Phylogenetic Frame Research Articles

Ruminant inner ear shape records 35 million years of neutral evolution

Extrinsic and intrinsic factors impact diversity. On deep-time scales, the extrinsic impact of climate and geology are crucial, but poorly understood. Here, we use the inner ear morphology of ruminant artiodactyls to test for a deep-time correlation between a low adaptive anatomical structure and both extrinsic and intrinsic variables. We apply geometric morphometric analyses in a phylogenetic frame to X-ray computed tomographic data from 191 ruminant species. Contrasting results across ruminant clades show that neutral evolutionary processes over time may strongly influence the evolution of inner ear morphology. Extant, ecologically diversified clades increase their evolutionary rate with decreasing Cenozoic global temperatures. Evolutionary rate peaks with the colonization of new continents. Simultaneously, ecologically restricted clades show declining or unchanged rates. These results suggest that both climate and paleogeography produced heterogeneous environments, which likely facilitated Cervidae and Bovidae diversification and exemplifies the effect of extrinsic and intrinsic factors on evolution in ruminants.

Lepidopteran caterpillars in the Cretaceous: were they a good food source for early birds?

Caterpillars are an omnipresent component in modern terrestrial faunas. Not surprisingly, they represent an important food source for larger animals. The oldest fossils of caterpillars are known from the Cretaceous. Yet, so far, only nine possible Cretaceous specimens have been reported. Here we expand the known record by four new specimens of caterpillars preserved in 99 million-year-old Kachin amber from Myanmar. The specimens cannot easily be interpreted in a taxonomic or phylogenetic frame. A simple morphometric comparison reveals that the new specimens differ in their relative body dimensions from those of the previously known specimens, expanding the morphological diversity of Cretaceous caterpillars. All caterpillars from the Cretaceous of which sizes are known are rather small, the largest definite one being only about 5 mm. Comparison to younger ambers reveals no clear directed preservation bias towards preserving only small caterpillars. In addition, the sizes of known adult lepidopterans from the Cretaceous are compatible with rather small caterpillars, although possibly slightly larger than the known ones. While small, the observed size range appears still to be within the size range of food items known to be consumed by modern birds. It therefore seems likely that also in the Cretaceous caterpillars were adequate food items for early birds.

Predator-Prey Dynamics of Intra-Host Simian Immunodeficiency Virus Evolution Within the Untreated Host.

The dynamic nature of the SIV population during disease progression in the SIV/macaque model of AIDS and the factors responsible for its behavior have not been documented, largely owing to the lack of sufficient spatial and temporal sampling of both viral and host data from SIV-infected animals. In this study, we detail Bayesian coalescent inference of the changing collective intra-host viral effective population size (Ne ) from various tissues over the course of infection and its relationship with what we demonstrate is a continuously changing immune cell repertoire within the blood. Although the relative contribution of these factors varied among hosts and time points, the adaptive immune response best explained the overall periodic dynamic behavior of the effective virus population. Data exposing the nature of the relationship between the virus and immune cell populations revealed the plausibility of an eco-evolutionary mathematical model, which was able to mimic the large-scale oscillations in Ne through virus escape from relatively few, early immunodominant responses, followed by slower escape from several subdominant and weakened immune populations. The results of this study suggest that SIV diversity within the untreated host is governed by a predator-prey relationship, wherein differing phases of infection are the result of adaptation in response to varying immune responses. Previous investigations into viral population dynamics using sequence data have focused on single estimates of the effective viral population size (Ne ) or point estimates over sparse sampling data to provide insight into the precise impact of immune selection on virus adaptive behavior. Herein, we describe the use of the coalescent phylogenetic frame- work to estimate the relative changes in Ne over time in order to quantify the relationship with empirical data on the dynamic immune composition of the host. This relationship has allowed us to expand on earlier simulations to build a predator-prey model that explains the deterministic behavior of the virus over the course of disease progression. We show that sequential viral adaptation can occur in response to phases of varying immune pressure, providing a broader picture of the viral response throughout the entire course of progression to AIDS.

The Role of Botanical Families in Medicinal Ethnobotany: A Phylogenetic Perspective.

Studies suggesting that medicinal plants are not chosen at random are becoming more common. The goal of this work is to shed light on the role of botanical families in ethnobotany, depicting in a molecular phylogenetic frame the relationships between families and medicinal uses of vascular plants in several Catalan-speaking territories. The simple quantitative analyses for ailments categories and the construction of families and disorders matrix were carried out in this study. A Bayesian approach was used to estimate the over- and underused families in the medicinal flora. Phylogenetically informed analyses were carried out to identify lineages in which there is an overrepresentation of families in a given category of use, i.e., hot nodes. The ethnobotanicity index, at a specific level, was calculated and also adapted to the family level. Two diversity indices to measure the richness of reported taxa within each family were calculated. A total of 47,630 use reports were analysed. These uses are grouped in 120 botanical families. The ethnobotanicity index for this area is 14.44% and the ethnobotanicity index at the family level is 68.21%. The most-reported families are Lamiaceae and Asteraceae and the most reported troubles are disorders of the digestive and nutritional system. Based on the meta-analytic results, indicating hot nodes of useful plants at the phylogenetic level, specific ethnopharmacological research may be suggested, including a phytochemical approach of particularly interesting taxa.

Phylogenetic association of Cyprinid (Schizothorax) inferred from complete mitochondrial genome

Whole mitochondrial DNA (mtDNA) of S.esocinusand S. plagiostomus was found to be 16,591 and 16,564 bp respectively with 13 protein-coding genes, 2 rRNAs genes, 22 tRNA genes and 2 non-coding region. For valuing the phylogenetic relationship of a species on the basis of whole mitogenome are considered to be a great importance. In this study, we sequenced whole mitogenome of S.esocinusand S. plagiostomus and compared with the whole mitogenome sequences of members of other families (Balitoridae, Nemanchillidae and Cobatidae). The monophyly of the family Cyprinidae and a clade comprising Balitoridae and Nemanchillidae while Cobatidae with paraphyletic origin was strongly supported by the resultant phylogenies, recognized that Cyprinidae was closely related with the family Cobatidae than other ones. The results indicated that whole mitochondrial genome has a great importance in studying variation in genes and phylogenetic relationship in the subfamily Schizothoracinae. This data offering the molecular phylogenetic frame work of important Schizothorax species found in Swat.

New material of Epiaceratherium and a new species of Mesaceratherium clear up the phylogeny of early Rhinocerotidae (Perissodactyla).

Reduction of the anterior dentition (i.e. incisors and canines) is a major adaptative trait of the Rhinocerotidae among Perissodactyla. However, the corresponding evolutionary sequence was lacking a robust phylogenetic frame to support it thus far. Here, we describe a new Oligocene species of Rhinocerotinae, Mesaceratherium sp. nov. from the Swiss locality of Bumbach (MP25 reference level). In addition, we identify the only known complete mandible of Epiaceratherium magnum, an early-branching rhinocerotid, as well as one of the earliest European rhinoceroses. We also compute a parsimony analysis based on morpho-anatomical characters to assess their phylogenetic position and elucidate the early evolution of the Rhinocerotidae. Our results allow to propose a new scenario for the reduction of the anterior dentition in which upper and lower dentitions would have undergone distinct evolutionary trajectories.

Flight, symmetry and barb angle evolution in the feathers of birds and other dinosaurs.

There has been much discussion over whether basal birds (e.g. Archaeopteryx and Confuciusornis) exhibited active flight. A recent study of barb angles has suggested they likely could not but instead may have exhibited a gliding phase. Pennaceous primary flight feathers were proposed to show significant shifts in barb angle values of relevance to the inference of flight in these extinct taxa. However, evolutionary trends in the evolution of these barb angle traits in extant volant taxa were not analysed in a phylogenetic frame. Neither the ancestral crown avian condition nor the condition in outgroup dinosaurs with symmetrical feathers were assessed. Here, we expand the fossil sample and reanalyse these data in a phylogenetic frame. We show that extant taxa, including strong flyers (e.g. some songbirds), show convergence on trailing barb angles and barb angle asymmetry observed in Mesozoic taxa that were proposed not to be active fliers. Trailing barb angles in these Mesozoic taxa are similar to symmetrical feathers in outgroup dinosaurs, indicating that selective regimes acted to modify primarily the leading-edge barb angles. These trends inform dynamics in feather shape evolution and challenge the notion that barb angle and barb angle ratios in extant birds directly inform the reconstruction of function in extinct stem taxa.

Behavioral and chemical antipredator mechanisms in ground beetles: an attempt to reconcile within a phylogenetic frame

Like other coleopterans, Carabids are recognized for the use of passive and active strategies against their enemies. They are known to produce dangerous and distasteful chemicals and to use anti-predator behaviors such crypsis/mimicry, gregariousness, intra- and interspecific helpful interactions, sound production and aposematism. While defensive chemicals have been an important element in the successful diversification of ground beetles, in many tribes of this wide adephagan family many other systems have evolved and discovered. Here we present a review on the current knowledge of the avoidance mechanisms in carabids, with a discussion of data on chemical products, morphological adaptations and behaviors used against vertebrate and invertebrate predators. The most widespread strategy is discouragement of the predators using pygidial gland secretions, but passive anti-predator strategies are also displayed as group-protecting behavior through intraspecific aggregations or communal roosting. Most adult carabids tend to be dark in color and thus less detectable, but chemically well-protected taxa use the opposite strategy, displaying bright colors related to mimicry or aposematism. In aposematic species, group-protecting behavior has probably evolved from intraspecific gregariousness into multispecies aggregations. Larval behavioral strategies are related more closely to the epigean or underground lifestyle. In surface-living larvae, cannibalism avoidance and the usage of defensive substances have been reported for Chlaeniini. In this tribe we found an interesting coincidence between a high level of toxicity/distastefulness and a complex larval behavior. Based mainly on the genus-level supertree of Beutel et al. (2008) and the phylogenetic analyses of Ober & Maddison (2008) we reconstructed the evolutionary relationships among the chemical classes isolated inside the tribes. The scenario shows that several semiochemical classes (quinone/benzoquinones, formic acid, m-cresol, methacrylic acid, isovaleric acid, ß-necrodol, benzaldehyde, etc.) found in carabids are at least in part related to their life style and habitat selection. The proposed relationship still lacks other chemical data of the missing genera/species and even if the knowledge of carabid anti-predator strategies still seems to be in the pioneer stage, future studies on carabid anti-predator behavior look very promising.

Bone histology of Azendohsaurus laaroussii: Implications for the evolution of thermometabolism in Archosauromorpha

AbstractThis paper is aimed at constraining the phylogenetic frame of the acquisition of endothermy by Archosauromorpha. We analyzed the bone histology of Azendohsaurus laaroussii. Stylopodial and zeugopodial bones show three tissue types: (1) avascular lamellar zonal bone formed at low growth rates; (2) a scaffold of parallel-fibered bone containing either small primary osteons or simple vascular canals; and (3) fibrolamellar bone formed at high growth rates. We used quantitative histology to infer the thermometabolic regime of this taxon. We define endothermy as the presence of any mechanism of nonshivering thermogenesis that increases both body temperature and resting metabolic rate. Thus, estimating the resting metabolic rate of an extinct organism may be a good proxy to infer its thermometabolic regime (endothermy vs. ectothermy). High resting metabolic rates have been shown to be primitive for the clade Prolacerta–Archosauriformes. Therefore, we inferred the resting metabolic rates of A. laaroussii, a sister group of this clade, and of 14 extinct related taxa, using phylogenetic eigenvector maps. All the inferences obtained are included in the range of variation of resting metabolic rates measured in mammals and birds, so we can reasonably assume that all these taxa (including Azendohsaurus) were endotherms. A parsimony optimization of the presence of endothermy on a phylogenetic tree of tetrapods shows that this derived character state was acquired by the last common ancestor of the clade Azendohsaurus–Archosauriformes and that there is a reversion in Crocodylia.

Plant Evolution: Phylogenetic Relationships between the Earliest Land Plants

The key structures and functions of land plants are most often studied in flowering plant models. However, the evolution of these traits (character states) is often difficult to infer, because we lack an accurate phylogenetic frame of reference. The potential branching order of the earliest land plants has now been further condensed, narrowing down potential reference frameworks for comparative studies.

A sneak peek into chromosome and genome size evolution among sisyrynchium taxa (Iridaceae: Iridoieae) SISYRINCHIUM TAXA (IRIDACEAE: IRIDOIDEAE)

Iridaceae is one of the largest Asparagales families with over 2030 species. Besides a wide morphological variation, this family presents great karyological variation including many polyploid taxa. Sisyrinchium is restricted to the New World and it holds a large amount of cytological data. Despite its importance in providing critical evidence to understand processes involved in genome evolution, cytological data is lacking for most of South American species of Sisyrinchium. Therefore, the present work aims to identify and characterize chromosome evolutionary trends among Sisyrinchium taxa of sect. Viperella. Chromosome numbers and genome sizes (GS) were determined for 16 and 17 taxa, respectively, from sect. Viperella; all reported here for the first time, except for S. alatum. Meiotic behavior, tetrad normality, pollen viability and morphology were also analyzed and revealed regular meiosis, high meiotic indexes and pollen viability (> 87%), except for Sisyrinchium sp. nov. aff. alatum (22.70%). The GS and chromosome number obtained were plotted onto a phylogenetic frame to identify transitions between character states and to locate where these transitions occurred throughout this group’s evolution. Based on our results, we suggest that the ancestral chromosome number for sect. Viperella is 2n = 18 and two independent polyploidization events occurred. Lower DNA content (2.17 ? 2C ? 2.97 pg) was the ancestral condition from which six major events took place towards GS increase. Despite the stability in base chromosome number (x = 9), evolutionary changes in karyotypes of this section involve primarily variation in DNA amount regardless of ploidy level, and secondly polyploidy and variation in chromosome size. Combining GS and chromosome number with molecular phylogeny, our data provides the first scenario for karyotype and genome evolution in Sisyrinchium, sect. Viperella, allowing us to suggest that mechanisms other than polyploidy were responsible for GS increase among these taxa.

Potential host number in cuckoo bees (Psithyrus subgen.) increases toward higher elevations

In severe and variable conditions, specialized resource selection strategies should be less fre- quent because extinction risks increase for species that depend on a single and unstable resource. Psithyrus (Bombus subgenus Psithyrus) are bumblebee parasites that usurp Bombus nests and display inter-specific variation in the number of hosts they parasitize. Using a phylogenetic comparative frame- work, we show that Psithyrus species at higher elevations display a higher number of hosts species com- pared with species restricted to lower elevations. Species inhabiting high elevations also cover a larger temperature range, suggesting that species able to occur in colder conditions may benefit from recruit- ment from populations occurring in warmer conditions. Our results provide evidence for an 'altitudinal niche breadth hypothesis' in parasitic species, showing a decrease in the parasites' specialization along the elevational gradient, and also suggesting that Rapoport's rule might apply to Psithyrus.

Facilitating wide hybridization in Hydrangea s. l. cultivars: A phylogenetic and marker-assisted breeding approach

Hydrangea s. l., belonging to the up-market segment of ornamental cultivars, currently faces a renaissance in horticulture. Hence, novel molecular- assisted breeding approaches are timely. Wide hybrid- ization, i.e. crosses between distantly related species, has been shown to be problematic. Recent studies have considerably improved our knowledge of the phyloge- netic relationships between the ornamental Hydrangea s. l. species. A fully resolved and highly supported phylogenetic tree is currently available, based on an extensive marker selection including 13 highly variable chloroplast markers. This robust phylogenetic frame- work includes the majority of widely cultivated Hydrangea s. l. species that have been the center of attention in a number of crossing projects. The present study is based on this highly supported phylogenetic hypothesis. Here, we aim to select the best candidates for future successful breeding projects, involving interspecific crosses of both closely and distantly related Hydrangea s. l. lineages. Therefore, we integrated the phylogenetic relatedness of potential parental lines along with genetic distances calculated from a wide plastid marker selection. Direct crosses between two species were found to be successful up to an average genetic distance of 0.01065, while failure could be expected at an average genetic distance of 0.01385 and higher. In order to overcome this genetic distance threshold, we propose Hydrangea arborescens, H. sargentiana, H. integrifolia ,a ndH. seemannii as the best candidates for future bridge-cross projects with currently available fertile hybrids. We expect that our results will allow breeders to overcome long-standing wide crossing difficulties and motivate breeding initia- tives of potential economic value.

Phylogeny in aid of the present and novel microbial lineages: diversity in Bacillus.

Bacillus represents microbes of high economic, medical and biodefense importance. Bacillus strain identification based on 16S rRNA sequence analyses is invariably limited to species level. Secondly, certain discrepancies exist in the segregation of Bacillus subtilis strains. In the RDP/NCBI databases, out of a total of 2611 individual 16S rDNA sequences belonging to the 175 different species of the genus Bacillus, only 1586 have been identified up to species level. 16S rRNA sequences of Bacillus anthracis (153 strains), B. cereus (211 strains), B. thuringiensis (108 strains), B. subtilis (271 strains), B. licheniformis (131 strains), B. pumilus (83 strains), B. megaterium (47 strains), B. sphaericus (42 strains), B. clausii (39 strains) and B. halodurans (36 strains) were considered for generating species-specific framework and probes as tools for their rapid identification. Phylogenetic segregation of 1121, 16S rDNA sequences of 10 different Bacillus species in to 89 clusters enabled us to develop a phylogenetic frame work of 34 representative sequences. Using this phylogenetic framework, 305 out of 1025, 16S rDNA sequences presently classified as Bacillus sp. could be identified up to species level. This identification was supported by 20 to 30 nucleotides long signature sequences and in silico restriction enzyme analysis specific to the 10 Bacillus species. This integrated approach resulted in identifying around 30% of Bacillus sp. up to species level and revealed that B. subtilis strains can be segregated into two phylogenetically distinct groups, such that one of them may be renamed.

Nuclear and plastid DNA sequences confirm the placement of the enigmatic Canacomyrica monticola in Myricaceae

AbstractPhylogenetic analyses of DNA sequences of the plastid rbcL gene were used to obtain a phylogenetic frame–work for the New Caledonian endemic genus Canacomyrica (monotypic). A further analysis of selected genera within Fagales combining DNA sequences of the rbcL gene, plastid trnL–F region and nuclear ITS region was also performed. In all analyses Canacomyrica fell into a well–supported clade in which it occupied a position as sister to the remaining genera of Myricaceae. A chromosome number of 2n = 16, consistent with Myricaceae, is reported for Canacomyrica for the first time. On the basis of the phylogenetic data and numerous shared morphological features, the original placement of Canacomyrica in Myricaceae is accepted. Canacomyrica is distinguished from other members of the family by the presence of staminodes in the female flower, a six–lobed perianth and a lamellular, laciniate style. The affinities of Myricaceae within Fagales are re–evaluated in the light of the unusual morphological features of Canacomyrica. The significance of staminodes in Canacomyrica is discussed with reference to pollination syndrome and incomplete suppression of male function in Myricaceae. A lectotype is designated for the name Canacomyrica monticola Guillaumin.

Mandibular gland secretions in alloxystine wasps (Hymenoptera, Cynipoidea, Charipidae): do ecological or phylogenetical constraints influence occurrence or composition?

Mandibular gland secretions were investigated in 28 taxa of alloxystine wasps (17 described and 11 potential, hitherto undescribed species) using GC-MS. In two selected species (Alloxysta pleuralis, A. victrix), the chemical patterns of the mandibular gland secretions remained constant and were not qualitatively influenced by different host systems; however, there was a considerable variation in quantity. A cluster analysis revealed the chemical composition to be independent of two different modes of resource utilisation which are characterized by the presence or absence of ants in the respective host system. These results support the idea of the prevalence of historical (phylogenetic) rather than actual ecological constraints. However, the chemotaxonomic applicability of such data on the subfamily level was limited, although a species status could be confirmed in some questionable taxa. By integrating morphological and biological characters, potential relationships of selected species and a hypothetical phylogenetic frame tree are proposed.

Éthologie et cognition : le cas des primates

Ethology and Cognition : the case of primate ethology There are two major boundaries within cognitive sciences ; 1-the anthropocentric definition of the concept of cognition which would prevent accepting that animals other than man have a cognition ; 2-the large gap between neurobiology, at the molecular or cellular level, at one end and psychology at the other end. Ethology is the study of the behavior of living beings considered as entities. This implies taking into account not only the motor outputs, the behaviors, but also, implicitly or explicitly, the related neural and endocrinological events. Ethology also implies studying the behavior within a phylogenetic frame. It is argued that this could help to fill the gap between neurobiology and psychology. In addition the study of cognition could be considered as having brought closer the field of ethology and that of comparative psychology. In this paper several domains of ethology related to the two cognitive concepts of representation and intentionality are examined, especially in nonhuman primates. These domains are spatial memory, vocal communication including the concept of "inferential communication", social cognition and still anecdotic examples of deception. Ethologists consider cognition not only within an evolution of cognitive processes but also that cognition is modulated by internal variables such as hormonal ones.