DNA from formalin-fixed tissue: extraction or repair? That is the question

Establishing effective DNA-based protocols for use on archival material fixed in formaldehyde (formalin) is a particularly challenging task. Formalin fixation induces cross-linking with nucleic acids and proteins, thereby reducing the amount and quality of the extracted DNA. Previous attempts have primarily focused on optimizing DNA extraction protocols. Here we focus on the use of enzymes capable of in vitro repair of DNA extracts prior to amplification of the nucleic acids by the polymerase chain reaction (PCR). The amplification success of mitochondrial DNA was greater using the repair enzyme assay (56%) than with the regular PCR assay (20%), and even more convincing results were obtained with the amplified nuclear ribosomal region (91% versus 21%). These results indicate that in vitro repair of DNA damage (depurinated sites, strand nicks and base modifications) increases the number of samples that amplify, amplify to a greater extent and amplify fewer ancillary bands and that DNA repair has been overlooked as a way of improving the efficiency of molecular methods used on formalin-fixed samples. Fidelity has not been specifically investigated, but preliminary results indicate that misincorporation is not a major problem.     

Intra-specific rDNA-ITS restriction site variation and an improved protocol to distinguish species and hybrids in the Daphnia longispina complex

A collaborative research effort was undertaken to evaluate the robustness of a recently developed genetic tool for species identification of members in the morphologically variable Daphnia longispina species complex. This genetic method, based on restriction fragment length polymorphism (RFLP) of the internal transcribed spacer region (ITS) of nuclear ribosomal DNA (rDNA) with restriction enzymes Mwo I and Sau96 I [Billiones et al., 2004. Hydrobiologia 526: 43–53], was applied to many different European populations. Results were compared with two or more independently obtained characters (morphology, allozymes, mitochondrial DNA (mtDNA), or cloned rDNA-ITS sequences). Individuals of most taxa were readily identified, but unexpected ITS-RFLP patterns were found in many individuals indicated by other markers to be D. galeata or one of its hybrids. Among 43 investigated D. galeata populations (902 specimen analysed by ITS-RFLP), deviant RFLP fragment patterns occurred in 26 (i.e., more than half) of the populations. The deviant patterns could be attributed to the loss of one single restriction site in the ITS2 region. This loss made the distinction of D. galeata from other species unreliable, and F1 hybrids could not be identified. Future users should be aware of this shortcoming of the Billions et al. [2004. Hydrobiologia 526: 43–53] protocol. As a solution to this problem, we present an improved genetic identification protocol based on a simple double digestion of the rDNA-ITS region with the restriction enzymes BsrB I and EagI. Sequence analyses of rDNA-ITS clones and preliminary testing indicate that the new protocol is unaffected by the rDNA variation which troubled the Mwo I/Sau96 I protocol. Further, the new protocol identifies all European species of the D. longispina complex, as well as their F1 hybrids. However, a wider screening is required to verify its general utility for all species, since yet unknown variation may occur. Guest editor: Piet Spaak Cladocera: Proceedings of the 7th International Symposium on Cladocera     

A taxonomic reappraisal of the European Daphnia longispina complex (Crustacea, Cladocera, Anomopoda)

The Daphnia longispina complex contains some of the most common water flea species in the northern hemisphere, and has been a model organism for many ecological and evolutionary studies. Nevertheless, the systematics and nomenclature of this group, in particular its Palaearctic members, have been in flux for the past 150 years; this hinders the correct interpretation of scientific results and promotes the erroneous use of species names. We revise the systematics of this species complex based on mitochondrial sequence variation (12S rDNA and COI) of representative populations across Europe, with a special focus on samples from type localities of the respective taxa. Combining genetic evidence and morphological assignments of analysed individuals, we propose a comprehensive revision of the European members of the D. longispina complex. We show that D. hyalina and D. rosea morphotypes have evolved several times independently, and we find no evidence to maintain these morphotypes as distinct biological species. Alpine individuals described as D. zschokkei are conspecific with the above-mentioned lineage. We suggest that this morphologically and ecologically plastic but genetically uniform hyalina–rosea–zschokkei clade should be identified as D. longispina (O. F. Müller, 1776). The valid name of Fennoscandian individuals labelled D. longispina sensu stricto in the recent literature is D. lacustris G. O. Sars, 1862. Additionally, we discovered another divergent lineage of this group, likely an undescribed species, in southern Norway. Our results present a solution for several prevailing taxonomic problems in the genus Daphnia , and have broad implications for interpretation of biogeographical patterns, and ecological and evolutionary studies.     

Molecular analysis of predation by carabid beetles (Carabidae) on the invasive Iberian slug Arion lusitanicus

The invasive Iberian slug, Arion lusitanicus, is spreading through Europe and poses a major threat to horticulture and agriculture. Natural enemies, capable of killing A. lusitanicus, may be important to our understanding of its population dynamics in recently invaded regions. We used polymerase chain reaction (PCR) to study predation on A. lusitanicus by carabid beetles in the field. A first multiplex PCR was developed, incorporating species-specific primers, and optimised in order to amplify parts of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene of large Arion slugs, including A. lusitanicus from the gut contents of the predators. A second multiplex PCR, targeting 12S rRNA mtDNA, detected predation on smaller Arion species and the field slug Deroceras reticulatum. Feeding trials were conducted to measure the effects of digestion time on amplicon detectability. The median detection times (the time at which 50% of samples tested positive) for A. lusitanicus and D. reticulatum DNA in the foreguts of Carabus nemoralis were 22 h and 20 h, respectively. Beetle activity-densities were monitored using pitfall traps, and slug densities were estimated using quadrats. Predation rates on slugs in the field by C. nemoralis in spring ranged from 16-39% (beetles positive for slug DNA) and were density dependent, with numbers of beetles testing positive being positively correlated with densities of the respective slug species. Carabus nemoralis was shown to be a potentially important predator of the alien A. lusitanicus in spring and may contribute to conservation biological control.     

Restoring <Emphasis Type="Italic">Daphnia lacustris</Emphasis> G.O. Sars, 1862 (Crustacea,Anomopoda): a cryptic species in the <Emphasis Type="Italic">Daphnia longispina</Emphasis> group

While molecular markers have revealed several distinct species within the Daphnia longispina group, there is a need to reconcile these species with traditional nomenclature. Here we show that one such species, called D. longispina in recent literature based on molecular markers, can reliably be associated with the described taxon Daphnia lacustris G.O. Sars, 1862. Both mitochondrial and nuclear molecular markers readily distinguish this species from others in the D. longispina group. D. lacustris is absent in the region from which D. longispina was first described (Denmark), and the designation D. longispina must be reserved for another widespread species represented by Danish lineages. While the diagnosis of D. lacustris (and other species of the D. longispina group) by molecular markers is unequivocal, distinguishing it morphologically from other species is still problematic. The presently known distribution range of D. lacustris includes most of Norway, northern Finland and a single lake in the Polish Tatra Mountains. Its typical habitat is oligotrophic lakes without intense fish predation. Guest editor: Piet Spaak Cladocera: Proceedings of the 7th International Symposium on Cladocera     

Long‐read sequence capture of the haemoglobin gene clusters across codfish species

Combining high‐throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short‐read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. Here, we demonstrate the power of combining targeted sequence capture with long‐read sequencing technology for comparative genomic analyses of the haemoglobin (Hb) gene clusters across eight species separated by up to 70 million years. Guided by the reference genome assembly of the Atlantic cod (Gadus morhua) together with genome information from draft assemblies of selected codfishes, we designed probes covering the two Hb gene clusters. Use of custom‐made barcodes combined with PacBio RSII sequencing led to highly continuous assemblies of the LA (~100 kb) and MN (~200 kb) clusters, which include syntenic regions of coding and intergenic sequences. Our results revealed an overall conserved genomic organization of the Hb genes within this lineage, yet with several, lineage‐specific gene duplications. Moreover, for some of the species examined, we identified amino acid substitutions at two sites in the Hbb1 gene as well as length polymorphisms in its regulatory region, which has previously been linked to temperature adaptation in Atlantic cod populations. This study highlights the use of targeted long‐read capture as a versatile approach for comparative genomic studies by generation of a cross‐species genomic resource elucidating the evolutionary history of the Hb gene family across the highly divergent group of codfishes.     

Daphnia Galeata × D. Longispina Hybrids in Western Norway

We describe the occurrence of D. galeata×longispina hybrids in two lakes of western Norway. Parental species and interspecific hybrids were characterised by both nuclear and mitochondrial molecular markers. In one of the populations, hybrids were shown to dominate the population over several years. A few individuals in both populations were probably not F1 hybrids, but possibly backcrosses or F2 hybrids. Most (possibly all) F1 hybrids were of D. galeata maternal origin. In addition, interspecific hybrids could be identified based on morphological characters, which were intermediate between the parental species. Interspecific hybridisation between these two species is remarkable, since they are distantly related.