Deletion bias in avian introns over evolutionary timescales

The role that introns play in the function and evolution of nuclear genomes is not fully understood. Recent models of intron evolution suggest that selection and drift may interact to maintain introns in multicellular organisms. In addition, deletion mutations are more likely to become fixed than insertion mutations. Examination of indel substitutions over macroevolutionary timescales in pigeons and doves (Aves: Columbiformes) reveals that deletion substitutions outnumber insertion substitutions by over six times. The length of indel events is variable.     

Evolution of beta satellite DNA sequences: evidence for duplication-mediated repeat amplification and spreading

In this article, we report studies on the evolutionary history of beta satellite repeats (BSR) in primates. In the orangutan genome, the bulk of BSR sequences was found organized as very short stretches of approximately 100 to 170 bp, embedded in a 60-kb to 80-kb duplicated DNA segment. The estimated copy number of the duplicon that carries BSR sequences ranges from 70 to 100 per orangutan haploid genome. In both macaque and gibbon, the duplicon mapped to a single chromosomal region at the boundary of the rDNA on the marker chromosome (chromosome 13 and 12, respectively). However, only in the gibbon, the duplicon comprised 100 bp of beta satellite. Thus, the ancestral copy of the duplicon appeared in Old World monkeys ( approximately 25 to approximately 35 MYA), whereas the prototype of beta satellite repeats took place in a gibbon ancestor, after apes/Old World monkeys divergence ( approximately 25 MYA). Subsequently, a burst in spreading of the duplicon that carries the beta satellite was observed in the orangutan, after lesser apes divergence from the great apes-humans lineage ( approximately 18 MYA). The analysis of the orangutan genome also indicated the existence of two variants of the duplication that differ for the length (100 or 170 bp) of beta satellite repeats. The latter organization was probably generated by nonhomologous recombination between two 100-bp repeated regions, and it likely led to the duplication of the single Sau3A site present in the 100-bp variant, which generated the prototype of Sau3A 68-bp beta satellite tandem organization. The two variants of the duplication, although with a different ratios, characterize the hominoid genomes from the orangutan to humans, preferentially involving acrocentric chromosomes. At variance to alpha satellite, which appeared before the divergence of New World and Old World monkeys, the beta satellite evolutionary history began in apes ancestor, where we have first documented a low-copy, nonduplicated BSR sequence. The first step of BSR amplification and spreading occurred, most likely, because the BSR was part of a large duplicon, which underwent a burst dispersal in great apes' ancestor after the lesser apes' branching. Then, after orangutan divergence, BSR acquired the clustered structural organization typical of satellite DNA.     

Retrotransposon-gene associations are widespread among D. melanogaster populations

We have surveyed 18 natural populations of Drosophila melanogaster for the presence of 23 retrotransposon-gene-association alleles (i.e., the presence of an LTR retrotransposon sequence in or within 1,000 bp of a gene) recently identified in the sequenced D. melanogaster genome. The identified associations were detected only in the D. melanogaster populations. The majority (61%) of the identified retrotransposon-gene associations were present only in the sequenced strain in which they were first identified. Thirty percent of the associations were detected in at least one of the natural populations, and 9% of the associations were detected in all of the D. melanogaster populations surveyed. Sequence analysis of an association allele present in all populations indicates that selection is a significant factor in the spread and/or maintenance of at least some of retroelement-gene associations in D. melanogaster.     

Positive selection at reproductive ADAM genes with potential intercellular binding activity

Many genes with a role in reproduction, including those implicated in fertilization and spermatogenesis, have been shown to evolve at a faster rate relative to genes associated with other functions and tissues. These survey studies usually group a wide variety of genes with different characteristics and evolutionary histories as reproductive genes based on their site of expression or function. We have examined the molecular evolution of the ADAM (a disintegrin and metalloprotease) gene family, a structurally and functionally diverse group of genes expressed in reproductive and somatic tissue to test whether a variety of protein characteristics such as phylogenetic clusters, tissue of expression, and proteolytic and adhesive function can group fast evolving ADAM genes. We found that all genes were evolving under purifying selection (d(N)/d(S) < 1), although reproductive ADAMs, including those implicated in fertilization and spermatogenesis, evolved at the fastest rate. Genes with a role in binding to cell receptors in endogenous tissue appear to be evolving under purifying selection, regardless of the tissue of expression. In contrast, positive selection of codon sites in the disintegrin/cysteine-rich adhesion domains was detected exclusively in ADAMs 2 and 32, two genes expressed in the testis with a potential role in sperm-egg adhesion. Positive selection was detected in the transmembrane/cytosolic tail region of ADAM genes expressed in a variety of tissues.     

Modifications of the falciform process in the eye of beloniformes (Teleostei: Atherinomorpha): evolution of a curtain-like septum in the eye

In order to comparatively analyze curtain-like septa in the eyes of visually orientated "close-to-surface-predators" among atherinomorph teleosts, we examined the eyes of 24 atherinomorph species under a binocular microscope with regard to the falciform process and related structures in the vitreous cavity. Additionally, falciform process samples were analyzed by transmission electron microscopy. All the studied representatives of the Cyprinodontiformes and Atheriniformes, and of one of the beloniform suborder, Adrianichthyioidei, possess a "typical" processus falciformis. In the eyes of the representatives of the other beloniform suborder, Belonoidei, however, pigmented structures that originate in the region of the optic disc and protrude into the vitreous cavity were noted. In the Hemiramphidae (halfbeaks) and Exocoetidae (flying fishes) these pigmented structures have a more cone-like shape, whereas in the Belonidae (needlefishes) and Scomberesocidae (sauries) horizontally oriented heavily pigmented curtain-like septa occur that divide the vitreous cavity dorsoventrally. It is suggested that the "typical" processus falciformis represents a plesiomorphic feature within the Atherinomorpha, whereas the pigmented modifications of the falciform process must be seen as a synapomorphic character state of the Belonoidei. The curtain-like septum of the Belonidae and Scomberesocidae might have evolved from the cone-like structures that are found in the Exocoetoidea. The functional significance of the pigmented structures in the eye is as yet not clear, except for the curtain-like septum found in Belonidae. It might play a role in visual orientation near the water surface at Snell's window.     

Marsupial relationships and a timeline for marsupial radiation in South Gondwana

Recent marsupials include about 280 species divided into 18 families and seven orders. Approximately 200 species live in Australia/New Guinea. The remaining species inhabit South America with some of these secondarily ranging into North America. In this study, we examine marsupial relationships and estimate their divergences times using complete mitochondrial (mt) genomes. The sampling, which includes nine new mtDNAs and a total number of 19 marsupial genomes, encompasses all extant orders and 14 families. The analysis identified a basal split between Didelphimorphia and remaining orders about 69 million years before present (MYBP), while other ordinal divergences were placed in Tertiary times. The monotypic South American order Microbiotheria (Dromiciops gliroides, Monito del Monte) was solidly nested among its Australian counterparts. The results suggest that marsupials colonized Australia twice from Antarctica/South America and that the divergence between Microbiotheria and its Australian relatives coincided with the geological separation of Antarctica and Australia. Within Australia itself, several of the deepest divergences were estimated to have taken place close to the Eocene/Oligocene transition.     

AFLP analysis of phylogenetic relationships among myrmecophytic species of Macaranga (Euphorbiaceae) and their allies

The palaeotropic pioneer tree genus Macaranga Thouars (Euphorbiaceae) is characterized by various types of mutualistic interactions with specific ant partners (mainly Crematogaster spp.). About 30 species are obligate ant-plants (myrmecophytes). We used amplified fragment length polymorphism (AFLP) markers to assess phylogenetic relationships among 108 Macaranga specimens from 43 species, including all available taxa from the three sections known to contain myrmecophytes. Eight primer combinations produced 426 bands that were scored as presence/absence characters. Banding patterns were analyzed phenetically, cladistically and by principal coordinates analysis. Monophyly of section Pruinosae is clearly supported. There is also good evidence for a monophyletic section Pachystemon that includes the puncticulata group. The monophyly of section Winklerianae and relationships between the three sections remain ambiguous. Section Pachystemon is subdivided into four well-supported monophyletic subclades that presumably correspond to taxonomic entities.We acknowledge the support by the Deutsche Forschungsgemeinschaft (DFG Fi606/4-1, DFG We1830/2-1, 4-1 and 4-2), which in part was granted in the frame of the DFG-SPP 1127 Radiations: origins of biological diversity. Part of the plant material was kindly supplied by Dr. H. Feldhaar (University of Würzburg), Dr. U. Moog (University of Kassel) and Dr. F. Slik (Leiden University Branch, Nationaal Herbarium Nederland). We thank the University of Malaysia (Dr. Rosli b. Hashim) and Taman Taman Sabah (Datuk Lamri Ali; Dr. J. Nais) for permits and logistic support, and EPU for permission to conduct research in Malaysia.