Not so ancient: the extant crown group of Nothofagus represents a post-Gondwanan radiation

This study uses a molecular-dating approach to test hypotheses about the biogeography of Nothofagus. The molecular modelling suggests that the present-day subgenera and species date from a radiation that most likely commenced between 55 and 40 Myr ago. This rules out the possibility of a reconciled all-vicariance hypothesis for the biogeography of extant Nothofagus. However, the molecular dates for divergences between Australasian and South American taxa are consistent with the rifting of Australia and South America from Antarctica. The molecular dates further suggest a dispersal of subgenera Lophozonia and Fuscospora between Australia and New Zealand after the onset of the Antarctic Circumpolar Current and west wind drift. It appears likely that the New Caledonian lineage of subgenus Brassospora diverged from the New Guinean lineage elsewhere, prior to colonizing New Caledonia. The molecular approach strongly supports fossil-based estimates that Nothofagus diverged from the rest of Fagales more than 84 Myr ago. However, the mid-Cenozoic estimate for the diversification of the four extant subgenera conflicts with the palynological interpretation because pollen fossils, attributed to all four extant subgenera, were widespread across the Weddellian province of Gondwana about 71 Myr ago. The discrepancy between the pollen and molecular dates exists even when confidence intervals from several sources of error are taken into account. In contrast, the molecular age estimates are consistent with macrofossil dates. The incongruence between pollen fossils and molecular dates could be resolved if the early pollen types represent extinct lineages, with similar types later evolving independently in the extant lineages.

The systematics and biology of the south African gall-inducing scale insect, Calycicoccus merwei brain (Hemiptera : Coccoidea : Eriococcidae)

The scale insect genus Calycicoccus Brain has a single described species, C. merwei Brain, which is endemic to southeastern South Africa. Females of C. merwei induce small, mostly conical galls on the foliage of their host tree, Apodytes dimidiata E. Meyer ex Arn. (Icacinaceae), which has a wider, mostly coastal distribution, than that currently known for the scale insect. Calycicoccus has been placed in the family Eriococcidae and may be related to the South American genus Aculeococcus Lepage. No other native eriococcid species have been described so far in South Africa, although the family is diverse in other Gondwanan regions. This paper summarizes the biology of C. merwei, redescribes the adult female, describes the adult male, the second-instar female and the first-instar nymphs for the first time, and reconsiders the phylogenetic relationships of the genus. The adult female is shown to have unusual abdominal segmentation, in that segment I is present both dorsally and ventrally, but a segment is absent ventrally on the middle abdomen. First-instar nymphs are sexually dimorphic; males have a larger and relatively narrower body, larger mouthparts, longer antennae and legs, and more thoracic dorsal setae compared with females. Molecular data from nuclear small-subunit ribosomal DNA (18S) and elongation factor 1 alpha (EF-1a) show C. merwei to have no close relatives among the Eriococcidae sampled to date. Instead, the Calycicoccus lineage is part of a polytomy near the base of the Eriococcidae. Molecular dating of the node suggests that the Calycicoccus lineage diverged from other eriococcids more than 100 Mya. These data support the placement of Calycicoccus as the only genus in the subfamily Calycicoccinae Brain.

Oligocene CO2 decline promoted C4 photosynthesis in grasses.

C4 photosynthesis is an adaptation derived from the more common C3 photosynthetic pathway that confers a higher productivity under warm temperature and low atmospheric CO2 concentration [1, 2]. C4 evolution has been seen as a consequence of past atmospheric CO2 decline, such as the abrupt CO2 fall 32-25 million years ago (Mya) [3-6]. This relationship has never been tested rigorously, mainly because of a lack of accurate estimates of divergence times for the different C4 lineages [3]. In this study, we inferred a large phylogenetic tree for the grass family and estimated, through Bayesian molecular dating, the ages of the 17 to 18 independent grass C4 lineages. The first transition from C3 to C4 photosynthesis occurred in the Chloridoideae subfamily, 32.0-25.0 Mya. The link between CO2 decrease and transition to C4 photosynthesis was tested by a novel maximum likelihood approach. We showed that the model incorporating the atmospheric CO2 levels was significantly better than the null model, supporting the importance of CO2 decline on C4 photosynthesis evolvability. This finding is relevant for understanding the origin of C4 photosynthesis in grasses, which is one of the most successful ecological and evolutionary innovations in plant history.

Biogeographic origin and radiation of the Old World crocidurine shrews (Mammalia: Soricidae) inferred from mitochondrial and nuclear genes.

The crocidurine shrews include the most speciose genus of mammals, Crocidura. The origin and evolution of their radiation is, however, poorly understood because of very scant fossil records and a rather conservative external morphology between species. Here, we use an alignment of 3560 base pairs of mitochondrial and nuclear DNA to generate a phylogenetic hypothesis for the evolution of Old World shrews of the subfamily Crocidurinae. These molecular data confirm the monophyly of the speciose African and Eurasian Crocidura, which also includes the fossorial, monotypic genus Diplomesodon. The phylogenetic reconstructions give further credit to a paraphyletic position of Suncus shrews, which are placed into at least two independent clades (one in Africa and sister to Sylvisorex and one in Eurasia), at the base of the Crocidura radiation. Therefore, we recommend restricting the genus Suncus to the Palaearctic and Oriental taxa, and to consider all the African Suncus as Sylvisorex. Using molecular dating and biogeographic reconstruction analyses, we suggest a Palaearctic-Oriental origin for Crocidura dating back to the Upper Miocene (6.8 million years ago) and several subsequent colonisations of the Afrotropical region by independent lineages of Crocidura.

The complex history of the olive tree: from Late Quaternary diversification of Mediterranean lineages to primary domestication in the northern Levant.

The location and timing of domestication of the olive tree, a key crop in Early Mediterranean societies, remain hotly debated. Here, we unravel the history of wild olives (oleasters), and then infer the primary origins of the domesticated olive. Phylogeography and Bayesian molecular dating analyses based on plastid genome profiling of 1263 oleasters and 534 cultivated genotypes reveal three main lineages of pre-Quaternary origin. Regional hotspots of plastid diversity, species distribution modelling and macrofossils support the existence of three long-term refugia; namely the Near East (including Cyprus), the Aegean area and the Strait of Gibraltar. These ancestral wild gene pools have provided the essential foundations for cultivated olive breeding. Comparison of the geographical pattern of plastid diversity between wild and cultivated olives indicates the cradle of first domestication in the northern Levant followed by dispersals across the Mediterranean basin in parallel with the expansion of civilizations and human exchanges in this part of the world.

Phylogeny of subtribe Gentianinae (Gentianaceae): biogeographic inferences despite limitations in temporal calibration points

The subtribe Gentianinae comprises ca. 425 species, most of them within the well-studied genus Gentiana and mainly distributed over the Eurasian continent. Phylogenetic relationships between Gentiana and its closest relatives, the climbing gentians (Crawfurdia, Tripterospermum) and the new genus Metagentiana, remain unclear. All three genera were recently found to be polyphyletic, possibly because of poor sampling of Tripterospermum and Crawfurdia. Highest diversity of Gentianinae occurs in the western Himalaya, but the absence of uncontroversial fossil evidence limits our understanding of its biogeography. In the present study, we generated ITS and atpB-rbcL sequences for 19 species of Tripterospermum, 9 of Crawfurdia and 11 of Metagentiana, together representing about 60 percent of the species diversity of these genera. Our results show that only Metagentiana is polyphyletic and divided into three monophyletic entities. No unambiguous synapomorphies were associated with the three Metagentiana entities. Different combinations of three approximate calibration points were used to generate three divergence time estimation scenarios. Although dating hypotheses were mostly inconsistent, they concurred in associating radiation of Gentiana to an orogenic phase of the Himalaya between 15 and 10 million years ago. Our study illustrates the conceptual difficulties in addressing the time frame of diversification in a group lacking sufficient fossil number and quality.

Colour-polymorphic snake species are older

Many characteristics, for example life-history traits, physiological tolerance to heat and cold, and energy requirements, contribute to a population's ability to persist in the face of climatic variation. Recent studies have suggested that the presence of intraspecific colour polymorphism could be another potential contributor to population resilience (e.g. to climate change) in ectothermic vertebrates such as reptiles. In the present study, we tested for a relationship between the presence of intraspecific colour polymorphism and the age of snake species. Using phylogenetic comparative methods, we demonstrate that the presence of intraspecific colour polymorphism is correlated with the age of a species, with polymorphic snake species being significantly older than monomorphic species. Understanding how species have dealt with past environmental modifications, such as climate change, can provide important insights into how they are likely to respond in the future to ongoing climate warming.

Temporal and spatial origin of Gesneriaceae in the New World inferred from plastid DNA sequences

Gesneriaceae are represented in the New World (NW) by a major clade (c. 1000 species) currently recognized as subfamily Gesnerioideae. Radiation of this group occurred in all biomes of tropical America and was accompanied by extensive phenotypic and ecological diversification. Here we performed phylogenetic analyses using DNA sequences from three plastid loci to reconstruct the evolutionary history of Gesnerioideae and to investigate its relationship with other lineages of Gesneriaceae and Lamiales. Our molecular data confirm the inclusion of the South Pacific Coronanthereae and the Old World (OW) monotypic genus Titanotrichum in Gesnerioideae and the sister-group relationship of this subfamily to the rest of the OW Gesneriaceae. Calceolariaceae and the NW genera Peltanthera and Sanango appeared successively sister to Gesneriaceae, whereas Cubitanthus, which has been previously assigned to Gesneriaceae, is shown to be related to Linderniaceae. Based on molecular dating and biogeographical reconstruction analyses, we suggest that ancestors of Gesneriaceae originated in South America during the Late Cretaceous. Distribution of Gesneriaceae in the Palaeotropics and Australasia was inferred as resulting from two independent long-distance dispersals during the Eocene and Oligocene, respectively. In a short time span starting at 34 Mya, ancestors of Gesnerioideae colonized several Neotropical regions including the tropical Andes, Brazilian Atlantic forest, cerrado, Central America and the West Indies. Subsequent diversification within these areas occurred largely in situ and was particularly extensive in the mountainous systems of the Andes, Central America and the Brazilian Atlantic forest. Only two radiations account for 90% of the diversity of Gesneriaceae in the Brazilian Atlantic forest, whereas half of the species richness in the northern Andes and Central America originated during the last 10 Myr from a single radiation.

Phylogenomics of C(4) photosynthesis in sedges (Cyperaceae): multiple appearances and genetic convergence.

C(4) photosynthesis is an adaptive trait conferring an advantage in warm and open habitats. It originated multiple times and is currently reported in 18 plant families. It has been recently shown that phosphoenolpyruvate carboxylase (PEPC), a key enzyme of the C(4) pathway, evolved through numerous independent but convergent genetic changes in grasses (Poaceae). To compare the genetics of multiple C(4) origins on a broader scale, we reconstructed the evolutionary history of the C(4) pathway in sedges (Cyperaceae), the second most species-rich C(4) family. A sedge phylogeny based on two plastome genes (rbcL and ndhF) has previously identified six fully C(4) clades. Here, a relaxed molecular clock was used to calibrate this tree and showed that the first C(4) acquisition occurred in this family between 19.6 and 10.1 Ma. According to analyses of PEPC-encoding genes (ppc), at least five distinct C(4) origins are present in sedges. Two C(4) Eleocharis species, which were unrelated in the plastid phylogeny, acquired their C(4)-specific PEPC genes from a single source, probably through reticulate evolution or a horizontal transfer event. Acquisitions of C(4) PEPC in sedges have been driven by positive selection on at least 16 codons (3.5% of the studied gene segment). These sites underwent parallel genetic changes across the five sedge C(4) origins. Five of these sites underwent identical changes also in grass and eudicot C(4) lineages, indicating that genetic convergence is most important within families but that identical genetic changes occurred even among distantly related taxa. These lines of evidence give new insights into the constraints that govern molecular evolution.

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.

Annonaceae substitution rates: a codon model perspective

The Annonaceae includes cultivated species of economic interest and represents an important source of information for better understanding the evolution of tropical rainforests. In phylogenetic analyses of DNA sequence data that are used to address evolutionary questions, it is imperative to use appropriate statistical models. Annonaceae are cases in point: Two sister clades, the subfamilies Annonoideae and Malmeoideae, contain the majority of Annonaceae species diversity. The Annonoideae generally show a greater degree of sequence divergence compared to the Malmeoideae, resulting in stark differences in branch lengths in phylogenetic trees. Uncertainty in how to interpret and analyse these differences has led to inconsistent results when estimating the ages of clades in Annonaceae using molecular dating techniques. We ask whether these differences may be attributed to inappropriate modelling assumptions in the phylogenetic analyses. Specifically, we test for (clade-specific) differences in rates of non-synonymous and synonymous substitutions. A high ratio of nonsynonymous to synonymous substitutions may lead to similarity of DNA sequences due to convergence instead of common ancestry, and as a result confound phylogenetic analyses. We use a dataset of three chloroplast genes (rbcL, matK, ndhF) for 129 species representative of the family. We find that differences in branch lengths between major clades are not attributable to different rates of non-synonymous and synonymous substitutions. The differences in evolutionary rate between the major clades of Annonaceae pose a challenge for current molecular dating techniques that should be seen as a warning for the interpretation of such results in other organisms.

Is the sword moss (Bryoxiphium) a preglacial Tertiary relict?

The disjunction of floras between East Asia, Southeast North America, West North America, and Southwest Eurasia has been interpreted in terms of the fragmentation of a once continuous mixed mesophytic forest that occurred throughout the Northern Hemisphere due to the climatic and geological changes during the late Tertiary. The sword moss, Bryoxiphium, exhibits a distribution that strikingly resembles that of the mesophytic forest elements such as Liriodendron and is considered as the only living member of an early Tertiary flora in Iceland. These hypotheses are tested here using molecular dating analyses and ancestral area estimations. The results suggest that the extant range of Bryoxiphium results from the fragmentation of a formerly wider range encompassing North America and Southeast Asia about 10 million years ago. The split of continental ancestral populations is too recent to match with a continental drift scenario but is spatially and temporally remarkably congruent with that observed in Tertiary angiosperm relict species. The timing of the colonization of Iceland from Macaronesian ancestors, about two million years ago, is, however, incompatible with the hypothesis that Bryoxiphium is the only living member of an early Tertiary flora of the island. Alaska was recurrently colonized from East Asia. The ability of Bryoxiphium to overcome large oceanic barriers is further evidenced by its occurrence on remote oceanic archipelagos. In particular, Madeira was colonized twice independently from American and East Asian ancestors, respectively. The striking range disjunction of Bryoxiphium is interpreted in terms of its mating system, as the taxon exhibits a very singular pattern of spatial segregation of the sexes.

Estimation des longueurs de branche et artefact sur la datation moléculaire

La phylogénie moléculaire fournit un outil complémentaire aux études paléontologiques et géologiques en permettant la construction des relations phylogénétiques entre espèces ainsi que l’estimation du temps de leur divergence. Cependant lorsqu’un arbre phylogénétique est inféré, les chercheurs se focalisent surtout sur la topologie, c'est-à-dire l’ordre de branchement relatif des différents nœuds. Les longueurs des branches de cette phylogénie sont souvent considérées comme des sous-produits, des paramètres de nuisances apportant peu d’information. Elles constituent cependant l’information primaire pour réaliser des datations moléculaires. Or la saturation, la présence de substitutions multiples à une même position, est un artefact qui conduit à une sous-estimation systématique des longueurs de branche. Nous avons décidé d’estimer l‘influence de la saturation et son impact sur l’estimation de l’âge de divergence. Nous avons choisi d’étudier le génome mitochondrial des mammifères qui est supposé avoir un niveau élevé de saturation et qui est disponible pour de nombreuses espèces. De plus, les relations phylogénétiques des mammifères sont connues, ce qui nous a permis de fixer la topologie, contrôlant ainsi un des paramètres influant la longueur des branches. Nous avons utilisé principalement deux méthodes pour améliorer la détection des substitutions multiples : (i) l’augmentation du nombre d’espèces afin de briser les plus longues branches de l’arbre et (ii) des modèles d’évolution des séquences plus ou moins réalistes. Les résultats montrèrent que la sous-estimation des longueurs de branche était très importante (jusqu'à un facteur de 3) et que l’utilisation d'un grand nombre d’espèces est un facteur qui influence beaucoup plus la détection de substitutions multiples que l’amélioration des modèles d’évolutions de séquences. Cela suggère que même les modèles d’évolution les plus complexes disponibles actuellement, (exemple: modèle CAT+Covarion, qui prend en compte l’hétérogénéité des processus de substitution entre positions et des vitesses d’évolution au cours du temps) sont encore loin de capter toute la complexité des processus biologiques. Malgré l’importance de la sous-estimation des longueurs de branche, l’impact sur les datations est apparu être relativement faible, car la sous-estimation est plus ou moins homothétique. Cela est particulièrement vrai pour les modèles d’évolution. Cependant, comme les substitutions multiples sont le plus efficacement détectées en brisant les branches en fragments les plus courts possibles via l’ajout d’espèces, se pose le problème du biais dans l’échantillonnage taxonomique, biais dû à l‘extinction pendant l’histoire de la vie sur terre. Comme ce biais entraine une sous-estimation non-homothétique, nous considérons qu’il est indispensable d’améliorer les modèles d’évolution des séquences et proposons que le protocole élaboré dans ce travail permettra d’évaluer leur efficacité vis-à-vis de la saturation.

Systématique et biogéographie du groupe Caesalpinia (famille Leguminosae)

Parmi les lignées des Caesalpinioideae (dans la famille des Leguminosae), l’un des groupes importants au sein duquel les relations phylogénétiques demeurent nébuleuses est le « groupe Caesalpinia », un clade de plus de 205 espèces, réparties présentement entre 14 à 21 genres. La complexité taxonomique du groupe Caesalpinia provient du fait qu’on n’arrive pas à résoudre les questions de délimitations génériques de Caesalpinia sensu lato (s.l.), un regroupement de 150 espèces qui sont provisoirement classées en huit genres. Afin d’arriver à une classification générique stable, des analyses phylogénétiques de cinq loci chloroplastiques et de la région nucléaire ITS ont été effectuées sur une matrice comportant un échantillonnage taxonomique du groupe sans précédent (~84% des espèces du groupe) et couvrant la quasi-totalité de la variation morphologique et géographique du groupe Caesalpinia. Ces analyses ont permis de déterminer que plusieurs genres du groupe Caesalpinia, tels que présentement définis, sont polyphylétiques ou paraphylétiques. Nous considérons que 26 clades bien résolus représentent des genres, et une nouvelle classification générique du groupe Caesalpinia est proposée : elle inclut une clé des genres, une description des 26 genres et des espèces acceptées au sein de ces groupes. Cette nouvelle classification maintient l’inclusion de douze genres (Balsamocarpon, Cordeauxia, Guilandina, Haematoxylum, Hoffmanseggia, Lophocarpinia, Mezoneuron, Pomaria, Pterolobium, Stenodrepanum, Stuhlmannia, Zuccagnia) et en abolit deux (Stahlia et Poincianella). Elle propose aussi de réinstaurer deux genres (Biancaea et Denisophytum), de reconnaître cinq nouveaux genres (Arquita, Gelrebia, Hererolandia, Hultholia et Paubrasilia), et d’amender la description de sept genres (Caesalpinia, Cenostigma, Coulteria, Erythrostemon, Libidibia, Moullava, Tara). Les résultats indiquent qu’il y aurait possiblement aussi une 27e lignée qui correspondrait au genre Ticanto, mais un échantillonage taxonomique plus important serait nécéssaire pour éclaircir ce problème. Les espèces du groupe Caesalpinia ont une répartition pantropicale qui correspond presque parfaitement aux aires du biome succulent, mais se retrouvent aussi dans les déserts, les prairies, les savanes et les forêts tropicales humides. À l’échelle planétaire, le biome succulent consiste en une série d’habitats arides ou semi-arides hautement fragmentés et caractérisés par l’absence de feu, et abrite souvent des espèces végétales grasses, comme les Cactacées dans les néo-tropiques et les Euphorbiacées en Afrique. L’histoire biogéographique du groupe Caesalpinia a été reconstruite afin de mieux comprendre l’évolution de la flore au sein de ce biome succulent. Ce portrait biogéographique a été obtenu grâce à des analyses de datations moléculaires et des changements de taux de diversification, à une reconstruction des aires ancestrales utilisant le modèle de dispersion-extinction-cladogenèse, et à la reconstruction de l’évolution des biomes et du port des plantes sur la phylogénie du groupe Caesalpinia. Ces analyses démontrent que les disjonctions trans-continentales entre espèces sœurs qui appartiennent au même biome sont plus fréquentes que le nombre total de changements de biomes à travers la phylogénie, suggérant qu’il y a une forte conservation de niches, et qu’il est plus facile de bouger que de changer et d’évoluer au sein d’un biome différent. Par ailleurs, contrairement à nos hypothèses initiales, aucun changement de taux de diversification n’est détecté dans la phylogénie, même lorsque les espèces évoluent dans des biomes différents ou qu’il y a changement de port de la plante, et qu’elle se transforme, par exemple, en liane ou herbacée. Nous suggérons que même lorsqu’ils habitent des biomes très différents, tels que les savanes ou les forêts tropicales humides, les membres du groupe Caesalpinia se retrouvent néanmoins dans des conditions écologiques locales qui rappellent celles du biome succulent. Finalement, bien que la diversité des espèces du biome succulent ne se compare pas à celle retrouvée dans les forêts tropicales humides, ce milieu se distingue par un haut taux d’espèces endémiques, réparties dans des aires disjointes. Cette diversité spécifique est probablement sous-estimée et mérite d’être évaluée attentivement, comme en témoigne la découverte de plusieurs nouvelles espèces d’arbres et arbustes de légumineuses dans la dernière décennie. Le dernier objectif de cette thèse consiste à examiner les limites au niveau spécifique du complexe C. trichocarpa, un arbuste des Andes ayant une population disjointe au Pérou qui représente potentiellement une nouvelle espèce. Des analyses morphologiques et moléculaires sur les populations présentes à travers les Andes permettent de conclure que les populations au Pérou représentent une nouvelle espèce, qui est génétiquement distincte et comporte des caractéristiques morphologiques subtiles permettant de la distinguer des populations retrouvées en Argentine et en Bolivie. Nous décrivons cette nouvelle espèce, Arquita grandiflora, dans le cadre d’une révision taxonomique du genre Arquita, un clade de cinq espèces retrouvées exclusivement dans les vallées andines.

Are Cape floral clades the same age? Contemporaneous origins of two lineages in the genistoids s.l. (Fabaceae)

The hypothesis that the elements of the modern species-rich flora of the Cape Floristic Region (CFR), South Africa, originated more or less simultaneously at the Miocene/Pliocene boundary, in response to the development of a mediterranean climate, has been challenged by numerous molecular dating estimates of Cape floral clades. These studies reveal a more gradual emergence, with the oldest clades originating in the Eocene, but others appearing later, some as recently as the Pliocene. That there are factors which might affect the dates recovered, such as choice of calibration point, analysis method, sampling density and the delimitation of Cape floral clades, suggests a need for further critical evaluation of the age estimates presented to date. In this study, the dates of origin of two Cape floral clades (the legume Crotalarieae p.p. and Podalyrieae) are estimated, constrained by a shared calibration point in a single analysis using an rDNA ITS phylogeny in which 633 taxa are sampled. The results indicate that these two clades arose contemporaneously 44-46 mya, not at the Miocene/Pliocene boundary as had been previously supposed. The contemporaneous origin of these Cape floral clades suggests that additional more inclusive analyses are needed before rejecting the hypothesis that a. single environmental trigger explains the establishment of Cape floral clades. (c) 2007 Elsevier Inc. All rights reserved.