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Thompson, Stacey L.
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Publications (10 of 13) Show all publications
Sullivan, A. R., Schiffthaler, B., Thompson, S. L., Street, N. R. & Wang, X.-R. (2017). Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae). Molecular biology and evolution, 34(7), 1689-1701
Open this publication in new window or tab >>Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae)
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2017 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 34, no 7, p. 1689-1701Article in journal (Refereed) Published
Abstract [en]

Plastid sequences are a cornerstone in plant systematic studies and key aspects of their evolution, such as uniparental inheritance and absent recombination, are often treated as axioms. While exceptions to these assumptions can profoundly influence evolutionary inference, detecting them can require extensive sampling, abundant sequence data, and detailed testing. Using advancements in high-throughput sequencing, we analyzed the whole plastomes of 65 accessions of Picea, a genus of similar to 35 coniferous forest tree species, to test for deviations from canonical plastome evolution. Using complementary hypothesis and data-driven tests, we found evidence for chimeric plastomes generated by interspecific hybridization and recombination in the clade comprising Norway spruce (P. abies) and 10 other species. Support for interspecific recombination remained after controlling for sequence saturation, positive selection, and potential alignment artifacts. These results reconcile previous conflicting plastid-based phylogenies and strengthen the mounting evidence of reticulate evolution in Picea. Given the relatively high frequency of hybridization and biparental plastid inheritance in plants, we suggest interspecific plastome recombination may be more widespread than currently appreciated and could underlie reported cases of discordant plastid phylogenies.

Place, publisher, year, edition, pages
OXFORD UNIV PRESS, 2017
Keywords
hybridization, chloroplast genomes, phylogenetic incongruence, recombination, reticulate evolution
National Category
Ecology
Identifiers
urn:nbn:se:umu:diva-137034 (URN)10.1093/molbev/msx111 (DOI)000402754400012 ()28383641 (PubMedID)
Available from: 2017-06-29 Created: 2017-06-29 Last updated: 2018-06-09Bibliographically approved
Roe, A. D., MacQuarrie, C. J. K., Gros-Louis, M.-C., Simpson, J. D., Lamarche, J., Beardmore, T., . . . Isabel, N. (2014). Fitness dynamics within a poplar hybrid zone: I. Prezygotic and postzygotic barriers impacting a native poplar hybrid stand. Ecology and Evolution, 4(9), 1629-1647
Open this publication in new window or tab >>Fitness dynamics within a poplar hybrid zone: I. Prezygotic and postzygotic barriers impacting a native poplar hybrid stand
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2014 (English)In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 4, no 9, p. 1629-1647Article in journal (Refereed) Published
Abstract [en]

Hybridization and introgression are pervasive evolutionary phenomena that provide insight into the selective forces that maintain species boundaries, permit gene flow, and control the direction of evolutionary change. Poplar trees (Populus L.) are well known for their ability to form viable hybrids and maintain their distinct species boundaries despite this interspecific gene flow. We sought to quantify the hybridization dynamics and postzygotic fitness within a hybrid stand of balsam poplar (Populus balsamifera L.), eastern cottonwood (P.deltoides Marsh.), and their natural hybrids to gain insight into the barriers maintaining this stable hybrid zone. We observed asymmetrical hybrid formation with P.deltoides acting as the seed parent, but with subsequent introgression biased toward P.balsamifera. Native hybrids expressed fitness traits intermediate to the parental species and were not universally unfit. That said, native hybrid seedlings were absent from the seedling population, which may indicate additional selective pressures controlling their recruitment. It is imperative that we understand the selective forces maintaining this native hybrid zone in order to quantify the impact of exotic poplar hybrids on this native system.

Keywords
Hybrid fitness, hybridization, introgression, postzygotic fitness, reproductive fitness, SNPs
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-90076 (URN)10.1002/ece3.1029 (DOI)000335267000011 ()
Available from: 2014-06-23 Created: 2014-06-17 Last updated: 2018-06-07Bibliographically approved
Roe, A. D., MacQuarrie, C. J. K., Gros-Louis, M.-C., Simpson, J. D., Lamarche, J., Beardmore, T., . . . Isabel, N. (2014). Fitness dynamics within a poplar hybrid zone: II. Impact of exotic sex on native poplars in an urban jungle. Ecology and Evolution, 4(10), 1876-1889
Open this publication in new window or tab >>Fitness dynamics within a poplar hybrid zone: II. Impact of exotic sex on native poplars in an urban jungle
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2014 (English)In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 4, no 10, p. 1876-1889Article in journal (Refereed) Published
Abstract [en]

Trees bearing novel or exotic gene components are poised to contribute to the bioeconomy for a variety of purposes such as bioenergy production, phytoremediation, and carbon sequestration within the forestry sector, but sustainable release of trees with novel traits in large-scale plantations requires the quantification of risks posed to native tree populations. Over the last century, exotic hybrid poplars produced through artificial crosses were planted throughout eastern Canada as ornamentals or windbreaks and these exotics provide a proxy by which to examine the fitness of exotic poplar traits within the natural environment to assess risk of exotic gene escape, establishment, and spread into native gene pools. We assessed postzygotic fitness traits of native and exotic poplars within a naturally regenerated stand in eastern Canada (Quebec City, QC). Pure natives (P.balsamifera and P.deltoides spp. deltoides), native hybrids (P.deltoidesxP.balsamifera), and exotic hybrids (trees bearing Populus nigra and P.maximowiczii genetic components) were screened for reproductive biomass, yield, seed germination, and fungal disease susceptibility. Exotic hybrids expressed fitness traits intermediate to pure species and were not significantly different from native hybrids. They formed fully viable seed and backcrossed predominantly with P.balsamifera. These data show that exotic hybrids were not unfit and were capable of establishing and competing within the native stand. Future research will seek to examine the impact of exotic gene regions on associated biotic communities to fully quantify the risk exotic poplars pose to native poplar forests.

Keywords
Anthropogenic disturbance, disease susceptibility, hybridization, Populus, postzygotic fitness, SNP genotyping, urban-forest interface
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-90859 (URN)10.1002/ece3.1028 (DOI)000336491600011 ()
Available from: 2014-07-17 Created: 2014-07-01 Last updated: 2018-06-07Bibliographically approved
Isabel, N., Lamothe, M. & Thompson, S. L. (2013). A second-generation diagnostic single nucleotide polymorphism (SNP)-based assay, optimized to distinguish among eight poplar (Populus L.) species and their early hybrids. Tree Genetics & Genomes, 9(2), 621-626
Open this publication in new window or tab >>A second-generation diagnostic single nucleotide polymorphism (SNP)-based assay, optimized to distinguish among eight poplar (Populus L.) species and their early hybrids
2013 (English)In: Tree Genetics & Genomes, ISSN 1614-2942, E-ISSN 1614-2950, Vol. 9, no 2, p. 621-626Article in journal (Refereed) Published
Abstract [en]

Rapid identification of Populus L. species and hybrids can be achieved with relatively little effort through the use of primer extension-based single nucleotide polymorphism (SNP) genotyping assays. We present an optimized set of 36 SNP markers from 28 gene regions that diagnose eight poplar species (Populus angustifolia James, Populus balsamifera L., Populus deltoides Bartram, Populus fremontii Watson, Populus laurifolia Ledeb., Populus maximowiczii Henry, Populus nigra L., and Populus trichocarpa Torr. & Gray). A total of 700 DNA sequences from six Populus species (1–15 individuals per species) were used to construct the array. A set of flanking and probe oligonucleotides was developed and tested. The accuracy of the SNP assay was validated by genotyping 448 putatively "pure" individuals from 14 species of Populus. Overall, the SNP assay had a high success rate (97.6 %) and will prove useful for the identification of all Aigeiros Duby and Tacamahaca Spach. species and their early-generation hybrids within natural populations and breeding programs. Null alleles and intraspecific polymorphisms were detected for a few locus/species combinations in the Aigeiros and Tacamahaca sections. When we attempted to genotype aspens of the section Populus (Populus alba L., Populus grandidentata Michx., Populus tremula L., and Populus tremuloides Michx.), the success rate of the SNP array decreased by 13 %, demonstrating moderate cross-sectional transferability.

Place, publisher, year, edition, pages
Springer Berlin/Heidelberg, 2013
Keywords
Genotyping array, Hybridization, Marker development, Poplars, Clone certification, Species identification
National Category
Genetics Botany
Identifiers
urn:nbn:se:umu:diva-67088 (URN)10.1007/s11295-012-0569-5 (DOI)000316366200025 ()
Available from: 2013-03-12 Created: 2013-03-12 Last updated: 2018-06-08Bibliographically approved
Nystedt, B., Street, N. R., Wetterbom, A., Zuccolo, A., Lin, Y.-C., Scofield, D. G., . . . Jansson, S. (2013). The Norway spruce genome sequence and conifer genome evolution. Nature, 497(7451), 579-584
Open this publication in new window or tab >>The Norway spruce genome sequence and conifer genome evolution
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2013 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 497, no 7451, p. 579-584Article in journal (Refereed) Published
Abstract [en]

Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.

Place, publisher, year, edition, pages
Nature Publishing Group, 2013
National Category
Earth and Related Environmental Sciences Botany
Identifiers
urn:nbn:se:umu:diva-76264 (URN)10.1038/nature12211 (DOI)000319556100035 ()
Available from: 2013-07-08 Created: 2013-07-08 Last updated: 2019-07-05Bibliographically approved
Talbot, P., Thompson, S. L., Schroeder, W. & Isabel, N. (2011). An efficient single nucleotide polymorphism assay to diagnose the genomic identity of poplar species and hybrids on the Canadian prairies. Canadian Journal of Forest Research, 41(5), 1102-1111
Open this publication in new window or tab >>An efficient single nucleotide polymorphism assay to diagnose the genomic identity of poplar species and hybrids on the Canadian prairies
2011 (English)In: Canadian Journal of Forest Research, ISSN 0045-5067, E-ISSN 1208-6037, Vol. 41, no 5, p. 1102-1111Article in journal (Refereed) Published
Abstract [en]

Hybridization frequently occurs among poplars, both naturally and artificially, hindering identification. Over 32 million clonal poplars, predominantly hybrids, have been planted throughout the Canadian prairies over the past century, making confirmation of genomic identity important. We developed a genotyping assay that rapidly diagnoses four compatible Populus species (Populus balsamifera L. and Populus deltoides Bartr. ex Marsh.: indigenous, Populus laurifolia Ledeb. and Populus nigra L.: exotics) and their hybrids found throughout this ecozone. First, we sequenced 23 genes from representative provenances of the four Populus species to discover single nucleotide polymorphisms (SNPs). Second, we developed and validated a medium-throughput genotyping assay of 26 diagnostic SNPs within these genes. We used this assay to genotype 198 trees from natural populations as well as 30 clones (pure species and hybrids), including those broadly distributed by Agriculture and Agri-Food Canada's Agroforestry Development Centre since 1910. This suite of SNPs has the resolving power to correctly identify pure species and hybrids of Populus. We confirmed the identity of clones of well-documented origin, complex hybrids with exotic components, and paternity of open-pollinated progenies from breeding programs. This diagnostic tool should prove useful for efficient molecular fingerprinting of breeding material and for further studies of interspecific gene flow on the Canadian prairies.

Place, publisher, year, edition, pages
Canadian Science Publishing, 2011
National Category
Forest Science
Identifiers
urn:nbn:se:umu:diva-67092 (URN)10.1139/X11-025 (DOI)000291446400018 ()
Available from: 2013-03-12 Created: 2013-03-12 Last updated: 2018-06-08Bibliographically approved
Thompson, S. L., Lamothe, M., Meirmans, P. G., Périnet, P. & Isabel, N. (2010). Repeated unidirectional introgression towards Populus balsamifera in contact zones of exotic and native poplars.. Molecular Ecology, 19(1), 132-145
Open this publication in new window or tab >>Repeated unidirectional introgression towards Populus balsamifera in contact zones of exotic and native poplars.
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2010 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 19, no 1, p. 132-145Article in journal (Refereed) Published
Abstract [en]

As the evolutionary significance of hybridization is largely dictated by its extent beyond the first generation, we broadly surveyed patterns of introgression across a sympatric zone of two native poplars (Populus balsamifera, Populus deltoides) in Quebec, Canada within which European exotic Populus nigra and its hybrids have been extensively planted since the 1800s. Single nucleotide polymorphisms (SNPs) that appeared fixed within each species were characterized by DNA-sequencing pools of pure individuals. Thirty-five of these diagnostic SNPs were employed in a high-throughput assay that genotyped 635 trees of different age classes, sampled from 15 sites with various degrees of anthropogenic disturbance. The degree of admixture within sampled trees was then assessed through Bayesian clustering of genotypes. Hybrids were present in seven of the populations, with 2.4% of all sampled trees showing spontaneous admixture. Sites with hybrids were significantly more disturbed than pure stands, while hybrids comprised both immature juveniles and trees of reproductive age. All three possible F1s were detected. Advanced-generation hybrids were consistently biased towards P. balsamifera regardless of whether hybridization had occurred with P. deltoides or P. nigra. Gene exchange between P. deltoides and P. nigra was not detected beyond the F1 generation; however, detection of a trihybrid demonstrates that even this apparent reproductive isolation does not necessarily result in an evolutionary dead end. Collectively, results demonstrate the natural fertility of hybrid poplars and suggest that introduced genes could potentially affect the genetic integrity of native trees, similar to that arising from introgression between natives.

Place, publisher, year, edition, pages
John Wiley & Sons, 2010
National Category
Forest Science
Identifiers
urn:nbn:se:umu:diva-67093 (URN)10.1111/j.1365-294X.2009.04442.x (DOI)20002578 (PubMedID)
Available from: 2013-03-12 Created: 2013-03-12 Last updated: 2018-06-08Bibliographically approved
Thompson, S. L., Choe, G., Ritland, K. & Whitton, J. (2008). Cryptic sex within male-sterile polyploid populations of the Easter daisy, Townsendia hookeri. International journal of plant sciences, 169(1), 183-193
Open this publication in new window or tab >>Cryptic sex within male-sterile polyploid populations of the Easter daisy, Townsendia hookeri
2008 (English)In: International journal of plant sciences, ISSN 1058-5893, E-ISSN 1537-5315, Vol. 169, no 1, p. 183-193Article in journal (Refereed) Published
Abstract [en]

After a transition from sexuality to asexuality, the evolutionary dynamics in apomictic lineages will largely depend on the frequency of recombination. We evaluated the presence and extent of asexuality and recombination within populations of the Easter daisy, Townsendia hookeri, from the Yukon Territory, Canada. Amplified fragment-length polymorphism (AFLP) fingerprints were used to genotype 78 individuals from four populations. Multilocus AFLP genotypes from each population were subjected to four tests for deviations from free recombination among loci, and the long-term frequency of sexuality was estimated for each population with a novel procedure. In addition, a sample of individuals was surveyed for genome size using flow cytometry, and pollen was assayed for male fertility. One male-fertile, diploid population showed evidence of rampant recombination. Two male-sterile populations (i.e., with aborted anthers) were tetraploid and asexual. The remaining population was male-sterile and included both triploids and tetraploids. Evidence of both sexuality and asexuality was uncovered in this mixed-ploidy population, at an equilibrium rate of approximately three sexual events every two generations. The presence and extent of sexuality differed with ploidy, while cryptic sex was uncovered within a morphologically asexual population, thus reinforcing the power of genome surveys to assess reproductive dynamics at the limit of a plant's geographical range.

Place, publisher, year, edition, pages
University of Chicago Press, 2008
Keywords
agamospermy, apomixis, asexual reproduction, polyploidy, recombination, sexuality rate, Townsendia hookeri
National Category
Biological Sciences
Identifiers
urn:nbn:se:umu:diva-67098 (URN)10.1086/523363 (DOI)000252245600015 ()
Available from: 2013-03-12 Created: 2013-03-12 Last updated: 2018-06-08Bibliographically approved
O'Connell, L. M., Ritland, K. & Thompson, S. L. (2008). Patterns of post-glacial colonization by western redcedar (Thuja plicata, Cupressaceae) as revealed by microsatellite markers. In: Botany - Botanique: . Paper presented at Symposium on Ethnobotany held at the 42nd Annual Meeting of the Canadian-Botanical-Association, JUN, 2006, Montreal, CANADA (pp. 194-203). Canadian Science Publishing (2)
Open this publication in new window or tab >>Patterns of post-glacial colonization by western redcedar (Thuja plicata, Cupressaceae) as revealed by microsatellite markers
2008 (English)In: Botany - Botanique, Canadian Science Publishing , 2008, no 2, p. 194-203Conference paper, Published paper (Refereed)
Abstract [en]

As knowledge of historical migration in response to climatic change allows insight into the dynamic nature of range shifts, patterns of post-glacial colonization were evaluated for the western redcedar (Thuja plicata Donn ex D. Don). We sampled and genotyped 620 trees from 23 populations across its range, including disjunct coastal and interior mesic sites. Genetic variation at eight microsatellite loci (mean alleles/locus = 10.30, mean expected heterozygosity = 0.755) was much higher than previous studies involving other markers, and inbreeding coefficients were predominantly positive (mean = 0.110). The two southernmost populations showed greatest genetic distances, while remaining populations clustered into three distinct geographic groups, comprising northern-coastal, central, and southern-interior populations, respectively. Genetic diversity decreased with latitude, while genetic and geographic distances were strongly correlated (r = 0.788). Our findings are consistent with independent routes of relatively recent colonization from one major refugium, located south of the glacial maximum, rather than ancient vicariant events. Regional bottlenecks, detected in the south of the range, may have resulted from local extinctions as the range of western redcedar advanced northward. Combined with inbreeding and the evolution of inbreeding tolerance, this may have promoted homozygosity for most classes of genetic markers as observed in other studies of this species.

Place, publisher, year, edition, pages
Canadian Science Publishing, 2008
Series
Botany ; 2008:86:2
Keywords
genetic diversity, mating system, microsatellite markers, population bottlenecks, post-glacial recolonization, Thuja plicata
National Category
Forest Science
Identifiers
urn:nbn:se:umu:diva-67097 (URN)10.1139/B07-124 (DOI)000255131000010 ()
Conference
Symposium on Ethnobotany held at the 42nd Annual Meeting of the Canadian-Botanical-Association, JUN, 2006, Montreal, CANADA
Available from: 2013-03-12 Created: 2013-03-12 Last updated: 2018-06-08Bibliographically approved
Thompson, S. L., Bérubé, Y., Bruneau, A. & Ritland, K. (2008). Three-gene identity coefficients demonstrate that clonal reproduction promotes inbreeding and spatial relatedness in yellow-cedar, Callitropsis nootkatensis. Evolution, 62(10), 2570-2579
Open this publication in new window or tab >>Three-gene identity coefficients demonstrate that clonal reproduction promotes inbreeding and spatial relatedness in yellow-cedar, Callitropsis nootkatensis
2008 (English)In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 62, no 10, p. 2570-2579Article in journal (Refereed) Published
Abstract [en]

Asexual reproduction has the potential to promote population structuring through matings between clones as well as through limited dispersal of related progeny. Here we present an application of three-gene identity coefficients that tests whether clonal reproduction promotes inbreeding and spatial relatedness within populations. With this method, the first two genes are sampled to estimate pairwise relatedness or inbreeding, whereas the third gene is sampled from either a clone or a sexually derived individual. If three-gene coefficients are significantly greater for clones than nonclones, then clonality contributes excessively to genetic structure. First, we describe an estimator of three-gene identity and briefly evaluate its properties. We then use this estimator to test the effect of clonality on the genetic structure within populations of yellow-cedar (Callitropsis nootkatensis) using a molecular marker survey. Five microsatellite loci were genotyped for 485 trees sampled from nine populations. Our three-gene analyses show that clonal ramets promote inbreeding and spatial structure in most populations. Among-population correlations between clonal extent and genetic structure generally support these trends, yet with less statistical significance. Clones appear to contribute to genetic structure through the limited dispersal of offspring from replicated ramets of the same clonal genet, whereas this structure is likely maintained by mating among these relatives.

Place, publisher, year, edition, pages
John Wiley & Sons, 2008
National Category
Forest Science
Identifiers
urn:nbn:se:umu:diva-67094 (URN)10.1111/j.1558-5646.2008.00470.x (DOI)18647338 (PubMedID)
Available from: 2013-03-12 Created: 2013-03-12 Last updated: 2018-06-08Bibliographically approved
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