Science · 2019 · 94 citations · 54 references
Life SciencesBiologyEvolutionary BiologyComparative GenomicsMammalogyPhylogeneticsEvolutionary RelationshipsMammalian EvolutionPhylogenetic AnalysisPhylogenetic Comparative MethodsPhylogenetic Sequence AnalysisPhylogenetic Tree ReconstructionAnimal PhylogenyAntler EvolutionIncomplete Lineage SortingIncomplete Lineage Sorting AnalysisMammalian OriginsMammalian Phylogenetic AnalysisPhylogenetic Tree InferenceReductions
Phylogeny and characteristics of ruminants Ruminants are a diverse group of mammals that includes families containing well-known taxa such as deer, cows, and goats. However, their evolutionary relationships have been contentious, as have the origins of their distinctive digestive systems and headgear, including antlers and horns (see the Perspective by Ker and Yang). To understand the relationships among ruminants, L. Chen et al. sequenced 44 species representing 6 families and performed a phylogenetic analysis. From this analysis, they were able to resolve the phylogeny of many genera and document incomplete lineage sorting among major clades. Interestingly, they found evidence for large population reductions among many taxa starting at approximately 100,000 years ago, coinciding with the migration of humans out of Africa. Examining the bony appendages on the head—the so-called headgear—Wang et al. describe specific evolutionary changes in the ruminants and identify selection on cancer-related genes that may function in antler development in deer. Finally, Lin et al. take a close look at the reindeer genome and identify the genetic basis of adaptations that allow reindeer to survive in the harsh conditions of the Arctic. Science , this issue p. eaav6202 , p. eaav6335 , p. eaav6312 ; see also p. 1130
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The Sequence Alignment/Map format and SAMtools
Heng Li, Alec Wysoker, Tim Fennell et al. · Bioinformatics · 2009 · 67.5K citations · Full text
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li, Richard Durbin · Bioinformatics · 2009 · 62.8K citations · Full text
KEGG: Kyoto Encyclopedia of Genes and Genomes
Hiroyuki Ogata, Susumu Goto, Kazushige Sato et al. · Nucleic Acids Research · 1999 · 32.4K citations · Full text