Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Evolution of Protein Molecules

http://webpages.icav.up.pt/PTDC/BIA-BEC/099934/2008/papers/Frankham_2005_Biological_Conservation.pdf

Genetics and extinction

The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.

/pdf/genome-sequence-of-the-brown-norway-rat-yields-insights-into-51an5rofp3.pdf

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

Mash extends the MinHash dimensionality-reduction technique to include a pairwise mutation distance and P value significance test, enabling the efficient clustering and search of massive sequence collections. Mash reduces large sequences and sequence sets to small, representative sketches, from which global mutation distances can be rapidly estimated. We demonstrate several use cases, including the clustering of all 54,118 NCBI RefSeq genomes in 33 CPU h; real-time database search using assembled or unassembled Illumina, Pacific Biosciences, and Oxford Nanopore data; and the scalable clustering of hundreds of metagenomic samples by composition. Mash is freely released under a BSD license (
 https://github.com/marbl/mash
 ).

/pdf/mash-fast-genome-and-metagenome-distance-estimation-using-3b84vfnedh.pdf

Mash: fast genome and metagenome distance estimation using MinHash.

9th International Feline Retrovirus Research Symposium 2008. Preface.

Mountain lions (Puma concolor) throughout North and South America are infected with puma lentivirus clade B (PLVB). A second, highly divergent lentiviral clade, PLVA, infects mountain lions in southern California and Florida. Bobcats (Lynx rufus) in these two geographic regions are also infected with PLVA, and to date, this is the only strain of lentivirus identified in bobcats. We sequenced full-length PLV genomes in order to characterize the molecular evolution of PLV in bobcats and mountain lions. Low sequence homology (88% average pairwise identity) and frequent recombination (1 recombination breakpoint per 3 isolates analyzed) were observed in both clades. Viral proteins have markedly different patterns of evolution; sequence homology and negative selection were highest in Gag and Pol and lowest in Vif and Env. A total of 1.7% of sites across the PLV genome evolve under positive selection, indicating that host-imposed selection pressure is an important force shaping PLV evolution. PLVA strains are highly spatially structured, reflecting the population dynamics of their primary host, the bobcat. In contrast, the phylogeography of PLVB reflects the highly mobile mountain lion, with diverse PLVB isolates cocirculating in some areas and genetically related viruses being present in populations separated by thousands of kilometers. We conclude that PLVA and PLVB are two different viral species with distinct feline hosts and evolutionary histories.

concolor) in North America (Lynx rufus) and Mountain Lions (Puma Evolution of Puma Lentivirus in Bobcats

/pdf/evolution-of-puma-lentivirus-in-bobcats-lynx-rufus-and-187r2vh7iw.pdf

Evolution of Puma Lentivirus in Bobcats ( Lynx rufus ) and MountainLions ( Puma concolor ) in North America

We isolated and sequenced two complete endogenous feline leukemia viruses (enFeLVs), designated enFeLV-AGTT and enFeLV-GGAG. In enFeLV-AGTT, the open reading frames are reminiscent of a functioning FeLVgenome, and the 5 and 3 long terminal repeat sequences are identical. Neither endogenous provirus isgenetically ﬁxed in cats but polymorphic, with 8.9 and 15.2% prevalence for enFeLV-AGTT and enFeLV-GGAG,respectively, among a survey of domestic cats. Neither provirus was found in the genomes of related species ofthe

Jill Pecon-Slattery

Papers

9th International Feline Retrovirus Research Symposium 2008. Preface.

concolor) in North America (Lynx rufus) and Mountain Lions (Puma Evolution of Puma Lentivirus in Bobcats

Evolution of Puma Lentivirus in Bobcats ( Lynx rufus ) and MountainLions ( Puma concolor ) in North America

Leukemia Viruses of Recent Origin Genomically Intact Endogenous Feline