A revisited phylogeography of Nautilus pompilius

Extinction in the Anthropocene.

The evolution of fruit-fly biology

Nautilus species are the only remaining cephalopods with an external shell. Targeted heavily by the shell trade across their distribution area, these species have a poorly known population structure and genetics. Molecular techniques have been used to assess levels of inter- and intra-population genetic diversity in isolated populations of Nautilus in the northern sections of the Great Barrier Reef (GBR), Australia and in the Coral Sea. Distinct populations, physically separated by depths in excess of 1,000 m were examined. RAPD analysis of genetic differences showed limited differentiation of the “Northern GBR” populations and the “Coral Sea” populations. Discrimination between the two geographic groups was observed from these data. In addition, partial sequencing of the CoxI gene region, yielded 575 bp of sequence, which was aligned for 43 samples and phylogenetic trees constructed to examine genetic relationships. Two distinct clades were resolved in the resulting trees, representing the “Northern GBR” and “Coral Sea” population groups. Inter- and intra-population relationships are presented and discussed. The differentiation of the Nautilus populations from the Northern section of the Great Barrier Reef and those from the Coral Sea were supported by two distinctly different methodologies and the significance of this separation and the potential evolutionary divergence of these two population groups is discussed.

Flatbacks at sea: understanding ecology in foraging populations

Global phylogeography of the dolphinfish ( Coryphaena hippurus): The influence of large effective population size and recent dispersal on the divergence of a marine pelagic cosmopolitan species

Latitudinal species diversity gradient of mushroom corals off eastern Australia: a baseline from the 1970s

Nautiloids are a charismatic group of marine molluscs best known for their rich fossil record, but today they are restricted to a handful of species in the family Nautilidae from around the Coral Triangle. Recent genetic work has shown a disconnect between traditional species, originally defined on shell characters, but now with new findings from genetic structure of various Nautilus populations. Here, three new species of Nautilus from the Coral Sea and South Pacific region are formally named using observations of shell and soft anatomical data augmented by genetic information: N.samoaensissp. nov. (from American Samoa), N.vitiensissp. nov. (from Fiji), and N.vanuatuensissp. nov. (from Vanuatu). The formal naming of these three species is timely considering the new and recently published information on genetic structure, geographic occurrence, and new morphological characters, including color patterns of shell and soft part morphology of hood, and will aid in managing these possibly endangered animals. As recently proposed from genetic analyses, there is a strong geographic component affecting taxonomy, with the new species coming from larger island groups that are separated by at least 200 km of deep water (greater than 800 m) from other Nautilus populations and potential habitats. Nautilid shells implode at depths greater than 800 m and depth therefore acts as a biogeographical barrier separating these species. This isolation, coupled with the unique, endemic species in each locale, are important considerations for the conservation management of the extant Nautilus species and populations.

BackgroundThe cox1-barcoding approach is currently extensively used for high-throughput species delimitation and discovery. However, this method has several limitations, particularly when organisms have large effective population sizes. Paradoxically, most common, abundant, and widely distributed species may be misclassified by this technique.ResultsWe conducted species delimitation analyses for two host-specific lineages of scab mites of the genus Caparinia, having small population sizes. Cox1 divergence between these lineages was high (7.4–7.8%) while that of nuclear genes was low (0.06–0.53%). This system was contrasted with the medically important American house dust mite, Dermatophagoides farinae, a globally distributed species with very large population size. This species has two distinct, sympatric cox1 lineages with 4.2% divergence. We tested several species delimitation algorithms PTP, GMYC, ABGD, BPP, STACEY and PHRAPL, which inferred different species boundaries for these entities. Notably, STACEY recovered the Caparinia lineages as two species and D. farinae as a single species. BPP agreed with these results when the prior on ancestral effective population sizes was set to expected values, although delimitation of Caparinia was still equivocal. No other cox1 species delimitation algorithms inferred D. farinae as a single species, despite the fact that the nuclear CPW2 gene shows some evidence for introgression between the cox1 groups. This indicates that the cox1-barcoding approach may result in excessive species splitting.ConclusionsOur research highlights the importance of using nuclear genes and demographic characteristics to infer species boundaries rather than relying on a single-gene barcoding approach, particularly for putative species having large effective population sizes.

Contrasting patterns of genetic structure in two species of the coral trout Plectropomus (Serranidae) from east and west Australia: Introgressive hybridisation or ancestral polymorphisms

The evolutionary history of large carnivorous mammals through the Ice Age have been investigated for the Italian peninsula. No endemisms are recorded in the mainland of Italy and large carnivore species composition reflected the similar fauna of European continent. Morpho-ecological adaptation of extinct Plio-Pleistocene species have been investigated throughout temporal PaleoCommunities (9 PCOMs – spanning 3.2 to 0.3 Ma) with statistical accuracy. Trophic apparatus of extant and extinct species was investigated with a geometric morphometric analysis of mandible shape while locomotory habits were assessed using long bone indices. The mandible shape analysis performed on extant Carnivora taxa confirms their morphological differences due principally to taxonomic affiliation (family). Although, when phylogenetic history is controlled with comparative methods, significant differences still to occur among taxa with different diets and between small and large forms (threshold posed at 7 kilograms). Interestingly, both mandibular regions (corpus and ascending ramus) are informative of Carnivora ecological adaptations and they result integrated at a macroevolutionary scale. This survey allows to consider geometric morphometric as a reliable technique to apply on fossil mandibles. Feeding habits have been predicted with a good degree of accuracy in several PlioPleistocene large carnivores on the basis of mandible shape data. The latter data –selecting only the corpus regionhave been considered also to perform a morphospace comparison between large carnivore guilds of Italian PCOMs and extant guilds representative of five mainland ecosystems worldwide. Disparity values computed for mandibular corpus shape of Plio-Pleistocene guilds did not differ significantly from extant guilds. Morphological variability in mandible shape is negatively influenced by number of species in each guild as well as number of prey confirming that ecomorph specialization does not occur at the extreme region of morphospace. Long bone proportions of Plio-Pleistocene large carnivores are grouped in the variability of extant species. Although some phenomena of morphological convergences occur among extinct and extant taxa because of similar locomotor adaptation (e.g. cursorial) and same body size constraint. These morphoecological data were also used to predict the relative adaptability of Plio-Pleistocene species to certain habitats (grassland and tropical). The macroecological analysis of presence/absence data confirms the striking relationship between the abundances of both predators and their prey thought Ice Age. On the other hand no morphoecological coordinate changes occurs between predators and their prey. It is noteworthy that large carnivores are overrepresented in the Italian fossil record and became rarer from Galerian to the Aurelian (also because of a possible interaction with human activities). A GIS model was then computed to compare large mammal communities toward Plio-Pleistocene in Italy. Structural changes occurred in large herbivore communities from Villafranchian through the Aurelian because of climate changes. On the other hand, the spatial structure of large carnivore communities was more affected by their prey during the Villafranchian, while in the Galerian and Aurelian there was a greater influence of uncontrolled factors like climate and human activity as well.

Diving into the deep-end: investigating tropical deep-reef fish assemblages

Under a neutral model, the stochastic lineage sorting that leads to gene monophyly proceeds slowly in large populations. Therefore, in many recent species with large population size, the genome will have mixed support for monophyly unless historical bottlenecks have accelerated coalescence. We use genealogical patterns in mitochondrial DNA and in introns of four nuclear loci to test for historical bottlenecks during the speciation and divergence of two temperate Lagenorhynchus dolphin species isolated by tropical Pacific waters (an antitropical distribution). Despite distinct morphologies, foraging behaviors, and mitochondrial DNAs, these dolphin species are polyphyletic at all four nuclear loci. The abundance of shared polymorphisms between these sister taxa is most consistent with the maintenance of large effective population sizes (5.09 x 10(4) to 10.9 x 10(4)) during 0.74-1.05 million years of divergence. A variety of population size histories are possible, however. We used gene tree coalescent probabilities to explore the rejection region for historical bottlenecks of different intensity given best estimates of effective population size under a strict isolation model of divergence. In L. obliquidens the data are incompatible with a colonization propagule of an effective size of 10 or fewer individuals. Although the ability to reject less extreme historical bottlenecks will require data from additional loci, the intermixed genealogical patterns observed between these dolphin sister species are highly probable only under an extended history of large population size. If similar demographic histories are inferred for other marine antitropical taxa, a parsimonious model for the Pleistocene origin of these distributions would not involve rare breaches of a constant dispersal barrier by small colonization propagules. Instead, a history of large population size in L. obliquidens and L. obscurus contributes to growing biological and environmental evidence that the equatorial barrier became permeable during glacial/interglacial cycles, leading to vicariant isolation of antitropical populations.

Under a neutral model, the stochastic lineage sorting that leads to gene monophyly proceeds slowly in large populations. Therefore, in many recent species with large population size, the genome will have mixed support for monophyly unless historical bottlenecks have accelerated coalescence. We use genealogical patterns in mitochondrial DNA and in introns of four nuclear loci to test for historical bottlenecks during the speciation and divergence of two temperate Lagenorhynchus dolphin species isolated by tropical Pacific waters (an antitropical distribution). Despite distinct morphologies, foraging behaviors, and mitochondrial DNAs, these dolphin species are polyphyletic at all four nuclear loci. The abundance of shared polymorphisms between these sister taxa is most consistent with the maintenance of large effective population sizes (5.09 × 104 to 10.9 × 104) during 0.74–1.05 million years of divergence. A variety of population size histories are possible, however. We used gene tree coalescent probabilities to explore the rejection region for historical bottlenecks of different intensity given best estimates of effective population size under a strict isolation model of divergence. In L. obliquidens the data are incompatible with a colonization propagule of an effective size of 10 or fewer individuals. Although the ability to reject less extreme historical bottlenecks will require data from additional loci, the intermixed genealogical patterns observed between these dolphin sister species are highly probable only under an extended history of large population size. If similar demographic histories are inferred for other marine antitropical taxa, a parsimonious model for the Pleistocene origin of these distributions would not involve rare breaches of a constant dispersal barrier by small colonization propagules. Instead, a history of large population size in L. obliquidens and L. obscurus contributes to growing biological and environmental evidence that the equatorial barrier became permeable during glacial/interglacial cycles, leading to vicariant isolation of antitropical populations.Corresponding Editor: S. Edwards

The processes underlying the distributional limits of both corals and coral reefs can be elucidated by examining coral communities at high latitudes. Coral-dominated communities in eastern Australia cover a latitudinal range of >2,500 km, from the northern Great Barrier Reef (11°S) to South West Rocks (31.5°S). Patterns of coral species richness from 11 locations showed a clear separation between the Great Barrier Reef and subtropical sites, with a further abrupt change at around 31°S. Differences in community structure between the Great Barrier Reef and more southern sites were mainly attributable to higher cover of massive corals, branching Acropora, dead coral and coralline algae on the Great Barrier Reef, and higher cover of macroalgae and bare rock at more southern sites. The absence of some major reef-building taxa (i.e., staghorn Acropora and massive Porites) from most subtropical sites coincided with the loss of reef accretion capacity. Despite high cover of hard corals in communities at up to 31°S, only Lord Howe Island contained areas of reef accretion south of the Great Barrier Reef. Factors that have been hypothesized to account for latitudinal changes in coral community structure include water temperature, aragonite saturation, light availability, currents and larval dispersal, competition between corals and other biota including macroalgae, reduced coral growth rates, and failure of coral reproduction or recruitment. These factors do not operate independently of each other, and they interact in complex ways.

Discovery mark tagging provided the first evidence of linkages between eastern Australian and Oceania Humpback whale breeding grounds and the Antarctic Area V feeding areas. Early investigation of movements of humpback whales in the Western Pacific led to the view that the Balleny Islands and the Ross Sea were the summer destinations for humpback whales from eastern Australia and the Oceania breeding grounds. Recent photo-identification (ID) studies provided further evidence of low levels of migratory interchange and complex linkages within Oceania and between eastern Australia and Oceania. We report here the migratory movement of three humpback whales (Megaptera novaeangliae) between Eastern Australia (E(i) breeding stock) and the Area V Antarctic feeding area in the vicinity of the Balleny Islands. Using photo-ID techniques, comparisons between a Balleny Island fluke catalogue (n = 11 individuals) and existing fluke catalogues from eastern Australia (n = 3,120 individuals) and Oceania (n = 725 individuals), yielded three matches to Hervey Bay, Byron Bay and Ballina in eastern Australia and no matches to Oceania. The eastern Australia catalogue (n = 3,120) was made up of Hervey Bay (n = 1,556), Byron Bay, (n = 916) and Ballina (n = 648). The Oceania catalogue (n = 725) is made up of Tonga (n = 282); New Caledonia (n = 160); French Polynesia (n = 159); New Zealand (n = 41); Cook Islands (n = 36); American Samoa (n = 31); Vanuatu, Niue, Samoa and Fiji (n = 11) and Norfolk Island (n = 5). Only three previous individual photo-ID matches have been reported between eastern Australia Breeding Stock E(i) and Antarctic Area V feeding areas in the vicinity of the Balleny Islands and the Ross Sea. Only one genotype match has been reported between Antarctic Area V feeding areas and Oceania breeding grounds. An analysis of the frequencies of whales seen and not seen in the Balleny Islands, Oceania and eastern Australia, relative to the expected frequencies, based on the estimated population sizes and the sizes of the catalogues, supports the hypothesis that Antarctic Area V waters, in the vicinity of the Balleny islands, is a summer feeding area for some eastern Australian humpback whales.