http://www.biomedcentral.com/bmcevolbiol/ The editor's pick of recent articles published by BMC Evolutionary Biology 2012-04-16T00:00:00Z Background: Ecological processes are increasingly being viewed as an important mode of diversification in the marine environment, where the high dispersal potential of pelagic organisms, and a lack of absolute barriers to gene flow may limit the occurrence of allopatric speciation through vicariance. Here we focus on the potential role of ecological partitioning in the diversification of a widely distributed group of marine protists, the planktonic foraminifera. Sampling was conducted in the tropical Arabian Sea, during the southwest (summer) monsoon, when pronounced environmental conditions result in a strong disparity in temperature, salinity and productivity between distinct northern and southern water masses. Results: We uncovered extensive genetic diversity within the Arabian Sea planktonic foraminifera, identifying 13 morphospecies, represented by 20 distinct SSU rRNA genetic types. Several morphospecies/genetic types displayed non-random biogeographical distributions, partitioning between the northern and southern water masses, giving a strong indication of independent ecological adaptations. Conclusions: We propose sea-surface primary productivity as the main factor driving the geographical segregation of Arabian Sea planktonic foraminifera, during the SW monsoon, with variations in symbiotic associations possibly playing a role in the specific ecological adaptations observed. Our findings suggest that ecological partitioning could be contributing to the high levels of 'cryptic' genetic diversity observed within the planktonic foraminifera, and support the view that ecological processes may play a key role in the diversification of marine pelagic organisms. http://www.biomedcentral.com/1471-2148/12/54 Heidi A Seears Kate F Darling Christopher M Wade BMC Evolutionary Biology 2012, 12:54 2012-04-16T00:00:00Z 10.1186/1471-2148-12-54 Foraminifera show ecological partitioning The distribution of species and genotypes of planktonic foraminifera in the Arabian Sea shows species-specific adaptations to different environmental conditions and suggests that ecological partitioning might play a role in the speciation process. /content/figures/1471-2148-12-54-toc.gif BMC Evolutionary Biology 1471-2148 12 54 2012-04-16T00:00:00Z XML Background: Cetaceans (whales, dolphins and porpoises) are a group of adapted marine mammals with an enigmatic history of transition from terrestrial to full aquatic habitat and rapid radiation in waters around the world. Throughout this evolution, the pathogen stress-response proteins must have faced challenges from the dramatic change of environmental pathogens in the completely different ecological niches cetaceans occupied. For this reason, cetaceans could be one of the most ideal candidate taxa for studying evolutionary process and associated driving mechanism of vertebrate innate immune systems such as Toll-like receptors (TLRs), which are located at the direct interface between the host and the microbial environment, act at the first line in recognizing specific conserved components of microorganisms, and translate them rapidly into a defense reaction. Results: We used TLR4 as an example to test whether this traditionally regarded pattern recognition receptor molecule was driven by positive selection across cetacean evolutionary history. Overall, the lineage-specific selection test showed that the dN/dS (omega) values along most (30 out of 33) examined cetartiodactylan lineages were less than 1, suggesting a common effect of functional constraint. However, some specific codons made radical changes, fell adjacent to the residues interacting with lipopolysaccharides (LPS), and showed parallel evolution between independent lineages, suggesting that TLR4 was under positive selection. Especially, strong signatures of adaptive evolution on TLR4 were identified in two periods, one corresponding to the early evolutionary transition of the terrestrial ancestors of cetaceans from land to semi-aquatic (represented by the branch leading to whale + hippo) and from semi-aquatic to full aquatic (represented by the ancestral branch leading to cetaceans) habitat, and the other to the rapid diversification and radiation of oceanic dolphins. Conclusions: This is the first study thus far to characterize the TLR gene in cetaceans. Our data present evidences that cetacean TLR4 has undergone adaptive evolution against the background of purifying selection in response to the secondary aquatic adaptation and rapid diversification in the sea. It is suggested that microbial pathogens in different environments are important factors that promote adaptive changes at cetacean TLR4 and new functions of some amino acid sites specialized for recognizing pathogens in dramatically contrasted environments to enhance the fitness for the adaptation and survival of cetaceans. http://www.biomedcentral.com/1471-2148/12/39 Tong Shen Shixia Xu Xiaohong Wang Wenhua Yu Kaiya Zhou Guang Yang BMC Evolutionary Biology 2012, 12:39 2012-03-24T00:00:00Z 10.1186/1471-2148-12-39 Innate immunity evolution of cetaceans The evolution of Toll-like receptors (TLRs) in cetaceans reveals the strong adaptive evolution of TLR4 during the habitat shift from land to water in this order, and during the rapid diversification of oceanic dolphins. /content/figures/1471-2148-12-39-toc.gif BMC Evolutionary Biology 1471-2148 12 39 2012-03-24T00:00:00Z PDF Background: House mice (Mus musculus) are commensals of humans and therefore their phylogeography can reflect human colonization and settlement patterns. Previous studies have linked the distribution of house mouse mitochondrial (mt) DNA clades to areas formerly occupied by the Norwegian Vikings in Norway and the British Isles. Norwegian Viking activity also extended further westwards in the North Atlantic with the settlement of Iceland, short-lived colonies in Greenland and a fleeting colony in Newfoundland in 1000 AD. Here we investigate whether house mouse mtDNA sequences reflect human history in these other regions as well. Results: House mice samples from Iceland, whether from archaeological Viking Age material or from modern-day specimens, had an identical mtDNA haplotype to the clade previously linked with Norwegian Vikings. From mtDNA and microsatellite data, the modern-day Icelandic mice also share the low genetic diversity shown by their human hosts on Iceland. Viking Age mice from Greenland had an mtDNA haplotype deriving from the Icelandic haplotype, but the modern-day Greenlandic mice belong to an entirely different mtDNA clade. We found no genetic association between modern Newfoundland mice and the Icelandic/ancient Greenlandic mice (no ancient Newfoundland mice were available). The modern day Icelandic and Newfoundland mice belong to the subspecies M. m. domesticus, the Greenlandic mice to M. m. musculus. Conclusions: In the North Atlantic region, human settlement history over a thousand years is reflected remarkably by the mtDNA phylogeny of house mice. In Iceland, the mtDNA data show the arrival and continuity of the house mouse population to the present day, while in Greenland the data suggest the arrival, subsequent extinction and recolonization of house mice - in both places mirroring the history of the European human host populations. If house mice arrived in Newfoundland with the Viking settlers at all, then, like the humans, their presence was also fleeting and left no genetic trace. The continuity of mtDNA haplotype in Iceland over 1000 years illustrates that mtDNA can retain the signature of the ancestral house mouse founders. We also show that, in terms of genetic variability, house mouse populations may also track their host human populations. http://www.biomedcentral.com/1471-2148/12/35 EP Jones K Skirnisson TH McGovern MTP Gilbert E Willerslev JB Searle BMC Evolutionary Biology 2012, 12:35 2012-03-19T00:00:00Z 10.1186/1471-2148-12-35 (Colonization patterns) of mice and men Colonization of the North Atlantic region by house mice, and the genetic diversity of individuals within these populations, closely mimics that of human settlers, reflecting the human history of colonization in this area /content/figures/1471-2148-12-35-toc.gif BMC Evolutionary Biology 1471-2148 12 35 2012-03-19T00:00:00Z XML Background: For a long time the presence of respiratory proteins in most insects has been considered unnecessary. However, in recent years it has become evident that globins belong to the standard repertoire of the insect genome. Like most other insect globins, the glob1 gene of Drosophila melanogaster displays a conserved expression pattern in the tracheae, the fat body and the Malpighian tubules. Results: Here we show that the recently discovered D. melanogaster globin genes glob2 and glob3 both display an unusual male-specific expression in the reproductive tract during spermatogenesis. Both paralogs are transcribed at equivalent mRNA levels and largely overlap in their cellular expression patterns during spermatogenesis. Phylogenetic analyses showed that glob2 and glob3 reflect a gene duplication event that occurred in the ancestor of the Sophophora subgenus at least 40 million years ago. Therefore, flies of the Drosophila subgenus harbor only one glob2/3-like gene. Conclusions: Phylogenetic and sequence analyses indicate an evolution of the glob2 and glob3 duplicates by a combination of sub- and neofunctionalization. Considering their restricted, testes-specific expression, an involvement of both globins in alleviating oxidative stress during spermatogenesis is conceivable. http://www.biomedcentral.com/1471-2148/12/34 Eva Gleixner Holger Herlyn Stefan Zimmerling Thorsten Burmester Thomas Hankeln BMC Evolutionary Biology 2012, 12:34 2012-03-19T00:00:00Z 10.1186/1471-2148-12-34 Gene duplication of Drosophila globins Drosophila gene duplicates, glob2 and glob3, evolved by a combination of sub- and neofunctionalization, with their expression in the male reproductive tract during spermatogenesis suggesting a possible role in the relief of oxidative stress during this process. /content/figures/1471-2148-12-34-toc.gif BMC Evolutionary Biology 1471-2148 12 34 2012-03-19T00:00:00Z XML Background: Morphostasis of traits in different species is necessary for reconstructing the evolutionary history of complex characters. Studies that place these species into a molecular phylogenetic context test hypotheses about the transitional stages that link divergent character states. For instance, the transition from a phagotrophic mode of nutrition to a phototrophic lifestyle has occurred several times independently across the tree of eukaryotes; one of these events took place within the Euglenida, a large group of flagellates with diverse modes of nutrition. Phototrophic euglenids form a clade that is nested within lineages of phagotrophic euglenids and that originated through a secondary endosymbiosis with green algae. Although it is clear that phototrophic euglenids evolved from phagotrophic ancestors, the morphological disparity between species representing these different nutritional modes remains substantial. Results: We cultivated a novel marine euglenid, Rapaza viridis n. gen. et sp. ("green grasper"), and a green alga, Tetraselmis sp., from the same environment. Cells of R. viridis were comprehensively characterized with light microscopy, SEM, TEM, and molecular phylogenetic analysis of small subunit rDNA sequences. Ultrastructural and behavioral observations demonstrated that this isolate habitually consumes a specific strain of Tetraselmis prey cells and possesses a functional chloroplast that is homologous with other phototrophic euglenids. A novel feeding apparatus consisting of a reduced rod of microtubules facilitated this first and only example of mixotrophy among euglenids. R. viridis also possessed a robust photoreception apparatus, two flagella of unequal length, euglenoid movement, and a pellicle consisting of 16 strips and one (square-shaped) whorl of posterior strip reduction. The molecular phylogenetic data demonstrated that R. viridis branches as the nearest sister lineage to phototrophic euglenids. Conclusions: The unusual combination of features in R. viridis combined with its molecular phylogenetic position completely conforms to the expected transitional stage that occurred during the early evolution of phototrophic euglenids from phagotrophic ancestors. The marine mixotrophic mode of nutrition, the preference for green algal prey cells, the structure of the feeding apparatus, and the organization of the pellicle are outstanding examples of morphostasis that clarify pivotal stages in the evolutionary history of this diverse group of microbial eukaryotes. http://www.biomedcentral.com/1471-2148/12/29 Aika Yamaguchi Naoji Yubuki Brian S Leander BMC Evolutionary Biology 2012, 12:29 2012-03-08T00:00:00Z 10.1186/1471-2148-12-29 Eugleid demonstrates evolutionary transition The novel euglenid, Rapaza viridis, displays both eukaryovorous behaviour and photosensory abilities, thus conforming to an evolutionary transitional stage expected to have taken place between current phototropic euglenids and their phagotropic ancestors. /content/figures/1471-2148-12-29-toc.gif BMC Evolutionary Biology 1471-2148 12 29 2012-03-08T00:00:00Z XML Background: In the laboratory, the Drosophila melanogaster heat shock protein Hsp90 can buffer the phenotypic effects of genetic variation. Laboratory experiments either manipulate Hsp90 activity pharmacologically, or they induce mutations with strong effects in the gene Hsp83, the single-copy fly gene encoding Hsp90. It is unknown whether observations from such laboratory experiments are relevant in the wild. Results: We here study naturally occurring mutations in Hsp83, and their effects on fitness and phenotypic buffering in flies derived from wild populations. We examined more than 4500 flies from 42 Drosophila populations distributed world-wide for insertions or deletions of mobile DNA in or near the Hsp83 gene. The insertions we observed occur at low population frequencies, and reduce Hsp83 gene expression. In competition experiments, mutant flies performed much more poorly than wild-type flies. Mutant flies were also significantly less fecund and shorter-lived than wild-type flies, as well as less well buffered against cryptic deleterious variation, as we show through inbreeding experiments. Specifically, in Hsp83 mutant flies female fecundity dropped to much lower levels after inbreeding than in wild-type flies. At even slightly elevated temperatures, inbred mutant Hsp83 populations went extinct, whereas inbred wild-type populations persisted. Conclusions: Our work shows that Hsp90, a regulator of the stress response and of signaling, helps buffer deleterious variation in fruit flies derived from wild population, and that its buffering role becomes even more important under heat stress. http://www.biomedcentral.com/1471-2148/12/25 Bing Chen Andreas Wagner BMC Evolutionary Biology 2012, 12:25 2012-02-27T00:00:00Z 10.1186/1471-2148-12-25 Drosophila heat shock mutations in the wild Naturally occurring mutations in the Drosophila Hsp83 gene result in fitness costs of reduced fecundity, lifespan, and buffering deleterious variation, demonstrating the importance of heat shock proteins in the wild. /content/figures/1471-2148-12-25-toc.gif BMC Evolutionary Biology 1471-2148 12 25 2012-02-27T00:00:00Z XML Background: The origin and modification of novel traits are important aspects of biological diversification. Studies combining concepts and approaches of developmental genetics and evolutionary biology have uncovered many examples of the recruitment, or co-option, of genes conserved across lineages for the formation of novel, lineage-restricted traits. However, little is known about the evolutionary history of the recruitment of those genes, and of the relationship between them -for example, whether the co-option involves whole or parts of existing networks, or whether it occurs by redeployment of individual genes with de novo rewiring. We use a model novel trait, color pattern elements on butterfly wings called eyespots, to explore these questions. Eyespots have greatly diversified under natural and sexual selection, and their formation involves genetic circuitries shared across insects. Results: We investigated the evolutionary history of the recruitment and co-recruitment of four conserved transcription regulators to the larval wing disc region where circular pattern elements develop. The co-localization of Antennapedia, Notch, Distal-less, and Spalt with presumptive (eye)spot organizers was examined in 13 butterfly species, providing the largest comparative dataset available for the system. We found variation between families, between subfamilies, and between tribes. Phylogenetic reconstructions by parsimony and maximum likelihood methods revealed an unambiguous evolutionary history only for Antennapedia, with a resolved single origin of eyespot-associated expression, and many homoplastic events for Notch, Distal-less, and Spalt. The flexibility in the (co-)recruitment of the targeted genes includes cases where different gene combinations are associated with morphologically similar eyespots, as well as cases where identical protein combinations are associated with very different phenotypes. Conclusions: The evolutionary history of gene (co-)recruitment is consistent with both divergence from a recruited putative ancestral network, and with independent co-option of individual genes. The diversity in the combinations of genes expressed in association with eyespot formation does not parallel diversity in characteristics of the adult phenotype. We discuss these results in the context of inferring homology. Our study underscores the importance of widening the representation of phylogenetic, morphological, and genetic diversity in order to establish general principles about the mechanisms behind the evolution of novel traits. http://www.biomedcentral.com/1471-2148/12/21 Leila T Shirai Suzanne V Saenko Roberto A Keller Maria A Jerónimo Paul M Brakefield Henri Descimon Niklas Wahlberg Patrícia Beldade BMC Evolutionary Biology 2012, 12:21 2012-02-15T00:00:00Z 10.1186/1471-2148-12-21 Eyespots show gene expression flexibility Gene expression associated with the development of butterfly eyespots shows great flexibility in the relationship between morphological phenotypes, genetic networks, and positional homologs and provides insight into the evolution of novel traits. /content/figures/1471-2148-12-21-toc.gif BMC Evolutionary Biology 1471-2148 12 21 2012-02-15T00:00:00Z XML Background: One of the big remaining challenges in evolutionary biology is to understand the evolution and maintenance of meiotic recombination. As recombination breaks down successful genotypes, it should be selected for only under very limited conditions. Yet, recombination is very common and phylogenetically widespread. The Red Queen Hypothesis is one of the most prominent hypotheses for the adaptive value of recombination and sexual reproduction. The Red Queen Hypothesis predicts an advantage of recombination for hosts that are coevolving with their parasites. We tested predictions of the hypothesis with experimental coevolution using the red flour beetle, Tribolium castaneum, and its microsporidian parasite, Nosema whitei. Results: By measuring recombination directly in the individuals under selection, we found that recombination in the host population was increased after 11 generations of coevolution. Detailed insights into genotypic and phenotypic changes occurring during the coevolution experiment furthermore helped us to reconstruct the coevolutionary dynamics that were associated with this increase in recombination frequency. As coevolved lines maintained higher genetic diversity than control lines, and because there was no evidence for heterozygote advantage or for a plastic response of recombination to infection, the observed increase in recombination most likely represented an adaptive host response under Red Queen dynamics. Conclusions: This study provides direct, experimental evidence for an increase in recombination frequency under host-parasite coevolution in an obligatory outcrossing species. Combined with earlier results, the Red Queen process is the most likely explanation for this observation. http://www.biomedcentral.com/1471-2148/12/18 Niels AG Kerstes Camillo Bérénos Paul Schmid-Hempel K Mathias Wegner BMC Evolutionary Biology 2012, 12:18 2012-02-13T00:00:00Z 10.1186/1471-2148-12-18 Support for Red Queen Hypothesis Greater levels of recombination are seen in populations of the red flour beetle, Tribolium castaneum, after 11 generations of experimental co-evolution with a microsporidian parasite compared to those grown without, supporting the predictions of the Red Queen Hypothesis. /content/figures/1471-2148-12-18-toc.gif BMC Evolutionary Biology 1471-2148 12 18 2012-02-13T00:00:00Z XML Background: Cave animals converge evolutionarily on a suite of troglomorphic traits, the best known of which are eyelessness and depigmentation. We studied 11 cave and 10 surface populations of Astyanax mexicanus in order to better understand the evolutionary origins of the cave forms, the basic genetic structuring of both cave and surface populations, and the degree to which present day migration among them affects their genetic divergence. Results: To assess the genetic structure within populations and the relationships among them we genotyped individuals at 26 microsatellite loci. We found that surface populations are similar to one another, despite their relatively large geographic separation, whereas the cave populations are better differentiated. The cave populations we studied span the full range of the cave forms in three separate geographic regions and have at least five separate evolutionary origins. Cave populations had lower genetic diversity than surface populations, correlated with their smaller effective population sizes, probably the result of food and space limitations. Some of the cave populations receive migrants from the surface and exchange migrants with one another, especially when geographically close. This admixture results in significant heterozygote deficiencies at numerous loci due to Wahlund effects. Cave populations receiving migrants from the surface contain small numbers of individuals that are intermediate in both phenotype and genotype, affirming at least limited gene flow from the surface. Conclusions: Cave populations of this species are derived from two different surface stocks denoted "old" and "new." The old stock colonized caves at least three times independently while the new stock colonized caves at least twice independently. Thus, the similar cave phenotypes found in these caves are the result of repeated convergences. These phenotypic convergences have occurred in spite of gene flow from surface populations suggesting either strong natural or sexual selection for alleles responsible for the cave phenotype in the cave environment. http://www.biomedcentral.com/1471-2148/12/9 Martina Bradic Peter Beerli Francisco J García-de León Sarai Esquivel-Bobadilla Richard L Borowsky BMC Evolutionary Biology 2012, 12:9 2012-01-23T00:00:00Z 10.1186/1471-2148-12-9 Blind Cavefish gene flow Cave populations of Mexican blind cavefish, Astyanax mexicanus, display lower genetic diversity than surface populations, despite migration from surface to cave, with phenotypic convergences occurring in spite of this gene flow, suggesting strong selection for the alleles responsible. /content/figures/1471-2148-12-9-toc.gif BMC Evolutionary Biology 1471-2148 12 9 2012-01-23T00:00:00Z XML Background: Non-human primate communication is thought to be fundamentally different from human speech, mainly due to vast differences in vocal control. The lack of these abilities in non-human primates is especially striking if compared to some marine mammals and bird species, which has generated somewhat of an evolutionary conundrum. What are the biological roots and underlying evolutionary pressures of the human ability to voluntarily control sound production and learn the vocal utterances of others? One hypothesis is that this capacity has evolved gradually in humans from an ancestral stage that resembled the vocal behavior of modern primates. Support for this has come from studies that have documented limited vocal flexibility and convergence in different primate species, typically in calls used during social interactions. The mechanisms underlying these patterns, however, are currently unknown. Specifically, it has been difficult to rule out explanations based on genetic relatedness, suggesting that such vocal flexibility may not be the result of social learning. Results: To address this point, we compared the degree of acoustic similarity of contact calls in free-ranging Campbell's monkeys as a function of their social bonds and genetic relatedness. We calculated three different indices to compare the similarities between the calls' frequency contours, the duration of grooming interactions and the microsatellite-based genetic relatedness between partners. We found a significantly positive relation between bond strength and acoustic similarity that was independent of genetic relatedness. Conclusion: Genetic factors determine the general species-specific call repertoire of a primate species, while social factors can influence the fine structure of some the call types. The finding is in line with the more general hypothesis that human speech has evolved gradually from earlier primate-like vocal communication. http://www.biomedcentral.com/1471-2148/11/362 Alban Lemasson Karim Ouattara Eric J Petit Klaus Zuberbühler BMC Evolutionary Biology 2011, 11:362 2011-12-16T00:00:00Z 10.1186/1471-2148-11-362 Its in the company you keep... Monkeys that spend time grooming each other develop similar call patterns, irrespective of genetic relatedness, revealing the effect that social interactions have on vocal calls and providing clues to the evolution of human speech. /content/figures/1471-2148-11-362-toc.gif BMC Evolutionary Biology 1471-2148 11 362 2011-12-16T00:00:00Z XML