Guha Dharmarajan

Relative performance of Bayesian clustering software for inferring population substructure and individual assignment at low levels of population differentiation

Traditional methods for characterizing genetic differentiation among populations rely on a priori grouping of individuals. Bayesian clustering methods avoid this limitation by using linkage and Hardy–Weinberg disequilibrium to decompose a sample of individuals into genetically distinct groups. There are several software programs available for Bayesian clustering analyses, all of which describe a decrease in the ability to detect distinct clusters as levels of genetic differentiation among populations decrease. However, no study has yet compared the performance of such methods at low levels of population differentiation, which may be common in species where populations have experienced recent separation or high levels of gene flow. We used simulated data to evaluate the performance of three Bayesian clustering software programs, PARTITION, STRUCTURE, and BAPS, at levels of population differentiation below FST=0.1. PARTITION was unable to correctly identify the number of subpopulations until levels of FST reached around 0.09. Both STRUCTURE and BAPS performed very well at low levels of population differentiation, and were able to correctly identify the number of subpopulations at FST around 0.03. The average proportion of an individual’s genome assigned to its true population of origin increased with increasing FST for both programs, reaching over 92% at an FST of 0.05. The average number of misassignments (assignments to the incorrect subpopulation) continued to decrease as FST increased, and when FST was 0.05, fewer than 3% of individuals were misassigned using either program. Both STRUCTURE and BAPS worked extremely well for inferring the number of clusters when clusters were not well-differentiated (FST=0.02–0.03), but our results suggest that FST must be at least 0.05 to reach an assignment accuracy of greater than 97%.

Spatio-temporal variation in the demographic attributes of a generalist mesopredator

Human land-use practices have dramatically altered the composition and configuration of native habitats throughout many ecosystems. Within heterogeneous landscapes generalist predators often thrive, causing cascading effects on local biological communities, yet there are few data to suggest how attributes of fragmentation influence local population dynamics of these species. We monitored 25 raccoon (Procyon lotor) populations from 2004 to 2009 in a fragmented agricultural landscape to evaluate the influence of local and landscape habitat attributes on spatial and temporal variation in demography. Our results indicate that agricultural ecosystems support increased densities of raccoons relative to many other rural landscapes, but that spatial and temporal variation in demography exists that is driven by non-agricultural habitat attributes rather than the availability of crops. At the landscape scale, both density and population stability were positively associated with the size and contiguity of forest patches, while at the local scale density was positively correlated with plant diversity and the density of tree cavities. In addition, populations occupying forest patches with greater levels of plant diversity and stable water resources exhibited less temporal variability than populations with limited plant species complexity or water availability. The proportion of populations comprised of females was most strongly influenced by the availability of tree cavities and soft mast. Despite the abundance of mesopredators in heterogeneous landscapes, our results indicate that all patches do not contribute equally to the regional abundance and persistence of these species. Thus, a clear understanding of how landscape attributes contribute to variation in demography is critical to the optimization of management strategies.

Effects of Culling on Mesopredator Population Dynamics

Anthropogenic changes in land use and the extirpation of apex predators have facilitated explosive growth of mesopredator populations. Consequently, many species have been subjected to extensive control throughout portions of their range due to their integral role as generalist predators and reservoirs of zoonotic disease. Yet, few studies have monitored the effects of landscape composition or configuration on the demographic or behavioral response of mesopredators to population manipulation. During 2007 we removed 382 raccoons (Procyon lotor) from 30 forest patches throughout a fragmented agricultural ecosystem to test hypotheses regarding the effects of habitat isolation on population recovery and role of range expansion and dispersal in patch colonization of mesopredators in heterogeneous landscapes. Patches were allowed to recolonize naturally and demographic restructuring of patches was monitored from 2008–2010 using mark-recapture. An additional 25 control patches were monitored as a baseline measure of demography. After 3 years only 40% of experimental patches had returned to pre-removal densities. This stagnant recovery was driven by low colonization rates of females, resulting in little to no within-patch recruitment. Colonizing raccoons were predominantly young males, suggesting that dispersal, rather than range expansion, was the primary mechanism driving population recovery. Contrary to our prediction, neither landscape connectivity nor measured local habitat attributes influenced colonization rates, likely due to the high dispersal capability of raccoons and limited role of range expansion in patch colonization. Although culling is commonly used to control local populations of many mesopredators, we demonstrate that such practices create severe disruptions in population demography that may be counterproductive to disease management in fragmented landscapes due to an influx of dispersing males into depopulated areas. However, given the slow repopulation rates observed in our study, localized depopulation may be effective at reducing negative ecological impacts of mesopredators in fragmented landscapes at limited spatial and temporal scales.

Serologic survey for selected infectious diseases in raccoons (Procyon lotor) in Indiana, USA.

The objective of this study was to characterize the antibody prevalence of important livestock and domestic animal pathogens in raccoons (Procyon lotor) trapped and sampled in 39 forest patches in north-central Indiana, USA, between 2004 and 2005. A total of 459 serum samples were tested for antibodies to Leptospira serovars, 512 for Canine distemper virus (CDV) antibodies, and 340 for antibodies to Porcine reproductive and respiratory syndrome virus (PRRSV). In total, 47, 16, and 0% of the samples were seropositive for at least one Leptospira serovar, CDV, and PRRSV, respectively. Most of the positive Leptospira results were to serovars grippotyphosa (36%), autum-nalis (22%), and hardjo (22%). No statistically significant correlation was found between antibody prevalence estimates for different Leptospira serovars. A significant association was found between body weight and antibodies for Leptospira serovars and CDV. In addition, age (adult vs. juvenile) was significantly associated with the presence of CDV antibody, with adults exhibiting a higher prevalence than juveniles. This study confirmed that raccoons in Indiana, USA, are exposed to different Leptospira interrogans serovars and CDV and that age and weight are associated with the presence of antibodies for both pathogens.

Development and characterization of 12 polymorphic microsatellite loci in the American dog tick (Dermacentor variabilis).

Twelve polymorphic microsatellite loci were developed for the American dog tick (Dermacentor variabilis), an important vector of infectious diseases in humans and animals. Four multiplexed panels comprising the loci were developed and 45 ticks collected from two raccoons (Procyon lotor) were genotyped. The number of alleles per locus ranged from nine to 30, and single locus heterozygosities ranged from 0.18 to 0.93. Data generated using these markers will further our understanding of factors affecting gene flow in D. variabilis, thus helping to elucidate the transmission dynamics of diseases associated with this vector.

Development and characterization of 14 polymorphic microsatellite loci in the raccoon tick (Ixodes texanus).

Fourteen polymorphic microsatellite loci were developed for the raccoon tick (Ixodes texanus). Three multiplexed panels comprising the loci were developed and 50 ticks collected from two infected raccoons (Procyon lotor) were genotyped. The number of alleles per locus ranged from five to 22, and single locus heterozygosities ranged from 0.46 to 0.94. Future research will further our understanding of I. texanus biology and help in elucidating the effects of life‐history variation on parasite population genetic structure, using I. texanus as a model organism.

Melding kin structure and demography to elucidate source and sink habitats in fragmented landscapes

The source-sink model undoubtedly is one of the most established paradigms for associating variance in population dynamics with heterogeneity in habitat quality. However, despite extensive theoretical support by the scientific community, the majority of studies seeking empirical validation for this model have lacked sufficient data to distinguish source and sink habitats, particularly for large or secretive mammals. Using relatively long-term mark-recapture and genetic data for a generalist mesopredator within a fragmented agricultural ecosystem, we show that use of a two-stage approach incorporating both genetic and demographic data can be a powerful tool for evaluating the population structure of organisms occupying complex ecological systems. We further demonstrate that a strong concordance exists between demographic attributes and underlying genetic expectations, suggesting evaluation of fine-scale genetic patterns alone may provide valuable insights into the population dynamics of species. These data...

Neglected leptospirosis in raccoons (Procyon lotor) in Indiana, USA

Background: Leptospirosis is a globally important zoonotic disease occurring clinically and subclinically in humans and animals. Objectives: To determine whether raccoons in Indiana carried leptospires in their kidneys. Animals and methods: Thirty-four raccoons were live-trapped from two forest patches in central Indiana. Following euthanasia, a portion of kidney (2 cm2) from each raccoon was homogenized and used for leptospiral culture. Leptospiral cultures were subjected to DNA extraction and various polymerase chain reaction (PCR) procedures reported previously. Serum sample from each raccoon was collected and antibody titers to leptospiral serovars were determined by microscopic agglutination test (MAT). Results: All leptospiral cultures were positive for Leptospira by various PCR procedures. The PCR with the primers targeting the conservative region of LipL32 gene was the most sensitive PCR in the detection of pathogenic leptospires. The variable LipL32 PCR amplicons were sequenced and compared to the reference strains available in GenBank. Twelve kidney cultures had Leptospira interrogans, eight had Leptospira kirschneri and two had Leptospira borgpetersenii. They were predominantly Grippotyphosa serogroup. Antileptospire antibodies were detected in 16 out of 34 raccoons (47.1%) by MAT. There were titers ≥ 1:80 in 16 raccoons (47.1%) and titers ≥ 1:400 in 3 raccoons (8.8%). The highest leptospiral serovar-specific seroreactivity among 34 raccoons was L. interrogans Bratislava (38.2%) and L. interrogans Grippotyphosa (32.4%). Conclusions: Raccoons in Indiana carry leptospiral organisms in kidneys and the leptospires are predominantly L. interrogans species and of the Grippotyphosa serogroup. Clinical importance: The raccoons serve as reservoir hosts that exposure sources to wildlife, livestock, pets and humans.