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Dawes, Tom; Forrest, Laura L. — 2020-03-06 <p>The hornwort Anthoceros agrestis is emerging as a model system for the study of symbiotic interactions and carbon fixation processes. It is an annual species with a remarkably small and compact genome. Single accessions of the plant have been shown to be related to the cosmopolitan perennial hornwort Anthoceros punctatus. We provide the first detailed insight into the evolutionary history of the two species. Due to the rather conserved nature of organellar loci, we sequenced multiple accessions in the Anthoceros agrestis-A.  punctatus complex using three nuclear regions: the ribosomal spacer ITS2, and exon and intron regions from the single-copy coding genes rbcS and phytochrome. We used phylogenetic and dating analyses to uncover the relationships between these two taxa. Our analyses resolve a lineage of genetically near-uniform European A. agrestis accessions and two non-European A. agrestis lineages. In addition, the cosmopolitan species Anthoceros punctatus forms two lineages, one of mostly European accessions, and another from India. All studied European A. agrestis accessions have a single origin, radiated relatively  recently (less than 1 million years ago), and are currently strictly associated with agroecosystem habitats</p>

Wang, Huai-Chun; Minh, Bui Quang; Susko, Edward; Roger, Andrew J. — 2017-08-04 Proteins have distinct structural and functional constraints at different sites that lead to site-specific preferences for particular amino acid residues as the sequences evolve. Heterogeneity in the amino acid substitution process between sites is not modeled by commonly used empirical amino acid exchange matrices. Such model misspecification can lead to artefacts in phylogenetic estimation such as long-branch attraction. Although sophisticated site-heterogeneous mixture models have been developed to address this problem in both Bayesian and maximum likelihood (ML) frameworks, their formidable computational time and memory usage severely limits their use in large phylogenomic analyses. Here we propose a posterior mean site frequency (PMSF) method as a rapid and efficient approximation to full empirical profile mixture models for ML analysis. The PMSF approach assigns a conditional mean amino acid frequency profile to each site calculated based on a mixture model fitted to the data using a preliminary guide tree. These PMSF profiles can then be used for in-depth tree-searching in place of the full mixture model. Compared with widely used empirical mixture models with k classes, our implementation of PMSF in IQ-TREE (http://www.iqtree.org) speeds up the computation by approximately k /1.5-fold and requires a small fraction of the RAM. Furthermore, this speedup allows, for the first time, full nonparametric bootstrap analyses to be conducted under complex site-heterogeneous models on large concatenated data matrices. Our simulations and empirical data analyses demonstrate that PMSF can effectively ameliorate long-branch attraction artefacts. In some empirical and simulation settings PMSF provided more accurate estimates of phylogenies than the mixture models from which they derive.

Iacarella, Josephine — 2022-02-11 <p><em><u><span lang="EN-US" style="border:none 1.0pt;padding:0in;">Aim</span></u><u><span lang="EN-US" style="border:none 1.0pt;padding:0in;">:</span></u> </em><span lang="EN-US" style="border:none 1.0pt;padding:0in;">Declining biodiversity across ecosystems and myriad human pressures necessitate high-level regional assessments for effective management. Evaluation of biodiversity patterns and stressor accumulation through beta diversity and cumulative effect analyses are two key methods for management prioritization. This study links these concepts to develop a novel cumulative effect metric based on beta diversity responses. </span></p> <p><em><u><span lang="EN-US" style="border:none 1.0pt;padding:0in;">Location:</span></u></em><em> </em><span lang="EN-US" style="border:none 1.0pt;padding:0in;">Fraser River basin, British Columbia, Canada.</span></p> <p><em><u><span lang="EN-US" style="border:none 1.0pt;padding:0in;">Methods:</span></u></em><em> </em><span lang="EN-US" style="border:none 1.0pt;padding:0in;">Multi-Site Generalized Dissimilarity Models were used to evaluate non-linear relationships between fish species compositional differences (</span><span lang="EN-US" style="border:none 1.0pt;padding:0in;">ζ<em>_n</em>, number of shared species across any number of watersheds compared)</span><span lang="EN-US" style="border:none 1.0pt;padding:0in;"> and human pressure, environmental, and geospatial differences among all watersheds and within low, mid-, and high elevation clusters. A cumulative effect metric was calculated as the sum of response values generated by the model for each human pressure variable specific to each watershed, when evaluated for </span><span lang="EN-US" style="border:none 1.0pt;padding:0in;">ζ₂</span><span lang="EN-US" style="border:none 1.0pt;padding:0in;">(equivalent to pairwise beta diversity). This metric was tested against the Local Contribution of each watershed to Beta Diversity to determine whether watersheds with unique communities had low cumulative effects and are therefore candidates for conservation, and conversely, whether watersheds with non-distinctive communities had high cumulative effects and warrant restoration. Species Contributions to Beta Diversity were also assessed across the basin.</span></p> <p><em><u><span lang="EN-US" style="border:none 1.0pt;padding:0in;">Results:</span></u></em><em> </em><span lang="EN-US" style="border:none 1.0pt;padding:0in;">Zeta diversity across low elevation watersheds indicated stronger filtering by human pressures than mid- and high elevations, which showed more stochastic community assembly. The relative importance and response to human pressures varied based on the diversity component (i.e., total diversity including compositional nestedness vs. turnover) and order of zeta (number of watersheds compared). Cumulative effects were negatively related to community uniqueness, supporting the use of these metrics for developing management priorities.</span></p> <p><em><u><span lang="EN-US" style="border:none 1.0pt;padding:0in;">Main Conclusions:</span></u></em><em> </em><span lang="EN-US" style="border:none 1.0pt;padding:0in;">This assessment contributes to biodiversity conservation efforts by identifying important watersheds, species, and human pressures to manage, as well as providing a cumulative effect metric directly based on biodiversity responses.</span></p>

Hleap, Jose Sergio; Littlefair, Joanne E.; Steinke, Dirk; Hebert, Paul D. N.; Cristescu, Melania E. — 2020-08-16 <p>Tissue extracts of 41 North American fish species were obtained from the Ministère des Forêts, de la Faune et des Parcs (Québec). The selected species were chosen to represent a diversity of families within the Actinopterygii, and to include some species known to be present at the Experimental Lakes Area. Muscle or fin tissue was extracted using Qiagen Blood and Tissue kits and equimolarised to 15ng/µl. Library preparation and next-generation sequencing (NGS) was performed by equimolarising the DNA and combining two replicate mock community libraries which were then PCR amplified and sequenced. Sequencing was conducted using 2x300bp Illumina MiSeq at the McGill University and Génome Québec Innovation Centre, Montréal.<br>  </p>

Therriault, Joseph; Pascoal, Tharick; Benedet, Andrea; Fernandez-Arias, Jaime; Wang, Tina; Berzgin, Gleb; Kang, Min Su; Lussier, Firoza; Chamoun, Mira; Savard, Melissa; Tissot, Cecile; Massarweh, Gassan; Soucy, Jean-Paul; Vitali, Paolo; Saha-Chaudhuri, Paramita; Gauthier, Serge; Rosa-Neto, Pedro — 2021-12-17 <p style="text-align:justify;"><b>Objective:</b> <span style="background:white;"> To assess the frequency of biologically-defined Alzheimer’s disease (AD) in relation to age, sex and <i>APOEε4</i>, as well as rates of discordance between clinically- and biologically defined AD. </span></p> <p style="text-align:justify;"><b>Methods:</b> <span style="background:white;">We assessed cognitively unimpaired (CU) elderly (n=166), amnestic MCI (n=77) and probable AD dementia (n=62) subjects who underwent evaluation by dementia specialists and neuropsychologists in addition to amyloi</span>d-PET with [¹⁸F]AZD4694<span style="background:white;"> and tau-PET with [¹⁸F]MK6240. Individuals were grouped according to their AD biomarker profile. Positive predictive value for biologically-defined AD was assessed in relation to clinical diagnosis. Frequency of AD biomarker profiles were assessed using logistic regressions with odds ratios and 95% CIs.</span></p> <p style="text-align:justify;"><b>Results:</b> <span style="background:white;">The clinical diagnosis of probable AD dementia demonstrated good agreement with biologically-defined AD (positive predictive value: 85.2%). 7.88% of CU elderly subjects were positive for both amyloid-PET and tau-PET. Frequency of biologically-defined AD increased with age (OR: 1.14; p&lt;0.0001) and frequency of <i>APOEε4</i> allele carriers (Single <i>ε4: </i>OR: 3.82; <i>p</i>&lt;0.0001; Double <i>ε4: </i>OR: 17.55, <i>p</i>&lt;0.0001). </span></p> <p style="text-align:justify;"><b>Discussion:</b> While we observed <span style="background:white;">strong, but not complete, agreement between clinically-defined “probable AD” dementia and biomarker positivity for both amyloid</span>-β<span style="background:white;"> and tau, we also observed that biologically-defined AD was not rare in CU elderly. A</span>bnormal tau-PET was almost exclusively observed in individuals with abnormal amyloid-PET. <span style="background:white;">Our results highlight that even in tertiary care memory clinics, detailed evaluation by dementia specialists systematically underestimates the frequency of biologically-defined AD and related entities. </span></p>

Arseneau, Jean-Rene; Steeves, Royce; Laflamme, Mark — 2016-10-19 The increasing use of high-throughput sequencing platforms has made the isolation of pure, high molecular weight DNA a primary concern for studies of a diverse range of organisms. Purification of DNA remains a significant challenge in many tissue and sample types due to various organic and inorganic molecules that co-precipitate with nucleic acids. Molluscs, for example, contain high concentrations of polysaccharides which often co-precipitate with DNA and can inhibit downstream enzymatic reactions. We modified a low-salt CTAB (MoLSC) extraction protocol to accommodate contaminant rich animal tissues and compared this method to a standard CTAB extraction protocol and two commercially available animal tissue DNA extraction kits using oyster adductor muscle. Comparisons of purity and molecular integrity showed that our in-house protocol yielded genomic DNA generally free of contaminants and shearing, whereas the traditional CTAB method and some of the commercial kits yielded DNA unsuitable for some applications of massively parallel sequencing (MPS). Our open-source MoLSC protocol provides a cost-effective, scalable, alternative DNA extraction method that can be easily optimized and adapted for sequencing applications in other contaminant rich samples.

Morris, Kimberley Y.; Bowman, Jeff; Schulte-Hostedde, Albrecht; Wilson, Paul J. — 2020-08-07 <p>The release of domestic organisms to the wild threatens biodiversity because the introduction of domestic genes through interbreeding can negatively impact wild conspecifics via outbreeding depression. In North America, farmed American mink (<i>Neovison vison</i>) frequently escape captivity, yet the impact of these events on functional genetic diversity of wild mink populations is unclear. We characterized domestic and wild mink in Ontario at 17 microsatellites located in functional genes and in a promoter region that is non-coding but thought to be associated with traits affected by domestication. We found low functional genetic diversity in both mink types, as only 4 of 17 genes were variable, and the number of alleles per locus were generally lower in captive mink than in wild mink. To determine if allele frequencies of wild populations were affected by domestic release events, we performed redundancy analysis and spatial analysis of principal components on four polymorphic loci (AR, ATN1, IGF-1, and TOB1). We found evidence to suggest domestic release events are affecting the functional genetic diversity of wild mink, as sPCA showed clear distinctions between wild individuals near mink farms and those located in areas without mink farms. This is further substantiated through RDA, where spatial location was associated with genetic variation of AR, ATN1, and IGF1.</p>

Gérardi, Sébastien; Laoué, Justine; Depardieu, Claire; Lamothe, Manuel; Bomal, Claude; Azaiez, Aïda; Gros-Louis, Marie-Claude; Laroche, Jerôme; Boyle, Brian; Hammerbacher, Almuth; Isabel, Nathalie; Bousquet, Jean — 2021-05-13 <p>Conifer forests worldwide are becoming increasingly vulnerable to the effects of climate change. Although the production of phenolic compounds (PCs) has been shown to be modulated by biotic and abiotic stresses, the genetic basis underlying the variation in their constitutive production level remains poorly documented in conifers. We used QTL mapping and RNA-Seq to explore the complex polygenic network underlying the constitutive production of PCs in a white spruce (<em>Picea glauca</em>) full-sib family for 2 years. QTL detection was performed for nine PCs and differentially expressed genes (DEGs) were identified between individuals with high and low PC contents for five PCs exhibiting stable QTLs across time. A total of 17 QTLs were detected for eight metabolites, including one major QTL explaining up to 91.3% of the neolignan-2 variance. The RNA-Seq analysis highlighted 50 DEGs associated with phenylpropanoid biosynthesis, several key transcription factors, and a subset of 137 genes showing opposite expression patterns in individuals with high levels of the flavonoids gallocatechin and taxifolin glucoside. A total of 19 DEGs co-localized with QTLs. Our findings represent a significant step toward resolving the genomic architecture of PC production in spruce and facilitate the functional characterization of genes and transcriptional networks responsible for differences in constitutive production of PCs in conifers.</p>

Blondel, Léa — 2020-12-03 <p class="paragraph"><span style="vertical-align:baseline;">Rare extreme “black swan” disturbances can impact ecosystems in many ways, such as destroying habitats, depleting resources, and causing high mortality. In rivers, for instance, exceptional floods that occur infrequently (e.g., so-called “50-year floods”) can strongly impact the abundance of fishes and other aquatic organisms. Beyond such ecological effects, these floods could also impact intraspecific diversity by elevating genetic drift or dispersal and by imposing strong selection, which could then influence the population’s ability to recover from disturbance. And yet, natural systems might be resistant (show little change) or resilient (show rapid recovery) even to rare extreme events – perhaps as a result of selection due to past events. We considered these possibilities in two rivers where native guppies experienced two extreme floods - one in 2005 and another in 2016. For each river, we selected four sites and used archived “historical” samples to compare levels of genetic diversity and phenotypic mean traits before versus after floods. Genetic diversity was represented by 33 neutral microsatellite markers, and phenotypic diversity was represented by body length and male melanic (black) color. We found that genetic diversity and population structure was mostly <i>resistant</i> to even these extreme floods; whereas the larger impacts on phenotypic diversity were short-lived, suggesting additional <i>resilience</i>. We discuss the determinants of these two outcomes for guppies facing floods, and then consider the general implications for the resistance and resilience of intraspecific variation to black swan disturbances. </span></p>

Schmidt, Chloé; Dray, Stéphane; Garroway, Colin J — 2022-03-28 <p>The processes that give rise to species richness gradients are not well understood, but may be linked to resource-based limits on the number of species a region can support. Ecological limits placed on regional species richness should also affect population demography, suggesting that these processes could also generate genetic diversity gradients. If true, we might better understand how broad-scale biodiversity patterns are formed by identifying the common causes of genetic diversity and species richness. We develop a hypothetical framework based on the consequences of regional variation in ecological limits set by resource availability and heterogeneity to simultaneously explain spatial patterns of species richness and neutral genetic diversity. Repurposing raw genotypic data spanning 38 mammal species sampled across 801 sites in North America, we show that estimates of genome-wide genetic diversity and species richness share spatial structure. Notably, species richness hotspots tend to harbor lower levels of within-species genetic variation. A structural equation model encompassing eco-evolutionary processes related to resource availability, habitat heterogeneity, and contemporary human disturbance supports the spatial patterns we detect. These results suggest broad-scale patterns of species richness and genetic diversity could both partly be caused by intraspecific demographic and evolutionary processes acting simultaneously across species.</p>