Phylogeny and biogeography of Muusoctopus (Cephalopoda: Enteroctopodidae)

Deep‐sea octopuses of the genus Muusoctopus are thought to have originated in the Pacific Northern Hemisphere and then diversified throughout the Pacific and into the rest of the World Ocean. However, this hypothesis was inferred only from molecular divergence times. Here, the ancestral distribution and dispersal routes are estimated by Bayesian analysis based on a new phylogeny including 38 specimens from the south‐eastern Pacific Ocean. Morphological data and molecular sequences of three mitochondrial genes (16S rRNA, COI and COIII) are presented. The morphological data confirm that specimens newly acquired from off the coast of Chile comprise two species: Muusoctopus longibrachus and the poorly described species, Muusoctopus eicomar. The latter is here redescribed and is clearly distinguished from M. longibrachus and other closely related species in the region. A gene tree was built using Bayesian analysis to infer the phylogenetic position of these species within the species group, revealing that a large genetic distance separates the two sympatric Chilean species. M. longibrachus is confirmed as the sister species of Muusooctopus eureka from the Falkland Islands; while M. eicomar is a sister species of Muusoctopus yaquinae from the North Pacific, most closely related to the amphi‐Atlantic species Muusoctopus januarii. Molecular divergence times and ancestral distribution analyses suggest that genus Muusoctopus may have originated in the North Atlantic: one lineage dispersed directly southward to the Magellan region and another dispersed southward along the Eastern Pacific to the Southern Ocean and Antarctica. The Muusoctopus species in the Southern Hemisphere have different phylogenetic origins and represent independent invasions of this region.     

Cryptic diversity in the lizard genus Plica (Squamata): phylogenetic diversity and Amazonian biogeography

Intra‐ and interspecific genetic diversity of the lizard species Plica plica (9 localities) and Plica umbra (19 localities) from the Brazilian Amazon was analysed using two mitochondrial (16S rDNA and CO1) and one nuclear (prolactin receptor – PRLR) genes. We generated a maximum‐likelihood and Bayesian hypotheses of phylogenetic relationships, and using the bPTP and ABGD lineage delimiting methods inferred the most likely number of lineages within each species. Both methods delimited five distinct lineages in Plica plica and six lineages within Plica umbra. The nominal subspecies of Plica umbra was comprised of one lineage, while Plica umbra ochrocollaris was comprised of five lineages. In majority of the cases, lineages were restricted to the interfluves of major Amazonian rivers, and different lineages occupied distinct areas of endemism. Phylogenetic relationships of the lineages are largely concordant with the hypothesized formation of the areas of endemism. The geographic structuring of the clades and the delimitation of these clades as distinct lineages suggest the possibility that these lineages represent species. If the observed diversity of lineages within the genus Plica is characteristic of squamate reptiles of the Amazon region, the diversity of squamates is grossly underestimated.     

Sensitivity analysis of Repast computational ecology models with R/Repast

Computational ecology is an emerging interdisciplinary discipline founded mainly on modeling and simulation methods for studying ecological systems. Among the existing modeling formalisms, the individual‐based modeling is particularly well suited for capturing the complex temporal and spatial dynamics as well as the nonlinearities arising in ecosystems, communities, or populations due to individual variability. In addition, being a bottom‐up approach, it is useful for providing new insights on the local mechanisms which are generating some observed global dynamics. Of course, no conclusions about model results could be taken seriously if they are based on a single model execution and they are not analyzed carefully. Therefore, a sound methodology should always be used for underpinning the interpretation of model results. The sensitivity analysis is a methodology for quantitatively assessing the effect of input uncertainty in the simulation output which should be incorporated compulsorily to every work based on in‐silico experimental setup. In this article, we present R/Repast a GNU R package for running and analyzing Repast Simphony models accompanied by two worked examples on how to perform global sensitivity analysis and how to interpret the results.     

Integration of habitat models to predict fish distributions in several watersheds of Northern Spain

Species distribution models and consensus models allow knowing the distribution of species in large areas where there is no field data and identifying the most important drivers for those distributions. In this study, seven individual models were used to obtain a consensus model to determine the potential distribution for six freshwater fish species in several watersheds of Northern Spain. Moreover, three different methods of model evaluation were used for performance comparison. Fish data were obtained from databases provided by different organisms related to aquatic systems containing information on 759 field sites sampled between October 2002 and June 2011 using electrofishing techniques. Dependent variables were obtained after filtering field sites according to a human pressure gradient analysis, while independent variables were derived from a Synthetic River Network for the study area. The ‘best’ individual models were obtained using Random Forest, Generalized Boosted Models and Generalized Additive Models, but with differing results among species and evaluation methods. The different consensus models revealed a high degree of adjustment between modelled and observed data. The most important factors related to fish distributions were the width of the valley floor, mean annual flow, average catchment elevation, distance to the sea, and total catchment area. The importance and critical limits of presence‐absence for these key variables differed among species. Use of these models could assist in the prioritization and selection of specific catchment and river reach actions for fish population management, restoration and/or conservation.     

Revision of the taxonomic position of the xylanolytic Bacillus sp. MIR32 reidentified as Bacillus halodurans and plasmid-mediated transformation of B. halodurans

Bacillus sp. MIR32 has been isolated using xylan as the only carbon source, and one of its xylanolytic enzymes has been extensively studied. Biochemical analysis first related this strain to Bacillus amyloliquefaciens, but further studies based on a comparison of 16S rDNA sequences, G+C content, and DNA-DNA hybridization showed that strain MIR32 should be classified as a member of the species Bacillus halodurans. This change is also supported by the typical phenotype observed and by the results of PCR amplification directed toward spacers in rDNA and tDNA genes, which were assayed and compared with those of B. halodurans DSM 497(T). Although among alkaliphilic bacilli competence development has not been experimentally demonstrated, in this work both B. halodurans MIR32 and DSM 497(T) were transformed according to a simple procedure developed in our laboratory, reaching 10(2)-10(3) stable transformants per microgram of plasmid DNA.     

Defining the importance of landscape metrics for large branchiopod biodiversity and conservation: the case of the Iberian Peninsula and Balearic Islands

The deficiency in the distributional data of invertebrate taxa is one of the major impediments acting on the bias towards the low awareness of its conservation status. The present study sets a basic framework to understand the large branchiopods distribution in the Iberian Peninsula and Balearic Islands. Since the extensive surveys performed in the late 1980s, no more studies existed updating the information for the whole studied area. The present study fills the gap, gathering together all available information on large branchiopods distribution since 1995, and analysing the effect of human population density and several landscape characteristics on their distribution, taking into consideration different spatial scales (100 m, 1 km and 10 km). In overall, 28 large branchiopod taxa (17 anostracans, 7 notostracans and 4 spinicaudatans) are known to occur in the area. Approximately 30% of the sites hosted multiple species, with a maximum of 6 species. Significant positive co-occurring species pairs were found clustered together, forming 4 different associations of large branchiopod species. In general, species clustered in the same group showed similar responses to analysed landscape characteristics, usually showing a better fit at higher spatial scales.     

Didymodon vulcanicus J.A.Jiménez,Hedd. & Frank Müll. (Pottiaceae), a new species from tropical Africa

Didymodon vulcanicus J.A.Jiménez, Hedd. & Frank Müll. is described and illustrated as a new species from volcanic regions of tropical Africa. The species is distinguished morphologically by its lanceolate or more rarely ovate-lanceolate leaves that are strongly incurved distally when dry, acute apices, upper and middle laminal cells arranged in longitudinal rows with a low dorsal papilla over the transverse walls which reaches the two immediate cells, basal cells not or hardly differentiated from the medial cells, and the presence of gemmae in the leaf axils. Drawings and light microscope photographs of the main characters are given, and possible confusion with other closely related taxa is discussed.     

A new species of Heteromyoxyuris (Nematoda: Oxyuridae), parasite of Perognathus flavus (Rodentia: Heteromyidae) from Mexico

Heteromyoxyuris otomii n. sp., which inhabits the intestinal caecum of Perognathus flavus (Heteromyidae), in Zaragoza, Hidalgo, Mexico, is described. This new species differs from the 2 other congeneric species in the morphology and length of lateral alae in males. Heteromyoxyuris deserti has simple lateral alae located at both sides of the body, whereas in the new species, these structures are double at both sides; in contrast, lateral alae of Heteromyoxyuris longejector begin at the posterior half of the body, whereas they arise in the first third in the new species. Heteromyoxyuris longejector was found in 2 new host species, i.e., Perognathus amplus and Chaetodipus hispidus. This record represents the first record for the species in Mexico, increasing its geographic distribution.