http://www.biomedcentral.com/bmcevolbiol/ The latest research articles published by BMC Evolutionary Biology 2009-07-02T00:00:00Z This is an RSS newsfeed from BioMed Central It is intended to be used with an RSS reader. For more information about RSS newsfeeds from BioMed Central, visit http://www.biomedcentral.com/info/about/rss/ Background: Central Asia and the Indian subcontinent represent an area considered as a source and a reservoir for human genetic diversity, with many markers taking root here, most of which are the ancestral state of eastern and western haplogroups, while others are local. Between these two regions, Terai (Nepal) is a pivotal passageway allowing, in different times, multiple population interactions, although because of its highly malarial environment, it was scarcely inhabited until a few decades ago, when malaria was eradicated. One of the oldest and the largest indigenous people of Terai is represented by the malaria resistant Tharus, whose gene pool could still retain traces of ancient complex interactions. Until now, however, investigations on their genetic structure have been scarce mainly identifying East Asian signatures. Results: High-resolution analyses of mitochondrial-DNA (including 34 complete sequences) and Y-chromosome (67 SNPs and 12 STRs) variations carried out in 173 Tharus (two groups from Central and one from Eastern Terai), and 104 Indians (Hindus from Terai and New Delhi and tribals from Andhra Pradesh) allowed the identification of three principal components: East Asian, West Eurasian and Indian, the last including both local and inter-regional sub-components, at least for the Y chromosome. Conclusions: Although remarkable quantitative and qualitative differences appear among the various population groups and also between sexes within the same group, many mitochondrial-DNA and Y-chromosome lineages are shared or derived from ancient Indian haplogroups, thus revealing a deep shared ancestry between Tharus and Indians. Interestingly, the local Y-chromosome Indian component observed in the Andhra-Pradesh tribals is present in all Tharu groups, whereas the inter-regional component strongly prevails in the two Hindu samples and other Nepalese populations.The complete sequencing of mtDNAs from unresolved haplogroups also provided informative markers that greatly improved the mtDNA phylogeny and allowed the identification of ancient relationships between Tharus and Malaysia, the Andaman Islands and Japan as well as between India and North and East Africa. Overall, this study gives a paradigmatic example of the importance of genetic isolates in revealing variants not easily detectable in the general population. http://www.biomedcentral.com/1471-2148/9/154 Simona Fornarino Maria Pala Vincenza Battaglia Ramona Maranta Alessandro Achilli Guido Modiano Antonio Torroni Ornella Semino Silvana Santachiara-Benerecetti BMC Evolutionary Biology 2009, 9:154 2009-07-02T00:00:00Z doi:10.1186/1471-2148-9-154 BMC Evolutionary Biology 1471-2148 9 154 2009-07-02T00:00:00Z PDF Background: Phylogenetic analyses of the Annonaceae consistently identify four clades: a basal clade consisting of Anaxagorea, and a small 'ambavioid' clade that is sister to two main clades, the 'long branch clade' (LBC) and 'short branch clade' (SBC). Divergence times in the family have previously been estimated using non-parametric rate smoothing (NPRS) and penalized likelihood (PL). Here we use an uncorrelated lognormal (UCLD) relaxed molecular clock in BEAST to estimate diversification times of the main clades within the family with a focus on the Asian genus Pseuduvaria within the SBC. Two fossil calibration points are applied, including the first use of the recently discovered Annonaceae fossil Futabanthus. The taxonomy and morphology of Pseuduvaria have been well documented, although no previous dating or biogeographical studies have been undertaken. Ancestral areas at internal nodes within Pseuduvaria are determined using dispersal-vicariance analysis (DIVA) and weighted ancestral area analysis (WAAA). Results: The divergence times of the main clades within the Annonaceae were found to deviate slightly from previous estimates that used different calibration points and dating methods. In particular, our estimate for the SBC crown (55.2-26.9 Mya) is much younger than previous estimates (62.5-53.1 +/- 3.6 Mya and ca. 58.76 Mya). Early diversification of Pseuduvaria was estimated to have occurred 15-8 Mya, possibly associated with the 'mid-Miocene climatic optimum.' Pseuduvaria is inferred to have originated in Sundaland in the late Miocene, ca. 8 Mya; subsequent migration events were predominantly eastwards towards New Guinea and Australia, although several migratory reversals are also postulated. Speciation of Pseuduvaria within New Guinea may have occurred after ca. 6.5 Mya, possibly coinciding with the formation of the Central Range orogeny from ca. 8 Mya. Conclusion: Our divergence time estimates within the Annonaceae are likely to be more precise as we used a UCLD clock model and calibrated the phylogeny using new fossil evidence. Pseuduvaria is shown to have dispersed from Sundaland after the late Miocene. The present-day paleotropical distribution of Pseuduvaria may have been achieved by long-distance dispersal, and speciation events might be explained by global climatic oscillations, sea level fluctuations, and tectonic activity. http://www.biomedcentral.com/1471-2148/9/153 Yvonne Su Richard Saunders BMC Evolutionary Biology 2009, 9:153 2009-07-02T00:00:00Z doi:10.1186/1471-2148-9-153 BMC Evolutionary Biology 1471-2148 9 153 2009-07-02T00:00:00Z PDF Background: Inbreeding and the loss of genetic diversity are known to be significant threats to small, isolated populations. Hymenoptera represent a special case regarding the impact of inbreeding. Haplodiploidy may permit purging of deleterious recessive alleles in haploid males, meaning inbreeding depression is reduced relative to diploid species. In contrast, the impact of inbreeding may be exacerbated in Hymenopteran species that have a single-locus complementary sex determination system, due to the production of sterile or inviable diploid males. We investigated the costs of brother-sister mating in the bumblebee Bombus terrestris. We compared inbred colonies that produced diploid males and inbred colonies that did not produce diploid males with outbred colonies. Mating, hibernation and colony founding took place in the laboratory. Once colonies had produced 15 offspring they were placed in the field and left to forage under natural conditions. Results: The diploid male colonies had a significantly reduced fitness compared to regular inbred and outbred colonies; they had slower growth rates in the laboratory, survived for a shorter time period under field conditions and produced significantly fewer offspring overall. No differences in success were found between non-diploid male inbred colonies and outbred colonies. Conclusions: Our data illustrate that inbreeding exacts a considerable cost in Bombus terrestris through the production of diploid males. We suggest that diploid males may act as indicators of the genetic health of populations, and that their detection could be used as an informative tool in hymenopteran conservation. We conclude that whilst haplodiploids may suffer less inbreeding depression than diploid species, they are still highly vulnerable to population fragmentation and reduced genetic diversity due to the extreme costs imposed by the production of diploid males. http://www.biomedcentral.com/1471-2148/9/152 Penelope Whitehorn Matthew Tinsley Mark Brown Ben Darvill Dave Goulson BMC Evolutionary Biology 2009, 9:152 2009-07-02T00:00:00Z doi:10.1186/1471-2148-9-152 BMC Evolutionary Biology 1471-2148 9 152 2009-07-02T00:00:00Z PDF Background: Although current molecular clock methods offer greater flexibility in modelling historical evolutionary events, calibration of the clock with dates from the fossil record is still problematic for many groups. Here we implement several new approaches in molecular dating to estimate evolutionary ages of Lacertidae, an Old World family of lizards with a poor fossil record and uncertain phylogeny. Four different models of rate variation are tested in a new program for Bayesian phylogenetic analysis called TreeTime, based on a combination of mitochondrial and nuclear gene sequences. We incorporate paleontological uncertainty into divergence estimates by expressing multiple calibration dates as a range of probabilistic distributions. We also test the reliability of our proposed calibrations by exploring effects of individual priors on posterior estimates. Results: According to the most reliable model, as indicated by Bayes factor comparison, modern lacertids arose shortly after the K/T transition and entered Africa about 45 million years ago, with the majority of their African radiation occurring in the Eocene and Oligocene. Our findings indicate much earlier origins for these clades than previously reported, and we discuss our results in light of paleogeographic trends during the Cenozoic. Conclusions: This study represents the first attempt to estimate evolutionary ages of a specific group of reptiles exhibiting uncertain phylogenetic relationships, molecular rate variation and a poor fossil record. Our results emphasize the sensitivity of molecular divergence dates to fossil calibrations, and support the use of combined molecular data sets and multiple, well-spaced dates from the fossil record as minimum node constraints. The bioinformatics program used here, TreeTime, is publicly available, and we recommend its use for molecular dating of taxa faced with similar challenges. http://www.biomedcentral.com/1471-2148/9/151 Christy Hipsley Lin Himmelmann Dirk Metzler Johannes Mueller BMC Evolutionary Biology 2009, 9:151 2009-07-01T00:00:00Z doi:10.1186/1471-2148-9-151 BMC Evolutionary Biology 1471-2148 9 151 2009-07-01T00:00:00Z PDF Background: Phylogenomic analyses recently became popular to address questions about deep metazoan phylogeny. Ribosomal proteins (RP) dominate many of these analyses or are, in some cases, the only genes included. Despite initial hopes, phylogenomic analyses including tens to hundreds of genes still fail to robustly place many bilaterian taxa. Results: Using the phylogenetic position of myzostomids as an example, we show that phylogenies derived from RP genes and mitochondrial genes produce incongruent results. Whereas the former support a position within a clade of platyzoan taxa, mitochondrial data recovers an annelid affinity, which is strongly supported by the gene order data and is congruent with morphology. Using hypothesis testing, our RP data significantly rejects the annelids affinity, whereas a platyzoan relationship is significantly rejected by the mitochondrial data. Conclusions: We conclude (i) that reliance of a set of markers belonging to a single class of macromolecular complexes might bias the analysis, and (ii) that concatenation of all available data might introduce conflicting signal into phylogenetic analyses. We therefore strongly recommend testing for data incongruence in phylogenomic analyses. Furthermore, judging all available data, we consider the annelid affinity hypothesis more plausible than a possible platyzoan affinity for myzostomids, and suspect long branch attraction is influencing the RP data. However, this hypothesis needs further confirmation by future analyses. http://www.biomedcentral.com/1471-2148/9/150 Christoph Bleidorn Lars Podsiadlowski Min Zhong Igor Eeckhaut Stefanie Hartmann Kenneth Halanych Ralph Tiedemann BMC Evolutionary Biology 2009, 9:150 2009-07-01T00:00:00Z doi:10.1186/1471-2148-9-150 BMC Evolutionary Biology 1471-2148 9 150 2009-07-01T00:00:00Z PDF Background: : Deacetylation of histones plays a fundamental role in gene silencing, and this is mediated by a corepressor complex containing Sin3 as an essential scaffold protein. In this report we examine the evolution of two proteins in this complex, the Sin3-associated proteins SAP30L and SAP30, by using an archive of protein sequences from 62 species. Results: : Our analysis indicates that in tetrapods SAP30L is more similar than SAP30 to the ancestral protein, and the two copies in this group originated by gene duplication which occurred after the divergence of Actinopterygii and Sarcopterygii about 450 million years ago (Mya). The phylogenetic analysis and biochemical experiments suggest that SAP30 has diverged functionally from the ancestral SAP30L by accumulating mutations that have caused attenuation of one of the original functions, association with the nuclear matrix. This function is mediated by a nuclear matrix association sequence, which consists of a conserved motif in the C-terminus and the adjacent nucleolar localization signal (NoLS). Conclusions: : These results add further insight into the evolution and function of proteins of the SAP30 family, which share many characteristic with nuclear scaffolding proteins that are intimately involved in regulation of gene expression. Furthermore, SAP30L seems essential to eukaryotic biology, as it is found in animals, plants, fungi, as well as some taxa of unicellular eukaryotes. http://www.biomedcentral.com/1471-2148/9/149 Keijo Viiri Taisto Heinonen Markku Maki Olli Lohi BMC Evolutionary Biology 2009, 9:149 2009-06-30T00:00:00Z doi:10.1186/1471-2148-9-149 BMC Evolutionary Biology 1471-2148 9 149 2009-06-30T00:00:00Z PDF Background: Many fungi are obligate biotrophs of plants, growing in live plant tissues, gaining direct access to recently photosynthesized carbon. Photosynthate within plants is transported from source to sink tissues as sucrose, which is hydrolyzed by plant glycosyl hydrolase family 32 enzymes (GH32) into its constituent monosaccharides to meet plant cellular demands. A number of plant pathogenic fungi also use GH32 enzymes to access plant-derived sucrose, but less is known about the sucrose utilization ability of mutualistic and commensal plant biotrophic fungi, such as mycorrhizal and endophytic fungi. The aim of this study was to explore the distribution and abundance of GH32 genes in fungi to understand how sucrose utilization is structured within and among major ecological guilds and evolutionary lineages. Using bioinformatic and PCR-based analyses, we tested for GH32 gene presence in all available fungal genomes and an additional 149 species representing a broad phylogenetic and ecological range of biotrophic fungi. Results: We detected 9 lineages of GH32 genes in fungi, 4 of which we describe for the first time. GH32 gene number in fungal genomes ranged from 0-12. Ancestral state reconstruction of GH32 gene abundance showed a strong correlation with nutritional mode, and gene family expansion was observed in several clades of pathogenic filamentous Ascomycota species. GH32 gene number was negatively correlated with animal pathogenicity and positively correlated with plant biotrophy, with the notable exception of mycorrhizal taxa. Few mycorrhizal species were found to have GH32 genes as compared to other guilds of plant-associated fungi, such as pathogens, endophytes and lichen-forming fungi. GH32 genes were also more prevalent in the Ascomycota than in the Basidiomycota. Conclusion: We found a strong signature of both ecological strategy and phylogeny on GH32 gene number in fungi. These data suggest that plant biotrophic fungi exhibit a wide range of ability to access plant-synthesized sucrose. Endophytic fungi are more similar to plant pathogens in their possession of GH32 genes, whereas most genomes of mycorrhizal taxa lack GH32 genes. Reliance on plant GH32 enzyme activity for C acquisition in these symbionts supports earlier predictions of possible plant control over C allocation in the mycorrhizal symbiosis. http://www.biomedcentral.com/1471-2148/9/148 Jeri Parrent Timothy James Rimvydas Vasaitis Andrew Taylor BMC Evolutionary Biology 2009, 9:148 2009-06-30T00:00:00Z doi:10.1186/1471-2148-9-148 BMC Evolutionary Biology 1471-2148 9 148 2009-06-30T00:00:00Z PDF Background: Evidence of multiple genetic criteria of mate choice is accumulating in numerous taxa. In many species, females have been shown to pair with genetically dissimilar mates or with extra-pair partners that are more genetically compatible than their social mates, thereby increasing their offsprings' heterozygosity which often correlates with offspring fitness. While most studies have focused on genetically promiscuous species, few studies have addressed genetically monogamous species, in which mate choice tends to be mutual. Results: Here, we used microsatellite markers to assess individual global heterozygosity and genetic similarity of pairs in a socially and genetically monogamous seabird, the black-legged kittiwake Rissa tridactyla. We found that pairs were more genetically dissimilar than expected by chance. We also identified fitness costs of breeding with genetically similar partners: (i) genetic similarity of pairs was negatively correlated with the number of chicks hatched, and (ii) offspring heterozygosity was positively correlated with growth rate and survival. Conclusion: These findings provide evidence that breeders in a genetically monogamous species may avoid the fitness costs of reproducing with a genetically similar mate. In such species that lack the opportunity to obtain extra-pair fertilizations, mate choice may therefore be under high selective pressure. http://www.biomedcentral.com/1471-2148/9/147 Herve Mulard Etienne Danchin Sandra Talbot Andrew Ramey Scott Hatch Joel White Fabrice Helfenstein Richard Wagner BMC Evolutionary Biology 2009, 9:147 2009-06-30T00:00:00Z doi:10.1186/1471-2148-9-147 BMC Evolutionary Biology 1471-2148 9 147 2009-06-30T00:00:00Z PDF Background: Snake venom toxins evolve more rapidly than other proteins through accelerated changes in the protein coding regions. Previously we have shown that accelerated segment switch in exons to alter targeting (ASSET) might play an important role in its functional evolution of viperid three-finger toxins. In this phenomenon, short sequences in exons are radically changed to unrelated sequences and hence affect the folding and functional properties of the toxins. Results: Here we analyzed other snake venom protein families to elucidate the role of ASSET in their functional evolution. ASSET appears to be involved in the functional evolution of three-finger toxins to a greater extent than in several other venom protein families. ASSET leads to replacement of some of the critical amino acid residues that affect the biological function in three-finger toxins as well as change the conformation of the loop that is involved in binding to specific target sites. Conclusion: ASSET could lead to novel functions in snake venom proteins. Among snake venom serine proteases, ASSET contributes to changes in three surface segments. One of these segments near the substrate binding region is known to affect substrate specificity, and its exchange may have significant implications for differences in isoform catalytic activity on specific target protein substrates. ASSET therefore plays an important role in functional diversification of snake venom proteins, in addition to accelerated point mutations in the protein coding regions. Accelerated point mutations lead to fine-tuning of target specificity, whereas ASSET leads to large-scale replacement of multiple functionally important residues, resulting in change or gain of functions. http://www.biomedcentral.com/1471-2148/9/146 Robin Doley Stephen Mackessy R Manjunatha Kini BMC Evolutionary Biology 2009, 9:146 2009-06-30T00:00:00Z doi:10.1186/1471-2148-9-146 BMC Evolutionary Biology 1471-2148 9 146 2009-06-30T00:00:00Z PDF Background: The seacoasts of the Japanese Arc are fringed by many gravel beaches owing to active tectonic uplift and intense denudation caused by heavy rainfall. These gravel beaches are inhabited by gobies of the genus Luciogobius that burrow into the gravel sediment and live interstitially. Although their habitat and morphology (e.g., reduced fins, elongated, scale-less body, and highly segmented vertebral column) are highly unusual among fishes, little is known on how their morphological evolution has facilitated the colonization of interstitial habitats and promoted extensive diversification. We conducted thorough sampling of Luciogobius and related species throughout Japan, and performed molecular phylogenetic analysis to explore the patterns of morphological evolution associated with gravel beach colonization. Results: An analysis of the mitochondrial cytochrome b gene suggested a remarkable diversity of previously unrecognized species. The species-level phylogeny based on six protein-coding nuclear genes clearly indicated that interstitial species cluster into two distinct clades, and that transitions from benthic or demersal habits to interstitial habits are strongly correlated with an increase in vertebral number. Colonization of gravel beach habitats is estimated to have occurred ca. 10 Ma, which coincides with the period of active orogenesis of the Japanese landmass. Different species of interstitial Luciogobius inhabit sediments with different granulometric properties, suggesting that microhabitat partitioning has been an important mechanism facilitating speciation in these fishes. Conclusions: This is the first study to document the adaptation to interstitial habitats by a vertebrate. Body elongation and excessive vertebral segmentation had been the key aspects enhancing body flexibility and fishes' ability to burrow into the gravel sediment. The rich diversity of coastal gravel habitats of the Japanese Arc has likely promoted the adaptive radiation of these unique gravel-dwelling fishes. http://www.biomedcentral.com/1471-2148/9/145 Tomohiko Yamada Tomoshige Sugiyama Nana Tamaki Atsushi Kawakita Makoto Kato BMC Evolutionary Biology 2009, 9:145 2009-06-28T00:00:00Z doi:10.1186/1471-2148-9-145 BMC Evolutionary Biology 1471-2148 9 145 2009-06-28T00:00:00Z PDF