Influence of artificial lights on the orientation of hatchlings of Eretmochelys imbricata in Pernambuco, Brazil

Sea turtle hatchlings, in natural abiotic conditions, emerge from their nests at night and go directly to the sea, following the moonlight's reflection in the ocean. Increased human activities such as tourism and artificial lights on the coasts, however, have interfered with the ability of sea turtle neonates to find their correct destination, negatively affecting their survival rates. Here we endeavored to assess the influence of artificial lights on the hatchlings of the sea turtle Eretmochelys imbricata (Linnaeus, 1766) in the south coast of the state of Pernambuco, Brazil. To that end, 10 experiments were conducted with 15 hatchlings/test subjects. Five experiments took place in artificially illuminated areas and five in non-illuminated areas. Circles with a 2 m radius were drawn on the sand a small 2–3 cm depression was made at the center of each circles. The neonates were then placed in the depressions to simulate their coming from a nest. After the neonates crossed the edge of the circles, their tracks were photographed and drawn on a diagram. To ascertain if the trajectories of the neonates differed between the two groups (hatchlings from illuminated versus non-illuminated nests), the Rayleigh test was used. The significance of those differences was tested using ANOVA. To evaluate similarities and significance of clusters, a Multi-Dimensional Scaling was used. The tracks of 86.67% (N = 65) of the hatchlings from nests at illuminated areas departed from their correct trajectory. The distribution of trajectories was considered random (V = 19.4895, p > 0.05) only for tracks originating from artificially illuminated areas. The movement patterns of hatchlings from illuminated and non-illuminated areas differed significantly (F < 0.0001, p < 0.01). Consistent with this, two distinct groups were identified, one from illuminated and one from non-illuminated areas. Therefore, we conclude that artificial illumination impacts the orientation of hawksbill hatchlings. This suggests that in order to protect this species it is necessary to safeguard its nesting areas from artificial lights

Molecular taxonomy via DNA barcodes for species identification in selected genera of Fabaceae

Fabaceae merupakan famili yang penting secara ekologi dan ekonomi karena manfaatnya yang tinggi sebagai sumber makanan, pupuk hijau, serta tanaman obat. Namun, di Indonesia Fabaceae telah dieksploitasi secara berlebihan di Indonesia dan beberapa spesies termasuk dalam kategori terancam punah. Untuk mendukung upaya konservasi dibutuhkan teknik identifikasi yang cepat dan akurat. Saat ini, identifikasi spesies melalui DNA barcode telah menjadi teknik klasifikasi taksonomi yang efektif. Penelitian ini bertujuan untuk mengevaluasi efektivitas penanda matK, rbcL, serta kombinasinya (matK+rbcL), sebagai DNA barcode dalam identifikasi spesies dari famili Fabaceae. Hasil penelitian menunjukkan bahwa matK+rbcL dan matK memiliki tingkat identifikasi tertinggi (90% dan 82,05%) pada tingkat spesies. Selain itu, matK memiliki rata-rata jarak interspesifik tertinggi (0.314) dan jarak intraspesifik (0.0030). Selanjutnya pohon filogenetik terbaik dihasilkan dengan metode Neighbour Joining. Berdasarkan analisis secara keseluruhan matK dan matK+rbcL merupakan barcode terbaik untuk spesies terpilih dalam penelitian ini.Fabaceae is an invaluable plant family with considerable ecological and economic importances for example as food sources, bio-fertilizer, and medicinal plants. However, Fabaceae has been overexploited in Indonesia and several species belong to this family are critically endangered. Due to morphological similarity, rapid and accurate identification of Fabaceae species is essential to support its conservation efforts. Nowadays, species identification through DNA barcoding has become an effective taxonomic classification tool. This study was aimed to evaluate the effectiveness of chloroplast markers, matK and rbcL and the combination (matK+rbcL), as DNA barcodes for the identification of seleted genera in Fabaceae. The result showed that matK+rbcL and matK had the highest level of identification (90% and 82.05%) of the investigated genera, respectively. Additionally, matK had the highest mean of interspesific distance (0.134) and intraspecific distance (0.003). The combined barcode matK+rbcL had the highest correct identification rate when comparing the morphological with molecular identification. Furthermore, the best phylogenetic tree was obtained using Neighbor Joining method. Based on the overall performance, matK and matK+rbcL were the best barcodes for the selected genera in this study

Distribuição geográfica e considerações ecológicas sobre a fauna de Testudines da Região Nordeste do Brasil

The knowledge of natural history of the Brazilian species of turtles is still insipient because most information about these animals are restricted to a few records of occurrence, which in general are sparse in the literature or even in museums. The paucity of knowledge prevents broader approaches on various ecological and evolutionary aspects, which are primordial for conservation planning and management of the group. The large geographical extent, the environmental complexity, and the degradation of biomes in Northeast Brazil make the systematization of environmental and biological data on turtles from this region, which are compiled and discussed in this paper, highly important to contribute to the characterization of the conservation status of these species and therefore to subsidize the diagnosis of the environments associated to them.O conhecimento da história natural das espécies brasileiras de cágados e tartarugas ainda é bastante incipiente, visto que a maior parte das informações sobre esses animais se restringe aos poucos registros de ocorrência, que em geral encontram-se esparsos na literatura ou mesmo em museus. Essa escassez de conhecimento dificulta abordagens mais amplas sobre vários aspectos ecológicos e evolutivosprimordiais em planos de conservação e manejo para esse grupo. A grande extensão geográfica, complexidade ambiental e degradação dos biomas no Nordeste fazem com que a sistematização dos dados ambientais e biológicos sobre os quelônios da Região, compilados e discutidos neste trabalho, sejam de suma importância para a caracterização do estado de conservação dessas espécies e, por consequência, auxiliem a subsidiar o diagnóstico dos ambientes associados

Evolutionary history of the Pectoral Sparrow Arremon taciturnus : evidence for diversification during the Late Pleistocene

We focus on reconstructing a spatiotemporal scenario of diversification of a widespread South American species, the Pectoral Sparrow Arremon taciturnus (Aves: Passerellidae). This species is widely distributed in both the humid and the dry forests of South America and therefore provides an interesting model for understanding the connection between different biomes of South America. We examined nucleotide sequences of the mitochondrial genes Cytochrome b (cyt-b) and NADH subunit 2 (ND2) from 107 specimens, and one nuclear marker (intron 7 of the beta-fibrinogen gene) from a subset of samples collected across the distribution ranges of A. t. taciturnus and A. t. nigrirostris. Six major lineages were recovered in the phylogenies that displayed high levels of variance of allele frequencies and corresponded to distinct geographical locations. The estimation of divergence times provided evidence that diversification of the six lineages of the Pectoral Sparrow occurred throughout the Late Pleistocene across major cis-Andean biomes and Amazonian interfluves. Our dataset for A. taciturnus provides further evidence that rivers in Amazonia constitute barriers promoting allopatric speciation, with occasional sharing of alleles among lineages, particularly those with adjacent distributions.Peer reviewe

Optimising high-throughput sequencing data analysis, from gene database selection to the analysis of compositional data: a case study on tropical soil nematodes

IntroductionHigh-throughput sequencing (HTS) provides an efficient and cost-effective way to generate large amounts of sequence data, providing a very powerful tool to analyze biodiversity of soil organisms. However, marker-based methods and the resulting datasets come with a range of challenges and disputes, including incomplete reference databases, controversial sequence similarity thresholds for delimitating taxa, and downstream compositional data analysis. MethodsHere, we use HTS data from a soil nematode biodiversity experiment to explore standardized HTS data processing procedures. We compared the taxonomic assignment performance of two main rDNA reference databases (SILVA and PR2). We tested whether the same ecological patterns are detected with Amplicon Sequence Variants (ASV; 100% similarity) versus classical Operational Taxonomic Units (OTU; 97% similarity). Further, we tested how different HTS data normalization methods affect the recovery of beta diversity patterns and the identification of differentially abundant taxa.ResultsAt this time, the SILVA 138 eukaryotic database performed better than the PR2 4.12 database, assigning more reads to family level and providing higher phylogenetic resolution. ASV- and OTU-based alpha and beta diversity of nematodes correlated closely, indicating that OTU-based studies represent useful reference points. For downstream data analyses, our results indicate that loss of data during subsampling under rarefaction-based methods might reduce the sensitivity of the method, e.g. underestimate the differences between nematode communities under different treatments, while the clr-transformation-based methods may overestimate effects. The Analysis of Compositions of Microbiome with Bias Correction approach (ANCOM-BC) retains all data and accounts for uneven sampling fractions for each sample, suggesting that this is currently the optimal method to analyze compositional data.DiscussionOverall, our study highlights the importance of comparing and selecting taxonomic reference databases before data analyses, and provides solid evidence for the similarity and comparability between OTU- and ASV-based nematode studies. Further, the results highlight the potential weakness of rarefaction-based and clr-transformation-based methods. We recommend future studies use ASV and that both the taxonomic reference databases and normalization strategies are carefully tested and selected before analyzing the data

Ecologia e conservação dos testudines, Nordeste do Brasil

Estudos que visem investigar a ecologia e diversidade genética das populações de testudines são essenciais para avaliar a resposta das comunidades aquáticas dos testudines aos impactos antrópicos e as modificações nos habitats destes animais. Pesquisas relativas a este tema são consideravelmente poucos nos ecossistemas de Caatinga e Mata Atlântica. Desta forma, no intuito de preencher uma lacuna no conhecimento sobre estas espécies, o presente estudo objetivou investigar o status de conservação das populações de testudines localizadas no domínio morfoclimático das Caatingas, na Área de Proteção Ambiental Chapada do Araripe, região de Semi Árido, Ceará, Nordeste do Brasil, no que se refere as suas estruturas populacionais e heterogeneidade gênica, além de compilar as ações cientificas referentes ao tema Testudines no nordeste do Brasil. Foram utilizadas duas armadilhas de convergência específicas para o clado Testudine, denominada Covo (armadilha com isca), seis dias por mês, durante um ano (agosto de 2011 a julho de 2012). Cada espécime capturado foi marcado, sexado, teve seus dados biométricos registrados e foram coletadas amostras biológicas para análise genética. Para efeito de comparação da variabilidade genética das populações de P. geoffroanus foram utilizadas amostras de testudines coletadas em dois pontos do domínio morfoclimático de Mata Atlântica, Mata do Privê em Camaragibe e Mata do Rio Paratibe em Paulista. Foram capturados na área de Caatinga 63 indivíduos, representando três espécies, 44 Phrynops geoffroanus, nove Kinosternon scorpioides e dez Mesoclemmys tuberculata. O tamanho da população estimado pelo método de Jolly-seber foi de 49.28±11 para K. scorpioides ,56±16.3 para M. tuberculata e 301.5±67,09 para P. geoffroanus. O índice de dimorfismo sexual calculado com a média dos valores da carapaça dos machos e fêmeas foi de 1.06 (desviado para fêmeas) para P. geoffroanus e 1.04 (desviado para machos) para K. scopioides. Não foi possível inferir a cerca de dimorfismo sexual ou razão sexual para a espécie M. tuberculata, pois foram capturadas apenas fêmeas. A análise da diversidade genética demonstrou que a população da Caatinga apresentou diversidade genética semelhante a das populações de Mata Atlântica, não havendo distância genética significativamente diferente entre os grupos (Caatinga e Mata Atlântica), que pode ser resultado provavelmente de uma explosão populacional ou intenso fluxo gênico, demonstrando que apesar das condições adversas da caatinga, a população estudada neste ambiente apresenta semelhante capacidade adaptativa que as populações da Mata Atlântica.Studies that aimed investigating the ecology and genetic diversity of populations of Testudines are essential to evaluate the response of aquatic communities of Testudines to human impacts and changes in the habitats of these animals. Research on this subject are few in the ecosystem of Caatinga and Atlantic Forest. Thus, in order to fill a gap in knowledge about these species, the present study aimed to investigate the conservation status of the Testudines populations located in the area of morphoclimatic Caatingas, Environmental Protection Area in the Araripe, Semi Arid region, Ceará, Northeast Brazil, regarding their population structure and genetic heterogeneity, and compile scientific actions related to the subject Testudines in northeastern Brazil. We used two traps convergence specific to clade Testudine called Covo (trap with bait), six days a month, for one year (August 2011 to July 2012). Each specimen captured was marked, sexed, had registered their biometric data and biological samples were collected for genetic analysis. For comparison of the genetic variability of populations of P. geoffroanus were used samples of Testudines collected at two points domain morphoclimatic Atlantic Forest, the Forest of Privê in Camaragibe and the Forest of Rio Paratibe in Paulista. Were captured in the area of Caatinga 63 individuals representing three species, 44 of Phrynops geoffroanus, nine of Kinosternon scorpioides and ten of Mesoclemmys tuberculata. Population size estimated by the Jolly-Seber method was 49.28±11 for K. scorpioides, 56±16.3 for M. tuberculata and 301.5 ± 67.09 for P. geoffroanus.The index of sexual dimorphism calculated the mean carapace of males and females was 1.06 (diverted for females) for P. geoffroanus and 1.04 (deflected males) for K. scopioides. We could not infer about sexual dimorphism and sex ratio for the species M. tuberculata, because only females were captured. Analysis of genetic diversity showed that the population of Caatinga showed similar genetic diversity of the populations of Atlantic forest, with genetic distance no significantly different between groups (Caatinga and Atlantic Forest), which may be the result probably of a population explosion or intense flow gene, demonstrating that despite the adverse conditions of the semi arid, the population studied in this environment presents similar adaptive capacity that populations of Atlantic Forest.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPE

Pliocene Origin, Ice Ages and Postglacial Population Expansion Have Influenced a Panmictic Phylogeography of the European Bee-Eater Merops apiaster

Oscillations of periods with low and high temperatures during the Quaternary in the northern hemisphere have influenced the genetic composition of birds of the Palearctic. During the last glaciation, ending about 12,000 years ago, a wide area of the northern Palearctic was under lasting ice and, consequently, breeding sites for most bird species were not available. At the same time, a high diversity of habitats was accessible in the subtropical and tropical zones providing breeding grounds and refugia for birds. As a result of long-term climatic oscillations, the migration systems of birds developed. When populations of birds concentrated in refugia during ice ages, genetic differentiation and gene flow between populations from distinct areas was favored. In the present study, we explored the current genetic status of populations of the migratory European bee-eater. We included samples from the entire Palearctic-African distribution range and analyzed them via mitochondrial and nuclear DNA markers. DNA data indicated high genetic connectivity and panmixia between populations from Europe, Asia and Africa. Negative outcomes of Fu&rsquo;s Fs and Tajima&rsquo;s D tests point to recent expansion events of the European bee-eater. Speciation of Merops apiaster started during the Pliocene around three million years ago (Mya), with the establishment of haplotype lineages dated to the Middle Pleistocene period circa 0.7 Mya. M. apiaster, which breed in Southern Africa are not distinguished from their European counterparts, indicating a recent separation event. The diversification process of the European bee-eater was influenced by climatic variation during the late Tertiary and Quaternary. Bee-eaters must have repeatedly retracted to refugia in the Mediterranean and subtropical Africa and Asia during ice ages and expanded northwards during warm periods. These processes favored genetic differentiation and repeated lineage mixings, leading to a genetic panmixia, which we still observe today

A alegoria da paisagem cultural brasileira

This text discusses protection of Brazil’s cultural landscape. Issues include intentions to regulate heritage preservation tool and conceptual implications of cultural landscape as cultural heritage. Recent turning points in Brazil are the suspension of the national cultural landscape instrument in 2014, and Unesco’s recognition, between 2012 and 2021, of four cultural landscapes in Brazil, despite the fact that this was still under discussion by Brazil’s national agency for heritage preservation. The text proposes a critical analysis of Brazil’s cultural landscape instrument in the field of cultural heritage, taking into account the roots of Brazilian culture formation, which includes the role of nation building and heritage preservation policies. The critique links Brazil’s cultural landscape to that which emerges from the struggle and resistance of the Brazilian people, therefore, to a mestizo landscape, which needs to be assimilated in an inclusive perspective of all subjects.O texto discute a proteção da paisagem cultural brasileira levando em conta a intenção de regulamentação de um instrumento de preservação patrimonial e as implicações conceituais da paisagem como patrimônio cultural. Toma-se como pontos de inflexão a suspensão do instrumento da chancela da Paisagem Cultural Brasileira em 2014, bem como o reconhecimento de quatro paisagens culturais do Brasil pela Unesco entre 2012 e 2021, quando este instrumento ainda está em discussão no âmbito do órgão nacional de preservação patrimonial. Neste sentido, o texto propõe uma reflexão crítica sobre o instrumento da paisagem cultural brasileira no campo do patrimônio cultural, ao lado das raízes que formam a cultura brasileira, questão associada ao contexto mais amplo que atravessa a formação nacional e, consequentemente, a regulamentação das políticas de preservação do patrimônio no Brasil. A crítica almeja atrelar a paisagem cultural brasileira àquela que emerge da luta e da resistência do povo brasileiro, portanto, a umapaisagem mestiça, que precisa ser assimilada numa perspectiva inclusiva de todos os sujeitos

Heat maps of interspecific genetic distances between Lamiaceae species sampled in Sumatra, Indonesia.

A- Interspecific genetic distances estimated using matK, B—rbcL and C- ITS regions. Scale bar is adjusted to the maximum genetic distance value of each marker.</p

Maximum likelihood tree estimated based on the <i>rbcL</i> sequences of Lamiaceae.

The tips of the tree labels display the species IDs. The subfamilies of the Lamiaceae family are highlighted in different colours. * Highlights juvenile specimens. (TIF)</p