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.

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.

Replication of hematopoietic stem cell niche

This thesis models the hematopoietic stem cell (HSC) niche by using decellularized extracellular matrix (ECM) scaffolds prepared by MS-5 cell line. The ECM replicates many of the properties of HSC niches in vivo, providing insights into expansion of HSCs that may have several applications in translational medicine.

Niche separation in burrowing seabirds in Bass Strait

Islands in north-central Bass Strait support significant populations of short-tailed shearwaters, little penguins, fairy prions and common diving-petrels. Dietary analyses showed that while penguins consume mainly fish, the other species primarily feed on krill. Together, these seabirds consume an estimated 1,270,200 tonnes of prey throughout Bass Strait during breeding.

Thermal niche, large-scale movements and implications of climate change for a critically endangered marine vertebrate

Climate change is expected to have a number of impacts on biological communities including range extensions and contractions. Recent analyses of multidecadal data sets have shown such monotonic shifts in the distribution of plankton communities and various fish species, both groups for which there is a large amount of historical data on distribution. However, establishing the implications of climate change for the range of endangered species is problematic as historic data are often lacking. We therefore used a different approach to predict the implications of climate change for the range of the critically endangered planktivourous leatherback turtle (Dermochelys coriacea). We used long-term satellite telemetry to define the habitat utilization of this species. We show that the northerly distribution limit of this species can essentially be encapsulated by the position of the 15°C isotherm and that the summer position of this isotherm has moved north by 330 km in the North Atlantic in the last 17 years. Consequently, conservation measures will need to operate over ever-widening areas to accommodate this range extension.

Sexual niche segregation and gender-specific individual specialisation in a highly dimorphic marine mammal

While sexual segregation is expected in highly dimorphic species, the local environment is a major factor driving the degree of resource partitioning within a population. Sexual and individual niche segregation was investigated in the Australian fur seal (Arctocephalus pusillus doriferus), which is a benthic foraging species restricted to the shallow continental shelf region of south-eastern Australia. Tracking data and the isotopic values of plasma, red blood cells and whiskers were combined to document spatial and dietary niche segregation throughout the year. Tracking data indicated that, in winter, males and females overlapped in their foraging habitat. All individuals stayed within central Bass Strait, relatively close (< 220 km) to the breeding colony. Accordingly, both genders exhibited similar plasma and red cell δ13C values. However, males exhibited greater δ13C intra-individual variation along the length of their whisker than females. This suggests that males exploited a greater diversity of foraging habitats throughout the year than their female counterparts, which are restricted in their foraging grounds by the need to regularly return to the breeding colony to suckle their pup. The degree of dietary sexual segregation was also surprisingly low, both sexes exhibiting a great overlap in their δ15N values. Yet, males displayed higher δ15N values than females, suggesting they fed upon a higher proportion of higher trophic level prey. Given that males and females exploit different resources (mainly foraging habitats), the degree of individual specialisation might differ between the sexes. Higher degrees of individual specialisation would be expected in males which exploit a greater range of resources. However, comparable levels of inter-individual variation in δ15N whisker values were found in the sampled males and females, and, surprisingly, all males exhibited similar seasonal and inter-annual variation in their δ13C whisker values, suggesting they all followed the same general dispersion pattern throughout the year.

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.

Elemental and molecular profiling of licit, illicit, and niche tobacco

The recognition of differences between regulated large-scale mass manufactured products and the uncontrolled cultivation of tobaccos for illicit purposes plays a significant role within identification of provenance. This research highlights X-ray fluorescence and Fourier transform infrared spectroscopy as useful analytical techniques for the rapid identification of tobacco samples of unknown provenance. Identification of key discriminative features within each technique allowed for the development of typical characteristic profiles for each type of tobacco. Analysis using X-ray fluorescence highlights chlorine, potassium, calcium and iron as key elemental indicators of tobacco provenance. Significant levels of chlorine seen within Snüs samples prompted attempts to visualise chlorine containing regions and structures within the sample. Scanning electron microscopy images showed crystalline structures visible within the Snüs tobacco, structures which Energy dispersive X-ray spectroscopy qualitatively confirmed to contain chlorine. Chloride levels within Snüs samples were quantified using ion chromatography with levels found to range between 0.87mgmL‾¹ and 1.28mg. Additionally, FTIR indicated that absorbances attributed to carbonyl stretching at 1050-1150cm‾¹, alkane bending at 1350-1480cm‾¹and amide I stretching at 1600-1700cm‾¹ highlighting a spectral fingerprint region that allowed for the clear differentiation between different types of tobaccos using PCA analysis, but was limited by differentiation between provenance of cigarettes and hand rolled tobacco. X-ray fluorescence and Fourier transform infrared spectroscopy yielded different information with regards tobacco discrimination and provenance, however both methods overall analysis time and cost reduced indicating usefulness as potential handheld analytical techniques in the field.

Early-life sexual segregation: ontogeny of isotopic niche differentiation in the Antarctic fur seal

Investigating the ontogeny of niche differentiation enables to determine at which life-stages sexual segregation arises, providing insights into the main factors driving resource partitioning. We investigated the ontogeny of foraging ecology in Antarctic fur seals (Arctocephalus gazella), a highly dimorphic species with contrasting breeding strategies between sexes. Sequential δ(13)C and δ(15)N values of whiskers provided a longitudinal proxy of the foraging niche throughout the whole life of seals, from weaning, when size dimorphism is minimal to the age of 5. Females exhibited an early-life ontogenetic shift, from a total segregation during their first year at-sea, to a similar isotopic niche as breeding females as early as age 2. In contrast, males showed a progressive change in isotopic niche throughout their development such that 5-year-old males did not share the same niche as territorial bulls. Interestingly, males and females segregated straight after weaning with males appearing to feed in more southerly habitats than females. This spatial segregation was of similar amplitude as observed in breeding adults and was maintained throughout development. Such early-life niche differentiation is an unusual pattern and indicates size dimorphism and breeding constraints do not directly drive sexual segregation contrary to what has been assumed in otariid seals.

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.

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.

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.

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.