Phylogenetic support values are not necessarily informative: the case of the Serialia hypothesis (a mollusk phylogeny)

Background: Molecular phylogenies are being published increasingly and many biologists rely on the most recent topologies. However, different phylogenetic trees often contain conflicting results and contradict significant background data. Not knowing how reliable traditional knowledge is, a crucial question concerns the quality of newly produced molecular data. The information content of DNA alignments is rarely discussed, as quality statements are mostly restricted to the statistical support of clades. Here we present a case study of a recently published mollusk phylogeny that contains surprising groupings, based on five genes and 108 species, and we apply new or rarely used tools for the analysis of the information content of alignments and for the filtering of noise (masking of random-like alignment regions, split decomposition, phylogenetic networks, quartet mapping). Results: The data are very fragmentary and contain contaminations. We show that that signal-like patterns in the data set are conflicting and partly not distinct and that the reported strong support for a "rather surprising result" (monoplacophorans and chitons form a monophylum Serialia) does not exist at the level of primary homologies. Split-decomposition, quartet mapping and neighbornet analyses reveal conflicting nucleotide patterns and lack of distinct phylogenetic signal for the deeper phylogeny of mollusks. Conclusion: Even though currently a majority of molecular phylogenies are being justified with reference to the 'statistical' support of clades in tree topologies, this confidence seems to be unfounded. Contradictions between phylogenies based on different analyses are already a strong indication of unnoticed pitfalls. The use of tree-independent tools for exploratory analyses of data quality are highly recommended. Concerning the new mollusk phylogeny more convincing evidence is needed

Molecular species identification of Central European ground beetles (Coleoptera: Carabidae) using nuclear rDNA expansion segments and DNA barcodes

<p>Abstract</p> <p>Background</p> <p>The identification of vast numbers of unknown organisms using DNA sequences becomes more and more important in ecological and biodiversity studies. In this context, a fragment of the mitochondrial cytochrome <it>c </it>oxidase I (COI) gene has been proposed as standard DNA barcoding marker for the identification of organisms. Limitations of the COI barcoding approach can arise from its single-locus identification system, the effect of introgression events, incomplete lineage sorting, numts, heteroplasmy and maternal inheritance of intracellular endosymbionts. Consequently, the analysis of a supplementary nuclear marker system could be advantageous.</p> <p>Results</p> <p>We tested the effectiveness of the COI barcoding region and of three nuclear ribosomal expansion segments in discriminating ground beetles of Central Europe, a diverse and well-studied invertebrate taxon. As nuclear markers we determined the 18S rDNA: V4, 18S rDNA: V7 and 28S rDNA: D3 expansion segments for 344 specimens of 75 species. Seventy-three species (97%) of the analysed species could be accurately identified using COI, while the combined approach of all three nuclear markers provided resolution among 71 (95%) of the studied Carabidae.</p> <p>Conclusion</p> <p>Our results confirm that the analysed nuclear ribosomal expansion segments in combination constitute a valuable and efficient supplement for classical DNA barcoding to avoid potential pitfalls when only mitochondrial data are being used. We also demonstrate the high potential of COI barcodes for the identification of even closely related carabid species.</p

Effective biodiversity monitoring needs a culture of integration

Despite conservation commitments, most countries still lack large-scale biodiversity monitoring programs to track progress toward agreed targets. Monitoring program design is frequently approached from a top-down, data-centric perspective that ignores the socio-cultural context of data collection. A rich landscape of people and organizations, with a diversity of motivations and expertise, independently engages in biodiversity monitoring. This diversity often leads to complementarity in activities across places, time periods, and taxa. In this Perspective, we propose a framework for aligning different efforts to realize large-scale biodiversity monitoring through a networked design of stakeholders, data, and biodiversity schemes. We emphasize the value of integrating independent biodiversity observations in conjunction with a backbone of structured core monitoring, thereby fostering broad ownership and resilience due to a strong partnership of science, society, policy, and individuals. Furthermore, we identify stakeholder-specific barriers and incentives to foster joint collaboration toward effective large-scale biodiversity monitoring

Redescription of Ischyromene lacazei Racovitza, 1908 (Isopoda: Sphaeromatidae) from the Mediterranean Coast of southern France

AbstractThe sphaeromatid species Ischyromene lacazei Racoviza, 1908 is rediagnosed, and new data on its morphology and distribution are given, based on new material from the type locality, the intertidal zones at Banyuls-sur-mer, southern France. Groups of specimens were found in empty shells of Balanus perforatus and Chthamalus stellatus (Crustacea: Balanomorpha); the formation of harems was not observed. The full redescription, further data and a discussion are provided in an accompanying Organisms Diversity and Evolution Electronic Supplement.See also Electronic Supplement at: http://www.senckenberg.de/odes/05-08.ht

Minimum conflict: a divide-and-conquer approach to phylogeny estimation

Fuellen G, Wägele JW, Giegerich R. Minimum conflict: a divide-and-conquer approach to phylogeny estimation. BIOINFORMATICS. 2001;17(12):1168-1178.Motivation: Fast and reliable phylogeny estimation is rapidly gaining importance as more and more genomic sequence information is becoming available, and the study of the evolution of genes and genomes accelerates our understanding in biology and medicine alike. Branch attraction phenomena due to unequal amounts of evolutionary change in different parts of the phylogeny are one major problem for current methods, placing the species that evolved fast in one part of the phylogenetic tree, and the species that evolved slowly in the other. Results: We describe a way to avoid the artifactual attraction of species that evolved slowly, by detecting shared old character states using a calibrated comparison with an outgroup. The corresponding focus on shared novel character states yields a fast and transparent phylogeny estimation algorithm, by application of the divide-and-conquer principle, and heuristic search: shared novelties give evidence of the exclusive common heritage (monophyly) of a subset of the species. They indicate conflict in a split of all species considered, if the split tears them apart. Only the split at the root of the phylogenetic tree cannot have such conflict. Therefore, we can work top-down, from the root to the leaves, by heuristically searching for a minimum-conflict split, and tackling the resulting two subsets in the same way. The algorithm, called 'minimum conflict phylogeny estimation' (MCOPE), has been validated successfully using both natural and artificial data. In particular, we reanalyze published trees, yielding more plausible phylogenies, and we analyze small 'undisputed' trees on the basis of alignments considering structural homology

Molecular phylogenetics: In spite of impressive advances, there remains a need for research on biological and methodical questions:

Die Erforschung der Stammesgeschichte der Organismen hat mit der Entwicklung der Molekulargenetik große Fortschritte gemacht. Wesentlich waren die Entwicklung der Sequenziertechniken für genomische DNA und effiziente heuristische Verfahren für die Datenanalyse. Die traditionelle Klassifikation der Tiere konnte mehrfach revidiert werden, es bleiben jedoch ungeklärte Fragen. Ergebnisse widersprechen sich oft, besonders wenn Ereignisse aus der Frühzeit der Evolution der Vielzeller rekonstruiert werden. In anderen Fällen lassen sich aus DNA-Daten errechnete Stammbäume nicht mit anatomischen Daten in Einklang bringen. Systematische Fehler der Algorithmen sowie die Verfügbarkeit von einem phylogenetischen Signal in den Daten müssen weiter erforscht werden.With the recent development of molecular genetics, research on the phylogeny of organisms has made great progress. In particular, the development of new DNA sequencing techniques and efficient heuristic methods for data analysis have been important. Repeatedly, the traditional classification of animals could be revised; however, there remain unanswered questions. The results are often contradictory, especially when events from the early days of the evolution of multicellular organisms are reconstructed. In other cases, phylogenetic trees obtained from DNA data do not match the anatomical data. Systematic errors of algorithms as well as the availability of a phylogenetic signal in the data need further investigation

Multiple colonization of the deep sea by the Asellota (Crustacea: Peracarida: Isopoda)

Despite its extreme environmental conditions the deep sea harbors a unique and species-rich fauna of mostly unknown age and phylogeny. Asellote isopods have undergone their most impressive radiation in the deep sea, being found at all depths down to the deepest trench. Here we present the first molecular evidence for the phylogenetic origin of this remarkable array of deep-sea crustaceans, based on 30 new DNA-sequences of the complete 18s rRNA gene of specimens collected at depths down to 4543&#xa0;m in the South Atlantic and South Polar Ocean. The results show that most of these isopod lineages belong to a single ancient clade. They evolved in situ in large oceanic depths and survived several climatic changes, but the lack of fossils and of a suitable molecular clock model prevents a precise dating of this radiation. The monophyly of typical deep-sea families, for example the Haploniscidae, Ischnomesidae or Munnopsidae, is well supported by different methods of analysis, while the monophyly of the Janiridae is rejected

Acropimpla leucostoma Cameron 1907

Acropimpla leucostoma (Cameron, 1907) (Fig. 2) Charitopimpla leucostoma Cameron, 1907. Tijdschr. Ent., 50: 97. Holotype: Ƥ, India: Sikkim (BMNH). Acropimpla leucostoma: Townes & Townes (1960). Diagnosis. Face yellow, usually with central black mark, yellow extending on inner orbits beyond antennal sockets; propodeum without or with very short stubs of median longitudinal carinae; clypeus, scutellum and metascutellum yellow; tergite 5 entirely black; ovipositor 2.50 x as long as hind tibia (Gupta & Tikar 1976). Distribution. Gupta and Tikar (1976) have previously recorded A. leucostoma from Vietnam on the basis of five female specimens collected from North Vietnam by Micholitz in October 1913. This species has been recorded from China, India, Sri Lanka, Myanmar, Laos, Indonesia, and Japan (Yu et al. 2005) (Fig. 7). Material examined. Ninh Binh, Cuc Phuong NP: 13 (RMNH), 225 m a.s.l., 01.XI– 20.XII. 2000, Malaise trap, leg. Mai P. Q.; Thua Thien-Hue, Phong Dien NP: 3 Ƥ (RMNH) 50–210 m a.s.l., 23.III–06.IV. 2001, Malaise trap, leg. C. V. Achterberg & R. de Vries; 1 Ƥ (RMNH), 50–100 m a.s.l., 24.III. 2001, at light, leg C. V. Achterberg; 1 Ƥ (RMNH), 50–100 m a.s.l., 25.III. 2001, hand net, leg. C. v. Achterberg; Dong Nai, Cat Tien NP: 1 Ƥ (RMNH), 100 m a.s.l., 01–09.X. 2005; 2 Ƥ (RMNH), 100 m a.s.l., 13–20.V. 2007, Malaise trap, leg. C. V. Achterberg & R. de Vries; Kon Tum, Chu Mom Ray NP: 1 Ƥ (RMNH), 700–900 m a. s. l., 26.IX–05.X. 2006, Malaise trap, leg. Mai P. Q. & Nguyen T. M.; Dak Lak, Chu Yang Sin NP: 2 Ƥ (RMNH), 800–940 m a.s.l., 02– 10.VI. 2007, Malaise trap, leg. C. V. Achterberg & R. de Vries; Phu Tho, Xuan Son NP: 1 Ƥ (IEBR), 200 m a.s.l., 07.XII. 2003, hand net, leg. Truong X. L., Ich. 087; 1 Ƥ (IEBR), 300 m a.s.l., 10.V. 2005, hand net, leg. Pham T. N., Ich. 089; Lai Chau, Hi Ngay, Muong Lay: 1 Ƥ (IEBR), 10.X. 2004, hand net, leg. Khuat D. L., Ich. 892; Ha Tinh, Huong Son, Son Kim: 1 Ƥ (IEBR), 07.V. 2004, hand net, leg. Truong X. L., Ich. 936; Vinh Phuc, Tam Dao NP: 1 Ƥ (ZFMK), 900 m a.s.l., 09.VIII. 2005, hand net, leg. Pham T. N., ZFMK HYM 2011 / 2.Published as part of Pham, Nhi Thi, Broad, Gavin R. & Wägele, Wolfgang J., 2011, The genus Acropimpla Townes (Hymenoptera: Ichneumonidae: Pimplinae) in Vietnam, with descriptions of three new species, pp. 1-12 in Zootaxa 2921 on page 4, DOI: 10.5281/zenodo.20054

FIGURE 3 in First record of the genus Zaglyptus Förster (Hymenoptera: Ichneumonidae: Pimplinae) from Vietnam, with description of one new species

FIGURE 3. Zaglyptus nigrolineatus: a. dorsal view; b. metapleuron; c. wings; d. ovipositor; e. face; f. dorsal view of scutellum and propodeum.Published as part of Pham, Nhi Thi, Broad, Gavin R. & Wägele, Wolfgang J., 2013, First record of the genus Zaglyptus Förster (Hymenoptera: Ichneumonidae: Pimplinae) from Vietnam, with description of one new species, pp. 483-492 in Zootaxa 3702 (5) on page 489, DOI: 10.11646/zootaxa.3702.5.7, http://zenodo.org/record/21753