Supermatrix phylogeny resolves goby lineages and reveals unstable root of Gobiaria.

Gobies, sleepers, and cardinalfishes represent major clades of a species rich radiation of small bodied, ecologically diverse percomorphs (Gobiaria). Molecular phylogenetics has been crucial to resolving broad relationships of sleepers and gobies (Gobioidei), but the phylogenetic placements of cardinalfishes and nurseryfishes, as reciprocal or sequential sister clades to Gobioidei, are uncertain. In order to evaluate relationships among and within families we used a phylogenetic data mining approach to generate densely sampled trees inclusive of all higher taxa. We utilized conspecific amino acid homology to improve alignment accuracy, included ambiguously identified taxa to increase taxon sampling density, and resampled individual gene alignments to filter rogue sequences before concatenation. This approach yielded the most comprehensive tree yet of Gobiaria, inferred from a sparse (17 percent-complete) supermatrix of one ribosomal and 22 protein coding loci (18,065 characters), comprised of 50 outgroup and 777 ingroup taxa, representing 32 percent of species and 68 percent of genera. Our analyses confirmed the lineage-based classification of gobies with strong support, identified sleeper clades with unforeseen levels of systematic uncertainty, and quantified competing phylogenetic signals that confound resolution of the root topology. We also discovered that multilocus data completeness was related to maximum likelihood branch support, and verified that the phylogenetic uncertainty of shallow relationships observed within goby lineages could largely be explained by supermatrix sparseness. These results demonstrate the potential and limits of publicly available sequence data for producing densely-sampled phylogenetic trees of exceptionally biodiverse groups.

Migratory flexibility in native Hawai'ian amphidromous fishes.

We assessed the prevalence of life history variation across four of the five native amphidromous Hawai'ian gobioids to determine whether some or all exhibit evidence of partial migration. Analysis of otolith Sr.: Ca concentrations affirmed that all are amphidromous and revealed evidence of partial migration in three of the four species. We found that 25% of Lentipes concolor (n = 8), 40% of Eleotris sandwicensis (n = 20) and 29% of Stenogobius hawaiiensis (n = 24) did not exhibit a migratory life-history. In contrast, all individuals of Sicyopterus stimpsoni (n = 55) included in the study went to sea as larvae. Lentipes concolor exhibited the shortest mean larval duration (LD) at 87 days, successively followed by E. sandwicensis (mean LD = 102 days), S. hawaiiensis (mean LD = 114 days) and S. stimpsoni (mean LD = 120 days). These findings offer a fresh perspective on migratory life histories that can help improve efforts to conserve and protect all of these and other at-risk amphidromous species that are subject to escalating anthropogenic pressures in both freshwater and marine environments.

Comparison of genetic structure in co-occurring freshwater eleotrids (Actinopterygii: Philypnodon) reveals cryptic species, likely translocation and regional conservation hotspots.

Freshwater systems are naturally fragmented and heterogeneous habitats that promote genetic sub-division and speciation for aquatic biota. Here we provide a novel nuclear genetic perspective (49 allozyme loci) complimented with updated mitochondrial data for the eleotrid genus Philypnodon to investigate broad genetic sub-structure across south-eastern Australia as a foundation for management and conservation. The genus is nominally comprised of two small benthic fishes with contrasting physical and ecological traits, namely the Flathead Gudgeon P. grandiceps and the Dwarf Flathead Gudgeon P. macrostomus. Extensive sample coverage included 99 sites across 5 major drainage divisions and 48 river basins. Nuclear markers revealed strong, geographically-based divergence and sub-structure, contrasting with shallower but largely congruent patterns for mtDNA. The results flag that each nominal species represents a hyper-cryptic species complex, including both broadly distributed and narrow-range taxa, with complicated biogeographic patterns. Predictions on dispersal and genetic structure based on ecological traits were only partially supported and varied by region, with the potential signature of human-assisted translocation evident in several catchments. Further intensive sampling in an important area of high genetic diversity, coastal south-east Queensland, is recommended to better resolve species boundaries and conservation units. The findings provide new insights on regional ecology and biogeography, demonstrating that even supposedly common species can, in reality, have complex conservation and management needs.

Species delineation and systematics of a hemiclonal hybrid complex in Australian freshwaters (Gobiiformes: Gobioidei: Eleotridae: Hypseleotris).

The rivers of southeastern Australia host a species complex within the carp gudgeon genus Hypseleotris that includes parental species and hemiclonal hybrid lineages. These hemiclones can be difficult to distinguish from their parent taxa, making delineation of species unusually difficult. We approach this historical taxonomic problem by using single nucleotide polymorphism (SNP) genotyping to distinguish individuals of each species and hemiclones, enabling us to quantify the variation among evolutionary lineages and assign names to the species. Hypseleotris klunzingeri remains valid and does not have any hemiclones. We describe Hypseleotris bucephala and Hypseleotris gymnocephala from the Murray-Darling Basin and Hypseleotris acropinna from the Murray-Darling as well as eastern coastal streams north of the Mary River, part of the range attributed to H. galii. We further split H. galii to distinguish a species from the Mary River, Hypseleotris moolooboolaensis. We designate a neotype and redescribe H. galii due to uncertainty about the source and species identity of specimens used in the original description. We reconcile previous taxonomies, provide new common names for parental species, and advocate using the scientific names of both parents when referring to the hemiclone hybrids to avoid confusion with previous common names that did not distinguish parental taxa and hemiclones.

Phylogeny, diversification, and biogeography of a hemiclonal hybrid system of native Australian freshwater fishes (Gobiiformes: Gobioidei: Eleotridae: Hypseleotris).

BACKGROUND: Carp gudgeons (genus Hypseleotris) are a prominent part of the Australian freshwater fish fauna, with species distributed around the western, northern, and eastern reaches of the continent. We infer a calibrated phylogeny of the genus based on nuclear ultraconserved element (UCE) sequences and using Bayesian estimation of divergence times, and use this phylogeny to investigate geographic patterns of diversification with GeoSSE. The southeastern species have hybridized to form hemiclonal lineages, and we also resolve relationships of hemiclones and compare their phylogenetic placement in the UCE phylogeny with a hypothesis based on complete mitochondrial genomes. We then use phased SNPs extracted from the UCE sequences for population structure analysis among the southeastern species and hemiclones. RESULTS: Hypseleotris cyprinoides, a widespread euryhaline species known from throughout the Indo-Pacific, is resolved outside the remainder of the species. Two Australian radiations comprise the bulk of Hypseleotris, one primarily in the northwestern coastal rivers and a second inhabiting the southeastern region including the Murray-Darling, Bulloo-Bancannia and Lake Eyre basins, plus coastal rivers east of the Great Dividing Range. Our phylogenetic results reveal cytonuclear discordance between the UCE and mitochondrial hypotheses, place hemiclone hybrids among their parental taxa, and indicate that the genus Kimberleyeleotris is nested within the northwestern Hypseleotris radiation along with three undescribed species. We infer a crown age for Hypseleotris of 17.3 Ma, date the radiation of Australian species at roughly 10.1 Ma, and recover the crown ages of the northwestern (excluding H. compressa) and southeastern radiations at 5.9 and 7.2 Ma, respectively. Range-dependent diversification analyses using GeoSSE indicate that speciation and extinction rates have been steady between the northwestern and southeastern Australian radiations and between smaller radiations of species in the Kimberley region and the Arnhem Plateau. Analysis of phased SNPs confirms inheritance patterns and reveals high levels of heterozygosity among the hemiclones. CONCLUSIONS: The northwestern species have restricted ranges and likely speciated in allopatry, while the southeastern species are known from much larger areas, consistent with peripatric speciation or allopatric speciation followed by secondary contact. Species in the northwestern Kimberley region differ in shape from those in the southeast, with the Kimberley species notably more elongate and slender than the stocky southeastern species, likely due to the different topographies and flow regimes of the rivers they inhabit.

DNA barcoding detects resurrected taxon Giuris laglaizei (Sauvage 1880) in Sulawesi, Indonesia: Bolano Sau Lake payangka phylogeny, phenotypic characters and implications for Giuris spp. conservation.

Background: The freshwater ichthyofauna of Wallacea is diverse and understudied. A baseline survey of Bolano Sau Lake in Parigi Moutong District, Central Sulawesi Province, Indonesia in 2019 found an eleotrid goby (local name payangka) with characters conforming to the genus Giuris, long considered monophyletic as G. margaritacea/G. margaritaceus but recently found to comprise at least eight species. This study focused on the molecular (DNA barcoding) identification and phenotypic characters of the payangka. Methods: Payangka samples were collected from August to December 2019 in collaboration with local fishermen, weighed and measured, and preserved in 75% ethanol. Length, weight, sex (n=111) and seventeen morphometric characters/six meristic counts (n=42) were recorded. DNA barcoding was performed on a fin clipping preserved in 96% ethanol. Homologous nucleotide sequences were obtained from public (GenBank and BOLD) databases, analysis conducted in MEGA X, and phylogenetic trees edited in the Interactive Tree of Life (iToL). Results: Within the polyphyletic Giuris clade, the payangka sequence resolved into a sub-clade identified as Giuris laglaizei (Sauvage 1880), a recently resurrected taxon, based on a sequence provided by Philippe Keith. The length-weight relationship (L = 0.0087∙W3.162) indicated mildly allometric positive growth. Size distribution differed significantly between male and female fish with significantly larger mean size of males (13.56 cm) than females (11.62 cm). The meristic formula was: D VI-I,8 A I,8 P 13 V I,5 C15. Phylogenic analysis indicated four Giuris species in wetlands around Tomini Bay and five in Sulawesi. Conclusions: This first record of G. laglaizei in Indonesia advances knowledge of Wallacean and Indo-Pacific gobioid biogeography and highlights the need for a revision of the conservation status of the taxa currently grouped under Giuris margaritacea/G. margaritaceus in the IUCN Red List and FishBase databases. The data will inform biodiversity and fisheries management at local and regional levels.

Morphological and molecular characterisation of a new species of Gyrodactylus von Nordmann, 1832 (Monogenoidea: Gyrodactylidae) of cichlid fishes (Perciformes) from Mexico.

Gyrodactylus mojarrae n. sp. is described from the gills of the Neotropical cichlids Thorichthys maculipinnis, Rocio octofasciata, Vieja zonata and V. fenestrata from several localities across southern Mexico. The new species is erected on the basis of the morphology of the haptoral elements (anchors, bars and hooks), and its phylogenetic position within the Gyrodactylidae is evaluated based on the analysis of partial sequences of the ITS1, 5.8 rRNA gene and ITS2. Gyrodactylus mojarrae n. sp. differs from other congeneric species by having hooks with a straight shaft and recurved point, pointed toe and convex heel, presence of reduced superficial anchor roots, by the number and disposition of spinelets of the male copulatory organ, and the absence of shield and lateral processes of the superficial bar. Molecular circumscription of isolates of G. mojarrae n. sp. from different host and hydrological basins showed that these isolates are conspecific and represent a distinct lineage from other congeners, including newly sequenced isolates of Gyodactylus sp. A and Gyrodactylus sp. B from Astyanax mexicanus (Characidae) and Gobiomorus dormitor (Eleotridae), respectively. Genetic affinities of Gyodactylus sp. A and B indicate that they might represent undescribed species infecting freshwater fish from the Americas.

Complete mitochondrial DNA sequence of marble goby, Oxyeleotris marmorata (Bleeker, 1852).

Marble goby, Oxyeleotris marmorata (Bleeker) is a large-scale invasive goby in China. In this study, the mitochondrial genome of marble goby was firstly determined. The entire mtDNA sequence was 16,556 bp in length with 13 protein-coding genes, 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and control region (CR). Its mitochondrial genome has the common features with those of other bony fishes with respect to gene arrangement, base composition, and tRNA structures.