Dung beetle radiations in Madagascar

Speciation on islands is affected by island size and the range of habitats and resources available and often also by limited interactions with other taxa. An ancestral population may evolve into a large number of species via an adaptive radiation. In Madagascar, most groups of animals and plants have radiated on the island, having arrived via oceanic dispersal during the long isolation of Madagascar. Characteristic features of Malagasy biota are exceptionally high level of endemism, high species richness as well as lack of many higher taxa that are dominant on the African mainland. Malagasy dung beetles are dominated by two tribes, Canthonini and Helictopleurina, with more than 250 endemic species. In this thesis I have reconstructed molecular phylogenies for the two tribes using several gene regions and different phylogenetic methods. Evolution of closely related species and among populations of the same species was examined with haplotype networks. The Malagasy Canthonini consists of three large lineages, while Helictopleurina forms a monophyletic group. The ancestors of each of the four clades colonised Madagascar at different times during Cenozoic. The subsequent radiations differ in terms of the number of extant species (from 37 to more than 100) and the level of ecological differentiation. In addition, Onthophagini (6 species) and Scarabaeini (3) have colonised Madagascar several times, but they have not radiated and the few species have not entered forests where Canthonini and Helictopleurina mostly occur. Among the three Canthonini radiations, speciation appears to have been mostly allopatric in the oldest and the youngest clades, while in the Epactoides clade sister species have diverged in their ecologies but have similar geographical distributions, indicating that speciation may have occurred in regional sympatry. The most likely isolating mechanisms have been rivers and forest refugia during dry and cool geological periods. Most species are generalists feeding on both carrion and dung, and competition among ecologically similar species may prevent their coexistence in the same communities. Some species have evolved to forage in the canopy and a few species have shifted to use cattle dung, a new resource in the open habitats following the introduction of cattle 1500 years ago. The latter shift has allowed species to expand their geographical ranges.Madagaskarin eläin- ja kasvilajisto on hyvin rikas, ja suurin osa lajeista on kotoperäisiä, eli ne ovat kehittyneet saarella ja ne esiintyvät vain siellä. Pääosin nykylajiston kantamuodot ovat saapuneet saarelle meriteitse kymmeniä miljoonia vuosia sitten saaren jo ollessa erkaantunut Afrikan mantereesta. Lajit ovat syntyneet saarella ja sopeutuneet sen moniin erilaisiin ympäristöihin. Toisaalta, eristyneisyytensä takia Madagaskarilta puuttuu monia eläinryhmiä, jotka esiintyvät runsaina manner-Afrikassa. Erityispiirteidensä ansiosta Madagaskar on oivallinen alue tutkia lajiutumista ja lajiryhmien kehittymistä. Madagaskarilta tunnetaan yli 250 kotoperäistä lantakuoriaislajia. Suurin osa lajeista kuuluu Canthonini- ja Helictopleurina-sukuryhmiin. Väitöskirjatutkimuksessani olen selvittänyt madagaskarilaisten lantakuoriaisten evoluutiota rakentamalla useaan geenialueeseen perustuvia sukupuita. Lajistoltaan suurempi sukuryhmistä, Canthonini, koostuu kolmesta erillisestä kehityslinjasta Kunkin linjan kantamuoto on saapunut saarelle viimeisen 65 miljoonan vuoden aikana. Helictopleurina-ryhmällä on vain yksi kantamuoto, joka saapui saarelle noin 30 miljoonaa vuotta sitten. Nämä neljä lantakuoriaislinjaa eroavat toisistaan lajimääriltään (37 yli 100 lajiin) sekä monilta ekologisilta piirteiltään. Suurin osa lajeista ei ole erikoistunut eri ravintoihin, mutta kahdella vanhimmalla linjalla on monipuolisempi ravinto kuin nuoremmilla ryhmillä. Kaikki neljä linjaa esiintyvät useissa metsätyypeissä, mutta erityisesti sademetsäalueella, jossa niille on parhaiten tarjolla ravintoa. Jotkin lajeista ovat kehittyneet asumaan puiden latvustossa, kun taas muutama laji on siirtynyt käyttämään lehmänlantaa avoimilla alueilla. Kumpikin näistä muutoksista on tapahtunut useaan kertaan. Lehmänlannan käyttö on mahdollistanut näiden lajien levittäytymisen koko saarelle, sillä karjaa kasvatetaan ympäri saarta. Saarella esiintyy myös Onthophagini- ja Scarabaeini-sukuryhmien lantakuoriaislajeja, mutta nämä ryhmät eivät ole pystyneet lajiutumaan saarella lähes lainkaan eivätkä leviämään sademetsiin. Todennäköisesti ne ovat saapuneet saarelle myöhemmin kuin Canthonini- ja Helictopleurina-ryhmät, ja kilpailu näiden aiemmin kehittyneiden ja siten saarelle paremmin sopeutuneiden lajien kanssa on estänyt uudempien ryhmien levittäytymisen

Trans-generational immune priming against American Foulbrood does not affect the performance of honeybee colonies

Honeybees are major pollinators for our food crops, but at the same time they face many stressors all over the world. One of the major threats to honeybee health are bacterial diseases, the most severe of which is the American Foulbrood (AFB). Recently a trans-generational vaccination approach against AFB has been proposed, showing strong potential in protecting the colonies from AFB outbreaks. Yet, what remains unstudied is whether the priming of the colony has any undesired side-effects. It is widely accepted that immune function is often a trade-off against other life-history traits, hence immune priming could have an effect on the colony performance. In this experiment we set up 48 hives, half of them with primed queens and half of them as controls. The hives were placed in six apiaries, located as pair of apiaries in three regions. Through a 2-year study we monitored the hives and measured their health and performance. We measured hive weight and frame contents such as brood amount, worker numbers, and honey yield. We studied the prevalence of the most common honeybee pathogens in the hives and expression of relevant immune genes in the offspring at larval stage. No effect of trans-generational immune priming on any of the hive parameters was found. Instead, we did find other factors contributing on various hive performance parameters. Interestingly not only time but also the region, although only 10 km apart from each other, had an effect on the performance and health of the colonies, suggesting that the local environment plays an important role in hive performance. Our results suggest that exploiting the trans-generational priming could serve as a safe tool in fighting the AFB in apiaries.Peer reviewe

Reconstructing the ecosystem context of a species: Honey-borne DNA reveals the roles of the honeybee

To assess a species’ impact on its environment–and the environment’s impact upon a species–we need to pinpoint its links to surrounding taxa. The honeybee (Apis mellifera) provides a promising model system for such an exercise. While pollination is an important ecosystem service, recent studies suggest that honeybees can also provide disservices. Developing a comprehensive understanding of the full suite of services and disservices that honeybees provide is a key priority for such a ubiquitous species. In this perspective paper, we propose that the DNA contents of honey can be used to establish the honeybee’s functional niche, as reflected by ecosystem services and disservices. Drawing upon previously published genomic data, we analysed the DNA found within 43 honey samples from Northern Europe. Based on metagenomic analysis, we find that the taxonomic composition of DNA is dominated by a low pathogenicity bee virus with 40.2% of the reads, followed by bacteria (16.7%), plants (9.4%) and only 1.1% from fungi. In terms of ecological roles of taxa associated with the bees or taxa in their environment, bee gut microbes dominate the honey DNA, with plants as the second most abundant group. A range of pathogens associated with plants, bees and other animals occur frequently, but with lower relative read abundance, across the samples. The associations found here reflect a versatile the honeybee’s role in the North-European ecosystem. Feeding on nectar and pollen, the honeybee interacts with plants–in particular with cultivated crops. In doing so, the honeybee appears to disperse common pathogens of plants, pollinators and other animals, but also microbes potentially protective of these pathogens. Thus, honey-borne DNA helps us define the honeybee’s functional niche, offering directions to expound the benefits and drawbacks of the associations to the honeybee itself and its interacting organisms.Peer reviewe

Morphological, Pathological, and Genetic Diversity of Colletotrichum Species Pathogens on Solanaceous Vegetable Crops in Bulgaria

Colletotrichum species are among the most devastating plant pathogens in a wide range of hosts. Their accurate identification requires a polyphasic approach, including geographical, ecological, morphological, and genetic data. Solanaceous crops are of significant economic importance for Bulgarian agriculture. Colletotrichum-associated diseases pose a serious threat to the yield and quality of production but are still largely unexplored. The aim of this study was to identify and characterize 26 pathogenic Colletotrichum isolates that threaten solanaceous crops based on morphological, pathogenic, and molecular data. DNA barcodes enabled the discrimination of three main taxonomic groups: C. acutatum, C. gloeosporioides, and C. coccodes. Three different species of acutatum complex (C. nymphaeae, C. godetiae, and C. salicis) and C. cigarro of the gloeosporioides complex were associated with fruit anthracnose in peppers and tomatoes. The C. coccodes group was divided in two clades: C. nigrum, isolated predominantly from fruits, and C. coccodes, isolated mainly from roots. Only C. salicis and C. cigarro produced sexual morphs. The species C. godetiae, C. salicis, and C. cigarro have not previously been reported in Bulgaria. Our results enrich the knowledge of the biodiversity and specific features of Colletotrichum species, which are pathogenic to solanaceous hosts, and may serve as a scientific platform for efficient disease control and resistance breeding

Quantifying uncertainty of taxonomic placement in DNA barcoding and metabarcoding

A crucial step in the use of DNA markers for biodiversity surveys is the assignment of Linnaean taxonomies (species, genus, etc.) to sequence reads. This allows the use of all the information known based on the taxonomic names. Taxonomic placement of DNA barcoding sequences is inherently probabilistic because DNA sequences contain errors, because there is natural variation among sequences within a species, and because reference data bases are incomplete and can have false annotations. However, most existing bioinformatics methods for taxonomic placement either exclude uncertainty, or quantify it using metrics other than probability. In this paper we evaluate the performance of the recently proposed probabilistic taxonomic placement method PROTAX by applying it to both annotated reference sequence data as well as to unknown environmental data. Our four case studies include contrasting taxonomic groups (fungi, bacteria, mammals and insects), variation in the length and quality of the barcoding sequences (from individually Sanger-sequenced sequences to short Illumina reads), variation in the structures and sizes of the taxonomies (800–130 000 species) and variation in the completeness of the reference data bases (representing 15–100% of known species). Our results demonstrate that PROTAX yields essentially unbiased probabilities of taxonomic placement, which means its quantification of species identification uncertainty is reliable. As expected, the accuracy of taxonomic placement increases with increasing coverage of taxonomic and reference sequence data bases, and with increasing ratio of genetic variation among taxonomic levels over within taxonomic levels. We conclude that reliable species-level identification from environmental samples is still challenging and that neglecting identification uncertainty can lead to spurious inference. A key aim for future research is the completion of taxonomic and reference sequence data bases and making these two types of data compatible

Complementary molecular information changes our perception of food web structure

Peer reviewe

DNA traces the origin of honey by identifying plants, bacteria and fungi

The regional origin of a food product commonly affects its value. To this, DNA-based identification of tissue remains could offer fine resolution. For honey, this would allow the usage of not only pollen but all plant tissue, and also that of microbes in the product, for discerning the origin. Here we examined how plant, bacterial and fungal taxa identified by DNA metabarcoding and metagenomics differentiate between honey samples from three neighbouring countries. To establish how the taxonomic contents of honey reflect the country of origin, we used joint species distribution modelling. At the lowest taxonomic level by metabarcoding, with operational taxonomic units, the country of origin explained the majority of variation in the data (70-79%), with plant and fungal gene regions providing the clearest distinction between countries. At the taxonomic level of genera, plants provided the most separation between countries with both metabarcoding and metagenomics. The DNA-based methods distinguish the countries more than the morphological pollen identification and the removal of pollen has only a minor effect on taxonomic recovery by DNA. As we find good resolution among honeys from regions with similar biota, DNA-based methods hold great promise for resolving honey origins among more different regions

Spatial subsidies in spider diets vary with shoreline structure: Complementary evidence from molecular diet analysis and stable isotopes

Peer reviewe

Morphological, Pathological and Genetic Diversity of the Colletotrichum Species, Pathogenic on Solanaceous Vegetable Crops in Bulgaria

Colletotrichum species are among the most devastating plant pathogens in a wide range of hosts. Their accurate identification requires a polyphasic approach, including geographical, ecological, morphological, and genetic data. Solanaceous crops are of significant economic importance for Bulgarian agriculture. Colletotrichum-associated diseases pose a serious threat to the yield and quality of production but are still largely unexplored. The aim of this study was to identify and characterize 26 pathogenic Colletotrichum isolates that threaten solanaceous crops based on morphological, pathogenic, and molecular data. DNA barcodes enabled the discrimination of three main taxonomic groups: C. acutatum, C. gloeosporioides, and C. coccodes. Three different species of acutatum complex (C. nymphaeae, C. godetiae, and C. salicis) and C. cigarro of the gloeosporioides complex were associated with fruit anthracnose in peppers and tomatoes. The C. coccodes group was divided in two clades: C. nigrum, isolated predominantly from fruits, and C. coccodes, isolated mainly from roots. Only C. salicis and C. cigarro produced sexual morphs. The species C. godetiae, C. salicis, and C. cigarro have not previously been reported in Bulgaria. Our results enrich the knowledge of the biodiversity and specific features of Colletotrichum species, which are pathogenic to solanaceous hosts, and may serve as a scientific platform for efficient disease control and resistance breeding

Origin of Madagascan Scarabaeini dung beetles (Coleoptera : Scarabaeidae) : dispersal from Africa

Madagascar, the world’s fourth largest island, has a long history of isolation (160 MY) and a wide range of climates and ecosystems which have in turn resulted in high levels of endemism across different taxonomic levels. Although Madagascar has a rich dung beetle fauna that belongs to various tribes only three species of the Scarabaeini are found there, namely Scarabaeus viettei, S. radama and S. sevoistra. These three species are superficially quite distinctive and have, consequently, had a relatively tortured taxonomic history since the first was described in1896. The morpholgical differences between these species resulted in them being placed in different genera at different times. However, currently, based on cladistic analysis, they are all classified in the genus Scarabaeus. In this study, two of the species, S. viettei and S. radama, were included in a phylogenetic analysis based on two mitochondrial gene regions - cytochrome oxidase I (COI) and 16S rRNA - and a 247 morphological and behavioural dataset of 23 members of the Scarabaeinae. A Bayesian phylogram supports the monophyly of the genus Scarabaeus, with the two species from Madagascar appearing sister to three species of Scarabaeus from southwest Africa. Estimated times of divergence based on published mutation rates of 0.012 and 0.0075 for COI indicate that a shared African/Madagascan origin occurred around 15.18 or 24.15 MYA, respectively. This study is another example in support of Madagascan fauna having an African origin with colonisation having occurred via dispersal as opposed to ancient vicariant events.http://www.brill.nl/iseab201