Bayesian total evidence dating reveals the recent crown radiation of penguins

The total-evidence approach to divergence-time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describing the diversification and fossilization process and can produce estimates that lead to erroneous conclusions. We address this shortcoming by providing a total-evidence method implemented in a Bayesian framework. This approach uses a mechanistic tree prior to describe the underlying diversification process that generated the tree of extant and fossil taxa. Previous attempts to apply the total-evidence approach have used tree priors that do not account for the possibility that fossil samples may be direct ancestors of other samples. The fossilized birth-death (FBD) process explicitly models the diversification, fossilization, and sampling processes and naturally allows for sampled ancestors. This model was recently applied to estimate divergence times based on molecular data and fossil occurrence dates. We incorporate the FBD model and a model of morphological trait evolution into a Bayesian total-evidence approach to dating species phylogenies. We apply this method to extant and fossil penguins and show that the modern penguins radiated much more recently than has been previously estimated, with the basal divergence in the crown clade occurring at ~12.7 Ma and most splits leading to extant species occurring in the last 2 million years. Our results demonstrate that including stem-fossil diversity can greatly improve the estimates of the divergence times of crown taxa. The method is available in BEAST2 (v. 2.4) www.beast2.org with packages SA (v. at least 1.1.4) and morph-models (v. at least 1.0.4).Comment: 50 pages, 6 figure

New material of Erketu ellisoni.

27 p. : ill. ; 26 cm. "October 22, 2010."Phylogenetic relationships among the diverse Cretaceous sauropods of East Asia have long been controversial. Debate has centered on whether there is any evidence for an endemic clade of Asian species ("Euhelopodidae") and on the placement of these taxa within the context of higher sauropod phylogeny. While most Cretaceous sauropod taxa from Asia are recognized as part of Somphospondyli, recent discoveries have suggested Brachiosauridae may have dispersed into Asia as well. We present new fossils and analyses bearing on these issues. Additional material of the holotype individual of Erketu ellisoni recovered on a subsequent visit to the type locality expands the character data available for this unique sauropod. Associated sauropod dorsal and caudal vertebrae were collected from the same horizon, at a location approximately 2 km from the holotype excavation. The dorsal vertebra exhibits synapomorphies suggesting a representative of Titanosauria co-occurred with Erketu ellisoni. These new specimens, as well as recent discoveries of contemporary Asian sauropod taxa, allow a basis for phylogenetic reappraisal of Erketu and related taxa. Phylogenetic results support a sister group relationship between the Asian Cretaceous sauropods Erketu and Qiaowanlong. Although Qiaowanlong was described as a brachiosaurid, it joins Erketu on the somphospondylian side of the Brachiosauridae-Somphospondyli divergence, erasing the evidence for the dispersal of Brachiosauridae into Asia

Insulin resistance indexes in women with premature ovarian insufficiency — a pilot study

  Objectives: Premature ovarian insufficiency (POI) is associated with hypoestrogenism and an increased risk of metabolic disorders. In many clinics, a variety of insulin resistance (IR) tests are used during routine clinical assessments. To date, there is no clear opinion about which of these tests should be applied in women with premature ovarian insufficiency (POI). Therefore, our preliminarily aim was to compare the most frequently used insulin resistance indexes in the clinical assessment of a group of POI women and a control group. Material and methods: Our retrospective study included 98 women with karyotypically normal spontaneous POI aged 18–39 years and a control group of 78 healthy women. Each patient was given an oral glucose tolerance test (OGTT) to evaluate their insulin release and insulin resistance. In addition, each woman’s insulin resistance (IR) was evaluated us­ing the homeostasis model assessment for insulin resistance (HOMA-IR), the quantitative insulin sensitivity check index (QUICKI), the fasting glucose-to-insulin ratio (FGIR), and Matsuda and McAuley indexes. The two groups’ glucose levels were compared at 0, 60 and 120 min of the OGTT. Results: At 0 and 60 min of the OGTT, the insulin levels of the POI women were significantly higher than those of the control group. The number of women in whom IR was detected using the various kits was comparable between the two groups. Conlusions: In conclusion, only the OGTT evaluation revealed a significant difference in insulin concentrations between the two study groups. The indexes most commonly used to detect IR did not detect differences in IR between the POI women and the members of the healthy control group. QUICKI detected significantly more women with IR within both study groups than other tests did

New material of Paleocene-eocene pellornis (aves: Gruiformes) clarifies the pattern and timing of the extant gruiform radiation

Pellornis mikkelseni is an early gruiform from the latest Paleocene-earliest Eocene Fur Formation of Denmark. At approximately 54 million years old, it is among the earliest clear records of the Gruiformes. The holotype specimen, and only material thus far recognised, was originally considered to comprise a partial postcranial skeleton. However, additional mechanical preparation of the nodule containing the holotype revealed that the skeleton is nearly complete and includes a well-preserved skull. In addition to extracting new information from the holotype, we identify and describe two additional specimens of P. mikkelseni which reveal further morphological details of the skeleton. Together, these specimens show that P. mikkelseni possessed a schizorhinal skull and shared many features with the well-known Paleogene Messelornithidae (“Messel rails”). To reassess the phylogenetic position of P. mikkelseni, we modified an existing morphological dataset by adding 20 characters, four extant gruiform taxa, six extinct gruiform taxa, and novel scorings based on the holotype and referred specimens. Phylogenetic analyses recover a clade containing P. mikkelseni, Messelornis, Songzia and crown Ralloidea, supporting P. mikkelseni as a crown gruiform. The phylogenetic position of P. mikkelseni illustrates that some recent divergence time analyses have underestimated the age of crown Gruiformes. Our results suggest a Paleocene origin for this important clade, bolstering evidence for a rapid early radiation of Neoaves following the end-Cretaceous mass extinction.</jats:p

Fossil record of penguins.

77 p. : ill., map ; 26 cm. "Issued June 3, 2010." Includes bibliographical references (p. 47-53).We present the first detailed description of Perudyptes devriesi, a basal penguin from the middle Eocene (~42 Ma) Paracas Formation of Peru, and a new analysis of all published extinct penguin species as well as controversial fragmentary specimens. The Perudyptes devriesi holotype includes key regions of the skull and significant postcranial material, thus helping to fill a major phylogenetic and stratigraphic (~20 million year) gap between the earliest fossil penguins (Waimanu manneringi and Waimanu tuatahi, ~58-61.6 Ma) and the next oldest partial skeletons. Perudyptes devriesi is diagnosable by five autapomorphies: (1) an anteroventrally directed postorbital process, (2) marked anterior expansion of the parasphenoid rostrum, (3) posterior trochlear ridge of the humerus projecting distal to the middle trochlear ridge and conformed as a large, broadly curved surface, (4) convex articular surface for the antitrochanter of the femur, and (5) extremely weak anterior projection of the lateral condyle of the tibiotarsus. The skull of Perudyptes is characterized by deep temporal fossae and an elongate, narrow beak that differs from other reported stem penguins in its short mandibular symphysis. The wing skeleton of Perudyptes preserves a combination of plesiomorphic features also observed in the basal penguin Waimanu and derived features shared with more crownward penguins. Features of the wing optimized as primitive for Sphenisciformes include retention of a discrete dorsal supracondylar tubercle on the humerus and presence of a modestly projected pisiform process on the carpometacarpus. Derived features present in Perudyptes and all more crownward penguins, but absent in Waimanu, include a more flattened humerus, development of a trochlea for the tendon of m. scapulotriceps at the distal end of the humerus, and bowing of the anterior face of the carpometacarpus. A combined molecular and morphological dataset for Spheniciformes was expanded by adding 25 osteological and soft tissue characters as well as 11 taxa. In agreement with previous results, Perudyptes devriesi is identified as one of the most basal members of Sphenisciformes. This analysis also confirms the placement of the middle/late Miocene (~11-13 Ma) fossil Spheniscus muizoni as a member of the Spheniscus clade and places the late Miocene (~10 Ma) Madrynornis mirandus as sister taxon to extant Eudyptes. These two species, known from relatively complete partial skeletons, are the oldest crown clade penguin fossils and represent well-corroborated temporal calibration points for the Spheniscus-Eudyptula divergence and Megadyptes-Eudyptes divergence, respectively. Our results reaffirm that the Miocene penguin taxon Palaeospheniscus, recently proposed to represent a member of the crown radiation, belongs outside of the crown clade Spheniscidae. The phylogenetic positions of small Eocene Antarctic penguin taxa (Delphinornis, Marambiornis, and Mesetaornis) recently proposed as possible direct ancestors to crown Spheniscidae were further evaluated using alternate coding strategies for incorporating scorings from isolated elements that preserve critical morphologies and are thought to represent these taxa, although they cannot yet be reliably assigned to individual species. Under all scoring regimes, Delphinornis, Marambiornis, and Mesetaornis were recovered as distantly related to Spheniscidae. Using synapomorphies identified in the primary analysis, we evaluated the phylogenetic position of fragmentary specimens, including the holotypes of valid but poorly known species, specimens currently unassignable to the species level, and morphologically distinct specimens that have not yet been named. All pre-Miocene specimens can be excluded from Spheniscidae based on presence of plesiomorphies lost in all crown penguins, consistent with a recent radiation for the penguin crown clade. This study provides additional support for a scenario of penguin evolution characterized by an origin of flightlessness near the K-T boundary, dispersal throughout the Southern Hemisphere during the early Paleogene, and a late Cenozoic origin for the crown clade Spheniscidae. Stratigraphic distribution and phylogenetic relationships of fossil penguins are consistent with distinct radiations during the Eocene, Oligocene, and Miocene. While the Eocene and Oligocene penguin faunas are similar in many respects, the Miocene fauna is characterized by smaller average size and novel cranial morphologies, suggesting that an ecological shift in diet occurred close to the origin of crown Spheniscidae

Ornithomimosaur remains

4 p. : 1 ill. ; 26 cm.Includes bibliographical references (p. 4).The 1998 American Museum of Natural History-Mongolian Academy of Sciences expedition uncovered partial ornithomimosaur remains from the Xanadu sublocality at Uhkaa Tolgod. The specimen includes the rostral portion of the snout, the anterior portion of the mandible, and vertebral fragments. These remains cannot be assigned with certainty to any known ornithomimosaur genus. Examination of these materials allows new comments on ornithomimosaur palatal anatomy

Cancellous bone and theropod dinosaur locomotion. Part I—an examination of cancellous bone architecture in the hindlimb bones of theropods

This paper is the first of a three-part series that investigates the architecture of cancellous (‘spongy’) bone in the main hindlimb bones of theropod dinosaurs, and uses cancellous bone architectural patterns to infer locomotor biomechanics in extinct non-avian species. Cancellous bone is widely known to be highly sensitive to its mechanical environment, and has previously been used to infer locomotor biomechanics in extinct tetrapod vertebrates, especially primates. Despite great promise, cancellous bone architecture has remained little utilized for investigating locomotion in many other extinct vertebrate groups, such as dinosaurs. Documentation and quantification of architectural patterns across a whole bone, and across multiple bones, can provide much information on cancellous bone architectural patterns and variation across species. Additionally, this also lends itself to analysis of the musculoskeletal biomechanical factors involved in a direct, mechanistic fashion. On this premise, computed tomographic and image analysis techniques were used to describe and analyse the three-dimensional architecture of cancellous bone in the main hindlimb bones of theropod dinosaurs for the first time. A comprehensive survey across many extant and extinct species is produced, identifying several patterns of similarity and contrast between groups. For instance, more stemward non-avian theropods (e.g. ceratosaurs and tyrannosaurids) exhibit cancellous bone architectures more comparable to that present in humans, whereas species more closely related to birds (e.g. paravians) exhibit architectural patterns bearing greater similarity to those of extant birds. Many of the observed patterns may be linked to particular aspects of locomotor biomechanics, such as the degree of hip or knee flexion during stance and gait. A further important observation is the abundance of markedly oblique trabeculae in the diaphyses of the femur and tibia of birds, which in large species produces spiralling patterns along the endosteal surface. Not only do these observations provide new insight into theropod anatomy and behaviour, they also provide the foundation for mechanistic testing of locomotor hypotheses via musculoskeletal biomechanical modelling

The evolution of mammalian brain size

Relative brain size has long been considered a reflection of cognitive capacities and has played a fundamental role in developing core theories in the life sciences. Yet, the notion that relative brain size validly represents selection on brain size relies on the untested assumptions that brain-body allometry is restrained to a stable scaling relationship across species and that any deviation from this slope is due to selection on brain size. Using the largest fossil and extant dataset yet assembled, we find that shifts in allometric slope underpin major transitions in mammalian evolution and are often primarily characterized by marked changes in body size. Our results reveal that the largest-brained mammals achieved large relative brain sizes by highly divergent paths. These findings prompt a reevaluation of the traditional paradigm of relative brain size and open new opportunities to improve our understanding of the genetic and developmental mechanisms that influence brain size

Effects of dietary mycotoxins and mycotoxin adsorbent additives on production performance, hematological parameters, and liver histology in juvenile Nile tilapia (Oreochromis niloticus)

Mycotoxins are fungal secondary metabolites that can adversely affect animals consuming contaminated feeds. This 71-day feeding trial was conducted to assess the effects of dietary deoxynivalenol plus zearalenone (DON+ZEN = 1.6 + 0.3 ppm), and fumonisins (FUM = 15 ppm), and three adsorbent additives on the production performance, hematological parameters, and liver histology of juvenile Nile tilapia. A mycotoxin-free diet (Control) formulated to contain 35% protein and 8% lipid was spiked with either DON+ZEN or FUM using contaminated corn meals replacing portions of non-spiked corn. Subsequently, three out of four DON+ZEN- and FUM-spiked diets were supplemented (0.5%) with an adsorbent. The research was carried out in a recirculating water system (2,500 L) with a controlled temperature of (25.9 ± 1.1°C), feeding was carried out twice a day at rates ranging from 5 to 8%. The experiment included nine treatments with five replications, each experimental unit consisting of an aquarium with a useful volume of 75-L and fifteen juvenile Nile tilapia (average initial weight of 4.0 ± 0.1 g). Mycotoxin-spiked diets without added adsorbent supported lower final biomass and survival of Nile tilapia relative to control and adsorbent containing diets (P ≤ 0.05). Histological examinations revealed liver inflammation evidenced by lymphocytic infiltration adjacent to pancreatic tissue in fish fed mycotoxin-spiked diets without added adsorbent. Mycotoxin contamination significantly increased HSI (hepato somatic index), which was reverted to the Control value or reduced further by adsorbent addition. Lowest and intermediate hematocrit values were observed in groups fed mycotoxin-spiked diets without and with added adsorbents, respectively. Our results reinforce the importance of using adsorbents and the need to investigate the effect of sub-lethal concentrations of mycotoxins in aquaculture feeds