Temporally stacked bee forage species distribution modeling for flower abundance mapping.

Predicting spatial distribution of flowering forage availability is critical for guiding migratory beekeeping decisions. Species distribution modelling (SDM) is widely used to predict the geographic distribution or species ranges. Stacked distributions of multiple species (S-SDM) have been used in predicting species richness or assemblages. Here, we present a method for stacking SDMs based on a temporal element, the flowering phenology of melliferous flora species. First, we used presence-only data for thirty key forage species used for honey production in Western Australia, combined with environmental variables for predicting the geographic distribution of species, using MaxEnt software. The output distribution grids were then stacked based on monthly flowering times of each species to develop grids representing the richness of flowering species by grid cell. While designed for modelling flowering forage availability for a migratory beekeeping system, the approach can be used for predicting temporal forage availability for a range of different fauna that rely on melliferous flora. •How to use temporally stacked species distribution modelling for generic distribution of flowering availability using presence-only data.•A procedure for developing flowering richness and availability grids.

Data representing climate-induced changes in the spatial distribution of key bee forage species for southwest Western Australia.

The dataset includes (i) species occurrence points, and (ii) Species Distribution Model (SDM) outputs under current conditions and a moderate emission (RCP 6.0) climate scenario, for 30 key bee forage species in southwest Western Australia (WA). Occurrence data were obtained from open data sources and through stakeholder engagement processes. SDM outputs were predicted using the Maxent algorithm with the change in species range analysed using QGIS software. The model outputs provide insight into the potential implications of climate change on important bee forage species in southwest WA, including dominant melliferous tree and shrub species. Changes in these species are likely to have repercussions to the ecological and social systems where a facilitatory relationship exists. This dataset is important for informing conservation efforts within the southwest Australian biodiversity hotspot.

Why bees are critical for achieving sustainable development.

Reductions in global bee populations are threatening the pollination benefits to both the planet and people. Whilst the contribution of bee pollination in promoting sustainable development goals through food security and biodiversity is widely acknowledged, a range of other benefits provided by bees has yet to be fully recognised. We explore the contributions of bees towards achieving the United Nation's Sustainable Development Goals (SDGs). Our insights suggest that bees potentially contribute towards 15 of the 17 SDGs and a minimum of 30 SDG targets. We identify common themes in which bees play an essential role, and suggest that improved understanding of bee contributions to sustainable development is crucial for ensuring viable bee systems.

Reconstruction of the ancestral marsupial karyotype from comparative gene maps.

BACKGROUND: The increasing number of assembled mammalian genomes makes it possible to compare genome organisation across mammalian lineages and reconstruct chromosomes of the ancestral marsupial and therian (marsupial and eutherian) mammals. However, the reconstruction of ancestral genomes requires genome assemblies to be anchored to chromosomes. The recently sequenced tammar wallaby (Macropus eugenii) genome was assembled into over 300,000 contigs. We previously devised an efficient strategy for mapping large evolutionarily conserved blocks in non-model mammals, and applied this to determine the arrangement of conserved blocks on all wallaby chromosomes, thereby permitting comparative maps to be constructed and resolve the long debated issue between a 2n = 14 and 2n = 22 ancestral marsupial karyotype. RESULTS: We identified large blocks of genes conserved between human and opossum, and mapped genes corresponding to the ends of these blocks by fluorescence in situ hybridization (FISH). A total of 242 genes was assigned to wallaby chromosomes in the present study, bringing the total number of genes mapped to 554 and making it the most densely cytogenetically mapped marsupial genome. We used these gene assignments to construct comparative maps between wallaby and opossum, which uncovered many intrachromosomal rearrangements, particularly for genes found on wallaby chromosomes X and 3. Expanding comparisons to include chicken and human permitted the putative ancestral marsupial (2n = 14) and therian mammal (2n = 19) karyotypes to be reconstructed. CONCLUSIONS: Our physical mapping data for the tammar wallaby has uncovered the events shaping marsupial genomes and enabled us to predict the ancestral marsupial karyotype, supporting a 2n = 14 ancestor. Futhermore, our predicted therian ancestral karyotype has helped to understand the evolution of the ancestral eutherian genome.

Globin gene structure in a reptile supports the transpositional model for amniote α- and ß-globin gene evolution.

The haemoglobin protein, required for oxygen transportation in the body, is encoded by α- and ß-globin genes that are arranged in clusters. The transpositional model for the evolution of distinct α-globin and ß-globin clusters in amniotes is much simpler than the previously proposed whole genome duplication model. According to this model, all jawed vertebrates share one ancient region containing α- and ß-globin genes and several flanking genes in the order MPG-C16orf35-(α-ß)-GBY-LUC7L that has been conserved for more than 410 million years, whereas amniotes evolved a distinct ß-globin cluster by insertion of a transposed ß-globin gene from this ancient region into a cluster of olfactory receptors flanked by CCKBR and RRM1. It could not be determined whether this organisation is conserved in all amniotes because of the paucity of information from non-avian reptiles. To fill in this gap, we examined globin gene organisation in a squamate reptile, the Australian bearded dragon lizard, Pogona vitticeps (Agamidae). We report here that the α-globin cluster (HBK, HBA) is flanked by C16orf35 and GBY and is located on a pair of microchromosomes, whereas the ß-globin cluster is flanked by RRM1 on the 3' end and is located on the long arm of chromosome 3. However, the CCKBR gene that flanks the ß-globin cluster on the 5' end in other amniotes is located on the short arm of chromosome 5 in P. vitticeps, indicating that a chromosomal break between the ß-globin cluster and CCKBR occurred at least in the agamid lineage. Our data from a reptile species provide further evidence to support the transpositional model for the evolution of ß-globin gene cluster in amniotes.

Physical map of two tammar wallaby chromosomes: a strategy for mapping in non-model mammals.

Marsupials are especially valuable for comparative genomic studies of mammals. Two distantly related model marsupials have been sequenced: the South American opossum (Monodelphis domestica) and the tammar wallaby (Macropus eugenii), which last shared a common ancestor about 70 Mya. The six-fold opossum genome sequence has been assembled and assigned to chromosomes with the help of a cytogenetic map. A good cytogenetic map will be even more essential for assembly and anchoring of the two-fold wallaby genome. As a start to generating a physical map of gene locations on wallaby chromosomes, we focused on two chromosomes sharing homology with the human X, wallaby chromosomes X and 5. We devised an efficient strategy for mapping large conserved synteny blocks in non-model mammals, and applied this to generate dense maps of the X and 'neo-X' regions and to determine the arrangement of large conserved synteny blocks on chromosome 5. Comparisons between the wallaby and opossum chromosome maps revealed many rearrangements, highlighting the need for comparative gene mapping between South American and Australian marsupials. Frequent rearrangement of the X, along with the absence of a marsupial XIST gene, suggests that inactivation of the marsupial X chromosome does not depend on a whole-chromosome repression by a control locus.

Platypus globin genes and flanking loci suggest a new insertional model for beta-globin evolution in birds and mammals.

BACKGROUND: Vertebrate alpha (alpha)- and beta (beta)-globin gene families exemplify the way in which genomes evolve to produce functional complexity. From tandem duplication of a single globin locus, the alpha- and beta-globin clusters expanded, and then were separated onto different chromosomes. The previous finding of a fossil beta-globin gene (omega) in the marsupial alpha-cluster, however, suggested that duplication of the alpha-beta cluster onto two chromosomes, followed by lineage-specific gene loss and duplication, produced paralogous alpha- and beta-globin clusters in birds and mammals. Here we analyse genomic data from an egg-laying monotreme mammal, the platypus (Ornithorhynchus anatinus), to explore haemoglobin evolution at the stem of the mammalian radiation. RESULTS: The platypus alpha-globin cluster (chromosome 21) contains embryonic and adult alpha- globin genes, a beta-like omega-globin gene, and the GBY globin gene with homology to cytoglobin, arranged as 5'-zeta-zeta'-alphaD-alpha3-alpha2-alpha1-omega-GBY-3'. The platypus beta-globin cluster (chromosome 2) contains single embryonic and adult globin genes arranged as 5'-epsilon-beta-3'. Surprisingly, all of these globin genes were expressed in some adult tissues. Comparison of flanking sequences revealed that all jawed vertebrate alpha-globin clusters are flanked by MPG-C16orf35 and LUC7L, whereas all bird and mammal beta-globin clusters are embedded in olfactory genes. Thus, the mammalian alpha- and beta-globin clusters are orthologous to the bird alpha- and beta-globin clusters respectively. CONCLUSION: We propose that alpha- and beta-globin clusters evolved from an ancient MPG-C16orf35-alpha-beta-GBY-LUC7L arrangement 410 million years ago. A copy of the original beta (represented by omega in marsupials and monotremes) was inserted into an array of olfactory genes before the amniote radiation (>315 million years ago), then duplicated and diverged to form orthologous clusters of beta-globin genes with different expression profiles in different lineages.