Leposoma osvaldoi avila-pires, 1995 (Squamata: Gymnophthalmidae): New records and distribution map in the state of Mato Grosso, Brazil

The present study provides the distribution map and reports new records of the gymnophthalmid lizard Leposoma osvaldoi Avila-Pires, 1995, from Mato Grosso state, Brazil, extending the known geographical distribution of the species ca. 42 km northeastern in straight line from the nearest record in the state. © 2011 Check List and Authors.

Lepidobatrachus asper Budgett,1899 (Amphibia: Anura: Ceratophryidae): New country record, distribution map and natural history notes

Lepidobatrachus asper is a large to medium frog known from the Chaco lowlands of Paraguay and Argentina. We provide the first species record for the Brazilian Chaco, which extends the species geographical distribution ca. 73 km northeast from Puerto Casado, Alto Paraguay Departament, Paraguay. We also provide a distribution map and information about the species habitat conditions and diet. The Brazilian Chaco is still poorly surveyed, and the rapid environmental degradation can lead to local extinctions of certain species. © 2013 Check List and Authors.

Geographical variation in mutualistic networks: similarity, turnover and partner fidelity

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

Implementing new northernmost records to modelling the distribution of Hypsiboas caingua (Anura: Hylidae) in South America

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Morphological and molecular evidence demonstrates the amphi-Atlantic distribution of Laurencia catarinensis (Ceramiales, Rhodophyta)

We performed morphological and molecular studies of Laurencia catarinensis from the Canary Islands. This species has an entangled habit, cushion-like tuft formation, cortical cell walls, slightly to markedly projecting near the apex, and lacking lenticular thickenings in medullary cells. We inferred its phylogenetic position by analyzing the chloroplast-encoded rbcL gene sequences from 41 samples. The results demonstrate that specimens of L. catarinensis from the Canary Islands, where it is referred to as L. intricata, and those from Brazil (including specimens from the type locality in Santa Catarina) form a monophyletic clade with low genetic divergence (0-0.9%). In contrast, specimens of L. intricata from the type locality in Cuba, Mexico, and the USA were clearly distinct from L. catarinensis collected in Brazil and the Canary Islands, as shown by high genetic divergence values (4.9-5.7%). The type material of L. catarinensis from Brazil allowed us to identify all samples from the Canarian Archipelago as L. catarinensis. These findings expand the known geographical distribution of L. catarinensis to the eastern Atlantic Ocean and demonstrate an amphi-Atlantic distribution of the species.

Spatial Distribution of Cryptic Species Diversity in European Freshwater Amphipods (Gammarus fossarum) as Revealed by Pyrosequencing

In order to understand and protect ecosystems, local gene pools need to be evaluated with respect to their uniqueness. Cryptic species present a challenge in this context because their presence, if unrecognized, may lead to serious misjudgement of the distribution of evolutionarily distinct genetic entities. In this study, we describe the current geographical distribution of cryptic species of the ecologically important stream amphipod Gammarus fossarum (types A, B and C). We use a novel pyrosequencing assay for molecular species identification and survey 62 populations in Switzerland, plus several populations in Germany and eastern France. In addition, we compile data from previous publications (mainly Germany). A clear transition is observed from type A in the east (Danube and Po drainages) to types B and, more rarely, C in the west (Meuse, Rhone, and four smaller French river systems). Within the Rhine drainage, the cryptic species meet in a contact zone which spans the entire G. fossarum distribution range from north to south. This large-scale geographical sorting indicates that types A and B persisted in separate refugia during Pleistocene glaciations. Within the contact zone, the species rarely co-occur at the same site, suggesting that ecological processes may preclude long-term coexistence. The clear phylogeographical signal observed in this study implies that, in many parts of Europe, only one of the cryptic species is present.

The effect of climate change on the potential distribution of the European Phlebotomus species and the parasite Leishmania infantum in 2011-2070. A climate envelope modeling approach

Aims: In the Mediterranean areas of Europe, leishmanisasis is one of the most emerging vector-borne diseases. Members of genus Phlebotomus are the primary vectors of the genus Leishmania. To track the human health effect of climate change it is a very important interdisciplinary question to study whether the climatic requirements and geographical distribution of the vectors of human pathogen organisms correlate with each other. Our study intended to explore the potential effects of ongoing climate change, in particular through a potential upward altitudinal and latitudinal shift of the distribution of the parasite Leishmania infantum, its vectors Phlebotomus ariasi, P. neglectus, P. perfiliewi, P. perniciosus, and P. tobbi, and some other sandfly species: P. papatasi, P. sergenti, and P. similis. Methods: By using a climate envelope modelling (CEM) method we modelled the current and future (2011-2070) potential distribution of 8 European sandfly species and L. infantum based on the current distribution using the REMO regional climate model. Results: We found that by the end of the 2060’s most parts of Western Europe can be colonized by sandfly species, mostly by P. ariasi and P. pernicosus. P. ariasi showed the greatest potential northward expansion. For all the studied vectors of L. infantum the entire Mediterranean Basin and South-Eastern Europe seemed to be suitable. L. infantum can affect the Eastern Mediterranean, without notable northward expansion. Our model resulted 1 to 2 months prolongation of the potentially active period of P. neglectus P. papatasi and P. perniciosus for the 2060’s in Southern Hungary. Conclusion: Our findings confirm the concerns that leishmanisais can become a real hazard for the major part of the European population to the end of the 21th century and the Carpathian Basin is a particularly vulnerable area.

Genetic diversity across geographical scales in marine coastal ecosystems: Holothuria arguinensis a model species

Coastal lagoons are considered one of the most productive areas of our planet harboring a large variety of habitats. Their transitional character, between terrestrial and marine environments, creates a very particular ecosystem with important variations of its environmental conditions. The organisms that are able to survive on these ecosystems frequently experience strong selective pressures and constrictions to gene flowwith marine populations, which could contribute to genetic divergence among populations inhabiting coastal lagoon and marine environments. Therefore, the main aims of this study are to asses the genetic diversity and population structure of Holothuria arguinensis across geographical ranges, to test the hypothesis of coastal lagoons as hotspots of genetic diversity in the Ria Formosa lagoon, and to determine the role of exporting standing genetic variation from the lagoon to open sea and their implications to recent geographical expansion events. To reach these objectives, we investigate the genetic structure of H. arguinensis using two mitochondrial DNA markers (COI and 16S) at different spatial scales: i) small, inside Ria Formosa coastal lagoon, South Portugal; 2) large, including most of the geographical distribution of this species (South and Western Portuguese coast and Canary islands); these results will allow us to compare the genetic diversity of lagoonal and marine populations of H. arguinensis. On this framework, its recent geographical expansion events, recorded by Rodrigues (2012) and González-Wangüemert and Borrero-Pérez (2012), will be analyzed considering the potential contribution from lagoonal genetic pool. Non-significant genetic structure and high haplotypic diversity were found inside the Ria Formosa coastal lagoon. Both genes were unable to detect significant genetic differentiation among lagoonal and marine localities, suggesting a high rate of gene flow. The results supported our hypotheses that coastal lagoons are not only acting as hotspots of genetic diversity, but also contributing for the genetic variability of the species, working as a source of new haplotypes and enhancing adaptation to the high variable conditions. Different genetic patterns of colonization were found on H. arguinensis, but they must be studied more deeply.

Distribution pattern of Galeus atlanticus in the Alborán Sea (south western Mediterranean) and some sexual character comparison with Galeus melastomus

Galeus atlanticus is a small-sized deepwater catshark living on the slope bottom of the Alborán Sea. Given its external similarities with Galeus melastomus, both species are often confused, which makes G. atlanticus a very poorly understood species both in terms of catches and biological aspects. For this study, a total of 741 G. atlanticus specimens, caught during scientific surveys from 1997 to 2003, were analysed. The distributional patterns were described and the reproductive status estimated. Galeus atlanticus occurred throughout the Alborán Sea, between the Strait of Gibraltar and Cape Gata, including the slope of the Island of Alborán. Its bathymetric range extended from 330 to 790 m and no size depth trends have been observed. Mature specimens, both males and females, were caught in all seasons of the year. Size at first maturity was significantly different between sexes, with estimates of 32.9 cm for males and 36.9 cm for females. The differential growth of some secondary sexual characteristics, such as clasper length in males and oviducal gland diameter in females, were compared with those of G. melastomus.

Spatial scale effects of sampling on the interpolation of species distribution models in the southwestern Amazon.

Knowledge of the geographical distribution of timber tree species in the Amazon is still scarce. This is especially true at the local level, thereby limiting natural resource management actions. Forest inventories are key sources of information on the occurrence of such species. However, areas with approved forest management plans are mostly located near access roads and the main industrial centers. The present study aimed to assess the spatial scale effects of forest inventories used as sources of occurrence data in the interpolation of potential species distribution models. The occurrence data of a group of six forest tree species were divided into four geographical areas during the modeling process. Several sampling schemes were then tested applying the maximum entropy algorithm, using the following predictor variables: elevation, slope, exposure, normalized difference vegetation index (NDVI) and height above the nearest drainage (HAND). The results revealed that using occurrence data from only one geographical area with unique environmental characteristics increased both model overfitting to input data and omission error rates. The use of a diagonal systematic sampling scheme and lower threshold values led to improved model performance. Forest inventories may be used to predict areas with a high probability of species occurrence, provided they are located in forest management plan regions representative of the environmental range of the model projection area.

Thermal requirements, field mortality and population phenology modelling of Paropsis atomaria Olivier, an emergent pest in subtropical hardwood plantations

Paropsis atomaria is a recently emerged pest of eucalypt plantations in subtropical Australia. Its broad host range of at least 20 eucalypt species and wide geographical distribution provides it the potential to become a serious forestry pest both within Australia and, if accidentally introduced, overseas. Although populations of P. atomaria are genetically similar throughout its range, population dynamics differ between regions. Here, we determine temperature-dependent developmental requirements using beetles sourced from temperate and subtropical zones by calculating lower temperature thresholds, temperature-induced mortality, and day-degree requirements. We combine these data with field mortality estimates of immature life stages to produce a cohort-based model, ParopSys, using DYMEX™ that accurately predicts the timing, duration, and relative abundance of life stages in the field and number of generations in a spring–autumn (September–May) field season. Voltinism was identified as a seasonally plastic trait dependent upon environmental conditions, with two generations observed and predicted in the Australian Capital Territory, and up to four in Queensland. Lower temperature thresholds for development ranged between 4 and 9 °C, and overall development rates did not differ according to beetle origin. Total immature development time (egg–adult) was approximately 769.2 ± S.E. 127.8 DD above a lower temperature threshold of 6.4 ± S.E. 2.6 °C. ParopSys provides a basic tool enabling forest managers to use the number of generations and seasonal fluctuations in abundance of damaging life stages to estimate the pest risk of P. atomaria prior to plantation establishment, and predict the occurrence and duration of damaging life stages in the field. Additionally, by using local climatic data the pest potential of P. atomaria can be estimated to predict the risk of it establishing if accidentally introduced overseas. Improvements to ParopSys’ capability and complexity can be made as more biological data become available.

Hierarchical models for 2D presence/absence data having ambiguous zeroes: With a biogeographical case study on dingo behaviour

This dissertation is primarily an applied statistical modelling investigation, motivated by a case study comprising real data and real questions. Theoretical questions on modelling and computation of normalization constants arose from pursuit of these data analytic questions. The essence of the thesis can be described as follows. Consider binary data observed on a two-dimensional lattice. A common problem with such data is the ambiguity of zeroes recorded. These may represent zero response given some threshold (presence) or that the threshold has not been triggered (absence). Suppose that the researcher wishes to estimate the effects of covariates on the binary responses, whilst taking into account underlying spatial variation, which is itself of some interest. This situation arises in many contexts and the dingo, cypress and toad case studies described in the motivation chapter are examples of this. Two main approaches to modelling and inference are investigated in this thesis. The first is frequentist and based on generalized linear models, with spatial variation modelled by using a block structure or by smoothing the residuals spatially. The EM algorithm can be used to obtain point estimates, coupled with bootstrapping or asymptotic MLE estimates for standard errors. The second approach is Bayesian and based on a three- or four-tier hierarchical model, comprising a logistic regression with covariates for the data layer, a binary Markov Random field (MRF) for the underlying spatial process, and suitable priors for parameters in these main models. The three-parameter autologistic model is a particular MRF of interest. Markov chain Monte Carlo (MCMC) methods comprising hybrid Metropolis/Gibbs samplers is suitable for computation in this situation. Model performance can be gauged by MCMC diagnostics. Model choice can be assessed by incorporating another tier in the modelling hierarchy. This requires evaluation of a normalization constant, a notoriously difficult problem. Difficulty with estimating the normalization constant for the MRF can be overcome by using a path integral approach, although this is a highly computationally intensive method. Different methods of estimating ratios of normalization constants (N Cs) are investigated, including importance sampling Monte Carlo (ISMC), dependent Monte Carlo based on MCMC simulations (MCMC), and reverse logistic regression (RLR). I develop an idea present though not fully developed in the literature, and propose the Integrated mean canonical statistic (IMCS) method for estimating log NC ratios for binary MRFs. The IMCS method falls within the framework of the newly identified path sampling methods of Gelman & Meng (1998) and outperforms ISMC, MCMC and RLR. It also does not rely on simplifying assumptions, such as ignoring spatio-temporal dependence in the process. A thorough investigation is made of the application of IMCS to the three-parameter Autologistic model. This work introduces background computations required for the full implementation of the four-tier model in Chapter 7. Two different extensions of the three-tier model to a four-tier version are investigated. The first extension incorporates temporal dependence in the underlying spatio-temporal process. The second extensions allows the successes and failures in the data layer to depend on time. The MCMC computational method is extended to incorporate the extra layer. A major contribution of the thesis is the development of a fully Bayesian approach to inference for these hierarchical models for the first time. Note: The author of this thesis has agreed to make it open access but invites people downloading the thesis to send her an email via the 'Contact Author' function.