https://www.cs.princeton.edu/~schapire/papers/ecolmod.pdf

Maximum entropy modeling of species geographic distributions

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Data Mining - Concepts and Techniques.

Prediction of species' distributions is central to diverse applications in ecology, evolution and conservation science. There is increasing electronic access to vast sets of occurrence records in museums and herbaria, yet little effective guidance on how best to use this information in the context of numerous approaches for modelling distributions. To meet this need, we compared 16 modelling methods over 226 species from 6 regions of the world, creating the most comprehensive set of model comparisons to date. We used presence-only data to fit models, and independent presence-absence data to evaluate the predictions. Along with well-established modelling methods such as generalised additive models and GARP and BIOCLIM, we explored methods that either have been developed recently or have rarely been applied to modelling species' distributions. These include machine-learning methods and community models, both of which have features that may make them particularly well suited to noisy or sparse information, as is typical of species' occurrence data. Presence-only data were effective for modelling species' distributions for many species and regions. The novel methods consistently outperformed more established methods. The results of our analysis are promising for the use of data from museums and herbaria, especially as methods suited to the noise inherent in such data improve.

/pdf/novel-methods-improve-prediction-of-species-distributions-3cmioqeu6v.pdf

Novel methods improve prediction of species' distributions from occurrence data

In the last two decades, interest in species distribution models (SDMs) of plants and animals has grown dramatically. Recent advances in SDMs allow us to potentially forecast anthropogenic effects on patterns of biodiversity at different spatial scales. However, some limitations still preclude the use of SDMs in many theoretical and practical applications. Here, we provide an overview of recent advances in this field, discuss the ecological principles and assumptions underpinning SDMs, and highlight critical limitations and decisions inherent in the construction and evaluation of SDMs. Particular emphasis is given to the use of SDMs for the assessment of climate change impacts and conservation management issues. We suggest new avenues for incorporating species migration, population dynamics, biotic interactions and community ecology into SDMs at multiple spatial scales. Addressing all these issues requires a better integration of SDMs with ecological theory.

Predicting species distribution: offering more than simple habitat models.

The increasing worldwide interest on the conservation of tropical forests reflects the conversion of over 50% of their area into agricultural lands and other uses. Understanding the distribution of remaining biodiversity across agricultural landscapes is an essential task to guide future conservation strategies. To understand the long-term effects of fragmentation on biodiversity, we investigated whether forest fragments in southeastern Brazil are under a taxonomic homogenization or heterogenization process. We estimated pre-deforestation species richness and composition based on a Species Distribution Modelling approach, and compared them to the observed patterns of - and {beta}-diversity. In particular, we asked (i) if changes in {beta}-diversity reveal convergence or divergence on species composition; (ii) if these changes are similar between forest fragments in Strictly Protected Areas (SPAs) (n=20) and within private lands (n=367) and in different regions of the state (West, Center, and Southeast). We detected steep reductions in observed local species richness in relation to our modeled predictions, and this was particularly true among forest fragments in non-protected private lands. The higher observed {beta} diversity indicated an overall biotic heterogenization process, consistent with the idea that the originally diverse vegetation is now reduced to small and isolated patches, with unique disturbance histories and impoverished communities derived from a large regional species pool. Since conservation of biodiversity extends beyond the boundaries of strictly Protected Areas, we advocate forest fragments are valuable for conservation in agricultural landscapes, with particular relevance for private lands, which represent the most exposed and neglected share of what is left.

/pdf/heterogenization-of-remaining-biodiversity-in-fragmented-3t2oiqt9tm.pdf

Heterogenization of remaining biodiversity in fragmented tropical forests across agricultural landscapes

Environmental and geographical space partitioning between core and peripheral Myrsine species (Primulaceae) of the Brazilian Atlantic Forest

Historically, macroecology and microecology have diverged with regard to the niche concept. A better understanding of functioning ecological systems, however, depends on an integrative approach to this concept at different spatial scales. A mixed approach, merging macro- and microscale by validating ecological niche modeling (ENM) with the results of in situ experiments and environmental data collection was used to understand if areas identified by ENM as highly suitable for adult palms are also adequate for seedling establishment. Syagrus weddelliana's (Arecaceae) distribution range falls within the Atlantic Rain Forest, and more specifically Serra dos Orgaos region (Rio de Janeiro state), southeastern Brazil. The following steps were performed: (a) ENM to delimit the area of occurrence of S. weddelliana and locate experimental areas; (b) a seed sowing experiment in areas with presence or absence of the species in areas of high or low environmental suitability at 36 experimental stations; and (c) characterization of each microhabitat which was related back to the macroscale results of ENM. Evidence of biotic and abiotic limitations was found for S. weddelliana distribution. Areas of higher suitability had lower seed predation rates and, consequently, higher seed germination rates. On the other hand, areas with low environmental suitability at the macroscale were divided into two types: areas with microhabitat similar to that of areas with high environmental suitability that had some germination despite high predation and areas with different environmental conditions that had no germination and high predation rates. Seedlings and adults had different abiotic requirements. Microhabitat conditions were more important for the initial establishment of S. weddelliana than macroclimatic variables. This finding demonstrates that macro- and microecological information works in a complementary way to a better understanding of the distribution of S. weddelliana.

https://www.onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.5300

Micro- or macroscale? Which one best predicts the establishment of an endemic Atlantic Forest palm?

First record of Pleroma boraceiense (Brade) P.J.F. Guim. & Justino (Melastomataceae) in Minas Gerais state, Brazil

Las areas protegidas actuan como pilares sobre los cuales se construyen las estrategias de conservacion. Ademas de las actividades humanas, los cambios climaticos globales son una preocupacion adicional para la conservacion de las especies. En el noreste de Brasil, el cambio climatico deberia conducir a un reemplazo de la vegetacion nativa actual por vegetacion semidesertica. Este estudio evalua si las areas protegidas de Caatinga pueden contribuir al mantenimiento de condiciones climaticas adecuadas para las aves en peligro de extincion a lo largo del tiempo frente a los cambios climaticos globales y el cambio de la cubierta terrestre. Utilizamos modelos de nicho ecologicos como capas de entrada en un programa de priorizacion espacial, en el que se utilizaron indices de estabilidad para ponderar los objetivos. Los resultados pronosticaron que la mayoria de lostaxa (18) tendran su idoneidad reducida en el futuro, y todos los taxa (23) tendran su nicho ecologico desplazado geograficamente. Sin embargo, nuestros resultados mostraron que el sistema de areas protegidas de Caatinga integrado con un conjunto de areas prioritarias puede mantener condiciones climaticas adecuadas para las aves en peligro de extincion ante el cambio climatico y el cambio de la cubierta terrestre. En promedio, el sistema de areas protegidas de Caatinga podria proteger las areas de estabilidad climatica al menos 1.7 veces mayor que los escenarios sin ella. Esto refuerza la importancia de las areas protegidas como estrategia de conservacion de la biodiversidad.

https://revistaeletronica.icmbio.gov.br/index.php/BioBR/article/download/1469/1156

Marinez Ferreira de Siqueira

Papers

Heterogenization of remaining biodiversity in fragmented tropical forests across agricultural landscapes

Environmental and geographical space partitioning between core and peripheral Myrsine species (Primulaceae) of the Brazilian Atlantic Forest

Micro- or macroscale? Which one best predicts the establishment of an endemic Atlantic Forest palm?

First record of Pleroma boraceiense (Brade) P.J.F. Guim. & Justino (Melastomataceae) in Minas Gerais state, Brazil

Could Protected Areas in Brazil’s Semi-Arid Conserve Endangered Birds Facing Climatic and Land Cover Changes?