RESUMO
Environmental gradients in the sea may coincide with phenotypic or genetic gradients resulting from an evolutionary balance between selection and dispersal. The population differentiation of the swimming crab, Liocarcinus depurator, an important by-catch species in the Mediterranean Sea and North-East Atlantic, was assessed using both genetic and morphometric approaches. A total of 472 specimens were collected along its distribution area, and 17 morphometric landmarks, one mitochondrial gene (COI) and 11 polymorphic microsatellite markers were scored in 350, 287 and 280 individuals, respectively. Morphometric data lacked significant differences, but genetic analyses showed significant genetic differentiation between Atlantic and Mediterranean populations, with a steeper gradient in COI compared to microsatellite markers. Interestingly, nuclear differentiation was due to an outlier locus with a gradient in the Atlantic-Mediterranean transition area overlapping with the mtDNA gradient. Such overlapping clines are likely to be maintained by natural selection. Our results suggest a scenario of past isolation with local adaptation and secondary contact between the two basins. Local adaptation during the process of vicariance may reinforce genetic differentiation at loci maintained by environmental selection even after secondary contact.
Assuntos
Braquiúros , DNA Mitocondrial , Repetições de Microssatélites , Animais , Braquiúros/genética , Mar Mediterrâneo , Repetições de Microssatélites/genética , DNA Mitocondrial/genética , Oceano Atlântico , Mitocôndrias/genética , Variação Genética , Genética Populacional , Núcleo Celular/genética , Seleção GenéticaRESUMO
On a planet experiencing constant human population growth, it is necessary to explore the anthropogenic effects on the genetic diversity of species, and specifically invasive species. Using an analysis that integrates comparative phylogeography, urban landscape genetics, macrogenetics and a systematic review, we explore the worldwide genetic diversity of the human commensal and anthropogenic species Rattus rattus and Rattus norvegicus. Based on metadata obtained considering 35 selected studies related to observed heterozygosity, measured by nuclear molecular markers (microsatellites, Single Nucleotide Polymorphisms-SNPs-, restrictition site-associated DNA sequencing -RAD-Seq-), socioeconomic and mobility anthropogenic factors were used as predictors of genetic diversity of R. rattus and R. norvegicus, using the Gini index, principal component analysis and Random Forest Regression as analysis methodology. Population density was on average the best predictor of genetic diversity in the Rattus species analyzed, indicating that the species respond in a particular way to the characteristics present in urban environments because of a combination of life history characteristics and human-mediated migration and colonization processes. To create better management and control strategies for these rodents and their associated diseases, it is necessary to fill the existing information gap in urban landscape genetics studies with more metadata repositories, with emphasis on tropical and subtropical regions of the world.
Assuntos
Espécies Introduzidas , Repetições de Microssatélites , Humanos , Ratos , Animais , Densidade Demográfica , Filogeografia , Polimorfismo de Nucleotídeo Único/genéticaRESUMO
Functional enrichment analysis is a cornerstone in bioinformatics as it makes possible to identify functional information by using a gene list as source. Different tools are available to compare gene ontology (GO) terms, based on a directed acyclic graph structure or content-based algorithms which are time-consuming and require a priori information of GO terms. Nevertheless, quantitative procedures to compare GO terms among gene lists and species are not available. Here we present a computational procedure, implemented in R, to infer functional information derived from comparative strategies. GOCompare provides a framework for functional comparative genomics starting from comparable lists from GO terms. The program uses functional enrichment analysis (FEA) results and implement graph theory to identify statistically relevant GO terms for both, GO categories and analyzed species. Thus, GOCompare allows finding new functional information complementing current FEA approaches and extending their use to a comparative perspective. To test our approach GO terms were obtained for a list of aluminum tolerance-associated genes in Oryza sativa subsp. japonica and their orthologues in Arabidopsis thaliana. GOCompare was able to detect functional similarities for reactive oxygen species and ion binding capabilities which are common in plants as molecular mechanisms to tolerate aluminum toxicity. Consequently, the R package exhibited a good performance when implemented in complex datasets, allowing to establish hypothesis that might explain a biological process from a functional perspective, and narrowing down the possible landscapes to design wet lab experiments.
Assuntos
Alumínio , Arabidopsis , Genômica/métodos , Biologia Computacional/métodos , Algoritmos , Ontologia Genética , Arabidopsis/genéticaRESUMO
In mosquitoes of medical importance, wing shape and size can vary with altitude, an aspect that can influence dispersion and, consequently, their vector capacity. Using geometric morphometry analysis, Aedes aegypti wing size and shape variation of males and females was studied in four altitudes in the second-smallest department in Colombia: 1,200 m (Tebaida), 1,400 m (Armenia), 1,500 m (Calarcá), and 1,700 m (Filandia). Wing shape in males (P < 0.001) and females (P < 0.001) was significantly different through the altitudinal gradient; in turn, wing size in males followed the altitudinal gradient males (R2 = 0.04946, P = 0.0002), females (R2 = 0.0011, P = 0.46). Wing allometry for males (P < 0.001) and females (P < 0.001) was significant. Likewise, the shape and size of the wings of males (P < 0.001) and females (P < 0.001) had significant fluctuating asymmetry. It is concluded that, in a small scale with an altitudinal variation of 500 meters, it is detected that the size and shape of the wings varied in A. aegypti, main vector the agents that cause dengue, chikungunya, and Zika. The fluctuating asymmetry is present in the individuals studied and could be associated with environmental effects caused by vector control campaigns present in some sampling locations.
Assuntos
Aedes/fisiologia , Asas de Animais/anatomia & histologia , Asas de Animais/fisiologia , Altitude , Animais , Febre de Chikungunya , Colômbia , Dengue , Feminino , Masculino , Mosquitos Vetores/anatomia & histologia , Infecção por Zika virusRESUMO
Urbanization is currently one the most important causes of biodiversity loss. The Colombian Andes is a well-known hotspot for biodiversity, however, it also exhibit high levels of urbanization, making it a useful site to document how species assemblages respond to habitat transformation. To do this, we compared the structure and composition of bird assemblages between rural and urban habitats in Armenia, a medium sized city located in the Central Andes of Colombia. In addition, we examined the influence of urban characteristics on bird species diversity within the city of Armenia. From September 2016 to February 2017 we performed avian surveys in 76 cells (250 x 250 m each) embedded within Armenia city limits; and in 23 cells (250 x 250 m each) in rural areas around Armenia. We found that bird diversity was significantly lower in urban habitats than in rural habitats, and differed in species composition by 29%. In urban cells, with higher abiotic noise intensity and higher impervious surface area, we found lower bird diversity than that in urban cells with higher guadual (Guadua angustifolia patches), and forested surface areas. We did not find segregation of urban cells according to the species composition, although additional bird surveys inside urban forests remnant are needed to be more conclusive about this aspect. Altogether, our results highlight the importance of green areas embedded within cities to conserve bird diversity through reducing the ecological impact of urbanization on avian biodiversity.
Assuntos
Biodiversidade , Aves/fisiologia , Meio Ambiente , Urbanização , Animais , Cidades , Colômbia , Ecossistema , Florestas , Humanos , Densidade Demográfica , Urbanização/tendênciasRESUMO
Constantly, aquatic ecosystems are under pressure by complex mixtures of contaminants whose effects are not always easy to evaluate. Due to this, organisms are sought in which early warning signs may be detected upon the presence of potentially toxic xenobiotic substances. Thereby, the study evaluated the incidence of deformities and other morphometric variations in the mentum and wing of Chironomus columbiensis exposed to water from some of the Colombian Andes affected by mining, agriculture, and cattle raising. Populations of C. columbiensis were subjected throughout their life cycle (24 days) for two generations (F1 and F2). Five treatments were carried out in controlled laboratory conditions (water from the site without impact, site of mining mercury, mining mercury + cyanide, cattle raising, and agriculture) and the respective control (reconstituted water). Thereafter, the percentage of deformities in the mentum was calculated, and for the morphometric analysis 29 landmarks were digitized for the mentum and 12 for the wing. As a result, four types of deformities were registered in the C. columbiensis mentum, like absence of teeth, increased number of teeth, fusion and space between teeth, none of them detected in the individuals from the control. Additionally, the highest incidence of deformity in F1 occurred in the treatment of mining mercury, while for F2 this took place in the treatments of mining mercury + cyanide, cattle raising and agriculture. Differences were also found with respect to the morphometric variations of the mentum and wing of C. columbiensis among the control and the treatments with water from the creeks intervened. The treatments of mining mercury + cyanide and agriculture had the highest morphological variation in the mentum and wing of C. columbiensis. The results suggest that the anthropogenic impacts evaluated generate alterations in the oral apparatus of the larval state of C. columbiensis and in the adult state provoke alterations in the wing shape (increased width and reduced basal area). These deformities may be related to multiple stress factors, among them the xenobiotics metabolized by the organisms under conditions of environmental contamination.
Assuntos
Chironomidae/efeitos dos fármacos , Poluentes Químicos da Água/toxicidade , Asas de Animais/anormalidades , Animais , Queixo/anormalidades , Chironomidae/anatomia & histologia , Chironomidae/crescimento & desenvolvimento , Monitoramento Ambiental/métodos , Incidência , Larva/anatomia & histologia , Larva/efeitos dos fármacos , Larva/crescimento & desenvolvimento , Poluentes Químicos da Água/análiseRESUMO
Characidium is a Neotropical fish genus. Its distribution ranges from eastern Panama to northern Argentina, and it is an important component of the Neotropical ichthyofauna present in the major rivers of South America. We here provide an approximation to the dispersal and historical distributions of Characidium. The biogeographic history of five species of the genus was analyzed through nuclear RAG-2 and mitochondrial 16S genes and a time-calibrated phylogenetic analysis using three outgroup species. A biogeographical reconstruction was performed to estimate ancestral geographic ranges and infer the historical events that impacted the geographic distributions of Characidium species. Our results showed Characidium as a monophyletic group. The molecular clock suggests that the most recent common ancestor of Characidium originated during the Eocene, about 50.2 Mya. In addition, different dispersion and vicariance events could be inferred, which possibly gave rise to the present geographical distribution of the genus. Our results point to the rise of the Andean mountains and sea fluctuations as being important events in the formations and delimitation of different rivers, which influenced the distribution of South American ichthyofauna.