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The biogeographic and demographic history of the house mouse, Mus musculus domesticus, has been closely linked to human history since pre-Neolithic times – this species first appeared in the Near East and subsequently dispersed westward with humans into regions with local Mus species. However, if this issue is now well known for the eastern Mediterranean, data are still lacking for the western Mediterranean, and especially for north-western Africa. In the present study, we combine morphological, geometric morphometric and genetic analyses to Mus remains from the Moroccan site of Rirha, dating to the Mauretanian period (5th to 1st century BC). Thanks to this multidisciplinary approach, we were able to confirm the first asserted record of the house mouse in a well-established archaeological context in the Maghreb. The morphometric and genetic results are largely congruent, with a single discrepancy observed for one specimen, which may be linked to possible hybridization between M. m. domesticus and M. spretus species. Further analyses are required on material from other North African sites dating to earlier chrono-cultural periods to better document the oldest appearance and the dispersal of the house mouse in the south-western Mediterranean through time. [ABSTRACT FROM AUTHOR]

Mobile devices for on-field DNA analysis have been used for medical diagnostics at the point-of-care, forensic investigations and environmental surveys, but still have to be validated for ancient DNA studies. We report here on a mobile laboratory that we setup using commercially available devices, including a compact real-time PCR machine, and describe procedures to perform DNA extraction and analysis from a variety of archeological samples within 4 hours. The process is carried out on 50 mg samples that are identified at the species level using custom TaqMan real-time PCR assays for mitochondrial DNA fragments. We evaluated the potential of this approach in museums lacking facilities for DNA studies by analyzing samples from the Enlène (MIS 2 layer) and the Portel-Ouest cave (MIS 3 deposits), and also performed experiments during an excavation campaign at the Roc-en-Pail (MIS 5) open-air site. Enlène Bovinae bone samples only yielded DNA for the extinct steppe bison (Bison priscus), whereas Portel-Ouest cave coprolites contained cave hyena (Crocuta crocuta spelaea) DNA together, for some of them, with DNA for the European bison sister species/subspecies (Bison schoetensacki/Bb1-X), thus highlighting the cave hyena diet. Roc-en-Pail Bovinae bone and tooth samples also contained DNA for the Bison schoetensacki/Bb1-X clade, and Cervidae bone samples only yielded reindeer (Rangifer tarandus) DNA. Subsequent DNA sequencing analyses confirmed that correct species identification had been achieved using our TaqMan assays, hence validating these assays for future studies. We conclude that our approach enables the rapid genetic characterization of tens of millennia-old archeological samples and is expected to be useful for the on-site screening of museums and freshly excavated samples for DNA content. Because our mobile laboratory is made up of commercially available instruments, this approach is easily accessible to other investigators. [ABSTRACT FROM AUTHOR]

Humans have a long history of transporting and trading plants, contributing to the evolution of domesticated plants. Theobroma cacao originated in the Neotropics from South America. However, little is known about its domestication and use in these regions. In this study, ceramic residues from a large sample of pre-Columbian cultures from South and Central America were analyzed using archaeogenomic and biochemical approaches. Here we show, for the first time, the widespread use of cacao in South America out of its native Amazonian area of origin, extending back 5000 years, likely supported by cultural interactions between the Amazon and the Pacific coast. We observed that strong genetic mixing between geographically distant cacao populations occurred as early as the middle Holocene, in South America, driven by humans, favoring the adaptation of T. cacao to new environments. This complex history of cacao domestication is the basis of today's cacao tree populations and its knowledge can help us better manage their genetic resources. [ABSTRACT FROM AUTHOR]

Nassariidae are a group of scavenging, predominantly marine, snails that are diversified on soft bottoms as well as on rocky shores, and are the subject of numerous research papers in ecology, ecotoxicology or paleontology. A weak and/or apparently continuous variation in shell characters has resulted in an intimidating taxonomy, with complex synonymy lists. Over 1320 extant nominal species have been described, of which 442 are currently regarded as valid. Above species level, the state of the art is equally hazy, with four subfamilies and twelve genera currently accepted, and many other names in the graveyard of synonymy. A molecular analysis based on three mitochondrial (COI, 16S, 12S) and two nuclear (28S, H3) markers was conducted. Our dataset includes 218 putative nassariid species, comprising 9 of the 12 valid genera, and 25 nominal genera represented by their type species. The monophyly of the Nassariidae as classically construed is not confirmed. Species of Antillophos , Engoniophos , Phos , Nassaria , Tomlinia and Anentome (formerly considered Buccinidae) are included inside the Nassariidae clade. Within the Nassariinae, the tree unexpectedly demonstrates that species from the Atlantic and the Indo-Pacific form different clades which represent several independent diversification events. Through an integrative approach, the reconstruction of ancestral states was addressed for eight characters supposedly informative for taxonomy. Using numerous fossil calibration points, Nassariidae appear to have originated 120 MYA ago in Atlantic temperate waters during the Lower Cretaceous. Our results have a profound impact on nassariid taxonomy, especially with regard to the validity of subfamily- and genus-level names. [ABSTRACT FROM AUTHOR]

In 2011, three specimens from an unknown species of tube-nosed bat (genus Murina) were collected in montane moist forest at altitudes between 1117 and 1682 m in the Ngoc Linh Nature Reserve of Vietnam. We sequenced the mitochondrial COI gene from Ngoc Linh bats and performed comparisons with Murina sequences available in the nucleotide databases. The results suggested that the three unidentified specimens belong to Murina lorelieae, a species recently described from a single specimen collected in southern China. Nucleotide distances between specimens from Ngoc Linh and southern China are exceptionally low for M. lorelieae (1.25%) in comparison with three other Murina species, i.e., Murina cyclotis, Murina feae, and Murina huttoni (3.9-5.5%). We suggest that M. lorelieae is adapted to montane forests, which may have facilitated long-distance dispersal events between southern China and Vietnam during glacial periods of the Pleistocene. Morphological comparisons based on body-size measurements and geometric morphometric analyses of the skulls showed differences between Vietnamese specimens and the Chinese holotype of M. lorelieae. We proposed that the Vietnamese specimens belong to a distinct subspecies, M. lorelieae ngoclinhensis. [ABSTRACT FROM AUTHOR]

The sequencing of the crustacean collection of the MNHN, Paris, constitutes a promising yet very challenging barcoding project. For the collection's crustacean specimens preserved in ethanol, some of which were collected up to 40 years ago, the conventional COI barcoding procedure of amplification with Folmer primers failed for more than half of the specimens (58%, n = 1920). We hypothesised that this failure may have been due to incompatible mismatches between the crustaceans targeted and the Folmer primer sequences and/or the amount of degradation of the DNA extracted from museum specimens. The comparison of the Folmer primers against the COI sequences from GenBank complete decapod mitochondrial genomes revealed that the annealing regions were, in fact, rather conserved, suggesting that the amplification failures were due more likely to the low quality of the DNA isolated. Using an alignment of all available decapod sequences we designed two internal primers in the middle of the barcoding COI region and also selected two additional external primers to be used as alternative to the standard Folmer primers. Using a two-overlapping-fragments amplification strategy and different primer combinations, our new protocol significantly increased the amplification success rate of the collection material from 42% with the Folmer primers to 84%, recovering an additional 364 complete barcodes and 443 minibarcodes (i.e. fragments of less than 400 base pairs), and expanding the species coverage from 254 to 397 barcoded crustaceans. [ABSTRACT FROM AUTHOR]

Abstract: Cancellariidae, or nutmeg shells, is a family of marine gastropods that feed on the body fluids and the egg cases of marine animals. The 300 or so living species are distributed worldwide, mostly on soft bottoms, from intertidal to depths of about 1000m. Although they are a key group for the understanding of neogastropod evolution, they are still poorly known in terms of anatomy, ecology and systematics. This paper reports the first mitochondrial multi-gene phylogenetic hypothesis for the group. Data were collected for 50 morphospecies, representative of 22 genera belonging to the three currently recognized subfamilies. Sequences from three genes (12S, 16S and COI) were analyzed with Maximum Likelihood analysis and Bayesian Inference, both as single gene datasets and in two partitioned concatenated alignment. Largely consistent topologies were obtained and discussed with respect to the traditional subfamilial arrangements. The obtained phylogenetic trees were also used to produce Robinson–Foulds supertrees. Our results confirmed the monophyly of the subfamily Plesiotritoninae, while Admetinae and Cancellariinae, as currently conceived, were retrieved as polyphyletic. Based on our findings we propose changes to the systematic arrangement of these subfamilies. At a lower taxonomic rank, our results highlighted the rampant homoplasy of many characters traditionally used to segregate genera, and thus the need of a critical re-evaluation of the contents of many genera (e.g. Nipponaphera, Merica, Sydaphera, Bivetia), the monophyly of which was not recovered. [Copyright &y& Elsevier]