Multi-taxa neo-taphonomic analysis of bone remains from barn owl pellets and cross-validation of observations: a case study from Dominica (Lesser Antilles)

Paleo- and neo-taphonomic analyses of bone assemblages rarely consider all the occurring taxa in a single study and works concerning birds of prey as accumulators of microvertebrate bone remains mostly focus on small mammals such as rodents and soricomorphs. However, raptors often hunt and consume a large range of taxa, including vertebrates such as small mammals, fishes, amphibians, squamates and birds. Bone remains of all these taxonomic groups are numerous in many paleontological and archaeological records, especially in cave deposits. To better characterize the predators at the origin of fossil and sub-fossil microvertebrate accumulations and the taphonomic history of the deposit, it is thus mandatory to conduct global and multi-taxa taphonomic approaches. The aim of this study is to provide an example of such a global approach through the investigation of a modern bone assemblage from a sample of pellets produced by the Lesser Antillean Barn Owl (Tyto insularis) in the island of Dominica. We propose a new methodology that allows us to compare different taxa (rodents, bats, squamates and birds) and to experiment with a cross-validation process using two observers for each taxonomic group to test the reliability of the taphonomic observations.1. Introduction 2. Materials and Methods 2.1. Owl Pellets Sampling 2.2. Prey Identification 2.3. Taphonomic Analysis 2.3.1. Anatomical Representation 2.3.2. Fragmentation 2.3.3. Surface Modifications 2.3.4. Size/Weight Classes of Preys 2.4. Cross-Validation of Observations 3. Results 3.1. Faunal Spectrum 3.2. Anatomical Representation 3.3. Fragmentation 3.4. Modifications of Bone Surface 4. Discussion 4.1. Diet of Tyto Insularis in Dominica 4.2. Taphonomic Impact of Tyto Insularis on Small Vertebrate Bone Assemblage 4.2.1. Remarks on the Size/Weight Classes of Preys 4.2.2. Anatomical Representation 4.2.3. Fragmentation 4.2.4. Digestion 4.3. Degree of Inter-Observer Differences and Potential Outcomes 4.4. Towards an “Inter-Taxa Calibration” 5. Conclusion

An improved chronology for the Middle Stone Age at El Mnasra cave, Morocco

North African coastal Middle Stone Age (MSA) sites are key to study the development and expansion of early H. sapiens. El Mnasra cave on the Atlantic coast of Morocco (Témara region) is a crucial site associated with MSA archaeological materials considered advanced cognitive hallmarks of behavioural innovation, such as numerous Nassariidae perforated shells, hematite pigments, bones industry and coastal resources exploitation. We provide new trapped-charges dates (OSL and combined US-ESR ages). Our Bayesian modelling strengthens the new lithostratigraphic interpretation of the cave stratigraphic units (US) and we propose an updated chronostratigraphic model for the Middle Stone Age archaeo-sequence of El Mnasra Cave. We confirm a human presence between 124–104 ka, earlier than what the previous OSL and US-ESR data showed. Our time range intervals allowed us to also extend the age of the MSA occupations considerably to the MIS 4/3 (~62–30 ka), marked by the disappearance of the Nassariidae perforated shells. Outstandingly, our model pushed back the age of the largest record of Nassariidae perforated shells and placed the age of their use by the Aterian groups at El Mnasra from the MIS 5d-5b (~115–94 ka)

Expanding phenotype of hereditary fibrosing poikiloderma with tendon contractures, myopathy, and pulmonary fibrosis caused by FAM111B mutations: Report of an additional family raising the question of cancer predisposition and a short review of early-onset poikiloderma.

journal article2017 Mar2017 03 19importedHereditary fibrosing poikiloderma with tendon contractures, myopathy, and pulmonary fibrosis (POIKTMP [MIM#615704]) is an extremely rare syndromic form of autosomal dominant poikiloderma. This genetic disorder was first identified in a South African family in 2006.1 To date, 3 families and 9 independent sporadic cases have been reported.2-4 Here we report an additional family of POIKTMP and expand the clinical spectrum. We describe, for the first time to our knowledge, a pancreatic cancer in the clinical course in 1 patient

VaRank: a simple and powerful tool for ranking genetic variants:

Background. Most genetic disorders are caused by single nucleotide variations (SNVs) or small insertion/deletions (indels). High throughput sequencing has broadened the catalogue of human variation, including common polymorphisms, rare variations or disease causing mutations. However, identifying one variation among hundreds or thousands of others is still a complex task for biologists, geneticists and clinicians. Results. We have developed VaRank, a command-line tool for the ranking of genetic variants detected by high-throughput sequencing. VaRank scores and prioritizes variants annotated either by Alamut Batch or SnpEff. A barcode allows users to quickly view the presence/absence of variants (with homozygote/heterozygote status) in analyzed samples. VaRank supports the commonly used VCF input format for variants analysis thus allowing it to be easily integrated into NGS bioinformatics analysis pipelines. VaRank has been successfully applied to disease-gene identification as well as to molecular diagnostics setup for several hundred patients. Conclusions. VaRank is implemented in Tcl/Tk, a scripting language which is platform-independent but has been tested only on Unix environment. The source code is available under the GNU GPL, and together with sample data and detailed documentation can be downloaded from http://www.lbgi.fr/VaRank/

BBS proteins interact genetically with the IFT pathway to influence SHH-related phenotypes

There are numerous genes for which loss-of-function mutations do not produce apparent phenotypes even though statistically significant quantitative changes to biological pathways are observed. To evaluate the biological meaning of small effects is challenging. Bardet–Biedl syndrome (BBS) is a heterogeneous autosomal recessive disorder characterized by obesity, retinopathy, polydactyly, renal malformations, learning disabilities and hypogenitalism, as well as secondary phenotypes including diabetes and hypertension. BBS knockout mice recapitulate most human phenotypes including obesity, retinal degeneration and male infertility. However, BBS knockout mice do not develop polydacyly. Here we showed that the loss of BBS genes in mice result in accumulation of Smoothened and Patched 1 in cilia and have a decreased Shh response. Knockout of Bbs7 combined with a hypomorphic Ift88 allele (orpk as a model for Shh dysfuction) results in embryonic lethality with e12.5 embryos having exencephaly, pericardial edema, cleft palate and abnormal limb development, phenotypes not observed in Bbs7−/− mice. Our results indicate that BBS genes modulate Shh pathway activity and interact genetically with the intraflagellar transport (IFT) pathway to play a role in mammalian development. This study illustrates an effective approach to appreciate the biological significance of a small effect

Limpet Shells from the Aterian Level 8 of El Harhoura 2 Cave (Témara, Morocco): Preservation State of Crossed-Foliated Layers

International audienceThe exploitation of mollusks by the first anatomically modern humans is a central question for archaeologists. This paper focuses on level 8 (dated around * 100 ka BP) of El Har-houra 2 Cave, located along the coastline in the Rabat-Témara region (Morocco). The large quantity of Patella sp. shells found in this level highlights questions regarding their origin and preservation. This study presents an estimation of the preservation status of these shells. We focus here on the diagenetic evolution of both the microstructural patterns and organic components of crossed-foliated shell layers, in order to assess the viability of further investigations based on shell layer minor elements, isotopic or biochemical compositions. The results show that the shells seem to be well conserved, with microstructural patterns preserved down to sub-micrometric scales, and that some organic components are still present in situ. But faint taphonomic degradations affecting both mineral and organic components are nonetheless evidenced, such as the disappearance of organic envelopes surrounding crossed-foliated lamellae, combined with a partial recrystallization of the lamellae. Our results provide a solid case-study of the early stages of the diagenetic evolution of crossed-foliated shell layers. Moreover, they highlight the fact that extreme caution must be taken before using fossil shells for palaeoenvironmental or geochronological reconstructions. Without thorough investigation, the alteration patterns illustrated here would easily have gone unnoticed. However, these degradations are liable to bias any proxy based on the elemental, isotopic or biochemical composition of the shells. This study also provides significant data concerning human subsistence behavior: the presence of notches and the good preservation state of limpet shells (no dissolution/recrystallization, no bioerosion and no abrasion/fragmentation aspects) would attest that limpets were gathered alive with tools by Middle Palaeolithic (Aterian) populations in North Africa for consumption

Zebrafish: a vertebrate tool for studying basal body biogenesis, structure, and function.

Understanding the role of basal bodies (BBs) during development and disease has been largely overshadowed by research into the function of the cilium. Although these two organelles are closely associated, they have specific roles to complete for successful cellular development. Appropriate development and function of the BB are fundamental for cilia function. Indeed, there are a growing number of human genetic diseases affecting ciliary development, known collectively as the ciliopathies. Accumulating evidence suggests that BBs establish cell polarity, direct ciliogenesis, and provide docking sites for proteins required within the ciliary axoneme. Major contributions to our knowledge of BB structure and function have been provided by studies in flagellated or ciliated unicellular eukaryotic organisms, specifically Tetrahymena and Chlamydomonas. Reproducing these and other findings in vertebrates has required animal in vivo models. Zebrafish have fast become one of the primary organisms of choice for modeling vertebrate functional genetics. Rapid ex-utero development, proficient egg laying, ease of genetic manipulation, and affordability make zebrafish an attractive vertebrate research tool. Furthermore, zebrafish share over 80 % of disease causing genes with humans. In this article, we discuss the merits of using zebrafish to study BB functional genetics, review current knowledge of zebrafish BB ultrastructure and mechanisms of function, and consider the outlook for future zebrafish-based BB studies

Mutations in the latent TGF-beta binding protein 3 (LTBP3) gene cause brachyolmia with amelogenesis imperfecta

Inherited dental malformations constitute a clinically and genetically heterogeneous group of disorders. Here, we report on four families, three of them consanguineous, with an identical phenotype, characterized by significant short stature with brachyolmia and hypoplastic amelogenesis imperfecta (AI) with almost absent enamel. This phenotype was first described in 1996 by Verloes et al. as an autosomal recessive form of brachyolmia associated with AI. Whole-exome sequencing resulted in the identification of recessive hypomorphic mutations including deletion, nonsense and splice mutations, in the LTBP3 gene, which is involved in the TGF-beta signaling pathway. We further investigated gene expression during mouse development and tooth formation. Differentiated ameloblasts synthesizing enamel matrix proteins and odontoblasts expressed the gene. Study of an available knockout mouse model showed that the mutant mice displayed very thin to absent enamel in both incisors and molars, hereby recapitulating the AI phenotype in the human disorder

A Novel Mutation Involving the Initiation Codon of FGF3 in a Family Described with Complete Inner Ear Agenesis, Microtia and Major Microdontia (LAMM Syndrome)

LAMM syndrome (OMIM #610706) is a rare autosomal recessive syndrome characterized by the association of Michel aplasia, microdontia and malformation of the external ear. Different mutations in FGF3 gene were reported in several families presenting with this syndrome. Clinical features and genetic results observed in a family with LAMM syndrome are reported. The diagnosis of isolated Michel aplasia was initially made in this family composed of two affected children. Microtia and microdontia was recently evidenced in both patients suggesting the diagnosis of LAMM syndrome. New auditory and orodental iconography was performed permitting to describe the patients’ phenotype in depth and to report rare findings of LAMM syndrome. The sequencing of FGF3 gene identified a novel missense mutation (c.2T>G), substituting the first initiator methionine in arginine, in the fibroblast growth factor 3 (FGF3) at the homozygous state in both patients. LAMM syndrome was confirmed and appropriate genetic counseling performed

Evidence for an Invasive Aphid “Superclone”: Extremely Low Genetic Diversity in Oleander Aphid (Aphis nerii) Populations in the Southern United States

The importance of genetic diversity in successful biological invasions is unclear. In animals, but not necessarily plants, increased genetic diversity is generally associated with successful colonization and establishment of novel habitats. The Oleander aphid, Aphis nerii, though native to the Mediterranean region, is an invasive pest species throughout much of the world. Feeding primarily on Oleander (Nerium oleander) and Milkweed (Asclepias spp.) under natural conditions, these plants are unlikely to support aphid populations year round in the southern US. The objective of this study was to describe the genetic variation within and among US populations of A. nerii, during extinction/recolonization events, to better understand the population ecology of this invasive species.We used five microsatellite markers to assess genetic diversity over a two year period within and among three aphid populations separated by small (100 km) and large (3,700 km) geographic distances on two host plant species. Here we provide evidence for A. nerii "superclones". Genotypic variation was absent in all populations (i.e., each population consisted of a single multilocus genotype (MLG) or "clone") and the genetic composition of only one population completely changed across years. There was no evidence of sexual reproduction or host races on different plant species.Aphis nerii is a well established invasive species despite having extremely low genetic diversity. As this aphid appears to be obligatorily asexual, it may share more similarities with clonally reproducing invasive plants, than with other animals. Patterns of temporal and geographic genetic variation, viewed in the context of its population dynamics, have important implications for the management of invasive pests and the evolutionary biology of asexual species