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131 results for “forest genetics”
Data from: Bee movement across heterogeneous tropical forests: multi-paternal genetic analyses reveal the importance of neighborhood composition for pollen-mediated gene flow
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Data from: Assessing the effects of land‑use intensity on small mammal community composition and genetic variation in Myodesglareolus and Microtus arvalis across grassland and forest habitats
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Patterns in the genetic structure of 49 lowland rain forest tree species co-distributed on opposite sides of the Northern Andes
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Landscape genetics Afromontane forest birds - microsatellite data
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Pollinator data from: Pollinator movement activity influences genetic diversity and differentiation of spatially isolated populations of clonal forest herbs
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Latitudinal trends in genetic diversity and distinctiveness of Quercus robur rear edge forest remnants call for new conservation priorities
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Data from: Genetic and phenotypic differentiation in a Neotropical passerine with a disjunct distribution in the Andean and Atlantic forests (Thamnophilus ruficapillus)
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Population dynamics of Amazonian floodplain forest species support spatial variation on genetic diversity but not range expansions through time
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Data from: Population genetic consequences of habitat fragmentation in ectomycorrhizal fungi with different dispersal mechanisms: Implications from ice-aged relict forests across the Japanese archipelago
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Data from: Morphological and genetic evidence for the Stigmatodon goniorachis complex (Tillandsioideae, Bromeliaceae) reveals a new species on inselbergs in the Brazilian Atlantic Forest
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Population genetics, demographic and evolutionary history of the Dudley’s lousewort, a rare redwood forest specialist (Pedicularis dudleyi)
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Data from: Phylogenomic approaches reveal how climate shapes patterns of genetic diversity in an African rain forest tree species
<p>The world's second largest expanse of tropical rain forest is in Central Africa and it harbours enormous species diversity. Population genetic studies have consistently revealed significant structure across central African rain forest plants, in particular a North-South genetic discontinuity around the equatorial line, in a continuous expanse of rain forest but where a climatic inversion is documented. Here, we took a phylogeographic approach by sequencing 351 nuclear markers in 112 individuals across the distribution of the African rain forest tree species Annickia affinis (Annonaceae). We showed for the first time that the North-South divide is the result of a single, major colonisation event across the climatic inversion from an ancestral population located in Gabon. We suggested that differences in ecological niche of populations located on either side of this inversion may have contributed to this phylogenetic discontinuity. We found evidence for inland dispersal, predominantly in northern areas, and variable demographic histories among genetic clusters, indicating that populations responded differently to past climate change. We show how newly-developed genomic tools can provide invaluable insights into our understanding of tropical rain forest evolutionary dynamics.</p>
Functional and genetic diversity changes through time in a cloud forest ant assemblage
<p>Climate change in the Neotropics is causing upslope range shifts. We used arrays of ant species collected in a cloud forest at 1,500 m in Área de Conservación Guanacaste (ACG), northwestern Costa Rica, collected in two time periods (1998-2000 and 2008-2011) to measure changes in species richness and diversity over a decade. Using metrics of community structure, we found that the species assemblage in the collections from the 1990s were significantly phylogenetically clustered and functionally less diverse as compared to collections from the early 2000's. At both time points, the assemblages were significantly phylogenetically clustered and while the difference in functional diversity between the time points was not significant, the ant assemblage has become lighter in color (on average) over time. When individual species are considered the overall pattern of replacement is consistent with the cloud forest ant assemblage being colonized by arrivals from lower-elevation forests. The invertebrate communities on cloud forested mountain tops are especially vulnerable to a changing climate as there are two factors working together; no higher terrain to which they can move and the invasion of more and more taxa from lower downslope. This vulnerability is already measurable.</p>
Data from: Genetic diversity of the rain tree (Albizia saman) in Colombian seasonally dry tropical forest for informing conservation and restoration interventions
<p><i>Albizia saman</i> is a multipurpose tree species of seasonally dry tropical forests (SDTFs) of Mesoamerica and northern South America typically cultivated in silvopastoral and other agroforestry systems around the world, a trend that is bound to increase in light of multimillion hectare commitments for forest and landscape restoration. The effective conservation and sustainable use of <i>A. saman</i> requires detailed knowledge of its genetic diversity across its native distribution range of which surprisingly little is known to date. We assessed the genetic diversity and structure of <i>A.saman</i> across twelve representative locations of SDTF in Colombia, and how they may have been shaped by past climatic changes and human influence. We found four different genetic groups which may be the result of differentiation due to isolation of populations in pre-glacial times. The current distribution and mixture of genetic groups across STDF fragments we observed might be the result of range expansion of SDTFs during the last glacial period followed by range contraction during the Holocene and human-influenced movement of germplasm associated with cattle ranching. Despite the fragmented state of the presumed natural <i>A. saman</i> stands we sampled we did not find any signs of inbreeding, suggesting that gene flow is not jeopardized in humanized landscapes. However, further research is needed to assess potential deleterious effects of fragmentation on progeny. Climate change is not expected to seriously threaten the <i>in situ</i> persistence of <i>A. saman</i> populations and might present opportunities for future range expansion. However, the sourcing of germplasm for tree planting activities needs to be aligned with the genetic affinity of reference populations across the distribution of Colombian SDTFs. We identify priority source populations for i<i>n situ</i> conservation based on their high genetic diversity, lack or limited signs of admixture and/or genetic uniqueness.</p>
Data from: Landscape genetics of leaf-toed geckos in the tropical dry forest of northern Mexico
Habitat fragmentation due to both natural and anthropogenic forces continues to threaten the evolution and maintenance of biological diversity. This is of particular concern in tropical regions that are experiencing elevated rates of habitat loss. Although less well-studied than tropical rain forests, tropical dry forests (TDF) contain an enormous diversity of species and continue to be threatened by anthropogenic activities including grazing and agriculture. However, little is known about the processes that shape genetic connectivity in species inhabiting TDF ecosystems. We adopt a landscape genetic approach to understanding functional connectivity for leaf-toed geckos (Phyllodactylus tuberculosus) at multiple sites near the northernmost limit of this ecosystem at Alamos, Sonora, Mexico. Traditional analyses of population genetics are combined with multivariate GIS-based landscape analyses to test hypotheses on the potential drivers of spatial genetic variation. Moderate levels of within-population diversity and substantial levels of population differentiation are revealed by FST and Dest. Analyses using STRUCTURE suggest the occurrence of from 2 to 9 genetic clusters depending on the model used. Landscape genetic analysis suggests that forest cover, stream connectivity, undisturbed habitat, slope, and minimum temperature of the coldest period explain more genetic variation than do simple Euclidean distances. Additional landscape genetic studies throughout TDF habitat are required to understand species-specific responses to landscape and climate change and to identify common drivers. We urge researchers interested in using multivariate distance methods to test for, and report, significant correlations among predictor matrices that can impact results, particularly when adopting least-cost path approaches. Further investigation into the use of information theoretic approaches for model selection is also warranted.
Data from: Forest trees in human modified landscapes: ecological and genetic drivers of recruitment failure in Dysoxylum malabaricum (Meliaceae)
Tropical agro-forest landscapes are global priority areas for biodiversity conservation. Little is known about the ability of these landscapes to sustain large late successional forest trees upon which much forest biodiversity depends. These landscapes are subject to fragmentation and additional habitat degradation which may limit tree recruitment and thus compromise numerous ecosystem services including carbon storage and timber production. Dysoxylum malabaricum is a large canopy tree species in the Meliaceae, a family including many important tropical timber trees. This species is found in highly fragmented forest patches within a complex agro-forest landscape of the Western Ghats biodiversity hot spot, South India. In this paper we combined a molecular assessment of inbreeding with ecological and demographic data to explore the multiple threats to recruitment of this tree species. An evaluation of inbreeding, using eleven microsatellite loci in 297 nursery-reared seedlings collected form low and high density forest patches embedded in an agro-forest matrix, shows that mating between related individuals in low density patches leads to reduced seedling performance. By quantifying habitat degradation and tree recruitment within these forest patches we show that increasing canopy openness and the increased abundance of pioneer tree species lead to a general decline in the suitability of forest patches for the recruitment of D. malabaricum. We conclude that elevated inbreeding due to reduced adult tree density coupled with increased degradation of forest patches, limit the recruitment of this rare late successional tree species. Management strategies which maintain canopy cover and enhance local densities of adult trees in agro-forest mosaics will be required to ensure D. malabaricum persists in these landscapes. Our study highlights the need for a holistic understanding of the incipient processes that threaten populations of many important and rare tropical tree species in human dominated agro-forest landscapes.
Data from: Interglacial genetic diversification of Moussonia deppeana (Gesneriaceae), a hummingbird-pollinated, cloud forest shrub in northern Mesoamerica
Recent empirical work on cloud forest-adapted species supports the role of both old divergences across major geographical areas and more recent divergences attributed to Pleistocene climate changes. The shrub Moussonia deppeana is distributed in northern Mesoamerica, with geographically disjunct populations. Based on sampling throughout the species range and employing plastid and nuclear markers, we (i) test whether the fragmented distribution is correlated with main evolutionary lineages, (ii) reconstruct its phylogeographical history to infer the history of cloud forest in northern Mesoamerica and (iii) evaluate a set of refugia/vicariance scenarios for the region and demographic patterns of the populations whose ranges expanded and tracked cloud forest conditions during the Last Glacial Maximum. We found a deep evolutionary split in M. deppeana about 6–3 Ma, which could be consistent with a Pliocene divergence. Comparison of variation in plastid and nuclear markers revealed several lineages mostly congruent with their isolated geographical distribution and restricted gene flow among groups. Results of species distribution modelling and coalescent simulations fit a model of multiple refugia diverging during interglacial cycles. The demographic history of M. deppeana is not consistent with an expanding–contracting cloud forest archipelago model during the Last Glacial Maximum. Instead, our data suggest that populations persisted across the geographical range throughout the glacial cycles, and experienced isolation and divergence during interglacial periods.
Data from: Morphology and genetics reveal an intriguing pattern of differentiation at a very small geographic scale in a bird species, the forest thrush Turdus lherminieri
Mobile organisms are expected to show population differentiation only over fairly large geographical distances. However, there is growing evidence of discrepancy between dispersal potential and realized gene flow. Here we report an intriguing pattern of differentiation at a very small spatial scale in the forest thrush (Turdus lherminieri), a bird species endemic to the Lesser Antilles. Analysis of 331 individuals from 17 sampling sites distributed over three islands revealed a clear morphological and genetic differentiation between these islands isolated by 40–50 km. More surprisingly, we found that the phenotypic divergence between the two geographic zones of the island of Guadeloupe was associated with a very strong genetic differentiation (Fst from 0.073–0.153), making this pattern a remarkable case in birds given the very small spatial scale considered. Molecular data (mitochondrial control region sequences and microsatellite genotypes) suggest that this strong differentiation could have occurred in situ, although alternative hypotheses cannot be fully discarded. This study suggests that the ongoing habitat fragmentation, especially in tropical forests, may have a deeper impact than previously thought on avian populations.
Data from: Mating system and genetic diversity of progenies before and after logging: a case study of Bagassa guianensis (Moraceae), a low-density dioecious tree of the Amazonian forest
The logging of large trees in tropical forests causes a decrease in the density of reproductive individuals, which likely affects the pattern of pollen dispersal and the mating system of the remaining trees in the population. Here, we investigate the impact of logging on mating system and genetic diversity of the low-density, thrip-pollinated, dioecious tree Bagassa guianensis within a 500-ha plot at Tapajós National Forest, Pará State, Brazil. Mating system parameters of the logged population were estimated using mixed-mating model. Six microsatellite loci were used to genotype 232 seeds from ten remnant female trees over three seasons (2006, 2007, and 2008). The data were compared with the mating system of the unlogged population of B. guianensis (18 female trees, 488 seeds) in the same plot. The overall number of alleles found in the open-pollinated progenies decreased after logging (K = 71 before logging and K = 57 after logging, considering the three after logging seasons pooled), as well as the average number of alleles per locus (A = 11.8 and 9.5, respectively). Similarly, the number of private alleles, which is defined in the context of this study as the number of alleles observed in the population exclusively before or after logging, also decreased after logging (15 and 1, respectively). However, the average number of alleles per locus and the observed and expected heterozygosities were not significantly higher before logging than after logging. Logging also did not affect the inbreeding of progenies in the population. Somewhat unexpectedly, the effective number of pollen donors was consistently higher after (N ep = 14.5 in 2006, 8.1 in 2007, and 6.3 in 2008) than before logging (N ep = 3.4), suggesting that the loss of alleles in the population was compensated by the higher heterogeneity in the pollen pool after the removal of the largest trees by logging. Potential causes explaining the patterns found here include the maintenance of large patches of forest around the logged plot and the species' ability to perform long-distance pollination by airborne thrips. Maintenance of landscape integrity as logged and unlogged forests around the exploited areas is recommended to enhance pollen migration and to avoid long-term losses in genetic diversity.
Data from: Does long distance pollen dispersal preclude inbreeding in tropical trees? Fragmentation genetics of Dysoxylum malabaricum in an agro-forest landscape
Tropical trees often display long distance pollen dispersal, even in highly fragmented landscapes. Understanding how patterns of spatial isolation influence gene flow and interact with background patterns of fine scale spatial genetic structure are critical for evaluating the genetic consequences of habitat fragmentation. In the endangered tropical timber tree Dysoxylum malabaricum (Meliaceae) we apply eleven microsatellite markers with paternity and parentage analysis to directly estimate contemporary gene flow across a large area (216 km2) in a highly fragmented agro-forest landscape. A comparison of genetic diversity and genetic structure in adult and juvenile life stages indicates an increase of differentiation and fine-scale spatial genetic structure (FSGS) over time. Paternity analysis and parentage analysis demonstrate high genetic connectivity across the landscape by pollen dispersal. A comparison between mother trees in forest patches with low and high densities of adult trees shows that the frequency of short distance mating increases, as does average kinship among mates in low density stands. We interpret this as an early warning sign of potentially negative genetic consequences of forest fragmentation. Single isolated trees, in contrast, frequently receive heterogeneous pollen from distances exceeding five kilometres. We discuss the processes leading to the observed patterns of gene flow and the implications of this for conservation management of D. malabaricum and tropical trees more generally.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.