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  • 1. Barker, Hilary L.
    et al.
    Riehl, Jennifer F.
    Bernhardsson, Carolina
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Rubert-Nason, Kennedy F.
    Holeski, Liza M.
    Ingvarsson, Pär K.
    Lindroth, Richard L.
    Linking plant genes to insect communities: Identifying the genetic bases of plant traits and community composition2019In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 19, p. 4404-4421Article in journal (Refereed)
    Abstract [en]

    Community genetics aims to understand the effects of intraspecific genetic variation on community composition and diversity, thereby connecting community ecology with evolutionary biology. Thus far, research has shown that plant genetics can underlie variation in the composition of associated communities (e.g., insects, lichen and endophytes), and those communities can therefore be considered as extended phenotypes. This work, however, has been conducted primarily at the plant genotype level and has not identified the key underlying genes. To address this gap, we used genome‐wide association mapping with a population of 445 aspen (Populus tremuloides) genets to identify the genes governing variation in plant traits (defence chemistry, bud phenology, leaf morphology, growth) and insect community composition. We found 49 significant SNP associations in 13 Populus genes that are correlated with chemical defence compounds and insect community traits. Most notably, we identified an early nodulin‐like protein that was associated with insect community diversity and the abundance of interacting foundation species (ants and aphids). These findings support the concept that particular plant traits are the mechanistic link between plant genes and the composition of associated insect communities. In putting the “genes” into “genes to ecosystems ecology”, this work enhances understanding of the molecular genetic mechanisms that underlie plant–insect associations and the consequences thereof for the structure of ecological communities.

  • 2.
    Bernhardsson, Carolina
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Ingvarsson, Pär
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Geographic structure and adaptive population differentiation in herbivore defence genes in European aspen (Populus tremula L., Salicaceae)2012In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 21, no 9, p. 2197-2207Article in journal (Refereed)
    Abstract [en]

    When a phenotypic trait is subjected to spatially variable selection and local adaptation, the underlying genes controlling the trait are also expected to show strong patterns of genetic differentiation since alternative alleles are favored in different geographical locations. Here we study 71 SNPs from seven genes associated with inducible defense responses in a sample of P. tremula collected from across Sweden. Four of these genes (PPO2, TI2, TI4 and TI5) show substantial population differentiation and a PCA conducted on the defense SNPs divides the Swedish population into three distinct clusters. Several defense SNPs show latitudinal clines, although these were not robust to multiple testing. However, five SNPs (located within TI4 and TI5) show strong longitudinal clines that remain significant after multiple test correction. Genetic geographical variation, supporting local adaptation, has earlier been confirmed in genes involved in the photoperiod pathway in P. tremula, but this is, to our knowledge, one of the first times that geographic variation has been found in genes involved in plant defense against antagonists.

  • 3.
    Bowd, Elle J.
    et al.
    Fenner School of Environment and Society, The Australian National University, Canberra, Australia.
    Egidi, Eleonora
    Hawkesbury Institute for the Environment, Western Sydney University, NSW, Penrith, Australia; Global Centre for Land-Based Innovation, Western Sydney University, NSW, Penrith, Australia.
    Lindenmayer, David B.
    Fenner School of Environment and Society, The Australian National University, Canberra, Australia.
    Wardle, David A.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Kardol, Paul
    Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden; Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Foster, Claire
    Fenner School of Environment and Society, The Australian National University, Canberra, Australia.
    Temporal dynamics of soil fungi in a pyrodiverse dry-sclerophyll forest2023In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 32, no 15, p. 4181-4198Article in journal (Refereed)
    Abstract [en]

    Fire is a major evolutionary and ecological driver that shapes biodiversity in forests. While above-ground community responses to fire have been well-documented, those below-ground are much less understood. However, below-ground communities, including fungi, play key roles in forests and facilitate the recovery of other organisms after fire. Here, we used internal transcribed spacer (ITS) meta-barcoding data from forests with three different times since fire [short (3 years), medium (13–19 years) and long (>26 years)] to characterize the temporal responses of soil fungal communities across functional groups, ectomycorrhizal exploration strategies and inter-guild associations. Our findings indicate that fire effects on fungal communities are strongest in the short to medium term, with clear distinctions between communities in forests with a short time (3 years) since fire, a medium time (13–19 years) and a long time (>26 years) since fire. Ectomycorrhizal fungi were disproportionately impacted by fire relative to saprotrophs, but the direction of the response varied depending on morphological structures and exploration strategies. For instance, short-distance ectomycorrhizal fungi increased with recent fire, while medium-distance (fringe) ectomycorrhizal fungi decreased. Further, we detected strong, negative inter-guild associations between ectomycorrhizal and saprotrophic fungi but only at medium and long times since fire. Given the functional significance of fungi, the temporal changes in fungal composition, inter-guild associations and functional groups after fire demonstrated in our study may have functional implications that require adaptive management to curtail.

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  • 4. Chauvet, S
    et al.
    van der Velde, M
    Imbert, E
    Guillemin, ML
    Mayol, M
    Riba, M
    Smulders, MJM
    Vosman, B
    Ericson, L
    Umeå University, Faculty of Science and Technology, Ecology and Environmental Science.
    Bijlsma, R
    Giles, BE
    Umeå University, Faculty of Science and Technology, Ecology and Environmental Science.
    Past and current gene flow in the selfing wind-dispersed species Mycelis muralis in western Europe2004In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 13, no 6, p. 1391-1407Article in journal (Refereed)
    Abstract [en]

    The distribution of genetic diversity in Mycelis muralis, or wall lettuce, was investigated at a European scale using 12 microsatellite markers to infer historical and contemporary forces from genetic patterns. Mycelis muralis has the potential for long-distance seed dispersal by wind, is mainly self-pollinated, and has patchily distributed populations, some of which may show metapopulation dynamics. A total of 359 individuals were sampled from 17 populations located in three regions, designated southern Europe (Spain and France), the Netherlands, and Sweden. At this within-region scale, contemporary evolutionary forces (selfing and metapopulation dynamics) are responsible for high differentiation between populations (0.34 < FST < 0.60) but, contrary to expectation, levels of within-population diversity, estimated by Nei's unbiased expected heterozygosity (HE) (0.24 < HE < 0.68) or analyses of molecular variance (50% of the variation found within-populations), were not low. We suggest that the latter results, which are unusual in selfing species, arise from efficient seed dispersal that counteracts population turnover and thus maintains genetic diversity within populations. At the European scale, northern regions showed lower allelic richness (A = 2.38) than populations from southern Europe (A = 3.34). In light of postglacial colonization hypotheses, these results suggest that rare alleles may have been lost during recolonization northwards. Our results further suggest that mutation has contributed to genetic differentiation between southern and northern Europe, and that Sweden may have been colonized by dispersers originating from at least two different refugia.

  • 5. Cole, Christopher T.
    et al.
    Ingvarsson, Pär K.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Pathway position constrains the evolution of an ecologically important pathway in aspens (Populus tremula L.)2018In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 16, p. 3317-3330Article in journal (Refereed)
    Abstract [en]

    Many ecological interactions of aspens and their relatives (Populus spp.) are affected by products of the phenylpropanoid pathway synthesizing condensed tannins (CTs), whose production involves trade-offs with other ecologically important compounds and with growth. Genes of this pathway are candidates for investigating the role of selection on ecologically important, polygenic traits. We analysed sequences from 25 genes representing 10 steps of the CT synthesis pathway, which produces CTs used in defence and lignins used for growth, in 12 individuals of European aspen (Populus tremula). We compared these to homologs from P.trichocarpa, to a control set of 77 P. tremula genes, to genome-wide resequencing data and to RNA-seq expression levels, in order to identify signatures of selection distinct from those of demography. In Populus, pathway position exerts a strong influence on the evolution of these genes. Nonsynonymous diversity, divergence and allele frequency shifts (Tajima's D) were much lower than for synonymous measures. Expression levels were higher, and the direction of selection more negative, for upstream genes than for those downstream. Selective constraints act with increasing intensity on upstream genes, despite the presence of multiple paralogs in most gene families. Pleiotropy, expression level, flux control and codon bias appear to interact in determining levels and patterns of variation in genes of this pathway, whose products mediate a wide array of ecological interactions for this widely distributed species.

  • 6. de Carvalho, Dulcineia
    et al.
    Ingvarsson, Pär K
    Umeå University, Faculty of Science and Technology, Ecology and Environmental Science.
    Joseph, Jeffrey
    Suter, Leonie
    Sedivy, Claudio
    Macaya-Sanz, David
    Cottrell, Joan
    Heinze, Berthold
    Schanzer, Ivan
    Lexer, Christian
    Admixture facilitates adaptation from standing variation in the European aspen (P. tremula L.), a widespread forest tree2010In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 19, no 8, p. 1638-1650Article in journal (Refereed)
    Abstract [en]

    Adaptation to new environments can start from new mutations or from standing variation already present in natural populations. Whether admixture constrains or facilitates adaptation from standing variation is largely unknown, especially in ecological keystone or foundation species. We examined patterns of neutral and adaptive population divergence in Populus tremula L., a widespread forest tree, using mapped molecular genetic markers. We detected the genetic signature of postglacial admixture between a Western and an Eastern lineage of P. tremula in Scandinavia, an area suspected to represent a zone of postglacial contact for many species of animals and plants. Stringent divergence-based neutrality tests provided clear indications for locally varying selection at the European scale. Six of 12 polymorphisms under selection were located less than 1 kb away from the nearest gene predicted by the Populus trichocarpa genome sequence. Few of these loci exhibited a signature of 'selective sweeps' in diversity-based tests, which is to be expected if adaptation occurs primarily from standing variation. In Scandinavia, admixture explained genomic patterns of ancestry and the nature of clinal variation and strength of selection for bud set, a phenological trait of great adaptive significance in temperate trees, measured in a common garden trial. Our data provide a hitherto missing direct link between past range shifts because of climatic oscillations, and levels of standing variation currently available for selection and adaptation in a terrestrial foundation species.

  • 7.
    De La Torre, Amanda R.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Univ British Columbia, Dept Forest & Conservat Sci, Ctr Forest Conservat Genet, Vancouver, BC V6T 1Z4, Canada.
    Roberts, David R.
    Aitken, Sally N.
    Genome-wide admixture and ecological niche modelling reveal the maintenance of species boundaries despite long history of interspecific gene flow2014In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 23, no 8, p. 2046-2059Article in journal (Refereed)
    Abstract [en]

    The maintenance of species boundaries despite interspecific gene flow has been a continuous source of interest in evolutionary biology. Many hybridizing species have porous genomes with regions impermeable to introgression, conferring reproductive barriers between species. We used ecological niche modelling to study the glacial and postglacial recolonization patterns between the widely hybridizing spruce species Picea glauca and P.engelmannii in western North America. Genome-wide estimates of admixture based on a panel of 311 candidate gene single nucleotide polymorphisms (SNP) from 290 genes were used to assess levels of admixture and introgression and to identify loci putatively involved in adaptive differences or reproductive barriers between species. Our palaeoclimatic modelling suggests that these two closely related species have a long history of hybridization and introgression, dating to at least 21000years ago, yet species integrity is maintained by a combination of strong environmental selection and reduced current interspecific gene flow. Twenty loci showed evidence of divergent selection, including six loci that were both F-st outliers and associated with climatic gradients, and fourteen loci that were either outliers or showed associations with climate. These included genes responsible for carbohydrate metabolism, signal transduction and transcription factors.

  • 8.
    Dibattista, Joseph D.
    et al.
    Redpath Museum and Department of Biology, McGill University, Montréal, Québec, Canada .
    Feldheim, Kevin A.
    Field Museum, Pritzker Laboratory for Molecular Systematics and Evolution, Chicago, IL, USA.
    Thibert-Plante, Xavier
    Redpath Museum and Department of Biology, McGill University, Montréal, Québec, Canada.
    Gruber, Samuel H.
    Division of Marine Biology and Fisheries, Rosenstiel School of Marine and Atmospheric Science, Miami, FL, USA.
    Hendry, Andrew P.
    Redpath Museum and Department of Biology, McGill University, Montréal, Québec, Canada.
    A genetic assessment of polyandry and breeding-site fidelity in lemon sharks2008In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 17, no 14, p. 3337-3351Article in journal (Refereed)
    Abstract [en]

    We here employ 11 microsatellite markers and recently developed litter reconstruction methods to infer mating system parameters (i.e. polyandry and breeding-site fidelity) at a lemon shark nursery site in Marquesas Key, Florida. Four hundred and eight juvenile or subadult sharks were genotyped over eight complete breeding seasons. Using this information, we were able to infer family structure, as well as fully or partially reconstruct genotypes of 46 mothers and 163 fathers. Multiple litter reconstruction methods were used, and novel simulations helped define apparent bias and precision of at least some mating system parameters. For Marquesas Key, we find that adult female lemon sharks display high levels of polyandry (81% of all litters sampled) and stronger fidelity to the nursery site than do males. Indeed, few male sharks sired offspring from more than one litter during the course of the study. These findings were quite similar to previous results from another lemon shark nursery site (Bimini, Bahamas), suggesting conserved mating system parameters despite significant variation in early life-history traits (i.e. body size and growth) among sites. The finding of at least some site fidelity in females also supports the need for careful conservation of each nursery.

  • 9. Du, Shuhui
    et al.
    Wang, Zhaoshan
    Ingvarsson, Pär K
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Wang, Dongsheng
    Wang, Junhui
    Wu, Zhiqiang
    Tembrock, Luke R.
    Zhang, Jianguo
    Multilocus analysis of nucleotide variation and speciation in three closely related Populus (Salicaceae) species2015In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, no 19, p. 4994-5005Article in journal (Refereed)
    Abstract [en]

    Historical tectonism and climate oscillations can isolate and contract the geographical distributions of many plant species, and they are even known to trigger species divergence and ultimately speciation. Here, we estimated the nucleotide variation and speciation in three closely related Populus species, Populus tremuloides, P.tremula and P.davidiana, distributed in North America and Eurasia. We analysed the sequence variation in six single-copy nuclear loci and three chloroplast (cpDNA) fragments in 497 individuals sampled from 33 populations of these three species across their geographic distributions. These three Populus species harboured relatively high levels of nucleotide diversity and showed high levels of nucleotide differentiation. Phylogenetic analysis revealed that P.tremuloides diverged earlier than the other two species. The cpDNA haplotype network result clearly illustrated the dispersal route from North America to eastern Asia and then into Europe. Molecular dating results confirmed that the divergence of these three species coincided with the sundering of the Bering land bridge in the late Miocene and a rapid uplift of the Qinghai-Tibetan Plateau around the Miocene/Pliocene boundary. Vicariance-driven successful allopatric speciation resulting from historical tectonism and climate oscillations most likely played roles inthe formation of the disjunct distributions and divergence of these three Populus species.

  • 10.
    Gao, Jie
    et al.
    State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
    Wang, Baosheng
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Mao, Ian-Feng
    State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
    Ingvarsson, Pär
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Zeng, Qing-Yin
    State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
    Demography and speciation history of the homoploid hybrid pine Pinus densata on the Tibetan Plateau2012In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 21, no 19, p. 4811-4827Article in journal (Refereed)
    Abstract [en]

    Pinus densata is an ecologically successful homoploid hybrid that inhabits vast areas of heterogeneous terrain on the south-eastern Tibetan Plateau as a result of multiple waves of colonization. Its region of origin, route of colonization onto the plateau and the directions of introgression with its parental species have previously been defined, but little is known about the isolation and divergence history of its populations. In this study, we surveyed nucleotide polymorphism over eight nuclear loci in 19 representative populations of P. densata and its parental species. Using this information and coalescence simulations, we assessed the historical changes in its population size, gene flow and divergence in time and space. The results indicate a late Miocene origin for P. densata associated with the recent uplift of south-eastern Tibet. The subsequent differentiation between geographical regions of this species began in the late Pliocene and was induced by regional topographical changes and Pleistocene glaciations. The ancestral P. densata population had a large effective population size but the central and western populations were established by limited founders, suggesting that there were severe bottlenecks during the westward migration out of the ancestral hybrid zone. After separating from their ancestral populations, population expansion occurred in all geographical regions especially in the western range. Gene flow in P. densata was restricted to geographically neighbouring populations, resulting in significant differentiation between regional groups. The new information on the divergence and demographic history of P. densata reported herein enhances our understanding of its speciation process on the Tibetan Plateau.

  • 11.
    Hall, David
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Ma, Xiao-Fei
    Program in Evolutionary Functional Genomics, Evolutionary Biology Center, Uppsala University.
    Ingvarsson, Pär K
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Adaptive evolution of the Populus tremula photoperiod pathway2011In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 20, no 7, p. 1463-1474Article in journal (Refereed)
    Abstract [en]

    Environmental cues entrain the circadian clock, a core component of the photoperiod pathway in plants, to daily and seasonal changes. The circadian clock mediates input signals from light and temperature receptors to downstream target genes through feedback loops. Several studies have shown that a correct timing of the circadian system is a fitness advantage and genes in photoperiod network have been implied to evolve in response to the diversifying selection in heterogeneous environment. In an attempt to quantify the extent of the historical patterns of selection on genes in the photoperiod pathway in the widely distributed tree species European aspen (Populus tremula) we obtained sequences for twenty-five of the genes in the network and these genes were compared to patterns of nucleotide diversity in 77 randomly chosen genes from across the genome of P. tremula. We found a significant reduction in synonymous diversity in photoperiod genes while non-synonymous diversity was in line with data from control genes. A substantial fraction of the genes show signs of selection, with eight genes showing signs of rapid protein evolution. In contrast to our expectations, genes closely associated with the core circadian clock show rapid protein evolution despite their central position in the pathway. Furthermore, selection on non-synonymous mutations is negatively correlated with synonymous diversity across all genes, indicating the action of recurrent selective sweeps.

  • 12.
    He, Li
    et al.
    College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China; Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China.
    Guo, Fei-Yi
    East China Survey and Planning Institute, National Forestry and Grassland Administration, Hangzhou, China; Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.
    Cai, Xin-Jie
    College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.
    Chen, Hong-Pu
    College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.
    Lian, Chun-Lan
    Asian Research Center for Bioresource and Environmental Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Nishitokyo, Tokyo, Japan.
    Wang, Yuan
    College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.
    Shang, Ce
    Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.
    Zhang, Yue
    Jiuzhaigou Nature Reserve Administration, Abazhou, China.
    Wagner, Natascha Dorothea
    Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Göttingen, Germany.
    Zhang, Zhi-Xiang
    Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.
    Hörandl, Elvira
    Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Göttingen, Germany.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Evolutionary origin and establishment of a dioecious diploid-tetraploid complex2023In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 32, no 11, p. 2732-2749Article in journal (Refereed)
    Abstract [en]

    Polyploids recurrently emerge in angiosperms, but most polyploids are likely to go extinct before establishment due to minority cytotype exclusion, which may be specifically a constraint for dioecious plants. Here we test the hypothesis that a stable sex-determination system and spatial/ecological isolation facilitate the establishment of dioecious polyploids. We determined the ploidy levels of 351 individuals from 28 populations of the dioecious species Salix polyclona, and resequenced 190 individuals of S. polyclona and related taxa for genomic diversity analyses. The ploidy survey revealed a frequency 52% of tetraploids in S. polyclona, and genomic k-mer spectra analyses suggested an autopolyploid origin for them. Comparisons of diploid male and female genomes identified a female heterogametic sex-determining factor on chromosome 15, which probably also acts in the dioecious tetraploids. Phylogenetic analyses revealed two diploid clades and a separate clade/grade of tetraploids with a distinct geographic distribution confined to western and central China, where complex mountain systems create higher levels of environmental heterogeneity. Fossil-calibrated phylogenies showed that the polyploids emerged during 7.6–2.3 million years ago, and population demographic histories largely matched the geological and climatic history of the region. Our results suggest that inheritance of the sex-determining system from the diploid progenitor as intrinsic factor and spatial isolation as extrinsic factor may have facilitated the preservation and establishment of polyploid dioecious populations.

  • 13. Hellgren, O
    et al.
    Bensch, S
    Malmqvist, Björn
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Bird hosts, blood parasites and their vectors--associations uncovered by molecular analyses of blackfly blood meals.2008In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 17, no 6, p. 1605-13Article in journal (Refereed)
    Abstract [en]

    The level of host specificity of blood-sucking invertebrates may have both ecological and evolutionary implications for the parasites they are transmitting. We used blood mealsfrom wild-caught blackflies for molecular identification of parasites and hosts to examine patterns of host specificity and how these may affect the transmission of avian blood parasites of the genus Leucocytozoon. We found that five different species of ornithophilic blackflies preferred different species of birds when taking their blood meals. Of the blackflies that contained avian blood meals, 62% were infected with Leucocytozoon parasites, consisting of 15 different parasite lineages. For the blackfly species, there was a significant association between the host width (measured as the genetic differentiation between the used hosts) and the genetic similarity of the parasites in their blood meals. The absence of similar parasite in blood meals from blackflies with different host preferences is interpreted as a result of the vector–host associations. The observed associations between blackfly species and host species are therefore likely to hinder parasites to be transmitted between different host-groups, resulting in ecologically driven associations between certain parasite lineages and hosts species.

  • 14. Ibrahim, Anan
    et al.
    Capo, Eric
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Department of Marine Biology, Institut de Ciències del Mar, CSIC, Barcelona, Spain.
    Wessels, Martin
    Martin, Isabel
    Meyer, Axel
    Schleheck, David
    Epp, Laura S.
    Anthropogenic impact on the historical phytoplankton community of Lake Constance reconstructed by multimarker analysis of sediment-core environmental DNA2021In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 30, no 13, p. 3040-3056Article in journal (Refereed)
    Abstract [en]

    During the 20th century, many lakes in the Northern Hemisphere were affected by increasing human population and urbanization along their shorelines and catchment, resulting in aquatic eutrophication. Ecosystem monitoring commenced only after the changes became apparent, precluding any examination of timing and dynamics of initial community change in the past and comparison of pre- and postimpact communities. Peri-Alpine Lake Constance (Germany) underwent a mid-century period of eutrophication followed by re-oligotrophication since the 1980s and is now experiencing warm temperatures. We extended the period for which monitoring data of indicator organisms exist by analysing historical environmental DNA (eDNA) from a sediment core dating back some 110 years. Using three metabarcoding markers-for microbial eukaryotes, diatoms and cyanobacteria-we revealed two major breakpoints of community change, in the 1930s and the mid-1990s. In our core, the latest response was exhibited by diatoms, which are classically used as palaeo-bioindicators for the trophic state of lakes. Following re-oligotrophication, overall diversity values reverted to similar ones of the early 20th century, but multivariate analysis indicated that the present community is substantially dissimilar. Community changes of all three groups were strongly correlated to phosphorus concentration changes, whereas significant relationships to temperature were only observed when we did not account for temporal autocorrelation. Our results indicate that each microbial group analysed exhibited a unique response, highlighting the particular strength of multimarker analysis of eDNA, which is not limited to organisms with visible remains and can therefore discover yet unknown responses and abiotic-biotic relationships.

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  • 15. Izabel-Shen, Dandan
    et al.
    Albert, Séréna
    Winder, Monika
    Farnelid, Hanna
    Nascimento, Francisco J. A.
    Quality of phytoplankton deposition structures bacterial communities at the water-sediment interface2021In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 30, no 14, p. 3515-3529Article in journal (Refereed)
    Abstract [en]

    Phytoplankton comprises a large fraction of the vertical carbon flux to deep water via the sinking of particulate organic matter (POM). However, despite the importance of phytoplankton in the coupling of benthic-pelagic productivity, the extent to which its deposition in the sediment affects bacterial dynamics at the water-sediment interface is poorly understood. Here, we conducted a microcosm experiment in which varying mixtures of diatom and cyanobacteria, representing phytoplankton-derived POM of differing quality, served as inputs to sediment cores. Characterization of 16S rRNA gene of the bacterial communities at the water-sediment interface showed that bacterial α-diversity was not affected by POM addition, while bacterial ?-diversity changed significantly along the POM quality gradient, with the variation driven by changes in relative abundance rather than in taxon replacement. Analysing individual taxa abundances across the POM gradient revealed two distinct bacterial responses, in which taxa within either diatom- or cyanobacteria-favoured groups were more phylogenetically closely related to one another than other taxa found in the water. Moreover, there was little overlap in taxon identity between sediment and water communities, suggesting the minor role played by sediment bacteria in influencing the observed changes in bacterial communities in the overlying water. Together, these results showed that variability in phytoplankton-originated POM can impact bacterial dynamics at the water-sediment interface. Our findings highlight the importance of considering the potential interactions between phytoplankton and bacteria in benthic-pelagic coupling in efforts to understand the structure and function of bacterial communities under a changing climate.

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  • 16. Jacquet, S.
    et al.
    Garros, C.
    Lombaert, E.
    Walton, C.
    Restrepo, J.
    Allene, X.
    Baldet, T.
    Cetre-Sossah, C.
    Chaskopoulou, A.
    Delecolle, J. -C
    Desvars, Amélie
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology.
    Djerbal, M.
    Fall, M.
    Gardes, L.
    De Garine-Wichatitsky, M.
    Goffredo, M.
    Gottlieb, Y.
    Fall, A. Gueye
    Kasina, M.
    Labuschagne, K.
    Lhor, Y.
    Lucientes, J.
    Martin, T.
    Mathieu, B.
    Miranda, M.
    Pages, N.
    Pereira Da Fonseca, I.
    Ramilo, D. W.
    Segard, A.
    Setier-Rio, M. -L
    Stachurski, F.
    Tabbabi, A.
    Seck, M. Talla
    Venter, G.
    Zimba, M.
    Balenghien, T.
    Guis, H.
    Chevillon, C.
    Bouyer, J.
    Huber, K.
    Colonization of the Mediterranean basin by the vector biting midge species Culicoides imicola: an old story2015In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, no 22, p. 5707-5725Article in journal (Refereed)
    Abstract [en]

    Understanding the demographic history and genetic make-up of colonizing species is critical for inferring population sources and colonization routes. This is of main interest for designing accurate control measures in areas newly colonized by vector species of economically important pathogens. The biting midge Culicoides imicola is a major vector of orbiviruses to livestock. Historically, the distribution of this species was limited to the Afrotropical region. Entomological surveys first revealed the presence of C. imicola in the south of the Mediterranean basin by the 1970s. Following recurrent reports of massive bluetongue outbreaks since the 1990s, the presence of the species was confirmed in northern areas. In this study, we addressed the chronology and processes of C. imicola colonization in the Mediterranean basin. We characterized the genetic structure of its populations across Mediterranean and African regions using both mitochondrial and nuclear markers, and combined phylogeographical analyses with population genetics and approximate Bayesian computation. We found a west/east genetic differentiation between populations, occurring both within Africa and within the Mediterranean basin. We demonstrated that three of these groups had experienced demographic expansions in the Pleistocene, probably because of climate changes during this period. Finally, we showed that C. imicola could have colonized the Mediterranean basin in the Late Pleistocene or Early Holocene through a single event of introduction; however, we cannot exclude the hypothesis involving two routes of colonization. Thus, the recent bluetongue outbreaks are not linked to C. imicola colonization event, but rather to biological changes in the vector or the virus.

  • 17.
    Mobley, Kenyon B.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Grandfathering in a new era of parentage analysis2011In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 20, no 6, p. 1080-1082Article in journal (Refereed)
    Abstract [en]

    The advent of DNA fingerprinting and microsatellite techniques has revolutionized the way in which we investigate genetic pedigrees in the wild (Pemberton 2008). With large and often incomplete data sets consisting of hundreds to thousands of individuals over multiple generations becoming commonplace, new methods in parentage analysis are being developed to rise to the next generation of questions and challenges. In this issue, Christie et al. (2011) provide a simple yet elegant solution to the problem of identifying missing parents and assessing hybrid fitness in a mixed population of wild and hatchery steelhead trout (Oncorhynchus mykiss) where not all individuals can be sampled effectively. They develop a new method of grandparent analysis where parental genotypes can be reconstructed using data from candidate grandparent crosses and F2 offspring genotypes, allowing for new explorations of hybridization, migration and gene flow in wild populations.

  • 18.
    Sunde, Johanna
    et al.
    Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.
    Yildirim, Yeserin
    Tibblin, Petter
    Bekkevold, Dorte
    Skov, Christian
    Nordahl, Oscar
    Larsson, Per
    Forsman, Anders
    Drivers of neutral and adaptive differentiation in pike (Esox lucius) populations from contrasting environments2022In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 31, no 4, p. 1093-1110Article in journal (Refereed)
    Abstract [en]

    Understanding how eco-evolutionary processes and environmental factors drive population differentiation and adaptation are key challenges in evolutionary biology of relevance for biodiversity protection. Differentiation requires at least partial reproductive separation, which may result from different modes of isolation such as geographic isolation (allopatry) or isolation by distance (IBD), resistance (IBR), and environment (IBE). Despite that multiple modes might jointly influence differentiation, studies that compare the relative contributions are scarce. Using RADseq, we analyse neutral and adaptive genetic diversity and structure in 11 pike (Esox lucius) populations from contrasting environments along a latitudinal gradient (54.9-63.6 degrees N), to investigate the relative effects of IBD, IBE and IBR, and to assess whether the effects differ between neutral and adaptive variation, or across structural levels. Patterns of neutral and adaptive variation differed, probably reflecting that they have been differently affected by stochastic and deterministic processes. The importance of the different modes of isolation differed between neutral and adaptive diversity, yet were consistent across structural levels. Neutral variation was influenced by interactions among all three modes of isolation, with IBR (seascape features) playing a central role, wheares adaptive variation was mainly influenced by IBE (environmental conditions). Taken together, this and previous studies suggest that it is common that multiple modes of isolation interactively shape patterns of genetic variation, and that their relative contributions differ among systems. To enable identification of general patterns and understand how various factors influence the relative contributions, it is important that several modes are simultaneously investigated in additional populations, species and environmental settings.

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  • 19.
    Tatarenkov, A.
    et al.
    Department of Marine Ecology, Tjärnö Marine Biological Laboratory, Göteborg University.
    Bergström, Lena
    Umeå University, Faculty of Science and Technology, Ecology and Environmental Science.
    Jönsson, Rita B.
    Department of Biology and Environmental Sciences, Kalmar University.
    Serrão, Ester A.
    CCMAR-Centre of Marine Sciences, University of Algarve, Gambelas, Portugal.
    Kautsky, Lena
    Department of Botany, Stockholm University.
    Johannesson, Kerstin
    Department of Marine Ecology, Tjärnö Marine Biological Laboratory, Göteborg University.
    Intriguing asexual life in marginal populations of the brown seaweed Fucus vesiculosus2005In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 14, no 2, p. 647-651Article in journal (Refereed)
    Abstract [en]

    Reproduction of attached large brown algae is known to occur only by sexual zygotes. Using microsatellites we show evolution of asexual reproduction in the bladder wrack promoting population persistence in the brackish water Baltic Sea (< 6 psu). Here a dwarf morph ofFucus vesiculosus is dominated by a single clone but clonal reproduction is also present in the common form of the species. We describe a possible mechanism for vegetative reproduction of attached algae, and conclude that clonality plays an important role in persistence and dispersal of these marginal populations, in which sexual reproduction is impaired by low salinity.

  • 20.
    Thibert-Plante, Xavier
    et al.
    Redpath Museum and Department of Biology, 859 Sherbrooke St. West, McGill University, Montréal, QC, Canada H3A 2K6.
    Hendry, Andrew P.
    Redpath Museum and Department of Biology, 859 Sherbrooke St. West, McGill University, Montréal, QC, Canada H3A 2K6.
    When can ecological speciation be detected with neutral loci?2010In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 19, no 11, p. 2301-2314Article in journal (Refereed)
    Abstract [en]

    It is not yet clear under what conditions empirical studies can reliably detect progress toward ecological speciation through the analysis of allelic variation at neutral loci. We use a simulation approach to investigate the range of parameter space under which such detection is, and is not, likely. We specifically test for the conditions under which divergent natural selection can cause a ‘generalized barrier to gene flow’ that is present across the genome. Our individual-based numerical simulations focus on how population divergence at neutral loci varies in relation to recombination rate with a selected locus, divergent selection on that locus, migration rate and population size. We specifically test whether genetic differences at neutral markers are greater between populations in different environments than between populations in similar environments. We find that this expected signature of ecological speciation can be detected under part of the parameter space, most consistently when divergent selection is strong and migration is intermediate. By contrast, the expected signature of ecological speciation is not reliably detected when divergent selection is weak or migration is low or high. These findings provide insights into the strengths and weaknesses of using neutral markers to infer ecological speciation in natural systems.

  • 21.
    Thompson, Stacey Lee
    et al.
    Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal QC H1X 2B2, Canada.
    Lamothe, Manuel
    Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal QC H1X 2B2, Canada.
    Meirmans, Patrick G
    Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal QC H1X 2B2, Canada.
    Périnet, Pierre
    Ministère des Ressources naturelles et de la Faune du Québec, 2700 Einstein, Québec, QC G1P 3W8, Canada.
    Isabel, Nathalie
    Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal QC H1X 2B2, Canada.
    Repeated unidirectional introgression towards Populus balsamifera in contact zones of exotic and native poplars.2010In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 19, no 1, p. 132-145Article in journal (Refereed)
    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.

  • 22.
    Thompson, Stacey Lee
    et al.
    Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
    Whitton, Jeannette
    Patterns of recurrent evolution and geographic parthenogenesis within apomictic polyploid Easter daises (Townsendia hookeri).2006In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 15, no 11, p. 3389-3400Article in journal (Refereed)
    Abstract [en]

    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.

  • 23.
    Wang, Baosheng
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Mao, Jian-Feng
    State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
    Gao, Jie
    State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
    Zhao, Wei
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Colonization of the Tibetan Plateau by the homoploid hybrid pine Pinus densata2011In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 20, no 18, p. 3796-3811Article in journal (Refereed)
    Abstract [en]

    Pinus densata is an intriguingly successful homoploid hybrid species that occupies vast areas of the southeastern Tibetan Plateau in which neither of its parental species are present, but the colonization processes involved are poorly understood. To shed light on how this species colonized and became established on the plateau, we surveyed paternally inherited chloroplast (cp) and maternally inherited mitochondrial (mt) DNA variation within and among 54 populations of P. densata and its putative parental species throughout their respective ranges. Strong spatial genetic structure of both cp and mtDNA were detected in P. densata populations. Mitotypes specific to P. densata were likely generated by complex recombination events. A putative ancestral hybrid zone in the northeastern periphery of P. densata was identified, and we propose that the species then colonized the plateau by migrating westwards. Along the colonization route, consecutive bottlenecks and surfing of rare alleles caused a significant reduction in genetic diversity and strong population differentiation. The direction and intensity of introgression from parental species varied among geographic regions. In western parts of its range, the species seems to have been isolated from seed and pollen flow from its parent species for a long time. The observed spatial distribution of genetic diversity in P. densata also appears to reflect the persistence of this species on the plateau during the last glaciation. Our results indicate that both ancient and contemporary population dynamics have contributed to the spatial distribution of genetic diversity in P. densata, which accordingly reflects its evolutionary history.

  • 24. Wang, Jing
    et al.
    Street, Nathaniel
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Park, Eung-Jun
    Liu, Jianquan
    Ingvarsson, Par K.
    Evidence for widespread selection in shaping the genomic landscape during speciation of Populus2020In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 29, no 6, p. 1120-1136Article in journal (Refereed)
    Abstract [en]

    Increasing our understanding of how evolutionary processes drive the genomic landscape of variation is fundamental to a better understanding of the genomic consequences of speciation. However, genome-wide patterns of within- and between- species variation have not been fully investigated in most forest tree species despite their global ecological and economic importance. Here, we use whole-genome resequencing data from four Populus species spanning the speciation continuum to reconstruct their demographic histories and investigate patterns of diversity and divergence within and between species. Using Populus trichocarpa as an outgroup species, we further infer the genealogical relationships and estimate the extent of ancient introgression among the three aspen species (Populus tremula, Populus davidiana and Populus tremuloides) throughout the genome. Our results show substantial variation in these patterns along the genomes with this variation being strongly predicted by local recombination rates and the density of functional elements. This implies that the interaction between recurrent selection and intrinsic genomic features has dramatically sculpted the genomic landscape over long periods of time. In addition, our findings provide evidence that, apart from background selection, recent positive selection and long-term balancing selection have also been crucial components in shaping patterns of genome-wide variation during the speciation process.

  • 25.
    Wang, Xi
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Ingvarsson, Pär K.
    Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Quantifying adaptive evolution and the effects of natural selection across the Norway spruce genome2023In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 32, no 19, p. 5288-5304Article in journal (Refereed)
    Abstract [en]

    Detecting natural selection is one of the major goals of evolutionary genomics. Here, we sequence whole genomes of 34 Picea abies individuals and quantify the amount of selection across the genome. Using an estimate of the distribution of fitness effects, we show that negative selection is very limited in coding regions, while positive selection is rare in coding regions but very strong in non-coding regions, suggesting the great importance of regulatory changes in evolution of Norway spruce. Additionally, we found a positive correlation between adaptive rate with recombination rate and a negative correlation between adaptive rate and gene density, suggesting a widespread influence from Hill-Robertson interference to efficiency of protein adaptation in P. abies. Finally, the distinct population statistics between genomic regions under either positive or balancing selection with that under neutral regions indicated impact from selection to genomic architecture of Norway spruce. Further gene ontology enrichment analysis for genes located in regions identified as undergoing either positive or long-term balancing selection also highlighted specific molecular functions and biological processes in that appear to be targets of selection in Norway spruce.

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