The evolution of antennal courtship in diplazontine parasitoid wasps (Hymenoptera, Ichneumonidae, Diplazontinae)

Background As predicted by theory, traits associated with reproduction often evolve at a comparatively high speed. This is especially the case for courtship behaviour which plays a central role in reproductive isolation. On the other hand, courtship behavioural traits often involve morphological and behavioural adaptations in both sexes; this suggests that their evolution might be under severe constraints, for instance irreversibility of character loss. Here, we use a recently proposed method to retrieve data on a peculiar courtship behavioural trait, i.e. antennal coiling, for 56 species of diplazontine parasitoid wasps. On the basis of a well-resolved phylogeny, we reconstruct the evolutionary history of antennal coiling and associated morphological modifications to study the mode of evolution of this complex character system. Results Our study reveals a large variation in shape, location and ultra-structure of male-specific modifications on the antennae. As for antennal coiling, we find either single-coiling, double-coiling or the absence of coiling; each state is present in multiple genera. Using a model comparison approach, we show that the possession of antennal modifications is highly correlated with antennal coiling behaviour. Ancestral state reconstruction shows that both antennal modifications and antennal coiling are highly congruent with the molecular phylogeny, implying low levels of homoplasy and a comparatively low speed of evolution. Antennal coiling is lost on two independent occasions, and never reacquired. A zero rate of regaining antennal coiling is supported by maximum parsimony, maximum likelihood and Bayesian approaches. Conclusions Our study provides the first comparative evidence for a tight correlation between male-specific antennal modifications and the use of the antennae during courtship. Antennal coiling in Diplazontinae evolved at a comparatively low rate, and was never reacquired in any of the studied taxa. This suggests that the loss of antennal coiling is irreversible on the timescale examined here, and therefore that evolutionary constraints have greatly influenced the evolution of antennal courtship in this group of parasitoid wasps. Further studies are needed to ascertain whether the loss of antennal coiling is irreversible on larger timescales, and whether evolutionary constraints have influenced courtship behavioural traits in a similar way in other groups.

Biomechanics on the Half Shell: Functional Performance Influences Patterns of Morphological Variation in the Emydid Turtle carapace

This study uses the carapace of emydid turtles to address hypothesized differences between terrestrial and aquatic species. Geometric morphometrics are used to quantify shell shape, and performance is estimated for two shell functions: shell strength and hydrodynamics. Aquatic turtle shells differ in shape from terrestrial turtle shells and are characterized by lower frontal areas and presumably lower drag. Terrestrial turtle shells are stronger than those of aquatic turtles; many-to-one mapping of morphology to function does not entirely mitigate a functional trade-off between mechanical strength and hydrodynamic performance. Furthermore, areas of morphospace characterized by exceptionally poor performance in either of the functions are not occupied by any emydid species. Though aquatic and terrestrial species show no significant differences in the rate of morphological evolution, aquatic species show a higher lineage density, indicative of a greater amount of convergence in their evolutionary history. The techniques employed in this study, including the modeling of theoretical shapes to assess performance in unoccupied areas of morphospace, suggest a framework for future studies of morphological variation.

Cell Types as Natural Kinds

Talk of different types of cells is commonplace in the biological sciences. We know a great deal, for example, about human muscle cells by studying the same type of cells in mice. Information about cell type is apparently largely projectible across species boundaries. But what defines cell type? Do cells come pre-packaged into different natural kinds? Philosophical attention to these questions has been extremely limited [see e.g., Wilson (Species: New Interdisciplinary Essays, pp 187-207, 1999; Genes and the Agents of Life, 2005; Wilson et al. Philos Top 35(1/2): 189-215, 2007)]. On the face of it, the problems we face in individuating cellular kinds resemble those biologists and philosophers of biology encountered in thinking about species: there are apparently many different (and interconnected) bases on which we might legitimately classify cells. We could, for example, focus on their developmental history (a sort of analogue to a species' evolutionary history); or we might divide on the basis of certain structural features, functional role, location within larger systems, and so on. In this paper, I sketch an approach to cellular kinds inspired by Boyd's Homeostatic Property Cluster Theory, applying some lessons from this application back to general questions about the nature of natural kinds.

Spatial and temporal variation in population genetic structure of wild Nile tilapia (Oreochromis niloticus) across Africa

Background: Reconstructing the evolutionary history of a species is challenging. It often depends not only on the past biogeographic and climatic events but also the contemporary and ecological factors, such as current connectivity and habitat heterogeneity. In fact, these factors might interact with each other and shape the current species distribution. However, to what extent the current population genetic structure reflects the past and the contemporary factors is largely unknown. Here we investigated spatio-temporal genetic structures of Nile tilapia (Oreochromis niloticus) populations, across their natural distribution in Africa. While its large biogeographic distribution can cause genetic differentiation at the paleo-biogeographic scales, its restricted dispersal capacity might induce a strong genetic structure at micro-geographic scales. Results: Using nine microsatellite loci and 350 samples from ten natural populations, we found the highest genetic differentiation among the three ichthyofaunal provinces and regions (Ethiopian, Nilotic and Sudano-Sahelian) (R(ST) = 0.38 - 0.69). This result suggests the predominant effect of paleo-geographic events at macro-geographic scale. In addition, intermediate divergences were found between rivers and lakes within the regions, presumably reflecting relatively recent interruptions of gene flow between hydrographic basins (R(ST) = 0.24 - 0.32). The lowest differentiations were observed among connected populations within a basin (R(ST) = 0.015 in the Volta basin). Comparison of temporal sample series revealed subtle changes in the gene pools in a few generations (F = 0 - 0.053). The estimated effective population sizes were 23 - 143 and the estimated migration rate was moderate (m similar to 0.094 - 0.097) in the Volta populations. Conclusions: This study revealed clear hierarchical patterns of the population genetic structuring of O. niloticus in Africa. The effects of paleo-geographic and climatic events were predominant at macro-geographic scale, and the significant effect of geographic connectivity was detected at micro-geographic scale. The estimated effective population size, the moderate level of dispersal and the rapid temporal change in genetic composition might reflect a potential effect of life history strategy on population dynamics. This hypothesis deserves further investigation. The dynamic pattern revealed at micro-geographic and temporal scales appears important from a genetic resource management as well as from a biodiversity conservation point of view.

Sediment core fossils in ancient Lake Ohrid: testing for faunal change since the Last Interglacial

Ancient Lake Ohrid is probably of early Pleistocene or Pliocene origin and amongst the few lakes in the world harbouring an outstanding degree of endemic biodiversity. Although there is a long history of evolutionary research in Lake Ohrid, particularly on molluscs, a mollusc fossil record has been missing up to date. For the first time, gastropod and bivalve fossils are reported from the basal, calcareous part of a 2.6 m long sediment succession (core Co1200) from the north-eastern part of Lake Ohrid. Electron spin resonance (ESR) dating of mollusc shells from the same stratigraphic level yielded an age of 130 ± 28 ka. Lithofacies III sediments, i.e. a stratigraphic subdivision comprising the basal succession of core Co1200 between 181.5–263 cm, appeared solid, greyish-white, and consisted almost entirely of silt-sized endogenic calcite (CaCO3>70%) and intact and broken mollusc shells. Here we compare the faunal composition of the thanatocoenosis with recent mollusc associations in Lake Ohrid. A total of 13 mollusc species (9 gastropod and 4 bivalve species) could be identified within Lithofacies III sediments. The value of sediment core fossils for reconstructing palaeoenvironmental settings was evaluated and the agreement between sediment and palaeontological proxies was tested. The study also aims at investigating major faunal changes since the Last Interglacial and searching for signs of extinction events. The combined findings of the ecological study and the sediment characteristics suggest deposition in a shallow water environment during the Last Interglacial. The fossil fauna exclusively included species also found in the present fauna, i.e. no extinction events are evident for this site since the Last Interglacial. The thanatocoenosis showed the highest similarity with recent Intermediate Layer (5–25 m water depth) mollusc assemblages. The demonstrated existence of a mollusc fossil record in Lake Ohrid sediment cores also has great significance for future deep drilling projects. It can be hoped that a more far reaching mollusc fossil record will then be obtained, enabling insight into the early evolutionary history of Lake Ohrid.

The origin of the 'Mycoplasma mycoides cluster' coincides with domestication of ruminants.

The 'Mycoplasma mycoides cluster' comprises the ruminant pathogens Mycoplasma mycoides subsp. mycoides the causative agent of contagious bovine pleuropneumonia (CBPP), Mycoplasma capricolum subsp. capripneumoniae the agent of contagious caprine pleuropneumonia (CCPP), Mycoplasma capricolum subsp. capricolum, Mycoplasma leachii and Mycoplasma mycoides subsp. capri. CBPP and CCPP are major livestock diseases and impact the agricultural sector especially in developing countries through reduced food-supply and international trade restrictions. In addition, these diseases are a threat to disease-free countries. We used a multilocus sequence typing (MLST) approach to gain insights into the demographic history of and phylogenetic relationships among the members of the 'M. mycoides cluster'. We collected partial sequences from seven housekeeping genes representing a total of 3,816 base pairs from 118 strains within this cluster, and five strains isolated from wild Caprinae. Strikingly, the origin of the 'M. mycoides cluster' dates to about 10,000 years ago, suggesting that the establishment and spread of the cluster coincided with livestock domestication. In addition, we show that hybridization and recombination may be important factors in the evolutionary history of the cluster.

Precambrian to Paleozoic zircon record in the Siviez-Mischabel basement (western Swiss Alps)

U–Pb zircon analyses from three meta-igneous and two metasedimentary rocks from the Siviez-Mischabel nappe in the western Swiss Alps are presented, and are used to derive an evolutionary history spanning from Paleoarchean crustal growth to Permian magmatism. The oldest components are preserved in zircons from metasedimentary albitic schists. The oldest zircon core in these schists is 3.4 Ga old. Detrital zircons reveal episodes of crustal growth in the Neoarchean (2.7–2.5 Ga), Paleoproterozoic (2.2–1.9 Ma) and Neoproterozoic (800–550 Ma, Pan-African event). The maximum age of deposition for the metasedimentary rocks is given by the youngest detrital zircons within both metasedimentary samples dated at ~490 Ma (Cambrian-Ordovician boundary). This is in the age range of two granitoid samples dated at 505 ± 4 and 482 ± 7 Ma, and indicates sedimentation and magmatism in an extensional setting preceding an Ordovician orogeny. The third felsic meta-igneous rock gives a Permian age of intrusion, and is part of a long-lasting Variscan to post-Variscan magmatic activity. The zircons record only minor disturbance of the U–Pb system during the Alpine orogeny.

What can a unicellular parasite tell us about mitochondrial biogenesis?

Most of what we know about mitochondrial biogenesis stems from work in yeast and mammals, which are quite closely related. To understand the conserved features of mitochondria and the evolutionary forces that shaped it, it is important to study a more diverse group of eukaryotes. The parasitic protozoan Trypanosoma brucei and its relatives are excellent systems to do so, since they appear to have diverged from other eukaryotes very early in evolution. This is reflected in a number of unique and extreme features in their mitochondrial biology, including a single continuous mitochondrion that contains a one unit mitochondrial genome that is physically connected across the two membranes with the basal body of the flagellum. Moreover, many mitochondrial transcripts have to be extensively edited in order to become functional mRNAs and organellar translation requires extensive import of cytosolic tRNAs. In my talk I will focus on the discovery and characterization of the elusive mitochondrial protein import system of the mitochondrial outer membrane of trypanosomes. In addition I will present data on a central outer membrane component of the mitochondrial genome inheritance system of T. brucei and compare it to the better characterized system of yeast. - I hope that I can convince you in my talk, that a better understanding of the mitochondrial biology in T. brucei will provide insights into both fundamentally conserved and fundamentally diverged aspects of mitochondrial biogenesis and thus of the evolutionary history of mitochondria in general.

Mitochondrial protein import receptors in Kinetoplastids reveal convergent evolution over large phylogenetic distances

Mitochondrial protein import is essential for all eukaryotes and mediated by hetero-oligomeric protein translocases thought to be conserved within all eukaryotes. We have identified and analysed the function and architecture of the non-conventional outer membrane (OM) protein translocase in the early diverging eukaryote Trypanosoma brucei. It consists of six subunits that show no obvious homology to translocase components of other species. Two subunits are import receptors that have a unique topology and unique protein domains and thus evolved independently of the prototype receptors ​Tom20 and ​Tom70. Our study suggests that protein import receptors were recruited to the core of the OM translocase after the divergence of the major eukaryotic supergroups. Moreover, it links the evolutionary history of mitochondrial protein import receptors to the origin of the eukaryotic supergroups.

Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers

Tropical rainforest hunter-gatherer populations worldwide share the pygmy phenotype, or small human body size. The evolutionary history of this phenotype is largely unknown. Here we studied DNA from the Batwa, a rainforest hunter-gatherer population from east central Africa, to identify regions of the Batwa genome that underlie the pygmy phenotype. We then performed population genomic analyses to study the evolution of these regions, including comparisons with the Baka, a west central African rainforest hunter-gatherer population. We conclude that the pygmy phenotype likely arose due to positive natural selection and that it arose possibly multiple times within Africa. These results support longstanding anthropological hypotheses that small body size confers an important selective advantage for human rainforest hunter-gatherers.

Synergies and trade-offs between insect and pathogen resistance in maize leaves and roots

Determining links between plant defence strategies is important to understand plant evolution and to optimize crop breeding strategies. Although several examples of synergies and trade-offs between defence traits are known for plants that are under attack by multiple organisms, few studies have attempted to measure correlations of defensive strategies using specific single attackers. Such links are hard to detect in natural populations because they are inherently confounded by the evolutionary history of different ecotypes. We therefore used a range of 20 maize inbred lines with considerable differences in resistance traits to determine if correlations exist between leaf and root resistance against pathogens and insects. Aboveground resistance against insects was positively correlated with the plant's capacity to produce volatiles in response to insect attack. Resistance to herbivores and resistance to a pathogen, on the other hand, were negatively correlated. Our results also give first insights into the intraspecific variability of root volatiles release in maize and its positive correlation with leaf volatile production. We show that the breeding history of the different genotypes (dent versus flint) has influenced several defensive parameters. Taken together, our study demonstrates the importance of genetically determined synergies and trade-offs for plant resistance against insects and pathogens.

Evidence for an Ancestral Association of Human Coronavirus 229E with Bats.

UNLABELLED We previously showed that close relatives of human coronavirus 229E (HCoV-229E) exist in African bats. The small sample and limited genomic characterizations have prevented further analyses so far. Here, we tested 2,087 fecal specimens from 11 bat species sampled in Ghana for HCoV-229E-related viruses by reverse transcription-PCR (RT-PCR). Only hipposiderid bats tested positive. To compare the genetic diversity of bat viruses and HCoV-229E, we tested historical isolates and diagnostic specimens sampled globally over 10 years. Bat viruses were 5- and 6-fold more diversified than HCoV-229E in the RNA-dependent RNA polymerase (RdRp) and spike genes. In phylogenetic analyses, HCoV-229E strains were monophyletic and not intermixed with animal viruses. Bat viruses formed three large clades in close and more distant sister relationships. A recently described 229E-related alpaca virus occupied an intermediate phylogenetic position between bat and human viruses. According to taxonomic criteria, human, alpaca, and bat viruses form a single CoV species showing evidence for multiple recombination events. HCoV-229E and the alpaca virus showed a major deletion in the spike S1 region compared to all bat viruses. Analyses of four full genomes from 229E-related bat CoVs revealed an eighth open reading frame (ORF8) located at the genomic 3' end. ORF8 also existed in the 229E-related alpaca virus. Reanalysis of HCoV-229E sequences showed a conserved transcription regulatory sequence preceding remnants of this ORF, suggesting its loss after acquisition of a 229E-related CoV by humans. These data suggested an evolutionary origin of 229E-related CoVs in hipposiderid bats, hypothetically with camelids as intermediate hosts preceding the establishment of HCoV-229E. IMPORTANCE The ancestral origins of major human coronaviruses (HCoVs) likely involve bat hosts. Here, we provide conclusive genetic evidence for an evolutionary origin of the common cold virus HCoV-229E in hipposiderid bats by analyzing a large sample of African bats and characterizing several bat viruses on a full-genome level. Our evolutionary analyses show that animal and human viruses are genetically closely related, can exchange genetic material, and form a single viral species. We show that the putative host switches leading to the formation of HCoV-229E were accompanied by major genomic changes, including deletions in the viral spike glycoprotein gene and loss of an open reading frame. We reanalyze a previously described genetically related alpaca virus and discuss the role of camelids as potential intermediate hosts between bat and human viruses. The evolutionary history of HCoV-229E likely shares important characteristics with that of the recently emerged highly pathogenic Middle East respiratory syndrome (MERS) coronavirus.

Taxonomy, phylogeny and molecular epidemiology of Echinococcus multilocularis: From fundamental knowledge to health ecology.

Alveolar echinococcosis, caused by the tapeworm Echinococcus multilocularis, is one of the most severe parasitic diseases in humans and represents one of the 17 neglected diseases prioritised by the World Health Organisation (WHO) in 2012. Considering the major medical and veterinary importance of this parasite, the phylogeny of the genus Echinococcus is of considerable importance; yet, despite numerous efforts with both mitochondrial and nuclear data, it has remained unresolved. The genus is clearly complex, and this is one of the reasons for the incomplete understanding of its taxonomy. Although taxonomic studies have recognised E. multilocularis as a separate entity from the Echinococcus granulosus complex and other members of the genus, it would be premature to draw firm conclusions about the taxonomy of the genus before the phylogeny of the whole genus is fully resolved. The recent sequencing of E. multilocularis and E. granulosus genomes opens new possibilities for performing in-depth phylogenetic analyses. In addition, whole genome data provide the possibility of inferring phylogenies based on a large number of functional genes, i.e. genes that trace the evolutionary history of adaptation in E. multilocularis and other members of the genus. Moreover, genomic data open new avenues for studying the molecular epidemiology of E. multilocularis: genotyping studies with larger panels of genetic markers allow the genetic diversity and spatial dynamics of parasites to be evaluated with greater precision. There is an urgent need for international coordination of genotyping of E. multilocularis isolates from animals and human patients. This could be fundamental for a better understanding of the transmission of alveolar echinococcosis and for designing efficient healthcare strategies.

New algorithms for automated phylogenetic reconstruction using artificial intelligence and data mining techniques

Academic and industrial research in the late 90s have brought about an exponential explosion of DNA sequence data. Automated expert systems are being created to help biologists to extract patterns, trends and links from this ever-deepening ocean of information. Two such systems aimed on retrieving and subsequently utilizing phylogenetically relevant information have been developed in this dissertation, the major objective of which was to automate the often difficult and confusing phylogenetic reconstruction process. ^ Popular phylogenetic reconstruction methods, such as distance-based methods, attempt to find an optimal tree topology (that reflects the relationships among related sequences and their evolutionary history) by searching through the topology space. Various compromises between the fast (but incomplete) and exhaustive (but computationally prohibitive) search heuristics have been suggested. An intelligent compromise algorithm that relies on a flexible “beam” search principle from the Artificial Intelligence domain and uses the pre-computed local topology reliability information to adjust the beam search space continuously is described in the second chapter of this dissertation. ^ However, sometimes even a (virtually) complete distance-based method is inferior to the significantly more elaborate (and computationally expensive) maximum likelihood (ML) method. In fact, depending on the nature of the sequence data in question either method might prove to be superior. Therefore, it is difficult (even for an expert) to tell a priori which phylogenetic reconstruction method—distance-based, ML or maybe maximum parsimony (MP)—should be chosen for any particular data set. ^ A number of factors, often hidden, influence the performance of a method. For example, it is generally understood that for a phylogenetically “difficult” data set more sophisticated methods (e.g., ML) tend to be more effective and thus should be chosen. However, it is the interplay of many factors that one needs to consider in order to avoid choosing an inferior method (potentially a costly mistake, both in terms of computational expenses and in terms of reconstruction accuracy.) ^ Chapter III of this dissertation details a phylogenetic reconstruction expert system that selects a superior proper method automatically. It uses a classifier (a Decision Tree-inducing algorithm) to map a new data set to the proper phylogenetic reconstruction method. ^

Changes in calcareous nannofossil assemblages across the Paleocene/Eocene transition from the paleo-equatorial Pacific Ocean

Quantitative analyses of selected calcareous nannofossils in deep-sea sections recovered from the paleo-equatorial Pacific (ODP Leg 199) provide new information about biostratigraphy, biochronology and the evolutionary history of calcareous nannofossils across the Paleocene/Eocene transition interval. The sediment cores from ODP Leg 199 represent the first continuous Paleocene/Eocene boundary sections ever to be sampled in the central equatorial Pacific Ocean. Calcareous nannofossil assemblages are studied to document the distribution of biostratigraphically useful taxa such as Ericsonia, Discoaster, Fasciculithus, Rhomboaster and Tribrachiatus. Focus is given to the evolution of the Rhomboaster-Tribrachiatus lineage in the lower Eocene interval at Site 1215, and on the stratigraphic relationship of these taxa relative to species in the genus Fasciculithus. Critical intervals of North Atlantic DSDP Site 550 have also been re-examined. The Tribrachiatus digitalis morphotype was described at Site 550 from an interval affected by down-hole contamination, partly originating from within the Tribrachiatus orthostylus range. The T. digitalis morphotype represents an evolutionary transitional form between T. contortus and T. orthostylus, entering the stratigraphic record within the range of the former species and disappearing within the lower part of the range of the latter species. The subzonal subdivision of Zone NP10 hence collapses. Lithological and colour variability reflecting orbital cyclicity occur in the lower Eocene of Site 1215, permitting a relative astronomical age calibration of the Tribrachiatus taxa. The distinct Rhomboaster spp.-Discoaster araneus association also occurs in the paleo-equatorial Pacific Ocean, together with a marked decrease in diversity of Fasciculithus spp. Site 1220 reveals a short peak abundance of Thoracosphaera spp. just above the P/E boundary interval, which probably reflects a stressed surface water environment.