The analysis of target enrichment data in phylogenetics lacks optimization toward using paralogues for phylogenetic reconstruction. We developed a novel approach of detecting paralogues and utilizing them for phylogenetic tree inference, by retrieving both ortho- and paralogous copies and creating orthologous alignments, from which the gene trees are built. We implemented this approach in ParalogWizard and demonstrate its performance in plant groups that underwent a whole genome duplication relatively recently: the subtribe Malinae (family Rosaceae), using Angiosperms353 as well as Malinae481 probes, the genus Oritrophium (family Asteraceae), using Compositae1061 probes, and the genus Amomum (family Zingiberaceae), using Zingiberaceae1180 probes.
View Article and Find Full Text PDFPremise: Custom probe design for target enrichment in phylogenetics is tedious and often hinders broader phylogenetic synthesis. The universal angiosperm probe set Angiosperms353 may be the solution. Here, we test the relative performance of Angiosperms353 on the Rosaceae subtribe Malinae in comparison with custom probes that we specifically designed for this clade.
View Article and Find Full Text PDFConifers often occur along steep gradients of diverse climates throughout their natural ranges, which is expected to result in spatially varying selection to local climate conditions. However, signals of climatic adaptation can often be confounded, because unraveled clines covary with signals caused by neutral evolutionary processes such as gene flow and genetic drift. Consequently, our understanding of how selection and gene flow have shaped phenotypic and genotypic differentiation in trees is still limited.
View Article and Find Full Text PDFGenetic admixture and plasticity along with propagule pressure, large seed dispersal distances and fast adaptation support successful establishment and spread of introduced species outside their native range. Consequently, introductions may display climatic niche shifts in the introduced range. Douglas-fir, a controversial forest and ornamental conifer represented by two ecologically different and hybridising varieties, was transferred multiple times outside the native range in North America.
View Article and Find Full Text PDFBiol Rev Camb Philos Soc
August 2019
Non-native tree (NNT) species have been transported worldwide to create or enhance services that are fundamental for human well-being, such as timber provision, erosion control or ornamental value; yet NNTs can also produce undesired effects, such as fire proneness or pollen allergenicity. Despite the variety of effects that NNTs have on multiple ecosystem services, a global quantitative assessment of their costs and benefits is still lacking. Such information is critical for decision-making, management and sustainable exploitation of NNTs.
View Article and Find Full Text PDFThe role of evolution in biological invasion studies is often overlooked. In order to evaluate the evolutionary mechanisms behind invasiveness, it is crucial to identify the source populations of the introduction. Studies in population genetics were carried out on L.
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Context: Tree species selection is one of the most important forest management decisions to enhance forest productivity and stand stability on a given site. Douglas-fir ( (Mirb.) Franco var.
Douglas-fir (Pseudotsuga menziesii) is one of numerous wide-range forest tree species represented by subspecies/varieties, which hybridize in contact zones. This study examined the genetic structure of this North American conifer and its two hybridizing varieties, coastal and Rocky Mountain, at intervarietal and intravarietal level. The genetic structure was subsequently associated with the Pleistocene refugial history, postglacial migration and intervarietal hybridization/introgression.
View Article and Find Full Text PDFAdmixture between genetically divergent populations facilitates genomic studies of the mechanisms involved in adaptation, reproductive isolation, and speciation, including mapping of the loci involved in these phenomena. Little is known about how pre- and postzygotic barriers will affect the prospects of "admixture mapping" in wild species. We have studied 93 mapped genetic markers (microsatellites, indels, and sequence polymorphisms, ∼60,000 data points) to address this topic in hybrid zones of Populus alba and P.
View Article and Find Full Text PDFClimatic history and ecology are considered the most important factors moulding the spatial pattern of genetic diversity. With the advent of molecular markers, species' historical fates have been widely explored. However, it has remained speculative what role ecological factors have played in shaping spatial genetic structures within species.
View Article and Find Full Text PDFSpatial genetic structure (SGS) holds the key to understanding the role of clonality in hybrid persistence, but multilocus SGS in hybrid zones has rarely been quantified. Here, the aim was to fill this gap for natural hybrids between two diploid, ecologically divergent European tree species with mixed sexual/asexual reproduction, Populus alba and P. tremula.
View Article and Find Full Text PDFContrasts between related diploid and polyploid taxa can serve as windows into the evolution of sexual systems. A recent study of a moving diploid-polyploid contact zone explores this topic in novel ways.
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