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opennotspecifiedOct 2022View details →

Figure 2 in Small islands and large biogeographic barriers have driven contrasting speciation patterns in Indo-Pacific sunbirds (Aves: Nectariniidae)

Figure 2. Simplified version of a combined maximum likelihood (ML) and Bayesian phylogenetic tree of Cinnyris and Leptocoma species sampled in Wallacea and the Sahul Shelf. In this figure, the outgroup is omitted and each major clade in the data is collapsed into a single branch. Tips representing focal populations are marked with coloured circles. Nodes are labelled with Bayesian probability/ ML bootstraps. Full versions of the ML and Bayesian trees, including all outgroup taxa, are provided in the Supporting Information (Figs S7, S8).

opennotspecifiedOct 2022View details →

Figure 3. A in Small islands and large biogeographic barriers have driven contrasting speciation patterns in Indo-Pacific sunbirds (Aves: Nectariniidae)

Figure 3. A, geographic distribution of Cinnyris jugularis (sensu Gill et al., 2022) haplotypes in Wallacea and the Sahul Shelf. Each circle represents an island and the fractions within the circle the haplotypes found on that island, proportioned to represent the frequency of each haplotype. The haplotypes are named according to the species-level divisions suggested by ABGD and coloured to represent the clades supported by our phylogenetic analyses. B, TCS haplotype network of Cinnyris haplotypes. Each circle represents a unique ND2–ND3 haplotype, sized to represent how many birds carried that haplotype. The hatch marks represent mutations between haplotypes, also given as numbers in brackets for the wider divergences. The unfilled, white nodes represent hypothetical ancestral states. C, Bayesian consensus tree of Cinnyris haplotypes. Nodes are labelled with Bayesian probabilities.

opennotspecifiedOct 2022View details →

Figure 5. A in Small islands and large biogeographic barriers have driven contrasting speciation patterns in Indo-Pacific sunbirds (Aves: Nectariniidae)

Figure 5. A, map of the Indo-Pacific with the range of the olive-backed sunbird shaded, as currently recognized by BirdLife International. Sampling sites of the birds included in our 697 bp partial ND2 analysis are marked with different triangles, according to the species they were assigned to by ABGD. Currently recognized subspecies are labelled (Gill et al., 2022). B, mean genetic distance (uncorrected p-distance) between each of the species recognized by ABGD, based on a 697 bp partial ND2 alignment. C, simplified version of a combined maximum likelihood (ML) and Bayesian phylogenetic tree of 697 bp of olive-backed sunbird ND2. In this figure the outgroup is omitted and each of the ABGD species is collapsed into a single branch. Nodes are labelled with Bayesian probability/ ML bootstraps.

opencc-by-4.0Feb 2023View details →

Vessel dimorphism and wood traits in lianas and trees among three contrasting environments

There are data and R-codes for "Vessel dimorphism and wood traits in lianas and trees among three contrasting environments" which will be published.

FIG. 6 in The Evolution of Courtship Behavior in Plethodontid Salamanders, Contrasting Patterns of Stasis and Diversification

FIG. 6.—The evolutionary origin and loss of key courtship traits in Rhŋacotriton and plethodontid genera. Character origins are shown with solid rectangles; character losses are shown with open rectangles: sff ¼ spermatophore deposition in front of the female, TSW ¼ tail-straddling walk, tpd ¼ transdermal pheromone delivery (tpd1 and tpd2), tbf ¼ turning back towards the female during TSW, tm ¼ tail massage during spermatophore pickup, opd ¼ olfactory pheromone delivery. The question marks on the Amphiuma and Hŋdromantes branches indicate that courtship behavior has not been adequately described. Dendrotriton is not shown on this tree but is the sister group to the Bolitoglossa-Pseudoeurŋcea lineage. The time of origin for each trait is bounded by the times at the ends of the branch on which it resides. Arrowhead pointing to the right indicates that the origin of traits on that branch precedes the date for the right end of the branch. Time-calibrated phylogeny based on Shen et al. (2016), using an independent-rate model (clock ¼ 2). Time scale shown in millions of years.

FIG. 4 in The Evolution of Courtship Behavior in Plethodontid Salamanders, Contrasting Patterns of Stasis and Diversification

FIG. 4.—Courtship in Desmognathus organi. (a) During bite and seize (bas) the male (foreground) holds the female̕s tail base in his jaws. The female holds her chin on the male̕s tail base in an apparent attempt to elicit tail-straddling walk. (b) During spermatophore deposition (SD), the male (right) aligns his hind limbs perpendicular to his body (align). Position of spermatophore indicated with ^. The female holds her chin over his undulating tail base in TSW position. (c) The male has moved forward after SD and has helped positioned the female over the spermatophore. The female has now departed from the spermatophore (base visible above the ^), while the male continues to arch his tail and extend on his hind limbs (extend).

FIG. 5 in The Evolution of Courtship Behavior in Plethodontid Salamanders, Contrasting Patterns of Stasis and Diversification

FIG. 5.—Olfactory pheromone delivery during turning back to the female (tbf) in Plethodon shermani (from Arnold 1976). (1) The dotted arrow shows the path of the male̕s head as he turns back towards the female during tailstraddling walk (TSW). (2) The path of the male̕s head as he slaps his mental gland across the female̕s nares. (3) The solid arrow shows the path of the male̕s head as he returns to TSW position. A video of a similar sequence is cataloged in Appendix S2.

FIG. 8 in The Evolution of Courtship Behavior in Plethodontid Salamanders, Contrasting Patterns of Stasis and Diversification

FIG. 8.—The evolutionary origin and loss of key courtship traits in the genus Desmognathus. Character origins are shown with solid rectangles; losses are shown with open rectangles: tbf ¼ turning back towards the female, tpd ¼ transdermal pheromone delivery (tpd1 and tpd2), ps ¼ pulling and snapping, rfh ¼ rub female head, bas ¼ bite and seize, fm ¼ forelimb movement, and fs ¼ forelimb strokes. Small solid circle denotes branch of origin for adjacent trait box. The time of origin or loss for each trait is bounded by the times at the ends of the branch on which it resides. Time-calibrated phylogeny based on Kozak et al. (2009); time scale shown in millions of years.

FIG. 3 in The Evolution of Courtship Behavior in Plethodontid Salamanders, Contrasting Patterns of Stasis and Diversification

FIG. 3.—Transdermal pheromone delivery in Eurŋcea aeilderae during an underwater courtship (from Arnold 1977). (A) Ventral view of the male̕s mental gland (MG), also showing three premaxillary teeth protruding through his upper lip. (B) The male̕s head during pulling, showing the backward motion that he uses to abrade the female̕s epidermis. (C) The male̕s position during pulling. The female is shaded. This image is based on a video recording cataloged in Appendix S2.

FIG. 1 in The Evolution of Courtship Behavior in Plethodontid Salamanders, Contrasting Patterns of Stasis and Diversification

FIG. 1.—Modular analysis of courtship in Rhŋacotriton and plethodontids. Modules are labeled: AP ¼ approach, HC ¼ head contact, TSW ¼ tailstraddling walk, SD ¼ spermatophore deposition, and POS ¼ positioning. Courtship sequences flow from left to right (as indicated by large arrows) and from top to bottom within modules. Behaviors shown in the same color occur in the same temporal context. Behaviors shown with different shades of the same color occur in a predictable sequence; those in lighter shades occurring earlier than those shown in darker shades. See Fig. 2 for inventory of behavior by module and submodule.

opencc-zeroMar 2023View details →

Data from: Contrasting patterns of disparity suggest differing constraints on the evolution of trilobite cephalic structures during the Cambrian 'explosion'

Trilobites are an abundant group of Palaeozoic euarthropods that appear abruptly in the fossil record c. 521 million years ago. Quantifying the development of morphological variation (or 'disparity') through time in fossil groups like trilobites is critical in understanding evolutionary radiations such as the Cambrian 'explosion'. Here, I use geometric morphometrics to quantify 'cumulative disparity' in functionally-important structures within the trilobite cephalon across their initial radiation during Cambrian Series 2. Overall cephalic disparity increased rapidly and attained a maximum within several million years. This pattern is dominated by the cephalic outline (in particular the genal spines), reflecting rapid, convergent expansion to the extremes of morphospace in a few early families. In contrast, removing the outline and focusing on structures such as the glabella and eye ridges (associated with feeding and vision, respectively) showed a more gradual increase in disparity, closer in line with taxonomic diversity and supporting the hypothesis of a relatively accurate trilobite fossil record. These contrasting patterns suggest that disparity in different structures was constrained in different ways, with extrinsic (ecological) factors likely having the biggest impact on overall disparity. It also implies that patterns of disparity in isolated substructures cannot necessarily be taken individually as representative of overall morphologies.

opencc-by-4.0Dec 2023View details →

Dominance of contrasting fungal functional groups influence nutrient cycling across four Japanese cool-temperate forest soils - Data repository

Soil data related to the publication Dominance of contrasting fungal functional groups influence nutrient cycling across four Japanese cool-temperate forest soils.

opencc-zeroApr 2023View details →

Data from: Contrasting demographic responses to size-selective harvesting among neighboring wild fish populations

Sustainable harvesting of wild populations relies on evidence-based knowledge to predict harvesting outcomes for species and the ecosystems they inhabit. Although harvesting may elicit compensatory density-dependence, it is generally size-selective, which induces additional pressures that are challenging to forecast. Furthermore, responses to harvest may be population-specific and whether generalizable patterns exist remains unclear. Taking advantage of Parks Canada's mandate to remove introduced brook trout (Salvelinus fontinalis) to restore alpine lakes in Canadian parks, we experimentally applied standardized size-selective harvesting rates (the largest ~64% annually) for three consecutive summers in five populations with different initial size structures. Four unharvested populations were used as controls. At reduced densities, harvested and control populations exhibited similar density-dependent increases in specific growth, juvenile survival, and earlier maturation. However, size-selective harvesting simultaneously induced changes to size and age structure that contrasted among harvested populations. Average body length decreased in three of five harvested populations, whereas it tended to increase in control populations over the three years. We also detected contrasting, population-specific changes in body length variability and ultimately in length- and age-at-harvest in harvested populations but not controls. Overall, populations with smaller, more homogeneous body sizes, and living at high densities were most resilient to size-selective harvesting, exhibiting the smallest change in size-at-age. In contrast, large-bodied populations exhibited more substantial size-structure changes following selective harvesting: large-bodied populations experienced either stabilizing or disruptive pressures, when initial length variability was high or low, respectively. Synthesis and application: Our results show that within species, size-selective harvesting inherently leads to more risk and uncertainty when harvesting populations with larger and more varied body sizes than smaller-bodied populations with less range in body size. Our study supports prioritizing regulations that protect harvested populations with larger and more varied body sizes. Such a management strategy would reduce the likelihood of eliciting unpredictable or undesirable demographic changes to fish populations with these attributes.

opencc-by-4.0Oct 2022View details →

Perceptual Contrast Reduces the JOLs of Small-font Words and Increases the JOLs of Large-font Words Compared with the No-contrast Conditions

The data and procedures in Experiment 1 & 2.

opencc-zeroJun 2023View details →

Contrasting mycorrhizal growth responses in native and invasive woody species are associated with distinct root trait syndromes

<ol> <li>Invasive plant species often express resource-acquisitive leaf traits that support rapid growth, but associated fine root traits and the role of microbial mutualists in invader whole-plant functioning remains poorly understood.</li> <li>We performed an experiment of 12 phylogenetically-grouped native and non-native, invasive woody species, grown with or without a common inoculum of arbuscular mycorrhizal fungi (AMF) across two nutrient levels. We measured 10 fine root traits associated with nutrient uptake and suitability of AMF colonization.</li> <li>The presence of AMF increased the growth rate of all species, but native species were significantly more dependent on AMF than invaders. Further, invaders expressed a distinct syndrome of first-order root traits, including longer, thinner roots of high specific root length, greater branching intensity, and lower tissue density, which are traits associated with rapid nutrient uptake and low AMF association. This syndrome was independent of phylogeny, AMF inoculation, and soil fertility.</li> <li>An acquisitive fine root trait syndrome for invaders supports high photosynthetic and growth rates, linking above- and below-ground functioning. The occurrence of this syndrome across phylogenetic groups indicates that lineages of woody invaders typically associated with arbuscular mycorrhizas may be generally less dependent on AMF than native species.</li> </ol>

opengpl-2.0Jun 2023View details →

Code for manuscript "Analysis of dynamic susceptibility contrast perfusion MRI using physics-informed deep learning"

This is the processing code and in vivo statistics for the manuscript "Analysis of dynamic susceptibility contrast perfusion MRI using physics-informed deep learning".

opencc-by-4.0Jun 2023View details →

Contrasting response of the water use efficiency to precipitation changes between the alpine meadow and alpine steppe over the Tibetan Plateau

The file of AlpineGrassland_GrowingSeason_WUE is dataset of the growing season water use efficiency of alpine grassland over the tibetan plateau during 1982-2014.

opencc-by-4.0Jun 2023View details →

Improving cell type identification with Gaussian noise-augmented single-cell RNA-seq contrastive learning

The benchmark datasets used to evaluate Gaussian noise augmentation-based scRNA-seq contrastive learning (GsRCL) against scRNA-seq cell-type identification tasks.

opencc-zeroJul 2023View details →

Data from: Genetic variation at innate and adaptive immune genes - contrasting patterns of differentiation and local adaptation in a wild gull

Immunogenetic variation in natural vertebrate populations is expected to respond to spatial and temporal fluctuations in pathogen assemblages. While spatial heterogeneity in pathogen-driven selection enhances local immunogenetic adaptations and population divergence, different immune genes may yield contrasting responses to the environment. Here, we investigated population differentiation at the key pathogen recognition genes of the innate and adaptive immune system in a colonial bird species, the black headed gull Chroicocephalus ridibundus. We assessed genetic variation at three toll-like receptor (TLR) genes (innate immunity) and the major histocompatibility complex (MHC) class I and II genes (adaptive immunity) in gulls from seven colonies scattered across Poland. As expected, we found much greater polymorphism at the MHC than TLRs. Population differentiation at the MHC class II, but not MHC-I, was significantly stronger than at neutral microsatellite loci, suggesting local adaptation. This could reflect spatial variation in the composition of extra-cellular parasite communities (e.g. helminths), possibly driven by sharp differences in habitat structure between colonies. Despite contrasting patterns of population differentiation, both MHC classes showed similar regimes of diversifying selection. Some significant population differentiation was also observed at TLRs, suggesting that innate immune receptors may respond to fine-scale spatial variation in pathogen pressure, although this pattern could have been enhanced by drift. Our results suggested that local adaptation at the pathogen recognition immune genes can be maintained at relatively small or moderate spatial scales in species with high dispersal potential and highlighted the complexity of immunogenetic responses of animals to heterogeneous environments.