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opencc-by-4.0Nov 2023View details →

Spectrophotometrical raw data of viability and total sugar content included in the paper "Promastigote EPS secretion and haptomonad biofilm formation as evolutionary adaptations of trypanosomatid parasites for colonizing honeybee hosts"

Raw data of spectrophotometrical data included in the paper: "Promastigote EPS secretion and haptomonad biofilm formation as evolutionary adaptations of trypanosomatid parasites for colonizing honeybee hosts" published in npj biofilms and Microbiomes.

Fig. 7 in Comparative osteology of paradoxical frogs (Hylidae: Pseudae) with comments on diagnostic features, evolutionary trends and potential aquatic adaptations

Fig. 7. Pelvic girdles in acetabular (left column) and dorsal (right column) views of representative pseudine species compared to that of Xenohyla. The pelvis of Pseudis minuta has been drawn from a dry specimen. Skeletal data from CT-scans available at Morphosource. Scale bars equal 1 mm. Anatomical abbreviations in section 2.2.5.

Fig. 6 in Comparative osteology of paradoxical frogs (Hylidae: Pseudae) with comments on diagnostic features, evolutionary trends and potential aquatic adaptations

Fig. 6. Pectoral girdles and forelimb bones of representative pseudine species compared to that of Xenohyla. Humerus in ventral view, radio-ulna in medial view, manus in plantar view, and close-up of finger in medial view. Skeletal data from CT-scans available at Morphosource. Scale bars equal 1 mm. Anatomical abbreviations in section 2.2.4.

Fig. 3 in Comparative osteology of paradoxical frogs (Hylidae: Pseudae) with comments on diagnostic features, evolutionary trends and potential aquatic adaptations

Fig. 3. Skulls of representative pseudine species in dorsal (left column), lateral (central column), and ventral (right column) views. Skeletal data from CT-scans available at Morphosource. Scale bars equal 1 mm. Anatomical abbreviations in section 2.2.1.

Fig. 10 in Comparative osteology of paradoxical frogs (Hylidae: Pseudae) with comments on diagnostic features, evolutionary trends and potential aquatic adaptations

Fig. 10. Evolutionary trends of digit morphology in pseudines. Schematic drawings of the distal part of finger IV (terminal phalanx, intercalary element, and penultimate phalanx) depict different character state combinations in pseudines and other hylids. See section 2.4 for methodological details.

Fig. 9 in Comparative osteology of paradoxical frogs (Hylidae: Pseudae) with comments on diagnostic features, evolutionary trends and potential aquatic adaptations

Fig. 9. Phylogenetic signal and homoplasy in the skeleton of pseudines and other hylids. Potential synapomorphies and autapomorphies are depicted as circles (if unambiguous) or squares (if ambiguous) on the scaffold tree, with color indicating the skeletal partition. Those unique within Hylidae are bordered in dark grey. A character distribution map indicates partition contribution to the whole data matrix. The homoplasy of each character is indicated by the homoplasy index (bottom left). See section 2.4 for methodological details.

Fig. 2 in Comparative osteology of paradoxical frogs (Hylidae: Pseudae) with comments on diagnostic features, evolutionary trends and potential aquatic adaptations

Fig. 2. Skeleton (in dorsal view) of Pseudis platensis compared to that of a tree-dwelling hylid. Skeletal data from CT-scans available at Morphosource.

Fig. 5 in Comparative osteology of paradoxical frogs (Hylidae: Pseudae) with comments on diagnostic features, evolutionary trends and potential aquatic adaptations

Fig. 5. Vertebral columns (in dorsal view) of representative pseudine species compared to that of Xenohyla. Close-ups are of the atlas-presacral II joint (in dorsal view) and the urostyle (in ventral view) of Pseudis platensis. Skeletal data from CT-scans available at Morphosource. Scale bars equal 1 mm. Anatomical abbreviations in section 2.2.3.

Fig. 1 in Comparative osteology of paradoxical frogs (Hylidae: Pseudae) with comments on diagnostic features, evolutionary trends and potential aquatic adaptations

Fig. 1. Geographic distribution map and phylogeny of paradoxical frogs (Pseudae). Species ranges are from Garda & Cannatella (2007) and timetree is from Duellman et al. (2016). The drawing (by ROG) is of an adult of Pseudis minuta. Abbreviations: L.bol, Lysapsus bolivianus; L.car, L. caraya; L.lae, L. laevis; L.lim, L. limellum; Ps.bol, Pseudis bolbodactyla; Ps.car, Ps. cardosoi; Ps.fus, Ps. fusca; Ps.min, Ps. minuta; Ps.par, Ps. paradoxa; Ps. pla, Ps. platensis; Ps.toc, Ps. tocantins; spp, species.

Fig. 4 in Comparative osteology of paradoxical frogs (Hylidae: Pseudae) with comments on diagnostic features, evolutionary trends and potential aquatic adaptations

Fig. 4. Hyolaryngeal complex (in ventral view) of Pseudis minuta (male; FCEN 19848). Red denotes bone and blue denotes cartilage. Scale bar equals 1 mm. Anatomical abbreviations in section 2.2.2.

Fig. 12 in Comparative osteology of paradoxical frogs (Hylidae: Pseudae) with comments on diagnostic features, evolutionary trends and potential aquatic adaptations

Fig. 12. Uniqueness of paradoxical frogs and convergence with aquatic taxa. Heatmap of 38 homoplastic characters showing clustering of Pseudae species with pipids and other aquatic frogs (phenogram on the left) and their distinctiveness amongst hylids (phylogenetic tree on the bottom). See section 2.4 for methodological details. Abbreviations: GD, Gower distance.

Fig. 11 in Comparative osteology of paradoxical frogs (Hylidae: Pseudae) with comments on diagnostic features, evolutionary trends and potential aquatic adaptations

Fig. 11. Evolutionary trends of selected characters of skull, pelvis, and limbs in pseudines and convergence with pipids. Optimization of 12 binary and multistate characters is depicted on the scaffold tree including all outgroup taxa, with color indicating the respective character state. Schematic drawings of skeletons depict different character state combinations in exemplar species (in bold) and the convergence of Pseudis and pipids. See section 2.4 for methodological details.

opencc-zeroFeb 2024View details →

Data from: Elevated evolutionary rates of biting biomechanics reveal patterns of extraordinary cranio-dental adaptations in some herbivorous dinosaurs

Adaptation to specialist ecologies is a key innovation that has contributed to the evolutionary success of many vertebrate clades, underpinning the acquisition of diverse skull morphologies. Dinosaurs, which dominated Mesozoic terrestrial faunas, acquired herbivory multiple times, including in clades historically regarded as predominantly carnivorous. The evolution of herbivory in theropod dinosaurs is linked to drastic changes in dental and craniomandibular functional morphology, yet whether such changes occurred more rapidly in herbivorous lineages compared to in carnivorous lineages remains untested in a phylogenetic framework. Here, we infer rates of phenotypic evolution in relative biting edge lengths to test the hypothesis that the acquisition of herbivory is associated with rapid changes in jaw biomechanics. We find elevated rates of biomechanical evolution in theropods with foreshortened and beaked skulls (Oviraptorosauria, Limusaurus), as well as in ceratopsians and Diplodocus. A reduced biting edge length and increased jaw efficiency unites these high-rate lineages, indicating selection for greater efficiency in biting biomechanics. Additionally, we hypothesise that extreme ontogenetic changes within species' lifetimes may be behind some instances of branch-wise elevated rates. Thus, we show how exceptional rates of biomechanical evolution can reveal signatures of adaptations within dinosaur lineages and potentially along ontogenetic sequences.

opencc-zeroJan 2022View details →

Data from: The evolutionary pathways for local adaptation in mountain hares

Understanding the evolution of local adaptations is a central aim of evolutionary biology and key for the identification of unique populations and lineages of conservation relevance. By combining RAD sequencing and whole-genome sequencing, we identify genetic signatures of local adaptation in mountain hares (Lepus timidus) from isolated and distinctive habitats of its wide distribution: Ireland, the Alps and Fennoscandia. We recovered full mitochondrial DNA sequences from whole-genome sequencing data and used it to recontruct the evolutionary relationships among mountain hare haplotypes.

opencc-zeroJan 2022View details →

Individual-based eco-evolutionary models for understanding adaptation in changing seas

As climate change threatens species' persistence, predicting the potential for species to adapt to rapidly changing environments is imperative for the development of effective conservation strategies. Eco-evolutionary individual-based models (IBMs) can be useful tools for achieving this objective. We performed a literature review to identify studies that apply these tools in marine systems. Our survey suggested that this is an emerging area of research fueled in part by developments in modeling frameworks that allow simulation of increasingly complex ecological, genetic, and demographic processes. The studies we identified illustrate the promise of this approach and advance our understanding of the capacity for adaptation to outpace climate change. These studies also identify limitations of current models and opportunities for further development. We discuss three main topics that emerged across studies: 1) effects of genetic architecture and non-genetic responses on adaptive potential; 2) capacity for gene flow to facilitate rapid adaptation; and 3) impacts of multiple stressors on persistence. Finally, we perform a set of simple simulations to demonstrate the approach and provide a framework for users to explore eco-evolutionary IBMs as tools for understanding adaptation in changing seas.

opencc-zeroJun 2022View details →

Data from: Compensatory adaptation and diversification subsequent to evolutionary rescue in a model adaptive radiation

Biological populations may survive lethal environmental stress through evolutionary rescue. The rescued populations typically suffer a reduction in growth performance and harbour very low genetic diversity compared with their parental populations. The present study addresses how population size and within-population diversity may recover through compensatory evolution, using the experimental adaptive radiation of bacterium Pseudomonas fluorescens. We exposed bacterial populations to an antibiotic treatment; and then imposed a one-individual-size population bottleneck on those surviving the antibiotic stress. During the subsequent compensatory evolution, population size increased and leveled off very rapidly. The increase of diversity was of slower paces and persisted longer. In the very early stage of compensatory evolution, populations of large sizes had a greater chance to diversify; however, this productivity-diversification relationship was not observed in later stages. Population size and diversity from the end of the compensatory evolution was not contingent on initial population growth performance. We discussed the possibility that our results be explained by the emergence of a "holey" fitness landscape under the antibiotic stress.

opencc-zeroAug 2022View details →

Evolutionary models demonstrate rapid and adaptive diversification of Australo-Papuan pythons

Lineages may diversify when they encounter available ecological niches. Adaptive divergence by ecological opportunity often appears to follow the invasion of a new environment with open ecological space. This evolutionary process is hypothesized to explain the explosive diversification of numerous Australian vertebrate groups following the collision of the Eurasian and Australian plates 25 million years ago. One of these groups is the pythons, which demonstrate their greatest phenotypic and ecological diversity in Australo-Papua (Australia and New Guinea). Here, using an updated and near complete time-calibrated phylogenomic hypothesis of the group, we show that following invasion of this region, pythons experienced a sudden burst of speciation rates coupled with multiple instances of accelerated phenotypic evolution in head and body shape and body size. These results are consistent with adaptive radiation theory with an initial rapid niche filling phase and later slow-down approaching niche saturation. We discuss these findings in the context of other Australo-Papuan adaptive radiations and the importance of incorporating adaptive diversification systems that are not extraordinarily species-rich but ecomorphologically diverse to understand how biodiversity is generated.

opencc-by-4.0Jun 2024View details →

Towards Adaptation in Multiobjective Evolutionary Algorithms for Integer Problems (Code and Dataset)

This is the code and the dataset for our paper published at IEEE WCCI/CEC 2024, <a href="https://2024.ieeewcci.org/">https://2024.ieeewcci.org</a>. Title: "Towards Adaptation in Multiobjective Evolutionary Algorithms for Integer Problems" Abstract: Parameter control refers to the techniques that dynamically adapt the parameter values of the evolutionary algorithm during the optimization process, such as population size, crossover rate, or operator selection. Adaptation can improve the performance and robustness of the algorithm, however, parameter control mechanisms themselves need to be designed and configured carefully. With this article, we contribute a systematic investigation of an adaptive, multi-objective algorithm that is designed for the optimisation of integer decision spaces. We find that (1) adaptation outperforms the best static configurations, and (2) performance of the multi-objective algorithm is often independent of the adaptation scheme's initial configuration.

opennotspecifiedMay 2015View details →

Fig. 3 in The hypothesis of adaptive radiation in evolutionary biology: hard facts about a hazy concept

Fig. 3 Systematic characteristics of the groups having possibly radiated. a Number of case studies (potentially several case studies per article) recorded for each category of organism: angiosperms (n =210), nonangiosperm terrestrial plants (n = 36), "algae", non-terrestrial chlorophyllian lineages (n = 9), tetrapods (n = 381), non-tetrapod vertebrates (n =121), hexapods (n =153), non-hexapod invertebrates (n = 90), fungi, Eumycetes (n =22), non-metazoan heterotrophic eukaryotes