On the taxonomic position of Tanacetum funkii (Anthemideae, Compositae)

In order to clarify the taxonomic position of the enigmatic SE Spanish endemic Tanacetum funkii Sch. Bip. ex Willk., a phylogenetic analysis based on nrDNA ITS sequence variation of representatives of Anthemideae (Compositae) was carried out together with morphological analyses of the type material. The observation of nearly identical (1 bp difference) sequences of ITS1 and ITS2 in T. funkii and Anthemis cotula L., along with the joint possession of a conical receptacle and subulate receptacular scales, argue for the conspecificity of these two taxa. As a consequence, T. funkii is transferred to the genus Anthemis L. and placed in the synonymy of Anthemis cotula, and a lectotype is designated

Weevils, weevils, weevils everywhere*

An overview is presented of the progress made on the taxonomy, classification and phylogeny of weevils in the 250 years since the first taxonomic descriptions of weevils by Carolus Linnaeus. The number of described weevils species is calculated to be about 62 000 and the likely total number of existing species 220 000, indicating that we have described just over a quarter of the diversity of this important group of beetles and that, at current rates of discovery and description, it will take another 650 years or so to describe the rest. Within the framework of the current concept of weevil phylogeny, a brief account is given of the seven main weevil lineages (families), and of the subfamilies of the largest of them, the Curculionidae, summarising their diversity, distribution and biology and identifying the major classificatory problems remaining in each. In conjunction with the phylogenetic hypothesis of weevil relationships and their fossil record, which is briefly summarised, the evolutionary history of weevils is mapped as a sequence of key evolutionary innovations that together have led to the phenomenal diversification and success of weevils. Key words: Curculionoidea, diversity, classification, phylogeny, evolutionary history.Fil: Oberprieler, Rolf. CSIRO Entomology; AustraliaFil: Marvaldi, Adriana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Provincia de Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Universidad Nacional de Cuyo. Instituto Argentino de Investigaciones de las Zonas Áridas; ArgentinaFil: Anderson, Robert S.. Canadian Museum of Nature; Canad

Can we use it? On the utility of de novo and reference-based assembly of Nanopore data for plant plastome sequencing

The chloroplast genome harbors plenty of valuable information for phylogenetic research. Illumina short-read data is generally used for de novo assembly of whole plastomes. PacBio or Oxford Nanopore long reads are additionally employed in hybrid approaches to enable assembly across the highly similar inverted repeats of a chloroplast genome. Unlike for PacBio, plastome assemblies based solely on Nanopore reads are rarely found, due to their high error rate and non-random error profile. However, the actual quality decline connected to their use has rarely been quantified. Furthermore, no study has employed reference-based assembly using Nanopore reads, which is common with Illumina data. Using Leucanthemum Mill. as an example, we compared the sequence quality of seven chloroplast genome assemblies of the same species, using combinations of two sequencing platforms and three analysis pipelines. In addition, we assessed the factors which might influence Nanopore assembly quality during sequence generation and bioinformatic processing. The consensus sequence derived from de novo assembly of Nanopore data had a sequence identity of 99.59% compared to Illumina short-read de novo assembly. Most of the errors detected were indels (81.5%), and a large majority of them is part of homopolymer regions. The quality of reference-based assembly is heavily dependent upon the choice of a close-enough reference. When using a reference with 0.83% sequence divergence from the studied species, mapping of Nanopore reads results in a consensus comparable to that from Nanopore de novo assembly, and of only slightly inferior quality compared to a reference-based assembly with Illumina data. For optimal de novo assembly of Nanopore data, appropriate filtering of contaminants and chimeric sequences, as well as employing moderate read coverage, is essential. Based on these results, we conclude that Nanopore long reads are a suitable alternative to Illumina short reads in plastome phylogenomics. Few errors remain in the finalized assembly, which can be easily masked in phylogenetic analyses without loss in analytical accuracy. The easily applicable and cost-effective technology might warrant more attention by researchers dealing with plant chloroplast genomes

GinJinn: An object‐detection pipeline for automated feature extraction from herbarium specimens

Premise The generation of morphological data in evolutionary, taxonomic, and ecological studies of plants using herbarium material has traditionally been a labor‐intensive task. Recent progress in machine learning using deep artificial neural networks (deep learning) for image classification and object detection has facilitated the establishment of a pipeline for the automatic recognition and extraction of relevant structures in images of herbarium specimens. Methods and Results We implemented an extendable pipeline based on state‐of‐the‐art deep‐learning object‐detection methods to collect leaf images from herbarium specimens of two species of the genus Leucanthemum . Using 183 specimens as the training data set, our pipeline extracted one or more intact leaves in 95% of the 61 test images. Conclusions We establish GinJinn as a deep‐learning object‐detection tool for the automatic recognition and extraction of individual leaves or other structures from herbarium specimens. Our pipeline offers greater flexibility and a lower entrance barrier than previous image‐processing approaches based on hand‐crafted features

Vertebrates are poor umbrellas for invertebrates: cross-taxon congruence in an Australian tropical savanna

Invertebrates are commonly ignored in conservation planning due to their vast diversity, difficulties with species identification, a poor understanding of their spatial patterns, and the impracticability of carrying out comprehensive sampling. Conservation planning for fauna is therefore often based on patterns of diversity and distribution of vertebrates, under the assumption that these are representative of animal diversity more generally. Here, we evaluate how well vertebrates act as umbrellas for invertebrate diversity and distribution in a highly diverse tropical savanna landscape, and we investigate the effect of vertebrate sampling intensity (i.e., number of surveys) on congruence results. We assessed congruence between each of the four classes of terrestrial vertebrates (amphibians, reptiles, birds, and mammals) and twelve invertebrate families (representing four dominant invertebrate taxa: ants, beetles, flies, and spiders) by applying a range of modeling approaches to analyze patterns of cross‐taxon congruence in species richness and composition across sampling sites. To investigate drivers of congruence, we applied generalized and distance‐based linear models to identify environmental associations of richness and composition for each taxon, then examined variation in environmental associations across taxa. Vertebrate and invertebrate richness was weakly (<30%) associated, and ~60% of the significant associations were negative. Correlations in species composition between vertebrate and invertebrate taxa were also weak, with a maximum of 13% congruence. In most cases, pairwise correlation scores using data from single surveys of vertebrates were only marginally lower than those from multiple surveys. Poor among‐site congruence between vertebrates and invertebrates was reflected by marked variation among taxa in their environmental associations. Our findings show that vertebrates are poor umbrellas for invertebrates in the tropical savannas of northern Australia in terms of geographic patterns of diversity and distribution and that this is not just an artifact of low vertebrate sampling intensity. Our study is one of the most comprehensive regional analyses of the congruence of vertebrate and invertebrate diversity, and it significantly adds to the growing evidence that empirical data on invertebrate diversity and distribution are required for conservation planning that effectively protects all faunal diversity

Entiminae Schoenherr 1823

Fil: Marvaldi, Adriana E.. Instituto Argentino de Investigaciones de las Zonas Áridas. Mendoza; ArgentinaFil: Lanteri, Analía Alicia. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Entomología; ArgentinaFil: del Río, María Guadalupe. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Entomología; ArgentinaFil: Oberprieler, Rolf G.. CSIRO Entomology. Canberra; Australi

Ploidy level in the genus Leucanthemum correlates with resistance to a specialist herbivore

Polyploidy is considered to be a major source of genetic diversity in plants. Genome duplication has been shown repeatedly to be associated with changes in biotic interactions, but little is known about whether species traits such as herbivore resistance consistently change with increasing ploidy level among closely related plant species. We tested whether larval survival and performance of the specialist root- mining moth Dichrorampha aeratana are influenced by the ploidy level of plant species in the genus Leucanthemum by experimentally infesting 16 different taxa with ploidy levels ranging from diploid to dodecaploid. We found that survival of D. aeratana larvae consistently decreased with increasing ploidy level, irrespective of whether phylogenetic distance among taxa was taken into account or not. The mass of larvae and the proportion of adults emerging from last-instar larvae, however, did not consistently change with increasing ploidy level. Root biomass and dry matter content of the Leucanthemum taxa were neither correlated with ploidy level nor correlated with survival or mass of D. aeratana larvae. In summary, our results provide evidence that in the genus Leucanthemum, resistance to the specialist root herbivore D. aeratana consistently increases with increasing plant ploidy level, but it remains unclear which characteristics associated with polyploidy account for the higher herbivore resistance