Geographic Life History Differences Predict Genomic Divergence Better than Mitochondrial Barcodes or Phenotype

Species diversity can be inferred using multiple data types, however, results based on genetic data can be at odds with patterns of phenotypic variation. Tiger beetles of the Cicindelidia politula (LeConte, 1875) species complex have been taxonomically problematic due to extreme phenotypic variation within and between populations. To better understand the biology and taxonomy of this group, we used mtDNA genealogies and multilocus nuclear analyses of 34,921 SNPs to elucidate its evolutionary history and evaluate the validity of phenotypically circumscribed species and subspecies. Genetic analyses recovered two divergent species that are also ecologically distinct, based on adult life history. These patterns are incongruous with the phenotypic variation that informed prior taxonomy, and most subspecies were not supported as distinct evolutionary lineages. One of the nominal subspecies was found to be a cryptic species; consequently, we elevate C. p. laetipennis (Horn, 1913) to a full species. Although nuclear and mtDNA datasets recovered broadly similar evolutionary units, mito-nuclear discordance was more common than expected, being observed between nearly all geographically overlapping taxonomic pairs. Additionally, a pattern of ‘mitochondrial displacement’ was observed, where mitochondria from one species unidirectionally displace others. Overall, we found that geographically associated life history factors better predict genomic divergence than phenotype and mitochondrial genealogies, and consequently taxon identifications based on mtDNA (e.g., DNA barcodes) may be misleading

Ronald Reagan a wyzwania epoki

Z wprowadzenia: "Śmierć Ronalda Reagana w czerwcu 2004 r. zamknęła znaczącą epokę w dziejach Europy i świata. Reagan symbolizował pokolenie polityków, którym przyszło działać w czasach szybkiej dekompozycji dwóch, wydawałoby się niepodważalnych pewników politycznych dominujących po drugiej wojnie światowej w świecie zachodnim. Z polityków tych był tym, który przyczynił się w olbrzymiej mierze do podważenia obu z nich."(...

O reakcjach podatników na opodatkowanie i przerzucalności podatków

Numerous governments’ growing interest in extending the tax base can be observed. The article discusses the conditions determining taxpayers’ attitudes and their reactions to taxation and the mechanisms of their most common conduct, i.e. tax shift. It takes into account the Polish scientists’, Adam Krzyżanowski’s and Roman Rybarski’s, output in the area in the twenty-year interwar period, as well as the contemporary experience with some new types of tax, such as bank tax that was imposed on some financial institutions.Obserwujemy wzmożone zainteresowanie rządów wielu państw zwiększaniem bazy podatkowej. Niniejszy artykuł dotyczy uwarunkowań determinujących postawę podatników i ich reakcji na opodatkowanie oraz mechanizmów najpowszechniejszego ich zachowania, czyli przerzucania podatków. Uwzględniono dorobek nauki polskiej w tym obszarze w okresie XX-lecia międzywojennego, Adama Krzyżanowskiego i Romana Rybarskiego, a także współczesne doświadczenia z nowymi rodzajami podatków, jak podatek od niektórych instytucji finansowych, nazywany podatkiem bankowym

Towards a catalogue of biodiversity databases: An ontological case study

Biodiversity informatics depends on digital access to credible information about species. Many online resources host species’ data, but the lack of categorisation for these resources inhibits the growth of this entire field. To explore possible solutions, we examined the (now retired) Biodiversity Information Projects of the World (BIPW) dataset created by the Biodiversity Information Standards (TDWG); this project, which ran from 2007-2015 (officially removed from the TDWG website in 2018) was an attempt at organising the Web's biodiversity databases into an indexed list. To do this, we applied a simple classification scheme to score databases within BIPW based on nine data categories, to characterise trends and current compositions of this biodiversity e-infrastructure. Primarily, we found that of 600 databases investigated from BIPW, only 315 (~53%) were accessible at the time of this writing, underscoring the precarious nature of the biodiversity information landscape. Many of these databases are still available, but suffer accessibility issues such as link rot, thus putting the information they contain in danger of being lost. We propose that a community-driven database of biodiversity databases with an accompanying ontology could facilitate efficient discovery of relevant biodiversity databases and support smaller databases – which have the greatest risk of being lost

The Hemiptera (Insecta) of Canada: Constructing a Reference Library of DNA Barcodes

<div><p>DNA barcode reference libraries linked to voucher specimens create new opportunities for high-throughput identification and taxonomic re-evaluations. This study provides a DNA barcode library for about 45% of the recognized species of Canadian Hemiptera, and the publically available R workflow used for its generation. The current library is based on the analysis of 20,851 specimens including 1849 species belonging to 628 genera and 64 families. These individuals were assigned to 1867 Barcode Index Numbers (BINs), sequence clusters that often coincide with species recognized through prior taxonomy. Museum collections were a key source for identified specimens, but we also employed high-throughput collection methods that generated large numbers of unidentified specimens. Many of these specimens represented novel BINs that were subsequently identified by taxonomists, adding barcode coverage for additional species. Our analyses based on both approaches includes 94 species not listed in the most recent Canadian checklist, representing a potential 3% increase in the fauna. We discuss the development of our workflow in the context of prior DNA barcode library construction projects, emphasizing the importance of delineating a set of reference specimens to aid investigations in cases of nomenclatural and DNA barcode discordance. The identification for each specimen in the reference set can be annotated on the Barcode of Life Data System (BOLD), allowing experts to highlight questionable identifications; annotations can be added by any registered user of BOLD, and instructions for this are provided.</p></div

A three dimensional visualization of taxonomic congruence between BINs and species identifications, based on morphology, for three families of Canadian Hemiptera (Aphididae, Cicadellidae, and Miridae).

<p>The taxonomists who identified these specimens are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0125635#pone.0125635.s012" target="_blank">S7 Table</a>. A robustly concordant BIN (one species per BIN, with many specimens in that BIN) occupies a forward position in the plane along the left wall, whereas discordant BINs (those with many specimens, and several species names) appear towards the upper right quadrant. The colors correspond to the concordance status of the same BIN on BOLD. In many cases, BINs that are concordant in this curated dataset are discordant on BOLD. This disparity highlights the utility of defining a reference set of specimens, as library specimens will be grouped by BOLD in BINs with misidentified specimens.</p

Proportion of data sources, and sequence length for all records in this study.

<p>These generalized-collection methods acquire a broad spectrum of taxa, and are valuable sources of diversity when combined with conventional museum collections, and research projects through BIO. Some specimens, especially those from museums, lack sequence data, but do have images, names, and associated metadata on BOLD.</p

Primers amplifying the COI barcode region of Hemiptera examined in this study.

<p>This table pairs with the primer-use heatmap in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0125635#pone.0125635.g002" target="_blank">Fig 2</a>, where the sequentially shaded numbers in the left columns connect primer sequences and citations with their amplification success, per hemipteran family, in this study. Primer sequences are provided with their first occurrence, and sequences for cocktail primer components are provided below. All cocktail primers are used in a 1:1 ratio.</p

Proportions of PCR amplifications by taxon, generated with particular primer pairs, for all Hemiptera specimens in this study.

<p>This heatmap pairs with <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0125635#pone.0125635.g001" target="_blank">Fig 1</a>, where the sequentially shaded numbers in the left columns connect primer sequences and citations with their use, per hemipteran family. Primer pairs appear in descending order of amplicon lengths, at left. The dot area is proportional to all amplification attempts for that primer/family, the total number of specimens analyzed per primer combination is adjacent to each dot, and the shading indicates the proportion of successful amplifications (illustrated in the key at lower left). All cocktail primers are used in a 1:1 ratio.</p

Ordinal-level summary for all data-release and library specimens.

<p>Shaded columns indicate library specimens, light columns indicate those from the data-release. This table provides a suborder level totals of specimens by taxon-based coverage, proportion of named specimens, BIN totals, species sharing barcodes, and those with >2% divergence. Specimens not assigned to family represent specimens with nomenclature-yet-to-be-confirmed, or specimens without DNA barcodes. The “Not Assigned” category is a workflow-filter that identifies specimens with species names consistent with the checklist, but whose higher taxonomy is not consistent with the checklist.</p><p>Ordinal-level summary for all data-release and library specimens.</p