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Fig. 8 in Taxonomic implications of describing a new species of Loimia (Annelida, Terebellidae) with two size-dependent morphotypes

Fig. 8. Phylogenetic reconstruction after Maximum Likelihood analyses of the cox1 fragment. Bootstrap support values (BS) above nodes.

Fig. 3 in Taxonomic implications of describing a new species of Loimia (Annelida, Terebellidae) with two size-dependent morphotypes

Fig. 3. Loimia davidi sp. nov., holotype (CEAB A.P. 935A), preserved. A–C. Chaetae from chaetiger 11. A. Alimbate capillary chaeta. B. Unilimbate capillary chaeta. C. Bilimbate capillary chaeta. — D–G. Chaetiger 12. D. Ventro-lateral section of thoracic parapodium. E. Uncini of the same, arranged in two rows, back to back. F. Single thoracic uncinus of the same. G. Detail of the uncinal growing region of the same. — H–I. Segment 25. H. Abdominal parapodium (arrow pointing to uncinal growing zone). I. Single abdominal uncinus of the same.

Fig. 1 in Taxonomic implications of describing a new species of Loimia (Annelida, Terebellidae) with two size-dependent morphotypes

Fig. 1. Loimia davidi sp. nov., holotype (CEAB A.P. 935A), living. A. Entire body in two fragments. B. Thorax and anterior abdomen, lateral view. C. Thorax, ventral view. D. Fragment of tube.

Fig. 6 in Taxonomic implications of describing a new species of Loimia (Annelida, Terebellidae) with two size-dependent morphotypes

Fig. 6. Loimia davidi sp. nov., paratype MNCN 16.01/19140. A. Alimbate capillary chaeta. B. Unilimbate capillary chaeta. C. Position of the thoracic uncini from segment 10. D. Single thoracic uncinus from segment 10 (thorax). E. Single abdominal uncinus from segment 22 (abdomen).

Fig. 7 in Taxonomic implications of describing a new species of Loimia (Annelida, Terebellidae) with two size-dependent morphotypes

Fig. 7. Loimia gigantea (Montagu, 1819), ARC-Loimia-IND2. A. Dorsolateral section of thoracic neuropodium 12, showing the uncinal growing zone (black arrow). B. View of entire abdominal neuropodium 4. C. Detail of the uncinal arrangement of abdominal neuropodium 4. D. Uncinus from thoracic neuropodium 8. E. Uncinus from abdominal neuropodium 4.

opencc-zeroAug 2022View details →

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Larval dispersal patterns and connectivity of Acropora on Florida's Coral Reef and its implications for restoration

Since the 1980s, populations of Acropora cervicornis and A. palmata have experienced severe declines due to disease and anthropogenic stressors; resulting in their listing as threatened, and their need for restoration. In this study, larval survival and competency data were collected and used to calibrate a very high-resolution hydrodynamic model (up to 100m) to determine the dispersal patterns of Acropora species along the Florida's Coral Reef. The resulting connectivity matrices was incorporated into a metapopulation model to compare strategies for restoring Acropora populations. This study found that Florida's Coral Reef was historically a well-connected system, and that spatially selective restoration may be able to stimulate natural recovery. Acropora larvae are predominantly transported northward along the Florida's Coral Reef, however southward transport also occurs, driven by tides and baroclinic eddies. Local retention and self-recruitment processes were strong for a broadcast spawner with a long pelagic larval duration. Model simulations demonstrate that it is beneficial to spread restoration effort across more reefs, rather than focusing on a few reefs. Differences in population patchiness between the Acropora cervicornis and A. palmata drive the need for different approaches to their management plans. This model can be used as a tool to address the species-specific management to restore genotypically diverse Acropora populations on the Florida's Coral Reef, and its methods could be expanded to other vulnerable populations.

opencc-by-4.0Aug 2022View details →

Data depository - "Quantifying the effect of wind on volcanic plumes: implications for plume modelling"

This depository contains all data to understand, evaluate, and build upon the research reported in the manuscript: "Quantifying the effect of wind on volcanic plumes: implications for plume modelling", submitted to Journal of Geophysical Research. Abstract The considerable effects that wind can have on estimates of mass eruption rates (MERs) in explosive eruptions based on volcanic plume height are well known but difficult to quantify rigorously. Many explicitly wind-affected plume models have the additional difficulty that they require the use of centerline heights of bent-over plumes, a parameter not easily obtained directly from observational data. We tested two such models by using the time series of varying plume heights and wind speeds of the 2010 Eyjafjallajökull eruption. The mapped fallout and photos taken during this eruption allow us to estimate the plume geometry and to empirically constrain input parameters for the two models tested. Two strategies are presented to correct the difference in maximum plume height and centerline height: (i) based on plume radius, and (ii) by using the plume type parameter ∏, which quantifies the relative influence of buoyancy and cross-wind on the plume dynamics, to discriminate weak, intermediate and strong plumes. The results indicate that it may be more appropriate to classify plumes as either wind-dominated, intermediate or buoyancy-dominated, where the relative effects of both wind and MER define the type. The analysis of the Eyjafjallajökull data shows that the MER estimates from both models are considerably improved when a plume-type dependent centreline-correction is applied and the wind entrainment coefficient β is refined. For this particular eruption, we find that the best value for β lies between 0.22 and 0.34, unlike previous suggestions that set this parameter to 0.50.

opencc-by-4.0Oct 2020View details →

The cost of self-promotion: Ecological and demographic implications of the mentor effect in natural Taraxacum populations

This data accompanies the pending publication "The cost of self-promotion: Ecological and demographic implications of the mentor effect in natural Taraxacum populations" by Lynn et al. The work is also published under Austin Lynn's PhD Dissertation, which is under embargo until 2022.

opencc-by-4.0Feb 2022View details →

Alternative splicing and genetic variation of MHC-E: Implications for rhesus cytomegalovirus-based vaccines

We used long-read sequencing to interrogate rhesus macaque (RM) MHC-E (Mamu-E) alternative splicing and genetic variations. Full-length Mamu-E RNA isoforms were recovered using the PacBio Iso-Seq method. Incomplete 5' ends of Mamu-E isoforms were confirmed using Sanger sequencing, where we identified three additional isoforms. Full-length human MHC-E (HLA-E) isoforms were also recovered using the PacBio Iso-Seq method. Isoform sequences and annotations are provided for both Mamu-E and HLA-E in addition to Mamu-E Sanger sequencing data. HLA-E annotations are reported using the hg38 reference, while Mamu-E annotations are shown using rhesus MHC Class I and II assemblies previously generated using Bacterial Artificial Cloning (BAC) technology (https://www.ncbi.nlm.nih.gov/nuccore/AC148696.1). Using PacBio Long Amplicon Analysis, we sequenced complete Mamu-E coding regions of 59 RMs and additionally captured 3' UTR polymorphism using mRNA-seq haplotype phasing analysis. The complete genotyping data for these animals are provided as well as animal metadata. Genotyping data is shown using the Mamu-E canonical isoform (Mamu-E1 from Iso-Seq analysis) as reference.

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Vegetation and vantage point influence visibility across diverse ecosystems: implications for animal ecology

Visual information can influence animal behavior and habitat use in diverse ways. Visibility is the property that relates 3D habitat structure to accessibility of visual information. Despite the importance of visibility in animal ecology, this property remains largely unstudied. Our objective was to assess how habitat structure from diverse environments and animal position within that structure can influence visibility. We gathered terrestrial lidar data (1 cm at 10 m) in four ecosystems (forest, shrub-steppe, prairie, and desert) to characterize viewsheds (i.e., estimates of visibility based on spatially explicit sightlines) from multiple vantage points. Both ecosystem-specific structure and animal position influenced potential viewsheds. Generally, as height of the vantage point above the ground increased, viewshed extent also increased, but the relationships were not linear. In low-structure ecosystems (prairie, shrub-steppe, and desert), variability in viewsheds decreased as vantage points increased to heights above the vegetation canopy. In the forest, however, variation in viewsheds was highest at intermediate heights, and markedly lower at the lowest and highest vantage points. These patterns are likely linked to the amount, heterogeneity, and distribution of vegetation structure occluding sightlines. Our work is the first to apply a new method that can be used to estimate viewshed properties relevant to animals (i.e., viewshed extent and variability). We demonstrate that these properties differ across terrestrial landscapes in complex ways that likely influence many facets of animal ecology and behavior.

Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa

In order to uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood (Populus trichocarpa) from much of its range in western North America. Extensive data from large-scale trait phenotyping (with spatial and temporal replications within a common garden) and genotyping (with a 34 K Populus single nucleotide polymorphism (SNP) array) of all accessions were used for gene discovery in a genome-wide association study (GWAS). We performed GWAS with 40 biomass, ecophysiology and phenology traits and 29 355 filtered SNPs representing 3518 genes. The association analyses were carried out using a Unified Mixed Model accounting for population structure effects among accessions. We uncovered 410 significant SNPs using a Bonferroni-corrected threshold (P < 1.7 × 10−6). Markers were found across 19 chromosomes, explained 1–13% of trait variation, and implicated 275 unique genes in trait associations. Phenology had the largest number of associated genes (240 genes), followed by biomass (53 genes) and ecophysiology traits (25 genes). The GWAS results propose numerous loci for further investigation. Many traits had significant associations with multiple genes, underscoring their genetic complexity. Genes were also identified with multiple trait associations within and/or across trait categories. In some cases, traits were genetically correlated while in others they were not.

Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa

FIG. 21 in Fossil wood from the lower Miocene of Myanmar (Natma Formation): palaeoenvironmental and biogeographic implications

FIG. 21. — Comparison between Eocene (Licht et al. 2014, 2015) and Miocene (this study) forest assemblage and diversity of Myanmar with the list of related fossil genera and supposed forest types they belong to. Underlined names are genera found in both formations. Yellow stars mark the schematic position of sampling sites.

FIG. 16 in Fossil wood from the lower Miocene of Myanmar (Natma Formation): palaeoenvironmental and biogeographic implications

FIG. 16. — Shoreoxylon cf. sumatraense Du, MNHN.F.50193: A, Ts, vessel often in groups, sometimes in clusters (arrows); B, Ts, long tangential lines of secretory canals (arrows) close to each other; C, D, Tls, 1-4-seriate rays; E, Tls, 3-seriate rays with a uniseriate row of six marginal cells (white arrow), abundant parenchyma (black arrow), 4-8 cells per strand; F, Rls, vessel-ray pits irregular in shape, simple with reduced borders (arrows); G, Ts, synthetic drawing of the transversal section (with only some vessels and rays displayed), visible bands of parenchyma as grey lines and recognized secretory canals as red dots, arranged mostly in long and closely spaced tangential lines; H, Rls, vasicentric tracheids (arrows); I, Rls, heterocellular ray with square or upright marginal cells (arrows). Scale bars: G, 1 cm; A, 1 mm; C, 500 µm; B, 330 µm; D, I, 200 µm; E, H, 100 µm; F, 50 µm. Abbreviations: see Fig. 2.

FIG. 13 in Fossil wood from the lower Miocene of Myanmar (Natma Formation): palaeoenvironmental and biogeographic implications

FIG. 13. — Dryobalanoxylon cf. javanense (Kräusel) Den Berger, MNHN.F.50190: A, Ts, Vessels seemingly exclusively solitary and long tangential line of secretory canals embedded in parenchyma bands (between arrows); B, Ts, synthetic drawing of the transversal section (with only some vessels and rays displayed); visible bands of parenchyma as grey lines and secretory canals as red dots, arranged mostly in long tangential lines; C, Ts, tyloses in vessels (arrow); D, Tls 1-6 seriate rays with some sheath cells (white arrows), vasicentric tracheids (black arrows) and fibre-tracheids (grey arrow); E, Ts, detail of secretory canals embedded in tangential bands of parenchyma; F, Rls, simple vessel-ray pits with reduced borders in irregular shapes; G, Rls, silica bodies (?) in ray cells; H, Rls, heterocellular ray with mostly 1-4 rows of square or upright marginal cells. Scale bars: B, 1 cm; A, 1 mm; C-E, H, 200 µm; F-G, 50 µm.

FIG. 12 in Fossil wood from the lower Miocene of Myanmar (Natma Formation): palaeoenvironmental and biogeographic implications

FIG. 12. — Dipterocarpoxylon cf. jammuense Guleria, Gupta & Srivastava, MNHN.F.50189: A, Ts, seemingly exclusively solitary vessels, vasicentric parenchyma, small pores interpreted as solitary secretory canals or in short lines (arrows); B, D, Ts, short lines of secretory canals (arrows); C, Tls, 1-6-seriate rays, with rows of uniseriate marginal cells up to 19 cells, frequent uniseriate rays and sheath cells present (arrow); E, Ts, vessel puggled with tyloses, surrounded par vasicentric parenchyma (black arrow), secretory canals solitary or in short lines, surrounded by parenchyma (white arrow); F, Rls, heterocellular rays with square or upright cells (black arrow) and procumbent cells (white arrow) mixed throughout the rays because of the presence of sheath cells, uniseriate rays and long row of marginal cells; G, Tls, vasicentric tracheids (arrow). Scale bars: A, B, 1 mm; C-F, 200 µm; G, 100 µm. Abbreviations: see Fig. 2.

FIG. 11 in Fossil wood from the lower Miocene of Myanmar (Natma Formation): palaeoenvironmental and biogeographic implications

FIG. 11. — Anisopteroxylon sp., MNHN.F.50188: A, Ts, strongly compressed wood, poorly distinguishable vessels, seemingly exclusively solitary, small pores that could be solitary secretory canals (arrows); B, Tls, simple perforation plates, vasicentric tracheids (arrows); C, D, Tls, 1-7-seriate rays with continuous sheath cells all around multiseriate rays (arrow); E, Rls, heterocellular rays with procumbent cells in median portion (white arrow) and square or upright marginal cells (black arrow), sometimes appearing with both types mixed due to sheath cells; F, Rls, silica bodies (?) in ray cells. Scale bars: A, C, 500 µm; B, D-E, 200 µm; F, 100 µm. Abbreviations: see Fig. 2.

FIG. 14 in Fossil wood from the lower Miocene of Myanmar (Natma Formation): palaeoenvironmental and biogeographic implications

FIG. 14. — Dryobalanoxylon sp., MNHN.F.50191: A, Ts, mostly solitary vessels and vasicentric to slightly aliform parenchyma, short line of secretory canals embedded in long tangential bands of parenchyma; B, Ts, synthetic drawing of the transversal section (with only some vessels and rays displayed), visible bands of parenchyma as grey lines and recognized secretory canals as red dots; C, Tls, vasicentric tracheids (arrows); D, Tls, simple perforation plates (arrows), 2-4 seriate homocellular to weakly heterocellular rays with a storied tendency at some places (segments); E, Tls, detail of a 4-seriate ray; F, Rls, heterocellular ray with one row of square marginal cells (arrow); G, Ts, solitary vessels with tyloses and surrounded by vasicentric to slightly aliform parenchyma. Scale bars: B, 1 cm; A, 500 µm; D, 250µm; F-G, 200 µm; C, E, 100 µm. Abbreviations: see Fig. 2.

FIG. 8 in Fossil wood from the lower Miocene of Myanmar (Natma Formation): palaeoenvironmental and biogeographic implications

FIG. 8. — Pahudioxylon bankurensis Chowdhury, Ghosh & Kazmi, MNHN.F.50183: A, Ts, solitary vessels or in radial multiples of 2-4, aliform parenchyma with marginal crystals (black arrow) and marginal parenchyma (white arrow); B, Ts, detail of aliform parenchyma with crystals in marginal cells; C, Tls, alternate intervessel pits, probably vestured (arrow); D, Tls, rays with storied tendency (arrows); E, Tls, 2-3 seriate, not storied rays with crystalliferous parenchyma (black arrow), strand of parenchyma made of 4 cells (white arrow); F, Rls, homocellular ray; G, Rls, sometimes but rarely crystals in marginal ray cells (arrow). Scale bars: A, 1 mm; D, 500 µm; B, E, 200 µm; F-G, 150 µm; C, 20 µm. Abbreviations: see Fig. 2.

FIG. 9 in Fossil wood from the lower Miocene of Myanmar (Natma Formation): palaeoenvironmental and biogeographic implications

FIG. 9. — Pahudioxylon cf. bankurensis Chowdhury, Ghosh & Kazmi, MNHN.F.50184: A, Ts, mostly solitary vessels, aliform parenchyma with crystals in marginal cells (black arrow), marginal parenchyma (bottom) and diffuse parenchyma (white arrow); B, Ts, detail of diffuse parenchyma (white arrow), often in contact with rays; C, Tls, storied rays in some parts of the section; D, Tls, 1-3-seriate homocellular rays in a non-storied part of the section; E, Rls, crystals in parenchyma strands, the strand on the left being diffuse parenchyma; F, Rls, homocellular ray; G, Tls, alternate intervessel pits, apparently vestured. Scale bars: A, 1 mm; C, 500 µm; B, D-E, 200 µm; F, 100 µm; G, 50 µm. Abbreviations: see Fig. 2.