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  • 151. Leonard, J.A.
    et al.
    Vilá, C.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Wayne, R.K.
    Legacy Lost: Genetic variability and population size of extirpated US gray wolves.2005In: Molecular Ecology, no 126, p. 198-206Article in journal (Refereed)
  • 152.
    Leonard, Jennifer A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ancient DNA applications for wildlife conservation2008In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 17, no 19, p. 4186-4196Article, review/survey (Refereed)
    Abstract [en]

    Ancient DNA analyses of historical, archaeological and paleontological remains can contribute important information for the conservation of populations and species that cannot be obtained any other way. In addition to ancient DNA analyses involving a single or few individuals, population level studies are now possible. Biases inherent in estimating population parameters and history from modern genetic diversity are exaggerated when populations are small or have been heavily impacted by recent events, as is common for many endangered species. Going directly back in time to study past populations removes many of the assumptions that undermine conclusions based only on recent populations. Accurate characterization of historic population size, levels of gene flow and relationships with other populations are fundamental to developing appropriate conservation and management plans. The incorporation of ancient DNA into conservation genetics holds a lot of potential, if it is employed responsibly.

  • 153.
    Leonard, Jennifer A
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionary Biology.
    Rohland, Nadin
    Glaberman, Scott
    Fleischer, Robert C
    Caccone, Adalgisa
    Hofreiter, Michael
    A rapid loss of stripes: the evolutionary history of the extinct quagga.2005In: Biol Lett, ISSN 1744-9561, Vol. 1, no 3, p. 291-5Article in journal (Refereed)
    Abstract [en]

    Twenty years ago, the field of ancient DNA was launched with the publication of two short mitochondrial (mt) DNA sequences from a single quagga (Equus quagga) museum skin, an extinct South African equid (Higuchi et al. 1984 Nature312, 282-284). This was the first extinct species from which genetic information was retrieved. The DNA sequences of the quagga showed that it was more closely related to zebras than to horses. However, quagga evolutionary history is far from clear. We have isolated DNA from eight quaggas and a plains zebra (subspecies or phenotype Equus burchelli burchelli). We show that the quagga displayed little genetic diversity and very recently diverged from the plains zebra, probably during the penultimate glacial maximum. This emphasizes the importance of Pleistocene climate changes for phylogeographic patterns in African as well as Holarctic fauna.

  • 154.
    Leonard, Jennifer A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Vilà, Carles
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Fox-Dobbs, Kena
    Koch, Paul L.
    Wayne, Robert K.
    Van Valkenburgh, Blaire
    Megafaunal extinctions and the disappearance of a specialized wolf ecomorph2007In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 17, no 13, p. 1146-1150Article in journal (Refereed)
    Abstract [en]

    The gray wolf (Canis lupus) is one of the few large predators to survive the Late Pleistocene megafaunal extinctions [1]. Nevertheless, wolves disappeared from northern North America in the Late Pleistocene, suggesting they were affected by factors that eliminated other species. Using skeletal material collected from Pleistocene permafrost deposits of eastern Beringia, we present a comprehensive analysis of an extinct vertebrate by exploring genetic (mtDNA), morphologic, and isotopic (delta(13)C, delta(15)N) data to reveal the evolutionary relationships, as well as diet and feeding behavior, of ancient wolves. Remarkably, the Late Pleistocene wolves are genetically unique and morphologically distinct. None of the 16 mtDNA haplotypes recovered from a sample of 20 Pleistocene eastern-Beringian wolves was shared with any modern wolf, and instead they appear most closely related to Late Pleistocene wolves of Eurasia. Moreover, skull shape, tooth wear, and isotopic data suggest that eastern-Beringian wolves were specialized hunters and scavengers of extinct megafauna. Thus, a previously unrecognized, uniquely adapted, and genetically distinct wolf ecomorph suffered extinction in the Late Pleistocene, along with other megafauna. Consequently, the survival of the species in North America depended on the presence of more generalized forms elsewhere.

  • 155.
    Leonard, Jennifer A
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Wayne, Robert K
    Native Great Lakes wolves were not restored2008In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 4, no 1, p. 95-98Article in journal (Refereed)
    Abstract [en]

    Wolves from the Great Lakes area were historically decimated due to habitat loss and predator control programmes. Under the protection of the US Endangered Species Act, the population has rebounded to approximately 3000 individuals. We show that the pre-recovery population was dominated by mitochondrial DNA haplotypes from an endemic American wolf referred to here as the Great Lakes wolf. In contrast, the recent population is admixed, and probably derives also from the grey wolf (Canis lupus) of Old World origin and the coyote (Canis latrans). Consequently, the pre-recovery population has not been restored, casting doubt on delisting actions.

  • 156.
    Leonard, Jennifer
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Shanks, Orin
    Hofreiter, E.
    Kreuz, Eva
    Hodges, Larry
    Ream, Walt
    Wayne, Robert K.
    Fleischer, Robert C.
    Animal DNA in PCR reagents plagues ancient DNA research2007In: Journal of Archaeological Science, ISSN 0305-4403, E-ISSN 1095-9238, Vol. 34, no 9, p. 1361-1366Article in journal (Refereed)
    Abstract [en]

    Molecular archaeology brings the tools of molecular biology to bear on fundamental questions in archaeology, anthropology, evolution, and ecology. Ancient DNA research is becoming widespread as evolutionary biologists and archaeologists discover the power of the polymerase chain reaction (PCR) to amplify DNA from ancient plant and animal remains. However, the extraordinary susceptibility of PCR to contamination by extraneous DNA is not widely appreciated. We report the independent observation of DNA from domestic animals in PCR reagents and ancient samples in four separate laboratories. Since PCR conditions used in ancient DNA analyses are extremely sensitive, very low concentrations of contaminating DNA can cause false positives. Previously unidentified animal DNA in reagents can confound ancient DNA research on certain domestic animals, especially cows, pigs, and chickens.

  • 157. Lewis, Cathryn M
    et al.
    Levinson, Douglas F
    Wise, Lesley H
    DeLisi, Lynn E
    Straub, Richard E
    Hovatta, Iiris
    Williams, Nigel M
    Schwab, Sibylle G
    Pulver, Ann E
    Faraone, Stephen V
    Brzustowicz, Linda M
    Kaufmann, Charles A
    Garver, David L
    Gurling, Hugh M D
    Lindholm, Eva
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Coon, Hilary
    Moises, Hans W
    Byerley, William
    Shaw, Sarah H
    Mesen, Andrea
    Sherrington, Robin
    O'Neill, F Anthony
    Walsh, Dermot
    Kendler, Kenneth S
    Ekelund, Jesper
    Paunio, Tiina
    Lännqvist, Jouko
    Peltonen, Leena
    O'Donovan, Michael C
    Owen, Michael J
    Wildenauer, Dieter B
    Maier, Wolfgang
    Nestadt, Gerald
    Blouin, Jean-Louis
    Antonarakis, Stylianos E
    Mowry, Bryan J
    Silverman, Jeremy M
    Crowe, Raymond R
    Cloninger, C Robert
    Tsuang, Ming T
    Malaspina, Dolores
    Harkavy-Friedman, Jill M
    Svrakic, Dragan M
    Bassett, Anne S
    Holcomb, Jennifer
    Kalsi, Gursharan
    McQuillin, Andrew
    Brynjolfson, Jon
    Sigmundsson, Thordur
    Petursson, Hannes
    Jazin, Elena
    Zoëga, Tomas
    Helgason, Tomas
    Genome scan meta-analysis of schizophrenia and bipolar disorder, part II: Schizophrenia2003In: American Journal of Human Genetics, ISSN 0002-9297, E-ISSN 1537-6605, Am J Hum Genet, ISSN 0002-9297, Vol. 73, no 1, p. 34-48Article in journal (Refereed)
    Abstract [en]

    Schizophrenia is a common disorder with high heritability and a 10-fold increase in risk to siblings of probands. Replication has been inconsistent for reports of significant genetic linkage. To assess evidence for linkage across studies, rank-based genome scan meta-analysis (GSMA) was applied to data from 20 schizophrenia genome scans. Each marker for each scan was assigned to 1 of 120 30-cM bins, with the bins ranked by linkage scores (1 = most significant) and the ranks averaged across studies (R(avg)) and then weighted for sample size (N(sqrt)[affected casess]). A permutation test was used to compute the probability of observing, by chance, each bin's average rank (P(AvgRnk)) or of observing it for a bin with the same place (first, second, etc.) in the order of average ranks in each permutation (P(ord)). The GSMA produced significant genomewide evidence for linkage on chromosome 2q (PAvgRnk<.000417). Two aggregate criteria for linkage were also met (clusters of nominally significant P values that did not occur in 1,000 replicates of the entire data set with no linkage present): 12 consecutive bins with both P(AvgRnk) and P(ord)<.05, including regions of chromosomes 5q, 3p, 11q, 6p, 1q, 22q, 8p, 20q, and 14p, and 19 consecutive bins with P(ord)<.05, additionally including regions of chromosomes 16q, 18q, 10p, 15q, 6q, and 17q. There is greater consistency of linkage results across studies than has been previously recognized. The results suggest that some or all of these regions contain loci that increase susceptibility to schizophrenia in diverse populations.

  • 158.
    Liden, K.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Eriksson, G.
    Nordqvist, B.
    Götherström, A.
    Bendixen, E.
    The wet and the wild followed by the dry and the tame - or did they occur at the same time?: Diet in Mesolithic Neolithic southern Sweden2004In: Antiquity, ISSN 0003-598X, no 78, p. 23-33Article in journal (Refereed)
  • 159.
    Lindberg, Julia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Björnerfeldt, Susanne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Bakken, Morten
    Vilà, Carles
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Saetre, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Selection for tameness modulates the expression of heme related genes in silver foxes2007In: Behavioral and Brain Functions, ISSN 1744-9081, E-ISSN 1744-9081, Vol. 3, p. 18-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: The genetic and molecular mechanisms of tameness are largely unknown. A line of silver foxes (Vulpes vulpes) selected for non-aggressive behavior has been used in Russia since the 1960's to study the effect of domestication. We have previously compared descendants of these selected (S) animals with a group of non-selected (NS) silver foxes kept under identical conditions, and showed that changes in the brain transcriptome between the two groups are small. Unexpectedly, many of the genes showing evidence of differential expression between groups were related to hemoproteins. RESULTS: In this study, we use quantitative RT-PCR to demonstrate that the activity of heme related genes differ between S and NS foxes in three regions of the brain. Furthermore, our analyses also indicate that changes in mRNA levels of heme related genes can be well described by an additive polygenic effect. We also show that the difference in genetic background between the two lines of foxes is limited, as estimated by mitochondrial DNA divergence. CONCLUSION: Our results indicate that selection for tameness can modify the expression of heme related genes in canid brain regions known to modulate emotions and behavior. The possible involvement of heme related genes in behavior is surprising. It is possible that hemoglobin modulates the behavior of canids by interaction with CO and NO signaling. Another possibility is that hemorphins, known to be produced after enzymatic cleavage of hemoglobin, are responsible for behavioral alterations. Thus, we hypothesize that hemoglobin metabolism can be a functionally relevant aspect of the domestic phenotype in foxes selected for tameness.

  • 160.
    Lindberg, Julia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Björnerfeldt, Susanne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Saetre, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Svartberg, Kenth
    Seehuus, Birgitte
    Bakken, Morten
    Vilà, Carles
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Selection for tameness has changed brain gene expression in silver foxes2005In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 15, no 22, p. R915-916Article in journal (Refereed)
  • 161.
    Lindell, Johan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Mendez-De La Cruz, Fausto R.
    Murphy, Robert W.
    Deep biogeographical history and cytonuclear discordance in the black-tailed brush lizard2008In: Biological Journal of the Linnean Society, ISSN 0024-4066, E-ISSN 1095-8312, Vol. 94, no 1, p. 89-104Article in journal (Refereed)
    Abstract [en]

    Molecular tools help us deduce historical events such as vicariance, dispersal, gene flow and speciation. However, our inferences are inevitably linked to the nature of the characters that we use to infer history. For example, the difference in inheritance patterns of mitochondrial DNA (mtDNA) and nuclear DNA (non-recombining maternal vs. recombining biparental inheritance) may lead us to propose different intraspecific histories. The peninsula of Baja California of north-western Mexico, a region affected by a complex geological history involving temporary seaways, permits evaluation of differences between these character types. We sequenced 1966 bp of mtDNA to reconstruct the genealogical history of Urosaurus nigricaudus (black-tailed brush lizard) from samples spanning the entire peninsula. The genealogy revealed several deep divergences, congruent with temporary vicariance events in the mid-peninsular, Loreto and Cape regions, as well as a major split across the Isthmus of La Paz, possibly resulting from a late Miocene seaway. The results support an emerging picture of the historical biogeography of Baja California, which suggests that key vicariance events are older than commonly perceived. The maternal genealogy of U. nigricaudus sharply contrasts with variation in allozymes that suggests very little differentiation across mitochondrial breaks, consistent with a pattern of ongoing gene flow. We interpret this cytonuclear discordance in relation to the historical biogeography of the region.

  • 162.
    Lindell, Johan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Murphy, Robert W.
    Simple identification of mitochondrial lienages in contact zones based on lineage-selective primers2008In: Molecular Ecology Resources, ISSN 1755-098X, Vol. 8, no 1, p. 66-73Article in journal (Refereed)
    Abstract [en]

    A variety of research projects focus on genetic variation among and within maternal lineages as encompassed by mitochondrial DNA (mtDNA). While mtDNA often differs substantially between species, large differences may also be found within species. The evaluation of such divergent lineages, for example in intraspecific contact zones (hybrid zones), commonly involves sequencing numerous individuals. Large-scale sequencing is both expensive and labour-intensive. Based on sequences from 15 individuals, we devised a simple and quick polymerase chain reaction assay for identification of divergent mtDNA lineages in a secondary contact zone of the side-blotched lizard (Uta stansburiana). The application uses lineage-selective primers to amplify a lineage-diagnostic product, and is based on each group of mtDNA haplotypes being a monophyletic assemblage of haplotypes sharing the same maternal ancestry, deeply divergent from the other group. The assay was tested on a larger sample (n = 147) of specimens from the contact zone, confirming its usefulness in quick and reliable identification of mtDNA lineages. This approach can be modified for other species, provided diagnostic lineage variation is available, and may also be performed in simple laboratory settings while conducting fieldwork.

  • 163. Linderholm, Anna
    et al.
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Lidén, Kerstin
    Holmlund, Gunilla
    Götherström, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Cryptic Contamination and Phylogenetic Nonsense2008In: PloS one, ISSN 1932-6203, Vol. 3, no 5, p. e2316-Article in journal (Refereed)
    Abstract [en]

    Ancient human DNA has been treated cautiously ever since the problems related to this type of material were exposed in the early 1990s, but as sequential genetic data from ancient specimens have been key components in several evolutionary and ecological studies, interest in ancient human DNA is on the increase again. It is especially tempting to approach archaeological and anthropological questions through this type of material, but DNA from ancient human tissue is notoriously complicated to work with due to the risk of contamination with modern human DNA. Various ways of authenticating results based on ancient human DNA have been developed to circumvent the problems. One commonly used method is to predict what the contamination is expected to look like and then test whether the ancient human DNA fulfils this prediction. If it does, the results are rejected as contamination, while if it does not, they are often considered authentic. We show here that human contamination in ancient material may well deviate from local allele frequencies or the distributions to be found among the laboratory workers and archaeologists. We conclude that it is not reliable to authenticate ancient human DNA solely by showing that it is different from what would be expected from people who have handled the material.

  • 164. Lindgren, G.
    et al.
    Backström, N.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Swenburne, J.
    Hellborg, L.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Einarsson, A.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Sandberg, K.
    Cothran, G.
    Vila, C.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Binns, M.
    Ellegren, H.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Limited number of patrilines in horse domestication.2004In: Nature Genetics, no 36, p. 335-336Article in journal (Refereed)
  • 165.
    Lindholm, Eva
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ekholm, Birgit
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Shaw, Sarah
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Jalonen, Paula
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Johansson, Gunnel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Pettersson, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Sherrington, Robin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Adolfsson, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    A schizophrenia-susceptibility locus at 6q25, in one of the world's largest reported pedigrees2001In: American Journal of Human Genetics, ISSN 0002-9297, E-ISSN 1537-6605, Vol. 69, no 1, p. 96-105Article in journal (Refereed)
  • 166.
    Lindholm, Eva
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Åberg, Karolina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ekholm, Birgit
    Pettersson, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Adolfsson, Rolf
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Reconstruction of Ancestral Haplotypes in a 12-Generation Schizophrenia Pedigree2004In: Psychiatric Genetics, ISSN 0955-8829, E-ISSN 1473-5873, Vol. 14, no 1, p. 1-8Article in journal (Refereed)
    Abstract [en]

    We searched for candidate chromosomal regions inherited identical by descent in 19 patients suffering from schizophrenia or schizoaffective disorder that are related 12 generations back, to an ancestral couple born in the middle of the seventeenth century. To accomplish this goal, we constructed complete chromosomal haplotypes for each patient using genotype data from 450 markers. In total, 12 haplotype regions (with sizes ranging from 0.6 to 10.9 cM) constituted by three markers each were identical in three or more of the affected individuals. The largest genomic segment was located on 6q25, a region previously shown to be significantly more frequent in patients than controls, and proposed to contain a schizophrenia susceptibility locus. For the remaining 11 candidate haplotypes, we estimated haplotype frequencies from all the 43 affected members collected from the same family and 46 unrelated control individuals. This analysis indicated that at least four of the 11 candidate haplotypes are ancestral, since the frequencies were significantly higher in patients than in controls. Five additional haplotypes showed higher estimated frequencies in the patients but the differences were not significant. Interestingly, five of these 11 genomic regions are located in, or close to, candidate regions previously suggested to contain susceptibility genes for schizophrenia. The regions are 5q21-23, 8p21-22, 10p13-15, 13q12-13 and 22q12-13. Several of these haplotypes are probably ancestral linkage disequilibrium blocks inherited from the original couple. There exists, however, the possibility that one or more of these regions harbour schizophrenia susceptibility loci that may have epistatic interactions among them.

  • 167. Lislevland, T
    et al.
    Byrkjedal, I
    Borge, T
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Saetre, G P
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Egg size in relation to sex of embryo, brood sex ratios and laying sequence in northern lapwings (Vanellus vanellus)2005In: Journal of Zoology, no 267, p. 81-87Article in journal (Refereed)
  • 168. Litvinchuk, Spartak N.
    et al.
    Mazepa, Glib O.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Pasynkova, Rosa A.
    Saidov, Abdusattor
    Satorov, Toszhiddin
    Chikin, Yuriy A.
    Shabanov, Dmitriy A.
    Crottini, Angelica
    Borkin, Leo J.
    Rosanov, Jury M.
    Stoeck, Matthias
    Influence of environmental conditions on the distribution of Central Asian green toads with three ploidy levels2011In: Journal of Zoological Systematics and Evolutionary Research, ISSN 0947-5745, E-ISSN 1439-0469, Vol. 49, no 3, p. 233-239Article in journal (Refereed)
    Abstract [en]

    We studied the distribution of Palearctic green toads (Bufo viridis subgroup), an anuran species group with three ploidy levels, inhabiting the Central Asian Amudarya River drainage. Various approaches (one-way, multivariate, components variance analyses and maximum entropy modelling) were used to estimate the effect of altitude, precipitation, temperature and land vegetation covers on the distribution of toads. It is usually assumed that polyploid species occur in regions with harsher climatic conditions (higher latitudes, elevations, etc.), but for the green toads complex, we revealed a more intricate situation. The diploid species (Bufo shaartusiensis and Bufo turanensis) inhabit the arid lowlands (from 44 to 789 m a.s.l.), while tetraploid Bufo pewzowi were recorded in mountainous regions (340-3492 m a.s.l.) with usually lower temperatures and higher precipitation rates than in the region inhabited by diploid species. The triploid species Bufo baturae was found in the Pamirs (Tajikistan) at the highest altitudes (2503-3859 m a.s.l.) under the harshest climatic conditions.

  • 169.
    Løe, Geir
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ecology and Evolution of Resistance to Herbivory: Trichome Production in Arabidopsis lyrata2006Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis, I examine variation in occurrence and performance of glabrous and trichome-producing plants of the perennial herb Arabidopsis lyrata. I combine field studies and genetic analysis to (1) examine the function of trichomes as a resistance character in natural populations, (2) compare the magnitude of population differentiation in trichome-production and at putatively neutral marker loci, (3) examine the molecular genetic basis of trichome-production, and (4) quantify the effects of herbivore removal on population growth and relative performance of glabrous and trichome-producing plants.

    In a survey of 30 populations of A. lyrata in Norway and Sweden, I documented spatiotemporal variation in damage from insect herbivores. With few exceptions, glabrous plants were more damaged by herbivorous insects than trichome-producing plants in polymorphic populations. Damage levels varied substantially among populations and among years. The intensity of herbivory quantified as mean leaf removal to glabrous plants was higher in polymorphic populations than in monomorphic glabrous populations.

    Within the Swedish range, populations were more strongly differentiated at the locus coding for glabrousness than at eight putatively neutral isozyme loci. This is consistent with the hypothesis that trichome production is subject to divergent selection.

    A study of the genetic basis of trichome production showed that glabrousness was associated with mutations in an orthologue to GLABROUS1, a regulatory gene known to cause glabrousness in A. thaliana. Comparative data indicate that the genetic basis of glabrousness varies among populations.

    Experimental removal of insect herbivores in a natural A. lyrata population increased population growth rate and the relative fitness of the glabrous morph. The results suggest that insect herbivory may influence both population dynamics and selection on trichome production in A. lyrata.

    List of papers
    1. Trichome production and spatiotemporal variation in herbivory in the perennial herb Arabidopsis lyrata
    Open this publication in new window or tab >>Trichome production and spatiotemporal variation in herbivory in the perennial herb Arabidopsis lyrata
    2007 (English)In: Oikos, ISSN 0030-1299, E-ISSN 1600-0706, Vol. 116, no 1, p. 134-142Article in journal (Refereed) Published
    Abstract [en]

    Allocation theory suggests that the optimal level of resistance against herbivores should vary with the risk of herbivory if allocation to resistance is costly. The perennial herb Arabidopsis lyrata has a genetically based polymorphism for- trichome production and occurs in a glabrous and a trichome-producing form. Leaf trichomes (hairs) can protect plants against insect herbivores, and may increase tolerance to drought and UV-radiation. To examine the functional significance of trichome production, we documented the frequency of glabrous plants and damage by insect herbivores in 30 A. lyrata populations in Sweden and Norway. The proportion of glabrous plants ranged from 0.10 to 0.71 (median = 0.44) in polymorphic populations; 7 of 12 populations in Norway and 14 of 18 populations in Sweden were monomorphic glabrous, i.e. with fewer than 5% trichome-producing plants. The mean proportion of the leaf area removed by herbivores varied substantially among populations and years. With few exceptions, glabrous plants were more damaged than trichome-producing plants in polymorphic populations. The intensity of herbivory quantified as the mean damage to glabrous plants tended to be higher in polymorphic populations than in populations monomorphic for the glabrous morph and was higher in Sweden than in Norway. In Norway, both the magnitude of herbivore damage and the frequency of trichome-producing plants tended to decrease with increasing altitude. The results indicate that leaf trichomes contribute to resistance against herbivorous insects in A. lyrata, and suggest that herbivore-mediated selection contributes to the maintenance of the polymorphism in trichome production.

    Keywords
    Spermatophyta, Angiospermae, Dicotyledones, Cruciferae, Arabidopsis, Herbivorous, Time variation, Spatial variation, Trichome
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-94036 (URN)10.1111/j.2006.0030-1299.15022.x (DOI)000243413600013 ()
    Available from: 2006-03-03 Created: 2006-03-03 Last updated: 2017-12-14
    2. Population structure in Arabidopsis lyrata: evidence for divergent selection on trichome production
    Open this publication in new window or tab >>Population structure in Arabidopsis lyrata: evidence for divergent selection on trichome production
    2004 (English)In: Evolution, Vol. 58, no 12, p. 2831-2836Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-94037 (URN)
    Available from: 2006-03-03 Created: 2006-03-03 Last updated: 2009-03-31Bibliographically approved
    3. Gene, phenotype and function: GLABROUS1 and resistance to herbivory in natural populations of Arabidopsis lyrata
    Open this publication in new window or tab >>Gene, phenotype and function: GLABROUS1 and resistance to herbivory in natural populations of Arabidopsis lyrata
    Show others...
    2007 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 16, no 2, p. 453-462Article in journal (Refereed) Published
    Abstract [en]

    The molecular genetic basis of adaptive variation is of fundamental importance for evolutionary dynamics, but is still poorly known. Only in very few cases has the relationship between genetic variation at the molecular level, phenotype and function been established in natural populations. We examined the functional significance and genetic basis of a polymorphism in production of leaf hairs, trichomes, in the perennial herb Arabidopsis lyrata. Earlier studies suggested that trichome production is subject to divergent selection. Here we show that the production of trichomes is correlated with reduced damage from insect herbivores in natural populations, and using statistical methods developed for medical genetics we document an association between loss of trichome production and mutations in the regulatory gene GLABROUS1. Sequence data suggest that independent mutations in this regulatory gene have provided the basis for parallel evolution of reduced resistance to insect herbivores in different populations of A. lyrata and in the closely related Arabidopsis thaliana. The results show that candidate genes identified in model organisms provide a valuable starting point for analysis of the genetic basis of phenotypic variation in natural populations.

    Keywords
    adaptation, Arabidopsis lyrata, association analysis, candidate gene, GLABROUS1, herbivory
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-94038 (URN)10.1111/j.1365-294X.2007.03109.x (DOI)000243305200017 ()17217357 (PubMedID)
    Available from: 2006-03-03 Created: 2006-03-03 Last updated: 2017-12-14Bibliographically approved
    4. Selection on trichome-production in a natural population of Arabidopsis lyrata
    Open this publication in new window or tab >>Selection on trichome-production in a natural population of Arabidopsis lyrata
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-94039 (URN)
    Available from: 2006-03-03 Created: 2006-03-03 Last updated: 2012-10-24
  • 170.
    Løe, Geir
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ågren, Jon
    Selection on trichome-production in a natural population of Arabidopsis lyrataManuscript (Other (popular science, discussion, etc.))
  • 171. Maldonado, J.E.
    et al.
    Hertel, F.
    Vila, C.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Discordant patterns of morphological variation in genetically divergent populations of ornate shrews (Sorex ornatus).2004In: Journal of Mammalogy, no 85, p. 886-896Article in journal (Refereed)
  • 172. Maldonado, JE
    et al.
    Leonard, JA
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Miranda, GA
    Ortega, J
    Wayne, RK
    Aguilera, RJ
    Then polymorphic microsatellite loci for the endangered Buena Vista Lake shrew (Sorex ornatus relictus).2006In: Molecular Ecology Notes, no 6, p. 349-352Article in journal (Refereed)
  • 173.
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ancient DNA as a Means to Investigate the European Neolithic2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The transition from a hunter-gatherer lifestyle to a farming lifestyle, i.e. the Neolithisation, is arguably the most important event in human prehistory. While the geography and dating of the Neolithisation is well known, the process is still under debate, especially if it occurred through diffusion of ideas or with migrating farmers. The process accelerated when alternative use of domesticated animals increased. Especially the use of dairy products, and the consumption of unprocessed milk, appears to be of importance. As milk consumption (lactose digestion) is dependent upon genetic components, it is debated whether the genetic disposition allowed for dairy production to evolve, or if the usages of dairy products added selection pressure that eventually lead to present day allele frequencies. Molecular genetics have the potential to solve this and similar questions, but only if the contamination problem, where authentic DNA can be distinguished from modern contaminating DNA, can be resolved.

    Here I investigate the nature and extent of contamination with modern human DNA in museum specimens and explore several approaches to minimise this contamination and to authenticate DNA results from ancient humans. I use real-time quantification, pyrosequencing and FLX-generated clonal sequencing assays to generate data on ancient humans and ancient dogs. I further use the techniques to study the development of lactase persistence and the nature of animal domestication.

    The results presented show that sample-based contamination is extensive, but can be minimised if treated with bleach. I retrieved authentic HVSI sequences from 30 Neolithic hunter-gatherers and farmers from Sweden, of which eighteen also yielded nuclear data indicating that the farmers had a higher frequency of the allele linked to lactase persistence compared to the hunter-gatherers. I conclude that genetic data from ancient humans as well as from ancient animals can be retrieved and used, but only under high stringency.

    List of papers
    1. Extensive human DNA contamination in extracts from ancient dog bones and teeth
    Open this publication in new window or tab >>Extensive human DNA contamination in extracts from ancient dog bones and teeth
    Show others...
    2005 (English)In: Molecular Biology and Evolution, ISSN 0737-4038, Vol. 22, no 10, p. 2040-2047Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-96064 (URN)
    Available from: 2007-08-31 Created: 2007-08-31 Last updated: 2009-03-31Bibliographically approved
    2. More on contamination: The use of asymmetric molecular behavior to identify authentic ancient human DNA
    Open this publication in new window or tab >>More on contamination: The use of asymmetric molecular behavior to identify authentic ancient human DNA
    Show others...
    2007 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 24, no 4, p. 998-1004Article in journal (Refereed) Published
    Abstract [en]

    Authentication of ancient human DNA results is an exceedingly difficult challenge due to the presence of modern contaminant DNA sequences. Nevertheless, the field of ancient human genetics generates huge scientific and public interest, and thus researchers are rarely discouraged by problems concerning the authenticity of such data. Although several methods have been developed to the purpose of authenticating ancient DNA (aDNA) results, while they are useful in faunal research, most of the methods have proven complicated to apply to ancient human DNA. Here, we investigate in detail the reliability of one of the proposed criteria, that of appropriate molecular behavior. Using real-time polymerase chain reaction (PCR) and pyrosequencing, we have quantified the relative levels of authentic aDNA and contaminant human DNA sequences recovered from archaeological dog and cattle remains. In doing so, we also produce data that describes the efficiency of bleach incubation of bone powder and its relative detrimental effects on contaminant and authentic ancient DNA. We note that bleach treatment is significantly more detrimental to contaminant than to authentic aDNA in the bleached bone powder. Furthermore, we find that there is a substantial increase in the relative proportions of authentic DNA to contaminant DNA as the PCR target fragment size is decreased. We therefore conclude that the degradation pattern in aDNA provides a quantifiable difference between authentic aDNA and modern contamination. This asymmetrical behavior of authentic and contaminant DNA can be used to identify authentic haplotypes in human aDNA studies.

    Keywords
    contamination, ancient DNA, authentication
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-96065 (URN)10.1093/molbev/msm015 (DOI)000245353200013 ()17255122 (PubMedID)
    Available from: 2007-08-31 Created: 2007-08-31 Last updated: 2017-12-13Bibliographically approved
    3. Barking up the wrong tree: Modern northern European dogs fail to explain their origin
    Open this publication in new window or tab >>Barking up the wrong tree: Modern northern European dogs fail to explain their origin
    Show others...
    2008 (English)In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 8, article id 71Article in journal (Refereed) Published
    Abstract [en]

    Background: Geographic distribution of the genetic diversity in domestic animals, particularly mitochondrial DNA, has often been used to infer centers of domestication. The underlying presumption is that phylogeographic patterns among domesticates were established during, or shortly after the domestication. Human activities are assumed not to have altered the haplogroup frequencies to any great extent. We studied this hypothesis by analyzing 24 mtDNA sequences in ancient Scandinavian dogs. Breeds originating in northern Europe are characterized by having a high frequency of mtDNA sequences belonging to a haplogroup rare in other populations (HgD). This has been suggested to indicate a possible origin of the haplogroup (perhaps even a separate domestication) in central or northern Europe. Results: The sequences observed in the ancient samples do not include the haplogroup indicative for northern European breeds (HgD). Instead, several of them correspond to haplogroups that are uncommon in the region today and that are supposed to have Asian origin. Conclusion: We find no evidence for local domestication. We conclude that interpretation of the processes responsible for current domestic haplogroup frequencies should be carried out with caution if based only on contemporary data. They do not only tell their own story, but also that of humans.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-96066 (URN)10.1186/1471-2148-8-71 (DOI)000254663500001 ()18307773 (PubMedID)
    Available from: 2007-08-31 Created: 2007-08-31 Last updated: 2017-12-14Bibliographically approved
    4. Ancient human DNA: authentication through FLX-sequenced PCR products in conjunction with bleach pre-treatment, quantitative PCR, assesment of assymetric behaviour and negative controls
    Open this publication in new window or tab >>Ancient human DNA: authentication through FLX-sequenced PCR products in conjunction with bleach pre-treatment, quantitative PCR, assesment of assymetric behaviour and negative controls
    Show others...
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-96067 (URN)
    Available from: 2007-08-31 Created: 2007-08-31 Last updated: 2010-01-14Bibliographically approved
    5. Different allele frequencies in the lactase gene in Scandinavian Neolithic populations and the development of dairy product consumtion
    Open this publication in new window or tab >>Different allele frequencies in the lactase gene in Scandinavian Neolithic populations and the development of dairy product consumtion
    Show others...
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-96068 (URN)
    Available from: 2007-08-31 Created: 2007-08-31 Last updated: 2010-01-14Bibliographically approved
  • 174.
    Malmström, Helena
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Gilbert, M. Thomas P.
    Thomas, Mark G.
    Brandström, Mikael
    Stora, Jan
    Molnar, Petra
    Andersen, Pernille K.
    Bendixen, Christian
    Holmlund, Gunilla
    Götherstrom, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Willerslev, Eske
    Ancient DNA Reveals Lack of Continuity between Neolithic Hunter-Gatherers and Contemporary Scandinavians2009In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 19, no 20, p. 1758-1762Article in journal (Refereed)
    Abstract [en]

    The driving force behind the transition from a foraging to a farming lifestyle in prehistoric Europe (Neolithization) has been debated for more than a century[1-3]. Of particular interest is whether population replacement or cultural exchange was responsible [3-5]. Scandinavia holds a unique place in this debate, for it maintained one of the last major hunter-gatherer complexes in Neolithic Europe, the Pitted Ware culture [6]. Intriguingly, these late hunter-gatherers existed in parallel to early farmers for more than a millennium before they vanished some 4,000 years ago [7, 8]. The prolonged coexistence of the two cultures in Scandinavia has been cited as an argument against population replacement between the Mesolithic and the present [7, 8]. Through analysis of DNA extracted from ancient Scandinavian human remains, we show that people of the Pitted Ware culture were not the direct ancestors of modern Scandinavians (including the Saami people of northern Scandinavia) but are more closely related to contemporary populations of the eastern Baltic region. Our findings support hypotheses arising from archaeological analyses that propose a Neolithic or post-Neolithic population replacement in Scandinavia [7]. Furthermore, our data are consistent with the view that the eastern Baltic represents a genetic refugia for some of the European hunter-gatherer populations.

  • 175.
    Malmström, Helena
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Götherström, Anders
    Gilbert, M Thomas P
    Brandström, Mikael
    Storå, Jan
    Molnar, Petra
    Bendixen, Christian
    Holmlund, Gunilla
    Willerslev, Eske
    Ancient human DNA: authentication through FLX-sequenced PCR products in conjunction with bleach pre-treatment, quantitative PCR, assesment of assymetric behaviour and negative controlsManuscript (Other (popular science, discussion, etc.))
  • 176.
    Malmström, Helena
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Linderholm, Anna
    Dalén, Love
    Lidén, Kerstin
    Evershed, Richard P
    Storå, Jan
    Molnar, Petra
    Gilbert, M Thomas P
    Willerslev, Eske
    Holmlund, Gunilla
    Different allele frequencies in the lactase gene in Scandinavian Neolithic populations and the development of dairy product consumtionManuscript (Other (popular science, discussion, etc.))
  • 177.
    Malmström, Helena
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Storå, Jan
    Dalén, Love
    Holmlund, Gunilla
    Götherström, Anders
    Extensive human DNA contamination in extracts from ancient dog bones and teeth2005In: Molecular Biology and Evolution, ISSN 0737-4038, Vol. 22, no 10, p. 2040-2047Article in journal (Refereed)
  • 178.
    Malmström, Helena
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Storå, Jan
    Dalén, Love
    Holmlund, Gunilla
    Götherström, Anders
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Extensive human DNA contamination in extracts from ancient dog bones and teeth.2005In: Mol Biol Evol, ISSN 0737-4038, Vol. 22, no 10, p. 2040-7Article in journal (Refereed)
    Abstract [en]

    Ancient DNA (aDNA) sequences, especially those of human origin, are notoriously difficult to analyze due to molecular damage and exogenous DNA contamination. Relatively few systematic studies have focused on this problem. Here we investigate the extent and origin of human DNA contamination in the most frequently used sources for aDNA studies, that is, bones and teeth from museum collections. To distinguish contaminant DNA from authentic DNA we extracted DNA from dog (Canis familiaris) specimens. We monitored the presence of a 148-bp human-specific and a 152-bp dog-specific mitochondrial DNA (mtDNA) fragment in DNA extracts as well as in negative controls. The total number of human and dog template molecules were quantified using real-time polymerase chain reaction (PCR), and the sequences were characterized by amplicon cloning and sequencing. Although standard precautions to avoid contamination were taken, we found that all samples from the 29 dog specimens contained human DNA, often at levels exceeding the amount of authentic ancient dog DNA. The level of contaminating human DNA was also significantly higher in the dog extracts than in the negative controls, and an experimental setup indicated that this was not caused by the carrier effect. This suggests that the contaminating human DNA mainly originated from the dog bones rather than from laboratory procedures. When cloned, fragments within a contaminated PCR product generally displayed several different sequences, although one haplotype was often found in majority. This leads us to believe that recognized criteria for authenticating aDNA cannot separate contamination from ancient human DNA the way they are presently used.

  • 179.
    Malmström, Helena
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Svensson, Emma M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Gilbert, M. Thomas P.
    Willerslev, Eske
    Götherström, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Holmlund, Gunilla
    More on contamination: The use of asymmetric molecular behavior to identify authentic ancient human DNA2007In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 24, no 4, p. 998-1004Article in journal (Refereed)
    Abstract [en]

    Authentication of ancient human DNA results is an exceedingly difficult challenge due to the presence of modern contaminant DNA sequences. Nevertheless, the field of ancient human genetics generates huge scientific and public interest, and thus researchers are rarely discouraged by problems concerning the authenticity of such data. Although several methods have been developed to the purpose of authenticating ancient DNA (aDNA) results, while they are useful in faunal research, most of the methods have proven complicated to apply to ancient human DNA. Here, we investigate in detail the reliability of one of the proposed criteria, that of appropriate molecular behavior. Using real-time polymerase chain reaction (PCR) and pyrosequencing, we have quantified the relative levels of authentic aDNA and contaminant human DNA sequences recovered from archaeological dog and cattle remains. In doing so, we also produce data that describes the efficiency of bleach incubation of bone powder and its relative detrimental effects on contaminant and authentic ancient DNA. We note that bleach treatment is significantly more detrimental to contaminant than to authentic aDNA in the bleached bone powder. Furthermore, we find that there is a substantial increase in the relative proportions of authentic DNA to contaminant DNA as the PCR target fragment size is decreased. We therefore conclude that the degradation pattern in aDNA provides a quantifiable difference between authentic aDNA and modern contamination. This asymmetrical behavior of authentic and contaminant DNA can be used to identify authentic haplotypes in human aDNA studies.

  • 180.
    Malmström, Helena
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Vilà, Carles
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Gilbert, M Thomas P
    Storå, Jan
    Willerslev, Eske
    Holmlund, Gunilla
    Götherström, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Barking up the wrong tree: Modern northern European dogs fail to explain their origin2008In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 8, article id 71Article in journal (Refereed)
    Abstract [en]

    Background: Geographic distribution of the genetic diversity in domestic animals, particularly mitochondrial DNA, has often been used to infer centers of domestication. The underlying presumption is that phylogeographic patterns among domesticates were established during, or shortly after the domestication. Human activities are assumed not to have altered the haplogroup frequencies to any great extent. We studied this hypothesis by analyzing 24 mtDNA sequences in ancient Scandinavian dogs. Breeds originating in northern Europe are characterized by having a high frequency of mtDNA sequences belonging to a haplogroup rare in other populations (HgD). This has been suggested to indicate a possible origin of the haplogroup (perhaps even a separate domestication) in central or northern Europe. Results: The sequences observed in the ancient samples do not include the haplogroup indicative for northern European breeds (HgD). Instead, several of them correspond to haplogroups that are uncommon in the region today and that are supposed to have Asian origin. Conclusion: We find no evidence for local domestication. We conclude that interpretation of the processes responsible for current domestic haplogroup frequencies should be carried out with caution if based only on contemporary data. They do not only tell their own story, but also that of humans.

  • 181.
    Mank, Judith E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Mating preferences, sexual selection and patterns of cladogenesis in ray-finned fishes2007In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 20, no 2, p. 597-602Article in journal (Refereed)
    Abstract [en]

    Evolutionary theory predicts that sexual selection may increase taxonomic diversity when emergent mating preferences result in reproductive isolation and therefore speciation. This theory has been invoked to explain patterns of diversity in ray-finned fishes (most notably in the cichlids), but the theory has not been tested comparatively in fish. Additionally, several other unrelated factors have been identified as promoters of cladogenesis, so it is unclear how important sexual selection might be in diversification. Using sister-clade analysis, I tested the relationship between the presence of sexually selected traits and taxonomic diversification in actinopterygiian fishes, a large clade that shows substantial diversity in mating preferences and related sexually selected traits. In all identified sister-families that differed with regard to the proportion of species manifesting sexually selected traits, sexual selection was correlated with increased diversification, and this association was significant across all sister clades (P = 0.02). This suggests that sexual selection, when present, is a substantial driver of diversification in the ray-finned fishes, and lends further empirical support to the theoretical link between mating preferences and accelerated cladogenesis.

  • 182.
    Mank, Judith E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    The evolution of sexually selected traits and antagonistic androgen expression in actinopterygiian fishes2007In: American Naturalist, ISSN 0003-0147, E-ISSN 1537-5323, Vol. 169, no 1, p. 142-149Article in journal (Refereed)
    Abstract [en]

    Many sexually selected traits in male fishes are controlled by testosterone. Directional selection for male ornaments could theoretically increase male testosterone levels over evolutionary time-scales, and when genetically correlated, female testosterone levels as well. Because of the negative fitness consequences of high testosterone, it is plausible that female choice for sexually selected traits in males results in decreased female reproductive fitness. I used comparative analysis to examine the association between male peak testosterone expression and sexually selected ornaments. I also tested for genetic correlation between male and female androgen levels. The presence of sexually selected traits in males was significantly correlated with increased peak androgen levels in males as well as females, and female testosterone levels were significantly correlated with male peak testosterone titers, although the slope was only marginally < 1. This suggests that selection to decouple high male and female testosterone levels is either weak or otherwise ineffective.

  • 183.
    Mank, Judith E.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Axelsson, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Fast-X on the Z: Rapid evolution of sex-linked genes in birds2007In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 17, no 5, p. 618-624Article in journal (Refereed)
    Abstract [en]

    Theoretical work predicts natural selection to be more efficient in the fixation of beneficial mutations in X-linked genes than in autosomal genes. This “fast-X effect” should be evident by an increased ratio of nonsynonymous to synonymous substitutions (dN/dS) for sex-linked genes; however, recent studies have produced mixed support for this expectation. To make an independent test of the idea of fast-X evolution, we focused on birds, which have female heterogamety (males ZZ, females ZW), where analogous arguments would predict a fast-Z effect. We aligned 2.8 Mb of orthologous protein-coding sequence of zebra finch and chicken from 172 Z-linked and 4848 autosomal genes. Zebra finch data were in the form of EST sequences from brain cDNA libraries, while chicken genes were from the draft genome sequence. The dN/dS ratio was significantly higher for Z-linked (0.110) than for all autosomal genes (0.085; P = 0.002), as well as for genes linked to similarly sized autosomes 1–10 (0.0948; P = 0.04). This pattern of fast-Z was evident even after we accounted for the nonrandom distribution of male-biased genes. We also examined the nature of standing variation in the chicken protein-coding regions. The ratio of nonsynonymous to synonymous polymorphism (pN/pS) did not differ significantly between genes on the Z chromosome (0.104) and on the autosomes (0.0908). In conjunction, these results suggest that evolution proceeds more quickly on the Z chromosome, where hemizygous exposure of beneficial nondominant mutations increases the rate of fixation.

  • 184.
    Mank, Judith E.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Parallel divergence and degradation of the avian W sex chromosome2007In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 22, no 8, p. 389-391Article in journal (Refereed)
    Abstract [en]

    Sex chromosomes are ubiquitous in birds but our understanding of how they originated and evolved has remained incomplete. Recent work by Tsuda et al. on tinamou and ratite birds suggests that, although all bird sex chromosomes evolved from the same pair of autosomes, the Z and W sex chromosomes have diverged from one another several times independently. This parallel evolution of the avian W presents a means for comparison in studies of sex chromosome evolution, which could help us understand more about the general forces that shape the development of all types of sex chromosome.

  • 185.
    Mank, Judith E.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Hultin-Rosenberg, Lina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Axelsson, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Rapid evolution of female-biased, but not male-biased, genes expressed in the avian brain2007In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 24, no 12, p. 2698-2706Article in journal (Refereed)
    Abstract [en]

    The powerful pressures of sexual and natural selection associated with species recognition and reproduction are thought to manifest in a faster rate of evolution in sex-biased genes, an effect that has been documented particularly for male-biased genes expressed in the reproductive tract. However, little is known about the rate of evolution for genes involved in sexually dimorphic behaviors, which often form the neurological basis of intrasexual competition and mate choice. We used microarray data, designed to uncover sex-biased expression patterns in embryonic chicken brain, in conjunction with data on the rate of sequence evolution for >4,000 coding regions aligned between chicken and zebra finch in order to study the role of selection in governing the molecular evolution for sex-biased and unbiased genes. Surprisingly, we found that female-biased genes, defined across a range of cutoff values, show a higher rate of functional evolution than both male-biased and unbiased genes. Autosomal male-biased genes evolve at a similar rate as unbiased genes. Sex-specific genomic properties, such as heterogeneity in genomic distribution and GC content, and codon usage bias for sex-biased classes fail to explain this surprising result, suggesting that selective pressures may be acting differently on the male and female brain.

  • 186.
    Mank, Judith E.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Hultin-Rosenberg, Lina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Webster, Matthew T.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.