Overcoming limitations of modelling rare species by using ensembles of small models

1. Species distribution models (SDMs) have become a standard tool in ecology and applied conservation biology. Modelling rare and threatened species is particularly important for conservation purposes. However, modelling rare species is difficult because the combination of few occurrences and many predictor variables easily leads to model overfitting. A new strategy using ensembles of small models was recently developed in an attempt to overcome this limitation of rare species modelling and has been tested successfully for only a single species so far. Here, we aim to test the approach more comprehensively on a large number of species including a transferability assessment. 2. For each species numerous small (here bivariate) models were calibrated, evaluated and averaged to an ensemble weighted by AUC scores. These 'ensembles of small models' (ESMs) were compared to standard Species Distribution Models (SDMs) using three commonly used modelling techniques (GLM, GBM, Maxent) and their ensemble prediction. We tested 107 rare and under-sampled plant species of conservation concern in Switzerland. 3. We show that ESMs performed significantly better than standard SDMs. The rarer the species, the more pronounced the effects were. ESMs were also superior to standard SDMs and their ensemble when they were independently evaluated using a transferability assessment. 4. By averaging simple small models to an ensemble, ESMs avoid overfitting without losing explanatory power through reducing the number of predictor variables. They further improve the reliability of species distribution models, especially for rare species, and thus help to overcome limitations of modelling rare species.

Species distribution of the Halophilous-psamophilous community along the coast of the Espirito-Santo state

The purpose of the present work was the study of the composition and distribution of the species in halophilous-psamophilous communities, utilizing the square method in 10 beaches of the Espirito Santo coast. The data of presence and cover of each species for the calculation of frequency and dominance, respectively, were obtained from twenty contiguous square of each of five 20 meters samplings, in a total of one hundred squares for each beach. Mariscus pedunculatus, Panicum racemosum, Ipomoea pes-caprae, I. littoralis and Blutaparon portulacoides were the most dominant species in the analyzed beaches.

Ecophysiology of Adonis distorta, a high-mountain species endemic of the Central Apennines

Morphological, anatomical and physiological plant and leaf traits of A. distorta, an endemic species of the Central Apennines on the Majella Massif, growing at 2,675 m a.s.l, were analyzed. The length of the phenological cycle starts immediately after the snowmelt at the end of May, lasting 128 ± 10 days. The low A. distorta height  (Hmax= 64 ± 4 mm) and total leaf area (TLA= 38 ± 9 cm2) associated to a high leaf mass area (LMA =11.8±0.6 mg cm−2) and a relatively high leaf tissue density (LTD = 124.6±14.3 mg cm−3) seem to be adaptive traits to the stress factors of the environment where it grows. From a physiological point of view, the high A. distorta photosynthetic rates (PN =19.6 ± 2.3 µmol m−2 s−1) and total chlorophyll content (Chla+b = 0.88 ± 0.13 mg g−1) in July are justified by the favorable temperature. PN decreases by 87% in September at the beginning of plant senescence. Photosynthesis and leaf respiration (RD) variations allow A. distorta to maintain a positive carbon balance during the growing season becoming indicative of the efficiency of plant carbon use. The results could be an important tool for conservation programmes of the A. distorta wild populations.

The invasion risk in the Pacific Northwest of two closely related grass species in the Genus Cortaderia

Thesis (Master's)--University of Washington, 2016-08

New status, species, distribution records and phylogeny for Australian mandibulate Chironomidae (Diptera)

All life-history stages of the Australian Podonominae (Chironomidae) genus Archaeochlus Brundin are revised, providing evidence for recognition of a separate clade, named here as Austrochlus Cranston. Based on molecular and morphological evidence, the clade contains two additional species: Austrochlus parabrundini Cranston, Edward and Cook sp. n. is described from Western Australia where its granite outcrop seepage habitat and geographical range is almost identical to that of the type species Austrochlus brundini Cranston, Edward and Colless (n. comb); Austrochlus centralaustralis Cranston, Edward and Cook sp. n. is described from ephemeral seepage/flows in the MacDonnell and James Ranges of central Australia. Molecular studies reported here confirm species distinctions, relationships to African taxa, and basal relationships within the Chironomidae. Modelled distributions provide evidence for range restriction by seasonal rainfall patterns.

Habitat predictive modelling of demersal fish species in the Azores

Dissertação de Mestrado, Estudos Integrados dos Oceanos, 25 de Março de 2013, Universidade dos Açores.

Mapping multi-species habitat use for marine conservation planning

Tese de Doutoramento, Ciências do Mar (Biologia Marinha)

Candidemia in a Brazilian tertiary care hospital: species distribution and antifungal susceptibility patterns

Recent studies have shown differences in the epidemiology of invasive infections caused by Candida species worldwide. In the period comprising August 2002 to August 2003, we performed a study in Santa Casa Complexo Hospitalar, Brazil, to determine Candida species distribution associated with candidemia and their antifungal susceptibility profiles to amphotericin B, fluconazole and itraconazole. Antifungal susceptibility was tested according to the broth microdilution method described in the NCCLS (M27A-2 method). Only one sample from each patient was analyzed (the first isolate). Most of the episodes had been caused by species other than C. albicans (51.6%), including C. parapsilosis (25.8%), C. tropicalis (13.3%), C. glabrata (3.3%), C. krusei (1.7%), and others (7.5%). Dose-dependent susceptibility to itraconazole was observed in 14.2% of strains, and dose-dependent susceptibility to fluconazole was found in 1.6%. Antifungal resistance was not found, probably related to low use of fluconazole. Further epidemiological surveillance is needed.

Predicting the impacts of climate change on the distribution and conservation of endemic forest land snails of Madeira Island

Climate change is emerging as one of the major threats to natural communities of the world’s ecosystems; and biodiversity hotspots, such as Madeira Island, might face a challenging future in the conservation of endangered land snails’ species. With this thesis, progresses have been made in order to properly understand the impact of climate on these vulnerable taxa; and species distribution models coupled with GIS and climate change scenarios have become crucial to understand the relations between species distribution and environmental conditions, identifying threats and determining biodiversity vulnerability. With the use of MaxEnt, important changes in the species suitable areas were obtained. Laurel forest species, highly dependent on precipitation and relative humidity, may face major losses on their future suitable areas, leading to the possible extinction of several endangered species, such as Leiostyla heterodon. Despite the complexity of the biological systems, the intrinsic uncertainty of species distribution models and the lack of information about land snails’ functional traits, this analysis contributed to a pioneer study on the impacts of climate change on endemic species of Madeira Island. The future inclusion of predictions of the effect of climate change on species distribution as part of IUCN assessments could contribute to species prioritizing, promoting specific management actions and maximizing conservation investment.

Species distribution and in vitro fluconazole susceptibility of clinical Candida isolates in a Brazilian tertiary-care hospital over a 3-year period

INTRODUCTION: In this study, we aimed at identifying Candida isolates obtained from blood, urine, tracheal secretion, and nail/skin lesions from cases attended at the Hospital Universitário de Londrina over a 3-year period and at evaluating fluconazole susceptibilities of the isolates. METHODS: Candida isolates were identified by polymerase chain reaction (PCR) using species-specific forward primers. The in vitro fluconazole susceptibility test was performed according to EUCAST-AFST reference procedure. RESULTS: Isolates were obtained from urine (53.4%), blood cultures (19.2%), tracheal secretion (17.8%), and nail/skin lesions (9.6%). When urine samples were considered, prevalence was similar in women (45.5%) and in men (54.5%) and was high in the age group >61 years than that in younger ones. For blood samples, prevalence was high in neonates (35%) and advanced ages (22.5%). For nail and skin samples, prevalence was higher in women (71.4%) than in men (28.6%). Candida albicans was the most frequently isolated in the hospital, but Candida species other than C. albicans accounted for 64% of isolates, including predominantly Candida tropicalis (33.2%) and Candida parapsilosis (19.2%). The trend for non-albicans Candida as the predominant species was noted from all clinical specimens, except from urine samples. All Candida isolates were considered susceptible in vitro to fluconazole with the exception of isolates belonging to the intrinsically less-susceptible species C. glabrata. CONCLUSIONS: Non-albicans Candida species were more frequently isolated in the hospital. Fluconazole resistance was a rare finding in our study.

Cross-scale determinants of palm species distribution

We investigate palm species distribution, richness and abundance along the Mokoti, a seasonally-dry river of southeastern Amazon and compare it to the patterns observed at a large scale, comprising the entire Brazilian territory. A total of 694 palms belonging to 10 species were sampled at the Mokoti River basin. Although the species showed diverse distribution patterns, we found that local palm abundance, richness and tree basal area were significantly higher from the hills to the bottomlands of the study region, revealing a positive association of these measures with moisture. The analyses at the larger spatial scale also showed a strong influence of vapor pressure (a measure of moisture content of the air, in turn modulated by temperature) and seasonality in temperature: the richest regions were those where temperature and humidity were simultaneously high, and which also presented a lower degree of seasonality in temperature. These results indicate that the distribution of palms seems to be strongly associated with climatic variables, supporting the idea that, by 'putting all the eggs in one basket' (a consequence of survival depending on the preservation of a single irreplaceable bud), palms have become vulnerable to extreme environmental conditions. Hence, their distribution is concentrated in those tropical and sub-tropical regions with constant conditions of (mild to high) temperature and moisture all year round.

Libellulidae (Insecta: Odonata) from Itapiracó reserve, Maranhão, Brazil: new records and species distribution information

In this work, I apply a simple protocol to species occurrence inventory of Odonata in a region of Maranhão state which has very few distributional records. Some relations between species occurrence and environmental characteristics are discussed, mainly in relation to the high occurrence of Erythemis. Eighteen new records are presented discussing the role of this approach to generate useful information for conservation purposes.

21st century climate change threatens mountain flora unequally across Europe

Continental-scale assessments of 21st century global impacts of climate change on biodiversity have forecasted range contractions for many species. These coarse resolution studies are, however, of limited relevance for projecting risks to biodiversity in mountain systems, where pronounced microclimatic variation could allow species to persist locally, and are ill-suited for assessment of species-specific threat in particular regions. Here, we assess the impacts of climate change on 2632 plant species across all major European mountain ranges, using high-resolution (ca. 100 m) species samples and data expressing four future climate scenarios. Projected habitat loss is greater for species distributed at higher elevations; depending on the climate scenario, we find 36-55% of alpine species, 31-51% of subalpine species and 19-46% of montane species lose more than 80% of their suitable habitat by 2070-2100. While our high-resolution analyses consistently indicate marked levels of threat to cold-adapted mountain florae across Europe, they also reveal unequal distribution of this threat across the various mountain ranges. Impacts on florae from regions projected to undergo increased warming accompanied by decreased precipitation, such as the Pyrenees and the Eastern Austrian Alps, will likely be greater than on florae in regions where the increase in temperature is less pronounced and rainfall increases concomitantly, such as in the Norwegian Scandes and the Scottish Highlands. This suggests that change in precipitation, not only warming, plays an important role in determining the potential impacts of climate change on vegetation.

Where will conflicts between alien and rare species occur after climate and land-use change? A test with a novel combined modelling approach

Protecting native biodiversity against alien invasive species requires powerful methods to anticipate these invasions and to protect native species assumed to be at risk. Here, we describe how species distribution models (SDMs) can be used to identify areas predicted as suitable for rare native species and also predicted as highly susceptible to invasion by alien species, at present and under future climate and land-use scenarios. To assess the condition and dynamics of such conflicts, we developed a combined predictive modelling (CPM) approach, which predicts species distributions by combining two SDMs fitted using subsets of predictors classified as acting at either regional or local scales. We illustrate the CPM approach for an alien invader and a rare species associated to similar habitats in northwest Portugal. Combined models predict a wider variety of potential species responses, providing more informative projections of species distributions and future dynamics than traditional, non-combined models. They also provide more informative insight regarding current and future rare-invasive conflict areas. For our studied species, conflict areas of highest conservation relevance are predicted to decrease over the next decade, supporting previous reports that some invasive species may contract their geographic range and impact due to climate change. More generally, our results highlight the more informative character of the combined approach to address practical issues in conservation and management programs, especially those aimed at mitigating the impact of invasive plants, land-use and climate changes in sensitive regions

Species distribution and antifungal susceptibility profile of Candida spp. bloodstream isolates from Latin American hospitals

From March 1999 to March 2000, we conducted a prospective multicenter study of candidemia involving five tertiary care hospitals from four countries in Latin America. Yeast isolates were identified by classical methods and the antifungal susceptibility profile was determined according to the National Committee for Clinical Laboratory Standards microbroth assay method. During a 12 month-period we were able to collect a total of 103 bloodstream isolates of Candida spp. C. albicans was the most frequently isolated species accounting for 42% of all isolates. Non-albicans Candida species strains accounted for 58% of all episodes of candidemia and were mostly represented by C. tropicalis (24.2%) and C. parapsilosis (21.3%). It is noteworthy that we were able to identify two cases of C. lusitaniae from different institutions. In our casuistic, non-albicans Candida species isolates related to candidemic episodes were susceptible to fluconazole. Continuously surveillance programs are needed in order to identify possible changes in the species distribution and antifungal susceptibility patterns of yeasts that may occurs after increasing the use of azoles in Latin American hospitals.