Utilizing paralogues for phylogenetic reconstruction has the potential to increase species tree support and reduce gene tree discordance in target enrichment data.

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. Discriminating between orthologues and paralogues reduced gene tree discordance and increased the species tree support in the case of the Malinae, but not for Oritrophium and Amomum. This may relate to the difference in the proportion of paralogous loci between the data sets, which was highest for the Malinae. Overall, retrieving paralogues for phylogenetic reconstruction following ParalogWizard has the potential to increase the species tree support and reduce gene tree discordance in target enrichment data, particularly if the proportion of paralogous loci is high.

Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae.

PREMISE: 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. We then address the impact of bioinformatically altering the performance of Angiosperms353 by replacing the original probe sequences with orthologs extracted from the Malus domestica genome. METHODS: To evaluate the relative performance of these probe sets, we compared the enrichment efficiency, locus recovery, alignment length, proportion of parsimony-informative sites, proportion of potential paralogs, the topology and support of the resulting species trees, and the gene tree discordance. RESULTS: Locus recovery was highest for our custom Malinae probe set, and replacing the original Angiosperms353 sequences with a Malus representative improved the locus recovery relative to Angiosperms353. The proportion of parsimony-informative sites was similar between all probe sets, while the gene tree discordance was lower in the case of the custom probes. DISCUSSION: A custom probe set benefits from data completeness and can be tailored toward the specificities of the project of choice; however, Angiosperms353 was equally as phylogenetically informative as the custom probes. We therefore recommend using both a custom probe set and Angiosperms353 to facilitate large-scale systematic studies, where financially possible.

Looking for the needle in a downsized haystack: Whole-exome sequencing unravels genomic signals of climatic adaptation in Douglas-fir (Pseudotsuga menziesii).

Conifers 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.A 40-year-old common garden experiment comprising 16 Douglas-fir (Pseudotsuga menziesii) provenances from a north-to-south gradient of approx. 1,000 km was analyzed, and genomic information was obtained from exome capture, which resulted in an initial genomic dataset of >90,000 single nucleotide polymorphisms. We used a restrictive and conservative filtering approach, which permitted us to include only SNPs and individuals in environmental association analysis (EAA) that were free of potentially confounding effects (LD, relatedness among trees, heterozygosity deficiency, and deviations from Hardy-Weinberg proportions). We used four conceptually different genome scan methods based on FST outlier detection and gene-environment association in order to disentangle truly adaptive SNPs from neutral SNPs.We found that a relatively small proportion of the exome showed a truly adaptive signal (0.01%-0.17%) when population substructuring and multiple testing was accounted for. Nevertheless, the unraveled SNP candidates showed significant relationships with climate at provenance origins, which strongly suggests that they have featured adaptation in Douglas-fir along a climatic gradient. Two SNPs were independently found by three of the employed algorithms, and one of them is in close proximity to an annotated gene involved in circadian clock control and photoperiodism as was similarly found in Populus balsamifera. Synthesis. We conclude that despite neutral evolutionary processes, phenotypic and genomic signals of adaptation to climate are responsible for differentiation, which in particular explain disparity between the well-known coastal and interior varieties of Douglas-fir.

Global effects of non-native tree species on multiple ecosystem services.

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. We present here a global assessment of NNT effects on the three main categories of ecosystem services, including regulating (RES), provisioning (PES) and cultural services (CES), and on an ecosystem disservice (EDS), i.e. pollen allergenicity. By searching the scientific literature, country forestry reports, and social media, we compiled a global data set of 1683 case studies from over 125 NNT species, covering 44 countries, all continents but Antarctica, and seven biomes. Using different meta-analysis techniques, we found that, while NNTs increase most RES (e.g. climate regulation, soil erosion control, fertility and formation), they decrease PES (e.g. NNTs contribute less than native trees to global timber provision). Also, they have different effects on CES (e.g. increase aesthetic values but decrease scientific interest), and no effect on the EDS considered. NNT effects on each ecosystem (dis)service showed a strong context dependency, varying across NNT types, biomes and socio-economic conditions. For instance, some RES are increased more by NNTs able to fix atmospheric nitrogen, and when the ecosystem is located in low-latitude biomes; some CES are increased more by NNTs in less-wealthy countries or in countries with higher gross domestic products. The effects of NNTs on several ecosystem (dis)services exhibited some synergies (e.g. among soil fertility, soil formation and climate regulation or between aesthetic values and pollen allergenicity), but also trade-offs (e.g. between fire regulation and soil erosion control). Our analyses provide a quantitative understanding of the complex synergies, trade-offs and context dependencies involved for the effects of NNTs that is essential for attaining a sustained provision of ecosystem services.

Forest stand productivity derived from site conditions: an assessment of old Douglas-fir stands (Pseudotsuga menziesii (Mirb.) Franco var. menziesii) in Central Europe.

KEY MESSAGE: Douglas-fir growth correlates with the climate, the soil moisture regime, and the soil nutrient status, reflecting a broad physiological amplitude. Even though planting this non-native tree species is suggested as a viable strategy to improve adaptiveness of European forests to a more extreme climate and to assure future productivity, the expected temperature increase may induce a decline in forest stand productivity for Douglas-fir in already warm and dry regions. 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 (Pseudotsuga menziesii (Mirb.) Franco var. menziesii), a non-native species from north-western America, is seen as an important additional species option for adapting Central European forests to a changing climate. AIMS: This study assesses Douglas-fir forest productivity derived from site conditions. We investigate climatic and physico-chemical soil characteristics and productivity of 28 mature Douglas-fir stands growing on siliceous, as well as carbonate bedrock material in southern Germany and north-eastern Austria. METHODS: The importance of climatic and physico-chemical soil characteristics was analyzed with the machine learning method Random Forests. RESULTS: The results show that Douglas-fir growth correlates with climate, soil moisture, and soil nutrient availability derived from ten climatic and physico-chemical soil parameters. CONCLUSION: The broad pH optimum between 4.5 and 7.2 reflects the broad physiological amplitude of Douglas-fir, and no significant differences were detectable between carbonate and siliceous bedrock. We also conclude that climate change may induce a forest stand productivity decline, because lower productivity with the highest mean summer temperature across our study range was observed at the warmest sites in Eastern Austria.

A few north Appalachian populations are the source of European black locust.

The 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 Robinia pseudoacacia L., a North American tree which is now one of the worst invasive tree species in Europe. We realized large-scale sampling in both the invasive and native ranges: 63 populations were sampled and 818 individuals were genotyped using 113 SNPs. We identified clonal genotypes in each population and analyzed between and within range population structure, and then, we compared genetic diversity between ranges, enlarging the number of SNPs to mitigate the ascertainment bias. First, we demonstrated that European black locust was introduced from just a limited number of populations located in the Appalachian Mountains, which is in agreement with the historical documents briefly reviewed in this study. Within America, population structure reflected the effects of long-term processes, whereas in Europe it was largely impacted by human activities. Second, we showed that there is a genetic bottleneck between the ranges with a decrease in allelic richness and total number of alleles in Europe. Lastly, we found more clonality within European populations. Black locust became invasive in Europe despite being introduced from a reduced part of its native distribution. Our results suggest that human activity, such as breeding programs in Europe and the seed trade throughout the introduced range, had a major role in promoting invasion; therefore, the introduction of the missing American genetic cluster to Europe should be avoided.

North American Douglas-fir (P. menziesii) in Europe: establishment and reproduction within new geographic space without consequences for its genetic diversity.

Genetic 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. Here, we compare climatic and genetic patterns of 38 native populations from North America with six old Pseudotsuga menziesii populations with natural regeneration in the introduced range in Central Europe. Following variety and geographic origin assessment of introduced populations, genotypic and climatic data were examined for signatures of inter-varietal gene flow, reduced genetic diversity, presence of fine-scale spatial genetic structure (SGS), dispersal patterns, and climate similarities between native and introduced range. In the introduced range, dominating coastal variety originated from a restricted area in the US, whereas the interior variety, with limited presence in the European sites, displayed wider geographic origin. Variety hybrids with contributing coastal, but not the interior parent were identified. Differences in genetic diversity between both ranges, but also among the parent and their respective offspring populations in Europe were not found. Old populations in general lacked any SGS, whereas natural regeneration revealed different patterns of SGS. Distances of propagule dispersal ranged between 2.5 and 92 m. The climate of the studied European introduced range was most similar to the climate of the coastal variety from the western Cascade range from which the majority of the analysed coastal European Douglas-fir, but not the European interior variety, was assigned to originate. The results we present here shed not only light on dynamics of invasive species in the introduced range in general, but also allow for refinement of climatic niche modeling when using lower than species level.

Intervarietal and intravarietal genetic structure in Douglas-fir: nuclear SSRs bring novel insights into past population demographic processes, phylogeography, and intervarietal hybridization.

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. Thirty-eight populations from the USA and Canada were genotyped for 13 nuclear SSRs and analyzed with simulations and traditional population genetic structuring methods. Eight genetic clusters were identified. The coastal clusters embodied five refugial populations originating from five distinct refugia. Four coastal refugial populations, three from California and one from western Canada, diverged during the Pleistocene (56.9-40.1 ka). The three Rocky Mountain clusters reflected distinct refugial populations of three glacial refugia. For Canada, ice covered during the Last Glacial Maximum, we present the following three findings. (1) One refugial population of each variety was revealed in the north of the distribution range. Additional research including paleodata is required to support and determine whether both northern populations originated from cryptic refugia situated south or north of the ice-covered area. (2) An interplay between intravarietal gene flow of different refugial populations and intervarietal gene flow by hybridization and introgression was identified. (3) The Canadian hybrid zone displayed predominantly introgressants of the Rocky Mountain into the coastal variety. This study provides new insights into the complex Quaternary dynamics of this conifer essential for understanding its evolution (outside and inside the native range), adaptation to future climates and for forest management.

Genomic admixture analysis in European Populus spp. reveals unexpected patterns of reproductive isolation and mating.

Admixture 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. tremula, two widespread, ecologically important forest trees. Using genotype and linkage information and recently developed analytical tools we show that (1) reproductive isolation between these species is much stronger than previously assumed but this cannot prevent the introgression of neutral or advantageous alleles, (2) unexpected genotypic gaps exist between recombinant hybrids and their parental taxa, (3) these conspicuous genotypic patterns are due to assortative mating and strong postzygotic barriers, rather than recent population history. We discuss possible evolutionary trajectories of hybrid lineages between these species and outline strategies for admixture mapping in hybrid zones between highly divergent populations. Datasets such as this one are still rare in studies of natural hybrid zones but should soon become more common as high throughput genotyping and resequencing become feasible in nonmodel species.

History or ecology? Substrate type as a major driver of spatial genetic structure in Alpine plants.

Climatic 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. With an unprecedented, dense large-scale sampling and genome-screening, we tested how ecological factors have influenced the spatial genetic structures in Alpine plants. Here, we show that species growing on similar substrate types, largely determined by the nature of bedrock, displayed highly congruent spatial genetic structures. As the heterogeneous and disjunctive distribution of bedrock types in the Alps, decisive for refugial survival during the ice ages, is temporally stable, concerted post-glacial migration routes emerged. Our multispecies study demonstrates the relevance of particular ecological factors in shaping genetic patterns, which should be considered when modelling species projective distributions under climate change scenarios.

Clonality and spatial genetic structure in Populus x canescens and its sympatric backcross parent P. alba in a Central European hybrid zone.

Spatial 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. Nuclear microsatellites were used to quantify clonality, SGS, and historical gene dispersal distances in up to 407 trees from an extensive Central European hybrid zone including three subpopulation replicates. The focus was on P. x canescens and its backcross parent P. alba, as these two genotypic classes co-occur and interact directly. Sexual recombination in both taxa was more prominent than previously thought, but P. x canescens hybrids tended to build larger clones extending over larger areas than P. alba. The 3.4 times stronger SGS in the P. x canescens genet population was best explained by a combination of interspecific gene flow, assortative mating, and increased clonality in hybrids. Clonality potentially contributes to the maintenance of hybrid zones of P. alba and P. tremula in time and space. Both clonality and SGS need to be taken into account explicitly when designing population genomics studies of locus-specific effects in hybrid zones.

Contact zones: natural labs for studying evolutionary transitions.

Contrasts 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.