Dan Graur’s research while affiliated with Tel Aviv University and other places

“[We are aware] of the general lack of information and knowledge regarding biological diversity and of the urgent need to develop scientific, technical, and institutional capacities to provide the basic understanding upon which to plan and implement appropriate measures.” (from the The United Nations “Earth Summit” Conference on Environment and Development, Rio de Janeiro. 1992).

Chimerism, the evolutionary perplexing outcome of fusion between conspecific individuals, is widely documented in nature. Several reports assign a variety of benefits to the state of chimerism, especially in cases of fusions between kins, rating a chimera as a congruous entity. For the first time, we describe here a follow-up study on chimeras of soft corals that occur only between ontogenetically immature conspecifics, prior to development of a histocompatibility recognition system. Four soft coral species from the Red Sea were investigated: Nephthea sp., Heteroxenia fuscescens, Parerythropodium fulvum fulvum and Clavularia hamra. Co-settlement of planulae resulted in high frequencies of spontaneous allogenic fusions between primary polyps. Tissue fusion between allogenic partners was confirmed histologically. During the observation periods (up to 450 d) chimeras were detached, or chimerism resulted in the death of 1 or more partners, or in morphological resorption of the partners. The results also document slower growth and growth-retarding disorders such as disruption of the structural patterns of polyp budding and polyp configuration. These cumulative effects were only manifested by individuals comprised of incongruous components. Such chimeras are likely to be less suited to field conditions than genetically homogeneous individuals, raising the ecological-evolutionary question of why soft-coral chimeras arose in the first place. We propose that juvenile cnidarian chimerism represents a case in which ontogenetic allorecognition is not infallible, and that it is further promoted by the gregarious settlement of larvae characteristic of many coral species.

Molecular phylogeneticists must frequently decide on a painful trade-off between the number of taxa and the number of sequences used in a study. Here, we illustrate the advantages of a method of combining quartet trees to solve this dilemma. We apply the method to a data set of 640 protein-sequence alignments from 4 to 24 eutherian taxa, and obtain a global eutherian phylogeny. In agreement with recent studies, we identify three major super-ordinal clades. The first clade is Afrotheria, a cluster of endemic African mammals. The second clade is an emended Laurasiatheria, consisting of Cetartiodactyla (cetaceans, ruminants, hippopotamuses, pigs, and tylopods), Perissodactyla (horses and rhinoceroses), Carnivora, Pholidota (pangolins), Chiroptera (bats), and Erinaceidae (hedgehogs). A tentatively identified third clade consists of some archontans (primates, flying lemurs, and tree shrews) as well as lagomorphs and rodents. Evolutionary relations within these major clades are well resolved. We also show that nuclear encoded proteins resolve eutherian phylogeny better than complete mitochondria. Finally, our results demonstrate that combining quartet trees provides a major opportunity to resolve unevenly sampled complex phylogenies.

A dynamic programming algorithm is developed for maximum-likelihood reconstruction of the set of all ancestral amino acid sequences in a phylogenetic tree. To date, exhaustive algorithms that find the most likely set of ancestral states (joint reconstruction) have running times that scale exponentially with the number of sequences and are thus limited to very few taxa. The time requirement of our new algorithm scales linearly with the number of sequences and is therefore applicable to practically any number of taxa. A detailed description of the new algorithm and an example of its application to cytochrome b sequences are provided.

The dioecious Red Sea soft coral Parerythropodium fulvum fulvum breeds its nonsymbiotic planula larvae on the surface of female colonies for less than a week. After completing their development, larvae crawl and settle near maternal colonies. Here we study the genetic polymorphism of developing larvae by the use of amplified fragment-length polymorphism markers. Four reproductive colonies from shallow water populations (two from a dense population and two from a less densely populated area 100 m away) were chosen, and ten larvae were randomly collected from each colony. DNA was analyzed by using three different primer combinations producing 61, 63, 63 polymorphic markers, respectively. All larvae exhibited different banding patterns from one another, illustrating the prominent role of sexual reproduction for the production of larvae. Nei's mean genetic distances for all 12 possible pair-wise combinations for larval origins revealed, in most cases, that sister larvae are genetically closer than larvae from different colonies and that larvae may be grouped into three statistical clusters in accordance with colony origin and population studied. The usefulness of molecular methodologies in coral population genetics is discussed.

Speciation and phenotypic plasticity are two extreme strategic modes enabling a given taxon to populate a broad ecological niche. One of the organismal models which stimulated Darwin's ideas on speciation was the Cirripedia (barnacles), to which he dedicated a large monograph. In several cases, including the coral-inhabiting barnacle genera Savignium and Cantellius (formerly Pyrgoma and Creusia, respectively), Darwin assigned barnacle specimens to morphological "varieties" (as opposed to species) within a genus. Despite having been the subject of taxonomic investigations and revisions ever since, the significance of these varieties has never been examined with respect to host-associated speciation processes. Here we provide evidence from molecular (12S mt rDNA sequences) and micromorphological (SEM) studies, suggesting that these closely related barnacle genera utilize opposite strategies for populating a suite of live-coral substrates. Cantellius demonstrates a relatively low genetic variability, despite inhabiting a wide range of corals. The species C. pallidus alone was found on three coral families, belonging to distinct higher-order classification units. In contrast, Savignium barnacles exhibit large between- and within-species variations with respect to both micromorphology and DNA sequences, with S. dentatum "varieties" clustering phylogenetically according to their coral host species (all of which are members of a single family). Thus, whereas Savignium seems to have undergone intense host-associated speciation over a relatively narrow taxonomic range of hosts, Cantellius shows phenotypic plasticity over a much larger range. This dichotomy correlates with differences in life-history parameters between these barnacle taxa, including host-infestation characteristics, reproductive strategies, and larval trophic type.

The observed and expected frequencies of occurrence of microsatellites in the yeast Saccharomyces cerevisiae were investigated. In all cases, the observed frequencies exceeded the expected ones. In contrast to predictions by Messier et al. (1996), there is no critical number of repeats beyond which the observed frequencies of microsatellites significantly exceed the frequencies expected in a random DNA sequence of the same size. Rather, the degree of deviation from expectation was found to be dependent on the length of the microsatellite. That is, a fourfold concatemeric repeat of 3 bp was found to deviate from expectation as much as three-fold concatemeric repeat of 4 bp. These findings suggest that microsatellites evolve through strand-slippage events, rather than recombination events. This, in turn, suggests that the chances of erroneous hybridizations leading to strand-slippage are length dependent.