A retroposon analysis of Afrotherian phylogeny

Recent comprehensive studies of DNA sequences support the monophyly of Afrotheria, comprising elephants, sirenians (dugongs and manatees), hyraxes, tenrecs, golden moles, aardvarks, and elephant shrews, as well as that of Paenungulata, comprising elephants, sirenians, and hyraxes. However, phylogenetic relationships among paenungulates, as well as among nonpaenungulates, have remained ambiguous. Here we applied an extensive retroposon analysis to these problems to support the monophyly of aardvarks, tenrecs, and golden moles, with elephant shrews as their sister group. Regarding phylogenetic relationships in Paenungulata, we could characterize only one informative locus, although we could isolate many insertions specific to each of three lineages, namely, Proboscidea, Sirenia, and Hyracoidea. These data prompted us to reexamine phylogenetic relationships among Paenungulata using 19 nuclear gene sequences resulting in three different analyses, namely, short interspersed element (SINE) insertions, nuclear sequence analyses, and morphological cladistics, supporting different respective phylogenies. We concluded that these three lineages diverged very rapidly in a very short evolutionary period, with the consequence that ancestral polymorphism present in the last common ancestor of Paenungulata results in such incongruence. Our results suggest the rapid fixation of many large-scale morphological synapomorphies for Tethytheria; implications of this in relation to the morphological evolution in Paenungulata are discussed.     

Ebriid phylogeny and the expansion of the Cercozoa

Ebria tripartita is a phagotrophic flagellate present in marine coastal plankton communities worldwide. This is one of two (possibly four) described extant species in the Ebridea, an enigmatic group of eukaryotes with an unclear phylogenetic position. Ebriids have never been cultured, are usually encountered in low abundance and have a peculiar combination of ultrastructural characters including a large nucleus with permanently condensed chromosomes and an internal skeleton composed of siliceous rods. Consequently, the taxonomic history of the group has been tumultuous and has included a variety of affiliations, such as silicoflagellates, dinoflagellates, 'radiolarians' and 'neomonads'. Today, the Ebridea is treated as a eukaryotic taxon incertae sedis because no morphological or molecular features have been recognized that definitively relate ebriids with any other eukaryotic lineage. We conducted phylogenetic analyses of small subunit rDNA sequences from two multi-specimen isolations of Ebria tripartita. The closest relatives to the sequences from Ebria tripartita are environmental sequences from a submarine caldera floor. This newly recognized Ebria clade was most closely related to sequences from described species of Cryothecomonas and Protaspis. These molecular phylogenetic relationships were consistent with current ultrastructural data from all three genera, leading to a robust placement of ebriids within the Cercozoa.     

Molecular evolution of the human Pgk-2 retroposon.

The human phosphoglycerate kinase (Pgk) gene family includes the functional, intronless Pgk-2 gene and the intronless psi hPgk-1 pseudogene, both of which are retroposons of the intron-containing Pgk-1 gene. The divergence of the Pgk-2 retroposon from Pgk-1 is compared with that of the psi hPgk-1 retroposon from Pgk-1 to reveal nucleotide characteristics diagnostic of functional genes. A comparison of the human and mouse Pgk genes indicates that Pgk-2 has evolved more rapidly than Pgk-1 since the two genes diverged early in mammalian evolution, but that the lack of introns in Pgk-2 may have diminished inter-exon variation. The hypothesis that codon bias is related to expression level is shown not to hold for the Pgk genes; however, the idea that a deficiency of TA and CG dinucleotides and an excess of TG and CT dinucleotides contributes to codon bias is supported. Finally, the hypothesis that the Pgk-2 retroposon initially included a copy of the Pgk-1 'housekeeping' promoter and subsequently evolved a tissue-specific promoter is examined and supported. It is concluded that this process involved the loss of the 5' CpG island present in the Pgk-1 gene, and that selection for cell type-specific expression of Pgk-2 at high levels has driven the divergence of this retroposon from its progenitor, Pgk-1.     

Genomic diversity and population structure of Mexican and Spanish bovine Lidia breed

The Lidia bovine breed is distinguished for its low genetic exchangeability given its selection on aggressive behavior, its management uniqueness and its subdivided structure. In this study, we present a comprehensive genome‐wide analysis of genetic diversity, population structure and admixture of 468 animals from Mexican and Spanish Lidia breed populations and 64 samples belonging to 10 Spanish native and American‐creole breeds using 37 148 single nucleotide polymorphisms. We found similar average inbreeding values in the Lidia breed, with different distributions within groups; variability of inbreeding values among Spanish lineages was significant and no differences were found among the Mexican sub‐populations. Together, the high F_IS of the lineages and the behavior of the runs of homozygosity are consequences of the lineage's small effective population sizes, contributing to their inbreeding increase. Population admixture analysis discarded any influence on the genetic structure of the Lidia populations from the Spanish native and American‐creole breeds. In addition, both Lidia populations depicted different genetic origins, with the exception of some Mexican individuals whose origins traced back to recent Spanish importations.     

Genomic analysis of the 67-kDa laminin receptor in normal and pathological tissues: circumstantial evidence for retroposon features.

We have cloned two cDNAs for the human 67-kDa laminin receptor (LR). In the present report we show that these clones hybridize to many restriction fragments in Southern experiments in human. This particular pattern is accounted for by the presence of up to 16 and 21 copies of the laminin receptor gene per haploid genome in human and mouse, respectively. In contrast, a single gene copy is found in chicken. Chromosomal localization reveals four main loci: LAMRP1, laminin receptor pseudogene 1 (Chr 3); LAMRP2, laminin receptor pseudogene 2 (Chr 12); LAMRP3, laminin receptor pseudogene 3 (Chr 14); LAMRP4, laminin receptor pseudogene 4 (Chr X). Comparison of our experimental results to the known features of processed retropseudogenes enabled us to conclude that the LR gene belongs to a retroposon family in mammals.     

Using a pericentromeric interspersed repeat to recapitulate the phylogeny and expansion of human centromeric segmental duplications

Despite considerable advances in sequencing of the human genome over the past few years, the organization and evolution of human pericentromeric regions have been difficult to resolve. This is due, in part, to the presence of large, complex blocks of duplicated genomic sequence at the boundary between centromeric satellite and unique euchromatic DNA. Here, we report the identification and characterization of an approximately 49-kb repeat sequence that exists in more than 40 copies within the human genome. This repeat is specific to highly duplicated pericentromeric regions with multiple copies distributed in an interspersed fashion among a subset of human chromosomes. Using this interspersed repeat (termed PIR4) as a marker of pericentromeric DNA, we recovered and sequence-tagged 3 Mb of pericentromeric DNA from a variety of human chromosomes as well as nonhuman primate genomes. A global evolutionary reconstruction of the dispersal of PIR4 sequence and analysis of flanking sequence supports a model in which pericentromeric duplications initiated before the separation of the great ape species (>12 MYA). Further, analyses of this duplication and associated flanking duplications narrow the major burst of pericentromeric duplication activity to a time just before the divergence of the African great ape and human species (5 to 7 MYA). These recent duplication exchange events substantially restructured the pericentromeric regions of hominoid chromosomes and created an architecture where large blocks of sequence are shared among nonhomologous chromosomes. This report provides the first global view of the series of historical events that have reshaped human pericentromeric regions over recent evolutionary time.     

Ancestry of SINE-R.C2 a human-specific retroposon

We have reported previously that a retroposon, containing a variable number of tandemly repeated nucleotide sequences, is present in the third intron of the human C2 gene. This element, termed SINE-R.C2, is a member of a large retroposon family derived from the endogenous retrovirus HERV-K10 and estimated to include a few thousand copies per haploid human genome. In the present study we analyzed genomic DNA from 175 humans from several ethnic groups including Americans of European and African descent, Chinese, Africans, Australians, Pacific Islanders, Japanese, and Koreans. They all contained SINE-R.C2, as indicated by Southern blotting. However, SINE-R.C2 was absent from the genome of nonhuman primates, although SINE-R-type elements were present in chimpanzees and gorillas and the HERV-K10 genome was apparently present in all primates except for New World monkeys. These results indicate that HERV-K10 was inserted into the genome after the divergence of New World monkeys; the prototype SINE-R element, after divergence of orangutans; and SINE-R.C2, after the split between humans and chimpanzees.     

Genomic insights into the phylogeny of Bacillus strains and elucidation of their secondary metabolic potential

The genus Bacillus constitutes a plethora of species that have medical, environmental, and industrial applications. While genus Bacillus has been the focus of several studies where genomic data have been used to resolve many taxonomic issues, there still exist several ambiguities. Through the use of in-silico genome-based methods, we tried to resolve the taxonomic anomalies of a large set of Bacillus genomes (n = 178). We also proposed species names for uncharacterized strains and reported genome sequence of a novel isolate Bacillus sp. RL. In the hierarchical clustering on genome-to-genome distances, we observed 11 distinct monophyletic clusters and investigated the functional pathways annotated as the property of these clusters and core-gene content of the entire dataset. Thus, we were able to assert the possible outlier strains (n = 17) for this genus. Analyses of secondary metabolite potential of each strain helped us unravel still unexplored diversity for various biosynthetic genes.     

Genomic structure and phylogeny of the plant pathogen Ralstonia solanacearum inferred from gene distribution analysis

In the present study, we investigated the gene distribution among strains of the highly polymorphic plant pathogenic beta-proteobacterium Ralstonia solanacearum, paying particular attention to the status of known or candidate pathogenicity genes. Based on the use of comparative genomic hybridization on a pangenomic microarray for the GMI1000 reference strain, we have defined the conditions that allowed comparison of the repertoires of genes among a collection of 18 strains that are representative of the biodiversity of the R. solanacearum species. This identified a list of 2,690 core genes present in all tested strains. As a corollary, a list of 2,338 variable genes within the R. solanacearum species has been defined. The hierarchical clustering based on the distribution of variable genes is fully consistent with the phylotype classification that was previously defined from the nucleotide sequence analysis of four genes. The presence of numerous pathogenicity-related genes in the core genome indicates that R. solanacearum is an ancestral pathogen. The results establish the long coevolution of the two replicons that constitute the bacterial genome. We also demonstrate the clustering of variable genes in genomic islands. Most genomic islands are included in regions with an alternative codon usage, suggesting that they originate from acquisition of foreign genes through lateral gene transfers. Other genomic islands correspond to genes that have the same base composition as core genes, suggesting that they either might be ancestral genes lost by deletion in certain strains or might originate from horizontal gene transfers.     

Marker-derived phylogeny of European cattle supports demic expansion of agriculture

Using frequencies of 86 genes from 23 loci of blood group systems, blood and milk proteins, the genetic relationships among 14 cattle breeds including four native Balkan and four synthetic Balkan-Alp breeds were studied. The dendrogram and nonlinear map construction shows a consensus ‘Balkan breed cluster’, an ‘Alp breed cluster’, an unstable position of synthetic breeds and well-separated American breeds. Positive partial correlations between genetic distance and time elapsed since introduction of farming while keeping geographical distances constant, and regular patterns over thousands of kilometres indicate that large-scale cattle population movements together with human migration (in the Neolithic age) from the Near East into Europe across the Balkans are the most likely explanation for the genetic distances observed in our data. More recent breed differentiation and selection do not yet blur this initial pattern of European cattle populations.     

Characterization of a recent retroposon insertion on mouse Chromosome 2 and localization of the cognate parental gene to Chromosome 11

The genomic sequence on mouse Chromosome (Chr) 2 corresponding to a previously identified novel cDNA has been characterized. The genomic organization of this locus, adjacent to the beta 2 microglobulin gene, has the properties of a processed gene or retroposon including the presence of a short flanking direct repeat, a polyadenylation signal/poly A tract, and the absence of introns. Analysis of inbred and wild-derived Mus DNAs reveals the retroposon to be a feature only of M. m. domesticus subspecies, suggesting that the insertion event is relatively recent. This notion is supported by the presence of an open reading frame and the lack of sequence divergence in the flanking direct repeats. The complex chromatin configuration characteristic of this region in mouse and human is not, therefore, related to this cDNA. The cognate parental gene encoding the cDNA was mapped to Chr 11. A further, more ancient retroposon present in many Mus species localizes to Chr 17. Received: 20 June 1997 / Accepted: 30 September 1997     

Applications of imaging methodologies to paleoanthropology: Beneficial results relating to the preservation,management and development of collections

The limited number of unearthed fossils and their accessibility are factors that hinder paleoanthropological studies. Original remains, but also osteological collections of extant specimens, have to be curated in optimal and adapted environments, and direct manipulation needs to be limited in order to preserve this irreplaceable patrimony. Imaging methodologies have recently provided ways for innovative advances in the preservation of these collections, as well as offering new perspectives to museographic displays and original scientific studies. Here, we describe recent examples of developments obtained from imaging methodologies and discuss methodological and ethical implications of these new “virtual” collections. Undeniably, “virtual anthropology” is an additional tool in our large set of analytical possibilities and for curators, with its specific constraints related to the particular nature of the analysed material. Finally, we suggest some possible guidelines for the optimisation of the preservation, management and development of collections while preserving their scientific exploitation.     

Domain organization of the ORF2 C-terminal region of the German cockroach retroposon R1

Using cosmid vector, a gene library of German cockroach Blattella germanica was constructed. From this library, clones containing full-length copies of two subfamilies of R1 retroposons were selected. Retroposons R1 of German cockroach belonging to different subfamilies were shown to be different in domain organization of the ORF2 C-terminal region. For the first time, retroposons transmembrane domains were identified in the sequences of R1. It was demonstrated that two retroposon R1 subfamilies of German cockroach arose as a result of intragenomic divergence rather than via horizontal transfer of alien mobile element into cockroach genome. The differences in domain organization appeared not as a result of saltatory recombination processes, but as a consequence of gradual mutation accumulation, which led to either degeneration, or to domain formation.     

Genomic pathways database and biological data management

In this paper, we discuss the properties of biological data and challenges it poses for data management, and argue that, in order to meet the data management requirements for 'digital biology', careful integration of the existing technologies and the development of new data management techniques for biological data are needed. Based on this premise, we present PathCase: Case Pathways Database System. PathCase is an integrated set of software tools for modelling, storing, analysing, visualizing and querying biological pathways data at different levels of genetic, molecular, biochemical and organismal detail. The novel features of the system include: (i) genomic information integrated with other biological data and presented starting from pathways; (ii) design for biologists who are possibly unfamiliar with genomics, but whose research is essential for annotating gene and genome sequences with biological functions; (iii) database design, implementation and graphical tools which enable users to visualize pathways data in multiple abstraction levels and to pose exploratory queries; (iv) a wide range of different types of queries including, 'path' and 'neighbourhood queries' and graphical visualization of query outputs; and (v) an implementation that allows for web (XML)-based dissemination of query outputs (i.e. pathways data in BIOPAX format) to researchers in the community, giving them control on the use of pathways data.     

To breed or not to breed: a model of partial migration

Migration is used by a number of species as a strategy for dealing with a seasonally variable environment. In many migratory species, only some individuals migrate within a given season (migrants) while the rest remain in the same location (residents), a phenomenon called ‘partial migration’. Most examples of partial migration considered in the literature (both empirically and theoretically) fall into one of two categories: either species where residents and migrants share a breeding ground and winter apart, or species where residents and migrants share an overwintering ground and breed apart. However, a third form of partial migration can occur when non‐migrating individuals actually forgo reproduction, essentially a special form of low‐frequency reproduction. While this type of partial migration is well documented in many taxa, it is not often included in the partial migration literature, and has not been considered theoretically to date. In this paper we present a model for this partial migration scenario and determine under what conditions an individual should skip a breeding opportunity (resulting in partial migration), and under what conditions individuals should breed every chance they get (resulting in complete migration). In a constant environment, we find that partial migration is expected to occur when the mortality cost of migration is high, and when individuals can greatly increase their fecundity by skipping a year before breeding. In a stochastic environment, we find that an individual should skip migration more frequently with increased risk of a bad year (higher probability and severity), with higher mortality cost of migration, and with lower mortality cost of skipping. We discuss these results in the context of empirical data and existing life history theory.