Perspective: transposable elements, parasitic DNA, and genome evolution

The nature of the role played by mobile elements in host genome evolution is reassessed considering numerous recent developments in many areas of biology. It is argued that easy popular appellations such as "selfish DNA" and "junk DNA" may be either inaccurate or misleading and that a more enlightened view of the transposable element-host relationship encompasses a continuum from extreme parasitism to mutualism. Transposable elements are potent, broad spectrum, endogenous mutators that are subject to the influence of chance as well as selection at several levels of biological organization. Of particular interest are transposable element traits that early evolve neutrally at the host level but at a later stage of evolution are co-opted for new host functions.     

The probability that beneficial mutations are lost in populations with periodic bottlenecks

Population bottlenecks affect the dynamics of evolution, increasing the probability that beneficial mutations will be lost. Recent protocols for the experimental study of evolution involve repeated bottlenecks-when fresh media are inoculated during serial transfer or when chemostat tubes are changed. Unlike population reductions caused by stochastic environmental factors, these bottlenecks occur at known, regular intervals and with a fixed dilution ratio. We derive the ultimate probability of extinction for a beneficial mutation in a periodically bottlenecked population, using both discrete and continuous approaches. We show that both approaches yield the same approximation for extinction probability. From this, we derive an approximate expression for an effective population size.     

Rapid evolution in the Nebria gregaria group (Coleoptera: Carabidae) and the paleogeography of the Queen Charlotte Islands

Morphological differentiation in the ground beetles of the Nebria gregaria group, found on the Queen Charlotte Islands, has been used as support for the glacial refugium proposed for the northwest coast of North America. Two members of this species group, N. charlottae and N. louiseae, are restricted to cobble beaches in this archipelago. A third, N. haida, is found only in alpine regions of the archipelago and the adjacent mainland. The remaining two species of the gregaria group, N. lituyae and N. gregaria, show highly restricted distributions in the mountains of the Alaska panhandle and on the beaches of the Aleutian Islands, respectively. To determine the relationships of the five species, we conducted phylogenetic analyses on nucleotide sequence data obtained from five regions of the mitochondrial DNA. In total, 1835 bp were analyzed. The results suggest that one species, N. lituyae, does not belong in the gregaria group, and that only seven mutations separated the two most divergent of the four remaining species. We also conducted random amplified polymorphic DNA fingerprinting analyses on genomic DNA extracted from the five species. Analyses of genetic diversity revealed a lack of molecular differentiation among the Queen Charlotte species, suggesting that these populations may be postglacial in origin and that together N. gregaria, N. charlottae, N. louiseae, and N. haida might represent local variations of a single species. These results are consistent with conclusions derived for the morphological and genetical differentiation among Gasterosteus populations in the archipelago.     

Sexual selection on plumage and behavior in an avian hybrid zone: experimental tests of male-male interactions

In western Panama, an unusual hybrid zone exists between white-collared manakins, Manacus candei, and golden-collared manakins, M. vitellinus. Unidirectional introgression of plumage traits from vitellinus into candei has created a region in which all definitively plumaged males have a collar that is lemon-colored. These males are nearly indistinguishable from white-collared candei genetically and morphometrically, but strongly resemble golden-collared vitellinus due to the introgression of secondary sexual plumage traits, particularly the lemon-colored collar. The introgression could be explained by sexual selection for golden-collared traits or by a series of mechanisms that do not invoke sexual selection (e.g., neutral diffusion, dominant allele). Sexual selection on male-male interactions implies behavioral differences among the plumage forms--specifically that golden- and lemon-collared males should be more aggressive than white-collared males. In contrast, the nonsexual hypotheses predict behavioral similarity between lemon- and white-collared males, based on their nearly identical genetics. We tested the sexual selection hypothesis experimentally, by presenting males with taxidermic mounts of the three forms. As response variables, we monitored vocalizations and attacks on the mounts by replicate subject males. Both golden-collared and lemon-collared males were more likely to attack than were white-collared males, as predicted under sexual selection but not by the nonsexual hypotheses. Lemon-collared males were more vocally reactive than either parental form, contrary to the prediction of the nonsexual hypotheses. Our study demonstrates that sexual selection on male-male interactions may play an important role in the dynamics of character evolution and hybrid zones.     

Adaptive life-history evolution in the livebearing fish Brachyrhaphis rhabdophora: genetic basis for parallel divergence in age and size at maturity and a test of predator-induced plasticity

I document a genetic basis for parallel evolution of life-history phenotypes in the livebearing fish Brachyrhaphis rhabdophora from northwestern Costa Rica. In previous work, I showed that populations of B. rhabdophora that co-occur with predators attain maturity at smaller sizes than populations that live in predator-free environments. I also demonstrated that this pattern of phenotypic divergence in life histories was independently repeated in at least five isolated drainages. However, life-history phenotypes measured from wild-caught fish could be attributed to environmental effects rather than to genetic differences among populations. In the present study, I reared male fish from four populations (two that co-occur with predators and two from predator-free environments) under four sets of environmental conditions. The pattern of phenotypic divergence in maturation size documented in the field between populations collected from different predation environments persisted after two generations in the laboratory. I also found a genetic basis for differences between populations in the age at which males attain maturity and in growth rates. By rearing fish in four different common environments, I tested for phenotypic plasticity in male life-history traits in response to nonlethal exposure to predators. There was a significant delay in the onset of sexual maturity in fish exposed to predators relative to those in the control, but no differences among treatments in size at maturity or growth rates. These results, coupled with previous work on B. rhabdophora, demonstrate a repeated pattern of parallel evolutionary divergence among genetically isolated populations that is strongly associated with predation.     

RECONNECTING CELL AND ANIMAL LINEAGES: WHAT DO CELL LINEAGES TELL US ABOUT THE EVOLUTION AND DEVELOPMENT OF SPIRALIA?

Cell lineage studies in the clade Eutrochozoa, and especially the Spiralia, remains a rich and relatively untapped source for understanding broad evolutionary developmental problems; including (1) the utility of cell timing formation for phylogenetic hypotheses; (2) the evolution of cell timing changes and its relation to heterochronic patterns; (3) stereotypy or lack thereof in rates of change of cell growth during evolution and its relation to both evolutionary history and current usage; and (4) how mosaic cleavage timing variation may be expected to differ from other groups. A compilation of available cell timing information was made from previous studies where each division was explicitly followed and the total number of cells followed was greater than 24. From that compilation, we performed a series of heuristic and quantitative analyses, including a phylogenetic analysis using cell timing data as characters and analyses of timing variation across all taxa. Our results show that: (1) cell lineage data reconstructs a phylogenetic hypothesis that has similarities, especially among the Mollusca. to the patterns found in morphological and molecular analyses; (2) the mesentoblast (4d) is a unique cell compared to other cell in that it speeds up and slows down relative to other cells in taxa with both unequal and equal cell sizes; (3) some cells that form in the same quartet at the same point in the cell lineage hierarchy have much lower variations than analogous other cells, arguing for architectural constraint or stabilizing selection acting on those cells; and (4) although variation in cell timing generally increases during development, timing of formation of progeny cells in the first quartet has lower variation than the parent cells, arguing that some regulation-like behavior might be present.     

Cladogenesis and loss of the marine life-history phase in freshwater galaxiid fishes (Osmeriformes: Galaxiidae)

Switches from migratory (diadromous) to nonmigratory (freshwater) life histories are known to have occurred repeatedly in some aquatic taxa. However, the significance of the loss of diadromy as an initiator for speciation remains poorly understood. The rivers of New Zealand's South Island house a species flock of recently derived nonmigratory galaxiid fishes known as the Galaxias vulgaris complex. Members of this complex are morphologically and genetically similar to the diadromous G. brevipinnis found in New Zealand and southeastern Australia. We hypothesised that South Island's G. vulgaris complex (at least 10 nonmigratory lineages) represents a number of independent radiations from a migratory G. brevipinnis stock, with repeated loss of diadromy. Sequence data were obtained for 31 ingroup samples (G. vulgaris complex and G. brevipinnis) plus four outgroup taxa. A well-resolved phylogeny based on 5039 base pairs of the mitochondrial genome suggests that diadromy has been lost on three separate occasions. Thus, speciation in these galaxiid fishes is partly an incidental phenomenon caused by switches from diadromous to nonmigratory strategies. However, much of the subsequent nonmigratory diversity is monophyletic, suggesting that drainage evolution (vicariance) has also played a major role in cladogenesis. Levels of sequence divergence among major ingroup lineages (1.6-12.7%) suggest that the radiation is considerably older relative to Northern Hemisphere (postglacial) complexes of salmonid, osmerid, and gasterosteid fishes. Sympatric taxa are not monophyletic, suggesting that their coexistence reflects secondary contact rather than sympatric speciation. The monophyly of New Zealand G. brevipinnis is well supported, but both mitochondrial DNA and nuclear sequences indicate that G. brevipinnis is paraphyletic on an intercontinental scale. The divergence (maximum 11.5%) between Tasmanian and New Zealand G. brevipinnis, although large, supports marine dispersal rather than vicariance as the principle biogeographic mechanism on an intercontinental scale.     

Migratory costs and the evolution of egg size and number in introduced and indigenous salmon populations

The trade-off between reproductive investment and migration should be an important factor shaping the evolution of life-history traits among populations following their radiation into habitats with different migratory costs and benefits. An experimentally induced difference in migratory rigor for families of chinook salmon (Oncorhynchus tshawytscha), of approximately 86 km and 413 m elevation, exacted a cost to somatic energy reserves (approximately 17% reduction in metabolizable mass) and ovarian investment (13.7% reduction in ovarian mass). This cost was associated with a reduction in egg size and paralleled the phenotypic pattern of divergence between two introduced New Zealand populations of common origin, presently breeding at sites with different migration distances. The genetic pattern of divergence of these same populations, detected under common rearing, was consistent with compensation for migratory costs (the population that migrates farther invested more in ovarian mass), but egg number more than egg size was associated with this evolution. These evolutionary patterns are consistent with what is known of the inheritance of these traits and with trade-offs and constraints favoring initial evolution in offspring number over offspring size. Analysis of egg number-size patterns of other Pacific salmon populations in their native range supported the hypothesis that migration strongly influences patterns of reproductive allocation, favoring a higher ratio of egg number to egg size with greater migration distance.