Use of Camera-Trapping to Estimate Puma Density and Influencing Factors in Central Brazil

Abstract: We used remotely triggered cameras to collect data on Puma (Puma concolor) abundance and occupancy in an area of tropical forest in Brazil where the species' status is poorly known. To evaluate factors influencing puma occupancy we used data from 5 sampling campaigns in 3 consecutive years (2005 to 2007) and 2 seasons (wet and dry), at a state park and a private forest reserve. We estimated puma numbers and density for the 2007 sampling data by developing a standardized individual identification method. We based individual identification on 1) time-stable parameters (SP; physical features that do not change over time), and 2) time-variable parameters (VP; marks that could change over time such as scars and botfly marks). Following individual identification we established a capture-recapture history and analyzed it using closed population capture-mark-recapture models. Puma capture probability was influenced by camera placement (roads vs. trails), sampling year, and prey richness. Puma occupancy was positively associated with species richness and there was a correlation between relative puma and jaguar (Panthera onca) abundance. Identifications enabled us to generate 8 VP histories for each photographed flank, corresponding to 8 individuals. We estimated the sampled population at 9 pumas (SE = 1.03, 95% CI = 8–10 individuals) translating to a density of 3.40 pumas/100 km². Information collected using camera-traps can effectively be used to assess puma population size in tropical forests. As habitat progressively disappears and South American felines become more vulnerable, our results support the critical importance of private forest reserves for conservation.     

Fluorescein-based amino acids for solid phase synthesis of fluorogenic protease substrates

An efficient synthesis of new type fluorescent amino acids is described. The Fmoc-protected dyes can be prepared in a four-step procedure with approximately 30% overall yield from aminofluoresceins and other inexpensive commercially available precursors. The dyes are much more photostable compared to fluorescein and exhibit constant pH-independent fluorescence that is advantageous in biological applications. The Fmoc-protected fluorescent amino acids are ready for use in solid phase peptide synthesis. As a proof of concept, a fluorogenic papain substrate was synthesized and employed for on-bead detection of the protease activity. By using a novel technique for quantitative analysis of bead fluorescence, a approximately 2.7-fold increase in mean bead brightness was measured and was attributed to substrate cleavage by papain. The new type fluorescent amino acids seem to be a promising tool for the synthesis of fluorescent peptide ligands and fluorogenic protease substrates.     

Positive and Negative Selection in the β-Esterase Gene Cluster of the Drosophila melanogaster Subgroup

We examine the pattern of molecular evolution of the β-esterase gene cluster, including the Est-6 and ψEst-6 genes, in eight species of the Drosophila melanogaster subgroup. Using maximum likelihood estimates of nonsynonymous/synonymous rate ratios, we show that the majority of Est-6 sites evolves under strong (48% of sites) or moderate (50% of sites) negative selection and a minority of sites (1.5%) is under significant positive selection. Est-6 sites likely to be under positive selection are associated with increased intraspecific variability. One positively selected site is responsible for the EST-6 F/S allozyme polymorphism; the same site is responsible for the EST-6 functional divergence between species of the melanogaster subgroup. For ψEst-6 83.7% sites evolve under negative selection, 16% sites evolve neutrally, and 0.3% sites are under positive selection. The positively selected sites of ψEst-6 are located at the beginning and at the end of the gene, where there is reduced divergence between D. melanogaster and D. simulans; these regions of ψEst-6 could be involved in regulation or some other function. Branch-site-specific analysis shows that the evolution of the melanogaster subgroup underwent episodic positive selection. Collating the present data with previous results for the β-esterase genes, we propose that positive and negative selection are involved in a complex relationship that may be typical of the divergence of duplicate genes as one or both duplicates evolve a new function. [Reviewing Editor: Dr. Martin Kreitman]     

Calycine colleters of seven species of Apocynaceae (Apocynoideae) from Brazil

The structure and organization of calycine colleters belonging to four genera of Apocynaceae are described. Calycine colleters were found in all species. All colleters had the same histological composition, but morphological differences were observed in four species. Most colleters were of the standard type, and possible deviations resulted in three morphological types: bifurcated, laminar, and sessile. Mechanisms of cell separation, proliferation, and elongation may explain the origin of the new types. As a consequence of morphological changes, the secretory surface was expanded in the bifurcated, laminar, and sessile glands. Most colleters were in a post-secretory phase, but a hydrophilic secretion was observed in Mandevilla pycnantha and Mesechites mansoana . A larger secretory surface, together with the extension of the secretory phase in adult flowers, were major shifts in the calycine colleters of Apocynaceae, and are possibly correlated with the functional and ecological aspects of these organs. Three patterns of distribution of calycine colleters were observed: alternate, opposite, or indefinitely distributed. The alternate pattern was not homogeneous, and three subtypes were recognized: four-, five-, and ten-grouped colleters. The number of calycine colleters was variable between taxa and even within the same species.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 152 , 387–398.     

Mitochondrial DNA Variation and Introgression in Siberian Taimen Hucho taimen

Siberian taimen Hucho taimen is the largest representative of the family Salmonidae inhabiting rivers of northern Eurasia. The species is under intensive aquaculture activity. To monitor natural taimen populations we have sequenced a portion (8,141 bp) of the mitochondrial (mt) genome in 28 specimens of H. taimen from six localities in the Amur River basin. Nucleotide variability is low (π = 0.0010), but structured in two divergent haplotype groups. A comparison of the data with the GenBank H. taimen mt genome ({"type":"entrez-nucleotide","attrs":{"text":"HQ897271","term_id":"325127000","term_text":"HQ897271"}}HQ897271) reveals significant differences between them in spite of the fact that the fish specimens come from neighboring geographical areas. The distribution of divergence is non-uniform with two highly pronounced divergent regions centered on two genes, ND3 and ND6. To clarify the pattern of divergence we sequenced the corresponding portion of the mt genome of lenok Brachymystax tumensis and analyzed the GenBank complete mt genomes of related species. We have found that the first and second divergent regions are identical between the GenBank H. taimen and two lenok subspecies, B. lenok and B. lenok tsinlingensis, respectively. Consequently, both divergent regions represent introgressed mtDNA resulting from intergeneric hybridization between the two lenok subspecies and H. taimen. Introgression is, however, not detected in our specimens. This plus the precise identity of the introgressed fragments between the donor and the recipient GenBank sequence suggests that the introgression is local and very recent, probably due to artificial manipulations involving taimen – lenok intergeneric hybridization. Human-mediated hybridization may become a major threat to aquatic biodiversity. Consequently we suggest that due attention needs to be given to this threat by means of responsible breeding program management, so as to prevent a potential spread of hybrid fishes that could jeopardize the resilience of locally adapted gene pools of the native H. taimen populations.     

Effects of multi-year droughts on fish assemblages of seasonally drying Mediterranean streams

1. This study analysed changes occurring in Mediterranean stream fish assemblages over a sequence of dry years followed by a generally wet period (1991–98). Variations in assemblage attributes were quantified at the basin and stream reach scales, and related to variables reflecting the occurrence of unusually dry or wet conditions. 2. Assemblage variability increased along with the resolution of analysis, with little changes in species richness, composition and rank abundances, but significant variation in individual species abundances. Fluctuations in relative abundances were significantly affected by variables reflecting the severity of summer droughts and the occurrence of rainy springs. These patterns were evident at the basin scale, while variability at individual stream reaches tended to be higher and less related to rainfall patterns. 3. At least three response guilds to rainfall variation could be identified: two of the four abundant and widespread species (chub and loach) declined following dry years, whereas the two other core species (nase and eel) declined after rainy spring; one scarce native species (stickleback) increased in dry years. 4. Except at the two most upstream reaches, the assemblages tended to recover quickly to previous configuration after the changes occurring during the sequence of dry years. 5. Temporal variability of local assemblages was concordant among reaches but did not follow any consistent spatial pattern. Instead, spatial patterns in assemblage attributes changed over time in response to environmental variability, with a tendency for a disruption of upstream–downstream gradients following dry years. 6. Results supported the view that present‐day droughts cause relatively small and transient changes to Mediterranean stream fish assemblages. However, longer and more severe droughts expected under altered future climates, may result in declines or local extinctions of the most sensitive species and their potential replacement by more resistant species. Changing drought regimes thus need to be duly considered in the development of conservation strategies for Mediterranean stream fish.     

Phylogenetic analysis of Micrathena and Chaetacis spiders (Araneae: Araneidae) reveals multiple origins of extreme sexual size dimorphism and long abdominal spines

The phylogenetic relationships amongst the New World spiny orb‐weaving spiders Micrathena and Chaetacis were assessed through parsimony and Bayesian analyses of morphological characters. A total of 146 characters was scored for ten outgroup taxa and 37 Micrathena and four Chaetacis species. The results indicate that Chaetacis nests within Micrathena and we propose Chaetacis as a junior synonym of Micrathena. Twelve subgeneric species groups of Micrathena are recognized and diagnosed. Species with extremely long spines evolved at least eight times in the genus and we suggest that this may be related to antipredator defences. Micrathena is primitively sexually monomorphic and extreme sexual size dimorphism has arisen at least six times in the genus. Most of these events are because of enlargement of the female in relation to the ancestral size, although in two cases sexual dimorphism was attained through male reduction, adding more data to the ‘giant females’ vs. ‘dwarf males’ controversy. The genus is probably of South American origin and has repeatedly invaded Central and North America. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 14–53.     

Fixation of metacentric chromosomes in populations of the common shrew Sorex araneus L. from populations of Eastern Europe

In this review, we discuss the processes of fixation of Robertsonian chromosome fusions in populations of the common shrew Sorex araneus L. Various Robertsonian fusions, accumulating in populations, create an illusion of large chromosomal rearrangements, reciprocal translocations of complete chromosome arms. The use of these rearrangements for phylogenetic reconstructions results in false conclusions. Robertsonian fusions accumulate in populations at such stages of the species evolution, when large open or subdivided populations prevail (populations of warm periods of Pleistocene and many present-day populations) and are fixed in small isolated populations and glacial refugia. The formation of monomorphic chromosome races requires a long time, several glaciation epochs during the whole Pleistocene.     

Gradients in stream fish assemblages across a Mediterranean landscape: contributions of environmental factors and spatial structure

1. Despite wide recognition that fish assemblages are influenced by factors operating over a range of spatial scales, little effort has been devoted to quantifying large‐scale variation and the multiscale dependencies of assemblage patterns and processes. This is particularly true for Mediterranean streams, where seasonally predictable drying‐up may lead to a strong association between assemblage attributes and large‐scale factors affecting the distribution of population sources and extinction likelihood. 2. The contribution of large‐scale factors to stream fish assemblage variation was quantified across a Mediterranean landscape, in south‐west Portugal. Fish abundance and species composition were estimated at 166 sites across third‐ to sixth‐order streams, in March–July 1998. Variance partitioning by redundancy analyses was used to analyse assemblage variation against three sets of predictor variables: environmental (catchment position, and geomorphic and hydrological factors), large‐scale spatial trends and neighbourhood effects. 3. Environmental variables and spatial trends accounted for 34.6% of the assemblage variation across the entire region, and for 36.6 and 57.8% within the two largest catchments (Mira and Seixe). Neighbourhood effects were analysed at the catchment scale, increasing the explained variation to 56.1% (Mira) and 70.7% (Seixe). 4. A prevailing environmental gradient was reflected in an increase in the abundance of all species and size‐classes in relation to catchment position, with more fish present in larger streams and in downstream reaches. Variables describing geomorphic and hydrological settings were less important in explaining assemblage variation. 5. Spatial trends always accounted for the smallest fraction of assemblage variation, and they were probably associated with historical barriers to fish dispersal. The strong neighbourhood effects may be related to spatially autocorrelated habitat conditions, but they are also a likely consequence of fish emigration/extinction and colonisation processes. 6. These results emphasise that a substantial proportion of fish assemblage variation in Mediterranean streams may be explained by large‐scale factors, irrespective of microhabitats and local biotic interactions. It is suggested that this pattern results to a large extent from the seasonal drying‐up, with the summer shortage of surface water limiting fish occurrence in headwaters, and consequently the key core areas for fish concentrating in larger streams and tributaries adjacent to large streams because of neighbourhood effects.