Social bonds and genetic ties: Kinship association and affiliation in a community of bonobos (Pan paniscus)

Studies of captive populations of bonobos suggest that females are more gregarious than males. This seems to contradict assumed sex-differences in kinship deriving from a speciestypical dispersal pattern of female exogamy and male philopatry. Here we present data on spatial associations and affiliative relations among members of one wild community (Eyengo) for which genetic relationships were identified by analysing mitochondrial and nuclear DNA. Our data from Lomako confirm the existence of spatial associations among resident females. In addition, they reveal strong social bonds between males and females. While most female-female associations did not last longer than one field season, long-term associations occurred predominantly between mixed-sex dyads and involved both close kin and unrelated individuals. Differences in social grooming appeared to be related to patterns of spatial association rather than to kinship. It is suggested that under natural conditions social organisation of bonobos is characterised by strong inter-sexual bonds. Males may benefit from bonding with females by increased reproductive success via rank acquisition. For females benefits may derive from inclusive fitness and reduced food competition. Preliminary evidence suggests that females also may benefit from protection by resident males against male intruders

Introducing "Frontiers in Zoology"

As a biological discipline, zoology has one of the longest histories. Today it occasionally appears as though, due to the rapid expansion of life sciences, zoology has been replaced by more or less independent sub-disciplines amongst which exchange is often sparse. However, the recent advance of molecular methodology into "classical" fields of biology, and the development of theories that can explain phenomena on different levels of organisation, has led to a re-integration of zoological disciplines promoting a broader than usual approach to zoological questions. Zoology has re-emerged as an integrative discipline encompassing the most diverse aspects of animal life, from the level of the gene to the level of the ecosystem. The new journal Frontiers in Zoology is the first Open Access journal focussing on zoology as a whole. It aims to represent and re-unite the various disciplines that look at animal life from different perspectives and at providing the basis for a comprehensive understanding of zoological phenomena on all levels of analysis. Frontiers in Zoology provides a unique opportunity to publish high quality research and reviews on zoological issues that will be internationally accessible to any reader at no cost

An algorithm for the determination and quantification of components of nucleic acid mixtures based on single sequencing reactions

BACKGROUND: Determination and quantification of nucleic acid components in a mixture is usually accomplished by microarray approaches, where the mixtures are hybridized against specific probes. As an alternative, we propose here that a single sequencing reaction from a mixture of nucleic acids holds enough information to potentially distinguish the different components, provided it is known which components can occur in the mixture. RESULTS: We describe an algorithm that is based on a set of linear equations which can be solved when the sequencing profiles of the individual components are known and when the number of sequenced nucleotides is larger than the number of components in the mixture. We have implemented the procedure for one type of sequencing approach, pyrosequencing, which produces a stepwise output of peaks that is particularly suitable for the procedure. As an example we use signature sequences from ribosomal RNA to distinguish and quantify several different species in a mixture. Using simulations, we show that the procedure may also be applicable for dideoxy sequencing on capillary sequencers, requiring only some instrument specific adaptations of protocols and software. CONCLUSION: The parallel sequencing approach described here may become a simple and cheap alternative to microarray experiments which aim at routine re-determination and quantification of known nucleic acid components from environmental samples or tissue samples

An evaluation of LSU rDNA D1-D2 sequences for their use in species identification

BACKGROUND: Identification of species via DNA sequences is the basis for DNA taxonomy and DNA barcoding. Currently there is a strong focus on using a mitochondrial marker for this purpose, in particular a fragment from the cytochrome oxidase I gene (COI). While there is ample evidence that this marker is indeed suitable across a broad taxonomic range to delineate species, it has also become clear that a complementation by a nuclear marker system could be advantageous. Ribosomal RNA genes could be suitable for this purpose, because of their global occurrence and the possibility to design universal primers. However, it has so far been assumed that these genes are too highly conserved to allow resolution at, or even beyond the species level. On the other hand, it is known that ribosomal gene regions harbour also highly divergent parts. We explore here the information content of two adjacent divergence regions of the large subunit ribosomal gene, the D1-D2 region. RESULTS: Universal primers were designed to amplify the D1-D2 region from all metazoa. We show that amplification products in the size between 800–1300 bp can be obtained across a broad range of animal taxa, provided some optimizations of the PCR procedure are implemented. Although the ribosomal genes occur in multiple copies in the genomes, we find generally very little intra-individual polymorphism (<< 0.1% on average) indicating that concerted evolution is very effective in most cases. Studies in two fish taxa (genus Cottus and genus Aphyosemion) show that the D1-D2 LSU sequence can resolve even very closely related species with the same fidelity as COI sequences. In one case we can even show that a mitochondrial transfer must have occurred, since the nuclear sequence confirms the taxonomic assignment, while the mitochondrial sequence would have led to the wrong classification. We have further explored whether hybrids between species can be detected with the nuclear sequence and we show for a test case of natural hybrids among cyprinid fish species (Alburnus alburnus and Rutilus rutilus) that this is indeed possible. CONCLUSION: The D1-D2 LSU region is a suitable marker region for applications in DNA based species identification and should be considered to be routinely used as a marker complementing broad scale studies based on mitochondrial markers

Galápagos and Californian sea lions are separate species: Genetic analysis of the genus Zalophus and its implications for conservation management

Wolf JBW, Tautz D, Trillmich F. Galápagos and Californian sea lions are separate species: genetic analysis of the genus Zalophus and its implications for conservation management. Frontiers in Zoology. 2007;4(1): 20.Background: Accurate formal taxonomic designations are thought to be of critical importance for the conservation of endangered taxa. The Galápagos sea lion (GSL), being appreciated as a key element of the Galápagos marine ecosystem, has lately been listed as 'vulnerable' by the IUCN. To date there is, however, hardly any scientific evidence, whether it constitutes a separate entity from its abundant Californian neighbour (CSL). In this paper, we delineate the taxonomic relationships within the genus Zalophus being comprised of the Galápagos sea lion, the Californian sea lion and the already extinct Japanese sea lion (JSL). Results: Using a set of different phylogenetic reconstruction approaches, we find support for monophyly of all three taxa without evidence of reticulation events. Molecular clock estimates place time to common ancestry of the Galápagos sea lion and the Californian sea lion at about 2.3 ± 0.5 mya. Genetic separation is further suggested by diagnostic SNPs in the mitochondrial and nuclear genome. Microsatellite markers confirm this trend, showing numerous private alleles at most of the 25 investigated loci. Microsatellite-based estimates of genetic differentiation between the Galápagos sea lion and the Californian sea lion indicate significant genetic differentiation. Gene diversity is 14% lower in the Galápagos sea lion than in the Californian sea lion, but there is no evidence for recent bottleneck events in the Galápagos sea lion. Conclusion: Based on molecular evidence we build a case for classifying the Galápagos sea lion (Zalophus wollebaeki), the Californian sea lion (Zalophus californianus) and the Japanese sea lion (Zalophus japonicus) as true species. As morphological characters do not necessarily fully reflect the rapid divergence on the molecular level, the study can be considered as a test case for deriving species status from molecular evidence. We further use the results to discuss the role of genetics in conservation policy for an organism that already is under the general protection of the habitat it lives in

Genome-wide acceleration of protein evolution in flies (Diptera)

BACKGROUND: The rate of molecular evolution varies widely between proteins, both within and among lineages. To what extent is this variation influenced by genome-wide, lineage-specific effects? To answer this question, we assess the rate variation between insect lineages for a large number of orthologous genes. RESULTS: When compared to the beetle Tribolium castaneum, we find that the stem lineage of flies and mosquitoes (Diptera) has experienced on average a 3-fold increase in the rate of evolution. Pairwise gene comparisons between Drosophila and Tribolium show a high correlation between evolutionary rates of orthologous proteins. CONCLUSION: Gene specific divergence rates remain roughly constant over long evolutionary times, modulated by genome-wide, lineage-specific effects. Among the insects analysed so far, it appears that the Tribolium genes show the lowest rates of divergence. This has the practical consequence that homology searches for human genes yield significantly better matches in Tribolium than in Drosophila. We therefore suggest that Tribolium is better suited for comparisons between phyla than the widely employed dipterans

A comparative assessment of mandible shape in a consomic strain panel of the house mouse (Mus musculus) - implications for epistasis and evolvability of quantitative traits

<p>Abstract</p> <p>Background</p> <p>Expectations of repeatedly finding associations between given genes and phenotypes have been borne out by studies of parallel evolution, especially for traits involving absence or presence of characters. However, it has rarely been asked whether the genetic basis of quantitative trait variation is conserved at the intra- or even at the interspecific level. This question is especially relevant for shape, where the high dimensionality of variation seems to require a highly complex genetic architecture involving many genes.</p> <p>Results</p> <p>We analyse here the genetic effects of chromosome substitution strains carrying <it>M. m. musculus </it>chromosomes in a largely <it>M. m. domesticus </it>background on mandible shape and compare them to the results of previously published QTL mapping data between <it>M. m. domesticus </it>strains. We find that the distribution of genetic effects and effect sizes across the genome is consistent between the studies, while the specific shape changes associated with the chromosomes are different. We find also that the sum of the effects from the different <it>M. m. musculus </it>chromosomes is very different from the shape of the strain from which they were derived, as well as all known wild type shapes.</p> <p>Conclusions</p> <p>Our results suggest that the relative chromosome-wide effect sizes are comparable between the long separated subspecies <it>M. m. domesticus </it>and <it>M. m. musculus</it>, hinting at a relative stability of genes involved in this complex trait. However, the absolute effect sizes and the effect directions may be allele-dependent, or are context dependent, i.e. epistatic interactions appear to play an important role in controlling shape.</p

The root of the East African cichlid radiations

<p>Abstract</p> <p>Background</p> <p>For decades cichlid fishes (Perciformes: Cichlidae) of the East African cichlid radiations (Teleostei: Cichlidae) have served as natural experimental subjects for the study of speciation processes and the search for potential speciation key factors. Despite numerous phylogenetic studies dealing with their intragroup relationships, surprisingly little is known about the phylogenetic placement and time of origin of this enigmatic group. We used multilocus DNA-sequence data from five nuclear and four mitochondrial genes and refined divergence time estimates to fill this knowledge gap.</p> <p>Results</p> <p>In concordance with previous studies, the root of the East African cichlid radiations is nested within the so called "Tilapias", which is a paraphyletic assemblage. For the first time, we clarified tilapiine intragroup relationships and established three new monophyletic groups:"Oreochromini", "Boreotilapiini" and a group with a distribution center in East/Central Africa, the "Austrotilapiini". The latter is the founder lineage of the East African radiations and emerged at the Miocene/Oligocene boundary at about 14 to 26 mya.</p> <p>Conclusion</p> <p>Our results provide the first resolved hypothesis for the phylogenetic placement of the megadiverse East African cichlid radiations as well as for the world's second most important aquaculture species, the Nile Tilapia, <it>Oreochromis niloticus</it>. Our analyses constitute not only a robust basis for African cichlid phylogenetics and systematics, but provide a valid and necessary framework for upcoming comparative phylogenomic studies in evolutionary biology and aquaculture.</p

Effects of a male meiotic driver on male and female transcriptomes in the house mouse

Not all genetic loci follow Mendel's rules, and the evolutionary consequences of this are not yet fully known. Genomic conflict involving multiple loci is a likely outcome, as restoration of Mendelian inheritance patterns will be selected for, and sexual conflict may also arise when sexes are differentially affected. Here, we investigate effects of the t haplotype, an autosomal male meiotic driver in house mice, on genome-wide gene expression patterns in males and females. We analysed gonads, liver and brain in adult same-sex sibling pairs differing in genotype, allowing us to identify t-associated differences in gene regulation. In testes, only 40% of differentially expressed genes mapped to the approximately 708 annotated genes comprising the t haplotype. Thus, much of the activity of the t haplotype occurs in trans, and as upregulation. Sperm maturation functions were enriched among both cis and trans acting t haplotype genes. Within the t haplotype, we observed more downregulation and differential exon usage. In ovaries, liver and brain, the majority of expression differences mapped to the t haplotype, and were largely independent of the differences seen in the testis. Overall, we found widespread transcriptional effects of this male meiotic driver in the house mouse genome