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opencc-zeroJan 2023View details →

Whole genome demographic models indicate divergent effective population size histories shape contemporary genetic diversity gradients in a montane bumble bee

Understanding historical range shifts and population size variation provides important context for interpreting contemporary genetic diversity. Methods to predict changes in species distributions and model changes in effective population size (Ne) using whole genomes make it feasible to examine how temporal dynamics influence diversity across populations. We investigate Ne variation and climate-associated range shifts to examine the origins of a previously observed latitudinal heterozygosity gradient in the bumble bee Bombus vancouverensis Cresson (Hymenoptera: Apidae: Bombus Latreille) in western North America. We analyze whole genomes from a latitude-elevation cline using sequentially Markovian coalescent models of Ne through time to test whether relatively low diversity in southern high-elevation populations is a result of long-term differences in Ne. We use Maxent models of the species range over the last 130,000 years to evaluate range shifts and stability. Ne fluctuates with climate across populations, but more genetically diverse northern populations have maintained greater Ne over the late Pleistocene and experienced larger expansions with climatically favorable time periods. Northern populations also experienced larger bottlenecks during the last glacial period which matched the loss of range area near these sites, however, bottlenecks were not sufficient to erode diversity maintained during periods of large Ne. A genome sampled from an island population indicated a severe postglacial bottleneck, indicating that large recent post-glacial declines are detectable if they have occurred. Genetic diversity was not related to niche stability or glacial-period bottleneck size. Instead, spatial expansions and increased connectivity during favorable climates likely maintain diversity in the north while restriction to high elevations maintains relatively low diversity despite greater stability in southern regions. Results suggest genetic diversity gradients reflect long-term differences in Ne dynamics and also emphasize the unique effects of isolation on insular habitats for bumble bees. Patterns are discussed in the context of conservation under climate change.

FIG. 3 in Changes in functional and taxonomic diversity and composition of corticolous lichens in an altitudinal gradient in Colombia

FIG. 3. — Lichen diversity and vegetation richness in the Chocó region of Valle del Cauca, Colombi: A, mean and standard error for alpha lichen diversity along the altitudinal gradient; B, mean and standard error for alpha lichen diversity by locality and microhabitat; C, beta lichen diversity; D, total lichen species richness (observed and rarefied) by locality.

FIG. 1 in Changes in functional and taxonomic diversity and composition of corticolous lichens in an altitudinal gradient in Colombia

FIG. 1. — Map of the department of Valle del Cauca, Colombia, showing the sampling points: Δ, Chucheros; Z, Pericos; •, El Queremal; O, Cerro El Inglés; ^, Pico Pance.

FIG. 5. — A in Changes in functional and taxonomic diversity and composition of corticolous lichens in an altitudinal gradient in Colombia

FIG. 5. — A, non-metric multidimensional scaling for composition of lichen species along the gradient (Stres=0.21); B, detrended correspondence analysis for the lichen functional traits along the gradient. In both graphs there is a clear separation between elevations, showing a gradient of species composition and functional traits along the altitudinal gradient. Locations: z, Alto Pance; +, Cerro El Inglés; X, El Queremal; •, Pericos; , Chucheros.

FIG. 2 in Changes in functional and taxonomic diversity and composition of corticolous lichens in an altitudinal gradient in Colombia

FIG. 2. — Number of species of the lichen families with higher diversity at each locality in the Chocó region of Valle del Cauca, Colombia.

FIG. 6 in Changes in functional and taxonomic diversity and composition of corticolous lichens in an altitudinal gradient in Colombia

FIG. 6. — Community Weighted Means (CWMs) of functional lichen traits along the altitudinal gradient in the Chocó region of Valle del Cauca, Colombia: A, crustose thallus; B, crustose thallus by microhabitat; C, foliose thallus; D, fruticose thallus; E, fruticose thallus by microhabitat; F, rhizines by microhabitat; G, cyanobacterial photobiont; H, vegetative propagules; I, ascoma; J, ascospore septation (septate, muriform and simple); K, thickness of the ascospore wall; L, size of the ascospores.

FIG. 7 in Changes in functional and taxonomic diversity and composition of corticolous lichens in an altitudinal gradient in Colombia

FIG. 7. — Functional diversity along the altitudinal gradient: A, relative Rao Index; B, functional Dominance.

FIG. 4 in Changes in functional and taxonomic diversity and composition of corticolous lichens in an altitudinal gradient in Colombia

FIG. 4. — Scatter plot for the alpha lichen diversity and tree density ratio in each study site in the Chocó region of Valle del Cauca, Colombia.

opencc-zeroAug 2023View details →

There and back to the present: a model-based framework to estimate phylogenetically constrained alpha diversity gradients

The imprint left by niche evolution on the variation of biological diversity across spatial and environmental gradients is still debated among ecologists. Furthermore, understanding to what extent dispersal limitation may reinforce or blur such an imprint is still a gap in our ecological knowledge. In this article we introduce a simulation approach coupled to Approximate Bayesian Computation (ABC) that parameterizes both the adaptation rate of species' niche positions over the evolution of a monophyletic lineage and the intensity of dispersal limitation associated with the variation of species alpha diversity among assemblages distributed across spatial and environmental gradients. The analytical tool was implemented in the R package mcfly. We evaluated the statistical performance of the analytical framework using simulated datasets, which confirmed the suitability of the analysis to estimate the adaptation rate parameter but showed to be less precise in relation to the dispersal limitation parameter. Also, we found that increased dispersal limitation levels improved the parameterization of the adaptation rate of species' niche positions in simulated datasets. Further, we evaluated the role played by niche evolution and dispersal limitation on species alpha diversity variation of Phyllostomidae bats across the Neotropics. The framework proposed here sheds light on the links between niche evolution, dispersal limitation and gradients of biological diversity, and thereby improved our understanding of evolutionary imprints on current biological diversity patterns.

opencc-by-4.0Aug 2023View details →

Replication Data for: "Marine latitudinal diversity gradients are generally absent in intertidal ecosystems"

Datasets used in the paper "Marine latitudinal diversity gradients are generally absent in intertidal ecosystems"

opencc-zeroSep 2023View details →

R codes from: Breakdown of the growth–mortality trade-off along a soil phosphorus gradient in diverse neotropical forest

An ecological paradigm predicts that plant species adapted to low resource availability grow slower and live longer than those adapted to high resource availability when growing together. We tested this by using hierarchical Bayesian analysis to quantify variations in growth and mortality of ~ 40,000 individual trees from > 400 species in response to limiting resources in the tropical forests of Panama. In contrast to theoretical expectations of the growth–mortality paradigm, we find that tropical tree species restricted to low-phosphorus soils simultaneously achieve faster growth rates and lower mortality rates than species restricted to high-phosphorus soils. This result demonstrates that adaptation to phosphorus limitation in diverse plant communities modifies the growth–mortality trade-off, with important implications for understanding long-term ecosystem dynamics.

opencc-by-4.0Dec 2015View details →

Fig. 1. SEM photos showing c.f in Latitudinal Diversity Gradients in Free-living Microorganisms - Hoogenraadia a Key Genus in Testate Amoebae Biogeography

Fig. 1. SEM photos showing c.f. Hoogenraadia humicola found from soils in Shennongjia Mountains of central China (the left picture is from Qin et al. 2011). This was previously identified as Planhoogenraadia africana by Qin et al. (2011). Scale bars: 50 µm (a) and 20 µm (b).

opencc-by-4.0Dec 2015View details →

Fig. 3 in Latitudinal Diversity Gradients in Free-living Microorganisms - Hoogenraadia a Key Genus in Testate Amoebae Biogeography

Fig. 3. Relationship between shell width and shell length of each species of the genus Hoogenraadia. The sample sizes on which these measurements are based is unclear as the older literature often doesn't specify the number of tests measured (see Table 1).

opencc-by-4.0Dec 2015View details →

Fig. 2 in Latitudinal Diversity Gradients in Free-living Microorganisms - Hoogenraadia a Key Genus in Testate Amoebae Biogeography

Fig. 2. Shell outline and SEM photos of six species of genus Hoogenraadia Gauthier-Lièvre and Thomas 1958, with scale bar 50 μm. a – H. cryptostoma Gauthier-Lièvre and Thomas 1958; b – H. sylvatica Vucetich 1974; c – H. africana Gauthier-Lièvre and Thomas 1958; d – H. humicola Bonnet 1976; e – H. ovata Bonnet 1976; f – H. asiatica Wang and Min 1987.