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opencc-by-4.0Jun 2023View details →

Host-associated genetic differentiation and origin of a recent host shift in the generalist parasitic weed Phelipanche ramosa

The branched broomrape, Phelipanche ramosa (L.) Pomel, is a parasitic weed that can infest several crops, notably tobacco, hemp and tomato. In western France, it has recently adapted to a new host, oilseed rape. We collected P. ramosa samples from fields cultivated with six different crops across Europe. Data from SSR markers and DNA sequences showed strong host-associated genetic differentiation. File SSRdata-Pramosa1611.txt contains sampling locations, host crops and microsatellite genotypes. Files BO1aligned.fas, ITSaligned.fas, RPL16aligned.fas and trnKtrnQaligned.fas contain aligned DNA sequences.

dryad40/100

Data from: Phenotypic plasticity and genetic diversity shed light on endemism of rare Boechera perstellata and its potential vulnerability to climate warming

Premise of the study: The rapid pace of contemporary environmental change puts many species at risk, especially rare species constrained by limited capacity to adapt or migrate due to low genetic diversity and/or fitness. But the ability to acclimate can provide another way to persist through change. We compared the capacity of rare Boechera perstellata (Braun's rockcress) and widespread B. laevigata to acclimate to change. Methods: We investigated the phenotypic plasticity of growth, biomass allocation, and leaf morphology of individuals of B. perstellata and B. laevigata propagated from seed collected from several populations throughout their ranges in a growth chamber experiment to assess their capacity to acclimate. Concurrently, we assessed the genetic diversity of sampled populations using 17 microsatellite loci to assess evolutionary potential. Key results: Plasticity was limited in both rare B. perstellata and widespread B. laevigata, but differences in the plasticity of root traits between species suggest that B. perstellata may have less capacity to acclimate to change. In contrast to its widespread congener, B. perstellata exhibited no plasticity in response to temperature and weaker plastic responses to water availability. As expected, B. perstellata also had lower levels of observed heterozygosity than B. laevigata at the species level, but population-level trends in diversity measures were inconsistent due to high heterogeneity among B. laevigata populations. Conclusions: Overall, the ability of phenotypic plasticity to broadly explain the rarity of B. perstellata vs. commonness of B. laevigata is limited. However, some contextual aspects of our plasticity findings compared with its relatively low genetic variability may shed light on the narrow range and habitat associations of B. perstellata and suggest its vulnerability to climate warming due to acclimatory and evolutionary constraints.

opencc-zeroSep 2023View details →

opencc-by-4.0Sep 2023View details →

Replication Data for "Exploring Genetic Improvement of the Carbon Footprint of Web Pages"

## Overview In this study, we explore automated reduction of the carbon footprint of web pages through genetic improvement, a process that produces alternative versions of a program by applying program transformations intended to optimize qualities of interest. We introduce a prototype tool that imposes transformations to HTML, CSS, and JavaScript code, as well as image resources, that minimize the quantity of data transferred and memory usage while also minimizing impact to the user experience (measured through loading time and number of changes imposed). In an evaluation,  our tool outperforms two baselines---the original page and randomized changes---in the average case on all projects for data transfer quantity, and 80% of projects for memory usage and load time, often with large effect size. Our results illustrate the applicability of genetic improvement to reduce the carbon footprint of web components, and offer lessons that can benefit the design of future tools. ## Data Contained in This Package - experiment_data/Subject Project-XX-X.xlsx Each spreadsheet contains data collected as part of our experiments, including the fitness scores of the final solutions.

Fig. 1 in High Genetic Diversity of Amoebae Belonging to the Genus Mayorella (Amoebozoa, Discosea, Dermamoebida) in Natural Habitats

Fig. 1. Diversity of locomotive and floating forms of studied strains: A–E – Mayorella sp. strain Belaya; F–J – Mayorella sp. strain 2Th5; K–O – Mayorella sp. strain FE 16; P–S – Mayorella sp. strain JJP2003. DIC and phase contrast images, scale bar is 20 μm.

Fig. 4 in High Genetic Diversity of Amoebae Belonging to the Genus Mayorella (Amoebozoa, Discosea, Dermamoebida) in Natural Habitats

Fig. 4. Phylogenetic tree based on SSU rRNA gene sequences for Mayorella species only, with few outgroups. Supports are indicated as PP/ BS; black dots indicate 1.0/100 PP/BS support. GTR + γ + I model of evolution; 1414 sites.

Fig. 3 in High Genetic Diversity of Amoebae Belonging to the Genus Mayorella (Amoebozoa, Discosea, Dermamoebida) in Natural Habitats

Fig. 3. Phylogenetic tree based on SSU rRNA gene sequences for all available Mayorella sequences and a wide sample of Discosea and Tubulinea taxa. Supports are indicated as PP/BS; black dots indicate 1.0/100 PP/BS support. GTR + γ + I model of evolution; 1554 sites.

Fig. 2 in High Genetic Diversity of Amoebae Belonging to the Genus Mayorella (Amoebozoa, Discosea, Dermamoebida) in Natural Habitats

Fig. 2. Diversity of locomotive and floating forms of studied strains: A–E – Mayorella sp. strain Amur_2; F–J – Mayorella sp. strain FE_2; K–O – Mayorella sp. strain Germany; P–T – Mayorella sp. strain FE_mz241; U–Y – Mayorella sp. strain Oklahoma. Scale bar is 20 μm.

figure 1 in Spatial genetic structure in the Eurasian otter (Lutra lutra) meta-population from its core range in Italy

figure 1 The area surveyed for collection of otter samples (40° 40' N, 39° 37' N). Red spots indicate the location of the collected samples. The blue lines highlight the main rivers (order 1) and their tributaries (order 2, 3 and 4 according to waterway hierarchy). The continuous red lines represent regional boundaries. In the inset, the current otter distribution (inferred from Balestrieri et al., 2016, modified) is reported in orange and the study area is defined by the black bold square.

figure 4 in Spatial genetic structure in the Eurasian otter (Lutra lutra) meta-population from its core range in Italy

figure 4 Principal Component Analysis (pca) performed on microsatellite genotypes (dots). Circles show the well-defined spatial groups. A) pca according to the belonging of genotypes to the six river basins: the Cilento basin (green dots); the Agri basin (pink dots); the Sinni basin (blue dots); the Lao basin (red dots); the Basento basin (orange dots); the Abatemarco basin (violet dots); black dots indicate the samples outside of the main river basins. Dashed line indicates geographically contiguous but genetically different genotypes. B) pca according to clusters inferred by STRUCTURE: genotypes assigned unambiguously to K2 (green dots), to K3 (yellow dots), to K5 (violet dots). Grey dots represent samples with mixed genotypes assignable to K1 and K4.

figure 3 in Spatial genetic structure in the Eurasian otter (Lutra lutra) meta-population from its core range in Italy

figure 3 Genetic structure and distribution of the Italian otter genotypes in the study area. A) Estimated population structure based on the analysis of 11 microsatellite loci according to STRUCTURE (K = 5). Each bar represents a sample analysed. B) Geographic visualisation of genotypes in the study area performed using QGIS 3.4.1 software with base layers acquired from http://www.pnc.miniambiente. it/. Each circle represents a sample analysed. The colours indicate the percentage of assignment of an individual to each cluster: in blue, K1; in green, K2; in orange, K3; in red, K4; in violet, K5. The bold blue lines highlight the main rivers, while the tiny blue lines show all other waterways.

figure 6 Mantel test for A in Spatial genetic structure in the Eurasian otter (Lutra lutra) meta-population from its core range in Italy

figure 6 Mantel test for A) the correlation between geographic distance (GGDsq) and genetic distance (LinGD) (Rxy = 0.264, P = 0.0001) and for B) the correlation between resistance distance (a measure of ecological distance) (ECO500) and LinGD (Rxy = 0.217, P = 0.0001).

FIGURE 16 in Split distribution, biogeography and morphological and genetic diversity of the Iberobathynellini Tribe in the family Parabathynellidae (Crustacea, Malacostraca, Bathynellacea)

FIGURE 16 Uropod: A. Iberobathynella andalusica; B. I. burgalensis; C. I. cornejoensis; D. I. lamasonensis; E. I. pedroi; F. Texanobathynella bowmani; G. I. paragracilipes; H. Guadalopebathynella puchi; I. Paraiberobathynella notenboomi; J. Hexaiberobathynella mateusi; K. Californibathynella californica; L. Montanabathynella pecosensis; M. Parabathynella motasi.

FIGURE 15 in Split distribution, biogeography and morphological and genetic diversity of the Iberobathynellini Tribe in the family Parabathynellidae (Crustacea, Malacostraca, Bathynellacea)

FIGURE 15 Male Th VIII: A. Iberobathynella burgalensis; B. I. lamasonensis; C. I. cornejoensis; D. I. andalusica; E. I. pedroi; F. Californibathynella californica; G. I. paragracilipes; H. Hexaiberobathynella hortezuelensis; I. Paraiberobathynella notenboomi; J. Guadalopebathynella puchi; K. Texanobathynella bowmani. L. Montanabathynella pecosensis; M. Parabathynella motasi. Abbreviations: Bsp, basipod; D.lb, dentate lobe; Endp, endopod; Exp, exopod; I.lb, inner lobe; O.lb, outer lobe.

FIGURE 13 Thoracopod I in Split distribution, biogeography and morphological and genetic diversity of the Iberobathynellini Tribe in the family Parabathynellidae (Crustacea, Malacostraca, Bathynellacea)

FIGURE 13 Thoracopod I: A. Iberobathynella lamasonensis; B. I. cornejoensis; C. Iberobathynella burgalensis; D. I. andalusica; E. I. paragracilipes; F. Hexaiberobathynella hortezuelensis; G. Paraiberobathynella notenboomi; H. I. pedroi; I. Guadalopebathynella puchi; J. Californibathynella californica; K. Texanobathynella aaronswinki; L. Montanabathynella pecosensis; M. Parabathynella motasi.

FIGURE 12 in Split distribution, biogeography and morphological and genetic diversity of the Iberobathynellini Tribe in the family Parabathynellidae (Crustacea, Malacostraca, Bathynellacea)

FIGURE 12 Maxilla (MxII): A. Iberobathynella burgalensis; B. I. cornejoensis; C. I. lamasonensis; D. I. andalusica; E. I. paragracilipes; F. Hexaiberobathynella hortezuelensis; G. Paraiberobathynella notenboomi; H. Guadalopebathynella puchi; I. Californibathynella californica; J. Texanobathynella aaronswinki; K. Montanabathynella pecosensis; L. Parabathynella motasi.

FIGURE 10 in Split distribution, biogeography and morphological and genetic diversity of the Iberobathynellini Tribe in the family Parabathynellidae (Crustacea, Malacostraca, Bathynellacea)

FIGURE 10 Mandible (Md): A. Iberobathynella cornejoensis; B. I. lamasonensis; E. I. pedroi; D. I. andalusica; E. I. burgalensis; F. I. paragracilipes; G. Paraiberobathynella notenboomi; H. Hexaiberobathynella hortezuelensis; I. Guadalopebathynella puchi; J. Californibathynella californica; K. Texanobathynella bowmani; L. Texanobathynella aaronswinki; M. Montanabathynella pecosensis; N. Parabathynella motasi.

FIGURE 9 in Split distribution, biogeography and morphological and genetic diversity of the Iberobathynellini Tribe in the family Parabathynellidae (Crustacea, Malacostraca, Bathynellacea)

FIGURE 9 Antenna (AII) A-L: A. Iberobathynella lamasonensis; B. I. burgalensis; C. I. andalusica; D. I. paragracilipes; E. Guadalopebathynella puchi; F. Californibathynella californica; G. Hexaiberobathynella hortezuelensis; H. Paraiberobathynella notenboomi; I. Texanobathynella aaronswinki; J. I. pedroi; K. Montanabathynella pecosensis; L. Parabathynella motasi. Labrum M-X: M. I. burgalensis; N. I. andalusica; O. I. cornejoensis; P. I. pedroi; Q. I. paragracilipes; R. Hexaiberobathynella hortezuelensis; S. Guadalopebathynella puchi; T. Californibathynella californica; U. Paraiberobathynella notenboomi; V. Texanobathynella aaronswinki; W. Montanabathynella pecosensis; X. Parabathynella motasi.

FIGURE 7 in Split distribution, biogeography and morphological and genetic diversity of the Iberobathynellini Tribe in the family Parabathynellidae (Crustacea, Malacostraca, Bathynellacea)

FIGURE 7 Ancestral State Reconstruction of: (A) Number of segments of AII (Ch.28); (B) Number of segments of exopod of ThII-III (Ch. 12) and (C) Number of segments of exopod of ThI (Ch. 9). Support for each node is provided by the size of circles indicating the posterior probabilities (PP). Coloured box depicted the state of the character.

FIGURE 8 in Split distribution, biogeography and morphological and genetic diversity of the Iberobathynellini Tribe in the family Parabathynellidae (Crustacea, Malacostraca, Bathynellacea)

FIGURE 8 Ancestral State Reconstruction of (A) Cuticle of female Th VIII (Ch.16) and (B) Number of segments female ThVIII. Support for each node is provided by the size of circles indicating the posterior probabilities (PP). Coloured box depicted the state of the character.

FIGURE 6 in Split distribution, biogeography and morphological and genetic diversity of the Iberobathynellini Tribe in the family Parabathynellidae (Crustacea, Malacostraca, Bathynellacea)

FIGURE 6 Phylogenetic tree from the combined analyses (morphological and molecular dataset). Support for each node is provided by the posterior probabilities (PP).