Biology subjects

Murienne, J.

Publications and source records attributed to Murienne, J..

8 recordsLinked to original sources

bioRxiv2024

A polytypic species revisited: Phylogenetic and morphological variation, taxonomic status, and geographical distribution of Trachops (Chiroptera: Phyllostomidae)

The taxonomic status of the neotropical bat genus Trachops has been reevaluated through an integrated study that incorporates morphological, morphometric, and molecular data across its extensive geographic range. Our research, which included previously unexamined regions, revealed substantial insights into the diversity within Trachops. The results support the elevation of T. cirrhosus ehrhardti to species status, due to genetic and morphological differences in southeastern Brazil specimens. Conversely, our comprehensive analysis found insufficient evidence to maintain the subspecific distinction of T. c. coffini, which lacks diagnosable morphological characters and is not genetically distinct from T. c. cirrhosus across its distribution range. Additionally, our findings challenge the previous belief of a latitudinal differentiation in body size for Trachops cirrhosus, as specimens from western South America and northeastern South America exhibit similar sizes to those from Central America. These results underscore the importance of revising the taxonomic framework for this bat genus, contributing to a more precise understanding of its evolutionary relationships, and further enhancing conservation efforts, considering the potential threats to the newly recognized T. ehrhardti in the imperiled Atlantic Forest of Brazil.

zoology↗

bioRxiv2023

Pangolin genomes offer key insights and resources for the world's most trafficked wild mammals

Pangolins form a group of scaly mammals that are trafficked at record numbers for their meat and medicinal properties. Despite their great conservation concern, knowledge of their evolution is limited by a paucity of genomic data. We aim to produce exhaustive genomic resources that include 3 238 orthologous genes and whole-genome polymorphisms to assess the evolution of all eight pangolin species. Robust orthologous gene-based phylogenies recovered the monophyly of the three genera of pangolins, and highlighted the existence of an undescribed species closely related to South-East Asian pangolins. Signatures of middle Miocene admixture between an extinct, possibly European, lineage and the ancestor of South-East Asian pangolins, provides new insights into the early evolutionary history of the group. Demographic trajectories and genome-wide heterozygosity estimates revealed contrasts between continental vs. island populations and species lineages, suggesting that conservation planning should consider intra-specific patterns. With the expected loss of genomic diversity from recent, extensive trafficking not yet been realized in pangolins, we recommend that populations are genetically surveyed to anticipate any deleterious impact of the illegal trade. Finally, we produce a complete set of genomic resources that will be integral for future conservation management and forensic endeavors required for conserving pangolins, including tracing their illegal trade. These include the completion of whole-genomes for pangolins through the first reference genome with long reads for the giant pangolin (Smutsia gigantea) and new draft genomes (~43x-77x) for four additional species, as well as a database of orthologous genes with over 3.4 million polymorphic sites.

genomics↗

bioRxiv2022

Phylogenomics Illuminates the Evolutionary History of Wild Silkmoths in Space and Time (Lepidoptera: Saturniidae)

AO_SCPLOWBSTRACTC_SCPLOWWild silkmoths (Saturniidae) are one of the most emblematic and most studied families of moths. Yet, the absence of a robust phylogenetic framework based on a comprehensive taxonomic sampling impedes our understanding of their evolutionary history. We analyzed 1,024 ultraconserved elements (UCEs) and their flanking regions to infer the relationships among 338 species of Saturniidae representing all described subfamilies, tribes, and genera. We investigated systematic biases in genomic data and performed dating and historical biogeographic analyses to reconstruct the evolutionary history of wild silkmoths in space and time. Using Gene Genealogy Interrogation, we showed that saturation of nucleotide sequence data blurred our understanding of early divergences and first biogeographic events. Our analyses support a Neotropical origin of saturniids, shortly after the Cretaceous-Paleogene extinction event (ca 64.0 [stem] - 52.0 [crown] Ma), and two independent colonization events of the Old World during the Eocene, presumably through the Bering Land Bridge. Early divergences strongly shaped the distribution of extant subfamilies as they showed very limited mobility across biogeographical regions, except for Saturniinae, a subfamily now present on all continents but Antarctica. Overall, our results provide a framework for in-depth investigations into the spatial and temporal dynamics of all saturniid lineages and for the integration of their evolutionary history into further global studies of biodiversity and conservation. Rather unexpectedly for a taxonomically well-known family such as Saturniidae, the proper alignment of taxonomic divisions and ranks with our phylogenetic results leads us to propose substantial rearrangements of the family classification, including the description of one new subfamily and two new tribes.

evolutionary biology↗

bioRxiv2021

Fast processing of environmental DNA metabarcoding sequence data using convolutional neural networks

1The intensification of anthropogenic pressures have increased consequences on biodiversity and ultimately on the functioning of ecosystems. To monitor and better understand biodiversity responses to environmental changes using standardized and reproducible methods, novel high-throughput DNA sequencing is becoming a major tool. Indeed, organisms shed DNA traces in their environment and this "environmental DNA" (eDNA) can be collected and sequenced using eDNA metabarcoding. The processing of large volumes of eDNA metabarcoding data remains challenging, especially its transformation to relevant taxonomic lists that can be interpreted by experts. Speed and accuracy are two major bottlenecks in this critical step. Here, we investigate whether convolutional neural networks (CNN) can optimize the processing of short eDNA sequences. We tested whether the speed and accuracy of a CNN are comparable to that of the frequently used OBITools bioinformatic pipeline. We applied the methodology on a massive eDNA dataset collected in Tropical South America (French Guiana), where freshwater fishes were targeted using a small region (60pb) of the 12S ribosomal RNA mitochondrial gene. We found that the taxonomic assignments from the CNN were comparable to those of OBITools, with high correlation levels and a similar match to the regional fish fauna. The CNN allowed the processing of raw fastq files at a rate of approximately 1 million sequences per minute which was 150 times faster than with OBITools. Once trained, the application of CNN to new eDNA metabarcoding data can be automated, which promises fast and easy deployment on the cloud for future eDNA analyses.

bioinformatics↗

bioRxiv2020

Characterizing the spatial signal of environmental DNA in river systems using a community ecology approach

Environmental DNA (eDNA) is gaining a growing popularity among scientists but its applicability to biodiversity research and management remains limited in river systems by the lack of knowledge about the spatial extent of the downstream transport of eDNA. Here, we assessed the ability of eDNA inventories to retrieve spatial patterns of fish assemblages along two large and species rich Neotropical rivers. We first examined overall community variation with distance through the distance decay of similarity and compared this pattern to capture-based samples. We then considered previous knowledge on individual species distributions, and compared it to the eDNA inventories for a set of 53 species. eDNA collected from 28 sites in the Maroni and 25 sites in the Oyapock rivers permitted to retrieve a decline of species similarity with distance between sites. The distance decay of similarity derived from eDNA was similar, and even more pronounced, than that obtained with capture-based methods (gil-nets). In addition, the species upstream-downstream distribution range derived from eDNA matched to the known distribution of most species. Our results demonstrate that environmental DNA does not represent an integrative measure of biodiversity across the whole upstream river basin but provide a relevant picture of local fish assemblages. Importantly, the spatial signal gathered from eDNA was therefore comparable to that gathered with local capture based methods, which describes fish fauna over a few hundred metres.

ecology↗

bioRxiv2020

At each site its diversity: DNA barcoding reveals remarkable earthworm diversity in neotropical rainforests of French Guiana

Despite their recognized essential role in soil, earthworms in tropical environments are still understudied. The aim of this study was to re-evaluate the diversity at the regional scale, as well as to investigate the environmental and spatial drivers of earthworm communities. We sampled earthworm communities across a range of habitats at six locations in French Guiana using three different sampling methods. We generated 1675 DNA barcodes and combined them with data from a previous study. Together, all sequences clustered into 119 MOTUs which were used as proxy to assess species richness. Only two MOTUs were common between the six locations and 20.2 % were singletons, showing very high regional species richness and a high number of rare species. A canonical redundancy analysis was used to identify key drivers of the earthworm community composition. The RDA results and beta-diversity calculations both show strong species turnover and a strong spatial effect, resulting from dispersal limitations that are responsible for the current community composition. Sampling in different microhabitats allowed the discovery of 23 MOTUs that are exclusively found in decaying trunks and epiphytes, highlighting hidden diversity of earthworms outside of soil.

ecology↗

bioRxiv2019

Climatic niche change of fish is faster at high latitude and in marine environments

Change in species climatic niches is a key mechanism influencing species distribution patterns. The question of which factors impact niche change remains a highly debated topic in evolutionary biology. Previous studies have proposed that rates of climatic niche change might be correlated with climatic oscillations at high latitude or adaptation to new environmental conditions. Yet, very few studies have asked if those factors are also predominant in aquatic environments. Here, we reconstruct the climatic niche changes of fish species on a new phylogeny encompassing 12,616 species. We first confirm that the rate of niche change is faster at high latitude and show that this association is steeper for freshwater than for marine species. We also show that freshwater species have slower rates of niche change than marine species. These results may be explained by the fact that freshwater species have larger climatic niche breadth and thermal safety margin than marine species at high latitude. Overall, our study sheds a new light on the environmental conditions and species features impacting rates of climatic niche change in aquatic habitats.

evolutionary biology↗

bioRxiv2019

Species better track the shifting isotherms in the oceans than on lands

Despite mounting evidence of species redistribution as climate warms, our knowledge of the coupling between species range shifts and isotherm shifts is limited. Compiling a global geo-database of 30,534 range shifts from 12,415 taxa, we show that only marine taxa closely track the shifting isotherms. In the oceans, the velocity of isotherm shifts interacts synergistically with anthropogenic disturbances and baseline temperatures such that isotherm tracking by marine life happens either in warm and undisturbed waters (e.g. Central Pacific Basin) or in colder waters where human activities are more pronounced (e.g. North Sea). On lands, increasing anthropogenic activities and temperatures negatively impact the capacity of terrestrial taxa to track isotherm shifts in latitude and elevation, respectively. This suggests that terrestrial taxa are lagging behind the shifting isotherms, most likely due to their wider thermal safety margin, more constrained physical environment for dispersal and higher availability of thermal microrefugia at shorter distances.

ecology↗