Estimation of gene flow into fragmented populations of Bursera simaruba (Burseraceae) in the dry-forest life zone of Puerto Rico

AbstractThe Black-whiskered Vireo (Vireo altiloquus) breeds from coastal southern Florida in the United States through the islands of the West Indies, and thus consists of several populations separated by large regions of uninhabitable space. I examined genetic variation within and among six migratory populations in the Florida Keys, Jamaica, and Puerto Rico, using random amplified polymorphic DNA (RAPD) markers and analysis of molecular variance (AMOVA). Calculations of variance components revealed that over 90% of the variance was among individuals; a significant portion also occurred among regional groups (Florida, Jamaica, and Puerto Rico). Variance between subpopulations within the regional groups was not significantly different from zero. This contrasts with the closely related Red-eyed Vireo (V. olivaceus) of continental North America, in which analyses of three widely separate geographic localities revealed that over 99% of the genetic variance was among individuals, with no significant variance detectable among localities. The greatest differences in V. altiloquus were detected between the Florida Keys populations and the populations from Jamaica and Puerto Rico; the latter two showed no significant differentiation. Estimates of gene flow from the AMOVA analog to Wright's F-statistics suggest that there is enough gene flow among regions to prevent differentiation by genetic drift. Although not strongly isolated, the Florida population of V. altiloquus is sufficiently differentiated to suggest reduced genetic exchange with the populations on Puerto Rico and Jamaica.Estructura Genética entre Poblaciones Migratorias de Vireo altiloquus con una Comparación con Vireo olivaceusResumen. Vireo altiloquus se reproduce desde la costa del sur de la Florida en los Estados Unidos hasta las islas de las Antillas, y por lo tanto presenta varias poblaciones separadas por extensas regiones de espacio no habitable. Examiné la variación genética dentro y entre seis poblaciones migratorias en los Cayos de la Florida, en Jamaica y en Puerto Rico, usando marcadores polimórficos de ADN amplificados al azar (RAPD) y análisis de varianza molecular (AMOVA). Los cálculos de los componentes de la varianza indicaron que más del 90% de la varianza se presentó entre individuos; una porción significativa también estuvo presente entre los grupos regionales (Florida, Jamaica y Puerto Rico). La varianza entre subpoblaciones dentro de grupos regionales no fue significativamente diferente de cero. Esto contrasta con los resultados para V. olivaceus de Norteamérica continental, donde los análisis de tres localidades alejadas revelaron que más del 99% de la varianza genética se registró entre individuos, sin varianza significativa detectable entre localidades. Las mayores diferencias en V. altiloquus fueron detectadas entre las poblaciones de los Cayos de la Florida y las poblaciones de Jamaica y Puerto Rico; las últimas dos no mostraron diferencias significativas. Las estimaciones de flujo génico a partir del AMOVA, análogo al estadístico F de Wright, sugieren que hay suficiente flujo génico entre las regiones para evitar diferenciación por deriva génica. Aunque no está muy aislada, la poblacion de V. altiloquus de la Florida se diferencia lo suficiente como para sugerir un intercambio génico reducido con las poblaciones de Puerto Rico y Jamaica.

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Fuel Conditions Associated with Native and Exotic Grasses in a Subtropical Dry Forest in Puerto Rico

Fire Ecology ◽

10.4996/fireecology.0803009 ◽

2012 ◽

Vol 8 (3) ◽

pp. 9-17 ◽

Cited By ~ 2

Author(s):

Jarrod M. Thaxton ◽

Skip J. Van Bloem ◽

Stefanie Whitmire

Keyword(s):

Puerto Rico ◽

Dry Forest ◽

Exotic Grasses

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Structure and Biomass of a Subtropical Dry Forest in Puerto Rico

Biotropica ◽

10.2307/2388750 ◽

1986 ◽

Vol 18 (2) ◽

pp. 89 ◽

Cited By ~ 137

Author(s):

Peter G. Murphy ◽

Ariel E. Lugo

Keyword(s):

Puerto Rico ◽

Dry Forest

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Genetic differentiation and limited gene flow among fragmented populations of New Zealand endemic Hector’s and Maui’s dolphins

Conservation Genetics ◽

10.1007/s10592-012-0347-9 ◽

2012 ◽

Vol 13 (4) ◽

pp. 987-1002 ◽

Cited By ~ 31

Author(s):

Rebecca M. Hamner ◽

Franz B. Pichler ◽

Dorothea Heimeier ◽

Rochelle Constantine ◽

C. Scott Baker

Keyword(s):

Gene Flow ◽

New Zealand ◽

Genetic Differentiation ◽

Fragmented Populations ◽

Limited Gene Flow

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Characterization of Dry-Season Phenology in Tropical Forests by Reconstructing Cloud-Free Landsat Time Series

Remote Sensing ◽

10.3390/rs13234736 ◽

2021 ◽

Vol 13 (23) ◽

pp. 4736

Author(s):

Xiaolin Zhu ◽

Eileen H. Helmer ◽

David Gwenzi ◽

Melissa Collin ◽

Sean Fleming ◽

...

Keyword(s):

Time Series ◽

Puerto Rico ◽

Tropical Forests ◽

Tropical Dry Forest ◽

Dry Season ◽

Dry Forest ◽

High Quality ◽

Forest Zone ◽

Fine Resolution ◽

Field Plots

Fine-resolution satellite imagery is needed for characterizing dry-season phenology in tropical forests since many tropical forests are very spatially heterogeneous due to their diverse species and environmental background. However, fine-resolution satellite imagery, such as Landsat, has a 16-day revisit cycle that makes it hard to obtain a high-quality vegetation index time series due to persistent clouds in tropical regions. To solve this challenge, this study explored the feasibility of employing a series of advanced technologies for reconstructing a high-quality Landsat time series from 2005 to 2009 for detecting dry-season phenology in tropical forests; Puerto Rico was selected as a testbed. We combined bidirectional reflectance distribution function (BRDF) correction, cloud and shadow screening, and contaminated pixel interpolation to process the raw Landsat time series and developed a thresholding method to extract 15 phenology metrics. The cloud-masked and gap-filled reconstructed images were tested with simulated clouds. In addition, the derived phenology metrics for grassland and forest in the tropical dry forest zone of Puerto Rico were evaluated with ground observations from PhenoCam data and field plots. Results show that clouds and cloud shadows are more accurately detected than the Landsat cloud quality assessment (QA) band, and that data gaps resulting from those clouds and shadows can be accurately reconstructed (R2 = 0.89). In the tropical dry forest zone, the detected phenology dates (such as greenup, browndown, and dry-season length) generally agree with the PhenoCam observations (R2 = 0.69), and Landsat-based phenology is better than MODIS-based phenology for modeling aboveground biomass and leaf area index collected in field plots (plot size is roughly equivalent to a 3 × 3 Landsat pixels). This study suggests that the Landsat time series can be used to characterize the dry-season phenology of tropical forests after careful processing, which will help to improve our understanding of vegetation–climate interactions at fine scales in tropical forests.

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Low coverage genomic data resolve the population divergence and gene flow history of an Australian rain forest fig wasp

10.1101/2020.02.21.959205 ◽

2020 ◽

Author(s):

Lisa Cooper ◽

Lynsey Bunnefeld ◽

Jack Hearn ◽

James M Cook ◽

Konrad Lohse ◽

...

Keyword(s):

Gene Flow ◽

Rain Forest ◽

Sequence Data ◽

Dry Forest ◽

Whole Genome Sequence ◽

Model Organisms ◽

Eastern Coast ◽

Population Divergence ◽

Fig Wasp ◽

History Of

AbstractPopulation divergence and gene flow are key processes in evolution and ecology. Model-based analysis of genome-wide datasets allows discrimination between alternative scenarios for these processes even in non-model taxa. We used two complementary approaches (one based on the blockwise site frequency spectrum (bSFS), the second on the Pairwise Sequentially Markovian Coalescent (PSMC)) to infer the divergence history of a fig wasp, Pleistodontes nigriventris. Pleistodontes nigriventris and its fig tree mutualist Ficus watkinsiana are restricted to rain forest patches along the eastern coast of Australia, and are separated into northern and southern populations by two dry forest corridors (the Burdekin and St. Lawrence Gaps). We generated whole genome sequence data for two haploid males per population and used the bSFS approach to infer the timing of divergence between northern and southern populations of P. nigriventris, and to discriminate between alternative isolation with migration (IM) and instantaneous admixture (ADM) models of post divergence gene flow. Pleistodontes nigriventris has low genetic diversity (π = 0.0008), to our knowledge one of the lowest estimates reported for a sexually reproducing arthropod. We find strongest support for an ADM model in which the two populations diverged ca. 196kya in the late Pleistocene, with almost 25% of northern lineages introduced from the south during an admixture event ca. 57kya. This divergence history is highly concordant with individual population demographies inferred from each pair of haploid males using PSMC. Our analysis illustrates the inferences possible with genome-level data for small population samples of tiny, non-model organisms and adds to a growing body of knowledge on the population structure of Australian rain forest taxa.

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Whole genome comparisons reveal panmixia among fall armyworm (Spodoptera frugiperda) from diverse locations

10.1101/2020.09.25.314005 ◽

2020 ◽

Author(s):

Katrina A. Schlum ◽

Kurt Lamour ◽

Caroline Placidi de Bortoli ◽

Rahul Banerjee ◽

Scott J. Emrich ◽

...

Keyword(s):

United States ◽

Puerto Rico ◽

Gene Flow ◽

Spodoptera Frugiperda ◽

Fall Armyworm ◽

The United States ◽

Genomic Diversity ◽

Whole Genome ◽

Long Distance ◽

Host Strains

AbstractThe fall armyworm (Spodoptera frugiperda (J.E. Smith)) is a highly polyphagous agricultural pest with long-distance migratory behavior threatening food security worldwide. This pest has a host range of >80 plant species, but two host strains are recognized based on their association with corn (C-strain) or rice and smaller grasses (R-strain). In this study, the population structure and genetic diversity in 55 S. frugiperda samples from Argentina, Brazil, Kenya, Puerto Rico and the United States (USA) were surveyed to further our understanding of whole genome nuclear diversity. Comparisons at the genomic level suggest panmixia in this population, other than a minor reduction in gene flow between the two overwintering populations in the continental USA that also corresponded to genetically distinct host strains. Two maternal lines were detected from analysis of mitochondrial genomes. We found members from the Eastern Hemisphere interspersed within both continental USA overwintering subpopulations, suggesting multiple individuals were likely introduced to Africa. Comparisons between laboratory-reared and field collected S. frugiperda support similar genomic diversity, validating the experimental use of laboratory strains. Our research is the largest diverse collection of United States S. frugiperda whole genome sequences characterized to date, covering eight continental states and a USA territory (Puerto Rico). The genomic resources presented provide foundational information to understand gene flow at the whole genome level among S. frugiperda populations.

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