Biologie // Biology

Permanent URI for this collectionhttps://hdl.handle.net/10393/12924

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Understanding pollen specialization in mason bees: a case study of six species
(Springer Science and Business Media LLC, 2020-10-26) McAulay, Megan K.; Killingsworth, Saff Z.; Forrest, Jessica R. K.
Many bee species are dietary specialists and restrict their pollen foraging to a subset of the available flowers. However, the reasons for specialization—and the reasons certain plant taxa support numerous specialists—are often unclear. Many bees specialize on the plant family Asteraceae, despite evidence its pollen is a poor food for non-specialists. Here, we studied six mason bee (Osmia) species, including three Asteraceae specialists, to test whether observed pollen-usage patterns reflect larval nutritional requirements, to investigate what aspects of Asteraceae pollen make it unsuitable for non-specialists, and to understand how Asteraceae specialists tolerate their seemingly low-quality diet. We reared larval bees on host and nonhost pollen and found that Asteraceae specialists could develop on nonhost provisions, but that other bees could not survive on Asteraceae provisions. These effects did not seem related to nutritional deficiencies, since Asteraceae provisions were not amino acid deficient, and we found no consistent differences in digestive efficiency among pollen types. However, Asteraceae specialists completed more foraging flights per larva, generally collected relatively larger provisions, and produced more frass (waste) than the other species, suggesting quantitative compensation for low food quality. Toxins, deficiencies in unmeasured nutrients, or aspects of pollen grain structure might explain poor survival of non-specialists on Asteraceae provisions. Our results suggest that floral host selection by specialist bees is not related to optimizing larval nutrition. We recommend further investigation of host-selection behaviour in adult bees and of pollen digestion in larvae to better understand the evolution of bee–flower associations.
Pollen specialisation is associated with later phenology in Osmia bees (Hymenoptera: Megachilidae)
(2022-11-24) Pelletier, Daniel; Forrest, Jessica
1. Species exhibit a range of specialisation in diet and other niche axes, with specialists typically thought to be more efficient in resource use but more vulnerable to extinction than generalists. Among herbivorous insects, dietary specialists seem more likely to lack acceptable host plants during the insect's feeding stage, owing to fluctuations in host-plant abundance or phenology. Like other herbivores, bee species vary in host breadth from pollen specialisation (oligolecty) to generalisation (polylecty). 2. Several studies have shown greater interannual variation in flowering phenology for earlier-flowering plants than later-flowering plants, suggesting that early-season bees may experience substantial year-to-year variation in the floral taxa available to them. 3. It was therefore reasoned that, among bees, early phenology could be a more viable strategy for generalists, which can use resources from multiple floral taxa, than for specialists. Consequently, it was expected that the median dates of collection of adult specimens to be earlier for generalist species than for specialists. To test this, phenology data and pollen diet information on 67 North American species of the bee genus Osmia was obtained. 4. Controlling for latitude and phylogeny, it was found that dietary generalisation is associated with significantly earlier phenology, with generalists active, on average, 11–14 days earlier than specialists. 5. This result is consistent with the generalist strategy being more viable than the specialist strategy for species active in early spring, suggesting that dietary specialisation may constrain the evolution of bee phenology—or vice versa.
Spring wildflower phenology and pollinator activity respond similarly to climatic variation in an eastern hardwood forest
(Springer Science and Business Media LLC, 2020-05-18) Sevenello, Manuel; Sargent, Risa D.; Forrest, Jessica R. K.
Climate warming could disrupt species interactions if organisms’ phenologies respond to climate change at different rates. Phenologies of plants and insects can be sensitive to temperature and timing of snowmelt; however, many important pollinators including ground-nesting bees have been little studied in this context. Without knowledge of the environmental cues affecting phenologies of co-occurring species, we have little ability to predict how species assemblages, and species interactions, will be affected by climate change. Here, we studied a hardwood forest understory over six years, to determine how spring temperatures, snowmelt timing, and photoperiod influence the phenology of two spring wildflowers (Anemone spp. and Trillium grandiflorum), activity of ground-nesting bees, and their temporal overlap. Surface degree-day accumulation was a better predictor of phenology for Anemone spp. (plant) and Nomada (bees) than were day of year (a proxy for photoperiod) or snowmelt date, whereas Trillium flowering appeared most sensitive to photoperiodic cues. Activity periods of Andrena and Lasioglossum bees were equally well described by degree-day accumulation and day of year. No taxon’s phenology was best predicted by snowmelt date. Despite these differences among taxa in their phenological responses, timing of bee activity and flowering responded similarly to variation in snowmelt date and early spring temperatures. Furthermore, temporal overlap between flowering and bee activity was similar over the years of this study and was unaffected by variability in snowmelt date or temperature. Nevertheless, the differences among some taxa in their phenological responses suggests that diverging temporal shifts are a possibility for the future.
Small wild bee abundance declines with distance into strawberry crops regardless of field margin habitat
(Elsevier BV, 2020-05) MacInnis, Gail; Buddle, Christopher M.; Forrest, Jessica R.K.
The preservation of pollinator habitat on croplands in the form of hedgerows, wildflower strips, and natural and semi-natural areas can help maintain and enhance wild bee populations in agricultural landscapes. However, there have been few comparisons of the effectiveness of different types of field-margin pollinator habitat in maintaining bee diversity and pollination of the focal crops. We compared wild bee abundance, species richness and community composition between strawberry crops bordered by hedgerows, and those bordered by larger expanses of natural land (forests). Strawberry is an ideal crop in which to investigate pollinator export from field margins as the rows are covered with straw, which reduces habitat for ground-nesting bees within the crop; thus, most wild pollinators need to enter the crop from the margins. We sampled bees in six strawberry fields with hedgerow margins and six strawberry fields with forested margins of at least 200 m in length, using a paired design. We examined strawberry pollen deposition at regular intervals into the fields, and the magnitude of pollinator export from the field margins towards the centre of the crops. We found that bees as a group were no more species-rich or abundant in crops bordered by forests than in crops bordered by hedgerows, although large-bodied bees were more abundant in the former than the latter. Regardless of field-margin type, we found that small wild bee abundance declined significantly from the edge to the centre of the crop, but honey bee (Apis mellifera L.) and large-bodied bee abundance did not. Strawberry pollen deposition also did not decline with distance into the crop. Although previous work indicates that small wild bees are more effective (yield-increasing) pollinators of strawberry on a per-visit basis, their limited foraging ranges suggest they may only pollinate areas near the crop margins, given typical field sizes in our area.
Higher‐latitude spring‐flowering herbs advance their phenology more than trees with warming temperatures
(Wiley, 2022-11-21) Alecrim, Evelyn F.; Sargent, Risa D.; Forrest, Jessica R. K.
The phenologies of co‐occurring trees and spring‐blooming understory herbs in northeastern North American hardwood forests appear to be regulated by different environmental drivers – air temperature and soil temperature/snowpack, respectively. Accordingly, it has been hypothesized that climate change–driven asymmetry in the advancement of canopy leaf‐out relative to the timing of understory growth could reduce photosynthetic rates and reproductive success of understory herbs through greater early‐season shading. To determine whether trees and spring‐flowering forest herbs are advancing their phenologies at different rates with respect to increasing global temperatures, we examined the phenological responses to warming of 10 species of trees and 11 species of spring‐flowering forest herbs (8045 observations from 965 sites) in northeastern North America using 13 years of data collected by citizen scientists under the auspices of the USA‐National Phenology Network. Contrary to expectation, the degree of advancement of leaf‐out as a function of temperature was greater in spring‐flowering forest herbs than in trees, with a mean response rate of −4.9 days/°C (95% BCI [−5.2, −4.6]) for spring‐flowering forest herbs vs. −3.3 days/°C (95% BCI [−3.5, −3.1]) for trees. However, the response to temperature was not consistent across the latitudinal range, with spring‐flowering forest herbs responding more strongly to warming than trees at middle (40–44°N) and higher (45–48°N) latitudes but not at lower latitudes (35–39°N). In contrast to previous suggestions, our study shows spring‐flowering forest herbs advancing their phenology at a higher rate than trees with respect to warming through most of the latitudinal range investigated, which could translate into a longer growing season and increased carbon uptake for spring‐flowering forest herbs as spring temperatures rise.
Pesticide-induced disturbances of bee gut microbiotas
(Oxford University Press (OUP), 2022-02-02) Hotchkiss, Michelle Z.; Poulain, Alexandre J.; Forrest, Jessica R. K.
Social bee gut microbiotas play key roles in host health and performance. Worryingly, a growing body of literature shows that pesticide exposure can disturb these microbiotas. Most studies examine changes in taxonomic composition in Western honey bee (Apis mellifera) gut microbiotas caused by insecticide exposure. Core bee gut microbiota taxa shift in abundance after exposure but are rarely eliminated, with declines in Bifidobacteriales and Lactobacillus near melliventris abundance being the most common shifts. Pesticide concentration, exposure duration, season and concurrent stressors all influence whether and how bee gut microbiotas are disturbed. Also, the mechanism of disturbance—i.e. whether a pesticide directly affects microbial growth or indirectly affects the microbiota by altering host health—likely affects disturbance consistency. Despite growing interest in this topic, important questions remain unanswered. Specifically, metabolic shifts in bee gut microbiotas remain largely uninvestigated, as do effects of pesticide-disturbed gut microbiotas on bee host performance. Furthermore, few bee species have been studied other than A. mellifera, and few herbicides and fungicides have been examined. We call for these knowledge gaps to be addressed so that we may obtain a comprehensive picture of how pesticides alter bee gut microbiotas, and of the functional consequences of these changes.
Field design can affect cross-pollination and crop yield in strawberry (Fragaria x ananassa D.)
(2020-02-15) MacInnis, Gail; Forrest, Jessica R. K.
The distance travelled by pollinators between successive flower visits can affect the quality of pollen transferred among plants. In cropping environments, especially monoculture systems, pollinators that travel between plants or rows may increase cross-pollination and consequently crop yield. However, the most commonly utilized crop pollinator, Apis mellifera L., tends to forage consecutively on nearest-neighbouring plants within rows. The level of cross-pollination can be further restricted in crops that are propagated by cloning. When a clonal variety is planted over large areas, the potential for outcrossed pollen deposition could be limited, regardless of pollinator flight distances. To investigate how pollinator movement and varietal diversity interact to affect crop pollination, we conducted an experiment with wild and honey bees in single- and multiple-variety strawberry fields. We hypothesized that the amount of cross-pollination provided by wild bees in multiple-variety strawberry fields would be greater than in single-variety fields, and greater than that provided by honey bees in either field type. We found that, indeed, flowers visited by wild bees produced larger strawberries than those visited by honey bees in multiple-variety plots, but only in the more self-incompatible of the two strawberry varieties tested. Strawberries resulting from honey bee pollination were of similar size regardless of the number of varieties planted in the field. Our results show that certain multiple-variety strawberry fields can benefit from the irregular foraging patterns of some solitary bee species, leading to increased cross-pollination and crop yield. Strawberry growers could take advantage of this effect by planting multiple varieties in close proximity and by supporting wild bee populations on farms.
Climate change fluctuations can increase population abundance and range size.
(2024-06) MacDonald, Jane Shaw; Lutscher, Frithjof; Bourgault, Yves
Climate change threatens many species by a poleward/upward movement of their thermal niche. While we know that faster movement has stronger impacts, little is known on how fluctuations of niche movement affect population outcomes. Environmental fluctuations often affect populations negatively, but theory and experiments have revealed some positive effects. We study how fluctuations around the average speed of the niche impact a species' persistence, abundance and realized niche width under climate change. We find that the outcome depends on how fluctuations manifest and what the relative time scale of population growth and climate fluctuations are. When populations are close to extinction with the average speed, fluctuations around this average accelerate population decline. However, populations not yet close to extinction can increase in abundance and/or realized niche width from such fluctuations. Long-lived species increase more when their niche size remains constant, short-lived species increase more when their niche size varies.
“Alternative” fuels contributing to mitochondrial electron transport: Importance of non-classical pathways in the diversity of animal metabolism
(2018-10-01) McDonald, Allison E.; Pichaud, Nicolas; Darveau, Charles-A.
The study of glycolysis, the TCA cycle, and oxidative phosphorylation in animals has yielded a wealth of information about bioenergetics. Less is known about how animals use fuels other than glucose and less characterized enzymes that are also used to provide electrons to the electron transport system. It has become clear that bioenergetic flexibility is employed by a wide variety of animals in order to successfully grow, maintain cells, and reproduce, and has contributed to the exploitation of new environments and ecological niches through evolution. In most cases, the discovery of these “alternative” fuels and non-classical pathways is relatively recent, but is starting to call into question long believed paradigms about the diversity of animal bioenergetics. We present several specific examples of these “alternatives” and the animals that use them and present some implications for animal mitochondrial physiology research.
High temperature sensitivity of bumblebee castes and the colony-level costs of thermoregulation in Bombus impatiens
(2023-09-12) Bretzlaff, Tiffany; Kerr, Jeremy T.; Darveau, Charles-A.
Physiological thermal limits often reflect species distribution, but the role that ambient temperature (Ta) plays in limiting species within their thermal environment remains unclear. Climate change-linked declines in bumblebees, an important pollinator group, leave questions regarding which aspect of their physiology is hindered under high Ta. As a eusocial species, bumblebees utilize their ability to thermoregulate as a superorganism to maintain nest temperature (Tn) within a narrow thermal window to buffer developing larvae from developmental defects. Thermoregulatory behaviours, such as thermogenesis to warm up and fanning to cool down the nest, are energetically expensive and it is uncertain how successful large colonies are at maintaining Tn within its optimal range. Using a common bumblebee species, Bombus impatiens, our study first established the critical thermal limits (CTmax) of workers, queens, drones and larvae to determine which caste is most thermally sensitive to heat. We found that larvae had significantly lower heat tolerance than adults, highlighting the importance of colonial thermoregulation. We then measured the energy expenditure of large colonies under acute thermal stress (5–40 °C) using flow-through respirometry while simultaneously quantifying Tn. Colonies that experienced Ta at or below optimal Tn (≤30 °C) were successful at thermoregulation. At 35 °C and above, however, Tn increased despite high energetic costs to the colony. Together our results demonstrate that high Ta poses a risk to colonies that fail to buffer thermally sensitive larvae from changes in Tn.
Flight energetics, caste dimorphism and scaling properties in the bumblebee Bombus impatiens
(2019-01-04) Billardon, Fannie; Darveau, Charles-A.
Animal size affects energetics of locomotion. Using female caste dimorphism in bumblebees, we assessed how body mass impacted morphological and physiological traits linked with flight. The allometric relationships obtained for workers wing surface area, wingbeat frequency, flight and resting metabolic rates could predict the trait values of queens that are more than four-fold larger. Flight success of queens decreased over time in part due to a large increase in body mass, and decrease in traits linked with flight, namely wingbeat frequency, metabolic rate, and the activity of metabolic enzymes tended to decrease. After taking into account temporal changes, body mass, flight wingbeat frequency and metabolic rate were repeatable. Finally, we found significant family resemblance for all traits measured, indicating that shared genes and/or environmental effects impact phenotypic variation. Together, we here show that the functional association between body morphology and flight physiology is robust, providing further insights into the mechanistic basis of metabolic rate scaling patterns during locomotion in animals.
Diversity in membrane composition is associated with variation in thermoregulatory capacity in hymenopterans
(2018-10-01) Rodríguez, Enrique; Weber, Jean-Michel; Darveau, Charles-A.
Thermoregulatory capacity varies widely among bees and wasps, but the cellular physiology required to support such thermogenic ability remains unclear. Studies conducted on ectothermic species living in varying temperature show that cellular membrane composition is adjusted to remain functional, a process named homeoviscous adaptation. We show that the fatty acid composition of flight muscle membranes varies with thermogenic capacity in species of bees and wasps. The relative abundance of palmitate (16:0) and linoleate (18:2) decreased, while oleate (18:1) increased with increasing thoracic temperature. Species selected for the study varied over ten-fold in body mass, which in turn affected species thoracic temperature and their fatty acids profile. Nevertheless, all analyses conducted show that thoracic temperature is the main driver of flight muscle membrane composition in hymenopterans with diverse thermoregulatory capacity. These findings are in line with the predictions based on the homeoviscous adaptation hypothesis and further show that thermogenic strategy used by insect species impacts cellular membrane composition.
Introduction à la biologie cellulaire et moléculaire
(2023) Beaulieu, Elaine
Un manuel libre pour les étudiantes et étudiants de premier cycle en biologie cellulaire et moléculaire à l’Université d’Ottawa. Cette ressource éducative libre (REL) est une traduction partielle et une adaptation des chapitres portant sur la biologie cellulaire et moléculaire du manuel libre Biology 2e de OpenStax. Dernière mise à jour : 2025.
Testing alternative hypotheses on the origin and speciation of Hawaiian katydids
(2022) Rakesh, Mohan; Aris-Brosou, Stephane; Xia, Xuhua
BACKGROUND: Hawaiian Islands offer a unique and dynamic evolutionary theatre for studying origin and speciation as the islands themselves sequentially formed by erupting undersea volcanos, which would subsequently become dormant and extinct. Such dynamics have not been used to resolve the controversy surrounding the origin and speciation of Hawaiian katydids in the genus Banza, whose ancestor could be from either the Old-World genera Ruspolia and Euconocephalus, or the New World Neoconocephalus. To address this question, we performed a chronophylogeographic analysis of Banza species together with close relatives from the Old and New Worlds. RESULTS: Based on extensive dated phylogeographic analyses of two mitochondrial genes (COX1 and CYTB), we show that our data are consistent with the interpretation that extant Banza species resulted from two colonization events, both by katydids from the Old World rather than from the New World. The first event was by an ancestral lineage of Euconocephalus about 6 million years ago (mya) after the formation of Nihoa about 7.3 mya, giving rise to B. nihoa. The second colonization event was by a sister lineage of Ruspolia dubia. The dating result suggests that this ancestral lineage first colonized an older island in the Hawaiian-Emperor seamount chain before the emergence of Hawaii Islands, but colonized Kauai after its emergence in 5.8 mya. This second colonization gave rise to the rest of the Banza species in two major lineages, one on the older northwestern islands, and the other on the newer southwestern islands. CONCLUSION: Chronophylogeographic analyses with well-sampled taxa proved crucial for resolving phylogeographic controversies on the origin and evolution of species colonizing a new environment.
Conservation of griseofulvin genes in the gsf gene cluster among fungal genomes
(2021) Aris, Parisa; Yan, Lihong; Wei, Yulong; Chang, Ying; Shi, Bihong; Xia, Xuhua
The polyketide griseofulvin is a natural antifungal compound and research in griseofulvin has been key in establishing our current understanding of polyketide biosynthesis. Nevertheless, the griseofulvin gsf biosynthetic gene cluster (BGC) remains poorly understood in most fungal species, including Penicillium griseofulvum where griseofulvin was first isolated. To elucidate essential genes involved in griseofulvin biosynthesis, we performed third-generation sequencing to obtain the genome of Penicillium griseofulvum strain D-756. Furthermore, we gathered publicly available genome of 11 other fungal species in which gsf gene cluster was identified. In a comparative genome analysis, we annotated and compared the gsf BGC of all 12 fungal genomes. Our findings show no gene rearrangements at the gsf BGC. Furthermore, seven gsf genes are conserved by most genomes surveyed whereas the remaining six were poorly conserved. This study provides new insights into differences between gsf BGC and suggests that seven gsf genes are essential in griseofulvin production.
Applications of Protein Secondary Structure Algorithms in SARS-CoV-2 Research
(2021) Kruglikov, Alibek; Rakesh, Mohan; Wei, Yulong; Xia, Xuhua
Since the outset of COVID-19, the pandemic has prompted immediate global efforts to sequence SARS-CoV-2, and over 450 000 complete genomes have been publicly deposited over the course of 12 months. Despite this, comparative nucleotide and amino acid sequence analyses often fall short in answering key questions in vaccine design. For example, the binding affinity between different ACE2 receptors and SARS-COV-2 spike protein cannot be fully explained by amino acid similarity at ACE2 contact sites because protein structure similarities are not fully reflected by amino acid sequence similarities. To comprehensively compare protein homology, secondary structure (SS) analysis is required. While protein structure is slow and difficult to obtain, SS predictions can be made rapidly, and a well-predicted SS structure may serve as a viable proxy to gain biological insight. Here we review algorithms and information used in predicting protein SS to highlight its potential application in pandemics research. We also showed examples of how SS predictions can be used to compare ACE2 proteins and to evaluate the zoonotic origins of viruses. As computational tools are much faster than wet-lab experiments, these applications can be important for research especially in times when quickly obtained biological insights can help in speeding up response to pandemics.
Does Saccharomyces cerevisiae Require Specific Post-Translational Silencing against Leaky Translation of Hac1up?
(2021) Tehfe, Ali; Roseshter, Talia; Wei, Yulong; Xia, Xuhua
HAC1 encodes a key transcription factor that transmits the unfolded protein response (UPR) from the endoplasmic reticulum (ER) to the nucleus and regulates downstream UPR genes in Saccharomyces cerevisiae. In response to the accumulation of unfolded proteins in the ER, Ire1p oligomers splice HAC1 pre-mRNA (HAC1u) via a non-conventional process and allow the spliced HAC1 (HAC1i) to be translated efficiently. However, leaky splicing and translation of HAC1u may occur in non-UPR cells to induce undesirable UPR. To control accidental UPR activation, multiple fail-safe mechanisms have been proposed to prevent leaky HAC1 splicing and translation and to facilitate rapid degradation of translated Hac1up and Hac1ip. Among proposed regulatory mechanisms is a degron sequence encoded at the 5' end of the HAC1 intron that silences Hac1up expression. To investigate the necessity of an intron-encoded degron sequence that specifically targets Hac1up for degradation, we employed publicly available transcriptomic data to quantify leaky HAC1 splicing and translation in UPR-induced and non-UPR cells. As expected, we found that HAC1u is only efficiently spliced into HAC1i and efficiently translated into Hac1ip in UPR-induced cells. However, our analysis of ribosome profiling data confirmed frequent occurrence of leaky translation of HAC1u regardless of UPR induction, demonstrating the inability of translation fail-safe to completely inhibit Hac1up production. Additionally, among 32 yeast HAC1 surveyed, the degron sequence is highly conserved by Saccharomyces yeast but is poorly conserved by all other yeast species. Nevertheless, the degron sequence is the most conserved HAC1 intron segment in yeasts. These results suggest that the degron sequence may indeed play an important role in mitigating the accumulation of Hac1up to prevent accidental UPR activation in the Saccharomyces yeast.
Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines
(2021) Xia, Xuhua
The design of Pfizer/BioNTech and Moderna mRNA vaccines involves many different types of optimizations. Proper optimization of vaccine mRNA can reduce dosage required for each injection leading to more efficient immunization programs. The mRNA components of the vaccine need to have a 5'-UTR to load ribosomes efficiently onto the mRNA for translation initiation, optimized codon usage for efficient translation elongation, and optimal stop codon for efficient translation termination. Both 5'-UTR and the downstream 3'-UTR should be optimized for mRNA stability. The replacement of uridine by N1-methylpseudourinine (Ψ) complicates some of these optimization processes because Ψ is more versatile in wobbling than U. Different optimizations can conflict with each other, and compromises would need to be made. I highlight the similarities and differences between Pfizer/BioNTech and Moderna mRNA vaccines and discuss the advantage and disadvantage of each to facilitate future vaccine improvement. In particular, I point out a few optimizations in the design of the two mRNA vaccines that have not been performed properly.
Dating the Common Ancestor from an NCBI Tree of 83688 High-Quality and Full-Length SARS-CoV-2 Genomes
(2021) Xia, Xuhua
All dating studies involving SARS-CoV-2 are problematic. Previous studies have dated the most recent common ancestor (MRCA) between SARS-CoV-2 and its close relatives from bats and pangolins. However, the evolutionary rate thus derived is expected to differ from the rate estimated from sequence divergence of SARS-CoV-2 lineages. Here, I present dating results for the first time from a large phylogenetic tree with 86,582 high-quality full-length SARS-CoV-2 genomes. The tree contains 83,688 genomes with full specification of collection time. Such a large tree spanning a period of about 1.5 years offers an excellent opportunity for dating the MRCA of the sampled SARS-CoV-2 genomes. The MRCA is dated 16 August 2019, with the evolutionary rate estimated to be 0.05526 mutations/genome/day. The Pearson correlation coefficient (r) between the root-to-tip distance (D) and the collection time (T) is 0.86295. The NCBI tree also includes 10 SARS-CoV-2 genomes isolated from cats, collected over roughly the same time span as human COVID-19 infection. The MRCA from these cat-derived SARS-CoV-2 is dated 30 July 2019, with r = 0.98464. While the dating method is well known, I have included detailed illustrations so that anyone can repeat the analysis and obtain the same dating results. With 16 August 2019 as the date of the MRCA of sampled SARS-CoV-2 genomes, archived samples from respiratory or digestive tracts collected around or before 16 August 2019, or those that are not descendants of the existing SARS-CoV-2 lineages, should be particularly valuable for tracing the origin of SARS-CoV-2.
Post-Alignment Adjustment and Its Automation
(2021) Xia, Xuhua
Multiple sequence alignment (MSA) is the basis for almost all sequence comparison and molecular phylogenetic inferences. Large-scale genomic analyses are typically associated with automated progressive MSA without subsequent manual adjustment, which itself is often error-prone because of the lack of a consistent and explicit criterion. Here, I outlined several commonly encountered alignment errors that cannot be avoided by progressive MSA for nucleotide, amino acid, and codon sequences. Methods that could be automated to fix such alignment errors were then presented. I emphasized the utility of position weight matrix as a new tool for MSA refinement and illustrated its usage by refining the MSA of nucleotide and amino acid sequences. The main advantages of the position weight matrix approach include (1) its use of information from all sequences, in contrast to other commonly used methods based on pairwise alignment scores and inconsistency measures, and (2) its speedy computation, making it suitable for a large number of long viral genomic sequences.

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