Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case.

Primates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the Cretaceous-Paleogene (K-Pg) boundary and the timing of diversification of the main crown groups remain controversial. Here, we analysed a data set of 372 taxa (367 Primates and 5 outgroups, 3.4 million aligned base pairs) that includes nine primate genomes. We systematically explore the effect of different interpretations of fossil calibrations and molecular clock models on primate divergence time estimates. We find that even small differences in the construction of fossil calibrations can have a noticeable impact on estimated divergence times, especially for the oldest nodes in the tree. Notably, choice of molecular rate model (autocorrelated or independently distributed rates) has an especially strong effect on estimated times, with the independent rates model producing considerably more ancient age estimates for the deeper nodes in the phylogeny. We implement thermodynamic integration, combined with Gaussian quadrature, in the program MCMCTree, and use it to calculate Bayes factors for clock models. Bayesian model selection indicates that the autocorrelated rates model fits the primate data substantially better, and we conclude that time estimates under this model should be preferred. We show that for eight core nodes in the phylogeny, uncertainty in time estimates is close to the theoretical limit imposed by fossil uncertainties. Thus, these estimates are unlikely to be improved by collecting additional molecular sequence data. All analyses place the origin of Primates close to the K-Pg boundary, either in the Cretaceous or straddling the boundary into the Palaeogene

Sex- and age-specific trends in mortality from suicide and undetermined death in Germany 1991–2002

BACKGROUND: Over the last decade, significant downward linear time trends in suicide mortality were observed in most Western countries. To date, it is not established whether those favourable time trends developed homogeneously for sex and age groups and how they were affected by the number of undetermined deaths. METHODS: Data on suicide mortality and undetermined death from 1991 to 2002 in Germany were obtained from the German Federal Statistical Office. For each year, the age-standardised suicide rate (SR), undetermined death rate (UDR) and total rate (SR+UDR) was calculated by direct standardisation separately for men and women. Time trends were analyzed by Poisson regression estimating the average annual percentage change (AAPC) of the rates for sex and four age groups (15–24, 25–44, 45–74, ≥ 75 years). RESULTS: A significant decline of the SR was observed in all age groups but was less pronounced among the younger ages, particularly among men aged 15–24 years (AAPC -0.7%, p = 0.041). The SR in the oldest male age group (≥ 75 years) declined much stronger (AAPC -3.5%, p < 0.001). In women, the AAPC of the SR ranged from -1.7% to -4.6%. The average annual percentage changes in the age groups 25 – 74 years did not differ substantially for SR and SR+UDR. In contrast, due to an increase of undetermined deaths for subjects ≥ 75 years, time trends in this age group were affected by the number of undetermined deaths, especially in women. CONCLUSION: Observing downward trends in suicide mortality with lower declines for younger subjects, prevention strategies should focus in particular on younger subjects

Dental eruption and growth in Hyracoidea (Mammalia, Afrotheria)

We investigated dental homologies, development, and growth in living and fossil hyracoids, and tested if hyracoids and other mammals show correlations between eruption patterns, gestation time, and age at maturity. Unlike living species, fossil hyracoids simultaneously possess replaced P1 and canine teeth. Fossil species also have shorter crowns, an upper and lower I3 locus, an upper I2, and a hypoconulid on m3. Prenatal specimens of the living $\textit{Procavia capensis}$ and $\textit{Heterohyrax brucei}$ show up to three tooth buds posterior to upper dI1 and anterior to the seven upper cheek teeth that consistently erupt; these include an anterior premolar but not a canine. Most lower cheek teeth finish eruption during growth in hyracoids, not after growth as in most other afrotherians. All hyracoids show the m1 at (lower) or near (upper) the beginning of eruption of permanent teeth; M3/m3 is the last permanent tooth to erupt. The living P. capensis erupts most lower antemolar loci before m2. In contrast, fossil hyraxes erupt lower antemolars after m2. While the early eruption of antemolars correlates with increased gestation time and age at maturity in primates and $\textit{Tupaia}$ (i.e., "Schultz's Rule"), and while modern hyraxes resemble some anthropoid primates in exhibiting long gestation and eruption of antemolars at or before molars, eruption patterns do not significantly co-vary with either life history parameter among afrotherians sampled so far. However, we do observe a shift in eruption timing and crown height in $\textit{Procavia}$ relative to fossil hyracoids, mirroring observations recently made for other ungulate-grade mammals.Collection of Fayum hyracoids has been funded by U.S. National Science Foundation grants to E. L. Simons (BCS-0114856), to ELS and E. R. Seiffert (BCS- 0416164), to ERS (BCS-0819186), and to ERS, J. G. Fleagle, G. F. Gunnell, and D. M. Boyer (BCS-1231288). Fieldwork was undertaken in collaboration with the Egyptian Mineral Resources Authority and the Egyptian Geological Museum, and was managed by P. Chatrath. RJA, LH, and DP acknowledge support from the Leverhulme Trust and the Department of Zoology, University of Cambridge. We thank C. Riddle and V. Yarborough for access to fossils and fossil preparation, and C. Soubiran for help with segmentation of extant hyrax CT scans. Some CTscan data presented in this work were produced thanks to the imaging facilities of the MRI Platform and of the LabEx CeMEB (Montpellier)

A new, large-bodied omnivorous bat (Noctilionoidea: Mystacinidae) reveals lost morphological and ecological diversity since the Miocene in New Zealand

A new genus and species of fossil bat is described from New Zealand's only pre-Pleistocene Cenozoic terrestrial fauna, the early Miocene St Bathans Fauna of Central Otago, South Island. Bayesian total evidence phylogenetic analysis places this new Southern Hemisphere taxon among the burrowing bats (mystacinids) of New Zealand and Australia, although its lower dentition also resembles Africa's endemic sucker-footed bats (myzopodids). As the first new bat genus to be added to New Zealand's fauna in more than 150 years, it provides new insight into the original diversity of chiropterans in Australasia. It also underscores the significant decline in morphological diversity that has taken place in the highly distinctive, semi-terrestrial bat family Mystacinidae since the Miocene. This bat was relatively large, with an estimated body mass of ~40 g, and its dentition suggests it had an omnivorous diet. Its striking dental autapomorphies, including development of a large hypocone, signal a shift of diet compared with other mystacinids, and may provide evidence of an adaptive radiation in feeding strategy in this group of noctilionoid bats

Digital reconstruction of the inner ear of Leptictidium auderiense (Leptictida, Mammalia) and North American leptictids reveals new insight into leptictidan locomotor agility

Leptictida are basal Paleocene to Oligocene eutherians from Europe and North America comprising species with highly specialized postcranial features including elongated hind limbs. Among them, the European Leptictidium was probably a bipedal runner or jumper. Because the semicircular canals of the inner ear are involved in detecting angular acceleration of the head, their morphometry can be used as a proxy to elucidate the agility in fossil mammals. Here we provide the first insight into inner ear anatomy and morphometry of Leptictida based on high-resolution computed tomography of a new specimen of Leptictidium auderiense from the middle Eocene Messel Pit (Germany) and specimens of the North American Leptictis and Palaeictops. The general morphology of the bony labyrinth reveals several plesiomorphic mammalian features, such as a secondary crus commune. Leptictidium is derived from the leptictidan groundplan in lacking the secondary bony lamina and having proportionally larger semicircular canals than the leptictids under study. Our estimations reveal that Leptictidium was a very agile animal with agility score values (4.6 and 5.5, respectively) comparable to Macroscelidea and extant bipedal saltatory placentals. Leptictis and Palaeictops have lower agility scores (3.4 to 4.1), which correspond to the more generalized types of locomotion (e.g., terrestrial, cursorial) of most extant mammals. In contrast, the angular velocity magnitude predicted from semicircular canal angles supports a conflicting pattern of agility among leptictidans, but the significance of these differences might be challenged when more is known about intraspecific variation and the pattern of semicircular canal angles in non-primate mammals

Relationships of Cetacea (Artiodactyla) Among Mammals: Increased Taxon Sampling Alters Interpretations of Key Fossils and Character Evolution

BACKGROUND: Integration of diverse data (molecules, fossils) provides the most robust test of the phylogeny of cetaceans. Positioning key fossils is critical for reconstructing the character change from life on land to life in the water. METHODOLOGY/PRINCIPAL FINDINGS: We reexamine relationships of critical extinct taxa that impact our understanding of the origin of Cetacea. We do this in the context of the largest total evidence analysis of morphological and molecular information for Artiodactyla (661 phenotypic characters and 46,587 molecular characters, coded for 33 extant and 48 extinct taxa). We score morphological data for Carnivoramorpha, Creodonta, Lipotyphla, and the raoellid artiodactylan Indohyus and concentrate on determining which fossils are positioned along stem lineages to major artiodactylan crown clades. Shortest trees place Cetacea within Artiodactyla and close to Indohyus, with Mesonychia outside of Artiodactyla. The relationships of Mesonychia and Indohyus are highly unstable, however--in trees only two steps longer than minimum length, Mesonychia falls inside Artiodactyla and displaces Indohyus from a position close to Cetacea. Trees based only on data that fossilize continue to show the classic arrangement of relationships within Artiodactyla with Cetacea grouping outside the clade, a signal incongruent with the molecular data that dominate the total evidence result. CONCLUSIONS/SIGNIFICANCE: Integration of new fossil material of Indohyus impacts placement of another extinct clade Mesonychia, pushing it much farther down the tree. The phylogenetic position of Indohyus suggests that the cetacean stem lineage included herbivorous and carnivorous aquatic species. We also conclude that extinct members of Cetancodonta (whales+hippopotamids) shared a derived ability to hear underwater sounds, even though several cetancodontans lack a pachyostotic auditory bulla. We revise the taxonomy of living and extinct artiodactylans and propose explicit node and stem-based definitions for the ingroup

Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology

The best European locality for complete Eocene mammal skeletons is Grube Messel, near Darmstadt, Germany. Although the site was surrounded by a para-tropical rain forest in the Eocene, primates are remarkably rare there, and only eight fragmentary specimens were known until now. Messel has now yielded a full primate skeleton. The specimen has an unusual history: it was privately collected and sold in two parts, with only the lesser part previously known. The second part, which has just come to light, shows the skeleton to be the most complete primate known in the fossil record.We describe the morphology and investigate the paleobiology of the skeleton. The specimen is described as Darwinius masillae n.gen. n.sp. belonging to the Cercamoniinae. Because the skeleton is lightly crushed and bones cannot be handled individually, imaging studies are of particular importance. Skull radiography shows a host of teeth developing within the juvenile face. Investigation of growth and proportion suggest that the individual was a weaned and independent-feeding female that died in her first year of life, and might have attained a body weight of 650-900 g had she lived to adulthood. She was an agile, nail-bearing, generalized arboreal quadruped living above the floor of the Messel rain forest.Darwinius masillae represents the most complete fossil primate ever found, including both skeleton, soft body outline and contents of the digestive tract. Study of all these features allows a fairly complete reconstruction of life history, locomotion, and diet. Any future study of Eocene-Oligocene primates should benefit from information preserved in the Darwinius holotype. Of particular importance to phylogenetic studies, the absence of a toilet claw and a toothcomb demonstrates that Darwinius masillae is not simply a fossil lemur, but part of a larger group of primates, Adapoidea, representative of the early haplorhine diversification

Is Homosexuality a Paraphilia? The Evidence For and Against

Whether homosexuality should be described as one among many paraphilic sexual interests or an altogether different dimension of sexual interest has long been discussed in terms of its political and social implications. The present article examined the question instead by comparing the major correlates and other features of homosexuality and of the paraphilias, including prevalence, sex ratio, onset and course, fraternal birth order, physical height, handedness, IQ and cognitive neuropsychological profile, and neuroanatomy. Although those literatures remain underdeveloped, the existing findings thus far suggest that homosexuality has a pattern of correlates largely, but not entirely, distinct from that identified among the paraphilias. At least, if homosexuality were deemed a paraphilia, it would be relatively unique among them, taxonometrically speaking