ESM Figure 1.tif - (A) Mean lnP(D) value with k = 1–20 for the 40 loci dataset. (B) Mean lnP(D) value with k = 1–20 for the 32 loci dataset from Next Gen Pop Gen: implementing a high-throughput approach to population genetics in boarfish (<i>Capros aper</i>)

The recently developed approach for microsatellite genotyping by sequencing (GBS) using individual combinatorial barcoding was further improved and used to assess the genetic population structure of boarfish (<i>Capros aper</i>) across the species' range. Microsatellite loci were developed <i>de novo</i> and genotyped by next-generation sequencing. Genetic analyses of the samples indicated that boarfish can be subdivided into at least seven biological units (populations) across the species' range. Furthermore, the recent apparent increase in abundance in the northeast Atlantic is better explained by demographic changes within this area than by influx from southern or insular populations. This study clearly shows that the microsatellite GBS approach is a generic, cost-effective, rapid and powerful method suitable for full-scale population genetic studies—a crucial element for assessment, sustainable management and conservation of valuable biological resources

Development of an environmental DNA assay and field validation for the detection of invasive pink salmon Oncorhynchus gorbuscha

1. Pink salmon Oncorhynchus gorbuscha was introduced from its native range in the Pacific to Northwest Russia several times since the 1950s. While this species has been regularly observed in rivers in northern Norway since then, there has been an upsurge in the numbers of odd-year O. gorbuscha individuals observed in rivers, particularly in northern Norway in recent years, and particularly in 2017 and 2019. 2. In the present pilot study, an assay was developed to detect O. gorbuscha from eDNA water samples. Positive control water samples were taken at two locations of the River Signaldalselva in northern Norway during the summer of 2019, when adults were spawning in the river. Samples showed positive detection of this species in the river, while negative control samples collected upstream migration barriers in central and southern Norway confirmed the absence of the target species. 3. These findings reveal that eDNA-based methods can be used to track the ongoing O. gorbuscha invasion of northern Europe and other regions where it might be or become invasive. ddPCR, eDNA, invasion, Norway, Oncorhynchus gorbuscha, pink salmon, qPCRpublishedVersio

Development of an environmental DNA assay and field validation for the detection of invasive pink salmon Oncorhynchus gorbuscha

1. Pink salmon Oncorhynchus gorbuscha was introduced from its native range in the Pacific to Northwest Russia several times since the 1950s. While this species has been regularly observed in rivers in northern Norway since then, there has been an upsurge in the numbers of odd-year O. gorbuscha individuals observed in rivers, particularly in northern Norway in recent years, and particularly in 2017 and 2019. 2. In the present pilot study, an assay was developed to detect O. gorbuscha from eDNA water samples. Positive control water samples were taken at two locations of the River Signaldalselva in northern Norway during the summer of 2019, when adults were spawning in the river. Samples showed positive detection of this species in the river, while negative control samples collected upstream migration barriers in central and southern Norway confirmed the absence of the target species. 3. These findings reveal that eDNA-based methods can be used to track the ongoing O. gorbuscha invasion of northern Europe and other regions where it might be or become invasive. ddPCR, eDNA, invasion, Norway, Oncorhynchus gorbuscha, pink salmon, qPC

microsatellite data

all abbreviations are given in Journal of Heredity articl

The Identification of a 1916 Irish Rebel: New Approach for Estimating Relatedness from Low Coverage Homozygous Genomes

Thomas Kent was an Irish rebel who was executed by British forces in the aftermath of the Easter Rising armed insurrection of 1916 and buried in a shallow grave on Cork prison’s grounds. In 2015, ninety-nine years after his death, a state funeral was offered to his living family to honor his role in the struggle for Irish independence. However, inaccuracies in record keeping did not allow the bodily remains that supposedly belonged to Kent to be identified with absolute certainty. Using a novel approach based on homozygous single nucleotide polymorphisms, we identified these remains to be those of Kent by comparing his genetic data to that of two known living relatives. As the DNA degradation found on Kent’s DNA, characteristic of ancient DNA, rendered traditional methods of relatedness estimation unusable, we forced all loci homozygous, in a process we refer to as 'forced homozygote approach'. The results were confirmed using simulated data for different relatedness classes. We argue that this method provides a necessary alternative for relatedness estimations, not only in forensic analysis, but also in ancient DNA studies, where reduced amounts of genetic information can limit the application of traditional methods.European Research CouncilIrish Research CouncilNSF gran

A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding

This study examines the potential of next-generation sequencing based 'genotyping-by-sequencing' (GBS) of microsatellite loci for rapid and cost-effective genotyping in large-scale population genetic studies. The recovery of individual genotypes from large sequence pools was achieved by PCR-incorporated combinatorial barcoding using universal primers. Three experimental conditions were employed to explore the possibility of using this approach with existing and novel multiplex marker panels and weighted amplicon mixture. The GBS approach was validated against microsatellite data generated by capillary electrophoresis. GBS allows access to the underlying nucleotide sequences that can reveal homoplasy, even in large datasets and facilitates cross laboratory transfer. GBS of microsatellites, using individual combinatorial barcoding, is potentially faster and cheaper than current microsatellite approaches and offers better and more data

A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding.

This study examines the potential of next-generation sequencing based 'genotyping-by-sequencing' (GBS) of microsatellite loci for rapid and cost-effective genotyping in large-scale population genetic studies. The recovery of individual genotypes from large sequence pools was achieved by PCR-incorporated combinatorial barcoding using universal primers. Three experimental conditions were employed to explore the possibility of using this approach with existing and novel multiplex marker panels and weighted amplicon mixture. The GBS approach was validated against microsatellite data generated by capillary electrophoresis. GBS allows access to the underlying nucleotide sequences that can reveal homoplasy, even in large datasets and facilitates cross laboratory transfer. GBS of microsatellites, using individual combinatorial barcoding, is potentially faster and cheaper than current microsatellite approaches and offers better and more data..S.V. and R.F. acknowledge funding from the Sea Change Strategy with the support of the Marine Institute and the Marine Research Sub-programme of the National Development Plan 2007–2013, co-financed by the European Regional Development Fund (Grant-Aid Agreement no. PBA/AF/07/004, EIRCOD). J.L.V.-C. acknowledges funding from the Spanish Ministerio de Economía y Competitividad (FPI BES-2010–038494 and EEBB-I-13–06270). G.H. acknowledges funding by the Irish Research Council (IRC) Graduate Research Education Programme (GREP). P.M. and J.C. acknowledge funding from the Beaufort Marine Research Award in Fish Population Genetics funded by the Irish Government under the Sea Change Programme. P.C.C. acknowledges funding from Science Foundation Ireland (SFI 12/IP/1308). E.D.F. acknowledges funding from Irish Research Council (IRC) (Funding Agency Ref no./nGOIPD/2013/320)

A novel human CD32 mAb blocks experimental immune haemolytic anaemia in Fc gamma RIIA transgenic mice

A fully human IgG1 kappa antibody (MDE-8) was generated, which recognised Fc-gamma receptor IIa (Fc?RIIa) molecules on CD32 transfectants, peripheral blood monocytes, polymorphonuclear cells and platelets. This antibody blocked Fc?RIIa ligand-binding via its F(ab')2 fragment. Overnight incubation of monocytes with F(ab')2 fragments of MDE-8 leads to a c. 60% decrease in cell surface expression of Fc?RIIa. MDE-8 whole antibody induced a concomitant c. 30% decrease of Fc?RI on THP-1 cells and monocytes. In humans Fc?RIIa plays an important role in the clearance of antibody-coated red blood cells in vivo. As an equivalent of Fc?RIIa does not exist in mice, the in vivo effect of MDE-8 was studied in an Fc?RIIa transgenic mouse model. In these mice, antibody-induced anaemia could readily be blocked by MDE-8. These data document a new human antibody that effectively blocks Fc?RIIa, induces modulation of both Fc?RIIa and Fc?RI from phagocytic cells, and ameliorates antibody-induced anaemia in vivo