Responses of five small mammal species to micro-scale variations in vegetation structure in secondary Atlantic Forest remnants, Brazil

<p>Abstract</p> <p>Background</p> <p>The Brazilian Atlantic Forest is highly endangered and only about 7% of the original forest remains, most of which consists of fragments of secondary forest. Small mammals in the Atlantic Forest have differential responses to this process of fragmentation and conversion of forest into anthropogenic habitats, and have varying abilities to occupy the surrounding altered habitats. We investigated the influence of vegetation structure on the micro-scale distribution of five small mammal species in six secondary forest remnants in a landscape of fragmented Atlantic Forest. We tested whether the occurrence of small mammal species is influenced by vegetation structure, aiming to ascertain whether species with different degrees of vulnerability to forest fragmentation (not vulnerable: <it>A. montensis</it>, <it>O. nigripes </it>and <it>G. microtarsus</it>; vulnerable: <it>M. incanus </it>and <it>D. sublineatus</it>; classification of vulnerability was based on the results of previous studies) are associated with distinct vegetation characteristics.</p> <p>Results</p> <p>Although vegetation structure differed among fragments, micro-scale distribution of most of the species was influenced by vegetation structure in a similar way in different fragments. Among the three species that were previously shown not to be vulnerable to forest fragmentation, <it>A. montensis </it>and <it>G. microtarsus </it>were present at locations with an open canopy and the occurrence of <it>O. nigripes </it>was associated to a low canopy and a dense understory. On the other hand, from the two species that were shown to be vulnerable to fragmentation, <it>M. incanus </it>was captured most often at locations with a closed canopy while the distribution of <it>D. sublineatus </it>was not clearly influenced by micro-scale variation in vegetation structure.</p> <p>Conclusion</p> <p>Results indicate the importance of micro-scale variation in vegetation structure for the distribution of small mammal species in secondary forest fragments. Species that are not vulnerable to fragmentation occurred at locations with vegetation characteristics of more disturbed forest, while one of the species vulnerable to fragmentation was found at locations with older forest characteristics. Results suggest that micro-habitat preferences may be an important factor influencing the capacity of small mammals to occupy altered habitats and, consequently, their vulnerability to forest fragmentation at a larger spatial scale.</p

Selection, diversity and evolutionary patterns of the MHC class II DAB in free-ranging Neotropical marsupials

<p>Abstract</p> <p>Background</p> <p>Research on the genetic architecture and diversity of the MHC has focused mainly on eutherian mammals, birds and fish. So far, studies on model marsupials used in laboratory investigations indicated very little or even no variation in MHC class II genes. However, natural levels of diversity and selection are unknown in marsupials as studies on wild populations are virtually absent. We used two endemic South American mouse opossums, <it>Gracilinanus microtarsus </it>and <it>Marmosops incanus</it>, to investigate characteristic features of MHC selection. This study is the first investigation of MHC selection in free-ranging Neotropical marsupials. In addition, the evolutionary history of MHC lineages within the group of marsupials was examined.</p> <p>Results</p> <p><it>G. microtarsus </it>showed extensive levels of MHC diversity within and among individuals as 47 MHC-DAB alleles and high levels of sequence divergence were detected at a minimum of four loci. Positively selected codon sites were identified, of which most were congruent with human antigen binding sites. The diversity in <it>M. incanus </it>was rather low with only eight observed alleles at presumably two loci. However, these alleles also revealed high sequence divergence. Again, positive selection was identified on specific codon sites, all congruent with human ABS and with positively selected sites observed in <it>G. microtarsus</it>. In a phylogenetic comparison alleles of <it>M. incanus </it>interspersed widely within alleles of <it>G. microtarsus </it>with four alleles being present in both species.</p> <p>Conclusion</p> <p>Our investigations revealed extensive MHC class II polymorphism in a natural marsupial population, contrary to previous assumptions. Furthermore, our study confirms for the first time in marsupials the presence of three characteristic features common at MHC loci of eutherian mammals, birds and fish: large allelic sequence divergence, positive selection on specific sites and trans-specific polymorphism.</p

Assessing the utility of statistical adjustments for imperfect detection in tropical conservation science

1. In recent years, there has been a fast development of models that adjust for imperfect detection. These models have revolutionised the analysis of field data, and their use has repeatedly demonstrated the importance of sampling design and data quality. There are, however, several practical limitations associated with the use of detectability models which restrict their relevance to tropical conservation science. 2. We outline the main advantages of detectability models, before examining their limitations associated with their applicability to the analysis of tropical communities, rare species and large-scale datasets. Finally, we discuss whether detection probability needs to be controlled before and/or after data collection. 3. Models that adjust for imperfect detection allow ecologists to assess data quality by estimating uncertainty, and to obtain adjusted ecological estimates of populations and communities. Importantly, these models have allowed informed decisions to be made about the conservation and management of target species. 4. Data requirements for obtaining unadjusted estimates are substantially lower than for detectability-adjusted estimates, which require relatively high detection/recapture probabilities and a number of repeated surveys at each location. These requirements can be difficult to meet in large-scale environmental studies where high levels of spatial replication are needed, or in the tropics where communities are composed of many naturally rare species. However, while imperfect detection can only be adjusted statistically, covariates of detection probability can also be controlled through study design. Using three study cases where we controlled for covariates of detection probability through sampling design, we show that the variation in unadjusted ecological estimates from nearly 100 species was qualitatively the same as that obtained from adjusted estimates. Finally, we discuss that the decision as to whether one should control for covariates of detection probability through study design or statistical analyses should be dependent on study objectives. 5. Synthesis and applications. Models that adjust for imperfect detection are an important part of an ecologist's toolkit, but they should not be uniformly adopted in all studies. Ecologists should never let the constraints of models dictate which questions should be pursued or how the data should be analysed, and detectability models are no exception. We argue for pluralism in scientific methods, particularly where cost-effective applied ecological science is needed to inform conservation policy at a range of different scales and in many different systems

Immigration Rates in Fragmented Landscapes – Empirical Evidence for the Importance of Habitat Amount for Species Persistence

BACKGROUND: The total amount of native vegetation is an important property of fragmented landscapes and is known to exert a strong influence on population and metapopulation dynamics. As the relationship between habitat loss and local patch and gap characteristics is strongly non-linear, theoretical models predict that immigration rates should decrease dramatically at low levels of remaining native vegetation cover, leading to patch-area effects and the existence of species extinction thresholds across fragmented landscapes with different proportions of remaining native vegetation. Although empirical patterns of species distribution and richness give support to these models, direct measurements of immigration rates across fragmented landscapes are still lacking. METHODOLOGY/PRINCIPAL FINDINGS: Using the Brazilian Atlantic forest marsupial Gray Slender Mouse Opossum (Marmosops incanus) as a model species and estimating demographic parameters of populations in patches situated in three landscapes differing in the total amount of remaining forest, we tested the hypotheses that patch-area effects on population density are apparent only at intermediate levels of forest cover, and that immigration rates into forest patches are defined primarily by landscape context surrounding patches. As expected, we observed a positive patch-area effect on M. incanus density only within the landscape with intermediate forest cover. Density was independent of patch size in the most forested landscape and the species was absent from the most deforested landscape. Specifically, the mean estimated numbers of immigrants into small patches were lower in the landscape with intermediate forest cover compared to the most forested landscape. CONCLUSIONS/SIGNIFICANCE: Our results reveal the crucial importance of the total amount of remaining native vegetation for species persistence in fragmented landscapes, and specifically as to the role of variable immigration rates in providing the underlying mechanism that drives both patch-area effects and species extinction thresholds

Selection, diversity and evolutionary patterns of the MHC class II DAB in free-ranging Neotropical marsupials-1

BB and DCB are additional marsupial β gene families. Some branches have been compressed for a better overview. The tree was constructed with the neighbour joining method (Kimura-2-parameter), bootstrap values >50 are indicated (1,000 replications). The scale bar represents genetic distance in nucleotide substitution per site. # following an allele's name indicates a pseudogene. = , open circle, = , filled circle; , in bold; , , . Chicken = , Axolotl = , Xenopus = Xenopus laevis, and .<p><b>Copyright information:</b></p><p>Taken from "Selection, diversity and evolutionary patterns of the MHC class II DAB in free-ranging Neotropical marsupials"</p><p>http://www.biomedcentral.com/1471-2156/9/39</p><p>BMC Genetics 2008;9():39-39.</p><p>Published online 5 Jun 2008</p><p>PMCID:PMC2442840.</p><p></p

Selection, diversity and evolutionary patterns of the MHC class II DAB in free-ranging Neotropical marsupials-2

A pseudogene. The bracket combining -DAB*03 and -DAB*04 signifies that these two alleles revealed identical SSCP patterns and the frequency value is therefore composed from both alleles. Numeration is according to the human DR1 molecule and asterisks indicate the human antigen binding sites (ABS) defined by [37].<p><b>Copyright information:</b></p><p>Taken from "Selection, diversity and evolutionary patterns of the MHC class II DAB in free-ranging Neotropical marsupials"</p><p>http://www.biomedcentral.com/1471-2156/9/39</p><p>BMC Genetics 2008;9():39-39.</p><p>Published online 5 Jun 2008</p><p>PMCID:PMC2442840.</p><p></p