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  • 1.
    Guschanski, Katerina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Warnefors, Maria
    Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance.
    Kaessmann, Henrik
    Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance.
    The evolution of duplicate gene expression in mammalian organs2017In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 27, no 9, p. 1461-1474Article in journal (Refereed)
    Abstract [en]

    Gene duplications generate genomic raw material that allows the emergence of novel functions, likely facilitating adaptive evolutionary innovations. However, global assessments of the functional and evolutionary relevance of duplicate genes in mammals were until recently limited by the lack of appropriate comparative data. Here, we report a large-scale study of the expression evolution of DNA-based functional gene duplicates in three major mammalian lineages (placental mammals, marsupials, egg-laying monotremes) and birds, on the basis of RNA sequencing (RNA-seq) data from nine species and eight organs. We observe dynamic changes in tissue expression preference of paralogs with different duplication ages, suggesting differential contribution of paralogs to specific organ functions during vertebrate evolution. Specifically, we show that paralogs that emerged in the common ancestor of bony vertebrates are enriched for genes with brain-specific expression and provide evidence for differential forces underlying the preferential emergence of young testis-and liver-specific expressed genes. Further analyses uncovered that the overall spatial expression profiles of gene families tend to be conserved, with several exceptions of pronounced tissue specificity shifts among lineage-specific gene family expansions. Finally, we trace new lineage-specific genes that may have contributed to the specific biology of mammalian organs, including the little-studied placenta. Overall, our study provides novel and taxonomically broad evidence for the differential contribution of duplicate genes to tissue-specific transcriptomes and for their importance for the phenotypic evolution of vertebrates.

    The full text will be freely available from 2018-03-05 12:59
  • 2.
    Malukiewicz, Joanna
    et al.
    Univ Fed Vicosa, Biochem & Mol Biol, Vicosa, MG, Brazil.;Arizona State Univ, Sch Human Evolut & Social Change, Tempe, AZ 85287 USA..
    Ackermann, Rebecca R.
    Univ Cape Town, Dept Archaeol, ZA-7700 Rondebosch, South Africa..
    Curi, Nelson H. A.
    Univ Fed Lavras, Dept Biol, Lavras, MG, Brazil..
    Dergam, Jorge A.
    Univ Fed Vicosa, Dept Anim Biol, Vicosa, MG, Brazil..
    Fuzessy, Lisieux F.
    Univ Fed Minas Gerais, Dept Plant Biol, Belo Horizonte, MG, Brazil..
    Guschanski, Katerina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Grativol, Adriana D.
    Univ Estadual Norte Fluminense, Ctr Biociencias & Biotecnol, Campos Dos Goytacazes, RJ, Brazil..
    Nicola, Patricia A.
    Univ Fed Vale Sao Francisco, Ctr Conservacao & Manejo Fauna Caatinga, Petrolina, Brazil..
    Pereira, Luiz C. M.
    Univ Fed Vale Sao Francisco, Ctr Conservacao & Manejo Fauna Caatinga, Petrolina, Brazil..
    Ruiz-Miranda, Carlos R.
    Univ Estadual Norte Fluminense, Ctr Biociencias & Biotecnol, Campos Dos Goytacazes, RJ, Brazil..
    Passamani, Marcelo
    Univ Fed Lavras, Dept Biol, Lavras, MG, Brazil..
    Silva, Daniel L.
    Univ Fed Vicosa, Dept Anim Biol, Vicosa, MG, Brazil..
    Stone, Anne C.
    Arizona State Univ, Sch Human Evolut & Social Change, Tempe, AZ 85287 USA..
    Genetic and morphological variation in natural and anthropogenic marmoset hybrids2016In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 159, no Suppl. 62, p. 217-218Article in journal (Other academic)
  • 3.
    Malukiewicz, Joanna
    et al.
    Univ Fed Vicosa, Dept Bioquim & Biol Mol, Avenida PH Rolfs s-n,Vicosa, BR-36570 Vicosa, MG, Brazil.;Arizona State Univ, Sch Life Sci, Tempe, AZ USA..
    Guschanski, Katerina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Grativol, Adriana D.
    Univ Estadual Norte Fluminense, Centro Biociencias & Biotecnol, Lab Ciencias Ambientais, Rio De Janeiro, RJ, Brazil..
    Oliveira, Maria Adelia B.
    Univ Fed Rural Pernambuco, Dept Morfol & Fisiol Anim, Recife, PE, Brazil..
    Ruiz-Miranda, Carlos R.
    Univ Estadual Norte Fluminense, Centro Biociencias & Biotecnol, Lab Ciencias Ambientais, Rio De Janeiro, RJ, Brazil..
    Stone, Anne C.
    Arizona State Univ, Sch Human Evolut & Social Change, Tempe, AZ USA..
    Application of PE-RADSeq to the study of genomic diversity and divergence of two Brazilian marmoset species (Callithrix jacchus and C-penicillata)2017In: American Journal of Primatology, ISSN 0275-2565, E-ISSN 1098-2345, Vol. 79, no 2, article id UNSP e22587Article in journal (Refereed)
    Abstract [en]

    Callithrix jacchus and C. penicillata are among the smallest anthropoid primates, are highly specialized tree gougers, and largely occupy Brazil's most extreme, semi-arid biomes. However, the underlying genomic factors that underpin the evolution of these species and their unique traits are under-investigated. Additionally, exotic populations of these two species are widely established throughout Brazil and hybridize with threatened native congers. Thus, both genomic and conservation factors call for a better understanding of C. jacchus and C. penicillata evolution. Here, we applied PE-RADseq to characterize genomic variation in these two species, using six C. jacchus and seven C. penicillata individuals. We identified an average of 7,463 and 5,180 SNPs/individual in C. penicillata and C. jacchus, respectively, and also found 1,395 variable sites that were represented in both species. C. penicillata showed overall higher levels of genetic diversity than C. jacchus at the variable sites present in both species. Additionally, among these variable sites, 106 showed relative interspecific divergence levels that were significantly higher than the genome-wide average. We further compared relative and absolute divergence for C. penicillata and C. jacchus between RAD loci associated with the 106 significantly diverged variable sites and all other RAD loci present in both species. The former RAD loci set showed significantly elevated relative and absolute divergence measures in comparison to the latter set. This convergence suggests that C. jacchus and C. penicillata may have diverged under a scenario of gene flow under secondary contact. Here, we demonstrate that RADseq is an efficient method to simultaneously discover and genotype a large number of markers and validate the utility of RADseq for examining Callithrix evolution.

  • 4.
    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.

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