Insights into recombination from population genetic variation

Patterns of genetic variation in natural populations are shaped by, and hence carry valuable information about, the underlying recombination process. In the past five years, the increasing availability of large-scale population genetic data on dense sets of markers, coupled with advances in statistical methods for extracting information from these data, have led to several important advances in our understanding of the recombination process in humans. These advances include the identification of large numbers of 'hotspots', where recombination appears to take place considerably more frequently than in the surrounding sequence, and the identification of DNA sequence motifs that are associated with the locations of these hotspots.     

Insights into the ecology and evolutionary success of crocodilians revealed through bite-force and tooth-pressure experimentation

Background

Crocodilians have dominated predatory niches at the water-land interface for over 85 million years. Like their ancestors, living species show substantial variation in their jaw proportions, dental form and body size. These differences are often assumed to reflect anatomical specialization related to feeding and niche occupation, but quantified data are scant. How these factors relate to biomechanical performance during feeding and their relevance to crocodilian evolutionary success are not known.

Methodology/Principal Findings

We measured adult bite forces and tooth pressures in all 23 extant crocodilian species and analyzed the results in ecological and phylogenetic contexts. We demonstrate that these reptiles generate the highest bite forces and tooth pressures known for any living animals. Bite forces strongly correlate with body size, and size changes are a major mechanism of feeding evolution in this group. Jaw shape demonstrates surprisingly little correlation to bite force and pressures. Bite forces can now be predicted in fossil crocodilians using the regression equations generated in this research.

Conclusions/Significance

Critical to crocodilian long-term success was the evolution of a high bite-force generating musculo-skeletal architecture. Once achieved, the relative force capacities of this system went essentially unmodified throughout subsequent diversification. Rampant changes in body size and concurrent changes in bite force served as a mechanism to allow access to differing prey types and sizes. Further access to the diversity of near-shore prey was gained primarily through changes in tooth pressure via the evolution of dental form and distributions of the teeth within the jaws. Rostral proportions changed substantially throughout crocodilian evolution, but not in correspondence with bite forces. The biomechanical and ecological ramifications of such changes need further examination.     

Insights into the adaptive significance of vertical pupil shape in snakes

Pupil shape in vertebrates ranges from circular to vertical, with multiple phylogenetic shifts in this trait. Our analyses challenge the widely held view that the vertical pupil evolved as an adaptation to enhance night vision. On functional grounds, a variable‐aperture vertical pupil (i) allows a nocturnal species to have a sensitive retina for night vision but avoid dazzle by day by adjusting pupil closure, and (ii) increases visual acuity by day, because a narrow vertical pupil can project a sharper image onto the retina in the horizontal plane. Detection of horizontal movement may be critical for predators that wait in ambush for moving prey, suggesting that foraging mode (ambush predation) as well as polyphasic activity may favour the evolution of vertical pupil shape. Camouflage (disruption of the circular outline of the eye) also may be beneficial for ambush predators. A comparative analysis in snakes reveals significant functional links between pupil shape and foraging mode, as well as between pupil shape and diel timing of activity. Similar associations between ambush predation and vertically slit pupils occur in lizards and mammals also, suggesting that foraging mode has exerted major selective forces on visual systems in vertebrates.     

Sensory ecology, receiver biases and sexual selection

During courtship, signals are sent between the sexes, and received signals contain information that forms the basis of decision making. Much is known about signal content, but less is known about signal design-what makes signals work efficiently? A consideration of design not only gives new insights into the evolution of signals (including novelty), but also allows the development of specific and testable predictions about the direction of evolution. Recently there has been increased interest in signal design, but this has resulted in some apparently divergent views in the literature.     

Quantitative genetic models of sexual selection

Modeling of R.A. Fisher's ideas about the evolution of male ornamentation using quantitative genetics began in the 1980s. Following an initial period of enthusiasm, interest in these models began to wane when theoretical studies seemed to show that the rapid evolution of ornaments would not occur if there were costs associated with female mate choice. Recent theoretical work has shown, however, that runaway evolution and other kinds of extensive diversification of ornaments and preferences can occur, even when female choice is costly. These new models highlight crucial parameters that profoundly influence evolutionary trajectories, but these parameters have been neglected in empirical studies. Here, we review quantitative genetic models of sexual selection with the aim of fostering communication and synergism between theoretical and empirical enterprises. We also point out several areas in which additional empirical work could distinguish between alternative models of evolution.     

Construction of a genetic linkage map in celery using DNA-based markers.

A F2 population of two celery cultivated types (Apium graveolens L. var. rapaceum and A. graveolens L. var. secalinum) was used to construct a linkage map consisting of 29 RFLP (restriction fragment length polymorphism), 100 RAPD (random amplified polymorphic DNA), four isozyme, one disease resistance, and one growth habit markers. The map contains 11 major groups and 9 small groups and has a total length of 803 cM with an average distance of 6.4 cM between two adjacent loci. Ten percent of the RAPDs segregated as codominant markers and their allelic homologies were tested by Southern hybridization. One-quarter of the dominant RAPDs were linked in repulsion phase, whereas the majority of them were linked to either codominant or dominant markers in coupling phase. About 10% of the markers showed significant segregation distortion. The detectable level of duplications in the celery genome was relatively low.     

Insights into the ecology of Schizosaccharomyces species in natural and artificial habitats

The fission yeast genus Schizosaccharomyces contains important model organisms for biological research. In particular, S. pombe is a widely used model eukaryote. So far little is known about the natural and artificial habitats of species in this genus. Finding out where S. pombe and other fission yeast species occur and how they live in their habitats can promote better understanding of their biology. Here we investigate in which substrates S. pombe, S. octosporus, S. osmophilus and S. japonicus are present. To this end about 2100 samples consisting of soil, tree sap fluxes, fresh fruit, dried fruit, honey, cacao beans, molasses and other substrates were analyzed. Effective isolation methods that allow efficient isolation of the above mentioned species were developed. Based on the frequency of isolating different fission yeast species in various substrates and on extensive literature survey, conclusions are drawn on their ecology. The results suggest that the primary habitat of S. pombe and S. octosporus is honeybee honey. Both species were also frequently detected on certain dried fruit like raisins, mango or pineapple to which they could be brought by the honey bees during ripening or during drying. While S. pombe was regularly isolated from grape mash and from fermented raw cacao beans S. octosporus was never isolated from fresh fruit. The main habitat of S. osmophilus seems to be solitary bee beebread. It was rarely isolated from raisins. S. japonicus was mainly found in forest substrates although it occurs on fruit and in fruit fermentations, too.

     

Insights into the mutational history and prevalence of SCA1 in the Indian population through anchored polymorphisms

There is a wide variation in prevalence of spinocerebellar ataxia type 1 (SCA1) in different populations. In the present study, we observed SCA1 in ∼22% (37/167 families) of the autosomal dominant cerebellar ataxias (ADCAs) in the Indian population. We investigated the role of various genetic factors like repeat length, interruption pattern and chromosomal background in predisposing the repeats to instability in these families. We analyzed 12 markers (9 SNPs and 3 microsatellite markers) and found 3 of them, spanning a region of ∼65 kbp to be linked with the disease locus in the Indian population. The haplotype C-4-C defined by rs1476464 (SNP9)-D6S288-rs2075974 (SNP1), which was extremely rare in nonaffected chromosomes (∼3%), was observed to be significantly (P<0.0000) associated with the expanded chromosomes in ∼44% of SCA1 families. This haplotype was found in all nonhuman primates. SNP1 (C/T), which showed a skewed allelic distribution between large (LN > 30 repeats) and small normal (SN ≤ 30 repeats) alleles (P<0.0000) had similar allelic distribution (P=0.3477) in LN and expanded alleles. Our study suggested that LN and expanded chromosomes linked with the ancestral C allele of SNP1 might have originated simultaneously during evolution by the lengthening of repeats. The LN alleles might have accumulated repeat stabilizing non-CAG interruptions during this process. Similar proportions of T allele in SN with single interruptions, LN and expanded chromosomes lend credence to the origin of expanded alleles from singly-interrupted chromosomes. Our analyses using markers linked (anchoring) to SCA1 suggest that prevalence of SCA1 is correlated to both repeat length and number of interruptions in the Indian population. The spectrum of these alleles also points toward the antiquity of SCA1 mutation in the Indian population.Electronic Supplementary Material Supplementary material is available for this article at     

Molecular markers in genetic and selection studies of maize

The review represents the literature data and the data of personal research demonstrating the modern achievements in molecular-genetic analysis of maize (Zea mays L.). The importance of the use of DNA-technologies in genetics, breeding and seed-production of maize is shown. The examples of application of molecular-genetic markers in breeding process to increase its efficacy are demonstrated.     

Insights into physiological and genetic mupirocin susceptibility in bifidobacteria

Mupirocin is an antibiotic commonly used in selective media for the isolation of bifidobacteria. However, little is known about the genetic traits responsible for bifidobacterial resistance to mupirocin. Our investigation demonstrates that all of the bifidobacteria tested exhibit a phenotype of generally high resistance to this antibiotic. The genotypic reason for bifidobacterial mupirocin resistance was further characterized by sequencing of the isoleucyl-tRNA synthetase gene (ileS) coupled with three-dimensional modeling of the encoded protein and cloning of the ileS gene of Bifidobacterium bifidum PRL2010 in a mupirocin-sensitive Escherichia coli strain. These analyses revealed key amino acid residues of the IleS protein that apparently are crucial for conferring a mupirocin resistance phenotype to bifidobacteria.     

Male reproductive success and sexual selection in northern water snakes determined by microsatellite DNA analysis

Male northern water snakes (Nerodia sipedon) have high variancein reproductive success relative to females. We used DNA-basedpaternity analyses from a 3-year study of two marsh populationsof water snakes to investigate the factors that contributeto variation in male success. Male traits investigated includedbody size, condition, tail length, home range size, activityduring the mating season, and genetic profile (genetic similarityto females, heterozygosity, and genetic variability [d²]).We successfully assigned > 80% of offspring to sires froma sample of 811 offspring from 45 litters. Male reproductivesuccess did not vary significantly with body size, tail length,condition, home range size, or the number of microsatelliteloci at which males were heterozygous, nor with other featuresof their genetic profiles. However, we found evidence of positive assortative mating by size in the marsh in which receptive femaleswere not spatially clumped. Also, males that were most activeduring the mating season were more successful, particularlywhere females were not clumped. We failed to find evidenceof selection acting on male size through variance in reproductivesuccess, indicating that sexual selection does not have an important influence on sexual size dimorphism in this species(males are smaller than females). We propose that males aresmaller than females because the lack of advantage to largesize allows males to adopt a low-energy, low-growth strategythat reduces their risk of predation outside the mating season.     

The depletion of genetic variance by sexual selection

Sexually selected traits display substantial genetic variance [1, 2], in conflict with the expectation that sexual selection will deplete it [3-5]. Condition dependence is thought to resolve this paradox [5-7], but experimental tests that relate the direction of sexual selection to the availability of genetic variance are lacking. Here, we show that condition-dependent expression is not sufficient to maintain genetic variance available to sexual selection in multiple male sexually selected traits. We employed an experimental design that simultaneously determined the quantitative genetic basis of nine male cuticular hydrocarbons (CHCs) of Drosophila bunnanda, the extent of condition dependence of these traits, and the strength and direction of sexual selection acting upon them. The CHCs of D. bunnanda are condition dependent, with 18% of the genetic variance in male body size explained by genetic variance in CHCs. Despite the presence of genetic variance in individual male traits, 98% of the genetic variance in CHCs was found to be orientated more than 88 degrees away from the direction of sexual selection and therefore unavailable to selection. A lack of genetic variance in male traits in the direction of sexual selection may represent a general feature of sexually selected systems, even in the presence of condition-dependent trait expression.     

An introduction to genetic quality in the context of sexual selection

This special issue of Genetica brings together empirical researchers and theoreticians to present the latest on the evolutionary ecology of genetic quality in the context of sexual selection. The work comes from different fields of study including behavioral ecology, quantitative genetics and molecular genetics on a diversity of organisms using different approaches from comparative studies, mathematical modeling, field studies and laboratory experiments. The papers presented in this special issue primarily focus on genetic quality in relation to (1) sources of genetic variation, (2) polyandry, (3) new theoretical developments and (4) comprehensive reviews.     

Evolution and ecology of MHC molecules: from genomics to sexual selection

In the past few years the DNA sequence database for molecules of the MHC (major histocompatibility complex) has expanded greatly, yielding a more complete picture of the long-term rates and patterns of evolution of the MHC in vertebrates. Sharing of MHC allelic lineages between long-diverged species (trans-species evolution) has been detected virtually wherever it is sought, but new analyses of linked neutral regions and the complexities of sequence convergence and microrecombination in the peptide binding region challenge traditional phylogenetic analyses. Methods for estimating the intensity of selection on MHC genes suggest that viability is important, but recent studies in natural populations of mammals give inconsistent results concerning mate choice. The complex and interacting roles of microrecombination, parasite-mediated selection and mating preferences for maintaining the extraordinary levels of MHC polymorphism observed are still difficult to evaluate.     

Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology

The recent development of metaproteomics has enabled the direct identification and quantification of expressed proteins from microbial communities in situ, without the need for microbial enrichment. This became possible by (1) significant increases in quality and quantity of metagenome data and by improvements of (2) accuracy and (3) sensitivity of modern mass spectrometers (MS). The identification of physiologically relevant enzymes can help to understand the role of specific species within a community or an ecological niche. Beside identification, relative and absolute quantitation is also crucial. We will review label-free and label-based methods of quantitation in MS-based proteome analysis and the contribution of quantitative proteome data to microbial ecology. Additionally, approaches of protein-based stable isotope probing (protein-SIP) for deciphering community structures are reviewed. Information on the species-specific metabolic activity can be obtained when substrates or nutrients are labeled with stable isotopes in a protein-SIP approach. The stable isotopes (¹³C, ¹⁵N, ³⁶S) are incorporated into proteins and the rate of incorporation can be used for assessing the metabolic activity of the corresponding species. We will focus on the relevance of the metabolic and phylogenetic information retrieved with protein-SIP studies and for detecting and quantifying the carbon flux within microbial consortia. Furthermore, the combination of protein-SIP with established tools in microbial ecology such as other stable isotope probing techniques are discussed.     

Assortative mating through a mechanism of sexual selection

We propose that assortative mating can arise through a mechanism of sexual selection by active female choice of partners based on a 'self-seeking like' decision rule. Using a mathematical model, we show that a gene can be selected that make females to choose mates that are similar to themselves with respect to an arbitrary tag, even if two independent and unlinked genes determine the preference and the tag. The necessary requisite for this process to apply is an asymmetry between partners, such that the female can choose the male but this one must always accept to mate. The fitness advantage is due to linkage disequilibrium built up between both genes. Simulations have been run to check the algebraic results and to analyse the influence of several factors on the evolution of the system. Any factor that favors linkage disequilibrium also favors the evolution of the preference allele. Moreover, in a large population subdivided in small subpopulations connected by migration, the assortative mating homogenizes the population genotypic structure for the tags in contrast to random mating that maintains most of the variation.     

A long-term genetic survey of an ungulate population reveals balancing selection acting on MHC through spatial and temporal fluctuations in selection

We explored a 13-year genetic survey of the major histocompatibility complex (MHC) and neutral loci of the Soay sheep population of St Kilda to test the existence and causes of balancing selection at the MHC. The sheep population experiences demographic fluctuations, partly driven by the nematode Teladorsagia circumcincta. The spatial differentiation detected at the MHC was comparable to that at neutral loci between 1988 and 1996, but significantly lower between 1996 and 2000. The rate of temporal genetic differentiation was higher at the MHC, but within the Eastern heft only. These comparisons of spatial and temporal divergence at MHC and non-MHC loci provide strong evidence of balancing selection at the MHC, acting through spatial and temporal heterogeneity in selection pressure. This heterogeneity could be due to fluctuations in the selection imposed by parasites, either directly, because the prevalence in T. circumcincta varies in space and time, or indirectly, because the fitness costs of infection may vary with resource availability.     

The ecology of sexual selection: Mean crowding of females and resource-defence polygyny

Summary Resource-defence polygyny is a mating system that offers an opportunity for strong sexual selection. I express the degree of aggregation or clustering of females at resources at the time of mating using Lloyd's measures of microspatial aggregation, mean crowding (m ^*) and patchiness (P). Here, I show that Lloyd's two ecological measures of aggregation can be used to quantify the relationship between resource-based polygyny and sexual selection. The advantage of using these measures is that some of the statistical machinery for estimating the degree of mean crowding and testing for density dependence in comparative ecological studies can be applied to estimating the strength of sexual selection and comparing different mating systems. When females vary in their tendency to aggregate with other females and males vary from one another in their ability to guard aggregations of females, a run-away process of sexual selection is possible. The largest aggregations of females have a higher proportion of the females most prone to aggregate or most tolerant of crowding. The males with the highest mating success have daughters more prone to aggregate and sons better at defending aggregated females against other males. As a result, females are selected to over-aggregate with respect to resources. The run-away process halts when single males cannot defend and maintain exclusive reproductive access to clusters of females as evidenced by extraharem copulations and paternity.     

Quantitative genetic models of sexual selection by male choice

There are many examples of male mate choice for female traits that tend to be associated with high fertility. I develop quantitative genetic models of a female trait and a male preference to show when such a male preference can evolve. I find that a disagreement between the fertility maximum and the viability maximum of the female trait is necessary for directional male preference (preference for extreme female trait values) to evolve. Moreover, when there is a shortage of available male partners or variance in male nongenetic quality, strong male preference can evolve. Furthermore, I also show that males evolve to exhibit a stronger preference for females that are more feminine (less resemblance to males) than the average female when there is a sexual dimorphism caused by fertility selection which acts only on females.