Phylogenetic assessment of the halophilic Australian gastropod Coxiella and South African Tomichia resolves taxonomic uncertainties, uncovers new species and supports a Gondwanan link.

Genetic and morphological data have suggested a Gondwanan connection between the three non-marine aquatic gastropod genera Coxiella Smith, 1894, Tomichia Benson, 1851 and Idiopyrgus Pilsbry, 1911. These genera have recently been included in the family Tomichiidae Wenz, 1938, however, further assessment of the validity of this family is warranted. Coxiella is an obligate halophile that occurs in Australian salt lakes while Tomichia occurs in saline and freshwater environments in southern Africa and Idiopyrgus is a freshwater taxon from South America. Despite their novel evolutionary and ecological characteristics, Coxiella, Tomichia and Idiopyrgus are poorly studied, and the lack of a contemporary taxonomic framework restricts our ability to assess the risk of declining habitat quality to these gastropods. We used data from mitochondrial (COI and 16S) and nuclear (28S and 18S) genes in 20 species from all three genera to undertake the most comprehensive phylogenetic test of the Tomichiidae to date. Bayesian and Maximum Likelihood phylogenetic analyses of a concatenated dataset (2974 bp) of all four genes strongly supported a monophyletic Tomichiidae. The COI analysis (n = 307) identified 14 reciprocally monophyletic lineages in Coxiella that comprised eight of the nine currently described species and at least six putative new species. Four distinct genetic clades of species with somewhat distinctive morphologies were found, each of which may constitute a distinct genera. In addition, four species of Tomichia were identified, including three described and one putatively new species. Current species descriptions of Coxiella do not account for the range of morphological variation observed within most described species, and although morphology is reasonably effective at delineating between clades, it is of limited use when trying to separate closely related Coxiella species. The improved understanding of the taxonomy and diversity of Tomichia and especially Coxiella will underpin future studies and conservation planning for these taxa.

Shedding light: a phylotranscriptomic perspective illuminates the origin of photosymbiosis in marine bivalves.

BACKGROUND: Photosymbiotic associations between metazoan hosts and photosynthetic dinoflagellates are crucial to the trophic and structural integrity of many marine ecosystems, including coral reefs. Although extensive efforts have been devoted to study the short-term ecological interactions between coral hosts and their symbionts, long-term evolutionary dynamics of photosymbiosis in many marine animals are not well understood. Within Bivalvia, the second largest class of mollusks, obligate photosymbiosis is found in two marine lineages: the giant clams (subfamily Tridacninae) and the heart cockles (subfamily Fraginae), both in the family Cardiidae. Morphologically, giant clams show relatively conservative shell forms whereas photosymbiotic fragines exhibit a diverse suite of anatomical adaptations including flattened shells, leafy mantle extensions, and lens-like microstructural structures. To date, the phylogenetic relationships between these two subfamilies remain poorly resolved, and it is unclear whether photosymbiosis in cardiids originated once or twice. RESULTS: In this study, we establish a backbone phylogeny for Cardiidae utilizing RNASeq-based transcriptomic data from Tridacninae, Fraginae and other cardiids. A variety of phylogenomic approaches were used to infer the relationship between the two groups. Our analyses found conflicting gene signals and potential rapid divergence among the lineages. Overall, results support a sister group relationship between Tridacninae and Fraginae, which diverged during the Cretaceous. Although a sister group relationship is recovered, ancestral state reconstruction using maximum likelihood-based methods reveals two independent origins of photosymbiosis, one at the base of Tridacninae and the other within a symbiotic Fraginae clade. CONCLUSIONS: The newly revealed common ancestry between Tridacninae and Fraginae brings a possibility that certain genetic, metabolic, and/or anatomical exaptations existed in their last common ancestor, which promoted both lineages to independently establish photosymbiosis, possibly in response to the modern expansion of reef habitats.

Integrated taxonomy reveals new threatened freshwater mussels (Bivalvia: Hyriidae: Westralunio) from southwestern Australia.

The freshwater mussel Westralunio carteri (Iredale, 1934) has long been considered the sole Westralunio species in Australia, limited to the Southwest and listed as vulnerable on the IUCN Red List and under Australian legislation. Here, we used species delimitation models based on COI mtDNA sequences to confirm existence of three evolutionarily significant units (ESUs) within this taxon and conducted morphometric analyses to investigate whether shell shape differed significantly among these ESUs. "W. carteri" I was found to be significantly larger and more elongated than "W. carteri" II and "W. carteri" II + III combined, but not different from "W. carteri" III alone. We recognise and redescribe "W. carteri" I as Westralunio carteri (Iredale, 1934) from western coastal drainages and describe "W. carteri" II and "W. carteri" III as Westralunio inbisi sp. nov. from southern and lower southwestern drainages. Two subspecies are further delineated: "W. carteri" II is formally described as Westralunio inbisi inbisi subsp. nov. from southern coastal drainages, and "W. carteri" III as Westralunio inbisi meridiemus subsp. nov. from the southwestern corner. Because this study profoundly compresses the range of Westralunio carteri northward and introduces additional southern and southwestern taxa with restricted distributions, new threatened species nominations are necessary.

A Molecular Survey of Ulva (Chlorophyta) in Temperate Australia Reveals Enhanced Levels of Cosmopolitanism.

The green algal genus Ulva includes a speciose group of marine macroalgae inhabiting shallow seas worldwide. Although algal blooms in Asia highlight the opportunistic nature of several "nuisance" species, recent research clearly reveals important positive benefits of Ulva. Applied research requires accurate, reliable, and rapid identification, however, identification of Ulva spp. has met with con-siderable difficulty. Consequently, many have turned to molecular markers to aid in taxonomy. Previous studies of plants and algae have relied heavily on ITS and rbcL. Recently, tufA has been presented as a suitable barcoding gene to facilitate species-level identification of green macroalgae and it is used here to explore the diversity of Ulva spp. in temperate Australia. Ninety Ulva specimens collected from 38 sites across five states were sequenced for this gene region with exemplars from each genetic group also sequenced for rbcL to test for congruence. Collections of Australian Ulva spp. were compared to samples from Asia and North America and exhibited trends consistent with recent studies in terms of species relationships. Results support an overwhelmingly cosmopolitan flora in temperate Australia that contrasts with other Australasian surveys of Ulva that report a greater number of endemics and new species. Four new records, as well as numerous range extensions for taxa already known from the country, are documented. Evidence for three nonindigenous Ulva species in temperate Australia is discussed.

Phylogeography of the Patelloida profunda group (Gastropoda: Lottidae): diversification in a dispersal-driven marine system.

In the last decade, greater than expected levels of genetic structure have been reported for many marine taxa with high dispersal capabilities. Although little-studied to date, it is predicted that taxa with poor dispersal abilities would exhibit even more genetic differentiation than high dispersal taxa. These systems may track biogeographical processes better than more dispersive taxa and, more critically, function as the 'lowest common denominators' in MPA design initiatives. We investigate phylogeographical patterns in the poorly dispersing, yet widely distributed Patelloida profunda group and related congeners across the Indo-west Pacific region. One hundred and twenty-five individuals were sequenced for COI mtDNA [593 base pairs (bp)] and 44 individuals were sequenced for 16S mtDNA (539 bp). Identified P. profunda group lineages are highly geographically structured, with 12 reciprocally monophyletic lineages reported from 13 localities. Divergences within Indian and Pacific basins range from d = 0.013 to 0.127 and between basins from d = 0.147 to 0.197. The latter split is ancient (> 15 Myr) and cannot be related to Plio-Pleistocene sea-level fluctuations, characteristic of previously reported divergences in the same region. Juxtaposed against this structure is genetic connectivity between two widely separated P. profunda populations that share a common haplotype (phiST = 0.001). This finding contrasts with previous work in the same geographical region and cautions strongly against single taxon indicators for designing conservation priorities or marine protected areas (MPAs). Historical and/or biological factors may play more significant roles than oceanography alone in determining the genetic structuring of taxa. In light of these findings, we discuss the difficulty in deriving biogeographical process or directionality from phylogenetic trees in dispersal-driven systems. Even with a well-resolved, highly supported topology, many equally parsimonious scenarios are possible.