The principles of classification and a classification of mammals. Bulletin of the AMNH ; v. 85

To discover interordinal relationships of living and fossil placental mammals and the time of origin of placentals relative to the Cretaceous-Paleogene (K-Pg) boundary, we scored 4541 phenomic characters de novo for 86 fossil and living species. Combining these data with molecular sequences, we obtained a phylogenetic tree that, when calibrated with fossils, shows that crown clade Placentalia and placental orders originated after the K-Pg boundary. Many nodes discovered using molecular data are upheld, but phenomic signals overturn molecular signals to show Sundatheria (Dermoptera + Scandentia) as the sister taxon of Primates, a close link between Proboscidea (elephants) and Sirenia (sea cows), and the monophyly of echolocating Chiroptera (bats). Our tree suggests that Placentalia first split into Xenarthra and Epitheria; extinct New World species are the oldest members of Afrotheria.

http://science.sciencemag.org/content/sci/339/6120/662.full.pdf

The Placental Mammal Ancestor and the Post–K-Pg Radiation of Placentals

The role of fossils in dating the tree of life has been misunderstood. Fossils can provide good "minimum" age estimates for branches in the tree, but "maximum" constraints on those ages are poorer. Current debates about which are the "best" fossil dates for calibration move to consideration of the most appropriate constraints on the ages of tree nodes. Because fossil-based dates are constraints, and because molecular evolution is not perfectly clock-like, analysts should use more rather than fewer dates, but there has to be a balance between many genes and few dates versus many dates and few genes. We provide "hard" minimum and "soft" maximum age constraints for 30 divergences among key genome model organisms; these should contribute to better understanding of the dating of the animal tree of life.

/pdf/paleontological-evidence-to-date-the-tree-of-life-5dhwbwgnyr.pdf

Paleontological Evidence to Date the Tree of Life

We present a draft genome sequence of the platypus, Ornithorhynchus anatinus This monotreme exhibits a fascinating combination of reptilian and mammalian characters For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles Analysis of the first monotreme genome aligned these features with genetic innovations We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation

/pdf/genome-analysis-of-the-platypus-reveals-unique-signatures-of-3ak256su45.pdf

Genome analysis of the platypus reveals unique signatures of evolution

Although the Human Genome Project was completed 4 years ago, the catalog of human protein-coding genes remains a matter of controversy. Current catalogs list a total of ≈24,500 putative protein-coding genes. It is broadly suspected that a large fraction of these entries are functionally meaningless ORFs present by chance in RNA transcripts, because they show no evidence of evolutionary conservation with mouse or dog. However, there is currently no scientific justification for excluding ORFs simply because they fail to show evolutionary conservation: the alternative hypothesis is that most of these ORFs are actually valid human genes that reflect gene innovation in the primate lineage or gene loss in the other lineages. Here, we reject this hypothesis by carefully analyzing the nonconserved ORFs—specifically, their properties in other primates. We show that the vast majority of these ORFs are random occurrences. The analysis yields, as a by-product, a major revision of the current human catalogs, cutting the number of protein-coding genes to ≈20,500. Specifically, it suggests that nonconserved ORFs should be added to the human gene catalog only if there is clear evidence of an encoded protein. It also provides a principled methodology for evaluating future proposed additions to the human gene catalog. Finally, the results indicate that there has been relatively little true innovation in mammalian protein-coding genes.

/pdf/distinguishing-protein-coding-and-noncoding-genes-in-the-3jn634pw9u.pdf

Distinguishing protein-coding and noncoding genes in the human genome

The biotic and geologic dynamics of the Great American Biotic Interchange are reviewed and revised Information on the Marine Isotope Stage chronology, sea level changes as well as Pliocene and Pleistocene vegetation changes in Central and northern South America add to a discussion of the role of climate in facilitating trans-isthmian exchanges Trans-isthmian land mammal exchanges during the Pleistocene glacial intervals appear to have been promoted by the development of diverse non-tropical ecologies

https://link.springer.com/content/pdf/10.1007%2Fs10914-010-9144-8.pdf

The Great American Biotic Interchange: Dispersals, Tectonics, Climate, Sea Level and Holding Pens

An appraisal of Paleogene floral and land mammal faunal dynamics in South America suggests that both biotic elements responded at rate and extent generally comparable to that portrayed by the global climate pattern of the interval. A major difference in the South American record is the initial as well as subsequent much greater diversity of both Neotropical and Austral floras relative to North American counterparts. Conversely, the concurrent mammal faunas in South America did not match, much less exceed, the diversity seen to the north. It appears unlikely that this difference is solely due to the virtual absence of immigrants subsequent to the initial dispersal of mammals to South America, and cannot be explained solely by the different collecting histories of the two regions. Possible roles played by non-mammalian vertebrates in niche exploitation remain to be explored.

Paleogene Land Mammal Faunas of South America; a Response to Global Climatic Changes and Indigenous Floral Diversity

The oldest Cenozoic mammalian assemblages in South America have been recovered from levels of the Han- sen Member of the Salamanca Formation, Punta Peligro locality in Argentina, and from the Santa Lucia Formation in Tiupampa, Bolivia. These faunas led to the recognition of the Peligran and Tiupampan South American Land Mammal Ages (SALMAs), each alternatively regarded as the oldest Paleocene SALMA. Due to the lack of radioisotopic dates for mammals bearing levels at these localities, no agreement has been reached yet about their relative ages. In this paper, the role of mammal faunas in age inference is discussed. Analysis of the SALMAs shows that the presence of non-therian mammals in the Peligran is of little consequence to the bio- chronological evaluation, reflecting instead a relict Mesozoic distribution. In contrast, therian mammals are particularly important in that (1) they were Lauraisan immigrants and (2) they support direct comparisons between the Tiupampa and Punta Peligro faunas. Parsimony and cluster analysis were used to quantitatively test hypotheses concerning the relative age of the Peligran and Tiupampan SALMAs. Our results support the hypothesis that the Tiupampan SALMA (early Danian) is older than the Peligran SALMA (early Selandian). This alignment results in an interpretation of the evolutionary history of South American land mammals that is more straightforward than the alternative.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1475-4983.2008.00835.x

Michael O. Woodburne

Papers

The Great American Biotic Interchange: Dispersals, Tectonics, Climate, Sea Level and Holding Pens

Paleogene Land Mammal Faunas of South America; a Response to Global Climatic Changes and Indigenous Floral Diversity

Biochronological relationships of the earliest south american paleogene mammalian faunas

Cenozoic mammals of North America : geochronology and biostratigraphy

3. Paleocene Biochronology: The Puercan Through Clarkforkian Land Mammal Ages