http://www.biomedcentral.com/bmcevolbiol/ The latest research articles published by BMC Evolutionary Biology 2013-05-26T00:00:00Z Background: A novel transient structure was observed in the spermatids of three ratite species using transmission electron microscopy. Results: The structure first appeared at the circular manchette stage of sperm development, was most prominent during the longitudinal manchette phase and disappeared abruptly prior to spermiation. It was composed of regularly-spaced finger-like projections which were closely associated with the outer nuclear membrane, giving the nucleus a cogwheel-like appearance. The projections were approximately 30 nm long and 14 nm wide. Although a similar structure has been described in certain lizard and crocodile species, this is the first report of a similar structure in the developing spermatids of birds. Conclusions: The potential value of non-traditional characters, such as spermiogenesis and sperm ultrastructure, as phylogenetic markers has recently been advocated. The morphologically unique structure found in ratite spermatids provides additional evidence of a possible phylogenetic link between the reptiles and birds. It also endorses the basal positioning of the ratites as a monophyletic group within the avian phylogenetic tree. http://www.biomedcentral.com/1471-2148/13/104 Lizette du Plessis John Soley BMC Evolutionary Biology 2013, null:104 2013-05-26T00:00:00Z doi:10.1186/1471-2148-13-104 /content/figures/1471-2148-13-104-toc.gif BMC Evolutionary Biology 1471-2148 ${item.volume} 104 2013-05-26T00:00:00Z PDF Background: PHOSPHATE1 (PHO1) gene family members have diverse roles in plant growth and development, and they have been studied in Arabidopsis, rice, and Physcomitrella. However, it has yet to be described in other plants. Therefore, we surveyed the evolutionary patterns of genomes within the plant PHO1 gene family, focusing on soybean (Glycine max) due to its economic importance. Results: Our data show that PHO1 genes could be classified into two major groups (Class I and Class II). Class I genes were only present and expanded in dicotyledonous plants and Selaginella moellendorffii; Class II genes were found in all land plants. Class I sequence losses in other lineages may be attributed to gene loss after duplication events in land plant evolution. Introns varied from 7 to 14, and ancestral state reconstruction analyses revealed that genes with 13 introns were ancestral, thus suggesting that the intron loss was a chief constituent of PHO1 gene evolution. In the soybean genome, only 12 PHO1-like genes (GmaPHO1) were detected at the mRNA level. These genes display tissue-specific or tissue-preferential expression patterns during soybean plant and fruit development. Class I genes were more broadly expressed than Class II. GmaPHO1 genes had altered expression in response to salt, osmotic, and inorganic phosphate stresses. Conclusions: Our study revealed that PHO1 genes originated from a eukaryotic ancestor and that two major classes formed in land plants. Class I genes are only present in dicots and lycophytes. GmaPHO1genes had diverse expression patterns in soybean, indicating their dramatic functional diversification. http://www.biomedcentral.com/1471-2148/13/103 Lingli He Man Zhao Yan Wang Junyi Gai Chaoying He BMC Evolutionary Biology 2013, null:103 2013-05-24T00:00:00Z doi:10.1186/1471-2148-13-103 /content/figures/1471-2148-13-103-toc.gif BMC Evolutionary Biology 1471-2148 ${item.volume} 103 2013-05-24T00:00:00Z PDF Background: Phylogenetic studies, particularly those based on rDNA sequences from plant roots and basidiomata, have revealed a strikingly high genetic diversity in the Sebacinales. However, the factors determining this genetic diversity at higher and lower taxonomic levels within this order are still unknown. In this study, we analysed patterns of genetic variation within two morphological species, Sebacina epigaea and S. incrustans, based on 340 DNA haplotype sequences of independent genetic markers from the nuclear (ITS + 5.8S + D1/D2, RPB2) and mitochondrial (ATP6) genomes for 98 population samples. By characterising the genetic population structure within these species, we provide insights into species boundaries and the possible factors responsible for genetic diversity at a regional geographic scale. Results: We found that recombination events are relatively common between natural populations within Sebacina epigaea and S. incrustans, and play a significant role in generating intraspecific genetic diversity. Furthermore, we also found that RPB2 and ATP6 genes display higher levels of intraspecific synonymous polymorphism. Phylogenetic and demographic analyses based on nuclear and mitochondrial loci revealed three distinct phylogenetic lineages within of each of the morphospecies S. epigaea and S. incrustans: one major and widely distributed lineage, and two geographically restricted lineages, respectively. We found almost no differential morphological or ecological characteristics that could be used to discriminate between these lineages. Conclusions: Our results suggest that recombination and negative selection have played significant roles in generating genetic diversity within these morphological species at small geographical scales. Concordance between gene genealogies identified lineages/cryptic species that have evolved independently for a relatively long period of time. These putative species were not associated with geographic provenance, geographic barrier, host preference or distinct phenotypic innovations. http://www.biomedcentral.com/1471-2148/13/102 Kai Riess Franz Oberwinkler Robert Bauer Sigisfredo Garnica BMC Evolutionary Biology 2013, null:102 2013-05-22T00:00:00Z doi:10.1186/1471-2148-13-102 /content/figures/1471-2148-13-102-toc.gif BMC Evolutionary Biology 1471-2148 ${item.volume} 102 2013-05-22T00:00:00Z PDF Background: Retrotransposons are a major component of the human genome constituting as much as 45%. The hominid specific SINE-VNTR-Alus are the youngest of these elements constituting 0.13% of the genome; they are therefore a practical and amenable group for analysis of both their global integration, polymorphic variation and their potential contribution to modulation of genome regulation. Results: Consistent with insertion into active chromatin we have determined that SVAs are more prevalent in genic regions compared to gene deserts. The consequence of which, is that their integration has greater potential to have affects on gene regulation. The sequences of SVAs show potential for the formation of secondary structure including G-quadruplex DNA. We have shown that the human specific SVA subtypes (E-F1) show the greatest potential for forming G-quadruplexes within the central tandem repeat component in addition to the 5' 'CCCTCT' hexamer. We undertook a detailed analysis of the PARK7 SVA D, located in the promoter of the PARK7 gene (also termed DJ-1), in a Hapmap cohort where we identified 2 variable number tandem repeat domains and 1 tandem repeat within this SVA with the 5' CCCTCT element being one of the variable regions. Functionally we were able to demonstrate that this SVA contains multiple regulatory elements that support reporter gene expression in vitro and further show these elements exhibit orientation dependency. Conclusions: Our data supports the hypothesis that SVAs integrate preferentially in to open chromatin where they could modify the existing transcriptional regulatory domains or alter expression patterns by a variety of mechanisms. http://www.biomedcentral.com/1471-2148/13/101 Abigail Savage Vivien Bubb Gerome Breen John Quinn BMC Evolutionary Biology 2013, null:101 2013-05-21T00:00:00Z doi:10.1186/1471-2148-13-101 /content/figures/1471-2148-13-101-toc.gif BMC Evolutionary Biology 1471-2148 ${item.volume} 101 2013-05-21T00:00:00Z PDF Background: Chromosomal inversions are increasingly being recognized as important in adaptive shifts and are expected to influence patterns of genetic variation, but few studies have examined genetic patterns in inversion polymorphisms across and within populations. Here, we examine genetic variation at 20 microsatellite loci and the alcohol dehydrogenase gene (Adh) located within and near the In(2L)t inversion of Drosophila melanogaster at three different sites along a latitudinal cline on the east coast of Australia. Results: We found significant genetic differentiation between the standard and inverted chromosomal arrangements at each site as well as significant, but smaller differences among sites in the same arrangement. Genetic differentiation between pairs of sites was higher for inverted chromosomes than standard chromosomes, while inverted chromosomes had lower levels of genetic variation even well away from inversion breakpoints. Bayesian clustering analysis provided evidence of genetic exchange between chromosomal arrangements at each site. Conclusions: The strong differentiation between arrangements and reduced variation in the inverted chromosomes are likely to reflect ongoing selection at multiple loci within the inverted region. They may also reflect lower effective population sizes of In(2L)t chromosomes and colonization of Australia, although there was no consistent evidence of a recent bottleneck and simulations suggest that differences between arrangements would not persist unless rates of gene exchange between them were low. Genetic patterns therefore support the notion of selection and linkage disequilibrium contributing to inversion polymorphisms, although more work is needed to determine whether there are spatially varying targets of selection within this inversion. They also support the idea that the allelic content within an inversion can vary between geographic locations. http://www.biomedcentral.com/1471-2148/13/100 W Kennington Ary Hoffmann BMC Evolutionary Biology 2013, null:100 2013-05-20T00:00:00Z doi:10.1186/1471-2148-13-100 /content/figures/1471-2148-13-100-toc.gif BMC Evolutionary Biology 1471-2148 ${item.volume} 100 2013-05-20T00:00:00Z PDF Background: Exceptionally preserved Palaeozoic faunas have yielded a plethora of trilobite-like arthropods, often referred to as lamellipedians. Among these, Artiopoda is supposed to contain taxa united by a distinctive appendage structure. This includes several well supported groups, Helmetiida, Nektaspida, and Trilobita, as well as a number of problematic taxa. Interrelationships remain unclear, and the position of the lamellipedian arthropods as a whole also remains the subject of debate. Results: Arthroaspis bergstroemi n. gen. n. sp., a new arthropod from the early Cambrian Sirius Passet Lagerstätte of North Greenland shows a striking combination of both dorsal and ventral characters of Helmetiida, Nektaspida, and Trilobita. Cladistic analysis with a broad taxon sampling of predominantly early Palaeozoic arthropods yields a monophyletic Lamellipedia as sister taxon to the Crustacea or Tetraconata. Artiopoda is resolved as paraphyletic, giving rise to the Marrellomorpha. Within Lamellipedia, a clade of pygidium bearing taxa is resolved that can be shown to have a broadly helmetiid-like tergite morphology in its ground pattern. This morphology is plesiomorphically retained in Helmetiida and in Arthroaspis, which falls basally into a clade containing Trilobita. The trilobite appendages, though similar to those of other lamellipedians in gross morphology, have a unique outward rotation of the anterior trunk appendages, resulting in a ‘hard wired’ lateral splay, different to that observed in other Lamellipedia. Conclusions: The combination of helmetiid, trilobite, and nektaspid characters in Arthroaspis gives important hints concerning character polarisation within the trilobite-like arthropods. The distinctive tergite morphology of trilobites, with its sophisticated articulating devices, is derived from flanged edge-to-edge articulating tergites forming a shield similar to the helmetiids, previously considered autapomorphic for that group. The stereotypical lateral splay of the appendages of lamellipedians is a homoplastic character shown to be achieved by several groups independently. http://www.biomedcentral.com/1471-2148/13/99 Martin Stein Graham Budd John Peel David Harper BMC Evolutionary Biology 2013, null:99 2013-05-11T00:00:00Z doi:10.1186/1471-2148-13-99 /content/figures/1471-2148-13-99-toc.gif BMC Evolutionary Biology 1471-2148 ${item.volume} 99 2013-05-11T00:00:00Z XML Background: Few studies on eurypterids have taken into account morphological changes that occur throughout postembryonic development. Here two species of eurypterid are described from the Pragian Beartooth Butte Formation of Cottonwood Canyon in Wyoming, and included in a phylogenetic analysis. Both species comprise individuals from a number of instars, and this allows for changes that occur throughout their ontogeny to be documented, and how ontogenetically variable characters can influence phylogenetic analysis to be tested. Results: The two species of eurypterid are described as Jaekelopterus howelli (Kjellesvig-Waering and St[latin small letter o with stroke]rmer, 1952) and Strobilopterus proteus sp. nov. Phylogenetic analysis places them within the Pterygotidae and Strobilopteridae respectively, both families within the Eurypterina. Jaekelopterus howelli shows positive allometry of the cheliceral denticles throughout ontogeny, while a number of characteristics including prosomal appendage length, carapace shape, lateral eye position, and relative breadth all vary during the growth of Strobilopterus proteus. Conclusions: The ontogeny of Strobilopterus proteus shares much in common with that of modern xiphosurans, however certain characteristics including apparent true direct development suggest a closer affinity to arachnids. The ontogenetic development of the genital appendage also supports the hypothesis that the structure is homologous to the endopods of the trunk limbs of other arthropods. Including earlier instars in the phylogenetic analysis is shown to destabilise the retrieved topology. Therefore, coding juveniles as individual taxa in an analysis is shown to be actively detrimental and alternative ways of coding ontogenetic data into phylogenetic analyses should be explored. http://www.biomedcentral.com/1471-2148/13/98 James Lamsdell Paul Selden BMC Evolutionary Biology 2013, null:98 2013-05-10T00:00:00Z doi:10.1186/1471-2148-13-98 /content/figures/1471-2148-13-98-toc.gif BMC Evolutionary Biology 1471-2148 ${item.volume} 98 2013-05-10T00:00:00Z PDF Background: Multiple infections of the same host by different strains of the same microparasite species are believed to play a crucial role during the evolution of parasite virulence. We investigated the role of specificity, relative virulence and relative dose in determining the competitive outcome of multiple infections in the Daphnia magna-Pasteuria ramosa host-parasite system. Results: We found that infections by P. ramosa clones (single genotype) were less virulent and produced more spores than infections by P. ramosa isolates (possibly containing multiple genotypes). We also found that two similarly virulent isolates of P. ramosa differed considerably in their within-host competitiveness and their effects on host offspring production when faced with coinfecting P. ramosa isolates and clones. Although the relative virulence of a P. ramosa isolate/clone appears to be a good indicator of its competitiveness during multiple infections, the relative dose may alter the competitive outcome. Moreover, spore counts on day 20 post-infection indicate that the competitive outcome is largely decided early in the parasite’s growth phase, possibly mediated by direct interference or apparent competition. Conclusions: Our results emphasize the importance of epidemiology as well as of various parasite traits in determining the outcome of within-host competition. Incorporating realistic epidemiological and ecological conditions when testing theoretical models of multiple infections, as well as using a wider range of host and parasite genotypes, will enable us to better understand the course of virulence evolution. http://www.biomedcentral.com/1471-2148/13/97 Frida Ben-Ami Jarkko Routtu BMC Evolutionary Biology 2013, null:97 2013-05-03T00:00:00Z doi:10.1186/1471-2148-13-97 /content/figures/1471-2148-13-97-toc.gif BMC Evolutionary Biology 1471-2148 ${item.volume} 97 2013-05-03T00:00:00Z XML Background: Tyrosinases, tyrosinase-related proteins, catechol oxidases and hemocyanins comprise the type-3 copper protein family and are involved in a variety of biological processes, including pigment formation, innate immunity and oxygen transport. Although this family is present in the three domains of life, its origin and early evolution are not well understood. Previous analyses of type-3 copper proteins largely have focussed on specific animal and plant phyla. Results: Here, we combine genomic, phylogenetic and structural analyses to show that the original type-3 copper protein possessed a signal peptide and may have been secreted (we designate proteins of this type the α subclass). This ancestral type-3 copper protein gene underwent two duplication events, the first prior to the divergence of the unikont eukaryotic lineages and the second before the diversification of animals. The former duplication gave rise to a cytosolic form (β) and the latter to a membrane-bound form (γ). Structural comparisons reveal that the active site of α and γ forms are covered by aliphatic amino acids, and the β form has a highly conserved aromatic residue in this position. The subsequent evolution of this gene family in modern lineages of multicellular eukaryotes is typified by the loss of one or more of these three subclasses and the lineage-specific expansion of one or both of the remaining subclasses. Conclusions: The diversity of type-3 copper proteins in animals and other eukaryotes is consistent with two ancient gene duplication events leading to α, β and γ subclasses, followed by the differential loss and expansion of one or more of these subclasses in specific kingdoms and phyla. This has led to many lineage-specific type-3 copper protein repertoires and in some cases the independent evolution of functionally-classified tyrosinases and hemocyanins. For example, the oxygen-carrying hemocyanins in arthropods evolved from a β-subclass tyrosinase, whilst hemocyanins in molluscs and urochordates evolved independently from an α-subclass tyrosinase. Minor conformational changes at the active site of α, β and γ forms can produce type-3 copper proteins with capacities to either carry oxygen (hemocyanins), oxidize diphenols (catechol oxidase) or o-hydroxylate monophenols (tyrosinases) and appear to underlie some functional convergences. http://www.biomedcentral.com/1471-2148/13/96 Felipe Aguilera Carmel McDougall Bernard Degnan BMC Evolutionary Biology 2013, null:96 2013-05-01T00:00:00Z doi:10.1186/1471-2148-13-96 /content/figures/1471-2148-13-96-toc.gif BMC Evolutionary Biology 1471-2148 ${item.volume} 96 2013-05-01T00:00:00Z XML Background: In evolutionary and conservation biology, parasitism is often highlighted as a major selective pressure. To fight against parasites and pathogens, genetic diversity of the immune genes of the major histocompatibility complex (MHC) are particularly important. However, the extensive degree of polymorphism observed in these genes makes it difficult to conduct thorough population screenings. Methods: We utilized a genotyping protocol that uses 454 amplicon sequencing to characterize the MHC class I in the endangered loggerhead sea turtle (Caretta caretta) and to investigate their evolution at multiple relevant levels of organization. Results: MHC class I genes revealed signatures of trans-species polymorphism across several reptile species. In the studied loggerhead turtle individuals, it results in the maintenance of two ancient allelic lineages. We also found that individuals carrying an intermediate number of MHC class I alleles are larger than those with either a low or high number of alleles. Conclusions: Multiple modes of evolution seem to maintain MHC diversity in the loggerhead turtles, with relatively high polymorphism for an endangered species. http://www.biomedcentral.com/1471-2148/13/95 Victor Stiebens Sonia Merino Frédéric J Chain Christophe Eizaguirre BMC Evolutionary Biology 2013, null:95 2013-04-30T00:00:00Z doi:10.1186/1471-2148-13-95 /content/figures/1471-2148-13-95-toc.gif BMC Evolutionary Biology 1471-2148 ${item.volume} 95 2013-04-30T00:00:00Z XML