BackgroundThe 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.ResultsWe 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.ConclusionThe 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.

ABSTRACT. A new eucryptodiran turtle, Xinjiangchelys qiguensis sp. nov. from the Upper Jurassic (Oxfordian ± ?Kimmeridgian) Qigu Formation of the southern Junggar Basin (north-west China) is described. The type material consists of a partial skeleton, including the complete carapace, plastron, nearly all cervical vertebrae, both scapulae, the pelvis and one ulna. It is clearly identi®able as a basal eucryptodire since it lacks the mesoplastron. It is distinguished from other species of Xinjiangchelys by several autapomorphies of the carapace and plastron, such as the ®rst and ®fth vertebrals extending on the peripherals, the plastron with three pairs of gulars, and an intergular which does not contact the hyoplastron. In the postcranium, the scapula with a long acromial and a small scapular process, the pelvis with a short ilial shaft and the elongated cervical vertebrae are characteristic. A new phylogenetic analysis of the in-group phylogeny of the Xinjiangchelyidae is proposed and discussed, resulting in a new classi®cation of the family. Xinjiangchelys (Toxocheloides) narynensis is regarded as a nomen dubium. Shartegemys is referred to Xinjiangchelys, whereas the holotypes of`Plesiochelys' chungkingensis and`P'. latimarginalis are excluded from the genus Xinjiangchelys but included in the Xinjiangchelyidae.KEY WORDS: Testudines, Eucryptodira, Xinjiangchelyidae, phylogeny, Upper Jurassic, Junggar Basin, China. I T has long been known that the Junggar Basin is very rich in fossil vertebrates and it is not surprising that this interesting region has been under study for many years. Much work was done during the expeditions of the Sino-Canadian Dinosaur Project (1987±90). They focused on the north-eastern and central parts of the Junggar Basin, where they collected several complete dinosaurs, turtles and other faunal elements from the Middle Jurassic Wucaiwan and Upper Jurassic Shishugou formations at the Jiangjunmiao and Pingfengshan localities.The new Sino-German Cooperation Project (SGP) (Maisch et al. 2001; Maisch et al. 2003) with teams from the Geological Survey No.1 of Xinjiang, the Nanjing Institute of Geology and Paleontology of the Academia Sinica, the Paleontology Institute of the Jilin University, Changchun, and the Institut fu Èr Geologie und Pala Èontologie der Universita Èt Tu Èbingen started extensive ®eldwork in 2000 around the city of Urumchi, along the southern margin of the Junggar Basin. The main outcrops investigated belong to the Middle Jurassic Toutunhe Formation and the Upper Jurassic Qigu Formation. The only fossil vertebrates hitherto described from this region are the ankylosaur Tianchisaurus nedegoapeferima and associated theropod remains from the Toutunhe Formation near Fukan (Dong 1993).In this paper we describe the ®rst vertebrate fossil, a well-preserved xinjiangchelyid turtle, from the Qigu Formation. It was found west of the Toutunhe River in the Liuhonggou section (Hendrix et al. 1992) approximately 40 km south-west of Urumchi. It clearly belongs to the genus Xinjiangchelys. ...

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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.

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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).

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.