Monitoring of species’ genetic diversity in Europe varies greatly and overlooks potential climate change impacts

Genetic monitoring of populations currently attracts interest in the context of the Convention on Biological Diversity but needs long-term planning and investments. However, genetic diversity has been largely neglected in biodiversity monitoring, and when addressed, it is treated separately, detached from other conservation issues, such as habitat alteration due to climate change. We report an accounting of efforts to monitor population genetic diversity in Europe (genetic monitoring effort, GME), the evaluation of which can help guide future capacity building and collaboration towards areas most in need of expanded monitoring. Overlaying GME with areas where the ranges of selected species of conservation interest approach current and future climate niche limits helps identify whether GME coincides with anticipated climate change effects on biodiversity. Our analysis suggests that country area, financial resources and conservation policy influence GME, high values of which only partially match species’ joint patterns of limits to suitable climatic conditions. Populations at trailing climatic niche margins probably hold genetic diversity that is important for adaptation to changing climate. Our results illuminate the need in Europe for expanded investment in genetic monitoring across climate gradients occupied by focal species, a need arguably greatest in southeastern European countries. This need could be met in part by expanding the European Union’s Birds and Habitats Directives to fully address the conservation and monitoring of genetic diversity

4inds_gDNA_cDNA

4inds_gDNA_cDN

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long_reads_cDNA_sequence

Zastosowanie oksymetrii tkankowej w anestezjologii i intensywnej terapii

Conventional monitoring during surgery and intensive care is not sufficiently sensitive to detect acute changes in vital organs perfusion, while its good quality is critical for maintaining their function. Disturbed vital organ perfusion may lead to the development of postoperative complications, including neurological sequel and renal failure. Near-infra-red spectroscopy (NIRS) represents one of up-to-date techniques of patient monitoring which is commonly used for the assessment of brain oximetry in thoracic aorta surgery, and – increasingly more often -in open-heart surgery. Algorithms for maintaining adequate brain saturation may result in a decrease of neurological complications and cognitive dysfunction following cardiac surgery. The assessment of kidney and visceral perfusion with tissue oximetry is gaining increasing interest during pediatric cardiac surgery. Attempts at decreasing complications by the use of brain oximetry during carotid endarterectomy, as well as thoracic and abdominal surgery demonstrated conflicting results. In recent years NIRS technique was proposed as a tool for muscle perfusion assessment under short term ischemia and reperfusion, referred to as vascular occlusion test (VOT). This monitoring extension allows for the identification of early disturbances in tissue perfusion. Results of recent studies utilizing VOT suggest that the muscle saturation decrease rate is reduced in septic shock patients, while decreased speed of saturation recovery on reperfusion is related to disturbed microcirculation. Being non-invasive and feasible technique, NIRS offers an improvement of preoperative risk assessment in cardiac surgery and promises more comprehensive intraoperative and ICU patient monitoring allowing for better outcome.Conventional monitoring during surgery and intensive care is not sufficiently sensitive to detect acute changes in vital organs perfusion, while its good quality is critical for maintaining their function. Disturbed vital organ perfusion may lead to the development of postoperative complications, including neurological sequel and renal failure. Nearinfra- red spectroscopy (NIRS) represents one of up-to-date techniques of patient monitoring which is commonly used for the assessment of brain oximetry in thoracic aorta surgery, and – increasingly more often -in open-heart surgery. Algorithms for maintaining adequate brain saturation may result in a decrease of neurological complications and cognitive dysfunction following cardiac surgery. The assessment of kidney and visceral perfusion with tissue oximetry is gaining increasing interest during pediatric cardiac surgery. Attempts at decreasing complications by the use of brain oximetry during carotid endarterectomy, as well as thoracic and abdominal surgery demonstrated conflicting results. In recent years NIRS technique was proposed as a tool for muscle perfusion assessment under short term ischemia and reperfusion, referred to as vascular occlusion test (VOT). This monitoring extension allows for the identification of early disturbances in tissue perfusion. Results of recent studies utilizing VOT suggest that the muscle saturation decrease rate is reduced in septic shock patients, while decreased speed of saturation recovery on reperfusion is related to disturbed microcirculation. Being non-invasive and feasible technique, NIRS offers an improvement of preoperative risk assessment in cardiac surgery and promises more comprehensive intraoperative and ICU patient monitoring allowing for better outcome

Host-parasite interactions in non-native invasive species are dependent on the levels of standing genetic variation at the immune locus

Abstract Background Parasites may mediate the success of biological invasions through their effect on host fitness and thus, on host population growth and stability. However, a release from the pressure of parasites is strongly related to the genetic differentiation of the host. In invasive host populations, the number of available genetic variants, allowing them to ‘fight’ the infection, are likely to be influenced by founder events and genetic drift. The level standing genetic variation of invasive populations may be crucial in successfully adapting to new environments and resisting diseases. We studied invasive populations of raccoon that experienced a random reduction in genetic diversity during the establishment and evaluated the relationship between host immune genetic diversity and intestinal parasites infection. Results We distinguished two different genetic clusters that are characterized by different sets of functionally relevant MHC-DRB alleles. Both clusters were characterized by considerably different allele-parasite associations and different levels of parasite infection. The specific resistance MHC-DRB alleles explained the lower prevalence of Digenea parasites. An increased infection intensity was related to the presence of two MHC-DRB alleles. One of these alleles significantly decreased in frequency over time, causing a decrease of Digenea abundance in raccoons in consecutive years. Conclusions Our findings suggest that intestinal parasites can exert selective pressure on an invasive host with lowered levels of immune genetic diversity and contribute to promoting local adaptation over time. The random genetic drift that created the two different genetic clusters in the invasive raccoon range imposed completely different MHC-parasite associations, strongly associated with the infection status of populations. Our findings underline the role of standing genetic variation in shaping host-parasite relationships and provide empirical support that functional genetic variation may be, at least partly, responsible for differences in the success of invasive populations

Testing genotyping strategies for ultra-deep sequencing of a co-amplifying gene family : MHC class I in a passerine bird

Characterization of highly duplicated genes, such as genes of the major histocompatibility complex (MHC), where multiple loci often co-amplify, has until recently been hindered by insufficient read depths per amplicon. Here, we used ultra-deep Illumina sequencing to resolve genotypes at exon 3 of MHC class I genes in the sedge warbler (Acrocephalus schoenobaenus). We sequenced 24 individuals in two replicates and used this data, as well as a simulated data set, to test the effect of amplicon coverage (range: 500-20 000 reads per amplicon) on the repeatability of genotyping using four different genotyping approaches. A third replicate employed unique barcoding to assess the extent of tag jumping, that is swapping of individual tag identifiers, which may confound genotyping. The reliability of MHC genotyping increased with coverage and approached or exceeded 90% within-method repeatability of allele calling at coverages of >5000 reads per amplicon. We found generally high agreement between genotyping methods, especially at high coverages. High reliability of the tested genotyping approaches was further supported by our analysis of the simulated data set, although the genotyping approach relying primarily on replication of variants in independent amplicons proved sensitive to repeatable errors. According to the most repeatable genotyping method, the number of co-amplifying variants per individual ranged from 19 to 42. Tag jumping was detectable, but at such low frequencies that it did not affect the reliability of genotyping. We thus demonstrate that gene families with many co-amplifying genes can be reliably genotyped using HTS, provided that there is sufficient per amplicon coverage