increasing measures of genetic diversity from south to north was found in the adaptive panel, but not in the neutral markers (SNPs or microsatellites). This may indicate divergent selective pressures in differing freshwater and marine environments between regional eulachon populations and that these adaptive diversity patterns not seen with neutral markers could be a consideration when determining genetic boundaries for conservation purposes. Estimates of effective population size (N(e)) were similar with the neutral SNP panel and microsatellites and may be utilized to monitor population status for eulachon where census sizes are difficult to obtain. Greater differentiation with the panel of putatively adaptive SNPs provided higher individual assignment accuracy compared to the neutral panel or microsatellites for stock identification purposes. This study presents the first SNPs that have been developed for eulachon, and analyses with these markers highlighted the importance of integrating genome-wide neutral and adaptive genetic variation for the applications of conservation and management.

Genetic structure of capelin (Mallotus villosus) in the northwest Atlantic Ocean.

Capelin (Mallotus villosus) is a commercially exploited, key forage-fish species found in the boreal waters of the North Pacific and North Atlantic Oceans. We examined the population structure of capelin throughout their range in the Canadian northwest Atlantic Ocean using genetic-based methods. Capelin collected at ten beach and five demersal spawning locations over the period 2002 through 2008 (N = 3,433 fish) were genotyped using six polymorphic microsatellite loci. Temporally distinct samples were identified at three beach spawning locations: Chance Cove, Little Lawn and Straitsview, Newfoundland. Four capelin stocks are assumed for fisheries management in the northwest Atlantic Ocean based on meristics, morphometrics, tag returns, and seasonal distribution patterns. Our results suggested groupings that were somewhat different than the assumed structure, and indicate at least seven genetically defined populations arising from two ancestral populations. The spatial mosaic of capelin from each of the two basal cluster groups explains much of the observed geographic variability amongst neighbouring samples. The genetic-defined populations were resolved at Jost's Dest ≥ 0.01 and were composed of fish collected 1) in the Gulf of St. Lawrence, 2) along the south and east coasts of Newfoundland, 3) along coastal northern Newfoundland and southern Labrador, 4) along coastal northern Labrador, 5) near the Saguenay River, and at two nearshore demersal spawning sites, 6) one at Grebes Nest off Bellevue Beach on the east coast of Newfoundland, and 7) one off the coast of Labrador at Domino Run. Moreover, the offshore demersal spawners on the Scotian Shelf and Southeast Shoal appeared to be related to the inshore demersal spawners at Grebes Nest and in Domino Run and to beach spawners from the Gulf of St. Lawrence.

Fifteen from one: a revision of the Galaxias olidus Günther, 1866 complex (Teleostei, Galaxiidae) in south-eastern Australia recognises three previously described taxa and describes 12 new species.

The systematics of the Galaxias olidus hyper-species complex from freshwater habitats in south-eastern, mainland Australia is revised. Galaxias olidus Günther 1866 is redescribed, Galaxias fuscus Mack 1936 and Galaxias ornatus Castelnau 1873, previously synonymised with G. olidus (sensu lato), are reinstated as valid taxa and redescribed, and 12 taxa are described as new: Galaxias aequipinnis sp. nov., Galaxias arcanus sp. nov., Galaxias brevissimus sp. nov., Galaxias gunaikurnai sp. nov., Galaxias lanceolatus sp. nov., Galaxias longifundus sp. nov., Galaxias mcdowalli sp. nov., Galaxias mungadhan sp. nov., Galaxias oliros sp. nov., Galaxias supremus sp. nov., Galaxias tantangara sp. nov., and Galaxias terenasus sp. nov. These species are morphologically similar and, whilst there is extensive overlap in meristic counts and morphometric characters, each can be diagnosed by unique combinations of characters, including allozyme loci and colour pattern; morphological diagnosis is improved greatly if based on freshly formalin-fixed material. Galaxias schomburgkii Peters 1868, Galaxias bongbong Macleay 1881, Galaxias kayi Ramsay & Ogilby 1886 and Galaxias oconnori Ogilby 1912 are retained as junior synonyms of G. olidus (sensu stricto). The types for Galaxias findlayi Macleay 1882 are lost and no specimens matching its description were collected or examined from the Mt. Kosciuszko region; it is also currently retained as a junior synonym of Galaxias olidus s.s. The species G. terenasus sp. nov. and G. arcanus sp. nov. are the most morphologically specialised in the complex and G. olidus s.s remains the most morphologically variable species. It also remains the most widespread taxon, though its previously known distribution is reduced, particularly in the south-west of its range. Nine species are narrow-range endemics, known from one, or only a few, locations, and these restricted distributions most probably reflect the fragmentation and reduction of former ranges caused by the effects of alien salmonids. Eleven species are of conservation concern, most are considered critically endangered.

Global biodiversity assessment and hyper-cryptic species complexes: more than one species of elephant in the room?

Several recent estimates of global biodiversity have concluded that the total number of species on Earth lies near the lower end of the wide range touted in previous decades. However, none of these recent estimates formally explore the real "elephant in the room", namely, what proportion of species are taxonomically invisible to conventional assessments, and thus, as undiagnosed cryptic species, remain uncountable until revealed by multi-gene molecular assessments. Here we explore the significance and extent of so-called "hyper-cryptic" species complexes, using the Australian freshwater fish Galaxias olidus as a proxy for any organism whose taxonomy ought to be largely finalized when compared to those in little-studied or morphologically undifferentiated groups. Our comprehensive allozyme (838 fish for 54 putative loci), mtDNA (557 fish for 605 bp of cytb), and morphological (1963-3389 vouchers for 17-58 characters) assessment of this species across its broad geographic range revealed a 1500% increase in species-level biodiversity, and suggested that additional taxa may remain undiscovered. Importantly, while all 15 candidate species were morphologically diagnosable a posteriori from one another, single-gene DNA barcoding proved largely unsuccessful as an a priori method for species identification. These results lead us to draw two strong inferences of relevance to estimates of global biodiversity. First, hyper-cryptic complexes are likely to be common in many organismal groups. Second, no assessment of species numbers can be considered "best practice" in the molecular age unless it explicitly includes estimates of the extent of cryptic and hyper-cryptic biodiversity. [Galaxiidae; global estimates; hyper-diverse; mountain galaxias; species counts; species richness.].

[Cloning and expression analysis of the NFκB inhibitor IκBα of ayu (Plecoglossus altivelis)].

The NFκB inhibitor (IκBα) is an integral part of NFκB/IκB signaling pathways, which plays roles in a variety of immune responses, such as bacterial infection resistance. By interacting with nuclear transcription factor NFκB, IκBα controls a variety of biological immune gene expressions. In this study, full-length cDNA (1341 bp) of the NFκB inhibitor IκBα (PaIκBα, GenBank Accession No. JN801027) of Plecoglossus altivelis was obtained by RACE and PCR, and included a 5' untranslated region (UTR) (64 bp), a 3' untranslated region (UTR) (341 bp) and an open reading frame (ORF) (936 bp) encoding a polypeptide of 311 amino acids. PaIκBα had high homology with other IκBαs, containing a conserved ankyrin repeat domain, which was required for interacting with NFκB, a PEST sequence in the C-terminus and a signal responsive domain in the N-terminus. The deduced amino acid sequence of PaIκBα shared 95% homology with Osmerus mordax, and 76%, 75%, 70%, and 68% homology with Salmo salar, Oncorhynchus mykiss, Nile tilapia, and Siniperca chuatsi, respectively. Phylogenetic analysis revealed that IκBα of ayu and Osmerus mordax, Salmo salar, Oncorhynchus mykiss, Nile tilapia, and Siniperca chuatsi were in the same phylogenetic tree. RT-PCR analysis showed that PaIκBα mRNA expression was highest in the liver, kidney, intestine, and gills, then followed by the spleen, brain and muscle, and was lowly expressed in the heart. Likewise, after Aeromonas hydrophila infection, the mRNA level of ayu PaIκBα in the liver was also up-regulated.

Diversity of Aplochiton fishes (Galaxiidea) and the taxonomic resurrection of A. marinus.

Aplochiton is a small genus of galaxiid fishes endemic to Patagonia and the Falkland Islands whose taxonomy is insufficiently resolved. Recent genetic analyses confirmed the existence of only two closely related species, Aplochiton taeniatus and Aplochiton zebra, while a third controversial species, Aplochiton marinus, remained lost to synonymy with A. taeniatus. Using an integrative taxonomy framework, we studied original samples and published sequences from a broad range in western Patagonia and the Falkland Islands, and generated robust species hypotheses based on single-locus (Cytochrome Oxidase subunit I; COI) species-delineation methods and known diagnostic morphological characters analyzed in a multivariate context. Results revealed three distinct evolutionary lineages that morphologically resemble, in important respects, existing nominal species descriptions. Interestingly, the lineage associated with A. marinus was unambiguously identifiable (100% accuracy) both from the genetic and morphological viewpoints. In contrast, the morphology of A. taeniatus and A. zebra overlapped substantially, mainly due to the high variability of A. taeniatus. Discriminant function analysis aided the identification of these species with 83.9% accuracy. Hence, for their unambiguous identification, genetic screening is needed. A. marinus has seldom been documented, and when recorded, it has always been found in sites with clear marine influence. It is possible that only A. marinus preserves a life cycle related to the sea akin to the hypothesized ancestral galaxiid. We did not find evidence of claimed diadromy in A. taeniatus or A. zebra, and, therefore, these should be regarded as freshwater species. Finally, a lack of phylogeographic patterns and overrepresentation of uncommon haplotypes suggested demographic expansions in recent evolutionary time, especially of A. zebra, in line with the hypothesis of large-scale range expansion and lineage spread in western Patagonia.

Balancing genetic uniqueness and genetic variation in determining conservation and translocation strategies: a comprehensive case study of threatened dwarf galaxias, Galaxiella pusilla (Mack) (Pisces: Galaxiidae).

Genetic markers are widely used to define and manage populations of threatened species based on the notion that populations with unique lineages of mtDNA and well-differentiated nuclear marker frequencies should be treated separately. However, a danger of this approach is that genetic uniqueness might be emphasized at the cost of genetic diversity, which is essential for adaptation and is potentially boosted by mixing geographically separate populations. Here, we re-explore the issue of defining management units, focussing on a detailed study of Galaxiella pusilla, a small freshwater fish of national conservation significance in Australia. Using a combination of microsatellite and mitochondrial markers, 51 populations across the species range were surveyed for genetic structure and diversity. We found an inverse relationship between genetic differentiation and genetic diversity, highlighting a long-term risk of deliberate isolation of G. pusilla populations based on protection of unique lineages. Instead, we adopt a method for identifying genetic management units that takes into consideration both uniqueness and genetic variation. This produced a management framework to guide future translocation and re-introduction efforts for G. pusilla, which contrasted to the framework based on a more traditional approach that may overlook important genetic variation in populations.

Molecular phylogeny and phylogeography of the Australian freshwater fish genus Galaxiella, with an emphasis on dwarf galaxias (G. pusilla).

The freshwater fauna of Southern Australia is primarily restricted to the southwestern and southeastern corners of the continent, and is separated by a large, arid region that is inhospitable to this biota. This geographic phenomenon has attracted considerable interest from biogeographers looking to explain evolutionary diversification in this region. Here, we employed phylogenetic and phylogeographic approaches to evaluate the effect of this barrier on a group of four galaxiid fish species (Galaxiella) endemic to temperate Southern Australia. We also tested if continental shelf width has influenced connectivity among populations during low sea levels when rivers, now isolated, could have been connected. We addressed these questions by sampling each species across its range using multiple molecular markers (mitochondrial cytochrome b sequences, nuclear S7 intron sequences, and 49 allozyme loci). These data also allowed us to assess species boundaries, to refine phylogenetic affinities, and to estimate species ages. Interestingly, we found compelling evidence for cryptic species in G. pusilla, manifesting as allopatric eastern and western taxa. Our combined phylogeny and dating analysis point to an origin for the genus dating to the early Cenozoic, with three of the four species originating during the Oligocene-Miocene. Each Galaxiella species showed high levels of genetic divergences between all but the most proximate populations. Despite extensive drainage connections during recent low sea levels in southeastern Australia, populations of both species within G. pusilla maintained high levels of genetic structure. All populations experienced Late Pleistocene-Holocene population growth, possibly in response to the relaxation of arid conditions after the last glacial maximum. High levels of genetic divergence and the discovery of new cryptic species have important implications for the conservation of this already threatened group of freshwater species.

A multilocus phylogeny of Asian noodlefishes Salangidae (Teleostei: Osmeriformes) with a revised classification of the family.

A group of small and transparent Asian noodlefishes (Osmeriformes: Salangidae) are commercially important fishery species, however, interrelationships among these fishes remain unresolved in previous studies using mitochondrial markers. We re-examine phylogenetic relationships of Salangidae by including complete taxon sampling, based on seven nuclear loci and one mitochondrial gene using a multilocus coalescence-based species-tree method. Our results show a well-resolved phylogeny of Salangidae that does not agree with previous hypotheses. The topology test suggests that our hypothesis represents the most likely phylogeny. Using the inferred species-tree as criterion, we recombine the rank of subfamilies and genera in the Salangidae, and erect a new genus Neosalangichthys. Our revised classification of Salangidae is well supported by reinterpreting previously proposed diagnostic characters. Finally, re-defined synapomorphic characters are used to erect a key to the genera of Salangidae.