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  • 1.
    Baas, Pauline
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    van der Valk, Tom
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Vigilant, Linda
    Ngobobo, Urbain
    Binyinyi, Escobar
    Nishuli, Radar
    Caillaud, Damien
    Guschanski, Katerina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Population-level assessment of genetic diversity and habitat fragmentation in critically endangered Grauer's gorillas2018In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 165, no 3, p. 565-575Article in journal (Refereed)
    Abstract [en]

    Objectives: The critically endangered Grauer's gorilla (Gorilla beringei graueri) has experienced an estimated 77% population decline within a single generation. Although crucial for informed conservation decisions, there is no clear understanding about population structure and distribution of genetic diversity across the species' highly fragmented range. We fill this gap by studying several core and peripheral Grauer's gorilla populations throughout their distribution range.

    Materials and Methods: We generated genetic profiles for a sampling of an unstudied population of Grauer's gorillas from within the species' core range at 13 autosomal microsatellite loci and combined them with previously published and newly generated data from four other Grauer's gorilla populations, two mountain gorilla populations, and one western lowland gorilla population.

    Results: In agreement with previous studies, the genetic diversity of Grauer's gorillas is intermediate, falling between western lowland and mountain gorillas. Among Grauer's gorilla populations, we observe lower genetic diversity and high differentiation in peripheral compared with central populations, indicating a strong effect of genetic drift and limited gene flow among small, isolated forest fragments.

    Discussion: Although genetically less diverse, peripheral populations are frequently essential for the long-term persistence of a species and migration between peripheral and core populations may significantly enrich the overall species genetic diversity. Thus, in addition to central Grauer's gorilla populations from the core of the distribution range that clearly deserve conservation attention, we argue that conservation strategies aiming to ensure long-term species viability should include preserving peripheral populations and enhancing habitat connectivity.

  • 2.
    Goldberg, Amy
    et al.
    Stanford Univ, Dept Biol, Stanford, CA, USA.
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Rosenberg, Noah A.
    Stanford Univ, Dept Biol, Stanford, CA, USA.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Neolithic familial migration contrasts Bronze Age male migration inferred from ancient X chromosomes2017In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 162, no S64, p. 196-196Article in journal (Other academic)
  • 3.
    Hedenstierna-Jonson, Charlotte
    et al.
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology. Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
    Kjellström, Anna
    Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden; Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden .
    Zachrisson, Torun
    Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
    Krzewińska, Maja
    Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
    Sobrado, Veronica
    Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
    Price, Neil
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology.
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Götherström, Anders
    Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
    Storå, Jan
    Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
    A female Viking warrior confirmed by genomics2017In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 164, no 4, p. 853-860Article in journal (Refereed)
    Abstract [en]

    OBJECTIVES: The objective of this study has been to confirm the sex and the affinity of an individual buried in a well-furnished warrior grave (Bj 581) in the Viking Age town of Birka, Sweden. Previously, based on the material and historical records, the male sex has been associated with the gender of the warrior and such was the case with Bj 581. An earlier osteological classification of the individual as female was considered controversial in a historical and archaeological context. A genomic confirmation of the biological sex of the individual was considered necessary to solve the issue.

    MATERIALS AND METHODS: Genome-wide sequence data was generated in order to confirm the biological sex, to support skeletal integrity, and to investigate the genetic relationship of the individual to ancient individuals as well as modern-day groups. Additionally, a strontium isotope analysis was conducted to highlight the mobility of the individual.

    RESULTS: The genomic results revealed the lack of a Y-chromosome and thus a female biological sex, and the mtDNA analyses support a single-individual origin of sampled elements. The genetic affinity is close to present-day North Europeans, and within Sweden to the southern and south-central region. Nevertheless, the Sr values are not conclusive as to whether she was of local or nonlocal origin.

    DISCUSSION: The identification of a female Viking warrior provides a unique insight into the Viking society, social constructions, and exceptions to the norm in the Viking time-period. The results call for caution against generalizations regarding social orders in past societies.

  • 4.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    The genomic footprints of Stone-Age Europeans2016In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 159, no Suppl. 62, p. 184-184Article in journal (Other academic)
  • 5.
    Jeong, Choongwon
    et al.
    Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA..
    Ozga, Andrew T.
    Univ Oklahoma, Dept Anthropol, Norman, OK 73019 USA..
    Witonsky, David
    Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA..
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Lewis, Cecil M.
    Univ Oklahoma, Dept Anthropol, Norman, OK 73019 USA..
    Aldenderfer, Mark
    Univ Calif Merced, Dept Anthropol, Merced, CA USA..
    Di Rienzo, Anna
    Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA..
    Warinner, Christina
    Univ Oklahoma, Dept Anthropol, Norman, OK 73019 USA..
    Long-term genetic stability and a high altitude East Asian origin for the peoples of the high valleys of the Himalayan arc2016In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 159, no Suppl. 62, p. 185-185Article in journal (Other academic)
  • 6. Khonsari, R H
    et al.
    Friess, M
    Nysjö, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Odri, G
    Malmberg, Filip
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Nyström, Ingela
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Messo, Elias
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Oral and Maxillofacial Surgery.
    Hirsch, Jan M
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Oral and Maxillofacial Surgery.
    Cabanis, E A M
    Kunzelmann, K H
    Salagnac, J M
    Corre, P
    Ohazama, A
    Sharpe, P T
    Charlier, P
    Olszewski, R
    Shape and volume of craniofacial cavities in intentional skull deformations2013In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 151, no 1, p. 110-119Article in journal (Refereed)
    Abstract [en]

    Intentional cranial deformations (ICD) have been observed worldwide but are especially prevalent in preColombian cultures. The purpose of this study was to assess the consequences of ICD on three cranial cavities (intracranial cavity, orbits, and maxillary sinuses) and on cranial vault thickness, in order to screen for morphological changes due to the external constraints exerted by the deformation device. We acquired CT-scans for 39 deformed and 19 control skulls. We studied the thickness of the skull vault using qualitative and quantitative methods. We computed the volumes of the orbits, of the maxillary sinuses, and of the intracranial cavity using haptic-aided semi-automatic segmentation. We finally defined 3D distances and angles within orbits and maxillary sinuses based on 27 anatomical landmarks and measured these features on the 58 skulls. Our results show specific bone thickness patterns in some types of ICD, with localized thinning in regions subjected to increased pressure and thickening in other regions. Our findings confirm that volumes of the cranial cavities are not affected by ICDs but that the shapes of the orbits and of the maxillary sinuses are modified in circumferential deformations. We conclude that ICDs can modify the shape of the cranial cavities and the thickness of their walls but conserve their volumes. These results provide new insights into the morphological effects associated with ICDs and call for similar investigations in subjects with deformational plagiocephalies and craniosynostoses.

  • 7.
    Malukiewicz, Joanna
    et al.
    Arizona State Univ, Sch Life Sci, Tempe, AZ 85287 USA..
    Hepp, Crystal M.
    No Arizona Univ, Sch Informat Comp & Cyber Syst, Flagstaff, AZ 86011 USA..
    Guschanski, Katerina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Stone, Anne C.
    Arizona State Univ, Sch Human Evolut & Social Change, Tempe, AZ 85287 USA.;Arizona State Univ, Inst Human Origins, Tempe, AZ 85287 USA..
    Phylogeny of the jacchus group of Callithrix marmosets based on complete mitochondrial genomes2017In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 162, no 1, p. 157-169Article in journal (Refereed)
    Abstract [en]

    ObjectivesTwo subgroups make up the marmoset genus Callithrix. The "aurita" group is composed of two species, whereas evolutionary relationships among the four species of the "jacchus" group remain unclear. To uncover these relationships, we first sequenced mitochondrial genomes for C. kuhlii and C. penicillata to complement data available for congeners. We then constructed a phylogenetic tree based on mtDNA heavy chain protein coding genes from several primates to untangle species relationships and estimate divergence times of the jacchus group. Materials and MethodsMtDNA genomes of C. kuhlii and C. penicillata were Sanger sequenced. These Callithrix mitogenomes were combined with other publically available primate mtDNA genomes. Phylogenies were produced using maximum likelihood and Bayesian inference. Finally, divergence times within the jacchus group of marmosets were estimated with Bayesian inference. ResultsIn our phylogenetic tree, C. geoffroyi was the sister to all other jacchus group species, followed by C. kuhlii, while C. jacchus and C. penicillata diverged most recently. Bayesian inference showed that C. jacchus and C. penicillata diverged approximately 0.70 MYA and that the jacchus group radiated approximately 1.30 MYA. DiscussionCallithrix nuclear and mtDNA phylogenies frequently result in polytomies and paraphyly. Here, we present a well-supported phylogenetic tree based on mitochondrial genome sequences, which facilitates the understanding of the divergence of the jacchus marmosets. Our results demonstrate how mitochondrial genomes can enrich Callithrix phylogenetic studies by alleviating some of the difficulties faced by previous mtDNA studies and allow formulation of hypotheses to test further under larger genomic-scale analyses.

  • 8.
    Pilloud, Marin A.
    et al.
    Univ Nevada, Anthropol, Reno, NV, USA.
    Somel, Mehmet
    Middle East Tech Univ, Ankara, Turkey.
    Haddow, Scott D.
    Univ Bordeaux, PACEA UMR, Bordeaux, France.
    Knusel, Christopher J.
    Univ Bordeaux, PACEA UMR, Bordeaux, France.
    Larsen, Clark Spencer
    Ohio State Univ, Anthropol, Columbus, OH, USA.
    Ozbasaran, Mihriban
    Istanbul Univ, Archaeol Dept, Istanbul, Turkey.
    Erdal, Omur Dilek
    Hacettepe Univ, Dept Anthropol, Ankara, Turkey.
    Baird, Douglas
    Univ Liverpool, Dept Archaeol Class & Egyptol, Liverpool, Merseyside, England.
    Pearson, Jessica
    Univ Liverpool, Dept Archaeol Class & Egyptol, Liverpool, Merseyside, England.
    Gotherstrom, Anders
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden.
    Stora, Jan
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Kilinc, Gulsah Merve
    Middle East Tech Univ, Ankara, Turkey.
    Ozer, Fusun
    Middle East Tech Univ, Ankara, Turkey.
    Koptekin, Dilek
    Middle East Tech Univ, Ankara, Turkey.
    Dagtas, Nihan Dilsad
    Middle East Tech Univ, Ankara, Turkey.
    Mobility in Neolithic Central Anatolia: A Comparison of Dental Morphometrics and aDNA2017In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 162, no S64, p. 316-316Article in journal (Other academic)
  • 9. Seldin, Michael F.
    et al.
    Tian, Chao
    Shigeta, Russell
    Scherbarth, Hugo R.
    Silva, Gabriel
    Belmont, John W.
    Kittles, Rick
    Gamron, Susana
    Allevi, Alberto
    Palatnik, Simon A.
    Alvarellos, Alejandro
    Paira, Sergio
    Caprarulo, Cesar
    Guilleron, Carolina
    Catoggio, Luis J.
    Prigione, Cristina
    Berbotto, Guillermo A.
    Garci­a, Mercedes A.
    Perandones, Carlos E.
    Pons-Estel, Bernardo A.
    Alarcon-Riquelme, Marta E.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Argentine population genetic structure: large variance in Amerindian contribution2007In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 132, no 3, p. 455-462Article in journal (Refereed)
    Abstract [en]

    Argentine population genetic structure was examined using a set of 78 ancestry informative markers (AIMs) to assess the contributions of European, Amerindian, and African ancestry in 94 individuals members of this population. Using the Bayesian clustering algorithm STRUCTURE, the mean European contribution was 78%, the Amerindian contribution was 19.4%, and the African contribution was 2.5%. Similar results were found using weighted least mean square method: European, 80.2%; Amerindian, 18.1%; and African, 1.7%. Consistent with previous studies the current results showed very few individuals (four of 94) with greater than 10% African admixture. Notably, when individual admixture was examined, the Amerindian and European admixture showed a very large variance and individual Amerindian contribution ranged from 1.5 to 84.5% in the 94 individual Argentine subjects. These results indicate that admixture must be considered when clinical epidemiology or case control genetic analyses are studied in this population. Moreover, the current study provides a set of informative SNPs that can be used to ascertain or control for this potentially hidden stratification. In addition, the large variance in admixture proportions in individual Argentine subjects shown by this study suggests that this population is appropriate for future admixture mapping studies.

  • 10.
    Somel, Mehmet
    et al.
    Middle E Tech Univ, Biol, Ankara, Turkey..
    Kilinc, Gulsah Merve
    Middle E Tech Univ, Biol, Ankara, Turkey..
    Ozer, Fusun
    Middle E Tech Univ, Biol, Ankara, Turkey..
    Omrak, Ayca
    Stockholm Univ, Archaeol, Stockholm, Sweden..
    Yaka, Reyhan
    Middle E Tech Univ, Biol, Ankara, Turkey..
    Donertas, Melike
    Middle E Tech Univ, Biol, Ankara, Turkey..
    Dagtas, Nihan D.
    Middle E Tech Univ, Biol, Ankara, Turkey..
    Yuncu, Eren
    Middle E Tech Univ, Biol, Ankara, Turkey..
    Koptekin, Dilek
    Middle E Tech Univ, Biol, Ankara, Turkey..
    Büyükkarakaya, Ali M.
    Hacettepe Univ, Anthropol, Stockholm, Sweden..
    Acan, Sinan C.
    Middle E Tech Univ, Biol, Ankara, Turkey..
    Alkan, Can
    Bilkent Univ, Comp Sci, Ankara, Turkey..
    Hodder, Ian
    Stanford Univ, Anthropol, Stanford, CA 94305 USA..
    Haddow, Scott
    Stanford Univ, Anthropol, Stanford, CA 94305 USA..
    Knüsel, Christopher
    Univ Bordeaux, Prehist, Bordeaux, France..
    Larsen, Clark S.
    Ohio State Univ, Anthropol, Columbus, OH 43210 USA..
    Erdal, Yilmaz S.
    Hacettepe Univ, Anthropol, Stockholm, Sweden..
    Bicakci, Erhan
    Istanbul Univ, Prehist, Istanbul, Turkey..
    Baird, Douglas
    Univ Liverpool, Archaeol, Liverpool L69 3BX, Merseyside, England..
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Togan, Inci
    Middle E Tech Univ, Biol, Ankara, Turkey..
    Götherström, Anders
    Stockholm Univ, Archaeol, Stockholm, Sweden.
    Archaeogenomic analysis of ancient Anatolians: first genetic indication for Neolithic cultural diffusion in the Near East2016In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 159, no Suppl. 62, p. 297-298Article in journal (Other academic)
  • 11. van Holst Pellekaan, Sheila M.
    et al.
    Ingman, Max
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology, Medical Genetics.
    Roberts-Thomson, June
    Harding, Rosalind M.
    Mitochondrial genomics identifies major haplogroups in Aboriginal Australians2006In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 131, no 2, p. 282-294Article in journal (Refereed)
    Abstract [en]

    We classified diversity in eight new complete mitochondrial genome sequences and 41 partial sequences from living Aboriginal Australians into five haplogroups. Haplogroup AuB belongs to global lineage M, and AuA, AuC, AuD, and AuE to N. Within N, we recognize subdivisions, assigning AuA to haplogroup S, AuD to haplogroup 0, AuC to P4, and AuE to P8. On available evidence, (S)AuA and (AuB)-Au-M are widespread in Australia. (AuC)-Au-P4 is found in the Riverine region of western New South Wales, and was identified by others in northern Australia. (AuD)-Au-O and (AuE)-Au-P8 were clearly identified only from central Australia. Our eight Australian full mt genome sequences, combined with 20 others (Ingman and Gyllensten [2003] Genome Res. 13:1600-1606) and compared with full mt genome sequences from regions to the north that include Papua New Guinea, Malaya, and Andaman and Nicobar Islands, show that ancestral connections between regions are deep and limited to clustering at the level of the N and M macro-haplogroups. The Australian-specific distribution of the five haplogroups identified indicates genetic isolation over a long period. Ancestral connections within Australia are deeper than those reflected by known linguistic or culturally based affinities. Applying a coalescence analysis to a gene tree for the coding regions of the eight genomic sequences, we made estimates of time depth that support a continuity of presence for the descendants of a founding population already established by 40,000 years ago.

  • 12.
    Vicente, Mário
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Ebbesen, Peter
    Aalborg Univ, Dept Hlth Sci & Technol, Aalborg, Denmark.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Schlebusch, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Genetic variation of southern Africa hunter-gatherers and the impact of admixture with farming and pastoralist populations2017In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 162, no S64, p. 395-395Article in journal (Other academic)
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