Competition may explain the fine-scale spatial patterns and genetic structure of two co-occurring plant congeners

1. The spatial distribution of individual plants within a population and the population’s genetic structure are determined by several factors, like dispersal, reproduction mode or biotic interactions. The role of interspecific interactions in shaping the spatial genetic structure of plant populations remains largely unknown. 2. Species with a common evolutionary history are known to interact more closely with each other than unrelated species due to the greater number of traits they share. We hypothesize that plant interactions may shape the fine genetic structure of closely related congeners. 3. We used spatial statistics (georeferenced design) and molecular techniques (ISSR markers) to understand how two closely related congeners, Thymus vulgaris (widespread species) and T. loscosii (narrow endemic) interact at the local scale. Specific cover, number of individuals of both study species and several community attributes were measured in a 10 × 10 m plot. 4. Both species showed similar levels of genetic variation, but differed in their spatial genetic structure. Thymus vulgaris showed spatial aggregation but no spatial genetic structure, while T. loscosii showed spatial genetic structure (positive genetic autocorrelation) at short distances. The spatial pattern of T. vulgaris’ cover showed significant dissociation with that of T. loscosii. The same was true between the spatial patterns of the cover of T. vulgaris and the abundance of T. loscosii and between the abundance of each species. Most importantly, we found a correlation between the genetic structure of T. loscosii and the abundance of T. vulgaris: T. loscosii plants were genetically more similar when they were surrounded by a similar number of T. vulgaris plants. 5. Synthesis. Our results reveal spatially complex genetic structures of both congeners at small spatial scales. The negative association among the spatial patterns of the two species and the genetic structure found for T. loscosii in relation to the abundance of T. vulgaris indicate that competition between the two species may account for the presence of adapted ecotypes of T. loscosii to the abundance of a competing congeneric species. This suggests that the presence and abundance of close congeners can influence the genetic spatial structure of plant species at fine scales.

Evolución de la vegetación en el sector biogeográfico Castellano Cantábrico durante el Cuaternario Final, a través del registro tobáceo

En esta memoria de Tesis Doctoral se aborda el estudio paleobotánico de seis yacimientos tobáceos situados en las localidades burgalesas de Tubilla del Agua, Sedano, Herrán, Tobera y Frías, y en la alavesa de Ocio. El registro fósil encontrado en estos afloramientos se analiza de forma conjunta con el objetivo de conocer la evolución de la vegetación en el sector biogeográfico Castellano Cantábrico. Este sector se considera el territorio para el cual los hallazgos paleobotánicos son representativos y extrapolables, en tanto que constituye una región homogénea desde el punto de vista florístico, que abarca todos los yacimientos prospectados. El contexto temporal en el que se enmarca este estudio es el final del Cuaternario, desde el Pleistoceno Medio hasta la actualidad. Este intervalo se ha establecido a partir de la edad de los depósitos estudiados, la cual ha sido determinada —para los yacimientos de los que no se disponía de edades fiables— mediante la datación de muestras extraídas de las diferentes unidades litológicas identificadas. Para ello han sido empleadas las técnicas de carbono-14, desequilibrio de las series del uranio y racemización de aminoácidos. Los resultados geocronológicos obtenidos junto con el análisis geomorfológico de los yacimientos han permitido vincular la génesis de las 13 unidades litológicas identificadas con diferentes estadíos climáticos. Estos abarcan un amplio rango de condiciones ambientales, desde las más extremas del Último Máximo Glacial, hasta las más benignas de los Estadíos Isotópicos Marinos interglaciares 1 y 5. Como resultado de la prospección de los depósitos de toba fueron recuperados 1.820 fósiles, la mayoría impresiones foliares, pero también moldes de estróbilos femeninos, ramas y corteza, así como 42 carbones y restos subfósiles de Pinus sp. La identificación taxonómica de estos restos se ha realizado fundamentalmente a partir del análisis de caracteres diagnósticos morfológicos. Como resultado de ello, han sido descritos 28 taxones pertenecientes a las subclases Bryidae, Polypodiidae, Pinidae y Magnoliidae. La flora de los yacimientos estudiados se puede clasificar en tres grupos en función de sus requerimientos ecológicos: (i) uno formado por dos especies de alta tolerancia a la continentalidad —Pinus nigra y Quercus faginea—, las cuales aparecen bien representadas en la mayoría de los depósitos; (ii) otro constituido fundamentalmente por un conjunto de árboles y arbustos que habitualmente tienen el papel de especies acompañantes en los bosques ibéricos submediterráneos y eurosiberianos; y (iii) un tercer grupo compuesto por taxones hidrófitos o edafohigrófilos asociados al ecosistema del fitohermo activo y la vegetación de ribera. En el capítulo de Discusión se propone y analiza la hipótesis de que P. nigra y Q. faginea habrían sido las especies protagonistas de la vegetación zonal del sector Castellano Cantábrico durante el Cuaternario Final. Estas podrían haber persistido como tal incluso durante las épocas más frías, debido a su amplia valencia ecológica y a la capacidad de reproducirse vegetativamente en el caso del quejigo. Por el contrario, los taxones mesofíticos y eurosiberianos pudieron haber sufrido la expansión y retracción de sus poblaciones al ritmo de las oscilaciones climáticas. Sin embargo, la orografía diversa del sector Castellano Cantábrico proporciona emplazamientos en los que se combinan las diversas variables fisiográficas, de tal forma que pudieron haber existido microrrefugios en los que encontraron cobijo algunos taxones mesotérmicos y eurosiberianos durante los periodos glaciales. Por último, la historia evolutiva reciente de la vegetación de este territorio ha estado marcada por la acción antrópica, la cual empezó a ser manifiesta a partir del Neolítico. Esta se tradujo en la degradación y reducción de la cubierta forestal, así como en la extinción del pino laricio del Sector Castellano Cantábrico en los dos últimos milenios. ABSTRACT This PhD Dissertation focuses in the study of six tufa formations located nearby the villages of Tubilla del Agua, Sedano, Herrán, Tobera y Frías, all of them in the province of Burgos, and Ocio, which belongs to the province of Álava. We analyze the palaeobotanical archives of these sites with the purpose of unveiling and understanding the evolution of the vegetation of the Castilian Cantabrian biogeographical sector. This area is considered to be the territory that is represented in the palaeobotanical sample of the studied tufa archives. It is the homogeneous phitogeographical area with the lowest rank that include all the sites. The time frame of this study is the last part of the Quaternary, since the Middle Pleistocene to the present time. This interval is defined by the age of the tufa deposits, which were dated —for the ones that there were not available datings— throughout the analysis of 20 tufa samples taken from the 13 identified lithostratigraphic units. The age of the samples has been determined by using the methods of radiocarbon, U-Th dating and amino acid racemization. Chronological results, along with the chronostratigraphic study of the sites has allowed us to relate the build-up of the 13 identified lithostratigraphic units with different climatic stages. These structures were deposited in a wide range of climatic conditions, from the most extreme ones of the Last Glacial Maximum, to the warmer ones of the Marine Isotopic Stages 1 and 5. A total of 1,820 fossils were recovered from the tufa deposits, most of them were leaf impressions, but also pine cones, branches and bark moulds, along with charcoal and Pinus nigra macro remains. The taxonomical identification of these remains has been done mainly through the analysis of morphological traits. As a result of this process, 28 taxa belonging to the subclass of Bryidae, Polypodiidae, Pinidae and Magnoliidae were identified. The persistency of some taxa can be traced along different climatic stages in this fossil record. This fossil flora can be classified in three different groups: (i) the first one would be composed of two species with high continental climate tolerance —Pinus nigra y Quercus faginea—, which can be found in most of the deposits, (ii) the second group would be mostly formed by trees and shrubs that usually grow in the Iberian forests as an accessory species and (iii) the third one is composed of hydrophytes or hydrophilic taxa associate to the streams, riparian zones or the active tufa ecosystem. In the Discussion chapter we propose and analyse the hypothesis that P.nigra and Q. faginea were the main species of the zonal vegetation of the Castilian Cantabrian biogeographical sector during the last part of the Quaternary. This species could have persisted due to their wide ecological amplitude and also due to the capacity of asexual reproduction in the cases of the oak. On the other hand, mesophitic taxa could have suffered the retraction and expansion of their population following the climate oscillations. However, the diverse orography of the Castilian Cantabrian biogeographical sector provides a variety of combinations of physiographic variables, which could have been suitable refuges for some of the mesophitic taxa. The recent evolutionary history of the vegetation in this territory has been affected by human activities, which started to be relevant since the Neolithic. This led to a reduction of the forests and eventually, to the extinction of P. nigra in the Castilian Cantabrian biogeographical sector in the last two thousands of years.

Distribution of haplotypes from a chromosome 21 region distinguishes multiple prehistoric human migrations

Despite mounting genetic evidence implicating a recent origin of modern humans, the elucidation of early migratory gene-flow episodes remains incomplete. Geographic distribution of haplotypes may show traces of ancestral migrations. However, such evolutionary signatures can be erased easily by recombination and mutational perturbations. A 565-bp chromosome 21 region near the MX1 gene, which contains nine sites frequently polymorphic in human populations, has been found. It is unaffected by recombination and recurrent mutation and thus reflects only migratory history, genetic drift, and possibly selection. Geographic distribution of contemporary haplotypes implies distinctive prehistoric human migrations: one to Oceania, one to Asia and subsequently to America, and a third one predominantly to Europe. The findings with chromosome 21 are confirmed by independent evidence from a Y chromosome phylogeny. Loci of this type will help to decipher the evolutionary history of modern humans.

Molecular evolution of integrins: Genes encoding integrin β subunits from a coral and a sponge

The integrin family of cell surface receptors is strongly conserved in higher animals, but the evolutionary history of integrins is obscure. We have identified and sequenced cDNAs encoding integrin β subunits from a coral (phylum Cnidaria) and a sponge (Porifera), indicating that these proteins existed in the earliest stages of metazoan evolution. The coral βCn1 and, especially, the sponge βPo1 sequences are the most divergent of the “β1-class” integrins and share a number of features not found in any other vertebrate or invertebrate integrins. Perhaps the greatest difference from other β subunits is found in the third and fourth repeats of the cysteine-rich stalk, where the generally conserved spacings between cysteines are highly variable, but not similar, in βCn1 and βPo1. Alternatively spliced cDNAs, containing a stop codon about midway through the full-length translated sequence, were isolated from the sponge library. These cDNAs appear to define a boundary between functional domains, as they would encode a protein that includes the globular ligand-binding head but would be missing the stalk, transmembrane, and cytoplasmic domains. These and other sequence comparisons with vertebrate integrins are discussed with respect to models of integrin structure and function.

Character displacement in some Cnemidophorus lizards revisited: A phylogenetic analysis

Ecological studies have demonstrated the role of competition in structuring communities; however, the importance of competition as a vehicle for evolution by natural selection and speciation remains unresolved. Study systems of insular faunas have provided several well known cases where ecological character displacement, coevolution of competitors leading to increased morphological separation, is thought to have occurred (e.g., anoline lizards and geospizine finches). Whiptail lizards (genus Cnemidophorus) from the islands of the Sea of Cortez and the surrounding mainland demonstrate a biogeographic pattern of morphological variation suggestive of character displacement. Two species of Cnemidophorus occur on the Baja peninsula, one relatively large (Cnemidophorus tigris) and one smaller (Cnemidophorus hyperythrus). Oceanic islands in the Sea of Cortez contain only single species, five of six having sizes intermediate to both species found on the Baja peninsula. On mainland Mexico C. hyperythrus is absent, whereas C. tigris is the smaller species in whiptail guilds. Here we construct a phylogeny using nucleotide sequences of the cytochrome b gene to infer the evolutionary history of body size change and historical patterns of colonization in the Cnemidophorus system. The phylogenetic analysis indicates that (i) oceanic islands have been founded at least five times from mainland sources by relatives of either C. tigris or C. hyperythrus, (ii) there have been two separate instances of character relaxation on oceanic islands for C. tigris, and (iii) there has been colonization of the oceanic island Cerralvo with retention of ancestral size for Cnemidophorus ceralbensis, a relative of C. hyperythrus. Finally, the phylogenetic analysis reveals potential cryptic species within mainland populations of C. tigris.

Chloroplast small heat shock proteins: Evidence for atypical evolution of an organelle-localized protein

Knowledge of the origin and evolution of gene families is critical to our understanding of the evolution of protein function. To gain a detailed understanding of the evolution of the small heat shock proteins (sHSPs) in plants, we have examined the evolutionary history of the chloroplast (CP)-localized sHSPs. Previously, these nuclear-encoded CP proteins had been identified only from angiosperms. This study reveals the presence of the CP sHSPs in a moss, Funaria hygrometrica. Two clones for CP sHSPs were isolated from a F. hygrometrica heat shock cDNA library that represent two distinct CP sHSP genes. Our analysis of the CP sHSPs reveals unexpected evolutionary relationships and patterns of sequence conservation. Phylogenetic analysis of the CP sHSPs with other plant CP sHSPs and eukaryotic, archaeal, and bacterial sHSPs shows that the CP sHSPs are not closely related to the cyanobacterial sHSPs. Thus, they most likely evolved via gene duplication from a nuclear-encoded cytosolic sHSP and not via gene transfer from the CP endosymbiont. Previous sequence analysis had shown that all angiosperm CP sHSPs possess a methionine-rich region in the N-terminal domain. The primary sequence of this region is not highly conserved in the F. hygrometrica CP sHSPs. This lack of sequence conservation indicates that sometime in land plant evolution, after the divergence of mosses from the common ancestor of angiosperms but before the monocot–dicot divergence, there was a change in the selective constraints acting on the CP sHSPs.

Hox cluster genomics in the horn shark, Heterodontus francisci

Reconstructing the evolutionary history of Hox cluster origins will lead to insights into the developmental and evolutionary significance of Hox gene clusters in vertebrate phylogeny and to their role in the origins of various vertebrate body plans. We have isolated two Hox clusters from the horn shark, Heterodontus francisci. These have been sequenced and compared with one another and with other chordate Hox clusters. The results show that one of the horn shark clusters (HoxM) is orthologous to the mammalian HoxA cluster and shows a structural similarity to the amphioxus cluster, whereas the other shark cluster (HoxN) is orthologous to the mammalian HoxD cluster based on cluster organization and a comparison with noncoding and Hox gene-coding sequences. The persistence of an identifiable HoxA cluster over an 800-million-year divergence time demonstrates that the Hox gene clusters are highly integrated and structured genetic entities. The data presented herein identify many noncoding sequence motifs conserved over 800 million years that may function as genetic control motifs essential to the developmental process.

Isoprenoid biosynthesis: The evolution of two ancient and distinct pathways across genomes

Isopentenyl diphosphate (IPP) is the central intermediate in the biosynthesis of isoprenoids, the most ancient and diverse class of natural products. Two distinct routes of IPP biosynthesis occur in nature: the mevalonate pathway and the recently discovered deoxyxylulose 5-phosphate (DXP) pathway. The evolutionary history of the enzymes involved in both routes and the phylogenetic distribution of their genes across genomes suggest that the mevalonate pathway is germane to archaebacteria, that the DXP pathway is germane to eubacteria, and that eukaryotes have inherited their genes for IPP biosynthesis from prokaryotes. The occurrence of genes specific to the DXP pathway is restricted to plastid-bearing eukaryotes, indicating that these genes were acquired from the cyanobacterial ancestor of plastids. However, the individual phylogenies of these genes, with only one exception, do not provide evidence for a specific affinity between the plant genes and their cyanobacterial homologues. The results suggest that lateral gene transfer between eubacteria subsequent to the origin of plastids has played a major role in the evolution of this pathway.

From tropics to tundra: Global convergence in plant functioning

Despite striking differences in climate, soils, and evolutionary history among diverse biomes ranging from tropical and temperate forests to alpine tundra and desert, we found similar interspecific relationships among leaf structure and function and plant growth in all biomes. Our results thus demonstrate convergent evolution and global generality in plant functioning, despite the enormous diversity of plant species and biomes. For 280 plant species from two global data sets, we found that potential carbon gain (photosynthesis) and carbon loss (respiration) increase in similar proportion with decreasing leaf life-span, increasing leaf nitrogen concentration, and increasing leaf surface area-to-mass ratio. Productivity of individual plants and of leaves in vegetation canopies also changes in constant proportion to leaf life-span and surface area-to-mass ratio. These global plant functional relationships have significant implications for global scale modeling of vegetation–atmosphere CO2 exchange.

Phylogenetic relationships among group II intron ORFs

Group II introns are widely believed to have been ancestors of spliceosomal introns, yet little is known about their own evolutionary history. In order to address the evolution of mobile group II introns, we have compiled 71 open reading frames (ORFs) related to group II intron reverse transcriptases and subjected their derived amino acid sequences to phylogenetic analysis. The phylogenetic tree was rooted with reverse transcriptases (RTs) of non-long terminal repeat retroelements, and the inferred phylogeny reveals two major clusters which we term the mitochondrial and chloroplast-like lineages. Bacterial ORFs are mainly positioned at the bases of the two lineages but with weak bootstrap support. The data give an overview of an apparently high degree of horizontal transfer of group II intron ORFs, mostly among related organisms but also between organelles and bacteria. The Zn domain (nuclease) and YADD motif (RT active site) were lost multiple times during evolution. Differences in domain structures suggest that the oldest ORFs were concise, while the ORF in the mitochondrial lineage subsequently expanded in three locations. The data are consistent with a bacterial origin for mobile group II introns.

Aminoacyl-tRNA synthetases database

Aminoacyl-tRNA synthetases (AARSs) are at the center of the question of the origin of life. They constitute a family of enzymes integrating the two levels of cellular organization: nucleic acids and proteins. AARSs arose early in evolution and are believed to be a group of ancient proteins. They are responsible for attaching amino acid residues to their cognate tRNA molecules, which is the first step in the protein synthesis. The role they play in a living cell is essential for the precise deciphering of the genetic code. The analysis of AARSs evolutionary history was not possible for a long time due to a lack of a sufficiently large number of their amino acid sequences. The emerging picture of synthetases’ evolution is a result of recent achievements in genomics [Woese,C., Olsen,G.J., Ibba,M. and Söll,D. (2000) Microbiol. Mol. Biol. Rev., 64, 202–236]. In this paper we present a short introduction to the AARSs database. The updated database contains 1047 AARS primary structures from archaebacteria, eubacteria, mitochondria, chloroplasts and eukaryotic cells. It is the compilation of amino acid sequences of all AARSs known to date, which are available as separate entries via the WWW at http://biobase s.ibch.poznan.pl/aars/.

Integrated fossil and molecular data reconstruct bat echolocation

Molecular and morphological data have important roles in illuminating evolutionary history. DNA data often yield well resolved phylogenies for living taxa, but are generally unattainable for fossils. A distinct advantage of morphology is that some types of morphological data may be collected for extinct and extant taxa. Fossils provide a unique window on evolutionary history and may preserve combinations of primitive and derived characters that are not found in extant taxa. Given their unique character complexes, fossils are critical in documenting sequences of character transformation over geologic time and may elucidate otherwise ambiguous patterns of evolution that are not revealed by molecular data alone. Here, we employ a methodological approach that allows for the integration of molecular and paleontological data in deciphering one of the most innovative features in the evolutionary history of mammals—laryngeal echolocation in bats. Molecular data alone, including an expanded data set that includes new sequences for the A2AB gene, suggest that microbats are paraphyletic but do not resolve whether laryngeal echolocation evolved independently in different microbat lineages or evolved in the common ancestor of bats and was subsequently lost in megabats. When scaffolds from molecular phylogenies are incorporated into parsimony analyses of morphological characters, including morphological characters for the Eocene taxa Icaronycteris, Archaeonycteris, Hassianycteris, and Palaeochiropteryx, the resulting trees suggest that laryngeal echolocation evolved in the common ancestor of fossil and extant bats and was subsequently lost in megabats. Molecular dating suggests that crown-group bats last shared a common ancestor 52 to 54 million years ago.