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Rapid advances in genomic tools for use in ecological contexts and non‐model systems allow unprecedented insight into interactions that occur beyond direct observation. We developed an approach that couples microbial forensics with molecular dietary analysis to identify species interactions and scavenging by invasive rats on native and introduced birds in Hawaii. First, we characterized bacterial signatures of bird carcass decay by conducting 16S rRNA high‐throughput sequencing on chicken (Gallus gallus domesticus) tissues collected over an 11‐day decomposition study in natural Hawaiian habitats. Second, we determined if field‐collected invasive black rats (Rattus rattus; n = 51, stomach and fecal samples) had consumed birds using molecular diet analysis with two independent PCR assays (mitochondrial Cytochrome Oxidase I and Cytochrome b genes) and Sanger sequencing. Third, we characterized the gut microbiome of the same rats using 16S rRNA high‐throughput sequencing and identified 15 bacterial taxa that were (a) detected only in rats that consumed birds (n = 20/51) and (b) were indicative of decaying tissue in the chicken decomposition experiment. We found that 18% of rats (n = 9/51) likely consumed birds as carrion by the presence of bacterial biomarkers of decayed tissue in their gut microbiome. One species of native bird (Myadestes obscurus) and three introduced bird species (Lophura leucomelanos, Meleagris gallopavo, Zosterops japonicus) were detected in the rats’ diets, with individuals from these species (except L. nycthemera) likely consumed through scavenging. Bacterial biomarkers of bird carcass decay can persist through rat digestion and may serve as biomarkers of scavenging. Our approach can be used to reveal trophic interactions that are challenging to measure through direct observation., We developed a novel three‐part approach using molecular dietary analysis and microbial forensics to reveal species interactions and scavenging by invasive rats on native and introduced birds in Hawaii. Our forensic genomic tool for use in ecological contexts is valuable for (a) detecting diet items in stomach and fecal samples, and (b) determining decomposition status of prey. Our method properly calibrated and replicated has great potential to detect and quantify species interactions that are remote, rare, and challenging to measure.

Age‐associated DNA‐methylation profiles have been used successfully to develop highly accurate biomarkers of age ("epigenetic clocks") in humans, mice, dogs, and other species. Here we present epigenetic clocks for African and Asian elephants. These clocks were developed using novel DNA methylation profiles of 140 elephant blood samples of known age, at loci that are highly conserved between mammalian species, using a custom Infinium array (HorvathMammalMethylChip40). We present epigenetic clocks for Asian elephants (Elephas maximus), African elephants (Loxodonta africana), and both elephant species combined. Two additional human‐elephant clocks were constructed by combining human and elephant samples. Epigenome‐wide association studies identified elephant age‐related CpGs and their proximal genes. The products of these genes play important roles in cellular differentiation, organismal development, metabolism, and circadian rhythms. Intracellular events observed to change with age included the methylation of bivalent chromatin domains, and targets of polycomb repressive complexes. These readily available epigenetic clocks can be used for elephant conservation efforts where accurate estimates of age are needed to predict demographic trends., DNA methylation aging clocks for African and Asian elephants. Some of these clocks apply to humans as well. Parts of the graphic were created by Hollis Burbank‐Hammerlund, Sandra Oviedo, and BioRender.com.

The intentional and unintentional movement of plants and animals by humans has transformed ecosystems and landscapes globally. Assessing when and how a species was introduced are central to managing these transformed landscapes, particularly in island environments. In the Gulf of Alaska, there is considerable interest in the history of mammal introductions and rehabilitating Gulf of Alaska island environments by eradicating mammals classified as invasive species. The Arctic ground squirrel (Urocitellus parryii) is of concern because it affects vegetation and seabirds on Gulf of Alaska islands. This animal is assumed to have been introduced by historic settlers; however, ground squirrel remains in the prehistoric archaeological record of Chirikof Island, Alaska, challenge this timeline and suggest they colonized the islands long ago. We used 3 lines of evidence to address this problem: direct radiocarbon dating of archaeological squirrel remains; evidence of prehistoric human use of squirrels; and ancient DNA analysis of dated squirrel remains. Chirikof squirrels dated to at least 2000 years ago, and cut marks on squirrel bones suggested prehistoric use by people. Ancient squirrels also shared a mitochondrial haplotype with modern Chirikof squirrels. These results suggest that squirrels have been on Chirikof longer than previously assumed and that the current population of squirrels is closely related to the ancient population. Thus, it appears ground squirrels are not a recent, human-mediated introduction and may have colonized the island via a natural dispersal event or an ancient human translocation.

We investigated the patterns of genetic diversity and structure of African forest elephants in a human‐modified landscape in the Gamba complex of protected areas (GCPA), a tropical wilderness area along the southwest coast of Gabon. We collected 298 elephant fecal samples from four sites (Sette Cama, Gamba area, Vera Plains, and Mayonami), along approximately 80 km of coastline from north to south. We used microsatellites and mitochondrial DNA (mtDNA) to successfully genotype 295 of the 298 fecal samples, and identified 213 individuals. Using sex markers, we identified 84 males and 118 females; we could not determine the sex of the remaining 11 individuals. We also characterized the sex, group size, and social status of crop‐raiding elephants and did not find characteristics distinguishing them from nonraiders. Overall, our mtDNA and microsatellite markers revealed that elephants in the research area maintain high levels of genetic variation and low levels of subdivision. Gene flow appears to be mostly mediated by male dispersal away from natal herds. Our structure analysis revealed two highly admixed genetic clusters, attributable to high connectivity among the protected areas. However, forest areas within the GCPA have become increasingly fragmented by human‐induced habitat modification. We detected a pattern of isolation by distance, accentuated by the presence of the town of Gamba between Sette‐Cama and Mayonami. We found a high degree of connectivity among sampling locations within the GCPA. This supports the importance of establishing agricultural best practices to reduce habitat loss that may sever gene exchange and to maintain connectivity, as well as to avoid human–elephant conflict that can result in retaliatory killing of elephants in this area. This study emphasizes the importance of conducting baseline monitoring of demographic data, genetic diversity, and structure to enable future comparisons to assess the long‐term impact of human‐induced habitat fragmentation.

Ectoparasites frequently vector pathogens from often unknown pathogen reservoirs to both human and animal populations. Simultaneous identification of the ectoparasite species, the wildlife host that provided their most recent blood meal(s), and their pathogen load would greatly facilitate the understanding of the complex transmission dynamics of vector-borne diseases. Currently, these identifications are principally performed using multiple polymerase chain reaction (PCR) assays. We developed an assay (EctoBaits) based on in-solution capture paired with high-throughput sequencing to simultaneously identify ectoparasites, host blood meals and pathogens. We validated our in-solution capture results using double-blind PCR assays, morphology and collection data. The EctoBaits assay effectively and efficiently identifies ectoparasites, blood meals, and pathogens in a single capture experiment, allowing for high-resolution taxonomic identification while preserving the DNA sample for future analyses.

Here, we present a set of RNA-based probes for whole mitochondrial genome in-solution enrichment, targeting a diversity of mammalian mitogenomes. This probes set was designed from seven mammalian orders and tested to determine the utility for enriching degraded DNA. We generated 63 mitogenomes representing five orders and 22 genera of mammals that yielded varying coverage ranging from 0 to >5400X. Based on a threshold of 70% mitogenome recovery and at least 10× average coverage, 32 individuals or 51% of samples were considered successful. The estimated sequence divergence of samples from the probe sequences used to construct the array ranged up to nearly 20%. Sample type was more predictive of mitogenome recovery than sample age. The proportion of reads from each individual in multiplexed enrichments was highly skewed, with each pool having one sample that yielded a majority of the reads. Recovery across each mitochondrial gene varied with most samples exhibiting regions with gaps or ambiguous sites. We estimated the ability of the probes to capture mitogenomes from a diversity of mammalian taxa not included here by performing a clustering analysis of published sequences for 100 taxa representing most mammalian orders. Our study demonstrates that a general array can be cost and time effective when there is a need to screen a modest number of individuals from a variety of taxa. We also address the practical concerns for using such a tool, with regard to pooling samples, generating high quality mitogenomes and detail a pipeline to remove chimeric molecules.

Herein, we compare functional muscle properties among convergent forms of large, obligate avian scavengers. We performed quantitative analyses of all the muscle masses and cross-sectional areas (CSA) of the wings and hindlimbs of five species from two families, Cathartidae (New World vultures; Cathartes aura and Vultur gryphus) and Accipitridae (Old World vultures and raptors; Gyps africanus, Aquila rapax, and Buteo lineatus). These species comprise two paraphyletic functional groups, raptors (Aquila and Buteo) and vultures (Gyps, Cathartes, and Vultur). Our ordination analyses based on all of the muscles of the wings, hindlimbs, and wing and hindlimb muscles combined produced patterns that appeared to be more related to phylogeny, with a hint of a functional signal in wing muscle CSA. However, when wing muscles were grouped according to their functional roles (upstroke, downstroke, and wing stabilization), the percentages of mass and CSA allocated to the upstroke and stabilizing muscles were 1.4–5% greater in the vultures than in the raptors. Conversely, when hindlimb muscles were grouped according to their roles in grasping and terrestrial locomotion, the percentages of mass and CSA allocated to grasping muscles were 5.9–14% greater in the raptors. Our results provide a baseline for future lines of inquiry aimed at understanding how muscle mass and CSA are affected differentially across locomotor modules, possibly in response to differential demands on wing and hindlimb function experienced by these disparate accipitriform clades.

Biodiversity conservation strategies are increasingly focused on regions outside national protected areas, where animals face numerous anthropogenic threats and must coexist with human settlements, livestock, and agriculture. The effects of these potential threats are not always clear, but they could have profound implications for population viability. We used savannah elephants (Loxodonta africana) as a case study to assess the physiological stress associated with living in a human-livestock-dominated landscape. We collected samples over two 3-month periods in 2007 and 2008. We used fecal DNA to identify 96 individual elephants in a community conservation area (CCA) and measured fecal glucocorticoid metabolite (FGM) concentrations as a proxy for stress. The CCA is community Maasai land managed for livestock and wildlife. We compared the FGM concentrations from the CCA to FGM concentrations of 40 elephants in Amboseli National Park and 32 elephants in the Maasai Mara National Reserve, where human settlements and intense livestock grazing were absent. In the CCA, we found no significant individual differences in FGM concentrations among the elephants in 2007 (p = 0.312) or 2008 (p = 0.412) and no difference between years (p = 0.616). The elephants in the CCA had similar FGM concentrations to the Maasai Mara population, but Amboseli elephants had significantly lower FGM concentrations than those in either Maasai Mara or the CCA (Tukey pairwise test, p < 0.001), due primarily to females excreting significantly lower FGM relative to males (p = 0.025). In the CCA, there was no relation among female group size, average pairwise group relatedness, and average group FGM concentration. We found no clear evidence of chronic stress in elephants living on CCA communal land, which is encouraging for conservation strategies promoting the protection of animals living outside protected areas. Conservacion Fuera de Areas Protegidas y el Efecto de Paisajes Dominados por Humanos sobre Hormonas del Estres en Elefantes Africanos Resumen Las estrategias de conservacion se enfocan cada vez mas hacia regiones fuera de areas nacionales protegidas, donde los animales enfrentan numerosas amenazas antropogenicas y deben coexistir con asentamientos humanos, ganado y agricultura. Los efectos de esas amenazas potenciales no siempre son claros, pero podrian tener implicaciones profundas para la viabilidad poblacional. Utilizamos elefantes africanos (Loxodonta africana) como un estudio de caso para evaluar el estres fisiologico asociado con vivir en un paisaje dominado por humanos y ganado. Recolectamos muestras en 2 periodos de 3 meses en 2007 y 2008. Utilizamos ADN fecal para identificar a 96 elefantes individuales en un area de conservacion comunitaria (ACC) y medimos las concentraciones del metabolito glucocorticoide fecal (MGF) como un indicador de estres. El ACC es tierra Maasai comunitaria manejada para ganado y vida silvestres. Comparamos las concentraciones de MGF en el ACC con las concentraciones de MGF de 40 elefantes del Parque Nacional Amboseli y 32 elefantes de la Reserva Nacional Maasai Mara, donde no hay asentamientos humanos ni pastoreo intensivo. En el ACC, no encontramos diferencias individuales significativas en las concentraciones de MGF entre los elefantes en 2007 (p = 0.312) ni 2008 (p = 0.412) ni entre anos (p = 0.616). Los elefantes en el ACC tuvieron concentraciones similares de MGF a la poblacion de Maasai Mara, pero los elefantes de Amboseli tuvieron concentraciones de MGF significativamente menores que las de Maasai Mara o el ACC. (prueba pareada de Tukey, p < 0.001), debido principalmente a que las hembras excretan significativamente menos MGF que los machos (p = 0.025). En el ACC, no hubo relacion entre el tamano del grupo de hembras, la similitud promedio de grupos pareados, ni la concentracion de MGF promedio del grupo. No encontramos evidencias claras de estres cronico en elefantes viviendo en el ACC, lo cual es alentador para las estrategias de conservacion que promueven la proteccion de animales que viven fuera de areas protegidas.

Prehensile-tailed porcupines (Coendou prehensilis), like other rodents, lack external sexual traits, making it difficult to non-invasively determine their gender. By exploiting genetic differences between the X and the Y chromosome, we developed a simple genetic test to determine the gender of Coendous from shed quills. We Sanger sequenced a short portion (195 bp) of the zinc finger protein gene of known male (XY) Coendous to identify positions that are polymorphic between the X and Y chromosomes at this locus. By directly sequencing this fragment, we were able to correctly determine (confirmed via anatomical sexing) the gender of male and female Coendous by the presences or absence of polymorphisms in the resulting chromatograms. This assay is simple, quick and is applicable to other porcupine species. Zoo Biol. 32:463–466, 2013. © 2013 Wiley Periodicals Inc.

We investigated the spatial genetic structure of the tiger meta-population in the Satpura–Maikal landscape of central India using population- and individual-based genetic clustering methods on multilocus genotypic data from 273 individuals. The Satpura–Maikal landscape is classified as a global-priority Tiger Conservation Landscape (TCL) due to its potential for providing sufficient habitat that will allow the long-term persistence of tigers. We found that the tiger meta-population in the Satpura–Maikal landscape has high genetic variation and very low genetic subdivision. Individual-based Bayesian clustering algorithms reveal two highly admixed genetic populations. We attribute this to forest connectivity and high gene flow in this landscape. However, deforestation, road widening, and mining may sever this connectivity, impede gene exchange, and further exacerbate the genetic division of tigers in central India.

Aim Habitat loss and fragmentation can influence the genetic structure of biological populations. Large terrestrial predators can often avoid genetic subdivision due to fragmentation because they have high rates of dispersal-mediated gene flow. Leopards (Panthera pardus) are found in a variety of habitats and are the most widely distributed of the large and middle-sized felids. We investigated the genetic diversity and population substructure of leopards (P.p fusca) in a fragmented meta-population comprised of four populations from five protected areas and inter-connecting corridors spread over an area of 45,000 km2 in central India. Location Kanha, Pench, Satpura and Melghat Tiger Reserves, and interconnecting corridors in the Satpura-Maikal Landscape of Central India. Methods We collected faecal samples and used genetic methods to identify individuals, estimate the genetic variation and evaluate the patterns of genetic substructuring within this meta-population of leopards. Results We identified 217 individual leopards using a panel of seven microsatellite loci. Leopards showed high levels of genetic diversity in all sampled populations. Spatial and non-spatial Bayesian analysis revealed at least two admixed genetic populations with indications of ongoing genetic subdivision. Genetic differentiation between populations was not explained by geographic distance. We identified nine individuals as migrants, most of which were assigned to reserves connected by corridors. Main conclusions Our study demonstrates that the leopard, an adaptable and vagile species, can become genetically differentiated with increased habitat fragmentation. Contrary to our hypothesis of panmixia, our results indicate that although leopards in this landscape are admixed, there is genetic substructuring at both the landscape and the fine-scale level. We conclude that this is due to habitat fragmentation and corridors are of immense value in maintaining genetic connectivity in this landscape.

Aim Dispersal is a critical component of animal ecology that is poorly understood for most species. In particular, savanna elephants (Loxodonta africana) have been studied for decades in national parks across Africa, but little is known about their dispersal into new or unused habitats or their population dynamics in human-dominated landscapes. We capitalized on a natural dispersal event of savanna elephants recolonizing communal land in southern Kenya to document their demographic characteristics and genetic relationships. Location Rift Valley province of Kenya. Methods We collected faecal samples and used genetic methods to identify individuals, estimate the sex ratio and evaluate the patterns of relatedness within the female groups and male aggregations. We also measured dung bolus circumference to assign age classes to individuals and estimate the age structure. Results We identified 112 individuals with a sex ratio not different from one (1.32:1.00). The age structure was skewed towards younger elephants (71%), suggesting the potential for rapid growth from reproduction. We detected significantly higher kinship levels within female groups (R = 0.124 ± 0.023), suggesting that family groups colonized the site, but found little support for higher-order genetic relationships among female groups. Males detected together were unrelated (R = 0.003 ± 0.030). Main conclusions Our results suggest that highly social mammals, such as savanna elephants, disperse into unoccupied habitat as family groups and that a young demographic structure and a large number of males might be expected in establishing populations. These findings highlight the potential value of indirect, non-invasive methods for assessing elephant herd and demographic characteristics when direct observations are difficult.

The ring-tailed coati (Nasua nasua) is the only coati species in which social groups contain an adult male year round, although most males live solitarily. We compared reproductive success of group living and solitary adult male coatis to determine the degree to which sociality affects reproductive success. Coati mating is highly seasonal and groups of female coatis come into oestrus during the same 1–2 week period. During the mating season, solitary adult males followed groups and fought with the group living male. This aggression was presumably to gain access to receptive females. We expected that high reproductive synchrony would make it difficult or impossible for the one group living male to monopolize and defend the group of oestrous females. However, we found that group living males sired between 67–91% of the offspring in their groups. This reproductive monopolization is much higher than other species of mammals with comparably short mating seasons. Clearly, living in a group greatly enhanced a male's reproductive success. At the same time, at least 50% of coati litters contained offspring sired by extra-group males (usually only one offspring per litter); thus, resident males could not prevent extra-group matings. The resident male’s reproductive advantage may reflect female preference for a resident male strong enough to fend off competing males.

Noninvasive survey methods based on analyzing DNA extracted from feces can be useful for carnivores that are difficult to study by other methods. Changes in fecal deposition patterns associated with reproduction in kit foxes (Vulpes macrotis) might affect results of such surveys. We used a trained dog to collect fresh scats on 2-km transects in the home ranges of 11 radiocollared female kit foxes in January, February, and March 2008 and determined sex of the individual that deposited the scats by amplifying the zinc finger protein gene. Female foxes give birth in mid-February to mid-March. We found a similar number of scats each month. In January, the sex ratio of the scats was not different from the expected 1∶1. However, in February there were almost 2 male scats for every female scat and in March there were >8 male scats for every female scat. Comparing March to January, there were more male scats on all 11 transects and fewer female scats on 10 of 11 transects. Around the time pups are born, ...

The small red brocket deer Mazama bororo is one of the most endangered deer in the Neotropics. The great morphological similarities with three other sympatric brocket deer species, coupled with the fact that they inhabit densely forested habitats complicate detection and prevent the use of traditional methodologies for accurate identification of species. The ability to determine the presence of this endangered species in an area is crucial for estimating its distribution range, and is critical for establishing conservation management strategies. Here we describe a fast and reliable noninvasive genetic method for species identification of Mazama species from faeces. We designed a primer set that amplifies a short 224-bp fragment of the cytochrome b and demonstrate its effectiveness in successful amplification of DNA isolated from both tissue and faecal samples. This fragment contains a BSTNI/ECORII digestion site that is unique to the endangered M. bororo. The digested polymerase chain reaction products yielded a 160-bp fragment that is clearly visible in a 2% agarose gel. Two other diagnostic sites were identified to differentiate the other three sympatric species, SspI (M. gouazoubira) and AflIII (M. americana, and M. nana).

Aim Human activities are major determinants of forest elephant ( Loxodonta africana cyclotis ) distribution in Gabon, but the types and intensity of disturbance that elephants can tolerate are not known. We conducted dung surveys within the Gamba Complex of Protected Areas in SW Gabon to examine (1) the feasibility of noninvasive faecal analyses for monitoring stress physiology, and (2) the influence of petroleum operations on stress levels in forest elephants.

Nonrandom patterns of mating and dispersal create fine-scale genetic structure in natural populations — especially of social mammals — with important evolutionary and conservation genetic consequences. Such structure is well-characterized for typical mammalian societies; that is, societies where social group composition is stable, dispersal is male-biased, and males form permanent breeding associations in just one or a few social groups over the course of their lives. However, genetic structure is not well understood for social mammals that differ from this pattern, including elephants. In elephant societies, social groups fission and fuse, and males never form permanent breeding associations with female groups. Here, we combine 33 years of behavioural observations with genetic information for 545 African elephants (Loxodonta africana), to investigate how mating and dispersal behaviours structure genetic variation between social groups and across age classes. We found that, like most social mammals, female matrilocality in elephants creates co-ancestry within core social groups and significant genetic differentiation between groups (ΦST = 0.058). However, unlike typical social mammals, male elephants do not bias reproduction towards a limited subset of social groups, and instead breed randomly across the population. As a result, reproductively dominant males mediate gene flow between core groups, which creates cohorts of similar-aged paternal relatives across the population. Because poaching tends to eliminate the oldest elephants from populations, illegal hunting and poaching are likely to erode fine-scale genetic structure. We discuss our results and their evolutionary and conservation genetic implications in the context of other social mammals.

The elephants of the Knysna region continue to survive, despite fears that there was only a single surviving female. Their range is larger than previously believed, and includes the Afromontane forest and mountain fynbos. The five individuals detected in this study were all females, and share a single mitochondrial DNA control region haplotype with individuals from Addo Elephant National Park. At least two of these elephants appear to be first-order relatives, and the others may be part of a single matrilineal group. The genetic diversity detected is lower than that found in most African savanna populations, but is higher than that found at Addo, where individuals represent the descendents of a severe population size bottleneck. Levels of genetic diversity are more similar to those detected at Kruger National Park, suggesting that the Knysna elephants represent a remnant of the once widespread populations of South Africa. Resume Les elephants de la region de Knysna ont survecu, meme si l'on a craint un moment qu'il ne subsiste qu'une seule femelle. Leur dispersion est plus vaste qu'on ne le croyait et comprend la foret afromontagnarde, le fynbos de montagne. Les cinq individus reperes lors de cette etude etaient tous des femelles et partagent un seul haplotype dans la region de controle de l'ADN mitochondrial avec les individus du Parc National d'Addo. Au moins deux de ces elephants semblent avoir des liens familiaux de premier ordre et les autres pourraient faire partie d'un meme groupe matrilineaire. La diversite genetique detectee est plus faible que celle qu'on trouve dans la plupart des populations des savanes africaines, mais elle est plus elevee que celle que l'on observe a Addo, ou les individus representent les descendants d'un seul residu extremement petit d'une population anterieure. Le niveau de diversite genetique est plus semblable a celui releve au Parc National Kruger, ce qui suggere que les elephants de Knysna sont un residu des populations autrefois repandues en Afrique du Sud.

The costs of inbreeding depression, as well as the opportunity costs of inbreeding avoidance, determine whether and which mechanisms of inbreeding avoidance evolve. In African elephants, sex-biased dispersal does not lead to the complete separation of male and female relatives, and so individuals may experience selection to recognize kin and avoid inbreeding. However, because estrous females are rare and male-male competition for mates is intense, the opportunity costs of inbreeding avoidance may be high, particularly for males. Here we combine 28 years of behavioural and demographic data on wild elephants with genotypes from 545 adult females, adult males, and calves in Amboseli National Park, Kenya, to test the hypothesis that elephants engage in sexual behaviour and reproduction with relatives less often than expected by chance. We found support for this hypothesis: males engaged in proportionally fewer sexual behaviours and sired proportionally fewer offspring with females that were natal family members or close genetic relatives (both maternal and paternal) than they did with nonkin. We discuss the relevance of these results for understanding the evolution of inbreeding avoidance and for elephant conservation.

Then polymorphic microsatellite loci for the endangered Buena Vista Lake shrew (Sorex ornatus relictus).

Noninvasive hair and fecal DNA sampling provides a means of collecting information on elusive species, while causing little or no disturbance. However, current methods of hair collection do not preclude multiple sampling, thus risking sample contamination. We developed a hair snare that prevents multiple sampling, is cost-effective, easy to construct, and safe for target and nontarget species. Our initial field tests on endangered San Joaquin kit foxes (Vulpes macrotis mutica) and swift foxes (Vulpes velox) suggest that this hair snare may be effective in collecting uncontaminated samples for DNA analysis.

Noninvasive faecal DNA sampling has the potential to provide a wealth of information necessary for monitoring and managing endangered species while eliminating the need to capture, handle or observe rare individuals. However, scoring problems, and subsequent genotyping errors, associated with this monitoring method remain a great concern as they can lead to misidentification of individuals and biased estimates. We examined a kit fox scat data set (353 scats; 80 genotypes) for genotyping errors using both genetic and GIS analyses, and evaluated the feasibility of combining both approaches to assess reliability of the faecal DNA results. We further checked the appropriateness of using faecal genotypes to study kit fox populations by describing information about foxes that we could deduce from the 'acceptable' scat genotypes, and comparing it to information gathered with traditional field techniques. Overall, genetic tests indicated that our data set had a low rate of genotyping error. Furthermore, examination of distributions of scat locations confirmed our data set was relatively error free. We found that analysing information on sex primer consistency and scat locations provided a useful assessment of scat genotype error, and greatly limited the amount of additional laboratory work that was needed to identify potentially 'false' scores. 'Acceptable' scat genotypes revealed information on sex ratio, relatedness, fox movement patterns, latrine use, and size of home range. Results from genetic and field data were consistent, supporting the conclusion that our data set had a very low rate of genotyping error and that this noninvasive method is a reliable approach for monitoring kit foxes.

Developing sound conservation strategies for carnivores in fragmented landscapes relies on accurate distribution information. Fecal (scat) surveys can provide an effective survey technique, especially when collection of scats is followed by genetic analysis of DNA extracted from scats. Furthermore, use of specially trained detection dogs to locate scats on survey routes may greatly enhance scat recovery. We evaluated utility of scat-detection dog surveys as a method to determine current distribution of kit foxes (Vulpes macrotis mutica). We used a trained dog to locate scats in core and satellite population areas with various densities and different habitat conditions. We compared number of scats found per kilometer on transects along different road and vegetation types. Scat-detection dog surveys detected the presence of kit foxes in each population area searched, regardless of relative fox density and vegetation type. We found a greater number of scats on unpaved than paved roads, suggesting unpaved roads are more appropriate for monitoring of foxes. Additionally, we found a greater number of scats in saltbush (Atriplex polycarpa) scrub than in non-native grassland. This result was strongly influenced by latitude, and was probably related to a north-south precipitation gradient. Our results demonstrate that scat-detection dog surveys can provide an effective conservation tool to map current kit fox distribution. This survey method has a wide application to other carnivore species, and can be used to survey multiple species simultaneously.

Specially trained detection dogs have been used to locate faeces (scats) for faecal analyses but their effectiveness has not been quantified. We evaluated detection and accuracy rates of dogs trained to find scats of endangered San Joaquin kit foxes (Vulpes macrotis mutica). Four dogs found from 0.43 to 5.37 presumptive kit fox scats per km of transect searched in two field sites where kit foxes and coyotes (Canis latrans) but not non-native red foxes (V. vulpes) were present. The unusually low detection rate (0.43 scats per km) by one dog (probably due to excessive panting in hot weather) was still similar to the average scat detection rate of two experienced humans. DNA tests of 1298 scats showed that all dogs were 100% accurate at distinguishing kit fox scats under our field conditions. Because red foxes are sympatric with kit foxes in some areas, we also conducted controlled discrimination experiments to see if trained dogs could distinguish between scats from kit and red foxes. Four dogs were 100% accurate at choosing a kit fox scat when red fox scats were present (n = 64 trials), but were less accurate at ignoring red fox scats in trials where a kit fox scat was absent.

The Pampas deer (Ozotoceros bezoarticus L. 1758) is the most endangered neotropical cervid, and in the past occupied a wide range of open habitats including grassland, pampas, savanna, and cerrado (Brazil) from 5 degrees to 41 degrees S. To better understand the effect of habitat fragmentation on gene flow and genetic variation, and to uncover genetic units for conservation, we examined DNA sequences from the mitochondrial control region of 54 individuals from six localities distributed throughout the present geographical range of the Pampas deer. Our results suggest that the control region of the Pampas deer is one of the most polymorphic of any mammal. This remarkably high variability probably reflects large historic population sizes of millions of individuals in contrast to numbers of fewer than 80,000 today. Gene flow between populations is generally close to one migrant per generation and, with the exception of two populations from Argentina, all populations are significantly differentiated. The degree of gene flow was correlated with geographical distance between populations, a result consistent with limited dispersal being the primary determinant of genetic differentiation between populations. The molecular genetic results provide a mandate for habitat restoration and reintroduction of Pampas deer so that levels of genetic variation can be preserved and historic patterns of abundance can be reconstructed. However, the source of individuals for reintroduction generally should be from populations geographically closest to those now in danger of extinction.

Sorex arizonae is a rare species that occupies a narrow range of habitat types in severalmountain ranges of New Mexico, Arizona and Northern Mexico. Here we identify and char-acterize six microsatellite loci for this species. We screened 63 individuals from four differ-ent localities from New Mexico and Arizona to analyse genetic variability. Alleles rangedfrom three to 16. Heterozygosity ranged from 40% to 78%. Most polymorphic loci were inHardy–Weinberg equilibrium with the exception of one locus. Primers appear to have rea-sonable cross-species applicability as five loci amplified in another shrew species ( Sorexmonticolus ). Keywords : Heterozygosity, microsatellites, polymorphic loci, rare species, Sorex arizonaeReceived 25 April 2005; revision accepted 20 May 2005 The Arizona shrew ( Sorex arizonae ) is one of the most restrictedshrews in North America. The species has a disjunctivemontane distribution in southern Arizona and New Mexico,and the Sierra Madre Occidental of Chihuahua, Mexico(Simons & Hoffmeister 2003). Currently, the Arizona shrewis listed by the Mexican and the US governments asendangered and species of special concern, respectively(Arita & Ceballos 1997).Microsatellites have been isolated and characterizedfor different shrews such as

Intraspecific patterns of mitochondrial DNA sequence variation were determined among California sea lions (Zalophus califomianus californianus) from three colonies along the Pacific coast of southern and Baja California and one colony in the Gulf of California. We found no variation in 368 base pairs (bp) of cytochrome b sequence among 40 sea lions from these localities, but analysis of 360 base pairs of control region revealed eleven genotypes. The four genotypes found in the Gulf of California population were unique and phylogenetically distinct from those found in sea lions along the Pacific coast. The average sequence divergence between Gulf and Southern California genotypes was 4.3%, suggesting a relatively long period of isolation. However, colonies along the Pacific coast, which are less than 200 km apart, shared mtDNA genotypes, indicating that recent genetic exchange has occurred between them. Therefore, we suggest that regional female philopatry exists in California sea lions. Regional boundaries may be related to oceanic currents or patchiness in the distribution of resources. Further research is needed to better understand the underlying causes of genetic differentiation in the California sea lion.

Artibeus jamaicensis is one of the most common bat species in the neotropics, with a welldefined polygynous social structure in caves. In order to study behaviour and to examine patterns of paternity and relatedness between different harem groups, we developed 14 microsatellite loci from two different enriched genomic libraries. We screened 125 individuals from two different bat colonies and found that polymorphism ranged from five to 13 alleles. Heterozygosity ranged from 63 to 95%. The primers amplified across 14 bat species, indicating their potential utility for population-level studies in several closely related bat species.