Impact of duplicate gene copies on phylogenetic analysis and divergence time estimates in butterflies.

BACKGROUND: The increase in availability of genomic sequences for a wide range of organisms has revealed gene duplication to be a relatively common event. Encounters with duplicate gene copies have consequently become almost inevitable in the context of collecting gene sequences for inferring species trees. Here we examine the effect of incorporating duplicate gene copies evolving at different rates on tree reconstruction and time estimation of recent and deep divergences in butterflies. RESULTS: Sequences from ultraviolet-sensitive (UVRh), blue-sensitive (BRh), and long-wavelength sensitive (LWRh) opsins,EF-1 and COI were obtained from 27 taxa representing the five major butterfly families (5535 bp total). Both BRh and LWRh are present in multiple copies in some butterfly lineages and the different copies evolve at different rates. Regardless of the phylogenetic reconstruction method used, we found that analyses of combined data sets using either slower or faster evolving copies of duplicate genes resulted in a single topology in agreement with our current understanding of butterfly family relationships based on morphology and molecules. Interestingly, individual analyses of BRh and LWRh sequences also recovered these family-level relationships. Two different relaxed clock methods resulted in similar divergence time estimates at the shallower nodes in the tree, regardless of whether faster or slower evolving copies were used, with larger discrepancies observed at deeper nodes in the phylogeny. The time of divergence between the monarch butterfly Danaus plexippus and the queen D. gilippus (15.3-35.6 Mya) was found to be much older than the time of divergence between monarch co-mimic Limenitis archippus and red-spotted purple L. arthemis (4.7-13.6 Mya), and overlapping with the time of divergence of the co-mimetic passionflower butterflies Heliconius erato and H. melpomene (13.5-26.1 Mya). Our family-level results are congruent with recent estimates found in the literature and indicate an age of 84-113 million years for the divergence of all butterfly families. CONCLUSION: These results are consistent with diversification of the butterfly families following the radiation of angiosperms and suggest that some classes of opsin genes may be usefully employed for both phylogenetic reconstruction and divergence time estimation.

Nonadditive effects of flower damage and hummingbird pollination on the fecundity of Mimulus luteus.

Flower herbivory and pollination have been described as interactive processes that influence each other in their effects on plant reproductive success. Few studies, however, have so far examined their joint effects in natural populations. In this paper we evaluate the influence of flower damage and pollination by the hummingbird Oreotrochilus leucopleurus on the fecundity of the Andean monkey flower Mimulus luteus. We performed a 2x2 factorial experiment, with artificial clipping of lower petals and selective exclusion of the hummingbird as main factors. In spite of the relatively low proportion (27.5%) of the variance in seed production accounted for by the full factorial model, artificial damage and hummingbird exclusion, as well as their interaction, were highly significant, indicating nonadditive effects of factors on plant fecundity. In the presence of hummingbirds, undamaged flowers had a seed production that was 1.7-fold higher than for damaged flowers, suggesting that the effect of flower damage on female reproductive success occurs probably as a consequence of hummingbird discrimination against damaged corollas. This result indicates that the impact of flower herbivory on plant fecundity was contingent on the presence or absence of hummingbirds, suggesting that pollinators may indirectly select for undamaged and probably resistant flower phenotypes. A second interaction effect revealed that undamaged flowers produced 78.5% more seeds in the absence of rather than in the presence of O. leucopleurus, raising the question of the ecological mechanism involved. We suggest that the strong territorial behavior exhibited by the bee Centris nigerrima may confine the foraging activities of the remaining bee species to safe sites within exclosures. Overall, our results provide evidence that hummingbird pollination and flower herbivory have interdependent effects on M. luteus fecundity, which indicates that it will be difficult to predict their ecological and evolutionary consequences unless interactions are analyzed in an integrated form.

Spatial organization of the pigeon tectorotundal pathway: an interdigitating topographic arrangement.

The retinotectofugal system is the main visual pathway projecting upon the telencephalon in birds and many other nonmammalian vertebrates. The ascending tectal projection arises exclusively from cells located in layer 13 of the optic tectum and is directed bilaterally toward the thalamic nucleus rotundus. Although previous studies provided evidence that different types of tectal layer 13 cells project to different subdivisions in Rt, apparently without maintaining a retinotopic organization, the detailed spatial organization of this projection remains obscure. We reexamined the pigeon tectorotundal projection using conventional tracing techniques plus a new method devised to perform small deep-brain microinjections of crystalline tracers. We found that discrete injections involving restricted zones within one subdivision retrogradely label a small fraction of layer 13 cells that are distributed throughout the layer, covering most of the tectal representation of the contralateral visual field. Double-tracer injections in one subdivision label distinct but intermingled sets of layer 13 neurons. These results, together with the tracing of tectal axonal terminal fields in the rotundus, lead us to propose a novel "interdigitating" topographic arrangement for the tectorotundal projection, in which intermingled sets of layer 13 cells, presumably of the same particular class and distributed in an organized fashion throughout the surface of the tectum, terminate in separate regions within one subdivision. This spatial organization has significant consequences for the understanding of the physiological and functional properties of the tectofugal pathway in birds.