Vladimir I. Gusarov

New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems

Metabarcoding approaches use total and typically degraded DNA from environmental samples to analyse biotic assemblages and can potentially be carried out for any kinds of organisms in an ecosystem. These analyses rely on specific markers, here called metabarcodes, which should be optimized for taxonomic resolution, minimal bias in amplification of the target organism group and short sequence length. Using bioinformatic tools, we developed metabarcodes for several groups of organisms: fungi, bryophytes, enchytraeids, beetles and birds. The ability of these metabarcodes to amplify the target groups was systematically evaluated by (i) in silico PCRs using all standard sequences in the EMBL public database as templates, (ii) in vitro PCRs of DNA extracts from surface soil samples from a site in Varanger, northern Norway and (iii) in vitro PCRs of DNA extracts from permanently frozen sediment samples of late‐Pleistocene age (∼16u2003000–50u2003000u2003years bp) from two Siberian sites, Duvanny Yar and Main River. Comparison of the results from the in silico PCR with those obtained in vitro showed that the in silico approach offered a reliable estimate of the suitability of a marker. All target groups were detected in the environmental DNA, but we found large variation in the level of detection among the groups and between modern and ancient samples. Success rates for the Pleistocene samples were highest for fungal DNA, whereas bryophyte, beetle and bird sequences could also be retrieved, but to a much lesser degree. The metabarcoding approach has considerable potential for biodiversity screening of modern samples and also as a palaeoecological tool.

Molecular phylogeny of the Athetini–Lomechusini–Ecitocharini clade of aleocharine rove beetles (Insecta)

Elven, E., Bachmann, L. & Gusarov V. I. (2012) Molecular phylogeny of the Athetini–Lomechusini–Ecitocharini clade of aleocharine rove beetles (Insecta). —Zoologica Scripta, 41, 617–636.

Phylogeny of the tribe Athetini (Coleoptera: Staphylinidae) inferred from mitochondrial and nuclear sequence data.

The Athetini are the largest and taxonomically most challenging tribe in the subfamily Aleocharinae. We present the first molecular phylogeny of Athetini. Nucleotide sequences were obtained from three genome regions for 58 athetine and 23 non-athetine species. The sequenced genes are cytochrome oxidase subunits 1 and 2 (2030bp), tRNA-Leucine 1 and 2 (154bp), 16S (628bp, partial sequence), NADH dehydrogenase subunit 1 (54bp, partial sequence), and the nuclear 18S gene (999bp, partial sequence). The Athetini were recovered as paraphyletic with respect to Lomechusini and Ecitocharini. Lomechusini were recovered as polyphyletic, with Myrmedonota grouping separately from Pella and Drusilla. The basal topology of Athetini remained largely unresolved but many apical clades were well supported, e.g. Geostiba+Earota, Pontomalota+Tarphiota, Mocyta+Atheta (Oxypodera)+Atheta (Mycetota), Liogluta+Atheta (Thinobaena)+Atheta (Oreostiba), and Lyprocorrhe+Atheta (Datomicra). The monophyly of Atheta was refuted, as several species of Atheta formed well supported clades with members of other genera. Additionally, the following groups were rejected: Strigotina (=Acrotonina) and Dimetrotina sensu Newton et al. (2000), Acrotona sensu Brundin (1952), Liogluta series (Yosii and Sawada, 1976), Atheta (Dimetrota) and Atheta (Alaobia) sensu Smetana (2004). New tribal placements are proposed for four genera: Halobrecta is removed from Athetini and provisionally placed in Oxypodini; Thendelecrotona is removed from Athetini and treated as Aleocharinae incertae sedis; Meronera and Thamiaraea are included in the Athetini.

Finding Evolutionary Processes Hidden in Cryptic Species

Cryptic species could represent a substantial fraction of biodiversity. However, inconsistent definitions and taxonomic treatment of cryptic species prevent informed estimates of their contribution to biodiversity and impede our understanding of their evolutionary and ecological significance. We propose a conceptual framework that recognizes cryptic species based on their low levels of phenotypic (morphological) disparity relative to their degree of genetic differentiation and divergence times as compared with non-cryptic species. We discuss how application of a more rigorous definition of cryptic species in taxonomic practice will lead to more accurate estimates of their prevalence in nature, better understanding of their distribution patterns on the tree of life, and increased abilities to resolve the processes underlying their evolution.

Molecular phylogeny of the beetle tribe Oxypodini (Coleoptera: Staphylinidae: Aleocharinae)

This is the first study to comprehensively address the phylogeny of the tribe Oxypodini Thomson and its phylogenetic relationships to other tribes within the staphylinid subfamily Aleocharinae. Using the hitherto largest molecular dataset of Aleocharinae comprising of 4599u2009bp for representatives of 22 tribes, the Oxypodini are recovered as non‐monophyletic. Members of the tribe belong to three distantly related lineages within the Aleocharinae: (i) the Amarochara group as sister clade to the tribe Aleocharini, (ii) the subtribe Tachyusina within a clade that also includes the tribes Athetini and Hygronomini, (iii) all other Oxypodini in a clade that also includes the tribes Placusini, Hoplandriini and Liparocephalini. Based on the inferred phylogeny, five subtribes of the Oxypodini are recognized: Dinardina Mulsant & Rey, Meoticina Seevers, Microglottina Fenyes, Oxypodina Thomson and Phloeoporina Thomson. The following changes in the classification of the Aleocharinae are proposed: (i) Amarochara Thomson is removed from the Oxypodini and placed in the tribe Aleocharini; (ii) the subtribe Taxicerina Lohse of the Athetini is reinstated as tribe Taxicerini to include Discerota Mulsant & Rey, Halobrecta Thomson (both removed from the Oxypodini) and Taxicera Mulsant & Rey; (iii) the subtribe Tachyusina Thomson is excluded from the Oxypodini and provisionally treated as tribe Tachyusini; (iv) the oxypodine subtribe name Blepharhymenina Klimaszewski & Peck is placed in synonymy with the subtribe name Dinardina Mulsant & Rey.

Cryptic Species – More Than Terminological Chaos: A Reply to Heethoff

Recently we discussed problems and challenges associated with inconsistent definitions and methods used to identify cryptic species, and how these hamper studies of their evolutionary significance. We proposed a conceptual framework that is focussed on evolutionary processes and advocated for a shift from patternto process-driven research concerning cryptic species, in order to circumvent these issues [1]. In his response, Heethoff [2] argued that cryptic species are merely a reflection of the limitations of applied taxonomy. He stated that cryptic species ‘represent nothing more than an incompatibility of species “concepts” in applied taxonomy’. As such, he rejected our proposed framework as an approach that ‘prioritizes the “evolutionary truth” of genetic over morphological species concepts’. In our opinion Heethoff’s conclusions are based on his misconceptions about the proposed framework.

Review of Anatheta Casey (Staphylinidae: Aleocharinae: Athetini), with Notes on Synonymy of Canastota Casey and Silusida Casey

Abstract Anatheta Casey 1910 (type species Sableta (Anatheta) planulicollis Casey 1910) is confirmed to be a valid genus separate from Sableta Casey 1910 (type species Sableta (s. str.) infulata Casey 1910). Two valid species are recognized in Anatheta: A. planulicollis (Casey 1910) (transferred from Sableta), and A. surrufa (Casey 1911) (transferred from Metaxya Mulsant et Rey 1873). Metaxya erudita Casey 1911 is recognized as a junior synonym of Anatheta planulicollis (Casey 1910). Sableta (Anatheta) curata Casey 1910 is not a member of Anatheta and is close to Acrotona Thomson 1859. Canastota Casey 1910 (type species Sableta (Canastota) canadensis Casey 1910), believed by Seevers (1978) to be very similar to Anatheta, is placed in synonymy with Silusida Casey 1906; Sableta (Canastota) canadensis Casey 1910 is placed in synonymy with Silusida marginella (Casey 1906). Lectotypes are designated for Metaxya erudita Casey 1911, Metaxya surrufa Casey 1911, Bolitochara marginella Casey 1893 and Sableta canadensis Casey 1910. Redescriptions and illustrations of distinctive structural features are provided for distinguishing Anatheta from other aleocharine genera and for recognizing the two valid species in the genus.

The importance of tracking introduced species: nine synonyms of Atheta (Dimetrotina) pasadenae Bernhauer, 1906 (Coleoptera, Staphylinidae, Aleocharinae).

Five species names are placed in synonymy with Atheta (Dimetrotina) pasadenae Bernhauer, 1906: Dimetrota vaniuscula Casey, 1911; Atheta pseudocoriaria Bernhauer, 1943 (non Cameron, 1939); A. zealandica Cameron, 1945; A. aucklandensis Pace, 1987 and A. pseudoinsulana Klimaszewski in Klimaszewski et al., 2002. Four names are confirmed to be junior synonyms of A. pasadenae: Atheta pseudolaticollis Erber & Hinterseher, 1992 (non Bernhauer, 1936, non Cameron, 1944); A. immucronata Pace, 1999; A. gulosa Tronquet, 2000 and A. atlantidum Smetana, 2004. Lectotypes are designated for A. pseudocoriaria Bernhauer, 1943; A. zealandica Cameron, 1945 (both designations are to be attributed to Richard A.B. Leschen); and A. pasadenae Bernhauer, 1906. Relationships among the subgenera Xenota Mulsant & Rey, 1874, Dimetrotina Casey, 1911, Oxypodera Bernhauer, 1915 and Mycetota Ádám, 1987 of the genus Atheta Thomson, 1858 are discussed. The name Mycetota Ádám, 1987 is placed in synonymy with Dimetrotina Casey, 1911 (treated as valid subgenus of Atheta), resulting in three new subgeneric assignments: Atheta (Dimetrotina) laticollis (Stephens, 1832), A. (D.) mucronata (Kraatz, 1859), and A. (D.) pasadenae Bernhauer, 1906. Atheta pasadenae is a species with almost cosmopolitan distribution, most likely originating from Africa and (unintentionally) introduced to Europe, North and South America, New Zealand, the Macaronesian islands, Tristan da Cunha archipelago, Juan Fernandez archipelago and Hawaii.