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opencc-zeroOct 2020View details →

Hidden in the DNA: insights on how multiple historical processes and natural history traits shaped patterns of cryptic diversity in an Amazon leaf-litter lizard Loxopholis osvaldoi (Squamata: Gymnophthalmidae).

Aim: To investigate cryptic diversity and diversification timing in the putatively low-dispersal Amazonian leaf-litter lizard Loxopholis osvaldoi, and to ask how geography (rivers, isolation by distance, IBD), ecological drivers (isolation by environment, IBE) and historical factors (climatic refugia) explain intraspecific genetic variation. Location: Central Amazonia, Brazil. Taxon: Squamata; Gymnophthalmidae; Loxopholis osvaldoi. Methods: We sequenced two mitochondrial and two nuclear markers in 157 individuals. Phylogeographic structure and the occurrence of independent evolving lineages where explored through phylogenetic and coalescent analyses. A species tree and divergence dates of lineages were inferred with BEAST, employing multiple DNA substitution rates. The potential genetic impacts of geographic distance among localities, the environment, and the position of localities in relation to main rivers were tested by Redundancy Analysis (RDA). Results: We detected 11 independently evolving and largely divergent intraspecific lineages. Lineage distribution patterns are complex and do not match any conspicuous barrier to gene flow, except for the Amazon River. Most lineages appear to have originated in the lower Miocene and Pliocene, in disagreement with the Pleistocene refuge hypothesis. IBD, IBE, and rivers appear to have acted in concert establishing and maintaining genetic structure. However, when controlling for other explanatory variables, IBD explains significantly more variation than rivers, IBE, or historical factors. Main conclusions: Our results strongly suggest that L. osvaldoi is a species complex. Future taxonomic work should use an integrative approach to explore whether morphological variation is present and congruent with the genetic data. While the use of a sensitive dating analysis allowed us to better describe the diversification history of L. osvaldoi, the lack of a spatial model of Neogene river dynamics prevents the test of specific, more informative river barrier hypotheses. The data suggest that non-linear correlation analyses (e.g. RDA) should be preferred to detect factors that affect phylogeographic patterns in the Amazon, instead of linear multiple regressions (e.g. Mantel tests). Given the high level of cryptic diversity detected within this and other Amazonian species, we caution against hypothesis tests based solely on the distribution of nominal taxa, which can provide a rather incomplete view of the processes behind Amazonian diversity.

opencc-zeroDec 2017View details →

Data from: Do an ecosystem engineer and environmental gradient act independently or in concert to shape juvenile plant communities? Tests with the leaf-cutter ant Atta laevigata in a Neotropical savanna

Background. Ecosystem Engineers are species that transform habitats in ways that influence other species. While the impacts of many engineers have been well described, our understanding of how their impact varies along environmental gradients remains limited. Although disentangling the effects of gradients and engineers on biodiversity is complicated – the gradients themselves can be altered by engineers – doing so is necessary to advance conceptual and mathematical models of ecosystem engineering. We used leaf-cutter ants (Atta spp.) to investigate the relative influence of gradients and environmental engineers on the abundance and species richness of woody plants. Methods. We conducted our research in South America's Cerrado. With a survey of plant recruits along a canopy cover gradient, and data on environmental conditions that influence plant recruitment, we fit statistical models that addressed the following questions: (1) Does A. laevigata modify the gradient in canopy cover found in our Cerrado site? (2) Do environmental conditions that influence woody plant establishment in the Cerrado vary with canopy cover or proximity to A. laevigata nests? (3) Do A. laevigata and canopy cover act independently or in concert to influence recruit abundance and species richness? Results. We found that environmental conditions previously shown to influence plant establishment in the Cerrado varied in concert with canopy cover, but that ants are not modifying the cover gradient or cover over nests. However, ants are modifying other local environmental conditions, and the magnitude and spatial extent of these changes is consistent across the gradient. In contrast to prior studies, we found that ant-related factors (e.g., proximity to nests, ant changes in surface conditions), rather than canopy cover, had the strongest effect on the abundance of plant recruits. However, the diversity of plants was influenced by both the engineer and the canopy cover gradient. Discussion. Atta laevigata in the Cerrado modify local conditions in ways that have strong but spatially restricted consequences for plant communities. We hypothesize that ants indirectly reduce seedling establishment by clearing litter and reducing soil moisture, which leads to seed and seedling desiccation. Altering soil nutrients could also reduce juvenile growth and survivorship; if so these indirect negative effects of engineering could exacerbate their direct effects of harvesting plants. The effects of Atta appear restricted to nest mounds, but they could be long-lasting because mounds persist long after a colony has died or migrated. Our results support the hypothesis that leaf-cutter ants play a dominant role in Cerrado plant demography. We suggest the ecological and economic footprint of these engineers may increase dramatically in coming decades due to the transformation of the Cerrado by human activities.

opencc-zeroDec 2017View details →

Data from: Vertical canopy gradient shaping the stratification of leaf-chewer-parasitoid interactions in a temperate forest

Knowledge about herbivores and their parasitoids in forest canopies remains limited, despite their diversity and ecological importance. Thus, it is important to understand the factors that shape the herbivore–parasitoid community structure, particularly the effect of vertical gradient. We investigated a quantitative community dataset of exposed and semiconcealed leaf‐chewing larvae and their parasitoids along a vertical canopy gradient in a temperate forest. We sampled target insects using an elevated work platform in a 0.2 ha broadleaf deciduous forest plot in the Czech Republic. We analyzed the effect of vertical position among three canopy levels (first [lowest], second [middle], and third [highest]) and tree species on community descriptors (density, diversity, and parasitism rate) and food web structure. We also analyzed vertical patterns in density and parasitism rate between exposed and semiconcealed hosts, and the vertical preference of the most abundant parasitoid taxa in relation to their host specificity. Tree species was an important determinant of all community descriptors and food web structure. Insect density and diversity varied with the vertical gradient, but was only significant for hosts. Both host guilds were most abundant in the second level, but only the density of exposed hosts declined in the third level. Parasitism rate decreased from the first to third level. The overall parasitism rate did not differ between guilds, but semiconcealed hosts suffered lower parasitism in the third level. Less host‐specific taxa (Ichneumonidae, Braconidae) operated more frequently lower in the canopy, whereas more host‐specific Tachinidae followed their host distribution. The most host‐specific Chalcidoidea preferred the third level. Vertical stratification of insect density, diversity, and parasitism rate was most pronounced in the tallest tree species. Therefore, our study contradicts the general paradigm of weak arthropod stratification in temperate forest canopies. However, in the network structure, vertical variation might be superseded by variation among tree species.

opencc-zeroDec 2012View details →

Data from: A modern ampelography: a genetic basis for leaf shape and venation patterning in Vitis vinifera

Terroir, the unique interaction between genotype, environment, and culture, is highly refined in domesticated grape, Vitis vinifera. Towards cultivating terroir, the science of ampelography tried to distinguish thousands of grape cultivars, without the aid of genetics. This led to sophisticated phenotypic analyses of natural variation in grape leaves, which within a palmate-lobed framework exhibit diverse patterns of blade outgrowth, hirsuteness, and venation patterning. Here, we provide a morphometric analysis of >1,200 V. vinifera accessions. Elliptical Fourier Descriptors provide a global analysis of leaf outlines and lobe positioning, while a Procrustes analysis quantitatively describes venation patterning. Correlation with previous ampelography suggests an important genetic component, which we confirm with estimates of heritability. We further use RNA-Seq of mutant varieties and perform a Genome-Wide Association Study (GWAS) to explore the genetic basis of leaf shape. Meta-analysis reveals a relationship between leaf morphology and hirsuteness, traits known to correlate with climate in the fossil record and extant species. Together, our data demonstrate a genetic basis for the intricate diversity present in grape leaves. We discuss the possibility of using grape leaves as a breeding target to preserve terroir in the face of anticipated climate change, a major problem facing viticulture.

FIGURE 6 in Taxonomy and biology of a new ambrosia gall midge Daphnephila urnicola sp. nov. (Diptera: Cecidomyiidae) inducing urn-shaped leaf galls on two species of Machilus (Lauraceae) in Taiwan

FIGURE 6. Diapausing first instar larva of Daphnephila urnicola sp.nov. in the leaf tissue of undeveloped galls on Machilus zuihoensis. A. the appearance of the adaxial surface of the leaf with first instar larva inside. B. cross section of leaf tissues showing initial gall with larval chamber and fungi. L= Larva, LC= larval chamber, and arrow= hyphae.

FIGURE 10 in Taxonomy and biology of a new ambrosia gall midge Daphnephila urnicola sp. nov. (Diptera: Cecidomyiidae) inducing urn-shaped leaf galls on two species of Machilus (Lauraceae) in Taiwan

FIGURE 10. Pictures showing opening area of mature galls of Daphnephila urnicola sp.nov. A–B. Apex of gall (longitudinal section) on Machilus zuihoensis (A, Bar = 80Μm) and on M. mushaensis (B, Bar = 180Μm), LC= larval chamber, NC= nutritive cell, S= secretory cell.. C–D. Longitudinal section of entire gall on Machilus zuihoensis (C) and on M. mushaensis (D); E–F. emergence hole and pupa skin on M. zuihoensis gall (E) and on M. mushaensis gall (F).

FIGURE 1 in Taxonomy and biology of a new ambrosia gall midge Daphnephila urnicola sp. nov. (Diptera: Cecidomyiidae) inducing urn-shaped leaf galls on two species of Machilus (Lauraceae) in Taiwan

FIGURE 1. Similar urn-shaped galls (mature phase) induced by D. urnicola sp.nov. on the leaves of two different species of Machilus (Lauraceae). A. M. zuihoensis. B. M. mushaensis.

FIGURE 5 in Taxonomy and biology of a new ambrosia gall midge Daphnephila urnicola sp. nov. (Diptera: Cecidomyiidae) inducing urn-shaped leaf galls on two species of Machilus (Lauraceae) in Taiwan

FIGURE 5. Strict consensus tree of Daphnephila species relationships based on COI gene data. Three equally parsimonious trees were acquired (length: 223). Bootstrap values greater than 50% for the MP inference, and the neighbor-joining (NJ) method, are shown above and below the branch, respectively. Individual specimens of D. urnicola collected from Machilus mushaensis and M. zuihoensis are labeled with M and Z in parentheses, respectively.

FIGURE 9. A in Taxonomy and biology of a new ambrosia gall midge Daphnephila urnicola sp. nov. (Diptera: Cecidomyiidae) inducing urn-shaped leaf galls on two species of Machilus (Lauraceae) in Taiwan

FIGURE 9. A. Dashed line showing plane of transverse section in B. B. Basal part of urn-shaped gall tissues on Machilus zuihoensis induced by Daphnephila urnicola sp.nov. at the later stage of the growth and differentiation phase (cross section). Bar = 50 Μm. LC= larval chamber, SC= sclerenchyma cells, P= parenchyma layer, V= vascular bundles, arrow= hyphae.

FIGURE 8 in Taxonomy and biology of a new ambrosia gall midge Daphnephila urnicola sp. nov. (Diptera: Cecidomyiidae) inducing urn-shaped leaf galls on two species of Machilus (Lauraceae) in Taiwan

FIGURE 8. Tissue of urn-shaped galls on Machilus zuihoensis induced by Daphnephila urnicola sp.nov. at the middle stage of growth and differentiation phase (longitudinal section). Bar = 500 Μm. L= Larva, LC= larval chamber, PT= plant tissue suberized, V= vascular tissue, arrow= secretory cells.

FIGURE 7 in Taxonomy and biology of a new ambrosia gall midge Daphnephila urnicola sp. nov. (Diptera: Cecidomyiidae) inducing urn-shaped leaf galls on two species of Machilus (Lauraceae) in Taiwan

FIGURE 7. Development of urn-shaped galls on Machilus zuihoensis and M. mushaensis at various stages of growth and differentiation phase. A. early stage, on Machilus zuihoensis. B. early stage, on M. mushaensis. C. middle stage, on M. zuihoensis. D. middle stage, on M. mushaensis. E. later stage, on M. zuihoensis. F. later stage, on M. mushaensis. Arrows= suberized host tissue.

FIGURE 2 in Taxonomy and biology of a new ambrosia gall midge Daphnephila urnicola sp. nov. (Diptera: Cecidomyiidae) inducing urn-shaped leaf galls on two species of Machilus (Lauraceae) in Taiwan

FIGURE 2. Map of Taiwan showing collecting sites of urn-shaped galls induced by Daphnephila urnicola sp.nov. on M. zuihoensis and on M. mushaensis. D site with only M. zuihoensis population, ● site with both M. zuihoensis and M. mushaensis populations, Δ site with only M. mushaensis population.

FIGURE 4 in Taxonomy and biology of a new ambrosia gall midge Daphnephila urnicola sp. nov. (Diptera: Cecidomyiidae) inducing urn-shaped leaf galls on two species of Machilus (Lauraceae) in Taiwan

FIGURE 4. Daphnephila urnicola sp. nov. A. female head, frontal view, scale bar= 0.6mm. B. male flagellomeres 8–12, scale bar= 0.25mm. C. female flagellomeres 7–12, scale bar= 0.25mm. D. male flagellomere 5, scale bar= 0.05mm. E. male palpus, scale bar= 0.05mm. F. male hind tarsal claw and empodium, scale bar= 0.04mm. G. male terminalia, dorsal view, scale bar= 0.1mm. H. larva, sternal spatula and adjacent papillae, ventral view, scale bar= 0.05mm. I. pupa, head, frontal view, scale bar= 0.25mm.

FIGURE 11. Female terminalia showing the pouch structure, a in Taxonomy and biology of a new ambrosia gall midge Daphnephila urnicola sp. nov. (Diptera: Cecidomyiidae) inducing urn-shaped leaf galls on two species of Machilus (Lauraceae) in Taiwan

FIGURE 11. Female terminalia showing the pouch structure, a mycangium-like fungal spore-carrying organ, of Daphnephila urnicola sp. nov. The structure is covered by an enlarged sheath on the 7th abdominal sternite. A. Lateral view, scale bar= 0.5 mm. B. Ventral-lateral view, scale bar= 0.5 mm. P= pouch and SS= seventh sternite.

opennotspecifiedJul 2022View details →

FIGURE. Drosera hirtella (a–i): a, b, c, habit of the "type morphotype"; d, habit of the "western morphotype"; e, rosette of the "type morphotype"; f, emerging inflorescence, highlighting the red scape with red eglandular trichomes characteristic of the species; g, fertile individuals of D. hirtella (left plant, with inflorescence emerging to the bottom) and D. lutescens (right plant, with inflorescence emerging to the top left) growing under shaded conditions side by side, highlighting the morphological differences between the two species regarding leaf shape and scape and indumentum color; h, i, flower. a–c, f and h at Serra do Cipó, MG; d and h at Chapada dos Veadeiros, GO; e at Diamantina, MG; g at Cristalina, GO. Photo credits: all by PMG. in A synopsis of the genus Drosera (Droseraceae) in Brazil

FIGURE. Drosera hirtella (a–i): a, b, c, habit of the "type morphotype"; d, habit of the "western morphotype"; e, rosette of the "type morphotype"; f, emerging inflorescence, highlighting the red scape with red eglandular trichomes characteristic of the species; g, fertile individuals of D. hirtella (left plant, with inflorescence emerging to the bottom) and D. lutescens (right plant, with inflorescence emerging to the top left) growing under shaded conditions side by side, highlighting the morphological differences between the two species regarding leaf shape and scape and indumentum color; h, i, flower. a–c, f and h at Serra do Cipó, MG; d and h at Chapada dos Veadeiros, GO; e at Diamantina, MG; g at Cristalina, GO. Photo credits: all by PMG.

opennotspecifiedJan 2015View details →

FIGURE 1. Oreocharis tsaii. A. Habit. B. Leaf. C–F. Corolla shapes. G–J. Opened corolla showing stamens and staminode. K–L. Calyx. M. Pistil. N in Oreocharis tsaii, a new species of Gesneriaceae from southern Yunnan, China

FIGURE 1. Oreocharis tsaii. A. Habit. B. Leaf. C–F. Corolla shapes. G–J. Opened corolla showing stamens and staminode. K–L. Calyx. M. Pistil. N. Capsule. Photographed by Yun-Hong Tan.