Ecological niche modelling and DNA sequencing support a new, morphologically cryptic beetle species unveiled by DNA barcoding

Background: DNA sequencing techniques used to estimate biodiversity, such as DNA barcoding, may reveal cryptic species. However, disagreements between barcoding and morphological data have already led to controversy. Species delimitation should therefore not be based on mtDNA alone. Here, we explore the use of nDNA and bioclimatic modelling in a new species of aquatic beetle revealed by mtDNA sequence data.

Methodology/Principal Findings: The aquatic beetle fauna of Australia is characterised by high degrees of endemism, including local radiations such as the genus Antiporus. Antiporus femoralis was previously considered to exist in two disjunct, but morphologically indistinguishable populations in south-western and south-eastern Australia. We constructed a phylogeny of Antiporus and detected a deep split between these populations. Diagnostic characters from the highly variable nuclear protein encoding arginine kinase gene confirmed the presence of two isolated populations. We then used ecological niche modelling to examine the climatic niche characteristics of the two populations. All results support the status of the two populations as distinct species. We describe the south-western species as Antiporus occidentalis sp.n.

Conclusion/Significance: In addition to nDNA sequence data and extended use of mitochondrial sequences, ecological niche modelling has great potential for delineating morphologically cryptic species. © 2011 Hawlitschek et al.

Concordance in phylogeography and ecological niche modelling identify dispersal corridors for reptiles in arid Australia

Aim: Using the rock-specialist agamid Ctenophorus caudicinctus as a model, we test hypothesized biogeographical dispersal corridors for lizards in the Australian arid zone (across the western sand deserts), and assess how these dispersal routes have shaped phylogeographical structuring. Location: Arid and semi-arid Australia. Methods: We sequenced a c. 1400 bp fragment of mtDNA (ND2) for 134 individuals of C. caudicinctus as well as a subset of each of the mtDNA clades for five nuclear loci (BDNF, BACH1, GAPD, NTF3, and PRLR). We used phylogenetic methods to assess biogeographical patterns within C. caudicinctus, including relaxed molecular clock analyses to estimate divergence times. Ecological niche modelling (Maxent) was employed to estimate the current distribution of suitable climatic envelopes for each lineage. Results: Phylogenetic analyses identified two deeply divergent mtDNA clades within C. caudicinctus - an eastern and western clade - separated by the Western Australian sand deserts. However, divergences pre-date the Pleistocene sand deserts. Phylogenetic analyses of the nuclear DNA data sets generally support major mtDNA clades, suggesting past connections between the western C. c. caudicinctus populations in far eastern Pilbara (EP) and the lineages to the east of the sand deserts. Ecological niche modelling supports the continued suitability of climatic conditions between the Central Ranges and the far EP for C. c. graafi. Main conclusions: Estimates of lineage ages provide evidence of divergence between eastern and western clades during the Miocene with subsequent secondary contact during the Pliocene. Our results suggest that this secondary contact occurred via dispersal between the Central Ranges and the far EP, rather than the more southerly Giles Corridor. These events precede the origins of the western sand deserts and divergence patterns instead appear associated with Miocene and Pliocene climate change.

Ecological allometries and niche use dynamics across Komodo dragon ontogeny

Ontogenetic allometries in ecological habits and niche use are key responses by which individuals maximize lifetime fitness. Moreover, such allometries have significant implications for how individuals influence population and community dynamics. Here, we examined how body size variation in Komodo dragons (Varanus komodoensis) influenced ecological allometries in their: (1) prey size preference, (2) daily movement rates, (3) home range area, and (4) subsequent niche use across ontogeny. With increased body mass, Komodo dragons increased prey size with a dramatic switch from small (≤10 kg) to large prey (≥50 kg) in lizards heavier than 20 kg. Rates of foraging movement were described by a non-linear concave down response with lizard increasinghourly movement rates up until ∼20 kg body mass before decreasing daily movement suggesting reduced foraging effort in larger lizards. In contrast, home range area exhibited a sigmoid response with increased body mass. Intrapopulation ecological niche use and overlap were also strongly structured by body size. Thus, ontogenetic allometries suggest Komodo dragon’s transition from a highly active foraging modeexploiting small prey through to a less active sit and wait feeding strategy focused on killing large ungulates. Further, our results suggest that as body size increases across ontogeny, the Komodo dragon exhibited marked ontogenetic niche shifts that enabled it to function as an entire vertebrate predator guild by exploiting prey across multiple trophic levels.

Remotely sensed hydroacoustics and observation data for predicting fish habitat suitability

This paper investigates the use of using remotely sensed observation and full coverage hydroacoustic datasets to quantify habitat suitability for a marine demersal fish, the blue-throated wrasse. Because of issues surrounding the detection of species using remotely sensed video techniques, the application of presence-only techniques are well suited for modeling demersal fish habitat suitability. Ecological-Niche Factor Analysis is used to compare analyses conducted using seafloor variables derived from hydroacoustics at three spatial scales; fine (56.25 m²), medium (506.25 m²) and coarse (2756.25 m²), to determine which spatial scale was most influential in predicting blue-throated wrasse habitat suitability. The coarse scale model was found to have the best predictive capabilities with a Boyce Index of 0.80±0.26. The global marginality and specialization values indicated that, irrespective of spatial scale, blue-throated wrasse prefer seafloor characteristics that are different to the mean available within the study site, but exhibit a relatively wide niche. Although variable importance varied over the three spatial scale models, blue-throated wrasse showed a strong preference for regions of shallow water, close to reef, with high rugosity and maximum curvature and low HSI-B values. Generally the spatial patterns in habitat suitability were well represented in the Marine National Park compared to adjacent waters. However, some significant differences in spatial patterns were observed. Interspersion and Juxtaposition Indexes for unsuitable and highly suitable habitat were significantly smaller inside the Marine National Park, while the Mean Shape Index of unsuitable habitat in the Marine National Park was significantly larger.

A parent focused child obesity prevention intervention improves some mother obesity risk behaviors : the Melbourne infant program

Background

The diets, physical activity and sedentary behavior levels of both children and adults in Australia are suboptimal. The family environment, as the first ecological niche of children, exerts an important influence on the onset of children's habits. Parent modeling is one part of this environment and a logical focus for child obesity prevention initiatives. The focus on parent's own behaviors provides a potential opportunity to decrease obesity risk behaviors in parents as well.
Objective

To assess the effect of a parent-focused early childhood obesity prevention intervention on first-time mothers' diets, physical activity and TV viewing time.
Methods

The Melbourne InFANT Program is a cluster-randomized controlled trial which involved 542 mothers over their newborn's first 18 months of life. The intervention focused on parenting skills and strategies, including parental modeling, and aimed to promote development of healthy child and parent behaviors from birth, including healthy diet, increased physical activity and reduced TV viewing time. Data regarding mothers' diet (food frequency questionnaire), physical activity and TV viewing times (self-reported questionnaire) were collected using validated tools at both baseline and post-intervention. Four dietary patterns were derived at baseline using principal components analyses including frequencies of 55 food groups. Analysis of covariance was used to measure the impact of the intervention.
Results

The scores of both the "High-energy snack and processed foods" and the "High-fat foods" dietary patterns decreased more in the intervention group: -0.22 ([MINUS SIGN]0.42;-0.02) and [MINUS SIGN]0.25 ([MINUS SIGN]0.50;-0.01), respectively. No other significant intervention vs. control effects were observed regarding total physical activity, TV viewing time, and the two other dietary patterns, i.e. "Fruits and vegetables" and "Cereals and sweet foods".
Conclusions

These findings suggest that supporting first-time mothers to promote healthy lifestyle behaviors in their infants impacts maternal dietary intakes positively. Further research needs to assess ways in which we might further enhance those lifestyle behaviors not impacted by the InFANT intervention.

Underestimated and severe : small mammal decline from the forests of south-eastern Australia since European settlement, as revealed by a top-order predator

In Australia, numerous small mammal species have suffered extinction or severe declines in distribution and abundance following European settlement. The extent of these declines from forested areas of south-eastern Australia, however, remains poorly understood. In this paper we use sub-fossil deposits of the sooty owl (Tyto tenebricosa tenebricosa) as a tool for understanding the diversity of the small mammal palaeocommunity. These results are compared to the contemporary sooty owl diet from the same geographical region to investigate the degree of small mammal decline following European settlement. Of 28 mammal species detected in sub-fossil deposits and considered prey items of the sooty owl at the time of European settlement, only 10 species were detected in the contemporary sooty owl diet. Numerous small mammal species have not only recently suffered severe declines in distribution and abundance but have also recently undergone niche contraction, as they occupied a greater diversity of regions and habitats at the time of European settlement. For some species our understanding of their true ecological niche and ecological potential is therefore limited. The species that underwent the greatest declines occupied open habitat types or were terrestrial. The severity of decline is also likely to have resulted in severe disruption of ecosystem functions, with wide scale ecosystem consequences. There is an urgent need to improve small mammal conservation, to maintain crucial ecosystem functions performed by small mammals. It is recommended that broad-scale exotic predator control programs are conducted which may also provide suitable conditions for the re-introduction of locally extinct species.

Long-term species, sexual and individual variations in foraging strategies of fur seals revealed by stable isotopes in whiskers

Background: Individual variations in the use of the species niche are an important component of diversity in trophic interactions. A challenge in testing consistency of individual foraging strategy is the repeated collection of information on the same individuals.

Methodology/Principal Findings: The foraging strategies of sympatric fur seals (Arctocephalus gazella and A. tropicalis) were examined using the stable isotope signature of serially sampled whiskers. Most whiskers exhibited synchronous delta C-13 and delta N-15 oscillations that correspond to the seal annual movements over the long term (up to 8 years). delta C-13 and delta N-15 values were spread over large ranges, with differences between species, sexes and individuals. The main segregating mechanism operates at the spatial scale. Most seals favored foraging in subantarctic waters (where the Crozet Islands are located) where they fed on myctophids. However, A. gazella dispersed in the Antarctic Zone and A. tropicalis more in the subtropics. Gender differences in annual time budget shape the seal movements. Males that do not perform any parental care exhibited large isotopic oscillations reflecting broad annual migrations, while isotopic values of females confined to a limited foraging range during lactation exhibited smaller changes. Limited inter-individual isotopic variations occurred in female seals and in male A. tropicalis. In contrast, male A. gazella showed large inter-individual variations, with some males migrating repeatedly to high-Antarctic waters where they fed on krill, thus meaning that individual specialization occurred over years.

Conclusions/Significance: Whisker isotopic signature yields unique long-term information on individual behaviour that integrates the spatial, trophic and temporal dimensions of the ecological niche. The method allows depicting the entire realized niche of the species, including some of its less well-known components such as age-, sex-, individual- and migration-related changes. It highlights intrapopulation heterogeneity in foraging strategies that could have important implications for likely demographic responses to environmental variability.

Behaviour and buoyancy regulation in the deepest-diving reptile : the leatherback turtle

In the face of the physical and physiological challenges of performing breath-hold deep dives, marine vertebrates have evolved different strategies. Although behavioural strategies in marine mammals and seabirds have been investigated in detail, little is known about the deepest-diving reptile – the leatherback turtle (Dermochelys coriacea). Here, we deployed tri-axial accelerometers on female leatherbacks nesting on St Croix, US Virgin Islands, to explore their diving strategy. Our results show a consistent behavioural pattern within dives among individuals, with an initial period of active swimming at relatively steep descent angles (∼–40 deg), with a stroke frequency of 0.32 Hz, followed by a gliding phase. The depth at which the gliding phase began increased with the maximum depth of the dives. In addition, descent body angles and vertical velocities were higher during deeper dives. Leatherbacks might thus regulate their inspired air-volume according to the intended dive depth, similar to hard-shelled turtles and penguins. During the ascent, turtles actively swam with a stroke frequency of 0.30 Hz but with a low vertical velocity (∼0.40 ms–1) and a low pitch angle (∼+26 deg). Turtles might avoid succumbing to decompression sickness (‘the bends’) by ascending slowly to the surface. In addition, we suggest that the low body temperature of this marine ectotherm compared with that of endotherms might help reduce the risk of bubble formation by increasing the solubility of nitrogen in the blood. This physiological advantage, coupled with several behavioural and physical adaptations, might explain the particular ecological niche the leatherback turtle occupies among marine reptiles.

Why fly the extra mile? Latitudinal trend in migratory fuel deposition rate as driver of trans-equatorial long-distance migration.

Trans-equatorial long-distance migrations of high-latitude breeding animals have been attributed to narrow ecological niche widths. We suggest an alternative hypothesis postulating that trans-equatorial migrations result from a possible increase in the rate at which body stores to fuel migration are deposited with absolute latitude; that is, longer, migrations away from the breeding grounds surpassing the equator may actually enhance fueling rates on the nonbreeding grounds and therewith the chance of a successful, speedy and timely migration back to the breeding grounds. To this end, we first sought to confirm the existence of a latitudinal trend in fuel deposition rate in a global data set of free-living migratory shorebirds and investigated the potential factors causing this trend. We next tested two predictions on how this trend is expected to impact the migratory itineraries on northward migration under the time-minimization hypothesis, using 56 tracks of high-latitude breeding shorebirds migrating along the East Asian-Australasian Flyway. We found a strong positive effect of latitude on fuel deposition rate, which most likely relates to latitudinal variations in primary productivity and available daily foraging time. We next confirmed the resulting predictions that (1) when flying from a stopover site toward the equator, migrants use long jumps that will take them to an equivalent or higher latitude at the opposite hemisphere; and (2) that from here onward, migrants will use small steps, basically fueling only enough to make it to the next suitable staging site. These findings may explain why migrants migrate "the extra mile" across the equator during the nonbreeding season in search of better fueling conditions, ultimately providing secure and fast return migrations to the breeding grounds in the opposite hemisphere.

Large-herbivore distribution and abundance : intra-and interspecific niche variation in the tropics

Determining the biological and environmental factors that limit the distribution and abundance of organisms is central to our understanding of the niche concept and crucial for predicting how species may respond to large-scale environmental change, such as global warming. However, detailed ecological information for the majority of species has been collected only at a local scale, and insufficient consideration has been given to geographical variation in intraspecific niche requirements. To evaluate the influence of environmental and biological factors on patterns of species distribution and abundance, we conducted a detailed, broadscale study across the tropical savannas of northern Australia on the ecology of three large, sympatric marsupial herbivores (family Macropodidae): the antilopine wallaroo (Macropus antilopinus), common wallaroo (M. robustus), and eastern grey kangaroo (M. giganteus). Using information on species abundance, climate, fire history, habitat, and resource availability, we constructed species' habitat models varying from the level of the complete distribution to smaller regional areas. Multiple factors affected macropod abundance, and the importance of these factors was dependent on the spatial scale of analyses. Fire regimes, water availability, geology, and soil type and climate were most important at the large scale, whereas aspects of habitat structure and interspecific species abundance were important at smaller scales. The distribution and abundance of eastern grey kangaroos and common wallaroos were strongly influenced by climate. Our results suggest that interspecific competition between antilopine wallaroos and eastern grey kangaroos may occur. The antilopine wallaroo and eastern grey kangaroo (grazers) preferred more nutrient-rich soils than the common wallaroo (grazer/browser), which we relate to differences in feeding modes. The abundance of antilopine wallaroos was higher on sites that were burned, whereas the abundance of common wallaroos was higher on unburned sites. Future climate change predicted for Australia has the capacity to seriously affect the abundance and conservation of macropod species in tropical savannas. The results of our models suggest that, in particular, the effects of changing climatic conditions on fire regimes, habitat structure, and water availability may lead to species declines and marked changes in macropod communities.

The dynamic regeneration niche of a forest following a rare disturbance event

Aim: Knowledge of how climate and fire regimes affect regeneration in foundation species is critical to the conservation of entire ecosystems. Different stages of regeneration often require different ecological conditions, but dynamic constraints on regeneration are poorly known for species that regenerate only after infrequent wildfires. Focussing on a long-lived, foundation tree species (Eucalyptus regnans), we tested the hypothesis that the relative importance of fire regime variables (fire severity and time since previous fire) and environmental gradients on post-fire regeneration would shift as seedlings developed. Location: South-eastern Australia. Methods: Following a large (> 59,000 ha) summer wildfire in 2009, we sampled 131 sites (61 burnt) annually for four years (2009-2012), representing the range of environmental conditions in which E. regnans occurs. We analysed the effect of fire severity, time since fire and environmental variables on early regeneration processes critical for post-fire species distributions: seedling establishment, seedling density and growth through different height stages (10 cm, 25 cm, 50 cm and 200 cm). Results: The regeneration niche of E. regnans was defined by different factors at different stages of development. Initially, seedlings established prolifically on burnt sites, regardless of severity. Three years into the regeneration process, high-severity fire became the dominant driver of seedling persistence and growth over 25 cm. Growth over 50 cm was dependent on environmental conditions relating to elevation and precipitation. Main conclusions: Our results describe how fire occurrence, fire severity and environmental gradients affected seedling establishment, persistence and growth. The dynamic constraints on regeneration likely reflect temporal changes in the biotic and abiotic environment and variation in resource requirements during the early post-fire years. Our findings will enable more accurate forecasts of species distributions to assist forest conservation in the face of global changes in climate and fire regimes.

Dietary niche overlap of free-roaming dingoes and domestic dogs: the role of human provided food

As both companion animals and opportunistic predators, dogs (Canis lupus spp.) have had a long and complex relationship with humans. In Australia, the dingo (C. l. dingo) was introduced 4,000 years ago and, other than humans, is now the continent's top mammalian predator. Domestic dogs (C. l. familiaris) were introduced by Europeans more recently and they interbreed with dingoes. This hybridization has caused growing concern about the roles that domestic dogs and dingoes play in shaping ecosystem processes. There is also considerable debate about whether anthropogenic environmental changes can alter the ecological roles of dingoes. We used scat analysis to test whether the dingo, as the longer-established predator, occupies a different dietary niche from that of free-roaming domestic dogs, irrespective of human influence. Our results demonstrate considerable dietary overlap between dingoes and domestic dogs in areas where humans provide supplementary food, providing evidence against our hypothesis. However, the consumption by dingoes of a greater diversity of prey, in association with historical differences in the interactions between dingoes and humans, suggests a partial separation of their dietary niche from that of domestic dogs. We conclude that anthropogenic changes in resource availability could prevent dingoes from fulfilling their trophic regulatory or pre-European roles. Effective management of human-provided food is therefore required urgently to minimize the potential for subsidized populations of dingoes and domestic dogs to negatively affect co-occurring prey.

Selecting umbrella species for conservation: a test of habitat models and niche overlap for beach-nesting birds

Umbrella species are rarely selected systematically from a range of candidate species. On sandy beaches, birds that nest on the upper beach or in dunes are threatened globally and hence are prime candidates for conservation intervention and putative umbrella species status. Here we use a maximum-likelihood, multi-species distribution modeling approach to select an appropriate conservation umbrella from a group of candidate species occupying similar habitats. We identify overlap in spatial extent and niche characteristics among four beach-nesting bird species of conservation concern, American oystercatchers (Haematopus palliatus), black skimmers (Rynchops niger), least terns (Sterna antillarum) and piping plovers (Charadrius melodus), across their entire breeding range in New Jersey, USA. We quantify the benefit and efficiency of using each species as a candidate umbrella on the remaining group. Piping plover nesting habitat encompassed 86% of the least tern habitat but only 15% and 13% of the black skimmer and American oystercatcher habitat, respectively. However, plovers co-occur with all three species across 66% of their total nesting habitat extent (~ 649 ha), suggesting their value as an umbrella at the local scale. American oystercatcher nesting habitat covers 100%, 99% and 47% of piping plover, least tern and black skimmer habitat, making this species more appropriate conservation umbrellas at a regional scale. Our results demonstrate that the choice of umbrella species requires explicit consideration of spatial scale and an understanding of the habitat attributes that an umbrella species represents and to which extent it encompasses other species of conservation interest. Notwithstanding the attractiveness of the umbrella species concept, local conservation interventions especially for breeding individuals in small populations may still be needed.

Evolutionary history of a secondary terrestrial Australian diving beetle (Coleoptera, Dytiscidae) reveals a lineage of high morphological and ecological plasticity

The evolution of a secondary terrestrial lifestyle in diving beetles (Coleoptera: Dytiscidae) has never been analysed in a phylogenetic framework before. Here we study Terradessus caecus Watts, a terrestrial species of the subfamily Hydroporinae endemic to Australia. We infer its phylogenetic placement using Bayesian inference and maximum-likelihood methods based on a multilocus molecular dataset. We also investigate the divergence time estimates of this lineage using a Bayesian relaxed clock approach. Finally, we infer ancestral ecological preferences using a likelihood approach. We recover T. caecus nested in the genus Paroster Sharp with strong support. Therefore, we establish a synonymy for both species of Terradessus with Paroster: Paroster caecus (Watts) n.comb. and Paroster anophthalmus (Brancucci & Monteith) n.comb. Paroster is an endemic Australian genus that has a remarkable number of subterranean species in underground aquifers with highly derived morphologies. Our results highlight one of the most remarkable radiations of aquatic beetles with independent ecological pathways likely linked to palaeoclimatic disruptions in the Neogene. Paroster caecus (Watts) n.comb. originated from a mid-Miocene split following the onset of an aridification episode that has been ongoing to the present day. The deep changes in ecological communities in association with the drying-out of palaeodrainage systems might have pushed this lineage to colonize a new niche in terrestrial habitats.