Ana Manjarrés-Hernández

Using modestr to download, import and clean species distribution records

Summary Data quality is one of the highest priorities for species distribution data warehouses, as well as one of the main concerns of data users. There is the need, however, for computational procedures with the facility to automatically or semi-automatically identify and correct errors and to seamlessly integrate expert knowledge and automated processes. New version modestr 2.0 (http://www.ipez.es/ModestR) makes it easy to download occurrence records from the Global Biodiversity Information Facility (GBIF), to import shape files with species range maps such as those available at the website of the International Union for Conservation of Nature (IUCN), to import KML files, to import CSV files with records of the users, to import ESRI ASCII grid probability files generated by distribution modelling software and show the resulting records on a map. modestr supports five different methods for cleaning the data: (i) data filtering when downloading records from GBIF, (ii) habitat data filtering, (iii) taxonomic disambiguation filtering, (iv) automatic spatial dispersion and environmental layer filters and (v) custom data filtering.

Ecological Factors and Diversification among Neotropical Characiforms

Morphological and DNA sequence data has been used to propose hypotheses of relationships within the Characiformes with minimal comparative discussion of causes underpinning the major intraordinal diversification patterns. We explore potential primary morphological factors controlling the early diversification process in some Neotropical characiforms as the first step to identifying factors contributing to the pronounced intraordinal morphological and species diversity. A phylogenetic reconstruction based on 16S rDNA (mitochondrial) and 18S rDNA (nuclear) genes provided the framework for the identification of the main morphological differences among the Acestrorhynchidae, Anostomidae, Characidae, Ctenoluciidae, Curimatidae, Cynodontidae, Gasteropelecidae, Prochilodontidae and Serrasalmidae. Results indicate an initial split into two major groupings: (i) species with long dorsal-fin bases relative to the size of other fins (Curimatidae, Prochilodontidae, Anostomidae, Serrasalmidae) which primarily inhabit lakes, swamps, and rivers (lineage I); and (ii) species with short dorsal-fin bases (Acestrorhynchidae, Gasteropelecidae, Characidae) which primarily inhabit creeks and streams (lineage II). The second diversification stage in lineage I involved substantial morphological diversification associated with trophic niche differences among the monophyletic families which range from detritivores to large item predators. Nonmonophyly of the Characidae complicated within lineage II analyzes but yielded groupings based on differences in pectoral and anal fin sizes correlated with life style differences.

Geospatial data of freshwater habitats for macroecological studies: an example with freshwater fishes

Global data sets are essential in macroecological studies. File formats of the few available data sets of freshwater ecosystems, however, are either incompatible with most macroecological software packages, incomplete, or of coarse spatial resolutions. We integrated more than 460 million geographical coordinates for freshwater habitats in the FRWater data set, partitioned into seven different habitats (lentic, wetlands, reservoirs, small rivers, large rivers, small ditches, large ditches, small channels, large channels, small drains and large drains) in ModestR (http://www.ipez.es/ModestR). A comprehensive collection of geospatial rasters was assembled, one for each of the seven freshwater habitats, with the area in km2 occupied by each habitat presented in cells of 5 arc-minute resolution. The utility of FRWater was evaluated using hierarchical partitioning via the identification of the contribution of the seven different freshwater habitats to both species richness and rarity. To this end, we used a data set of 836,123 geographical records of the 16,216 species of freshwater fishes recognized as valid by systematists at the end of 2014. Areas in North America and Europe are the most detailed in the FRWater data set, evidencing the higher quality of data sources in those regions. The number of geographical coordinates is much lower for Africa, Asia, Australia, and South America where many water bodies remain unmapped. In light of the variation in information quality at continental levels, we performed and present comparative analyses for Europe versus South America at local (5ʹ × 5ʹ grid cells) and regional (5° × 5° grid cells) scales. The relative contribution of small rivers to both species richness and rarity was highest under almost all analyses, followed by lentic habitats and large rivers. The areas of different habitats moreover explained a relatively high proportion of the observed variance in geographic rarity. Our findings corroborate previous findings that the greater contribution of small rivers to species richness is probably due to these habitats promoting geographical rarity. Hence, species richness is favored by the isolation resultant from, and the refuges associated with, small river basins and via the diversification processes promoted by such isolation.

A procedure to assess the spatial variability in the importance of abiotic factors affecting distributions: the case of world freshwater fishes

Abstract Understanding the factors shaping species’ distributions is a key longstanding topic in ecology with unresolved issues. The aims were to test whether the relative contribution of abiotic factors that set the geographical range of freshwater fish species may vary spatially and/or may depend on the geographical extent that is being considered. The relative contribution of factors, to discriminate between the conditions prevailing in the area where the species is present and those existing in the considered extent, was estimated with the instability index included in the R package SPEDInstabR. We used 3 different extent sizes: 1) each river basin where the species is present (local); 2) all river basins where the species is present (regional); and 3) the whole Earth (global). We used a data set of 16,543 freshwater fish species with a total of 845,764 geographical records, together with bioclimatic and topographic variables. Factors associated with temperature and altitude show the highest relative contribution to explain the distribution of freshwater fishes at the smaller considered extent. Altitude and a mix of factors associated with temperature and precipitation were more important when using the regional extent. Factors associated with precipitation show the highest contribution when using the global extent. There was also spatial variability in the importance of factors, both between species and within species and from region to region. Factors associated with precipitation show a clear latitudinal trend of decreasing in importance toward the equator.

Completeness of national freshwater fish species inventories around the world

The aim was to discriminate the countries with relatively comprehensive inventories of freshwater fishes from those with insufficiently prospected inventories. We used a data set of 16,734 freshwater fish species with a total of 1,373,449 occurrence records. Accumulation curves relating the increase in the number of species to the number of records, and completeness values obtained after extrapolating these curves to estimate the total number of predicted species were calculated for each country using the RWizard application KnowBR. Using the final slope values of the accumulation curves, the obtained completeness values, and the ratio between the number of records and the observed species, maps and plots representing the location of good, fair and poor quality inventories at country level were obtained. Inventory completeness ranged from 5.3% (Guinea-Bissau) to 108.4% (United Kingdom), with a pooled mean of 65.9%. We observed that a completeness higher than 90%, a slope lower than 0.02 and a ratio of records/species observed greater than 15 were good thresholds for identifying countries with good quality inventories; only 26 countries met these requirements, mainly located in Europe and North America. However, more than 71% of countries worldwide have inventories that can be categorised as of poor quality. Furthermore, even those countries with relatively accurate national inventories possess a high variability in the completeness of their provincial or regional inventories.