| 1. |
- Niemi, MEK, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 2. |
- Kanai, M, et al.
(författare)
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- 2023
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swepub:Mat__t
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| 3. |
- Arndt, D. S., et al.
(författare)
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STATE OF THE CLIMATE IN 2017
- 2018
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Ingår i: Bulletin of The American Meteorological Society - (BAMS). - : American Meteorological Society. - 0003-0007 .- 1520-0477. ; 99:8, s. S1-S310
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Forskningsöversikt (refereegranskat)
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| 4. |
- Teslovich, Tanya M., et al.
(författare)
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Biological, clinical and population relevance of 95 loci for blood lipids
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 466:7307, s. 707-713
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Tidskriftsartikel (refereegranskat)abstract
- Plasma concentrations of total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol and triglycerides are among the most important risk factors for coronary artery disease (CAD) and are targets for therapeutic intervention. We screened the genome for common variants associated with plasma lipids in >100,000 individuals of European ancestry. Here we report 95 significantly associated loci (P<5 x 10(-8)), with 59 showing genome-wide significant association with lipid traits for the first time. The newly reported associations include single nucleotide polymorphisms (SNPs) near known lipid regulators (for example, CYP7A1, NPC1L1 and SCARB1) as well as in scores of loci not previously implicated in lipoprotein metabolism. The 95 loci contribute not only to normal variation in lipid traits but also to extreme lipid phenotypes and have an impact on lipid traits in three non-European populations (East Asians, South Asians and African Americans). Our results identify several novel loci associated with plasma lipids that are also associated with CAD. Finally, we validated three of the novel genes-GALNT2, PPP1R3B and TTC39B-with experiments in mouse models. Taken together, our findings provide the foundation to develop a broader biological understanding of lipoprotein metabolism and to identify new therapeutic opportunities for the prevention of CAD.
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| 5. |
- Blunden, Jessica, et al.
(författare)
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State of the Climate in 2012
- 2013
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Ingår i: Bulletin of The American Meteorological Society - (BAMS). - 0003-0007 .- 1520-0477. ; 94:8, s. S1-S258
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Tidskriftsartikel (refereegranskat)abstract
- For the first time in serveral years, the El Nino-Southern Oscillation did not dominate regional climate conditions around the globe. A weak La Ni a dissipated to ENSOneutral conditions by spring, and while El Nino appeared to be emerging during summer, this phase never fully developed as sea surface temperatures in the eastern conditions. Nevertheless, other large-scale climate patterns and extreme weather events impacted various regions during the year. A negative phase of the Arctic Oscillation from mid-January to early February contributed to frigid conditions in parts of northern Africa, eastern Europe, and western Asia. A lack of rain during the 2012 wet season led to the worst drought in at least the past three decades for northeastern Brazil. Central North America also experienced one of its most severe droughts on record. The Caribbean observed a very wet dry season and it was the Sahel's wettest rainy season in 50 years. Overall, the 2012 average temperature across global land and ocean surfaces ranked among the 10 warmest years on record. The global land surface temperature alone was also among the 10 warmest on record. In the upper atmosphere, the average stratospheric temperature was record or near-record cold, depending on the dataset. After a 30-year warming trend from 1970 to 1999 for global sea surface temperatures, the period 2000-12 had little further trend. This may be linked to the prevalence of La Ni a-like conditions during the 21st century. Heat content in the upper 700 m of the ocean remained near record high levels in 2012. Net increases from 2011 to 2012 were observed at 700-m to 2000-m depth and even in the abyssal ocean below. Following sharp decreases in to the effects of La Ni a, sea levels rebounded to reach records highs in 2012. The increased hydrological cycle seen in recent years continued, with more evaporation in drier locations and more precipitation in rainy areas. In a pattern that has held since 2004, salty areas of the ocean surfaces and subsurfaces were anomalously salty on average, while fresher areas were anomalously fresh. Global tropical cyclone activity during 2012 was near average, with a total of 84 storms compared with the 1981-2010 average of 89. Similar to 2010 and 2011, the North Atlantic was the only hurricane basin that experienced above-normal activity. In this basin, Sandy brought devastation to Cuba and parts of the eastern North American seaboard. All other basins experienced either near-or below-normal tropical cyclone activity. Only three tropical cyclones reached Category 5 intensity-all in Bopha became the only storm in the historical record to produce winds greater than 130 kt south of 7 N. It was also the costliest storm to affect the Philippines and killed more than 1000 residents. Minimum Arctic sea ice extent in September and Northern Hemisphere snow cover extent in June both reached new record lows. June snow cover extent is now declining at a faster rate (-17.6% per decade) than September sea ice extent (-13.0% per decade). Permafrost temperatures reached record high values in northernmost Alaska. A new melt extent record occurred on 11-12 July on the Greenland ice sheet; 97% of the ice sheet showed some form of melt, four times greater than the average melt for this time of year. The climate in Antarctica was relatively stable overall. The largest maximum sea ice extent since records begain in 1978 was observed in September 2012. In the stratosphere, warm air led to the second smallest ozone hole in the past two decades. Even so, the springtime ozone layer above Antarctica likely will not return to its early 1980s state until about 2060. Following a slight decline associated with the global 2 emissions from fossil fuel combustion and cement production reached a record 9.5 +/- 0.5 Pg C in 2011 and a new record of 9.7 +/- 0.5 Pg C is estimated for 2012. Atmospheric CO2 concentrations increased by 2.1 ppm in 2012, to 392.6 ppm. In spring 2012, 2 concentration exceeded 400 ppm at 7 of the 13 Arctic observation sites. Globally, other greenhouse gases including methane and nitrous oxide also continued to rise in concentration and the combined effect now represents a 32% increase in radiative forcing over a 1990 baseline. Concentrations of most ozone depleting substances continued to fall.
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| 6. |
- Isabel, Nathalie, et al.
(författare)
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A second-generation diagnostic single nucleotide polymorphism (SNP)-based assay, optimized to distinguish among eight poplar (Populus L.) species and their early hybrids
- 2013
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Ingår i: Tree Genetics & Genomes. - : Springer Berlin/Heidelberg. - 1614-2942 .- 1614-2950. ; 9:2, s. 621-626
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 7. |
- Nystedt, Björn, et al.
(författare)
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The Norway spruce genome sequence and conifer genome evolution
- 2013
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 497:7451, s. 579-584
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 8. |
- O'Connell, Lisa M., et al.
(författare)
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Patterns of post-glacial colonization by western redcedar (Thuja plicata, Cupressaceae) as revealed by microsatellite markers
- 2008
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Ingår i: Botany - Botanique. - : Canadian Science Publishing. ; , s. 194-203
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Konferensbidrag (refereegranskat)abstract
- 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.
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| 9. |
- Sullivan, Alexis R., et al.
(författare)
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Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae)
- 2017
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Ingår i: Molecular biology and evolution. - : OXFORD UNIV PRESS. - 0737-4038 .- 1537-1719. ; 34:7, s. 1689-1701
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 10. |
- Talbot, Patricia, et al.
(författare)
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An efficient single nucleotide polymorphism assay to diagnose the genomic identity of poplar species and hybrids on the Canadian prairies
- 2011
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Ingår i: Canadian Journal of Forest Research. - : Canadian Science Publishing. - 0045-5067 .- 1208-6037. ; 41:5, s. 1102-1111
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 11. |
- Thompson, Stacey Lee, et al.
(författare)
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A novel mating system analysis for modes of self-oriented mating applied to diploid and polyploid arctic Easter daisies (Townsendia hookeri).
- 2006
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Ingår i: Heredity. - : Nature Publishing Group. - 0018-067X .- 1365-2540. ; 97:2, s. 119-126
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Tidskriftsartikel (refereegranskat)abstract
- We have developed a new model for mating system analysis, which attempts to distinguish among alternative modes of self-oriented mating within populations. This model jointly estimates the rates of outcrossing, selfing, automixis and apomixis, through the use of information in the family structure given by dominant genetic marker data. The method is presented, its statistical properties evaluated, and is applied to three arctic Easter daisy populations, one consisting of diploids, the other two of tetraploids. The tetraploids are predominantly male sterile and reported to be apomictic while the diploids are male fertile. In each Easter daisy population, 10 maternal arrays of six progeny were assayed for amplified fragment length polymorphism markers. Estimates, confirmed with likelihood ratio tests of mating hypotheses, showed apomixis to be predominant in all populations (ca. 70%), but selfing or automixis was moderate (ca. 25%) in tetraploids. It was difficult to distinguish selfing from automixis, and simulations confirm that with even very large sample sizes, the estimates have a very strong negative statistical correlation, for example, they are not independent. No selfing or automixis was apparent in the diploid population, instead, moderate levels of outcrossing were detected (23%). Low but significant levels of outcrossing (2-4%) seemed to occur in the male-sterile tetraploid populations; this may be due to genotyping error of this level. Overall, this study shows apomixis can be partial, and provides evidence for higher levels of inbreeding in polyploids compared to diploids and for significant levels of apomixis in a diploid plant population.
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| 12. |
- Thompson, Stacey Lee
(författare)
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A simple procedure for joint estimation of the long-term rates of sexuality and mutation in predominantly clonal populations, for use with dominant molecular markers
- 2007
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Ingår i: Molecular Ecology Notes. - : Blackwell Publishing. - 1471-8278 .- 1471-8286. ; 7:4, s. 567-569
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Tidskriftsartikel (refereegranskat)abstract
- In highly clonal populations, mutation can contribute to the rate of apparent sexuality. To remove this bias, a method is presented that jointly estimates the rates of sexuality (Ns) and mutation (N mu) for populations, based upon levels of single-locus vs. multilocus clonal identity. This effectively haploid model assumes equilibrium, and can be used with dominant molecular data and in conjunction with organisms of various ploidies. Simulations indicate that while equilibrium can take thousands of generations to attain, and afterwards have a large evolutionary variance, the method gives approximate estimates of Ns.
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| 13. |
- Thompson, Stacey Lee, et al.
(författare)
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Cryptic sex within male-sterile polyploid populations of the Easter daisy, Townsendia hookeri
- 2008
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Ingår i: International journal of plant sciences. - : University of Chicago Press. - 1058-5893 .- 1537-5315. ; 169:1, s. 183-193
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 14. |
- Thompson, Stacey Lee, et al.
(författare)
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Patterns of recurrent evolution and geographic parthenogenesis within apomictic polyploid Easter daises (Townsendia hookeri).
- 2006
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Ingår i: Molecular Ecology. - : Blackwell Publishing. - 0962-1083 .- 1365-294X. ; 15:11, s. 3389-3400
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Tidskriftsartikel (refereegranskat)abstract
- Geographic patterns of parthenogenesis and the number of transitions from sexual diploidy to asexual (apomictic) autopolyploidy were examined for 40 populations of the Easter daisy, Townsendia hookeri. Analyses of pollen diameter and stainability characterized 15 sexual diploid and 25 apomictic polyploid populations from throughout the plant's western North American range. Sexual diploids were restricted to two Wisconsin refugia: Colorado/Wyoming, south of the ice sheets, and northern Yukon/Beringia. Chloroplast DNA sequencing uncovered 17 polymorphisms within the ndhF gene and trnK intron, yielding 10 haplotypes. Phylogenetic analyses indicated that five exclusively polyploid haplotypes were derived from four haplotypes that are shared among ploidies, conservatively inferring a minimum of four origins of apomictic polyploidy. Three of these apomictic polyploid origins were derived from southern sexual diploids, while the fourth origin was derived from northern sexual diploids. Analyses of regional diversity were suggestive of a formerly broad distribution for sexual diploids that has become subsequently fragmented, possibly due to the last round of glaciation. As sexual diploids were exclusively found north and south of the glacial maximum, while formerly glaciated areas were exclusively inhabited by asexual polyploids derived from both northern and southern sexual lineages, it is more likely that patterns of glaciation, as opposed to a particular latitudinal trend, played a causal role in the establishment of the observed pattern of geographic parthenogenesis in Easter daisies.
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| 15. |
- Thompson, Stacey Lee, et al.
(författare)
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Repeated unidirectional introgression towards Populus balsamifera in contact zones of exotic and native poplars.
- 2010
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Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 19:1, s. 132-145
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 16. |
- Thompson, Stacey Lee, et al.
(författare)
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Three-gene identity coefficients demonstrate that clonal reproduction promotes inbreeding and spatial relatedness in yellow-cedar, Callitropsis nootkatensis
- 2008
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Ingår i: Evolution. - : John Wiley & Sons. - 0014-3820 .- 1558-5646. ; 62:10, s. 2570-2579
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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