Barcoding a partir de posos de café - Explorando la biodiversidad de gasterópodos pterópodos a partir de posos de frascos de colección

Despite their cosmopolitan occurrence and massive plankton sampling during expeditions, the genetic diversity within Pteropoda Cuvier, 1804 is still largely unexplored. In this study we present a next-generation environmental barcoding approach to zooplankton bulk samples, which were collected during the circumglobal 2010 Malaspina expedition to evaluate pteropod diversity. We introduce a technique that avoids destructive procedures and leaves material intact for further morphological investigations. We extracted DNA out of the dregs (organic material such as mucus or body parts) of 27 sample containers for molecular barcoding (average 100-260 bp of COI). We were able to identify 7128 operational taxonomic units corresponding to the species composition contained in the examined samples. Among them were three species of thecosome pteropods, Creseis acicula, Creseis virgula and Cavolinia inflexa, which are discussed with respect to their taxonomy and their geographic distribution. Unidentified gymnosomes were also present in our samples from warmer regions in oceanic waters of the southern Indian Ocean. To facilitate identification of species, it is beneficial to create a better database of pteropod COI barcodes. Furthermore, gathering environmental barcoding data on a broad global scale will help to better understand species abundance and distribution of pteropods in the world’s oceans, and potentially those of other planktonic organisms.A pesar de su presencia cosmopolita y las actividades de muestreo masivo de plancton durante las expediciones, la diversidad genética dentro de los Pteropoda Cuvier, 1804 está todavía inexplorada en gran medida. En este estudio se presenta una aproximación desde el barcoding ambiental aplicada a muestras generales de zooplancton recogidas durante la expedición circumglobal “Malaspina 2010”, con el fin de evaluar la diversidad de pterópodos. Se introduce una técnica que evita procedimientos destructivos de tal modo que el material permanece intacto para futuras investigaciones morfológicas. Extrajimos ADN de los posos (material orgánico como moco o partes del cuerpo) de 27 recipientes de muestras para el barcoding (promedio de 100- 260 bp de COI). Se pudieron identificar 7128 “OTUs” correspondientes a la composición de las especies contenidas en las muestras examinadas. Entre ellas se encontraron tres especies de pterópodos tecosomados, Creseis acicula, Creseis virgula y Cavolinia inflexa, cuya taxonomía y distribución geográfica son discutidas. Gimnosomados no identificados procedentes de regiones más templadas de aguas oceánicas del sur del Océnao Indico también estaban presentes. Para facilitar la identificación de especies, es beneficioso crear una base de datos ampliada de códigos de barras COI de pterópodos. Además, la recopilación de datos de barcoding ambiental a una escala mundial amplia ayudará a comprender mejor la abundancia y distribución de especies de pterópodos en los océanos del mundo y de otros posibles organismos planctónicos

A novel approach for reliable qualitative and quantitative prey spectra identification of carnivorous plants combining DNA metabarcoding and macro photography

Prey spectra (the number and composition of captured arthropods) represent a crucial aspect of carnivorous plant ecology, yet remain poorly studied. Traditional morphology-based approaches for prey identification are time-intensive, require specialists with considerable knowledge of arthropod taxonomy, and are hampered by high numbers of unidentifiable (i.e., heavily digested) prey items. We examined prey spectra of three species of closely-related annual Drosera (Droseraceae, sundews) from tropical northern Australia using a novel DNA metabarcoding approach with in-situ macro photography as a plausibility control and to facilitate prey quantity estimations. This new method facilitated accurate analyses of carnivorous plant prey spectra (even of heavily digested prey lacking characteristic morphological features) at a taxonomic resolution and level of completeness far exceeding morphology-based methods and approaching the 100% mark at arthropod order level. Although the three studied species exhibited significant differences in detected prey spectra, little prey specialisation was observed and habitat or plant population density variations were likely the main drivers of prey spectra dissimilarity

Arthropod dark taxa provide new insights into diversity responses to bark beetle infestations

Natural disturbances are increasing around the globe, also impacting protected areas. Although previous studies have indicated that natural disturbances result in mainly positive effects on biodiversity, these analyses mostly focused on a few well established taxonomic groups, and thus uncertainty remains regarding the comprehensive impact of natural disturbances on biodiversity. Using Malaise traps and meta-barcoding, we studied a broad range of arthropod taxa, including dark and cryptic taxa, along a gradient of bark beetle disturbance severities in five European national parks. We identified order-level community thresholds of disturbance severity and classified barcode index numbers (BINs; a cluster system for DNA sequences, where each cluster corresponds to a species) as negative or positive disturbance indicators. Negative indicator BINs decreased above thresholds of low to medium disturbance severity (20%-30% of trees killed), whereas positive indicator BINs benefited from high disturbance severity (76%-98%). BINs allocated to a species name contained nearly as many positive as negative disturbance indicators, but dark and cryptic taxa, particularly Diptera and Hymenoptera in our data, contained higher numbers of negative disturbance indicator BINs. Analyses of changes in the richness of BINs showed variable responses of arthropods to disturbance severity at lower taxonomic levels, whereas no significant signal was detected at the order level due to the compensatory responses of the underlying taxa. We conclude that the analyses of dark taxa can offer new insights into biodiversity responses to disturbances. Our results suggest considerable potential for forest management to foster arthropod diversity, for example by maintaining both closed-canopy forests (>70% cover) and open forests (<30% cover) on the landscape

DNA metabarcoding for biodiversity monitoring in a national park: Screening for invasive and pest species

DNA metabarcoding was utilized for a large-scale, multiyear assessment of biodiversity in Malaise trap collections from the Bavarian Forest National Park (Germany, Bavaria). Principal component analysis of read count-based biodiversities revealed clustering in concordance with whether collection sites were located inside or outside of the National Park. Jaccard distance matrices of the presences of barcode index numbers (BINs) at collection sites in the two survey years (2016 and 2018) were significantly correlated. Overall similar patterns in the presence of total arthropod BINs, as well as BINs belonging to four major arthropod orders across the study area, were observed in both survey years, and are also comparable with results of a previous study based on DNA barcoding of Sanger-sequenced specimens. A custom reference sequence library was assembled from publicly available data to screen for pest or invasive arthropods among the specimens or from the preservative ethanol. A single 98.6% match to the invasive bark beetle Ips duplicatus was detected in an ethanol sample. This species has not previously been detected in the National Park

Relationship of insect biomass and richness with land use along a climate gradient

Recently reported insect declines have raised both political and social concern. Although the declines have been attributed to land use and climate change, supporting evidence suffers from low taxonomic resolution, short time series, a focus on local scales, and the collinearity of the identified drivers. In this study, we conducted a systematic assessment of insect populations in southern Germany, which showed that differences in insect biomass and richness are highly context dependent. We found the largest difference in biomass between semi-natural and urban environments (−42%), whereas differences in total richness (−29%) and the richness of threatened species (−56%) were largest from semi-natural to agricultural environments. These results point to urbanization and agriculture as major drivers of decline. We also found that richness and biomass increase monotonously with increasing temperature, independent of habitat. The contrasting patterns of insect biomass and richness question the use of these indicators as mutual surrogates. Our study provides support for the implementation of more comprehensive measures aimed at habitat restoration in order to halt insect declines

Enseignants et enseignements au cœur de la transmission des savoirs

Ce recueil est consacré à la question de la transmission des savoirs abordée non pas comme un transfert individuel, de personne à personne, dans le cadre de la famille ou de l’atelier, mais comme un système formel combinant de façon plus structurée un ou des enseignements. Cette problématique a fait l’objet de très nombreuses conférences, d’une extrême diversité, présentées lors du 143e Congrès national des sociétés historiques et scientifiques tenu à Paris, en 2018. Leur point commun est principalement de s’interroger sur la transmission des savoirs par l’enseignement, son éventuelle formalisation, ses acteurs, ses méthodes et ses outils, voire ses enjeux. Le Congrès national des sociétés historiques et scientifiques rassemble chaque année universitaires, membres de sociétés savantes et jeunes chercheurs. Ce recueil est issu de travaux présentés lors du 143e Congrès sur le thème « La transmission des savoirs »

The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life

DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life’s species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between ‘Barcode Index Numbers’ (BINs) and ‘species’ that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description. This article is part of the themed issue ‘From DNA barcodes to biomes’

Türkiye'de Chilo partellus (Swinhoe) (Lepidoptera : Crambidae)'un yumurta parazitoidlerinin DNA barkodu kullanılarak belirlenmiş ilk kaydı

Chilo partellus (Swinhoe) (Lepidoptera: Crambidae) mısır ve diğer tahıl ürünlerinde zararlı olan ve önemli ürün kayıplarına neden olan istilacı bir türdür. Bu böceğin Türkiye'deki varlığı ilk kez 2014 yılında Türkiye'nin Doğu Akdeniz Bölgesi'nin bazı illerinin mısır alanlarında kaydedilmiştir. Bu zararlı için insektisitler veya diğer zararlı mücadele metodları her zaman yeterli kontrolü sağlamamakta, biyolojik mücadele ise önemli bir alternatif olarak düşünülmektedir. Ancak biyolojik metodların başarılı bir şekilde uygulanması için zararlının doğal düşmanlarının ilk adımda iyi tanımlanmış olması gerekmektedir, Morfolojiye dayanan klasik teşhis metodlarıyla bunu gerçekleştirmek oldukça zordur. Moleküler tekniklerdeki son gelişmeler, böcek türlerinin ve onların parazitoidlerinin daha doğru tanılanmasına olanak vermektedir. Dolayısıyla bu çalışmanın amacı C. partellus' un yumurta parazitoidlerini, moleküler metodlar kullanarak tanılamaktır. Bu zararlının parazitlenmiş yumurtaları, 2014 yılının eylül ve ekim ayları ile 2015 yılı eylül ayında Türkiye'nin Hatay ilindeki mısır alanlarından toplanmıştır. Yumurtalar daha sonra laboratuvar koşullarında kültüre alınmış ve çıkış yapan erginlerin moleküler analizleri yapılmıştır. DNA barkod ile İki yerel doğal düşman, Trichogramma brassicae Bezdenko (Hymenoptera: Trichogrammatidae) ve Telenomus busseolae (Gahan) (Hymenoptera: Platygasteridae) C. partellus'un yumurta parazitoidleri olarak ilk kez kaydedilmiştir.Chilo partellus (Swinhoe) (Lepidoptera: Crambidae) is an invasive insect species attacking maize (Zea mays L.) and other cereal crops causing important yield losses. The occurrence of this insect in Turkey was first reported in maize growing areas of some provinces in the East Mediterranean region of Turkey in 2014. Chemical or other pest control methods do not always provide acceptable control of this pest, so biological control is considered an important alternative. However, for a successful biological control, the first step is to reliably identify the natural enemies of a target pest, which is difficult to achieve using methods based on morphology. Recent developments in molecular techniques allow more reliable identification of insect species and their parasitoids. Therefore, the aim of this study was to identify the egg parasitoids of C. partellus by molecular methods. Parasitized eggs were collected from maize fields in Hatay province, Turkey, from September to October 2014 and in September 2015. Eggs were maintained in the laboratory and emerging adult parasitoids were subjected to molecular analysis. Using DNA barcoding, two native natural enemies, Trichogramma brassicae Bezdenko (Hymenoptera: Trichogrammatidae) and Telenomus busseolae (Gahan) (Hymenoptera: Platygastridae) were identified as egg parasitoids of C. partellus for the first time in Turkey

High genetic variation within mitochondrial CO1 in Middle European Thanasimus formicarius (Linné, 1758) (Coleoptera: Cleridae)

Gerstmeier, Roland, Morinière, Jérôme, Hendrich, Lars (2019): High genetic variation within mitochondrial CO1 in Middle European Thanasimus formicarius (Linné, 1758) (Coleoptera: Cleridae). Zootaxa 4674 (3): 386-392, DOI: https://doi.org/10.11646/zootaxa.4674.3.