Bonobos Fall within the Genomic Variation of Chimpanzees
Anne Fischer,Kay Prüfer,Jeffrey M. Good,Michel Halbwax,Victor Wiebe,Claudine André,Rebeca Atencia,Lawrence Mugisha,Susan E. Ptak,Svante Pääbo +9 more
TLDR
While chimpanzees retain genomic variation that predates bonobo-chimpanzee speciation, extensive lineage sorting has occurred within bonobos such that much of their genome traces its ancestry back to a single common ancestor that postdates their origin as a group separate from chimpanzees.Abstract:
To gain insight into the patterns of genetic variation and evolutionary relationships within and between bonobos and chimpanzees, we sequenced 150,000 base pairs of nuclear DNA divided among 15 autosomal regions as well as the complete mitochondrial genomes from 20 bonobos and 58 chimpanzees. Except for western chimpanzees, we found poor genetic separation of chimpanzees based on sample locality. In contrast, bonobos consistently cluster together but fall as a group within the variation of chimpanzees for many of the regions. Thus, while chimpanzees retain genomic variation that predates bonobo-chimpanzee speciation, extensive lineage sorting has occurred within bonobos such that much of their genome traces its ancestry back to a single common ancestor that postdates their origin as a group separate from chimpanzees.read more
Citations
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TL;DR: This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.
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The bonobo genome compared with the chimpanzee and human genomes
Kay Prüfer,Kasper Munch,Ines Hellmann,Keiko Akagi,Jason R. Miller,Brian P. Walenz,Sergey Koren,Granger G. Sutton,Chinnappa D. Kodira,Roger Winer,James R. Knight,James C. Mullikin,Stephen Meader,Chris P. Ponting,Gerton Lunter,Saneyuki Higashino,Asger Hobolth,Julien Y. Dutheil,Emre Karakoc,Can Alkan,Can Alkan,Saba Sajjadian,Claudia Rita Catacchio,Mario Ventura,Mario Ventura,Tomas Marques-Bonet,Tomas Marques-Bonet,Evan E. Eichler,Claudine André,Rebeca Atencia,Lawrence Mugisha,Jörg Junhold,Nick Patterson,Michael Siebauer,Jeffrey M. Good,Anne Fischer,Susan E. Ptak,Michael Lachmann,David E. Symer,Thomas Mailund,Mikkel H. Schierup,Aida M. Andrés,Janet Kelso,Svante Pääbo +43 more
TL;DR: The sequencing and assembly of the bonobo genome is reported to study its evolutionary relationship with the chimpanzee and human genomes, and it is found that more than three per cent of the human genome is more closely related to either theBonobo or the chimpanzees genome than these are to each other.
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Chimpanzee genomic diversity reveals ancient admixture with bonobos
Marc de Manuel,Martin Kuhlwilm,Peter Frandsen,Peter Frandsen,Vitor C. Sousa,Vitor C. Sousa,Tariq Desai,Javier Prado-Martinez,Javier Prado-Martinez,Jessica Hernandez-Rodriguez,Isabelle Dupanloup,Isabelle Dupanloup,Oscar Lao,Pille Hallast,Pille Hallast,Joshua M. Schmidt,José María Heredia-Genestar,Andrea Benazzo,Guido Barbujani,Benjamin M. Peter,Lukas F. K. Kuderna,Ferran Casals,Samuel Angedakin,Mimi Arandjelovic,Christophe Boesch,Hjalmar S. Kühl,Linda Vigilant,Kevin E. Langergraber,John Novembre,Marta Gut,Ivo Gut,Arcadi Navarro,Arcadi Navarro,Frands Carlsen,Aida M. Andrés,Hans R. Siegismund,Aylwyn Scally,Laurent Excoffier,Laurent Excoffier,Chris Tyler-Smith,Sergi Castellano,Yali Xue,Christina Hvilsom,Tomas Marques-Bonet,Tomas Marques-Bonet +44 more
TL;DR: It is found that chimpanzee population substructure makes genetic information a good predictor of geographic origin at country and regional scales and also provides population-specific genetic markers that may be valuable for conservation efforts.
References
More filters
Journal ArticleDOI
MUSCLE: multiple sequence alignment with high accuracy and high throughput
TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
Journal ArticleDOI
Inference of population structure using multilocus genotype data
TL;DR: Pritch et al. as discussed by the authors proposed a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations, which can be applied to most of the commonly used genetic markers, provided that they are not closely linked.
Journal ArticleDOI
MrBayes 3: Bayesian phylogenetic inference under mixed models
TL;DR: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models to analyze heterogeneous data sets and explore a wide variety of structured models mixing partition-unique and shared parameters.
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