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Demography and mating system shape the genome-wide impact of purifying selection in Arabis alpina.

https://arctichealth.org/en/permalink/ahliterature287993
Source
Proc Natl Acad Sci U S A. 2018 Jan 23;115(4):816-821
Publication Type
Article
Date
Jan-23-2018
Author
Benjamin Laenen
Andrew Tedder
Michael D Nowak
Per Toräng
Jörg Wunder
Stefan Wötzel
Kim A Steige
Yiannis Kourmpetis
Thomas Odong
Andreas D Drouzas
Marco C A M Bink
Jon Ågren
George Coupland
Tanja Slotte
Source
Proc Natl Acad Sci U S A. 2018 Jan 23;115(4):816-821
Date
Jan-23-2018
Language
English
Publication Type
Article
Abstract
Plant mating systems have profound effects on levels and structuring of genetic variation and can affect the impact of natural selection. Although theory predicts that intermediate outcrossing rates may allow plants to prevent accumulation of deleterious alleles, few studies have empirically tested this prediction using genomic data. Here, we study the effect of mating system on purifying selection by conducting population-genomic analyses on whole-genome resequencing data from 38 European individuals of the arctic-alpine crucifer Arabis alpina We find that outcrossing and mixed-mating populations maintain genetic diversity at similar levels, whereas highly self-fertilizing Scandinavian A. alpina show a strong reduction in genetic diversity, most likely as a result of a postglacial colonization bottleneck. We further find evidence for accumulation of genetic load in highly self-fertilizing populations, whereas the genome-wide impact of purifying selection does not differ greatly between mixed-mating and outcrossing populations. Our results demonstrate that intermediate levels of outcrossing may allow efficient selection against harmful alleles, whereas demographic effects can be important for relaxed purifying selection in highly selfing populations. Thus, mating system and demography shape the impact of purifying selection on genomic variation in A. alpina These results are important for an improved understanding of the evolutionary consequences of mating system variation and the maintenance of mixed-mating strategies.
Notes
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PubMed ID
29301967 View in PubMed
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The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic.

https://arctichealth.org/en/permalink/ahliterature304476
Source
Mol Ecol Resour. 2020 Oct 15; :
Publication Type
Journal Article
Date
Oct-15-2020
Author
Michael D Nowak
Siri Birkeland
Terezie Mandáková
Rimjhim Roy Choudhury
Xinyi Guo
Anna Lovisa S Gustafsson
Abel Gizaw
Audun Schrøder-Nielsen
Marco Fracassetti
Anne K Brysting
Loren Rieseberg
Tanja Slotte
Christian Parisod
Martin A Lysak
Christian Brochmann
Author Affiliation
Natural History Museum, University of Oslo, Oslo, Norway.
Source
Mol Ecol Resour. 2020 Oct 15; :
Date
Oct-15-2020
Language
English
Publication Type
Journal Article
Abstract
The Arctic is one of the most extreme terrestrial environments on the planet. Here, we present the first chromosome-scale genome assembly of a plant adapted to the high Arctic, Draba nivalis (Brassicaceae), an attractive model species for studying plant adaptation to the stresses imposed by this harsh environment. We used an iterative scaffolding strategy with data from short-reads, single-molecule long reads, proximity ligation data, and a genetic map to produce a 302 Mb assembly that is highly contiguous with 91.6% assembled into eight chromosomes (the base chromosome number). To identify candidate genes and gene families that may have facilitated adaptation to Arctic environmental stresses, we performed comparative genomic analyses with nine non-Arctic Brassicaceae species. We show that the D. nivalis genome contains expanded suites of genes associated with drought and cold stress (e.g., related to the maintenance of oxidation-reduction homeostasis, meiosis, and signaling pathways). The expansions of gene families associated with these functions appear to be driven in part by the activity of transposable elements. Tests of positive selection identify suites of candidate genes associated with meiosis and photoperiodism, as well as cold, drought, and oxidative stress responses. Our results reveal a multifaceted landscape of stress adaptation in the D. nivalis genome, offering avenues for the continued development of this species as an Arctic model plant.
PubMed ID
33058468 View in PubMed
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Multiple Genetic Trajectories to Extreme Abiotic Stress Adaptation in Arctic Brassicaceae.

https://arctichealth.org/en/permalink/ahliterature306584
Source
Mol Biol Evol. 2020 07 01; 37(7):2052-2068
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
07-01-2020
Author
Siri Birkeland
A Lovisa S Gustafsson
Anne K Brysting
Christian Brochmann
Michael D Nowak
Author Affiliation
Natural History Museum, University of Oslo, Oslo, Norway.
Source
Mol Biol Evol. 2020 07 01; 37(7):2052-2068
Date
07-01-2020
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Abstract
Extreme environments offer powerful opportunities to study how different organisms have adapted to similar selection pressures at the molecular level. Arctic plants have adapted to some of the coldest and driest biomes on Earth and typically possess suites of similar morphological and physiological adaptations to extremes in light and temperature. Here, we compare patterns of molecular evolution in three Brassicaceae species that have independently colonized the Arctic and present some of the first genetic evidence for plant adaptations to the Arctic environment. By testing for positive selection and identifying convergent substitutions in orthologous gene alignments for a total of 15 Brassicaceae species, we find that positive selection has been acting on different genes, but similar functional pathways in the three Arctic lineages. The positively selected gene sets identified in the three Arctic species showed convergent functional profiles associated with extreme abiotic stress characteristic of the Arctic. However, there was little evidence for independently fixed mutations at the same sites and for positive selection acting on the same genes. The three species appear to have evolved similar suites of adaptations by modifying different components in similar stress response pathways, implying that there could be many genetic trajectories for adaptation to the Arctic environment. By identifying candidate genes and functional pathways potentially involved in Arctic adaptation, our results provide a framework for future studies aimed at testing for the existence of a functional syndrome of Arctic adaptation in the Brassicaceae and perhaps flowering plants in general.
PubMed ID
32167553 View in PubMed
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Multiple Genetic Trajectories to Extreme Abiotic Stress Adaptation in Arctic Brassicaceae.

https://arctichealth.org/en/permalink/ahliterature311289
Source
Mol Biol Evol. 2020 07 01; 37(7):2052-2068
Publication Type
Comparative Study
Journal Article
Research Support, Non-U.S. Gov't
Date
07-01-2020
Author
Siri Birkeland
A Lovisa S Gustafsson
Anne K Brysting
Christian Brochmann
Michael D Nowak
Author Affiliation
Natural History Museum, University of Oslo, Oslo, Norway.
Source
Mol Biol Evol. 2020 07 01; 37(7):2052-2068
Date
07-01-2020
Language
English
Publication Type
Comparative Study
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Adaptation, Biological
Amino Acid Substitution
Arctic Regions
Brassicaceae - genetics
Evolution, Molecular
Selection, Genetic
Abstract
Extreme environments offer powerful opportunities to study how different organisms have adapted to similar selection pressures at the molecular level. Arctic plants have adapted to some of the coldest and driest biomes on Earth and typically possess suites of similar morphological and physiological adaptations to extremes in light and temperature. Here, we compare patterns of molecular evolution in three Brassicaceae species that have independently colonized the Arctic and present some of the first genetic evidence for plant adaptations to the Arctic environment. By testing for positive selection and identifying convergent substitutions in orthologous gene alignments for a total of 15 Brassicaceae species, we find that positive selection has been acting on different genes, but similar functional pathways in the three Arctic lineages. The positively selected gene sets identified in the three Arctic species showed convergent functional profiles associated with extreme abiotic stress characteristic of the Arctic. However, there was little evidence for independently fixed mutations at the same sites and for positive selection acting on the same genes. The three species appear to have evolved similar suites of adaptations by modifying different components in similar stress response pathways, implying that there could be many genetic trajectories for adaptation to the Arctic environment. By identifying candidate genes and functional pathways potentially involved in Arctic adaptation, our results provide a framework for future studies aimed at testing for the existence of a functional syndrome of Arctic adaptation in the Brassicaceae and perhaps flowering plants in general.
PubMed ID
32167553 View in PubMed
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RAD-seq data point to a northern origin of the arctic-alpine genus Cassiope (Ericaceae).

https://arctichealth.org/en/permalink/ahliterature268645
Source
Mol Phylogenet Evol. 2015 Dec 9;95:152-160
Publication Type
Article
Date
Dec-9-2015
Author
Yan Hou
Michael D Nowak
Virginia Mirré
Charlotte Sletten Bjorå
Christian Brochmann
Magnus Popp
Source
Mol Phylogenet Evol. 2015 Dec 9;95:152-160
Date
Dec-9-2015
Language
English
Publication Type
Article
Abstract
Many arctic-alpine plants display a highly disjunct distribution between the Arctic/Boreal regions and the southern Asian mountains. Two main hypotheses have been proposed to explain the origin of this biogeographic pattern: (1) south-to-north migration in the late Pliocene/early Pleistocene, and (2) north-to-south migration during the Miocene. The genus Cassiope is disjunctly distributed between the Arctic/Boreal regions and the Himalayan-Hengduan Mountains (HHM) and was selected to test these hypotheses. We constructed a fossil-calibrated phylogeny of Ericaceae using two plastid regions to estimate the crown group age of Cassiope, and used sequence data from thousands of loci produced by restriction site associated DNA sequencing (RAD-seq) to reconstruct the phylogeny of Cassiope. We also performed Bayesian divergence time analysis and biogeographic analysis. The Cassiope crown group was estimated to have originated in the Miocene, which predates the onset of Northern hemisphere glaciation. All HHM species formed a clade together with one eastern Siberian species, and this clade was sister to all other Arctic/Boreal species. This topology implies a northern origin of Cassiope, which is confirmed by our biogeographic analysis. Our results thus suggest that the ancient north-to-south migration hypothesis is most consistent with the origin of Cassiope.
PubMed ID
26691641 View in PubMed
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Thousands of RAD-seq Loci Fully Resolve the Phylogeny of the Highly Disjunct Arctic-Alpine Genus Diapensia (Diapensiaceae).

https://arctichealth.org/en/permalink/ahliterature266813
Source
PLoS One. 2015;10(10):e0140175
Publication Type
Article
Author
Yan Hou
Michael D Nowak
Virginia Mirré
Charlotte S Bjorå
Christian Brochmann
Magnus Popp
Source
PLoS One. 2015;10(10):e0140175
Language
English
Publication Type
Article
Abstract
Restriction-site associated DNA sequencing (RAD-seq) has recently become an important method to generate genome-wide molecular data for species delimitation, phylogeography, and population genetic studies. However, very few empirical studies have so far tested its applicability in phylogenetic reconstruction. The alpine-arctic genus Diapensia was selected to study the origin of the disjunction between the Arctic and the Himalayan-Hengduan Mountains (HHM). However, a previous phylogenetic analysis based on one nuclear and four plastid DNA regions failed to resolve the oldest divergences in Diapensia as well as the relationship between the two HHM species. Here we reconstruct a fully resolved phylogeny of Diapensia and address the conflict between the currently accepted taxonomy and the gene trees in the HHM species using RAD-seq. Based on a data set containing 2,650 loci selected to maximize the number of parsimony informative sites and allowing for a high level of missing data (51%), the phylogeny of Diapensia was fully resolved and each of the four species was reciprocally monophyletic. Whereas the arctic D. lapponica was inferred as sister to the HHM clade in the previous study, the RAD-seq data resolved the two arctic species as sisters to the HHM clade. Similar relationships were inferred from a differently filtered data set with far fewer loci (114) and less missing data (21%), but with lower support and with one of the two HHM species as non-monophyletic. Bayesian concordance analysis and Patterson's D-statistic tests suggested that admixture has occurred between the two HHM species.
PubMed ID
26448557 View in PubMed
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6 records – page 1 of 1.