Larissa Rosa de Oliveira

DNA barcoding meets molecular scatology: short mtDNA sequences for standardized species assignment of carnivore noninvasive samples

Although species assignment of scats is important to study carnivore biology, there is still no standardized assay for the identification of carnivores worldwide, which would allow large‐scale routine assessments and reliable cross‐comparison of results. Here, we evaluate the potential of two short mtDNA fragments [ATP6 (126 bp) and cytochrome oxidase I gene (COI) (187 bp)] to serve as standard markers for the Carnivora. Samples of 66 species were sequenced for one or both of these segments. Alignments were complemented with archival sequences and analysed with three approaches (tree‐based, distance‐based and character‐based). Intraspecific genetic distances were generally lower than between‐species distances, resulting in diagnosable clusters for 86% (ATP6) and 85% (COI) of the species. Notable exceptions were recently diverged species, most of which could still be identified using diagnostic characters and uniqueness of haplotypes or by reducing the geographic scope of the comparison. In silico analyses were also performed for a 110‐bp cytochrome b (cytb) segment, whose identification success was lower (70%), possibly due to the smaller number of informative sites and/or the influence of misidentified sequences obtained from GenBank. Finally, we performed case studies with faecal samples, which supported the suitability of our two focal markers for poor‐quality DNA and allowed an assessment of prey DNA co‐amplification. No evidence of prey DNA contamination was found for ATP6, while some cases were observed for COI and subsequently eliminated by the design of more specific primers. Overall, our results indicate that these segments hold good potential as standard markers for accurate species‐level identification in the Carnivora.

Anomalous colour in Neotropical mammals: a review with new records for Didelphis sp. (Didelphidae, Didelphimorphia) and Arctocephalus australis (Otariidae, Carnivora)

Anomalous colourations occur in many tropical vertebrates. However, they are considered rare in wild populations, with very few records for the majority of animal taxa. We report two new cases of anomalous colouration in mammals. Additionally, we compiled all published cases about anomalous pigmentation registered in Neotropical mammals, throughout a comprehensive review of peer reviewed articles between 1950 and 2010. Every record was classified as albinism, leucism, piebaldism or eventually as undetermined pigmentation. As results, we report the new record of a leucistic specimen of opossum (Didelphis sp.) in southern Brazil, as well as a specimen of South American fur seal (Arctocephalus australis) with piebaldism in Uruguay. We also found 31 scientific articles resulting in 23 records of albinism, 12 of leucism, 71 of piebaldism and 92 records classified as undetermined pigmentation. Anomalous colouration is apparently rare in small terrestrial mammals, but it is much more common in cetaceans and michrochiropterans. Out of these 198 records, 149 occurred in cetaceans and 30 in bats. The results related to cetaceans suggest that males and females with anomolous pigmentation are reproductively successful and as a consequence their frequencies are becoming higher in natural populations. In bats, this result can be related to the fact these animals orient themselves primarily through echolocation, and their refuges provide protection against light and predation. It is possible that anomalous colouration occurs more frequently in other Neotropical mammal orders, which were not formally reported. Therefore, we encourage researchers to publish these events in order to better understand this phenomenon that has a significant influence on animal survival.

Sexual size dimorphism in Myotis nigricans (Schinz, 1821) (Chiroptera: Vespertilionidae) from south Brazil

Among Vespertilionidae species, sexual size dimorphism is very well documented, in which females are larger than males. The differences are mainly in body weight, skull measurements and forearm length. Studies have discussed some hypothesis for this phenomenon. However, very little information is known about sexual size dimorphism in Myotis nigricans (Schinz, 1821) in Brazil. In this sense, the goal of this paper is to present a study of this phenomenon in the species. For this, we present a quantitative analysis of sexual size dimorphism assessed by traditional morphometrics. Ten skull measurements in addition to the forearm length of adult specimens were taken. Results of traditional morphometrics revealed sexual size dimorphism in five skull measurements and in the forearm length. Females were larger than males. These differences can be attributed to natural selection on large female size for increase fecundity. Bat females of the Vespertilionidae family are usually larger than males in order to perform parental care appropriately and to provide a successful reproductive process.

Size and shape variability in the skull of Myotis nigricans (Schinz, 1821) (Chiroptera: Vespertilionidae) from two geographic areas in Brazil

We present a quantitative analysis of sexual dimorphism and geographic variation in the skull of Myotis nigricans (Schinz, 1821) assessed by geometric morphometrics. Differences in size and shape of skulls were investigated using 30 landmarks plotted on two-dimensional images of lateral and ventral views. Results of geometric morphometrics revealed sexual dimorphism in the centroid size of the skull in both views. Females were larger than males. Nevertheless, there was no sexual dimorphism in skull shape of M. nigricans. Geographic variation was detected in size and shape of the skull. South Brazilian specimens were significantly larger than Ceará specimens only in the lateral view. Differences in skull shape were statistically significant in both views: specimens from South Brazil were brevirostri and presented a more expanded skull in the posterior region while Ceará specimens were longirostri and do not present any expansion in the brain case. Ecological factors for these phenomena are discussed in the text.

A family history of serious complications due to BCG vaccination is a tool for the early diagnosis of severe primary immunodeficiency

Severe Combined Immunodeficiency (SCID) is one of the most severe forms of primary immunodeficiency (PID). Complications of BCG vaccination, especially disseminated infection and its most severe forms, are known to occur in immunodeficient patients, particularly in SCID. A carefully taken family history before BCG injection as well as delaying vaccination if PID is suspected could be a simple and effective method to avoid inappropriate vaccination of an immunodeficient child in some cases until the prospect of newborn screening for SCID has been fully developed. We describe a patient with a very early diagnosis of SCID, which was suspected on the basis of the previous death of two siblings younger than one year due to severe complications secondary to the BCG vaccine. We suggest that a family history of severe or fatal reactions to BCG should be included as a warning sign for an early diagnosis of SCID.

A hunted population in recovery: Effective population size for South American sea lions from Patagonia

Effective population size ( N e ) is a parameter of central importance in evolutionary biology and conservation. Factors such as unequal sex ratios of breeding individuals, periodic fluctuation in population size and variance in reproductive success can affect the N e in general. At present, South American sea lions, Otaria flavescens, from northern Patagonia, Argentina, belongs to one of the several populations that are recovering from overhunting which occurred in the early 20th century. Here, we present the estimate of N e for this population that takes into account the effects of their polygynous mating system and variation in population size through time. The resultant overall N e ’s were 4171 ± 2450 or 4745 ± 2681 breeding animals depending on the inclusion of peripheral adult males. The estimated N e ’s are not critical, because they are close to the average mean minimum viable population for vertebrates (5000 breeding adults). Even though the northern Patagonian population of O. flavescens is increasing its abundance is still far below its historical numbers. The N e estimated should be considered the minimum range to be maintained, especially in light of bycatch related to fishery interactions along the Patagonian coast. We emphasise the importance of estimating N e for future management plans of the species within different populations.

Depredation of domestic herds by pumas based on farmer’s information in Southern Brazil

BackgroundLarge carnivores such as pumas are frequently killed due to conflicts with human populations involving predation on domestic herds. In Southern Brazil, traditional pasture systems, where animals feed without specific husbandry practices is typical, becoming the herds vulnerable to puma attacks. The aim of this study was to examine the conflict between local people and pumas in a Protected Areas mosaic in southern Brazil.MethodsForty-five face-to-face interviews with local people were performed during the year of 2011, using a structured questionnaire with open and closed questions about puma attack episodes in some farms. Based on responses, the conflict and puma attacks were described, and the characteristics of attacked farms and estimated financial losses were evaluated. The first respondents were indicated by the Local Environmental Agency, and the others were indicated by the first one and so on, which is known as “snow-ball” method.ResultsOur data suggested that pumas used to attack in unfavorable conditions of visibility (foggy days) and on easier prey (e.g. sheep). Most of the attacks reported were close to forested areas and were focused on free herds during feeding activities. Some farmers said they gave up their sheep breeding activity due to losses caused by puma attacks. However, some farmers could over estimate their losses. Moreover, pumas were considered a threat to domestic herds and respondents mentioned cases of illegal puma hunting in the area. The results of questionnaires suggested that puma attack episodes were related to fragmentation of their habitat associated to incorrect management of herds in the farms studied. The diagnosis of this type of conflict and the characterization of most attacked sites are extremely important to create strategies to prevent and control attacks by wild carnivores.ConclusionsDeep changes in husbandry practices added to educational programs should be implemented, in order to maintain the sustainability of rural activities as well as the survival of pumas in southern Brazil.

Revalidation of Tursiops gephyreus Lahille, 1908 (Cetartiodactyla: Delphinidae) from the southwestern Atlantic Ocean

Historically, the taxonomic status of the bottlenose dolphins, Tursiops, has been confusing. Over 20 nominal species have been described in, or transferred to, the genus, but most them have been synonymized under T. truncatus, the type species of the genus. Here, we review the taxonomic status of Tursiops gephyreus Lahille, 1908, from the southwestern Atlantic Ocean (SWA), a taxon long considered as either synonym or subspecies of T. truncatus. We examined a total of 280 bottlenose dolphin skulls, including the lectotype of T. gephyreus. We examined all specimens for morphological (14 characters) and morphometric (29 measurements) differences. Univariate and multivariate analyses were conducted to test differences between groups. Based on qualitative and quantitative analyses of skulls as well as the vertebrae number of Tursiops specimens from SWA, we recognized 2 distinct morphological forms of bottlenose dolphins in the region, consistent with treatment of 2 species under the “diagnosable version of the Phylogenetic Species Concept.” Six qualitative characters are reliable for the identification of both species in the SWA, but the shape of the nasal process of the right premaxilla alone is sufficient to separate the species. Furthermore, the total number of vertebrae is higher in T. truncatus (62–64) than in T. gephyreus (57–59). Based on these results, we propose the revalidation of T. gephyreus. Since T. gephyreus was recognized as inhabiting the estuaries and the surf zone alongside the Rio Grande do Sul in Brazil, Uruguay, and Argentina coasts, the conservation efforts must take into account that this region presents similar threats to the species.

Bottlenose dolphin communities from the southern Brazilian coast: do they exchange genes or are they just neighbours?

The genetic structure of bottlenose dolphin communities found along the southern Brazilian coast is reported in this study. Genetic structure analysis using biopsy samples from free ranging dolphins and tissue samples from stranded dolphins revealed a fine-scale population structure among three distinct groups. The first genetically distinct group was composed of resident dolphins of Laguna with a high degree of site fidelity. The second group was composed of one photo-identified dolphin, previously recognised by its interaction with fishermen, and dolphins that stranded near the mouth of Tramandai Lagoon. Moderate nuclear and low mitochondrial gene diversity was found in dolphins of those coastal communities, whereas most of the dolphins stranded along the coast showed markedly higher levels of gene diversity at both markers. These stranded dolphins of unknown origin formed the third distinct group, which may be part of a larger offshore community. These results demonstrate the presence of at least three bottlenose dolphin clusters along this portion of the Brazilian coast, with the coastal specimens appearing to be only neighbours of a larger offshore community that eventually strands along the coast, highlighting the importance of the establishment of management and conservation measures for the species at a local scale.

Effective population size for South American sea lions along the Peruvian coast: the survivors of the strongest El Niño event in history

The South American sea lion, Otaria flavescens , has been considered vulnerable and under the threat of extinction in Peru due to the drastic demographic changes as a result of the impact of low food availability and the unusual timing of the severe El Nino event of 1997–1998. We present the first estimate of effective population size ( N e ) for the species that takes into account the effects of mating system and variation in population size in different generations caused by the severe El Nino event of 1997–1998. The resulting N e was 7715 specimens. We believe that the estimated N e for the Peruvian population is not a critical value, because it is higher than the mean minimum viable population generally accepted for vertebrates (ca. 5000 breeding adults). However, the viability of O. flavescens on the Peruvian coast may depend primarily on local availability of food resources. Climatic change models predict stronger and more frequent El Nino events. In this sense, the N e of 7715 should be considered as a value to be maintained in order to keep the population large enough to avoid inbreeding or to retain adaptive genetic variation to survive to future El Nino events. Moreover, this N e estimate is important data in discussions about resuming culling activities, based on the statement of an increasing competition between fishery activity and sea lions during El Nino events. Thus, this N e should be taken into account in future management plans to ensure the conservation of the species on the Peruvian coast.