Phylogenetic analysis of plastid and nuclear DNA sequences reveals a rapid late Miocene radiation of the temperate bamboo tribe Arundinarieae (Poaceae, Bambusoideae)

Background: Arundinarieae are a large tribe of temperate woody bamboos for which phylogenetics are poorly understood because of limited taxon sampling and lack of informative characters. Aims: This study assessed phylogenetic relationships, origins and classification of Arundinarieae. Methods: DNA sequences (plastid trnL-F; nuclear ITS) were used for parsimony and Bayesian inference including 41 woody bamboo taxa. Divergence dates were estimated using a relaxed Bayesian clock. Results: Arundinarieae were monophyletic but their molecular divergence was low compared to the tropical Bambuseae. Ancestors of the Arundinarieae lineage were estimated to have diverged from the other bamboos 23 (15-30) million years ago (Mya). However, the Arundinarieae radiation occurred 10 (6-16) Mya compared to 18 (11-25) Mya for the tropical Bambuseae. Some groups could be defined within Arundinarieae, but they do not correspond to recognised subtribes such as Arundinariinae or Shibataeinae. Conclusions: Arundinarieae are a relatively ancient bambusoid lineage that underwent a rapid radiation in the late Miocene. The radiation coincides with the continental collision of the Indo-Australian and Eurasian Plates. Arundinarieae are distributed primarily in East Asia and the Himalayas to northern Southeast Asia. It is unknown whether they were present in Asia long before their radiation, but we believe recent dispersal is a more likely scenario. Keywords: Arundinarieae; Bambuseae; internal transcribed spacer (ITS); molecular clock; phylogenetics; radiation; temperate bamboos; Thamnocalaminae; trnL-F

Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling.

In this paper we included a very broad representation of grass family diversity (84% of tribes and 42% of genera). Phylogenetic inference was based on three plastid DNA regions rbcL, matK and trnL-F, using maximum parsimony and Bayesian methods. Our results resolved most of the subfamily relationships within the major clades (BEP and PACCMAD), which had previously been unclear, such as, among others the: (i) BEP and PACCMAD sister relationship, (ii) composition of clades and the sister-relationship of Ehrhartoideae and Bambusoideae + Pooideae, (iii) paraphyly of tribe Bambuseae, (iv) position of Gynerium as sister to Panicoideae, (v) phylogenetic position of Micrairoideae. With the presence of a relatively large amount of missing data, we were able to increase taxon sampling substantially in our analyses from 107 to 295 taxa. However, bootstrap support and to a lesser extent Bayesian inference posterior probabilities were generally lower in analyses involving missing data than those not including them. We produced a fully resolved phylogenetic summary tree for the grass family at subfamily level and indicated the most likely relationships of all included tribes in our analysis.

Phylogeny and circumscription of Sapindaceae revisited: molecular sequence data, morphology and biogeography support recognition of a new family, Xanthoceraceae

Background and aims Recent studies have adopted a broad definition of Sapindaceae that includes taxa traditionally placed in Aceraceae and Hippocastanaceae, achieving monophyly but yielding a family difficult to characterize and for which no obvious morphological synapomorphy exists. This expanded circumscription was necessitated by the finding that the monotypic, temperate Asian genus Xanthoceras, historically placed in Sapindaceae tribe Harpullieae, is basal within the group. Here we seek to clarify the relationships of Xanthoceras based on phylogenetic analyses using a dataset encompassing nearly 3/4 of sapindaceous genera, comparing the results with information from morphology and biogeography, in particular with respect to the other taxa placed in Harpullieae. We then re-examine the appropriateness of maintaining the current broad, morphologically heterogeneous definition of Sapindaceae and explore the advantages of an alternative family circumscription. Methods Using 243 samples representing 104 of the 142 currently recognized genera of Sapindaceae s. lat. (including all in Harpullieae), sequence data were analyzed for nuclear (ITS) and plastid (matK, rpoB, trnD-trnT, trnK-matK, trnL-trnF and trnS-trnG) markers, adopting the methodology of a recent family-wide study, performing single-gene and total evidence analyses based on maximum likelihood (ML) and maximum parsimony (MP) criteria, and applying heuristic searches developed for large datasets, viz, a new strategy implemented in RAxML (for ML) and the parsimony ratchet (for MP). Bootstrap analyses were performed for each method to test for congruence between markers. Key results Our findings support earlier suggestions that Harpullieae are polyphyletic: Xanthoceras is confirmed as sister to all other sampled taxa of Sapindaceae s. lat.; the remaining members belong to three other clades within Sapindaceae s. lat., two of which correspond respectively to the groups traditionally treated as Aceraceae and Hippocastanaceae, together forming a clade sister to the largely tropical Sapindaceae s. str., which is monophyletic and morphologically coherent provided Xanthoceras is excluded. Conclusion To overcome the difficulties of a broadly circumscribed Sapindaceae, we resurrect the historically recognized temperate families Aceraceae and Hippocastanaceae, and describe a new family, Xanthoceraceae, thus adopting a monophyletic and easily characterized circumscription of Sapindaceae nearly identical to that used for over a century.

Specific duplication and dorsoventrally asymmetric expression patterns of Cycloidea-like genes in zygomorphic species of Ranunculaceae.

Floral bilateral symmetry (zygomorphy) has evolved several times independently in angiosperms from radially symmetrical (actinomorphic) ancestral states. Homologs of the Antirrhinum majus Cycloidea gene (Cyc) have been shown to control floral symmetry in diverse groups in core eudicots. In the basal eudicot family Ranunculaceae, there is a single evolutionary transition from actinomorphy to zygomorphy in the stem lineage of the tribe Delphinieae. We characterized Cyc homologs in 18 genera of Ranunculaceae, including the four genera of Delphinieae, in a sampling that represents the floral morphological diversity of this tribe, and reconstructed the evolutionary history of this gene family in Ranunculaceae. Within each of the two RanaCyL (Ranunculaceae Cycloidea-like) lineages previously identified, an additional duplication possibly predating the emergence of the Delphinieae was found, resulting in up to four gene copies in zygomorphic species. Expression analyses indicate that the RanaCyL paralogs are expressed early in floral buds and that the duration of their expression varies between species and paralog class. At most one RanaCyL paralog was expressed during the late stages of floral development in the actinomorphic species studied whereas all paralogs from the zygomorphic species were expressed, composing a species-specific identity code for perianth organs. The contrasted asymmetric patterns of expression observed in the two zygomorphic species is discussed in relation to their distinct perianth architecture.

Phylogeny of shrews (Soricidae) : taxonomic and biogeographic implications

Résumé Les Soricidae sont l'une des plus grandes familles de mammifères avec plus de 300 espèces décrites. Elle a été récemment divisée en trois sous-familles, les Soricidae, qui sont distribuées dans la région Holarctique, les Crocidurinae en Afrique et en Eurasie, et les Myosoricinae en Afrique. La diversité spécifique de cette famille a conduit à des interprétations taxonomiques multiples, qui sont à l'origine de polémiques entre spécialistes, et même les premiers résultats moléculaires ont été fortement contradictoires. Le but de cette thèse est donc d'appliquer des meilleures techniques sur des échantillons mieux ciblés, afin de résoudre les contradictions taxonomiques et comprendre l'histoire de cette famille. Par le biais de marqueurs génétiques mitochondriaux et nucléaires, j'ai étudié: (i) Les relations taxonomiques à différent niveaux hiérarchiques au sein des Soricidae, c'est-à dire, entre les sous-familles, tribus, et genres, ainsi qu'au sein de deux complexes d'espèces largement distribués, et d'une espèce européenne, le but étant d'établir la congruence entre les données génétiques et les interprétations morphologiques classiques. (ii) Les relations biogéographiques, soit l'origine potentielle des différentes sous-familles, tribus, et genres, le nombre d'échanges intercontinentaux, ainsi que la structure phylogéographique à un niveau (péri)-spécifique, afin d'établir l'histoire de la diversification de cette famille. Les analyses combinées d'ADN mitochondrial et nucléaire ont montré un rapport clair entre les taxa à un niveau taxonomique élevé, mettant en évidence les rapports entre les sous-familles, les tribus, et les genres. Bien que Myosorex constitue un groupe monophylétique distinct, sa définition en tant que sous-famille séparée ne peut pas être reconnue. Ainsi, nous proposons d'attribuer un niveau de tribu pour ce clade (inclus dans les Crocidurinae). Nous avons également montré l'inclusion du genre Anourosorex dans les Soricinae et non en position basale dans les Soricidae. Au sein des Crocidurinae, Suncus s'est révélé être paraphylétique, et le genre Diplomesodon devrait être considéré d'un point de vue génétique comme invalide, puisque il se trouve au sein du clade du genre Crocidura. À un niveau taxonomique plus bas, nous avons montré la monophylie de deux complexes d'espèces largement distribués, le groupe de C. suaveolens et de C. olivieri. Néanmoins à l'intérieur de ceux-ci, des différences majeures avec la classification morphologique se sont révélées. Par exemples, C. sibirica n'est pas une espèce valide, les analyses de phylogénie moléculaire ne montrant pas de variations génétiques entre celle-ci et un échantillon de la localité type de C. suaveolens. D'un point de vue biogéographique, les fluctuations climatiques et les activités tectoniques des 20 derniers millions d'années ont fortement influencé la diversité actuelle des Soricidae. À un niveau taxonomique élevé, l'apparition de connexions de terre temporaires entre le Vieux et le Nouveau Monde au Miocène moyen ont mené à plusieurs colonisations indépendantes de l'Amérique par les Soricinae. Celles-ci ónt conduit à une diversification d'une tribu (Notiosoricini), ainsi que de genres (par ex: Cryptotis, Blarina) et d'un sous-genre (Otisorex) endémique au Néarctique. Dans le Vieux Monde, les barrières entre l'Afrique et Eurasie étaient plus perméables, menant à plusieurs échanges bidirectionnels de Crocidurinae. La diversification des clades principaux s'est produite au Miocène, certains clades étant endémiques d'Afrique ou d'Eurasie, tandis que d'autres se sont diversifiés à travers le Vieux Monde. À un niveau spécifique ou péri-spécifique, la fluctuation climatique du Pliocène et les glaciations du Pléistocène ont fortement divisé les populations dans tout le Paléarctique, menant à des entités génétiques distinctes. En Europe, les populations du groupe de C. suaveolens ont été divisées en une lignée Sud-Ouest et une Sud-Est, alors qu'au Proche-Orient et au Moyen-Orient, la diversité de clades est plus importante. En conclusion, mes études ont révélé que du Miocène à nos jours, la diversification des Soricidae a été provoquée par la colonisation de nouveaux habitats (dispersion), ainsi que par l'isolement des populations par diverses barrières (vicariance). Abstract The Soricidae is one of the largest mammalian families with more than 300 species described. It has been recently divided into three subfamilies, the Soricinae, which are distributed in the Holartic region, the Crocidurinae in Africa and Eurasia, and the Myosoricinae in Africa. The specific diversity of this family have led to multiple systematic interpretations and controversies between authors. Fortunately, today, cytotaxonomic, allozymic and molecular studies have permitted to clarify some uncertainties. Nevertheless, the Soricidae remains still poorly known. In this thesis, we aim at understanding with the use of mitochondrial and nuclear markers: (i) the taxonomic relationships at different hierarchical levels within Soricidae, i.e., between the subfamilies, tribes, and genera, as well as within two largely distributed species complexes, and within a European species, the goal being to establish congruence between the genetic data and traditional morphological interpretations; (ii) the biogeographic relationships, especially the potential origin of the different subfamilies, tribes, and genera, the number of transcontinental exchanges, as well as the phylogeographic structure at a (peri)-specific level, in order to establish the history of the genetic diversification of this family. The combined analyses of mitochondrial and nuclear DNA highlight for the first time a clear relationship between taxa at a high taxonomical level, permitting to distinguish the relationships between subfamilies, tribes, and genera. Although Myosorex formed a distinct monophyletic group, its definition as a distinct sub-family cannot be advocated. Thus, we propose to attribute a tribe level for this Glade (included within the Crocidurinae). Additionally, this combination of genes pleads in favour of the inclusion of the genus Anourosorex within the Soricinae and not in a basal position within the Soricidae. Within the Crocidurinae, Suncus appeared to be paraphyletic, and Diplomesodon should be considered from a genetic point of view as invalid, and is presently considered as Crocidura. At a lower taxonomic level, we showed the monophyly of two widely distributed species complexes, the C. suaveolens group and the C. olivieri group. Nevertheless within those, we showed major differences compared to morphological classification. For examples, C. sibirica revealed to not be a valid species, the molecular phylogenetic analyses failed to evidence genetical variations between it and samples of the type locality of C. suaveolens. In a biogeographic point of view, the climatic fluctuations and the tectonic plate activities of the last 20 Myr have strongly influenced the actual diversity of the family. At a high taxonomic level, the successive land bridge connections between the Old and the New World, which occurred during the Middle Miocene, have led to several independent colonisations of America by Soricinae, and a subsequent diversification of endemic Nearctic's tribe (Notiosoricini), genera (e.g. Cryptotis, Blaring) and sub-genus (Otisorex) within the Soricinae. Within the Old World, the barriers between Africa and Eurasia were more permeable, leading to several bidirectional exchanges within the Crocidurinae. The diversification of major clades occurred through the Miocene, some clades being endemic to Africa or Eurasia, whereas others diversified through the Old World. At a species level or a peri-specific level, the Pliocene climatic fluctuation and the Pleistocene glaciations have strongly divided the populations throughout the Palaearctic, leading to well defined genetic entities. In Europe, populations of the C. suaveolens group were split in a classical south-western and south-eastern lineage. In contrast, the Near East and the Middle East reveal many differentiated clades. In conclusion, our studies revealed that, from the Miocene to present, the diversification and speciation events within the Soricidae were caused by natural colonisation of new habitats (dispersion) and isolation of populations by various barriers (vicariance).

Non-monophyly of the woody bamboos (Bambuseae; Poaceae): a multi-gene region phylogenetic analysis of Bambusoideae s.s.

The taxonomy of Bambusoideae is in a state of flux and phylogenetic studies are required to help resolve systematic issues. Over 60 taxa, representing all subtribes of Bambuseae and related non-bambusoid grasses were sampled. A combined analysis of five plastid DNA regions, trnL intron, trnL-F intergenic spacer, atpB-rbcL intergenic spacer, rps16 intron, and matK, was used to study the phylogenetic relationships among the bamboos in general and the woody bamboos in particular. Within the BEP clade (Bambusoideae s.s., Ehrhartoideae, Pooideae), Pooideae were resolved as sister to Bambusoideae s.s. Tribe Bambuseae, the woody bamboos, as currently recognized were not monophyletic because Olyreae, the herbaceous bamboos, were sister to tropical Bambuseae. Temperate Bambuseae were sister to the group consisting of tropical Bambuseae and Olyreae. Thus, the temperate Bambuseae would be better treated as their own tribe Arundinarieae than as a subgroup of Bambuseae. Within the tropical Bambuseae, neotropical Bambuseae were sister to the palaeotropical and Austral Bambuseae. In addition, Melocanninae were found to be sister to the remaining palaeotropical and Austral Bambuseae. We discuss phylogenetic and morphological patterns of diversification and interpret them in a biogeographic context.

Energy consumption of European and African shrews

Is the extremely high oxygen consumption of shrews due to an unusually high basal metabolism? In an attempt to answer this long-standing question, we have measured the oxygen consumption of 13 species of shrews of different origin: from Europe - Sorex araneus, S. Minutus, Neomys fodiens, Crocidura russula, and Suncus etruscus; from Africa - Crocidura bottegi, C. bicolor, C. jouvenetae; C. poensis, C. theresae, C. Wimmeri, C. flavescens, and C. giffardi, The measurements, taken over a period of 20-30 minutes, were made in small, closed-system chambers at 25°C. The metabolic rat our shrews of the subfamily Soricinae lies between the eman and minimum values of the Soricini (M=126.2 W0.52 cal/h and M=82.6 W0.53 cal/h, respectively), as recorded in the literature. Zhe average for the African Crocidurinae is much lower (M= 43.6 W0.67). The metabolic rate of the European Croccidura russula agrees with that of the African species. Thus, the Crocidurinae are characterized by a relatively low metabolic rate; the Soricinae, and in particular the tribe of the Soricini, by an extremely high metabolic rate. The tribes Neomyini and Blarinini occupy an intermediate position. These differences are also to be found at the level of the basal metabolism. This main difference between the two sub-families can most likely be explained by evolution in geographical isolation under differential climatic conditions: the Crocidurinae having evolved in tropical Africa and the Soricinae in temperate Eurasia

Putative adverse outcome pathways relevant to neurotoxicity.

The Adverse Outcome Pathway (AOP) framework provides a template that facilitates understanding of complex biological systems and the pathways of toxicity that result in adverse outcomes (AOs). The AOP starts with an molecular initiating event (MIE) in which a chemical interacts with a biological target(s), followed by a sequential series of KEs, which are cellular, anatomical, and/or functional changes in biological processes, that ultimately result in an AO manifest in individual organisms and populations. It has been developed as a tool for a knowledge-based safety assessment that relies on understanding mechanisms of toxicity, rather than simply observing its adverse outcome. A large number of cellular and molecular processes are known to be crucial to proper development and function of the central (CNS) and peripheral nervous systems (PNS). However, there are relatively few examples of well-documented pathways that include causally linked MIEs and KEs that result in adverse outcomes in the CNS or PNS. As a first step in applying the AOP framework to adverse health outcomes associated with exposure to exogenous neurotoxic substances, the EU Reference Laboratory for Alternatives to Animal Testing (EURL ECVAM) organized a workshop (March 2013, Ispra, Italy) to identify potential AOPs relevant to neurotoxic and developmental neurotoxic outcomes. Although the AOPs outlined during the workshop are not fully described, they could serve as a basis for further, more detailed AOP development and evaluation that could be useful to support human health risk assessment in a variety of ways.

Genotype-phenotype analysis of Jervell and Lange-Nielsen syndrome in six families from Saudi Arabia.

We sought to explore the genotype-phenotype of Jervell and Lange-Nielsen syndrome (JLNS) patients in Saudi Arabia. We have also assessed the plausible effect of consanguinity into the pathology of JLNS. Six families with at least one JLNS-affected member attended our clinic between 2011 and 2013. Retrospective and prospective clinical data were collected and genetic investigation was performed. Pathogenic mutations in the KCNQ1 gene were detected in all JLNS patients. The homozygous mutations detected were Leu273Phe, Asp202Asn, Ile567Thr, and c.1486_1487delCT and compound heterozygous mutations were c.820_ 830del and c.1251+1G>T. All living JLNS patients except one had a QTc of >500 ms and a history of recurrent syncope. β-Blockers abolished the cardiac-related events in all patients except two siblings with homozygous Ile567Thr mutation. Four of the six mutations were originally reported in autosomal dominant long QT syndrome (LQTS) patients. Eighty percent of the heterozygote mutation carriers showed prolongation of QTc, but majority of these reported no symptoms attributable to arrhythmias. Mutations detected in this study will be advantageous in tribe and region-specific cascade screening of LQTS in Saudi Arabia.

Back to Gondwanaland: can ancient vicariance explain (some) Indian Ocean disjunct plant distributions?

Oceans, or other wide expanses of inhospitable environment, interrupt present day distributions of many plant groups. Using molecular dating techniques, generally incorporating fossil evidence, we can estimate when such distributions originated. Numerous dating analyses have recently precipitated a paradigm shift in the general explanations for the phenomenon, away from older geological causes, such as continental drift, in favour of more recent, long-distance dispersal (LDD). For example, the 'Gondwanan vicariance' scenario has been dismissed in various studies of Indian Ocean disjunct distributions. We used the gentian tribe Exaceae to reassess this scenario using molecular dating with minimum (fossil), maximum (geological), secondary (from wider analyses) and hypothesis-driven age constraints. Our results indicate that ancient vicariance cannot be ruled out as an explanation for the early origins of Exaceae across Africa, Madagascar and the Indian subcontinent unless a strong assumption is made about the maximum age of Gentianales. However, both the Gondwanan scenario and the available evidence suggest that there were also several, more recent, intercontinental dispersals during the diversification of the group.

Subfamilial and tribal relationships of Ranunculaceae: evidence from eight molecular markers

The first molecular phylogenies of the flowering plant family Ranunculaceae were published more than twenty years ago, and have led to major changes in the infrafamilial classification. However, the current phylogeny is not yet well supported, and relationships among subfamilies and tribes of Ranunculaceae remain an open question. Eight molecular markers from the three genomes (nuclear, chloroplast and mitochondrial) were selected to investigate these relationships, including new markers for the family (two homologs of the nuclear CYCLOIDEA gene, the chloroplast gene ndhF, and the mitochondrial intron nad4-I1). The combination of multiple markers led to better resolution and higher support of phylogenetic relationships among subfamilies of Ranunculaceae, and among tribes within subfamily Ranunculoideae. Our results challenge the monophyly of Ranunculoideae as currently circumscribed due to the position of tribe Adonideae (Ranunculoideae), sister to Thalictroideae. We suggest that Thalictroideae could be merged with Ranunculoideae in an enlarged single subfamily.