Department of Biological Sciences
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- ItemBMP3 is a novel locus involved in the causality of ocular coloboma(2022) Fox, Sabrina C.; Widen, Sonya A.; Asai-Coakwell, Mika; Havrylov, Serhiy; Benson, Matthew; Prichard, Lisa; Baddam, Pranidhi; Graf, Daniel; Lehmann, Ordan J.; Waskiewicz, Andrew J.Coloboma, a congenital disorder characterized by gaps in ocular tissues, is caused when the choroid fissure fails to close during embryonic development. Several loci have been associated with coloboma, but these represent less than 40% of those that are involved with this disease. Here, we describe a novel coloboma-causing locus, BMP3. Whole exome sequencing and Sanger sequencing of patients with coloboma identified three variants in BMP3, two of which are predicted to be disease causing. Consistent with this, bmp3 mutant zebrafish have aberrant fissure closure. bmp3 is expressed in the ventral head mesenchyme and regulates phosphorylated Smad3 in a population of cells adjacent to the choroid fissure. Furthermore, mutations in bmp3 sensitize embryos to Smad3 inhibitor treatment resulting in open choroid fissures. Micro CT scans and Alcian blue staining of zebrafish demonstrate that mutations in bmp3 cause midface hypoplasia, suggesting that bmp3 regulates cranial neural crest cells. Consistent with this, we see active Smad3 in a population of periocular neural crest cells, and bmp3 mutant zebrafish have reduced neural crest cells in the choroid fissure. Taken together, these data suggest that Bmp3 controls Smad3 phosphorylation in neural crest cells to regulate early craniofacial and ocular development.
- ItemGlobal urban environmental change drives adaptation in white clover(2022) Santangelo, James S.; Ness, Rob W.; Cohan, Beata; Flaherty, LeahUrbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural clines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale.
- ItemUser testing for serious game design: improving the player experience(2022) Shaw, Ross; Sperano, Isabelle; Andruchow, Robert; Cobzas, DanaThis case study reflects on our use of user testing during a research project in which we designed a serious video game, “Life on the Edge.” The target audience of the game is first-year post-secondary biology students. As we designed the game, user testing was a critical component that allowed us to identify issues. Any issues that interfere with the flow or enjoyment of a video game can be distracting to players. In what follows, we will describe the research design and discuss the processes for testing a serious video game that will allow you to identify game issues successfully. How you recruit participants, test players, and prioritize player feedback is a component of effective user testing and improving your game. With user testing, we were able to identify problems in the game, prioritize them, and address them. By using variable user testing methods, you can adapt to the changing needs of your game project and develop a successful serious video game.
- ItemAncient hybridization patterns between bighorn and thinhorn sheep(2021) Santos, Sarah H. D.; Peery, Rhiannon M.; Miller, Joshua M.; Dao, Anh; Lyu, Feng-Hua; Li, Xin; Li, Meng-Hua; Coltman, David W.Whole-genome sequencing has advanced the study of species evolution, including the detection of genealogical discordant events such as ancient hybridization and incomplete lineage sorting (ILS). The evolutionary history of bighorn (Ovis canadensis) and thinhorn (Ovis dalli) sheep present an ideal system to investigate evolutionary discordance due to their recent and rapid radiation and putative secondary contact between bighorn and thinhorn sheep subspecies, specifically the dark pelage Stone sheep (O. dalli stonei) and predominately white Dall sheep (O. dalli dalli), during the last ice age. Here, we used multiple genomes of bighorn and thinhorn sheep, together with snow (O. nivicola) and the domestic sheep (O. aries) as outgroups, to assess their phylogenomic history, potential introgression patterns and their adaptive consequences. Among the Pachyceriforms (snow, bighorn and thinhorn sheep) a consistent monophyletic species tree was retrieved; however, many genealogical discordance patterns were observed. Alternative phylogenies frequently placed Stone and bighorn as sister clades. This relationship occurred more often and was less divergent than that between Dall and bighorn. We also observed many blocks containing introgression signal between Stone and bighorn genomes in which coat colour genes were present. Introgression signals observed between Dall and bighorn were more random and less frequent, and therefore probably due to ILS or intermediary secondary contact. These results strongly suggest that Stone sheep originated from a complex series of events, characterized by multiple, ancient periods of secondary contact with bighorn sheep.
- ItemA phylogeographic contact zone for Arctic grayling (Thymallus arcticus) in Alberta, Canada(2021) Reilly, Jessica R.; Miller, Joshua M.Arctic Grayling Thymallus arcticus are a salmonid with a Holarctic distribution, extending from north-eastern Eurasia through north-western North America. Throughout their range, Arctic Grayling face a number of threats including angling mortality, habitat fragmentation and loss and climate change. Thus, there is a need to protect the species through targeted management actions. Genetic information can assist in determining the appropriate scale for these actions through description of Designatable Units (DUs). Here we use newly collected mitochondrial DNA sequence data to assess the phylogeographic structure of Arctic Grayling in Alberta, Canada and link these with previously collected mitochondrial and microsatellite data to determine how many DUs may exist across Canada. Our assessment of 831 base pairs of sequence data in 96 individuals found two deeply divergent lineages in Alberta. When combined with 22 previously collected sequences our results highlight that Alberta is a contact zone for the observed lineages of Arctic Grayling in North America. Reassessment of nine microsatellites genotyped in 1,116 individuals further highlighted inter-basin divergence, likely the result of historical processes. Given the divergence and geographic distribution of the genetic diversity, Arctic Grayling in Canada merit consideration for separate DUs in future species status assessments and management plans. Continuing research should aim to expand sampling geographically (e.g. regions east of Great Slave Lake and along the Arctic coastline) to clarify possible colonization routes, and add to or synthesize work on Arctic Grayling behaviour, morphology, and life-history to address the limited understanding of local adaptions within this species.