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.

Contemporary genetic, historical genetic and morphological data sets for the Yellow-tufted Honeyeater Lichenostomus melanops

Understanding the evolutionary history of threatened populations can improve their conservation management. Re-establishment of past but recent gene flow could re-invigorate threatened populations and replenish genetic diversity, necessary for population persistence. One of the four nominal subspecies of the common yellow-tufted honeyeater, Lichenostomus melanops cassidix, is critically endangered despite substantial conservation efforts over 55 years. Using a combination of morphometric, genetic and modelling approaches we tested for its evolutionary distinctiveness and conservation merit. We confirmed that cassidix has at least one morphometric distinction. It also differs genetically from the other subspecies in allele frequencies but not phylogenetically, implying that its evolution was recent. Modelling historical distribution supported the lack of vicariance and suggested a possibility of gene flow among subspecies at least since the late Pleistocene. Multi-locus coalescent analyses indicated that cassidix diverged from its common ancestor with neighbouring subspecies gippslandicus sometime from the mid-Pleistocene to the Holocene, and that it has the smallest historical effective population size of all subspecies. It appears that cassidix diverged from its ancestor with gippslandicus through a combination of drift and local selection. From patterns of genetic subdivision on two spatial scales and morphological variation we concluded that cassidix, gippslandicus and (melanops + meltoni) are diagnosable as subspecies. Low genetic diversity and effective population size of cassidix may translate to low genetic fitness and evolutionary potential, thus managed gene flow from gippslandicus is recommended for its recovery.

Origin and evolution of Cycladophora davisiana (Radiolaria) in DSDP Hole 19-192, Northwest Pacific

This paper documents the evolutionary history of Cycladophora davisiana Ehrenberg from an uppermost Miocene to Pleistocene sedimentary record in the high-latitude Northwest Pacific. It apparently evolved from C. sakaii Motoyama through a series of intermediates. C. sakaii has a relatively large shell with an external spongy layer. The evolutionary transition is characterized by a relatively rapid decrease in thorax size with a reduction of the spongy appendage. This change occurred during about 0.4 m.y. from 2.8 to 2.4 Ma without cladogenesis. Following this interval, a decrease in thorax size continued gradually up to the Recent, resulting in a very small morphology. Although the population of C. davisiana first appeared at about 2.5 Ma, some morphotypic specimens may occur in earlier periods as indistinguishable very small endmembers in the C. sakaii populations. Timing of the first appearance events both of morphotypic specimens and of a population of C. davisiana in Site 192 and previously reported cores does not disprove the idea that C. davisiana evolved first in the Northwest Pacific region, and later migrated into other regions of the world ocean. Biometrics clearly indicate no direct phylogenetic relationships between C. davisiana and C. cornutoides Kling in the studied core. Thus, the latter species, which was originally described as a variation and later elevated to a subspecies of the former species, is separated from the former species and raised to the species rank.

Petrology and carbon and oxygen stable isotopic composition of macrofossils and sediments from the Blake-Bahama Formation, DSDP Hole 93-603B

Strata that record the evolutionary history of the North American continental margin in a region that serves as the basin margin interface between allochthonous sedimentation from the continent and pelagic sedimentation from the oceanic realm were recovered at Deep Sea Drilling Project Site 603, on the lower continental rise. The lowermost unit recovered at this site is composed of upper Berriasian-Aptian interbedded laminated limestone and bioturbated limestone with sandstone to claystone turbidites. This unit can be correlated with the Blake-Bahama Formation in the western North Atlantic. Studies of the laminated and bioturbated limestones were used to determine the depositional environment. Geochemical and petrographic studies suggest that the laminated limestones were deposited from the suspended particulate loads of the nepheloid layer associated with weak bottom-current activity as well as moderate to poorly oxygenated bottom-water conditions. Fragments of macrofossils are also found in the Blake-Bahama Formation drilled at Site 603. Twelve specimens and their host sediment were analyzed for their carbon and oxygen isotopic composition. The macrofossil samples chosen for analysis consist of nine samples of Inoceramus, two ammonite aptychi, and one belemnite sample. Depletion in 18O is observed in recrystallized specimens. The ammonite aptychi have been diagenetically altered and/or exhibit evidence of isotopic fractionation by the organism. Oxygen isotope paleotemperatures obtained from five well-preserved specimens - four of Inoceramus and one of a belemnite - suggest that bottom-water temperatures in the North Atlantic Basin during the Early Cretaceous were very warm, at least 11°C.

Planktonic foraminiferal stratigraphy and datum levels of ODP Leg 182 sites

Planktonic foraminifers from Ocean Drilling Program Leg 182, Holes 1126B and 1126C, 1128B and 1128C, 1130A and 1130B, 1132B, and 1134A and 1134B confirm the neritic record that during the early Miocene the Great Australian Bight region was in a cool-temperate regime with abundant Globoturborotalita woodi. Warm marine environments started to develop in the later part of the early Miocene, and the region became warm temperate to subtropical in the early middle Miocene with abundant Globigerinoides, Orbulina, and Globorotalia, corresponding to global warming at the Miocene climatic optimum. Fluctuations between cool- and warm-temperate conditions prevailed during the late Miocene, as indicated by abundant Globoconella conoidea and Menardella spp. A major change in planktonic foraminiferal assemblages close to the Miocene/Pliocene boundary not only drove many Miocene species into extinction but also brought about such new species as Globorotalia crassaformis and Globoconella puncticulata. Warm-temperate environments continued into the early and mid-Pliocene before being replaced by cooler conditions, supporting numerous Globoconella inflata and Globigerina quinqueloba. Based on data from this study and published results from the Australia-New Zealand region, we established a local planktonic foraminifer zonation scheme for separating the southern Australian Neogene (SAN) into Zones SAN1 to SAN19 characterizing the Miocene and Zones SAN20 to SAN25 characterizing the Pliocene. The Neogene sections from the Great Australian Bight are bounded by hiatuses of ~0.5 to >3 m.y. in duration, although poor core recovery in some holes obscured a proper biostratigraphic resolution. A total of 15 hiatuses, numbered 1 to 15, were identified as synchronous events from the base of the Miocene to the lower part of the Pleistocene. We believe that these are local manifestations of major third-order boundaries at about (1) 23.8, (2) 22.3, (3) 20.5, (4) 18.7, (5) 16.4, (6) 14.8, (7) 13.5, (8) 11.5, (9) 9.3, (10) 7.0, (11) 6.0, (12) 4.5, (13) 3.5, (14) 2.5, and (15) 1.5 Ma, respectively. This hiatus-bounded Neogene succession samples regional transgressions and stages of southern Australia and reveals its stepwise evolutionary history.

(Table 1) Number of alleles per locus and heterozygosity of Arctic charr (Salvelinus alpinus) populations in Iceland

The ecological theory of adaptive radiation predicts that the evolution of phenotypic diversity within species is generated by divergent natural selection arising from different environments and competition between species. Genetic connectivity among populations is likely also to have an important role in both the origin and maintenance of adaptive genetic diversity. Our goal was to evaluate the potential roles of genetic connectivity and natural selection in the maintenance of adaptive phenotypic differences among morphs of Arctic charr, Salvelinus alpinus, in Iceland. At a large spatial scale, we tested the predictive power of geographic structure and phenotypic variation for patterns of neutral genetic variation among populations throughout Iceland. At a smaller scale, we evaluated the genetic differentiation between two morphs in Lake Thingvallavatn relative to historically explicit, coalescent-based null models of the evolutionary history of these lineages. At the large spatial scale, populations are highly differentiated, but weakly structured, both geographically and with respect to patterns of phenotypic variation. At the intralacustrine scale, we observe modest genetic differentiation between two morphs, but this level of differentiation is nonetheless consistent with strong reproductive isolation throughout the Holocene. Rather than a result of the homogenizing effect of gene flow in a system at migration-drift equilibrium, the modest level of genetic differentiation could equally be a result of slow neutral divergence by drift in large populations. We conclude that contemporary and recent patterns of restricted gene flow have been highly conducive to the evolution and maintenance of adaptive genetic variation in Icelandic Arctic charr.

Late Oligocene rapid transformations in the South China Sea

Lithobiostratigraphic data indicate that the double reflectors on the seismic profile through Ocean Drilling Program (ODP) Site 1148 represent two unconformities that coincide, respectively, with the lower/upper Oligocene boundary at ~488 mcd, and Oligocene-Miocene boundary at 460 mcd. Two other unconformities, at ~478 and 472 mcd, respectively, were also identified within the upper Oligocene section. Together they erased a sediment record of about 3 Ma from this locality in a period of very active seafloor spreading. The existence of 32.8 Ma marine sediment at the terminated depth (850 mcd) indicates that the initial breakup of the South China Sea (SCS) was probably during 34-33 Ma, close to the Eocene-Oligocene boundary. High sedimentation rates of 60-115 m/my from the much expanded, N350 m lower Oligocene section resulted from rifting and rapid subsidence between 33 and 29 Ma. The mid-Oligocene unconformity at ~28.5 Ma, which also occurred in many parts of the Indo-West Pacific region, was probably related to a significant uplift of the Himalayan-Tibetan Plateau to the west and the initial collision between Indonesia and Australia in the south. A narrowed Indonesian seaway may have accounted for the late Oligocene warming and chalk deposition in the northern South China Sea including the Site 1148 locality. The unconformities and slumps near the Oligocene-Miocene boundary indicate a very unstable tectonic regime, probably corresponding to changes in the rotation of different land blocks and the seafloor spreading ridge from nearly E-W to NE-SW, as recognized earlier at magnetic Anomaly 7. This 25 Ma event also saw the first New Guinea terrane docking at the northern Australian craton. The low sedimentation rate of ~15 m/my in the early to middle Miocene may correspond to another period of rapid seafloor spreading and rapid widespread subsidence that effectively caused sediment source areas to retreat with a rapidly rising sea level. The isostatic nature of these late Oligocene unconformities and slumps with several major collision-uplift events indicate that the rapid changes in the early evolutionary history of the South China Sea were mainly responding to regional tectonic reconfiguration including the uplift-driven southeast extrusion of the Indochina subcontinent.