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Mitogenomics reveals high synteny and long evolutionary histories of sympatric cryptic nematode species
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Species with seemingly identical morphology but with distinct genetic differences are abundant in the marine environment and frequently co-occur in the same habitat. Such cryptic species are typically delineated using a limited number of mitochondrial and/or nuclear marker genes, which do not yield information on gene order and gene content of the genomes under consideration. We used next-generation sequencing to study the composition of the mitochondrial genomes of four sympatrically distributed cryptic species of the Litoditis marina species complex (PmI, PmII, PmIII, and PmIV). The ecology, biology, and natural occurrence of these four species are well known, but the evolutionary processes behind this cryptic speciation remain largely unknown. The gene order of the mitochondrial genomes of the four species was conserved, but differences in genome length, gene length, and codon usage were observed. The atp8 gene was lacking in all four species. Phylogenetic analyses confirm that PmI and PmIV are sister species and that PmIII diverged earliest. The most recent common ancestor of the four cryptic species was estimated to have diverged 16 MYA. Synonymous mutations outnumbered nonsynonymous changes in all protein-encoding genes, with the Complex IV genes (coxI-III) experiencing the strongest purifying selection. Our mitogenomic results show that morphologically similar species can have long evolutionary histories and that PmIII has several differences in genetic makeup compared to the three other species, which may explain why it is better adapted to higher temperatures than the other species.
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RBINS Staff Publications 2016
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Spatiotemporal variation and sediment retention effects on nematode communities associated with Halimeda opuntia (Linnaeus) Lamouroux (1816) and Sargassum polyceratium Montagne (1837) seaweeds in a tropical phytal ecosystem
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Nematodes play an important role in ecological processes and are one of the most abundant meiofaunal organisms associated with seaweeds. Yet, knowledge on seaweed bed ecosystems is limited. Nematodes associated with Sargassum polyceratium and Halimeda opuntia were compared in two transects, 80 m apart and parallel to the beach line in Cupe Beach, Brazil. The temporal variation during the dry and rainy seasons and the effect of sediment retention by the seaweed on nematode density and composition were investigated. The differences in nematode communities between the two seasons were mainly caused by the increase in density of the most abundant genera in the rainy season. A significant difference was observed between the nematode communities of the two transects for H. opuntia. The nematode communities of both seaweed species did not differ significantly in the same transect. The genus Euchromadora was dominant in both seaweed species. The amount of sediment retained by the seaweeds did not affect the overall nematode density. However, it was positively correlated with the density of Draconema and Euchromadora in both seaweeds, and both genera were exclusively found associated with seaweeds. This result opposes the idea that the more sediment retained by the seaweed, the higher the nematode overall density and the higher the number of nematodes originally coming from the sediment.
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RBINS Staff Publications 2016
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Coexisting cryptic species of the Litoditis marina complex (Nematoda) show differential resource use and have distinct microbiomes with high intraspecific variability
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Differences in resource use or in tolerances to abiotic conditions are often invoked as potential mechanisms underlying the sympatric distribution of cryptic species. Additionally, the microbiome can provide physiological adaptations of the host to environmental conditions. We determined the intra- and interspecific variability of the microbiomes of three cryptic nematode species of the Litoditis marina species complex that co-occur, but show differences in abiotic tolerances. Roche 454 pyrosequencing of the microbial 16S rRNA gene revealed distinct bacterial communities characterized by a substantial diversity (85-513 OTUs) and many rare OTUs. The core microbiome of each species contained only very few OTUs (2-6), and four OTUs were identified as potentially generating tolerance to abiotic conditions. A controlled experiment in which nematodes from two cryptic species (Pm1 and Pm3) were fed with either an E. coli suspension or a bacterial mix was performed, and the 16S rRNA gene was sequenced using the MiSeq technology. OTU richness was 10-fold higher compared to the 454 data set and ranged between 1118 and 7864. This experiment confirmed the existence of species-specific microbiomes, a core microbiome with few OTUs, and high interindividual variability. The offered food source affected the bacterial community and illustrated different feeding behaviour between the cryptic species, with Pm3 exhibiting a higher degree of selective feeding than Pm1. Morphologically similar species belonging to the same feeding guild (bacterivores) can thus have substantial differences in their associated microbiomes and feeding strategy, which in turn may have important ramifications for biodiversity-ecosystem functioning relationships.
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RBINS Staff Publications 2016
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Let the dead speak…comments on Dibble et al.'s reply to “Evidence supporting an intentional burial at La Chapelle-aux-Saints”
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In a reply to our paper presenting new evidence supporting an intentional Neanderthal burial at La Chapelle-aux-Saints (Corrèze, France), Dibble et al. (2014) reviewed our data in relation to the original Bouyssonie publications. They conclude that alternative hypotheses can account for the preservation of the human remains within a pit. Here we present new data from our recent excavations and highlight several misinterpretations of the Bouyssonie publications, which, when taken together refute most of their arguments. Moreover, we show that the different hypotheses proposed by Dibble et al. cannot work together and fail to provide a credible explanation for the deposit, reinforcing our demonstration that the burial hypothesis remains the most parsimonious explanation for the preservation of the Neanderthal skeletal material at La Chapelle-aux-Saints.
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RBINS Staff Publications 2016
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Change in Historical Range of the Ural Owl in Europe
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A carpometacarpus recovered during archaeological excavations in the town of Quaregnon is the westernmost find ever reported in Europe of a Ural Owl (Strix uralensis), and the first occurrence for Belgium. Both the morphology of the skeletal element and its measurements rule out an identification as any of the other Strigiformes from the Western Palearctic. The provenance of this specimen, that dates to the medieval period (10th-12th centuries AD), is discussed. It is hypothesized that the bird was a wild animal, but the available evidence does not unequivocally determine whether it belonged to a local, breeding population that went extinct or if it came from a more distant population. However, a survey of other zooarchaeological finds of Ural Owl in Europe shows that the species occurred farther west in the past, outside the present natural breeding range. This suggests that Ural Owl may have found suitable nesting biotopes in Belgium and northern France during the medieval period.
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RBINS Staff Publications 2016
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Unraveling geological and geographical provenances of querns and mills during Roman times at the northern frontier of the Roman Empire (Belgium, Northern France, Southern Netherlands, Western germany): a multidisciplinary research project.
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RBINS Staff Publications 2016
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Manufacture and diffusion of whetstones during Roman times in Northern Gaul (Belgium and Northern France).
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RBINS Staff Publications 2016
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Geochemical sourcing of flint artifacts from Western Belgium and the German Rhineland: testing hypotheses on Gravettian period mobility and raw material economy
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Identifying the geological and geographical origin of lithic raw materials is critical to effectively address prehistoric forager raw material economies and mobility strategies. Currently, Paleolithic archaeology in Belgium lacks a systematic sourcing strategy to effectively substantiate detailed interpretations of prehistoric hunter-gatherer behavioral change across time and space. This pilot study evaluates the potential to “fingerprint” flint from the Mons Basin, western Belgium, using the laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) technique and a multivariate statistical analysis of 87 geological samples and 39 Gravettian period chipped stone artifacts. We reappraise two hypotheses raised by previous scholars based on visual raw material identification: (1) the Gravettian occupants of Maisières-Canal supplied themselves with “black flint” from one single source; (2) the sites Rhens and Koblenz-Metternich yielded artifacts indicative of long-distance transfer of western Belgian flint into the German Rhineland, ca. 260 km from the primary source area. Our results demonstrate the validity of LA-ICP-MS data with flint and compositional data analysis for fingerprinting discrete geological formations from the Mons Basin. We suggest multiple source provisioning for Maisières-Canal. Geochemical characterization of other potential flint sources is required to validate the long-distance transfer hypothesis of western Belgian “black flint” into the German Rhineland.
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RBINS Staff Publications 2016
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The genetic history of Ice Age Europe
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Modern humans arrived in Europe ˊ45,000 years ago, but little is known about their genetic composition before the start of farming ˊ8,500 years ago. Here we analyse genome-wide data from 51 Eurasians from ˊ45,000–7,000 years ago. Over this time, the proportion of Neanderthal DNA decreased from 3–6\% to around 2\%, consistent with natural selection against Neanderthal variants in modern humans. Whereas there is no evidence of the earliest modern humans in Europe contributing to the genetic composition of present-day Europeans, all individuals between ˊ37,000 and ˊ14,000 years ago descended from a single founder population which forms part of the ancestry of present-day Europeans. An ˊ35,000-year-old individual from northwest Europe represents an early branch of this founder population which was then displaced across a broad region, before reappearing in southwest Europe at the height of the last Ice Age ˊ19,000 years ago. During the major warming period after ˊ14,000 years ago, a genetic component related to present-day Near Easterners became widespread in Europe. These results document how population turnover and migration have been recurring themes of European prehistory.
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13th International Symposium on Aquatic Oligochaeta, Brno, Czech Republic, 7–11 September, 2015
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RBINS Staff Publications 2016
