A new specimen of Solnhofia parsonsi from the Upper Jurassic (Kimmeridgian) Plattenkalk deposits of Painten (Bavaria, Germany) and comments on the relationship between limb taphonomy and habitat ecology in fossil turtles.

The limestones of the Solnhofen area in southern Germany are one of the most important fossil Lagerstätten from the entire Mesozoic era, especially famous for the exquisitely preserved vertebrates. The turtles from the Solnhofen Limestone have been always of special interest because they include some of the best-preserved specimens from the Mesozoic. Here, we describe a new turtle specimen from the Torleite Formation (Kimmeridgian) of Painten and refer it to the thalassochelydian turtle Solnhofia parsonsi based on the presence of a unique combination of characters. The far majority of morphological differences from previously published specimens can be explained by ontogeny as the new specimen represents a larger, more ossified, and presumably older individual. Additionally, the specimen from Painten is the first described specimen of S. parsonsi preserving the largely complete and articulated limbs, the preservation of which indicates that the taxon did not possess stiffened paddles present in more pelagic marine turtles and is consistent with a previously inferred nearshore marine lifestyle. Contrary to previous inferences, we argue that taphonomic preservation of digits in articulated fossil turtles from laminated deposits cannot be used alone to infer marine or freshwater habitat. Finally, the new specimen from Painten is only the second, for which detailed information on its stratigraphic position and locality of origin are known.

The smallest eating the largest: the oldest mammalian feeding traces on dinosaur bone from the Late Jurassic of the Junggar Basin (northwestern China).

Reconstructing trophic interactions in ancient ecosystems is an important and fascinating branch of palaeontological research. Here we describe small bioerosional traces that are preserved on sauropod bone from the early Late Jurassic Qigu Formation (Oxfordian) of Liuhuanggou gorge in the southern Junggar Basin (Xinjiang Province, northwestern China). The most likely producers of these traces are tiny Mesozoic mammals as evinced by the small size of the traces as well as by their paired and opposed arrangement. The feeding traces are only superficially preserved on the bone surface and most likely were inflicted unintentionally during feeding. The occurrence of the bite marks along small ridges and the "gnawed" appearance of the bone surface points to selective feeding on the remaining soft tissues of the dinosaur carcass. The traces represent the oldest direct evidence for mammalian feeding behaviour in the fossil record. Additionally, these traces expand the known range of the early mammalian feeding repertoire significantly and shed light on the palaeobiology and palaeoecology of early mammals, a field that has remained evasive for a long time.

The Beaver's Phylogenetic Lineage Illuminated by Retroposon Reads.

Solving problematic phylogenetic relationships often requires high quality genome data. However, for many organisms such data are still not available. Among rodents, the phylogenetic position of the beaver has always attracted special interest. The arrangement of the beaver's masseter (jaw-closer) muscle once suggested a strong affinity to some sciurid rodents (e.g., squirrels), placing them in the Sciuromorpha suborder. Modern molecular data, however, suggested a closer relationship of beaver to the representatives of the mouse-related clade, but significant data from virtually homoplasy-free markers (for example retroposon insertions) for the exact position of the beaver have not been available. We derived a gross genome assembly from deposited genomic Illumina paired-end reads and extracted thousands of potential phylogenetically informative retroposon markers using the new bioinformatics coordinate extractor fastCOEX, enabling us to evaluate different hypotheses for the phylogenetic position of the beaver. Comparative results provided significant support for a clear relationship between beavers (Castoridae) and kangaroo rat-related species (Geomyoidea) (p < 0.0015, six markers, no conflicting data) within a significantly supported mouse-related clade (including Myodonta, Anomaluromorpha, and Castorimorpha) (p < 0.0015, six markers, no conflicting data).

Retroposon insertion patterns of neoavian birds: strong evidence for an extensive incomplete lineage sorting era.

More than 150 Ma, the avian lineage separated from that of other dinosaurs and later diversified into the more than 10,000 species extant today. The early neoavian bird radiations most likely occurred in the late Cretaceous (more than 65 Ma) but left behind few if any molecular signals of their archaic evolutionary past. Retroposed elements, once established in an ancestral population, are highly valuable, virtually homoplasy-free markers of species evolution; after applying stringent orthology criteria, their phylogenetically informative presence/absence patterns are free of random noise and independent of evolutionary rate or nucleotide composition effects. We screened for early neoavian orthologous retroposon insertions and identified six markers with conflicting presence/absence patterns, whereas six additional retroposons established before or after the presumed major neoavian radiation show consistent phylogenetic patterns. The exceptionally frequent conflicting retroposon presence/absence patterns of neoavian orders are strong indicators of an extensive incomplete lineage sorting era, potentially induced by an early rapid successive speciation of ancestral Neoaves.

Retroposon insertions provide insights into deep lagomorph evolution.

The homogenous mammalian order Lagomorpha comprises about 80 species in two families, Ochotonidae (pikas) and Leporidae (rabbits and hares). However, the phylogenetic relationships among leporids are controversial. Molecular data, particularly from mitochondrial sequences, give highly homoplasious signals. To resolve the controversy between mitochondrial and nuclear data, we analyzed genomic orthologous retroposon insertion sites, a virtually homoplasy-free marker system. From a differential screen of rabbit genomic data for intronic retroposon insertions of CSINE elements, we polymerase chain reaction-amplified and sequenced 11 retroposons in eight representative lagomorphs. We found three retroposons shared among all lagomorphs but absent in outgroups, four confirmed the monophyly of leporids, and three significantly supported Pronolagus as the sister group to all other leporids. One retroposon supported the monophyly of Lepus. The position of Pronolagus outside of the remaining leporids supports the sequence-based signals of nuclear genes and clearly refutes the misleading signals of mitochondrial genes.

Waves of genomic hitchhikers shed light on the evolution of gamebirds (Aves: Galliformes).

BACKGROUND: The phylogenetic tree of Galliformes (gamebirds, including megapodes, currassows, guinea fowl, New and Old World quails, chicken, pheasants, grouse, and turkeys) has been considerably remodeled over the last decades as new data and analytical methods became available. Analyzing presence/absence patterns of retroposed elements avoids the problems of homoplastic characters inherent in other methodologies. In gamebirds, chicken repeats 1 (CR1) are the most prevalent retroposed elements, but little is known about the activity of their various subtypes over time. Ascertaining the fixation patterns of CR1 elements would help unravel the phylogeny of gamebirds and other poorly resolved avian clades. RESULTS: We analyzed 1,978 nested CR1 elements and developed a multidimensional approach taking advantage of their transposition in transposition character (TinT) to characterize the fixation patterns of all 22 known chicken CR1 subtypes. The presence/absence patterns of those elements that were active at different periods of gamebird evolution provided evidence for a clade (Cracidae + (Numididae + (Odontophoridae + Phasianidae))) not including Megapodiidae; and for Rollulus as the sister taxon of the other analyzed Phasianidae. Genomic trace sequences of the turkey genome further demonstrated that the endangered African Congo Peafowl (Afropavo congensis) is the sister taxon of the Asian Peafowl (Pavo), rejecting other predominantly morphology-based groupings, and that phasianids are monophyletic, including the sister taxa Tetraoninae and Meleagridinae. CONCLUSION: The TinT information concerning relative fixation times of CR1 subtypes enabled us to efficiently investigate gamebird phylogeny and to reconstruct an unambiguous tree topology. This method should provide a useful tool for investigations in other taxonomic groups as well.

The first haramiyoid mammal from Asia.

A lower molar of a haramiyoid mammal is described from the Toutunhe Formation of Liuhuanggou near Urumqi in the southern Junggar Basin, Xinjiang, China. It is referred to Eleutherodon sp., otherwise exclusively known from the Upper Bathonian of England. It is the first record of the order Haramiyida from Asia and the first Mesozoic mammal described from the southern Junggar Basin. Apart from the English specimens of Eleutherodon and Staffia from the Upper Jurassic of East Africa, it is the geologically youngest haramiyoid known. It is the first vertebrate taxon from the Toutunhe Formation that is probably not endemic and lends some support to the dating of the Formation as late Middle Jurassic, probably Bathonian.

A relict trematosauroid (Amphibia: Temnospondyli) from the Middle Jurassic of the Junggar Basin (NW China).

A temnospondyl ilium from the uppermost Toutunhe Formation (Middle Jurassic, Callovian) of the southern Junggar Basin is described. Among the known temnospondyls it is very unusual in morphology because of its very long and slender shaft. It compares closely only to the ilium of one of the latest known trematosaurids from the Ladinian of southern Germany. The Toutunhe Formation has also yielded vertebrae and skull fragments of temnospondyls which belong to the brachyopid Gobiops from the Upper Jurassic of Mongolia. Brachyopoid ilia do not, however, display a morphology similar to that of the new specimen. It is therefore concluded that this specimen represents a second taxon of temnospondyl from the Toutunhe Formation, which probably represents the latest surviving trematosauroid. The Trematosauroidea, which was hitherto exclusively known from the Lower to early Upper Triassic, therefore joins the Brachyopoidea--and possibly the Capitosauroidea --as another group of temnospondyls which survived the end--Triassic mass extinction.