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Population analysis of retrotransposons in giraffe genomes supports RTE decline and widespread LINE1 activity in Girafdae

Background: The majority of structural variation in genomes is caused by insertions of transposable elements (TEs). In mammalian genomes, the main TE fraction is made up of autonomous and non-autonomous non-LTR retrotransposons commonly known as LINEs and SINEs (Long and Short Interspersed Nuclear Elements). Here we present one of the first population-level analysis of TE insertions in a non-model organism, the giraffe. Giraffes are ruminant artiodactyls, one of the few mammalian groups with genomes that are colonized by putatively active

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A novel Giraffidae-specific interspersed repeat with a microsatellite, originally found in an intron of a ruminant paralogous p97bcnt gene

The ruminant-specific p97bcnt gene (bcntp97) is a paralogous gene that includes a region derived from a retrotransposable element 1 (RTE-1). The region comprises an exon (RTE-1 exon) encoding 325 amino acids in the middle of the p97bcnt protein. To understand how the bcntp97 paralog evolved, we examined its organization in several ruminants. We found a 700-base pair (bp) insert in the 5Vintron of the RTE- 1 exon in giraffe bcntp97. This insert is missing in the corresponding regions of bovine

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Pushing the boundary? Testing the “functional elongation hypothesis” of the giraffe’s neck

Although giraffes maintain the usual mammalian cervical number of seven vertebrae, their first thoracic vertebra (T1) exhibits aberrant anatomy and has been hypothesized to functionally elongate the neck. We test this “functional elongation hypothesis” by combining phylogenetically informed analyses of neck length, three-dimensional (3D) vertebral shape, and of the functional significance of shape differences across a broad sample of ruminants and camelids. Digital bone models of the cervicothoracic transition were subjected to 3D geometric morphometric analysis revealing how the shape

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The systematic position of Hoplitomerycidae (Ruminantia) revisited

Hoplitomeryx Leinders was originally described only on cranial characters. The type specimens were found during the 1970’s in karstic fissure fillings, most likely of Messinian age, in Gargano (Apulia, southeastern Italy), between Poggio Imperiale (418490300 N, 158210580 E) and Apricena (418470060 N, 158260410 E). During the 1990’s, Hoplitomeryx remains were also discovered in the lower Tortonian layered calcarenites near Scontrone (Abruzzo, central Italy; 41845015.550 N, 14802013.230 E). The skull fragments, teeth, and jawbones from both localities have been examined. The

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Molecular and Morphological Phylogenies of Ruminantia and the Alternative Position of the Moschidae

The ruminants constitute the largest group of ungulates, with >190 species, and its distribution is widespread throughout all continents except Australia and Antarctica. Six families are traditionally recognized within the suborder Ruminantia: Antilocapridae (pronghorns), Bovidae (cattle, sheep, and antelopes), Cervidae (deer), Giraffidae (giraffes and okapis), Moschidae (musk deer), and Tragulidae (chevrotains). The interrelationships of the families have been an area of controversy among morphology, palaeontology, and molecular studies, and almost all possible evolutionary scenarios have been proposed in the literature.

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The phylogeny of Cetartiodactyla: The importance of dense taxon sampling, missing data, and the remarkable promise of cytochrome b to provide reliable species-level phylogenies

We perform Bayesian phylogenetic analyses on cytochrome b sequences from 264 of the 290 extant cetartiodactyl mammals (whales plus even-toed ungulates) and two recently extinct species, the ‘Mouse Goat’ and the ‘Irish Elk’. Previous primary analyses have included only a small portion of the species diversity within Cetartiodactyla, while a complete supertree analysis lacks resolution and branch lengths limiting its utility for comparative studies. The benefits of using a single-gene approach include rapid phylogenetic estimates for a large number of

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New artiodactyl ruminant mammal from the late Oligocene of Pakistan

Dental and postcranial material of the bovid−like ruminant Palaeohypsodontus zinensis sp. nov. is reported from the Oligocene of the Bugti Hills (Balochistan, Pakistan). This finding extends the geographic distribution of this dentally highly derived ruminant, which was previously restricted to the early Oligocene of Mongolia and China. The inclusion of Palaeohypsodontus within the Bovidae is disputed on the basis of astragalus characters, and the taxonomic status of the Oligo−Miocene Eurasian bovid−like ruminants is briefly discussed. It is concluded that the

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First comprehensive morphological analysis on the metapodials of Giraffidae

Giraffids are a group of relict pecoran ruminants with only two living taxa. During the Miocene, however, this group was much more diverse, with more than 20 different species showing a wide range of variability. In addition to many other parts of the skeleton this variability is also represented in their metapodials. We find inter-specific anatomical differences in the giraffid metapodials; each taxon evaluated possesses a unique combination of limb morphologies. The proximo-palmar/plantar metapodial surface provides useful characteristics and allows

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Evolution of ruminant headgear: a review

The horns, ossicones and antlers of ruminants are familiar and diverse examples of cranial appendages. We collectively term ruminant cranial appendages ‘headgear’; this includes four extant forms: antlers (in cervids), horns (in bovids), pronghorns (in pronghorn antelope) and ossicones (in giraffids). Headgear evolution remains an open and intriguing question because phylogenies (molecular and morphological), adult headgear structure and headgear development (where data are available) all suggest different pictures of ruminant evolution. We discuss what is known about the evolution of

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