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Turbinals are bony or cartilaginous structures that are present in the nasal cavity of most tetrapods. They are involved in key functions such as olfaction, heat, and moisture conservation, as well as protection of the respiratory tract. Despite recent studies that challenged long‐standing hypotheses about their physiological and genomic correlation, turbinals remain largely unexplored, particularly for non‐mammalian species. Herein, we review and synthesise the current knowledge of turbinals using an integrative approach that includes comparative anatomy, physiology, histology and genomics. In addition, we provide synonyms and correspondences of tetrapod turbinals from about 80 publications. This work represents a first step towards drawing hypotheses of homology for the whole clade, and provides a strong basis to develop new research avenues. [ABSTRACT FROM AUTHOR]

Thomasomys is the most diverse genus of the Sigmodontinae subfamily, comprising at least 51 species. Despite recent systematic advances, the monophyly of this genus, the proposed species groups and their content, and the species limits are not yet firmly established. Using a well‐sampled mitochondrial dataset, we aim to test the monophyly of the genus, infer phylogenetic relationships among species and species groups and test the limits between valid species and candidate species. For this, we used a large matrix of 272 partial non‐redundant sequences of the cytochrome b mitochondrial gene from 40 valid and 20 candidate species. Using probabilistic approaches on this dataset, we inferred Thomasomys phylogenetic relationships and explored species boundaries using four unilocus species delimitation methods (ABGD, ASAP, bPTP and GMYC). Thomasomys sensu stricto was recovered monophyletic and well‐supported, excluding a Peruvian lineage misidentified as part of the genus. Analyses consistently recovered 10 well‐supported major clades and several paraphyletic or polyphyletic species. Delimitation methods and genetic divergences estimated that Thomasomys comprises between 81 and 93 putative species, thus potentially doubling the species diversity of Thomasomys. Such a result clearly calls for an urgent taxonomic revision of this genus and the use of further molecular loci within an integrative taxonomic approach to describe its diversity and understand its evolutionary history. [ABSTRACT FROM AUTHOR]

The early diversification of tetrapods into terrestrial environments involved adaptations of their locomotor apparatus that allowed for weight support and propulsion on heterogeneous surfaces. Many lineages subsequently returned to the water, while others conquered the aerial environment, further diversifying under the physical constraints of locomoting through continuous fluid media. While many studies have explored the relationship between locomotion in continuous fluids and body mass, none have focused on how continuous fluid media have impacted the macroevolutionary patterns of limb shape diversity.We investigated whether mammals that left terrestrial environments to use air and water as their main locomotor environment experienced constraints on the morphological evolution of their forelimb, assessing their degree of morphological disparity and convergence. We gathered a comprehensive sample of more than 800 species that cover the extant family‐level diversity of mammals, using linear measurements of the forelimb skeleton to determine its shape and size.Among mammals, fully aquatic groups have the most disparate forelimb shapes, possibly due to the many different functional roles performed by flippers or the relaxation of constraints on within‐flipper bone proportions. Air‐based locomotion, in contrast, is linked to restricted forelimb shape diversity. Bats and gliding mammals exhibit similar morphological patterns that have resulted in partial phenotypic convergence, mostly involving the elongation of the proximal forelimb segments.Thus, whereas aquatic locomotion drives forelimb shape diversification, aerial locomotion constrains forelimb diversity. These results demonstrate that locomotion in continuous fluid media can either facilitate or limit morphological diversity and more broadly that locomotor environments have fostered the morphological and functional evolution of mammalian forelimbs. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Anomaluromorpha is a particularly puzzling suborder of Rodentia. Endemic to Africa, this clade includes the extant genera Idiurus, Anomalurus, Zenkerella, and Pedetes. These rodents present an hystricomorphous condition of the skull, characterized by a large infraorbital foramen, which evolved independently within the mouse‐related clade over a span of approximately 57 million years. They exhibit a high disparity in craniomandibular and dental morphology that has kept their phylogenetic affinities disputed for a long time. Given the past significance of masticatory morphotypes in establishing the classification of Rodentia, we propose to explore variations in the masticatory apparatus of Anomaluromorpha in order to evaluate whether its related features can offer additional data for systematics and contribute to our understanding of the complexity of hystricomorphy. In order to do so, we used traditional dissection and diffusible iodine‐based contrast‐enhanced computed tomography (diceCT) to accurately describe and compare the anatomy of the specimens. We found that the muscle morphology displays clear differentiation among each anomaluromorph taxonomic unit. Specifically, the masseteric complex of Anomaluromorpha exhibits distinctive synapomorphies such as the infraorbital part of the zygomaticomandibularis muscle being separated into a rostral and orbital part and an absence of a posterior part of the zygomaticomandibularis. Additionally, the orbital portion of the infraorbital part originates from a well‐marked ridge and fossa at the level of its area of origin on the anteromedial wall of the orbital cavity, a feature that is absent in other members of the mouse‐related clade. This evident bony feature, among others, is strongly associated with muscular anatomy and can contribute to ascertaining the taxonomic status of extinct representatives of the clade. Finally, we showed that the hystricomorphy of Anomaluromorpha largely differs from those of Ctenohystrica and Dipodoidea and that the definition of this morphotype is complex and cannot be reduced simply to the size of the opening of the infraorbital foramen. [ABSTRACT FROM AUTHOR]

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With their past and current diversities, West Indian caviomorph rodents dominate the terrestrial mammalian fauna of the Caribbean archipelago. Many of these species have recently become extinct, including the emblematic giant forms known as Heptaxodontidae. The higher-level systematics and content of this family have been widely disputed over the last decades (i.e., membership in Cavioidea vs. Chinchilloidea vs. Octodontoidea). Here we analyzed the phylogenetic signal provided by several characters of the caviomorph inner ear to adress the phylogenetic affinities of the West Indian heptaxodontids. For this, we assembled an exhaustive taxonomic sampling (N = 100) of extant North and South American caviomorphs (including representatives of all families) and a wide array of West Indian forms among octodontoid echimyids (extant and extinct capromyines, as well as extinct heteropsomyines), and some heptaxodontid subfossil taxa such as Amblyrhiza, Clidomys, and Elasmodontomys. Geometric morphometrics and comparative phylogenetic methods were employed to explore shape differences of the inner ear and their potential systematic implications. Our results show that: (1) allometry is a major contributor to shape variation in the bony labyrinth; (2) shape variation bears a strong phylogenetic signal, providing diagnostic characters for Caviidae and Erethizontoidea; and (3) Amblyrhiza and Clidomys are morphologically closer to Chinchilloidea with which they have potential phylogenetic affinities. Elasmodontomys remains a problematic taxon as it exhibits inner ear features that are consistent with either Chinchilloidea or Octodontoidea, depending on how the allometric component is evaluated. [ABSTRACT FROM AUTHOR]

Olfactory receptor (OR) genes represent the largest multigenic family in mammalian genomes and encode proteins that bind environmental odorant molecules. The OR repertoire is extremely variable among species and is subject to many gene duplications and losses, which have been linked to ecological adaptations in mammals. Although they have been studied on a broad taxonomic scale (i.e. placental), finer sampling has rarely been explored in order to better capture the mechanisms that drove the evolution of the OR repertoire. Among placental mammals, rodents are well-suited for this task, as they exhibit diverse life history traits, and genomic data are available for most major families and a diverse array of lifestyles. In this study, 53 rodent published genomes were mined for their OR subgenomes. We retrieved more than 85,000 functional and pseudogene OR sequences that were subsequently classified into phylogenetic clusters. Copy number variation among rodents is similar to that of other mammals. Using our OR counts along with comparative phylogenetic approaches, we demonstrated that ecological niches such as diet, period of activity, and a fossorial lifestyle strongly impacted the proportion of OR pseudogenes. Within the OR subgenome, phylogenetic inertia was the main factor explaining the relative variations of the 13 OR gene families. However, a striking exception was a convergent 10-fold expansion of the OR family 14 among the phylogenetically divergent subterranean mole-rat lineages belonging to Bathyergidae and Spalacidae families. This study illustrates how the diversity of the OR repertoire has evolved among rodents, both shaped by selective forces stemming from species life history traits and neutral evolution along the rodent phylogeny. [ABSTRACT FROM AUTHOR]

Understanding palaeodiversity dynamics through time and space is a central goal of macroevolution. Estimating palaeodiversity dynamics has been historically addressed with fossil data because it directly reflects the past variations of biodiversity. Unfortunately, some groups or regions lack a good fossil record, and dated phylogenies can be useful to estimate diversification dynamics. Recent methodological developments have unlocked the possibility to investigate palaeodiversity dynamics by using phylogenetic birth‐death models with non‐homogeneous rates through time and across clades. One of them seems particularly promising to detect clades whose diversity has declined through time. However, empirical applications of the method have been hampered by the lack of a robust, accessible implementation of the whole procedure, therefore requiring users to conduct all the steps of the analysis by hand in a time‐consuming and error‐prone way.Here we propose an automation of Morlon et al. (2011) clade‐shift model with additional features accounting for recent developments, and we implement it in the R package RPANDA. We also test the approach with simulations focusing on its ability to detect shifts of diversification and to infer palaeodiversity dynamics. Finally, we illustrate the automation by investigating the palaeodiversity dynamics of Cetacea, Vangidae, Parnassiinae and Cycadales.Simulations showed that we accurately detected shifts of diversification although false shift detections were higher for time‐dependent diversification models with extinction. The median global error of palaeodiversity dynamics estimated with the automated model is low, showing that the method can capture diversity declines. We detected shifts of diversification for three of the four empirical examples considered (Cetacea, Parnassiinae and Cycadales). Our analyses unveil a waxing‐and‐waning pattern due to a phase of negative net diversification rate embedded in the trees after isolating recent radiations.Our work makes it possible to easily apply non‐homogeneous models of diversification in which rates can vary through time and across clades to reconstruct palaeodiversity dynamics. By doing so, we detected palaeodiversity declines among three of the four groups tested, highlighting that such periods of negative net diversification might be common. We discuss the extent to which this approach might provide reliable estimates of extinction rates, and we provide guidelines for users. [ABSTRACT FROM AUTHOR]

The evolution of endothermy in vertebrates is a major research topic in recent decades that has been tackled by a myriad of research disciplines including paleontology, anatomy, physiology, evolutionary and developmental biology. The ability of most mammals to maintain a relatively constant and high body temperature is considered a key adaptation, enabling them to successfully colonize new habitats and harsh environments. It has been proposed that in mammals the anterior nasal cavity, which houses the maxilloturbinal, plays a pivotal role in body temperature maintenance, via a bony system supporting an epithelium involved in heat and moisture conservation. The presence and the relative size of the maxilloturbinal has been proposed to reflect the endothermic conditions and basal metabolic rate in extinct vertebrates. We show that there is no evidence to relate the origin of endothermy and the development of some turbinal bones by using a comprehensive dataset of µCT-derived maxilloturbinals spanning most mammalian orders. Indeed, we demonstrate that neither corrected basal metabolic rate nor body temperature significantly correlate with the relative surface area of the maxilloturbinal. Instead, we identify important variations in the relative surface area, morpho-anatomy, and complexity of the maxilloturbinal across the mammalian phylogeny and species ecology. The maxilloturbinal, an area of the mammalian nasal cavity, has been proposed to play a pivotal role in body temperature maintenance. Here, the authors use computed tomographic data to show that neither corrected basal metabolic rate nor body temperature significantly correlate with the relative surface area of the maxilloturbinal. [ABSTRACT FROM AUTHOR]

Copyright of Il Capitale Culturale: Studies on the Value of Cultural Heritage is the property of Il Capitale Culturale Studies on the Value of Cultural Heritage and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Analysis of the incisor enamel microstructure of extinct and extant West Indian caviomorph rodents emphasizes a clear microstructural distinction between the Echimyidae (Capromyinae and Heteropsomyinae) among Octodontoidea and the "Heptaxodontidae", whose phylogenetic affinities are debated. All capromyines and heteropsomyines have a pattern of enamel characterized by a rectangular crystallite arrangement, which is biomechanically strongest in limiting crack propagation most efficiently (subtype [Sbt.] 3 of multiserial Hunter-Schreger bands [HSBs]). This enamel condition is exclusive to all mainland octodontoids. In stark contrast, "heptaxodontids" sampled here exhibit much less derived enamel subtypes of multiserial HSBs, with parallel to acute angular crystallite arrangement (Sbt. 1 [Clidomys], Sbt. 1–2 [Elasmodontomys], and low acute Sbt. 2 [Amblyrhiza]), less well adapted for prevention of crack propagation. The incisor enamel microstructure of Amblyrhiza and Clidomys is consistent with a chinchilloid assignment, as reflected by the anatomy of their auditory region and their unusual dental pattern. For Elasmodontomys, the primitive condition of its incisor enamel is difficult to reconcile with its highly nested phylogenetic position within the Octodontoidea clade (among the Capromyinae), as recently inferred from aDNA analyses. The different enamel patterns among extinct and extant West Indian caviomorphs indicate distinct high-level taxonomic groups, but restricted to the Octochinchilloi (Octodontoidea and Chinchilloidea) among Caviomorpha. The great diversity of caviomorphs on the Caribbean islands resulted from intra-archipelago diversification through time, but their high-level phylogenetic diversity can only be explained by distinct sources, implying de facto multiple (potentially time-staggered) natural colonizations of the West Indies. The chinchilloid-compatible enamel and dental pattern characterizing Borikenomys from lower Oligocene deposits in Puerto Rico strongly suggest a link with some of the recently-extinct "heptaxodontids", which would substantiate their much greater antiquity in the Caribbean islands. [ABSTRACT FROM AUTHOR]

Copyright of Revue de l'Histoire des Religions is the property of Librairie Armand Colin and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The conclusion of this collection of studies endeavors to recapture five major questions that this special issue of the Journal of Jesuit Studies poses on the subject of martyrdom: Is this gesture a form of imitation of Christ (or imitatio Christi) or is it itself a sacrifice? How does it get rid of the shadow of suicide or voluntary death? How do the singularity of its experience and the community within which and in the name of which it is exercised articulate? Can martyrdom be defined as a renunciation of human love, and in this sense as the ultimate step in a process of conversion? How does martyrdom take its place in the writing of the religious history of the modern era, in particular, as far as the Society of Jesus is concerned, in the historiography of the nineteenth century? These five questions open this collection of essays to a field of research that remains to be pursued. [ABSTRACT FROM AUTHOR]

The account of the sacrifice performed by Noah on leaving the ark (Gen. 8.20-1) is certainly one of the most enigmatic moments in the first chapters of Genesis. How are we to understand this sacrifice, which God does not command, but which immediately precedes a radical transformation of the discourse that God addresses to Noah, a discourse which might seem to return to his very first address to Adam, but which in reality introduces between man and the animals the weapon of a domination by terror. We will be interested in the different interpretations that have marked this story in Christian exegesis and in the various manifestations of the iconography that has been used to convey it. [ABSTRACT FROM AUTHOR]

The West Indies are a natural laboratory for the study of biogeography and evolution, especially for mammals. The modality of their arrival in the Caribbean islands is a highly controversial issue, and palaeontological evidence remains particularly elusive. Lower Oligocene deposits of Puerto Rico (c. 29.5 Ma) have recently yielded the oldest archipelago rodents, with teeth of two chinchilloid caviomorphs of South American origin. Here we report the discovery of additional dental remains from the same level, testifying to the occurrence of another rodent group. Their morphology is singular but otherwise characteristic of North/Central American geomyin geomorphs (including extant kangaroo rats, pocket mice, and pocket gophers), and leads us to propose here a new taxon: Caribeomys merzeraudi gen. et sp. nov. The evidence of geomorphs in the West Indies challenges the view that all extinct and extant Antillean rodents derived from South American sources. The morphological singularity of this Puerto Rican geomorph also suggests an early split of this insular lineage from coeval mainland counterparts, and its dispersal towards the West Indies sometime around the Eocene–Oligocene transition. This unexpected rodent adds to the few cases of Antillean terrestrial vertebrates of North American origins, such as solenodonotan eulipotyphlans. In the absence of subaerial land connections between both landmasses, an overwater dispersal may explain mid‐Palaeogene colonization of the West Indies by geomorph rodents. [ABSTRACT FROM AUTHOR]

Biotic interactions between Africa and Eurasia across the Levant have invoked particular attention among scientists aiming to unravel early human dispersals. However, it remains unclear whether behavioral capacities enabled early modern humans to surpass the Saharo-Arabian deserts or if climatic changes triggered punctuated dispersals out of Africa. Here, we report an unusual subfossil assemblage discovered in a Judean Desert's cliff cave near the Dead Sea and dated to between ~42,000 and at least 103,000 y ago. Paleogenomic and morphological comparisons indicate that the specimens belong to an extinct subspecies of the eastern African crested rat, Lophiomys imhausi maremortum subspecies nova, which diverged from the modern eastern African populations in the lateMiddle Pleistocene ~226,000 to 165,000 y ago. The reported paleomitogenome is the oldest so far in the Levant, opening the door for future paleo-DNA analyses in the region. Species distribution modeling points to the presence of continuous habitat corridors connecting eastern Africa with the Levant during the Last Interglacial ~129,000 to 116,000 y ago, providing further evidence of the northern ingression of African biomes into Eurasia and reinforcing previous suggestions of the critical role of climate change in Late Pleistocene intercontinental biogeography. Furthermore, our study complements other paleoenvironmental proxies with local--instead of interregional--paleoenvironmental data, opening an unprecedented window into the Dead Sea rift paleolandscape. [ABSTRACT FROM AUTHOR]

Background. Ecological adaptations of mammals are reflected in the morphological diversity of their feeding apparatus, which includes differences in tooth crown morphologies, variation in snout size, or changes in muscles of the feeding apparatus. The adaptability of their feeding apparatus allowed them to optimize resource exploitation in a wide range of habitats. The combination of computer-assisted X-ray microtomography (μ-CT) with contrast-enhancing staining protocols has bolstered the reconstruction of three-dimensional (3D) models of muscles. This new approach allows for accurate descriptions of muscular anatomy, as well as the quick measurement of muscle volumes and fiber orientation. Ant- and termite-eating (myrmecophagy) represents a case of extreme feeding specialization, which is usually accompanied by tooth reduction or complete tooth loss, snout elongation, acquisition of a long vermiform tongue, and loss of the zygomatic arch. Many of these traits evolved independently in distantly-related mammalian lineages. Previous reports on South American anteaters (Vermilingua) have shown major changes in the masticatory, intermandibular, and lingual muscular apparatus. These changes have been related to a functional shift in the role of upper and lower jaws in the evolutionary context of their complete loss of teeth and masticatory ability. Methods. We used an iodine staining solution (I2KI) to perform contrast-enhanced μ-CT scanning on heads of the pygmy (Cyclopes didactylus), collared (Tamandua tetradactyla) and giant (Myrmecophaga tridactyla) anteaters. We reconstructed the musculature of the feeding apparatus of the three extant anteater genera using 3D reconstructions complemented with classical dissections of the specimens. We performed a description of the musculature of the feeding apparatus in the two morphologically divergent vermilinguan families (Myrmecophagidae and Cyclopedidae) and compared it to the association of morphological features found in other myrmecophagous placentals. Results. We found that pygmy anteaters (Cyclopes) present a relatively larger and architecturally complex temporal musculature than that of collared (Tamandua) and giant (Myrmecophaga) anteaters, but shows a reduced masseter musculature, including the loss of the deep masseter. The loss of this muscle concurs with the loss of the jugal bone in Cyclopedidae. We show that anteaters, pangolins, and aardvarks present distinct anatomies despite morphological and ecological convergences. [ABSTRACT FROM AUTHOR]

Olfaction and thermoregulation are key functions for mammals. The former is critical to feeding, mating, and predator avoidance behaviors, while the latter is essential for homeothermy. Aquatic and amphibious mammals face olfactory and thermoregulatory challenges not generally encountered by terrestrial species. In mammals, the nasal cavity houses a bony system supporting soft tissues and sensory organs implicated in either olfactory or thermoregulatory functions. It is hypothesized that to cope with aquatic environments, amphibious mammals have expanded their thermoregulatory capacity at the expense of their olfactory system. We investigated the evolutionary history of this potential trade-off using a comparative dataset of three-dimensional (3D) CT scans of 189 skulls, capturing 17 independent transitions from a strictly terrestrial to an amphibious lifestyle across small mammals (Afrosoricida, Eulipotyphla, and Rodentia). We identified rapid and repeated loss of olfactory capacities synchronously associated with gains in thermoregulatory capacity in amphibious taxa sampled from across mammalian phylogenetic diversity. Evolutionary models further reveal that these convergences result from faster rates of turbinal bone evolution and release of selective constraints on the thermoregulatory-olfaction trade-off in amphibious species. Lastly, we demonstrated that traits related to vital functions evolved faster to the optimum compared to traits that are not related to vital functions. [ABSTRACT FROM AUTHOR]

Aim: To determine the historical dynamics of colonization and whether the relative timing of colonization predicts diversification rate in the species‐rich, murine rodent communities of Indo‐Australia. Location: Indo‐Australian Archipelago including the Sunda shelf of continental Asia, Sahul shelf of continental Australia, the Philippines and Wallacea of Indonesia. Taxon: Order Rodentia, Family Muridae. Methods: We used a fossil‐calibrated molecular phylogeny and Bayesian biogeographical modelling to infer the frequency and temporal sequence of biogeographical transitions among Sunda, Sahul, the Philippines and Wallacea. We estimated diversification rates for each colonizing lineage using a method‐of‐moments estimator of net diversification and Bayesian mixture model estimates of diversification rate shifts. Results: We identified 17 biogeographical transitions, including nine originating from Sunda, seven originating from Sulawesi and broader Wallacea and one originating from Sahul. Wallacea was colonized eight times, the Phillipines five times, Sunda twice and Sahul twice. Net diversification rates ranged from 0.2 to 2.12 species/lineage/My with higher rates in secondary and later colonizers than primary colonizers. The highest rates were in the genus Rattus and their closest relatives, irrespective of colonization history. Main Conclusions: Our inferences from murines demonstrate once again the substantial role of islands as sources of species diversity in terrestrial vertebrates of the IAA with most speciation events occurring on islands. Sulawesi and broader Wallacea have been a major source of colonists for both island and continental systems. Crossings of Wallace's Line were more common than subsequent transitions across Lydekker's Line to the east. While speciation following colonization of oceanic archipelagos and large islands is consistent with adaptive radiation theory and ideas regarding ecological opportunity, we did not observe a strong signal of incumbency effects. Rather, subsequent colonists of landmasses radiated unhindered by previous radiations. [ABSTRACT FROM AUTHOR]

Retinal ganglion cells (RGC), cone photoreceptors (cones), horizontal cells (HC) and amacrine cells (AC) are the first classes of neurons produced in the retina. However, an important question is how this diversity of cell states is transcriptionally produced. Here we profiled 6,067 single retinal cells to provide a comprehensive transcriptomic atlas showing the diversity of the early developing mouse retina. RNA velocities unveiled dynamics of cell-cycle coordination of early retinogenesis and define the transcriptional sequences at work during the hierarchical production of early cell-fate specification. We show that RGC maturation follows six waves of gene expression, with older-generated RGCs transcribing increasing amount of guidance cues for young peripheral RGC axons that express the matching receptors. Spatial transcriptionally-deduced features in subpopulations of RGCs allowed us to define novel molecular markers that are spatially restricted. Finally, the isolation of such a spatially restricted population, ipsilateral RGCs, allowed us to identify their molecular identity at the time they execute axon guidance decisions. Together, these data represent a valuable resource shedding light on transcription factor sequences and guidance cue dynamics during mouse retinal development. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Mammalogy is the property of Oxford University Press / USA and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Anomaluroidea, commonly known as the “scaly‐tailed squirrels,” are an emblematic group of tropical African mammals that includes gliding forms. The family Anomaluridae was until recently represented by three genera: the flying scaly‐tailed squirrels (Anomalurus), the flying mouse (Idiurus) and the flightless scaly‐tailed squirrels (Zenkerella). Idiurus and Zenkerella have long been grouped into the Zenkerellinae subfamily, and Zenkerella was interpreted as a rare case of evolutionary reversal to non‐gliding lifestyle. Recent studies have demonstrated that Zenkerella is sister to all other modern anomalurids, and represents in fact the monogeneric family Zenkerellidae. The Anomalurus genus was split into Anomalurus and Anomalurops, but no study has ever considered all Anomalurus species together in a phylogeny to test the status of Anomalurops. Here, we used mitogenomic next‐generation sequencing to infer the phylogenetic relationships among all extant anomalurids and to estimate their divergence ages. We found that the arboreal Zenkerella is the sister group of all extant gliding anomalurids (Idiurus and Anomalurus). We confirmed that Anomaluroidea only evolved the gliding adaptation once. A comparison based on morphological traits indicates that Zenkerella harbours several unique morphological features. We propose new morphological characters for the novel classification of modern Anomaluroidea, which includes the families Zenkerellidae and Anomaluridae. Using different calibration schemes, we demonstrated that classical dating methods relying only on mitogenomes provide rather young Miocene estimates between Zenkerellidae and the Anomaluridae. The use of published nuclear genes, internal calibrations and tip dating converged towards an Eocene split between gliding and non‐gliding scaly‐tailed squirrels, which is in agreement with the African fossil record. Finally, we provide the first exhaustive species‐level molecular phylogenetic inference for the genus Anomalurus. We found that Anomalurus beecrofti is the sister group of all other species of Anomalurus and branched off during the Miocene. [ABSTRACT FROM AUTHOR]

Mosaic-tailed rodents of the genus Melomys belong to the Australasian old endemic murine radiation and exhibit a rat-like morphology with arboreal or scansorial specializations. Here we report a new population of Melomys burtoni from the island of Halmahera (in the North Moluccas, Indonesia). Our molecular phylogenetic results highlight close relationships and recent evolutionary divergences among M. burtoni from Halmahera and the Australo-Papuan taxa M. burtoni and M. lutillus and other Moluccan taxa, including M. paveli. Multivariate as well as geometric morphometric analyses of cranial, and dental features support the recognition of M. burtoni from Halmahera as a slightly distinctive insular population, preventing us from elevating it as a new taxa. This population is recorded from lowland secondary forest and forest edge habitats in south-central Halmahera. As with other Moluccan endemic murines, colonization by an Australo-Papuan ancestor and subsequent isolation is the probable mode of diversification for M. burtoni in Halmahera. The discovery of Melomys in Halmahera fills a previously puzzling gap in knowledge of the murine fauna of the Moluccas and the biogeography of the Wallacean region. [ABSTRACT FROM AUTHOR]

The taxonomic position of Annandale's rat, Rattus annandalei (Bonhote, 1903), has been uncertain given its mix of Rattus-like and Sundamys-like morphological features. Annandale's rat and all described species in Sundamys (the lowland S. muelleri and the montane S. maxi and S. infraluteus) are endemic to Sundaland, a center of diversification and endemism for their tribe, the Rattini. Using mitochondrial genomes and 3 nuclear markers (rag1, rbp3, ghr), we provide the 1st phylogenetic framework for Sundamys. We find that R. annandalei is nested within Sundamys and that the 4 species likely diverged during the Pleistocene. We move R. annandalei to Sundamys and provide an emended diagnosis for Sundamys. Using geometric morphometric analyses of skulls and mandibles, we identify morphological differences between lowland and highland species of Sundamys that may be associated with adaptations to distinct diets. [ABSTRACT FROM AUTHOR]

Echimyidae is one of the most speciose and ecologically diverse rodent families in the world, occupying a wide range of habitats in the Neotropics. However, a resolved phylogeny at the genus-level is still lacking for these 22 genera of South American spiny rats, including the coypu (Myocastorinae), and 5 genera of West Indian hutias (Capromyidae) relatives. Here, we used Illumina shotgun sequencing to assemble 38 new complete mitogenomes, establishing Echimyidae, and Capromyidae as the first major rodent families to be completely sequenced at the genus-level for their mitochondrial DNA. Combining mitogenomes and nuclear exons, we inferred a robust phylogenetic framework that reveals several newly supported nodes as well as the tempo of the higher level diversification of these rodents. Incorporating the full generic diversity of extant echimyids leads us to propose a new higher level classification of two subfamilies: Euryzygomatomyinae and Echimyinae. Of note, the enigmatic Carterodon displays fast-evolving mitochondrial and nuclear sequences, with a long branch that destabilizes the deepest divergences of the echimyid tree, thereby challenging the sister-group relationship between Capromyidae and Euryzygomatomyinae. Biogeographical analyses involving higher level taxa show that several vicariant and dispersal events impacted the evolutionary history of echimyids. The diversification history of Echimyidae seems to have been influenced by two major historical factors, namely (1) recurrent connections between Atlantic and Amazonian Forests and (2) the Northern uplift of the Andes. [ABSTRACT FROM AUTHOR]

Recent phylogenetic studies and taxonomic reviews have led to nearly complete resolution of the phylogenetic divisions within the old world rats and mice (Muridae, Murinae). The Micromys division and Pithecheir division are two notable exceptions where groupings of species into these divisions based on morphology and arboreal lifestyle have not been supported by phylogenetic evidence. Several enigmatic species from these divisions have been missing from molecular studies, preventing a rigorous revision of phylogenetic relationships. In this study, we sequenced for the first time one mitochondrial and three nuclear genes from South-East Asian keystone species of these two arboreal divisions: Hapalomys delacouri ( Micromys division), Lenothrix canus and Pithecheir parvus ( Pithecheir division). We also complemented the molecular data already available for the two divisions with new data from Sundaic Chiropodomys, Indian Vandeleuria oleracea and the recently described Sulawesian Margaretamys christinae. Using this new phylogenetic framework and molecular dating methodologies, our study allows some more detailed classification of the former Micromys and Pithecheir divisions, while confirming their polyphyletic status. Specifically, the former Micromys division should now be split into four monotypic divisions: Chiropodomys, Hapalomys, Micromys and Vandeleuria divisions. The former Pithecheir division is likely to be refined and restricted to Pithecheir and probably Pithecheirops, whereas Lenothrix and Margaretamys should now be recognized as representatives of the Dacnomys division. Our findings have profound implications with regard to the systematics of Murinae, as well as to the early evolution of murine morphology and dental characters. [ABSTRACT FROM AUTHOR]

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Chromatin condensation plays an important role in the regulation of gene expression. Recently, it was shown that the transcriptional activation of Hoxd genes during vertebrate digit development involves modifications in 3D interactions within and around the HoxD gene cluster. This reorganization follows a global transition from one set of regulatory contacts to another, between two topologically associating domains (TADs) located on either side of the HoxD locus. Here, we use 3D DNA FISH to assess the spatial organization of chromatin at and around the HoxD gene cluster and report that although the two TADs are tightly associated, they appear as spatially distinct units. We measured the relative position of genes within the cluster and found that they segregate over long distances, suggesting that a physical elongation of the HoxD cluster can occur. We analyzed this possibility by super-resolution imaging (STORM) and found that tissues with distinct transcriptional activity exhibit differing degrees of elongation. We also observed that the morphological change of the HoxD cluster in developing digits is associated with its position at the boundary between the two TADs. Such variations in the fine-scale architecture of the gene cluster suggest causal links among its spatial configuration, transcriptional activation, and the flanking chromatin context. [ABSTRACT FROM AUTHOR]

Birds vary greatly in their life-history strategies, including their breeding systems, which range from brood parasitism to a system with multiple nonbreeding helpers at the nest. By far the most common arrangement, however, is where both parents participate in raising the young. The traits associated with parental care have been suggested to affect dispersal propensity and lineage diversification, but to date tests of this potential relationship at broad temporal and spatial scales have been limited. Here, using data from a globally distributed group of corvoid birds in concordance with state-dependent speciation and extinction models, we suggest that pair breeding is associated with elevated speciation rates. Estimates of transition between breeding systems imply that cooperative lineages frequently evolve biparental care, whereas pair breeders rarely become cooperative. We further highlight that these groups have differences in their spatial distributions, with pair breeders overrepresented on islands, and cooperative breeders mainly found on continents. Finally, we find that speciation rates appear to be significantly higher on islands compared to continents. These results imply that the transition from cooperative breeding to pair breeding was likely a significant contributing factor facilitating dispersal across tropical archipelagos, and subsequent world-wide phylogenetic expansion among the core Corvoidea. [ABSTRACT FROM AUTHOR]

Background: Longitudinal axons grow parallel to the embryonic midline to connect distant regions of the central nervous system. Previous studies suggested that repulsive midline signals guide pioneer longitudinal axons by blocking their entry into the floor plate; however, the role of midline attractants, and whether attractant signals may cooperate with repulsive signals, remains unclear. In this study we investigated the navigation of a set of pioneer longitudinal axons, the medial longitudinal fasciculus, in mouse embryos mutant for the Netrin/Deleted in Colorectal Cancer (DCC) attractants, and for Slit repellents, as well as the responses of explanted longitudinal axons in vitro. Results: In mutants for Netrin1 chemoattractant or DCC receptor signaling, longitudinal axons shifted away from the ventral midline, suggesting that Netrin1/DCC signals act attractively to pull axons ventrally. Analysis of mutants in the three Slit genes, including Slit1/2/3 triple mutants, suggest that concurrent repulsive Slit/Robo signals push pioneer axons away from the ventral midline. Combinations of mutations between the Netrin and Slit guidance systems provided genetic evidence that the attractive and repulsive signals balance against each other. This balance is demonstrated in vitro using explant culture, finding that the cues can act directly on longitudinal axons. The explants also reveal an unexpected synergy of Netrin1 and Slit2 that promotes outgrowth. Conclusions: These results support a mechanism in which longitudinal trajectories are positioned by a push-pull balance between opposing Netrin and Slit signals. Our evidence suggests that longitudinal axons respond directly and simultaneously to both attractants and repellents, and that the combined signals constrain axons to grow longitudinally. [ABSTRACT FROM AUTHOR]

Aim Islands and archipelagos have played an important role in the development of ecological and evolutionary theories. Using a newly compiled molecular phylogeny we infer the biogeographical history of a monarch flycatcher genus, Myiagra, which is distributed across the Indo-Pacific. We subsequently integrate biogeographical and ecomorphological data to examine the role of dispersal and trait evolution in the build-up of avian assemblages. Location Australia, the Moluccas, New Guinea and Pacific islands. Methods We generated a taxonomically densely sampled mitochondrial DNA dataset that included almost all species and subspecies of the reciprocally monophyletic genera Myiagra and Arses. We then used maximum likelihoood and Bayesian inference to infer their phylogenetic relationships. To reconstruct their biogeographical history, we first dated the tree topology and then used Lagrange to infer ancestral geographical areas. Finally, we combined ancestral area reconstructions with information on ecomorphological traits to infer mechanisms underlying community assembly. Results We provide the first comprehensive molecular phylogenetic reconstruction for Myiagra and Arses monarch flycatchers. Our phylogenetic reconstruction reveals a relatively recent diversification from the Miocene associated with several major dispersal events. Ancestral area reconstruction reveals several independent colonizations of the Moluccas, Melanesia, Fiji and the Micronesian islands. Ancestral state reconstruction of ecological traits suggests that the diversity of traits in co-occurring species of monarch flycatchers results from independent colonization events and ecological niche conservatism rather than in situ diversification. Main conclusions Three waves of colonization, non-overlapping in time, led to independent speciation events in the Bismarcks, Fiji and the Moluccas, in addition to in situ speciation events on remote islands of Micronesia, the Solomons, Vanuatu and Samoa. Few of these colonizations have led to the co-occurrence of congenerics or species with similar ecomorphological profiles on the same island. Thus, we suggest that priority effects might prevent new colonizers from establishing themselves if they share high levels of ecological similarity with resident species. We conclude that historical dispersal to and colonization of new islands, combined with ecologically deterministic priority effects, drove the assembly of insular monarch flycatcher communities across the Indo-Pacific. [ABSTRACT FROM AUTHOR]

We describe Halmaheramys bokimekot Fabre, Pagès, Musser, Fitriana, Semiadi & Helgen gen. et sp. nov., a new genus and species of murine rodent from the North Moluccas, and study its phylogenetic placement using both molecular and morphological data. We generated a densely sampled mitochondrial and nuclear DNA data set that included most genera of Indo- Pacific Murinae, and used probabilistic methodologies to infer their phylogenetic relationships. To reconstruct their biogeographical history, we first dated the topology and then used a Lagrange analysis to infer ancestral geographic areas. Finally, we combined the ancestral area reconstructions with temporal information to compare patterns of murine colonization among Indo-Pacific archipelagos. We provide a new and comprehensive molecular phylogenetic reconstruction for Indo- Pacific Murinae, with a focus on the Rattus division. Using previous results and those presented in this study, we define a new Indo- Pacific group within the Rattus division, composed of Bullimus, Bunomys, Paruromys, Halmaheramys, Sundamys, and Taeromys. Our phylogenetic reconstructions revealed a relatively recent diversification from the Middle Miocene to Plio- Pleistocene associated with several major dispersal events. We identified two independent Indo- Pacific dispersal events from both western and eastern Indo- Pacific archipelagos to the isolated island of Halmahera, which led to the speciations of H. bokimekot gen. et sp. nov. and Rattus morotaiensis Kellogg, 1945. We propose that a Middle Miocene collision between the Halmahera and Sangihe arcs may have been responsible for the arrival of the ancestor of Halmaheramys to eastern Wallacea. Halmaheramys bokimekot gen. et sp. nov. is described in detail, and its systematics and biogeography are documented and illustrated. © 2013 The Linnean Society of London [ABSTRACT FROM AUTHOR]

Fabre, P.-H., Galewski, T., Tilak, M.-k. & Douzery, E.J.P. (2012) Diversification of South American spiny rats (Echimyidae): a multigene phylogenetic approach. - Zoologica Scripta, 00, 000-000. We investigated the phylogenetic relationships of 14 Echimyidae (spiny rats), one Myocastoridae (nutrias) and one Capromyidae (hutias) genera based on three newly sequenced nuclear genes ( APOB, GHR and RBP3) and five previously published markers (the nuclear RAG1 and vWF, and the mitochondrial cytochrome b, 12S rRNA and 16S rRNA). We recovered a well-supported phylogeny within the Echimyidae, although the evolutionary relationships among arboreal echimyid taxa remain unresolved. Molecular divergence times estimated using a Bayesian relaxed molecular clock suggest a Middle Miocene origin for most of the extant echimyid genera. Echimyidae seems to constitute an example of evolutionary radiation with high species diversity, yet they exhibit only narrow skull morphological changes, and the arboreal and terrestrial taxa are shown to retain numerous plesiomorphic features. The most recent common ancestor of spiny rats is inferred to be a ground-dwelling taxon that has subsequently diverged into fossorial, semiaquatic and arboreal habitats. The arboreal clade polytomy and ancestral character estimations suggest that the colonization of the arboreal niche constituted the keystone event of the echimyid radiation. However, biogeographical patterns suggest a strong influence of allopatric speciation in addition to ecology-driven diversification among South American spiny rats. [ABSTRACT FROM AUTHOR]

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Adaptive radiation is the rapid diversification of a single lineage into many species that inhabit a variety of environments or use a variety of resources and differ in traits required to exploit these. Why some lineages undergo adaptive radiation is not well-understood, but filling unoccupied ecological space appears to be a common feature. We construct a complete, dated, species-level phylogeny of the endemic Vangidae of Madagascar. This passerine bird radiation represents a classic, but poorly known, avian adaptive radiation. Our results reveal an initial rapid increase in evolutionary lineages and diversification in morphospace after colonizing Madagascar in the late Oligocene some 25 Mya. A subsequent key innovation involving unique bill morphology was associated with a second increase in diversification rates about 10 Mya. The volume of morphospace occupied by contemporary Madagascan vangas is in many aspects as large (shape variation)-or even larger (size variation)-as that of other better-known avian adaptive radiations, including the much younger Galapagos Darwin's finches and Hawaiian honeycreepers. Morphological space bears a close relationship to diet substrate use, and foraging movements, and thus our results demonstrate the great extent of the evolutionary diversification of the Madagascan vangas. [ABSTRACT FROM AUTHOR]

Background: Development of phylogenetic methods that do not rely on fossils for the study of evolutionary processes through time have revolutionized the field of evolutionary biology and resulted in an unprecedented expansion of our knowledge about the tree of life. These methods have helped to shed light on the macroevolution of many taxonomic groups such as the placentals (Mammalia). However, despite the increase of studies addressing the diversification patterns of organisms, no synthesis has addressed the case of the most diversified mammalian clade: the Rodentia. Results: Here we present a rodent maximum likelihood phylogeny inferred from a molecular supermatrix. It is based on 11 mitochondrial and nuclear genes that covers 1,265 species, i.e., respectively 56% and 81% of the known specific and generic rodent diversity. The inferred topology recovered all Rodentia clades proposed by recent molecular works. A relaxed molecular clock dating approach provided a time framework for speciation events. We found that the Myomorpha clade shows a greater degree of variation in diversification rates than Sciuroidea, Caviomorpha, Castorimorpha and Anomaluromorpha. We identified a number of shifts in diversification rates within the major clades: two in Castorimorpha, three in Ctenohystrica, 6 within the squirrel-related clade and 24 in the Myomorpha clade. The majority of these shifts occurred within the most recent familial rodent radiations: the Cricetidae and Muridae clades. Using the topological imbalances and the time line we discuss the potential role of different diversification factors that might have shaped the rodents radiation. Conclusions: The present glimpse on the diversification pattern of rodents can be used for further comparative meta-analyses. Muroid lineages have a greater degree of variation in their diversification rates than any other rodent group. Different topological signatures suggest distinct diversification processes among rodent lineages. In particular, Muroidea and Sciuroidea display widespread distribution and have undergone evolutionary and adaptive radiation on most of the continents. Our results show that rodents experienced shifts in diversification rate regularly through the Tertiary, but at different periods for each clade. A comparison between the rodent fossil record and our results suggest that extinction led to the loss of diversification signal for most of the Paleogene nodes. [ABSTRACT FROM AUTHOR]

Background: Crows and ravens (Passeriformes: Corvus) are large-brained birds with enhanced cognitive abilities relative to other birds. They are among the few non-hominid organisms on Earth to be considered intelligent and well-known examples exist of several crow species having evolved innovative strategies and even use of tools in their search for food. The 40 Corvus species have also been successful dispersers and are distributed on most continents and in remote archipelagos. Results: This study presents the first molecular phylogeny including all species and a number of subspecies within the genus Corvus. We date the phylogeny and determine ancestral areas to investigate historical biogeographical patterns of the crows. Additionally, we use data on brain size and a large database on innovative behaviour and tool use to test whether brain size (i) explains innovative behaviour and success in applying tools when foraging and (ii) has some correlative role in the success of colonization of islands. Our results demonstrate that crows originated in the Palaearctic in the Miocene from where they dispersed to North America and the Caribbean, Africa and Australasia. We find that relative brain size alone does not explain tool use, innovative feeding strategies and dispersal success within crows. Conclusions: Our study supports monophyly of the genus Corvus and further demonstrates the direction and timing of colonization from the area of origin in the Palaearctic to other continents and archipelagos. The Caribbean was probably colonized from North America, although some North American ancestor may have gone extinct, and the Pacific was colonized multiple times from Asia and Australia. We did not find a correlation between relative brain size, tool use, innovative feeding strategies and dispersal success. Hence, we propose that all crows and ravens have relatively large brains compared to other birds and thus the potential to be innovative if conditions and circumstances are right. [ABSTRACT FROM AUTHOR]

A central paradigm in island biogeography has been the unidirectional "downstream" colonization of islands from continents (source to sink) based on the idea that less-diverse island communities are easier to invade than biologically more-diverse continental communities. Recently, several cases of "upstream" colonization (from islands to continents) have been documented, challenging the traditional view. However, all these cases have involved individual island species that have colonized mainland regions. Here, using molecular phylogenetic data, divergence time estimates, lineage diversity distributions, and ancestral area analyses, we reconstruct the spread of a species-rich (>700 species) passerine bird radiation (core Corvoidea) from its late Eocene/Oligocene origin in the emerging proto-Papuan archipelago north of Australia, including multiple colonizations from the archipelago to Southeast Asia. Thus, islands apparently provided the setting for the initiation of a major songbird radiation that subsequently invaded all other continents. Morphological and behavioral adaptations of the core Corvoidea as generalist feeders in open habitats, which facilitated dispersal and colonization, apparently evolved in the descendants of sedentary forest birds that invaded the proto-Papuan archipelago. The archipelago evidently provided islands of the right size, number, and proximity to continental areas to support the adaptation and diversification of vagile colonizers that went on to increase avian diversity on a global scale. [ABSTRACT FROM AUTHOR]

The pattern of contralaterally and ipsilaterally projecting retinal ganglion cell (RGC) axons at the optic chiasm is essential for the establishment of binocular vision. Contralateral axons cross the chiasm midline as they progress from the optic nerve to the optic tract. In contrast, ipsilateral axons deviate from the chiasm and continue in the ipsilateral optic tract, avoiding the chiasm midline. The molecular mechanism underlying this phenomenon is not completely understood. Here we show that the Sonic Hedgehog (Shh) receptor Boc is enriched in ipsilateral RGCs of the developing retina. Together with the presence of Shh at the midline, this complementary expression pattern led us to hypothesize that Shh might repel ipsilateral RGC axons at the chiasm. Consistent with this hypothesis, we found that only Boc-positive RGC axons retract in vitro in response to Shh and that this response is lost in Boc mutant RGCs. In vivo, we show that Boc is required for the normal segregation of ipsilateral axons at the optic chiasm and, conversely, that Boc expression in contralateral RGCs prevents their axons from crossing the optic chiasm. Together, these results suggest that Shh repels ipsilateral RGC axons at the optic chiasm via its receptor Boc. This work identifies a novel molecular pathway required for the segregation of axons at the optic chiasm. [ABSTRACT FROM AUTHOR]

This paper focuses on veto supertree methods; i.e., methods that aim at producing a conservative synthesis of the relationships agreed upon by all source trees. We propose desirable properties that a supertree should satisfy in this framework, namely the non-contradiction property (PC) and the induction property (PI). The former requires that the supertree does not contain relationships that contradict one or a combination of the source topologies, whereas the latter requires that all topological information contained in the supertree is present in a source tree or collectively induced by several source trees. We provide simple examples to illustrate their relevance and that allow a comparison with previously advocated properties. We show that these properties can be checked in polynomial time for any given rooted supertree. Moreover, we introduce the PhySIC method (PHYlogenetic Signal with Induction and non-Contradiction). For k input trees spanning a set of n taxa, this method produces a supertree that satisfies the above-mentioned properties in O(kn3 + n4) computing time. The polytomies of the produced supertree are also tagged by labels indicating areas of conflict as well as those with insufficient overlap. As a whole, PhySIC enables the user to quickly summarize consensual information of a set of trees and localize groups of taxa for which the data require consolidation. Lastly, we illustrate the behaviour of PhySIC on primate data sets of various sizes, and propose a supertree covering 95% of all primate extant genera. The PhySIC algorithm is available at http://atgc.lirmm.fr/cgi-bin/PhySIC. [ABSTRACT FROM AUTHOR]

In the spinal cord, sonic hedgehog (Shh) is secreted by the floor plate to control the generation of distinct classes of ventral neurons along the dorsoventral axis. Genetic and in vitro studies have shown that Shh also later acts as a midline-derived chemoattractant for commissural axons. However, the receptor(s) responsible for Shh attraction remain unknown. Here we show that two Robo-related proteins, Boc and Cdon, bind specifically to Shh and are therefore candidate receptors for the action of Shh as an axon guidance ligand. Boc is expressed by commissural neurons, and targeted disruption of Boc in mouse results in the misguidance of commissural axons towards the floor plate. RNA-interference-mediated knockdown of Boc impairs the ability of rat commissural axons to turn towards an ectopic source of Shh in vitro. Taken together, these data suggest that Boc is essential as a receptor for Shh in commissural axon guidance. [ABSTRACT FROM AUTHOR]