Uncovering patterns of the evolution of genomic sequence entropy and complexity.

The lack of consensus concerning the biological meaning of entropy and complexity of genomes and the different ways to assess these data hamper conclusions concerning what are the causes of genomic entropy variation among species. This study aims to evaluate the entropy and complexity of genomic sequences of several species without using homologies to assess relationships among these variables and non-molecular data (e.g., the number of individuals) to seek a trigger of interspecific genomic entropy variation. The results indicate a relationship among genomic entropy, genome size, genomic complexity, and the number of individuals: species with a small number of individuals harbors large genome, and hence, low entropy but a higher complexity. We defined that the complexity of a genome relies on the entropy of each DNA segment within genome. Then, the entropy and complexity of a genome reflects its organization solely. Exons of vertebrates harbor smaller entropies than non-exon regions (likely by the repeats that accumulated from duplications), whereas other taxonomic groups do not present this pattern. Our findings suggest that small initial population might have defined current genomic entropy and complexity: actual genomes are less complex than ancestral ones. Besides, our data disagree with the relationship between phenotype and genomic entropies previously established. Finally, by establishing the relationship between genomic entropy/complexity with the number of individuals and genome size, under an evolutive perspective, ideas concerning the genomic variability may emerge.

Local host-tick coextinction in neotropical forest fragments.

Ticks are obligatory parasites with complex life cycles that often depend on larger bodied vertebrates as final hosts. These traits make them particularly sensitive to local coextinction with their host. Loss of wildlife abundance and diversity should thus lead to loss of tick abundance and diversity to the point where only generalist tick species remain. However, direct empirical tests of these hypotheses are lacking, despite their relevance to our understanding of tick-borne disease emergence in disturbed environments. Here, we compare vertebrate and tick communities across 12 forest islands and peninsulas in the Panama Canal that ranged 1000-fold in size (2.6-2811.3 ha). We used drag sampling and camera trapping to directly assess the abundance and diversity of communities of questing ticks and vertebrate hosts. We found that the abundance and species richness of ticks were positively related to those of wildlife. Specialist tick species were only present in fragments where their final hosts were found. Further, less diverse tick communities had a higher relative abundance of the generalist tick species Amblyomma oblongoguttatum, a potential vector of spotted fever group rickettsiosis. These findings support the host-parasite coextinction hypothesis, and indicate that loss of wildlife can indeed have cascading effects on tick communities. Our results also imply that opportunities for pathogen transmission via generalist ticks may be higher in habitats with degraded tick communities. If these patterns are general, then tick identities and abundances serve as useful bioindicators of ecosystem health, with low tick diversity reflecting low wildlife diversity and a potentially elevated risk of interspecific disease transmission via remaining host species and generalist ticks.

Inference of Developmental Gene Regulatory Networks Beyond Classical Model Systems: New Approaches in the Post-genomic Era.

The advent of high-throughput sequencing (HTS) technologies has revolutionized the way we understand the transformation of genetic information into morphological traits. Elucidating the network of interactions between genes that govern cell differentiation through development is one of the core challenges in genome research. These networks are known as developmental gene regulatory networks (dGRNs) and consist largely of the functional linkage between developmental control genes, cis-regulatory modules, and differentiation genes, which generate spatially and temporally refined patterns of gene expression. Over the last 20 years, great advances have been made in determining these gene interactions mainly in classical model systems, including human, mouse, sea urchin, fruit fly, and worm. This has brought about a radical transformation in the fields of developmental biology and evolutionary biology, allowing the generation of high-resolution gene regulatory maps to analyze cell differentiation during animal development. Such maps have enabled the identification of gene regulatory circuits and have led to the development of network inference methods that can recapitulate the differentiation of specific cell-types or developmental stages. In contrast, dGRN research in non-classical model systems has been limited to the identification of developmental control genes via the candidate gene approach and the characterization of their spatiotemporal expression patterns, as well as to the discovery of cis-regulatory modules via patterns of sequence conservation and/or predicted transcription-factor binding sites. However, thanks to the continuous advances in HTS technologies, this scenario is rapidly changing. Here, we give a historical overview on the architecture and elucidation of the dGRNs. Subsequently, we summarize the approaches available to unravel these regulatory networks, highlighting the vast range of possibilities of integrating multiple technical advances and theoretical approaches to expand our understanding on the global gene regulation during animal development in non-classical model systems. Such new knowledge will not only lead to greater insights into the evolution of molecular mechanisms underlying cell identity and animal body plans, but also into the evolution of morphological key innovations in animals.

Biodiversity conservation gaps in the Brazilian protected areas.

Although Brazil is a megadiverse country and thus a conservation priority, no study has yet quantified conservation gaps in the Brazilian protected areas (PAs) using extensive empirical data. Here, we evaluate the degree of biodiversity protection and knowledge within all the Brazilian PAs through a gap analysis of vertebrate, arthropod and angiosperm occurrences and phylogenetic data. Our results show that the knowledge on biodiversity in most Brazilian PAs remain scant as 71% of PAs have less than 0.01 species records per km2. Almost 55% of Brazilian species and about 40% of evolutionary lineages are not found in PAs, while most species have less than 30% of their geographic distribution within PAs. Moreover, the current PA network fails to protect the majority of endemic species. Most importantly, these results are similar for all taxonomic groups analysed here. The methods and results of our countrywide assessment are suggested to help design further inventories in order to map and secure the key biodiversity of the Brazilian PAs. In addition, our study illustrates the most common biodiversity knowledge shortfalls in the tropics.

Vertebrate road kill survey on a highway in southern Brazil / Levantamento de vertebrados atropelados em rodovias do sul do Brasil

Highways are a major factor acting in the decline of several wildlife populations. Impact occurs due to the continuous flow of motor vehicles over tracks and collision with animals using the same area. This study aimed to list road killed wild vertebrates found in highways in the Pampa Biome, state of Rio Grande do Sul, over an entire year. The taxa found (amphibians, reptiles, birds and mammals) were identified to species level and their frequency of occurrence was seasonally registered. Along 2,160 km, we found 318 road killed individuals, totaling 65 species. This number represents an average of 0.147 road killed specimens by kilometer (that is, 1 individual each 7 km). Of these, seven species are under threat of extinction in the state of Rio Grande do Sul. We also found a seasonal pattern among road kills, in which the highest number of road killed animals was registered in the summer and spring months. These results contribute to increase knowledge about which species are most impacted by road kill on highways of the Pampa Biome. Such data can be used as an indicator for the implementation of measures by competent bodies to mitigate impacts of highways in the state of Rio Grande do Sul.(AU)

As rodovias são um fator provocador de declínio populacional de diversas espécies da fauna silvestre. O impacto ocorre devido ao contínuo fluxo de veículos automotores sobre as pistas e a colisão dos mesmos com animais que também utilizam essa área. O presente estudo teve por finalidade listar os vertebrados silvestres encontrados atropelados em rodovias no bioma Pampa, no Estado do Rio Grande do Sul, ao longo de um ano. Os táxons encontrados (anfíbios, répteis, aves e mamíferos) foram identificados em nível específico e a sua frequência de ocorrência foi registrada de forma sazonal. Em 2.160 km de estrada percorridos, foram encontrados 318 indivíduos atropelados, totalizando 65 espécies. Essa quantia representa uma média de 0,147 espécimes atropelados por quilômetro (ou seja, 01 indivíduo atropelado a cada 07 Km). Destas, sete espécies estão sob ameaça de extinção no Estado do Rio Grande do Sul. Foram observados padrões sazonais nos atropelamentos, sendo que os meses de verão e da primavera apresentaram o maior número de animais atropelados. Os resultados do estudo contribuem para o conhecimento de quais espécies da fauna silvestre são mais impactadas por atropelamentos no bioma Pampa. Estes dados poderão ser utilizados como orientação na implantação de medidas por órgãos competentes, afim de mitigar o impacto de rodovias no Estado do Rio Grande do Sul.(AU)

Nodal signalling and asymmetry of the nervous system.

The role of Nodal signalling in nervous system asymmetry is still poorly understood. Here, we review and discuss how asymmetric Nodal signalling controls the ontogeny of nervous system asymmetry using a comparative developmental perspective. A detailed analysis of asymmetry in ascidians and fishes reveals a critical context-dependency of Nodal function and emphasizes that bilaterally paired and midline-unpaired structures/organs behave as different entities. We propose a conceptual framework to dissect the developmental function of Nodal as asymmetry inducer and laterality modulator in the nervous system, which can be used to study other types of body and visceral organ asymmetries. Using insights from developmental biology, we also present novel evolutionary hypotheses on how Nodal led the evolution of directional asymmetry in the brain, with a particular focus on the epithalamus. We intend this paper to provide a synthesis on how Nodal signalling controls left-right asymmetry of the nervous system.This article is part of the themed issue 'Provocative questions in left-right asymmetry'.

Homology of the fifth epibranchial and accessory elements of the ceratobranchials among gnathostomes: insights from the development of ostariophysans.

Epibranchials are among the main dorsal elements of the gill basket in jawed vertebrates (Gnathostomata). Among extant fishes, chondrichthyans most resemble the putative ancestral condition as all branchial arches possess every serially homologous piece. In osteichthyans, a primitive rod-like epibranchial 5, articulated to ceratobranchial 5, is absent. Instead, epibranchial 5 of many actinopterygians is here identified as an accessory element attached to ceratobranchial 4. Differences in shape and attachment of epibranchial 5 in chondrichthyans and actinopterygians raised suspicions about their homology, prompting us to conduct a detailed study of the morphology and development of the branchial basket of three ostariophysans (Prochilodus argenteus, Characiformes; Lophiosilurus alexandri and Pseudoplatystoma corruscans, Siluriformes). Results were interpreted within a phylogenetic context of major gnathostome lineages. Developmental series strongly suggest that the so-called epibranchial 5 of actinopterygians does not belong to the epal series because it shares the same chondroblastic layer with ceratobranchial 4 and its ontogenetic emergence is considerably late. This neomorphic structure is called accessory element of ceratobranchial 4. Its distribution among gnathostomes indicates it is a teleost synapomorphy, occurring homoplastically in Polypteriformes, whereas the loss of the true epibranchial 5 is an osteichthyan synapomorphy. The origin of the accessory element of ceratobranchial 4 appears to have occurred twice in osteichthyans, but it may have a single origin; in this case, the accessory element of ceratobranchial 4 would represent a remnant of a series of elements distally attached to ceratobranchials 1-4, a condition totally or partially retained in basal actinopterygians. Situations wherein a structure is lost while a similar neomorphic element is present may lead to erroneous homology assessments; these can be avoided by detailed morphological and ontogenetic investigations interpreted in the light of well-supported phylogenetic hypotheses.

Desarrollo de los Miembros en los Vertebrados / Limb Development in Vertebrates

Los miembros de los vertebrados son estructuras complejas con tres ejes a considerar, proximal-distal, anterior-posterior y dorsal-ventral. La batería de genes involucrados en la formación de estas estructuras está bastante conservada en la evolución. El esbozo del miembro está compuesto de células mesenquimáticas indiferenciadas que derivan del mesodermo lateral somático cubiertas por ectodermo. La cresta apical ectodérmica es un centro productor de señales para el desarrollo y se ubica en el margen distal del esbozo de miembro. La zona de progreso esta a continuación y permite el crecimiento del miembro. El tipo de estructuras formadas a lo largo del eje proximal distal es especificado por los genes Hox. La proteína Sonic Hedgehog está involucrada en la regulación de la actividad de un segundo centro de señales conocido como zona de actividad polarizante. Los miembros también tienen una polaridad dorso ventral. La proteína WNT7A secretada desde el ectodermo dorsal, instruye a las células mesenquimales circundantes a diferenciarse en estructuras dorsales mientras que Engrailed 1 expresado en el ectodermo ventral, inhibe la expresión de WNT7A en esta zona del esbozo de miembro promoviendo la formación de estructuras ventrales.

Members of vertebrates are complex structures with three lines to consider, proximal-distal, anterior-posterior and dorsal-ventral. The battery of genes involved in the formation of these structures is well conserved in evolution. The outline of the member is composed of undifferentiated mesenchymal cells derived from somatic lateral mesoderm covered by ectoderm. The apical ectodermal ridge is a signal producing center for development and is located in the distal margin of the outline of a member. The area of progress is below and allows the growth of the member. The type of structures formed along the proximal distal axis is specified by Hox genes. Sonic Hedgehog protein is involved in regulating the activity of a second signaling center known as the zone of polarizing activity. Members also have a dorsal ventral polarity. The Wnt protein secreted from the dorsal ectoderm, instructs the surrounding mesenchymal cells to differentiate into dorsal structures whereas Engrailed 1 expressed in the ventral ectoderm, inhibit the expression of WNT7A outline in this membership area promoting the formation of ventral structures.

A fauna de vertebrados do campus da Universidade Estadual de Londrina, região norte do estado do Paraná, Brasil / The vertebrates’ fauna from Universidade Estadual de Londrina campus, northern Paraná State, Brazil

Este trabalho teve como objetivo fazer um levantamento da fauna de vertebrados do campus da Universidade Estadual de Londrina (UEL), pela compilação da literatura, com vistas a auxiliar o seu manejo e preservação. Foram registradas 250 espécies, sendo nove de peixes, 15 de anfíbios, 16 de répteis, 32 de mamíferos e 178 de aves. Duas espécies, o gato-do-mato Leopardus tigrinus e a jandaia-de-testa-vermelha Aratinga auricapillus figuram em listas de fauna ameaçada de extinção. A maioria das espécies, no entanto, não é estenóica ou endêmica da área, o que condiz com um ambiente perturbado e muito freqüentado pela população humana. O assoreamento do ribeirão Esperança, a redução de áreas verdes e a impermeabilização do solo podem reduzir a diversidade de espécies em médio a longo prazos.

This work had the objective to make a survey of vertebrates’ fauna from Universidade Estadual de Londrina (UEL) campus, for the compilation of literature, in order to help its management and preservation. 250 species were identified, being nine of fish, 15 of amphibians, 16 of reptiles, 32 of mammals and 178 of birds. Two species, the gato-do-mato Leopardus tigrinus and the jandaia-da-testa-vermelha Aratinga auricapillus, are in the list of species threatened by extinction. Most species, however, are not stenoecious or endemic to the area, which corresponds to an environment under stress and often visited by humans. Despite UEL’s rich diversity of wild animals, the burying of stream Esperança, the reduction of green areas and waterproofing of the ground can reduce de diversity of species in a medium or long term.

Static allometry and animal genitalia.

A survey of 117 species of arthropods and 17 species of vertebrates showed a strong trend for male genitalia to have relatively low static allometric values. This trend contrasts with the allometry of other structures under sexual selection, which usually show steep allometric slopes. The trend to low allometric genital values is less consistent in mammals than in arthropods. Data not in accord with the previous the "one-size-fits-all" explanation for low allometric slopes in genitalia, which was based on sexual selection by female choice, suggest a more general version that includes both natural selection and sexual selection, and involves both mechanical fit and stimulation. Less-complete data on the female genitalia of arthropods suggest a trend to similar low allometric slopes, and may also be explained by mechanical fit and stimulatory one-size-fits-all arguments.

Coincident scales of forest feedback on climate and conservation in a diversity hot spot.

The dynamic relationship between vegetation and climate is now widely acknowledged. Climate influences the distribution of vegetation; and through a number of feedback mechanisms vegetation affects climate. This implies that land-use changes such as deforestation will have climatic consequences. However, the spatial scales at which such feedbacks occur remain largely unknown. Here, we use a large database of precipitation and tree cover records for an area of the biodiversity-rich Atlantic forest region in south eastern Brazil to investigate the forest-rainfall feedback at a range of spatial scales from ca 10(1)-10(4) km2. We show that the strength of the feedback increases up to scales of at least 10(3) km2, with the climate at a particular locality influenced by the pattern of landcover extending over a large area. Thus, smaller forest fragments, even if well protected, may suffer degradation due to the climate responding to land-use change in the surrounding area. Atlantic forest vertebrate taxa also require large areas of forest to support viable populations. Areas of forest of ca 10(3) km2 would be large enough to support such populations at the same time as minimizing the risk of climatic feedbacks resulting from deforestation.

Vertebrate floor plate transiently expresses a compound recognized by antisera raised against subcommissural organ secretion.

Located along the ventral midline of the neural tube, the floor plate (FP) performs an essential role in central nervous system development, especially in the patterning of the ventral region of the neural tube and axonal guidance. Several studies have been directed to the identification of molecules mediating some of the functions of the FP. Most of the models proposed for floor plate actions involve contact-mediated- and/or gradients of diffusible-signals acting throughout the nervous tissue. This report presents and discusses findings showing that the FP cells secrete a novel compound, which is recognized by antisera raised against secretory products of the subcommissural organ (SCO). This immunoreactive compound appears to be very similar to one of the glycoproteins secreted by the SCO. This immunoreactivity is expressed transiently during central nervous system development, and its rostro-caudal extension along the anterior-posterior axis of the FP displays some species variations. However, a constant feature in all species investigated is that this immunoreactive compound is highly expressed in the FP located in the mesencephalic-metencephalic boundary. The distribution of this compound is compatible with basal and apical pathways of release from FP cells. The former might participate in the formation of some brain commissures. The latter might involve the use of the cerebrospinal fluid as a route for performing actions on distant targets, a pathway somehow disregarded by most models accounting for morphogen actions.

Utilización del suero caprino como sustituto del suero de ternera donante en el crecimiento de algunos cultivos primarios de vertebrados / Use of goats serum as a substitute for doner calf serum in the growth of some primary cultures of vertebrates

Se utilizó el suero caprino para la preparación de cultivos primarios de fibroblastos de embrión de pollo y riñón de hámster, los cuales fueron posteriormente inoculados con el virus de la encefalomielitis equina del Este en comparación con los cultivos obtenidos mediante el suero de ternera donante. La utilización del suero caprino para nuestros propósitos en este trabajo, constituye una opción de gran interés para el desarrollo en el campo de las investigaciones científicas y la economía del país