Understanding evolutionary rescue and parallelism in response to environmental stress.

Evolutionary rescue, the process by which populations facing environmental stress avoid extinction through genetic adaptation, is a critical area of study in evolutionary biology. The order in which mutations arise and get established will be relevant to the population's rescue. This study investigates the degree of parallel evolution at the genotypic level between independent populations facing environmental stress and subject to different demographic regimes. Under density regulation, 2 regimes exist: In the first, the population can restore positive growth rates by adjusting its population size or through adaptive mutations, whereas in the second regime, the population is doomed to extinction unless a rescue mutation occurs. Analytical approximations for the likelihood of evolutionary rescue are obtained and contrasted with simulation results. We show that the initial level of maladaptation and the demographic regime significantly affect the level of parallelism. There is an evident transition between these 2 regimes. Whereas in the first regime, parallelism decreases with the level of maladaptation, it displays the opposite behavior in the rescue/extinction regime. These findings have important implications for understanding population persistence and the degree of parallelism in evolutionary responses as they integrate demographic effects and evolutionary processes.

Community-wide genome sequencing reveals 30 years of Darwin's finch evolution.

A fundamental goal in evolutionary biology is to understand the genetic architecture of adaptive traits. Using whole-genome data of 3955 of Darwin's finches on the Galápagos Island of Daphne Major, we identified six loci of large effect that explain 45% of the variation in the highly heritable beak size of Geospiza fortis, a key ecological trait. The major locus is a supergene comprising four genes. Abrupt changes in allele frequencies at the loci accompanied a strong change in beak size caused by natural selection during a drought. A gradual change in Geospiza scandens occurred across 30 years as a result of introgressive hybridization with G. fortis. This study shows how a few loci with large effect on a fitness-related trait contribute to the genetic potential for rapid adaptive radiation.

Desaparecimento radical: o mimetismo de Thayer no olhar de Lacan / Radical disappearance: Thayer's mimicry in Lacan's gaze

Resumo: Este artigo buscou investigar o mimetismo em Thayer, articulado a um recorte do conceito de olhar no seminário 11. Visto que, no campo do mimetismo, Lacan só entrou em contato com Thayer indiretamente, exploramos um ponto de encontro teórico entre os autores ainda não discutido na literatura. O ponto de encontro é a lei formulada por Thayer que impele os animais a buscarem mais do que a camuflagem, mas o desaparecimento da cena. Concluímos que o olhar, como a luz em Lacan, é o que produz esse efeito de desaparecimento radical na natureza.

Abstract: This article aims to investigate Thayer's concept of mimicry and to discuss it together with the concept of the gaze in seminar 11. Since Lacan only knew Thayer indirectly, we explored a theoretical meeting point between the two that has not yet been discussed. The meeting point is a law formulated by Thayer that describes how animals seek more than mimicry, but the disappearance of the scene. We conclude that the gaze, as a point of light in Lacan, is what produces that radical disappearance effect in Nature.

Sífilis mimetizando lúpus eritematoso sistêmico: um relato de caso / Syphilis mimicking systemic lupus erythematosus: a case report / Sífilis que simula lupus eritematoso sistémico: informe de un caso

O Lúpus Eritematoso Sistêmico (LES) é uma patologia crônica, de origem autoimune e inflamatória. As diversas manifestações clínicas existentes em pacientes acometidos pelo LES, sejam elas sistêmicas ou órgãos-alvo, possibilitam variados diagnósticos diferenciais. Dentre as manifestações clínicas que possibilitam estes diagnósticos está o acometimento cutâneo, com vasta variabilidade de apresentação. Da mesma forma, a sífilis também possui apresentação cutânea, tornando possível o diferencial de diagnóstico com outras patologias, inclusive o próprio LES. O presente estudo tem como objetivo relatar um caso de sífilis mimetizando lúpus eritematoso sistêmico, descrever o quadro clínico apresentado pelo paciente, bem como as ferramentas utilizadas para diagnóstico, e a posterior abordagem terapêutica. O caso relatado refere-se a um paciente de 29 anos, do sexo masculino, procedente de Campos Novos (SC), que apresentou um quadro clínico e laboratorial de lúpus-like induzido por uma infecção aguda de sífilis. A resolução completa de critérios inflamatórios de LES ocorreu após tratamento correto da doença infecciosa, com total melhora clínica e sorológica.

Systemic lupus erythematosus (SLE) is a chronic autoimmune inflammatory disease. The various clinical manifestations in SLE patients, both systemic and in target organs, allow for various differential diagnoses. Among the clinical manifestations that aid in diagnosis are the cutaneous injuries, which have a wide range of presentations. Syphilis also has cutaneous manifestations, which aid in the differential diagnosis from other pathologies, including SLE. The present study aims to report a case of syphilis mimicking SLE, describe the clinical condition presented by the patient, the tools used for diagnosis, and the therapeutic approach. The case reported refers to a 29- year-old male patient from Campos Novos (SC), who showed a clinical and laboratory lupus-like condition induced by an acute syphilis infection. The full resolution of SLE inflammatory criteria occurred following appropriate treatment for the infectious disease, with complete clinical and serological improvement.

El lupus eritematoso sistémico (LES) es una enfermedad inflamatoria autoinmune crónica. Las diversas manifestaciones clínicas de los pacientes con LES, tanto sistémicas como en órganos diana, permiten realizar varios diagnósticos diferenciales. Entre las manifestaciones clínicas que ayudan al diagnóstico se encuentran las lesiones cutáneas, que tienen una amplia gama de presentaciones. La sífilis también tiene manifestaciones cutáneas, que ayudan al diagnóstico diferencial con otras patologías, incluido el LES. El presente estudio tiene como objetivo comunicar un caso de sífilis que simula un LES, describir el cuadro clínico presentado por la paciente, las herramientas utilizadas para el diagnóstico y el abordaje terapéutico. El caso relatado se refiere a un paciente masculino de 29 años, natural de Campos Novos (SC), que presentó un cuadro clínico y de laboratorio semejante al lupus, inducido por una infección aguda por sífilis. La resolución completa de los criterios inflamatorios del LES ocurrió tras el tratamiento adecuado de la enfermedad infecciosa, con mejoría clínica y serológica completa.

Relatos da pandemia: ser mulher e mãe em tempos de covid-19 / Pandemic reports: being a woman and mother in covid-19 times / Relatos de la pandemia: ser mujer y madre en tiempos del covid-19

Partindo da pergunta "Como tem sido ser mulher e mãe em tempos de pandemia?", o presente estudo convidou mulheres que são mães, em redes sociais virtuais, a partilhar um relato de suas experiências com a readaptação parental em função do distanciamento social causado pela pandemia de covid-19. O objetivo foi refletir sobre a experiência de ser mulher e mãe em tempos de covid-19 e distanciamento social, apontando algumas ressonâncias do cenário pandêmico na subjetividade dessas mulheres. O estudo teve como base o referencial psicanalítico, tanto na construção da pesquisa e análise dos relatos quanto na sua discussão. A análise dos cerca de 340 relatos coletados, os quais variaram de uma breve frase a longos parágrafos, apontou para uma série de questionamentos, pontos de análise e reflexões. A pandemia, e o decorrente distanciamento social, parece ter colocado uma lente de aumento sobre as angústias das mulheres que são mães, evidenciando sentimentos e sofrimentos sempre presentes. Destacaram-se, nos relatos, a sobrecarga das mulheres com as tarefas de cuidado dos filhos e da casa, a culpa, a solidão, a exaustão, e o sentimento de que não havia espaço nesse contexto para "ser mulher", sendo isso entendido especialmente a questões estéticas e de vaidade.(AU)

Starting from the question "How does it feel to be a woman and a mother in pandemic times?", this study invited women who are mothers, in virtual social networks, to share their experiences regarding parental adaptations due to social distancing caused by the COVID-19 pandemic. The objective was to reflect on the experience of being a woman and a mother in the context of COVID-19 and of social distancing, pointing out some resonances of the pandemic scenario in the subjectivity of these women. The study was based on the psychoanalytical framework, both in the construction of the research and analysis of the reports and in their discussion. The analysis of about 340 collected reports, which ranged from a brief sentence to long paragraphs, pointed to a series of questions, analysis topics, and reflections. The pandemic, and the resulting social distancing, seems to have placed a magnifying glass over the anguish of women who are mothers, showing ever-present feelings and suffering. The reports highlighted women's overload with child and house care tasks, the guilt, loneliness, exhaustion, and the feeling that there was no space in this context to "be a woman," and it extends to aesthetic and vanity related questions especially.(AU)

A partir de la pregunta "¿cómo te sientes siendo mujer y madre en tiempos de pandemia?", este estudio invitó por las redes sociales a mujeres que son madres a compartir un relato de sus experiencias sobre la readaptación parental en función del distanciamiento social causado por la pandemia del covid-19. Su objetivo fue reflexionar sobre la experiencia de ser mujer y madre en tiempos del covid-19 y el distanciamiento social, señalando algunas resonancias del escenario pandémico en la subjetividad de estas mujeres. Este estudio se basó en el marco psicoanalítico, tanto en la construcción de la investigación y análisis de los informes como en su discusión. El análisis de los casi 340 relatos, que variaron de una pequeña frase a largos párrafos, generó en las investigadoras una serie de cuestionamientos y reflexiones. La pandemia y el consecuente distanciamiento social parece haber agrandado las angustias de las mujeres que son madres, evidenciando sentimientos y sufrimientos siempre presentes. En los relatos destacan la sobrecarga de las mujeres con las tareas de cuidado de los hijos y del hogar, la culpa, la soledad, el cansancio, así como el sentimiento de que no hay espacio em este contexto para "ser mujer", relacionado principalmente a cuestiones estéticas y de vanidad.(AU)

Population genomics and geographic dispersal in Chagas disease vectors: Landscape drivers and evidence of possible adaptation to the domestic setting.

Accurate prediction of vectors dispersal, as well as identification of adaptations that allow blood-feeding vectors to thrive in built environments, are a basis for effective disease control. Here we adopted a landscape genomics approach to assay gene flow, possible local adaptation, and drivers of population structure in Rhodnius ecuadoriensis, an important vector of Chagas disease. We used a reduced-representation sequencing technique (2b-RADseq) to obtain 2,552 SNP markers across 272 R. ecuadoriensis samples from 25 collection sites in southern Ecuador. Evidence of high and directional gene flow between seven wild and domestic population pairs across our study site indicates insecticide-based control will be hindered by repeated re-infestation of houses from the forest. Preliminary genome scans across multiple population pairs revealed shared outlier loci potentially consistent with local adaptation to the domestic setting, which we mapped to genes involved with embryogenesis and saliva production. Landscape genomic models showed elevation is a key barrier to R. ecuadoriensis dispersal. Together our results shed early light on the genomic adaptation in triatomine vectors and facilitate vector control by predicting that spatially-targeted, proactive interventions would be more efficacious than current, reactive approaches.

Sympatric cleptobiotic stingless bees have species-specific cuticular profiles that resemble their hosts.

Stingless bees are the largest group of eusocial pollinators with diverse natural histories, including obligate cleptobionts (genus Lestrimelitta) that completely abandoned flower visitation to rely on other stingless bees for food and nest materials. Species of Lestrimeliita are thought to specialize upon different host species, and deception through chemical similarity has been proposed as a mechanism to explain this phenomenon. In the Yucatan Peninsula of Mexico, Scaptotrigona pectoralis is a species chemically distinct from, and not preferred as a host by, locally widespread Lestrimeliita niitkib; witnessing attacks on S. pectoralis colonies offered the opportunity to test the sensory deception hypothesis to cletoparasitism. Analysis of cuticular profiles revealed that the Lestrimelitta attacking S. pectoralis differed significantly in odour bouquet to L. niitkib and, in contrast, it resembled that of S. pectoralis. Further analyses, including morphometrics, mtDNA barcoding, and the examination of taxonomic features, confirmed the existence of two sympatric Lestrimelitta species. The results give support to the hypothesis of chemical deception as a cleptobiotic strategy in Lestrimelitta sp. This is the first evidence that sympatric cleptobionts of the same genus select hosts in accordance with species-specific cuticular profiles, with possible consequences for ecological adaptation and the evolution of these remarkable organisms and the community of stingless bee hosts.

Productivity of strawberry genotypes in the south and southwest mesoregion of Minas Gerais / Produtividade de genótipos de morangueiro na mesoregião sul e sudoeste de Minas Gerais

The strawberry is a perennial plant of temperate climate belonging to the Rosaceae family, much appreciated for presenting a fleshy and succulent receptacle as an edible part. Among small fruits, in Brazil it represents the species of greatest economic expression. The breeding of the strawberry aims to meet the demands of the market, mainly regarding the quality of the fruit required by consumers. Thus, the selection of genotypes that have good quality, productivity and adaptation is extremely important for the development of culture in the country, as well as for making seedlings available at lower prices. The objective of this work was to evaluate the agronomic performance and productivity of experimental strawberry genotypes in the city of Alfenas, Minas Gerais. For this, the experiment was carried out in the premises of the José do Rosário Vellano University (UNIFENAS), Alfenas-MG, in an experimental area of the Olericulture and Experimentation Sector (21025'45''S, 45056'50 "W, 880 m altitude). The experimental design used was completely randomized, with eleven treatments, distributed in seven experimental genotypes, namely MDA01, MDA06, MCA 119, MFA444, MDA19, MDA11 and MDA23, and four commercial cultivars taken as control, being them Pircinque, Albion, Aromas and Festival, in eight repetitions. The following characteristics were evaluated total production per plant (grams of strawberries per plant-1), average weight of fruits per plant (grams/fruit-1), total number of fruits per plant and number of stolons (seedlings) per plant. The experimental genotypes that showed the highest total productivity and average fruit weight were MDA01, MDA23 and MDA19. These materials are presented as promising for the strawberry breeding program in the region and should be reevaluated under other edaphoclimatic conditions and/or used as parents in new crossings for the next stages of the program.

O morangueiro é uma planta perene de clima temperado pertencente à família das Rosáceas, muito apreciado por apresentar um receptáculo carnoso e suculento como parte comestível. Entre os frutos pequenos, no Brasil representa a espécie de maior expressão econômica. O melhoramento genético do morangueiro visa atender às demandas do mercado, principalmente, quanto ao quesito qualidade do fruto exigido pelos consumidores. Dessa forma, a seleção de genótipos que apresentem boa qualidade, produtividade e adaptação, é de extrema importância para o desenvolvimento da cultura no país, bem como para a disponibilização de mudas com menores preços. Objetivou-se com este trabalho avaliar o desempenho agronômico e a produtividade de genótipos experimentais de morangueiro no município de Alfenas, Minas Gerais. O experimento foi conduzido nas dependências da Universidade José do Rosário Vellano (UNIFENAS), em área experimental do Setor de Olericultura e Experimentação. O delineamento experimental utilizado foi inteiramente casualizado, com onze tratamentos, distribuídos em sete genótipos experimentais provenientes do banco de germoplasma da Universidade Federal de Lavras, sendo eles MDA01, MDA06, MCA 119, MFA444, MDA19, MDA11 e MDA23, e quatro cultivares comerciais tidas como controle, sendo elas Pircinque, Albion, Aromas e Festival, em oito repetições. Foram avaliadas as seguintes características: produção total por planta (gramas de morangos por planta), peso médio de frutos por planta (gramas/fruto), número total de frutos por planta e quantidade de estolões emitidos (mudas) por planta. Os genótipos experimentais que apresentaram os maiores índices de produtividade total e peso médio dos frutos foram MDA01, MDA23 e MDA19. Estes materiais se apresentam como promissores para o programa de melhoramento genético do morangueiro na região e devem ser reavaliados em outras condições edafoclimáticas e/ou utilizados como genitores em novos cruzamentos para as próximas etapas do programa.

Expression pattern of CRYAB and CTGF genes in two pig breeds at different altitudes / [Padrão de expressão dos genes CRYAB e CTGF em duas raças de suínos em altitudes diferentes]

Tibetan pigs are characterized by significant phenotypic differences relative to lowland pigs. Our previous study demonstrated that the genes CRYAB and CTGF were differentially expressed in heart tissues between Tibetan (highland breed) and Yorkshire (lowland breed) pigs, indicating that they might participate in hypoxia adaptation. CRYAB (ɑB-crystallin) and CTGF (connective tissue growth factor) have also been reported to be associated with lung development. However, the expression patterns of CRYAB and CTGF in lung tissues at different altitudes and their genetic characterization are not well understood. In this study, qRT-PCR and western blot of lung tissue revealed higher CRYAB expression levels in highland and middle-highland Tibetan and Yorkshire pigs than in their lowland counterparts. With an increase in altitude, the expression level of CTGF increased in Tibetan pigs, whereas it decreased in Yorkshire pigs. Furthermore, two novel single-nucleotide polymorphism were identified in the 5' flanking region of CRYAB (g.39644482C>T and g.39644132T>C) and CTGF (g.31671748A>G and g.31671773T>G). The polymorphism may partially contribute to the differences in expression levels between groups at the same altitude. These findings provide novel insights into the high-altitude hypoxia adaptations of Tibetan pigs.

Porcos tibetanos são caracterizados por diferenças fenotípicas significativas em relação aos porcos de planície. Nosso estudo anterior demonstrou que os genes CRYAB e CTGF eram expressos diferentemente nos tecidos do coração entre os porcos tibetanos (raça das terras altas) e Yorkshire (raça das terras baixas), indicando que eles poderiam participar da adaptação à hipoxia. CRYAB (ɑB-crystallin) e CTGF (fator de crescimento do tecido conjuntivo) também foram relatados como estando associados ao desenvolvimento pulmonar. Entretanto, os padrões de expressão do CRYAB e CTGF nos tecidos pulmonares em diferentes altitudes e sua caracterização genética não são bem compreendidos. Neste estudo, o qRT-PCR e a mancha ocidental de tecido pulmonar revelou níveis de expressão de CRYAB mais elevados em porcos tibetanos e Yorkshire de altitude e média altitude do que em seus pares de planície. Com um aumento na altitude, o nível de expressão do CTGF aumentou nos porcos tibetanos, enquanto diminuiu nos porcos Yorkshire. Além disso, foram identificados dois novos polimorfismos de um único nucleotídeo na região flanqueadora de CRYAB (g.39644482C>T e g.39644132T>C) e CTGF (g.31671748A>G e g.31671773T>G). O polimorfismo pode contribuir parcialmente com as diferenças nos níveis de expressão entre grupos a uma mesma altitude. Estas descobertas proporcionam novos conhecimentos sobre as adaptações de hipoxia a alta altitude dos porcos tibetanos.

Performance of sweet potato genotypes in Brazilian regions

The average yield of sweet potato (Ipomoea batatas (L.) Lam.) in Brazil is below the crop potential, and appropriate cultural practices and more productive cultivars are needed to improve crop yield. The Beauregard sweet potato cultivar, originally from the United States, has shown high productive potential. This study evaluated the performance of features of agronomic importance of the Beauregard cultivar in comparison to local cultivars and eight sweet-potato clones in Brazilian regions. For that purpose, two sets of experiments were carried out. The first set evaluated eight sweet potato clones and cultivars Beauregard, Olho Roxo and Ourinhos in Brasília-DF and Itabaiana-SE using as criteria two foliage and six root traits. In the second set, two sweet potato clones (9 and 75), and Beauregard, Brazlândia Branca and Canadense cultivars were evaluated in Piacatú-SP, Brasília-DF, PAD-DF, Canoinhas-SC and Altamira-PA, for the traits: commercial, non-commercial, and total yield. Beauregard presented little foliage production but great root yield across the different environments. Since it has low dry matter content, acceptance of this cultivar may be limited in some regions. None of the sweet potato clones showed stable yield to justify a commercial launch.

Trophic relationships among three species of ornamental fish from the region of Lake Amanã, Amazon / Relações tróficas entre três espécies de peixes ornamentais da região do lago de Amanã, Amazonas

The present study objectified to evaluate the trophic relationships and the possible aggressive mimicry involving Carnegiella strigata, Carnegiella marthae and Gnathocharax steindachneri, in lowland forest streams. Samplings occurred in November 2002, March and August 2003 in Amanã Sustainable Development Reserve (ASDR). The total of 943 fish was caught, being 79.43% of C. marthae, 3.18% of C. strigata and 17.39% of G. steindachneri. Stomach contents, degree of stomach repletion, relative volume and frequency of occurrence of food items were evaluated. Thirteen food items were identified, and the presence of terrestrial and aquatic insects indicates the high dependence of these species and the flooded forest. Low feeding overlap was observed between Carnegiella strigata and C. marthae compared to Gnathocharax steindachneri. However, the overlap between the two Carnegiella species was relatively high, which could explain the low frequency of syntopic occurrence among these species, suggesting a possible case of competitive exclusion.(AU)

Este estudo teve como objetivo analisar as relações tróficas e a possível existência de uma relação de mimetismo agressivo envolvendo Carnegiella strigata, Carnegiella marthae e Gnathocharax steindachneri, em igarapés de terra firme. As coletas ocorreram em novembro de 2002, março e agosto de 2003 e foram realizadas na Reserva de Desenvolvimento Sustentável de Amanã (RDSA). Foram capturados 943 peixes, onde C. marthae representou 79,43%, C. strigata 3,18% e G. steindachneri 17,39%. Foram analisados os conteúdos estomacais e verificados grau de repleção, volume relativo e frequência de ocorrência dos alimentos. Foram identificados 13 itens alimentares, onde insetos terrestres e aquáticos denotaram alto grau de dependência destas espécies em relação à floresta alagada. Ocorreu baixa sobreposição alimentar das espécies Carnegiella strigata e C. marthae em relação a Gnathocharax steindachneri. Entretanto, a sobreposição entre as duas espécies de Carnegiella foi relativamente alta, o que poderia explicar a baixa frequência de ocorrência sintópica entre essas espécies, sugerindo um possível caso de exclusão competitiva.(AU)

Trophic relationships among three species of ornamental fish from the region of Lake Amanã, Amazon / Relações tróficas entre três espécies de peixes ornamentais da região do lago de Amanã, Amazonas

The present study objectified to evaluate the trophic relationships and the possible aggressive mimicry involving Carnegiella strigata, Carnegiella marthae and Gnathocharax steindachneri, in lowland forest streams. Samplings occurred in November 2002, March and August 2003 in Amanã Sustainable Development Reserve (ASDR). The total of 943 fish was caught, being 79.43% of C. marthae, 3.18% of C. strigata and 17.39% of G. steindachneri. Stomach contents, degree of stomach repletion, relative volume and frequency of occurrence of food items were evaluated. Thirteen food items were identified, and the presence of terrestrial and aquatic insects indicates the high dependence of these species and the flooded forest. Low feeding overlap was observed between Carnegiella strigata and C. marthae compared to Gnathocharax steindachneri. However, the overlap between the two Carnegiella species was relatively high, which could explain the low frequency of syntopic occurrence among these species, suggesting a possible case of competitive exclusion.

Este estudo teve como objetivo analisar as relações tróficas e a possível existência de uma relação de mimetismo agressivo envolvendo Carnegiella strigata, Carnegiella marthae e Gnathocharax steindachneri, em igarapés de terra firme. As coletas ocorreram em novembro de 2002, março e agosto de 2003 e foram realizadas na Reserva de Desenvolvimento Sustentável de Amanã (RDSA). Foram capturados 943 peixes, onde C. marthae representou 79,43%, C. strigata 3,18% e G. steindachneri 17,39%. Foram analisados os conteúdos estomacais e verificados grau de repleção, volume relativo e frequência de ocorrência dos alimentos. Foram identificados 13 itens alimentares, onde insetos terrestres e aquáticos denotaram alto grau de dependência destas espécies em relação à floresta alagada. Ocorreu baixa sobreposição alimentar das espécies Carnegiella strigata e C. marthae em relação a Gnathocharax steindachneri. Entretanto, a sobreposição entre as duas espécies de Carnegiella foi relativamente alta, o que poderia explicar a baixa frequência de ocorrência sintópica entre essas espécies, sugerindo um possível caso de exclusão competitiva.

Comparative Analysis of Three Bradyrhizobium diazoefficiens Genomes Show Specific Mutations Acquired during Selection for a Higher Motility Phenotype and Adaption to Laboratory Conditions.

Microbial genomes are being extensively studied using next-generation sequencing technologies in order to understand the changes that occur under different selection regimes. In this work, the number and type of mutations that have occurred in three Bradyrhizobium diazoefficiens USDA 110T strains under laboratory conditions and during selection for a more motile phenotypic variant were analyzed. Most of the mutations found in both processes consisted of single nucleotide polymorphisms, single nucleotide deletions or insertions. In the case of adaptation to laboratory conditions, half of the changes occurred within intergenic regions, and around 80% were insertions. When the more motile phenotypic variant was evaluated, eight single nucleotide polymorphisms and an 11-bp deletion were found, although none of them was directly related to known motility or chemotaxis genes. Two mutants were constructed to evaluate the 11-bp deletion affecting the alpha subunit of 2-oxoacid:acceptor oxidoreductase (AAV28_RS30705-blr6743). The results showed that this single deletion was not responsible for the enhanced motility phenotype. IMPORTANCE The genetic and genomic changes that occur under laboratory conditions in Bradyrhizobium diazoefficiens genomes remain poorly studied. Only a few genome sequences of this important nitrogen-fixing species are available, and there are no genome-wide comparative analyses of related strains. In the present work, we sequenced and compared the genomes of strains derived from a parent strain, B. diazoefficiens USDA 110, that has undergone processes of repeated culture in the laboratory environment, or phenotypic selection toward antibiotic resistance and enhanced motility. Our results represent the first analysis in B. diazoefficiens that provides insights into the specific mutations that are acquired during these processes.

Robustness and predictability of evolution in bottlenecked populations.

Deterministic and stochastic evolutionary processes drive adaptation in natural populations. The strength of each component process is determined by the population size: deterministic components prevail in very large populations, while stochastic components are the driving mechanisms in small ones. Many natural populations, however, experience intermittent periods of growth, moving through states in which either stochastic or deterministic processes prevail. This growth is often countered by population bottlenecks, which abound in both natural and laboratory populations. Here we investigate how population bottlenecks shape the process of adaptation. We demonstrate that adaptive trajectories in populations experiencing regular bottlenecks can be naturally scaled in time units of generations; with this scaling the time courses of adaptation, fitness variance, and genetic diversity all become relatively insensitive to the timing of population bottlenecks, provided the bottleneck size exceeds a few thousand individuals. We also include analyses at the genotype level to investigate the impact of population bottlenecks on the predictability and distribution of evolutionary pathways. Irrespective of the timing of population bottlenecks, we find that predictability increases with population size. We also find that predictability of the adaptive pathways increases in increasingly rugged fitness landscapes. Overall, our work reveals that both the adaptation rate and the predictability of evolutionary trajectories are relatively robust to population bottlenecks.

Spatial distribution of Brazilian bovine taurine breeds associated with climatic, physical and socioeconomic variables / [Distribuição espacial de raças taurinas bovinas brasileiras associada a variáveis climáticas, físicas e socioeconômicas]

The objective of this study was to evaluate the spatial distribution of purebred Bos taurus taurus bovine breeds raised in Brazil in association with climatic, physical and socioeconomic variables. The breeds Aberdeen Angus, Ayrshire, Braford, Brangus, Charolais, Devon, Flemish, Hereford, Pinzgauer, Shorthorn and Simental were classified according to their aptitude (milk, meat or dual-purpose). They were spatialized according to their aptitude using state and municipal information. The milk breeds were found in the states of Rio Grande do Sul and Santa Catarina, while the dual-purpose breeds were found in Minas Gerais and Rio Grande do Sul states and the beef breeds were concentrated in the southern region. Only the Aberdeen Angus meat breed showed higher dispersion in other regions. Meat and dual-purpose breeds tended to be raised in regions with lower maximum temperature, average temperature, thermal amplitude and temperature-humidity index. Dual-purpose breeds were found in municipalities with high humidity and altitude, but with a low gross domestic product, little technical guidance received from cooperatives and the government, low control of diseases and parasites, as well as low use of pasture rotation systems. The spatial distribution of Brazilian bovine taurine breeds, regardless of aptitude, was related to climatic, physical and socioeconomic factors.(AU)

O objetivo deste estudo foi avaliar a distribuição espacial de raças bovinas puras Bos taurus taurus criadas no Brasil, associadas a variáveis climáticas, físicas e socioeconômicas. As raças Aberdeen Angus, Ayrshire, Braford, Brangus, Charolês, Devon, Flamenga, Hereford, Pinzgauer, Shorthorn e Simental foram classificadas de acordo com sua aptidão (leite, carne ou duplo-propósito). Elas foram espacializadas de acordo com sua aptidão a partir de informações estaduais e municipais. As raças leiteiras foram encontradas nos estados do Rio Grande do Sul e de Santa Catarina, enquanto as raças de duplo-propósito foram encontradas nos estados de Minas Gerais e Rio Grande do Sul, e as raças de carne concentraram-se na região Sul. Apenas a raça de carne Aberdeen Angus apresentou maior dispersão nas demais regiões. As raças de carne e de duplo-propósito tendem a ser criadas em regiões com menores temperatura máxima, temperatura média, amplitude térmica e índice de temperatura e umidade. As raças de duplo-propósito foram encontradas em municípios com alta umidade e altitude, mas com baixo produto interno bruto, pouca orientação técnica recebida de cooperativas e do governo, baixo controle de doenças e de parasitas e baixo uso de sistema de rotação de pastagens. A distribuição espacial das raças taurinas bovinas brasileiras, independentemente da aptidão, foi relacionada a fatores climáticos, físicos e socioeconômicos.(AU)

Inferring Adaptive Codon Preference to Understand Sources of Selection Shaping Codon Usage Bias.

Alternative synonymous codons are often used at unequal frequencies. Classically, studies of such codon usage bias (CUB) attempted to separate the impact of neutral from selective forces by assuming that deviations from a predicted neutral equilibrium capture selection. However, GC-biased gene conversion (gBGC) can also cause deviation from a neutral null. Alternatively, selection has been inferred from CUB in highly expressed genes, but the accuracy of this approach has not been extensively tested, and gBGC can interfere with such extrapolations (e.g., if expression and gene conversion rates covary). It is therefore critical to examine deviations from a mutational null in a species with no gBGC. To achieve this goal, we implement such an analysis in the highly AT rich genome of Dictyostelium discoideum, where we find no evidence of gBGC. We infer neutral CUB under mutational equilibrium to quantify "adaptive codon preference," a nontautologous genome wide quantitative measure of the relative selection strength driving CUB. We observe signatures of purifying selection consistent with selection favoring adaptive codon preference. Preferred codons are not GC rich, underscoring the independence from gBGC. Expression-associated "preference" largely matches adaptive codon preference but does not wholly capture the influence of selection shaping patterns across all genes, suggesting selective constraints associated specifically with high expression. We observe patterns consistent with effects on mRNA translation and stability shaping adaptive codon preference. Thus, our approach to quantifying adaptive codon preference provides a framework for inferring the sources of selection that shape CUB across different contexts within the genome.

Photochemical efficiency correlated with candidate gene expression promote coffee drought tolerance.

The aim of this study was to identify the correlation between photochemical efficiency and candidate genes expression to elucidate the drought tolerance mechanisms in coffee progenies (Icatu Vermelho IAC 3851-2 × Catimor UFV 1602-215) previously identified as tolerant in field conditions. Four progenies (2, 5, 12 and 15) were evaluated under water-deficit conditions (water deficit imposed 8 months after transplanting seedlings to the pots) and under irrigated system. Evaluations of physiological parameters and expression of candidate genes for drought tolerance were performed. Progeny 5 showed capacity to maintain water potential, which contributed to lower qP variation between irrigated and deficit conditions. However, the increases of qN and NPQ in response to stress indicate that this progeny is photochemically responsive to small variations of Ψam protecting the photosystem and maintaining qP. Data obtained for progeny 12 indicated a lower water status maintenance capacity, but with increased qN and NPQ providing maintenance of the ɸPSII and ETR parameters. A PCA analysis revealed that the genes coding regulatory proteins, ABA-synthesis, cellular protectors, isoforms of ascorbate peroxidase clearly displayed a major response to drought stress and discriminated the progenies 5 and 12 which showed a better photochemical response. The genes CaMYB1, CaERF017, CaEDR2, CaNCED, CaAPX1, CaAPX5, CaGolS3, CaDHN1 and CaPYL8a were up-regulated in the arabica coffee progenies with greater photochemical efficiency under deficit and therefore contributing to efficiency of the photosynthesis in drought tolerant progenies.

Understanding the Adaptive Evolutionary Histories of South American Ancient and Present-Day Populations via Genomics.

The South American continent is remarkably diverse in its ecological zones, spanning the Amazon rainforest, the high-altitude Andes, and Tierra del Fuego. Yet the original human populations of the continent successfully inhabited all these zones, well before the buffering effects of modern technology. Therefore, it is likely that the various cultures were successful, in part, due to positive natural selection that allowed them to successfully establish populations for thousands of years. Detecting positive selection in these populations is still in its infancy, as the ongoing effects of European contact have decimated many of these populations and introduced gene flow from outside of the continent. In this review, we explore hypotheses of possible human biological adaptation, methods to identify positive selection, the utilization of ancient DNA, and the integration of modern genomes through the identification of genomic tracts that reflect the ancestry of the first populations of the Americas.