Factors affecting southern water vole (Arvicola sapidus) detection and occupancy probabilities in Mediterranean farmland

Failure to detect a species at sites where it is present (i.e. imperfect detection) is known to occur frequently, but this is often disregarded in monitoring programs and metapopulation studies. Here we modelled for the first time the probability of patch occupancy by a threatened small mammal, the southern water vole (Arvicola sapidus, while accounting for the probability of detection given occupancy. Based on replicated presence sign surveys conducted in autumn (November–December 2013) and winter (February–March 2014) in a farmland landscape, we used occupancy detection modelling to test the effects of vegetation, sampling effort, observer experience, and rainfall on detection probability. We then assessed whether occupancy was related to patch size, isolation, vegetation, or presence of water, after correcting for imperfect detection. The mean detection probabilities of water vole signs in autumn (0.71) and winter (0.81) indicated that false absences may be generated in about 20–30% of occupied patches surveyed by a single observer on a single occasion. There was no statistical support for the effects of covariates on detectability. After controlling for imperfect detection, the mean probabilities of occupancy in autumn (0.31) and winter (0.29) were positively related to patch size and presence of water, and negatively so, albeit weakly, to patch isolation. Overall, our study underlined the importance of accounting for imperfect detection in sign surveys of small mammals such as water voles, pointing out the need to use occupancy detection modelling together with replicate surveys for accurately estimating occupancy and the factors affecting it.

Giardia survey in live-trapped small domestic and wild mammals in four regions in the southwest region of the State of São Paulo, Brazil

For the first time, a survey on Giardia in the live-trapped small domestic and wild mammals was perfomed in four regions of state of the São Paulo, Brazil, with special attention to the parasitism of Rattus rattus rattus by Giardia. This species was found infected in all studied sites: Botucatu (15.4%), Conchas (28.5%), Itaporanga (38.7%) and São Roque (100 %). Two new hosts and their frequency of infection were described for Giardia in Nectomys squamipes, an aquatic rodent and in Bolomys lasiurus, a forest rodent (100 % and 14.3 %, respectively). Both G. muris and G. duodenalis groups were found in scrapings of intestinal mucosa of those rodents. Mixed infection was observed in some animals. It is important to emphasize the infection by G. duodenalis in the black rat as this species lives as a comensal with man and in N. squamipes as it may contaminate small streams used for domestic consumption. Therefore, further investigation will be necessary to elucidate the potential of these rodents to act as reservoirs of Giardia for man.

Small regulatory RNAs in mammals

Mammalian cells harbor numerous small non-protein-coding RNAs, including small nucleolar RNAs (snoRNAs), microRNAs (miRNAs), short interfering RNAs (siRNAs) and small double-stranded RNAs, which regulate gene expression at many levels including chromatin architecture, RNA editing, RNA stability, translation, and quite possibly transcription and splicing. These RNAs are processed by multistep pathways from the introns and exons of longer primary transcripts, including protein-coding transcripts. Most show distinctive temporal- and tissue-specific expression patterns in different tissues, including embryonal stem cells and the brain, and some are imprinted. Small RNAs control a wide range of developmental and physiological pathways in animals, including hematopoietic differentiation, adipocyte differentiation and insulin secretion in mammals, and have been shown to be perturbed in cancer and other diseases. The extent of transcription of non-coding sequences and the abundance of small RNAs suggests the existence of an extensive regulatory network on the basis of RNA signaling which may underpin the development and much of the phenotypic variation in mammals and other complex organisms and which may have different genetic signatures from sequences encoding proteins.

The management of large mammals in relation to male strategies and conflict with people

Many large mammals such as elephant, rhino and tiger often come into conflict with people by destroying agricultural crops and even killing people, thus providing a deterrent to conservation efforts. The males of these polygynous species have a greater variance in reproductive success than females, leading to selection pressures favouring a ‘high risk-high gain’ strategy for promoting reproductive success. This brings them into greater conflict with people. For instance, adult male elephants are far more prone than a member of a female-led family herd to raid agricultural crops and to kill people. In polygynous species, the removal of a certain proportion of ‘surplus’ adult males is not likely to affect the fertility and growth rate of the population. Hence, this could be a management tool which would effectively reduce animal-human conflict, and at the same time maintain the viability of the population. Selective removal of males would result in a skewed sex ratio. This would reduce the ‘effective population size’ (as opposed to the total population or census number), increase the rate of genetic drift and, in small populations, lead to inbreeding depression. Plans for managing destructive mammals through the culling of males will have to ensure that the appropriate minimum size in the populations is being maintained.

Soviet-American Cooperative Research on Marine Mammals. Volume 1- Pinnipeds: Under Project V.6. Marine Mammals, of the US-USSR Agreement on Cooperation in the Field of Environmental Protection

Some 25 to 30 yr ago, when we as students were beginning our respective careers and were developing for the first time our awareness of marine mammals in the waters separating western North America from eastern Asia, we had visions of eventually bridging the communication gap which existed between our two countries at that time. Each of us was anxious to obtain information on the distribution, biology, and ecological relations of "our" seals and walruses on "the other side," beyond our respective political boundari~s where we were not permitted to go to study them. We were concerned that the resource management practices on the other side of the Bering and Chukchi Seas, implemented in isolation, on a purely unilateral basis, might endanger the species which we had come to know and were striving to conserve. At once apparent to both of us was the need for free exchange of biological information between our two countries and, ultimately, joint management of our shared resources. In a small way, we and others made some initial efforts to generate that exchange by personal correspondence and through vocal interchange at the annual meetings of the North Pacific Fur Seal Commission. By the enabling Agreement on Cooperation in the Field of Environmental Protection, reached between our two countries in 1972, our earlier visions at last came true. Since that time, within the framework of the Marine Mammal Project under Area V of that Agreement, we and our colleagues have forged a strong bond of professional accord and respect, in an atmosphere of free intercommunication and mutual understanding. The strength and utility of this arrangement from the beginning of our joint research are reflected in the reports contained in this, the first compendium of our work. The need for a series of such a compendia became apparent to us in 1976, and its implementation was agreed on by the regular meeting of the Project in La Jolla, Calif., in January 1977. Obviously, the preparation and publication of this first volume has been excessively delayed, in part by continuing political distrust between our governments but mainly by increasing demands placed on the time of the contributors. In this period of growing environmental concern in both countries, we and our colleagues have been totally immersed in other tasks and have experienced great difficulty in drawing together the works presented here. Much of the support for doing so was provided by the State of Alaska, through funding for Organized Research at the University of Alaska-Fairbanks. For its ultimate completion in publishable form we wish to thank Helen Stockholm, Director of Publications, Institute of Marine Science, University of Alaska, and her staff, especially Ruth Hand, and the numerous referees narned herein who gave willingly oftheir time to review each ofthe manuscripts critically and to provide a high measure of professionalism to the final product. (PDF file contains 110 pages.)

Distribution and abundance of humpback whales (Megaptera novaeangliae) and other marine mammals off the northern Washington coast

We examined the summer distribution of marine mammals off the northern Washington coast based on six ship transect surveys conducted between 1995 and 2002, primarily from the NOAA ship McArthur. Additionally, small boat surveys were conducted in the same region between 1989 and 2002 to gather photographic identification data on humpback whales (Megaptera novaeangliae) and killer whales (Orcinus orca) to examine movements and population structure. In the six years of ship survey effort, 706 sightings of 15 marine mammal species were made. Humpback whales were the most common large cetacean species and were seen every year and a total of 232 sightings of 402 animals were recorded during ship surveys. Highest numbers were observed in 2002, when there were 79 sightings of 139 whales. Line-transect estimates for humpback whales indicated that about 100 humpback whales inhabited these waters each year between 1995 and 2000; in 2002, however, the estimate was 562 (CV= 0.21) whales. A total of 191 unique individuals were identified photographically and mark recapture estimates also indicated that the number of animals increased from under 100 to over 200 from 1995 to 2002. There was only limited interchange of humpback whales between this area and feeding areas off Oregon and California. Killer whales were also seen on every ship survey and represented all known ecotypes of the Pacific Northwest, including southern and northern residents, transients, and offshore-type killer whales. Dall’s porpoise (Phocoenoides dalli) were the most frequently sighted small cetacean; abundance was estimated at 181−291 individuals, except for 2002 when we observed dramatically higher numbers (876, CV= 0.30). Northern fur seals (Callorhinus ursinus) and elephant seals (Mirounga angustirostris) were the most common pinnipeds observed. There were clear habitat differences related to distance offshore and water depth for different species.

Stable carbon isotope analyses show dominance of C3 grasses in the feed selected by small herbivores at the alpine meadow at the Tibetan Plateau

Muscle samples were collected from small herbivorous mammals (Ochotona curzoniae, Microtus oecnomus, Myospalax fontanierii and Lepus oiostolus) at the alpine meadow ecosystem at the Tibetan Plateau in order to address variability in stable carbon isotope composition. Stable carbon isotope values of muscles remain steady and show no significant variations (-25.72 to -27.04 parts per thousand) among the four small mammal species. Based on the mass balance theory of stable isotopes, it is proposed that small herbivorous mammals mainly (or totally) rely on C3 grasses as food supply, and there is few or no distribution of C4 grasses at the ecosystem. The results reflect our previous study on the isotope patterns of plant species. Thus, stable carbon isotope analysis of muscles provides a method to address dietary selection and dietary variability in herbivores. In addition, stable carbon isotopic analyses can be used to address changes in vegetation distributions in ecosystem and paleovegetaion and paleoclimate.

Trophic role of small cetaceans and seals in Irish waters

Understanding the role of marine mammals in specific ecosystems and their interactions with fisheries involves, inter alia, an understanding of their diet and dietary requirements. In this thesis, the foraging ecology of seven marine mammal species that regularly occur in Irish waters was investigated by reconstructing diet using hard parts from digestive tracts and scats. Of the species examined, two (striped and Atlantic white-sided dolphin) can be considered offshore species or species inhabiting neritic waters, while five others usually inhabit more coastal areas (white-beaked dolphin, harbour porpoise, harbour seal and grey seal); the last species studied was the bottlenose dolphin whose population structure is more complex, with coastal and offshore populations. A total of 13,028 prey items from at least 81 different species (62 fish species, 14 cephalopods, four crustaceans, and a tunicate) were identified. 28% of the fish species were identified using bones other than otoliths, highlighting the importance of using all identifiable structures to reconstruct diet. Individually, each species of marine mammal presented a high diversity of prey taxa, but the locally abundant Trisopterus spp. were found to be the most important prey item for all species, indicating that Trisopterus spp. is probably a key species in understanding the role of these predators in Irish waters. In the coastal marine mammals, other Gadiformes species (haddock, pollack, saithe, whiting) also contributed substantially to the diet; in contrast, in pelagic or less coastal marine mammals, prey was largely comprised of planktivorous fish, such as Atlantic mackerel, horse mackerel, blue whiting, and mesopelagic prey. Striped dolphins and Atlantic white-sided dolphins are offshore small cetaceans foraging in neritic waters. Differences between the diet of striped dolphins collected in drift nets targeting tuna and stranded on Irish coasts showed a complex foraging behaviour; the diet information shows that although this dolphin forages mainly in oceanic waters it may occasionally forage on the continental shelf, feeding on available prey. The Atlantic white-sided dolphin diet showed that this species prefers to feed over the continental edge, where planktivorous fish are abundant. Some resource partitioning was found in bottlenose dolphins in Irish waters consistent with previous genetic and stable isotope analysis studies. Bottlenose dolphins in Irish waters appears to be generalist feeders consuming more than 30 prey species, however most of the diet comprised a few locally abundant species, especially gadoid fish including haddock/pollack/saithe group and Trisopterus spp., but the contribution of Atlantic hake, conger eels and the pelagic planktivorous horse mackerel were also important. Stomach content information suggests that three different feeding behaviours might occur in bottlenose dolphin populations in Irish waters; firstly a coastal behaviour, with animals feeding on prey that mainly inhabit areas close to the coast; secondly an offshore behaviour where dolphins feed on offshore species such as squid or mesopelagic fish; and a third more complex behaviour that involves movements over the continental shelf and close to the shelf edge. The other three coastal marine mammal species (harbour porpoise, harbour seal and grey seal) were found to be feeding on similar prey and competition for food resources among these sympatric species might occur. Both species of seals were found to have a high overlap (more than 80%) in their diet composition, but while grey seals feed on large fish (>110mm), harbour seals feed mostly on smaller fish (<110mm), suggesting some spatial segregation in foraging. Harbour porpoises and grey seals are potentially competing for the same food resource but some differences in prey species were found and some habitat partitioning might occur. Direct interaction (by catch) between dolphins and fisheries was detected in all species. Most of the prey found in the stomach contents from both stranded and by catch dolphins were smaller sizes than those targeted by commercial fisheries. In fact, the total annual food consumption of the species studied was found to be very small (225,160 tonnes) in comparison to fishery landings for the same area (~2 million tonnes). However, marine mammal species might be indirectly interacting with fisheries, removing forage fish. Incorporating the dietary information obtained from the four coastal species, an ECOPATH food web model was established for the Irish Sea, based on data from 2004. Five trophic levels were found, with bottlenose dolphins and grey and harbour seals occurring at the highest trophic level. A comparison with a previous model based on 1973 data suggests that while the overall Irish Sea ecosystem appears to be “maturing”, some indices indicate that the 2004 fishery was less efficient and was targeting fish at higher trophic levels than in 1973, which is reflected in the mean trophic level of the catch. Depletion or substantial decrease of some of the Irish Sea fish stocks has resulted in a significant decline in landings in this area. The integration of diet information in mass-balance models to construct ecosystem food-webs will help to understand the trophic role of these apex predators within the ecosystem.

Urban mammals: what does the future hold? An analysis of the factors affecting patterns of use of residential gardens in Great Britain

1Urban areas are predicted to grow significantly in the foreseeable future because of increasing human population growth. Predicting the impact of urban development and expansion on mammal populations is of considerable interest due to possible effects on biodiversity and human-wildlife conflict. 2The British government has recently announced a substantial housing programme to meet the demands of its growing population and changing socio-economic profile. This is likely to result in the construction of high-density, low-cost housing with small residential gardens. To assess the potential effects of this programme, we analysed the factors affecting the current pattern of use of residential gardens by a range of mammal species using a questionnaire distributed in wildlife and gardening magazines and via The Mammal Society. 3Twenty-two species/species groups were recorded. However, the pattern of garden use by individual species was limited, with only six species/species groups (bats, red fox Vulpes vulpes, grey squirrel Sciurus carolinensis, hedgehog Erinaceus europaeus, mice, voles) recorded as frequent visitors to > 20% of gardens in the survey. 4There was a high degree of association between the variables recorded in the study, such that it was difficult to quantify the effects of individual variables. However, all species/species groups appeared to be negatively affected by the increased fragmentation and reduced proximity of natural and semi-natural habitats, decreasing garden size and garden structure, but to differing degrees. Patterns of garden use were most clearly affected by house location (city, town, village, rural), with garden use declining with increasing urbanization for the majority of species/species groups, except red foxes and grey squirrels. Increasing urbanization is likely to be related to a wide range of interrelated factors, any or all of which may affect a range of mammal species. 5Overall, the probable effects of the planned housing development programme in Britain are not likely to be beneficial to mammal populations, although the pattern of use examined in this study may represent patterns of habitat selection by species rather than differences in distribution or abundance. Consequently, additional data are required on the factors affecting the density of species within urban environments.

Adaptive evolution toward larger size in mammals

The notion that large body size confers some intrinsic advantage to biological species has been debated for centuries. Using a phylogenetic statistical approach that allows the rate of body size evolution to vary across a phylogeny, we find a long-term directional bias toward increasing size in the mammals. This pattern holds separately in 10 of 11 orders for which sufficient data are available and arises from a tendency for accelerated rates of evolution to produce increases, but not decreases, in size. On a branch-by-branch basis, increases in body size have been more than twice as likely as decreases, yielding what amounts to millions and millions of years of rapid and repeated increases in size away from the small ancestral mammal. These results are the first evidence, to our knowledge, from extant species that are compatible with Cope’s rule: the pattern of body size increase through time observed in the mammalian fossil record. We show that this pattern is unlikely to be explained by several nonadaptive mechanisms for increasing size and most likely represents repeated responses to new selective circumstances. By demonstrating that it is possible to uncover ancient evolutionary trends from a combination of a phylogeny and appropriate statistical models, we illustrate how data from extant species can complement paleontological accounts of evolutionary history, opening up new avenues of investigation for both.

Carnivore mammals in a fragmented landscape in northeast of Sao Paulo State, Brazil

Sao Paulo is the most developed state in Brazil and little of its native vegetation remains. In Luiz Antonio and Santa Rita do Passa Quatro municipalities, only small fragments of cerrado (Brazilian savanna) physiognomies (cerrado, cerrado sensu stricto) and of semideciduous forest have been left, surrounded by eucalyptus silviculture and sugar-cane agriculture. However, that vegetation mosaic still shelters large mammals, including several carnivore species. To detect the carnivores present in such a mosaic area (50,000 ha), and to find out how they use the landscape, we recorded them through 21 camera traps and 21 track plots, during 18 months. Species richness, diversity and relative frequency were evaluated according to the habitat. Ten species were recorded, some of them locally threatened to extinction (Puma concolor, Leopardus pardalis, Chrysocyon brachyurus). Species diversity did not significantly differ among fragments, and although most species preferred one or another habitat, the carnivore community as a whole explored all the study area regardless of the vegetation cover;eucalyptus plantations were as used by the carnivores as the native fragments. Therefore, it seems possible to maintain such animals in agricultural landscapes, where some large native fragments are left and the matrix is permeable to native fauna.

New insights into trypanosomatid U5 small nuclear ribonucleoproteins

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Cloning and molecular characterization of Trypanosoma cruzi U2, U4, U5, and U6 small nuclear RNAs

Small nuclear RNAs (snRNAs) are important factors in the functioning of eukaryotic cells that form several small complexes with proteins; these ribonucleoprotein particles (U snRNPs) have an essential role in the pre-mRNA processing, particularly in splicing, catalyzed by spliceosomes, large RNA-protein complexes composed of various snRNPs. Even though they are well defined in mammals, snRNPs are still not totally characterized in certain trypanosomatids as Trypanosoma cruzi. For this reason we subjected snRNAs (U2, U4, U5, and U6) from T. cruzi epimastigotes to molecular characterization by polymerase chain reaction (PCR) and reverse transcription-PCR. These amplified sequences were cloned, sequenced, and compared with those other of trypanosomatids. Among these snRNAs, U5 was less conserved and U6 the most conserved. Their respective secondary structures were predicted and compared with known T. brucei structures. In addition, the copy number of each snRNA in the T. cruzi genome was characterized by Southern blotting.

Functional and historical determinants of shape in the scapula of Xenarthran mammals: Evolution of a complex morphological structure

The mammalian scapula is a complex morphological structure, composed of two ossification plates that fuse into a single structure. Most studies on morphological differentiation in the scapula have considered it to be a simple, spatially integrated structure, primarily influenced by the important locomotor function presented by this element. We used recently developed geometric morphometric techniques to test and quantify functional and phylogenetic influences on scapular shape variation in fossil and extant xenarthran mammals. The order Xenarthra is well represented in the fossil record and presents a stable phylogenetic hypothesis for its genealogical history. In addition, its species present a large variety of locomotor habits. Our results show that approximately half of the shape variation in the scapula is due to phylogenetic heritage. This is contrary to the view that the scapula is influenced only by functional demands. There are large-scale shape transformations that provide biomechanical adaptation for the several habits (arboreality, terrestriality, and digging), and small scale-shape transformations (mostly related to the coracoid process) that are not influenced by function. A nonlinear relationship between morphometric and phylogenetic distances indicates the presence of a complex mixture of evolutionary processes acting on shape differentiation of the scapula. J. Morphol. 241,251-263, 1999. (C) 1999 Wiley-Liss, Inc.

A comparison of mucosal surface area and villous histology in small intestines of the brazilian free-tailed bat (Tadarida brasiliensis) and the mouse (Mus musculus)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)