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131 results for “forest genetics”
Western columbine genetics across HJ Andrews Experimental Forest meadow communities
Woody plant encroachment is diminishing meadow and grassland habitat on a global scale. Increased woody cover influences local conditions such as light/shade environments, local soil characteristics, understory plant community structure, and disturbance regimes. Woody encroachment may also affect landscape-scale biological processes, such as herbaceous plant population structure, through reducing the total cover and continuity of open habitat and eroding mutualistic interactions, such as plant-pollinator interaction networks. A major concern is that habitat fragmentation will have a cascading effect if one or more mutualistic partners is adversely affected. For example, if pollinators are sensitive to disturbance, fragmentation may reduce rates of gene flow among sub-populations of plants, which is predicted to decrease effective population sizes and diminish adaptive potential (i.e. the capacity to respond to selective pressures through the evolution of genetically-based and heritable traits). Alpine meadows of the Cascade Mountains, which support diverse wildflower and pollinator communities, have shrunk dramatically over the last century as a result of forest encroachment. We posited that, as meadows become smaller and less connected, pollinators may abandon the smallest meadows and focus foraging efforts on the largest, most connected meadows with the most resources. This could expedite the decline and ultimate collapse of meadow communities through reducing adaptive potential across sub-populations of plants. We focus on a plant-pollinator interaction between a common, nectar-producing plant, Aquilegia formosa (western columbine), and rufous hummingbird (Selasphorus rufus) pollinators in four montane meadow complexes in the H.J. Andrews experimental forest, Oregon, USA (HJA). Using hummingbird movement data from SA028 (see H.J. Andrews project database), we first ask whether further forest encroachment in the HJA may alter hummingbird movement patterns among me
Data from 'Tracability of Forest Reproductive Material with the quality label 'Plant van Hier': A DNA database with genetic profiles of native autochthonous tree and shrub species of Flanders, Belgium'
<h2>Background</h2> <p>Indigenous trees and shrubs play an important role in multifunctional forest management. They form a significant part of the biodiversity in our forests. Forest reproductive material (FRM) of autochthonous Flemish origin is sold under the quality label ‘Plant van Hier’, a certification mark of the Agency for Nature and Forests. To ensure the provenance of the seedlings, we developed a DNA-database of genetic profiles of potential parent trees, using species-specific genetic markers. This database enables the traceability of FRM of the ‘Plant van Hier’ label throughout the entire production chain; from seed harvesting and cultivation to planting by the end user.</p> <p>This database contains the genetic profiles of almost all possible parent trees present within 27 Flemish autochthonous seed orchards of eight ecologically important tree and shrub species: <em>Carpinus betulus</em>, <em>Corylus avellana</em>, <em>Frangula alnus</em>, <em>Populus tremula</em>, <em>Sorbus aucuparia</em>, <em>Tilia cordata</em>, <em>Tilia platyphyllos,</em> and <em>Ulmus laevis</em>. The profiles were established using microsatellite markers (11 to 24 markers per species). New genetic markers were developed for <em>Carpinus betulus</em> and <em>Ulmus laevis</em>. PCR products were run on an ABI 3500 Genetic Analyser (Thermo Fisher Scientific).</p> <h2>Files</h2> <p>The files will be updated when new genotypes are added to the seed orchards. The current data files contain data from genotypes collected in the period 2018-2023. </p> <h3>Species_genotypes</h3> <p>These files contain the genetic fingerprints of the parent trees of autochthonous Flemish seed orchards. Missing data is indicated as ‘MD’. For <em>Carpinus betulus</em>, an octoploid species, the allelic phenotype is given instead of the genotype as the number of times that an allele occurs on a specific locus is not known.</p> <p>The next metadata is additionally given:<br>- Species: the Latin name of the species<br>- Seed_orchard: the name of the seed orchard in which the genotypes are located<br>- Code_seed_orchard: the code of the seed orchard in which the genotypes are located as given in the Register of Flemish Forest Reproductive Material (‘Register bosbouwkundig uitgangsmateriaal’; inbo.be)<br>- Genotype: the fieldname given to the genotype<br>- Origin: the location where the genotype was collected in Flanders, Belgium. Genotypes were collected from natural stands which are assumed to have an autochthonous origin. When the specific location is unknown, the location ‘Flanders’ is given. <br>- Year_sampled: the year in which the genotypes were sampled in the respective seed orchard for genetic analysis.</p> <h3>Species_binsets</h3> <p>These files contain the binsets and allele names that are used to score the alleles of the genotypes in the programme Geneious Prime 2019.3.2 (<a href="https://www.geneious.com">https://www.geneious.com</a>). For <em>Tilia platyphyllos </em>and <em>Tilia cordata</em>, the same binsets were used.</p>
Population genomics reveals differences in genetic structure between two endemic arboreal rodent species in threatened cloud forest habitat
<p>SNPs obtained by UNEAK pipeline for <em>Habromys schmidlyi </em>and <em>Reithrodontomys microdon</em>. </p> <p>Pleae cite as: </p> <p>Colunga-Salas P., T Marines-Macías, G Hernández-Canchola, S Barbosa, C Ramírez, JB Searle, L León-Paniagua. 2022. <strong>Population genomics reveals differences in genetic structure between two endemic arboreal rodent species in threatened cloud forest habitat</strong>. Mammalian Reasearch. Doi: 10.1007/s13364-022-00667-x</p>
Data from: Drift happens: molecular genetic diversity and differentiation among populations of jewelweed (Impatiens capensis Meerb.) reflect fragmentation of floodplain forests
Landscape features often shape patterns of gene flow and genetic differentiation in plant species. Populations that are small and isolated enough also become subject to genetic drift. We examined patterns of gene flow and differentiation among 12 floodplain populations of the selfing annual jewelweed (Impatiens capensis Meerb.) nested within four river systems and two major watersheds in Wisconsin, USA. Floodplain forests and marshes provide a model system for assessing the effects of habitat fragmentation within agricultural/urban landscapes and for testing whether rivers act to genetically connect dispersed populations. We generated a panel of 12,856 single nucleotide polymorphisms and assessed genetic diversity, differentiation, gene flow, and drift. Clustering methods revealed strong population genetic structure with limited admixture and highly differentiated populations (mean multilocus FST = 0.32, FST' = 0.33). No signals of isolation by geographic distance or environment emerged, but alleles may flow along rivers given that genetic differentiation increased with river distance. Differentiation also increased in populations with fewer private alleles (R2 = 0.51) and higher local inbreeding (R2 = 0.22). Populations varied greatly in levels of local inbreeding (FIS = 0.2 to 0.9) and FIS declined in smaller, more isolated populations. These results suggest that genetic drift dominates other forces in structuring these Impatiens populations. In rapidly changing environments, species must migrate or genetically adapt. Habitat fragmentation limits both processes, potentially compromising the ability of species to persist in fragmented landscapes.
Data and modeling results for publication: Landscape genetics indicate recently increased habitat fragmentation in African forest-associated chafers
<ul> <li>DNA sequences: <em>cox1</em> and ITS1 alignments</li> <li>spatial records (in hypervolume archive)</li> <li>spatial principal component 1-3 used for <em>hypervolume</em> models (in hypervolume archive)</li> <li>Present and past species distribution models (SDMs): <ul> <li><em>biomod2</em> ensemble SDMs <ul> <li>Present</li> <li>Holocene Altithermal</li> <li>Last Glacial Maximum</li> </ul> </li> <li><em>biomod2</em> SDMs for single PMIP3 models <ul> <li>Present</li> <li>Holocene Altithermal</li> <li>Last Glacial Maximum</li> </ul> </li> <li><em>hypervolume</em> SDMs</li> </ul> </li> <li>landscape connectivity models <ul> <li>circuitscape (for F0, F1, and F2)</li> <li>least cost corridors and paths (for F0, F1, and F2)</li> </ul> </li> </ul>
Data from: Context matters: the landscape matrix determines the population genetic structure of temperate forest herbs across Europe
<p>Context. Plant populations in agricultural landscapes are mostly fragmented and their functional connectivity often depends on seed and pollen dispersal by animals. However, little is known about how the interactions of seed and pollen dispersers with the agricultural matrix translate into gene flow among plant populations.</p> <p>Objectives. We aimed to identify effects of the landscape structure on the genetic diversity within, and the genetic differentiation among, spatially isolated populations of three temperate forest herbs. We asked, whether different arable crops have different effects, and whether the orientation of linear landscape elements relative to the gene dispersal direction matters.</p> <p>Methods. We analysed the species' population genetic structures in seven agricultural landscapes across temperate Europe using microsatellite markers. These were modelled as a function of landscape composition and configuration, which we quantified in buffer zones around, and in rectangular landscape strips between, plant populations.</p> <p>Results. Landscape effects were diverse and often contrasting between species, reflecting their association with different pollen- or seed dispersal vectors. Differentiating crop types rather than lumping them together yielded higher proportions of explained variation. Some linear landscape elements had both a channelling and hampering effect on gene flow, depending on their orientation.</p> <p>Conclusions. Landscape structure is a more important determinant of the species' population genetic structure than habitat loss and fragmentation <i>per se</i>. Landscape planning with the aim to enhance the functional connectivity among spatially isolated plant populations should consider that even species of the same ecological guild might show distinct responses to the landscape structure.</p>
Data from: Seeing the Forest for the trees: Assessing genetic offset predictions from Gradient Forest
<p><span>Gradient Forest (GF) is a machine learning algorithm designed to analyze spatial patterns of biodiversity as a function of environmental gradients. An offset measure between the GF predicted environmental association of adapted alleles and a new environment (GF Offset), is increasingly being used to predict the loss of environmentally adapted alleles under rapid environmental change, but remains mostly untested for this purpose. Here we explore the robustness of GF Offset to assumption violations, and its relationship to measures of fitness, using SLiM simulations with explicit genome architecture and a spatial metapopulation. We evaluate measures of GF Offset in: (1) a neutral model with no environmental adaptation; (2) a monogenic "population genetic" model with a single environmentally adapted locus; and (3) a polygenic "quantitative genetic" model with two adaptive traits, each adapting to a different environment. We found GF Offset to be broadly correlated with fitness offsets under both single locus and polygenic architectures. However, neutral demography, genomic architecture, and the nature of the adaptive environment can all confound relationships between GF Offset and fitness. GF Offset is a promising tool, but it is important to understand its limitations and underlying assumptions, especially when used in the context of predicting maladaptation.</span></p>
Fig. 1 in Winter Diet Of The Common Genet, Genetta Genetta (Carnivora, Viverridae), And The African Golden Wolf, Canis Anthus (Carnivora, Canidae), In Altitudinal Locality Of The Edough Forest (Northeastern Algeria)
Fig. 1. Geographical situation of the study locality. (with indication of the three transects: 1, 2 and 3). Source: https://journals.openedition.org/physio-geo/docannexe/image/4217/img-1.jpg. Modified by Boukheroufa (present work).
How ancient forest fragmentation and riparian connectivity generate high levels of genetic diversity in a micro-endemic Malagasy tree
<p>This repository contains all the scripts and most of the intermediary files necessary to replicate the analyses of the preprint "<strong>How ancient forest fragmentation and riparian connectivity generate high levels of genetic diversity in a micro-endemic Malagasy tree</strong>" submitted to Molecular Ecology and available at:</p> <p><a href="https://www.biorxiv.org/content/10.1101/2020.11.25.394544v1">https://www.biorxiv.org/content/10.1101/2020.11.25.394544v5</a></p> <p>Within each of the different zipped folders a readme.txt file briefly explains how the analyses are organized.</p> <p>This version of the dataset has been revised in agreement with the manuscript revision to answer the comments of the first two rounds of reviews in Peer Community In Evolutionary Biolology (PCI-EvolBiol; <a href="https://evolbiol.peercommunityin.org/">https://evolbiol.peercommunityin.org/</a>) by M. Navascues (Recommender), Katharina Budde (reviewer) and Yurena Arjona (reviewer), as well as two rounds of reviews in Molecular Ecology. All PCIevolbiol comments, response and changes are documented on the PCIevolbiol website.</p>
Data and code from: Evaluating genomic offset predictions in a forest tree with high population genetic structure
<p>Predicting how tree populations will respond to climate change is an urgent societal concern. An increasingly popular way to make such predictions is the genomic offset (GO) approach, which aims to use genomic and climate data to identify populations that may experience climate maladaptation in the near future. More precisely, GO tries to represent the change in allele frequencies required to maintain the current gene-climate relationships under climate change. However, the GO approach has major limitations and, despite promising validation of its predictions using height data from common gardens, it still lacks broad empirical testing. In the present study, we evaluated the consistency and empirical validity of GO predictions in maritime pine (<em>Pinus pinaster</em> Ait.), a tree species from southwestern Europe and North Africa with a marked population genetic structure. First, gene-climate relationships were estimated using 9,817 SNPs genotyped in 454 trees from 34 populations; and candidate SNPs potentially involved in climate adaptation were identified. Second, GO was predicted using four methods, namely Gradient Forest (GF), Redundancy Analysis (RDA), latent factor mixed model (LFMM) and Generalised Dissimilarity Modeling (GDM), two sets of SNPs (candidate and control SNPs) and five climate general circulation models (GCMs) to account for uncertainty in future climate predictions. Last, the empirical validity of GO predictions was evaluated within a Bayesian framework by estimating the associations between GO predictions and two independent data sources: mortality data from National Forest Inventories (NFI), and mortality and height data from five common gardens in contrasting environments. We found high variability in GO predictions across methods, SNP sets and GCMs. Regarding validation, GO predictions with GDM and GF (and to a lesser extent RDA) based on the candidate SNPs showed the strongest and most consistent associations with mortality rates in common gardens and NFI plots. We found almost no association between GO predictions and tree height in common gardens, most likely due to the overwhelming effect of population genetic structure on tree height in this species. Our study demonstrates the imperative to validate GO predictions with a range of independent data sources before they can be used as informative and reliable metrics in conservation or management strategies.</p>
Figure 2 in Genetic structure of Trypanosoma congolense "forest type" circulating in domestic animals and tsetse flies in the South-West region of Cameroon
Figure 2. NJ Tree based on Cavalli-Sforza and Edwards chord distance matrix of T. congolense "forest type" circulating in tsetse flies and domestic animals of Fontem.
Database of Pines from the Forests paper: "Intraspecific Variation in Pines from the Trans-Mexican Volcanic Belt Grown Under Two Watering Regimes: Implications for Management of Genetic Resources"
<p>Raw data from the Forests paper: "Intraspecific Variation in Pines from the Trans-Mexican Volcanic Belt Grown under Two Watering Regimes: Implications for Management of Genetic Resources" Forests <strong>2018</strong> <em>9</em>(2), 71. doi:<a href="http://dx.doi.org/10.3390/f9020071">10.3390/f9020071. </a></p> <p>The database correspond to seedlings of four Mexican pines: <em>P. oocarpa, P. patula</em> and <em>P. pseudostrobus</em>, that were submitted to two watering treatments: Field Capacity (FC) and Drought-Stress (DS), during 90 days. Growth and biomass, survival and ontogenetic score were measured.</p>
Fig. 2 in Genetic and morphological differentiation among populations of the narrowly endemic and karst forest-adapted Pilea pteridophylla (Urticaceae)
Fig. 2 Morphological variation among individuals of Pilea pteridophylla sampled along its distribution range in the tropical karst forest of southern Mexico. Plot of individual scores for the first two components of the principal component analysis using morphological data. Coloured symbols represent the two populations recognized for the species: red circles, Tabasco; and blue circles, Chiapas. Ellipses correspond to the 95% confidence intervals estimated for each population. The lines represent the dispersion of the individuals within each population
Fig. 3 in Genetic and morphological differentiation among populations of the narrowly endemic and karst forest-adapted Pilea pteridophylla (Urticaceae)
Fig. 3 Statistical parsimony networks of rps16-trnQ, trnL-trnF and rps16-trnQ + trnL-trnF dataset using the gaps as missing data. Coloured symbols represent the two populations recognized for the species: red circles, Tabasco; and blue circles, Chiapas. Open-white circles represent the number of mutational steps between haplotypes. The size of the circles is proportional to the frequency of each haplo-
Fig. 1 in Genetic and morphological differentiation among populations of the narrowly endemic and karst forest-adapted Pilea pteridophylla (Urticaceae)
Fig. 1 Mountain karst forests of Mexico and the studied species Pilea pteridophylla A. K. Monro (Urticaceae). A Geographic distribution of the Mountain karst forests of Mexico. B Individual from the Chiapas population. C Individual from the Tabasco population
Fungal community composition and genetic potential regulate fine root decay in northern temperate forests
<p>Understanding how genetic differences among soil microorganisms regulate spatial patterns in litter decay remains a persistent challenge in ecology. Despite fine root litter accounting for ~50% of total litter production in forest ecosystems, far less is known about the microbial decay of fine roots relative to aboveground litter. Here, we evaluated whether fine root decay occurred more rapidly where fungal communities have a greater genetic potential for litter decay. Additionally, we tested if linkages between decay and fungal genes can be adequately captured by delineating saprotrophic and ectomycorrhizal fungal functional groups based on whether they have genes encoding certain ligninolytic class II peroxidase enzymes, which oxidize lignin and polyphenolic compounds. To address these ideas, we used a litterbag study paired with fungal DNA barcoding to characterize fine root decay rates and fungal community composition at the landscape scale in northern temperate forests, and we estimated the genetic potential of fungal communities for litter decay using publicly available genomes. Fine root decay occurred more rapidly where fungal communities had a greater genetic potential for decay, especially of cellulose and hemicellulose. Fine root decay was positively correlated with ligninolytic saprotrophic fungi and negatively correlated with ECM fungi with ligninolytic peroxidases, likely because these saprotrophic and ectomycorrhizal functional groups had the highest and lowest genetic potentials for plant cell wall degradation, respectively. These fungal variables overwhelmed direct environmental controls, suggesting fungal community composition and genetic variation are primary controls over fine root decay in temperate forests at regional scales.</p>
Archived Data - Genetic breaks caused by ancient forest fragmentation: phylogeography of Staudtia kamerunensis (Myristicaceae) reveals distinct clusters in the Congo Basin
<p>List of the 400 genotyped <em>Staudtia kamerunensis</em><em> </em>accessions from Central Africa included in Vanden Abeele & Matvijev et al. 2023 - Tree Genetics & Genomes, and the corresponding alleles for each of the 14 microsatellite markers (0-0 indicates missing alleles)</p>
Data from: Past forest-cover explains current genetic differentiation in the Carpathian newt (Lissotriton montandoni), but not in the smooth newt (L. vulgaris)
<p class="MsoNormal"><strong>Aim:</strong><strong><span> </span></strong><span>Current genetic variation and differentiation are expected to reflect the effects of past rather than present landscapes due to time lags, i.e., the time necessary for genetic diversity to reach equilibrium and reflect demography. </span>Time lags can affect our ability to infer landscape use and model connectivity, and also obscure the genetic consequences of recent landscape changes<span>. In this work, we test if past forest-cover better explains contemporary patterns of genetic differentiation in two closely related but ecologically distinct newt species – <em>Lissotriton montandoni</em> and <em>L. vulgaris</em>. </span></p> <p class="MsoNormal"><span><strong>Location: </strong></span><span><span>Carpathian Mountains and foothills.</span></span></p> <p class="MsoNormal"><span><strong>Methods: </strong>Genetic differentiation between populations was related with landscape resistance optimized with tools from landscape genetics, for multiple timeframes, using forest-cover data from 1963 to 2015. Analyses were conducted for </span><span><span>pairs of populations at distances from 1 to 50 km.</span></span></p> <p class="MsoNormal"><span><strong>Results:</strong></span><span><strong><span> </span></strong></span><span><span>We </span></span><span>find evidence for a time lag in <em>L. montandoni</em>, with forest-cover from 40 years ago (ca. 10 newt generations) better explaining current genetic differentiation. In <em>L. vulgaris</em>, current genetic differentiation was better predicted by present land-cover models with lower resistance given to open-forests. This result may reflect the generalist ecology of<em> L. vulgaris</em>, its lower effective population sizes and exposure to habitat destruction and fragmentation.</span></p> <p class="MsoNormal"><strong>Main conclusions:</strong><span> <span>Our study provides evidence for time lags in <em>L. montandoni</em>, showing that the genetic consequences of landscape change for some species are not yet evident. Our findings highlight the interspecific variation in time lag prevalence, and demonstrate that current patterns of genetic differentiation should be interpreted in the context of historical landscape changes.</span></span></p>
Data from: The city and forest bird flock together in a common garden: Genetic and environmental effects drive urban phenotypic divergence
Open the record for dataset details and reuse information.
Data and code from: Evaluating genomic offset predictions in a forest tree with high population genetic structure
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Allen Brain Atlas
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OpenNeuro
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