A Review of the Mitogenomic Phylogeny of the Chondrichthyes

The phylogenetic analysis of the Chondrichthyes has been the subject of intense debate over the past two decades. The principal relationships within the group based on the analysis of morphological traits are inconsistent with the available molecular topologies, and the phylogeny of these animals is highly controversial, at all levels, ranging from superorders to families and even the genera within families. With the recent development of new generation sequencing (NGS), many phylogenies are now being inferred based on the complete genome of the species. In 2015 and 2016 alone, around 21 new elasmobranch genomes were made available in GenBank. In this context, the principal objective of the present study was to infer the phylogeny of the sharks and rays based on the complete mitochondrial genomes available in the literature. A total of 73 mitogenomes of chondrichthyan species were analyzed. The phylogenetic trees generated rejected the “Hypnosqualea” hypothesis and confirmed the monophyly of the Neoselachii and Batoidea as sister groups of the sharks. These mitogenomic analyses provided ampler and more complete insights into the relationships between the sharks and rays, in particular, the topologies obtained by the analyses revealed a number of incongruities in certain groups of sharks and rays, and the interrelationships between them

Análise populacional de Scomberomorus cavalla (Cuvier, 1829) (Perciformes, Scombridae) da costa Norte e Nordeste brasileira

Scomberomorus cavalla is a pelagic fish species widely distributed on the Atlantic west coast, and a noticeable decrease in its capture level in the USA and Gulf of Mexico is occurring, compared to the levels reached by the species in the past. Likewise, in some areas of Brazil, there has been indication of over-harvesting. However, there are no molecular studies focusing on the management of such an important item. Thus, in the present study, 380 nucleotide base pairs of the mitochondrial DNA D-Loop region of samples from Macapá, Bragança, and Fortaleza were sequenced. Phylogenetic and population analyses revealed that there is only one panmitic population, and low levels of genetic variability were verified. These results, as well as the noticed over-harvesting of S. cavalla, represent very important data to determine the management of such stock in order to prevent a collapse or the risk of future extinction.Scomberomorus cavalla é uma espécie de peixe pelágico amplamente distribuído na costa oeste do Atlântico, e uma diminuição no seu nível de captura tem sido verificada nos E.U.A e Golfo do México, comparada com os níveis alcançados pela espécie no passado. Da mesma forma, em algumas áreas do Brasil, há indícios de sobre-exploração. Entretanto, não existem estudos moleculares que visam o manejo deste importante item. Desta forma, no presente estudo, foram seqüenciados 380 pares de bases nucleotídicas da região da Alça-D do DNA mitocondrial de amostras provenientes de desembarque em Macapá, Bragança e Fortaleza. As análises filogenéticas e populacionais revelaram que há apenas uma população panmítica e baixos níveis de variabilidade genética foram observados. Estes resultados, assim como a observada sobre-exploração de S. cavala, representam dados muito importantes para o estabelecimento do manejo deste estoque a fim de prevenir um colapso ou risco de extinção no futuro

FILOGENIA MOLECULAR DE CLUPEIFORMES E O POSICIONAMENTO DE ALGUNS TÁXONS DAS REGIÕES DO ATLÂNTICO OCIDENTAL E AMAZÔNIA

The taxonomy of herrings, sardines and anchovies from morphological and molecular characters has been largely approached, but the phylogenetic relationships among most of the taxa are little resolved. The present study of the mitochondrial ribosomal 16S gene using, adding sequence data for 14 species of Neotropical sardines from both marine and freshwater habitats, 10 of which appear for the first time in molecular phylogenetic analysis. Results from Bayesian, Maximum Likelihood and Parsimony analyses strongly support the monophyly of the families Pristigasteridae and Engraulidae, but were not able to recover the monophyly of the family Clupeidae. In addition, Chirocentridae and Sundasalangidae, appear in polytomic arrangements among some Clupeidae/Clupeiformes lineages. Curiously, Odontognathus mucronatus and Pellona harroweri, a Western Atlantic species which were included in a molecular phylogenetic analysis for the first time were key species, breaking up the monophyly of both Pellona and Ilisha inside the Pristigasteridae. Additional examples of paraphyly and/or polyphyly were observed for several traditional genera, such as Sardinella, Anchoa and Engraulis. The present analysis successfully resolved some relevant aspects of its taxonomy and opened several questions that will demand additional sampling effort and new phylogenetic analyses to better clarify the taxonomy of this rich group of fishes.Keywords: Clupeiformes, molecular phylogeny, Amazonian, sardines, mitochondrial.A taxonomia dos arenques, sardinhas e anchovas a partir de caracteres morfológicos e moleculares tem sido amplamente abordada, mas as relações filogenéticas entre a maioria dos táxons são pouco resolvidas. O presente estudo utilizou o gene ribossômico mitocondrial 16S, e adicionando dados de sequência para 14 espécies de sardinha neotropical de habitats marinhos e de água doce, 10 das quais aparecem pela primeira vez em análises filogenéticas moleculares. Os resultados das análises bayesiana, máxima verossimilhança e parcimônia suportam fortemente a monofilia das famílias Pristigasteridae e Engraulidae, mas não foram capazes de recuperar a monofilia da família Clupeidae. Chirocentridae e Sundasalangidae, aparecem em arranjos politômicos entre algumas linhagens de Clupeidae/Clupeiformes. Curiosamente, Odontognathus mucronatus e Pellona harroweri, espécies do Atlântico Ocidental que foram incluídas em uma análise filogenética molecular pela primeira vez, sendo espécies-chave, quebraram a monofilia de Pellona e Ilisha dentro de Pristigasteridae. Exemplos adicionais de parafilia e/ou polifilia foram observados para vários gêneros tradicionais, como Sardinella, Anchoa e Engraulis. A presente análise resolveu com sucesso alguns aspectos relevantes de sua taxonomia e abriu várias questões que exigirão um esforço adicional de amostragem e novas análises filogenéticas para melhor esclarecer a taxonomia desse rico grupo de peixes.Palavras-chaves: Clupeiformes, filogenia molecular, Amazônia, sardinhas, mitocondrial

Ictiofauna comercial de Gurupá, Pará / Commercial ichthyofauna in Gurupá, Pará

A pesca é uma das mais antigas atividades praticadas pelo homem. O pescado é uma das principais fontes de proteínas inserida diariamente no cardápio dos povos da Amazônia. Neste trabalho foram capturadas e identificadas espécies de peixes em Gurupá – PA, município pertencente ao arquipélago do Marajó, localizado na foz do rio Amazonas, o maior arquipélago fluvio-marinho do mundo, com mais de 50.000 Km². Foram coletadas informações sobre os peixes mais importantes comercialmente para a região, durante os anos 2014 e 2015 a partir de vistitas semanais aos mercados de peixes da cidade. Foi registrado 30 espécies, distribuídas em 26 gêneros e 15 famílias. As famílias mais representativas foram Cichlidae e Pimelodidae (6 espécies cada), seguida por Serrasalmidae (4 espécies), por fim Erythrinidae e Pristigasteridae (2 espécies cada) as demais famílias apresentaram uma única espécie de peixe. Tais peixes são conhecidos popularmente como, filhote, pacú, curimatã, mapará, piramutaba, sarda e pirarucu. Como esperado, foi notado uma grande diversidade de espécies comercializadas em Gurupá, pois a Amazônia é conhecida como um hotspots para novas espécies de peixes de água doce. A atividade de pesca é de suma importante para a população gurupaense, assim como para os povos de toda a região Amazônica

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear un derstanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5–7 vast areas of the tropics remain understudied.8–11 In the American tropics, Amazonia stands out as the world’s most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepre sented in biodiversity databases.13–15 To worsen this situation, human-induced modifications16,17 may elim inate pieces of the Amazon’s biodiversity puzzle before we can use them to understand how ecological com munities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple or ganism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region’s vulnerability to environmental change. 15%–18% of the most ne glected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lostinfo:eu-repo/semantics/publishedVersio

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear understanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5,6,7 vast areas of the tropics remain understudied.8,9,10,11 In the American tropics, Amazonia stands out as the world's most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepresented in biodiversity databases.13,14,15 To worsen this situation, human-induced modifications16,17 may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple organism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region's vulnerability to environmental change. 15%–18% of the most neglected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lost

Secondary Metabolites Found among the Species <i>Trattinnickia rhoifolia</i> Willd

Plant-derived products may represent promising strategies in the treatment of Neglected Tropical Diseases (NTDs). From this perspective, it is observed that the Amazon phytogeographic region contains the tribe Canarieae of the Burseraceae family, composed of trees and shrubs supplied with resin channels. Its uses in folk medicine are related to aromatic properties, which have numerous medicinal applications and are present in reports from traditional peoples, sometimes as the only therapeutic resource. Despite its economic and pharmacological importance in the region, and although the family is distributed in all tropical and subtropical regions of the world, most of the scientific information available is limited to Asian and African species. Therefore, the present work aimed to review the secondary metabolites with possible pharmacological potential of the species Trattinnickia rhoifolia Willd, popularly known as “Breu sucuruba”. To this end, an identification key was created for chemical compounds with greater occurrence in the literature of the genus Trattinnickia. The most evident therapeutic activities in the consulted studies were antimicrobial, antioxidant, anti-inflammatory, antiviral, antifungal, anesthetic and antiparasitic. An expressive chemical and pharmacological relevance of the species was identified, although its potential is insufficiently explored, mainly in the face of the NTDs present in the Brazilian Amazon

Patterns of Genetic Variability in Island Populations of the Cane Toad (<i>Rhinella marina</i>) from the Mouth of the Amazon

<div><p>The Amazonian coast has several unique geological characteristics resulting from the interaction between drainage pattern of the Amazon River and the Atlantic Ocean. It is one of the most extensive and sedimentologically dynamic regions of the world, with a large number of continental islands mostly formed less than 10,000 years ago. The natural distribution of the cane toad (<i>Rhinella marina</i>), one of the world’s most successful invasive species, in this complex Amazonian system provides an intriguing model for the investigation of the effects of isolation or the combined effects of isolation and habitat dynamic changes on patterns of genetic variability and population differentiation. We used nine fast-evolving microsatellite loci to contrast patterns of genetic variability in six coastal (three mainlands and three islands) populations of the cane toad near the mouth of the Amazon River. Results from Bayesian multilocus clustering approach and Discriminant Analyses of Principal Component were congruent in showing that each island population was genetically differentiated from the mainland populations. All <i>F</i>_<i>ST</i> values obtained from all pairwise comparisons were significant, ranging from 0.048 to 0.186. Estimates of both recent and historical gene flow were not significantly different from zero across all population pairs, except the two mainland populations inhabiting continuous habitats. Patterns of population differentiation, with a high level of population substructure and absence/restricted gene flow, suggested that island populations of <i>R</i>. <i>marina</i> are likely isolated since the Holocene sea-level rise. However, considering the similar levels of genetic variability found in both island and mainland populations, it is reliable to assume that they were also isolated for longer periods. Given the genetic uniqueness of each cane toad population, together with the high natural vulnerability of the coastal regions and intense human pressures, we suggest that these populations should be treated as discrete units for conservation management purposes.</p></div

Adult toads (<i>Rhinella marina</i>) collected in Bailique Island showing deformities.

<p>(A and D) Individuals with Hemimelia (partially missing limb); (B, C and E) Digit bent at joint; (F) Forked digits; Polydactyly (G) (Photographs: Adam R. Bessa-Silva and Davidson Sodré). Scales = 1 cm.</p