A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms

Since the completion of the human genome project, the diversity of genome sequencing data produced for non-human primates has increased exponentially. Papio baboons are well-established biological models for studying human biology and evolution. Despite substantial interest in the evolution of Papio, the systematics of these species has been widely debated, and the evolutionary history of Papio diversity is not fully understood. Alu elements are primate-specific transposable elements with a well-documented mutation/insertion mechanism and the capacity for resolving controversial phylogenetic relationships. In this study, we conducted a whole genome analysis of Alu insertion polymorphisms unique to the Papio lineage. To complete these analyses, we created a computational algorithm to identify novel Alu insertions in next-generation sequencing data. We identified 187,379 Alu insertions present in the Papio lineage, yet absent from M. mulatta [Mmul8.0.1]. These elements were characterized using genomic data sequenced from a panel of twelve Papio baboons: two from each of the six extant Papio species. These data were used to construct a whole genome Alu-based phylogeny of Papio baboons. The resulting cladogram fully-resolved relationships within Papio. These data represent the most comprehensive Alu-based phylogenetic reconstruction reported to date. In addition, this study produces the first fully resolved Alu-based phylogeny of Papio baboons.

• Publication year

  2018

• Venue

  Mobile DNA

• Publication date

  2018-04-05

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1186/s13100-018-0118-3PMID 29632618PMCID 5885306
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Primate taxonomy

  2018cited by this paper
• Alu Insertion Polymorphisms as Evidence for Population Structure in Baboons

  2017cited by this paper
• Database resources of the National Center for Biotechnology Information

  2017cited by this paper
• Rethinking the dispersal of Homo sapiens out of Africa

  2015cited by this paper
• Evidence for archaic adaptive introgression in humans

  2015cited by this paper
• Database resources of the National Center for Biotechnology Information

  2014cited by this paper
• Out of Africa, but how and when? The case of hamadryas baboons (Papio hamadryas).

  2014cited by this paper
• The landscape of Neandertal ancestry in present-day humans

  2014cited by this paper
• Why primate models matter

  2014cited by this paper
• Baboon phylogeny as inferred from complete mitochondrial genomes

  2013influential reference
• Baboons as a model to study genetics and epigenetics of human disease.

  2013cited by this paper
• Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM

  2013cited by this paper
• Fast gapped-read alignment with Bowtie 2

  2012influential reference
• An Alu-Based Phylogeny of Lemurs (Infraorder: Lemuriformes)

  2012cited by this paper
• An Alu-based phylogeny of gibbons (hylobatidae).

  2012cited by this paper
• Insights into hominid evolution from the gorilla genome sequence

  2012influential reference
• Kinda baboons (Papio kindae) and grayfoot chacma baboons (P. ursinus griseipes) hybridize in the Kafue river valley, Zambia

  2011cited by this paper
• Comparative and demographic analysis of orang-utan genomes

  2011cited by this paper
• The Sequence Read Archive

  2010cited by this paper
• LINEs and SINEs of primate evolution

  2010cited by this paper
• The Baboon in Biomedical Research

  2009cited by this paper
• Mitochondrial phylogeography of baboons (Papio spp.) – Indication for introgressive hybridization?

  2009cited by this paper
• Diverse cis factors controlling Alu retrotransposition: what causes Alu elements to die?

  2009cited by this paper
• Behavioral variation and reproductive success of male baboons (Papio anubis × Papio hamadryas) in a hybrid social group

  2008cited by this paper
• Evolution of Human Retrosequences: Alu

  2008cited by this paper
• Baboons

  2008cited by this paper
• Active Alu retrotransposons in the human genome.

  2008cited by this paper
• Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

  2007cited by this paper
• A mobile element-based evolutionary history of guenons (tribe Cercopithecini)

  2007cited by this paper
• SINEs of a nearly perfect character.

  2006cited by this paper
• Initial sequence of the chimpanzee genome and comparison with the human genome

  2005cited by this paper
• A mobile element based phylogeny of Old World monkeys.

  2005cited by this paper
• Demand for Nonhuman Primate Resources in the Age of Biodefense

  2005cited by this paper
• Mitochondrial evidence for the origin of hamadryas baboons.

  2004cited by this paper
• Crossing the Red Sea: phylogeography of the hamadryas baboon, Papio hamadryas hamadryas

  2004cited by this paper
• Genetic variation of recent Alu insertions in human populations

  2004cited by this paper
• Database resources of the National Center for Biotechnology Information: update

  2004cited by this paper
• LINE-mediated retrotransposition of marked Alu sequences

  2003cited by this paper
• Genetic variation among world populations: inferences from 100 Alu insertion polymorphisms.

  2003cited by this paper
• Alu elements and hominid phylogenetics

  2003cited by this paper
• Alu repeats and human genomic diversity

  2002influential reference
• PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4.0b10

  2002cited by this paper
• Human L1 element target‐primed reverse transcription in vitro

  2002cited by this paper
• Animal experiments: The great primate debate

  2002cited by this paper
• Mammalian retroelements.

  2002cited by this paper
• Sodium-lithium countertransport activity is linked to chromosome 5 in baboons.

  2001cited by this paper
• Immigration and hybridization patterns of yellow and anubis baboons in and around Amboseli, Kenya

  2001cited by this paper
• A proper study for mankind: Analogies from the Papionin monkeys and their implications for human evolution.

  2001cited by this paper
• Initial sequencing and analysis of the human genome

  2001influential reference
• SINE insertions in cladistic analyses and the phylogenetic affiliations of Tarsius bancanus to other primates.

  2001cited by this paper
• Molecular phylogeny of the major hylobatid divisions.

  2001cited by this paper
• Sodium-Lithium Countertransport Activity Is Linked to Chromosome 5 in Baboons

  2001cited by this paper
• Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity.

  2001cited by this paper
• Non‐human primates: essential partners in biomedical research

  2001cited by this paper
• SINE insertions: powerful tools for molecular systematics.

  2000cited by this paper
• An Alu insertion polymorphism in a baboon hybrid zone.

  1999cited by this paper
• Species richness, species range size and ecological specialisation among African primates: geographical patterns and conservation implications

  1999cited by this paper
• Repeats in genomic DNA: mining and meaning.

  1998cited by this paper
• Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa.

  1997cited by this paper
• RNA template requirements for target DNA-primed reverse transcription by the R2 retrotransposable element

  1995cited by this paper
• Species, Subspecies, and Baboon Systematics

  1993cited by this paper
• Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition.

  1993cited by this paper
• The baboon: an ideal model in biomedical research.

  1992cited by this paper
• The Human Community as a Primate Society [and Comments]

  1991cited by this paper
• A human-specific subfamily of Alu sequences.

  1991cited by this paper
• Characteristics of hamadryas-like male baboons living in anubis baboon troops in the Awash hybrid zone, Ethiopia.

  1991cited by this paper
• Structure and variability of recently inserted Alu family members.

  1990cited by this paper
• The Evolution of Human Behavior: Primate Models.

  1987cited by this paper
• Effects of ovariectomy on iliac trabecular bone in baboons (Papio anubis)

  1986cited by this paper
• Relationship of Lipoprotein Cholesterol Concentrations to Experimental Atherosclerosis in Baboons

  1981cited by this paper
• A comparison of anubis baboons, hamadryas baboons and their hybrids at a species border in Ethiopia.

  1973cited by this paper
• The major features of evolution

  1955cited by this paper
• Simpson, George Gaylord. The Major Features of Evolution. Columbia University Press, New York City, New York. xx plus 434 pp., 52 figs., 28 tables. 1953. Price $7.50

  1954cited by this paper
• Major Features Of Evolution

  1954cited by this paper
• LSU Digital Commons LSU Digital Commons Papio baboon species indicative Alu elements Papio baboon species indicative Alu elements

  year unknowncited by this paper
• LSU Digital Commons LSU Digital Commons Phylogeny of the macaques (Cercopithecidae: Macaca) based on Phylogeny of the macaques (Cercopithecidae: Macaca) based on Alu elements Alu elements

  year unknowncited by this paper

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  2025cites this paper
• Flexible reproductive seasonality in Africa-dwelling papionins is associated with low environmental productivity and high climatic unpredictability

  2024cites this paper
• The identification of retro-DNAs in primate genomes as DNA transposons mobilizing via retrotransposition

  2023cites this paper
• A Comprehensive Overview of Baboon Phylogenetic History

  2023cites this paper
• Cebidae Alu Element Alignments and a Complex Non-Human Primate Radiation

  2022cites this paper
• A Pleistocene assemblage of near-modern Papio hamadryas from the Middle Awash study area, Afar Rift, Ethiopia.

  2022cites this paper
• Selection against admixture and gene regulatory divergence in a long-term primate field study

  2021cites this paper
• March Mammal Madness and the power of narrative in science outreach

  2021cites this paper
• Identification and characterization of retro-DNAs, a new type of retrotransposons originated from DNA transposons, in primate genomes

  2020cites this paper
• Divergence of 3' ends as a driver of Short Interspersed Nuclear Element (SINE) evolution in the Salicaceae.

  2020cites this paper
• Alu master copies serve as the drivers of differential SINE transposition in recent primate genomes.

  2020cites this paper
• The role of mobile elements in recent primate genomes

  2020cites this paper
• The comparative genomics and complex population history of Papio baboons

  2019cites this paper
• Amplification Dynamics of Platy-1 Retrotransposons in the Cebidae Platyrrhine Lineage

  2019cites this paper
• TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data

  2019cites this paper
• Characterization and Amplification of Retrotransposable Elements Platy-1 and Alu in the Cebidae Lineage of Platyrrhine Primates

  2019influential citation
• Alu insertion polymorphisms shared by Papio baboons and Theropithecus gelada reveal an intertwined common ancestry

  2019cites this paper
• Comparative Genomics Analysis Reveals High Levels of Differential Retrotransposition among Primates from the Hominidae and the Cercopithecidae Families

  2019cites this paper
• Sexual selection in the Kinda baboon.

  2019cites this paper
• Sensitivity of the polyDetect computational pipeline for phylogenetic analyses.

  2019influential citation
• Comparative genomics analysis reveals high levels of differential DNA transposition among primates

  2019cites this paper
• Computational Analysis of Papionini Evolution Using Alu Insertions

  2018influential citation