Viral metagenomic analysis of feces of wild small carnivores

Background: Recent studies have clearly demonstrated the enormous virus diversity that exists among wild animals. This exemplifies the required expansion of our knowledge of the virus diversity present in wildlife, as well as the potential transmission of these viruses to domestic animals or humans. Methods: In the present study we evaluated the viral diversity of fecal samples (n = 42) collected from 10 different species of wild small carnivores inhabiting the northern part of Spain using random PCR in combination with next-generation sequencing. Samples were collected from American mink (Neovison vison), European mink (Mustela lutreola), European polecat (Mustela putorius), European pine marten (Martes martes), stone marten (Martes foina), Eurasian otter (Lutra lutra) and Eurasian badger (Meles meles) of the family of Mustelidae; common genet (Genetta genetta) of the family of Viverridae; red fox (Vulpes vulpes) of the family of Canidae and European wild cat (Felis silvestris) of the family of Felidae. Results: A number of sequences of possible novel viruses or virus variants were detected, including a theilovirus, phleboviruses, an amdovirus, a kobuvirus and picobirnaviruses. Conclusions: Using random PCR in combination with next generation sequencing, sequences of various novel viruses or virus variants were detected in fecal samples collected from Spanish carnivores. Detected novel viruses highlight the viral diversity that is present in fecal material of wild carnivores.

Note sur l'évolution des populations de Copépodes pélagiques de l'upwelling mauritanien (mars-avril 1972)

The evolution of a plankton copepod population in the Mauritania upwelling was studied by following a drogue for 9 days, from the point of upwelling till the water-mass dives under offshore waters. The Shannon index of specific diversity and the tropic structure allow separation into several stages in the studied succession. The upwelling brings near the shore a rather poor, highly diverse fauna, with a low filter-feeder rate. The phytoplanktonic development induces an increase in the copepod number. The filter-feeders become dominant and the diversity decreases. When the increase of copepod number stops, the diversity decreases and the omnivore and carnivore rate increases.

Inferring Population Genetic Structure in Widely and Continuously Distributed Carnivores: The Stone Marten (Martes foina) as a Case Study

The stone marten is a widely distributed mustelid in the Palaearctic region that exhibits variable habitat preferences in different parts of its range. The species is a Holocene immigrant from southwest Asia which, according to fossil remains, followed the expansion of the Neolithic farming cultures into Europe and possibly colonized the Iberian Peninsula during the Early Neolithic (ca. 7,000 years BP). However, the population genetic structure and historical biogeography of this generalist carnivore remains essentially unknown. In this study we have combined mitochondrial DNA (mtDNA) sequencing (621 bp) and microsatellite genotyping (23 polymorphic markers) to infer the population genetic structure of the stone marten within the Iberian Peninsula. The mtDNA data revealed low haplotype and nucleotide diversities and a lack of phylogeographic structure, most likely due to a recent colonization of the Iberian Peninsula by a few mtDNA lineages during the Early Neolithic. The microsatellite data set was analysed with a) spatial and non-spatial Bayesian individual-based clustering (IBC) approaches (STRUCTURE, TESS, BAPS and GENELAND), and b) multivariate methods [discriminant analysis of principal components (DAPC) and spatial principal component analysis (sPCA)]. Additionally, because isolation by distance (IBD) is a common spatial genetic pattern in mobile and continuously distributed species and it may represent a challenge to the performance of the above methods, the microsatellite data set was tested for its presence. Overall, the genetic structure of the stone marten in the Iberian Peninsula was characterized by a NE-SW spatial pattern of IBD, and this may explain the observed disagreement between clustering solutions obtained by the different IBC methods. However, there was significant indication for contemporary genetic structuring, albeit weak, into at least three different subpopulations. The detected subdivision could be attributed to the influence of the rivers Ebro, Tagus and Guadiana, suggesting that main watercourses in the Iberian Peninsula may act as semi-permeable barriers to gene flow in stone martens. To our knowledge, this is the first phylogeographic and population genetic study of the species at a broad regional scale. We also wanted to make the case for the importance and benefits of using and comparing multiple different clustering and multivariate methods in spatial genetic analyses of mobile and continuously distributed species.

Pan-biogeografia dos gêneros Didelphis, Philander, Metachirus, Chironectes e Lutreolina (Didelphimorphia: Didelphidae)

A ordem Didelphimorphia, de marsupiais americanos, apresenta 19 gêneros e 96 espécies, todos membros da família Didelphidae, que é dividida em duas subfamílias, Caluromyinae e Didelphinae. A subfamília Didelphinae contém (não apenas) as tribos Didelphini e Metachirini. A tribo Didelphini compreende 15 espécies de quatro gêneros: Chironectes (1 espécie), Lutreolina (1), Didelphis (6) e Philander (7) e a tribo Metachirini é monotípica, com apenas uma espécie do gênero Metachirus. Estes cinco gêneros encontram-se distribuídos amplamente pelas Américas, desde o sul do Canadá até a região central da Argentina. O objetivo deste estudo foi buscar identificar e explicar, através de análise pan-biogeográfica, os padrões de distribuição das espécies destes cinco gêneros. Para tal, foi feito um levantamento em banco de dados, coleções científicas e artigos científicos para a obtenção de dados sobre as localidades de registro de cada espécie. Estas foram então marcadas em mapas e a partir destes, as localidades de ocorrência foram conectadas com linhas de menor distância para formação dos traços individuais. Pela sobreposição dos traços individuais chegou-se aos traços generalizados e do encontro destes, aos nós biogeográficos. Os pontos de ocorrência foram também plotados em mapas de biomas para análise. Encontramos três traços generalizados e dois nós biogeográficos, um no centro da Bolívia na província biogeográfica de Puna e outro na Argentina, na província de Misiones. Quatro espécies não participaram de nenhum dos traços generalizados, provavelmente devido à sua distribuição mais restrita (Philander deltae, P. andersoni, P. olrogi e P. mcilhennyi). Chironectes minimus e Metachirus nudicaudatus tiveram seus traços coincidentes com dois traços generalizados, o que está de acordo com suas divisões de subespécies. Identificamos os diferentes padrões existentes para o norte da América do Sul (Venezuela) já apontado por diversos autores, porém apenas quando analisadas as subespécies em separado. Alguns limites para a distribuição das espécies puderam ser identificados, como por exemplo o istmo de Tehuantepec, no México, para Chironectes minimus e Metachirus nudicaudatus e o limite da região neotropical para P. opossum e D. marsupialis. O limite de distribuição sul de Philander opossum e P. frenatus é provavelmente o rio Paraguai, que deve servir de barreira para o contato entre as duas espécies. A descaracterização dos ambientes naturais pelo desmatamento vem alterando os padrões naturais de distribuição das espécies, com o registro de espécies de áreas abertas em biomas de mata. Lutreolina crassicaudata apresenta distribuição disjunta, ocupando duas áreas de vegetação aberta, uma no noroeste e outra no centro e sudeste da América do Sul, padrão provavelmente gerado pelos períodos de retração e expansão de áreas de savana do Mioceno superior ao Holoceno, levando à captura destes enclaves de vegetação aberta, com seu isolamento por áreas de floresta. Os nós e traços generalizados aqui identificados coincidiram com os encontrados por outros autores. Apesar da pan-biogeografia poder ser usada para propor áreas de proteção ambiental, nos locais em que encontramos os nós biogeográficos já existem unidades de conservação, não havendo assim necessidade de propor novas áreas no caso desses marsupiais. Ainda existe uma grande necessidade de um melhor conhecimento da distribuição e taxonomia das espécies estudadas, o que promoveria um melhor entendimento dos padrões biogeográficos existentes

Avaliação de aspectos hematológicos, bioquímicos e de hemoparasitas em população de Didelphis aurita Wied-Neuwied, 1826 (Didelphimorphia: Didelphidae) da Serra dos Órgãos, RJ

A Floresta Tropical Atlântica apresenta uma enorme biodiversidade, e está atualmente sujeita a inúmeras pressões como a perda de área pela intensa ocupação humana, agricultura, pecuária, urbanização e industrialização. Esses impactos têm provocado desmatamento e fragmentação florestal, processos que interferem na manutenção das populações animais, inclusive afetando os ciclos silvestres de parasitas e microorganismos. Didelphis aurita é um marsupial da Mata Atlântica com alta capacidade adaptativa a ambientes perturbados. Esta espécie onívora é tolerante à fragmentação florestal, podendo sobreviver em ambientes silvestres, rurais, suburbanos e urbanos, tendo importância na conexão dos ciclos silvestres e urbanos de diversos agentes. Este trabalho teve por objetivo descrever aspectos hematológicos, bioquímicos e de hemoparasitas em Didelphis aurita de duas áreas da Serra dos Órgãos/ RJ, uma área fragmentada e outra de mata contínua. Entre julho de 2011 e fevereiro de 2012 foram capturados 61 animais que tiveram amostras de sangue avaliadas. Os resultados expressos como média desvio padrão foram: Volume Globular 38,66 % ( 4,97); Hemácias 5,40 ( 0,75) x106/mm3; Hemoglobina 12,78 ( 1,68) g/dL; VGM 71,69 ( 3,56) fl; CHGM 33,01 ( 0,63) %; Plaquetas 514,70 ( 323,10) x 103/mm3; Leucócitos 19.678,52 ( 10.152,26)/mm3; Basófilos 0,59 ( 0,72) %; Eosinófilos 13,79 ( 6,94)%; Bastonetes 0,77 ( 2,04) %; Segmentados 41,12 ( 13,95) %; Linfócitos 41,97 ( 12,97) %; Monócitos 1,75 ( 1,51)%. Para parâmetros bioquímicos encontramos os seguintes resultados: Proteínas totais 8,50 ( 1,68); albumina 3,03 ( 0,69); globulina 5,44 ( 1,66); uréia 83,57 ( 20,11); creatinina 0,44 ( 0,13); ALT 85,01 ( 65,65); AST 314,55 ( 130,58); FA 420,38 ( 371,89); GGT 19,40 ( 8,51). Os parâmetros hematócrito, hemoglobina, hematimetria, ALT, AST e FA foram maiores nos machos do que nas fêmeas. Adultos apresentaram valores de proteína plasmática total, leucócitos, hematócrito, hemoglobina, hematimetria, albumina, proteínas totais, creatinina e GGT maiores do que jovens, e o inverso ocorreu para plaquetas, globulina e FA. Animais do Fragmento apresentaram valores de massa corporal e albumina menores do que os do Garrafão, e o inverso ocorreu para GGT e globulina. Babesiasp. ocorreu em 26,6% da população, sendo mais freqüente em adultos. Estes resultados são os primeiros parâmetros de referência para Didelphis aurita na Serra dos Órgãos, contribuindo para o estudo desta espécie.

Dinâmica populacional e caracterização conquiliomorfológica de Diplodon ellipticus Spix in Wagner, 1827 (Bivalvia: Unionoida: Hyriidae) da lagoa dos Caiçaras (Piraí, Rio de Janeiro, Brasil)

No presente estudo monitoramos uma população de Diplodon ellipticus Spix in Wagner, 1827 da lagoa dos Caiçaras, Piraí, Rio de Janeiro, e avaliamos alguns aspectos conquiliomorfológicos da larva e do adulto, a relação peso-comprimento, os padrões populacionais tais como crescimento, mortalidade e expectativa de vida, e o ciclo larval. Amostragens mensais foram realizadas de novembro/2012 a novembro/2013 em três pontos da lagoa. Em cada ponto, definimos uma area de 15 m2, que foi subdividida em 15 quadrados de 1m2 cada. Os bivalves foram procurados por três coletores, usando mãos e pés, totalizando 45 minutos de coleta/área. Posteriormente, foram medidos com um paquímetro em relação ao comprimento total, marcados e devolvidos a lagoa. Quinze bivalves foram coletados e analisados em laboratório durante dois anos. Os fatores abióticos (condutividade, temperatura da água, temperatura do ambiente, umidade, pH e oxigênio dissolvido) foram mensurados e amostragens do sedimento e da água foram realizados em cada ponto. Os indivíduos foram agrupados em classes de comprimento com intervalo de 2,0 mm para análise da estrutura de comprimento da população. Os parâmetros de curva de crescimento foram estimados pela rotina ELEFAN (distribuição de frequência) e pelo método de Gulland-Holt (marcação e recaptura), ambos no programa FISAT. A mortalidade foi calculada pelo método da curva de captura convertida em comprimento e a expectativa de vida foi calculada pela equação invertida de von Bertalanffy. Ao todo, 3474 bivalves foram marcados e 1849 recapturados, alguns deles mais de uma vez. O menor bivalve recapturado mediu 23,58 mm e foi recapturado 127 dias depois com 25,50 mm e o maior bivalve recapturado mediu 62,14 mm e foi recapturado 31 dias depois com 62,20 mm. Pelo método indireto analizamos 6922 bivalves com comprimentos variando de 11,37 a 62,49 mm. A maior frequência de comprimento foi encontrada em tamanhos intermediários de 44-46 mm, como foi observado em outras populações de Diplodon. A análise do crescimento, mortalidade e expectativa de vida foram similares em ambos os métodos, por isso, utilizamos em conjunto para ajustar a curva de crescimento da população. A relação peso-comprimento foi alta (r = 0,7-0,8). A avaliação do ciclo reprodutivo indica uma continuidade no desenvolvimento larval ao longo dos meses, à exceção de janeiro/2014. Contabilizamos um total de 54.617 gloquídios, havendo mais indivíduos grávidos com gloquídios (n=5) nos meses de julho e setembro de 2014. Padrão similar foi encontrado em outras espécies de bivalves de água doce, inclusive em Diplodon ellipticus no estado do Paraná. Os gloquídios maduros foram encontrados em amplitudes de temperaturas de 20,1-25,27C e acreditamos que a temperatura pode influenciar na liberação dos mesmos. Os bivalves com o maior e o menor número de gloquídios foram encontrados em novembro/2013 (n= 4759) e setembro/2014 (n= 212), respectivamente. A correlação entre o comprimento do marsúpio e o tamanho da ninhada foi testada pela primeira vez nesse gênero e foi significativa (r= 0,303 , p<0,05). As informações deste estudo são relevantes ao conhecimento da espécie e às futuras ações de gestão que tenham como objetivo preservar as espécies de Diplodon

Estado de conservación de la ictiofauna arrecifal en sitios de buceo turístico de cuatro regiones del Archipiélago Sabana-Camagüey, Cuba.

Los peces constituyen uno de los atractivos principales en los arrecifes coralinos para el buceo turístico, por lo cual resulta necesario monitorear su abundancia y valores estéticos. El objetivo de esta investigación fue evaluar el estado de conservación de las asociaciones de peces arrecifales en cuatro de los principales polos turísticos del Archipiélago Sabana-Camagüey, Cuba en el año 2010. Se muestrearon 23 sitios de buceo turísticos en áreas adyacentes a las regiones de Varadero (5 sitios), cayos de Villa Clara (6 sitios), Cayo Coco (6 sitios) y Santa Lucia (6 sitios). En cada uno de ellos se realizaron seis réplicas de censos visuales de todas las especies de peces en recorridos lineales de 50 m de largo por 2 m de ancho, ocupando un área total de 600 m2. El puntaje más alto de conservación lo presentó los cayos de Villa Clara (37), siguiéndole en orden decreciente Cayo Coco (35), y con valores más bajos Varadero (24) y Santa Lucia (22). Los puntajes de las cuatro regiones fueron inferiores a los encontrados en otros arrecifes de Cuba y el Caribe. Los valores de Varadero y Santa Lucia se correspondieron con los de arrecifes de hábitats degradados y sometidos a explotación pesquera. En general, en la mayoría de las regiones predominaron peces de talla pequeña (<20 cm) pertenecientes a las familias Pomacentridae y Labridae y hubo poca abundancia de peces carnívoros y herbívoros de mediana (20-40 cm) y gran talla (>40 cm). ABSTRACT Fish are one of the main attractions on coral reefs for diving tourism; therefore, it is necessary to monitor their condition and aesthetic values. The objective of this research was to evaluate the status of reef fish assemblages in four tourist areas of Sabana-Camaguey Archipelago, Cuba in 2010. Twentythree tourist diving sites were sampled in adjacent areas to regions of Varadero (five sites), Villa Clara keys (6 sites), Coco key (6 sites) and Santa Lucia (6 sites). In each region, six replicated visual census of all fish species were conducted along belt transects of 50 m length and 2 m width, occupying a total area of 600 m2. The highest conservation score was obtained by Villa Clara keys (37), followed in decreasing order by Coco key (35), and with lower values Varadero (24) and St. Lucia (22). The scores of the four regions were lower than the values of other Cuban and Caribbean reefs. The values of Varadero and Santa Lucia corresponded to reefs with degraded habitats and subject to overfishing. In general, small fish (< 20 cm) from families Pomacentridae and Labridae, and low abundance of carnivore and herbivore fish of middle (20-40 cm) and large size (> 40 cm) predominated in most regions.

A few observations on the biology of Tachysurus thalassinus Ruppell from Veraval (Gujarat)

The length-weight relationship of T. thalassinus differed in the sexes and, therefore separate equations were obtained; for males log W = -5.1728 4- 3.0495 log L; and for females log W = -5.7456 + 3.2798 log L. The spawning period of this species appears to be restricted to a short period from October to November. Fecundity has been found to range from 33 to 55 mature eggs in specimens of the size range 421-564mm. The sex ratio of males to females was 1.8:1. T. thalassinus is a bottom carnivore, crustaceans ranking first in food followed by fishes, mollusc and polychaetes.

Preliminary observations on the morphometric characteristics, length weight relationship, food and fedding habits and fecundity of Saurida tumbil (Bloch) off Bombay coast

Fifteen morphometric and four meristic characters of Saurida tumbil were studied and their relationships with total length and head length were established. The length weight relationship worked out to be W= -5.6055 L(super)3.291. The fish is a carnivore, feeding mainly on small fishes, molluscs and crustaceans. Larger fishes are selective feeders on fish. It is a long protracted spawner. Fecundity varied from 6008 to 17384 eggs in specimens of size group 212-420 mm. Fecundity-total length, fecundity-total weight of fish and fecundity - total weight of ovary relationships were worked out to be F=0.9414 L(super)1.6626, F=180.7069 W(super)0.7531 and F=3153.0375 W(super)0.8278 respectively.

Comparative molecular cytogenetic studies in the order Carnivora: mapping chromosomal rearrangements onto the phylogenetic tree

We have made a set of chromosome-specific painting probes for the American mink by degenerate oligonucleotide primed-PCR (DOP-PCR) amplification of flow-sorted chromosomes. The painting probes were used to delimit homologous chromosomal segments among human, red fox, dog, cat and eight species of the family Mustelidae, including the European mink, steppe and forest polecats, least weasel, mountain weasel, Japanese sable, striped polecat, and badger. Based on the results of chromosome painting and G-banding, comparative maps between these species have been established. The integrated map demonstrates a high level of karyotype conservation among mustelid species. Comparative analysis of the conserved chromosomal segments among mustelids and outgroup species revealed 18 putative ancestral autosomal segments that probably represent the ancestral chromosomes, or chromosome arms, in the karyotype of the most recent ancestor of the family Mustelidae. The proposed 2n = 38 ancestral Mustelidae karyotype appears to have been retained in some modern mustelids, e.g., Martes, Lutra, ktonyx, and Vormela. The derivation of the mustelid karyotypes from the putative ancestral state resulted from centric fusions, fissions, the addition of heterochromatic arms, and occasional pericentric inversions. Our results confirm many of the evolutionary conclusions suggested by other data and strengthen the topology of the carnivore phylogenetic tree through the inclusion of genome-wide chromosome rearrangements. Copyright (C) 2002 S. KargerAG, Basel.

Studies on the food habits of three species of Mastacembelidae

To identify the food habits of three species of Mastacembelidae namely Mastacembelus armatus, Mastacembelus pancalus and Macrognathus aculeatus, the gut content analysis was performed by three methods i.e. occurrence method, points method and index of fullness method. All three species were found to consume prawn, molluscs, insects, earth warm, debris and plant materials. M. armatus and M. pan cal us were found to feed mainly on animal food items and 84.68% of different types of animal food were taken by M. armatus and 62.72% by M. pancalus. M. aculeatus was found to consume 44.86% of different types of animal food items, 53.51% of debris and plant materials which indicated that this fish feeds almost equally on animal and plant food. Analysis of the food habits showed that both M. armatus and M. pancalus are carnivore in nature with higher feeding preference for animal food namely prawn, crabs, fishes, molluscs etc. On the other hand, M. aculeatus is an omnivore in nature feeding almost equally on animal and plant food.

Diel feeding patterns, rate of gastric evacuation and foods of Indian sandwhiting, Sillago sihama in Mulki estuary, west coast of India

Diel feeding chronology of sandwhiting, Sillago sihama was examined from stomach collections taken during the months of April, July and December'99 in Mulki estuary along Dakshina Kannada coast, India. Significant differences in mean stomach content weight were found between several consecutive 3 hour periods with peak fullness occurring in early morning and evening hours. The rate of gastric evacuation of natural food (crustacea, polychaetes and fish) was measured in the field was best described by an exponential model, with an estimated evacuation time of 8.0 h at a temperature of 28.5 ± 1.2°C. Stomach content analysis indicated that this species is a carnivore on a wide range of benthic, epibenthic and planktonic prey. The principal food items of S. sihama were crustaceans, polychaetes and fish. Fishes less than 100 mm TL preferred mainly crustaceans while larger ones depends on polychaetes, crustaceans and fish. The feeding activity of S. sihama was influenced by tidal cycle.

Evolutionary implications of multiple SINE insertions in an intronic region from diverse mammals

An analysis of the nuclear beta-fibrinogen intron 7 locus from 30 taxa representing 12 placental orders of mammals reveals the enriched occurrences of short interspersed clement (SINE) insertion events. Mammalian-wide interspersed repeats (MIRs) are present at orthologous sites of all examined species except those in the order Rodentia. The higher substitution rate in mouse and a rare MIR deletion from rat account for the absence of MIR in the rodents. A minimum of five lineage-specific SINE sequences are also found to have independently inserted into this intron in Carnivora, Artiodactyla and Lagomorpha. In the case of Carnivora, the unique amplification pattern of order-specific CAN SINE provides important evidence for the "pan-carnivore" hypothesis of this repeat element and reveals that the CAN SINE family may still be active today. Particularly interesting is the finding that all identified lineage-specific SINE elements show a strong tendency to insert within or in very close proximity to the preexisting MIRs for their efficient integrations, suggesting that the MIR clement is a hot spot for successive insertions of other SINEs. The unexpected MIR excision as a result of a random deletion in the rat intron locus and the non-random site targeting detected by this study indicate that SINEs actually have a greater insertional flexibility and regional specificity than had previously been recognized. Implications for SINE sequence evolution upon and following integration, as well as the fascinating interactions between retroposons and the host genomes are discussed.

The sequence and de novo assembly of the giant panda genome

Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.

Novel frenatins from the skin of the Australasian Giant White-lipped tree frog, Litoria infrafrenata: cloning of precursor cDNAs and identification in defensive skin secretion.

The Australasian anuran amphibian genus Litoria, contains many phenotypically-diverse species as a result of radial evolution of an ancestral species into different biotopes much in the manner of the indigenous marsupial mammals. In common with members of the Central/South American genus Phyllomedusa, their specialized skin granular glands are factories for the production of a plethora of biologically-active peptides. Here we report a more detailed study of those present in the defensive skin secretion of the Australasian giant white-lipped tree frog, Litoria infrafrenata, and, for the first time, we have identified three novel frenatins by deduction of primary structures from cDNAs that were cloned from a library constructed from lyophilized skin secretion using a recently-developed technique. All open-reading frames consisted of a putative signal peptide and an acidic pro-region followed by a single copy of a frenatin peptide. Processed peptides corresponding in molecular mass to the deduced molecular masses of frenatins (named 1.1, 3, 3.1 and 4.1) were identified in the same secretion sample using HPLC and mass spectroscopy. The application of this technique thus permits parallel peptidomic and transcriptomic analyzes on the same lyophilized skin secretion sample circumventing sacrifice of specimens from endangered herpetofauna.