Testing the link between the latitudinal gradient in species richness and rates of molecular evolution

Numerous hypotheses have been proposed to explain latitudinal gradients in species richness, but all are subject to ongoing debate. Here we examine Rohde's (1978, 1992) hypothesis, which proposes that climatic conditions at low latitudes lead to elevated rates of speciation. This hypothesis predicts that rates of molecular evolution should increase towards lower latitudes, but this prediction has never been tested. We discuss potential links between rates of molecular evolution and latitudinal diversity gradients, and present the first test of latitudinal variation in rates of molecular evolution. Using 45 phylogenetically independent, latitudinally separated pairs of bird species and higher taxa, we compare rates of evolution of two mitochondrial genes and DNA-DNA hybridization distances. We find no support for an effect of latitude on rate of molecular evolution. This result casts doubt on the generality of a key component of Rohde's hypothesis linking climate and speciation.

Combining molecular evolution and environmental genomics to unravel adaptive processes of MHC class IIB diversity in European minnows (Phoxinus phoxinus)

Host-pathogen interactions are a major evolutionary force promoting local adaptation. Genes of the major histocompatibility complex (MHC) represent unique candidates to investigate evolutionary processes driving local adaptation to parasite communities. The present study aimed at identifying the relative roles of neutral and adaptive processes driving the evolution of MHC class IIB (MHCIIB) genes in natural populations of European minnows (Phoxinus phoxinus). To this end, we isolated and genotyped exon 2 of two MHCIIB gene duplicates (DAB1 and DAB3) and 1665 amplified fragment length polymorphism (AFLP) markers in nine populations, and characterized local bacterial communities by 16S rDNA barcoding using 454 amplicon sequencing. Both MHCIIB loci exhibited signs of historical balancing selection. Whereas genetic differentiation exceeded that of neutral markers at both loci, the populations' genetic diversities were positively correlated with local pathogen diversities only at DAB3. Overall, our results suggest pathogen-mediated local adaptation in European minnows at both MHCIIB loci. While at DAB1 selection appears to favor different alleles among populations, this is only partially the case in DAB3, which appears to be locally adapted to pathogen communities in terms of genetic diversity. These results provide new insights into the importance of host-pathogen interactions in driving local adaptation in the European minnow, and highlight that the importance of adaptive processes driving MHCIIB gene evolution may differ among duplicates within species, presumably as a consequence of alternative selective regimes or different genomic context.

Multiscale phylogeography: glacial history and autopolyploidy of Biscutella laevigata L. (Brassicaceae) in the Western Alps

Résumé Les changements climatiques du Quaternaire ont eu une influence majeure sur la distribution et l'évolution des biota septentrionaux. Les Alpes offrent un cadre spatio-temporel bien étudié pour comprendre la réactivité de la flore et le potentiel d'adaptation d'une espèce végétale face aux changements climatiques. Certaines hypothèses postulent une diversification des espèces en raison de la disparition complète de la flore des Alpes et d'un isolement important des espèces dans des refuges méridionaux durant les dernières glaciations (Tabula Rasa). Une autre hypothèse stipule le maintien de poches de résistance pour la végétation au coeur des Alpes (Nunataks). Comme de nombreuses espèces végétales présentant un grand succès écologique semblent avoir réagi aux glaciations par la multiplication de leur génome (autopolyploïdie), leur étude en milieu naturel devrait permettre de comprendre les avantages inhérents à la polyploïdie. Biscutella laevigata est un modèle emblématique de biogéographie historique, diverses études ayant montré que des populations diploïdes sont actuellement isolées dans les zones restées déglacées durant le dernier maximum glaciaire, alors que des tétraploïdes ont recolonisé l'ensemble des zones alpines mises à nu par le retrait des glaciers. Si le contexte périglaciaire semble avoir favorisé ce jeune complexe autopolyploïde, les circonstances et les avantages de cette mutation génomique ne sont pas encore clairs. Y a-t-il eu de multiples événements de polyploïdisation ? Dans quelle mesure affecte(nt)il(s) la diversité génétique et le potentiel évolutif des polyploïdes ? Les polyploïdes ont-ils une grande flexibilité génomique, favorisant une radiation adaptative, ou doivent-ils leur succès à une grande plasticité écologique ? Cette étude aborde ces questions à différentes échelles spatiales et temporelles. L'échelle régionale des Alpes occidentales permet d'aborder les facteurs distaux (aspects historiques), alors que l'échelle locale cherche à appréhender les facteurs proximaux (mécanismes évolutifs). Dans les Alpes occidentales, des populations ont été densément échantillonnées et étudiées grâce à (1) leur cytotype, (2) leur appartenance taxonomique, (3) leur habitat et (4) des marqueurs moléculaires de l'ADN chloroplastique, en vue d'établir leurs affinités évolutives. Á l'échelle locale, deux systèmes de population ont été étudiés : l'un où les populations persistent en périphérie de l'aire de distribution et l'autre au niveau du front actif de colonisation, en marge altitudinale. Les résultats à l'échelle des Alpes occidentales révèlent les sites d'intérêt (refuges glaciaires, principales barrières et voies de recolonisation) pour une espèce représentative des pelouses alpines, ainsi que pour la biodiversité régionale. Les Préalpes ont joué un rôle important dans le maintien de populations à proximité immédiate des Alpes centrales et dans l'évolution du taxon, voire de la végétation. Il est aussi démontré que l'époque glaciaire a favorisé l'autopolyploïdie polytopique et la recolonisation des Alpes occidentales par des lignées distinctes qui s'hybrident au centre des Alpes, influençant fortement leur diversité génétique et leur potentiel évolutif. L'analyse de populations locales en situations contrastées à l'aide de marqueurs AFLP montre qu'au sein d'une lignée présentant une grande expansion, la diversité génétique est façonnée par des forces évolutives différentes selon le contexte écologique et historique. Les populations persistant présentent une dispersion des gènes restreinte, engendrant une diversité génétique assez faible, mais semblent adaptées aux conditions locales de l'environnement. À l'inverse, les populations colonisant la marge altitudinale sont influencées par les effets de fondation conjugués à une importante dispersion des gènes et, si ces processus impliquent une grande diversité génétique, ils engendrent une répartition aléatoire des génotypes dans l'environnement. Les autopolyploïdes apparaissent ainsi comme capables de persister face aux changements climatiques grâce à certaines facultés d'adaptation locale et de grandes capacités à maintenir une importante diversité génétique lors de la recolonisation post-glaciaire. Summary The extreme climate changes of the Quaternary have had a major influence on species distribution and evolution. The European Alps offer a great framework to investigate flora reactivity and the adaptive potential of species under changing climate. Some hypotheses postulate diversification due to vegetation removal and important isolation in southern refugia (Tabula Rasa), while others explain phylogeographic patterns by the survival of species in favourable Nunataks within the Alps. Since numerous species have successfully reacted to past climate changes by genome multiplication (autopolyploidy), studies of such taxa in natural conditions is likely to explain the ecological success and the advantages of autopolyploidy. Early cytogeographical surveys of Biscutella laevigata have shed light on the links between autopolyploidy and glaciations by indicating that diploids are now spatially isolated in never-glaciated areas, while autotetraploids have recolonised the zones covered by glaciers- during the last glacial maximum. A periglacial context apparently favoured this young autopolyploid complex but the circumstances and the advantages of this genomic mutation remain unclear. What is the glacial history of the B. laevigata autopolyploid complex? Are there multiple events of polyploidisation? To what extent do they affect the genetic diversity and the evolutionary potential of polyploids? Is recolonisation associated with adaptive processes? How does long-term persistence affect genetic diversity? The present study addresses these questions at different spatiotemporal scales. A regional survey at the Western Alps-scale tackles distal factors (evolutionary history), while local-scale studies explore proximal factors (evolutionary mechanisms). In the Western Alps, populations have been densely sampled and studied from the (1) cytotypic, (2) morphotaxonomic, (3) habitat point of views, as well as (4) plastid DNA molecular markers, in order to infer their relationships and establish the maternal lineages phylogeography. At the local scale, populations persisting at the rear edge and populations recolonising the attitudinal margin at the leading edge have been studied by AFLPs to show how genetic diversity is shaped by different evolutionary forces across the species range. The results at the regional scale document the glacial history of a widespread species, representative of alpine meadows, in a regional area of main interest (glacial refugia, main barriers and recolonisation routes) and points out to sites of interest for regional biodiversity. The external Alps have played a major role in the maintenance of populations near the central Alps during the Last Glacial Maximum and influenced the evolution of the species, and of vegetation. Polytopic autopolyploidy in different biogeographic districts is also demonstrated. The species has had an important and rapid radiation because recolonisation took place from different refugia. The subsequent recolonisation of the Western Alps was achieved by independent lineages that are presently admixing in the central Alps. The role of the Pennic summit line is underlined as a great barrier that was permeable only through certain favourable high-altitude passes. The central Alps are thus viewed as an important crossroad where genomes with different evolutionary histories are meeting and admixing. The AFLP analysis and comparison of local populations growing in contrasted ecological and historical situations indicate that populations persisting in the external Alps present restricted gene dispersal and low genetic diversity but seem in equilibrium with their environment. On the contrary, populations colonising the attitudinal margin are mainly influenced by founder effects together with great gene dispersal and genotypes have a nearly random distribution, suggesting that recolonisation is not associated with adaptive processes. Autopolyploids that locally persist against climate changes thus seem to present adaptive ability, while those that actively recolonise the Alps are successful because of their great capacity to maintain a high genetic diversity against founder effects during recolonisation.

L'épigénétique, moteur de l'évolution d'un vertébré asexué

L’objectif de cette thèse est de déterminer l’étendue de la variabilité épigénétique, plus particulièrement du polymorphisme de méthylation de l’ADN, non liée à la variabilité génétique dans les populations asexuées en milieu naturel. Cette évaluation nous a permis de mieux cerner l’importance que peuvent avoir les processus épigénétiques en écologie et en évolution. Le modèle biologique utilisé est l’hybride clonal du complexe gynogénétique Chrosomus eos-neogaeus. Malgré une homogénéité génétique, une importante variabilité phénotypique est observée entre les hybrides d’une même lignée clonale mais retrouvés dans des environnements différents. L’influence des processus épigénétiques apporte une explication sur ce paradoxe. L’épigénétique se définit comme une modification de l’expression des gènes sans changement de la séquence d’ADN. La diversité des phénotypes peut entre autre s’expliquer par des patrons de méthylation différentiels des gènes et/ou des allèles des gènes entre les hybrides génétiquement identiques. La diversité des lignées épiclonales peut quant à elle s’expliquer par la colonisation de plusieurs lignées épiclonales, s’établir en réponse à l’environnement ou de façon aléatoire. Plusieurs méthodes seront utilisées afin de survoler le génome des hybrides clonaux pour mettre en évidence le polymorphisme de méthylation de l’ADN à l’échelle de l’individu et entre les individus de différentes populations.

First steps in experimental cancer evolution

Evolutionary processes play a central role in the development, progression and response to treatment of cancers. The current challenge facing researchers is to harness evolutionary theory to further our understanding of the clinical progression of cancers. Central to this endeavour will be the development of experimental systems and approaches by which theories of cancer evolution can be effectively tested. We argue here that the experimental evolution approach – whereby evolution is observed in real time and which has typically employed microorganisms – can be usefully applied to cancer. This approach allows us to disentangle the ecological causes of natural selection, identify the genetic basis of evolutionary changes and determine their repeatability. Cell cultures used in cancer research share many of the desirable traits that make microorganisms ideal for studying evolution. As such, experimental cancer evolution is feasible and likely to give great insight into the selective pressures driving the evolution of clinically destructive cancer traits. We highlight three areas of evolutionary theory with importance to cancer biology that are amenable to experimental evolution: drug resistance, social evolution and resource competition. Understanding the diversity, persistence and evolution of cancers is vital for treatment and drug development, and an experimental evolution approach could provide strategic directions and focus for future research.

Using experimental evolution to explore natural patterns between bacterial motility and resistance to bacteriophages

Resistance of bacteria to phages may be gained by alteration of surface proteins to which phages bind, a mechanism that is likely to be costly as these molecules typically have critical functions such as movement or nutrient uptake. To address this potential trade-off, we combine a systematic study of natural bacteria and phage populations with an experimental evolution approach. We compare motility, growth rate and susceptibility to local phages for 80 bacteria isolated from horse chestnut leaves and, contrary to expectation, find no negative association between resistance to phages and bacterial motility or growth rate. However, because correlational patterns (and their absence) are open to numerous interpretations, we test for any causal association between resistance to phages and bacterial motility using experimental evolution of a subset of bacteria in both the presence and absence of naturally associated phages. Again, we find no clear link between the acquisition of resistance and bacterial motility, suggesting that for these natural bacterial populations, phage-mediated selection is unlikely to shape bacterial motility, a key fitness trait for many bacteria in the phyllosphere. The agreement between the observed natural pattern and the experimental evolution results presented here demonstrates the power of this combined approach for testing evolutionary trade-offs.

The behavior and natural history of Chartergellus, a little-known genus of neotropical social wasps (Vespidae Polistinae Epiponini)

This study reviews published data on the behavior and natural history of Chartergellus and presents the first observations on social interactions in this genus of tropical swarm-founding wasps. Observations of Chartergellus golfitensis in Costa Rica and C. punctatior in Colombia showed that queens perform a post-oviposition egg-guarding vigil, and a bending display like that characteristic of epiponine social wasps that lack consistent morphological differences between workers and queens and have caste determination in the adult stage. Young, old, and queen (egg-laying) females of C. golfitensis showed small differences that indicate color changes with age, and structural differences that could be due to seasonal or colony-cycle changes in developmental conditions, but do not rule out the possibility of pre-adult caste determination, a phenomenon that needs to be carefully distinguished from pre-adult caste bias. Sexual dimorphism and the behavior of males at the nest in C. golfitensis is described, as well as the aggressive and avoidance behavior of females toward males. Nest structure in both species is as described previously for Chartergellus species, but some anomalies and their possible evolutionary significance are discussed. Cell initiation by an egg-laying queen, a behavior never seen by workers, and by a young female with slightly developed ovaries, may be vestiges of ancestral solitary reproductive traits where developed ovaries are associated with cell construction. © 2010 Dipartimento di Biologia Evoluzionistica dell'Università, Firenze, Italia.

Pollination ecology and reproductive success in isolated populations of flowering plants: Primula apennina Widmer, Dictamnus albus L. and Convolvulus lineatus L.

This research focuses on reproductive biology and pollination ecology of entomophilous angiosperms, with particular concern to reproductive success in small and isolated populations of species that occur at their distribution limits or are endemic. I considered three perennial herbs as model species: Primula apennina Widmer, Dictamnus albus L. and Convolvulus lineatus L. I carried out field work on natural populations and performed laboratory analyses on specific critical aspects (resource allocation, pollen viability, stigmatic receptivity, physiological self-incompatibility, seed viability), through which I analysed different aspects related to plant fitness, such as production of viable seed, demographic structure of populations, type and efficiency of plant-pollinator system, and limiting factors.

Pliocene-Pleistocene stack of globally distributed benthic stable oxygen isotope records

We present a 5.3-Myr stack (the ''LR04'' stack) of benthic d18O records from 57 globally distributed sites aligned by an automated graphic correlation algorithm. This is the first benthic delta18O stack composed of more than three records to extend beyond 850 ka, and we use its improved signal quality to identify 24 new marine isotope stages in the early Pliocene. We also present a new LR04 age model for the Pliocene-Pleistocene derived from tuning the delta18O stack to a simple ice model based on 21 June insolation at 65 N. Stacked sedimentation rates provide additional age model constraints to prevent overtuning. Despite a conservative tuning strategy, the LR04 benthic stack exhibits significant coherency with insolation in the obliquity band throughout the entire 5.3 Myr and in the precession band for more than half of the record. The LR04 stack contains significantly more variance in benthic delta18O than previously published stacks of the late Pleistocene as the result of higher resolution records, a better alignment technique, and a greater percentage of records from the Atlantic. Finally, the relative phases of the stack's 41- and 23-kyr components suggest that the precession component of delta18O from 2.7-1.6 Ma is primarily a deep-water temperature signal and that the phase of d18O precession response changed suddenly at 1.6 Ma.

Patterns and ecosystem consequences of shark declines in the ocean

Whereas many land predators disappeared before their ecological roles were studied, the decline of marine apex predators is still unfolding. Large sharks in particular have experienced rapid declines over the last decades. In this study, we review the documented changes in exploited elasmobranch communities in coastal, demersal, and pelagic habitats, and synthesize the effects of sharks on their prey and wider communities. We show that the high natural diversity and abundance of sharks is vulnerable to even light fishing pressure. The decline of large predatory sharks reduces natural mortality in a range of prey, contributing to changes in abundance, distribution, and behaviour of small elasmobranchs, marine mammals, and sea turtles that have few other predators. Through direct predation and behavioural modifications, top-down effects of sharks have led to cascading changes in some coastal ecosystems. In demersal and pelagic communities, there is increasing evidence of mesopredator release, but cascading effects are more hypothetical. Here, fishing pressure on mesopredators may mask or even reverse some ecosystem effects. In conclusion, large sharks can exert strong top-down forces with the potential to shape marine communities over large spatial and temporal scales. Yet more empirical evidence is needed to test the generality of these effects throughout the ocean.

Location and ages of terrestrial peatlands located on continental shelves and in coastal sediments

This synthesis dataset contains records of freshwater peat and lake sediments from continental shelves and coastal areas. Information included is site location (when available), thickness and description of terrestrial sediments as well as underlying and overlying sediments, dates (when available), and references.

GENETIC VARIATION, LOCAL ADAPTATION AND POPULATION STRUCTURE IN NORTH AMERICAN RED OAK SPECIES, QUERCUS RUBRA L. AND Q. ELLIPSOIDALIS E. J. HILL

Forest trees, like oaks, rely on high levels of genetic variation to adapt to varying environmental conditions. Thus, genetic variation and its distribution are important for the long-term survival and adaptability of oak populations. Climate change is projected to lead to increased drought and fire events as well as a northward migration of tree species, including oaks. Additionally, decline in oak regeneration has become increasingly concerning since it may lead to decreased gene flow and increased inbreeding levels. This will in turn lead to lowered levels of genetic diversity, negatively affecting the growth and survival of populations. At the same time, populations at the species’ distribution edge, like those in this study, could possess important stores of genetic diversity and adaptive potential, while also being vulnerable to climatic or anthropogenic changes. A survey of the level and distribution of genetic variation and identification of potentially adaptive genes is needed since adaptive genetic variation is essential for their long-term survival. Oaks possess a remarkable characteristic in that they maintain their species identity and specific environmental adaptations despite their propensity to hybridize. Thus, in the face of interspecific gene flow, some areas of the genome remain differentiated due to selection. This characteristic allows the study of local environmental adaptation through genetic variation analyses. Furthermore, using genic markers with known putative functions makes it possible to link those differentiated markers to potential adaptive traits (e.g., flowering time, drought stress tolerance). Demographic processes like gene flow and genetic drift also play an important role in how genes (including adaptive genes) are maintained or spread. These processes are influenced by disturbances, both natural and anthropogenic. An examination of how genetic variation is geographically distributed can display how these genetic processes and geographical disturbances influence genetic variation patterns. For example, the spatial clustering of closely related trees could promote inbreeding with associated negative effects (inbreeding depression), if gene flow is limited. In turn this can have negative consequences for a species’ ability to adapt to changing environmental conditions. In contrast, interspecific hybridization may also allow the transfer of genes between species that increase their adaptive potential in a changing environment. I have studied the ecologically divergent, interfertile red oaks, Quercus rubra and Q. ellipsoidalis, to identify genes with potential roles in adaptation to abiotic stress through traits such as drought tolerance and flowering time, and to assess the level and distribution of genetic variation. I found evidence for moderate gene flow between the two species and low interspecific genetic differences at most genetic markers (Lind and Gailing 2013). However, the screening of genic markers with potential roles in phenology and drought tolerance led to the identification of a CONSTANS-like (COL) gene, a candidate gene for flowering time and growth. This marker, located in the coding region of the gene, was highly differentiated between the two species in multiple geographical areas, despite interspecific gene flow, and may play a role in reproductive isolation and adaptive divergence between the two species (Lind-Riehl et al. 2014). Since climate change could result in a northward migration of trees species like oaks, this gene could be important in maintaining species identity despite increased contact zones between species (e.g., increased gene flow). Finally I examined differences in spatial genetic structure (SGS) and genetic variation between species and populations subjected to different management strategies and natural disturbances. Diverse management activities combined with various natural disturbances as well as species specific life history traits influenced SGS patterns and inbreeding levels (Lind-Riehl and Gailing submitted).