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.

Fine-scale effects of habitat loss and fragmentation despite large-scale gene flow for some regionally declining woodland bird species

Habitat loss and associated fragmentation effects are well-recognised threats to biodiversity. Loss of functional connectivity (mobility, gene flow and demographic continuity) could result in population decline in altered habitat, because smaller, isolated populations are more vulnerable to extinction. We tested whether substantial habitat reduction plus fragmentation is associated with reduced gene flow in three 'decliner' woodland-dependent bird species (eastern yellow robin, weebill and spotted pardalote) identified in earlier work to have declined disproportionately in heavily fragmented landscapes in the Box-Ironbark forest region in north-central Victoria, Australia. For these three decliners, and one 'tolerant' species (striated pardalote), we compared patterns of genetic diversity, relatedness, effective population size, sex-ratios and genic (allele frequency) differentiation among landscapes of different total tree cover, identified population subdivision at the regional scale, and explored fine-scale genotypic (individual-based genetic signature) structure. Unexpectedly high genetic connectivity across the study region was detected for 'decliner' and 'tolerant' species. Power analysis simulations suggest that moderate reductions in gene flow should have been detectable. However, there was evidence of local negative effects of reduced habitat extent and structural connectivity: slightly lower effective population sizes, lower genetic diversity, higher within-site relatedness and altered sex-ratios (for weebill and eastern yellow robin) in 10 x 10 km 'landscapes' with low vegetation cover. We conclude that reduced structural connectivity in the Box-Ironbark ecosystem may still allow sufficient gene flow to avoid the harmful effects of inbreeding in our study species. Although there may still be negative consequences of fragmentation for demographic connectivity, the high genetic connectivity of mobile bird species in this system suggests that reconnecting isolated habitat patches may be less important than increasing habitat extent and/or quality if these need to be traded off.

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.

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.

A species in decline: genetic diversity and conservation of the Victorian eastern barred bandicoot, Perameles gunnii

The eastern barred bandicoot, Perameles gunnii, has undergone a dramatic decline in distribution and abundance on the mainland of Australia during the twentieth century. In 1988 a captive breeding program was initiated to reduce the chance of extinction. With the extinction of the last wild mainland population in the early 1990s, reintroductions from captive-bred P. gunnii have met limited success, and currently only two extant populations persist in predator proof enclosures in the State of Victoria. With ~20 years of breeding, there are concerns that the genetic diversity within the breeding program has declined and may inhibit current and future success of the program. We have used ten nuclear microsatellite loci and sequencing of two partial mitochondrial genes (cytochrome oxidase I and ATPase 6) to determine genetic diversity within current Victorian P. gunnii. These diversity estimates are compared with historic samples from the captive breeding program dating back to 1995, historic samples from the last wild mainland population found at Hamilton in 1992 and contemporary Tasmanian wild populations. Results indicate that the captive P. gunnii population in the State of Victoria has lost significant genetic diversity through time. Genetic diversity is also reduced in populations at Hamilton Community Parklands and Mount Rothwell. Samples from the last wild population at Hamilton collected in 1992, along with samples from Tasmanian P. gunnii, had significantly greater genetic diversity than contemporary mainland populations. The results are discussed with reference to management options for maintaining genetic diversity within Victorian P. gunnii, including crossing Victorian and Tasmanian P. gunnii to increase genetic diversity, adaptability and evolutionary potential.

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.

Microsatellites revealed no genetic differentiation between hatchery and contemporary wild populations of striped catfish, Pangasianodon hypophthalmus (Sauvage 1878) in Vietnam

Aquaculture of the striped catfish, Pangasianodon hypophthalmus (Sauvage 1878), in Vietnam has become one of the fastest growing primary food production sectors in the world. Although a demand on quantity of fingerlings is currently reached, it is likely that the long term quality of the stocks may be uncertain due to lacking of genetic broodstock management measures. The present study employed five microsatellite loci to investigate levels of genetic variation of the stripped catfish of the current wild stocks as well as of the selected hatcheries in Vietnam. The study included four hatchery populations and two wild populations spawned in 2005 in the Mekong and Bassac Rivers, and one wild population (spawned in 2006) in the Bassac River. The results showed no genetic differentiation among populations as revealed by F_ST and a model-based clustering method. AMOVA also showed no genetic differentiation between pooled wild and pooled hatchery populations while variation within groups was significant. Genetic variation of wild (mean number of alleles per locus, A = 4.80–6.20; allelic richness, A_r = 4.54–5.06; mean effective number of alleles per locus, A_e = 2.86–3.20; observed heterozygosity, H_o = 0.62–0.65; expected heterozygosity, H_e = 0.62–0.64) and hatchery populations (A = 4.60–5.20; A^_r = 4.10–4.83; A_e = 2.80–3.11; H_o = 0.61–0.66; H_e = 0.61–0.64) were not statistically different. There were no evidences for recent genetic bottleneck in all populations. Therefore it is implied that the hatchery stocks of striped catfish in Vietnam were founded from sufficient numbers of brooders and current population size is large. The domestication process is in an early stage.

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.

The role and contribution of private land in Victoria to biodiversity conservation and the protected area system

The distribution and attributes of properties involved in three major programs for biodiversity protection on private land in Victoria, Australia, was investigated to determine their role in relation to the reserve system. Overlaying of dowsets in a geographic information system, with particular emphasis on property distribution in relation to bioregional and population centres, was undertaken. Land for Wildlife agreements had greater numbers of properties and total area protected in all bioregions throughout the State, yet average protected area sizes were lower than those of conservation covenants and Trust for Nature reserves. A combination of large bioregional area and human population size tended to attract more private conservation properties and, to a lesser extent, the total area they protected. The potential contribution that such properties made to biodiversity conservation varied between bioregions. Inclusion of properties within a national reserve framework is proposed to improve the coordination and effectiveness of conservation measures.

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.

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.