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

Forest Fragmentation and Selective Logging Have Inconsistent Effects on Multiple Animal-Mediated Ecosystem Processes in a Tropical Forest

Forest fragmentation and selective logging are two main drivers of global environmental change and modify biodiversity and environmental conditions in many tropical forests. The consequences of these changes for the functioning of tropical forest ecosystems have rarely been explored in a comprehensive approach. In a Kenyan rainforest, we studied six animal-mediated ecosystem processes and recorded species richness and community composition of all animal taxa involved in these processes. We used linear models and a formal meta-analysis to test whether forest fragmentation and selective logging affected ecosystem processes and biodiversity and used structural equation models to disentangle direct from biodiversity-related indirect effects of human disturbance on multiple ecosystem processes. Fragmentation increased decomposition and reduced antbird predation, while selective logging consistently increased pollination, seed dispersal and army-ant raiding. Fragmentation modified species richness or community composition of five taxa, whereas selective logging did not affect any component of biodiversity. Changes in the abundance of functionally important species were related to lower predation by antbirds and higher decomposition rates in small forest fragments. The positive effects of selective logging on bee pollination, bird seed dispersal and army-ant raiding were direct, i.e. not related to changes in biodiversity, and were probably due to behavioural changes of these highly mobile animal taxa. We conclude that animal-mediated ecosystem processes respond in distinct ways to different types of human disturbance in Kakamega Forest. Our findings suggest that forest fragmentation affects ecosystem processes indirectly by changes in biodiversity, whereas selective logging influences processes directly by modifying local environmental conditions and resource distributions. The positive to neutral effects of selective logging on ecosystem processes show that the functionality of tropical forests can be maintained in moderately disturbed forest fragments. Conservation concepts for tropical forests should thus include not only remaining pristine forests but also functionally viable forest remnants

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

Morphology and Taxonomy of Isopoda Anthuroidea (Crustacea) from Sulawesi with description of six new species

This is a first inventory of Isopoda Anthuroidea from near-shore marine sites in Sulawesi. The material was collected from reefs, sea-grass beds and mangroves of the Minahasa Peninsula in North Sulawesi. Specimens were washed out from benthos samples collected in shallow water. The new species Hyssura reptans sp. nov., Kupellonura indonesica sp. nov., Kupellonura macaroni sp. nov., Pendanthura bangkaensis sp. nov., Expanathura marcoi sp. nov., and Colanthura gerungi sp. nov. are described. We discovered that in Colanthura the mandible is fused to the cephalothorax, a unique feature among isopods. Expanathura collaris (Kensley, 1979) is described from Bangka Island and several differences between other Indo-Pacific populations are discussed.</p

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

Best systematist practice transferred to molecular data

Fuellen G, Wägele JW, Giegerich R. Best systematist practice transferred to molecular data. ORGANISMS DIVERSITY &amp; EVOLUTION. 2001;1(4):257-272.In the first part of the paper, we give a short description of the "minimum conflict" phylogeny estimation algorithm that analyzes molecular data in a way that resembles traditional best practice in morphological systematics. The algorithm calculates the tree from the root to the leaves, focussing on the detection of shared novel (synapomorphic) character states. Following the encaptic order of monophyla, at each step an outgroup serves to distinguish shared novel from shared old character states. The group of species under consideration is split in such a way that no synapomorphies of subgroups are torn apart, indicating that the split divides the group into two monophyla. In the second part of the paper, we describe the validation of our method with both natural and artificial data. Our method is very fast in theory, enabling the analysis of large quantities of data on a genomic scale. A Perl prototype is available on the World-Wide Web, via http://bibiserv.techfak.unibielefeld.de/m cope/

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