scholarly journals A landscape genetic analysis of swamp rabbits (Sylvilagus aquaticus) suggests forest canopy cover enhances gene flow in an agricultural matrix

2018 ◽  
Vol 96 (6) ◽  
pp. 622-632 ◽  
Author(s):  
Leah K. Berkman ◽  
Clayton K. Nielsen ◽  
Charlotte L. Roy ◽  
Edward J. Heist
Keyword(s):  
Gene Flow ◽  
Genetic Distance ◽  
Canopy Cover ◽  
Population Connectivity ◽  
Causal Modeling ◽  
Suitable Habitat ◽  
Southern Illinois ◽  
Landscape Features ◽  
Tree Canopy Cover ◽  
Landscape Genetic

Habitat loss and fragmentation pose a continued and immediate threat to wildlife and create a persistent need for ecological information at the landscape scale to guide conservation efforts. Landscape features influence population connectivity for many species and genetic analyses can be employed to determine which of these features are most important. Because population connectivity through dispersal is important to the persistence of swamp rabbits (Sylvilagus aquaticus (Bachman, 1837)) at the northern edge of their range, we used a landscape genetic approach to relate gene flow to landscape features that may impact dispersal success. We tested resistance values for attributes of land cover, watercourse corridors, canopy cover, and roads and used causal modeling and redundancy analysis to relate these representations of landscapes to genetic distance for swamp rabbits in southern Illinois, USA. Models that included canopy cover had the strongest correlations with genetic distance and were supported by our methods whereas other models were not. We concluded that high tree canopy cover enhances gene flow and landscape connectivity for swamp rabbits in southern Illinois. Our study provides important empirical evidence that landscape variables may impact the habitat connectivity of swamp rabbits. Preserving dispersal routes for swamp rabbits should focus on improving canopy cover, in both bottomland and upland, to connect suitable habitat.

scholarly journals Population and landscape genetic analysis of the Malayan sun bear Helarctos malayanus

2019 ◽  
Vol 21 (1) ◽  
pp. 123-135
Author(s):  
Miriam N. Kunde ◽  
Renata F. Martins ◽  
Joe Premier ◽  
Joerns Fickel ◽  
Daniel W. Förster
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Unknown Origin ◽  
Population Connectivity ◽  
The Sun ◽  
Conservation Action ◽  
Helarctos Malayanus ◽  
Assignment Probability ◽  
Sun Bear ◽  
Landscape Genetic

AbstractConservation genetics can provide data needed by conservation practitioners for their decisions regarding the management of vulnerable or endangered species, such as the sun bear Helarctos malayanus. Throughout its range, the sun bear is threatened by loss and fragmentation of its habitat and the illegal trade of both live bears and bear parts. Sharply declining population numbers and population sizes, and a lack of natural dispersal between populations all threaten the genetic diversity of the remaining populations of this species. In this first population genetics study of sun bears using microsatellite markers, we analyzed 68 sun bear samples from Cambodia to investigate population structure and genetic diversity. We found evidence for two genetically distinct populations in the West and East of Cambodia. Ongoing or recent gene flow between these populations does not appear sufficient to alleviate loss of diversity in these populations, one of which (West Cambodia) is characterized by significant inbreeding. We were able to assign 85% of sun bears of unknown origin to one of the two populations with high confidence (assignment probability ≥ 85%), providing valuable information for future bear reintroduction programs. Further, our results suggest that developed land (mostly agricultural mosaics) acts as a barrier to gene flow for sun bears in Cambodia. We highlight that regional sun bear conservation action plans should consider promoting population connectivity and enforcing wildlife protection of this threatened species.

scholarly journals Using empirical datasets to quantify uncertainty in inferences of landscape genetic resistance due to variation of individual-based genetic distance metrics

2021 ◽  
Author(s):  
Joscha Beninde ◽  
Alain C. Frantz
Keyword(s):  
Gene Flow ◽  
Genetic Distance ◽  
Genetic Resistance ◽  
List Type ◽  
Distance Metrics ◽  
Factorial Correspondence Analysis ◽  
Landscape Resistance ◽  
Landscape Factors ◽  
Landscape Genetic ◽  
The Impact

AbstractEstimates of gene flow are commonly based on inferences of landscape resistance in ecological and evolutionary research and they frequently inform decision-making processes in conservation management. It is therefore imperative that inferences of a landscape factors relevance and its resistance are robust across approaches and reflect real-world gene flow instead of methodological artefacts. Here, we tested the impact of 160 different individual-based pairwise genetic metrics on consistency of landscape genetic inferences.We used three empirical datasets that adopted individual-based sampling schemes and varied in scale (35-25,000 km2) and total number of samples (184-790) and comprise the wild boar, Sus scrofa, the red fox, Vulpes vulpes and the common wall lizard, Podarcis muralis. We made use of a machine-learning algorithm implemented in ResistanceGA to optimally fit resistances of landscape factors to genetic distance metrics and ranked their importance. Employed for nine landscape factors this resulted in 4,320 unique combinations of dataset, landscape factor and genetic distance metric, which provides the basis for quantifying uncertainty in inferences of landscape resistance.Our results demonstrate that there are clear differences in Akaike information criteria (AICc)-based model support and marginal R2-based model fit between different genetic distance metrics. Metrics based on between 1-10 axes of eigenvector-based multivariate analyses (Factorial correspondence analysis, FCA; Principal component analysis, PCA) outperformed more widely used metrics, including the proportion of shared alleles (DPS), with AICc and marginal R2 values often an order of magnitude greater in the former. Across datasets, inferences of the directionality of a landscape factors influence on gene flow, e.g. facilitating or impeding it, changed across different genetic distance metrics. The directionality of the inferred resistance was largely consistent when considering metrics based on between 1-10 FCA/PCA axes.Inferences of landscape genetic resistance need to be corroborated using calculations of multiple individual-based pairwise genetic distance metrics. Our results call for the adoption of eigenvector-based quantifications of pairwise genetic distances. Specifically, a preliminary step of analysis should be incorporated, which explores model ranks across genetic distance metrics derived from FCA and PCA, and, contrary to findings of a simulation study, we demonstrate that it suffices to quantify these distances spanning the first ten axes only.

scholarly journals Evidence for human-mediated range expansion and gene flow in an invasive grass

2018 ◽  
Vol 285 (1882) ◽  
pp. 20181125 ◽  
Author(s):  
Tina M. Arredondo ◽  
Gina L. Marchini ◽  
Mitchell B. Cruzan
Keyword(s):  
Gene Flow ◽  
Genetic Distance ◽  
Canopy Cover ◽  
Invasive Grass ◽  
Single Nucleotide ◽  
Brachypodium Sylvaticum ◽  
Dispersal Mechanism ◽  
Genome Wide ◽  
Urban Rural ◽  
Landscape Feature

Cities and adjacent regions represent foci of intense human activity and provide unique opportunities for studying human-mediated dispersal and gene flow. We examined the effect of landscape features on gene flow in the invasive grass Brachypodium sylvaticum across an urban–rural interface at the edge of its expanding range. We used genome-wide single-nucleotide polymorphism surveys of individuals from 22 locations. Resistance surfaces were created for each landscape feature, using ResistanceGA to optimize resistance parameters. Our S tructure analysis identified three distinct clusters, and diversity analyses support the existence of at least three local introductions. Multiple regression on distance matrices showed no evidence that development, roads, canopy cover or agriculture had a significant influence on genetic distance in B. sylvaticum . Geographical distance was a mediocre predictor of genetic distance and reflected geographical clustering. The model of rivers acting as a conduit explained a large portion of variation in genetic distance, but the lack of evidence of directional gene flow eliminated hydrochory as a dispersal mechanism. These results and observations of the distribution of populations in disturbed sites indicate that the influence of rivers on patterns of dispersal of B. sylvaticum probably reflects seed dispersal due to human recreational activity.

Zoning, land use, and urban tree canopy cover: The importance of scale

2013 ◽  
Vol 12 (2) ◽  
pp. 191-199 ◽  
Author(s):  
Sarah K. Mincey ◽  
Mikaela Schmitt-Harsh ◽  
Richard Thurau
Keyword(s):  
Land Use ◽  
Canopy Cover ◽  
Tree Canopy ◽  
Urban Tree ◽  
Tree Canopy Cover ◽  
Urban Tree Canopy

scholarly journals Diversity of Medicinal Plants among Different Tree Canopies

2021 ◽  
Vol 13 (5) ◽  
pp. 2640
Author(s):  
Muhammad Zubair ◽  
Akash Jamil ◽  
Syed Bilal Hussain ◽  
Ahsan Ul Haq ◽  
Ahmad Hussain ◽  
...  
Keyword(s):  
Medicinal Plants ◽  
Coniferous Forest ◽  
Canopy Cover ◽  
Local Communities ◽  
Tree Canopy ◽  
Tree Cover ◽  
Open Spaces ◽  
Floral Diversity ◽  
Tree Canopy Cover ◽  
Closed Canopy

The moist temperate forests in Northern Pakistan are home to a variety of flora and fauna that are pivotal in sustaining the livelihoods of the local communities. In these forests, distribution and richness of vegetation, especially that of medicinal plants, is rarely reported. In this study, we carried out a vegetation survey in District Balakot, located in Northeastern Pakistan, to characterize the diversity of medicinal plants under different canopies of coniferous forest. The experimental site was divided into three major categories (viz., closed canopy, open spaces, and partial tree cover). A sampling plot of 100 m2 was established on each site to measure species diversity, dominance, and evenness. To observe richness and abundance, the rarefaction and rank abundance curves were plotted. Results revealed that a total of 45 species representing 34 families were available in the study site. Medicinal plants were the most abundant (45%) followed by edible plants (26%). Tree canopy cover affected the overall growth of medicinal plants on the basis of abundance and richness. The site with partial canopy exhibited the highest diversity, dominance, and abundance compared to open spaces and closed canopy. These findings are instrumental in identifying the wealth of the medicinal floral diversity in the northeastern temperate forest of Balakot and the opportunity to sustain the livelihoods of local communities with the help of public/private partnership.

scholarly journals Estimating Forest Canopy Cover by Multiscale Remote Sensing in Northeast Jiangxi, China

Land ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 433
Author(s):  
Xiaolan Huang ◽  
Weicheng Wu ◽  
Tingting Shen ◽  
Lifeng Xie ◽  
Yaozu Qin ◽  
...  
Keyword(s):  
Remote Sensing ◽  
Large Scale ◽  
Forest Canopy ◽  
Canopy Cover ◽  
Google Earth ◽  
Tree Canopy ◽  
Landsat Data ◽  
High Resolution Data ◽  
Modis Ndvi ◽  
Tree Canopy Cover

This research was focused on estimation of tree canopy cover (CC) by multiscale remote sensing in south China. The key aim is to establish the relationship between CC and woody NDVI (NDVIW) or to build a CC-NDVIW model taking northeast Jiangxi as an example. Based on field CC measurements, this research used Google Earth as a complementary source to measure CC. In total, 63 sample plots of CC were created, among which 45 were applied for modeling and the remaining 18 were employed for verification. In order to ascertain the ratio R of NDVIW to the satellite observed NDVI, a 20-year time-series MODIS NDVI dataset was utilized for decomposition to obtain the NDVIW component, and then the ratio R was calculated with the equation R = (NDVIW/NDVI) *100%, respectively, for forest (CC >60%), medium woodland (CC = 25–60%) and sparse woodland (CC 1–25%). Landsat TM and OLI images that had been orthorectified by the provider USGS were atmospherically corrected using the COST model and used to derive NDVIL. R was multiplied for the NDVIL image to extract the woody NDVI (NDVIWL) from Landsat data for each of these plots. The 45 plots of CC data were linearly fitted to the NDVIWL, and a model with CC = 103.843 NDVIW + 6.157 (R2 = 0.881) was obtained. This equation was applied to predict CC at the 18 verification plots and a good agreement was found (R2 = 0.897). This validated CC-NDVIW model was further applied to the woody NDVI of forest, medium woodland and sparse woodland derived from Landsat data for regional CC estimation. An independent group of 24 measured plots was utilized for validation of the results, and an accuracy of 83.0% was obtained. Thence, the developed model has high predictivity and is suitable for large-scale estimation of CC using high-resolution data.

scholarly journals Habitat associations and conservation status of an endemic forest dwarf chameleon (Bradypodion sp.) from South Africa

Oryx ◽  
2006 ◽  
Vol 40 (2) ◽  
pp. 183-188 ◽  
Author(s):  
Walter J. Reisinger ◽  
Devi M. Stuart-Fox ◽  
Barend F.N. Erasmus
Keyword(s):  
South Africa ◽  
Conservation Status ◽  
Canopy Cover ◽  
Iucn Red List ◽  
Habitat Associations ◽  
Suitable Habitat ◽  
Area Of Occupancy ◽  
Forest Interior ◽  
Forest Remnants ◽  
Iucn Red List Criteria

We quantified habitat associations and evaluated the conservation status of a recently identified, undescribed species of dwarf chameleon, Bradypodion sp. nov. Dhlinza, endemic to scarp forest remnants in KwaZulu-Natal Province, South Africa. At the microhabitat scale the Dhlinza dwarf chameleon was found more often in forest gaps and near paths than highly disturbed edges or forest interior. Chameleon presence was not explained by forest physiognomic variables such as vine cover, shrub and tree density, or canopy cover. Presence near gaps may be better explained by the combined effects of the thermal microenvironment and food availability. The species is moderately common where it occurs, with estimated densities of 4.7, 8.7 and 29.7 individuals per ha within forest interior, edges and gaps respectively. At the landscape scale, the chameleon occurs only in three remnant forests: the Dhlinza, Entumeni and Ongoye Forests. The species' extent of occurrence was estimated to be 88 km2 and its area of occupancy 49 km2. Based on the small area of remaining suitable habitat, this species meets the requirements for categorization as Endangered according to IUCN Red List criteria.

Habitat differentiation between estuarine and inland Hibiscus tiliaceus L. (Malvaceae) as revealed by retrotransposon-based SSAP marker

2011 ◽  
Vol 59 (6) ◽  
pp. 515 ◽  
Author(s):  
Tian Tang ◽  
Lian He ◽  
Feng Peng ◽  
Suhua Shi
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Distance ◽  
Genetic Variance ◽  
Genetic Relationships ◽  
Principal Coordinate Analysis ◽  
Geographical Isolation ◽  
Tidal Zone ◽  
Ecological Scale ◽  
Habitat Differentiation

Hibiscus tiliaceus L. (Malvaceae) is a pantropical coastal tree that extends to the tidal zone. In this study, the retrotransposon sequence-specific amplified polymorphism (SSAP) technique was used in order to understand the genetic variation between four population pairs of H. tiliaceus from repeated estuarine and inland habitat contrasts in China. The estuarine populations were consistently more genetic variable compared with the inland ones, which may be attributed to extensive gene flow via water-drifted seeds and/or retrotransposon activation in stressful estuarine environments. An AMOVA revealed that 8.9% of the genetic variance could be explained by the habitat divergence within site, as compared with only 4.9% to geographical isolation between sites, which indicates significant habitat differentiation between the estuarine and inland populations. The estuarine populations were less differentiated (ΦST = 0.115) than the inland (ΦST = 0.152) implying frequent gene interchange in the former. Accordingly, the principal coordinate analysis of genetic distance between individuals revealed that genetic relationships are not fully consistent with the geographic association. These results suggest that despite substantial gene flow via sea-drifted seeds, habitat-related divergent selection could be one of the primary mechanisms that drive habitat differentiation in H. tiliaceus at a local ecological scale.

The Influence of Gene Flow on Genetic Distance

1975 ◽  
Vol 109 (969) ◽  
pp. 597-601 ◽  
Author(s):  
M. Slatkin ◽  
T. Maruyama
Keyword(s):  
Gene Flow ◽  
Genetic Distance
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