Restrospective genetic monitoring of the threatened Yellow marsh saxifrage (Saxifraga hirculus) reveals genetic erosion but provides valuable information for conservation strategies

Aim: Retrospective genetic monitoring, comparing genetic diversity of extant populations with historical samples, can provide valuable and often unique insights into evolutionary processes informing conservation strategies. The Yellow marsh saxifrage (Saxifraga hirculus) is listed as ‘critically endangered’ in Ireland with only two extant populations. We quantified genetic changes over time and identified genotypes in extant populations that could be used as founders for reintroductions to sites where the species is extinct.

Location: Ireland.

Methods: Samples were obtained from both locations where the species is currently found, including the most threatened site at the Garron Plateau, Co. Antrim, which held only 13 individuals during 2011. Herbarium samples covering the period from 1886 to 1957 were obtained including plants from the same area as the most threatened population, as well as three extinct populations. In total, 422 individuals (319 present-day and 103 historical) were genotyped at six microsatellite loci. Species distribution modelling was used to identify areas of potentially suitable habitat for reintroductions.

Results: Level of phenotypic diversity within the most threatened population was significantly lower in the present-day compared with historical samples but levels of observed heterozygosity and number of alleles, whilst reduced, did not differ significantly. However, Bayesian clustering analysis suggested gradual lineage replacement over time. All three measures of genetic diversity were generally lower at the most threatened population compared with the more substantial extant populations in Co. Mayo. Species distribution modelling suggested that habitat at one site where the species is extinct may be suitable for reintroduction.

Main conclusions: The dominant genetic lineage in the most threatened population is rare elsewhere; thus, care needs to be taken when formulating any potential reintroduction programme. Our findings highlight both the need for genetic monitoring of threatened populations, but also for its swift implementation before levels of diversity become critically low.

Factors influencing success of clinical genome sequencing across a broad spectrum of disorders

To assess factors influencing the success of whole-genome sequencing for mainstream clinical diagnosis, we sequenced 217 individuals from 156 independent cases or families across a broad spectrum of disorders in whom previous screening had identified no pathogenic variants. We quantified the number of candidate variants identified using different strategies for variant calling, filtering, annotation and prioritization. We found that jointly calling variants across samples, filtering against both local and external databases, deploying multiple annotation tools and using familial transmission above biological plausibility contributed to accuracy. Overall, we identified disease-causing variants in 21% of cases, with the proportion increasing to 34% (23/68) for mendelian disorders and 57% (8/14) in family trios. We also discovered 32 potentially clinically actionable variants in 18 genes unrelated to the referral disorder, although only 4 were ultimately considered reportable. Our results demonstrate the value of genome sequencing for routine clinical diagnosis but also highlight many outstanding challenges.

Favorable effect on acute and chronic graft-versus-host disease with cyclophosphamide and in vivo anti-CD52 monoclonal antibodies for marrow transplantation from HLA-identical sibling donors for acquired aplastic anemia

Between August 1989 and November 2003, 33 patients at our center with acquired aplastic anemia underwent bone marrow transplantation (BMT) from HLA-identical sibling donors with cyclophosphamide and in vivo anti-CD52 monoclonal antibodies (MoAb) for conditioning. The median age at BMT was 17 years (range, 4-46 years). Before BMT, 58% were heavily transfused (>50 transfusions), and 42% had previously experienced treatment failure with antithymocyte globulin-based immunosuppressive therapy. Unmanipulated bone marrow was used as the source of stem cells in all patients except 1. Graft-versus-host disease (GVHD) prophylaxis was with cyclosporine alone in 19 (58%) patients; 14 received anti-CD52 MoAb in addition to cyclosporine. The conditioning regimen was well tolerated without significant acute toxicity. Graft failure was seen in 8 patients (primary, n = 4; secondary, n = 4). Of those whose grafts failed, 4 survived long-term (complete autologous recovery, n = 2; rescue with previously stored marrow, n = 1; second allograft, n = 1). The cumulative incidence of graft failure and grade II to IV acute and chronic GVHD was 24%, 14%, and 4%, respectively. None developed extensive chronic GVHD. With a median follow-up of 59 months, the 5-year survival was 81% (95% confidence interval, 68%-96%). No unexpected early or late infectious or noninfectious complications were observed. We conclude that the conditioning regimen containing cyclophosphamide and anti-CD52 MoAb is well tolerated and effective for acquired aplastic anemia with HLA-matched sibling donors. The favorable effect on the incidence and severity of GVHD is noteworthy in this study and warrants further investigation.

Sir Robert Hart Photo Collection on Flickr

The photographs in this album were selected with the assistance of the Sir Robert Hart Research Project, which is a collaboration between Special Collections & Archives in the Library, the School of Modern History & Anthropology, Queen’s University Belfast, and the Institute of Modern History at the Chinese Academy of Social Sciences (CASS) in Beijing. The research project is creating an annotated photobook from the Sir Robert Hart Photo Collection (originally donated in the 1970s) and the Irons Collection. The photographs here reflect those that will be included in the book.