Identification of an ancient endogenous retrovirus,predating the divergence of the placental mammals

The evolutionary arms race between mammals and retroviruses has long been recognized as one of the oldest host–parasite interactions. Rapid evolution rates in exogenous retroviruses have often made accurate viral age estimations highly problematic. Endogenous retroviruses (ERVs), however, integrate into the germline of their hosts, and are subjected to their evolutionary rates. This study describes, for the first time, a retroviral orthologue predating the divergence of placental mammals, giving it a minimum age of 104–110 Myr. Simultaneously, other orthologous selfish genetic elements (SGEs), inserted into the ERV sequence, provide evidence for the oldest individual mammalian-wide interspersed repeat and medium-reiteration frequency interspersed repeat mammalian repeats, with the same minimum age. The combined use of shared SGEs and reconstruction of viral orthologies defines new limits and increases maximum ‘lookback’ times, with subsequent implications for the field of paleovirology.     

Molecular evidence on plant divergence times

Estimation of divergence times from sequence data has become increasingly feasible in recent years. Conflicts between fossil evidence and molecular dates have sparked the development of new methods for inferring divergence times, further encouraging these efforts. In this paper, available methods for estimating divergence times are reviewed, especially those geared toward handling the widespread variation in rates of molecular evolution observed among lineages. The assumptions, strengths, and weaknesses of local clock, Bayesian, and rate smoothing methods are described. The rapidly growing literature applying these methods to key divergence times in plant evolutionary history is also reviewed. These include the crown group ages of green plants, land plants, seed plants, angiosperms, and major subclades of angiosperms. Finally, attempts to infer divergence times are described in the context of two very different temporal settings: recent adaptive radiations and much more ancient biogeographic patterns.     

Evolution of the placenta during the early radiation of placental mammals

The chorioallantoic placenta is an organ of gaseous exchange that exhibits a high degree of structural diversity. One factor determining oxygen transfer across the placenta, the diffusion distance, is in part dependent on the number of cell layers separating maternal from fetal blood. This interhaemal barrier occurs in three principal variants. The focus of this review is on determining how the barrier evolved in placental mammals. The analysis was based on current knowledge of placental structure, as far as possible using ultrastructural data, and on current views about the evolution of placental mammals, derived from molecular phylogenetics. We show that epitheliochorial placentation, the least invasive type, is a derived state and discuss factors that may have determined its evolution with reference to conflict theory, as applied to the allocation of resources between mother and fetus. It is not yet possible to determine which of the two more invasive types of placentation occurred in the last common ancestor of crown placentals. Depending on tree topology and taxon sampling, the result achieved is either endotheliochorial, haemochorial or unresolved. Finally we discuss other factors important to placental gas exchange and point to physiological variables that might become amenable to phylogenetic analysis.     

Molecular evidence for deep phylogenetic divergence in Mandrillus sphinx

Mandrills (Mandrillus sphinx) are forest primates indigenous to western central Africa. Phylogenetic analysis of 267 base pairs (bp) of the cytochrome b gene from 53 mandrills of known and 17 of unknown provenance revealed two phylogeographical groups, with haplotypes differentiated by 2.6% comprising seven synonymous transitions. The distribution of the haplotypes suggests that the Ogooué River, Gabon, which bisects their range, separates mandrill populations in Cameroon and northern Gabon from those in southern Gabon. The haplotype distribution is also concordant with that of two known mandrill simian immunodeficiency viruses, suggesting that these two mandrill phylogroups have followed different evolutionary trajectories since separation.     

Morphofunctional characteristics of the lipids in the early embryogeny of placental mammals]

The comparative cytological study of lipids points to species specific character of lipid metabolism in early embryogenesis of placentate mammals. The general level of lipid metabolism is genetically determined in oogenesis being expressed by different loading of the ooplasm with substances of lipoid nature. At the cleavage stage lipids play a plastic role. Their significance as functionally active complexes is manifested in the period of the blastocyst formation, which is dependent on morphological differentiation and the beginning of the trophoblast functioning as an early metabolic organ.     

Molecular and functional evidence for early divergence of an endothelin-like system during metazoan evolution: analysis of the Cnidarian, hydra

A novel putative endothelin-converting enzyme (ECE) has been cloned from hydra, a freshwater invertebrate that belongs to the second oldest phylum of the animal kingdom. As an integral component of the endothelin system, vertebrate ECE functions in the activation of endothelin (ET) peptides. Vertebrate ETs are (1) the most potent vasoconstrictors known in mammals; and (2) function as essential signaling ligands during development of tissues derived from neural crest cells. To date, only a limited number of immunocytochemical studies have suggested the presence of endothelin-like peptides in invertebrates. Based on structural and functional analyses, we present evidence for a functional endothelin-like system in hydra that is involved in both muscle contraction and developmental processes. These findings indicate the broad use of endothelin systems in metazoans and also indicate that this type of signaling system arose early in evolution even before divergence of protostomes and deuterostomes.     

Joint reconstruction of divergence times and life-history evolution in placental mammals using a phylogenetic covariance model

Violation of the molecular clock has been amply documented, and is now routinely taken into account by molecular dating methods. Comparative analyses have revealed a systematic component in rate variation, relating it to the evolution of life-history traits, such as body size or generation time. Life-history evolution can be reconstructed using Brownian models. However, the resulting estimates are typically uncertain, and potentially sensitive to the underlying assumptions. As a way of obtaining more accurate ancestral trait and divergence time reconstructions, correlations between life-history traits and substitution rates could be used as an additional source of information. In this direction, a Bayesian framework for jointly reconstructing rates, traits, and dates was previously introduced. Here, we apply this model to a 17 protein-coding gene alignment for 73 placental taxa. Our analysis indicates that the coupling between molecules and life history can lead to a reevaluation of ancestral life-history profiles, in particular for groups displaying convergent evolution in body size. However, reconstructions are sensitive to fossil calibrations and to the Brownian assumption. Altogether, our analysis suggests that further integrating inference of rates and traits might be particularly useful for neontological macroevolutionary comparative studies.     

Molecular dating and biogeography of the early placental mammal radiation

The timing and phylogenetic hierarchy of early placental mammal divergences was determined based on combined DNA sequence analysis of 18 gene segments (9779 bp) from 64 species. Using rooted and unrooted phylogenies derived from distinct theoretical approaches, strong support for the divergence of four principal clades of eutherian mammals was achieved. Minimum divergence dates of the earliest nodes in the placental mammal phylogeny were estimated with a quartet-based maximum-likelihood method that accommodates rate variation among lineages using conservative fossil calibrations from nine different nodes in the eutherian tree. These minimum estimates resolve the earliest placental mammal divergence nodes at periods between 64 and 104 million years ago, in essentially every case predating the Cretaceous-Tertiary (K-T) boundary. The pattern and timing of these divergences allow a geographic interpretation of the primary branching events in eutherian history, likely originating in the southern supercontinent Gondwanaland coincident with its breakup into Africa and South America 95-105 million years ago. We propose an integrated genomic, paleontological, and biogeographic hypothesis to account for these earliest splits on the placental mammal family tree and address current discrepancies between fossil and molecular evidence.     

Resolving the relationships of Paleocene placental mammals

The ‘Age of Mammals’ began in the Paleocene epoch, the 10 million year interval immediately following the Cretaceous–Palaeogene mass extinction. The apparently rapid shift in mammalian ecomorphs from small, largely insectivorous forms to many small‐to‐large‐bodied, diverse taxa has driven a hypothesis that the end‐Cretaceous heralded an adaptive radiation in placental mammal evolution. However, the affinities of most Paleocene mammals have remained unresolved, despite significant advances in understanding the relationships of the extant orders, hindering efforts to reconstruct robustly the origin and early evolution of placental mammals. Here we present the largest cladistic analysis of Paleocene placentals to date, from a data matrix including 177 taxa (130 of which are Palaeogene) and 680 morphological characters. We improve the resolution of the relationships of several enigmatic Paleocene clades, including families of ‘condylarths’. Protungulatum is resolved as a stem eutherian, meaning that no crown‐placental mammal unambiguously pre‐dates the Cretaceous–Palaeogene boundary. Our results support an Atlantogenata–Boreoeutheria split at the root of crown Placentalia, the presence of phenacodontids as closest relatives of Perissodactyla, the validity of Euungulata, and the placement of Arctocyonidae close to Carnivora. Periptychidae and Pantodonta are resolved as sister taxa, Leptictida and Cimolestidae are found to be stem eutherians, and Hyopsodontidae is highly polyphyletic. The inclusion of Paleocene taxa in a placental phylogeny alters interpretations of relationships and key events in mammalian evolutionary history. Paleocene mammals are an essential source of data for understanding fully the biotic dynamics associated with the end‐Cretaceous mass extinction. The relationships presented here mark a critical first step towards accurate reconstruction of this important interval in the evolution of the modern fauna.     

The evolution of placental mammals.

Based on morphological, virological, biochemical and molecular biological data, it is proposed that the presence of endogenous retrovirus particles in the placental cytotrophoblasts of many mammals is indicative of some beneficial action provided by the virus in relation to cell fusion, syncytiotrophoblast formation and the creation of the placenta. Further, it is hypothesised that the germ line retroviral infection of some primitive mammal-like species resulted in the evolution of the placental mammals.     

Sex chromosomes of basal placental mammals

Placental (eutherian) mammals are currently classified into four superordinal clades (Afrotheria, Xenarthra, Laurasiatheria and Supraprimates) of which one, the Afrotheria (a unique lineage of African origin), is generally considered to be basal. Therefore, Afrotheria provide a pivotal evolutionary link for studying fundamental differences between the sex chromosomes of human/mouse (both representatives of Supraprimates and the index species for studies of sex chromosomes) and those of the distantly related marsupials. In this study, we use female fibroblasts to investigate classical features of X chromosome inactivation including replication timing of the X chromosomes and Barr body formation. We also examine LINE-1 accumulation on the X chromosomes of representative afrotherians and look for evidence of a pseudoautosomal region (PAR). Our results demonstrate that asynchronous replication of the X chromosomes is common to Afrotheria, as with other mammals, and Barr body formation is observed across all Placentalia, suggesting that mechanisms controlling this evolved before their radiation. Finally, we provide evidence of a PAR (which marsupials lack) and demonstrate that LINE1 is accumulated on the afrotherian and xenarthran X, although this is probably not due to transposition events in a common ancestor, but rather ongoing selection to retain recently inserted LINE1 on the X.     

Ovum lipids of placental mammals]

Morphocytochemical peculiarities of lipids from oocytes of some mammals and man were studied. The human oocytes, according to the structure and content of yolk, bear a close relation to a hare and a rabbit much differing from gametes of predatory animals (dog, cat), artiodactyla (sow), rodents (golden hamster). By thin layer chromatography on silicagel, a detailed lipid composition was established in the rabbit's oocytes, with neutral lipid and phospholipids (kefalin, lecitin, sfingomyelin) dominating. In addition, cholesterin was found.     

Retroposed elements as archives for the evolutionary history of placental mammals

Reconstruction of the placental mammalian (eutherian) evolutionary tree has undergone diverse revisions, and numerous aspects remain hotly debated. Initial hierarchical divisions based on morphology contained many misgroupings due to features that evolved independently by similar selection processes. Molecular analyses corrected many of these misgroupings and the superordinal hierarchy of placental mammals was recently assembled into four clades. However, long or rapid evolutionary periods, as well as directional mutation pressure, can produce molecular homoplasies, similar characteristics lacking common ancestors. Retroposed elements, by contrast, integrate randomly into genomes with negligible probabilities of the same element integrating independently into orthologous positions in different species. Thus, presence/absence analyses of these elements are a superior strategy for molecular systematics. By computationally scanning more than 160,000 chromosomal loci and judiciously selecting from only phylogenetically informative retroposons for experimental high-throughput PCR applications, we recovered 28 clear, independent monophyly markers that conclusively verify the earliest divergences in placental mammalian evolution. Using tests that take into account ancestral polymorphisms, multiple long interspersed elements and long terminal repeat element insertions provide highly significant evidence for the monophyletic clades Boreotheria (synonymous with Boreoeutheria), Supraprimates (synonymous with Euarchontoglires), and Laurasiatheria. More importantly, two retropositions provide new support for a prior scenario of early mammalian evolution that places the basal placental divergence between Xenarthra and Epitheria, the latter comprising all remaining placentals. Due to its virtually homoplasy-free nature, the analysis of retroposon presence/absence patterns avoids the pitfalls of other molecular methodologies and provides a rapid, unequivocal means for revealing the evolutionary history of organisms.     

Strong morphological support for the molecular evolutionary tree of placental mammals

The emerging molecular evolutionary tree for placental mammals differs greatly from morphological trees, leading to repeated suggestions that morphology is uninformative at this level. This view is here refuted empirically, using an extensive morphological and molecular dataset totalling 17 431 characters. When analysed alone, morphology indeed is highly misleading, contradicting nearly every clade in the preferred tree (obtained from the molecular or the combined data). Widespread homoplasy overrides historical signal. However, when added to the molecular data, morphology surprisingly increases support for most clades in the preferred tree. The homoplasy in the morphology is incongruent with all aspects of the molecular signal, while the historical signal in the morphology is congruent with (and amplifies) the historical signal in the molecular data. Thus, morphology remains relevant in the genomic age, providing vital independent corroboration of the molecular tree of mammals.     

Molecular phylogenetic evidence for ancient divergence of lizard taxa on either side of Wallace's Line

Wallace's Line, separating the terrestrial faunas of South East Asia from the Australia-New Guinea region, is the most prominent and well-studied biogeographical division in the world. Phylogenetically distinct subgroups of major animal and plant groups have been documented on either side of Wallace's Line since it was first proposed in 1859. Despite its importance, the temporal history of fragmentation across this line is virtually unknown and the geological foundation has rarely been discussed. Using molecular phylogenetics and dating techniques, we show that the split between taxa in the South East Asian and the Australian-New Guinean geological regions occurred during the Late Jurassic to Early Cretaceous in two independent lizard clades. This estimate is compatible with the hypothesis of rifting Gondwanan continental fragments during the Mesozoic and strongly rejects the hypothetical origin of various members of the Australian-New Guinean herpetofauna as relatively recent invasions from South East Asia. Our finding suggests an ancient fragmentation of lizard taxa on either side of Wallace's Line and provides further evidence that the composition of modern global communities has been significantly affected by rifting and accretion of Gondwanan continental plates during the Middle to Late Mesozoic.