Identification of a Novel PNMA-MS1 Gene in Marsupials Suggests the LTR Retrotransposon-Derived PNMA Genes Evolved Differently in Marsupials and Eutherians

Two major gene families derived from Ty3/Gypsy long terminal repeat (LTR) retrotransposons were recently identified in mammals. The sushi-ichi retrotransposon homologue (SIRH) family comprises 12 genes: 11 in eutherians including Peg10 and Peg11/Rtl1 that have essential roles in the eutherian placenta and 1 that is marsupial specific. Fifteen and 12 genes were reported in the second gene family, para-neoplastic antigen MA (PNMA), in humans and mice, respectively, although their biological functions and evolutionary history remain largely unknown. Here, we identified two novel candidate PNMA genes, PNMA-MS1 and -MS2 in marsupials. Like all eutherian-specific PNMA genes, they exhibit the highest homology to a Gypsy12_DR (DR, Danio rerio) Gag protein. PNMA-MS1 is conserved in both Australian and South American marsupial species, the tammar wallaby and grey short-tailed opossum. However, no PNMA-MS1 orthologue was found in eutherians, monotremes or non-mammalian vertebrates. PNMA-MS1 was expressed in the ovary, mammary gland and brain during development and growth in the tammar, suggesting that PNMA-MS1 may have acquired a marsupial-specific function. However, PNMA-MS2 seems to be a pseudogene. The absence of marsupial orthologues of eutherian PNMA genes suggests that the retrotransposition events of the Gypsy12_DR-related retrotransposons that gave rise to the PNMA family occurred after the divergence of marsupials and eutherians.     

Probable diphyletic formation of the mammalian middle ear: Monotremata and Theria

The first steps in the formation of the middle ear of the mammalian type, with the tympanum and three auditory ossicles, have only been passed by higher cynodonts. They have an incipient malleus, which developed from the anterior process of the articulare rather than the retroarticular process, which is rudimentary in cynodonts. The tympanic bone is formed of the anterior projections of the angulare. In some gorgonopians, the retroarticular process is elongated and curved anteriorly, resembling the malleus of mammals; however, this is only convergent similarity.     

Recent evidence for evolution of the genetic code.

The genetic code, formerly thought to be frozen, is now known to be in a state of evolution. This was first shown in 1979 by Barrell et al. (G. Barrell, A. T. Bankier, and J. Drouin, Nature [London] 282:189-194, 1979), who found that the universal codons AUA (isoleucine) and UGA (stop) coded for methionine and tryptophan, respectively, in human mitochondria. Subsequent studies have shown that UGA codes for tryptophan in Mycoplasma spp. and in all nonplant mitochondria that have been examined. Universal stop codons UAA and UAG code for glutamine in ciliated protozoa (except Euplotes octacarinatus) and in a green alga, Acetabularia. E. octacarinatus uses UAA for stop and UGA for cysteine. Candida species, which are yeasts, use CUG (leucine) for serine. Other departures from the universal code, all in nonplant mitochondria, are CUN (leucine) for threonine (in yeasts), AAA (lysine) for asparagine (in platyhelminths and echinoderms), UAA (stop) for tyrosine (in planaria), and AGR (arginine) for serine (in several animal orders) and for stop (in vertebrates). We propose that the changes are typically preceded by loss of a codon from all coding sequences in an organism or organelle, often as a result of directional mutation pressure, accompanied by loss of the tRNA that translates the codon. The codon reappears later by conversion of another codon and emergence of a tRNA that translates the reappeared codon with a different assignment. Changes in release factors also contribute to these revised assignments. We also discuss the use of UGA (stop) as a selenocysteine codon and the early history of the code.     

A new hypothesis on the evolution of the genetic code

Summary Starting from the assumption that specific steric and energetic interactions between amino acids and their respective anticodons could exist, the evolution of the genetic code is deduced from purely chemical and physical reasons. In this model the amino acids are intercalated between the two first anticodon bases and their carbon bound hydrogen atoms are assumed to penetrate into the electron clouds of the bases. By these means a gain in energy and a fixation of the amino acid is obtained in such a way that the anticodon nucleotides could be determinant for the nature of the amino acids.     

Facultative adjustment of mammalian sex ratios in support of the Trivers-Willard hypothesis: evidence for a mechanism

Evolutionary theory predicts that mothers of different condition should adjust the birth sex ratio of their offspring in relation to future reproductive benefits. Published studies addressing variation in mammalian sex ratios have produced surprisingly contradictory results. Explaining the source of such variation has been a challenge for sex-ratio theory, not least because no mechanism for sex-ratio adjustment is known. I conducted a meta-analysis of previous mammalian sex-ratio studies to determine if there are any overall patterns in sex-ratio variation. The contradictory nature of previous results was confirmed. However, studies that investigated indices of condition around conception show almost unanimous support for the prediction that mothers in good condition bias their litters towards sons. Recent research on the role of glucose in reproductive functioning have shown that excess glucose favours the development of male blastocysts, providing a potential mechanism for sex-ratio variation in relation to maternal condition around conception. Furthermore, many of the conflicting results from studies on sex-ratio adjustment would be explained if glucose levels in utero during early cell division contributed to the determination of offspring sex ratios.     

Evolutionary genetic models of the ovarian time bomb hypothesis for the evolution of genomic imprinting

At a small number of loci in eutherian mammals, only one of the two copies of a gene is expressed; the other is silenced. Such loci are said to be "imprinted," with some having the maternally inherited allele inactivated and others showing paternal inactivation. Several hypotheses have been proposed to explain how such a genetic system could evolve in the face of the selective advantages of diploidy. In this study, we examine the "ovarian time bomb" hypothesis, which proposes that imprinting arose through selection for reduced risk of ovarian trophoblastic disease in females. We present three evolutionary genetic models that incorporate both this selection pressure and the effect of deleterious mutations to elucidate the conditions under which imprinting could evolve. Our findings suggest that the ovarian time bomb hypothesis can explain why some growth-enhancing genes active in early embryogenesis [e.g., mouse insulin-like growth factor 2 (Igf2)] have evolved to be maternally rather than paternally inactive and why the opposite imprinting status has evolved at some growth-inhibiting loci [e.g., mouse insulin-like growth factor 2 receptor (Igf2r)].     

壳斗演化的假说及分子系统学和化石证据

壳斗作为壳斗科Fagaceae的重要特征, 其起源、演化和多样性形成长期以来为系统学家们所关注, 有众多的观点和假说。本文在综合这些假说的基础上, 结合分子系统学和大化石证据, 讨论了壳斗演化的规律。研究结果支持壳斗具枝性性质, 来源于二歧聚伞花序最外侧小枝的假说。在比较3个壳斗演化模型的基础上, 根据4种分子系统关系的一致性重建了壳斗的演化历史: 壳斗是单系起源; 水青冈属的2果4裂瓣壳斗是最早分化的壳斗类型, 三棱栎型壳斗是较晚分化的类型; 并支持具有内裂瓣的金鳞果类型壳斗可能与其他横切面为圆形的壳斗有较近的共同祖先。这一结果也得到了多个大化石证据的支持。壳斗科多个分子系统关系的一致性和壳斗化石证据共同证实了壳斗演化的规律是从开裂向裂瓣融合、逐步简化、多向发展; 支持开裂壳斗、坚果三角形、较小、具棱或狭翅是祖征, 融合壳斗、坚果圆形、较大、不具棱是衍征。这些结果为进一步探索壳斗科的演化历史和系统发育提供了新的证据。     

Complete-genome phylogenetic approach to varicella-zoster virus evolution: genetic divergence and evidence for recombination

Recent studies of varicella-zoster virus (VZV) DNA sequence variation, involving large numbers of globally distributed clinical isolates, suggest that this virus has diverged into at least three distinct genotypes designated European (E), Japanese (J), and mosaic (M). In the present study, we determined and analyzed the complete genomic sequences of two M VZV strains and compared them to the sequences of three E strains and two J strains retrieved from GenBank (including the Oka vaccine preparation, V-Oka). Except for a few polymorphic tandem repeat regions, the whole genome, representing approximately 125,000 nucleotides, is highly conserved, presenting a genetic similarity between the E and J genotypes of approximately 99.85%. These analyses revealed that VZV strains distinctly segregate into at least four genotypes (E, J, M1, and M2) in phylogenetic trees supported by high bootstrap values. Separate analyses of informative sites revealed that the tree topology was dependent on the region of the VZV genome used to determine the phylogeny; collectively, these results indicate the observed strain variation is likely to have resulted, at least in part, from interstrain recombination. Recombination analyses suggest that strains belonging to the M1 and M2 genotypes are mosaic recombinant strains that originated from ancestral isolates belonging to the E and J genotypes through recombination on multiple occasions. Furthermore, evidence of more recent recombination events between M1 and M2 strains is present in six segments of the VZV genome. As such, interstrain recombination in dually infected cells seems to figure prominently in the evolutionary history of VZV, a feature it has in common with other herpesviruses. In addition, we report here six novel genomic targets located in open reading frames 51 to 58 suitable for genotyping of clinical VZV isolates.     

An hypothesis and evidence concerning the genetic components controlling tumor formation in Nicotiana

Summary The evidence discussed in this paper demonstrates unuqual genetic contribution of N. debneyi-tabacum and N. longiflora to the development of tumors in hybrids between them. Tumor formation depends upon the presence of a specific longiflora chromosome fragment in an otherwise debneyi-tabacum background and consequently is transmitted as a dominant trait. Tumor expression remains relatively constant among those segregants which carry the complete complements of N. debneyi-tabacum or N. tabacum along with the longiflora chromosome, but tumors fail to develop on plants with a few debneyi chromosomes on a diploid longiflora background. These results suggest that gene(s) on a single longiflora chromosome fragment are sufficient, whereas from N. debneyi or N. tabacum a large number of genes distributed over many chromosomes are required for tumor formation. An hypothesis concerning genetic components controlling tumor initiation (I) and expression (ee) is proposed, supported by these observations, and by previous studies both genetic and physiological, on another tumorous hybrid between N. glauca and N. langsdorffii. (I) and (ee), representing unequal contributions from two evolutionarily diverse species, must both be present in the hybrid for tumors to develop. Evidence is presented to indicate that N. longiflora and N. langsdorffii, belonging to the section Alatae, represent species carrying (I) and that N. debneyi, N. tabacum and N. glauca, belonging to different sections of the genus Nicotiana, are (ee) carriers. It is predicted that genetic analyses will reveal that the genes for tumor initiation (I) will be carried invariably by species of the section Alatae, or the so-called plus group of Näf, and genes modifying expression (ee) by species from other sections but belonging to the so-called minus group. Specific characterization of (I) and (ee) in biochemical terms is under investigation.     

Age-specific reproductive success: evidence for the selection hypothesis

Age-specific reproductive success has been demonstrated in many species. Three hypotheses have been raised to explain this general phenomenon: the experience hypothesis based on age-specific reproductive experience, the effort hypothesis based on age-specific reproductive effort, and the selection hypothesis based on progressive disappearance of phenotypes due to variation in individual productivity and survival. We used data from a long-term study of Leach's storm-petrels (Oceanodroma leucorhoa) to present a single test of mutually exclusive predictions about the relationship between early breeding success and longevity. There should be no correlation between early breeding success and longevity under the experience hypothesis, a negative correlation under the effort hypothesis, and a positive correlation under the selection hypothesis. We found a significant (P < 0.0001) positive relationship between success in the first two breeding attempts and longevity in this population of long-lived seabirds, strongly suggesting that low-productivity parents were also less likely to survive early breeding. These data provide some of the strongest support to date for the selection hypothesis.     

Moving up the hierarchy: A hypothesis on the evolution of a genetic sex determination pathway

A hypothesis on the evolutionary origin of the genetic pathway of sex determination in the nematode Caenorhabditis elegans is presented here. It is suggested that the pathway arose in steps, driven by frequency-dependent selection for the minority sex at each step, and involving the sequential acquisition of dominant negative, neomorphic genetic switches, each one reversing the action of the previous one. A central implication is that the genetic pathway evolved in reverse order from the final step in the hierarchy up to the first. The possible applicability of the model to the other well-characterized sex determination pathway, that of Drosophila melanogaster, and to sex determination in mammals, is discussed, along with some potential implications for pathway evolution in general. Finally, the specific molecular and population genetic questions that the model raises are described and some tests are proposed.     

Energetic trade-offs between brain size and offspring production: Marsupials confirm a general mammalian pattern

Recently, Weisbecker and Goswami presented the first comprehensive comparative analysis of brain size, metabolic rate, and development periods in marsupial mammals. In this paper, a strictly energetic perspective is applied to identify general mammalian correlates of brain size evolution. In both marsupials and placentals, the duration or intensity of maternal investment is a key correlate of relative brain size, but here I show that allomaternal energy subsidies may also play a role. In marsupials, an energetic constraint on brain size in adults is only revealed if we consider both metabolic and reproductive rates simultaneously, because a strong trade-off between encephalization and offspring production masks the positive correlation between basal metabolic rate and brain size in a bivariate comparison. In conclusion, starting from an energetic perspective is warranted to elucidate relations between ecology, social systems, life history, and brain size in all mammals.     

A hypothesis for the evolution of sex

Summary Sex is one of the most creative of the major transitions in Evolution and its existence allows faster and wider mobility of species in the ‘History of Life’. We postulate that sex evolved from prokaryotes in the tail of the fitness distribution curve for a given environment. Once sex was established we have the potential for the evolution of species and the rich flowering of organisms in a relatively short period of time.     

The Opossum genome reveals further evidence for regulatory evolution in mammalian diversification

The sequencing of the euchromatic genome of a marsupial, the opossum Monodelphis domestica, identifies shared and unique features of marsupial and placental genomes and reveals a prominent role for the evolution of non-protein-coding elements.