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  • 1. Arandjelovic, M.
    et al.
    Guschanski, Katerina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
    Schubert, G.
    Harris, T. R.
    Thalmann, O.
    Siedel, H.
    Vigilant, L.
    Two-step multiplex polymerase chain reaction improves the speed and accuracy of genotyping using DNA from noninvasive and museum samples2009In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 9, no 1, p. 28-36Article in journal (Refereed)
    Abstract [en]

    Many studies in molecular ecology rely upon the genotyping of large numbers of low‐quantity DNA extracts derived from noninvasive or museum specimens. To overcome low amplification success rates and avoid genotyping errors such as allelic dropout and false alleles, multiple polymerase chain reaction (PCR) replicates for each sample are typically used. Recently, two‐step multiplex procedures have been introduced which drastically increase the success rate and efficiency of genotyping. However, controversy still exists concerning the amount of replication needed for suitable control of error. Here we describe the use of a two‐step multiplex PCR procedure that allows rapid genotyping using at least 19 different microsatellite loci. We applied this approach to quantified amounts of noninvasive DNAs from western chimpanzee, western gorilla, mountain gorilla and black and white colobus faecal samples, as well as to DNA from ~100‐year‐old gorilla teeth from museums. Analysis of over 45 000 PCRs revealed average success rates of > 90% using faecal DNAs and 74% using museum specimen DNAs. Average allelic dropout rates were substantially reduced compared to those obtained using conventional singleplex PCR protocols, and reliable genotyping using low (< 25 pg) amounts of template DNA was possible. However, four to five replicates of apparently homozygous results are needed to avoid allelic dropout when using the lowest concentration DNAs (< 50 pg/reaction), suggesting that use of protocols allowing routine acceptance of homozygous genotypes after as few as three replicates may lead to unanticipated errors when applied to low‐concentration DNAs.

  • 2.
    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.

  • 3.
    Guschanski, Katerina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany.
    Caillaud, Damien
    Robbins, Martha M.
    Vigilant, Linda
    Females Shape the Genetic Structure of a Gorilla Population2008In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 18, no 22, p. 1809-1814Article in journal (Refereed)
  • 4.
    Guschanski, Katerina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Krause, Johannes
    Sawyer, Susanna
    Valente, Luis M.
    Bailey, Sebastian
    Finstermeier, Knut
    Sabin, Richard
    Gilissen, Emmanuel
    Sonet, Gontran
    Nagy, Zoltan T.
    Lenglet, Georges
    Mayer, Frieder
    Savolainen, Vincent
    Next-Generation Museomics Disentangles One of the Largest Primate Radiations2013In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 62, no 4, p. 539-554Article in journal (Refereed)
    Abstract [en]

    Guenons (tribe Cercopithecini) are one of the most diverse groups of primates. They occupy all of sub-Saharan Africa and show great variation in ecology, behavior, and morphology. This variation led to the description of over 60 species and subspecies. Here, using next-generation DNA sequencing (NGS) in combination with targeted DNA capture, we sequenced 92 mitochondrial genomes from museum-preserved specimens as old as 117 years. We infer evolutionary relationships and estimate divergence times of almost all guenon taxa based on mitochondrial genome sequences. Using this phylogenetic framework, we infer divergence dates and reconstruct ancestral geographic ranges. We conclude that the extraordinary radiation of guenons has been a complex process driven by, among other factors, localized fluctuations of African forest cover. We find incongruences between phylogenetic trees reconstructed from mitochondrial and nuclear DNA sequences, which can be explained by either incomplete lineage sorting or hybridization. Furthermore, having produced the largest mitochondrial DNA data set from museum specimens, we document how NGS technologies can “unlock” museum collections, thereby helping to unravel the tree-of-life. [Museum collection; next-generation DNA sequencing; primate radiation; speciation; target capture.]

  • 5.
    Guschanski, Katerina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Olivieri, G.
    Funk, S. M.
    Radespiel, U.
    MtDNA reveals strong genetic differentiation among geographically isolated populations of the golden brown mouse lemur, Microcebus ravelobensis2007In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 8, no 4, p. 809-821Article in journal (Refereed)
  • 6.
    Guschanski, Katerina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Max Planck Inst Evolutionary Anthropol, Leipzig, Germany.
    Vigilant, Linda
    McNeilage, Alastair
    Gray, Maryke
    Kagoda, Edwin
    Robbins, Martha M.
    Counting elusive animals: Comparing field and genetic census of the entire mountain gorilla population of Bwindi Impenetrable National Park, Uganda2009In: Biological Conservation, ISSN 0006-3207, E-ISSN 1873-2917, Vol. 142, no 2, p. 290-300Article in journal (Refereed)
    Abstract [en]

    Accurate population size estimates are an essential part of every effective management plan for conserving endangered species. However, censusing rare and elusive wild animals is challenging and often relies on counting indirect signs, such as nests or feces. Despite widespread use, the accuracy of such estimates has rarely been evaluated. Here we compare an estimate of population size derived solely from field data with that obtained from a combination of field and genetic data for the critically endangered population of mountain gorillas (Gorilla beringei beringei) in Bwindi Impenetrable National Park, Uganda. After genotyping DNA from 384 fecal samples at 16 microsatellite loci, the population size estimate was reduced by 10.1% to 302 individuals, compared with 336 gorillas estimated using the traditional nest-count based method alone. We found that both groups and lone silverbacks were double-counted in the field and that individuals constructed multiple nests with an overall rate of 7.8%, resulting in the overestimation of the population size in the absence of genetic data. Since the error associated with the traditional field method exceeded the estimated population growth of 5% in the last 4 years, future genetic censusing will be needed to determine how the population size is changing. This study illustrates that newly improved molecular methods allow fast, efficient and relatively affordable genotyping of several hundred samples, suggesting that genetic censusing can be widely applied to provide accurate and reliable population size estimates for a wide variety of species. (C) 2008 Elsevier Ltd. All rights reserved.

  • 7.
    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.

  • 8.
    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.

  • 9.
    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.

  • 10. Meunier, Julien
    et al.
    Lemoine, Frederic
    Soumillon, Magali
    Liechti, Angelica
    Weier, Manuela
    Guschanski, Katerina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ Lausanne, Ctr Integrat Genom, Lausanne, Switzerland.
    Hu, Haiyang
    Khaitovich, Philipp
    Kaessmann, Henrik
    Birth and expression evolution of mammalian microRNA genes2013In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 23, no 1, p. 34-45Article in journal (Refereed)
    Abstract [en]

    MicroRNAs (miRNAs) are major post-transcriptional regulators of gene expression, yet their origins and functional evolution in mammals remain little understood due to the lack of appropriate comparative data. Using RNA sequencing, we have generated extensive and comparable miRNA data for five organs in six species that represent all main mammalian lineages and birds (the evolutionary outgroup) with the aim to unravel the evolution of mammalian miRNAs. Our analyses reveal an overall expansion of miRNA repertoires in mammals, with threefold accelerated birth rates of miRNA families in placentals and marsupials, facilitated by the de novo emergence of miRNAs in host gene introns. Generally, our analyses suggest a high rate of miRNA family turnover in mammals with many newly emerged miRNA families being lost soon after their formation. Selectively preserved mammalian miRNA families gradually evolved higher expression levels, as well as altered mature sequences and target gene repertoires, and were apparently mainly recruited to exert regulatory functions in nervous tissues. However, miRNAs that originated on the X chromosome evolved high expression levels and potentially diverse functions during spermatogenesis, including meiosis, through selectively driven duplication-divergence processes. Overall, our study thus provides detailed insights into the birth and evolution of mammalian miRNA genes and the associated selective forces.

  • 11. Olivieri, Gillian
    et al.
    Zimmermann, Elke
    Randrianambinina, Blanchard
    Rasoloharijaona, Solofonirina
    Rakotondravony, Daniel
    Guschanski, Katerina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Radespiel, Ute
    The ever-increasing diversity in mouse lemurs: Three new species in north and northwestern Madagascar2007In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 43, no 1, p. 309-327Article in journal (Refereed)
  • 12. Rosengaus, Rebeca B.
    et al.
    Cornelisse, Tara
    Guschanski, Katerina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Traniello, James F. A.
    Inducible immune proteins in the dampwood termite Zootermopsis angusticollis2007In: The Science of Nature: Naturwissenschaften, ISSN 0028-1042, E-ISSN 1432-1904, Vol. 94, no 1, p. 25-33Article in journal (Refereed)
  • 13. Roy, Justin
    et al.
    Arandjelovic, Mimi
    Bradley, Brenda J.
    Guschanski, Katerina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Max Planck Inst Evolutionary Anthropol, Dept Primatol, Leipzig, Germany.
    Stephens, Colleen R.
    Bucknell, Dan
    Cirhuza, Henry
    Kusamba, Chifundera
    Kyungu, Jean Claude
    Smith, Vince
    Robbins, Martha M.
    Vigilant, Linda
    Recent divergences and size decreases of eastern gorilla populations2014In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 10, no 11, article id 20140811Article in journal (Refereed)
    Abstract [en]

    Compared with other African apes, eastern gorillas (Gorilla beringei) have been little studied genetically. We used analysis of autosomal DNA genotypes obtained from non-invasively collected faecal samples to estimate the evolutionary histories of the two extant mountain gorilla populations and the closely related eastern lowland gorillas. Our results suggest that eastern lowland gorillas and mountain gorillas split beginning some 10 000 years ago, followed 5000 years ago by the split of the two mountain gorilla populations of Bwindi Impenetrable National Park and the Virungas Massif. All three populations have decreased in effective population size, with particularly substantial 10- fold decreases for the mountain gorillas. These dynamics probably reflect responses to habitat changes resulting from climate fluctuations over the past 20 000 years as well as increasing human influence in this densely populated region in the last several thousand years.

  • 14. Sawyer, Susanna
    et al.
    Krause, Johannes
    Guschanski, Katerina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ Lausanne, Ctr Integrat Genom, Lausanne, Switzerland.
    Savolainen, Vincent
    Paeaebo, Svante
    Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA2012In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 3, article id e34131Article in journal (Refereed)
    Abstract [en]

    DNA that survives in museum specimens, bones and other tissues recovered by archaeologists is invariably fragmented and chemically modified. The extent to which such modifications accumulate over time is largely unknown but could potentially be used to differentiate between endogenous old DNA and present-day DNA contaminating specimens and experiments. Here we examine mitochondrial DNA sequences from tissue remains that vary in age between 18 and 60,000 years with respect to three molecular features: fragment length, base composition at strand breaks, and apparent C to T substitutions. We find that fragment length does not decrease consistently over time and that strand breaks occur preferentially before purine residues by what may be at least two different molecular mechanisms that are not yet understood. In contrast, the frequency of apparent C to T substitutions towards the 5'-ends of molecules tends to increase over time. These nucleotide misincorporations are thus a useful tool to distinguish recent from ancient DNA sources in specimens that have not been subjected to unusual or harsh treatments.

  • 15. Thalmann, Olaf
    et al.
    Wegmann, Daniel
    Spitzner, Marie
    Arandjelovic, Mimi
    Guschanski, Katerina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Max Planck Inst Evolutionary Anthropol, Leipzig, Germany.
    Leuenberger, Christoph
    Bergl, Richard A.
    Vigilant, Linda
    Historical sampling reveals dramatic demographic changes in western gorilla populations2011In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 11, article id 85Article in journal (Refereed)
    Abstract [en]

    Background: Today many large mammals live in small, fragmented populations, but it is often unclear whether this subdivision is the result of long-term or recent events. Demographic modeling using genetic data can estimate changes in long-term population sizes while temporal sampling provides a way to compare genetic variation present today with that sampled in the past. In order to better understand the dynamics associated with the divergences of great ape populations, these analytical approaches were applied to western gorillas (Gorilla gorilla) and in particular to the isolated and Critically Endangered Cross River gorilla subspecies (G. g. diehli). Results: We used microsatellite genotypes from museum specimens and contemporary samples of Cross River gorillas to infer both the long-term and recent population history. We find that Cross River gorillas diverged from the ancestral western gorilla population similar to 17,800 years ago (95% HDI: 760, 63,245 years). However, gene flow ceased only similar to 420 years ago (95% HDI: 200, 16,256 years), followed by a bottleneck beginning similar to 320 years ago (95% HDI: 200, 2,825 years) that caused a 60 fold decrease in the effective population size of Cross River gorillas. Direct comparison of heterozygosity estimates from museum and contemporary samples suggests a loss of genetic variation over the last 100 years. Conclusions: The composite history of western gorillas could plausibly be explained by climatic oscillations inducing environmental changes in western equatorial Africa that would have allowed gorilla populations to expand over time but ultimately isolate the Cross River gorillas, which thereafter exhibited a dramatic population size reduction. The recent decrease in the Cross River population is accordingly most likely attributable to increasing anthropogenic pressure over the last several hundred years. Isolation of diverging populations with prolonged concomitant gene flow, but not secondary admixture, appears to be a typical characteristic of the population histories of African great apes, including gorillas, chimpanzees and bonobos.

  • 16.
    van der Valk, Tom
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Durazo, Frida Lona
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ Toronto, Dept Anthropol, Mississauga, ON, Canada..
    Dalen, Love
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden..
    Guschanski, Katerina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Whole mitochondrial genome capture from faecal samples and museum-preserved specimens2017In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 17, no 6, p. e111-e121Article in journal (Refereed)
    Abstract [en]

    Population-scale molecular studies of endangered and cryptic species are often limited by access to high-quality samples. The use of noninvasively collected samples or museum-preserved specimens reduces the pressure on modern populations by removing the need to capture and handle live animals. However, endogenous DNA content in such samples is low, making shotgun sequencing a financially prohibitive approach. Here, we apply a target enrichment method to retrieve mitochondrial genomes from 65 museum specimens and 56 noninvasively collected faecal samples of two endangered great ape species, Grauer's gorilla and the eastern chimpanzee. We show that the applied method is suitable for a wide range of sample types that differ in endogenous DNA content, increasing the proportion of target reads to over 300-fold. By systematically evaluating biases introduced during target enrichment of pooled museum samples, we show that capture is less efficient for fragments shorter or longer than the baits, that the proportion of human contaminating reads increases postcapture although capture efficiency is lower for human compared to gorilla fragments with a gorilla-generated bait, and that the rate of jumping PCR is considerable, but can be controlled for with a double-barcoding approach. We succeed in capturing complete mitochondrial genomes from faecal samples, but observe reduced capture efficiency as sequence divergence increases between the bait and target species. As previously shown for museum specimens, we demonstrate here that mitochondrial genome capture from field-collected faecal samples is a robust and reliable approach for population-wide studies of nonmodel organisms.

  • 17. Vigilant, Linda
    et al.
    Guschanski, Katerina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Using genetics to understand the dynamics of wild primate populations2009In: Primates, ISSN 0032-8332, E-ISSN 1610-7365, Vol. 50, no 2, p. 105-120Article in journal (Refereed)
    Abstract [en]

    While much can be learned about primates by means of observation, the slow life history of many primates means that even decades of dedicated effort cannot illuminate long-term evolutionary processes. For example, while the size of a contemporary population can be estimated from field censuses, it is often desirable to know whether a population has been constant or changing in size over a time frame of hundreds or thousands of years. Even the nature of “a population” is open to question, and the extent to which individuals successfully disperse among defined populations is also difficult to estimate by using observational methods alone. Researchers have thus turned to genetic methods to examine the size, structure, and evolutionary histories of primate populations. Many results have been gained by study of sequence variation of maternally inherited mitochondrial DNA, but in recent years researchers have been increasingly focusing on analysis of short, highly variable microsatellite segments in the autosomal genome for a high-resolution view of evolutionary processes involving both sexes. In this review we describe some of the insights thus gained, and discuss the likely impact on this field of new technologies such as high-throughput DNA sequencing.

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