Melody E. Roelke

A Molecular Phylogeny of Living Primates

Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (∼8 Mb) from 186 primates representing 61 (∼90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species.

The Consequences of Demographic Reduction and Genetic Depletion in the Endangered Florida Panther

The Florida panther has recently suffered severe range and demographic contraction, leaving a remarkably low level of genetic diversity. This exerts a severe fitness cost, manifested by spermatozoal defects, cryptorchidism, cardiac abnormalities and infectious diseases that threaten the survival of the subspecies.

Genetic Restoration of the Florida Panther

Return of the Florida Panther The Florida panther is an endangered lineage that has been the target of extensive human management to maintain genetic diversity within a small population. Now, Johnson et al. (p. 1641; see the Perspective by Packer) provide comprehensive genetic and demographic analyses of a project to rescue the Florida panther from inbreeding, low genetic diversity, inbreeding depression, and demographic stochasticity by outcrossing it to Texas pumas. The genetics and reproductive fitness traits of different panther populations and their crosses reveal the benefits of outcrossing on survival, genetic diversity, male reproductive characteristics, and population demography. Recovery of the Florida panther population is attributed to the benefits of admixture with panthers from Texas. 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.

Climate extremes promote fatal co-infections during canine distemper epidemics in African lions.

Extreme climatic conditions may alter historic host-pathogen relationships and synchronize the temporal and spatial convergence of multiple infectious agents, triggering epidemics with far greater mortality than those due to single pathogens. Here we present the first data to clearly illustrate how climate extremes can promote a complex interplay between epidemic and endemic pathogens that are normally tolerated in isolation, but with co-infection, result in catastrophic mortality. A 1994 canine distemper virus (CDV) epidemic in Serengeti lions (Panthera leo) coincided with the death of a third of the population, and a second high-mortality CDV epidemic struck the nearby Ngorongoro Crater lion population in 2001. The extent of adult mortalities was unusual for CDV and prompted an investigation into contributing factors. Serological analyses indicated that at least five “silent” CDV epidemics swept through the same two lion populations between 1976 and 2006 without clinical signs or measurable mortality, indicating that CDV was not necessarily fatal. Clinical and pathology findings suggested that hemoparsitism was a major contributing factor during fatal epidemics. Using quantitative real-time PCR, we measured the magnitude of hemoparasite infections in these populations over 22 years and demonstrated significantly higher levels of Babesia during the 1994 and 2001 epidemics. Babesia levels correlated with mortalities and extent of CDV exposure within prides. The common event preceding the two high mortality CDV outbreaks was extreme drought conditions with wide-spread herbivore die-offs, most notably of Cape buffalo (Syncerus caffer). As a consequence of high tick numbers after the resumption of rains and heavy tick infestations of starving buffalo, the lions were infected by unusually high numbers of Babesia, infections that were magnified by the immunosuppressive effects of coincident CDV, leading to unprecedented mortality. Such mass mortality events may become increasingly common if climate extremes disrupt historic stable relationships between co-existing pathogens and their susceptible hosts.

Ancient papillomavirus-host co-speciation in Felidae.

BackgroundEstimating evolutionary rates for slowly evolving viruses such as papillomaviruses (PVs) is not possible using fossil calibrations directly or sequences sampled over a time-scale of decades. An ability to correlate their divergence with a host species, however, can provide a means to estimate evolutionary rates for these viruses accurately. To determine whether such an approach is feasible, we sequenced complete feline PV genomes, previously available only for the domestic cat (Felis domesticus, FdPV1), from four additional, globally distributed feline species: Lynx rufus PV type 1, Puma concolor PV type 1, Panthera leo persica PV type 1, and Uncia uncia PV type 1.ResultsThe feline PVs all belong to the Lambdapapillomavirus genus, and contain an unusual second noncoding region between the early and late protein region, which is only present in members of this genus. Our maximum likelihood and Bayesian phylogenetic analyses demonstrate that the evolutionary relationships between feline PVs perfectly mirror those of their feline hosts, despite a complex and dynamic phylogeographic history. By applying host species divergence times, we provide the first precise estimates for the rate of evolution for each PV gene, with an overall evolutionary rate of 1.95 × 10-8 (95% confidence interval 1.32 × 10-8 to 2.47 × 10-8) nucleotide substitutions per site per year for the viral coding genome.ConclusionOur work provides evidence for long-term virus-host co-speciation of feline PVs, indicating that viral diversity in slowly evolving viruses can be used to investigate host species evolution. These findings, however, should not be extrapolated to other viral lineages without prior confirmation of virus-host co-divergence.

SEROPREVALENCE OF INFECTIOUS DISEASE AGENTS IN FREE-RANGING FLORIDA PANTHERS (FELIS CONCOLOR CORYI)

Serum samples obtained from 38 free-ranging Florida panthers (Felis concolor coryi) in southern Florida, March 1978 through February 1991, were tested for antibodies against eight bacterial, parasitic, and viral disease agents. Sera were positive for antibodies against feline panleukopenia virus (FPV) (78%), feline calicivirus (56%), feline immunodeficiency virus/puma lentivirus (37%), feline enteric coronavirus/feline infectious peritonitis virus (19%), and Toxoplasma gondii (9%). All samples were seronegative for Brucella spp., feline rhinotracheitis virus, and pseudorabies virus. In addition, all the animals tested were negative for feline leukemia virus p27 antigen as determined by enzyme-linked immunosorbent assay. Feline panleukopenia virus was considered to be a potentially significant disease agent; FPV antibodies occurred in the highest prevalences in older age classes (P = 0.027) and in panthers living in the dense mixed hardwood swamps in the western portion of their range compared to the open cypress and sawgrass prairies to the east (P = 0.096). Because <50 animals remain in this relict population and the probable resultant depression of genetic diversity and lowered disease resistance, FPV or other disease agents could contribute to the extinction of this endangered subspecies.

REPRODUCTIVE CHARACTERISTICS OF MALE FLORIDA PANTHERS: COMPARATIVE STUDIES FROM FLORIDA, TEXAS, COLORADO, LATIN AMERICA, AND NORTH AMERICAN ZOOS

Testicular volume, semen traits, and pituitary-gonadal hormones were measured in populations of Felis concolor from Florida, Texas, Colorado, Latin America, and North American zoos. More Florida panthers ( F. concolor coryi ) were unilaterally cryptorchid (one testicle not descended into the scrotum) than other populations (43.8 versus 3.9%, respectively). Florida panthers also had lower testicular and semen volumes, poorer sperm progressive motility, and more morphologically abnormal sperm, including a higher incidence of acrosomal defects and abnormal mitochondrial sheaths. Transmission electron microscopy revealed discontinuities in the acrosome, extraneous acrosomal material under the plasma membrane, and remnants of the golgi complex under the acrosome. No differences were detected in mean-circulating follicle-stimulating hormone, luteinizing hormone, or testosterone between Florida panthers and other populations of mountain lions. Seminal traits and concentrations of follicle-stimulating hormone, luteinizing hormone, and testosterone were similar between cryptorchid and noncryptorchid Florida panthers. Animals with F. concolor coryi ancestry were categorized on the basis of amount of genetic variation (low = type A; medium = type B; high = captive Piper stock). Compared to counterparts, type A Florida panthers had the lowest testicular volume and sperm-motility ratings and were the only animals exhibiting unilateral cryptorchidism. These results demonstrate the existence of major morphological and physiological differences among populations of F. concolor , a finding potentially related to differences in genetic diversity.

Molecular evidence for species-level distinctions in clouded leopards.

Among the 37 living species of Felidae, the clouded leopard (Neofelis nebulosa) is generally classified as a monotypic genus basal to the Panthera lineage of great cats. This secretive, mid-sized (16-23 kg) carnivore, now severely endangered, is traditionally subdivided into four southeast Asian subspecies (Figure 1A). We used molecular genetic methods to re-evaluate subspecies partitions and to quantify patterns of population genetic variation among 109 clouded leopards of known geographic origin (Figure 1A, Tables S1 ans S2 in the Supplemental Data available online). We found strong phylogeographic monophyly and large genetic distances between N. n. nebulosa (mainland) and N. n. diardi (Borneo; n = 3 individuals) with mtDNA (771 bp), nuclear DNA (3100 bp), and 51 microsatellite loci. Thirty-six fixed mitochondrial and nuclear nucleotide differences and 20 microsatellite loci with nonoverlapping allele-size ranges distinguished N. n. nebulosa from N. n. diardi. Along with fixed subspecies-specific chromosomal differences, this degree of differentiation is equivalent to, or greater than, comparable measures among five recognized Panthera species (lion, tiger, leopard, jaguar, and snow leopard). These distinctions increase the urgency of clouded leopard conservation efforts, and if affirmed by morphological analysis and wider sampling of N. n. diardi in Borneo and Sumatra, would support reclassification of N. n. diardi as a new species (Neofelis diardi).

Genetics and Pathogenesis of Feline Infectious Peritonitis Virus

Coronavirus sequence analyses demonstrate distinctive circulating strains in natural populations.

A homozygous single-base deletion in MLPH causes the dilute coat color phenotype in the domestic cat

Three proteins have been described in humans and mice as being essential for even distribution, transport, and translocation of pigment granules, with defects in these molecules giving rise to lighter skin/coat color. The dilute phenotype in domestic cats affects both eumelanin and phaeomelanin pigment pathways; for example, black pigmentation combined with dilute appears gray and orange pigments appear cream. The dilute pigmentation segregates as a fully penetrant, autosomal recessive trait. We conducted classical linkage mapping with microsatellites in a large multigeneration pedigree of domestic cats and detected tight linkage for dilute on cat chromosome C1 (theta=0.08, LOD=10.81). Fine-mapping identified a genomic region exhibiting conserved synteny to human chromosome 2, which included one of the three dilute candidate genes, melanophilin (MLPH). Sequence analysis in dilute cats identified a single base pair deletion in exon 2 of MLPH transcripts that introduces a stop codon 11 amino acids downstream, resulting in the truncation of the bulk of the MLPH protein. The occurrence of this homozygous variant in 97 unrelated dilute cats representing 26 cat breeds and random-bred cats, along with 89 unrelated wild-type cats representing 29 breeds and random-bred cats, supports the finding that dilute is caused by this single mutation in MLPH (p<0.00001). Single-nucleotide polymorphism analyses in dilute individuals identified a single haplotype in dilute cats, suggesting that a single mutation event in MLPH gave rise to dilute in domestic cats.