Adaptive introgression: a plant perspective Suarez-Gonzalez, Adriana; Lexer, Christian; Cronk, Quentin C. B.
Biology letters,
03/2018, Letnik:
14, Številka:
3
Journal Article
Recenzirano
Odprti dostop
Introgression is emerging as an important source of novel genetic variation, alongside standing variation and mutation. It is adaptive when such introgressed alleles are maintained by natural ...selection. Recently, there has been an explosion in the number of studies on adaptive introgression. In this review, we take a plant perspective centred on four lines of evidence: (i) introgression, (ii) selection, (iii) phenotype and (iv) fitness. While advances in genomics have contributed to our understanding of introgression and porous species boundaries (task 1), and the detection of signatures of selection in introgression (task 2), the investigation of adaptive introgression critically requires links to phenotypic variation and fitness (tasks 3 and 4). We also discuss the conservation implications of adaptive introgression in the face of climate change. Adaptive introgression is particularly important in rapidly changing environments, when standing genetic variation and mutation alone may only offer limited potential for adaptation. We conclude that clarifying the magnitude and fitness effects of introgression with improved statistical techniques, coupled with phenotypic evidence, has great potential for conservation and management efforts.
Premise of the study: Plann automates the process of annotating a plastome sequence in GenBank format for either downstream processing or for GenBank submission by annotating a new plastome based on ...a similar, well-annotated plastome. Methods and Results: Plann is a Perl script to be executed on the command line. Plann compares a new plastome sequence to the features annotated in a reference plastome and then shifts the intervals of any matching features to the locations in the new plastome. Plann's output can be used in the National Center for Biotechnology Information's tbl2asn to create a Sequin file for GenBank submission. Conclusions: Unlike Web-based annotation packages, Plann is a locally executable script that will accurately annotate a plastome sequence to a locally specified reference plastome. Because it executes from the command line, it is ready to use in other software pipelines and can be easily rerun as a draft plastome is improved.
In order to uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood (Populus trichocarpa) from much of its range in western North America. ...Extensive data from large‐scale trait phenotyping (with spatial and temporal replications within a common garden) and genotyping (with a 34 K Populus single nucleotide polymorphism (SNP) array) of all accessions were used for gene discovery in a genome‐wide association study (GWAS). We performed GWAS with 40 biomass, ecophysiology and phenology traits and 29 355 filtered SNPs representing 3518 genes. The association analyses were carried out using a Unified Mixed Model accounting for population structure effects among accessions. We uncovered 410 significant SNPs using a Bonferroni‐corrected threshold (P < 1.7 × 10⁻⁶). Markers were found across 19 chromosomes, explained 1–13% of trait variation, and implicated 275 unique genes in trait associations. Phenology had the largest number of associated genes (240 genes), followed by biomass (53 genes) and ecophysiology traits (25 genes). The GWAS results propose numerous loci for further investigation. Many traits had significant associations with multiple genes, underscoring their genetic complexity. Genes were also identified with multiple trait associations within and/or across trait categories. In some cases, traits were genetically correlated while in others they were not.
Populus trichocarpa is widespread across western North America spanning extensive variation in photoperiod, growing season and climate. We investigated trait variation in P. trichocarpa using over ...2000 trees from a common garden at Vancouver, Canada, representing replicate plantings of 461 genotypes originating from 136 provenance localities.
We measured 40 traits encompassing phenological events, biomass accumulation, growth rates, and leaf, isotope and gas exchange-based ecophysiology traits. With replicated plantings and 29 354 single nucleotide polymorphisms (SNPs) from 3518 genes, we estimated both broad-sense trait heritability (H
2) and overall population genetic structure from principal component analysis.
Populus trichocarpa had high phenotypic variation and moderate/high H
2 for many traits. H
2 ranged from 0.3 to 0.9 in phenology, 0.3 to 0.8 in biomass and 0.1 to 0.8 in ecophysiology traits. Most traits correlated strongly with latitude, maximum daylength and temperature of tree origin, but not necessarily with elevation, precipitation or heat: moisture indices. Trait H
2 values reflected trait correlation strength with geoclimate variables. The population genetic structure had one significant principal component (PC1) which correlated with daylength and showed enrichment for genes relating to circadian rhythm and photoperiod.
Robust relationships between traits, population structure and geoclimate in P. trichocarpa reflect patterns which suggest that range-wide geographical and environment gradients have shaped its genotypic and phenotypic variability.
As molecular phylogenetic analyses incorporate ever‐greater numbers of loci, cases of cytonuclear discordance – the phenomenon in which nuclear gene trees deviate significantly from organellar gene ...trees – are being reported more frequently. Plant examples of topological discordance, caused by recent hybridization between extant species, are well known. However, examples of branch‐length discordance are less reported in plants relative to animals. We use a combination of de novo assembly and reference‐based mapping using short‐read shotgun sequences to construct a robust phylogeny of the plastome for multiple individuals of all the common Populus species in North America. We demonstrate a case of strikingly high plastome divergence, in contrast to little nuclear genome divergence, in two closely related balsam poplars, Populus balsamifera and Populus trichocarpa (Populus balsamifera ssp. trichocarpa). Previous studies with nuclear loci indicate that the two species (or subspecies) diverged since the late Pleistocene, whereas their plastomes indicate deep divergence, dating to at least the Pliocene (6–7 Myr ago). Our finding is in marked contrast to the estimated Pleistocene divergence of the nuclear genomes, previously calculated at 75 000 yr ago, suggesting plastid capture from a ‘ghost lineage’ of a now‐extinct North American poplar.
Natural hybrid zones in forest trees provide systems to study the transfer of adaptive genetic variation by introgression. Previous landscape genomic studies in Populus trichocarpa, a keystone tree ...species, indicated genomic footprints of admixture with its sister species Populus balsamifera and identified candidate genes for local adaptation. Here, we explored the patterns of introgression and signals of local adaptation in P. trichocarpa and P. balsamifera, employing genome resequencing data from three chromosomes in pure species and admixed individuals from wild populations. Local ancestry analysis in admixed P. trichocarpa revealed a telomeric region in chromosome 15 with P. balsamifera ancestry, containing several candidate genes for local adaptation. Genomic analyses revealed signals of selection in certain genes in this region (e.g. PRR5, COMT1), and functional analyses based on gene expression variation and correlations with adaptive phenotypes suggest distinct functions of the introgressed alleles. In contrast, a block of genes in chromosome 12 paralogous to the introgressed region showed no signs of introgression or signatures of selection. We hypothesize that the introgressed region in chromosome 15 has introduced modular or cassette‐like variation into P. trichocarpa. These linked adaptive mutations are associated with a block of genes in chromosome 15 that appear to have undergone neo‐ or subfunctionalization relative to paralogs in a duplicated region on chromosome 12 that show no signatures of adaptive variation. The association between P. balsamifera introgressed alleles with the expression of adaptive traits in P. trichocarpa supports the hypothesis that this is a case of adaptive introgression in an ecologically important foundation species.
The western black cottonwood (Populus trichocarpa) was the first tree to have its genome fully sequenced and has emerged as the model species for the study of secondary growth and wood formation. It ...is also a good candidate species for the production of lignocellulosic biofuels. Here, we present and make available to the research community the results of the sequencing of the transcriptome of developing xylem in 20 accessions with high-throughput next generation sequencing technology. We found over 0.5 million putative single nucleotide polymorphisms (SNPs) in 26 595 genes that are expressed in developing secondary xylem. More than two-thirds of all SNPs were found in annotated exons, with 18% and 14% in regions of the genome annotated as introns and intergenic, respectively, where only 3% and 4% of sequence reads mapped. This suggests that the current annotation of the poplar genome is remarkably incomplete and that there are many transcripts and novel genes waiting to be annotated. We hope that this resource will stimulate further research in expression profiling, detection of alternative splicing and adaptive evolution in poplar.
The extinction of species before they are discovered and named (dark extinction, DE) is widely inferred as a significant part of species loss in the 'pre-taxonomic' period (approx. 1500-1800 CE) and, ...to some extent, in the 'taxonomic period' (approx. 1800-present) as well. The discovery of oceanic islands and other pristine habitats by European navigators and the consequent introduction of destructive mammals, such as rats and goats, started a process of anthropogenic extinction. Much ecosystem change happened before systematic scientific recording, so has led to DE. Statistical methods are available to robustly estimate DE in the 'taxonomic period'. For the 'pre-taxonomic period', simple extrapolation can be used. The application of these techniques to world birds, for example, suggests that approximately 56 DEs occurred in the 'taxonomic period' (1800-present) and approximately 180 in the 'pre-taxonomic period' (1500-1800). Targeting collection activities in extinction hotspots, to make sure organisms are represented in collections before their extinction, is one way of reducing the number of extinct species without a physical record (providing that collection efforts do not themselves contribute to species extinction).
Establishing links between phenotypes and molecular variants is of central importance to accelerate genetic improvement of economically important plant species. Our work represents the first ...genome-wide association study to the inherently complex and currently poorly understood genetic architecture of industrially relevant wood traits.
Here, we employed an Illumina Infinium 34K single nucleotide polymorphism (SNP) genotyping array that generated 29 233 high-quality SNPs in c. 3500 broad-based candidate genes within a population of 334 unrelated Populus trichocarpa individuals to establish genomewide associations.
The analysis revealed 141 significant SNPs (α ≤ 0.05) associated with 16 wood chemistry/ ultrastructure traits, individually explaining 3–7% of the phenotypic variance. A large set of associations (41% of all hits) occurred in candidate genes preselected for their suggested a priori involvement with secondary growth. For example, an allelic variant in the FRA8 ortholog explained 21% of the total genetic variance in fiber length, when the trait's heritability estimate was considered. The remaining associations identified SNPs in genes not previously implicated in wood or secondary wall formation.
Our findings provide unique insights into wood trait architecture and support efforts for population improvement based on desirable allelic variants.
Aquilegia × miniana (J.F.Macbr. & Payson) Cronk,
hybr. & stat. nov.
is the correct name for the hybrid
Aquilegia flavescens
S.Watson × A. formosa Fisch. & DC. var. formosa. In 1916 Payson and ...Macbride, while exploring the mountains of Idaho, found populations of
Aquilegia
that were pink in flower colour and appeared intermediate between the yellow-flowered
A. flavescens
and red-flowered
A. formosa
. They named these plants A. flavescens var. miniana J.F.Macbr. & Payson. There has been uncertainty over whether their type collections (in GH, RM, MO, US, E, CM, CAS, NY) do indeed represent hybrids or pink-flowered morphs of
A. flavescens
. Using a Wells diagram, the holotype (in the Gray Herbarium of Harvard University) is shown to be intermediate, allowing its identification as a clear hybrid. However, some of the isotype material is indistinguishable from
A. flavescens
. The holotype matches material from British Columbia that has been determined to be of hybrid origin using molecular and morphological data. A. flavescens var. miniana J.F.Macbr. & Payson is, therefore, an available name for the hybrid, which is here raised to the status of hybrid binomial.
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