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

Evolutionary history of black grouse major histocompatibility complex class IIB genes revealed through single locus sequence-based genotyping

Background: Gene duplications are frequently observed in the Major Histocompatibility Complex (MHC) of many species, and as a consequence loci belonging to the same MHC class are often too similar to tell apart. In birds, single locus genotyping of MHC genes has proven difficult due to concerted evolution homogenizing sequences at different loci. But studies on evolutionary history, mode of selection and heterozygosity correlations on the MHC cannot be performed before it is possible to analyse duplicated genes separately. In this study we investigate the architecture and evolution of the MHC class IIB genes in black grouse. We developed a sequence-based genotyping method for separate amplification of the two black grouse MHC class IIB genes BLB1 and BLB2. Based on this approach we are able to study differences in structure and selection between the two genes in black grouse and relate these results to the chicken MHC structure and organization. Results: Sequences were obtained from 12 individuals and separated into alleles using the software PHASE. We compared nucleotide diversity measures and employed selection tests for BLB1 and BLB2 to explore their modes of selection. Both BLB1 and BLB2 are transcribed and display classic characteristics of balancing selection as predicted for expressed MHC class IIB genes. We found evidence for both intra- and interlocus recombination or gene conversion, as well as indication for positive but differential selection at both loci. Moreover, the two loci appear to be linked. Phylogenetic analyses revealed orthology of the black grouse MHC class IIB genes to the respective BLB loci in chicken. Conclusions: The results indicate that the duplication of the BLB gene occurred before the species divergence into black grouse, chicken and pheasant. Further, we conclude that BLB1 and BLB2 in black grouse are subjected to homogenizing concerted evolution due to interlocus genetic exchange after species divergence. The loci are in linkage disequilibrium, which is in line with the theory of tightly coevolving genes within the MHC under the minimal essential MHC hypothesis. Our results support the conclusion that MHC form and function in birds derived from studies on the domesticated chicken are not artefacts of the domestication process

Signatures of historical selection on MHC reveal different selection patterns in the moor frog (Rana arvalis)

MHC genes are key components in disease resistance and an excellent system for studying selection acting on genetic variation in natural populations. Current patterns of variation in MHC genes are likely to be influenced by past and ongoing selection as well as demographic fluctuations in population size such as those imposed by post-glacial recolonization processes. Here, we investigated signatures of historical selection and demography on an MHC class II gene in 12 moor frog populations along a 1700-km latitudinal gradient. Sequences were obtained from 207 individuals and consecutively assigned into two different clusters (northern and southern clusters, respectively) in concordance with a previously described dual post-glacial colonization route. Selection analyses comparing the relative rates of non-synonymous to synonymous substitutions (dN/dS) suggested evidence of different selection patterns in the northern and the southern clusters, with divergent selection prevailing in the south but uniform positive selection predominating in the north. Also, models of codon evolution revealed considerable differences in the strength of selection: The southern cluster appeared to be under strong selection while the northern cluster showed moderate signs of selection. Our results indicate that the MHC alleles in the north diverged from southern MHC alleles as a result of differential selection patterns

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-0

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

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

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