Pablo Vargas

Regulation of dendritic cell migration by CD74, the MHC class II-associated invariant chain.

Dendritic cells (DCs) sample peripheral tissues of the body in search of antigens to present to T cells. This requires two processes, antigen processing and cell motility, originally thought to occur independently. We found that the major histocompatibility complex II–associated invariant chain (Ii or CD74), a known regulator of antigen processing, negatively regulates DC motility in vivo. By using microfabricated channels to mimic the confined environment of peripheral tissues, we found that wild-type DCs alternate between high and low motility, whereas Ii-deficient cells moved in a faster and more uniform manner. The regulation of cell motility by Ii depended on the actin-based motor protein myosin II. Coupling antigen processing and cell motility may enable DCs to more efficiently detect and process antigens within a defined space.

Unparalleled rates of species diversification in Europe

The most rapid species radiations have been reported from ‘evolutionary laboratories’, such as the Andes and the Cape of South Africa, leading to the prevailing view that diversification elsewhere has not been as dramatic. However, few studies have explicitly assessed rates of diversification in northern regions such as Europe. Here, we show that carnations (Dianthus, Caryophyllaceae), a well-known group of plants from temperate Eurasia, have diversified at the most rapid rate ever reported in plants or terrestrial vertebrates. Using phylogenetic methods, we found that the majority of species of carnations belong to a lineage that is remarkably species-rich in Europe, and arose at the rate of 2.2–7.6 species per million years. Unlike most previous studies that have inferred rates of diversification in young diverse groups, we use a conservative approach throughout that explicitly incorporates the uncertainties associated with phylogenetic inference, molecular dating and incomplete taxon sampling. We detected a shift in diversification rates of carnations coinciding with a period of increase in climatic aridity in the Pleistocene, suggesting a link between climate and biodiversity. This explosive radiation suggests that Europe, the continent with the worlds best-studied flora, has been underestimated as a cradle of recent and rapid speciation.

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.

A role for lipid bodies in the cross-presentation of phagocytosed antigens by MHC class I in dendritic cells

Dendritic cells (DCs) have the striking ability to cross-present exogenous antigens in association with major histocompatibility complex (MHC) class I to CD8(+) T cells. However, the intracellular pathways underlying cross-presentation remain ill defined. Current models involve cytosolic proteolysis of antigens by the proteasome and peptide import into endoplasmic reticulum (ER) or phagosomal lumen by the transporters associated with antigen processing (TAP1 and TAP2). Here, we show that DCs expressed an ER-resident 47 kDa immune-related GTPase, Igtp (Irgm3). Igtp resides on ER and lipid body (LB) membranes where it binds the LB coat component ADFP. Inactivation of genes encoding for either Igtp or ADFP led to defects in LB formation in DCs and severely impaired cross-presentation of phagocytosed antigens to CD8(+) T cells but not antigen presentation to CD4(+) T cells. We thus define a new role for LB organelles in regulating cross-presentation of exogenous antigens to CD8(+) T lymphocytes in DCs.

Biogeographic patterns in Mediterranean and Macaronesian species of Saxifraga (Saxifragaceae) inferred from phylogenetic analyses of ITS sequences

A biogeographic study of Saxifraga section Saxifraga was performed based on phylogenetic analyses of ITS (internal transcribed spacer) sequences of nuclear ribosomal DNA. ITS sequences from 21 species and 31 populations were examined to identify colonization patterns for the two species of Saxifraga occurring in Macaronesia and for S. globulifera in the west Mediterranean basin. Phylogenetic analysis of the sequence data yield a single most parsimonious tree with many of the major clades well supported by bootstrap and decay values. The ITS tree provided resolution at specific and populational levels that points to two biogeographic patterns within the genus. In contrast to the molecular evidence provided by other authors for a Mediterranean origin of several Macaronesian genera of angiosperms, our results indicate that the Madeiran archipelago was colonized a single time by a species of Saxifraga originating from the Eurosiberian region. On the other hand, the molecular evidence also suggests that populations of S. globulifera from North Africa have been isolated for a long time from populations occurring in the Iberian Peninsula, and that the endemic S. reuteriana has evolved from the Iberian populations of S. globulifera. The Mediterranean Sea has probably been an effective isolating barrier for some plant groups that occur in Europe and North Africa.

Coalescent simulations reveal hybridization and incomplete lineage sorting in Mediterranean Linaria.

We examined the phylogenetic history of Linaria with special emphasis on the Mediterranean sect. Supinae (44 species). We revealed extensive highly supported incongruence among two nuclear (ITS, AGT1) and two plastid regions (rpl32-trnLUAG, trnS-trnG). Coalescent simulations, a hybrid detection test and species tree inference in *BEAST revealed that incomplete lineage sorting and hybridization may both be responsible for the incongruent pattern observed. Additionally, we present a multilabelled *BEAST species tree as an alternative approach that allows the possibility of observing multiple placements in the species tree for the same taxa. That permitted the incorporation of processes such as hybridization within the tree while not violating the assumptions of the *BEAST model. This methodology is presented as a functional tool to disclose the evolutionary history of species complexes that have experienced both hybridization and incomplete lineage sorting. The drastic climatic events that have occurred in the Mediterranean since the late Miocene, including the Quaternary-type climatic oscillations, may have made both processes highly recurrent in the Mediterranean flora.

Phylogenetics of Olea (Oleaceae) based on plastid and nuclear ribosomal DNA sequences: Tertiary climatic shifts and lineage differentiation times

BACKGROUND AND AIMS The genus Olea (Oleaceae) includes approx. 40 taxa of evergreen shrubs and trees classified in three subgenera, Olea, Paniculatae and Tetrapilus, the first of which has two sections (Olea and Ligustroides). Olive trees (the O. europaea complex) have been the subject of intensive research, whereas little is known about the phylogenetic relationships among the other species. To clarify the biogeographical history of this group, a molecular analysis of Olea and related genera of Oleaceae is thus necessary. METHODS A phylogeny was built of Olea and related genera based on sequences of the nuclear ribosomal internal transcribed spacer-1 and four plastid regions. Lineage divergence and the evolution of abaxial peltate scales, the latter character linked to drought adaptation, were dated using a Bayesian method. KEY RESULTS Olea is polyphyletic, with O. ambrensis and subgenus Tetrapilus not sharing a most recent common ancestor with the main Olea clade. Partial incongruence between nuclear and plastid phylogenetic reconstructions suggests a reticulation process in the evolution of subgenus Olea. Estimates of divergence times for major groups of Olea during the Tertiary were obtained. CONCLUSIONS This study indicates the necessity of revising current taxonomic boundaries in Olea. The results also suggest that main lines of evolution were promoted by major Tertiary climatic shifts: (1) the split between subgenera Olea and Paniculatae appears to have taken place at the Miocene-Oligocene boundary; (2) the separation of sections Ligustroides and Olea may have occurred during the Early Miocene following the Mi-1 glaciation; and (3) the diversification within these sections (and the origin of dense abaxial indumentum in section Olea) was concomitant with the aridification of Africa in the Late Miocene.

Polyploid speciation inHedera (Araliaceae): Phylogenetic and biogeographic insights based on chromosome counts and ITS sequences

Variation in chromosome number and internal transcribed sequences (ITS) of nrDNA is used to infer phylogenetic relationships of a wide range ofHedera species. Polyploidy was found to be frequent inHedera, with diploid, tetraploid, hexaploid and octoploid populations being detected. Nucleotide additivity occurs in the ITS sequences of one tetraploid (H. hibernica) and two hexaploid species (H. maderensis, H. pastuchovii), suggesting that all three species originated by allopolyploidisation. ITS sequence polymorphism and nucleotide characters may indicate the presence of an ancient genome persistent only in some allopolyploid species. Phylogenetic analyses of ITS sequence data reveal two lineages ofHedera: one containing all sequences belonging to extant diploids plus the tetraploidH. algeriensis, and a second that includes this ancient ITS type and others exclusive to several polyploid species. The origin of the polyploids is evaluated on the basis of morphology, chromosome counts, ITS sequence polymorphism, and phylogenetic analyses. Reconstruction of reticulate evolution inHedera agrees with two allopolyploid areas on both sides of the Mediterranean basin. Morphological, molecular and cytological evidence also suggests an active dispersal ofHedera populations that may account for three independent introductions in Macaronesia.

Invaders of pollination networks in the Galapagos Islands: emergence of novel communities.

The unique biodiversity of most oceanic archipelagos is currently threatened by the introduction of alien species that can displace native biota, disrupt native ecological interactions, and profoundly affect community structure and stability. We investigated the threat of aliens on pollination networks in the species-rich lowlands of five Galápagos Islands. Twenty per cent of all species (60 plants and 220 pollinators) in the pooled network were aliens, being involved in 38 per cent of the interactions. Most aliens were insects, especially dipterans (36%), hymenopterans (30%) and lepidopterans (14%). These alien insects had more links than either endemic pollinators or non-endemic natives, some even acting as island hubs. Aliens linked mostly to generalized species, increasing nestedness and thus network stability. Moreover, they infiltrated all seven connected modules (determined by geographical and phylogenetic constraints) of the overall network, representing around 30 per cent of species in two of them. An astonishingly high proportion (38%) of connectors, which enhance network cohesiveness, was also alien. Results indicate that the structure of these emergent novel communities might become more resistant to certain type of disturbances (e.g. species loss), while being more vulnerable to others (e.g. spread of a disease). Such notable changes in network structure as invasions progress are expected to have important consequences for native biodiversity maintenance.

Seed dispersal networks in the Galápagos and the consequences of alien plant invasions.

Alien plants are a growing threat to the Galápagos unique biota. We evaluated the impact of alien plants on eight seed dispersal networks from two islands of the archipelago. Nearly 10 000 intact seeds from 58 species were recovered from the droppings of 18 bird and reptile dispersers. The most dispersed invaders were Lantana camara, Rubus niveus and Psidium guajava, the latter two likely benefiting from an asynchronous fruit production with most native plants, which facilitate their consumption and spread. Lava lizards dispersed the seeds of 27 species, being the most important dispersers, followed by small ground finch, two mockingbirds, the giant tortoise and two insectivorous birds. Most animals dispersed alien seeds, but these formed a relatively small proportion of the interactions. Nevertheless, the integration of aliens was higher in the island that has been invaded for longest, suggesting a time-lag between alien plant introductions and their impacts on seed dispersal networks. Alien plants become more specialized with advancing invasion, favouring more simplified plant and disperser communities. However, only habitat type significantly affected the overall network structure. Alien plants were dispersed via two pathways: dry-fruited plants were preferentially dispersed by finches, while fleshy fruited species were mostly dispersed by other birds and reptiles.