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      The difference between trivial and scientific names: There were never any true cheetahs in North America

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      Genome Biology
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          Abstract

          Dobrynin et al. (Genome Biol 16:277, 2015) recently published the complete genome of the cheetah ( Acinonyx jubatus) and provided an exhaustive set of analyses supporting the famously low genetic variation in the species, known for several decades. Their genetic analyses represent state-of-the-art and we do not criticize them. However, their interpretation of the results is inconsistent with current knowledge of cheetah evolution. Dobrynin et al. suggest that the causes of the two inferred bottlenecks at ∼ 100,000 and 10,000 years ago were immigration by cheetahs from North America and end-Pleistocene megafauna extinction, respectively, but the first explanation is impossible and the second implausible.

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          Stratigraphic placement and age of modern humans from Kibish, Ethiopia.

          In 1967 the Kibish Formation in southern Ethiopia yielded hominid cranial remains identified as early anatomically modern humans, assigned to Homo sapiens. However, the provenance and age of the fossils have been much debated. Here we confirm that the Omo I and Omo II hominid fossils are from similar stratigraphic levels in Member I of the Kibish Formation, despite the view that Omo I is more modern in appearance than Omo II. 40Ar/39Ar ages on feldspar crystals from pumice clasts within a tuff in Member I below the hominid levels place an older limit of 198 +/- 14 kyr (weighted mean age 196 +/- 2 kyr) on the hominids. A younger age limit of 104 +/- 7 kyr is provided by feldspars from pumice clasts in a Member III tuff. Geological evidence indicates rapid deposition of each member of the Kibish Formation. Isotopic ages on the Kibish Formation correspond to ages of Mediterranean sapropels, which reflect increased flow of the Nile River, and necessarily increased flow of the Omo River. Thus the 40Ar/39Ar age measurements, together with the sapropel correlations, indicate that the hominid fossils have an age close to the older limit. Our preferred estimate of the age of the Kibish hominids is 195 +/- 5 kyr, making them the earliest well-dated anatomically modern humans yet described.
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            Pinnacle Point Cave 13B (Western Cape Province, South Africa) in context: The Cape Floral kingdom, shellfish, and modern human origins.

            Genetic and anatomical evidence suggests that Homo sapiens arose in Africa between 200 and 100ka, and recent evidence suggests that complex cognition may have appeared between ~164 and 75ka. This evidence directs our focus to Marine Isotope Stage (MIS) 6, when from 195-123ka the world was in a fluctuating but predominantly glacial stage, when much of Africa was cooler and drier, and when dated archaeological sites are rare. Previously we have shown that humans had expanded their diet to include marine resources by ~164ka (±12ka) at Pinnacle Point Cave 13B (PP13B) on the south coast of South Africa, perhaps as a response to these harsh environmental conditions. The associated material culture documents an early use and modification of pigment, likely for symbolic behavior, as well as the production of bladelet stone tool technology, and there is now intriguing evidence for heat treatment of lithics. PP13B also includes a later sequence of MIS 5 occupations that document an adaptation that increasingly focuses on coastal resources. A model is developed that suggests that the combined richness of the Cape Floral Region on the south coast of Africa, with its high diversity and density of geophyte plants and the rich coastal ecosystems of the associated Agulhas Current, combined to provide a stable set of carbohydrate and protein resources for early modern humans along the southern coast of South Africa during this crucial but environmentally harsh phase in the evolution of modern humans. Humans structured their mobility around the use of coastal resources and geophyte abundance and focused their occupation at the intersection of the geophyte rich Cape flora and coastline. The evidence for human occupation relative to the distance to the coastline over time at PP13B is consistent with this model. Copyright © 2010 Elsevier Ltd. All rights reserved.
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              Genomic legacy of the African cheetah, Acinonyx jubatus

              Background Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations. Results Here the genome sequence of wild-born African cheetahs reveals extreme genomic depletion in SNV incidence, SNV density, SNVs of coding genes, MHC class I and II genes, and mitochondrial DNA SNVs. Cheetah genomes are on average 95 % homozygous compared to the genomes of the outbred domestic cat (24.08 % homozygous), Virunga Mountain Gorilla (78.12 %), inbred Abyssinian cat (62.63 %), Tasmanian devil, domestic dog and other mammalian species. Demographic estimators impute two ancestral population bottlenecks: one >100,000 years ago coincident with cheetah migrations out of the Americas and into Eurasia and Africa, and a second 11,084–12,589 years ago in Africa coincident with late Pleistocene large mammal extinctions. MHC class I gene loss and dramatic reduction in functional diversity of MHC genes would explain why cheetahs ablate skin graft rejection among unrelated individuals. Significant excess of non-synonymous mutations in AKAP4 (p 80 %) pleiomorphic sperm. Conclusions The study provides an unprecedented genomic perspective for the rare cheetah, with potential relevance to the species’ natural history, physiological adaptations and unique reproductive disposition. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0837-4) contains supplementary material, which is available to authorized users.
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                Author and article information

                Contributors
                faurby@mncn.csic.es
                Journal
                Genome Biol
                Genome Biol
                Genome Biology
                BioMed Central (London )
                1474-7596
                1474-760X
                5 May 2016
                5 May 2016
                2016
                : 17
                : 89
                Affiliations
                [ ]Section of Biology and Environmental Science, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Øst Denmark
                [ ]Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales, CSIC, Calle José Gutiérrez Abascal 2, 28006 Madrid, Spain
                [ ]Swedish Museum of Natural History, Department of Palaeobiology, Box 50007, 10405 Stockholm, Sweden
                [ ]Section for Ecoinformatics & Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
                Article
                943
                10.1186/s13059-016-0943-y
                4858926
                27150269
                c7657aa7-ce1b-4893-ba31-46f8e1d870bd
                © Faurby et al. 2016

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 23 December 2015
                : 11 April 2016
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100008394, Natur og Univers, Det Frie Forskningsråd;
                Award ID: 4090-00227
                Award Recipient :
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                © The Author(s) 2016

                Genetics
                Genetics

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