A revision of the gudgeon genus Hypseleotris (Gobiiformes: Gobioidei: Eleotridae) of northwest Australia, describing three new species and synonymizing the genus Kimberleyeleotris.

Species within the northwest Australian clade of Hypseleotris (six species) and the genus Kimberleyeleotris (two species) are reviewed following the recording of new populations in the region and a molecular study of the group that identified three undescribed candidate species. Based on the analysis of extensive morphological and nuclear and mitochondrial molecular datasets, Kimberleyeleotris is here formally synonymised with Hypseleotris. Furthermore, three species from the Kimberley region, Western Australia, are described to science: Hypseleotris maranda sp. nov., Hypseleotris wunduwala sp. nov., and Hypseleotris garawudjirri sp. nov. The presence of, or number of scales across the head and body, the pattern of sensory papillae on the head, fin ray counts, dorsal and anal fin colouration (particularly in breeding males), and body depth, can be used to distinguish the members of the northwest Australia lineage. Furthermore, the newly described species were genetically separated from all northwest Australian congeners by K2P distances ranging from 7.8-11.3% based on the CO1 gene, and 7.7-16.3 % based on the entire mitochondrial genome. Two of the new species, H. maranda sp. nov. and H. wunduwala sp. nov., have extremely narrow ranges being found in single sub-catchments of the Roe and King Edward Rivers respectively. On the other hand, H. garawudjirri sp. nov. is moderately widespread, being found across the Charnley, Calder, and Sale rivers. While the conservation risk to H. maranda sp. nov. and H. wunduwala sp. nov. is inherently high due to their small range, there are currently no obvious local threatening processes to either of these species given their remote locations that are little impacted by human activities.

Diversification of the sleepers (Gobiiformes: Gobioidei: Eleotridae) and evolution of the root gobioid families.

Eleotridae (sleepers) and five smaller families are the earliest diverging lineages within Gobioidei. Most inhabit freshwaters in and around the Indo-Pacific, but Eleotridae also includes species that have invaded the Neotropics as well as several inland radiations in the freshwaters of Australia, New Zealand, and New Guinea. Previous efforts to infer phylogeny of these families have been based on sets of mitochondrial or nuclear loci and have yielded uncertain resolution of clades within Eleotridae. We expand the taxon sampling of previous studies and use genomic data from nuclear ultraconserved elements (UCEs) to infer phylogeny, then calibrate the hypothesis with recently discovered fossils. Our hypothesis clarifies ambiguously resolved relationships, provides a timescale for divergences, and indicates the core crown Eleotridae diverged over a short period 24.3-26.3 Ma in the late Oligocene. Within Eleotridae, we evaluate diversification dynamics with BAMM and find evidence for an overall slowdown in diversification over the past 35 Ma, but with a sharp increase 3.5 Ma in the genus Mogurnda, a clade of brightly colored species found in the freshwaters of Australia and New Guinea.

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.

Delayed Adaptive Radiation among New Zealand Stream Fishes: Joint Estimation of Divergence Time and Trait Evolution in a Newly Delineated Island Species Flock.

Adaptive radiations are generally thought to occur soon after a lineage invades a region offering high levels of ecological opportunity. However, few adaptive radiations beyond a handful of exceptional examples are known, so a comprehensive understanding of their dynamics is still lacking. Here, we present a novel case of an island species flock of freshwater fishes with a radically different tempo of adaptive history than that found in many popular evolutionary model systems. Using a phylogenomic data set combined with simultaneous Bayesian estimation of divergence times and trait-based speciation and extinction models, we show that the New Zealand Gobiomorphus gudgeons comprise a monophyletic assemblage, but surprisingly, the radiation did not fully occupy freshwater habitats and explosively speciate until more than 10 myr after the lineage invaded the islands. This shift in speciation rate was not accompanied by an acceleration in the rate of morphological evolution in the freshwater crown clade relative to the other species, but is correlated with a reduction in head pores and scales as well as an increase in egg size. Our results challenge the notion that clades always rapidly exploit ecological opportunities in the absence of competing lineages. Instead, we demonstrate that adaptive radiation can experience a slow start before undergoing accelerated diversification and that lineage and phenotypic diversification may be uncoupled in young radiations. [Adaptive radiation; Eleotridae; freshwater; Gobiomorphus; New Zealand.].

Revision of the genus Hannia (Teleostei, Terapontidae), with description of a new species, Hannia wintoni, from the Kimberley, Western Australia.

The systematics of the genus Hannia Vari 1978, endemic to freshwater habitats of remote north-western Australia, is revised in light of recent collections in the region and a molecular study of the group that identified an undescribed candidate species. A new freshwater fish species (Hannia wintoni sp. nov) is described based on analysis of multiple nuclear genetic markers (53 allozyme loci), mitochondrial DNA sequence data (601 bp cytochrome b) and morphology (examination of a suite of 66 morphometric and meristic characters). Head profile, postorbital length, maximum length, preopercular spines and pectoral-fin rays are characters that best distinguish H. wintoni sp. nov from its only congener, H. greewayi. While the existing description of H. greenwayi is robust and accurate, we present a number of additional characters that enhance to the original description, based on type and fresh material. Information on the known distribution, habitats and conservation status of the two species is summarised. The new species is a narrow-range endemic.

A revision of the bioregionalisation of freshwater fish communities in the Australian Monsoonal Tropics.

The Australian freshwater fish fauna is very unique, but poorly understood. In the Australian Monsoonal Tropics (AMT) biome of northern Australia, the number of described and candidate species has nearly doubled since the last attempt to analyse freshwater fish species composition patterns and determine a bioregionalisation scheme. Here, we utilise the most complete database of catchment-scale freshwater fish distributions from the AMT to date to: (a) reanalyze spatial patterns of species richness, endemism and turnover of freshwater fishes; (b) propose a biogeographic regionalisation based on species turnover; (c) assess the relationship between species turnover and patterns of environmental change and historic drainage connectivity; and (d) identify sampling gaps. Biogeographic provinces were identified using an agglomerative cluster analysis of a Simpson's beta (ß sim) dissimilarity matrix. A generalised dissimilarity model incorporating eighteen environmental variables was used to investigate the environmental correlates of species turnover. Observed and estimated species richness and endemism were calculated and inventory completeness was estimated based on the ratio of observed to estimated species richness. Three major freshwater fish biogeographic provinces and 14 subprovinces are proposed. These differ substantially from the current bioregionalisation scheme. Species turnover was most strongly influenced by environmental variables that are interpreted to reflect changes in terrain (catchment relief and confinement), geology and climate (runoff perenniality, stream density), and biotic responses to climate (net primary productivity). Past connectivity between rivers during low sea-level events is also influential highlighting the importance of historical processes in explaining contemporary patterns of biodiversity in the AMT. The inclusion of 49 newly discovered species and candidate species only reinforced known focal points of species richness and endemism in the AMT. However, a number of key sampling gaps remain that need to be filled to fully characterise the proposed bioregionalisation.

Cryptic biodiversity in the freshwater fishes of the Kimberley endemism hotspot, northwestern Australia.

The prevalence of unrecognised cryptic species impairs biodiversity estimates, clouds biological research and hinders conservation planning. As the rate of cryptic species detection increases globally, research is needed to determine how frequent cryptic species are, whether they are more common in given management regions, and whether these patterns are consistent across taxonomic groups. The Kimberley region in remote northwestern Australia harbours some of the most speciose, and morphologically and functionally diverse, endemic animal and plant communities on the continent. The rugged and changeable landscape also appears to contain a large proportion of cryptic terrestrial species, raising the question of whether similar patterns are also found among aquatic taxa, which have yet to be studied using integrative systematic approaches. If true, then the actual levels of aquatic biodiversity are yet to be fully realised. Here we conducted a molecular assessment of where species boundaries may exist in the Kimberley regions' most speciose freshwater fish family, the Terapontidae (grunters), with a combined morphological assessment of the regions' most speciose terapontid genus, Syncomistes. Assessment of nuclear markers (54 allozyme loci), sequence data (mitochondrial cytochrome b (cytb); nuclear recombination activation gene one (RAG1)) and 31 meristic and 36 morphometric characters provides evidence for 13 new candidate species across three different genera. Many of these candidate species are narrow range endemics. Our findings raise several questions about the evolutionary origin of the Kimberley's endemic fish fauna and highlight the likelihood that freshwater fish species diversity in the Kimberley is severely under-represented by current systematic frameworks, with significant implications for ecological research, conservation and management.

A revision of the grunter genus Syncomistes (Teleostei, Terapontidae, Syncomistes) with descriptions of seven new species from the Kimberley region, northwestern Australia.

The systematics of the genus Syncomistes Vari, 1978 endemic to freshwater habitats of remote northwestern Australia, is reviewed in light of recent collections in the region and a fine scale molecular study of the group that identified new taxa. Based primarily on external morphology, seven taxa are described as new: Syncomistes bonapartensis sp. nov., S. carcharus sp. nov., S. dilliensis sp. nov., S. holsworthi sp. nov., S. moranensis sp. nov., S. wunambal sp. nov. and S. versicolor sp. nov. The species complexes Syncomistes butleri Vari, 1978 and S. trigonicus Vari, 1978 are resolved and redescribed, and S. kimberleyensis Vari, 1978 and S. rastellus Vari Hutchins, 1978 are redescribed based on juvenile and adult specimens. Finally, a neotype is provided for S. trigonicus sensu stricto in place of the destroyed holotype. Meristic and morphometric data are collected and analysed for the entire genus. Syncomistes have a broad range of meristic and morphometric character differences between species, and juveniles and adults, as well as variations in colour. The head, particularly feeding structures such as the jaw and dentition, were found to be the most important morphological features in discriminating between taxa. Some characters undergo distinct ontogenetic shifts in form, which are discussed. Of note, four of the new species, and seven from the entire genus, are narrow-range endemics, each found in single river systems, and are thus of conservation concern.