Genomic correlates of recombination rate and its variability across eight recombination maps in the western honey bee (Apis mellifera L.)

Background

Meiotic recombination has traditionally been explained based on the structural requirement to stabilize homologous chromosome pairs to ensure their proper meiotic segregation. Competing hypotheses seek to explain the emerging findings of significant heterogeneity in recombination rates within and between genomes, but intraspecific comparisons of genome-wide recombination patterns are rare. The honey bee (Apis mellifera) exhibits the highest rate of genomic recombination among multicellular animals with about five cross-over events per chromatid.

Results

Here, we present a comparative analysis of recombination rates across eight genetic linkage maps of the honey bee genome to investigate which genomic sequence features are correlated with recombination rate and with its variation across the eight data sets, ranging in average marker spacing ranging from 1 Mbp to 120 kbp. Overall, we found that GC content explained best the variation in local recombination rate along chromosomes at the analyzed 100 kbp scale. In contrast, variation among the different maps was correlated to the abundance of microsatellites and several specific tri- and tetra-nucleotides.

Conclusions

The combined evidence from eight medium-scale recombination maps of the honey bee genome suggests that recombination rate variation in this highly recombining genome might be due to the DNA configuration instead of distinct sequence motifs. However, more fine-scale analyses are needed. The empirical basis of eight differing genetic maps allowed for robust conclusions about the correlates of the local recombination rates and enabled the study of the relation between DNA features and variability in local recombination rates, which is particularly relevant in the honey bee genome with its exceptionally high recombination rate.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1281-2) contains supplementary material, which is available to authorized users.     

HotSpotter: efficient visualization of driver mutations

Background

Driver mutations are positively selected during the evolution of cancers. The relative frequency of a particular mutation within a gene is typically used as a criterion for identifying a driver mutation. However, driver mutations may occur with relative infrequency at a particular site, but cluster within a region of the gene. When analyzing across different cancers, particular mutation sites or mutations within a particular region of the gene may be of relatively low frequency in some cancers, but still provide selective growth advantage.

Results

This paper presents a method that allows rapid and easy visualization of mutation data sets and identification of potential gene mutation hotspot sites and/or regions. As an example, we identified hotspot regions in the NFE2L2 gene that are potentially functionally relevant in endometrial cancer, but would be missed using other analyses.

Conclusions

HotSpotter is a quick, easy-to-use visualization tool that delivers gene identities with associated mutation locations and frequencies overlaid upon a large cancer mutation reference set. This allows the user to identify potential driver mutations that are less frequent in a cancer or are localized in a hotspot region of relatively infrequent mutations.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1044) contains supplementary material, which is available to authorized users.     

Linking political and scientifically derived targets for global biodiversity conservation: implications for the expansion of the global network of protected areas

Despite the global network of protected areas covers 12% of the world's land surface, its performance is still unsatisfactory. Although political and scientifically sound conservation targets usually portray different pictures of the task ahead, we show that in terms of priority areas for expanding the global network of reserves, there is much agreement between the political targets of the Convention on Biological Diversity (CBD), and the scientifically derived goals endorsed by international conservation organizations. Here we analyse four global databases to identify priority areas for fulfilling the CBD target of representing 10% of every ecological region within protected areas, and compare the distribution of priority regions for fulfilling that political target, with the distribution of the priority areas for global biodiversity conservation identified by Conservation International, the WWF, and the Wildlife Conservation Society on scientific basis. For 63% (549) of the world's terrestrial ecoregions the CBD 10% target is still not met; fulfilling it requires protecting another 4.6% of the Earth's land surface (6,239,894 km²). Yet, at least 78% of the priority regions for fulfilling that target lay within priority regions for the main global conservation strategies. By pursuing the political target set by the CBD much ancillary gains in terms of other global conservation objectives can be obtained.     

Reserve selection in the Succulent Karoo,South Africa: coping with high compositional turnover

The Succulent Karoo biome is home to the world's richest succulent flora. It has approximately 1954 endemic plant species, and is the only semi-arid region to qualify as a hotspot of global significance. Despite its importance, only 2% of the biome is currently protected. Based on its flora, the biome can be divided into 12 bioregions, reflecting its high compositional turnover in relation to environmental and geographical gradients. Only three of these bioregions (the Gariep Centre, the Namaqualand Rocky Hills and the Tanqua Karoo) contain National Parks, and three contain large (over 10000 ha) provincial reserves (the Gariep Centre, the Namaqualand Rocky Hills and the Little Karoo). The current reserve system does little to conserve biodiversity, with only one reserve significantly conserving Red Data Book (RDB) plant diversity. Using a RDB plant species database of 3874 records at a quarter degree scale (QDS = 15×15), we used hotspot analyses and iterative reserve selection algorithms to identify possible locations for future reserves. The hotspot analysis and iterative analyses yielded similar results for the top 11 QDS, mainly due to very high local endemism. Also because of the local endemism and the high species turnover within the biome, the real-world iterative algorithm (starting with the seven already reserved QDS) selected a very large total number of QDS (59% of the total in the biome) to conserve all RDB species. As a possible alternative to conservation planning based on QDS, we also assessed priorities at the scale of bioregions, but showed that representation at this geographic level misses important areas defined at a finer scale. We suggest that if the objective is to maximise the retention of RDB species in the landscape (to pre-empt extinction by scheduling the allocation of limited conservation resources), at least the top 5% of QDS (n=11) selected by the iterative procedure, and identified as the core conservation sequence by analysis of endemicity and threat, should be given priority for reservation. Less extensive and, in some cases, less formal conservation action can be applied to QDS later in the sequence, based on species-specific monitoring and action plans. Of the 11 core areas, four fall in a node centred on the Vanrhynsdorp Centre, two fall in a node centred on the Kamiesberg, and the remaining five are isolated. With existing reserves, the core areas capture 50% of the RDB flora in 8% of the biome.     

Conservation of Freshwater Biodiversity: a Comparison of Different Area Selection Methods

The biodiversity of freshwater systems is endangered, especially in Mediterranean semiarid areas such as the south east of the Iberian Peninsula, whose rich and endemic biota is threatened by the development of surrounding land-crop irrigation. For this reason, the prioritization of areas for biodiversity conservation is an urgent target. In this study we used data records of water beetles from a province of the southeast of Spain for assessing priority areas for freshwater biodiversity conservation. We compare the performance of various area-selection methods, ranging from scoring procedures to complementarity-based algorithms, which are based on different criteria such as richness, rarity and vulnerability. The complementarity approaches were more efficient than methods using scoring or richness and rarity hotspots for representing conservation targets in a given number of areas and for identifying the minimum set of areas containing all species at least once. Within these, the richness-based algorithm was more efficient than rarity-based algorithm. Crucial target habitats for aquatic biodiversity conservation in the area studied are streams at medium altitude, hypersaline streams, and endorreic and karstic complexes.     

Geographic patterns in the distribution of Palearctic songbirds

A database was created of digitized equal area distribution maps of 3,036 phylogenetic species of Palearctic songbirds. Biogeographic patterns are reported for two data sets: (1) including all passeriform bird species reported as breeding within the boundaries of our study map, (2) passeriform species restricted in their distribution to our study region, thus excluding the partly extra-limital taxa. With respect to the data set excluding partly extra-limital taxa, the average range size is 238 grid cells (grid cell area: 4,062 km²). Analysis of the geographic distribution of species richness for the full data set showed several hotspot regions, mostly located in mountainous areas. The index of range-size rarity identified similar hotspot regions as that for species richness, albeit that the range-size rarity de-emphasized the central Siberian hotspot. Range-size rarity hotspots that are not evident on the measure of species richness concern a great number of islands. Much more prominent on the index of range-size rarity are the Atlas Mountains of northern Africa, the Jabal al Akhdar region in NE Libya, and the eastern border of the Mediterranean. Restricting the analysis of geographic variation to the 25% of the species with smallest ranges resulted in a greatly simplified pattern of hotspots. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Hotspots and richness pattern of grasshopper species in cultural landscapes

The success of the hotspot approach for biodiversity conservation depends on the spatial scale and the indicator species used. In this study, we investigated grasshopper species richness in Switzerland at a 1 ha resolution including a total of 111 species. We compared the representativeness of common and of endangered grasshopper species for the overall grasshopper species richness and we assessed the efficiency of the hotspot approach for grasshopper conservation. The pattern of overall grasshopper species richness was well represented by both the number of common and the number of endangered grasshopper species. For evaluating the efficiency of different hotspot approaches for conservation, we compared hotspots of common species, hotspots of endangered species (rarity hotspots), and hotspots of all grasshopper species (richness hotspots). Among these hotspot types, richness hotspots not only featured most common grasshopper species, but they even contained more endangered species than the rarity hotspots. The combination of rarity hotspots and hotspots of common species featured more species than the other combinations of hotspot types. However, the gain of combining two hotspot types compared to the single-hotspot approach was low (max. 3 species). About 24% of the species were not contained in any of the hotspots. These grasshopper species require species-specific action plans. As rarity hotspots were located in areas that are rather strongly affected by landscape change, species richness in rarity hotspots may decrease in the future. We conclude that, for grasshoppers, the hotspot approach on the 1 ha scale can be an effective way to conserve a high proportion of species richness.     

National ecosystem services mapping at multiple scales ⿿ The German exemplar

The EU Biodiversity Strategy 2020 requires the Member States of the European Union to map and assess ecosystem services. This paper presents a procedure for developing a national framework of ecosystem service indicators for Germany that is applicable at different scales and is transferable to other countries. The framework was set up to use existing indicators or datasets and to be compatible with international typologies of ecosystem services and their indicators. Starting with an evaluation of the importance of different ecosystem services for Germany and an analysis of existing monitoring systems, we define suitable indicators for mapping ecosystem services nationwide. We demonstrate how both the supply of and demand for ecosystem services can be mapped with different indicators and datasets and how these indicators have to be adapted for use at different scales. Subsequently, we analyze the resulting maps to draw conclusions about the suitability of the different indicators and their complementarity. Furthermore, we show synergies and trade-offs between ecosystem services in Germany and discuss the applicability of the ecosystem services concept for decision making and spatial planning.     

The Tenebrionidae of California: A Time Sensitive Snapshot Assessment

Due to a diversity of habitats and its geologic history, the US state of California hosts a spectacular assemblage of darkling beetle species (Coleoptera: Tenebrionidae). In addition to being part of the California Floristic Province, one of 34 global biodiversity hotspots identified by Conservation International, California also has additional areas which are parts of the Great Basin, Mojave, and Sonoran deserts. California is divided into nine floristic regions. Each region is assessed in terms of faunal composition and endemism. A “snapshot” of our present knowledge of the Tenebrionidae indicates that 447 currently recognized species, representing 108 genera, occur in California of which one hundred and ninety are endemic. California is compared to other nearby regions in diversity and endemism. An analysis of currently valid species vs a more realistic species account based on unpublished records of likely synonyms and known species yet to be described in the scientific literature is presented. The California Floristic Region, rather than other more arid parts of California, has the highest number of total and endemic species. Because of their high diversity and endemism, tenebrionids could potentially provide a valuable tool for monitoring the environment for conservation purposes.     

Performance of an automated conservation status assessment for the megadiverse vascular flora of Brazil

Conservation status assessments are one of the key scientific measures to inform solutions aiming at minimizing the biodiversity crisis of the Anthropocene, being the IUCN’s Red List approach the most widely used and accepted tool for species-level assessment. However, Red Lists are time-consuming because they necessarily rely on expert evaluation. Thus, the development of automated tools, able to handle the huge increasingly amount of data in less time, are useful for guiding conservation actions. In this sense, the aim of this research is to evaluate an automated preliminary conservation status assessment for all known endemic flora from the megadiverse Brazil. Vascular taxa were derived from the Brazilian Flora 2020 project and occurrences were retrieved from GBIF and SpeciesLink. Data was filtered and then evaluated with the aid of ConR package and high resolution nationwide vegetation maps. The current approach estimates that 28.78 % (22.72–43.75 %) of the endemic flora is threatened by extinction, with different patterns between the six Brazilian ecoregions: from 30.75 % (Amazonia’s lower) to 100 % (Pantanal’s best/upper). The high variation in the estimate is because more than a fifth of the vascular flora is poorly known (<3 records). Accuracy assessment reveals a good agreement between the reference from the Brazilian Flora 2020 project and a binary classification (threatened/not- or near-threatened), with an overall accuracy of 61.67 % (58.84–64.47 %), but with limited capacity to distinguish between the IUCN’s threat levels (Critically Endangered, Endangered and Vulnerable to extinction). Bromeliaceae and Orchidaceae are the families with higher estimated number, proportion in relation to the whole family and uncertainty of estimated threatened species, reflecting that herb is the life form with far more threatened species, followed by shrubs. The presented approach can serve as rapid assessment tool for optimizing efforts and to identify potentially threatened species and hotspots of species that could be considered for timely and effective conservation actions. As a practical recommendation, botanists could prioritize the assessment of the species indicated here as threatened, as there is a high chance of confirming this status, and efforts can be properly addressed for their conservation. Moreover, the automated approach can be useful for monitoring the progress of conservation targets. Finally, further scientific research is urgent to fill the knowledge gap on the Brazilian flora aiming at its conservation.