DOI: 10.5061/dryad.b2rbnzshp
title: Analysis of biodiversity data suggests that mammal species are hidden in predictable places

description: Research in the biological sciences is hampered by the Linnean shortfall,
 which describes the number of hidden species that are suspected of
 existing without formal species description. Using machine learning and
 species delimitation methods, we built a predictive model that
 incorporates some 5.0 × 105 data points for 117 species traits, 3.3 × 106
 occurrence records, and 9.1 × 105 gene sequences from 4,310 recognized
 species of mammals. Delimitation results suggest that there are hundreds
 of undescribed species in class Mammalia. Predictive modeling indicates
 that most of these hid- den species will be found in small-bodied taxa
 with large ranges characterized by high variability in temperature and
 precipitation. As demonstrated by a quantitative analysis of the
 literature, such taxa have long been the focus of taxonomic research. This
 analysis supports taxonomic hypotheses regarding where undescribed
 diversity is likely to be found and highlights the need for investment in
 taxonomic research to overcome the Linnean shortfall.
description: Genetic data: We downloaded all available mammalian DNA sequences
 for the mitochondrial genes cytochrome-c oxidase I (COI) and cytochrome-b
 (cytb) from the NIH genetic sequence database, GenBank. For each gene, we
 grouped sequences by species and then manually checked all species records
 for errors (e.g., subspecies, duplicates, extinct species, etc.). To
 ensure standardization across groups, we updated all sequence taxonomy to
 reflect that of the Mammal Diversity Database (MDD) published by the
 American Society of Mammologists. Following taxonomic standardization, we
 grouped sequence records for each gene by family and generated multiple
 sequence alignments for COI and cytb independently using MUSCLE v3.5. We
 then visually inspected each family-level alignment for gaps and removed
 problematic sequences causing severe gaps or misalignment that could not
 be resolved through reverse complement or manual correction.
 Geographic data: We first downloaded all geographic coordinates
 for class Mammalia from the Global Biodiversity Information Facility
 (GBIF) and used these to extract data from several GIS layers, including
 elevation, the 19 BIOCLIM layers at 1-km resolution pertaining to
 temperature and precipitation available from the World- Clim database,
 population density, gross domestic product, light pollution, protected
 areas, anthropogenic biomes, and GlobCover by the European Space Agency.
 We then curated these occurrence records using the R package, Coordinate
 Cleaner. 
description: Genetic data: Sequence alignments are organized taxonomically in
 folders corresponding to orders and families. Within each family folder
 there are alignment files titled "COI_unique.fas" and
 "cytb_unique.fas" that contain family-level alignments for COI
 and cytb, respectively. Certain groups may be missing one or both files,
 indicating that there was not enough sequence data to generate an
 alignment for that particular group. Geographic data:
 Occurrence records are organized taxonomically in folders corresponding to
 orders and families. Within each family folder there are species files
 containing the corresponding species geographic data. Files titled
 "genus_species.csv" contain a list of all coordinates gathered
 for said species. Files titled "genus_species_clean.txt" contain
 the results of Coordinate Cleaner curation, with each row after the
 species name representing a specific flag, and values of "FALSE"
 meaning the occurrence was flagged and discarded and values of
 "TRUE" meaning the occurrence was kept. Files titled
 "genus_species_var.txt" contains values extracted from GIS
 layers using the species curated occurrence records. Please see
 "README.txt" and "supplemental_var.xlsx" files for
 more detailed information on GIS layers used and descriptions of values
 extracted. Each family folder also contains a "family_var.txt"
 file, which contains values from all of the
 "genus_species_var.txt" files located within the family folder.
 Similarly, each order folder also contains an "order_var.txt"
 file, which contains values from all of the "family_var.txt"
 files located within the order folder. Certain groups may be missing one
 or more files, indicating that there was not enough occurrence data to
 generate occurrence files for that particular group.