HomeRange: A global database of mammalian home ranges

Motivation

Home range is a common measure of use of space by animals because it provides ecological information that is useful for conservation applications. In macroecological studies, values are typically aggregated to species means to examine general patterns of use of space by animals. However, this ignores the environmental context in which the home range was estimated and does not account for intraspecific variation in home range size. In addition, the focus of macroecological studies on home ranges has historically been biased towards terrestrial mammals. The use of aggregated numbers and the terrestrial focus limit our ability to examine home-range patterns across different environments, their variation in time and variation between different levels of organization. Here, we introduce HomeRange, a global database with 75,611 home-range values across 960 different species of mammals, including terrestrial, aquatic and aerial species.

Main types of variables contained

The dataset contains estimates of home ranges of mammals, species names, methodological information on data collection, method of home-range estimation, period of data collection, study coordinates and name of location, in addition to species traits derived from the studies, such as body mass, life stage, reproductive status and locomotor habit.

Spatial location and grain

The collected data are distributed globally. Across studies, the spatial accuracy varies, with the coarsest resolution being 1°.

Time period and grain

The data represent information published between 1939 and 2022. Across studies, the temporal accuracy varies; some studies report start and end dates specific to the day, whereas for other studies only the month or year is reported.

Major taxa and level of measurement

Mammalian species from 24 of the 27 different taxonomic orders. Home-range estimates range from individual-level values to population-level averages.

Software format

Data are supplied as a comma-delimited text file (.csv) and can be loaded directly into R using the “HomeRange” R package ( https://github.com/SHoeks/HomeRange ).     

Influence of seasonal variation to the population growth and ecophysiology of Typha domingensis (Typhaceae)

Journal of Plant Research - Precipitation is an important climatic element that defines the hydrological regime, and its seasonal variation produces annual dry and wet periods in some areas. This...     

A chromosome-level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex-determining gene in the flatfish Solea senegalensis

Sex determination (SD) shows huge variation among fish and a high evolutionary rate, as illustrated by the Pleuronectiformes (flatfishes). This order is characterized by its adaptation to demersal life, compact genomes and diversity of SD mechanisms. Here, we assembled the Solea senegalensis genome, a flatfish of great commercial value, into 82 contigs (614 Mb) combining long- and short-read sequencing, which were next scaffolded using a highly dense genetic map (28,838 markers, 21 linkage groups), representing 98.9% of the assembly. Further, we established the correspondence between the assembly and the 21 chromosomes by using BAC-FISH. Whole genome resequencing of six males and six females enabled the identification of 41 single nucleotide polymorphism variants in the follicle stimulating hormone receptor (fshr) consistent with an XX/XY SD system. The observed sex association was validated in a broader independent sample, providing a novel molecular sexing tool. The fshr gene displayed differential expression between male and female gonads from 86 days post-fertilization, when the gonad is still an undifferentiated primordium, concomitant with the activation of amh and cyp19a1a, testis and ovary marker genes, respectively, in males and females. The Y-linked fshr allele, which included 24 nonsynonymous variants and showed a highly divergent 3D protein structure, was overexpressed in males compared to the X-linked allele at all stages of gonadal differentiation. We hypothesize a mechanism hampering the action of the follicle stimulating hormone driving the undifferentiated gonad toward testis.     

Mapping of resistance to the potato cyst nematode Globodera rostochiensis from the wild potato species Solanum vernei

A population of diploid potato (Solanum tuberosum) was used for the genetic analysis and mapping of a locus for resistance to the potato cyst nematode Globodera rostochiensis, introgressed from the wild potato species Solanum vernei. Resistance tests of 108 genotypes of a F₁ population revealed the presence of a single locus with a dominant allele for resistance to G. rostochiensis pathotype Ro1. This locus, designated GroV1, was located on chromosome 5 with RFLP markers. Fine-mapping was performed with RAPD and SCAR markers. The GroV1 locus was found in the same region of the potato genome as the S. tuberosum ssp. andigena H1 nematode resistance locus. Both resistance loci could not excluded to be allelic. The identification of markers flanking the GroV1 locus offers a valuable strategy for marker-assisted selection for introgression of this nematode resistance.Abbreviations BSA bulked segregant analysis - RAPD random-amplified polymorphic DNA - RFLP restriction fragment length polymorphism - SCAR sequence-characterized amplified region     

Alteration of tobacco floral organ identity by expression of combinations of Antirrhinum MADS-box genes

Floral organ identity is largely controlled by the spatially restricted expression of several MADS-box genes. In Antirrhinum majus these organ identity genes include DEF, GLO and PLE . Single and double mutant analyses indicated that the type of organ found in a particular whorl is dependent on which combination of these genes is expressed there. This paper reports the ectopic expression of Antirrhinum organ identity genes, alone and in combinations, in transgenic tobacco. Although the phenotypes are broadly in agreement with the genetic predictions, several unexpected features are observed which provide information concerning the action of the organ identity genes. The presumed tobacco homologue of DEF, NTDEF , has been isolated and used to investigate the influence of ectopic expression of the Antirrhinum organ identity genes on the endogenous tobacco genes. Analysis of the spatial and temporal expression patterns of NTDEF and NTGLO reveals that the boundaries are not coincident and that differences exist in the regulatory mechanisms of the two genes concerning both induction and maintenance of gene expression. Evidence is provided which indicates that organ development is sensitive to the relative levels of organ identity gene expression. Expression of the organ identity genes outside the flower or inflorescence produced no effects, suggesting that additional factors are required to mediate their activity. These results demonstrate that heterologous genes can be used to predictably influence floral organ identity but also reveal the existence of unsuspected control mechanisms.     

Genetic and environmental variation in anther,pollen and pistil dimensions in sesame

Measurements of anther (length, width, depth), pollen grain (percent fertility, polar diameter, equatorial diameter, polar diameter/equatorial diameter ratio, volume) and pistil (stigma length, style length, ovary length, total pistil length, stigma width, style width, ovary width) were taken on 12 diverse sesame (Sesamum indicum L.) genotypes on each of four collection dates in 1994. Highly significant differences among genotype means were obtained for all characters except polar diameter. Highly significant differences among environment (collection date) means were found for ten of the 15 characters measured. Highly significant genotype x environment interactions were obtained for all characters except anther length. For the anther characters measured, relatively high repeatability values were found, ranging from 99.8% for length to 87.6% for depth. For the pollen grain characters measured, the repeatability values ranged from 67.6% for percent fertility to 23.1% for polar diameter. For the pistil characters measured, the repeatability values ranged from 94.0% for style width to 49.6% for total pistil length. These results indicate that genotype and environment influence anther, pollen grain and pistil characters. Variation in some of these morphological aspects could influence the consistency and interpretation of male transmission studies on both the applied and evolutionary levels.     

A genetic map of potato (Solanum tuberosum) integrating molecular markers,including transposons,and classical markers

A genetic map of potato (Solanum tuberosum L.) integrating molecular markers with morphological and isozyme markers was constructed using a backcross population of 67 diploid potato plants. A general method for map construction is described that differs from previous methods employed in potato and other outbreeding plants. First, separate maps for the female and male parents were constructed. The female map contained 132 markers, whereas the male map contained 138 markers. Second, on the basis of the markers in common the two integrated parental maps were combined into one with the computer programme JoinMap. This combined map consisted of 175 molecular markers, 10 morphological markers and 8 isozyme markers. Ninety-two of the molecular markers were derived from DNA sequences flanking either T-DNA inserts in potato or reintegrated maize transposable elements originating from these T-DNA constructs. Clusters of distorted segregation were found on chromosomes 1,2,8 and 11 for the male parent and chromosome 5 for both parents. The total length of the combined map is 1120 cM.     

Yeast communities as descriptors of habitat use by the Drosophila fasciola subgroup (repleta group) in Atlantic rain forests

Yeast communities associated with four species of the Drosophila fasciola subgroup (repleta group) in tropical rain forests were surveyed in an abandoned orchard, and rain forest sites of Rio de Janeiro and Ilha Grande, State of Rio de Janeiro, Brazil. Adult flies of Drosophila carolinae, Drosophila coroica, Drosophila fascioloides and Drosophila onca frequently carried Candida colliculosa, Geotrichum sp, Kloeckera apiculata and a Pichia membranaefaciens-like species. The most frequent yeasts in the crop of flies included Candida collicullosa, C. krusei, Pichia kluyveri and a P. membranaefaciens-like species. The physiological abilities and species composition of these yeast communities differed from those of other forest-inhabiting Drosophila. The narrow feeding niches of the fasciola subgroup suggested the use of only part of the substrates available to the flies as food in the forest environment, as noted previously for cactophilic Drosophila serido (mulleri subgroup of the repleta group) in a sand dune ecosystem. The cactophilic yeasts that were isolated have not been previously found in forests. The fasciola subgroup probably used epiphytic cactus substrates as breeding and feeding sites in the forest. The physiological profile of yeasts associated with the fasciola flies was broader than that of yeasts associated with the cactophilic Drosophila serido, suggesting that the fasciola subgroup represents an older lineage from which the South American repleta species evolved.     

Effects of Auxin and Phenobarbital on Morphogenesis and Production of Digitoxin in Digitalis Callus

Pieces of callus obtained from seedlings of Digitalis purpureawere grown on solid Murashige-Skoog's medium supplemented with1 mg liter^–1 BA and 0.1 mg liter^–1 IAA or NAA, withor without phenobarbital (40 mg liter^–1). The replacementof the natural auxin IAA by the synthetic auxin NAA increasedcallus growth and inhibited organogenesis, whereas the additionof phenobarbital had the opposite effect. Morphometric measurementsrevealed a high ratio of vacuole to cytoplasm (v/v) in calluscells. This ratio was affected by the different treatments inthe same way as the fresh weight. The activity of mitochondrialcytochrome P450scc (the enzyme that provides the precursor,pregnenolone, for the biosynthesis of cardenolide in foxgloveplants) was detected in the relevant fraction of callus grownunder all experimental conditions, and its activity was increasedby the addition of phenobarbital. The different treatments testedincreased the cardenolide content and quantifiable amounts ofdigitoxin were detected in all callus tissues. It is of specialinterest that phenobarbital added to the culture medium increasedthe accumulation of digitoxin. The mechanism affecting the developmentand production of cardenolide in callus tissues of D. purpureaby phenobarbital and the replacement of IAA by NAA is discussed. (Received July 18, 1994; Accepted December 14, 1994)