Slow and steady wins the race: Diversification rate is independent from body size and lifestyle in Malagasy skinks (Squamata: Scincidae: Scincinae)

Research data are available on the Mendeley Data platform (https://doi.org/10.17632/xfx2yhw949.2), which include datasets, input files and R scripts of the analyses.Appendix A. Supplementary material Supplementary data to this article can be found online at https://doi. org/10.1016/j.ympev.2022.107635Most of the unique and diverse vertebrate fauna that inhabits Madagascar derives from in situ diversification from colonisers that reached this continental island through overseas dispersal. The endemic Malagasy Scincinae lizards are amongst the most species-rich squamate groups on the island. They colonised all bioclimatic zones and display many ecomorphological adaptations to a fossorial (burrowing) lifestyle. Here we propose a new phylogenetic hypothesis for their diversification based on the largest taxon sampling so far compiled for this group. We estimated divergence times and investigated several aspects of their diversification (diversification rate, body size and fossorial lifestyle evolution, and biogeography). We found that diversification rate was constant throughout most of the evolutionary history of the group, but decreased over the last 6–4 million years and independently from body size and fossorial lifestyle evolution. Fossoriality has evolved from fully quadrupedal ancestors at least five times independently, which demonstrates that even complex morphological syndromes – in this case involving traits such as limb regression, body elongation, modification of cephalic scalation, depigmentation, and eyes and ear-opening regression – can evolve repeatedly and independently given enough time and eco-evolutionary advantages. Initial diversification of the group likely occurred in forests, and the divergence of sand-swimmer genera around 20 Ma appears linked to a period of aridification. Our results show that the large phenotypic variability of Malagasy Scincinae has not influenced diversification rate and that their rich species diversity results from a constant accumulation of lineages through time. By compiling large geographic and trait-related datasets together with the computation of a new time tree for the group, our study contributes important insights on the diversification of Malagasy vertebrates.Portuguese National Funds through FCT (Fundação para a Ciência e a Tecnologia) supported this work with the projects UIDP/50027/2020 and PTDC/BIA-EVL/31254/2017Contract grant to AC [2020.00823.CEECIND/CP1601/CT0003PD/BD/128493/2017SFRH/BD/102495/2014SFRH/BPD/111015/2015Agencia Española de Investigación, with a Juan de la Cierva-Formación grant [FCI2019-039443-I/AEI/10.13039/501100011033]Swedish Research Council [2019-05191]Swiss National Science Foundation [PCEFP3_187012]Swedish Research Council [VR: 2019-04739

Identification of HIR, EDS1 and PAD4 Genes Reveals Differences between Coffea Species That May Impact Disease Resistance

This research was co-funded by Foundation for Science and Technology (FCT) and FEDER funds through PORNorte under the project CoffeeRES ref. PTDC/ASP-PLA/29779/2017, and by FCT UNIT LEAF (UID/AGR/04129/2020).The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/agronomy13040992/s1Coffee, a widely consumed important agricultural product, is mainly produced from two species, Coffea arabica (Arabica coffee) and C. canephora (Robusta coffee). Timor Hybrid (HDT) is a population resulting from a natural cross between C. arabica and C. canephora. HDT derivatives have a high spectrum of resistance to different races of Hemileia vastatrix (Hv), the causal agent of coffee leaf rust. A RNAseq database, obtained from HDT832/2 leaves inoculated with Hv (Host Resistance) and Uromyces vignae (Uv, Nonhost Resistance), showed the presence of genes implicated in the hypersensitive response and salicylic acid pathway. Hypersensitive Induced Reaction (HIR) gene family, Enhanced Disease Susceptibility1 gene (EDS1), and Phytoalexin Deficient 4 (PAD4) gene are involved in host and nonhost resistance. Relative expression calculated by RT-qPCR was used to confirm and expand the transcriptome analysis. HDTHIR4, HDTEDS1, and HDTPAD4 showed the highest upregulation in response to Hv and Uv inoculation, confirming a similar trend in host and nonhost resistance in HDT. HIR and EDS1/PAD4 gene families were characterized for the first time in the three available Coffea genomes. HIR genes were quite conserved between Coffea species. Surprisingly, EDS1 and PAD4 genes revealed major differences in gene structure. The PAD4 predicted protein from C. arabica does not include both conserved domains of the EDS1/PAD4 family, and the EDS1 putative protein from C. canephora includes a formin domain unusual in the same protein family. The variability shown by EDS1/PAD4 gene family may impact the disease resistance response of Coffea species, which can be surveyed for the gene sequences that will produce a more resistant phenotype.Foundation for Science and Technology (FCT)FEDER PTDC/ASP-PLA/29779/2017FCT UNIT LEAF (UID/AGR/04129/2020

Bases para el establecimiento de una Marca de Calidad de Biomasa en Castilla y León -BIOCACyL

La realización de este trabajo “Bases para el establecimiento de una marca de calidad de Biomasa en Castilla y León – BIOCACyL”, se debe a la necesidad planteada por el Centro Tecnológico CARTIF sobre el establecimiento de una marca de calidad/garantía para la biomasa producida en la Comunidad de Castilla y León.Departamento de Ingeniería Química y Tecnología del Medio AmbienteMáster en Gestión de la Prevención de Riesgos Laborales, Calidad y Medio Ambient

Can the use of an auditory feedback device improve the gait pattern of paediatric patients with hemiparesis?

Postprint (published version

The chloroplast protein HCF164 is predicted to be associated with Coffea SH 9 resistance factor against Hemileia vastatrix

This work was funded by Portuguese national funds through FCT—Fundação para a Ciência e Tecnologia, I.P., under the Projects: UID/AGR/04129/2020 of LEAF; UIDP/04378/2020 and UIDB/04378/2020 of UCIBIO; and LA/P/0140/2020 of i4HB and FCT and FEDER funds through PORNorte under the projects: HDT-Coffee (PTDC/ASP-PLA/32429/2017) and CoffeeRES (PTDC/ASP-PLA/29779/2017). H.A. was supported by Portuguese national funds through FCT within the scope of the Stimulus of Scientific Employment—Individual Support (CEECIND/00399/2017/CP1423/CT0004). A.O. was supported at the University of Bristol by Oracle for Research and the Biological and Biotechnological Sciences Research Council ([BB/X009831/1] and [BBW003449/1]). All molecular modelling work was carried out using the computational facilities of the Advanced Computing Research Centre, University of Bristol (http://www.bris.ac.uk/acrc).To explore the connection between chloroplast and coffee resistance factors, designated as SH1 to SH9, whole genomic DNA of 42 coffee genotypes was sequenced, and entire chloroplast genomes were de novo assembled. The chloroplast phylogenetic haplotype network clustered individuals per species instead of SH factors. However, for the first time, it allowed the molecular validation of Coffea arabica as the maternal parent of the spontaneous hybrid “Híbrido de Timor”. Individual reads were also aligned on the C. arabica reference genome to relate SH factors with chloroplast metabolism, and an in-silico analysis of selected nuclear-encoded chloroplast proteins (132 proteins) was performed. The nuclear-encoded thioredoxin-like membrane protein HCF164 enabled the discrimination of individuals with and without the SH9 factor, due to specific DNA variants linked to chromosome 7c (from C. canephora-derived sub-genome). The absence of both the thioredoxin domain and redox-active disulphide center in the HCF164 protein, observed in SH9 individuals, raises the possibility of potential implications on redox regulation. For the first time, the identification of specific DNA variants of chloroplast proteins allows discriminating individuals according to the SH profile. This study introduces an unexplored strategy for identifying protein/genes associated with SH factors and candidate targets of H. vastatrix effectors, thereby creating new perspectives for coffee breeding programs.CoffeeRES CEECIND/00399/2017/CP1423/CT0004, PTDC/ASP-PLA/29779/2017University of Bristol by Oracle for ResearchBiotechnology and Biological Sciences Research Council BB/X009831/1, BBW003449/1 BBSRCUniversity of BristolFundação para a Ciência e a Tecnologia LA/P/0140/2020, UID/AGR/04129/2020, UIDB/04378/2020, UIDP/04378/2020 FCTEuropean Regional Development Fund PTDC/ASP-PLA/32429/2017 ERD

Ploidy effects on the relationship between floral phenotype, reproductive investment, and fitness in an autogamous species complex

This research was supported by a grant from the Spanish Ministry of Economy and Competitiveness (CGL2014‐59886‐JIN), the Organismo Autónomo de Parques Nacionales (Ref: 2415/2017), and the Ministry of Science and Innovation (PID2019‐111294GB‐I00/SRA/10.13039/5011000 11033), including FEDER funds. A.J.M.‐P. was funded by the European Commission under the Marie Sklodowska‐Curie Action Cofund 2016 EU agreement 754446 and the UGR Research and Knowledge Transfer—Athenea3i. A.G.‐M. was supported by the OUTevolution project (PID2019‐ 111294GB‐I00/SRA/10.13039/501100011033)Premise: The relationships between reproductive investment, phenotype, and fitness have been broadly studied in cross-pollinated plants in contrast to selfing species, which are considered less interesting in this area because they are supposed to be a dead end in any evolutionary pathway. Still, selfing plants are unique systems to study these questions since the position of reproductive structures and traits related to flower size play an important role in female and male pollination success. Methods: Erysimum incanum s.l. is a selfing species complex that has three levels of ploidy (diploids, tetraploids, and hexaploids) and traits that are typically associated with the selfing syndrome. Here, we used 1609 plants belonging to these three ploidies to characterize the floral phenotype and spatial configuration of reproductive structures, reproductive investment (pollen and ovule production), and plant fitness. Then, we used structural equation modelling to analyze the relationship between all these variables across ploidy levels. Results: An increase in ploidy level leads to bigger flowers with anthers exserted farther and more pollen and ovules. In addition, hexaploid plants had higher absolute values for herkogamy, which is positively correlated with fitness. Ovule production significantly mediated the natural selection acting on different phenotypic traits and pollen production, a pattern that is maintained across ploidies. Conclusions: The changes in floral phenotypes, reproductive investment, and fitness with ploidy level suggest that genome duplication can be a driver for transitions in reproductive strategy by modifying the investment in pollen and ovules and linking them with plant phenotype and fitness.European Commission 754446FEDERMinistry of Science and Innovation PID2019‐111294GB‐I00/SRA/10.13039/501100011033Organismo Autónomo de Parques Nacionales 2415/2017Spanish Ministry of Economy and Competitiveness CGL2014‐59886‐JINUniversidad de Granad

Serosurvey for selected pathogens in Iberian roe deer

<p>Abstract</p> <p>Background</p> <p>The roe deer is the most abundant and widespread wild Eurasian cervid. Its populations are expanding and increasingly in contact with livestock. This may affect the distribution of infectious diseases shared with other wild and domestic ungulates.</p> <p>Methods</p> <p>We investigated the antibody seroprevalence against Pestivirus, Herpesvirus, Bluetongue (BT) virus, <it>M. avium paratuberculosis </it>(MAP), and <it>Brucella </it>sp. in 519 roe deer from different regions in Spain, south-western Europe.</p> <p>Results</p> <p>No antibodies were detected against BT and <it>Brucella </it>sp. However, antibodies were detected against Pestivirus (1.5%), Herpesvirus (0.2%) and MAP (9.2%). MAP antibodies were detected in seven of the eight populations (range 5-16.4%).</p> <p>Conclusions</p> <p>The detection of MAP antibodies in samples from most roe deer populations suggests that contact with MAP is widespread in this wildlife species. The highest prevalence was detected in sites with abundant dairy cattle and frequent use of liquid manure on pastures. Considering the results obtained regarding exposure to different pathogens, we suggest that antibody prevalences in this non-gregarious browser are largely determined by environmental factors, potentially modulating vector populations or pathogen survival in the environment.</p

Identification of HIR, EDS1 and PAD4 genes reveals differences between Coffea species that may impact disease resistance

Coffee, a widely consumed important agricultural product, is mainly produced from two species, Coffea arabica (Arabica coffee) and C. canephora (Robusta coffee). Timor Hybrid (HDT) is a population resulting from a natural cross between C. arabica and C. canephora. HDT derivatives have a high spectrum of resistance to different races of Hemileia vastatrix (Hv), the causal agent of coffee leaf rust. A RNAseq database, obtained from HDT832/2 leaves inoculated with Hv (Host Resistance) and Uromyces vignae (Uv, Nonhost Resistance), showed the presence of genes implicated in the hypersensitive response and salicylic acid pathway. Hypersensitive Induced Reaction (HIR) gene family, Enhanced Disease Susceptibility1 gene (EDS1), and Phytoalexin Deficient 4 (PAD4) gene are involved in host and nonhost resistance. Relative expression calculated by RT-qPCR was used to confirm and expand the transcriptome analysis. HDTHIR4, HDTEDS1, and HDTPAD4 showed the highest upregulation in response to Hv and Uv inoculation, confirming a similar trend in host and nonhost resistance in HDT. HIR and EDS1/PAD4 gene families were characterized for the first time in the three available Coffea genomes. HIR genes were quite conserved between Coffea species. Surprisingly, EDS1 and PAD4 genes revealed major differences in gene structure. The PAD4 predicted protein from C. arabica does not include both conserved domains of the EDS1/PAD4 family, and the EDS1 putative protein from C. canephora includes a formin domain unusual in the same protein family. The variability shown by EDS1/PAD4 gene family may impact the disease resistance response of Coffea species, which can be surveyed for the gene sequences that will produce a more resistant phenotype.This research was co-funded by Foundation for Science and Technology (FCT) and FEDER funds through PORNorte under the project CoffeeRES ref. PTDC/ASP-PLA/29779/2017, and by FCT UNIT LEAF (UID/AGR/04129/2020)info:eu-repo/semantics/publishedVersio