Significant patterns of population genetic structure and limited gene flow in a threatened macropodid marsupial despite continuous habitat in southeast Queensland, Australia

Many endangered species worldwide are found in remnant populations, often within fragmented landscapes. However, when possible, an understanding of the natural extent of population structure and dispersal behaviour of threatened species would assist in their conservation and management. The brush-tailed rock-wallaby (Petrogale penicillata), a once abundant and widespread rock-wallaby species across southeastern Australia, has become nearly extinct across much of the southern part of its range. However, the northern part of the species’ range still sustains many small colonies closely distributed across suitable habitat, providing a rare opportunity to investigate the natural population dynamics of a listed threatened species. We used 12 microsatellite markers to investigate genetic diversity, population structure and gene flow among brush-tailed rock-wallaby colonies within and among two valley regions with continuous habitat in southeast Queensland. We documented high and significant levels of population genetic structure between rock-wallaby colonies embedded in continuous escarpment habitat and forest. We found a strong and significant pattern of isolation-by-distance among colonies indicating restricted gene flow over a small geographic scale ( <10 km) and conclude that gene flow is more likely limited by intrinsic factors rather than environmental factors. In addition, we provide evidence that genetic diversity was significantly lower in colonies located in a more isolated valley region compared to colonies located in a valley region surrounded by continuous habitat. These findings shed light on the processes that have resulted in the endangered status of rock-wallaby species in Australia and they have strong implications for the conservation and management of both the remaining ‘connected’8 brush-tailed rock-wallaby colonies in the northern parts of the species’8 range and the remnant endangered populations in the south.     

Population structure of brush-tailed rock-wallaby (Petrogale penicillata) colonies inferred from analysis of faecal DNA

Genetic data obtained using faecal DNA were used to elucidate the population structure of four brush-tailed rock-wallaby (Petrogale penicillata) colonies located in Wollemi National Park, New South Wales. The results suggested that the four sampled colonies are genetically differentiated and do not form a panmictic unit. Based on assignment tests, approximately 5% of sampled individuals were inferred to be dispersers and both male and female migrants were detected. Multilocus spatial autocorrelation analyses provided evidence for increased philopatry among females compared to males within the largest colony in the valley. Females in close spatial proximity were more genetically similar than expected under a random distribution of females, and females separated by more than 400 m were less genetically similar than expected. In contrast, there was no evidence of a significant clustering of related males. This suggests that within-colony dispersal is male biased. We also investigated the best strategies for conserving genetic diversity in this population. All of the four sampled colonies were found to contain distinct components of the genetic diversity of the Wolgan Valley P. penicillata population and loss of any colony is likely to result in the loss of unique alleles. Conservation and management plans should take into account that these colonies represent genetically differentiated discrete subpopulations. This approach is also the best strategy for maintaining the genetic diversity of the populations in this valley.     

Restricted mating dispersal and strong breeding group structure in a mid-sized marsupial mammal (Petrogale penicillata)

Ecological genetic studies have demonstrated that spatial patterns of mating dispersal, the dispersal of gametes through mating behaviour, can facilitate inbreeding avoidance and strongly influence the structure of populations, particularly in highly philopatric species. Elements of breeding group dynamics, such as strong structuring and sex-biased dispersal among groups, can also minimize inbreeding and positively influence levels of genetic diversity within populations. Rock-wallabies are highly philopatric mid-sized mammals whose strong dependence on rocky terrain has resulted in series of discreet, small colonies in the landscape. Populations show no signs of inbreeding and maintain high levels of genetic diversity despite strong patterns of limited gene flow within and among colonies. We used this species to investigate the importance of mating dispersal and breeding group structure to inbreeding avoidance within a 'small' population. We examined the spatial patterns of mating dispersal, the extent of kinship within breeding groups, and the degree of relatedness among brush-tailed rock-wallaby breeding pairs within a colony in southeast Queensland. Parentage data revealed remarkably restricted mating dispersal and strong breeding group structuring for a mid-sized mammal. Breeding groups showed significant levels of female kinship with evidence of male dispersal among groups. We found no evidence for inbreeding avoidance through mate choice; however, anecdotal data suggest the importance of life history traits to inbreeding avoidance between first-degree relatives. We suggest that the restricted pattern of mating dispersal and strong breeding group structuring facilitates inbreeding avoidance within colonies. These results provide insight into the population structure and maintenance of genetic diversity within colonies of the threatened brush-tailed rock-wallaby.     

Nematode community structure in the brush-tailed rock-wallaby, Petrogale penicillata: Implications of captive breeding and the translocation of wildlife

Despite an increasing appreciation of the disease risks associated with wild-life translocations, the effects which captive breeding programs exert on parasite communities remain understudied. This may be attributed, in part, to the current lack of rapid and cost-effective techniques for comparing parasite assemblages between host populations. Terminal restriction fragment length polymorphism (T-RFLP) analysis of the rDNA region encompassing the internal transcribed spacers (ITS-1 and ITS-2) and 5.8S rRNA gene was used to characterise bursate nematode communities (suborder Strongylida) across two captive and two non-captive colonies of the threatened brush-tailed rock-wallaby, Petrogale penicillata. A clone library was constructed and a restriction enzyme selected to differentiate the predominant operational taxonomic units (OTUs) by the unique peak profiles they generated. The prevalence, intensity of infection and comparative structure of strongylid assemblages was evaluated for each of the host colonies. Compared to wild conspecifics, captive wallabies exhibited a reduced prevalence of infection and significantly lower faecal egg counts. T-RFLP revealed that a high proportion of the OTUs co-occurred across three of the four study locations. Despite this, the composition of strongylid assemblages was significantly different between the colonies, even when host translocation events had occurred. These results suggest that captive breeding programs may exert a profound impact on parasitic helminth assemblages. Developing efficient techniques for characterising community dynamics in potentially pathogenic organisms is critical to the long term success of species recovery efforts worldwide.     

Hematology and serum biochemistry of the brush-tailed rock-wallaby (Petrogale penicillata)

In Australia the brush-tailed rock-wallaby (Petrogale penicillata) is the subject of a national recovery plan, and several sites have been selected for reintroductions. Condition of wild populations and individual animals can be monitored using hematologic and serum biochemistry analytes, and hematologic variables have been correlated with postrelease survival in other species. Prior to such monitoring, reference values for blood variables are required, but these data have not been available for the brush-tailed rock-wallaby. During four trapping periods from November 2004 to August 2005, 116 blood samples were collected from 44 brush-tailed rock-wallabies in a wild colony in southeast Queensland. Some variables varied with sex, age, method of restraint, lactation demands, and trapping period. After partitioning, when required, reference ranges for hematology and serum biochemistry variables were established. This study provides the most comprehensive serum biochemistry reference range for any macropodid marsupial yet published.     

Fine-scale spatial genetic correlation analyses reveal strong female philopatry within a brush-tailed rock-wallaby colony in southeast Queensland

We combine spatial data on home ranges of individuals and microsatellite markers to examine patterns of fine-scale spatial genetic structure and dispersal within a brush-tailed rock-wallaby (Petrogale penicillata) colony at Hurdle Creek Valley, Queensland. Brush-tailed rock-wallabies were once abundant and widespread throughout the rocky terrain of southeastern Australia; however, populations are nearly extinct in the south of their range and in decline elsewhere. We use pairwise relatedness measures and a recent multilocus spatial autocorrelation analysis to test the hypotheses that in this species, within-colony dispersal is male-biased and that female philopatry results in spatial clusters of related females within the colony. We provide clear evidence for strong female philopatry and male-biased dispersal within this rock-wallaby colony. There was a strong, significant negative correlation between pairwise relatedness and geographical distance of individual females along only 800 m of cliff line. Spatial genetic autocorrelation analyses showed significant positive correlation for females in close proximity to each other and revealed a genetic neighbourhood size of only 600 m for females. Our study is the first to report on the fine-scale spatial genetic structure within a rock-wallaby colony and we provide the first robust evidence for strong female philopatry and spatial clustering of related females within this taxon. We discuss the ecological and conservation implications of our findings for rock-wallabies, as well as the importance of fine-scale spatial genetic patterns in studies of dispersal behaviour.     

Estimating population size by genotyping faeces.

Population size is a fundamental biological parameter that is difficult to estimate. By genotyping coyote (Canis latrans) faeces systematically collected in the Santa Monica Mountains near Los Angeles, California, we exemplify a general, non-invasive method to census large mammals. Four steps are involved in the estimation. First, presumed coyote faeces are collected along paths or roadways where coyotes, like most carnivores, often defaecate and mark territorial boundaries. Second, DNA is extracted from the faeces and species identity and sex is determined by mitochondrial DNA and Y-chromosome typing. Third, hypervariable microsatellite loci are typed from the faeces. Lastly, rarefaction analysis is used to estimate population size from faecal genotypes. This method readily provides a point count estimate of population size and sex ratio. Additionally, we show that home range use paternity and kinship can be inferred from the distribution and relatedness patterns of faecal genotypes.     

Individual genetic diversity correlates with the size and spatial isolation of natal colonies in a bird metapopulation

The genetic consequences of small population size and isolation are of central concern in both population and conservation biology. Organisms with a metapopulation structure generally show effective population sizes that are much smaller than the number of mature individuals and this can reduce genetic diversity especially in small sized and isolated subpopulations. Here, we examine the association between heterozygosity and the size and spatial isolation of natal colonies in a metapopulation of lesser kestrels (Falco naumanni). For this purpose, we used capture-mark-recapture data to determine the patterns of immigration into the studied colonies, and 11 highly polymorphic microsatellite markers that allowed us to estimate genetic diversity of locally born individuals. We found that individuals born in smaller and more isolated colonies were genetically less diverse. These colonies received a lower number of immigrants, supporting the idea that both reduced gene flow and small population size are responsible for the genetic pattern observed. Our results are particularly intriguing because the lesser kestrel is a vagile and migratory species with great movement capacity and dispersal potential. Overall, this study provides evidence of the association between individual heterozygosity and the size and spatial isolation of natal colonies in a highly mobile vertebrate showing relatively frequent dispersal and low genetic differentiation among local subpopulations.     

Mitochondrial DNA structure and colony expansion dynamics of New Zealand fur seals (Arctocephalus forsteri) around Banks Peninsula

New Zealand fur seals are one of many pinniped species that survived the commercial sealing of the eighteenth and nineteenth centuries in dangerously low numbers. After the enforcement of a series of protection measures in the early twentieth century, New Zealand fur seals began to recover from the brink of extinction. We examined the New Zealand fur seal populations of Banks Peninsula, South Island, New Zealand using the mitochondrial DNA control region. We identified a panmictic population structure around Banks Peninsula. The most abundant haplotype in the area showed a slight significant aggregated structure. The Horseshoe Bay colony showed the least number of shared haplotypes with other colonies, suggesting a different origin of re-colonisation of this specific colony. The effective population size of the New Zealand fur seal population at Banks Peninsula was estimated at approximately 2500 individuals. The exponential population growth rate parameter for the area was 35, which corresponds to an expanding population. In general, samples from adjacent colonies shared 4.4 haplotypes while samples collected from colonies separated by between five and eight bays shared 1.9 haplotypes. The genetic data support the spill-over dynamics of colony expansion already suggested for this species. Approximate Bayesian computations analysis suggests re-colonisation of the area from two main clades identified across New Zealand with a most likely admixture coefficient of 0.41 to form the Banks Peninsula population. Approximate Bayesian computations analysis estimated a founder population size of approximately 372 breeding individuals for the area, which then rapidly increased in size with successive waves of external recruitment. The population of fur seals in the area is probably in the late phase of maturity in the colony expansion dynamic.     

Can functional classification of tropical trees predict population dynamics after disturbance?

Question: How far can we simplify the fioristic complexity of a tropical rainforest into functional groups in order to predict tree population dynamics after logging‐induced disturbance? Location: Paracou experimental site, French Guiana. Methods: We used data from over 15 years in control and disturbed plots from a silvicultural trial started in 1984. We selected 53 common tree species assigned to five functional groups based on potential size and light requirement. For each species, we quantified: the fate, i.e. variation in population size, and dynamic processes, i.e. mortality, recruitment and growth, driving this fate. We investigated the links between dynamic processes, fate and functional groups. Results: Disturbance stimulated growth and recruitment for most species, but had a heterogeneous impact on mortality. Species fate in disturbed plots depended on recruitment and was more favourable than in control plots. The functional classification was more predictive for most separate dynamic processes than for species fate: after disturbance, significant differences were found between all functional groups for growth. Pioneer+heliophilous species showed significantly higher recruitment rates. Mortality of shade‐tolerant species slightly increased and of mid‐tolerant and heliophilous species decreased. Conclusions: A combination of three species classifications separately built from the growth, recruitment and mortality processes is more informative than a global classification combining the processes. Identifying the pioneer+heliophilous species on the basis of their growth rate is crucial to predict species fate after disturbance. We showed that potential growth rate could be used as a reliable indicator to identify this group.     

Size–abundance relationships in Florida ant communities reveal how ants break the energetic equivalence rule

1. Ants are among the most abundant terrestrial organisms, yet little is known of how ant communities divide resources because it is difficult to measure the number of individuals in colonies and the density of colonies. 2. The body size–abundance relationships of the ants of five upland ecosystems in Florida were examined. The study tested whether abundance, energy use, and total biomass were distributed among species and body sizes as predicted by Damuth's energetic equivalence rule. Estimates of average worker body size, colony size, colony mass, and field metabolic rates were used to examine the relationships among body sizes, energy use, and total biomass. 3. Analyses revealed significant variation in energy use and did not support the energetic equivalence hypothesis. Specifically, the energy use and total standing biomass of species with large workers and colonies was much greater than smaller species. 4. These results suggest that larger species with larger colonies account for a disproportionate fraction of the total abundance and biomass of ants. A general model of resource allocation in colonies provides a possible explanation for why ants do not conform to the predictions of the energetic equivalence rule and for why ants are so abundant.     

A comparison of methods for estimating plant population size

Assessing local population size is one of the most common tasks in biodiversity monitoring. Population size estimates are not only important for conservation management and population threat assessment; they also enter many other analyses in landscape ecology and conservation. It is therefore concerning that methods for estimating plant population sizes are not standardized. We surveyed the literature and found that the most commonly used methods are counting either all or only flowering individuals on a site, as well as counting individuals in random plots or plots on transects. Sometimes, these methods are combined in the same study, without assurance that they produce comparable results. We therefore conducted a field study, in which we obtained population size estimates from all four methods for six different calcareous grassland species at 18 study sites. Our results demonstrate not only substantial differences between overall count rates generated by the different methods, but methods that surveyed the whole population also systematically yielded lower counts when species were less visible and when the area was larger, suggesting that these methods suffer from biases that could distort species and site comparisons. We conclude that estimates from different methods should not be mixed, and that plot or transect based surveys have likely smaller biases for large areas or poorly visible individuals, and are therefore preferable.     

Estimating Population Growth and Recruitment Rates Across the Range of American Common Eiders

Sound management of bird populations rests upon an adequate understanding of their population dynamics. Our study evaluated recruitment and population growth rates of 14 American common eider (Somateria mollissima dresseri) colonies from Labrador, Nova Scotia, Quebec, Canada, and Maine, USA, during various periods between 1970 and 2019. We used Pradel mark-recapture models to estimate colony-specific growth rates and the relative contributions of survival and recruitment on growth. We also validated this approach using annual nest counts (~8,000 pairs) conducted between 2003 and 2019 during down harvest operations in 3 colonies located in the Saint Lawrence estuary in Quebec. There was generally a good agreement between estimates derived using the 2 approaches. We considered that capture-recapture data were suitable to estimate population trends of common eiders in other colonies, especially for colonies where accurate nest monitoring is impaired by dense vegetation. The breeding abundance declined at major colonies in Maine and Nova Scotia and increased or was stable in Quebec and Labrador. Female survival contributed the most to population growth, but variation in recruitment among colonies was more important than variation in survival to explain population growth. Management measures should thus strive to maximize local recruitment in colonies with declining populations. The assumption that apparent survival probabilities were homogeneous throughout an individual capture history was violated at several colonies in Quebec and Labrador. Using recaptures and band recoveries, we showed that the lower apparent survival for newly marked individuals compared to females that had been recaptured at least once was caused by a difference in site fidelity rather than true survival. But <1% of recaptured females dispersed to another colony for breeding, indicating that the lower site fidelity could be related to heterogeneity in capture probability among individuals. © 2021 The Wildlife Society.     

Nondestructive DNA sampling from bumblebee faeces

Genetic studies provide valuable data to inform conservation strategies for species with small or declining populations. In these circumstances, obtaining DNA samples without harming the study organisms is highly desirable. Excrements are increasingly being used as a source of DNA in such studies, but such approaches have rarely been applied to arthropods. Bumblebees are ecologically and economically important as pollinators; however, some species have recently suffered severe declines and range contractions across much of Western Europe and North America. We investigated whether bumblebee faeces could be used for the extraction of DNA suitable for genotyping using microsatellite markers. We found that DNA could be extracted using a Chelex method from faecal samples collected either in microcapillary tubes or on filter paper, directly from captured individuals. Our results show that genotypes scored from faecal samples are identical to those from tissue samples. This study describes a reliable, consistent and efficient noninvasive method of obtaining DNA from bumblebees for use in population genetic studies. This approach should prove particularly useful in breeding and conservation programs for bumblebees and may be broadly applicable across insect taxa.     

Non-invasive assessment of parasitic nematode species diversity in wild Soay sheep using molecular markers

Considerable effort has been put into detecting and identifying parasitic nematodes in live ruminants, but to date most studies are limited to a small group of nematodes and/or to experimentally infected sheep. In this study, a PCR-based assay using species-specific primer pairs, located in the second internal transcribed spacer ribosomal DNA, was developed to identify nine different species from six different families of parasitic nematodes in a wild, unmanaged and naturally infected population of sheep. Each primer pair was tested for its specificity and sensitivity and it exclusively amplified the species it was designed for and exhibited a high degree of sensitivity. The method was applied to eggs and cultured larvae to identify the parasitic nematodes present in a pooled faecal sample from several host individuals with unknown parasite burden. To test detection reliability, a faecal sample from an individual with known parasite burden (through post-mortem analysis) was also examined. All species present could be correctly identified by PCR, but detecting very low levels and/or early stages of infection proved to be difficult. The method was also tested for its applicability to high through-put screening of faecal samples.     

Reliable genotyping of the koala (Phascolarctos cinereus) using DNA isolated from a single faecal pellet

The koala, an Australian icon, has been added to the threatened species list. Rationale for the listing includes proposed declines in population size, threats to populations (e.g. disease) and loss and fragmentation of habitat. There is now an urgent need to obtain accurate data to assess the status of koala populations in Australia, to ensure the long‐term viability of this species. Advances in genetic techniques have enabled DNA analysis to study and inform the management of wild populations; however, sampling of individual koalas is difficult in tall, often remote, eucalypt forest. The collection of faecal pellets (scats) from the forest floor presents an opportunistic sampling strategy, where DNA can be collected without capturing or even sighting an individual. Obtaining DNA via noninvasive sampling can be used to rapidly sample a large proportion of a population; however, DNA from noninvasively collected samples is often degraded. Factors influencing DNA quality and quantity include environmental exposure, diet and methods of sample collection, storage and DNA isolation. Reduced DNA quality and quantity can introduce genotyping errors and provide inaccurate DNA profiles, reducing confidence in the ability of such data to inform management/conservation strategies. Here, we present a protocol that produces a reliable individual koala genotype from a single faecal pellet and highlight the importance of optimizing DNA isolation and analysis for the species of interest. This method could readily be adapted for genetic studies of mammals other than koalas, particularly those whose diet contains high proportions of volatile materials that are likely to induce DNA damage.     

Using pedigree reconstruction to estimate population size: genotypes are more than individually unique marks

Estimates of population size are critical for conservation and management, but accurate estimates are difficult to obtain for many species. Noninvasive genetic methods are increasingly used to estimate population size, particularly in elusive species such as large carnivores, which are difficult to count by most other methods. In most such studies, genotypes are treated simply as unique individual identifiers. Here, we develop a new estimator of population size based on pedigree reconstruction. The estimator accounts for individuals that were directly sampled, individuals that were not sampled but whose genotype could be inferred by pedigree reconstruction, and individuals that were not detected by either of these methods. Monte Carlo simulations show that the population estimate is unbiased and precise if sampling is of sufficient intensity and duration. Simulations also identified sampling conditions that can cause the method to overestimate or underestimate true population size; we present and discuss methods to correct these potential biases. The method detected 2–21% more individuals than were directly sampled across a broad range of simulated sampling schemes. Genotypes are more than unique identifiers, and the information about relationships in a set of genotypes can improve estimates of population size.     

Microsatellite markers uncover cryptic species of Odontotermes (Termitoidae: Termitidae) from Peninsular Malaysia

Termites from the genus Odontotermes are known to contain numerous species complexes that are difficult to tell apart morphologically or with mitochondrial DNA sequences. We developed markers for one such cryptic species complex, that is, Odontotermes srinakarinensis sp. nov. from Maxwell Hill Forest Reserve (Perak, Malaysia), and characterised them using a sample of 41 termite workers from three voucher samples from the same area. We then genotyped 150 termite individuals from 23 voucher samples/colonies of this species complex from several sites in Peninsular Malaysia. We analysed their population by constructing dendograms from the proportion of shared-alleles between individuals and genetic distances between colonies; additionally, we examined the Bayesian clustering pattern of their genotype data. All methods of analysis indicated that there were two distinct clusters within our data set. After the morphologies of specimens from each cluster were reexamined, we were able to separate the two species morphologically and found that a single diagnostic character found on the mandibles of its soldiers could be used to separate the two species quite accurately. The additional species in the clade was identified as Odontotermes denticulatus after it was matched to type specimens at the NHM London and Cambridge Museum of Zoology.     

Weather and herbivores influence fertility in the endangered fern Botrychium multifidum (S.G. Gmel.) Rupr

Fluctuations in local weather conditions and other stochastic processes are important factors affecting species population persistence. We studied two differently sized populations of the rare and declining fern species Botrychium multifidum for 4 and 5 years, respectively. Individually marked plants in permanent plots were followed to detect trends in population size, reproductive success and dormancy in relation to local precipitation and temperature. Our applied logistic regression model suggests that the shortage of precipitation during summer decreases fertility in the next year in both populations. Invertebrate herbivory of the fertile part of the plant additionally diminishes the output of spores. We found the population size to be stable with a very low percentage of each population composed of juvenile plants. Stochastic processes and low recruitment could easily lead to the extinction of these populations.     

Integration of genetic and demographic data to assess population risk in a continuously distributed species

The identification and demographic assessment of biologically meaningful populations is fundamental to species’ ecology and management. Although genetic tools are used frequently to identify populations, studies often do not incorporate demographic data to understand their respective population trends. We used genetic data to define subpopulations in a continuously distributed species. We assessed demographic independence and variation in population trends across the distribution. Additionally, we identified potential barriers to gene flow among subpopulations. We sampled greater sage-grouse (Centrocercus urophasianus) leks from across their range (≈175,000 Km²) in Wyoming and amplified DNA at 14 microsatellite loci for 1761 samples. Subsequently, we assessed population structure in unrelated individuals (n = 872) by integrating results from multiple Bayesian clustering approaches and used the boundaries to inform our assessment of long-term population trends and lek activity over the period of 1995–2013. We identified four genetic clusters of which two northern ones showed demographic independence from the others. Trends in population size for the northwest subpopulation were statistically different from the other three genetic clusters and the northeast and southwest subpopulations demonstrated a general trend of increasing proportion of inactive leks over time. Population change from 1996 to 2012 suggested population growth in the southern subpopulations and decline, or neutral, change in the northern subpopulations. We suggest that sage-grouse subpopulations in northern Wyoming are at greater risk of extirpation than the southern subpopulations due to smaller census and effective population sizes and higher variability within subpopulations. Our research is an example of incorporating genetic and demographic data and provides guidance on the identification of subpopulations of conservation concern.