Genomics. On choosing mammalian genomes for sequencing

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.

Microarray and proteomic analysis of the cardioprotective effects of cold blood cardioplegia in the mature and aged male and female

Recently we have shown that the cardioprotection afforded by cardioplegia is modulated by age and gender and is significantly decreased in the aged female. In this report we use microarray and proteomic analyses to identify transcriptomic and proteomic alterations affecting cardioprotection using cold blood cardioplegia in the mature and aged male and female heart. Mature and aged male and female New Zealand White rabbits were used for in situ blood perfused cardiopulmonary bypass. Control hearts received 30 min sham ischemia and 120 min sham reperfusion. Global ischemia (GI) hearts received 30 min of GI achieved by cross-clamping of the aorta. Cardioplegia (CP) hearts received cold blood cardioplegia prior to GI. Following 30 min of GI the hearts were reperfused for 120 min and then used for RNA and protein isolation. Microarray and proteomic analyses were performed. Functional enrichment analysis showed that mitochondrial dysfunction, oxidative phosphorylation and calcium signaling pathways were significantly enriched in all experimental groups. Glycolysis/gluconeogenesis and the pentose phosphate pathway were significantly changed in the aged male only (P < 0.05), while glyoxylate/dicarboxylate metabolism was significant in the aged female only (P < 0.05). Our data show that specific pathways associated with the mitochondrion modulate cardioprotection with CP in the aged and specifically in the aged female. The alteration of these pathways significantly contributes to decreased myocardial functional recovery and myonecrosis following ischemia and may be modulated to allow for enhanced cardioprotection in the aged and specifically in the aged female.

[Combining phylogenetic information: concept, methodology, and challenges]

The DNA sequences, morphological and other homologous characters can be used to infer the origins and histories of biological taxa. Combining all the phylogenetic information available can produce more inclusive phylogenies, improve our understanding of living organisms, and enable biologists to prompt and test hypotheses on a larger scale and with stronger statistical power. In this article, the concept of combining phylogenetic information and its comparison with traditional analysis were reviewed. The most popular approaches of supertree and supermatrix were discussed in detail, and novel ways were presented. Although the combining analysis is facing rigid challenges from data and foundation, it is currently the only approach for realization of the Tree(Net) of Life, and its development will definitely expand our knowledge of evolution on the earth and contribute to the progress of evolutionary related disciplines.

Transcriptomic and proteomic analysis of global ischemia and cardioprotection in the rabbit heart

Cardioplegia is used to partially alleviate the effects of surgically induced global ischemia injury; however, the molecular mechanisms involved in this cardioprotection remain to be elucidated. To improve the understanding of the molecular processes modulating the effects of global ischemia and the cardioprotection afforded by cardioplegia, we constructed rabbit heart cDNA libraries and isolated, sequenced, and identified a compendium of nonredundant cDNAs for use in transcriptomic and proteomic analyses. New Zealand White rabbits were used to compare the effects of global ischemia and cardioplegia compared with control (nonischemic) hearts. The effects of RNA and protein synthesis on the cardioprotection afforded by cardioplegia were investigated separately by preperfusion with either alpha-amanitin or cycloheximide. Our results demonstrate that cardioplegia partially ameliorates the effects of global ischemia and that the cardioprotection is modulated by RNA- and protein-dependent mechanisms. Transcriptomic and proteomic enrichment analyses indicated that global ischemia downregulated genes/proteins associated with mitochondrial function and energy production, cofactor catabolism, and the generation of precursor metabolites of energy. In contrast, cardioplegia significantly increased differentially expressed genes/proteins associated with the mitochondrion and mitochondrial function and significantly upregulated the biological processes of muscle contraction, involuntary muscle contraction, carboxylic acid and fatty acid catabolic processes, fatty acid beta-oxidation, and fatty acid metabolic processes.

The opossum genome: insights and opportunities from an alternative mammal

The strategic importance of the genome sequence of the gray, short-tailed opossum, Monodelphis domestica, accrues from both the unique phylogenetic position of metatherian (marsupial) mammals and the fundamental biologic characteristics of metatherians that distinguish them from other mammalian species. Metatherian and eutherian (placental) mammals are more closely related to one another than to other vertebrate groups, and owing to this close relationship they share fundamentally similar genetic structures and molecular processes. However, during their long evolutionary separation these alternative mammals have developed distinctive anatomical, physiologic, and genetic features that hold tremendous potential for examining relationships between the molecular structures of mammalian genomes and the functional attributes of their components. Comparative analyses using the opossum genome have already provided a wealth of new evidence regarding the importance of noncoding elements in the evolution of mammalian genomes, the role of transposable elements in driving genomic innovation, and the relationships between recombination rate, nucleotide composition, and the genomic distributions of repetitive elements. The genome sequence is also beginning to enlarge our understanding of the evolution and function of the vertebrate immune system, and it provides an alternative model for investigating mechanisms of genomic imprinting. Equally important, availability of the genome sequence is fostering the development of new research tools for physical and functional genomic analyses of M. domestica that are expanding its versatility as an experimental system for a broad range of research applications in basic biology and biomedically oriented research.

State of cat genomics

Our knowledge of cat family biology was recently expanded to include a genomics perspective with the completion of a draft whole genome sequence of an Abyssinian cat. The utility of the new genome information has been demonstrated by applications ranging from disease gene discovery and comparative genomics to species conservation. Patterns of genomic organization among cats and inbred domestic cat breeds have illuminated our view of domestication, revealing linkage disequilibrium tracks consequent of breed formation, defining chromosome exchanges that punctuated major lineages of mammals and suggesting ancestral continental migration events that led to 37 modern species of Felidae. We review these recent advances here. As the genome resources develop, the cat is poised to make a major contribution to many areas in genetics and biology.

Identification of SNPs and INDELS in swine transcribed sequences using short oligonucleotide microarrays

Background

Genome-wide detection of single feature polymorphisms (SFP) in swine using transcriptome profiling of day 25 placental RNA by contrasting probe intensities from either Meishan or an occidental composite breed with Affymetrix porcine microarrays is presented. A linear mixed model analysis was used to identify significant breed-by-probe interactions.

Results

Gene specific linear mixed models were fit to each of the log₂ transformed probe intensities on these arrays, using fixed effects for breed, probe, breed-by-probe interaction, and a random effect for array. After surveying the day 25 placental transcriptome, 857 probes with a q-value ≤ 0.05 and |fold change| ≥ 2 for the breed-by-probe interaction were identified as candidates containing SFP. To address the quality of the bioinformatics approach, universal pyrosequencing assays were designed from Affymetrix exemplar sequences to independently assess polymorphisms within a subset of probes for validation. Additionally probes were randomly selected for sequencing to determine an unbiased confirmation rate. In most cases, the 25-mer probe sequence printed on the microarray diverged from Meishan, not occidental crosses. This analysis was used to define a set of highly reliable predicted SFPs according to their probability scores.

Conclusion

By applying a SFP detection method to two mammalian breeds for the first time, we detected transition and transversion single nucleotide polymorphisms, as well as insertions/deletions which can be used to rapidly develop markers for genetic mapping and association analysis in species where high density genotyping platforms are otherwise unavailable.

SNPs and INDELS discovered by this approach have been publicly deposited in NCBI's SNP repository dbSNP. This method is an attractive bioinformatics tool for uncovering breed-by-probe interactions, for rapidly identifying expressed SNPs, for investigating potential functional correlations between gene expression and breed polymorphisms, and is robust enough to be used on any Affymetrix gene expression platform.

Large-scale sequencing and the new animal phylogeny

Although comparisons of gene sequences have revolutionised our understanding of the animal phylogenetic tree, it has become clear that, to avoid errors in tree reconstruction, a large number of genes from many species must be considered: too few genes and stochastic errors predominate, too few taxa and systematic errors appear. We argue here that, to gather many sequences from many taxa, the best use of resources is to sequence a small number of expressed sequence tags (1000-5000 per species) from as many taxa as possible. This approach counters both sources of error, gives the best hope of a well-resolved phylogeny of the animals and will act as a central resource for a carefully targeted genome sequencing programme.

Chromosome localization of microsatellite markers in the shrews of the Sorex araneus group

The extremely high rate of karyotypic evolution that characterizes the shrews of the Sorex araneus group makes this group an exceptionally interesting model for population genetics and evolutionary studies. Here, we attempted to map 46 microsatellite markers at the chromosome arm level using flow-sorted chromosomes from three karyotypically different taxa of the Sorex araneus group (S. granarius and the chromosome races Cordon and Novosibirsk of S. araneus). The most likely localizations were provided for 35 markers, among which 25 were each unambiguously mapped to a single locus on the corresponding chromosomes in the three taxa, covering the three sexual chromosomes (XY1Y2) and nine of the 18 autosomal arms of the S. araneus group. The results provide further evidence for a high degree of conservation in genome organization in the S. araneus group despite the presence of numerous Robertsonian rearrangements. These markers can therefore be used to compare the genetic structure among taxa of the S. araneus group at the chromosome level and to study the role of chromosomal rearrangements in the genetic diversification and speciation process of this group.

Status and applications of genomic resources for the gray, short-tailed opossum, Monodelphis domestica, an American marsupial model for comparative biology

Owing to its small size, favourable reproductive characteristics, and simple husbandry, the gray, short-tailed opossum, Monodelphis domestica, has become the most widely distributed and intensively utilised laboratory-bred research marsupial in the world today. This article provides an overview of the current state and future projections of genomic resources for this species and discusses the potential impact of this growing resource base on active research areas that use M. domestica as a model system. The resources discussed include: fully arrayed, bacterial artificial chromosome (BAC) libraries; an expanding linkage map; developing full-genome BAC-contig and chromosomal fluorescence in situ hybridisation maps; public websites providing access to the M. domestica whole-genome-shotgun sequence trace database and the whole-genome sequence assembly; and a new project underway to create an expressed-sequence database and microchip expression arrays for functional genomics applications. Major research areas discussed span a variety of genetic, evolutionary, physiologic, reproductive, developmental, and behavioural topics, including: comparative immunogenetics; genomic imprinting; reproductive biology; neurobiology; photobiology and carcinogenesis; genetics of lipoprotein metabolism; developmental and behavioural endocrinology; sexual differentiation and development; embryonic and fetal development; meiotic recombination; genome evolution; molecular evolution and phylogenetics; and more.

Evolutionary analysis of a large mtDNA translocation (numt) into the nuclear genome of the Panthera genus species

Translocation of cymtDNA into the nuclear genome, also referred to as numt, has been reported in many species, including several closely related to the domestic cat (Felis catus). We describe the recent transposition of 12,536 bp of the 17 kb mitochondrial genome into the nucleus of the common ancestor of the five Panthera genus species: tiger, P. tigris; snow leopard, P. uncia; jaguar, P. onca; leopard, P. pardus; and lion, P. leo. This nuclear integration, representing 74% of the mitochondrial genome, is one of the largest to be reported in eukaryotes. The Panthera genus numt differs from the numt previously described in the Felis genus in: (1) chromosomal location (F2-telomeric region vs. D2-centromeric region), (2) gene make up (from the ND5 to the ATP8 vs. from the CR to the COII), (3) size (12.5 vs. 7.9 kb), and (4) structure (single monomer vs. tandemly repeated in Felis). These distinctions indicate that the origin of this large numt fragment in the nuclear genome of the Panthera species is an independent insertion from that of the domestic cat lineage, which has been further supported by phylogenetic analyses. The tiger cymtDNA shared around 90% sequence identity with the homologous numt sequence, suggesting an origin for the Panthera numt at around 3.5 million years ago, prior to the radiation of the five extant Panthera species.

Species choice for comparative genomics: being greedy works

Several projects investigating genetic function and evolution through sequencing and comparison of multiple genomes are now underway. These projects consume many resources, and appropriate planning should be devoted to choosing which species to sequence, potentially involving cooperation among different sequencing centres. A widely discussed criterion for species choice is the maximisation of evolutionary divergence. Our mathematical formalization of this problem surprisingly shows that the best long-term cooperative strategy coincides with the seemingly short-term “greedy” strategy of always choosing the next best single species. Other criteria influencing species choice, such as medical relevance or sequencing costs, can also be accommodated in our approach, suggesting our results' broad relevance in scientific policy decisions.

What would happen if sequencing centres around the world were to choose genomes without consulting each other and without devising long-term strategies? When several parties are involved in decisions with interacting consequences, experience teaches that cooperation and planning are usually necessary to guarantee the best result. Similarly, in computer science, “greedy” algorithms—which construct solutions by iteratively taking the best immediate choice—are rarely the best option to solve a problem. The authors show, however, that in the context of choosing species for comparative genomics, cooperation and planning can be kept to a minimum without affecting the quality of the global result: a greedy algorithm applied to the problem of maximising the evolutionary divergence among species chosen from a known phylogeny is proven to guarantee optimal solutions.

Genomic inferences from Afrotheria and the evolution of elephants

Recent genetic studies have established that African forest and savanna elephants are distinct species with dissociated cytonuclear genomic patterns, and have identified Asian elephants from Borneo and Sumatra as conservation priorities. Representative of Afrotheria, a superordinal clade encompassing six eutherian orders, the African savanna elephant was among the first mammals chosen for whole-genome sequencing to provide a comparative understanding of the human genome. Elephants have large and complex brains and display advanced levels of social structure, communication, learning and intelligence. The elephant genome sequence might prove useful for comparative genomic studies of these advanced traits, which have appeared independently in only three mammalian orders: primates, cetaceans and proboscideans.

Subtree power analysis and species selection for comparative genomics

Sequence comparison across multiple organisms aids in the detection of regions under selection. However, resource limitations require a prioritization of genomes to be sequenced. This prioritization should be grounded in two considerations: the lineal scope encompassing the biological phenomena of interest, and the optimal species within that scope for detecting functional elements. We introduce a statistical framework for optimal species subset selection, based on maximizing power to detect conserved sites. Analysis of a phylogenetic star topology shows theoretically that the optimal species subset is not in general the most evolutionarily diverged subset. We then demonstrate this finding empirically in a study of vertebrate species. Our results suggest that marsupials are prime sequencing candidates.

Gene conversion and functional divergence in the beta-globin gene family

Different models of gene family evolution have been proposed to explain the mechanism whereby gene copies created by gene duplications are maintained and diverge in function. Ohta proposed a model which predicts a burst of nonsynonymous substitutions following gene duplication and the preservation of duplicates through positive selection. An alternative model, the duplication-degeneration-complementation (DDC) model, does not explicitly require the action of positive Darwinian selection for the maintenance of duplicated gene copies, although purifying selection is assumed to continue to act on both copies. A potential outcome of the DDC model is heterogeneity in purifying selection among the gene copies, due to partitioning of subfunctions which complement each other. By using the d(N)/ d(S) (omega) rate ratio to measure selection pressure, we can distinguish between these two very different evolutionary scenarios. In this study we investigated these scenarios in the beta-globin family of genes, a textbook example of evolution by gene duplication. We assembled a comprehensive dataset of 72 vertebrate beta-globin sequences. The estimated phylogeny suggested multiple gene duplication and gene conversion events. By using different programs to detect recombination, we confirmed several cases of gene conversion and detected two new cases. We tested evolutionary scenarios derived from Ohta's model and the DDC model by examining selective pressures along lineages in a phylogeny of beta-globin genes in eutherian mammals. We did not find significant evidence for an increase in the omega ratio following major duplication events in this family. However, one exception to this pattern was the duplication of gamma-globin in simian primates, after which a few sites were identified to be under positive selection. Overall, our results suggest that following gene duplications, paralogous copies of beta-globin genes evolved under a nonepisodic process of functional divergence.

Mammalian phylogenomics comes of age

The relatively new field of phylogenomics is beginning to reveal the potential of genomic data for evolutionary studies. As the cost of whole genome sequencing falls, anticipation of complete genome sequences from divergent species, reflecting the major lineages of modern mammals, is no longer a distant dream. In this article, we describe how comparative genomic data from mammals is progressing to resolve long-standing phylogenetic controversies, to refine dogma on how chromosomes evolve and to guide annotation of human and other vertebrate genomes.

Human, mouse, and rat genome large-scale rearrangements: stability versus speciation

Using paired-end sequences from bacterial artificial chromosomes, we have constructed high-resolution synteny and rearrangement breakpoint maps among human, mouse, and rat genomes. Among the >300 syntenic blocks identified are segments of over 40 Mb without any detected interspecies rearrangements, as well as regions with frequently broken synteny and extensive rearrangements. As closely related species, mouse and rat share the majority of the breakpoints and often have the same types of rearrangements when compared with the human genome. However, the breakpoints not shared between them indicate that mouse rearrangements are more often interchromosomal, whereas intrachromosomal rearrangements are more prominent in rat. Centromeres may have played a significant role in reorganizing a number of chromosomes in all three species. The comparison of the three species indicates that genome rearrangements follow a path that accommodates a delicate balance between maintaining a basic structure underlying all mammalian species and permitting variations that are necessary for speciation.

Genomics. A dog's breakfast?

The genomes of human, mouse, and rat have been sequenced. Now, as O'Brien and Murphy announce in their Perspective, the genome sequence derby is heating up with the addition of dog to the list (Kirkness et al.). As they explain, even though the coverage of the dog genome (1.5x) is lower than that of mouse (8x), there are many valuable insights to be gained from comparing the sequence of dog with those of mouse and human.

A cattle-human comparative map built with cattle BAC-ends and human genome sequence

As a step toward the goal of adding the cattle genome to those available for multispecies comparative genome analysis, 40,224 cattle BAC clones were end-sequenced, yielding 60,547 sequences (BAC end sequences, BESs) after trimming with an average read length of 515 bp. Cattle BACs were anchored to the human and mouse genome sequences by BLASTN search, revealing 29.4% and 10.1% significant hits (E < e-5), respectively. More than 60% of all cattle BES hits in both the human and mouse genomes are located within known genes. In order to confirm in silico predictions of orthologyand their relative position on cattle chromosomes, 84 cattle BESs with similarity to sequences on HSA11 were mapped using a cattle-hamster radiation hybrid (RH) panel. Resulting RH maps of BTA15 and BTA29 cover approximately 85% of HSA11 sequence, revealing a complex patchwork shuffling of segments not explained by a simple translocation followed by internal rearrangements. Overlay of the mouse conserved syntenies onto HSA11 revealed that segmental boundaries appear to be conserved in all three species. The BAC clone-based comparative map provides a foundation for the evolutionary analysis of mammalian karyotypes and for sequencing of the cattle genome.

The Feline Genome Project

The compilation of a dense gene map and eventually a whole genome sequence (WGS) of the domestic cat holds considerable value for human genome annotation, for veterinary medicine, and for insight into the evolution of genome organization among mammals. Human association and veterinary studies of the cat, its domestic breeds, and its charismatic wild relatives of the family Felidae have rendered the species a powerful model for human hereditary diseases, for infectious disease agents, for adaptive evolutionary divergence, for conservation genetics, and for forensic applications. Here we review the advantages, rationale, and present strategy of a feline genome project, and we describe the disease models, comparative genomics, and biological applications posed by the full resolution of the cat's genome.

A comparative study of white blood cell counts and disease risk in carnivores

In primates, baseline levels of white blood cell (WBC) counts are related to mating promiscuity. It was hypothesized that differences in the primate immune system reflect pathogen risks from sexually transmitted diseases (STDs). Here, we test for the generality of this result by examining hypotheses involving behavioural, ecological and life-history factors in carnivores. Again, we find a significant correlation in carnivores between mating promiscuity and elevated levels of WBC counts. In addition, we find relationships with measures of sociality, substrate use and life-history parameters. These comparative results across independent taxonomic orders indicate that the evolution of the immune system, as represented by phylogenetic differences in basal levels of blood cell counts, is closely linked to disease risk involved with promiscuous mating and associated variables. We found only limited support for an association between the percentage of meat in the diet and WBC counts, which is consistent with the behavioural and physiological mechanisms that carnivores use to avoid parasite transmission from their prey. We discuss additional comparative questions related to taxonomic differences in disease risk, modes of parasite transmission and implications for conservation biology.

Deciding among green plants for whole genome studies

Recent comparative DNA-sequencing studies of chloroplast, mitochondrial and ribosomal genes have produced an evolutionary tree relating the diversity of green-plant lineages. By coupling this phylogenetic framework to the explosion of information on genome content, plant-genomic efforts can and should be extended beyond angiosperm crop and model systems. Including plant species representative of other crucial evolutionary nodes would produce the comparative information necessary to understand fully the organization, function and evolution of plant genomes. The simultaneous development of genomic tools for green algae, bryophytes, 'seed-free' vascular plants and gymnosperms should provide insights into the bases of the complex morphological, physiological, reproductive and biochemical innovations that have characterized the successful transition of green plants to land.

Future directions in protein function prediction

New directions in computational methods for the prediction of protein function are discussed. THEMATICS, a method for the location and characterization of the active sites of enzymes, is featured. THEMATICS, for Theoretical Microscopic Titration Curves, is based on well-established finite-difference Poisson-Boltzmann methods for computing the electric field function of a protein. THEMATICS requires only the structure of the subject protein and thus may be applied to proteins that bear no similarity in structure or sequence to any previously characterized protein. The unique features of catalytic sites in proteins are discussed. Discussion of the chemical basis for the predictive powers of THEMATICS is featured in this paper. Some results are given for three illustrative examples: HIV-1 protease, human apurinic/apyrimidinic endonuclease, and human adenosine kinase.

Convergences in the modular and areal organization of the forebrain of mammals: implications for the reconstruction of forebrain evolution

Early efforts to reconstruct the course of the evolution of the human brain relied on comparing the brains of a few related mammals with brains at successively higher levels of complexity. This Clark or ladder of levels approach is now seen as having limited usefulness in that species are not easily assigned to levels, and extant mammals are now recognized as mosaics of primitive and derived features. In addition, direction of change does not necessarily proceed from simple to complex, small to large, or diffuse to differentiated. A modern cladistic approach reconstructs the brains of ancestors by identifying brain characters within and across phylogenetic groups (clades), and uses parsimony or likelihood to infer direction of change and distinguish ancestral features from independently evolved convergences. Unfortunately, an idealized cladistic approach is often difficult to realize because characters may be hard to identify and validate, key species may be unavailable for study, and broadly based comparative studies can be costly, poorly funded, and labor intensive. Thus, many investigators pursue a truncated approach that is superficially Clark-like but conceptually cladistic. A truncated approach that relies on the extensive study of a few species may compensate for weaknesses by including niche-matched species that offer the opportunity to estimate the likelihood of similar brain features evolving as convergent adaptations. Because inferences about the brains of the primate ancestor are often made from the brains of tree shrews, we compare the brains of squirrel-like tree shrews with the brains of diurnal squirrels, and suggest that many of the primate-like features of the visual system of tree shrews arose independently of those in primates.

Factors influencing the identification of transcription factor binding sites by cross-species comparison

As the number of sequenced genomes has grown, the questions of which species are most useful and how many genomes are sufficient for comparison have become increasingly important for comparative genomics studies. We have systematically addressed these questions with respect to phylogenetic footprinting of transcription factor (TF) binding sites in the gamma-proteobacteria, and have evaluated the statistical significance of our motif predictions. We used a study set of 166 Escherichia coli genes that have experimentally identified TF binding sites upstream of the gene, with orthologous data from nine additional gamma-proteobacteria for phylogenetic footprinting. Just three species were sufficient for approximately 74.0% of the motif predictions to correspond to the experimentally reported E. coli sites, and important characteristics to consider when choosing species were phylogenetic distance, genome size, and natural habitat. We also performed simulations using randomized data to determine the critical maximum a posteriori probability (MAP) values for statistical significance of our motif predictions (P = 0.05). Approximately 60% of motif predictions containing sites from just three species had average MAP values above these critical MAP values. The inclusion of a species very closely related to E. coli increased the number of statistically significant motif predictions, despite substantially increasing the critical MAP value.

Vertebrate genome sequencing: building a backbone for comparative genomics

The human genome sequence provides a reference point from which we can compare ourselves with other organisms. Interspecies comparison is a powerful tool for inferring function from genomic sequence and could ultimately lead to the discovery of what makes humans unique. To date, most comparative sequencing has focused on pair-wise comparisons between human and a limited number of other vertebrates, such as mouse. Targeted approaches now exist for mapping and sequencing vertebrate bacterial artificial chromosomes (BACs) from numerous species, allowing rapid and detailed molecular and phylogenetic investigation of multi-megabase loci. Such targeted sequencing is complementary to current whole-genome sequencing projects, and would benefit greatly from the creation of BAC libraries from a diverse range of vertebrates.

Resolution of the early placental mammal radiation using Bayesian phylogenetics

Molecular phylogenetic studies have resolved placental mammals into four major groups, but have not established the full hierarchy of interordinal relationships, including the position of the root. The latter is critical for understanding the early biogeographic history of placentals. We investigated placental phylogeny using Bayesian and maximum-likelihood methods and a 16.4-kilobase molecular data set. Interordinal relationships are almost entirely resolved. The basal split is between Afrotheria and other placentals, at about 103 million years, and may be accounted for by the separation of South America and Africa in the Cretaceous. Crown-group Eutheria may have their most recent common ancestry in the Southern Hemisphere (Gondwana).

A radiation hybrid mapping panel for the rhesus macaque

The genomes of nonhuman primates have recently become highly visible candidates for full genome analysis, as they provide powerful models of human disease and a better understanding of the evolution of the human genome. We describe the creation of a 5000 rad radiation hybrid (RH) mapping panel for the rhesus macaque. Duplicate genotypes of 84 microsatellite and coding gene sequence tagged sites from six macaque chromosomes produced an estimated whole genome retention frequency of 0.33. To test the mapping ability of the panel, we constructed RH maps for macaque chromosomes 7 and 9 and compared them to orthologous locus orders in existing human and baboon maps derived from different methodologies. Concordant marker order between all three species maps suggests that the current panel represents a powerful mapping resource for generating high-density comparative maps of the rhesus macaque and other species genomes.