Puma genomes from North and South America provide insights into the genomic consequences of inbreeding.

Pumas are the most widely distributed felid in the Western Hemisphere. Increasingly, however, human persecution and habitat loss are isolating puma populations. To explore the genomic consequences of this isolation, we assemble a draft puma genome and a geographically broad panel of resequenced individuals. We estimate that the lineage leading to present-day North American pumas diverged from South American lineages 300-100 thousand years ago. We find signatures of close inbreeding in geographically isolated North American populations, but also that tracts of homozygosity are rarely shared among these populations, suggesting that assisted gene flow would restore local genetic diversity. The genome of a Florida panther descended from translocated Central American individuals has long tracts of homozygosity despite recent outbreeding. This suggests that while translocations may introduce diversity, sustaining diversity in small and isolated populations will require either repeated translocations or restoration of landscape connectivity. Our approach provides a framework for genome-wide analyses that can be applied to the management of similarly small and isolated populations.

Noninvasive individual and species identification of jaguars (Panthera onca), pumas (Puma concolor) and ocelots (Leopardus pardalis) in Belize, Central America using cross-species microsatellites and faecal DNA.

There is a great need to develop efficient, noninvasive genetic sampling methods to study wild populations of multiple, co-occurring, threatened felids. This is especially important for molecular scatology studies occurring in challenging tropical environments where DNA degrades quickly and the quality of faecal samples varies greatly. We optimized 14 polymorphic microsatellite loci for jaguars (Panthera onca), pumas (Puma concolor) and ocelots (Leopardus pardalis) and assessed their utility for cross-species amplification. Additionally, we tested their reliability for species and individual identification using DNA from faeces of wild felids detected by a scat detector dog across Belize in Central America. All microsatellite loci were successfully amplified in the three target species, were polymorphic with average expected heterozygosities of HE = 0.60 ± 0.18 (SD) for jaguars, HE = 0.65 ± 0.21 (SD) for pumas and HE = 0.70 ± 0.13 (SD) for ocelots and had an overall PCR amplification success of 61%. We used this nuclear DNA primer set to successfully identify species and individuals from 49% of 1053 field-collected scat samples. This set of optimized microsatellite multiplexes represents a powerful tool for future efforts to conduct noninvasive studies on multiple, wild Neotropical felids.

Genetic restoration of the Florida panther.

The rediscovery of remnant Florida panthers (Puma concolor coryi) in southern Florida swamplands prompted a program to protect and stabilize the population. In 1995, conservation managers translocated eight female pumas (P. c. stanleyana) from Texas to increase depleted genetic diversity, improve population numbers, and reverse indications of inbreeding depression. We have assessed the demographic, population-genetic, and biomedical consequences of this restoration experiment and show that panther numbers increased threefold, genetic heterozygosity doubled, survival and fitness measures improved, and inbreeding correlates declined significantly. Although these results are encouraging, continued habitat loss, persistent inbreeding, infectious agents, and possible habitat saturation pose new dilemmas. This intensive management program illustrates the challenges of maintaining populations of large predators worldwide.

Development and testing of an optimized method for DNA-based identification of jaguar (Panthera onca) and puma (Puma concolor) faecal samples for use in ecological and genetic studies.

The elusive nature and endangered status of most carnivore species imply that efficient approaches for their non-invasive sampling are required to allow for genetic and ecological studies. Faecal samples are a major potential source of information, and reliable approaches are needed to foster their application in this field, particularly in areas where few studies have been conducted. A major obstacle to the reliable use of faecal samples is their uncertain species-level identification in the field, an issue that can be addressed with DNA-based assays. In this study we describe a sequence-based approach that efficiently distinguishes jaguar versus puma scats, and that presents several desirable properties: (1) considerably high amplification and sequencing rates; (2) multiple diagnostic sites reliably differentiating the two focal species; (3) high information content that allows for future application in other carnivores; (4) no evidence of amplification of prey DNA; and (5) no evidence of amplification of a nuclear mitochondrial DNA insertion known to occur in the jaguar. We demonstrate the reliability and usefulness of this approach by evaluating 55 field-collected samples from four locations in the highly fragmented Atlantic Forest biome of Brazil and Argentina, and document the presence of one or both of these endangered felids in each of these areas.

Identificación de individuos de jaguares (Panthera onca) y pumas (Puma concolor) a partir de morfometría de sus huellas (Carnivora: Felidae)

Identification of individual jaguars (Panthera onca) and pumas (Puma concolor) based on footprint morphometry (Carnivora: Felidae). Estimating feline abundance becomes particularly difficult, sometimes impossible, due to their elusive behavior and extensive space requirements. Available techniques are expensive and/or poorly efficient, therefore alternative methods are needed. The objective of this study was to assess the possibility of identifying individual jaguars and pumas based on morphometric analyses of their tracks. The footprints of five jaguars and four pumas were drawn and the foot (hind or fore foot, left or right foot) and the substrate were recorded. We took 16 measures from each footprint including lengths, widths, areas and angles. Variables were analyzed by using Principal Component Analysis (PCA) and substituted by the first Principal Component (PC) (> 70 % variance). We assessed the effect of the substrate and type of foot by means of paired t-student tests, and found differences between fore and hind feet and footprints from the same individual when made on soil or sand. No differences were found between right or left feet. The footprints changed over time as revealed by Multiple ANOVA. Different individuals could be identifyied based on discriminant analyses with more than 70 % confidence. We conclude that this method is feasible and can be useful when studying endangered felines. Rev. Biol. Trop. 56 (4): 1893-1904. Epub 2008 December 12.

Estimar la abundancia de felinos resulta particular-mente difícil o, incluso imposible, debido a su comportamiento críptico y sus amplios requerimiento espaciales. Las técnicas disponibles para estimar abundancia son costosas y poco eficientes, por lo que es necesario proponer métodos alternativos. El objetivo de este trabajo fue evaluar la capacidad de identificación de individuos utilizando el análisis morfométrico de huellas en yaguares y pumas. Para ello, se dibujaron huellas de cinco yaguares y cuatro pumas, registrándose el tipo de pata que dio origen a la huella y el sustrato. Para cada huella se tomaron 16 mediciones morfológicas de ángulos, largos, anchos y áreas. Las variables de largos, anchos y áreas fueron analizadas con un Análisis de Componentes Principales (ACP) y sustituidas por el primer componente principal (más del 70 % de la varianza en todos los casos). Se evaluó el efecto del sustrato y del tipo de pata a partir de pruebas t-pareadas, encontrándose diferencias entre huellas del mismo individuo dibujadas a partir de arena o tierra (t-pareadas p < 0.05), así como diferencias en todas las variables para patas delanteras y traseras (t-pareadas p < 0.05 en todos los casos). No se encontraron diferencias entre patas izquierdas o derechas. El efecto de la edad de la huella se estudió con Análisis Múltiples de Varianza, en los que se revelaron diferencias en las variables con respecto a la edad de la huella. Se realizaron análisis discriminantes por especies, sustrato de la huella y tipo de pata, para determinar la capacidad del método de discriminar entre individuos. Se obtuvo una adecuada separación de los individuos con más del 70 % de confianza. Se concluye que este método es factible y puede ser de gran utilidad especialmente en el caso de felinos amenazados.

[Identification of individual jaguars (Panthera onca) and pumas (Puma concolor) based on footprint morphometry (Carnivora: Felidae)]. / Identificación de individuos de jaguares (Panthera onca) y pumas (Puma concolor) a partir de morfometría de sus huellas (Carnivora: Felidae).

Estimating feline abundance becomes particularly difficult, sometimes impossible, due to their elusive behavior and extensive space requirements. Available techniques are expensive and/or poorly efficient, therefore alternative methods are needed. The objective of this study was to assess the possibility of identifying individual jaguars and pumas based on morphometric analyses of their tracks. The footprints of five jaguars and four pumas were drawn and the foot (hind or fore foot, left or right foot) and the substrate were recorded. We took 16 measures from each footprint including lengths, widths, areas and angles. Variables were analyzed by using Principal Component Analysis (PCA) and substituted by the first Principal Component (PC) (> 70% variance). We assessed the effect of the substrate and type of foot by means of paired t-student tests, and found differences between fore and hind feet and footprints from the same individual when made on soil or sand. No differences were found between right or left feet. The footprints changed over time as revealed by Multiple ANOVA. Different individuals could be identifyied based on discriminant analyses with more than 70% confidence. We conclude that this method is feasible and can be useful when studying endangered felines.

Conflitos causados pela predação de rebanhos domésticos por grandes felinos em comunidades quilombolas na Mata Atlântica / Conflicts caused by predation on domestic livestock by large cats in quilombola communities in the Atlantic Forest

A predação de rebanhos domésticos por onças-pintadas (Panthera onca) e onças-pardas (Puma concolor) foi quantificada de 1998 a 2000 e a opinião local para resolver o conflito foi investigada em duas comunidades quilombolas na Mata Atlântica. Os responsáveis pelas propriedades foram entrevistados regularmente de maio de 2000 a janeiro de 2001. A predação foi dependente do número de animais domésticos nas propriedades, foi aparentemente seletiva e possivelmente sazonal. O prejuízo econômico foi alto quando associado com o baixo número de criações. A população expressou uma visão bastante negativa frente à presença de onças e a maior parte (54 por cento) sugeriu o extermínio desses animais. Conhecer a percepção local é fundamental para adotar um planejamento participativo que reduza as perdas dos proprietários e garanta a conservação dos grandes felinos.

Domestic livestock predation by jaguars (Panthera onca) and pumas (Puma concolor) was recorded from 1998 to 2000 and local opinion to solve the conflict was investigated in two quilombola communities in the Atlantic Forest. The householders were interviewed regularly from May 2000 to January 2001. Predation depended on the number of domestic animals per household, and was apparently selective and possibly seasonal. The economic damage was high when associated with the low livestock number. People's attitude towards predators was negative and most of those surveyed (54 percent) suggested these animals should be eliminated. Knowing the local perception is essential to adopt a participative management to reduce household losses and to guarantee large cats' conservation.

The late Miocene radiation of modern Felidae: a genetic assessment.

Modern felid species descend from relatively recent (<11 million years ago) divergence and speciation events that produced successful predatory carnivores worldwide but that have confounded taxonomic classifications. A highly resolved molecular phylogeny with divergence dates for all living cat species, derived from autosomal, X-linked, Y-linked, and mitochondrial gene segments (22,789 base pairs) and 16 fossil calibrations define eight principal lineages produced through at least 10 intercontinental migrations facilitated by sea-level fluctuations. A ghost lineage analysis indicates that available felid fossils underestimate (i.e., unrepresented basal branch length) first occurrence by an average of 76%, revealing a low representation of felid lineages in paleontological remains. The phylogenetic performance of distinct gene classes showed that Y-chromosome segments are appreciably more informative than mitochondrial DNA, X-linked, or autosomal genes in resolving the rapid Felidae species radiation.