Placental Clades Research Articles

Evolution of a Human-Specific De Novo Open Reading Frame and Its Linked Transcriptional Silencer.

In the human genome, two short open reading frames (ORFs) separated by a transcriptional silencer and a small intervening sequence stem from the gene SMIM45. The two ORFs show different translational characteristics, and they also show divergent patterns of evolutionary development. The studies presented here describe the evolution of the components of SMIM45. One ORF consists of an ultra-conserved 68 amino acid (aa) sequence, whose origins can be traced beyond the evolutionary age of divergence of the elephant shark, ~462 MYA. The silencer also has ancient origins, but it has a complex and divergent pattern of evolutionary formation, as it overlaps both at the 68 aa ORF and the intervening sequence. The other ORF consists of 107 aa. It develops during primate evolution but is found to originate de novo from an ancestral non-coding genomic region with root origins within the Afrothere clade of placental mammals, whose evolutionary age of divergence is ~99 MYA. The formation of the complete 107 aa ORF during primate evolution is outlined, whereby sequence development is found to occur through biased mutations, with disruptive random mutations that also occur but lead to a dead-end. The 107 aa ORF is of particular significance, as there is evidence to suggest it is a protein that may function in human brain development. Its evolutionary formation presents a view of a human-specific ORF and its linked silencer that were predetermined in non-primate ancestral species. The genomic position of the silencer offers interesting possibilities for the regulation of transcription of the 107 aa ORF. A hypothesis is presented with respect to possible spatiotemporal expression of the 107 aa ORF in embryonic tissues.

Evolutionary anatomical and functional characteristics of the intrinsic shoulder and brachial muscles in the northern anteater (Tamandua mexicana).

Tamandua mexicana is an anteater species native from Mexico to Peru. This species is of great evolutionary interest because it belongs to one of the oldest clades of placental mammals in the American continent. This study aimed to describe the origin, insertion, and arterial supply of the intrinsic shoulder and brachial muscles of T. mexicana. We also compared the masses of the functional groups. Gross dissections were performed on both thoracic limbs of 13 cadavers. ANOVA followed by Tukey's test was used for statistical analyses. The subscapularis muscle presents a hiatus to the common tendon of the caput breve of the biceps brachii and coracobrachialis muscles. A variant accessory muscle, the m. articularis humeri lateralis, was found on the lateral surface of the shoulder joint. M. deltoideus pars acromialis has two bellies. The teres major muscle is perforated by the aponeurotic origin of the m. tensor fasciae antebrachii. The triceps brachii has two capita longi. The caput mediale is fused with the m. anconeus medialis. The caput laterale can have an accessory belly as an anatomical variant. Among the functional groups, a significant difference was found between the elbow extensors and flexors, with the latter having the lowest mass. In conclusion, the intrinsic muscles of T. mexicana presented unique features for the species, as well as arrangements in mass distribution that evidence a possible evolutionary convergence among species of the Superorder Xenarthra.

Afrotheria

Elephants and sea cows and tenrecs; hyraxes and aardvarks and sengis and golden moles. What do these very divergent and different looking mammals have in common? They are each other's closest living relatives, and all belong to the placental mammal clade Afrotheria ('African beasts'), which is one of the four major clades of placental mammals along with Xenarthra (anteaters, sloths, armadillos), Euarchontoglires (e.g. rodents, rabbits, primates), and Laurasiatheria (e.g. bats, carnivorans, odd-toed and even-toed ungulates) (Figure 1). Unlike many animal groups that were recognized and named long ago based on anatomical features, the Afrotheria emerged as a natural clade only in the 1990s when molecular techniques were applied to the problem of placental mammal classification. The recognition of Afrotheria represents a triumph of molecular phylogenetics and brings together a fantastically diverse assemblage of placental mammals with widely disparate ecological and morphological adaptations. Although Afrotheria was not previously proposed based on studies of anatomical characters, additional support for the monophyly of this clade comes from geography and the fossil record. Specifically, the six extant orders in Afrotheria share with each other early fossil representatives that are known from Africa or along the margins of the ancient Tethys Sea, hence Afrotheria.

The effects of fossil taxa, hypothetical predicted ancestors, and a molecular scaffold on pseudoextinction analyses of extant placental orders.

Pseudoextinction analyses, which simulate extinction in extant taxa, use molecular phylogenetics to assess the accuracy of morphological phylogenetics. Previous pseudoextinction analyses have shown a failure of morphological phylogenetics to place some individual placental orders in the correct superordinal clade. Recent work suggests that the inclusion of hypothetical ancestors of extant placental clades, estimated by ancestral state reconstructions of morphological characters, may increase the accuracy of morphological phylogenetic analyses. However, these studies reconstructed direct hypothetical ancestors for each extant taxon based on a well-corroborated molecular phylogeny, which is not possible for extinct taxa that lack molecular data. It remains to be determined if pseudoextinct taxa, and by proxy extinct taxa, can be accurately placed when their immediate hypothetical ancestors are unknown. To investigate this, we employed molecular scaffolds with the largest available morphological data set for placental mammals. Each placental order was sequentially treated as pseudoextinct by exempting it from the molecular scaffold and recoding soft morphological characters as missing for all its constituent species. For each pseudoextinct data set, we omitted the pseudoextinct taxon and performed a parsimony ancestral state reconstruction to obtain hypothetical predicted ancestors. Each pseudoextinct order was then evaluated in seven parsimony analyses that employed combinations of fossil taxa, hypothetical predicted ancestors, and a molecular scaffold. In treatments that included fossils, hypothetical predicted ancestors, and a molecular scaffold, only 8 of 19 pseudoextinct placental orders (42%) retained the same interordinal placement as on the molecular scaffold. In treatments that included hypothetical predicted ancestors but not fossils or a scaffold, only four placental orders (21%) were recovered in positions that are congruent with the scaffold. These results indicate that hypothetical predicted ancestors do not increase the accuracy of pseudoextinct taxon placement when the immediate hypothetical ancestor of the taxon is unknown. Hypothetical predicted ancestors are not a panacea for morphological phylogenetics.

On the alleged perissodactyl affinities of the “condylarth” Escribania chubutensis and other endemic South American ungulate-like placentals

ABSTRACT Evolutionary relationships of the endemic South American ungulates (SANUs), both to each other and to other major placental clades, have been robustly debated for more than a century. Morphological evidence has not provided unambiguous resolution of these controversies, although recent paleoproteomic and paleogenomic analyses have supplied unequivocal evidence that at least Litopterna and Notoungulata are most closely related to each other and then to crown Perissodactyla. A recent study based on morphological characters has gone much further, claiming that litopterns and South American condylarths are stem to, or even nested within, Perissodactyla, but are not otherwise related to any North American clades of archaic ungulates. This study also concluded that the alleged shared presence of perissodactyls in Paleogene South America and India, along with several other biological groups, is evidence of a fluid biotic interchange early in the Cenozoic. Our assessment of this study revealed various conceptual and methodological errors, including misinterpretation of homologies, scoring errors, and failure to include relevant taxa such as Notoungulata. Our corrected phylogenetic analysis, performed with essentially the same taxon/character sampling and searching options, recovered all litopterns and their relatives in a single monophyletic clade, separate from the one representing Perissodactyla s.s. Both clades are clearly derived from Laurasian ungulate ancestors. In addition to the absence of true perissodactyls in Paleogene South America, most of the biological groups postulated as shared by both continents are not found in Paleogene strata of India. In sum, there is no meaningful evidence supporting the alleged multiclade, multiterrain biotic interchange.

Historical biogeography of smoothhound sharks (genus Mustelus) of Southern Africa reveals multiple dispersal events from the Northern Hemisphere

Members of the smoothhound shark genus Mustelus display a widespread distribution pattern across ocean basins with a high degree of sub-regional endemism. The patterns and processes that resulted in smoothhound biodiversity and present-day distribution remain largely unknown. We infer the phylogenetic relationships of the genus Mustelus, based on sequence data (3474 bp) from three mitochondrial genes (CR, NADH-2 and 12S-16SrRNA) and a nuclear gene (KBTBD2) from seven species of Mustelus distributed across the eastern Atlantic- and Indo-Pacific oceans. Using the CR and KBTBD2 dataset, we infer the phylogeographic placement of Old World Mustelus, with particular reference to species from southern Africa. Using a near-complete phylogeny of the genus including Old World and New World species of Mustelus and publicly available sequences of the NADH-2 gene, we found supporting evidence indicating a major cladogenic event separating placental and aplacental species. Biogeographical analyses further revealed that the radiation of Mustelus in the southern African region was driven primarily by long-distance dispersal during the upper Miocene to lower Pleistocene. The placement of the placental blackspotted smoothhound Mustelus punctulatus at the base of the placental non-spotted clade suggests the secondary loss of black spots in the genus, and this was also supported by the ancestral state reconstruction. The results furthermore suggest that the Southern Hemisphere species of the genus arose from multiple separate dispersal events from the Northern Hemisphere which is in line with the earliest record of Mustelus in the Northern Hemisphere.

The Extent of Metaplastic Hard Tissue Within the Appendicular Skeleton of the Nine‐Banded Armadillo (Dasypus novemcinctus)

The developmental and functional advantages of vertebrate metaplastic hard tissue is still relatively unclear. Metaplastic tissue forms from the direct transformation of one cell type to another. Specifically, mineralization of preformed dense connective tissue results in intratendinous metaplastic tissue, and has been described in a variety of taxa and elements including turtle shell, reptilian osteoderms, sturgeon scutes, dinosaur cranial and vertebral elements, ossified tendons, portions of bird skeletons, and tendinous entheses in mammalian bone. However, histological analysis of the extent of metaplastic hard tissues, both across Mammalia and within individual mammalian bones, is lacking. Here we serially sectioned both tibiae of a nine‐banded armadillo, Dasypus novemcinctus [Xenarthra: Cingulata], transversely and longitudinally to identify the existence and possible patterns of metaplastic hard tissue. All skeletal elements were processed using standard procedure for the preparation of undecalcified bone. We found evidence of metaplastic hard tissue in the tibial crest, as well as the medial side of the diaphysis and the proximal lateral side of the tibia. The metaplastic tissue in the tibial crest appears interstitially within a primary woven bone matrix. Along the lateral side, metaplastic tissue forms a thin patch in the mid‐cortex superficial to compact coarse cancellous bone. The presence of metaplastic hard tissue seems consistent with tendinous insertions through fibrous entheses along the length of the tibia and tibial crest. The entrapment of metaplastic tissue within the tibia is likely due to appositional bone growth at the enthesis. However, the presence of metaplastic hard tissue on the medial side of the mid‐diaphyseal and proximal portion of the tibia does not appear to be associated with any tendinous insertions. Previously, unassociated metaplastic tissue was found extensively in osteoderms, ankylosaur tail clubs, and dinosaur cranial ornamentation such as the parietal frill of Triceratops. Study of metaplastic hard tissue in modern bone, independent of tendinous insertions, can improve our understanding of its potential biomechanical advantages and thereby possibly provide clues to its use in ornamentation and within the appendicular skeleton. Metaplastic hard tissues have likely been misidentified and understudied in previous investigations of modern hard tissue microstructure. Additionally, because Xenarthra is proposed to be one of the four original clades of placental mammals, analysis of metaplastic tissue in the skeleton of D. novemcinctus could have implications for early mammalian bone development patterns.Support or Funding InformationPartial funding was provided by Montana State University Undergraduate Scholar’s ProgramFigure 1

Molecular evolution of autophagy rate-limiting factor LAMP2 in placental mammals

Autophagy is the cellular process of removal of misfolded or damaged macromolecules and organelles. Experimental studies have demonstrated autophagy as a major mechanism of lifespan extension in long-lived mammals such as bats and mole rat rodents. Moreover, the role of this biological process has been well documented in protection against age-associated diseases and viral infection. However, studies on the molecular adaptive changes of autophagy factors during evolution are scarce. Here, we conducted a bioinformatics study of the molecular evolution of the Lysosomal Associated Membrane Protein 2 (LAMP2), as a rate-limiting factor in the lysosomal degradation stage of autophagy (the communal step of two of autophagy types: macroautophagy and chaperone-mediated). Analyzing LAMP2 across placental mammals, our phylogenetic-based maximum likelihood analyses indicate that the majority of the coding sites undergo purifying selection. However, around 27% of sites display a relaxation of purifying constraints (average ω = 0.42128), among which, 14 particular sites undergo positive selection (ω > 1). These sites are mostly located in the first luminal domain of LAMP2 (N-domain), with a hotspot region in the 135–144 codons interval. Therefore, the N-domain may account for the functional diversity and regulation of LAMP2. In addition, the identified positive selection sites could act as key regulatory sites in the LAMP2 function. On the other hand, testing the rate of evolution in LAMP2 along different clades of placental mammals revealed a relatively relaxed evolution in LAMP2 along megabats’ clade. It is not clear yet whether an expedited evolution of LAMP2 in megabats has contributed to their reported up-regulation of autophagy. Finally, our data indicate positive selection sites along the ancestral branch of the clades of rodents, mouse-related rodents, and mole-rats; and suggest the potentially important regulatory role of these sites in LAMP2. Identifying the residues under positive selection, our findings pave the way for future experimental investigations to define how these selective substitutions have functionally affected autophagy.

Xenarthran Synsacrum Morphology and Evolution

Xenarthra is unique in having striking features in the axial skeleton, usually very different from the rest of the eutherian clades. Some of these features are widely spread among the members of the group (e.g., the presence of xenarthrales in most cingulates and all pilosans, and the synsacrum with sacroischial union to the pelvis in almost all xenarthrans) and others are restricted to some taxa (e.g., deviated number of cervical vertebrae in Bradypus and Choloepus). In this study, we aim to explore the great diversity of vertebral elements composing the xenarthran synsacrum within a phylogenetic framework. Vertebral counts of the adult synsacrum was obtained from almost all extant genera, with the exception of Calyptophractus, and several fossils. The modal number of vertebrae from the adult synsacrum was mapped onto a composite phylogeny of Xenarthra. The ancestral number of synsacrals for Xenarthra was recovered as ambiguous, although one of the optimizations recorded a number of six synsacrals, probably three iliac and three post-iliac vertebrae. The clade Cingulata is characterized by a high number of vertebrae forming the synsacrum (eight synsacrals), which is fused to the ischium through the tip of the transverse processes of the most posterior vertebrae. In pilosans, the ancestral number of synsacral vertebrae seems to be lower, probably formed by five or six vertebrae, and the union with the ischium is achieved through the base of the transverse processes of the most posterior vertebrae. Two exceptions stand out, one involving the extant suspensory sloths and Megalocnus, and the other involving a family of ground sloths, the Mylodontidae. A probable relationship of the synsacral number in the different taxa to the lifestyles is discussed.

The natural selection of metabolism explains curvature in allometric scaling

I simulate the natural selection of metabolism and mass to explain the curvature in the metabolic allometry for placental and marsupial mammals. The simulation model starts with a single ancestor in each clade at the Cretaceous–Palaeogene boundary 65 million years ago. The release of inter‐specific competition by the extinction of dinosaurs make it possible for each clade to diversify into a multitude of species across a wide range of empty niches. The selection of mass in these species depends on the net assimilated energy that depends on 1) the handling of the resources in the different niches, and on 2) mass‐specific metabolism that defines the pace of the handling process. The model is fitted to explain the maximum observed body masses over time and the current inter‐specific allometry for metabolism. The selection of mass‐specific metabolism is found to bend the metabolic allometry over time, even when all species have the same selection on the per‐generation time‐scale of natural selection. This is because the smaller species evolve over a larger number of generations than the larger species. The strongest curvature is in the placental clade, where the estimated rate of exponential increase in mass‐specific metabolism is 9.3 × 10−9 (95% CI: 7.3 × 10−9 – 1.1 × 10−8) on the per‐generation time‐scale. This is an order of magnitude larger than the estimate for marsupials, in agreement with an average metabolism that is 30% larger in placentals relative to marsupials of similar 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.

Inactivation of thermogenic UCP1 as a historical contingency in multiple placental mammal clades.

Mitochondrial uncoupling protein 1 (UCP1) is essential for nonshivering thermogenesis in brown adipose tissue and is widely accepted to have played a key thermoregulatory role in small-bodied and neonatal placental mammals that enabled the exploitation of cold environments. We map ucp1 sequences from 133 mammals onto a species tree constructed from a ~51-kb sequence alignment and show that inactivating mutations have occurred in at least 8 of the 18 traditional placental orders, thereby challenging the physiological importance of UCP1 across Placentalia. Selection and timetree analyses further reveal that ucp1 inactivations temporally correspond with strong secondary reductions in metabolic intensity in xenarthrans and pangolins, or in six other lineages coincided with a ~30 million-year episode of global cooling in the Paleogene that promoted sharp increases in body mass and cladogenesis evident in the fossil record. Our findings also demonstrate that members of various lineages (for example, cetaceans, horses, woolly mammoths, Steller's sea cows) evolved extreme cold hardiness in the absence of UCP1-mediated thermogenesis. Finally, we identify ucp1 inactivation as a historical contingency that is linked to the current low species diversity of clades lacking functional UCP1, thus providing the first evidence for species selection related to the presence or absence of a single gene product.

Orientation of the lateral semicircular canal in Xenarthra and its links with head posture and phylogeny.

The orientation of the semicircular canals of the inner ear in the skull of vertebrates is one of the determinants of the capacity of this system to detect a given rotational movement of the head. Past functional studies on the spatial orientation of the semicircular canals essentially focused on the lateral semicircular canal (LSC), which is supposedly held close to horizontal during rest and/or alert behaviors. However, they generally investigated this feature in only a few and distantly related taxa. Based on 3D-models reconstructed from µCT-scans of skulls, we examined the diversity of orientations of the LSC within one of the four major clades of placental mammals, that is, the superorder Xenarthra, with a data set that includes almost all extant genera and two extinct taxa. We observed a wide diversity of LSC orientations relative to the basicranium at both intraspecific and interspecific scales. The estimated phylogenetic imprint on the orientation of the LSC was significant but rather low within the superorder, though some phylogenetic conservatism was detected for armadillos that were characterized by a strongly tilted LSC. A convergence between extant suspensory sloths was also detected, both genera showing a weakly tilted LSC. Our preliminary analysis of usual head posture in extant xenarthrans based on photographs of living animals further revealed that the LSC orientation in armadillos is congruent with a strongly nose-down head posture. It also portrayed a more complex situation for sloths and anteaters. Finally, we also demonstrate that the conformation of the cranial vault and nuchal crests as well as the orientation of the posterior part of the petrosal may covary with the LSC orientation in Xenarthra. Possible inferences for the head postures of extinct xenarthrans such as giant ground sloths are discussed in the light of these results.

Orientation selectivity in the visual cortex of the nine-banded armadillo.

Orientation selectivity in primary visual cortex (V1) has been proposed to reflect a canonical computation performed by the neocortical circuitry. Although orientation selectivity has been reported in all mammals examined to date, the degree of selectivity and the functional organization of selectivity vary across mammalian clades. The differences in degree of orientation selectivity are large, from reports in marsupials that only a small subset of neurons are selective to studies in carnivores, in which it is rare to find a neuron lacking selectivity. Furthermore, the functional organization in cortex varies in that the primate and carnivore V1 is characterized by an organization in which nearby neurons share orientation preference while other mammals such as rodents and lagomorphs either lack or have only extremely weak clustering. To gain insight into the evolutionary emergence of orientation selectivity, we examined the nine-banded armadillo, a species within the early placental clade Xenarthra. Here we use a combination of neuroimaging, histological, and electrophysiological methods to identify the retinofugal pathways, locate V1, and for the first time examine the functional properties of V1 neurons in the armadillo (Dasypus novemcinctus) V1. Individual neurons were strongly sensitive to the orientation and often the direction of drifting gratings. We uncovered a wide range of orientation preferences but found a bias for horizontal gratings. The presence of strong orientation selectivity in armadillos suggests that the circuitry responsible for this computation is common to all placental mammals.NEW & NOTEWORTHY The current study shows that armadillo primary visual cortex (V1) neurons share the signature properties of V1 neurons of primates, carnivorans, and rodents. Furthermore, these neurons exhibit a degree of selectivity for stimulus orientation and motion direction similar to that found in primate V1. Our findings in armadillo visual cortex suggest that the functional properties of V1 neurons emerged early in the mammalian lineage, near the time of the divergence of marsupials.

What was the ancestral function of decidual stromal cells? A model for the evolution of eutherian pregnancy

In human and mouse, decidual stromal cells (DSC) are necessary for the establishment (implantation) and the maintenance of pregnancy by preventing inflammation and the immune rejection of the semi-allograft conceptus. DSC originated along the stem lineage of eutherian mammals, coincidental with the origin of invasive placentation. Surprisingly, in many eutherian lineages decidual cells are lost after the implantation phase of pregnancy, making it unlikely that DSC are necessary for the maintenance of pregnancy in these animals. In order to understand this variation, we review the literature on the fetal-maternal interface in all major eutherian clades Euarchontoglires, Laurasiatheria, Xenarthra and Afrotheria, as well as the literature about the ancestral eutherian species. We conclude that maintaining pregnancy may not be a shared derived function of DSC among all eutherian mammals. Rather, we propose that DSC originated to manage the inflammatory reaction associated with invasive implantation. We envision that this happened in a stem eutherian that had invasive placenta but still a short gestation. We further propose that extended gestation evolved independently in the major eutherian clades explaining why the major lineages of eutherian mammals differ with respect to the mechanisms maintaining pregnancy.

Shotgun Mitogenomics Provides a Reference Phylogenetic Framework and Timescale for Living Xenarthrans.

Xenarthra (armadillos, sloths, and anteaters) constitutes one of the four major clades of placental mammals. Despite their phylogenetic distinctiveness in mammals, a reference phylogeny is still lacking for the 31 described species. Here we used Illumina shotgun sequencing to assemble 33 new complete mitochondrial genomes, establishing Xenarthra as the first major placental clade to be fully sequenced at the species level for mitogenomes. The resulting data set allowed the reconstruction of a robust phylogenetic framework and timescale that are consistent with previous studies conducted at the genus level using nuclear genes. Incorporating the full species diversity of extant xenarthrans points to a number of inconsistencies in xenarthran systematics and species definition. We propose to split armadillos into two distinct families Dasypodidae (dasypodines) and Chlamyphoridae (euphractines, chlamyphorines, and tolypeutines) to better reflect their ancient divergence, estimated around 42 Ma. Species delimitation within long-nosed armadillos (genus Dasypus) appeared more complex than anticipated, with the discovery of a divergent lineage in French Guiana. Diversification analyses showed Xenarthra to be an ancient clade with a constant diversification rate through time with a species turnover driven by high but constant extinction. We also detected a significant negative correlation between speciation rate and past temperature fluctuations with an increase in speciation rate corresponding to the general cooling observed during the last 15 My. Biogeographic reconstructions identified the tropical rainforest biome of Amazonia and the Guiana Shield as the cradle of xenarthran evolutionary history with subsequent dispersions into more open and dry habitats.

Collagen Sequence Analysis of the Extinct Giant Ground Sloths Lestodon and Megatherium.

For over 200 years, fossils of bizarre extinct creatures have been described from the Americas that have ranged from giant ground sloths to the ‘native’ South American ungulates, groups of mammals that evolved in relative isolation on South America. Ground sloths belong to the South American xenarthrans, a group with modern although morphologically and ecologically very different representatives (anteaters, armadillos and sloths), which has been proposed to be one of the four main eutherian clades. Recently, proteomics analyses of bone collagen have recently been used to yield a molecular phylogeny for a range of mammals including the unusual ‘Malagasy aardvark’ shown to be most closely related to the afrotherian tenrecs, and the south American ungulates supporting their morphological association with condylarths. However, proteomics results generate partial sequence information that could impact upon the phylogenetic placement that has not been appropriately tested. For comparison, this paper examines the phylogenetic potential of proteomics-based sequencing through the analysis of collagen extracted from two extinct giant ground sloths, Lestodon and Megatherium. The ground sloths were placed as sister taxa to extant sloths, but with a closer relationship between Lestodon and the extant sloths than the basal Megatherium. These results highlight that proteomics methods could yield plausible phylogenies that share similarities with other methods, but have the potential to be more useful in fossils beyond the limits of ancient DNA survival.

The ear region of earliest known elephant relatives: new light on the ancestral morphotype of proboscideans and afrotherians.

One of the last major clades of placental mammals recognized was the Afrotheria, which comprises all main endemic African mammals. This group includes the ungulate-like paenungulates, and among them the elephant order Proboscidea. Among afrotherians, the petrosal anatomy remains especially poorly known in Proboscidea. We provide here the first comparative CT scan study of the ear region of the two earliest known proboscideans (and paenungulates), Eritherium and Phosphatherium, from the mid Palaeocene and early Eocene of Morocco. It is helpful to characterize the ancestral morphotype of Proboscidea to understand petrosal evolution within proboscideans and afrotherians. The petrosal structure of these two taxa shows several differences. Eritherium is more primitive than Phosphatherium and closer to the basal paenungulate Ocepeia in several traits (inflated tegmen tympani, very deep fossa subarcuata and ossified canal for ramus superior of stapedial artery). Phosphatherium, however, retains plesiomorphies such as a true crus commune secundaria. A cladistic analysis of petrosal traits of Eritherium and Phosphatherium among Proboscidea results in a single tree with a low level of homoplasy in which Eritherium, Phosphatherium and Numidotherium are basal. This contrasts with previous phylogenetic studies showing homoplasy in petrosal evolution among Tethytheria. It suggests that evolutionary modalities of petrosal characters differ with the taxonomic level among Afrotheria: noticeable convergences occurred among the paenungulate orders, whereas little homoplasy seems to have occurred at intra-ordinal level in orders such as Proboscidea. Most petrosal features of both Eritherium and Phosphatherium are primitive. The ancestral petrosal morphotype of Proboscidea was not specialized but was close to the generalized condition of paenungulates, afrotherians, and even eutherians. This is consistent with cranial and dental characters of Eritherium, suggesting that the ancestral morphotypes of the different paenungulate orders were close to each other. Specializations occurred rapidly after the ordinal radiation of Paenungulata.

Why do Xenarthrans matter?: Table 1.

Xenarthrans possess a suite of characteristics that make them among the most unusual of mammals. Understanding the functional significance of these traits is one prominent reason why xenarthrans matter. In addition, Xenarthra is currently considered one of the basal clades of placental mammals, and the only one to originate in South America. Consequently, studies of xenarthrans can provide important insights into the evolution of early placentals. The fossil record contains hundreds of recognized species of xenarthrans but this rich evolutionary history is currently distilled into just 31 extant species. Preserving this heritage through various conservation initiatives is yet another reason why xenarthrans matter. This Special Feature on xenarthrans provides an overview of current work and identifies many areas requiring further study. It is our hope that this Special Feature will raise the profile of xenarthrans among mammalogists and perhaps entice some to consider addressing one or more of the many lin...

Paleogene Xenarthra and the evolution of South American mammals

Recent studies show Xenarthra to be even more isolated systematically from other placental mammals than traditionally thought. The group not only represents 1 of 4 primary placental clades, but proposed links to other fossorial mammal taxa (e.g., Pholidota, Palaeanodonta) have been contradicted. No unambiguous Paleocene fossil xenarthran remains are known, and Eocene remains consist almost exclusively of isolated cingulate osteoderms and isolated postcrania of uncertain systematic provenance. Cingulate skulls are unknown until the late middle Eocene, and the oldest sloth and anteater skulls are early Oligocene and early Miocene age, respectively; there are no nearly complete xenarthran skeletons until the early Miocene. Ecological reconstructions of early xenarthrans based on extant species and the paleobiology of extinct Neogene taxa suggest the group's progenitors were myrmecophagous with digging and perhaps some climbing adaptations. The earliest cingulates were terrestrial diggers and likely myrmecoph...