Estimating population size of the black-eared miner, with an assessment of landscape-scale habitat requirements

The decline of the Black-eared Miner Manorina melanotis has been caused primarily by habitat degradation and vegetation clearance. To better direct conservation actions for this species there was a need to assess habitat requirements on a regional-scale and to estimate the population size using quantitative methods. We used vegetation mapping and the current distribution of the Black-eared Miner to determine regional-scale habitat requirements. These findings were combined with the results of distance sampling to provide population estimates. The species is restricted to large tracts of intact mallee in the Murray Mallee of southeastern Australia that have not been burnt for at least 45 years. The density· of Black-eared Miners is highest in areas that are dominated by mallee- Triodia associations and have not been intensively grazed. The Bookmark Biosphere Reserve supports an estimated 501 (270-927, 95% CI) colonies, containing 3758 (2026-6954) phenotypically pure Black-eared Miners, 2255 (1 215-4170) hybrids and small numbers of Yellow-throated Miners Manorina flavigula. However, the effective population size is considerably smaller (390 Black-eared Miners '(21 0-726) and 234 hybrids (126-433)), due to a skewed adult sex ratio (1 female: 1.81 males) and complex social organization. A smaller population also persists in the Murray Sunset National Park containing 53 (32-85) Black-eared Miner/hybrid colonies. Both populations face a high risk of extinction from large-scale wildfire. The endangered status of the species under IUCN criteria remains warranted.

Mortality rates, prevalence of malnutrition, and prevalence of lost pregnancies among the drought-ravaged population of Tete province Mozambique

Background: Tete Province, Mozambique has experienced chronic food insecurity and a dramatic fall in livestock numbers due to the cyclic problems characterized by the floods in 2000 and severe droughts in 2002 and 2003. The Province has been a beneficiary of emergency relief programs, which have assisted >22% of the population. However, these programs were not based on sound epidemiological data, and they have not established baseline data against which to assess the impact of the programs. Objective: The objective of this study was to document mortality rates, causes of death, the prevalence of malnutrition, and the prevalence of lost pregnancies after 2.5 years of humanitarian response to the crisis. Methods: A two-stage, 30-cluster household survey was conducted in the Cahora Bassa and Changara districts from 22 October to 08 November 2004. A total of 838 households were surveyed, with a population size of 4,688 people. Results: Anthropometric data were collected among children 6-59 months of age. In addition, crude mortality rates (CMRs), under five mortality rates (U5MRs), causes of deaths, and prevalence of lost pregnancies were determined among the sample population. The prevalence of malnutrition was 8.0% (95% confidence interval (CI)=6.2-9.8%) for acute malnutrition, 26.9% (95% CI=24.0-29.9%) for being underweight, and 37.0% (95% CI=33.8-40.2%) for chronic malnutrition. Boys were more likely to be underweight than were girls (odds ratio (OR)=1.34; 95% CI=1.00, 1.82; p<0.05) after controlling for age, household size, and food aid beneficiary status. Similarly, children 30-59 months of age were significantly less likely to suffer from acute malnutrition (OR=0.45; 95% CI=0.26, 0.79; p<0.01) and less likely to be underweight (OR=0.37; 95% CI=0.27, 0.51; p<0.01) than children 6-29 months of age, after adjusting for the other, aforementioned factors. The proportion of lost pregnancies was estimated at 7.7% (95% CI=4.5-11.0%). A total of 215 deaths were reported during the year preceding the survey. Thirty-nine (18.1%) children <5 years of age died. The CMR was 1.23/10 000/day (95% CI=1.08-1.38), and an U5MR was 1.03/10 000/day (95% CI=0.71-1.35). Diarrheal diseases, malaria, tuberculosis, and human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) accounted for more than two-thirds of all deaths. Conclusions: The observed CMR in Tete Province, Mozambique is three times higher than the baseline rate for sub-Saharan Africa and 1.4 times higher than the CMR cut-off point used to define excess mortality in emergencies. The current humanitarian response in Tete Province would benefit from an improved alignment of food aid programming in conjunction with diarrheal disease control, HIV/AIDS, and malaria prevention and treatment programs. The impact of the food programs would be improved if mutually acceptable food aid programme objectives, verifiable indicators relevant to each objective, and beneficiary targets and selection criteria are developed. Periodic re-assessments and evaluations of the impact of the program and evidenced-based decision-making urgently are needed to avert a chronic dependency on food aid.

Factors influencing population dynamics in island and mainland populations of the Swamp Antechinus (Antechinus minimus)

Simultaneously analysing demographic processes of small mammals living in different ecological contexts may help to understand mechanisms that influence the growth and decline of these populations. The size and demography of swamp antechinus (Antechinus minimus) populations located in a coastal mainland habitat and on a small offshore island in south-eastern Australia were investigated. Large demographic differences occurred between the two ecosystems, with the island population density often 100 times greater than that on the mainland. The swamp antechinus in the mainland habitat was influenced by extrinsic climatic forces, with juvenile recruitment, individual body mass and overall population size being affected by rainfall, a factor likely to influence food availability for the species. However, the island population did not appear to be affected by drought to the same degree where allochthonous marine nutrient inputs may have offset any drought-induced reduction in primary production. Significantly greater juvenile recruitment in the island habitats combined with restricted emigration and potentially reduced predation and interspecific competition are likely to be responsible for the high population densities on the island. Although island populations appear robust, future conservation efforts should focus on mainland populations given the genetic deficiencies in the island populations.

Inbreeding and testicular abnormalities in a bottlenecked population of koalas (Phascolarctos cinereus)

Habitat destruction and fragmentation, interactions with introduced species or the relocation of animals to form new populations for conservation purposes may result in a multiplication of population bottlenecks. Examples are the translocations of koalas to French Island and its derivative Kangaroo Island population, with both populations established as insurance policies against koala extinction. In terms of population size, these conservation programs were success stories. However, the genetic story could be different. We conducted a genetic investigation of French and Kangaroo Island koalas by using 15 microsatellite markers, 11 of which are described here for the first time. The results confirm very low genetic diversity. French Island koalas have 3.8 alleles per locus and Kangaroo Island koalas 2.4. The present study found a 19% incidence of testicular abnormality in kangaroo Island animals. Internal relatedness, an individual inbreeding coefficient, was not significantly different in koalas with testicular abnormalities from that in other males, suggesting the condition is not related to recent inbreeding. It could instead result from an unfortunate selection of founder individuals carrying alleles for testicular abnormalities, followed by a subsequent increase in these alleles’ frequencies through genetic drift and small population-related inefficiency of selection. Given the low diversity and possible high prevalence of deleterious alleles, the genetic viability of the population remains uncertain, despite its exponential growth so far. This stands as a warning to other introductions for conservation reasons.

Continued population recovery by Australian fur seals

Australian fur seals (Arctocephalus pusillus doriferus) are conspicuous, top-level predators in coastal waters of south-eastern Australia that were over-harvested during the 1800s and have had a delayed recovery. A previous species-wide estimate of live pups in 2002 recorded a near-doubling of annual pup production and a 5% annual growth rate since the 1980s. To determine if pup production increased after 2002, we estimated live pup numbers in 2007. Pups were recorded at 20 locations: 10 previously known colonies, three newly recognised colonies and seven haul-out sites where pups are occasionally born. Two colonies adjacent to the Victorian coast accounted for 51% of live pups estimated: Seal Rocks (5660 pups, 25.9%) and Lady Julia Percy Island (5574 pups, 25.5%). Although some colonies were up and some were down in pup numbers, the 2007 total of 21 882±187 (s.e.) live pups did not differ significantly from a recalculated estimate of 21 545±184 in 2002, suggesting little change to overall population size. However, the colonisation of three new sites between 2002 and 2007 indicates population recovery has continued.

Densities of individually marked migrants away from the marking site to estimate population sizes : a test with three wader populations

Capsule Population estimates based on the mark–resighting method can be a useful alternative to population-wide counts.

Aims To investigate whether the mark–resighting method can be used as an alternative to counts to estimate the size of wader populations.

Methods Individual colour-marking and subsequent resightings allowed accurate estimates of annual survival for three populations of waders, on which basis we could estimate the actual number of marked birds alive. Densities of marked birds were determined on sites away (2000–4300 km) from the ringing locations expecting marked birds to be randomly distributed among non-marked conspecifics. Population sizes are estimated by combining these densities with the number of marked birds alive.

Results We found indications that the distribution of marked birds was indeed random in the locations away from the site of marking. The estimated population size of Red Knot Calidris canutus canutus was in accordance with the most recent estimates based on counts. Our estimate of the Calidris c. islandica population was somewhat lower, and that of the Bar-tailed Godwit Limosa lapponica taymyrensis population was considerably lower than the latest estimates based on counts.

Conclusion Population estimates based on the mark–resighting method can be a useful alternative for, or addition to, population-wide counts, as long as the assumption of random distribution of marked birds at the reading sites is taken into account. We conclude that the Afro-Siberian Bar-tailed Godwit population has recently decreased in size or has been substantially overestimated during the counts.

Population genetic structure, gene flow and sex-biased dispersal in frillneck lizards (Chlamydosaurus kingii)

By using both mitochondrial and nuclear multiloci markers, we explored population genetic structure, gene flow and sex-specific dispersal of frillneck lizards (Chlamydosaurus kingii) sampled at three locations, separated by 10 to 50 km, in a homogenous savannah woodland in tropical Australia. Apart from a recombinant lizard, the mitochondrial analyses revealed two nonoverlapping haplotypes/populations, while the nuclear markers showed that the frillneck lizards represented three separate clusters/populations. Due to the small population size of the mtDNA, fixation may occur via founder effects and/or drift. We therefore suggest that either of these two processes, or a combination of the two, are the most likely causes of the discordant results obtained from the mitochondrial and the nuclear markers. In contrast to the nonoverlapping mitochondrial haplotypes, in 12 out of 74 lizards, mixed nuclear genotypes were observed, hence revealing a limited nuclear gene flow. Although gene flow should ultimately result in a blending of the populations, we propose that the distinct nuclear population structure is maintained by frequent fires resulting in local bottlenecks, and concomitant spatial separation of the frillneck lizard populations. Limited mark-recapture data and the difference in distribution of the mitochondrial and nuclear markers suggest that the mixed nuclear genotypes were caused by juvenile male-biased dispersal.

Geographical variation and population structure in the White-rumped Sandpiper Calidris fuscicollis as shown by morphology, mitochondrial DNA and carbon isotope ratios

We studied the population structure of a high arctic breeding wader bird species, the White-rumped Sandpiper Calidris fuscicollis. Breeding adults, chicks and juveniles were sampled at seven localities throughout the species' breeding range in arctic Canada in 1999. The mitochondrial control region was analysed by DNA sequencing, feathers were analysed for carbon isotope ratios (C13/C12) by isotope ratio mass spectrometry, and morphological measurements were analysed using principal component analyses, taking the effect of sex into account (identified by molecular genetic methods). In general, our results support the notion that the White-rumped Sandpiper is a monotypic species with no subspecies, and most of the morphological and genetic variation occurs within sites. Nevertheless, some differences between sites were found. Birds from the two northernmost sites (Ellesmere and Devon Islands) had relatively longer bill and wing and shorter tarsus than birds sampled further south, possibly reflecting genetic differences between populations. The carbon isotope ratios were higher at the easternmost site (Baffin Island), revealing differences in the isotope content of the food. The mtDNA sequences showed no significant differentiation between sites and no pattern of isolation-by-distance was found. Based on the mtDNA variation, the species was estimated to have a long-term effective population size of approximately 9,000 females. The species shows no clear evidence of any population expansion or decline. Our results indicate that carbon isotope ratios, and possibly also certain mtDNA haplotypes, may be useful as tools for identifying the breeding origin of White-rumped Sandpipers on migration and wintering sites.

Use of expert knowledge to elicit population trends for the koala (Phascolarctos cinereus)

Aim: The koala is a widely distributed Australian marsupial with regional populations that are in rapid decline, are stable or have increased in size. This study examined whether it is possible to use expert elicitation to estimate abundance and trends of populations of this species. Diverse opinions exist about estimates of abundance and, consequently, the status of populations. Location: Eastern and south-eastern Australia Methods: Using a structured, four-step question format, a panel of 15 experts estimated population sizes of koalas and changes in those sizes for bioregions within four states. They provided their lowest plausible estimate, highest plausible estimate, best estimate and their degree of confidence that the true values were contained within these upper and lower estimates. We derived estimates of the mean population size of koalas and associated uncertainties for each bioregion and state. Results: On the basis of estimates of mean population sizes for each bioregion and state, we estimated that the total number of koalas for Australia is 329,000 (range 144,000-605,000) with an estimated average decline of 24% over the past three generations and the next three generations. Estimated percentage of loss in Queensland, New South Wales, Victoria and South Australia was 53%, 26%, 14% and 3%, respectively. Main conclusions: It was not necessary to achieve high levels of certainty or consensus among experts before making informed estimates. A quantitative, scientific method for deriving estimates of koala populations and trends was possible, in the absence of empirical data on abundances.

A single panmictic population of endemic red crabs, Gecarcoidea natalis, on Christmas Island with high levels of genetic diversity

The red crab, Gecarcoidea natalis, is endemic to Christmas Island in the Indian Ocean and largely responsible for shaping the unique ecosystem found throughout the island's rainforests. However, the introduction and establishment of supercolonies of the highly invasive yellow crazy ant, Anoplolepis gracilipes, has decimated red crab numbers over the last several decades. This poses a significant risk to the future conservation of G. natalis and consequently threatens the integrity of the unique island ecosystem. Here we undertook a population genetic analysis of G. natalis using a combination of 11 microsatellite markers and sequencing of the mitochondrial cytochrome oxidase subunit I gene from samples collected on Christmas Island as well as a single location from North Keeling Island (located approximately 900 km west of Christmas Island). The genetic results indicate that G. natalis is a single panmictic population on Christmas Island, with no spatial genetic structure or restricted gene flow apparent between sampled locations. Further, G. natalis from North Keeling Island are not genetically distinct and are recent immigrants from Christmas Island. The effective population size of G. natalis has likely remained large and stable on Christmas Island throughout its evolutionary history with relatively moderate to high levels of genetic diversity in microsatellite loci and mitochondrial haplotypes assessed in this study. For management purposes G. natalis can be considered a single panmictic population, which should simplify conservation efforts for the genetic management of this iconic island species. © 2014 Springer Science+Business Media Dordrecht.

Using climatic suitability thresholds to identify past, present and future population viability

Often climatic niche models predict that any change in climatic conditions will impact species abundance or distribution. However, the accuracy of models that just incorporate climatic information to predict future species habitat use is widely debated. Alternatively, environmental conditions may simply need to be above some minimum threshold of climatic suitability, at which point, other factors drive population size. Using the example of nesting sites of loggerhead sea turtles (Caretta caretta) in the Mediterranean (n = 105), we developed climatic niche models to examine whether a climatic suitability threshold could be identified as a climatic indicator in order for large populations of a widespread species to exist. We then assessed the climatic suitability of sites above and below this threshold in the past (∼1900) and future (∼2100). Most large sites that are currently above the climatic threshold were above the threshold in the past and future, particularly when future nesting seasonality shifted to start 1–2 months earlier. Our analyses highlight the importance of future phenological shifts for maintaining suitability. Our results provide a positive outlook for sea turtle conservation, suggesting that climatic conditions may remain suitable in the future at sites that currently support large nesting populations. Our study also provides an alternative way of interpreting the outputs of climatic niche models, by generating a threshold as an index of a minimum climatic suitability required to sustain large populations. This type of approach offers the possibility to benefit from information provided by climate-driven models, while reducing their inherent uncertainties.

Three molecular markers show no evidence of population genetic structure in the gouldian finch (Erythrura gouldiae)

Assessment of genetic diversity and connectivity between regions can inform conservation managers about risk of inbreeding, potential for adaptation and where population boundaries lie. The Gouldian finch (Erythrura gouldiae) is a threatened species in northern Australia, occupying the savannah woodlands of the biogeographically complex monsoon tropics. We present the most comprehensive population genetic analysis of diversity and structure the Gouldian finch using 16 microsatellite markers, mitochondrial control region and 3,389 SNPs from genotyping-by-sequencing. Mitochondrial diversity is compared across three related, co-distributed finches with different conservation threat-statuses. There was no evidence of genetic differentiation across the western part of the range in any of the molecular markers, and haplotype diversity but not richness was lower than a common co-distributed species. Individuals within the panmictic population in the west may be highly dispersive within this wide area, and we urge caution when interpreting anecdotal observations of changes to the distribution and/or flock sizes of Gouldian finch populations as evidence of overall changes to the population size of this species.