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High-throughput sequences were generated from DNA and cDNA from four Southern white rhinoceros (Ceratotherium simum simum) located in the Taronga Western Plain Zoo in Australia. Virome analysis identified reads that were similar to Mus caroli endogenous gammaretrovirus (McERV). Previous analysis of perissodactyl genomes did not recover gammaretroviruses. Our analysis, including the screening of the updated white rhinoceros (Ceratotherium simum) and black rhinoceros (Diceros bicornis) draft genomes identified high-copy orthologous gammaretroviral ERVs. Screening of Asian rhinoceros, extinct rhinoceros, domestic horse, and tapir genomes did not identify related gammaretroviral sequences in these species. The newly identified proviral sequences were designated SimumERV and DicerosERV for the white and black rhinoceros retroviruses, respectively. Two long terminal repeat (LTR) variants (LTR-A and LTR-B) were identified in the black rhinoceros, with different copy numbers associated with each (n = 101 and 373, respectively). Only the LTR-A lineage (n = 467) was found in the white rhinoceros. The African and Asian rhinoceros lineages diverged approximately 16 million years ago. Divergence age estimation of the identified proviruses suggests that the exogenous retroviral ancestor of the African rhinoceros ERVs colonized their genomes within the last 8 million years, a result consistent with the absence of these gammaretroviruses from Asian rhinoceros and other perissodactyls. The black rhinoceros germ line was colonized by two lineages of closely related retroviruses and white rhinoceros by one. Phylogenetic analysis indicates a close evolutionary relationship with ERVs of rodents including sympatric African rats, suggesting a possible African origin of the identified rhinoceros gammaretroviruses. IMPORTANCE Rhinoceros genomes were thought to be devoid of gammaretroviruses, as has been determined for other perissodactyls (horses, tapirs, and rhinoceros). While this may be true of most rhinoceros, the African white and black rhinoceros genomes have been colonized by evolutionarily young gammaretroviruses (SimumERV and DicerosERV for the white and black rhinoceros, respectively). These high-copy endogenous retroviruses (ERVs) may have expanded in multiple waves. The closest relative of SimumERV and DicerosERV is found in rodents, including African endemic species. Restriction of the ERVs to African rhinoceros suggests an African origin for the rhinoceros gammaretroviruses. [ABSTRACT FROM AUTHOR]

The Lophiodontidae is an emblematic and well-documented Eocene family of perissodactyls from Western Europe. However, after more than a century and a half of studies, lophiodontids still display a complex systematics associated with blurry intraspecific variation and a poorly known early radiation. The locality of La Borie, located near the city of Toulouse, France, has yielded numerous remains of Eolophiodon laboriense. This abundance of remains allows for the first time the study of the intraspecific variation of a basal lophiodontid. The variation has been investigated for dental and cranio-mandibular characters, notably dental polymorphism, size variation and sexual dimorphism. The intraspecific variation of E. laboriense is high with more than 20 polymorphic characters of the dentition, including many additional crests and conules. This dental polymorphism is similar to the one observed in the Bartonian lophiodontid Lophiodon lautricense. E. laboriense also displays an important degree of sexual dimorphism, with male specimens having broader and longer mandibles with larger canines than females. Despite this high intraspecific variation, the low size variation of teeth and the consistency of diagnostic characters strengthen the validity of the genus Eolophiodon and does not impact the previous lophiodontid phylogeny. [ABSTRACT FROM AUTHOR]

The evolution of mammalian genomes has been shaped by interactions with endogenous retroviruses (ERVs). In this study, we investigated the distribution and diversity of ERVs in the mammalian order Perissodactyla, with a view to understanding their impact on the evolution of modern equids (family Equidae). We characterize the major ERV lineages in the horse genome in terms of their genomic distribution, ancestral genome organization, and time of activity. Our results show that subsequent to their ancestral divergence from rhinoceroses and tapirs, equids acquired four novel ERV lineages. We show that two of these ERV lineages proliferated extensively in the lineage leading to modern horses, and one contains loci that are actively transcribed in specific tissues. In addition, we show that the white rhinoceros has resisted germ line colonization by retroviruses for more than 54 million years--longer than any other extant mammalian species. The map of equine ERVs that we provide here will be of great utility to future studies aiming to investigate the potential functional roles of equine ERVs and their impact on equine evolution. [ABSTRACT FROM AUTHOR]

Tapirs are the only group among the perissodactyls for which no recent description of the gastrointestinal tract (GIT) exists. Historical depictions of the GIT of tapirs suggest a similarity to the GIT of equids, but do not resolve the question whether the isthmus at the caeco-colical junction, and at the transition from the proximal colon to the colon transversum-both evident in horses-occur in tapirs as well. Here, we describe the macroscopic anatomy of the GIT of a captive, adult lowland tapir ( Tapirus terrestris). While similar to equids in terms of the overall design and, in particular, the two mentioned isthmuses, the proximal colon of the tapir appeared less pronounced than in other perissodactyls, resulting in a GIT in which the caecum appeared as the most voluminous fermentation chamber. This finding is supported by the particular location of the ileo-caecal junction, which does not visibly separate the caecum from the colon, or the caecum head from the caecum body, but enters the caecum body in its upper third. [ABSTRACT FROM AUTHOR]

The Eocene–Oligocene transition (~ 34 Ma) was one of the most pronounced episodes of climate change of the Cenozoic. In order to investigate this episode of global climate cooling in North America, we analyzed the carbon and oxygen stable isotope composition of the carbonate component of 19 perissodactyl (horse and rhino) tooth enamel samples from the Eocene–Oligocene rocks of the Cypress Hills Formation (southwestern Saskatchewan, Canada); we then compared the results with previously published data from the US Great Plains (Nebraska, South Dakota, and Wyoming). Average (± 1σ) perissodactyl enamel δ 13 C values (vs. V-PDB) in the Eocene (− 8.8 ± 0.3‰) and Oligocene (− 9.0 ± 0.3‰) are indistinguishable, suggesting no major change in mean annual precipitation in Saskatchewan across the transition. The δ 13 C values in Saskatchewan indicate the presence of arid ecosystems and are slightly higher than those in the US Great Plains, suggesting drier conditions at higher latitudes. With respect to oxygen isotopes, average (± 1σ) perissodactyl enamel δ 18 O values (vs. V-SMOW) in the Eocene (19.8 ± 2.0‰) and Oligocene (20.1 ± 3.6‰) are also indistinguishable, suggesting no change in the δ 18 O of meteoric precipitation across the transition in Saskatchewan. Enamel δ 18 O variability is much larger in the Oligocene vs. Eocene, indicating a large increase in temperature seasonality. This increase in enamel δ 18 O variability is much larger than that recorded in the US Great Plains, suggesting that higher latitudes are more sensitive to major episodes of climate change with respect to temperature seasonality. Finally, our data indicate no major change in the Oligocene vs. Eocene latitudinal gradient in local water δ 18 O in North America, which suggests no change in mean annual temperature gradients across the transition. This result supports the hypothesis that ascribes the climate change of the transition to a drop in atmospheric p CO 2 because climate models show that this mechanism produces uniform cooling at mid-latitudes. [ABSTRACT FROM AUTHOR]

In 1997, coal extraction at the John Henry Mine in western King County, Washington, USA, exposed bedding planes in Eocene sandstone that contained numerous bird and mammal tracks. By the time scientists arrived at the site several months later, the track-bearing surfaces had mostly been obliterated by landslides. Several track specimens were collected but not curated, described, or studied. In 2011, the specimens were found in a storage room at the University of Washington Burke Museum of History and Culture, triggering an investigation that yielded many photographs of the fossil site taken at the time of the 1997 discovery. Perissodactyl mammal tracks are named herein asOplidcatylapes eocenicaichnogenus and ichnospecies nov. Photographs also show a trackway containing eight footprints that have prominent claw impressions. These tracks are inferred to have been made by a creodont, but because of the absence of specimens or track casts to serve as holotypes, ichnotaxonomic names have not been assigned. [ABSTRACT FROM AUTHOR]

In the past few decades, many new discoveries have provided numerous transitional fossils that show the evolution of hoofed mammals from their primitive ancestors. We can now document the origin of the odd-toed perissodactyls, their early evolution when horses, brontotheres, rhinoceroses, and tapirs can barely be distinguished, and the subsequent evolution and radiation of these groups into distinctive lineages with many different species and interesting evolutionary transformations through time. Similarly, we can document the evolution of the even-toed artiodactyls from their earliest roots and their great radiation into pigs, peccaries, hippos, camels, and ruminants. We can trace the complex family histories in the camels and giraffes, whose earliest ancestors did not have humps or long necks and looked nothing like the modern descendants. Even the Proboscidea and Sirenia show many transitional fossils linking them to ancient ancestors that look nothing like modern elephants or manatees. All these facts show that creationist attacks on the fossil record of horses and other hoofed mammals are completely erroneous and deceptive. Their critiques of the evidence of hoofed mammal evolution are based entirely on reading trade books and quoting them out of context, not on any firsthand knowledge or training in paleontology or looking at the actual fossils. [ABSTRACT FROM AUTHOR]

Two mitochondrial genes, the protein-coding cytochrome c oxidase subunit II (COII) gene and a portion of the 12S rRNA gene, were used for phylogenetic investigation of the mammalian order Perissodactyla. The primary objective of the study was to utilize the extensive fossil record of perissodactyls for calibrating molecular clocks and comparing estimates of divergence times using both genes and two fossil calibration points. Secondary objectives included clarification of previously unresolved relationships within Tapiridae and comparison of the results of separate and combined analyses of two genes. Analyses included several perissodactyl lineages representing all three families (Tapiridae, Equidae, and Rhinocerotidae), most extant genera, all four species of tapirs, two to four species of rhinoceros, and two species of Equus. The application of a relatively recent fossil calibration point and a relatively ancient calibration point produced greatly different estimates of evolutionary rates and divergence times for both genes, even though a relative rates test did not find significant rate differences among taxa. A likelihood-ratio test, however, rejected a molecular clock for both genes. Neither calibration point produced estimates of divergence times consistent with paleontological evidence over a range of perissodactyl radiations. The combined analysis of both genes produces a well-resolved phylogeny with Perissodactyla that conforms to traditional views of interfamilial relationships and supports monophyly of neotropical tapirs. Combining the data sets increases support for most nodes but decreases the support for a neotropical tapir clade because the COII and 12S rRNA data sets are in conflict for tapir relationships. [ABSTRACT FROM AUTHOR]