Showing papers by "William J. Murphy published in 2011"

Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification

Abstract: Previous analyses of relations, divergence times, and diversification patterns among extant mammalian families have relied on supertree methods and local molecular clocks. We constructed a molecular supermatrix for mammalian families and analyzed these data with likelihood-based methods and relaxed molecular clocks. Phylogenetic analyses resulted in a robust phylogeny with better resolution than phylogenies from supertree methods. Relaxed clock analyses support the long-fuse model of diversification and highlight the importance of including multiple fossil calibrations that are spread across the tree. Molecular time trees and diversification analyses suggest important roles for the Cretaceous Terrestrial Revolution and Cretaceous-Paleogene (KPg) mass extinction in opening up ecospace that promoted interordinal and intraordinal diversification, respectively. By contrast, diversification analyses provide no support for the hypothesis concerning the delayed rise of present-day mammals during the Eocene Period.

Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens

Abstract: The advent of next-generation sequencing technologies (NGSTs) has transformed the way in which scientists approach a myriad of biological questions (Hawkins et al. 2010). Even with NGSTs' growing familiarity and broad range of applications such as ChIP-seq, RNA-seq, and genome-wide association studies, NGSTs still have the potential to influence the field of population genetics and phylogenetics with new methods to obtain genomic sequences of rare, difficult to sample, or extinct species (Millar et al. 2008). The ability to uncover the phylogenetic history of recently extinct species has rapidly improved due to the reduced cost and increased sequence capacity of NGSTs (Gilbert et al. 2007, 2008; Miller et al. 2008, 2009); however, obstacles do remain. The difficulties with applying NGSTs to phylogenetic problems do not lie with the sequencing technology itself, but with the preparative procedures for isolation and sequencing of large, orthologous DNA regions across multiple divergent species (Summerer 2009). This problem is exacerbated for museum specimens, where DNA quality varies greatly between samples and contamination levels are often high (Millar et al. 2008). Generation of whole genome sequences for museum specimens, or even complete mitochondrial DNA (mtDNA) genome sequences, is not cost-effective for most laboratories due to the large amount of sequencing required for adequate genome coverage of a single individual. Capture hybridization methods are routinely used for genomic-scale enrichments of modern target DNA from the same species (Summerer 2009; Mamanova et al. 2010) and also for recovery of DNA from museum or fossil specimens by largely removing contaminants from the final product (Krause et al. 2010). However, capture hybridization techniques have not been applied to assembling phylogenetic data sets across divergent sets of taxa (e.g., millions of years of genetic divergence), largely due to lack of appropriate probes and lack of exploration of hybridization conditions to allow for heterologous sequence capture. Enrichment for target sequences by PCR (which has been the standard for most previous museum DNA studies) requires closely related reference sequences and painstaking efforts to design many oligonucleotide primers to amplify very short regions of the DNA of interest. Capture hybridization and sequencing of targeted loci from museum specimens promises to be a more flexible, cost-effective, and efficient approach than other enrichment procedures for degraded samples. Here we describe the application of capture hybridization and selection techniques to recover mitochondrial DNA from 13 Sunda colugo (Galeopterus variegatus) museum specimens of varying ages (47–170 yr old) that represent major geographical locations throughout the Southeast Asian mainland and archipelago (Supplemental Fig. S1; Table 1). Colugos are arboreal mammals that are widely distributed throughout Southeast Asia and have the most extensive gliding membrane (patagium) of any known mammal. This allows them to glide for very large distances, the longest recorded being 136 m (Lim 2007). Colugos are rarely kept in captivity and are elusive in the wild (Lim 2007), factors that have obscured their evolutionary history for decades. Under current taxonomy, colugos comprise a unique mammalian order (Dermoptera) and are classified as two species: the Sunda colugo (Galeopterus variegatus) and the Philippine colugo (Cynocephalus volans) (Wilson and Reeder 2005). However, recent mtDNA and nuclear DNA data provide compelling evidence that the geographically widespread Sunda colugo in fact represents multiple species distributed throughout Southeast Asia (Janecka et al. 2008) and suggest that further genetic sampling may identify many additional divergent populations and/or species. Because of the extreme difficulty obtaining fresh tissue or DNA samples from colugos, we further explored this question using collections of museum specimens and devised a comprehensive method for capture, selection, and recovery of divergent mtDNA fragments using NGST. Table 1. USNM Sunda colugo specimens

The historical biogeography of Mammalia

Abstract: Palaeobiogeographic reconstructions are underpinned by phylogenies, divergence times and ancestral area reconstructions, which together yield ancestral area chronograms that provide a basis for proposing and testing hypotheses of dispersal and vicariance. Methods for area coding include multi-state coding with a single character, binary coding with multiple characters and string coding. Ancestral reconstruction methods are divided into parsimony versus Bayesian/likelihood approaches. We compared nine methods for reconstructing ancestral areas for placental mammals. Ambiguous reconstructions were a problem for all methods. Important differences resulted from coding areas based on the geographical ranges of extant species versus the geographical provenance of the oldest fossil for each lineage. Africa and South America were reconstructed as the ancestral areas for Afrotheria and Xenarthra, respectively. Most methods reconstructed Eurasia as the ancestral area for Boreoeutheria, Euarchontoglires and Laurasiatheria. The coincidence of molecular dates for the separation of Afrotheria and Xenarthra at approximately 100 Ma with the plate tectonic sundering of Africa and South America hints at the importance of vicariance in the early history of Placentalia. Dispersal has also been important including the origins of Madagascar's endemic mammal fauna. Further studies will benefit from increased taxon sampling and the application of new ancestral area reconstruction methods.

Comparison of noninvasive genetic and camera-trapping techniques for surveying snow leopards

Abstract: The endangered snow leopard (Panthera uncia) is widely but sparsely distributed throughout the mountainous regions of central Asia. Detailed information on the status and abundance of the snow leopard is limited because of the logistical challenges faced when working in the rugged terrain it occupies, along with its secretive nature. Camera-trapping and noninvasive genetic techniques have been used successfully to survey this felid. We compared noninvasive genetic and camera-trapping snow leopard surveys in the Gobi Desert of Mongolia. We collected 180 putative snow leopard scats from 3 sites during an 8-day period along 37.74 km of transects. We then conducted a 65-day photographic survey at 1 of these sites, approximately 2 months after scat collection. In the site where both techniques were used noninvasive genetics detected 5 individuals in only 2 days of fieldwork compared to 7 individuals observed in the 65-day camera-trapping session. Estimates of population size from noninvasive genetics ranged be...

A gene catalogue of the euchromatic male-specific region of the horse Y chromosome: comparison with human and other mammals.

Abstract: Studies of the Y chromosome in primates, rodents and carnivores provide compelling evidence that the male specific region of Y (MSY) contains functional genes, many of which have specialized roles in spermatogenesis and male-fertility. Little similarity, however, has been found between the gene content and sequence of MSY in different species. This hinders the discovery of species-specific male fertility genes and limits our understanding about MSY evolution in mammals. Here, a detailed MSY gene catalogue was developed for the horse – an odd-toed ungulate. Using direct cDNA selection from horse testis, and sequence analysis of Y-specific BAC clones, 37 horse MSY genes/transcripts were identified. The genes were mapped to the MSY BAC contig map, characterized for copy number, analyzed for transcriptional profiles by RT-PCR, examined for the presence of ORFs, and compared to other mammalian orthologs. We demonstrate that the horse MSY harbors 20 X-degenerate genes with known orthologs in other eutherian species. The remaining 17 genes are acquired or novel and have so far been identified only in the horse or donkey Y chromosomes. Notably, 3 transcripts were found in the heterochromatic part of the Y. We show that despite substantial differences between the sequence, gene content and organization of horse and other mammalian Y chromosomes, the functions of MSY genes are predominantly related to testis and spermatogenesis. Altogether, 10 multicopy genes with testis-specific expression were identified in the horse MSY, and considered likely candidate genes for stallion fertility. The findings establish an important foundation for the study of Y-linked genetic factors governing fertility in stallions, and improve our knowledge about the evolutionary processes that have shaped Y chromosomes in different mammalian lineages.

Reduced genetic diversity and isolation of remnant ocelot populations occupying a severely fragmented landscape in southern Texas

Abstract: The ocelot Leopardus pardalis has become a conservation priority in the US as a result of severe population decline and loss of habitat during the 20th century. Only two small populations remain in this country. Their short-term viability is threatened by the disappearance of dense thornshrub communities, human-caused mortality and demographic stochasticity. The influence these factors have on ocelot persistence must be considered to develop effective conservation initiatives. We therefore examined neutral genetic diversity and connectivity among ocelots in the US and northeastern Mexico using 25 autosomal microsatellites and a 395-bp segment of the mitochondrial control region. Genetic variation was lowest in the population occurring on Laguna Atascosa National Wildlife Refuge, Texas (autosomal microsatellite HE = 0.399 and mtDNA-haplotype diversity = 0) and highest in northeastern Mexico (0.637 and 0.73, respectively), while intermediate on private lands in Willacy County, Texas (0.553 and 0.252, respectively). Significant genetic differentiation between the two Texas populations was observed, despite their close proximity (� 30 km). Both populations were also significantly divergent from northeastern Mexico. The absence of any detectable gene flow implies that the human modified landscape of the Lower Rio Grande Valley in southern Texas acts as a strong barrier to ocelot movement, disrupting metapopulation dynamics and contributing to loss of diversity. As a consequence, continued genetic erosion among the Texas populations is expected. The lack of movement through the fragmented landscape also suggests it is unlikely ocelots will recolonize unoccupied habitat patches along the Lower Rio Grande and the delta interior where agriculture and urban land uses predominate. The continued rapid development will exacerbate this problem. These factors threaten the persistence of the Texas populations and limit their recovery. Translocations are necessary to link ocelot populations in the US.

Accelerated Evolution of CES7, a Gene Encoding a Novel Major Urinary Protein in the Cat Family

Abstract: Cauxin is a novel urinary protein recently identified in the domestic cat that regulates the excretion of felinine, a pheromone precursor involved in sociochemical communication and territorial marking of domestic and wild felids. Understanding the evolutionary history of cauxin may therefore illuminate molecular adaptations involved in the evolution of pheromone-based communication, recognition, and mate selection in wild animals. We sequenced the gene encoding cauxin, CES7, in 22 species representing all major felid lineages, and multiple outgroups and showed that it has undergone rapid evolutionary change preceding and during the diversification of the cat family. A comparison between feline cauxin and orthologous carboxylesterases from other mammalian lineages revealed evidence of strong positive Darwinian selection within and between several cat lineages, enriched at functionally important sites of the protein. The higher rate of radical amino acid replacements in small felids, coupled with the lack of felinine and extremely low levels of cauxin in the urine of the great cats (Panthera), correlates with functional divergence of this gene in Panthera, and its putative loss in the snow leopard. Expression studies found evidence for several alternatively spliced transcripts in testis and brain, suggesting additional roles in male reproductive fitness and behavior. Our work presents the first report of strong positive natural selection acting on a major urinary protein of nonrodent mammals, providing evidence for parallel selection pressure on the regulation of pheromones in different mammalian lineages, despite the use of different metabolic pathways. Our results imply that natural selection may drive rapid changes in the regulation of pheromones in urine among the different cat species, which in turn may influence social behavior, such as territorial marking and conspecific recognition, therefore serving as an important mechanism for the radiation of this group of mammals.