Mating system and reproductive skew in the black rhinoceros

Linking diet switching to reproductive performance across populations of two critically endangered mammalian herbivores

Optimal foraging theory predicts that animals maximise energy intake by consuming the most valuable foods available. When resources are limited, they may include lower-quality fallback foods in their diets. As seasonal herbivore diet switching is understudied, we evaluate its extent and effects across three Kenyan reserves each for Critically Endangered eastern black rhino (Diceros bicornis michaeli) and Grevy's zebra (Equus grevyi), and its associations with habitat quality, microbiome variation, and reproductive performance. Black rhino diet breadth increases with vegetation productivity (NDVI), whereas zebra diet breadth peaks at intermediate NDVI. Black rhino diets associated with higher vegetation productivity have less acacia (Fabaceae: Vachellia and Senegalia spp.) and more grass suggesting that acacia are fallback foods, upending conventional assumptions. Larger dietary shifts are associated with longer calving intervals. Grevy's zebra diets in high rainfall areas are consistently grass-dominated, whereas in arid areas they primarily consume legumes during low vegetation productivity periods. Whilst microbiome composition between individuals is affected by the environment, and diet composition in black rhino, seasonal dietary shifts do not drive commensurate microbiome shifts. Documenting diet shifts across ecological gradients can increase the effectiveness of conservation by informing habitat suitability models and improving understanding of responses to resource limitation.

Comparative analysis of gestation in three rhinoceros species (Diceros bicornis; Ceratotherium simum; Rhinoceros unicornis)

This comparative analysis evaluated endocrine profiles and gestation length data of captive pregnant black rhinoceros (Diceros bicornis), white rhinoceros (Ceratotherium simum), and greater one-horned (GOH) rhinoceros (Rhinoceros unicornis). Hormone profiles were collected over three decades as part of pregnancy diagnoses. After the third month of gestation, the luteo-placental shift in progesterone production in pregnant rhinoceroses causes a significant increase in the concentration of faecal progesterone metabolites. We defined a laboratory-specific value of 1000 ng/g faeces as a threshold for incipient feto-placental progesterone production. Using this value allowed a comparison between species and revealed significant individual differences within a species. The mean ± SEM gestation days for reaching the 1000 ng/g faeces threshold were 89.5 ± 2.9 (range 56-138 days; n = 39) in black, 96.0 ± 2.6 (58-138; n = 39) in white, and 117.8 ± 5.3 (74-173; n = 19) in GOH rhinoceroses. For the calculations of gestation length, we complemented our results from three decades of reproductive monitoring with data from the literature, resulting in about 70 values for each species. Gestation length in the black, the white and the GOH rhinoceros was 460.6 ± 1.5 (range: 436 - 486), 503.8 ± 1.3 (range: 480 - 525) and 480.5 ± 1.1 (range: 453 - 505) days, respectively. Daylight length significantly affected gestation length, while the sex of offspring had no effect. On average, pregnancies with parturitions in spring and summer were one week shorter than those in autumn and winter. Although rhinoceroses are non-seasonal breeders, most parturitions in captivity occur in autumn and winter. We also analysed preconception endocrine profiles in the white rhinoceros. Conceptions in this species occurred after oestrous cycles of approximately 35 days (n = 18), 70 days (n = 3), 15 days (n = 1), after periods of ovarian inactivity (n = 5), and during a foal heat within one month after stillbirth parturition (n = 1). In conclusion, this study provides a comprehensive overview of gestational parameters in three rhinoceros species.

Dancing to a different tune: changing reproductive seasonality in an introduced chital deer population

Male and female reproductive behaviour is typically synchronised. In species such as those in the family Cervidae, reproductive timing is often cued by photoperiod, although in females, it can be dependent on body condition. When a species is introduced to a novel environment, the environment changes, or responses of the sexes to such cues differ, asynchronous reproductive behaviour between males and females may occur. We investigated the seasonality of reproductive behaviour in introduced chital deer in northern Queensland by examining male antler phase in relation to female conception rates. We then analysed the influence of different variables likely to affect the timing of male and female reproductive physiology. The lowest percentage of chital in hard antler in any 1 month in this study was 35% (Fig. 1), but the average value was closer to 50%, thus there was a seasonal peak in antler phase linked with photoperiod. Females conceived at any time of year, but were strongly influenced by the amount of rainfall 3 months prior to conception. This resulted in varying conception peaks year-to-year that often did not correspond to the male’s peak in hard antler. In this system, a proportion of males and females were physiologically and behaviourally ready to mate at any time of the year. We predict that differences in the timing of the peaks between the males and females will lead to increased reproductive skew (variation in reproductive success among individual males). This pattern may select for different mating strategies or physiological mechanisms to increase reproductive success.Fig. 1

Female reproductive skew exacerbates the extinction risk from poaching in the eastern black rhino

Variation in individual demographic rates can have large consequences for populations. Female reproductive skew is an example of structured demographic heterogeneity where females have intrinsic qualities that make them more or less likely to breed. The consequences of reproductive skew for population dynamics are poorly understood in non-cooperatively breeding mammals, especially when coupled with other drivers such as poaching. We address this knowledge gap with population viability analyses using an age-specific, female-only, individual-based, stochastic population model built with long-term data for three Kenyan populations of the Critically Endangered eastern black rhino (Diceros bicornis michaeli). There was substantial reproductive skew, with a high proportion of females not breeding or doing so at very low rates. This had a large impact on the projected population growth rate for the smaller population on Ol Jogi. Moreover, including female reproductive skew exacerbates the effects of poaching, increasing the probability of extinction by approximately 70% under a simulated poaching pressure of 5% offtake per year. Tackling the effects of reproductive skew depends on whether it is mediated by habitat or social factors, with potential strategies including habitat and biological management respectively. Investigating and tackling reproductive skew in other species requires long-term, individual-level data collection.

Age structure changes indicate direct and indirect population impacts in illegally harvested black rhino

Overharvesting affects the size and growth of wildlife populations and can impact population trajectories. Overharvesting can also severely alter population structure and may result in changes in spatial organisation, social dynamics and recruitment. Understanding the relationship between overharvesting and population growth is therefore crucial for the recovery of exploited species. The black rhinoceros (Diceros bicornis; black rhino) is a long-lived megaherbivore native to sub-Saharan Africa, listed as Critically Endangered on the IUCN Red List of Threatened Species. Since 2009, the targeted illegal killing of rhino for their horns has escalated dramatically in South Africa. Given their slow life trajectories, spatial structure and social dynamics, black rhino may be susceptible to both direct and indirect impacts of overharvesting. Our study compared black rhino demography before and during extensive poaching to understand the impact of illegal killing. The population exhibited significant changes in age structure after four years of heavy poaching; these changes were primarily explained by a decrease in the proportion of calves over time. Population projections incorporating both direct poaching removals and decreased fecundity/recruitment were most similar to the observed demographic profile in 2018, suggesting that indirect impacts are also contributing to the observed population trajectory. These indirect impacts are likely a result of decreased density, through processes such as reduced mate-finding, population disturbance and/or increased calf predation. This study illustrates the combined effect of direct and indirect impacts on an endangered species, providing a more comprehensive approach by which to evaluate exploited populations.

Mate choice, reproductive success and inbreeding in white rhinoceros: New insights for conservation management

Improving our sparse knowledge of the mating and reproductive behaviour of white rhinoceros (Ceratotherium simum Burchell, 1817) is essential for the effective conservation of this iconic species. By combining morphological, physiological and habitat data with paternity assignments of 104 known mother-offspring pairs collected over a period of 13 years, we provide the most comprehensive analysis of the mating system in this species. We show that while the overall mating system was promiscuous, and both males and females produced more offspring when mating with several partners, half of all females with multiple offspring were monogamous. Additionally, we find that mating and reproductive success varied significantly among territorial males in two independent sets of males. In females, however, variation in the mating and the reproductive success was not larger than expected by random demographic fluctuations. Horn size, testosterone metabolite concentration, territory size, habitat openness and the volume of preferred food within the territory did not seem to influence male mating or reproductive success. Moreover, there was no sign of inbreeding avoidance: females tended to mate more frequently with closely related males, and one daughter produced a progeny with her father. The lack of inbreeding avoidance, in combination with the skew in male reproductive success, the partial monogamy in females and the territorial-based mating system, jeopardizes the already low genetic variation in the species. Considering that the majority of populations are restricted to fenced reserves and private farms, we recommend taking preventive measures that aim to reduce inbreeding in white rhinoceros. A video abstract can be viewed here.

Gut microbiome differences between wild and captive black rhinoceros - implications for rhino health

A number of recent studies have shown the importance of the mammalian gut microbiome in host health. In the context of endangered species, a few studies have examined the relationship between the gut microbiome in wild versus captive populations due to digestive and other health issues. Unfortunately, the results seem to vary across taxa in terms of captive animals having higher, lower, or equivalent microbiome diversity relative to their wild counterparts. Here, we focus on the black rhinoceros as captive animals suffer from a number of potentially dietary related health effects. We compared gut microbiomes of wild and captive black rhinos to test for differences in taxonomic diversity (alpha and beta) and in functional diversity of the microbiome. We incorporated a more powerful metagenomic shotgun sequencing approach rather than a targeted amplification of the 16S gene for taxonomic assignment of the microbiome. Our results showed no significant differences in the alpha diversity levels between wild and captive black rhinos, but significant differences in beta diversity. We found that bacterial taxa traditionally associated with ruminant guts of domesticated animals had higher relative abundances in captive rhinos. Our metagenomic sequencing results suggest that unknown gut microbes of wild rhinos are being replaced by those found in conventional human-domesticated livestock. Wild rhinos have significantly different functional bacterial communities compared to their captive counterparts. Functional profiling results showed greater abundance of glycolysis and amino acid synthesis pathways in captive rhino microbiomes, representing an animal receiving sub-optimal nutrition with a readily available source of glucose but possibly an imbalance of necessary macro and micronutrients. Given the differences observed between wild and captive rhino gut microbiomes, we make a number of recommendations for potentially modifying captive gut microbiome to better reflect their wild counterparts and thereby hopefully improve overall rhino health in captivity.

Effects of age and sex ratios on offspring recruitment rates in translocated black rhinoceros

Success of animal translocations depends on improving postrelease demographic rates toward establishment and subsequent growth of released populations. Short-term metrics for evaluating translocation success and its drivers, like postrelease survival and fecundity, are unlikely to represent longer-term outcomes. We used information theory to investigate 25 years of data on black rhinoceros (Diceros bicornis) translocations. We used the offspring recruitment rate (ORR) of translocated females-a metric integrating survival, fecundity, and offspring recruitment at sexual maturity-to detect determinants of success. Our unambiguously best model (AICω = 0.986) predicted that ORR increases with female age at release as a function of lower postrelease adult rhinoceros sex ratio (males:females). Delay of first postrelease reproduction and failure of some females to recruit any calves to sexual maturity most influenced the pattern of ORRs, and the leading causes of recruitment failure were postrelease female death (23% of all females) and failure to calve (24% of surviving females). We recommend translocating older females (≥6 years old) because they do not exhibit the reproductive delay and low ORRs of juveniles (<4 years old) or the higher rates of recruitment failure of juveniles and young adults (4-5.9 years old). Where translocation of juveniles is necessary, they should be released into female-biased populations, where they have higher ORRs. Our study offers the unique advantage of a long-term analysis across a large number of replicate populations-a science-by-management experiment as a proxy for a manipulative experiment, and a rare opportunity, particularly for a large, critically endangered taxon such as the black rhinoceros. Our findings differ from previous recommendations, reinforce the importance of long-term data sets and comprehensive metrics of translocation success, and suggest attention be shifted from ecological to social constraints on population growth and species recovery, particularly when translocating species with polygynous breeding systems.

Reproductive performance parameters in a large population of game-ranched white rhinoceroses (Ceratotherium simum simum)

The population of free-roaming white rhinoceroses (Ceratotherium simum) is under serious threat. Captive breeding of this species is therefore becoming more important, but this is challenging and often not successful. Obtaining reproductive reference values is a crucial aspect of improving these breeding results. In this study performed between 2008 and 2016, reproductive performance was analysed in 1,354 animals kept in a 8000 hectares game-ranched environment. Descriptive statistics of this captive population showed an average annual herd growth (%) of 7 .0±0.1 (min -9 –max 15). Average calving rates were calculated as an annual calving rate of 20% and biennial calving rate of 37% adult females calving per year. Females had a median age of 83.2 months at first calving (IQR 72.9–110.7) and inter-calving intervals of 29.2 (IQR 24.6–34.8) months. Furthermore, translocations of animals did not interfere with reproductive success in terms of inter-calving periods or age at first calving. Multivariate models showed a clear seasonal calving pattern with a significant increase of the number of calvings during December–April when compared to April–December. Our results did not show any significant skewed progeny sex ratios. Weather observations showed no significant influence of rain or season on sex ratios of the calves.

The reproductive success of black rhinoceroses in the Hluhluwe–iMfolozi Park, KwaZulu-Natal, South Africa

Black rhinoceroses (Diceros bicornis) are endangered and the southern-central sub-species (Diceros bicornis minor) is considered critically endangered. We assessed the reproductive lifehistories of black rhinoceroses in Hluhluwe–iMfolozi Park (HiP), KwaZulu-Natal, South Africa, to determine whether this historically important donor sub-population was meeting regional reproductive targets. Detailed life-history information for known individuals (n = 79–120) was used to investigate reproductive parameters between 1998 and 2013. Mean age at sexual maturity was 12 years, which exceeded a target period of 7 years and 5 months. The mean inter-calving interval was 3 years and 8 months – 8 months longer than the recommended 3 years. The poor population performance of the HiP black rhinoceroses could be a result of poor habitat quality, poor animal condition, females losing their first calves, predation of calves or a negative social effect of annual live-harvesting of the population. However, we believe that the estimated ecological carrying capacity of black rhinoceroses at HiP (a figure used to ascertain whether the population can be harvested at all) may be incorrect, leading to the poor reproductive performance. We recommend that the accuracy of the ecological carrying capacity estimate be assessed as a matter of urgency and that a moratorium be placed on the live-harvesting of individuals until the estimate has been refined.Conservation implications: Our results provide key data which can be used to refine black rhinoceros breeding targets in South Africa and the region more broadly

Factors affecting genotyping success in giant panda fecal samples

Fecal samples play an important role in giant panda conservation studies. Optimal preservation conditions and choice of microsatellites for giant panda fecal samples have not been established. In this study, we evaluated the effect of four factors (namely, storage type (ethanol (EtOH), EtOH −20 °C, 2-step storage medium, DMSO/EDTA/Tris/salt buffer (DETs) and frozen at −20 °C), storage time (one, three and six months), fragment length, and repeat motif of microsatellite loci) on the success rate of microsatellite amplification, allelic dropout (ADO) and false allele (FA) rates from giant panda fecal samples. Amplification success and ADO rates differed between the storage types. Freezing was inferior to the other four storage methods based on the lowest average amplification success and the highest ADO rates (P < 0.05). The highest microsatellite amplification success was obtained from either EtOH or the 2-step storage medium at three storage time points. Storage time had a negative effect on the average amplification of microsatellites and samples stored in EtOH and the 2-step storage medium were more stable than the other three storage types. We only detected the effect of repeat motif on ADO and FA rates. The lower ADO and FA rates were obtained from tri- and tetra-nucleotide loci. We suggest that freezing should not be used for giant panda fecal preservation in microsatellite studies, and EtOH and the 2-step storage medium should be chosen on priority for long-term storage. We recommend candidate microsatellite loci with longer repeat motif to ensure greater genotyping success for giant panda fecal studies.

Standardising Home Range Studies for Improved Management of the Critically Endangered Black Rhinoceros

Comparisons of recent estimations of home range sizes for the critically endangered black rhinoceros in Hluhluwe-iMfolozi Park (HiP), South Africa, with historical estimates led reports of a substantial (54%) increase, attributed to over-stocking and habitat deterioration that has far-reaching implications for rhino conservation. Other reports, however, suggest the increase is more likely an artefact caused by applying various home range estimators to non-standardised datasets. We collected 1939 locations of 25 black rhino over six years (2004-2009) to estimate annual home ranges and evaluate the hypothesis that they have increased in size. A minimum of 30 and 25 locations were required for accurate 95% MCP estimation of home range of adult rhinos, during the dry and wet seasons respectively. Forty and 55 locations were required for adult female and male annual MCP home ranges, respectively, and 30 locations were necessary for estimating 90% bivariate kernel home ranges accurately. Average annual 95% bivariate kernel home ranges were 20.4 ± 1.2 km(2), 53 ± 1.9% larger than 95% MCP ranges (9.8 km(2) ± 0.9). When home range techniques used during the late-1960s in HiP were applied to our dataset, estimates were similar, indicating that ranges have not changed substantially in 50 years. Inaccurate, non-standardised, home range estimates and their comparison have the potential to mislead black rhino population management. We recommend that more care be taken to collect adequate numbers of rhino locations within standardized time periods (i.e., season or year) and that the comparison of home ranges estimated using dissimilar procedures be avoided. Home range studies of black rhino have been data deficient and procedurally inconsistent. Standardisation of methods is required.

Male reproductive success is correlated with testosterone in the eastern black rhinoceros (Diceros bicornis michaeli)

Among natural populations of polygynous species, males often vary in their lifetime reproductive success. However, in managed populations of endangered species, either in situ or as part of captive breeding programmes, it is important to understand why differences in reproductive success occur. The European captive population of the critically endangered eastern black rhinoceros is currently under-performing relative to their wild counterparts, with low reproductive output and high reproductive skew limiting growth and genetic diversity. To investigate why over 40% of captive males fail to breed, faecal samples were collected weekly from 23 males at 12 institutions across Europe for 4-32 months. Testosterone metabolite concentration was compared between proven and non-proven males and a number of intrinsic and extrinsic factors that could influence reproductive success were also investigated. Males that sired within the last 3½ years had significantly higher androgen concentrations than non-proven males, and average testosterone was positively correlated with the number of offspring sired per year spent in the reproductive age class. Proven and non-proven males did not differ in their body condition, or in average faecal glucocorticoid concentration. Differences in individual temperament were associated with adrenal activity, but did not correlate with reproductive category. Highest testosterone concentrations were observed in proven males that were housed with females during oestrus, and lowest concentrations in non-proven females not housed with females at all during the study period. Further work is necessary to determine whether proven males had higher testosterone due to underlying differences associated with quality, or whether external stimuli such as access to females could influence testosterone concentration and increase a male's chances of becoming a successful breeder.

Sex-biased inbreeding effects on reproductive success and home range size of the critically endangered black rhinoceros

A central premise of conservation biology is that small populations suffer reduced viability through loss of genetic diversity and inbreeding. However, there is little evidence that variation in inbreeding impacts individual reproductive success within remnant populations of threatened taxa, largely due to problems associated with obtaining comprehensive pedigree information to estimate inbreeding. In the critically endangered black rhinoceros, a species that experienced severe demographic reductions, we used model selection to identify factors associated with variation in reproductive success (number of offspring). Factors examined as predictors of reproductive success were age, home range size, number of nearby mates, reserve location, and multilocus heterozygosity (a proxy for inbreeding). Multilocus heterozygosity predicted male reproductive success (p< 0.001, explained deviance >58%) and correlated with male home range size (p < 0.01, r(2) > 44%). Such effects were not apparent in females, where reproductive success was determined by age (p < 0.01, explained deviance 34%) as females raise calves alone and choose between, rather than compete for, mates. This first report of a 3-way association between an individual male's heterozygosity, reproductive output, and territory size in a large vertebrate is consistent with an asymmetry in the level of intrasexual competition and highlights the relevance of sex-biased inbreeding for the management of many conservation-priority species. Our results contrast with the idea that wild populations of threatened taxa may possess some inherent difference from most nonthreatened populations that necessitates the use of detailed pedigrees to study inbreeding effects. Despite substantial variance in male reproductive success, the increased fitness of more heterozygous males limits the loss of heterozygosity. Understanding how individual differences in genetic diversity mediate the outcome of intrasexual competition will be essential for effective management, particularly in enclosed populations, where individuals have restricted choice about home range location and where the reproductive impact of translocated animals will depend upon the background distribution in individual heterozygosity.

Kinship and social behavior of lowland tapirs (Tapirus terrestris) in a central Amazon landscape

We tested the hypothesis that tapirs tolerate individuals from adjacent and overlapping home ranges if they are related. We obtained genetic data from fecal samples collected in the Balbina reservoir landscape, central Amazon. Samples were genotyped at 14 microsatellite loci, of which five produced high quality informative genotypes. Based on an analysis of 32 individuals, we inferred a single panmictic population with high levels of heterozygosity. Kinship analysis identified 10 pairs of full siblings or parent-offspring, 10 pairs of half siblings and 25 unrelated pairs. In 10 cases, the related individuals were situated on opposite margins of the reservoir, suggesting that tapirs are capable of crossing the main river, even after damming. The polygamous model was the most likely mating system for Tapirus terrestris. Moran's I index of allele sharing between pairs of individuals geographically close (<3 km) was similar to that observed between individual pairs at larger distances (>3 km). Confirming this result, the related individuals were not geographically closer than unrelated ones (W = 188.5; p = 0.339). Thus, we found no evidence of a preference for being close to relatives and observed a tendency for dispersal. The small importance of relatedness in determining spatial distribution of individuals is unusual in mammals, but not unheard of. Finally, non-invasive sampling allowed efficient access to the genetic data, despite the warm and humid climate of the Amazon, which accelerates DNA degradation.

Impacts of environmental pressures on the reproductive physiology of subpopulations of black rhinoceros (Diceros bicornis bicornis) in Addo Elephant National Park, South Africa

Black rhinoceros are an icon for international conservation, yet little is known about their physiology due to their secretive nature. To overcome these challenges, non-invasive methods were used to monitor rhinoceros in two sections of Addo Elephant National Park, South Africa, namely Addo and Nyathi. These sections were separated by a public road, and the numbers of elephants, predators and tourists were higher in Addo. Faecal samples (n = 231) were collected (from July 2007 to November 2010) from known individuals and analysed for progestagen and androgen metabolite (FPM and FAM, respectively) concentrations. As biotic factors could impact reproduction, we predicted that demographics, FPM and FAM would vary between sections and with respect to season (calendar and wet/dry), climate and age of the rhinoceros. Mean FPM concentrations from pregnant females were seven times higher (P < 0.05) than samples from non-pregnant rhinoceros. Positive relationships were found between monthly temperatures and FPM from non-pregnant females (r (2) = 0.25, P = 0.03) and the percentage of calves born (r = 0.609, P = 0.04). Although FAM peaked in the spring, when the majority of calves (40%) were conceived, no seasonal patterns in male androgen concentrations were found with respect to month of conception and parturition. Females in Addo had a longer inter-calving interval and were less likely to be pregnant (P < 0.05) compared with those in Nyathi. The biotic stressors (e.g. predators and more competitors) within Addo section could be affecting the reproductive physiology of the rhinoceros negatively. Enhanced knowledge about how black rhinoceros populations respond to environmental stressors could guide management strategies for improving reproduction.

Hierarchical polygyny in multiparous lesser flat-headed bats

How males gain access to mates and the potential for female choice will determine whether polygyny can operate at several levels, from within litters and groups to the wider population. Female lesser flat-headed bats (Tylonycteris pachypus) form maternity groups in bamboo stems. Unusually for bats, they are multiparous, providing the opportunity to test whether multi-level polygyny differs among males depending on whether they roost with females, with males or are solitary. We genotyped 662 individuals from 54 internodes and analysed parentage of 165 litters. Our results revealed 170 sets of paternal twins/triplets, of which 96 were full-sibs and 74 were half-sibs. We found that males captured roosting with females typically sired more offspring overall than did other males and also showed a greater tendency to monopolize paternity within both litters and roosting groups. In comparison, males that sired fewer full-sibs were assigned more maternal half-sibs. These latter individuals, which included solitary males and those from all-male groups, might gain copulations either via roaming with furtive mating or during visits by females. Indeed, female lesser flat-headed bats store sperm, so could benefit from multiple mating to reduce genetic incompatibilities. At the same time, however, we found no evidence of outbreeding. Finally, relatedness and mtDNA analyses revealed that polygyny also operated within matrilineal kin, suggesting a system that might promote social cohesiveness. Future studies of individual movements will help to determine the extent to which mixed paternities in litters, matrilines and groups are driven by male or female behaviour.

Neotropical bats: estimating species diversity with DNA barcodes

DNA barcoding using the cytochrome c oxidase subunit 1 gene (COI) is frequently employed as an efficient method of species identification in animal life and may also be used to estimate species richness, particularly in understudied faunas. Despite numerous past demonstrations of the efficiency of this technique, few studies have attempted to employ DNA barcoding methodologies on a large geographic scale, particularly within tropical regions. In this study we survey current and potential species diversity using DNA barcodes with a collection of more than 9000 individuals from 163 species of Neotropical bats (order Chiroptera). This represents one of the largest surveys to employ this strategy on any animal group and is certainly the largest to date for land vertebrates. Our analysis documents the utility of this tool over great geographic distances and across extraordinarily diverse habitats. Among the 163 included species 98.8% possessed distinct sets of COI haplotypes making them easily recognizable at this locus. We detected only a single case of shared haplotypes. Intraspecific diversity in the region was high among currently recognized species (mean of 1.38%, range 0-11.79%) with respect to birds, though comparable to other bat assemblages. In 44 of 163 cases, well-supported, distinct intraspecific lineages were identified which may suggest the presence of cryptic species though mean and maximum intraspecific divergence were not good predictors of their presence. In all cases, intraspecific lineages require additional investigation using complementary molecular techniques and additional characters such as morphology and acoustic data. Our analysis provides strong support for the continued assembly of DNA barcoding libraries and ongoing taxonomic investigation of bats.

Cross-species amplification of bovid microsatellites in central African duikers (genus Cephalophus) and other sympatric artiodactyls

The present study set out to evaluate cross-species amplification of 34 bovid microsatellites in six central African duikers: Cephalophus callipygus, C. monticola, C. silvicultor, C. nigrifrons, C. dorsalis and C. leucogaster. Of these loci, 16 amplified across all species and appeared polymorphic when initially tested in polyacrylamide gel electrophoresis. Twelve of these loci were subsequently assembled into three multiplex panels of four loci each. These multiplexes successfully amplified across all six duiker species in the present study and the sympatric artiodactyls Tragelaphus spekei and Hyemoschus aquaticus. The only exception was the locus BM848 that did not amplify from C. leucogaster. For species with sufficient sample sizes (C. callipygus and C. monticola), the number of alleles ranged from three to ten and four to fifteen, respectively. Three loci deviated from Hardy-Weinberg equilibrium in C. callipygus and five in C. monticola. We attribute the latter result to possibilities of local population substructuring or to an excess of homozygotes because of null alleles. These multiplex assemblies will greatly facilitate studies of individual identification, parentage analysis, population size estimation and fine-scale analyses of population genetic structure in central African artiodactyls.

Species on the menu of a generalist predator, the eastern red bat (Lasiurus borealis): using a molecular approach to detect arthropod prey

One of the most difficult interactions to observe in nature is the relationship between a predator and its prey. When direct observations are impossible, we rely on morphological classification of prey remains, although this is particularly challenging among generalist predators whose faeces contain mixed and degraded prey fragments. In this investigation, we used a polymerase chain reaction and sequence-based technique to identify prey fragments in the guano of the generalist insectivore, the eastern red bat (Lasiurus borealis), and evaluate several hypotheses about prey selection and prey defences. The interaction between bats and insects is of significant evolutionary interest because of the adaptive nature of insect hearing against echolocation. However, measuring the successes of predator tactics or particular prey defences is limited because we cannot normally identify these digested prey fragments beyond order or family. Using a molecular approach, we recovered sequences from 89% of the fragments tested, and through comparison to a reference database of sequences, we were able to identify 127 different species of prey. Our results indicate that despite the robust jaws of L. borealis, most prey taxa were softer-bodied Lepidoptera. Surprisingly, more than 60% of the prey species were tympanate, with ears thought to afford protection against these echolocating bats. Moths of the family Arctiidae, which employ multiple defensive strategies, were not detected as a significant dietary component. Our results provide an unprecedented level of detail for the study of predator-prey relationships in bats and demonstrate the advantages which molecular tools can provide in investigations of complex ecological systems and food-web relationships.

Effects of storage type and time on DNA amplification success in tropical ungulate faeces

The present study compares the effect of three storage media (silica, RNAlater®, ethanol) and time to extraction (1 week, 1 month and 3 months) on mitochondrial and nuclear marker amplification success in faecal DNA extracts from a sympatric community of small to medium-sized Central African forest ungulates (genera Cephalophus, Tragelaphus, Hyemoschus). The effect of storage type and time on nuclear DNA concentrations, genotyping errors and percentage recovery of consensus genotypes was also examined. Regardless of storage method, mitochondrial and nuclear amplification success was high in DNA extracted within the first week after collection. Over longer storage periods, RNAlater yielded better amplification success rates in the mitochondrial assay. However, samples stored on silica showed (i) highest nuclear DNA concentrations, (ii) best microsatellite genotyping success, (iii) lowest genotyping errors, and (iv) greatest percentage recovery of the consensus genotype. The quantity of nuclear DNA was generally a good predictor of microsatellite performance with 83% amplification success or greater achieved with sample DNA concentrations of ≥ 50 pg/µL. If faecal DNA samples are to be used for nuclear microsatellite analyses, we recommend silica as the best storage method. However, for maximum mitochondrial amplification success, RNAlater appears to be the best storage medium. In contrast, ethanol appeared inferior to the other two methods examined here and should not be used to store tropical ungulate faeces. Regardless of storage method, samples should be extracted as soon as possible after collection to ensure optimal recovery of DNA.

Patterns of paternity and group fission in wild multimale mountain gorilla groups

To understand variation among social systems, it is essential to know the relative reproductive success of individuals in group-living species. Particularly interesting for such studies are taxa such as mountain gorillas in which both one-male and multimale groups are common, because of the opportunity to estimate the costs and benefits to males of pursuing different reproductive strategies. We genotyped 68 individuals from two groups of multimale mountain gorilla groups in Bwindi Impenetrable National Park, Uganda to determine the distribution of paternity among the males. In both groups, the dominant male sired the majority of offspring. One group underwent a fission, and we found that the eight offspring assigned to the dominant silverback (and their mothers) remained with their father, while the two offspring of unknown paternity ended up in the small group headed by the formerly subordinate silverback. This is consistent with the proposal that the outcome of group fission in primates is not only influenced by maternal relationships among individuals, but also by patrilineal relationships. Results of this study show that subordinate males may gain reproductive benefits even while queuing for dominance status. Despite ecological differences between Bwindi and the Virunga Volcanoes, male mountain gorillas living in both populations benefit from remaining in multimale groups.

Molecular analysis of predation: a review of best practice for DNA-based approaches

Molecular analysis of predation, through polymerase chain reaction amplification of prey remains within the faeces or digestive systems of predators, is a rapidly growing field, impeded by a lack of readily accessible advice on best practice. Here, we review the techniques used to date and provide guidelines accessible to those new to this field or from a different molecular biology background. Optimization begins with field collection, sample preservation, predator dissection and DNA extraction techniques, all designed to ensure good quality, uncontaminated DNA from semidigested samples. The advantages of nuclear vs. mitochondrial DNA as primer targets are reviewed, along with choice of genes and advice on primer design to maximize specificity and detection periods following ingestion of the prey by the predators. Primer and assay optimization are discussed, including cross-amplification tests and calibratory feeding experiments. Once primers have been made, the screening of field samples must guard against (through appropriate controls) cross contamination. Multiplex polymerase chain reactions provide a means of screening for many different species simultaneously. We discuss visualization of amplicons on gels, with and without incorporation of fluorescent primers. In more specialized areas, we examine the utility of temperature and denaturing gradient gel electrophoresis to examine responses of predators to prey diversity, and review the potential of quantitative polymerase chain reaction systems to quantify predation. Alternative routes by which prey DNA might get into the guts of a predator (scavenging, secondary predation) are highlighted. We look ahead to new technologies, including microarrays and pyrosequencing, which might one day be applied to this field.

Paternal kin discrimination: the evidence and likely mechanisms

One of the most important assumptions of kin selection theory is that individuals behave differently towards kin than non-kin. In mammals, there is strong evidence that maternal kin are distinguished from non-kin via familiarity. However, little is known about whether or not mammals can also recognize paternal kin as many female mammals, including primates, mate with multiple males near the time of conception, potentially concealing paternal kinship. Genetic data in several mammalian species with a promiscuous mating system and male-biased dispersal reveal a high skew in male reproduction which leads to co-residing paternal half-siblings. In most primates, individuals also form stable bisexual groups creating opportunities for males to interact with their offspring. Here I consider close paternal kin co-resident in the same social group, such as father-offspring and paternal half-siblings (i.e. animals sharing the same father but who were born to different mothers) and review mammalian studies of paternal kin discrimination. Furthermore, I summarize the most likely mechanisms of paternal kin discrimination (familiarity and phenotype matching). When familiarity is the underlying mechanism, mothers and/or the sire could mediate familiarity among paternal half-siblings as well as between fathers and offspring assuming mothers and/or fathers can assess paternity. When animals use phenotype matching, they might use their fathers' template (when the father is present) or self (when the father is absent) to assess paternal kinship in others. Available evidence suggests that familiarity and phenotype matching might be used for paternal kin discrimination and that both mechanisms might apply to a wide range of social mammals characterized by a high skew in male reproduction and co-residence of paternal kin. Among primates, suggested evidence for phenotype matching can often have an alternative explanation, which emphasizes the crucial importance of controlling for familiarity as a potential confounding variable. However, the mechanism/s used to identify paternal kin might differ within a species (as a function of each individual's specific circumstances) as well as among species (depending upon the key sensory modalities of the species considered). Finally, I discuss the possible cues used in paternal kin discrimination and offer suggestions for future studies.