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Integrative & Comparative Biology

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Integrative & Comparative Biology - Volume 49 Number 6 December 2009 - Back cover

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Integrative & Comparative Biology - Volume 49 Number 6 December 2009 - Front cover

Mon, 16 Nov 2009 07:17:52 PST

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Mon, 16 Nov 2009 07:17:52 PST

Integrative & Comparative Biology - Volume 49 Number 6 December 2009

Mon, 16 Nov 2009 07:17:52 PST

Genomics and vertebrate adaptive radiation: A celebration of the first cichlid genome

Hulsey, C. D., Renn, S. C. P. — Mon, 16 Nov 2009 07:17:51 PST

Cichlid genomics and phenotypic diversity in a comparative context

Hulsey, C. D. — Mon, 16 Nov 2009 07:17:51 PST

Cichlid fishes provide an excellent natural system for integrating studies of genomics and adaptive radiation. Cichlids are unique in comprising a substantial fraction of all vertebrate species, possessing unique jaw structures, displaying an exceptional range of breeding systems, and exhibiting rampant phenotypic convergence. The rate of divergence in cichlid jaws, teeth, color patterns, visual systems, reproductive biology, and mating behaviors is unparalleled among vertebrates. I discuss ways rapid divergence in cichlids and other adaptive radiations make understanding the genomic basis of adaptive divergence more tractable. Then, I briefly overview some major findings and insights into vertebrate adaptation that have been gained through cichlid genetic studies. Finally, I discuss the extensive evolutionary replication provided by cichlid adaptive radiations and their potential for studies of genotype-to-phenotype mapping.

Gene duplication and differential gene expression play an important role in the diversification of visual pigments in fish

Hofmann, C. M., Carleton, K. L. — Mon, 16 Nov 2009 07:17:51 PST

Sensory systems provide crucial information about an organism's external environment and, thus, are often subject to strong natural selection. Because of the large variation in the intensity and spectral quality of light in aquatic environments, studies of sensory adaptation have focused on the visual systems of fish for over a half a century. Recently, the molecular genetic mechanisms that determine the spectral sensitivity of visual pigments have been characterized in several fishes including zebrafish, guppies, medaka, killifish, bream, and cichlids. The results of these studies suggest that teleost fish have incredibly diverse visual systems. In this paper, we review the role that opsin duplication and differential gene expression have played in the diversification of visual pigments. We compare our findings in cichlids to five other taxonomic groups and highlight the ways that their similarities and differences may provide new insights into the molecular genetic basis of sensory adaptation and diversification.

Interspecific profiling of gene expression informed by comparative genomic hybridization: A review and a novel approach in African cichlid fishes

Machado, H. E., Pollen, A. A., Hofmann, H. A., Renn, S. C.P. — Mon, 16 Nov 2009 07:17:51 PST

Modern genomic approaches have facilitated great progress in our understanding of the molecular and genetic underpinnings of ecological and evolutionary processes. Analysis of gene expression through heterologous hybridization in particular has enabled genome-scale studies in many ecologically and evolutionarily interesting species. However, these studies have been hampered by the difficulty of comparing—on a common array platform—gene-expression profiles across species due to sequence divergence altering the dynamics of hybridization. All too often, comparisons of expression profiles across species were limited to contrasting lists of gene or even of just functional categories. Here we review these issues and propose a novel solution. Exploiting the diverse cichlid lineages of East Africa as our model-system, we then present results from an experimental case study that compares the neural gene-expression profiles of males and females of two species that differ in mating system. Using a single microarray platform that contains genes from one species, Astatotilapia burtoni, we conducted a total of 16 direct comparisons for neural gene-expression level between individual males and females from a pair of sister species, the polygynous Enantiopus melanogenys and the monogamous Xenotilapia flavipinnis. Next, we conducted a meta-analysis with previously published data from two different intra-specific expression studies to determine whether sex-specific neural gene expression is more closely associated with behavioral phenotype than it is with gonadal sex. Our results indicate that the gene expression profiles are species-specific to a large extent, as relatively few genes show conserved expression patterns associated with either sex. Finally, we describe how competitive genomic DNA hybridizations between the two focal species allow us to assess the degree to which divergence of sequences biases the results. We propose a masking technique that correlates interspecific expression ratios obtained with cDNA with hybridization ratios obtained with genomic DNA for the same set of species and determines threshold sequence divergence to reduce false positives. Our approach should be applicable to a wide range of interesting questions related to the evolution and ecology of gene expression.

Maternal care and altered social phenotype in a recently collected stock of Astatotilapia burtoni cichlid fish

Renn, S. C. P., Carleton, J. B., Magee, H., Nguyen, M. L. T., Tanner, A. C. W. — Mon, 16 Nov 2009 07:17:51 PST

For over 30 years, the African cichlid fish, Astatotilapia burtoni, has been an important model system for studying the mechanisms underlying socially mediated behavioral change, with the focus being the dominance behavior of males. A recently collected wild-stock (WS) of this species invigorates interest in parallel studies of females’ behavior. Here, we describe a robust ‘good-mother’ phenotype, increased maternal affiliation in fry, and subtle differences in males’ behavior that are exhibited by this new stock. While the females of both the laboratory-stock (LS) and the WS brood the developing fry in their buccal cavity, only the WS continues to provide maternal care after initial release of the fry while the LS engage in filial cannibalism. We show that weight loss during starvation, either during brooding or with restriction of food, is greater in the LS than in the WS; thus, the observed behavioral differences may be tied to metabolic differences. The WS also exhibits a robust androgen response to challenge during the maternal care phase. Given the increasing power of genomic tools available for this species, the comparison of these two stocks will offer the opportunity to investigate the genetic and genomic basis of behavioral differences.

Using Drosophila for studying fundamental processes in hearing

Lu, Q., Senthilan, P. R., Effertz, T., Nadrowski, B., Gopfert, M. C. — Mon, 16 Nov 2009 07:17:51 PST

Apart from detecting sounds, vertebrate ears occasionally produce sounds. These spontaneous otoacoustic emissions are the most compelling evidence for the existence of the cochlear amplifier, an active force-generating process within the cochlea that resides in the motility of the hair cells. Insects have neither a cochlea nor hair cells, yet recent studies demonstrate that an active process that is equivalent to the cochlear amplifier occurs in at least some insect ears; like hair cells, the chordotonal sensory neurons that mediate hearing in Drosophila actively generate forces that augment the minute vibrations they transduce. This neuron-based force-generation, its impact on the ear's macroscopic performance, and the underlying molecular mechanism are the topics of this article, which summarizes some of the recent findings on how the Drosophila organ of hearing works. Functional parallels with vertebrate auditory systems are described that recommend the fly for the study of fundamental processes in hearing.

Active touch, exploratory movements, and sensory prediction

Hartmann, M. J. Z. — Mon, 16 Nov 2009 07:17:51 PST

The relation between somatosensory input and motor output is asymmetric. Somatosensation is associated with every movement an animal makes, but movement is not required for somatosensation. This symposium paper proposes a classification scheme for movement, in which movements are placed along a continuum that describes the role that somatosensory information plays during the movement. Fine sensorimotor control—manipulation and exploration—are found to fall to one extreme of the spectrum, and exploratory movements in particular are shown to possess characteristics that clearly distinguish them from other varieties of movement. Specifically, the exploratory process must permit animals to extract an object's features independently of the sequence of movements executed to explore the object. Based in part on our work on the rat vibrissal system, we suggest that exploration of objects may consist of two complementary levels of sensorimotor prediction operating in parallel. At the cognitive level, the animal might move so as to perform hypothesis testing about the identity or nature of the object. The particular hypothesis tests chosen by the animal might be implemented through sequences of control-level predictions that could be generated at the level of the brainstem and cerebellum.

The influence of viscous hydrodynamics on the fish lateral-line system

Windsor, S. P., McHenry, M. J. — Mon, 16 Nov 2009 07:17:51 PST

Fish exhibit many behaviors that involve sensing water flows with their lateral-line system. In many situations, viscosity affects how the flow interacts with the body of the fish and the neuromasts of the lateral line. Here we discuss how viscosity influences the stimulus to the fish lateral-line system. The movement of a fish's body creates flows that can interfere with the detection of external signals, but these flows can also serve as a source of information about nearby obstacles and the fish's own hydrodynamic performance. The viscous boundary layer on the surface of the skin alters external signals by attenuating the low-frequency components of stimuli. The stimulus to each neuromast depends on the interaction of the fluid surrounding the neuromast and the structural properties of that neuromast, including the number of mechanosensory hair cells it contains. A consideration of the influences of viscosity on flow, at both the whole-body and receptor levels, offers the promise of a more comprehensive understanding of the signals involved in behaviors mediated by the lateral-line system.

Environmental influences in the evolution of tetrapod hearing sensitivity and middle ear tuning

Gridi-Papp, M., Narins, P. M. — Mon, 16 Nov 2009 07:17:51 PST

Vertebrates inhabit and communicate acoustically in most natural environments. We review the influence of environmental factors on the hearing sensitivity of terrestrial vertebrates, and on the anatomy and mechanics of the middle ears. Evidence suggests that both biotic and abiotic environmental factors affect the evolution of bandwidth and frequency of peak sensitivity of the hearing spectrum. Relevant abiotic factors include medium type, temperature, and noise produced by nonliving sources. Biotic factors include heterospecific, conspecific, or self-produced sounds that animals are selected to recognize, and acoustic interference by sounds that other animals generate. Within each class of tetrapods, the size of the middle ear structures correlates directly to body size and inversely to frequency of peak sensitivity. Adaptation to the underwater medium in cetaceans involved reorganization of the middle ear for novel acoustic pathways, whereas adaptation to subterranean life in several mammals resulted in hypertrophy of the middle ear ossicles to enhance their inertial mass for detection of seismic vibrations. The comparative approach has revealed a number of generalities about the effect of environmental factors on hearing performance and middle ear structure across species. The current taxonomic sampling of the major tetrapod groups is still highly unbalanced and incomplete. Future expansion of the comparative evidence should continue to reveal general patterns and novel mechanisms.

Animal Osmoregulation. Tim Bradley.

Somero, G. N. — Mon, 16 Nov 2009 07:17:52 PST

The Genial Gene. Deconstructing Darwinian Selfishness. Joan Roughgarden.

Byers, J. — Mon, 16 Nov 2009 07:17:52 PST

Evolution of Communicative Flexibility - Complexity, Creativity, and Adaptability in Human and Animal Communication. D. Kimbrough Oller and Ulrike Griebel editors.

Miller, C. T., Osmanski, M. — Mon, 16 Nov 2009 07:17:52 PST

Evolution, Second Edition. Douglas J. Futuyma.

Mooi, R. — Mon, 16 Nov 2009 07:17:52 PST

Not By Design: Retiring Darwin's Watchmaker. John O. Reiss.

Hodge, A.-M. C. — Mon, 16 Nov 2009 07:17:52 PST

The Rise of Amphibians: 365 Million Years of Evolution. Robert Carroll.

Sues, H.-D. — Mon, 16 Nov 2009 07:17:52 PST

In the Light of Evolution, Volume II: Biodiversity and Extinction. John C. Avise, Stephen P. Hubbell, and Francisco J. Ayala, editors (National Research Council).

Voirin, B. — Mon, 16 Nov 2009 07:17:52 PST

Ecological Developmental Biology: Integrating Epigenetics, Medicine and Evolution. Scott F. Gilbert and David Epel.

Davidowitz, G. — Mon, 16 Nov 2009 07:17:52 PST

Insect Species Conservation. T. R. New.

Haddad, N. — Mon, 16 Nov 2009 07:17:52 PST

Sperm Biology - An Evolutionary Perspective. Tim R. Birkhead, Dave J. Hosken, and Scott Pitnick, editors.

Morrow, E. H. — Mon, 16 Nov 2009 07:17:52 PST

Morphological selection in an extreme flow environment: body shape and waterfall-climbing success in the Hawaiian stream fish Sicyopterus stimpsoni

Mon, 16 Nov 2009 07:17:52 PST