Song Trait Similarity in Great Tits Varies with Social Structure

For many animals, long-range signalling is essential to maintain contact with conspecifics. In territorial species, individuals often have to balance signalling towards unfamiliar potential competitors (to solely broadcast territory ownership) with signalling towards familiar immediate neighbours (to also maintain so-called “dear enemy” relations). Hence, to understand how signals evolve due to these multilevel relationships, it is important to understand how general signal traits vary in relation to the overall social environment. For many territorial songbirds dawn is a key signalling period, with several neighbouring individuals singing simultaneously without immediate conflict. In this study we tested whether sharing a territory boundary, rather than spatial proximity, is related to similarity in dawn song traits between territorial great tits (Parus major) in a wild personality-typed population. We collected a large dataset of automatized dawn song recordings from 72 unique male great tits, during the fertile period of their mate, and compared specific song traits between neighbours and non-neighbours. We show here that both song rate and start time of dawn song were repeatable song traits. Moreover, neighbours were significantly more dissimilar in song rate compared to non-neighbours, while there was no effect of proximity on song rate similarity. Additionally, similarity in start time of dawn song was unrelated to sharing a territory boundary, but birds were significantly more similar in start time of dawn song when they were breeding in close proximity of each other. We suggest that the dissimilarity in dawn song rate between neighbours is either the result of neighbouring great tits actively avoiding similar song rates to possibly prevent interference, or a passive consequence of territory settlement preferences relative to the types of neighbours. Neighbourhood structuring is therefore likely to be a relevant selection pressure shaping variation in territorial birdsong.     

Effects of physical connection and genetic identity of neighbouring ramets on root-placement patterns in two clonal species

Root-placement patterns were examined in the clonal species Glechoma hederacea and Fragaria vesca when grown with different types of neighbours. Three different patterns were predicted as consequences of different types of interactions between roots: the avoidance pattern if root growth decreases in the presence of neighbouring roots; the intrusive pattern if root growth increases towards neighbouring roots; and the unresponsive pattern if root growth is unaffected by neighbouring roots. Experiments were conducted in which physical connection between ramets, and the genetic identity of neighbouring ramets, were manipulated. The patterns of distribution of entire root systems and elongation rates of individual roots were measured. Root systems and individual roots of G. hederacea avoided contact with roots of neighbouring ramets, irrespective of connection to the neighbour and its genetic or specific identity. In contrast, F. vesca roots grew equally towards and away from intraspecific ramet neighbours and their elongation was stimulated by contact with roots of G. hederacea ramets. These results demonstrate that root-placement patterns of plants grown with different types of neighbours vary between species, and suggest that factors additional to resource depletion could be involved in their development.     

A hierarchical approach to aligning collinear regions of genomes

MOTIVATION: As a first approximation, similarity between two long orthologous regions of genomes can be represented by a chain of local similarities. Within such a chain, pairs of successive similarities are collinear (non-conflicting), i.e. segments involved in the nth similarity precede in both sequences segments involved in the (n+1)th similarity. However, when all similarities between two long sequences are considered, usually there are many conflicts between them. Although some conflicts can be avoided by masking transposons or low-complexity sequences, selecting only those similarities that reflect orthology and, thus, belong to the evolutionarily true chain is not trivial. RESULTS: We propose a simple, hierarchical algorithm of finding the true chain of local similarities. Starting from similarities with low P-values, we resolve each pairwise conflict by deleting a similarity with a higher P-value. This greedy approach constructs a chain of similarities faster than when a chain optimal with respect to some global criterion is sought, and makes more sense biologically.     

Genetic relatedness and female spatial organization in a solitary carnivore,the raccoon,Procyon lotor

Among mammals, some of the most common types of cohesive social groupings originate from natal philopatry through the extended mother family. This retention of females within social groups (i.e. the nonrandom dispersion of female relatives in space) should affect population genetic structure. We examined the relationship between genetic relatedness and female spatial organization in a wild population of the North-American raccoon, Procyon lotor, a solitary carnivore in east Tennessee. Multilocus genetic band-sharing data and 3(1/2) years of radiotelemetry observations were used to study the spatial and genetic relationships among 38 adult females. DNA amplification employing primers of arbitrary sequence (random amplified polymorphic DNA; RAPD) indicated that female philopatry in raccoons led to a greater likelihood of neighbours being more related than expected by chance. Genetic distance based on RAPD band frequency was positively correlated with spatial distance among females (P = 0.0001) and genetic similarity was positively correlated with the extent of home-range overlap (P = 0.0028). Philopatry seemed biased towards females; average female-female similarities were greater than average male-male similarities (P = 0.0001), or average male-female similarities (P = 0.0001). High home-range overlap among some females with low or moderate levels of band sharing indicated that maternal inheritance of space was not a prerequisite for establishing or sharing home ranges. Female philopatry was the most probable explanation for the nonrandom spatial and genetic association of raccoons in east Tennessee.     

The effect of neighbours and females on dawn and daytime singing behaviours by male chipping sparrows

Bird song may play an important role for communication among territorial neighbours, but the effect of neighbours on song use is still not well known. My previous field observations suggested that male chipping sparrows, Spizella passerina, use the dawn chorus for interactions among neighbouring males, and use day song for female attraction. To determine how these social factors may influence dawn and daytime singing behaviour, I conducted a series of experiments in which I removed the male neighbours or the female mate of territorial males during 1998-2000. Following removal of all neighbouring males, the solitary male either stopped or reduced his dawn chorus (N=9), but did not change his daytime singing behaviour. After one of the neighbouring males was returned to his territory, the focal male resumed and increased his dawn bout, accompanied with close-range countersinging. Following the removal of a territorial male's mate, the widowed male did not change the dawn chorus, but significantly increased his day song. This study thus revealed that, in chipping sparrows, the presence or absence of neighbouring males has a significant effect on the dawn chorus singing behaviour of territorial males. The presence or absence of a male's mate, in contrast, has a strong influence on a male's daytime singing behaviour. This study also supports the hypothesis that the dawn chorus and daytime song have different functions.     

Pushy males and choosy females: courtship disruption and mate choice in the lekking great snipe

We studied the effects of male disruptive behaviour on female mate choice and male mating success in the great snipe, Gallinago media, a lekking bird. Harassment from neighbouring males, a widespread behaviour in lekking animals, was the most prevalent cause of females leaving a male territory. Several lines of evidence show that females did not prefer to mate with males able to protect them from harassment. Males that obtained mating success were no less likely to suffer disruptions and females were no less likely to be disrupted when with their preferred male. Females returned to the male they later mated with, despite being repeatedly chased away by neighbours. The probability that an individual female returned and solicited mating from a male was 15 times higher for the male she was chased away from compared to the neighbour that chased her away. Females returned as often or more to the territory owner after being disrupted, compared to after leaving the territory without being harassed. Our results suggest that female great snipes are extremely choosy, but also that females do not gain direct benefits (harassment avoidance) by mating with certain males. Females appear to have neither direct nor indirect preferences for dominance that could give them such benefits: females appeared choosy despite, not because of, harassment. If females gain indirect benefits (genetically superior offspring) by being choosy, this is also likely to be unrelated to any dominance among males.     

A study of the evolution of coxsackievirus A24 variant in Ghana by viral RNA fingerprinting analysis

An epidemic of acute haemorrhagic conjunctivities (AHC) caused by coxsackievirus A24 variant (CA24v) was reported in Accra, Ghana in May 1987. We studied 7 of the viral strains collected from May to November, 1987, by RNA genome fingerprinting. Pairwise comparisons of the oligonucleotide maps showed that genetic similarity among them ranged from between 60.0 to 84.7 %.Using base sequence variations deduced from genetic similarity among the isolates, isolation time of the strains and the rate of nucleotide substitution (estimated in a previous paper, Miyamura et al., 1990), we calculated divergence times and constructed a phylogenetic tree. This tree indicated that all the 7 strains had diverged from each other from 11 to 26 months before the AHC epidemic in Accra. CA24v may have been introduced into the country or the neighbouring area, at least, more than two years earlier, i. e. in the early half of 1985.     

Bower quality,number of decorations and mating success of male satin bowerbirds (Ptilonorhynchus violaceus): an experimental analysis

Bowerbirds build large bowers of twigs decorated with brightly coloured objects at display sites where males court females. The bower and its decorations are hypothesized to influence female choice in these birds. However, there have been no empirical tests of this hypothesis. Data from two years of field research on the satin bowerbird (Ptilonorhynchus violaceus) show: (1) an extremely skewed distribution of matings among males, and (2) a consistent pattern of female preference for particular males, especially those with well-constructed, highly-decorated bowers. These results support the hypothesis that bower quality is important in influencing female mating preferences. In particular, they support the ‘marker’ hypothesis, which suggests that the construction of bowers evolved to provide females with information about the relative quality of males.     

Tactic for bower acquisition by male cichlids,Cyathopharynx furcifer,in Lake Tanganyika

A tactic for bower acquisition by male cichlids,Cyathopharynx furcifer, was studied in Lake Tanganyika. Males held crater-shaped bowers of sand within their territories, which were located adjacent to each other. Females visited bowers to spawn eggs, subsequently brooding the eggs in their mouths. Some individuals held territories without bowers near those of males with bowers. Although only the males with bowers succeeded in reproduction, they were apparently exhausted by bower maintenance and reproduction, and often deserted their bowers. These were soon occupied by males which had held nearby territories without bowers, such males then engaging in reproductive activity. Although the construction of new bowers by males was observed, such was unsuccessful, probably because too much energy was required and/or the optimal space for bowers was limited. Direct aggression by males without bowers against bower-holding males to deprive the bowers was not observed, possibly due to the high costs of such competition. Therefore, waiting for bower desertion by other males may be the best bower acquisition tactic for males without bowers.     

Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions

MOTIVATION: Most approaches in predicting protein function from protein-protein interaction data utilize the observation that a protein often share functions with proteins that interacts with it (its level-1 neighbours). However, proteins that interact with the same proteins (i.e. level-2 neighbours) may also have a greater likelihood of sharing similar physical or biochemical characteristics. We speculate that functional similarity between a protein and its neighbours from the two different levels arise from two distinct forms of functional association, and a protein is likely to share functions with its level-1 and/or level-2 neighbours. We are interested in finding out how significant is functional association between level-2 neighbours and how they can be exploited for protein function prediction. RESULTS: We made a statistical study on recent interaction data and observed that functional association between level-2 neighbours is clearly observable. A substantial number of proteins are observed to share functions with level-2 neighbours but not with level-1 neighbours. We develop an algorithm that predicts the functions of a protein in two steps: (1) assign a weight to each of its level-1 and level-2 neighbours by estimating its functional similarity with the protein using the local topology of the interaction network as well as the reliability of experimental sources and (2) scoring each function based on its weighted frequency in these neighbours. Using leave-one-out cross validation, we compare the performance of our method against that of several other existing approaches and show that our method performs relatively well.     

Bilateral similarity function: A novel and universal method for similarity analysis of biological sequences

Bilateral similarity function is designed for analyzing the similarities of biological sequences such as DNA, RNA secondary structure or protein in this paper. The defined function can perform comprehensive comparison between sequences remarkably well, both in terms of the Hamming distance of two compared sequences and the corresponding location difference. Compared with the existing methods for similarity analysis, the examination of similarities/dissimilarities illustrates that the proposed method with the computational complexity of O(N) is effective for these three kinds of biological sequences, and bears the universality for them.     

Dietary shifts,niche relationships and reproductive output of coexisting Kestrels and Long-eared Owls

Summary Food samples of breeding Kestrels (Falco tinnunculus) and Long-eared Owls (Asio otus) were collected in the peak and low phase of their preferred prey (Microtus voles) in western Finland. Diets of pairs that bred as neighbours (1 km) with interspecifics were compared with those of non-neighbours. In both species, neighbouring pairs fed less on Microtus voles and more on alternative prey than did non-neighbours. Competition theory predicts that diet overlap should be lower during prey shortage and that diet similarity should be especially reduced in neighbouring pairs. Observations were consistent with expectations: diet similarity was lower in the low vole years and neighbouring pairs showed less diet overlap that non-neighbours. Differences in habitat composition and prey availability at the sample sites should not confuse the results. In addition to the high diet similarity, hunting habitats and nest sites of the species overlapped almost completely; they only showed clear temporal segregation in hunting. Probably because of food competition, the neighbouring pairs of both species produced significantly fewer young than the non-neighbours. These results contrast with the view that the diet composition and dietary shift of rodent-feeding predatory birds can be interpreted in terms of simple opportunistic foraging. In the breeding season, interspecific competition for food seems to be an important factor that affects the niches of these species, especially in northern areas, where the seasonal low phase of voles in spring and the number of alternative prey are lower than in more southern areas.     

Preferences for coloured bower decorations can be explained in a nonsexual context

The sensory bias model of sexual selection suggests that elaborate male secondary sexual traits evolved to exploit biases in the female's sensory system. Such biases may have evolved in a nonsexual context. Male bowerbirds build and decorate elaborate structures, bowers, which function as targets of female choice. The colour of decorations used on bowers appears to be important in determining a male's mating success. We tested two predictions made by the sensory bias model, using cache presentation experiments of artificially coloured grapes made to captive bowerbirds of five species. We first searched for evidence of ancestral biases for certain colours that could explain current colour preferences across species. We found no single parsimonious explanation for ancestral patterns of colour preference across the family. We next tested whether female preference patterns could be explained in a nonsexual, foraging, context. For both of the species where sufficient data could be collected, female foraging preferences for grapes were significantly related to male preferences for grapes used as bower decorations. Our results suggest that choice of bower decoration colour may have evolved to exploit a bias in the female's sensory system, originally shaped by selection on foraging practices. Copyright 2003 Published by Elsevier Ltd on behalf of The Association for the Study of Animal Behaviour.      

Female Mate Preference for Males Having Long and Symmetric Fins in the Bower-holding Cichlid Cyathopharynx furcifer

Female mate preference in a bower-holding cichlid, Cyathopharynx furcifer, was studied in Lake Tanganyika. Most males held territories with crater-shaped bowers in sand, but some males held territories without bowers. Territories were distributed adjacently and females visited them to spawn. After engaging in circling behaviour with the male, a female deposited eggs in the bower. Soon after spawning, the female picked the eggs up into her mouth and brooded them in places away from male territories. Female mate choice appeared to follow three steps: 1) females visited only bower-holding male territories, and more frequently visited territories of males that performed courtship displays at a higher frequency and had longer pelvic fins; 2) females preferred to start circling with males having longer and more symmetrical pelvic fins; 3) females chose males with more symmetrical pelvic fins as their mates. Less than 7% of females that visited male territories spawned eggs in the bowers. In contrast to other bower-holding species, bower size did not correlate with male reproductive success in C. furcifer. Bowers may therefore be essential as spawning sites or may function as a species recognition character for females. Female choice may be dependent instead on males having long and symmetrical pelvic fins apparent during the circling behaviour carried out in the bowers.     

HUMF13A01 in autochthonous Basques and in genetically related populations

A population gentics study was carried out on 678 Basque individuals using the short tandem repeat HUMF13A01. Thirteen different alleles were detected. This population is in Hardy-Weinberg equilibrium. The singularity of the Basque population’s HUMF13A01 allele frequencies is displayed in the European context, through some genetic similarities are shown, especially with some neighbouring and culturally related populations, and with other populations with which Basques may have shared ancient common roots, such as the Sardinians.     

Variation in plant performance in a grassland: Species‐specific and neighbouring root mass effects

Question: What characteristics of local biotic neighbourhood is the best proxy of competitive effects experienced by plants in a herbaceous community: (1) total above‐ground biomass, (2) root mass or (3) relative above‐ground abundance of selected species? Location: Grassland at ca. 1100 m a.s.l. in the Krkono?e Mts., northern Czech Republic. Methods: We implanted two phytometer species, Antho‐xanthum alpinum and Festuca rubra, into a mountain grassland, and examined their response to local variation in (1) total above‐ground biomass, (2) root mass at three soil depths, and (3) relative abundance of individual species above‐ground. Results : Performance of both phytometer species was determined much more consistently by the mass of neighbouring roots and by species composition of neighbours than by the total above‐ground biomass. The two phytometer species showed different responses to these parameters. The most important relationships were (1) negative relationship between performance of Anthoxanthum and mass of neighbouring roots at 0–3 cm, (2) positive relationship between performance of Festuca and mass of neighbouring roots at 3–6 cm, and (3) negative relationship between performance of Festuca and relative abundance of Festuca in the neighbourhood. Conclusions: Neighbouring root mass and above‐ground species composition are better determinants of biotic interactions than total above‐ground biomass of neighbours in the studied mountain grassland. However, the relationships found are not necessarily due to variation in competitive intensity but can be due to other hidden factors as well, e.g. local availability of resources.     

Nonrandom mating in pikas Ochotona princeps: evidence for inbreeding between individuals of intermediate relatedness

The extent and effect of inbreeding in natural populations remain largely undetermined. Pikas Ochotona princeps have been considered a likely candidate for close inbreeding in natural populations due to observations of frequent juvenile philopatry (colonization of natal home range or neighbouring home range) and high levels of spatial overlap and social tolerance between neighbouring individuals of the opposite sex. A 4-year investigation of inbreeding in pikas, however, has revealed that dispersal and mating patterns are uncoupled in this species, i.e. explained by different hypotheses. DNA fingerprinting analysis revealed that band-sharing scores between mated pairs, identified via parentage analysis, were not commensurate with band-sharing among known first-order relatives, but were similar to scores for a small sample of known second-order relatives (i.e. half-siblings, grandparent-grandchild pairs). Band-sharing scores between mated pairs were then compared with those between potential mated pairs within the population to assess whether mating was random or nonrandom with respect to genetic similarity. The results of Monte Carlo randomization tests show that pikas mated with individuals with intermediate genetic similarity in greater proportion than would be expected by chance. These data suggest mate choice in pikas may be based upon intermediate levels of relatedness.     

High gene flow promotes the genetic homogeneity of arable weed populations at the landscape level

To determine whether weed populations growing in neighbouring fields were genetically isolated, we investigated the genetic contamination of Alopecurus myosuroides populations in organic fields by populations in conventional fields. Herbicide resistance was used as a marker for gene flow to organic populations, which are not under herbicide selective pressure. Organic fields contained on average 74.5% herbicide-resistant plants (80.1% in conventional fields). Identical resistance alleles were found in neighbouring organic and conventional fields. AFLP analysis revealed that populations from organic and conventional fields had similar neutral genetic diversity. Massive pollen flow from conventional fields is likely chiefly responsible for the genetic makeup of A. myosuroides populations from organic fields. Using a demo-genetic model, we propose that demographic collapses of populations due to effective weed control enhance gene flow towards these populations. Fields with a low weed density could act as ‘genetic sinks’ that would facilitate the diffusion of genes from neighbouring, dense weed populations. Populations of allogamous wind-pollinated weed species like A. myosuroides occurring in neighbouring fields are therefore clearly not independent units. Adaptive evolution and management of such weeds should thus be considered on a scale broader than the field.     

Community-level education accelerates the cultural evolution of fertility decline

Explaining why fertility declines as populations modernize is a profound theoretical challenge. It remains unclear whether the fundamental drivers are economic or cultural in nature. Cultural evolutionary theory suggests that community-level characteristics, for example average education, can alter how low-fertility preferences are transmitted and adopted. These assumptions have not been empirically tested. Here, we show that community-level education accelerates fertility decline in a way that is neither predicted by individual characteristics, nor by the level of economic modernization in a population. In 22 high-fertility communities in Poland, fertility converged on a smaller family size as average education in the community increased—indeed community-level education had a larger impact on fertility decline than did individual education. This convergence was not driven by educational levels being more homogeneous, but by less educated women having fewer children than expected, and more highly educated social networks, when living among more highly educated neighbours. The average level of education in a community may influence the social partners women interact with, both within and beyond their immediate social environments, altering the reproductive norms they are exposed to. Given a critical mass of highly educated women, less educated neighbours may adopt their reproductive behaviour, accelerating the pace of demographic transition. Individual characteristics alone cannot capture these dynamics and studies relying solely on them may systematically underestimate the importance of cultural transmission in driving fertility declines. Our results are inconsistent with a purely individualistic, rational-actor model of fertility decline and suggest that optimization of reproduction is partly driven by cultural dynamics beyond the individual.     

Lack of structure in the gene pool of the highly polyploid ornamental chrysanthemum

Selection of clonally propagated chrysanthemums is mostly performed on F1 hybrids using phenotypic characteristics without the use of molecular information. We applied 448 amplified fragment length polymorphism markers to a set of 81 accessions, mainly from the European gene pool, covering the different horticultural types (cut, pot and garden varieties) and originating from the most important European chrysanthemum breeders. The average pairwise genetic similarity of 0.69 was moderate to rather high. Neighbour-joining clustering resulted in no grouping of the accessions, either by their common origin or their horticultural type, or by similarities in important phenotypic characteristics. The structure of the dendrogram could not be supported by bootstrap analysis. Furthermore, network analysis using SplitsTree, principal coordinate analysis via DARwin or analysis of the population with structure did not differentiate reliable and invariable clusters. Therefore, we tested the marker saturation by plotting the mean coefficient of variation for every pairwise similarity of the bootstrap analysis against the different numbers of markers. We showed that the number of markers is sufficient for a precise estimate of genetic similarity and that the lack of bootstrap support is not due to a low genetic diversity or a lack of marker information, but most likely resulted from the breeding history of the cultivars, involving repeated backcrosses and the exchange of genotypes between breeders.