Contrasting quantitative traits and neutral genetic markers for genetic resource assessment of Mesoamerican Cedrela odorata

We compared within-population variability and degree of population differentiation for neutral genetic markers (RAPDS) and eight quantitative traits in Central American populations of the endangered tree, Cedrela odorata. Whilst population genetic diversity for neutral markers (Shannon index) and quantitative traits (heritability, coefficient of additive genetic variation) were uncorrelated, both marker types revealed strong differentiation between populations from the Atlantic coast of Costa Rica and the rest of the species' distribution. The degree of interpopulation differentiation was higher for RAPD markers (F-ST 0.67 for the sampled Mesoamerican range) than for quantitative traits (Q(ST) = 0.30). Hence, the divergence in quantitative traits was lower than could have been achieved by genetic drift alone, suggesting that balancing selection for similar phenotypes in different populations of this species. Nevertheless, a comparison of pair-wise estimates of population differentiation in neutral genetic markers and quantitative traits revealed a strong positive correlation (r = 0.66) suggesting that, for C. odorata, neutral marker divergence could be used as a surrogate for adaptive gene divergence for conservation planning. The utility of this finding and suggested further work are discussed.

Assumption-free estimation of heritability from genome-wide identity-by-descent sharing between full siblings

The study of continuously varying, quantitative traits is important in evolutionary biology, agriculture, and medicine. Variation in such traits is attributable to many, possibly interacting, genes whose expression may be sensitive to the environment, which makes their dissection into underlying causative factors difficult. An important population parameter for quantitative traits is heritability, the proportion of total variance that is due to genetic factors. Response to artificial and natural selection and the degree of resemblance between relatives are all a function of this parameter. Following the classic paper by R. A. Fisher in 1918, the estimation of additive and dominance genetic variance and heritability in populations is based upon the expected proportion of genes shared between different types of relatives, and explicit, often controversial and untestable models of genetic and non-genetic causes of family resemblance. With genome-wide coverage of genetic markers it is now possible to estimate such parameters solely within families using the actual degree of identity-by-descent sharing between relatives. Using genome scans on 4,401 quasi-independent sib pairs of which 3,375 pairs had phenotypes, we estimated the heritability of height from empirical genome-wide identity-by-descent sharing, which varied from 0.374 to 0.617 (mean 0.498, standard deviation 0.036). The variance in identity-by-descent sharing per chromosome and per genome was consistent with theory. The maximum likelihood estimate of the heritability for height was 0.80 with no evidence for non-genetic causes of sib resemblance, consistent with results from independent twin and family studies but using an entirely separate source of information. Our application shows that it is feasible to estimate genetic variance solely from within- family segregation and provides an independent validation of previously untestable assumptions. Given sufficient data, our new paradigm will allow the estimation of genetic variation for disease susceptibility and quantitative traits that is free from confounding with non-genetic factors and will allow partitioning of genetic variation into additive and non-additive components.

Genetic structure of a reef-building coral from thermally distinct environments on the Great Barrier Reef

Adaptation to localised thermal regimes is facilitated by restricted gene flow, ultimately leading to genetic divergence among populations and differences in their physiological tolerances. Allozyme analysis of six polymorphic loci was used to assess genetic differentiation between nine populations of the reef-building coral Acropora millepora over a latitudinal temperature gradient on the inshore regions of the Great Barrier Reef (GBR). Small but significant genetic differentiation indicative of moderate levels of gene flow (pairwise F-ST 0.023 to 0.077) was found between southern populations of A. millepora in cooler regions of the GBR and the warmer, central or northern GBR populations. Patterns of genetic differentiation at these putatively neutral allozyme loci broadly matched experimental variation in thermal tolerance and were consistent with local thermal regimes (warmest monthly-averages) for the A. millepora populations examined. It is therefore hypothesized that natural selection has influenced the thermal tolerance of the A. millepora populations examined and greater genetic divergence is likely to be revealed by examination of genetic markers under the direct effects of natural selection.

The origin of the pelagobenthic metazoan life cycle: what's sex got to do with it?

The biphasic (pelagobenthic) life cycle is found throughout the animal kingdom, and includes gametogenesis, embryogenesis, and metamorphosis. From a tangled web of hypotheses on the origin and evolution of the metazoan pelagobenthic life cycle, current opinion appears to favor a simple, larval-like holopelagic ancestor that independently settled multiple times to incorporate a benthic phase into the life cycle. This hypothesis derives originally from Haeckel's (1874) Gastraea theory of ontogeny recapitulating phylogeny, in which the gastrula is viewed as the recapitulation of a gastracan ancestor that evolved via selection on a simple, planktonic hollow ball of cells to develop the capacity to feed. Here, we propose an equally plausible hypothesis that the origin of the metazoan pelagobenthic life cycle was a direct consequence of sexual reproduction in a likely holobenthic ancestor. In doing so, we take into account new insights from poriferan development and from molecular phylogenies. In this scenario, the gastrula does not represent a recapitulation, but simply an embryological stage that is an outcome of sexual reproduction. The embryo can itself be considered as the precursor to a biphasic lifestyle, with the embryo representing one phase and the adult another phase. This hypothesis is more parsimonious because it precludes the need for multiple, independent origins of the benthic form. It is then reasonable to consider that multilayered, ciliated embryos ultimately released into the water column are subject to natural selection for dispersal/longevity/feeding that sets them on the evolutionary trajectory towards the crown metazoan planktonic larvae. These new insights from poriferan development thus clearly support the intercalation hypothesis of bilaterian larval evolution, which we now believe should be extended to discussions of the origin of biphasy in the metazoan last common ancestor.

Attribution of social dominance and maleness to schematic faces

We report findings which suggest perception of 'higher order' attributes such as gender and social dominance are perceived from a schematic face. To investigate a large population, the first two experiments were carried out in both the traditional manner and on the Internet. Results obtained from both were not significantly different so the data sets were combined. Lowered eyebrow position was a strong indicator of both social dominance and the male gender. A schematic face with a sad mouth resulted in the face's being viewed as less dominant and less male. Eyegaze direction also was investigated and discussed in terms of dyadic influence. Evidence supported the assumption that both social dominance and the male gender are perceived through similar facial configurations on a schematic face. Limitations include the use of schematic face pairs, and the presentation of single faces in research is discussed.

The effects of ingroup-outgroup membership on minority influence when group membership is determined by a trivial categorisation

Two experiments are reported which investigate the influence of ingroup and outgroup minority influence where group membership was determined according to a trivial dimension. The results of the first experiment replicate an earlier study and show that an ingroup minority has significantly more influence than an outgroup minority. In the second study the connotations associated with membership of the ingroup and outgroup (positive/negative) were experimentally manipulated. When ingroup/outgroup membership was associated with a positive/negative image respectively, the ingroup minority had the most influence. However, when ingroup/outgroup membership was associated with a negative/positive image, as predicted, an outgroup minority had more influence than an ingroup minority. These results are interpreted as supporting an intergroup analysis of minority influence processes.

The evolution of learning systems:to Bayes or not to be

Bayesian algorithms pose a limit to the performance learning algorithms can achieve. Natural selection should guide the evolution of information processing systems towards those limits. What can we learn from this evolution and what properties do the intermediate stages have? While this question is too general to permit any answer, progress can be made by restricting the class of information processing systems under study. We present analytical and numerical results for the evolution of on-line algorithms for learning from examples for neural network classifiers, which might include or not a hidden layer. The analytical results are obtained by solving a variational problem to determine the learning algorithm that leads to maximum generalization ability. Simulations using evolutionary programming, for programs that implement learning algorithms, confirm and expand the results. The principal result is not just that the evolution is towards a Bayesian limit. Indeed it is essentially reached. In addition we find that evolution is driven by the discovery of useful structures or combinations of variables and operators. In different runs the temporal order of the discovery of such combinations is unique. The main result is that combinations that signal the surprise brought by an example arise always before combinations that serve to gauge the performance of the learning algorithm. This latter structures can be used to implement annealing schedules. The temporal ordering can be understood analytically as well by doing the functional optimization in restricted functional spaces. We also show that there is data suggesting that the appearance of these traits also follows the same temporal ordering in biological systems. © 2006 American Institute of Physics.

An in-vitro-in-vivo model for the transdermal delivery of cholecalciferol for the purposes of rodent management

The natural selection of anticoagulant resistant rats has resulted in a need for an alternative to anticoagulant rodenticides which differs in both active ingredient and in the method of dosing. Cholecalciferol toxicity to rodents using the dermal route is demonstrated using a variety of penetration enhancing formulations in two in-vitro models and finally in-vivo. A 1 ml dose of 50/50 (v/v) DMSO/ethanol containing 15% (v/v) PEG 200 and 20% (w/v) cholecalciferol was judged as 'sufficiently effective' in line with the European Union's Biocidal Products Regulation (No. 528/2012) during in-vivo studies. This dose was found to cause 100% mortality in a rat population in 64.4 h (±22 h).

A comparative study of life history and gene flow in darters (Pisces: Percidae)

Gene flow, or the exchange of genes between populations, is important because it determines the evolutionary trajectory of a species, including the relative influences of genetic drift and natural selection in the process of population differentiation. Gene flow differs among species because of variation in dispersal capability and abundances across taxa, and historical forces related to geological or lineage history. Both history and ecology influence gene flow in potentially complicated ways, and accounting for their effects remains an important problem in evolutionary biology. This research is a comparative study of gene flow and life-history in a monophyletic group of stream fishes, the darters. As a first step in disentangling historical and ecological effects, I reconstructed the phylogenetic relationships of the study species from nucleotide sequences in the mtDNA control region. I then used this phylogeny and regional glaciation history to infer historical effects on life-history evolution and gene flow in 15 species of darters. Gene flow was estimated indirectly, using information from 20 resolvable and polymorphic allozyme loci. When I accounted for historical effects, comparisons across taxa revealed that gene flow rates were closely associated with differences in clutch sizes and reproductive investment patterns. I hypothesized that differences in larval dispersal among taxa explained this relationship. Results from a field study of larval drift were consistent with this hypothesis. Finally, I asked whether there was an interaction between species' ecology and genetic differentiation across biogeographically distinct regions. Information from allozymes and mtDNA sequences revealed that life history plays an important role in the magnitude of species divergence across biogeographic boundaries. These results suggested an important association between life histories and rates of speciation following an allopatric isolation event. This research, along with other studies from the literature, further illustrates the enormous potential of North American freshwater fishes as a system for studying speciation processes. ^

Colony-specific calcification and mortality under ocean acidification in the branching coral Montipora digitata

Ocean acidification (OA) threatens calcifying marine organisms including reef-building corals. In this study, we examined the OA responses of individual colonies of the branching scleractinian coral Montipora digitata. We exposed nubbins of unique colonies (n = 15) to ambient or elevated pCO2 under natural light and temperature regimes for 110 days. Although elevated pCO2 exposure on average reduced calcification, individual colonies showed unique responses ranging from declines in positive calcification to negative calcification (decalcification) to no change. Similarly, mortality was greater on average in elevated pCO2, but also showed colony-specific patterns. High variation in colony responses suggests the possibility that ongoing OA may lead to natural selection of OA-tolerant colonies within a coral population.

The Roles of Phenotypic Plasticity and Plant-Microbe Interactions in the Evolution of Complex Traits in Boechera stricta

All organisms live in complex habitats that shape the course of their evolution by altering the phenotype expressed by a given genotype (a phenomenon known as phenotypic plasticity) and simultaneously by determining the evolutionary fitness of that phenotype. In some cases, phenotypic evolution may alter the environment experienced by future generations. This dissertation describes how genetic and environmental variation act synergistically to affect the evolution of glucosinolate defensive chemistry and flowering time in Boechera stricta, a wild perennial herb. I focus particularly on plant-associated microbes as a part of the plant’s environment that may alter trait evolution and in turn be affected by the evolution of those traits. In the first chapter I measure glucosinolate production and reproductive fitness of over 1,500 plants grown in common gardens in four diverse natural habitats, to describe how patterns of plasticity and natural selection intersect and may influence glucosinolate evolution. I detected extensive genetic variation for glucosinolate plasticity and determined that plasticity may aid colonization of new habitats by moving phenotypes in the same direction as natural selection. In the second chapter I conduct a greenhouse experiment to test whether naturally-occurring soil microbial communities contributed to the differences in phenotype and selection that I observed in the field experiment. I found that soil microbes cause plasticity of flowering time but not glucosinolate production, and that they may contribute to natural selection on both traits; thus, non-pathogenic plant-associated microbes are an environmental feature that could shape plant evolution. In the third chapter, I combine a multi-year, multi-habitat field experiment with high-throughput amplicon sequencing to determine whether B. stricta-associated microbial communities are shaped by plant genetic variation. I found that plant genotype predicts the diversity and composition of leaf-dwelling bacterial communities, but not root-associated bacterial communities. Furthermore, patterns of host genetic control over associated bacteria were largely site-dependent, indicating an important role for genotype-by-environment interactions in microbiome assembly. Together, my results suggest that soil microbes influence the evolution of plant functional traits and, because they are sensitive to plant genetic variation, this trait evolution may alter the microbial neighborhood of future B. stricta generations. Complex patterns of plasticity, selection, and symbiosis in natural habitats may impact the evolution of glucosinolate profiles in Boechera stricta.

Premotor Mechanisms for Orofacial Coordination

The mouth, throat, and face contain numerous muscles that participate in a large variety of orofacial behaviors. The jaw and tongue can move independently, and thus require a high degree of coordination among the muscles that move them to prevent self-injury. However, different orofacial behaviors require distinct patterns of coordination between these muscles. The method through which motor control circuitry might coordinate this activity has yet to be determined. Electrophysiological, immunohistochemical, and retrograde tracing studies have attempted to identify populations of premotor neurons which directly send information to orofacial motoneurons in an effort to identify sources of coordination. Yet these studies have not provided a complete picture of the population of neurons which monosynaptically connect to jaw and tongue motoneurons. Additionally, while many of these studies have suggested that premotor neurons projecting to multiple motor pools may play a role in coordination of orofacial muscles, no clear functional roles for these neurons in the coordination of natural orofacial movements has been identified.

In this dissertation, I took advantage of the recently developed monosynaptic rabies virus to trace the premotor circuits for the jaw-closing masseter muscle and tongue-protruding genioglossus muscle in the neonatal mouse, uncovering novel premotor inputs in the brainstem. Furthermore, these studies identified a set of neurons which form boutons onto motor neurons in multiple motor pools, providing a premotor substrate for orofacial coordination. I then combined a retrogradely traveling lentivirus with a split-intein mediated split-Cre recombinase system to isolate and manipulate a population of neurons which project to both left and right jaw-closing motor nuclei. I found that these bilaterally projecting neurons also innervate multiple other orofacial motor nuclei, premotor regions, and midbrain regions implicated in motor control. I anatomically and physiologically characterized these neurons and used optogenetic and chemicogenetic approaches to assess their role in natural jaw-closing behavior, specifically with reference to bilateral masseter muscle electromyogram (EMG) activity. These studies identified a population of bilaterally projecting neurons in the supratrigeminal nucleus as essential for maintenance of an appropriate level of masseter activation during natural chewing behavior in the freely moving mouse. Moreover, these studies uncovered two distinct roles of supratrigeminal bilaterally projecting neurons in bilaterally synchronized activation of masseter muscles, and active balancing of bilateral masseter muscle tone against an excitatory input. Together, these studies identify neurons which project to multiple motor nuclei as a mechanism by which the brain coordinates orofacial muscles during natural behavior.

Seawater carbonate chemistry and Celleporella hyalina biological processes during experiments, 2011

Increased anthropogenic CO2 emissions in the last two centuries have lead to rising sea surface temperature and falling ocean pH, and it is predicted that current global trends will worsen over the next few decades. There is limited understanding of how genetic variation among individuals will influence the responses of populations and species to these changes. A microcosm system was set up to study the effects of predicted temperature and CO2 levels on the bryozoan Celleporella hyalina. In this marine species, colonies grow by the addition of male, female and feeding modular individuals (zooids) and can be physically subdivided to produce a clone of genetically identical colonies. We studied colony growth rate (the addition of zooids), reproductive investment (the ratio of sexual to feeding zooids) and sex ratio (male to female zooids) in four genetically distinct clonal lines. There was a significant effect of clone on growth rate, reproductive investment and sex ratio, with clones showing contrasting responses to the various temperature and pH combinations. Overall, decreasing pH and increasing temperature caused reduction of growth, and eventual cessation of growth was often observed at the highest temperature, especially during the latter half of the 15-day trials. Reproductive investment increased with increasing temperature and decreasing pH, varying more widely with temperature at the lowest pH. The increased production of males, a general stress response of the bryozoan, was seen upon exposure to reduced pH, but was not expressed at the highest temperature tested, presumably due to the frequent cessation of growth. Further to the significant effect of pH on the measured whole-colony parameters, observation by scanning electron microscopy revealed surface pitting of the calcified exoskeleton in colonies that were exposed to increased acidity. Studying ecologically relevant processes of growth and reproduction, we demonstrate the existence of relevant levels of variation among genetic individuals which may enable future adaptation via non-mutational natural selection to falling pH and rising temperature.

The onset of lactase persistence in Europe

The genomic region containing the lactase (LCT) gene shows one of the strongest signals of positive selection in Europeans, detectable using a range of approaches including haplotype length, linked microsatellite variation and population-differentiation-based tests. Lactase is the enzyme that carries out the digestion of the milk sugar lactose. Its expression decreases at some point after the weaning period is over in most mammals and in around 68% of all living adult humans. However, in some humans, particularly those from populations with a history of dairying, lactase is expressed throughout adulthood. This trait is called lactase persistence (LP), and in people of European ancestry, it is associated with a single mutation (-13910*T). Evidence from the detection of dairy fat residues in potsherds, and allele frequencies in ancient DNA samples suggest that LP arose after dairying practices had developed. However, the reasons why LP may have been advantageous are still debated, and the respective contribution of demography and natural selection remains to be disentangled. This paper discusses various studies, from archaeology to population genetics, that have shed some light on the subject by investigating the evolution of LP in Europe.