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Publications (10 of 12) Show all publications
Wang, J., Ding, J., Tan, B., Robinson, K. M., Michelson, I. H., Johansson, A., . . . Ingvarsson, P. K. (2018). A major locus controls local adaptation and adaptive life history variation in a perennial plant. Genome Biology, 19, Article ID 72.
Open this publication in new window or tab >>A major locus controls local adaptation and adaptive life history variation in a perennial plant
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2018 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 19, article id 72Article in journal (Refereed) Published
Abstract [en]

Background: The initiation of growth cessation and dormancy represent critical life history trade offs between survival and growth and have important fitness effects in perennial plants Such adaptive life history traits often show strong local adaptation along environmental gradients but, despite then importance, the genetic architecture of these traits remains poorly understood.

Results: We integrate whole genome re sequencing with environmental and phenotypic data from common garden experiments to investigate the genomic basis of local adaptation across a latitudinal gradient in European aspen (Populus tremula). A single genomic region containing the PtFT2 gene mediates local adaptation in the timing of bud set and explains 65% of the observed genetic variation in bud set This locus is the likely target of a recent selective sweep that originated right before or during colonization of northern Scandinavia following the last glaciation Field and greenhouse experiments confirm that variation in PtFT2 gene expression affects the phenotypic variation in bud set that we observe in wild natural populations.

Conclusions: Our results reveal a major effect locus that determines the timing of bud set and that has facilitated rapid adaptation to shorter growing seasons and colder climates in European aspen. The discovery of a single locus explaining a substantial fraction of the variation in a key life-history trait is remarkable, given that such traits are generally considered to be highly polygenic. These findings provide a dramatic illustration of how loci of large effect for adaptive traits can arise and be maintained over large geographical scales in natural populations.

Place, publisher, year, edition, pages
BioMed Central, 2018
Keywords
Populus tremula, Local adaptation, Genomic basis, PtFT2, Adaptive traits, Selective sweep
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-150175 (URN)10.1186/s13059-018-1444-y (DOI)000434210500001 ()29866176 (PubMedID)
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation
Note

Originally included in thesis in manuscript form.

Available from: 2018-07-18 Created: 2018-07-18 Last updated: 2018-08-14Bibliographically approved
Lin, Y.-C., Wang, J., Delhomme, N., Schiffthaler, B., Sundström, G., Zuccolo, A., . . . Street, N. R. (2018). Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen. Proceedings of the National Academy of Sciences of the United States of America, 115(46), E10970-E10978
Open this publication in new window or tab >>Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen
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2018 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 46, p. E10970-E10978Article in journal (Refereed) Published
Abstract [en]

The Populus genus is one of the major plant model systems, but genomic resources have thus far primarily been available for poplar species, and primarily Populus trichocarpa (Torr. & Gray), which was the first tree with a whole-genome assembly. To further advance evolutionary and functional genomic analyses in Populus, we produced genome assemblies and population genetics resources of two aspen species, Populus tremula L. and Populus tremuloides Michx. The two aspen species have distributions spanning the Northern Hemisphere, where they are keystone species supporting a wide variety of dependent communities and produce a diverse array of secondary metabolites. Our analyses show that the two aspens share a similar genome structure and a highly conserved gene content with P. trichocarpa but display substantially higher levels of heterozygosity. Based on population resequencing data, we observed widespread positive and negative selection acting on both coding and noncoding regions. Furthermore, patterns of genetic diversity and molecular evolution in aspen are influenced by a number of features, such as expression level, coexpression network connectivity, and regulatory variation. To maximize the community utility of these resources, we have integrated all presented data within the PopGenIE web resource (PopGenIE.org).

Place, publisher, year, edition, pages
NATL ACAD SCIENCES, 2018
Keywords
genome assembly, natural selection, coexpression, population genetics, Populus
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-154950 (URN)10.1073/pnas.1801437115 (DOI)000449934400020 ()30373829 (PubMedID)2-s2.0-85056516875 (Scopus ID)
Available from: 2019-01-07 Created: 2019-01-07 Last updated: 2019-01-07Bibliographically approved
Wang, J., Street, N., Scofield, D. & Ingvarsson, P. (2016). Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species. Genetics, 202(3), 1185-1200
Open this publication in new window or tab >>Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species
2016 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 202, no 3, p. 1185-1200Article in journal (Refereed) Published
Abstract [en]

A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of PopulusPopulus tremulaP. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.

Place, publisher, year, edition, pages
Genetics Society of America, 2016
Keywords
Populus, whole-genome resequencing, nucleotide polymorphism, recombination, natural selection
National Category
Natural Sciences Evolutionary Biology Genetics
Research subject
Genetics
Identifiers
urn:nbn:se:umu:diva-117941 (URN)10.1534/genetics.115.183152 (DOI)000371596400026 ()
Available from: 2016-03-07 Created: 2016-03-07 Last updated: 2018-06-07Bibliographically approved
Wang, J. (2016). The genomic signatures of adaptive evolution in Populus. (Doctoral dissertation). Umeå: Umeå University
Open this publication in new window or tab >>The genomic signatures of adaptive evolution in Populus
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Understanding the genetic basis of adaptive evolution, and how natural selection has shaped patterns of polymorphism and divergence within and between species are enduring goals of evolutionary genetics. In this thesis, I used whole genome re-sequencing data to characterize the genomic signatures of natural selection along different evolutionary timescales in three Populus species: Populus tremula, P. tremuloides and P. trichocarpa. First, our study shows multiple lines of evidence suggesting that natural selection, due to both positive and purifying selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. Second, we characterize the evolution of genomic divergence patterns between two recently diverged aspen species: P. tremula and P. tremuloides. Our findings indicate that the two species diverged ~2.2-3.1 million years ago, coinciding with the severing of the Bering land bridge and the onset of dramatic climatic oscillations during the Pleistocene. We further explore different mechanisms that may explain the heterogeneity of genomic divergence, and find that variation in linked selection and recombination likely plays a key role in generating the heterogeneous genomic landscape of differentiation between the two aspen species. Third, we link whole-genome polymorphic data with local environmental variables and phenotypic variation in an adaptive trait to investigate the genomic basis of local adaptation in P. tremula along a latitudinal gradient across Sweden. We find that a majority of single nucleotide polymorphisms (SNPs) (>90%) identified as being involved in local adaptation are tightly clustered in a single genomic region on chromosome 10. The signatures of selection at this region are more consistent with soft rather than hard selective sweeps, where multiple adaptive haplotypes derived from standing genetic variation sweep through the populations simultaneously, and where different haplotypes rise to high frequency in different latitudinal regions. In summary, this thesis uses phylogenetic comparative approaches to elucidate how various evolutionary forces have shaped genome-wide patterns of sequence evolution in Populus.

Place, publisher, year, edition, pages
Umeå: Umeå University, 2016. p. 52
Keywords
Populus, adaptive evolution, natural selection, genomic diversity and divergence, recombination, Next-generation sequencing, local adaptation
National Category
Ecology
Identifiers
urn:nbn:se:umu:diva-120286 (URN)978-91-7601-463-9 (ISBN)
Public defence
2016-06-08, KB3B1, KBC-huset, Umeå, 13:00 (English)
Opponent
Supervisors
Note

The research in this thesis was supported by the Swedish research council (to Pär K. Ingvarsson) and the JC Kempe Memorial Scholarship Foundation (to Jing Wang). The PhD study of Jing Wang in Sweden was funded by the State Scholarship from China Scholarship council.

Available from: 2016-05-18 Created: 2016-05-13 Last updated: 2018-06-07Bibliographically approved
Wang, J., Street, N., Scofield, D. & Ingvarsson, P. (2016). Variation in linked selection and recombination drive genomic divergence during allopatric speciation of European and American aspens. Molecular biology and evolution, 33(7), 1754-1767
Open this publication in new window or tab >>Variation in linked selection and recombination drive genomic divergence during allopatric speciation of European and American aspens
2016 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 33, no 7, p. 1754-1767Article in journal (Refereed) Published
Abstract [en]

Despite the global economic and ecological importance of forest trees, the genomic basis of differential adaptation and speciation in tree species is still poorly understood. Populus tremula and P. tremuloides are two of the most widespread tree species in the Northern Hemisphere. Using whole-genome re-sequencing data of 24 P. tremula and 22 P. tremuloidesindividuals, we find that the two species diverged ~2.2-3.1 million years ago, coinciding with the severing of the Bering land bridge and the onset of dramatic climatic oscillations during the Pleistocene. Both species have experienced substantial population expansions following long-term declines after species divergence. We detect widespread and heterogeneous genomic differentiation between species, and in accordance with the expectation of allopatric speciation, coalescent simulations suggest that neutral evolutionary processes can account for most of the observed patterns of genetic differentiation. However, there is an excess of regions exhibiting extreme differentiation relative to those expected under demographic simulations, which is indicative of the action of natural selection. Overall genetic differentiation is negatively associated with recombination rate in both species, providing strong support for a role of linked selection in generating the heterogeneous genomic landscape of differentiation between species. Finally, we identify a number of candidate regions and genes that may have been subject to positive and/or balancing selection during the speciation process.

Keywords
Populus tremula, P. tremuloides, whole-genome re-sequencing, demographic histories, heterogeneous genomic differentiation, linked selection, recombination
National Category
Evolutionary Biology
Research subject
Genetics; evolutionary genetics
Identifiers
urn:nbn:se:umu:diva-118326 (URN)10.1093/molbev/msw051 (DOI)000378767100009 ()
Available from: 2016-03-16 Created: 2016-03-16 Last updated: 2018-06-07Bibliographically approved
Peng, Y., Tian, B., Tian, X., Wang, J., Hensen, I. & Liu, J. (2015). Range expansion during the Pleistocene drove morphological radiation of the fir genus (Abies, Pinaceae) in the Qinghai-Tibet Plateau and Himalayas. Botanical journal of the Linnean Society, 179(3), 444-453
Open this publication in new window or tab >>Range expansion during the Pleistocene drove morphological radiation of the fir genus (Abies, Pinaceae) in the Qinghai-Tibet Plateau and Himalayas
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2015 (English)In: Botanical journal of the Linnean Society, ISSN 0024-4074, E-ISSN 1095-8339, Vol. 179, no 3, p. 444-453Article in journal (Refereed) Published
Abstract [en]

Range expansion caused by climate oscillations in the past probably promoted morphological radiation in a few plant groups. In this study, we aim to test this hypothesis through phylogeographical analysis of the cold-tolerant fir genus (Abies) in the Qinghai-Tibet Plateau (QTP) and Himalayas, where it comprises 12 described species. We examined sequence variation in two maternally inherited mitochondrial (mt) DNA fragments (nad5-4 and nad7-1) and two paternally inherited plastid DNA fragments (trnS-G and trnL-F) for 733 individuals from 75 populations of the species in a monophyletic group. Only six mtDNA haplotypes were recovered, but five were shared between multiple species and one occurred at a high frequency, providing strong evidence of range expansion. Forty-three plastid DNA haplotypes were detected, 19 of which were shared between species and three occurred at high frequency. Network, mismatch and Bayesian skyline plot analyses of all plastid DNA haplotypes from this clade clearly suggested range expansion. This expansion was dated as having occurred during the longest and most extensive glaciation in the Pleistocene. Our results therefore supported the range expansion hypothesis for this clade of Abies during the Pleistocene; expansion probably drove the morphological radiation of the clade in the QTP and Himalayas, although it remains unclear whether the different morphotypes should be acknowledged as independent, reproductively isolated species.

Place, publisher, year, edition, pages
Wiley-Blackwell, 2015
Keywords
climate change, climate oscillations, phylogeography, speciation
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:umu:diva-109411 (URN)10.1111/boj.12329 (DOI)000364530100007 ()
Available from: 2015-09-27 Created: 2015-09-27 Last updated: 2018-06-07Bibliographically approved
Wang, J., Scofield, D., Street, N. & Ingvarsson, P. (2015). Variant calling using NGS data in European aspen (Populus tremula) (1ed.). In: Sablok, G., Kumar, S., Ueno, S., Kuo, J., Varotto, C. (Eds.) (Ed.), Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches: (pp. 43-61). Springer
Open this publication in new window or tab >>Variant calling using NGS data in European aspen (Populus tremula)
2015 (English)In: Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches / [ed] Sablok, G., Kumar, S., Ueno, S., Kuo, J., Varotto, C. (Eds.), Springer, 2015, 1, p. 43-61Chapter in book (Refereed)
Abstract [en]

Analysis of next-generation sequencing (NGS) data is rapidly becoming an important source of information for genetics and genomics studies. The utility of such data does, however, rely crucially on the accuracy and quality of SNP and genotype calling. Identification of genetic variants (SNPs and short indels) from NGS data is an area of active research and many recent statistical methods have been developed to both improve and quantify the large uncertainty associated with genotype calling. The detection of genetic variants from NGS data is prone to errors, due to multiple factors such as base-calling, alignment errors and read coverage. Here we highlight some of the issues and review and exemplify some of the recent methods that have been developed for genotype calling. We also provide guidelines for their application to whole-genome re-sequencing data using a data set based on a number of European aspen (Populus tremula) individuals each sequenced to a depth of about 20x coverage per individual.

Place, publisher, year, edition, pages
Springer, 2015 Edition: 1
Keywords
Next generation sequencing, variant calling, single nucleotide polymorphism (SNP), pre-processing, alignment, post-processing, filtering
National Category
Biological Sciences
Identifiers
urn:nbn:se:umu:diva-102803 (URN)10.1007/978-3-319-17157-9_4 (DOI)978-3-319-17156-2 (ISBN)
Available from: 2015-05-05 Created: 2015-05-05 Last updated: 2018-06-07Bibliographically approved
Wang, J., Abbott, R., Ingvarsson, P. & Liu, J. (2014). Increased genetic divergence between two closely related fir species in areas of range overlap. Ecology and Evolution, 4(7), 1019-1029
Open this publication in new window or tab >>Increased genetic divergence between two closely related fir species in areas of range overlap
2014 (English)In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 4, no 7, p. 1019-1029Article in journal (Refereed) Published
Abstract [en]

Because of introgressive hybridization, closely related species can be more similar to each other in areas of range overlap (parapatry or sympatry) than in areas where they are geographically isolated from each other (allopatry). Here, we report the reverse situation based on nuclear genetic divergence between two fir species, Abies chensiensis and Abies fargesii, in China, at sites where they are parapatric relative to where they are allopatric. We examined genetic divergence across 126 amplified fragment length polymorphism (AFLP) markers in a set of 172 individuals sampled from both allopatric and parapatric populations of the two species. Our analyses demonstrated that AFLP divergence was much greater between the species when comparisons were made between parapatric populations than between allopatric populations. We suggest that selection in parapatry may have largely contributed to this increased divergence.

Keywords
Abies chensiensis, Abies fargesii, allopatry, genetic divergence, natural selection, parapatry.
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:umu:diva-87740 (URN)10.1002/ece3.1007 (DOI)000333809000013 ()
Available from: 2014-04-08 Created: 2014-04-08 Last updated: 2018-06-08Bibliographically approved
Lockwood, J., Aleksic, J., Zou, J., Wang, J., Liu, J. & Renner, S. (2013). A new phylogeny for the genus Picea from plastid, mitochondrial adn nuclear sequences. Molecular Phylogenetics and Evolution, 69(3), 717-727
Open this publication in new window or tab >>A new phylogeny for the genus Picea from plastid, mitochondrial adn nuclear sequences
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2013 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 69, no 3, p. 717-727Article in journal (Refereed) Published
Abstract [en]

Studies over the past ten years have shown that the crown groups of most conifer genera are only about 15–25 Ma old. The genus Picea (spruces, Pinaceae), with around 35 species, appears to be no exception. In addition, molecular studies of co-existing spruce species have demonstrated frequent introgression. Per- haps not surprisingly therefore previous phylogenetic studies of species relationships in Picea, based mostly on plastid sequences, suffered from poor statistical support. We therefore generated mitochon- drial, nuclear, and further plastid DNA sequences from carefully sourced material, striking a balance between alignability with outgroups and phylogenetic signal content. Motif duplications in mitochon- drial introns were treated as characters in a stochastic Dollo model; molecular clock models were cali- brated with fossils; and ancestral ranges were inferred under maximum likelihood. In agreement with previous findings, Picea diverged from its sister clade 180 million years ago (Ma), and the most recent common ancestor of today’s spruces dates to 28 Ma. Different from previous analyses though, we find a large Asian clade, an American clade, and a Eurasian clade. Two expansions occurred from Asia to North America and several between Asia and Europe. Chinese P. brachytyla, American P. engelmannii, and Nor- way spruce, P. abies, are not monophyletic, and North America has ten, not eight species. Divergence times imply that Pleistocene refugia are unlikely to be the full explanation for the relationships between the European species and their East Asian relatives. Thus, northern Norway spruce may be part of an Asian species complex that diverged from the southern Norway spruce lineage in the Upper Miocene, some 6 Ma, which can explain the deep genetic gap noted in phylogeographic studies of Norway spruce. The large effective population sizes of spruces, and incomplete lineage sorting during speciation, mean that the interspecific relationships within each of the geographic clades require further studies, especially based on genomic information and population genetic data. 

Keywords
Molecular clocks, Historical biogeography, Mitochondrial nad introns, Stochastic Dollo model, Secondary structure-based alignment, North American spruces, Fossil calibration
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:umu:diva-84060 (URN)10.1016/j.ympev.2013.07.004 (DOI)23871916 (PubMedID)
Available from: 2013-12-14 Created: 2013-12-14 Last updated: 2018-06-08Bibliographically approved
Peng, Y., Yin, S., Wang, J., Tian, B., Ren, G., Guo, Q. & Liu, J. (2012). Phylogeographic analysis of the fir species in southern China suggests complex origin and genetic admixture. Annals of Forest Science, 69(3), 409-416
Open this publication in new window or tab >>Phylogeographic analysis of the fir species in southern China suggests complex origin and genetic admixture
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2012 (English)In: Annals of Forest Science, ISSN 1286-4560, E-ISSN 1297-966X, Vol. 69, no 3, p. 409-416Article in journal (Refereed) Published
Abstract [en]

Context

Fir species are mainly distributed across the high latitudes, preferring cold climates. The phylogeographic origins of those subtropical fir species that occur in low latitudes in southern China remain elusive, as does the nature of any inter-lineage hybridization.

Aims

In fir species, mitochondrial DNA (mtDNA) is mater- nally inherited and chloroplast DNA (cpDNA) is paternally inherited, and the genetic variations in the two make them particularly useful for examining species’ hybridizations and evolutionary histories.

Materials

and methods We sequenced four DNA frag- ments: two of mtDNA and two of cpDNA for 161 individuals from four subtropical endangered fir species (Abies beshan- zuensis, Abies ziyuanensis, Abies yuanbaoshanensis, and Abies fanjingshanensis) and two more northerly distributed ones (Abies recurvata and Abies fargesii) from central and southwest China.

Results

Three mitotypes and four chlorotypes were recov- ered from the four southern species. In most populations, individuals share a single fixed mitotype and chlorotype. Three mitotypes clustered into two distinct clades, each associated with one of the northern species examined. For four chlorotypes, one occurred in A. ziyuanensis, A. beshan- zuensis, A. fargesii, and A. recurvata, another in A. ziyua- nensis and A. recurvata, the remaining two differed from others by two mutations exclusively in A. fanjingshanenis and A. yuanbaoshanensis.

Conclusion

Phylogeographic origins of the subtropical fir species are complex, and genetic admixtures occurred dur- ing the evolutionary history of A. ziyuanensis. The geno- typed populations further provide basic frames for genetic delimitation and effective conservation of these endangered species in the future. 

Keywords
Fir species, mtDNA, cpDNA, Phylogeography, Genetic admixture
National Category
Ecology
Identifiers
urn:nbn:se:umu:diva-84059 (URN)
Available from: 2013-12-14 Created: 2013-12-14 Last updated: 2018-06-08Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-3793-3264

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