Evolution of Protein Molecules

A DNA test to sex most birds.

Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

/pdf/fast-tree-computing-large-minimum-evolution-trees-with-4grq0gwfpy.pdf

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

General Themes: G.A. Parker, Sperm Competition and the Evolution of Ejaculates: Towards a Theory Base. A.P. Moller, Sperm Competition and Sexual Selection. W.G. Eberhard, Female Roles in Sperm Competition. J. Wright, Paternity and Paternal Care. Taxonomic Treatments: L.F. Delph and K. Havens, Pollen Competition in Flowering Plants. D.R. Levitan, Sperm Limitation, Gamete Competition and Sexual Selection in External Fertilizers. N.K. Michiels, Mating Conflicts and Sperm Competition in Simultaneous Hermaphrodites. B. Baur, Sperm Competition in Molluscs. M.A. Elgar, Sperm Competition and Sexual Selection in Spiders and Other Arachnids. L.W. Simmons and M.T. Siva-Jothy, Sperm Competition in Insects: Mechanisms and the Potential for Selection. C.W. Petersen and R.R. Warner, Sperm Competition in Fishes. T.R. Halliday, Sperm Competition in Amphibians. M. Olsson and T. Madsen, Sexual Selection and Sperm Competition in Reptiles. T.R. Birkhead, Sperm Competition in Birds: Mechanisms and Function. D.A. Taggart, W.G. Breed, P.D. Temple-Smith, A. Purvis, and G. Shimmin, Reproduction, Mating Strategies and Sperm Competition in Marsupials and Monotremes. M. Gomendio, A.H. Harcourt, and E.R.S. Roldan, Sperm Competition in Mammals. T.R. Birkhead and A.P. Moller, Sperm Competition, Sexual Selection and Different Routes to Fitness. Index.

Sperm competition and sexual selection

http://webpages.icav.up.pt/PTDC/BIA-BEC/099934/2008/papers/Frankham_2005_Biological_Conservation.pdf

Genetics and extinction

Sperm size varies enormously among species, but the reasons for this variation remain obscure. Since it has been suggested that swimming velocity increases with sperm length, earlier studies proposed longer (and therefore faster) sperm are advantageous under conditions of intense sperm competition. Nonetheless, previous work has been equivocal, perhaps because the intensity of sperm competition was measured indirectly. DNA profiling now provides a more direct measure of the number of offspring sired by extrapair males, and thus a more direct method of assessing the potential for sperm competition. Using a sample of 21 species of passerine birds for which DNA profiling data were available, we found a positive relation between sperm length and the degree of extrapair paternity. A path analysis, however, revealed that this relationship arises only indirectly through the positive relationship between the rate of extrapair paternity and length of sperm storage tubules (SSTs) in the female. As sperm length is correlated positively with SST length, an increase in the intensity of sperm competition leads to an increase in sperm length only through its effect on SST length. Why females vary SST length with the intensity of sperm competition is not clear, but one possibility is that it increases female control over how sperm are used in fertilization. Males, in turn, may respond on an evolutionary time scale to changes in SST size by increasing sperm length to prevent displacement from rival sperm. Previous theoretical analyses predicting that sperm size should decrease as sperm competition becomes more intense were not supported by our findings. We suggest that future models of sperm-size evolution consider not only the role of sperm competition, but also how female control and manipulation of ejaculates after

The evolution of sperm size in birds.

In a sample of 20 species of North American passerine birds we found no relation between sperm size and mating system like that previously reported in mammals (Gomendio & Roldan (Proc. R. Soc. Lond. B 243, 181 (1991)). Instead, we found a positive correlation between sperm length and the length of female sperm storage tubules (SSTS) and a negative correlation between sperm length and the number of SSTS. Both of these correlations suggest that the more than fivefold variation in sperm size we found among species can be explained by sperm competition for access to storage sites (SSTS) in females. As longer sperm appear to be able to swim faster, selection should favour long sperm when SSTS are in short supply; sperm long enough to fill an SST might also prevent access to SSTS by the sperm of other males. Conversely, selection should favour shorter sperm when there is an advantage to sperm layering within an SST promoting a last-male mating advantage. Although we conclude that sperm competition influences sperm size in birds, little is known about the interactions between sperm and SSTS. It seems clear, however, that detailed study of this interaction will provide a new dimension to the study of avian mating systems.

Sperm size and sperm competition in birds.

Sperm competition should select for increased sperm production if the probability of fertilization by a specific male is proportional to the relative number of sperm inseminated. A review of the literature generally supports the predicted positive association between sperm production or allocation and various measures of the presumed intensity of sperm competition. However, it is not clear how increased sperm competition is related to extra-pair paternity, and it remains unknown whether certainty of paternity should be associated with relative testis size. Based on a large sample of bird species with information on extra-pair paternity gathered from the literature, we demonstrate that testis mass is related positively to the level of extra-pair paternity, after controlling for body size and phylogeny. Although large testes may be necessary to avoid sperm depletion in species in which males frequently engage in multi-pair copulations, we argue that selection has favoured increased testis mass in situations of more intense sperm competition in order to retaliate against copulations by rival males. The fact the males are not always successful in retaliating against rival ejaculates further suggests that females may largely control the allocation of paternity in birds and that increased sperm production by males may simply be a male strategy to make the best of a bad situation.

Extra-pair paternity, sperm competition and the evolution of testis size in birds

Severe bottlenecks can reduce genetic diversity and increase inbreeding as individuals are forced to mate with close relatives, but it is unknown at what minimum population size the negative fitness consequences of bottlenecks are expressed. The New Zealand avifauna contains a large number of species that have gone through bottlenecks of varying severity, providing an exceptional opportunity to test this question by using the comparative method. Using decreased hatchability as a measure of fitness costs, we found that hatching failure was significantly greater among both native and introduced species that had passed through bottlenecks of <150 individuals. Comparisons between pre- and postbottleneck populations of introduced species suggest that hatching problems arise even in populations founded by <600 individuals. Our study confirms that hatching failure is widespread and persistent among birds passing through severe bottlenecks and that the population sizes at which this fitness cost is expressed are several times greater than the number of individuals currently used to found most new populations of endangered species. We recommend that conservation managers revise the protocols they use for reintroductions or they may unwittingly reduce the long-term viability of the species they are trying to save.

https://www.pnas.org/content/pnas/101/2/558.full.pdf

Hatching failure increases with severity of population bottlenecks in birds

Begging by nestling birds can be conspicuous and loud. Such displays are thought to function in signalling nestling condition and securing parental care, but they also may inadvertently attract the attention of predators. We compared the structure of nestling begging calls to the risk of predation among 24 species of birds breeding in a forest community in central Arizona. After controlling for body size and phylogeny, we found that species subject to greater nest predation had calls with higher frequency (pitch) and lower amplitude (loudness) than species subject to lower rates of nest predation. As these acoustic features make it difficult for potential predators to pinpoint the source of a sound, our results suggest that an increased risk of predation has led to the evolution of begging calls that minimize locatability. The relationship between call structure and the risk of predation also supports the hypothesis that attracting predators is a direct cost of begging and that such costs can constrain any evolutionary escalation in the intensity of nestling begging.

James V. Briskie

Papers

The evolution of sperm size in birds.

Sperm size and sperm competition in birds.

Extra-pair paternity, sperm competition and the evolution of testis size in birds

Hatching failure increases with severity of population bottlenecks in birds

Nest predation and the evolution of nestling begging calls