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15 records – page 1 of 2.

Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA.

https://arctichealth.org/en/permalink/ahliterature130568
Source
Mol Ecol. 2012 Apr;21(8):1806-15
Publication Type
Article
Date
Apr-2012
Author
Sanne Boessenkool
Laura S Epp
James Haile
Eva Bellemain
Mary Edwards
Eric Coissac
Eske Willerslev
Christian Brochmann
Author Affiliation
National Centre for Biosystematics, Natural History Museum, University of Oslo, Oslo, Norway. sanneboessenkool@gmail.com
Source
Mol Ecol. 2012 Apr;21(8):1806-15
Date
Apr-2012
Language
English
Publication Type
Article
Keywords
Animals
DNA - analysis - isolation & purification
DNA Contamination
DNA Primers - genetics
Fossils
Geologic Sediments - chemistry
Humans
Ice
Perissodactyla - classification - genetics
Polymerase Chain Reaction - methods
Sequence Analysis, DNA - methods
Siberia
Abstract
Analyses of degraded DNA are typically hampered by contamination, especially when employing universal primers such as commonly used in environmental DNA studies. In addition to false-positive results, the amplification of contaminant DNA may cause false-negative results because of competition, or bias, during the PCR. In this study, we test the utility of human-specific blocking primers in mammal diversity analyses of ancient permafrost samples from Siberia. Using quantitative PCR (qPCR) on human and mammoth DNA, we first optimized the design and concentration of blocking primer in the PCR. Subsequently, 454 pyrosequencing of ancient permafrost samples amplified with and without the addition of blocking primer revealed that DNA sequences from a diversity of mammalian representatives of the Beringian megafauna were retrieved only when the blocking primer was added to the PCR. Notably, we observe the first retrieval of woolly rhinoceros (Coelodonta antiquitatis) DNA from ancient permafrost cores. In contrast, reactions without blocking primer resulted in complete dominance by human DNA sequences. These results demonstrate that in ancient environmental analyses, the PCR can be biased towards the amplification of contaminant sequences to such an extent that retrieval of the endogenous DNA is severely restricted. The application of blocking primers is a promising tool to avoid this bias and can greatly enhance the quantity and the diversity of the endogenous DNA sequences that are amplified.
PubMed ID
21988749 View in PubMed
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Conservation Genomics in a Changing Arctic.

https://arctichealth.org/en/permalink/ahliterature308281
Source
Trends Ecol Evol. 2020 02; 35(2):149-162
Publication Type
Journal Article
Review
Date
02-2020
Author
Jocelyn P Colella
Sandra L Talbot
Christian Brochmann
Eric B Taylor
Eric P Hoberg
Joseph A Cook
Author Affiliation
Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA. Electronic address: jcolella.jc@gmail.com.
Source
Trends Ecol Evol. 2020 02; 35(2):149-162
Date
02-2020
Language
English
Publication Type
Journal Article
Review
Keywords
Arctic Regions
Biodiversity
Climate change
Conservation of Natural Resources
Ecosystem
Genomics
Abstract
Although logistically challenging to study, the Arctic is a bellwether for global change and is becoming a model for questions pertinent to the persistence of biodiversity. Disruption of Arctic ecosystems is accelerating, with impacts ranging from mixing of biotic communities to individual behavioral responses. Understanding these changes is crucial for conservation and sustainable economic development. Genomic approaches are providing transformative insights into biotic responses to environmental change, but have seen limited application in the Arctic due to a series of limitations. To meet the promise of genome analyses, we urge rigorous development of biorepositories from high latitudes to provide essential libraries to improve the conservation, monitoring, and management of Arctic ecosystems through genomic approaches.
PubMed ID
31699414 View in PubMed
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Genetics of cryptic speciation within an Arctic mustard, Draba nivalis.

https://arctichealth.org/en/permalink/ahliterature263623
Source
PLoS One. 2014;9(4):e93834
Publication Type
Article
Date
2014
Author
A Lovisa S Gustafsson
Inger Skrede
Heather C Rowe
Galina Gussarova
Liv Borgen
Loren H Rieseberg
Christian Brochmann
Christian Parisod
Source
PLoS One. 2014;9(4):e93834
Date
2014
Language
English
Publication Type
Article
Keywords
Amplified Fragment Length Polymorphism Analysis
Arctic Regions
Chromosome Mapping
Fertility - genetics
Flowers - genetics
Genetic Speciation
Microsatellite Repeats - genetics
Mustard Plant - genetics - growth & development
Pollen - genetics
Quantitative Trait Loci - genetics
Reproductive Isolation
Seeds - genetics
Abstract
Crossing experiments indicate that hybrid sterility barriers frequently have developed within diploid, circumpolar plant species of the genus Draba. To gain insight into the rapid evolution of postzygotic reproductive isolation in this system, we augmented the linkage map of one of these species, D. nivalis, and searched for quantitative trait loci (QTLs) associated with reproductive isolation. The map adds 63 new dominant markers to a previously published dataset of 31 co-dominant microsatellites. These markers include 52 amplified fragment length polymorphisms (AFLPs) and 11 sequence-specific amplified polymorphisms (SSAPs) based on retrotransposon sequence. 22 markers displaying transmission ratio distortion were further included in the map. We resolved eight linkage groups with a total map length of 894 cM. Significant genotype-trait associations, or quantitative trait loci (QTL), were detected for reproductive phenotypes including pollen fertility (4 QTLs), seed set (3 QTLs), flowering time (3 QTLs) and number of flowers (4 QTLs). Observed patterns of inheritance were consistent with the influence of both nuclear-nuclear interactions and chromosomal changes on these traits. All seed set QTLs and one pollen fertility QTL displayed underdominant effects suggestive of the involvement of chromosomal rearrangements in hybrid sterility. Interestingly, D. nivalis is predominantly self-fertilizing, which may facilitate the establishment of underdominant loci and contribute to reproductive isolation.
Notes
Cites: Bioinformatics. 2003 May 1;19(7):889-9012724300
Cites: Evolution. 2013 Sep;67(9):2547-6024033166
Cites: Nucleic Acids Res. 1995 Nov 11;23(21):4407-147501463
Cites: Mol Gen Genet. 1997 Feb 27;253(6):687-949079879
Cites: Philos Trans R Soc Lond B Biol Sci. 1998 Feb 28;353(1366):287-3059533126
Cites: Nature. 2013 Dec 5;504(7478):135-724196712
Cites: Evolution. 2001 Jan;55(1):1-2411263730
Cites: Mol Biol Evol. 2001 May;18(5):882-9211319272
Cites: Evolution. 2001 Jun;55(6):1085-9411475044
Cites: Mol Biol Evol. 2001 Dec;18(12):2315-2211719581
Cites: Genetics. 2001 Dec;159(4):1701-1611779808
Cites: J Hered. 2002 Jan-Feb;93(1):77-812011185
Cites: Mol Ecol. 2005 Aug;14(9):2621-3516029465
Cites: Cytogenet Genome Res. 2005;110(1-4):441-716093696
Cites: Curr Opin Genet Dev. 2005 Dec;15(6):621-716219458
Cites: Proc Natl Acad Sci U S A. 2006 Jan 24;103(4):972-516418291
Cites: Nature. 2006 Mar 23;440(7083):524-716554818
Cites: Genetics. 2006 May;173(1):419-3416204214
Cites: Nature. 2006 Oct 5;443(7111):521-417024082
Cites: Theor Appl Genet. 2006 Nov;113(8):1551-6116988816
Cites: Theor Appl Genet. 2007 Feb;114(4):627-3617160537
Cites: Syst Biol. 2006 Dec;55(6):949-5617345676
Cites: Nat Protoc. 2006;1(6):2746-5217406531
Cites: Science. 2007 Aug 17;317(5840):910-417702935
Cites: Mol Genet Genomics. 2007 Oct;278(4):361-7017690909
Cites: Nat Rev Genet. 2007 Dec;8(12):973-8217984973
Cites: Heredity (Edinb). 2008 Jan;100(1):71-817940548
Cites: New Phytol. 2008;178(2):436-4718208468
Cites: Proc Natl Acad Sci U S A. 2005 May 3;102 Suppl 1:6522-615851676
Cites: Plant Cell. 2008 Feb;20(2):249-5818296625
Cites: Science. 2008 Apr 25;320(5875):484-618436777
Cites: Philos Trans R Soc Lond B Biol Sci. 2008 Sep 27;363(1506):3023-3618579476
Cites: Philos Trans R Soc Lond B Biol Sci. 2008 Sep 27;363(1506):3009-2118579478
Cites: Evolution. 2008 Aug;62(8):1840-5118485112
Cites: Mol Ecol. 2009 Feb;18(3):375-40219143936
Cites: Science. 2009 Feb 6;323(5915):737-4119197053
Cites: Heredity (Edinb). 2009 Mar;102(3):293-30219066622
Cites: Proc Natl Acad Sci U S A. 2009 Jun 16;106 Suppl 1:9939-4619528641
Cites: Nat Rev Genet. 2010 Mar;11(3):175-8020051985
Cites: Ann Bot. 2010 Sep;106(3):439-5520576737
Cites: PLoS Biol. 2010;8(9). pii: e1000500. doi: 10.1371/journal.pbio.100050020927411
Cites: Trends Ecol Evol. 2010 Nov;25(11):660-920817305
Cites: Genome Biol Evol. 2011;3:812-2921903731
Cites: Evolution. 2011 Oct;65(10):2959-7221967435
Cites: Trends Ecol Evol. 2012 Jan;27(1):27-3921978464
Cites: Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):E981-822460791
Cites: Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16240-522988127
Cites: Evolution. 2013 Jan;67(1):225-4023289574
Cites: J Evol Biol. 2013 Feb;26(2):229-4623323997
Cites: Mol Ecol Resour. 2013 Sep;13(5):765-7523795753
Cites: Theor Appl Genet. 2004 Aug;109(3):451-6315168022
PubMed ID
24691072 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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Glacial survival may matter after all: nunatak signatures in the rare European populations of two west-arctic species.

https://arctichealth.org/en/permalink/ahliterature99865
Source
Mol Ecol. 2011 Jan;20(2):376-93
Publication Type
Article
Date
Jan-2011
Author
Kristine B Westergaard
Inger G Alsos
Magnus Popp
Torstein Engelskjøn
Kjell I Flatberg
Christian Brochmann
Author Affiliation
Tromsø University Museum, NO-9037 Tromsø, Norway National Centre for Biosystematics, Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318 Oslo, Norway University Centre in Svalbard, PO Box 156, NO-9171 Longyearbyen, Norway NTNU Museum of Natural History and Archaeology, NO-7491 Trondheim, Norway.
Source
Mol Ecol. 2011 Jan;20(2):376-93
Date
Jan-2011
Language
English
Publication Type
Article
Abstract
Biogeographers claimed for more than a century that arctic plants survived glaciations in ice-free refugia within the limits of the North European ice sheets. Molecular studies have, however, provided overwhelming support for postglacial immigration into northern Europe, even from the west across the Atlantic. For the first time we can here present molecular evidence strongly favouring in situ glacial persistence of two species, the rare arctic-alpine pioneer species Sagina caespitosa and Arenaria humifusa. Both belong to the 'west-arctic element' of amphi-Atlantic disjuncts, having their few and only European occurrences well within the limits of the last glaciation. Sequencing of non-coding regions of chloroplast DNA revealed only limited variation. However, two very distinct and partly diverse genetic groups, one East and one West Atlantic, were detected in each species based on amplified fragment length polymorphisms (AFLPs), excluding postglacial dispersal from North America as explanation for their European occurrences. Patterns of genetic diversity and distinctiveness indicate that glacial populations existed in East Greenland and/or Svalbard (A. humifusa) and in southern Scandinavia (S. caespitosa). Despite their presumed lack of long-distance dispersal adaptations, intermixed populations in several regions indicate postglacial contact zones. Both species are declining in Nordic countries, probably due to climate change-induced habitat loss. Little or no current connectivity between their highly fragmented and partly distinct populations call for conservation of several populations in each geographic region.
PubMed ID
21156004 View in PubMed
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Highly overlapping winter diet in two sympatric lemming species revealed by DNA metabarcoding.

https://arctichealth.org/en/permalink/ahliterature260214
Source
PLoS One. 2015;10(1):e0115335
Publication Type
Article
Date
2015
Author
Eeva M Soininen
Gilles Gauthier
Frédéric Bilodeau
Dominique Berteaux
Ludovic Gielly
Pierre Taberlet
Galina Gussarova
Eva Bellemain
Kristian Hassel
Hans K Stenøien
Laura Epp
Audun Schrøder-Nielsen
Christian Brochmann
Nigel G Yoccoz
Source
PLoS One. 2015;10(1):e0115335
Date
2015
Language
English
Publication Type
Article
Abstract
Sympatric species are expected to minimize competition by partitioning resources, especially when these are limited. Herbivores inhabiting the High Arctic in winter are a prime example of a situation where food availability is anticipated to be low, and thus reduced diet overlap is expected. We present here the first assessment of diet overlap of high arctic lemmings during winter based on DNA metabarcoding of feces. In contrast to previous analyses based on microhistology, we found that the diets of both collared (Dicrostonyx groenlandicus) and brown lemmings (Lemmus trimucronatus) on Bylot Island were dominated by Salix while mosses, which were significantly consumed only by the brown lemming, were a relatively minor food item. The most abundant plant taxon, Cassiope tetragona, which alone composes more than 50% of the available plant biomass, was not detected in feces and can thus be considered to be non-food. Most plant taxa that were identified as food items were consumed in proportion to their availability and none were clearly selected for. The resulting high diet overlap, together with a lack of habitat segregation, indicates a high potential for resource competition between the two lemming species. However, Salix is abundant in the winter habitats of lemmings on Bylot Island and the non-Salix portion of the diets differed between the two species. Also, lemming grazing impact on vegetation during winter in the study area is negligible. Hence, it seems likely that the high potential for resource competition predicted between these two species did not translate into actual competition. This illustrates that even in environments with low primary productivity food resources do not necessarily generate strong competition among herbivores.
PubMed ID
25635852 View in PubMed
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Late Pleistocene origin of the entire circumarctic range of the arctic-alpine plant Kalmia procumbens.

https://arctichealth.org/en/permalink/ahliterature289792
Source
Mol Ecol. 2017 Oct; 26(20):5773-5783
Publication Type
Journal Article
Date
Oct-2017
Author
Hajime Ikeda
Pernille Bronken Eidesen
Valentin Yakubov
Vyacheslav Barkalov
Christian Brochmann
Hiroaki Setoguchi
Author Affiliation
Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan.
Source
Mol Ecol. 2017 Oct; 26(20):5773-5783
Date
Oct-2017
Language
English
Publication Type
Journal Article
Keywords
Arctic Regions
Bayes Theorem
Biological Evolution
Climate
Ericaceae - genetics
Genetics, Population
Models, Genetic
Phylogeny
Abstract
The circumarctic ranges of arctic-alpine plants are thought to have been established in the late Pliocene/early Pleistocene, when the modern arctic tundra was formed in response to climate cooling. Previous findings of range-wide genetic structure in arctic-alpine plants have been thought to support this hypothesis, but few studies have explicitly addressed the temporal framework of the genetic structure. Here, we estimated the demographic history of the genetic structure in the circumarctic Kalmia procumbens using sequences of multiple nuclear loci and examined whether its genetic structure reflects prolonged isolation throughout the Pleistocene. Both Bayesian clustering and phylogenetic analyses revealed genetic distinction between alpine and arctic regions, whereas detailed groupings were somewhat discordant between the analyses. By assuming a population grouping based on the phylogenetic analyses, which likely reflects a deeper intraspecific divergence, we conducted model-based analyses and demonstrated that the intraspecific genetic divergence in K. procumbens likely originated during the last glacial period. Thus, there is no need to postulate range separation throughout the Pleistocene to explain the current genetic structure in this species. This study demonstrates that range-wide genetic structure in arctic-alpine plants does not necessarily result from the late Pliocene/early Pleistocene origin of their circumarctic ranges and emphasizes the importance of a temporal framework of the current genetic structure for understanding the biogeographic history of the arctic flora.
PubMed ID
28815785 View in PubMed
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Late Pleistocene origin of the entire circumarctic range of the arctic-alpine plant Kalmia procumbens.

https://arctichealth.org/en/permalink/ahliterature285018
Source
Mol Ecol. 2017 Aug 16;
Publication Type
Article
Date
Aug-16-2017
Author
Hajime Ikeda
Pernille Bronken Eidesen
Valentin Yakubov
Vyacheslav Barkalov
Christian Brochmann
Hiroaki Setoguchi
Source
Mol Ecol. 2017 Aug 16;
Date
Aug-16-2017
Language
English
Publication Type
Article
Abstract
The circumarctic ranges of arctic-alpine plants are thought to have been established in the late Pliocene/early Pleistocene, when the modern arctic tundra was formed in response to climate cooling. Previous findings of range-wide genetic structure in arctic-alpine plants have been thought to support this hypothesis, but few studies have explicitly addressed the temporal framework of the genetic structure. Here, we estimated the demographic history of the genetic structure in the circumarctic Kalmia procumbens using sequences of multiple nuclear loci and examined whether its genetic structure reflects prolonged isolation throughout the Pleistocene. Both Bayesian clustering and phylogenetic analyses revealed genetic distinction between alpine and arctic regions, whereas detailed groupings were somewhat discordant between the analyses. By assuming a population grouping based on the phylogenetic analyses, which likely reflects a deeper intraspecific divergence, we conducted model-based analyses and demonstrated that the intraspecific genetic divergence in K. procumbens likely originated during the last glacial period. Thus, there is no need to postulate range separation throughout the Pleistocene to explain the current genetic structure in this species. This study demonstrates that range-wide genetic structure in arctic-alpine plants does not necessarily result from the late Pliocene/early Pleistocene origin of their circumarctic ranges and emphasizes the importance of a temporal framework of the current genetic structure for understanding the biogeographic history of the arctic flora.
PubMed ID
28815785 View in PubMed
Less detail

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
Less detail

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
Less detail

15 records – page 1 of 2.