The ecogenetic link between demography and evolution: can we bridge the gap between theory and data?

Calls to understand the links between ecology and evolution have been common for decades. Population dynamics, i.e. the demographic changes in populations, arise from life history decisions of individuals and thus are a product of selection, and selection, on the contrary, can be modified by such dynamical properties of the population as density and stability. It follows that generating predictions and testing them correctly requires considering this ecogenetic feedback loop whenever traits have demographic consequences, mediated via density dependence (or frequency dependence). This is not an easy challenge, and arguably theory has advanced at a greater pace than empirical research. However, theory would benefit from more interaction between related fields, as is evident in the many near-synonymous names that the ecogenetic loop has attracted. We also list encouraging examples where empiricists have shown feasible ways of addressing the question, ranging from advanced data analysis to experiments and comparative analyses of phylogenetic data.     

Atelinae phylogenetic relationships: The trichotomy revived?

This research examines phylogenetic relationships between members of the Atelinae subfamily (Alouatta, Ateles, Brachyteles, and Lagothrix), based on analysis of three genetic regions. Two loci, cytochrome c oxidase subunit II (COII) and the hypervariable I portion of the control region, are part of the mitochondrial genome. The other is a single-copy nuclear gene, Aldolase A Intron V. Analysis of these genetic regions provides support for tribe Alouattini containing the Alouatta species, while tribe Atelini contains the other three genera. However, these three genetic regions produce conflicting results for relationships among tribe Atelini members. Previous genetic studies supported grouping Brachyteles with Lagothrix, leaving Ateles in a separate subclade. The present data sets vary based on the genetic region analyzed and method of analysis suggesting all possible cladistic relationships. These results are more consistent with investigations of morphology and behavior among these primates. The primary cause of discrepancy between this study and previous genetic studies is postulated to reside in increased sampling in the present study of genetic variation among members of the Atelinae, specifically Ateles. The present study utilized samples of Ateles from all postulated species for this genetically variable primate, while previous studies used only one or two species of Ateles. This paper demonstrates that shifting relationships are produced when different species of Ateles are used to reconstruct phylogenies. This research concludes that a trichotomy should still be supported between members of tribe Atelini until further analyses, which include additional Atelinae haplotypes are conducted.     

Evolution of the primate β-Globin gene region: Nucleotide sequence of the δ-β-globin Intergenic region of gorilla and phylogenetic relationships between African Apes and Man

Summary A 6.0-kb DNA fragment from Gorilla gorilla including the 5 part of the -globin gene and about 4.5 kb of its upstream flanking region was cloned and sequenced. The sequence was compared to the human, chimpanzee, and macaque - intergenic region. This analysis reveals four tandemly repeated sequences (RS), at the same location in the four species, showing a variable number of repeats generating both intraspecific (polymorphism) and interspecific variability. These tandem arrays delimit five regions of unique sequence called IG for intergenic. The divergence for these IG sequences is 1.85 ± 0.22% between human and gorilla, which is not significantly different from the value estimated in the same region between chimpanzee and human (1.62 ± 0.21%). The CpG and TpA dinucleotides are avoided. CpGs evolve faster than other sequence sites but do not confuse phylogenetic inferences by producing parallel mutations in different lineages. About 75% of CpG doublets have become TpG or CpA since the common ancestor, in agreement with the methylation/deamination pattern. Comparison of this intergenic region gives information on branching order within Hominoidea. Parsimony and distance-based methods when applied to the - intergenic region provide evidence (although not statistically significant) that human and chimpanzee are more closely related to each other than to gorilla. CpG sites are indeed rich in information by carrying substitutions along the short internal branch. Combining these results with those on the — intergenic region, shows in a statistically significant way that chimpanzee is the closest relative of human. Offprint requests to: P. Perrin-Pecontal     

The relationships between EEG θ and β oscillations and the level of creativity

The interrelations between the level of creativity and both the baseline power and event-related desynchronization/synchronization (ED/ES) of θ and β rhythms during a figural creative task (Torrance’s “Incomplete Figures” test) were studied under the conditions of different motivations. A higher motivation was caused by instruction “to create most unique images” as opposed to the instruction “to create images.” The subjects, right-handed students (14 males and 14 females), were divided into two groups with high and low originality scores (OSs). The baseline power and the ED/ES of the θ₂ and β rhythms of the subjects were found to depend on the level of creativity and person’s sex only in response to the instruction “to create images.” Male subjects with higher OSs differed from those with lower OSs in a stronger ED of the θ₂ rhythm in temporal-parietal-occipital brain regions, whereas these differences were absent in female subjects. Task performance was accompanied by ED of β₁ rhythm in men with higher OSs, whereas in women with higher OSs, ES was recorded in the same band. Only in women with high OSs did analysis of β_{1, 2} reference power show a higher β₁ power in the caudal hemispheric regions as compared to the frontal ones. High-OS subjects of different genders also differed in the lateral patterns of activity in the electrode loci Fp_1/2 (β₁) and Fp_1/2, F_7/8 (β₂). Our results suggest that a high level of creativity in men and women is related to sex-dependent specific patterns of frontal-occipital and lateral activities of θ and β rhythm oscillators in the brain cortex.     

The influence of snow on lynx and coyote movements: does morphology affect behavior?

Summary We studied sympatric lynx (Lynx canadensis) and coyotes (Canis latrans) to assess how morphological disadvantages to locomotion over snow affected movement patterns. Both species are of similar size and mass, but the feet of lynx are much larger, and coyotes were found to have 4.1–8.8 times the foot-load (ratio of body mass to foot area) of lynx. This resulted in greater mean sinking depths of coyote limbs, although the magnitude of the difference was less than that in foot-load. Coyotes exhibited stronger use of behavioral patterns that reduced negative effects of snow on movements. Coyotes were most abundant at low elevations where snow was shallow, whereas lynx were mostly at higher elevations. Coyotes also used areas at both elevations where snow was shallower than average, while lynx used areas where snow was deeper. further, both species used travel routes where snow was shallower than it was near the track. Coyotes traveled on harder snow and used trails more frequently, thereby tending to reduce sinking depths to those similar to lynx. The behavioral repertoire of coyotes reduced the morphological advantage of large feet possessed by lynx; however, overall sinking depths were still greater in coyotes. Snowshoe hares (Lepus americanus) were the main prey of both species, and their foot-load was less than that of either predator. Hare kills by coyotes occurred after fewer bounds than did those by lynx, and the large difference between foot-loads of both species of predators may have forced coyotes to ambush rather than chase hares, as did lynx.     

Goodbye Halteria? The thoracic morphology of Endopterygota (Insecta) and its phylogenetic implications

Characters of the thorax of 30 representatives of all endopterygote orders and four hemimetabolous outgroup taxa were examined. In total, 126 characters potentially useful for phylogenetic reconstruction are discussed and presented as a data matrix. The thoracic features were analysed with different approaches combined with an additional large set of morphological data. Endopterygota were confirmed as monophyletic and new morphological autapomorphies of the group are suggested. The highly controversial Strepsiptera are not placed as sistergroup of Diptera (Halteria‐concept) but consistently as sistergroup of Coleoptera. This clade was mainly supported by characters associated with posteromotorism. The traditionally proposed relationship of Neuropterida + Coleoptera was not confirmed. Hymenoptera was placed as sistergroup of all remaining orders in parsimony analyses. The inclusion of Strepsiptera + Coleoptera in Mecopterida in parsimony analyses is probably artificial and potential thoracic autapomorphies of Mecopterida in the traditional sense are suggested. Mecopterida are confirmed as a clade in Bayesian analyses. Amphiesmenoptera and Antliophora are well supported. The paraphyly of Mecoptera is due to a clade comprising Nannochoristidae and Siphonaptera + Diptera. The phylogenetic reconstruction using characters of the thorax is impeded by functional constraints, parallel losses, a general trend to reinforce the skeleton and to simplify the muscular apparatus, and also by different specializations occurring in potential outgroup taxa. The addition of a large additional morphological data set only partly compensated for these problems. It is apparent that the inclusion of more outgroup and ingroup taxa is required, notably presumably basal representatives of Mecoptera, Trichoptera, and Diptera. This may reduce the effect of an artificial attraction of branches caused by homoplasy, notably character losses occurring within different lineages.© The Willi Hennig Society 2010.     

Molecular evidence for the hybridity ofIlex × wandoensis and the phylogenetic study of KoreanIlex based on ITS sequence data

In this study, internal transcribed spacer (ITS) regions within the nuclear ribosomal DNA of KoreanIlex were analyzed in order to investigate any molecular evidence thatI. × wandoensis could serve as a putative hybrid betweenI. cornuta andI. integra. We also sought to clearly identify taxonomic relationships and problems caused by consecutive external morphological characters among taxa in the genus. We sequenced 20 clones fromI. × wandoensis and found these individuals displayed intra-genomic polymorphisms within ITS regions. The analysis of the clones clearly demonstrated the presence of discrete sequences from bothI. cornuta andI. integra, thereby confirmingI. × wandoensis is a species that was formed by crossingI. cornuta andI. integra. Lastly, the subgenusIlex, which contains the evergreen species, failed to form a monophyletic group in a strict consensus tree that was prepared based upon ITS regions.I. crenata var.microphylla in the subgenus KoreaIlex, which has presented taxonomic problems previously, formed an independent clade within the consensus tree, thereby showing distinction fromI. crenata.) Genetic discontinuity ofI. macropoda andI. Macropoda for.pseudo-macropoda individuals couldn't be confirmed.     

Further support for the phylogenetic relationships within Euphorbia L. (Euphorbiaceae) from nrITS and trnL–trnF IGS sequence data

The cosmopolitan genus Euphorbia is one of the largest plant genera with an extreme phenotypic plasticity ranging from globose succulents to large shrubs and trees adapted to very divergent habitats like forests or deserts. We compiled the current knowledge about the evolution of Euphorbia by reconstructing a molecular phylogeny based on nearly all available internal transcribed spacer (nrITS) sequence data from previous investigations and sequences of newly sampled species. We compared the results with phylogenetic analyses based on a combined data set of nrITS and trnL–trnF intergenic spacer sequences of a subset of taxa. Apart from a few exceptions, the results correspond well to recently published studies based on different molecular markers. The genus Euphorbia is divided into four major clades, of which the clade comprising subgen. Rhizanthium is restricted to Africa and Madagascar, whereas the remaining three clades are distributed over several continents. Our results support the hypothesis that Euphorbia evolved in Africa from progenitors of subgen. Esula.     

Is there a link between shell morphology and parasites of zebra mussels?

The shell morphology of zebra mussels, Dreissena polymorpha, was analyzed to determine if alterations in shell shape and asymmetry between valves were related to its infection status, i.e. infected or not by microparasites like ciliates Ophryoglena spp. or intracellular bacteria Rickettsiales-like organisms (RLOs), and by macroparasites like trematodes Phyllodistomum folium and Bucephalus polymorphus. For microparasites, two groups of mussels were observed depending on shell measurements. Mussels with the more concave shells were the most parasitized by ciliates. This could be more a consequence than a cause and we hypothesized that a modification of the water flow through the mantle cavity could promote the infection with a ciliate. There were more RLOs present in the most symmetrical individuals. A potential explanation involved a canalization of the left-right asymmetry as a by-product of the parasite infection. Trematode infections were associated with different responses in valve width. Females infected by P. folium displayed significantly higher symmetry in valve width compared with non-infected congeners, whereas the infection involved an opposite pattern in males. B. polymorphus was also linked to a decrease in valve width asymmetry. This study suggested that a relationship exists between parasitism and shell morphology through the physiological condition of host zebra mussels.     

Addressing the conflict between partner notification and patient confidentiality in serodiscordant relationships: How can Ubuntu help?

This study evaluates the conflict between patient confidentiality and partner notification in sero‐discordant relationships, and argues the thesis that based on a theoretical formulation of Ubuntu, a health provider is obliged to facilitate friendly relationships in which individuals are true subjects and/or objects of communal friendship. In serodiscordant relationships, the health professional can fulfil this obligation by notifying “others” (particularly a partner with whom an HIV positive patient has a “present” and “actual relationship”) of their spouse's HIV seroconversion, since without such relevant information a partner (subject) of an HIV positive patient cannot “appropriately” care for the patient's condition (object). There is a need to move away from the medical traditional emphasis that has for so long put primacy on doctor‐patient confidentiality as is the case with the Health Professions Council of South Africa Guidelines (Booklet 12) which favours patient confidentiality over partner notification. Given empirical evidence to support effectiveness of partner notification amongst sero‐discordant couples, there is thus, a need to focus emphasis on latter. This shift is necessary for achieving the United Nations’ Sustainable Development of Goal of ending HIV/AIDS epidemic by 2030. I proposed in this study that African ethics, specifically Ubuntu, will do a better job than current ethical frameworks at ensuring that partner notification receives more emphasis in the care of serodiscordant couples. If this framework is integrated into ethical guidelines and codes, it would significantly enhance the care of serodiscordant couples, as well as further boost global effort at ending HIV/AIDS epidemic by 2030.     

Is congruence between data partitions a reliable predictor of phylogenetic accuracy? Empirically testing an iterative procedure for choosing among phylogenetic methods

The relationship between phylogenetic accuracy and congruence between data partitions collected from the same taxa was explored for mitochondrial DNA sequences from two well-supported vertebrate phylogenies. An iterative procedure was adopted whereby accuracy, phylogenetic signal, and congruence were measured before and after modifying a simple reconstruction model, equally weighted parsimony. These modifications included transversion parsimony, successive weighting, and six-parameter parsimony. For the data partitions examined, there is a generally positive relationship between congruence and phylogenetic accuracy. If congruence increased without decreasing resolution or phylogenetic signal, this increased congruence was a good predictor of accuracy. If congruence increased as a result of poor resolution, the degree of congruence was not a good predictor of accuracy. For all sets of data partitions, six-parameter parsimony methods show a consistently positive relationship between congruence and accuracy. Unlike successive weighting, six-parameter parsimony methods were not strongly influenced by the starting tree.     

On the phylogenetic position of Myzostomida: can 77 genes get it wrong?

Background  

Phylogenomic analyses recently became popular to address questions about deep metazoan phylogeny. Ribosomal proteins (RP) dominate many of these analyses or are, in some cases, the only genes included. Despite initial hopes, phylogenomic analyses including tens to hundreds of genes still fail to robustly place many bilaterian taxa.     

Notentera ivanovi Joffe et al., 1997: a contribution to the question of phylogenetic relationships between ‘turbellarians’ and the parasitic Plathelminthes (Neodermata)

Notentera ivanovi is a parasitic platyhelminth found in the gut of a polychaete, Nephthys ciliata. N. ivanovi has no mouth, pharynx, or intestine; the dorsal epidermis of adult animals forms a thick pad which is very similar to gut epithelia even at the light microscopic level. Structure of ciliary rootlets and dermal glands with peculiar striated secretion bodies point to close relationships with the Fecampiidae, though other important characters imply placing the genus Notentera in a separate family. In mature sperm of N. ivanovi, the axonemes are fully incorporated; they are directed from proximal to distal, as in the Neodermata. We argue that new family, Notenteridae, should be included in the taxon Fecampiida. We also suggest that all Plathelminthes with neodermatan type of spermiogenesis (Fecampiidae, Urastomidae, and Neodermata) form a monophyletic branch within the Plathelminthes Neoophora. This revised version was published online in July 2006 with corrections to the Cover Date.     

Does body contact contribute towards repairing relationships?: The association between flipper-rubbing and aggressive behavior in captive bottlenose dolphins

Bottlenose dolphins exhibit complex social affiliations that may be shaped by interactions among individuals. Affiliative body contact among dolphins may repair deteriorated relationships or reduce tension within the group following aggressive interactions. We investigated the time-series association between one type of contact behavior (flipper-rubbing) and aggression by continuous observation of three captive bottlenose dolphins. For all three dolphin pairs, the elapsed time to aggressive events was significantly greater following flipper-rubbing. In two dolphin pairs comprised of a young male and an adult female, one-zero score of inter-opponent flipper-rubbing was higher for 10 min following aggressive bouts (post-AG periods) than for the same length of control (Ctrl) periods. For all three focal pairs, one-zero score of third-party rubbing was higher for post-AG than Ctrl periods. Neither the direction of rubbing nor the identity of the partner that approached prior to rubbing showed any significant tendencies. Flipper-rubbing may contribute to restore friendly relationships between former opponents or reduce conflicts in at least juvenile-adult female associations. Our results also give preliminary suggestions of the functions of third-party flipper-rubbing among bottlenose dolphins, including tension easing by the third party, or displacement as a result of aggressive interactions.     

Morphology, sociality, and ecology: can morphology predict pairing behavior in coral reef fishes?

Morphology can contain valuable information about the ecological performance of reef fishes, but it has rarely been used in combination with social traits. Social behavior is known to influence the ecological role of fishes; however, the ecological basis for pairing in reef fishes is not well understood. Field observations of 2,753 individuals, in 47 species in six families of biting reef fishes (Acanthuridae, Chaetodontidae, Kyphosidae, Labridae, Pomacanthidae, Siganidae), were used in combination with six morphological measurements, to examine the morphology of fishes in different social systems. A principal components analysis of morphological traits segregated species with high proportions of pairing individuals from non-pairing species along principal component 1, explaining 40.8 % of the variation. Pairing species were characterized by large eyes, concave foreheads, pointed snouts, deep bodies, and small maximum sizes. There was a significant positive relationship between these morphological traits (i.e., scores on PC1) and the prevalence of pairing within the Chaetodontidae (r ² = 0.59; P = 0.026), Siganidae (r ² = 0.72; P = 0.004), and Acanthuridae (r ² = 0.82; P < 0.001). This was consistent when traits were corrected for phylogenetic effects. No pattern was evident in the scarine Labridae (r ² = 0.15; P = 0.17). The morphological characteristics found among pairing species suggest that pairing species share common ecological traits, including foraging for small prey items in micro-topographically complex environments such as reef crevices. These ecological traits may have played a role in the evolution of pairing behavior and subsequently led to the development of reproductive patterns based on monogamy.