Afrotheria: plate tectonics meets genomics

NOX family NADPH oxidases in mammals: Evolutionary conservation and isoform-defining sequences

NADPH oxidases are superoxide-producing enzymes that play a role in host defense, biosynthetic pathways, as well as cellular signaling. Humans have 7 NOX isoforms (NOX1-5, DUOX1,2), while mice and rats lack NOX5 and therefore have only 6 NOX isoforms. Whether all human NOX isoforms or their subunits (CYBA, NCF1, 2, 4, NOXO1, NOXA1, DUOXA1, 2) are present and conserved in other mammalian species is unknown. In this study, we have analyzed the conservation of the NOX family during mammalian evolution using an in-silico approach. Complete genomic sequences of 164 mammalian species were available. The possible absence of genes coding for NOX isoforms was investigated using the NCBI orthologs database followed by manual curation. Conservation of a given NOX isoform during mammalian evolution was evaluated by multiple alignment and identification of highly conserved sequences. There was no convincing evidence for the absence of NOX2, 3, 4, and DUOX1, 2 in all the available mammalian genome. However, NOX5 was absent in 27 of 31 rodent, in 2 of 3 lagomorph and in 2 out of 18 bat species. NOX1 was absent in all sequenced Afrotheria and Monotremata species, as well as in 3 of 18 bat species. NOXA1 was absent in all Afrotheria and in 3 out of 4 Eulipotyphla species. We also investigated amino acid sequence conservation among given NOX isoforms. Highly conserved sequences were observed for most isoforms except for NOX5. Interestingly, the highly conserved region of NOX2 sequence was relatively small (11 amino acids), as compared to NOX1, 3, 4. The highly conserved domains are different from one NOX isoform to the other, raising the possibility of distinct evolutionary conserved functional domains. Our results shed a new light on the essentiality of different NOX isoforms. We also identified isoform-defining sequences, i.e., hitherto undescribed conserved domains within specific NOX isoforms.

Phylogenomic analyses reveal a Gondwanan origin and repeated out of India colonizations into Asia by tarantulas (Araneae: Theraphosidae)

The study of biogeography seeks taxa that share a key set of characteristics, such as timescale of diversification, dispersal ability, and ecological lability. Tarantulas are ideal organisms for studying evolution over continental-scale biogeography given their time period of diversification, their mostly long-lived sedentary lives, low dispersal rate, and their nevertheless wide circumtropical distribution. In tandem with a time-calibrated transcriptome-based phylogeny generated by PhyloBayes, we estimate the ancestral ranges of ancient tarantulas using two methods, DEC+j and BBM, in the context of their evolution. We recover two ecologically distinct tarantula lineages that evolved on the Indian Plate before it collided with Asia, emphasizing the evolutionary significance of the region, and show that both lineages diversified across Asia at different times. The most ancestral tarantulas emerge on the Americas and Africa 120 Ma-105.5 Ma. We provide support for a dual colonization of Asia by two different tarantula lineages that occur at least 20 million years apart, as well as a Gondwanan origin for the group. We determine that their current distributions are attributable to a combination of Gondwanan vicariance, continental rafting, and geographic radiation. We also discuss emergent patterns in tarantula habitat preferences through time.

Phylogenomics and the Genetic Architecture of the Placental Mammal Radiation

The genomes of placental mammals are being sequenced at an unprecedented rate. Alignments of hundreds, and one day thousands, of genomes spanning the rich living and extinct diversity of species offer unparalleled power to resolve phylogenetic controversies, identify genomic innovations of adaptation, and dissect the genetic architecture of reproductive isolation. We highlight outstanding questions about the earliest phases of placental mammal diversification and the promise of newer methods, as well as remaining challenges, toward using whole genome data to resolve placental mammal phylogeny. The next phase of mammalian comparative genomics will see the completion and application of finished-quality, gapless genome assemblies from many ordinal lineages and closely related species. Interspecific comparisons between the most hypervariable genomic loci will likely reveal large, but heretofore mostly underappreciated, effects on population divergence, morphological innovation, and the origin of new species.

Are there phylogenetic differences in salivary tannin-binding proteins between browsers and grazers, and ruminants and hindgut fermenters?

While feeding, mammalian browsers (primarily eat woody plants) encounter secondary metabolites such as tannins. Browsers may bind these tannins using salivary proteins, whereas mammalian grazers (primarily eat grasses that generally lack tannins) likely would not. Ruminant browsers rechew their food (ruminate) to increase the effectiveness of digestion, which may make them more effective at binding tannins than nonruminants. Few studies have included a sufficient number of species to consider possible scaling with body mass or phylogenetic effects on salivary proteins. Controlling for phylogeny, we ran inhibition radial diffusion assays of the saliva of 28 species of African herbivores that varied in size, feeding strategy, and digestive system. We could not detect the presence of salivary proline-rich proteins that bind tannins in any of these species. However, using the inhibition radial diffusion assay, we found considerable abilities to cope with tannins in all species, albeit to varying degrees. We found no differences between browsers and grazers in the effectiveness of their salivary proteins to bind to and precipitate tannins, nor between ruminants and nonruminants, or scaling with body mass. Three species bound all tannins, but their feeding niches included one browser (gray duiker), one mixed feeder (bush pig), and one grazer (red hartebeest). Five closely related species of small ruminant browsers were very effective in binding tannins. Megaherbivores, considered generalists on account of their large body size, were capable of binding tannins. However, the grazing white rhinoceros was almost as effective at binding tannins as the megaherbivore browsers. We conclude, contrary to earlier predictions, that there were no differences in the relative salivary tannin-binding capability that was related to common ancestry (phylogeny) or to differences in body size.

Lineage-independent retrotransposition of UTP14 associated with male fertility has occurred multiple times throughout mammalian evolution

In mammals, gamete production is essential for reproductive success. This is particularly true for males where large quantities of sperm are produced to fertilize a limited number of eggs released by the female. Because of this, new genes associated with increased spermatogenic efficiency have been accumulating throughout the evolution of therian mammals. Many of these new genes are testis-specific retrotransposed copies of housekeeping genes located on the X chromosome. Of particular interest are retrotransposed copies of UTP14 that are present in many distantly related eutherian mammals. Analysis of genomic data available in ENSEMBL indicates that these UTP14 retrogenes have arisen independently in the various eutherian clades. They represent an interesting aspect of evolution whereby new homologues of UTP14 have become independently fixed in multiple mammalian lineages due to the reproductive advantage that may be conferred to males. Surprisingly, these genes may also be lost, even after being present within a lineage for millions of years. This phenomenon may potentially be used to delineate evolutionary trees in closely related groups of mammals, particularly in the case of South American primates. Studying these retrogenes will yield new insights into the evolutionary history of male gamete production and the phylogeny of eutherian mammals.

The evolution of micro-cursoriality in mammals

In this study we report on the evolution of micro-cursoriality, a unique case of cursoriality in mammals smaller than 1 kg. We obtained new running speed and limb morphology data for two species of elephant-shrews (Elephantulus spp., Macroscelidae) from Namaqualand, South Africa, which we compared with published data for other mammals. Elephantulus maximum running speeds were higher than most mammals smaller than 1 kg. Elephantulus also possess exceptionally high metatarsal:femur ratios (1.07) that are typically associated with fast unguligrade cursors. Cursoriality evolved in the Artiodactyla, Perissodactyla, and Carnivora coincident with global cooling and the replacement of forests with open landscapes in the Oligocene and Miocene. The majority of mammal species, though, remained non-cursorial, plantigrade, and small (< 1 kg). The extraordinary running speed and digitigrady of elephant-shrews was established in the Early Eocene in the earliest macroscelid Prodiacodon, but was probably inherited from Paleocene, Holarctic stem macroscelids. Micro-cursoriality in macroscelids evolved from the plesiomorphic plantigrade foot of the possum-like ancestral mammal earlier than in other mammalian crown groups. Micro-cursoriality evolved first in forests, presumably in response to selection for rapid running speeds facilitated by local knowledge, in order to avoid predators. During the Miocene, micro-cursoriality was pre-adaptive to open, arid habitats, and became more derived in the newly-evolved Elephantulus and Macroscelides elephant-shrews with trail running.

Gestating for 22 months: luteal development and pregnancy maintenance in elephants

The corpus luteum, a temporally established endocrine gland, formed on the ovary from remaining cells of the ovulated follicle, plays a key role in maintaining the early mammalian pregnancy by secreting progesterone. Despite being a monovular species, 2-12 corpora lutea (CLs) were found on the elephant ovaries during their long pregnancy lasting on average 640 days. However, the function and the formation of the additional CLs and their meaning remain unexplained. Here, we show from the example of the elephant, the close relationship between the maternally determined luteal phase length, the formation of multiple luteal structures and their progestagen secretion, the timespan of early embryonic development until implantation and maternal recognition. Through three-dimensional and Colour Flow ultrasonography of the ovaries and the uterus, we conclude that pregnant elephants maintain active CL throughout gestation that appear as main source of progestagens. Two LH peaks during the follicular phase ensure the development of a set of 5.4 ± 2.7 CLs. Accessory CLs (acCLs) form prior to ovulation after the first luteinizing hormone (LH) peak, while the ovulatory CL (ovCL) forms after the second LH peak. After five to six weeks (the normal luteal phase lifespan), all existing CLs begin to regress. However, they resume growing as soon as an embryo becomes ultrasonographically apparent on day 49 ± 2. After this time, all pregnancy CLs grow significantly larger than in a non-conceptive luteal phase and are maintained until after parturition. The long luteal phase is congruent with a slow early embryonic development and luteal rescue only starts 'last minute', with presumed implantation of the embryo. Our findings demonstrate a highly successful reproductive solution, different from currently described mammalian models.

Phylogeny and taxonomy of the round-eared sengis or elephant-shrews, genus Macroscelides (Mammalia, Afrotheria, Macroscelidea)

The round-eared sengis or elephant-shrews (genus Macroscelides) exhibit striking pelage variation throughout their ranges. Over ten taxonomic names have been proposed to describe this variation, but currently only two taxa are recognized (M. proboscideus proboscideus and M. p. flavicaudatus). Here, we review the taxonomic history of Macroscelides, and we use data on the geographic distribution, morphology, and mitochondrial DNA sequence to evaluate the current taxonomy. Our data support only two taxa that correspond to the currently recognized subspecies M. p. proboscideus and M. p. flavicaudatus. Mitochondrial haplotypes of these two taxa are reciprocally monophyletic with over 13% uncorrected sequence divergence between them. PCA analysis of 14 morphological characters (mostly cranial) grouped the two taxa into non-overlapping clusters, and body mass alone is a relatively reliable distinguishing character throughout much of Macroscelides range. Although fieldworkers were unable to find sympatric populations, the two taxa were found within 50 km of each other, and genetic analysis showed no evidence of gene flow. Based upon corroborating genetic data, morphological data, near sympatry with no evidence of gene flow, and differences in habitat use, we elevate these two forms to full species.

ARTADE2DB: improved statistical inferences for Arabidopsis gene functions and structure predictions by dynamic structure-based dynamic expression (DSDE) analyses

Recent advances in technologies for observing high-resolution genomic activities, such as whole-genome tiling arrays and high-throughput sequencers, provide detailed information for understanding genome functions. However, the functions of 50% of known Arabidopsis thaliana genes remain unknown or are annotated only on the basis of static analyses such as protein motifs or similarities. In this paper, we describe dynamic structure-based dynamic expression (DSDE) analysis, which sequentially predicts both structural and functional features of transcripts. We show that DSDE analysis inferred gene functions 12% more precisely than static structure-based dynamic expression (SSDE) analysis or conventional co-expression analysis based on previously determined gene structures of A. thaliana. This result suggests that more precise structural information than the fixed conventional annotated structures is crucial for co-expression analysis in systems biology of transcriptional regulation and dynamics. Our DSDE method, ARabidopsis Tiling-Array-based Detection of Exons version 2 and over-representation analysis (ARTADE2-ORA), precisely predicts each gene structure by combining two statistical analyses: a probe-wise co-expression analysis of multiple transcriptome measurements and a Markov model analysis of genome sequences. ARTADE2-ORA successfully identified the true functions of about 90% of functionally annotated genes, inferred the functions of 98% of functionally unknown genes and predicted 1,489 new gene structures and functions. We developed a database ARTADE2DB that integrates not only the information predicted by ARTADE2-ORA but also annotations and other functional information, such as phenotypes and literature citations, and is expected to contribute to the study of the functional genomics of A. thaliana. URL: http://artade.org.

Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals

As a consequence of recent developments in molecular phylogenomics, all extant orders of placental mammals have been grouped into 3 lineages: Afrotheria, Xenarthra, and Boreotheria, which originated in Africa, South America, and Laurasia, respectively. Despite this advancement, the order of divergence of these 3 lineages remains unresolved. Here, we performed extensive retroposon analysis with mammalian genomic data. Surprisingly, we identified a similar number of informative retroposon loci that support each of 3 possible phylogenetic hypotheses: the basal position for Afrotheria (22 loci), Xenarthra (25 loci), and Boreotheria (21 loci). This result indicates that the divergence of the placental common ancestor into the 3 lineages occurred nearly simultaneously. Thus, we examined whether these molecular data could be integrated into the geological context by incorporating recent geological data. We obtained firm evidence that complete separation of Gondwana into Africa and South America occurred 120 +/- 10 Ma. Accordingly, the previous reported time frame (division of Pangea into Gondwana and Laurasia at 148-138 Ma and division of Gondwana at 105 Ma) cannot be used to validate mammalian divergence order. Instead, we use our retroposon results and the recent geological data to propose that near-simultaneous divisions of continents leading to isolated Africa, South America, and Laurasia caused nearly concomitant divergence of the ancient placental ancestor into 3 lineages, Afrotheria, Xenarthra, and Boreotheria, approximately 120 Ma.

A new perspective on phylogeny and evolution of tetraodontiform fishes (Pisces: Acanthopterygii) based on whole mitochondrial genome sequences: basal ecological diversification?

Background

The order Tetraodontiformes consists of approximately 429 species of fishes in nine families. Members of the order exhibit striking morphological diversity and radiated into various habitats such as freshwater, brackish and coastal waters, open seas, and deep waters along continental shelves and slopes. Despite extensive studies based on both morphology and molecules, there has been no clear resolution except for monophyly of each family and sister-group relationships of Diodontidae + Tetraodontidae and Balistidae + Monacanthidae. To address phylogenetic questions of tetraodontiform fishes, we used whole mitochondrial genome (mitogenome) sequences from 27 selected species (data for 11 species were newly determined during this study) that fully represent all families and subfamilies of Tetraodontiformes (except for Hollardinae of the Triacanthodidae). Partitioned maximum likelihood (ML) and Bayesian analyses were performed on two data sets comprising concatenated nucleotide sequences from 13 protein-coding genes (all positions included; third codon positions converted into purine [R] and pyrimidine [Y]), 22 transfer RNA and two ribosomal RNA genes (total positions = 15,084).

Results

The resultant tree topologies from the two data sets were congruent, with many internal branches showing high support values. The mitogenomic data strongly supported monophyly of all families and subfamilies (except the Tetraodontinae) and sister-group relationships of Balistidae + Monacanthidae and Tetraodontidae + Diodontidae, confirming the results of previous studies. However, we also found two unexpected basal splits into Tetraodontoidei (Triacanthidae + Balistidae + Monacanthidae + Tetraodontidae + Diodontidae + Molidae) and Triacanthodoidei (Ostraciidae + Triodontidae + Triacanthodidae).

Conclusion

This basal split into the two clades has never been reported and challenges previously proposed hypotheses based on both morphology and nuclear gene sequences. It is likely that the basal split had involved ecological diversification, because most members of Tetraodontoidei exclusively occur in shallow waters (freshwater, brackish and coastal waters, and open seas), while those of Triacanthodoidei occur mainly in relatively deep waters along continental shelves and slopes except for more derived ostraciids. This suggests that the basal split between the two clades led to subsequent radiation into the two different habitats.

Genome size: a novel genomic signature in support of Afrotheria

Molecular phylogenetic analyses suggest an emerging phylogeny for the extant Placentalia (eutherian) that radically departs from morphologically based constructions of the past. Placental mammals are partitioned into four supraordinal clades: Afrotheria, Xenarthra, Laurasiatheria, and Euarchontoglires. Afrotheria form an endemic African clade that includes elephant shrews, golden moles, tenrecs, aardvarks, hyraxes, elephants, dugongs, and manatees. Datamining databases of genome size (GS) shows that till today just one afrotherian GS has been evaluated, that of the aardvark Orycteropus afer. We show that the GSs of six selected representatives across the Afrotheria supraordinal group are among the highest for the extant Placentalia, providing a novel genomic signature of this enigmatic group. The mean GS value of Afrotheria, 5.3 +/- 0.7 pg, is the highest reported for the extant Placentalia. This should assist in planning new genome sequencing initiatives.

Additional material of the enigmatic Early Miocene mammal Kelba and its relationship to the order Ptolemaiida

Kelba quadeemae, a fossil mammal from the Early Miocene of East Africa, was originally named on the basis of three isolated upper molars. Kelba has previously been interpreted as a creodont, a pantolestid, an insectivoran, and a hemigaline viverrid. The true affinities of this taxon have remained unclear because of the limited material and its unique morphology relative to other Miocene African mammals. New material of Kelba from several East African Miocene localities, most notably a skull from the Early Miocene locality of Songhor in Western Kenya, permits analysis of the affinities of Kelba and documents the lower dentition of this taxon. Morphological comparison of this new material clearly demonstrates that Kelba is a member of the order Ptolemaiida, a poorly understood group whose fossil record was previously restricted to the Oligocene Fayum deposits of northern Egypt. Phylogenetic analysis supports the monophyly of the Ptolemaiida, including Kelba, and recovers two monophyletic clades within the order. We provide new family names for these groups and an emended diagnosis for the order. The discovery of ptolemaiidans from the Miocene of East Africa is significant because it extends the known temporal range of the order by >10 million years and the geographic range by >3,200 km. Although the higher-level affinities of the Ptolemaiida remain obscure, their unique morphology and distribution through a larger area of Africa (and exclusively Africa) lend support to the idea that Ptolemaiida may have an ancient African origin.

Discovery of alpha-defensins in basal mammals

Alpha-defensins are essential molecules of the innate immune system that have broad spectrum antimicrobial activity against a range of bacteria and viruses. To date, alpha-defensins have only been identified in the Euarchontoglires branch of the mammals. This has led to speculation that alpha-defensins may be specific to this group, a somewhat surprising finding, given their importance in the immune system. The mammalian genome project provided us with the opportunity to search for alpha-defensins in previously unexamined mammalian superorders. Using hidden Markov model (HMM) profile searching, we report the discovery of alpha-defensins in the African savanna elephant, the lesser hedgehog tenrec, and the nine-banded armadillo genomes representing two of the most basal mammalian superorders, Afrotheria and Xenarthra. Furthermore, we identify an alpha-defensin-like gene in the gray short-tailed opossum, suggesting that alpha-defensins may have evolved much earlier than previously thought, before the divergence of placental mammals and marsupials approximately 130 mya.

A higher-level MRP supertree of placental mammals

BACKGROUND

The higher-level phylogeny of placental mammals has long been a phylogenetic Gordian knot, with disagreement about both the precise contents of, and relationships between, the extant orders. A recent MRP supertree that favoured 'outdated' hypotheses (notably, monophyly of both Artiodactyla and Lipotyphla) has been heavily criticised for including low-quality and redundant data. We apply a stringent data selection protocol designed to minimise these problems to a much-expanded data set of morphological, molecular and combined source trees, to produce a supertree that includes every family of extant placental mammals.

RESULTS

The supertree is well-resolved and supports both polyphyly of Lipotyphla and paraphyly of Artiodactyla with respect to Cetacea. The existence of four 'superorders'--Afrotheria, Xenarthra, Laurasiatheria and Euarchontoglires--is also supported. The topology is highly congruent with recent (molecular) phylogenetic analyses of placental mammals, but is considerably more comprehensive, being the first phylogeny to include all 113 extant families without making a priori assumptions of suprafamilial monophyly. Subsidiary analyses reveal that the data selection protocol played a key role in the major changes relative to a previously published higher-level supertree of placentals.

CONCLUSION

The supertree should provide a useful framework for hypothesis testing in phylogenetic comparative biology, and supports the idea that biogeography has played a crucial role in the evolution of placental mammals. Our results demonstrate the importance of minimising poor and redundant data when constructing supertrees.

Phylogeny and Biogeography of a Cosmopolitan Frog Radiation: Late Cretaceous Diversification Resulted in Continent-Scale Endemism in the Family Ranidae

Ranidae is a large anuran group with a nearly cosmopolitan distribution. We investigated the phylogenetic relationships and early biogeographic history of ranid frogs, using 104 representatives of all subfamilies and families, sampled from throughout their distribution. Analyses of approximately 1570 bp of nuclear gene fragments (Rag-1, rhod, Tyr) and approximately 2100 bp of the mitochondrial genome (12S rRNA, tRNAVAL, 16S rRNA) indicate that the monophyly of several taxa can be rejected with high confidence. Our tree is characterized by a clear historical association of each major clade with one Gondwanan plate. This prevalence of continent-scale endemism suggests that plate tectonics has played a major role in the distribution of ranid frogs. We performed dispersal-vicariance analyses, as well as analyses constrained by paleogeographic data, to estimate ancestral distributions during early ranid diversification. Additionally, we used molecular clock analyses to evaluate whether these scenarios fit the temporal framework of continental breakup. Our analyses suggest that a scenario in which the ancestors of several clades (Rhacophorinae, Dicroglossinae, Raninae) reached Eurasia via the Indian subcontinent, and the ancestor of Ceratobatrachinae entered via the Australia-New Guinea plate, best fits the paleogeographic models and requires the fewest number of dispersal/vicariance events. However, several alternatives, in which part of the ranid fauna colonized Laurasia from Africa, are not significantly worse. Most importantly, all hypotheses make clear predictions as to where to expect key fossils and where to sample other living ranids, and thus constitute a strong basis for further research.

Molecular clocks: four decades of evolution

During the past four decades, the molecular-clock hypothesis has provided an invaluable tool for building evolutionary timescales, and has served as a null model for testing evolutionary and mutation rates in different species. Molecular clocks have also influenced the development of theories of molecular evolution. As DNA-sequencing technologies have progressed, the use of molecular clocks has increased, with a profound effect on our understanding of the temporal diversification of species and genomes.

Ribosomal RNA kink-turn motif--a flexible molecular hinge

Ribosomal RNA K-turn motifs are asymmetric internal loops characterized by a sharp bend in the phosphodiester backbone resulting in "V" shaped structures, recurrently observed in ribosomes and showing a high degree of sequence conservation. We have carried out extended explicit solvent molecular dynamics simulations of selected K-turns, in order to investigate their intrinsic structural and dynamical properties. The simulations reveal an unprecedented dynamical flexibility of the K-turns around their X-ray geometries. The K-turns sample, on the nanosecond timescale, different conformational substates. The overall behavior of the simulations suggests that the sampled geometries are essentially isoenergetic and separated by minimal energy barriers. The nanosecond dynamics of isolated K-turns can be qualitatively considered as motion of two rigid helix stems controlled by a very flexible internal loop which then leads to substantial hinge-like motions between the two stems. This internal dynamics of K-turns is strikingly different for example from the bacterial 5S rRNA Loop E motif or BWYV frameshifting pseudoknot which appear to be rigid in the same type of simulations. Bistability and flexibility of K-turns was also suggested by several recent biochemical studies. Although the results of MD simulations should be considered as a qualitative picture of the K-turn dynamics due to force field and sampling limitations, the main advantage of the MD technique is its ability to investigate the region close to K-turn ribosomal-like geometries. This part of the conformational space is not well characterized by the solution experiments due to large-scale conformational changes seen in the experiments. We suggest that K-turns are well suited to act as flexible structural elements of ribosomal RNA. They can for example be involved in mediation of large-scale motions or they can allow a smooth assembling of the other parts of the ribosome.

Deep Time and the Search for Anthropoid Origins

Recent fossil discoveries, phylogenetic analyses, revised reconstructions of continental drift, and accumulating molecular evidence have all yielded new information relating to anthropoid origins within the broader context of primate evolution. There is an emerging consensus among molecular studies that four superorders of eutherian mammals can be recognized: Afrotheria, Euarchontoglires (to which primates belong), Laurasiatheria, and Xenarthra. Overall, molecular phylogenies for mammals agree with some statistical analyses of the primate fossil record in indicating an early origin for primates around 85 Ma ago, and the divergence of haplorhines and strepsirrhines at ca. 77 Ma. Such an ancient date for the origin of haplorhines is some 17 Ma prior to the first known possible primate, and some 22 Ma before the earliest fossil evidence of undoubted euprimates. Because anthropoid fossils date back at least to the late Eocene and perhaps to the middle Eocene, and given indications of an early origin for primates, it is unlikely that ancestral anthropoids arose within any other currently known clade of fossil primates (adapiforms, omomyiforms, strepsirrhines, or tarsiiforms). Implications of new molecular, morphological, and biogeographic lines of evidence are explored with respect to the likely time and place of the origin of anthropoids. Four competing, testable hypotheses are reviewed in detail: 1) the Paratethyan hypothesis, 2) the continental Asian hypothesis, 3) the Indo-Madagascar hypothesis, and 4) the African hypothesis. A case is made that current evidence best supports a relatively ancient Gondwanan origin for primates, as well as a Gondwanan (African or Indo-Madagascan) origin for anthropoids at least as old as that of any other currently documented major primate clade. Available fossil evidence at present seems to be most compatible with the African hypothesis, but it is noteworthy that primates are included not in Afrotheria but in Euarchontoglires.

Planetary biology--paleontological, geological, and molecular histories of life

The history of life on Earth is chronicled in the geological strata, the fossil record, and the genomes of contemporary organisms. When examined together, these records help identify metabolic and regulatory pathways, annotate protein sequences, and identify animal models to develop new drugs, among other features of scientific and biomedical interest. Together, planetary analysis of genome and proteome databases is providing an enhanced understanding of how life interacts with the biosphere and adapts to global change.

Parabrachio-cortical connections with the lateral hemisphere in the madagascan hedgehog tenrec: prominent projections to layer 1, weak projections from layer 6

The present study was undertaken to further characterize and subdivide the rhinal cortex (insular and perirhinal areas) in the hedgehog tenrec (Echinops telfairi), a placental mammal with a rather low encephalisation index. Injections of wheat germ agglutinin-horseradish peroxidase into the dorsolateral pontine tegmentum revealed a prominent layer 1 projection to several rhinal target areas, while the rhinal cortex only stained weakly for the calcitonin gene-related peptide. Among the regions retrogradely labeled following tracer injections into the rhinal cortex, the parabrachial nucleus was considered the main origin of the tegmento-cortical projection. This conclusion was based on the circumscribed pattern of termination, as well as the differences noted between the pattern of anterograde labeling and the pattern obtained by thyrosine hydroxylase immunohistochemistry. The tracer injections into the dorsolateral tegmentum also revealed numerous retrogradely labeled cells in the layer 5 of the dorsomedial frontal cortex. In contrast, the rhinal cortex only showed few labeled cells and most of these cells were located in the layer 6/7. A comparison with other species indicates that the tenrec's parabrachial nucleus gives rise to the most extensive cortical projections but receives the least prominent input from the lateral cerebral hemisphere. The layer 6/7 projection may be a common mammalian feature but it is overshadowed by the layer 5 projection in higher mammals.

Hippocampal fields in the hedgehog tenrec. Their architecture and major intrinsic connections

The Madagascan lesser hedgehog tenrec was investigated to get insight into the areal evolution of the hippocampal formation in mammals with poorly differentiated brains. The hippocampal subdivisions were analyzed using cyto- and chemoarchitectural criteria; long associational and commissural connections were demonstrated with tracer techniques. The hedgehog tenrec shows a well differentiated dentate gyrus, CA3 and CA1. Their major intrinsic connections lie within the band of variations known from other species. The dentate hilar region shows calretinin-positive mossy cells with extensive projections to the molecular layer. The calbindin- and enkephalin-positive granule mossy fibers form a distinct endbulb and do not invade the CA1 as reported in the erinaceous hedgehog. Isolated granule cells with basal dendrites were also noted. A CA2 region is hard to identify architecturally; its presence is suggested due to its contralateral connections. Subicular and perisubicular regions are clearly present along the dorsal aspects of the hemisphere, but we failed to identify them unequivocally along the caudal and ventral tip of the hippocampus. A temporal portion of the subiculum, if present, differs in its chemoarchitecture from its dorsal counterpart. The perisubicular region, located medially adjacent to the dorsal subiculum may be equivalent to the rat's presubiculum; evidence for the presence of a parasubiculum was rather weak.

Islands on the plains: metapopulation dynamics and female biased dispersal in hyraxes (Hyracoidea) in the Serengeti National Park

Two species of hyrax, Heterohyrax brucei and Procavia johnstoni, inhabit rock outcrops, or kopjes, in the Serengeti National Park, Tanzania. Such distinct 'island' habitats provide an excellent model to investigate natural metapopulation dynamics with distinct small populations with extinction and colonization events, as well as migration between populations. Allele frequencies, genetic variability and genetic distances between populations were calculated based on DNA microsatellite markers. The genetic diversity in both species of hyrax, especially P. johnstoni, was surprisingly low: allelic diversity ranged from 2 to 7 alleles per locus. This may have been induced by colonization by a small number of individuals from single source populations. F-statistics, assignment tests and calculations of pairwise relatedness all indicated female-biased dispersal in H. brucei but not P. johnstoni. Values of FIS in P. johnstoni showed an excess of homozygotes indicative of high rates of inbreeding; evidence for inbreeding could not be detected in H. brucei. Although female dispersal patterns in H. brucei seem to prevent inbreeding and consequently reduce risk of local extinction, this seems not to be the case in P. johnstoni.