Population connectivity of Buller's albatrosses

The Diomedeidae (Albatrosses) family is comprised of 22 recognised species, 13 are of high conservation concern because they are experiencing population declines. The taxonomy of albatrosses has always been problematic, which makes it difficult to estimate the number and size of breeding groups within a species. The Northern Buller’s Albatross (Thalassarche bulleri platei) and Southern Buller’s Albatross (Thalassarche bulleri bulleri) (Robertson & Nunn 1998; Turbott 1990) were recognised as separate species until 2006. A review of morphological data provided a basis for defining them as one species (Thalassarche bulleri); a result that was supported by international conservation agreements. However, there was no genetic data available at the time to corroborate the taxonomic change. The species status of Buller’s Albatross ssp. is an important issue because they are consistently recorded in the top five observed seabird interactions with commercial fishing vessels within New Zealand's Exclusive Economic Zone. Despite their prevalence in fisheries interactions, the relative impact of commercial fishing activity on northern and southern populations is unknown. Incidental mortality of albatrosses in commercial fisheries is recognised as a primary source of population disturbance. The overall goal of this thesis research was to investigate the genetic differences between the two sub-species of Buller’s Albatross. DNA was isolated from blood samples collected from a total of 73 birds from two Northern Buller’s Albatross colonies (n = 26) and two Southern Buller’s Albatross colonies (n = 47). The degree of genetic differentiation between the Northern and Southern taxa was estimated using DNA sequences from a 221 bp fragment of the mitochondrial control region, Domain II (CRII). The genetic differentiation between regional colony groups was high (pairwise ΦST = 0.621, p < 0.00001). Two haplogroups were identified within Northern Buller’s Albatross, while Southern Buller’s Albatross samples composed a single haplogroup. An analysis of molecular variance did not find any significant population structuring at the colony level. All individuals sampled from fisheries bycatch (n = 97) were assigned with maximum probability to either Northern (n = 19) or Southern Buller’s Albatross (n = 78; P = 1.00). The DNA sequences differences found in the mitochondrial control region can be used to assign provenance of T. bulleri ssp. samples, which will be a useful conservation management tool. In addition, a genome wide set of markers was obtained using a Genotyping by Sequencing approach. DNA was digested using restriction enzymes, fragments were labeled adaptor sequences, and shotgun sequenced on an Illumina platform by AgResearch. The Stacks pipeline was used to filter the sequences and obtain a set of single nucleotide polymorphism (SNP) markers across the genome. Estimates of genetic diversity and gene flow were conducted for 26 319 putative loci comprised of 54,061 single nucleotide polymorphisms. Estimates of genetic diversity were consistent across datasets with both taxa exhibiting similar levels of nucleotide diversity (Northern π ≈ 0.002 – 0.004; Southern π ≈ 0.002 – 0.003). However, estimates of genetic differentiation increased slightly as filtering protocols became increasingly restrictive (FST ≈ 0.019 – 0.048). This low level of differentiation was supported by admixture analyses, which identified two distinct ‘clusters’, one corresponding to T. b. platei and the second to T. b. bulleri. The results of this research demonstrate that Northern and Southern Buller’s Albatrosses are two genetically distinct groups

Challenges and opportunities for integrating structural variants into conservation genomics.

Reduced costs and increased accessibility of whole-genome sequencing (WGS) technologies continue to facilitate the use of genomic data to inform conservation management. Whole- genome single nucleotide polymorphisms (SNPs) are increasingly used to estimate population diversity and differentiation to inform translocations, identify signatures of local adaptation or hybridisation and introgression, and inform conservation breeding programs. In general, these conservation management interventions aim to ensure populations have sufficient genetic diversity to adapt to environmental change. However, SNPs are but one type of variant and may not holistically capture genetic diversity or evolutionary potential. Structural variants (SVs), which are large variants typically defined as ≥50bp in length, include deletions, duplications, insertions, inversions and translocations. SVs have been found to be a significant source of genetic diversity as they intersect with genes and gene regions more frequently and impact more genomic content overall than SNPs. Further, mounting evidence indicates that SVs play an important role in the evolution of adaptive traits. However, SVs remain largely understudied in a conservation context. To date, the majority of SV research has taken place in well-resourced fields (e.g., primary industry and human health) and the minimum sequencing and bioinformatic thresholds to leverage conservation genomics data for SV studies is unclear. This thesis aims to explore the challenges and opportunities associated with studying SVs in non-model species of conservation concern, and to identify potential strategies for incorporating SVs into the conservation genomics toolbox. Chapter 2, published as a Perspective in the Molecular Ecology ‘Whole Genome Sequencing in Molecular Ecology’ Special Issue, is a product of all of the learnings of this thesis. In this Perspective, my co-authors and I discuss the relative performance of sequencing technologies and bioinformatic approaches in a conservation context. We examine the wider literature for emerging tools and strategies aimed at investigating SVs in small populations. Insights gained from these well resourced fields are likely to inform approaches best suited to investigating SVs in non-model organisms, especially since there is very little research outside these well studied species and fewer still that investigate SVs in a conservation context. We also argue that advances like long-read sequencing and genome graphs will be increasingly utilised in conservation genomics. In the meantime, gaps remain in our understanding of the limitations and expected systematic biases introduced by short-read data for population SV studies in non-model organisms. Extensive benchmarking studies within the human genomics space demonstrate that whole genome short-read sequence data is prone to high false-positive rates and systematic biases towards detecting smaller SVs. However, short-read resequence data is currently one of the most common WGS data types available for species of conservation concern. Further, the resources required to establish and validate a reliable ‘truth’ set for SV benchmarking and validation are likely unattainable for many threatened species. In Chapter 3 we leverage an unprecedented population-level short-read resequence data set and a high-quality, chromosomally assembled reference genome for the critically endangered kākāpō (Strigops habroptilus) to explore four strategies for SV discovery and genotyping. My coauthors and I compare variability in SV call sets and genotype consistency to explore how this may impact SV population studies. We find a high level of variability in SV type, size distribution, and number of SVs per chromosome between the four approaches. However, SVs successfully recover known population structure in the dataset. These results indicate that, although SV studies with short- read data may be informative, caution should be exercised when interpreting results. Taking the insights gained from Chapter 3, in Chapter 4 we shift our focus to the most endangered breeding bird in Aotearoa New Zealand, the New Zealand fairy tern/tara iti (Sternula nereis davisae). Tara iti are one of three subspecies that include the Australian fairy tern (Sternula nereis nereis) and New Caledonian fairy tern (Sternula nereis exsul). All taxa are either highly threatened or experiencing declines due to anthropogenic disturbance, introduced predators and a changing climate. Observation data indicates that tara iti have persisted as a small population since the 1950’s, but this is likely an underestimate. To investigate the level of genome-wide diversity within, and population differentiation between tara iti and the closely related Australian fairy tern, we utilise short-read WGS data aligned to a chromosomally scaffolded reference genome for the common tern (Sterna hirundo) to detect SNPs and SVs. Overall, there was a high level of congruence between SNP and SV data. For example, we observed much lower levels of heterozygosity in SNP data and a high proportion of fixed SVs in tara iti. This is consistent with the expectation of a persistently small population size for tara iti. In addition, both SNP and SV data demonstrated a high level population differentiation between the two taxa. These results represent the ‘first steps’ towards integrating SNPs and SVs to better inform conservation management of tara iti and have implications for the taxonomic status of the fairy tern species complex. In Chapter 2 we highlight the exciting promise of genome graphs, which capture population variation in genome structure and sequence by aligning multiple reference individuals. Genome graphs can facilitate the discovery and genotyping of large and complex variants, because they remove any bias that comes from having a single linear reference genome. In Chapter 5 we present the first steps towards a kākāpō pangenome. We target 12 individuals in the kākāpō population, including 10 highly represented ‘founding’ individuals, to generate long-read data using Oxford Nanopore Technology. Using a high-quality chromosomally assembled kākāpō reference genome (Jane’s genome) as a guide, we target chromosome 7 for graph construction as it contains four functional genes of interest (Toll-like Receptors, or TLRs). Assemblies for seven individuals alongside Jane’s genome were used to construct the graph. We observe depth outliers along the length of the graphs for chromosome 7 and each TLR, likely indicating poorly assembled and/or highly repetitive regions. When examining the graph topology for each of the four TLRs, we observe large putative SVs in two of them. However, more work is required to determine whether these represent assembly errors or reflect true variation. These results are exciting as they represent the first known attempt to implement genome graphs in a species of conservation concern. Finally, Chapter 6 provides a summary of the main findings of this thesis and revisits the exciting promise of integrating SVs into the conservation genomics toolkit. The appendices contain two additional manuscripts that I co-authored during my PhD and a collation of reports prepared for Te Arai and Mangawhai Shorebirds Trust and Department of Conservation. This combined research represents an exciting step towards the integration of SVs into conservation decision frameworks for species of conservation concern globally

Phylogenetic relationships, population connectivity, and development of genetic assignment testing in Buller's Albatross (Thalassarche bulleri ssp.)

The Diomedeidae (Albatrosses) family is comprised of 22 recognised species, 13 are of high conservation concern because they are experiencing population declines. The taxonomy of albatrosses has always been problematic, which makes it difficult to estimate the number and size of breeding groups within a species. The Northern Buller’s Albatross (Thalassarche bulleri platei) and Southern Buller’s Albatross (Thalassarche bulleri bulleri) (Robertson & Nunn 1998; Turbott 1990) were recognised as separate species until 2006. A review of morphological data provided a basis for defining them as one species (Thalassarche bulleri); a result that was supported by international conservation agreements. However, there was no genetic data available at the time to corroborate the taxonomic change. The species status of Buller’s Albatross ssp. is an important issue because they are consistently recorded in the top five observed seabird interactions with commercial fishing vessels within New Zealand's Exclusive Economic Zone. Despite their prevalence in fisheries interactions, the relative impact of commercial fishing activity on northern and southern populations is unknown. Incidental mortality of albatrosses in commercial fisheries is recognised as a primary source of population disturbance.  The overall goal of this thesis research was to investigate the genetic differences between the two sub-species of Buller’s Albatross. DNA was isolated from blood samples collected from a total of 73 birds from two Northern Buller’s Albatross colonies (n = 26) and two Southern Buller’s Albatross colonies (n = 47). The degree of genetic differentiation between the Northern and Southern taxa was estimated using DNA sequences from a 221 bp fragment of the mitochondrial control region, Domain II (CRII). The genetic differentiation between regional colony groups was high (pairwise ΦST = 0.621, p < 0.00001). Two haplogroups were identified within Northern Buller’s Albatross, while Southern Buller’s Albatross samples composed a single haplogroup. An analysis of molecular variance did not find any significant population structuring at the colony level. All individuals sampled from fisheries bycatch (n = 97) were assigned with maximum probability to either Northern (n = 19) or Southern Buller’s Albatross (n = 78; P = 1.00). The DNA sequences differences found in the mitochondrial control region can be used to assign provenance of T. bulleri ssp. samples, which will be a useful conservation management tool.  In addition, a genome wide set of markers was obtained using a Genotyping by Sequencing approach. DNA was digested using restriction enzymes, fragments were labeled adaptor sequences, and shotgun sequenced on an Illumina platform by AgResearch. The Stacks pipeline was used to filter the sequences and obtain a set of single nucleotide polymorphism (SNP) markers across the genome. Estimates of genetic diversity and gene flow were conducted for 26 319 putative loci comprised of 54,061 single nucleotide polymorphisms. Estimates of genetic diversity were consistent across datasets with both taxa exhibiting similar levels of nucleotide diversity (Northern π ≈ 0.002 – 0.004; Southern π ≈ 0.002 – 0.003). However, estimates of genetic differentiation increased slightly as filtering protocols became increasingly restrictive (FST ≈ 0.019 – 0.048). This low level of differentiation was supported by admixture analyses, which identified two distinct ‘clusters’, one corresponding to T. b. platei and the second to T. b. bulleri. The results of this research demonstrate that Northern and Southern Buller’s Albatrosses are two genetically distinct groups.</p

Increased Blood Pressure Variability Is Associated with Worse Neurologic Outcome in Acute Anterior Circulation Ischemic Stroke

Background. Although research suggests that blood pressure variability (BPV) is detrimental in the weeks to months after acute ischemic stroke, it has not been adequately studied in the acute setting. Methods. We reviewed acute ischemic stroke patients from 2007 to 2014 with anterior circulation stroke. Mean blood pressure and three BPV indices (standard deviation, coefficient of variation, and successive variation) for the intervals 0-24, 0-72, and 0-120 hours after admission were correlated with follow-up modified Rankin Scale (mRS) in ordinal logistic regression models. The correlation between BPV and mRS was further analyzed by terciles of clinically informative stratifications. Results. Two hundred and fifteen patients met inclusion criteria. At all time intervals, increased systolic BPV was associated with higher mRS, but the relationship was not significant for diastolic BPV or mean blood pressure. This association was strongest in patients with proximal stroke parent artery vessel occlusion and lower mean blood pressure. Conclusion. Increased early systolic BPV is associated with worse neurologic outcome after ischemic stroke. This association is strongest in patients with lower mean blood pressure and proximal vessel occlusion, often despite endovascular or thrombolytic therapy. This hypothesis-generating dataset suggests potential benefit for interventions aimed at reducing BPV in this patient population

Neurohospitalist Practice, Perspectives, and Burnout

Background and purposeNeurohospitalist neurology is a fast-growing subspecialty with a variety of practice settings featuring neurohospitalist models of care. Since inception, the subspecialty has responded to new challenges in resident training, hospital reimbursement, practice, and burnout.MethodsTo characterize neurohospitalists' current practice and perspectives, we surveyed the neurohospitalists and trainees affiliated with the Neurohospitalist Society using an electronic survey distributed through the society listserv.ResultsOf 501 individuals surveyed by e-mail, 119 began the survey (23.8% response rate), with 88.2% self-identifying as neurohospitalists. Most neurohospitalists (63%) are 10 years or less out of training, devoting 70% of their professional time to inpatient clinical activities while also performing administrative or teaching activities. Only 38% are employed by an academic department. Call schedules are common, with 75% of neurohospitalists participating in a hospital or emergency call schedule, while 55% provide telemedicine services. The majority (97%) of neurohospitalists primarily care for adults, most commonly treating patients with cerebrovascular disease, seizures, and delirium/encephalopathy. The majority (87%) are overall pleased with their work, but 36% report having experienced burnout.ConclusionsNeurohospitalists are a diverse group of neurologists primarily practicing in the inpatient setting while performing a variety of additional activities. They provide a wide array of clinical expertise for acute neurological diseases and neurological emergencies that require hospitalization, including stroke, seizure, and encephalopathy. Neurohospitalists in general are very pleased with their work, while burnout, as in neurology and other areas of medicine, remains a concern

Handbook of Food Analysis Instruments

This monograph published by Taylor&Francis Publishing House contains versatile instrumentation that is applied in food analysis. More than 40 authors, experts from different fields, took part in writing comprehensive chapters related to various aspects of microscopic, chromatographic, UV VIS, electrochemical, Fluorescence, Electrophoresis, AFM and IR techniques applied in food analysis. In the beginning of this book, authors provide comprehensive statistic relevant to analytical chemistry. Also, extraction and preparation methods in food analysis are extensively explained. The readers can get an insight in several free chapters of this Monograph (issued on line in 2016) available for free in 2021