@article {6522, title = {Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections}, journal = {Biodiversity Data Journal}, volume = {11}, year = {2023}, month = {Oct-27-2023}, pages = {e102317}, abstract = {

Intentionally preserved biological material in natural history collections represents a vast repository of biodiversity. Advances in laboratory and sequencing technologies have made these specimens increasingly accessible for genomic analyses, offering a window into the genetic past of species and often permitting access to information that can no longer be sampled in the wild. Due to their age, preparation and storage conditions, DNA retrieved from museum and herbarium specimens is often poor in yield, heavily fragmented and biochemically modified. This not only poses methodological challenges in recovering nucleotide sequences, but also makes such investigations susceptible to environmental and laboratory contamination. In this paper, we review the practical challenges associated with making the recovery of DNA sequence data from museum collections more routine. We first review key operational principles and issues to address, to guide the decision-making process and dialogue between researchers and curators about when and how to sample museum specimens for genomic analyses. We then outline the range of steps that can be taken to reduce the likelihood of contamination including laboratory set-ups, workflows and working practices. We finish by presenting a series of case studies, each focusing on protocol practicalities for the application of different mainstream methodologies to museum specimens including: (i) shotgun sequencing of insect mitogenomes, (ii) whole genome sequencing of insects, (iii) genome skimming to recover plant plastid genomes from herbarium specimens, (iv) target capture of multi-locus nuclear sequences from herbarium specimens, (v) RAD-sequencing of bird specimens and (vi) shotgun sequencing of ancient bovid bone samples.

}, issn = {1314-2828, 1314-2836}, doi = {10.3897/bdj.11.e102317}, url = {http://dx.doi.org/10.3897/bdj.11.e102317}, author = {Ferrari, Giada and Esselens, Lore and Hart, Michelle and Janssens, Steven and Kidner, Catherine and Mascarello, Maurizio and Pe{\~n}alba, Joshua and Pezzini, Fl{\'a}via and von Rintelen, Thomas and Sonet, Gontran and Vangestel, Carl and Virgilio, Massimiliano and Hollingsworth, Peter} } @article {6509, title = {Large-scale and small-scale population genetic structure of the medically important gastropod species Bulinus truncatus (Gastropoda, Heterobranchia)}, volume = {15}, year = {2022}, month = {Sep-19-2022}, abstract = {

Abstract Background Gastropod snails remain strongly understudied, despite their important role in transmitting parasitic diseases. Knowledge of their distribution and population dynamics increases our understanding of the processes driving disease transmission. We report the first study to use high-throughput sequencing (HTS) to elucidate the population genetic structure of the hermaphroditic snail Bulinus truncatus (Gastropoda, Heterobranchia) on a regional (17\–150\ km) and inter-regional (1000\–5400\ km) scale. This snail species acts as an intermediate host of Schistosoma haematobium and Schistosoma bovis, which cause human and animal schistosomiasis respectively. Methods Bulinus truncatus snails were collected in Senegal, Cameroon, Egypt and France and identified through DNA barcoding. A single-end genotyping-by-sequencing (GBS) library, comprising 87 snail specimens from the respective countries, was built and sequenced on an Illumina HiSeq 2000 platform. Reads were mapped against S. bovis and S. haematobium reference genomes to identify schistosome infections, and single nucleotide polymorphisms (SNPs) were scored using the Stacks pipeline. These SNPs were used to estimate genetic diversity, assess population structure and construct phylogenetic trees of B. truncatus. Results A total of 10,750 SNPs were scored and used in downstream analyses. The phylogenetic analysis identified five clades, each consisting of snails from a single country but with two distinct clades within Senegal. Genetic diversity was low in all populations, reflecting high selfing rates, but varied between locations due to habitat variability. Significant genetic differentiation and isolation by distance patterns were observed at both spatial scales, indicating that gene flow is not strong enough to counteract the effects of population bottlenecks, high selfing rates and genetic drift. Remarkably, the population genetic differentiation on a regional scale (i.e. within Senegal) was as large as that between populations on an inter-regional scale. The blind GBS technique was able to pick up parasite DNA in snail tissue, demonstrating the potential of HTS techniques to further elucidate the role of snail species in parasite transmission. Conclusions HTS techniques offer a valuable toolbox to further investigate the population genetic patterns of intermediate schistosome host snails and the role of snail species in parasite transmission. Graphical Abstract

}, issn = {1756-3305}, doi = {10.1186/s13071-022-05445-x}, url = {http://dx.doi.org/10.1186/s13071-022-05445-x}, author = {Maes, Tim and De Corte, Zo{\"e} and Vangestel, Carl and Virgilio, Massimiliano and Smitz, Nathalie and Djuikwo-Teukeng, F{\'e}licit{\'e} F. and Papadaki, Maria Ioanna and Huyse, Tine} } @article {6507, title = {DNA barcoding echinoderms from the East Coast of South Africa. The challenge to maintain DNA data connected with taxonomy}, journal = {PLoS ONE}, volume = {17}, year = {2022}, month = {Oct-10-2022}, pages = {e0270321}, abstract = {

Echinoderms are marine water invertebrates that are represented by more than 7000 extant species, grouped in five classes and showing diverse morphologies (starfish, sea lilies, feather stars, sea urchins, sea cucumbers, brittle and basket stars). In an effort to further study their diversity, DNA barcodes (DNA fragments of the 5\’ end of the cytochrome c oxidase subunit I gene, COI) have been used to complement morphological examination in identifying evolutionary lineages. Although divergent clusters of COI sequences were reported to generally match morphological species delineations, they also revealed some discrepancies, suggesting overlooked species, ecophenotypic variation or multiple COI lineages within one species. Here, we sequenced COI fragments of 312 shallow-water echinoderms of the East Coast of South Africa (KwaZulu-Natal Province) and compared morphological identifications with species delimitations obtained with four methods that are exclusively based on COI sequences. We identified a total of 103 morphospecies including 18 that did not exactly match described species. We also report 46 COI sequences that showed large divergences (\>5\% p-distances) with those available to date and publish the first COI sequences for 30 species. Our analyses also identified discordances between morphological identifications and COI-based species delimitations for a considerable proportion of the morphospecies studied here (49/103). For most of them, further investigation is necessary to keep a sound connection between taxonomy and the growing importance of DNA-based research.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0270321}, url = {http://dx.doi.org/10.1371/journal.pone.0270321}, author = {Sonet, Gontran and Smitz, Nathalie and Vangestel, Carl and Samyn, Yves}, editor = {Chiang, Tzen-Yuh} } @article {6501, title = {Population genomics of introduced Nile tilapia Oreochromis niloticus (Linnaeus, 1758) in the Democratic Republic of the Congo: Repeated introductions since colonial times with multiple sources}, journal = {Molecular Ecology}, volume = {31}, year = {2022}, month = {May-07-2022}, pages = {3304 {\textendash} 3322}, issn = {0962-1083, 1365-294X}, doi = {10.1111/mec.16479}, url = {http://dx.doi.org/10.1111/mec.16479}, author = {Geraerts, Mare and Vangestel, Carl and Artois, Tom and Fernandes, Jorge Manuel de Oliveira and Jorissen, Michiel W. P. and Chocha Manda, Auguste and Danadu Mizani, C{\'e}lestin and Smeets, Karen and Snoeks, Jos and Sonet, Gontran and Tingbao, Yang and Van Steenberge, Maarten and Vreven, Emmanuel and Lunkayilakio Wamuini, Soleil and Vanhove, Maarten P. M. and Huyse, Tine} } @article {6496, title = {A masculinizing supergene underlies an exaggerated male reproductive morph in a spider}, journal = {Nature Ecology \& Evolution}, volume = {6}, year = {2022}, month = {Dec-23-2021}, pages = {195 {\textendash} 206}, issn = {2397-334X}, doi = {10.1038/s41559-021-01626-6}, url = {http://dx.doi.org/10.1038/s41559-021-01626-6}, author = {Hendrickx, Frederik and De Corte, Zo{\"e} and Sonet, Gontran and Van Belleghem, Steven M. and K{\"o}stlbacher, Stephan and Vangestel, Carl} } @article {6487, title = {Female need for paternal care shapes variation in extra-pair paternity in a cooperative breeder}, journal = {Behavioral Ecology}, volume = {31}, year = {2020}, month = {Nov-01-2020}, pages = {548 - 558}, issn = {1045-2249}, doi = {10.1093/beheco/arz215}, url = {https://academic.oup.com/beheco/article/31/2/548/5700537}, author = {Cousseau, Laurence and Van de Loock, Dries and Githiru, Mwangi and Vangestel, Carl and Lens, Luc}, editor = {Ridley, Amanda} } @article {4689, title = {First genomic study on Lake Tanganyika sprat Stolothrissa tanganicae: a lack of population structure calls for integrated management of this important fisheries target species}, journal = {BMC Evolutionary Biology}, volume = {19}, year = {2019}, month = {Jan-12-2019}, pages = {6}, doi = {10.1186/s12862-018-1325-8}, url = {https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-018-1325-8}, author = {De Keyzer, Els L. R. and De Corte, Zo{\"e} and Van Steenberge, Maarten and Raeymaekers, Joost A. M. and Calboli, Federico C. F. and Kmentov{\'a}, Nikol and N{\textquoteright}Sibula Mulimbwa, Th{\'e}ophile and Virgilio, Massimiliano and Vangestel, Carl and Mulungula, Pascal Masilya and Volckaert, Filip A. M. and Vanhove, Maarten P. M.} } @article {4688, title = {Evolution at two time frames: Polymorphisms from an ancient singular divergence event fuel contemporary parallel evolution}, journal = {PLOS Genetics}, volume = {14}, year = {2018}, month = {Jan-11-2019}, pages = {e1007796}, doi = {10.1371/journal.pgen.1007796}, url = {http://dx.plos.org/10.1371/journal.pgen.1007796}, author = {Van Belleghem, Steven M. and Vangestel, Carl and De Wolf, Katrien and De Corte, Zo{\"e} and M{\"o}st, Markus and Rastas, Pasi and De Meester, Luc and Hendrickx, Frederik}, editor = {Schierup, Mikkel H.} } @article {4672, title = {Finding loci associated to partial resistance to white pine blister rust in sugar pine (Pinus lambertiana Dougl.).}, journal = {Tree Genetics \& Genomes}, volume = {13}, year = {2017}, month = {Jan-10-2017}, issn = {1614-2942}, doi = {10.1007/s11295-017-1190-4}, url = {http://link.springer.com/10.1007/s11295-017-1190-4}, author = {V{\'a}zquez-Lobo, Alejandra and De La Torre, Amanda R. and Mart{\'\i}nez-Garc{\'\i}a, Pedro J. and Vangestel, Carl and Wegzryn, Jill L. and Calic, Irina and Burton, Deems and Davis, Dean and Kinloch, Bohun and Vogler, Detlev and Neale, David B.} } @article {4671, title = {Linking phenotype, genotype and environment to unravel genetic components underlying cold hardiness in coastal Douglas-fir (Pseudotsuga menziesii var. menziesii)}, journal = {Tree Genetics \& Genomes}, volume = {14}, year = {2018}, month = {Jan-02-2018}, pages = {10}, issn = {1614-2942}, doi = {10.1007/s11295-017-1225-x}, url = {http://link.springer.com/10.1007/s11295-017-1225-x}, author = {Vangestel, Carl and Eckert, Andrew J. and Wegrzyn, Jill L. and St. Clair, J. Bradley and Neale, David B.} } @article {4658, title = {Patterns of neutral and adaptive genetic diversity across the natural range of sugar pine (Pinus lambertiana Dougl.)}, journal = {Tree Genetics \& Genomes}, volume = {12}, year = {2016}, month = {Jan-06-2016}, issn = {1614-2942}, doi = {10.1007/s11295-016-0998-7}, url = {http://link.springer.com/10.1007/s11295-016-0998-7}, author = {Vangestel, Carl and V{\'a}zquez-Lobo, Alejandra and Mart{\'\i}nez-Garc{\'\i}a, Pedro J. and Calic, Irina and Wegrzyn, Jill L. and Neale, David B.} }