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A DNA barcode examination of the Laminariaceae (Phaeophyceae) in Canada reveals novel biogeographical and evolutionary insights
(Taylor and Francis, 2010) McDevit, Daniel, C.; Saunders, Gary, W.
DNA barcoding is becoming a widely applied tool for the rapid and accurate identification of eukaryotic species. In this study we used the DNA barcode for large-scale screening of the brown algal family Laminariaceae in Canada. With the examination of 194 COI-5P (5′ end of cytochrome c oxidase 1) sequences (150 newly determined) from representatives of this family, we confirmed the presence of 12 species in Canadian waters (Cymathaere triplicata, Laminaria digitata, L. ephemera, L. setchellii, L. solidungula, L. yezoensis, Macrocystis integrifolia, Nereocystis leutkeana, Postelsia palmaeformis, Saccharina groenlandica, S. latissima and S. sessilis). Saccharina groenlandica, a species with a history of taxonomic confusion, was found in the Pacific, Hudson Bay (subarctic) and Atlantic Canada extending greatly our comprehension of the biogeography of this species. Additionally, COI-5P data from S. latissima, combined with ITS results, provided insights into historical distributional patterns and uncovered a hybridization zone between incipient species in this complex. These discoveries highlight how the growth of a worldwide barcode database for the assignment of individuals to genetic species will uncover new perspectives on biogeography and species diversity on a global scale.
A DNA barcode examination of the red algal family Dumontiaceae in Canadian waters reveals substantial cryptic species diversity. 1. The foliose Dilsea–Neodilsea complex and Weeksia
(Canadian Science Publishing, 2008) Saunders, Gary, W.
The field of DNA barcoding is working towards generating a genetic system for the quick and accurate identification of eukaryotic species. For the more systematic minded, however, DNA barcoding offers a new approach towards screening and uniting large numbers of biological specimens in genetic groups as a first step towards assigning them to species and genera in an approach best termed “molecular-assisted alpha taxonomy”. This approach is particularly amenable in organisms with simple morphologies, a propensity for convergence, extensive phenotypic plasticity, and life histories with an alternation of heteromorphic generations. It is hard to imagine a group of organisms better defined by all of these traits than the marine macroalgae. In an effort to assess the utility of the DNA barcode (COI-5′) for testing the current concepts of biodiversity of marine macroalgae in Canada, a study to assess species diversity in the red algal family, Dumontiaceae, was initiated. Through this work I confirm the presence in Canadian waters of Dilsea californica (J. Agardh) Kuntze, Dilsea integra (Kjellman) Rosenvinge, and Neodilsea borealis (I.A. Abbott) Lindstrom of the Dilsea–Neodilsea complex, and Weeksia coccinea (Harvey) Lindstrom for the genus Weeksia. However, our work has uncovered two additional species of the former complex, Dilsea lindstromiae Saunders sp. nov. and Dilsea pygmaea (Setchell) Setchell, and an additional species of the latter, Weeksia reticulata Setchell, effectively doubling representation of these foliose dumontiacean genera in Canadian waters.
A molecular assessment of species diversity and generic boundaries in the red algal tribes Polysiphonieae and Streblocladieae (Rhodomelaceae, Rhodophyta) in Canada
(Taylor and Francis, 2018) Savoie, Amanda, M.; Saunders, Gary, W.
Sequence data generated during a Canadian barcode survey (COI-5P) of the tribes Polysiphonieae and Streblocladieae, a large and taxonomically challenging group of red algae, revealed significant taxonomic confusion and hidden species diversity. Polysiphonia pacifica Hollenberg, P. paniculata Montagne, P. stricta (Dillwyn) Greville and Vertebrata fucoides (Hudson) Kuntze were all complexes of two or more genetically distinct yet overlooked species. One variety of P. pacifica was elevated to the rank of species as P. determinata (Hollenberg) Savoie & Saunders, stat. nov. Several new additions to the Canadian flora were recorded including P. kapraunii Stuercke & Freshwater and P. morrowii Harvey. Subsequent multi-gene (COI-5P, LSU and rbcL) phylogenetic analyses confirmed that the genus Polysiphonia Greville was polyphyletic, and currently assigned species resolved with many other genera. Polysiphonia sensu stricto was restricted to a group of species that formed a monophyletic lineage with the type, Polysiphonia stricta. Carradoriella P.C.Silva was resurrected based on the South African species Carradoriella virgata (C.Agardh) P.C.Silva. Species previously attributed to Polysiphonia were transferred to Carradoriella, Leptosiphonia and Vertebrata as well as to three new genera described here: Acanthosiphonia gen. nov., based on A. echinata (Harvey) comb. nov.; Eutrichosiphonia gen. nov. for E. confusa (Hollenberg) comb. nov. and E. sabulosia (B.Kim & M.S.Kim) comb. nov.; and Kapraunia gen. nov., which includes K. schneideri (Stuercke & Freshwater) comb. nov. and three additional species.
A molecular phylogenetic and DNA barcode assessment of the tribe Pterosiphonieae (Ceramiales, Rhodophyta) emphasizing the Northeast Pacific
(Canadian Science Publishing, 2016) Savoie, Amanda, M.; Saunders, Gary, W.
Sequence data (COI-5P and rbcL) for North American members of the tribe Pterosiphonieae were compared with collections from around the world. Phylogenetic analyses resolved Pterosiphonia as polyphyletic and many species required transfer to other genera. In our analyses Pterosiphonia sensu stricto included only the type species P. cloiophylla (C. Agardh) Falkenberg and P. complanata (Clemente) Falkenberg, as well as the South African species P. stegengae sp. nov. A new genus, Xiphosiphonia gen. nov., was described for X. ardreana (Maggs & Hommersand) comb. nov., X. pennata (C. Agardh) comb. nov., and X. pinnulata (Kützing) comb. nov. Some Asian, European and North American species previously attributed to Pterosiphonia were transferred to Symphyocladia including S. baileyi (Harvey) comb. nov., S. dendroidea (Montagne) comb. nov., S. plumosa nom. nov. (for P. gracilis Kylin), and S. tanakae (S. Uwai & M. Masuda) comb. nov. We also described two new North American species, Symphyocladia brevicaulis sp. nov. and S. rosea sp. nov. Other species formed a well-supported clade for which the genus name Polyostea Ruprecht was resurrected. Included in Polyostea were P. arctica (J. Agardh) comb. nov., P. bipinnata (Postels & Ruprecht) Ruprecht, P. hamata (E.S. Sinova) comb. nov., and P. robusta (N.L. Gardner) comb. nov.
A revision of the genus Cryptonemia (Halymeniaceae, Rhodophyta) in Bermuda, western Atlantic Ocean, including five new species and C. bermudensis (Collins & M. Howe) comb. nov.
(Taylor and Francis, 2018) Schneider, Craig, W.; Lane, Christopher, E.; Saunders, Gary, W.
Cryptonemia specimens collected in Bermuda over the past two decades were analysed using gene sequences encoding the large subunit of the nuclear ribosomal DNA and the large subunit of RuBisCO as genetic markers to elucidate their phylogenetic positions. They were additionally subjected to morphological assessment and compared with historical collections from the islands. Six species are presently found in the flora including C. bermudensis comb. nov., based on Halymenia bermudensis, and the following five new species: C. abyssalis, C. antricola, C. atrocostalis, C. lacunicola and C. perparva. Of the eight species known in the western Atlantic flora prior to this study, none is found in Bermuda. Specimens reported in the islands in the 1900s attributed to C. crenulata and C. luxurians are representative of the new species, C. antricola and C. atrocostalis, respectively.
Activity and Distribution of Paxillin, Focal Adhesion Kinase, and Cadherin Indicate Cooperative Roles during Zebrafish Morphogenesis
(2003) Crawford, Bryan, D.; Henry, Clarissa, A.; Clason, Todd, A.; Becker, Amanda, L.; Hille, Merrill, B.
We investigated the focal adhesion proteins paxillin and Fak, and the cell-cell adhesion protein cadherin in developing zebrafish (Danio rerio) embryos. Cadherins are expressed in presomitic mesoderm where they delineate cells. The initiation of somite formation coincides with an increase in the phosphorylation of Fak, and the accumulation of Fak, phosphorylated Fak, paxillin, and fibronectin at nascent somite boundaries. In the notochord, cadherins are expressed on cells during intercalation, and phosphorylated Fak accumulates in circumferential rings where the notochord cells contact laminin in the perichordal sheath. Subsequently, changes in the orienta- tions of collagen fibers in the sheath suggest that Fak-mediated adhesion allows longitudinal expansion of the notochord, but not lateral expansion, resulting in notochord elongation. Novel observations showed that focal adhesion kinase and paxillin concentrate at sites of cell-cell adhesion in the epithelial enveloping layer and may associate with actin cytoskeleton at epithelial junctions containing cadherins. Fak is phosphorylated at these epithelial junctions but is not phosphorylated on Tyr397, implicating a noncanonical mechanism of regulation. These data suggest that Fak and paxillin may function in the integration of cadherin-based and integrin-based cell adhesion during the morphogenesis of the early zebrafish embryo.
Activity-Based Labeling of Matrix Metalloproteinases in Living Vertebrate Embryos
(PLOS, 2012) Keow, Johnathan Y.; Pond, Eric D.; Cisar, Justin S.; Cravatt, Benjamin F.; Crawford, Bryan D.
Extracellular matrix (ECM) remodeling is a physiologically and developmentally essential process mediated by a family of zinc-dependent extracellular proteases called matrix metalloproteinases (MMPs). In addition to complex transcriptional control, MMPs are subject to extensive post-translational regulation. Because of this, classical biochemical, molecular and histological techniques that detect the expression of specific gene products provide useful but limited data regarding the biologically relevant activity of MMPs. Using benzophenone-bearing hydroxamate-based probes that interact with the catalytic zinc ion in MMPs, active proteases can be covalently ‘tagged’ by UV cross-linking. This approach has been successfully used to tag MMP-2 in vitro in tissue culture supernatants, and we show here that this probe tags proteins with mobilities consistent with known MMPs and detectable gelatinolytic activity in homogenates of zebrafish embryos. Furthermore, because of the transparency of the zebrafish embryo, UV-photocroslinking can be accomplished in vivo, and rhodamated benzophenone probe is detected in striking spatial patterns consistent with known distributions of active matrix remodeling in embryos. Finally, in metamorphosing Xenopus tadpoles, this probe can be used to biotinylate active MMP-2 by injecting it and cross-linking it in vivo, allowing the protein to be subsequently extracted and biochemically identified.
Ancient DNA SNP-panel data suggests stability in bluefin tuna genetic diversity despite centuries of fluctuating catches in the eastern Atlantic and Mediterranean
(Nature Research, 2021-10-20) Andrews, Adam J.; Puncher, Gregory N.; Bernal‑Casasola, Darío; Di Natale, Antonio; Massari, Francesco; Onar, Vedat; Toker, Nezir Yaşar; Hanke, Alex; Pavey, Scott A.; Savojardo, Castrense; Martelli, Pier Luigi; Casadio, Rita; Cilli, Elisabetta; Morales‑Muñiz, Arturo; Mantovani, Barbara; Tinti, Fausto; Cariani, Alessia
Atlantic bluefin tuna (Thunnus thynnus; BFT) abundance was depleted in the late 20th and early 21st century due to overfishing. Historical catch records further indicate that the abundance of BFT in the Mediterranean has been fluctuating since at least the 16th century. Here we build upon previous work on ancient DNA of BFT in the Mediterranean by comparing contemporary (2009–2012) specimens with archival (1911–1926) and archaeological (2nd century BCE–15th century CE) specimens that represent population states prior to these two major periods of exploitation, respectively. We successfully genotyped and analysed 259 contemporary and 123 historical (91 archival and 32 archaeological) specimens at 92 SNP loci that were selected for their ability to differentiate contemporary populations or their association with core biological functions. We found no evidence of genetic bottlenecks, inbreeding or population restructuring between temporal sample groups that might explain what has driven catch fluctuations since the 16th century. We also detected a putative adaptive response, involving the cytoskeletal protein synemin which may be related to muscle stress. However, these results require further investigation with more extensive genome-wide data to rule out demographic changes due to overfishing, and other natural and anthropogenic factors, in addition to elucidating the adaptive drivers related to these.
Antimycobacterial 1,4-napthoquinone natural products from Moneses uniflora
(Elsevier, 2018-10) Li, Haoxin; Bos, Allyson; Jean, Stéphanie; Webster, Duncan; Robichaud, Gilles A.; Johnson, John A.; Gray, Christopher A.
A new 1,4-naphthoquinone derivative, 5,8-dihydro-3-hydroxychimaphilin (4) and five known compounds (1, 2 and 5–7) were isolated from an extract of the Canadian medicinal plant Moneses uniflora that significantly inhibited the growth of Mycobacterium tuberculosis H37Ra. The structure of 4 was established through analysis of NMR and MS data and the absolute configuration of the glycone of 5 was determined by chemical transformation and comparison with standards prepared from D- and L-glucose. All compounds isolated were screened against Mycobacterium tuberculosis (H37Ra) and the mammalian HEK 293 cell line and, with the exception of compounds 5 and 7, exhibited marked selectivity in their bioactivity: Compound 1 exhibited potent antimycobacterial activity (IC50 of 5.4 μM) and moderate cytotoxicity (IC50 of 30 μM); compounds 2, 4 and 6 showed moderate antimycobacterial activity (IC50 values from 28 – 47 μM) without affecting the viability of mammalian cells; compound 5 displayed moderate activity in both assays (IC50 values of 44 and 55 μM respectively); and compound 7 was not active in either assay. These data suggest that the Moneses napthaquinone derivatives elicit biological responses in mycobacterial and mammalian cells through disparate modes of action that warrant further investigation
Assigning morphological variants of Fucus (Fucales, Phaeophyceae) in Canadian waters to recognized species using DNA barcoding
(Canadian Science Publishing, 2008) Kucera, Hana; Saunders, Gary, W.
The intertidal brown algal genus Fucus (Phaeophyceae) consists of individuals with a generally dichotomously branched habit. Morphological variability within species, combined with morphological similarity between species, renders field identification difficult. In light of recent taxonomic revisions, which reduced 10 taxa traditionally recognized in Canada to four species, we tested the utility of the DNA barcode (mitochondrial cytochrome oxidase 1, 5′) for assigning individuals to these species. We sequenced the DNA barcode for 125 specimens representing all morphologies recognized. We confirmed our results by sequencing the internal transcribed spacer region for 66 specimens. This is the first study to establish that the DNA barcode successfully assigns different morphologies of brown algae to known species as well as other single-gene molecular markers currently used. Furthermore, the results uncovered substantial phenotypic plasticity in Pacific Fucus distichus, from moss-like fragments embedded in estuarine mud, strap-like morphs on exposed rocky coasts, to “spiralis”-like morphs in the upper intertidal whereas phenotypic expression for this species was more restricted in the Atlantic.
Chromosomal inversions in the Atlantic cod genome: implications for management of Canada’s Northern cod stock
(Elsevier, 2019-08-29) Puncher, Gregory Neils; Rowe, Sherrylynn; Rose, George A.; Leblanc, Nathalie M.; Parent, Geneviève J.; Wang, Yanjun; Pavey, Scott A.
Following stock collapse and over twenty years of moratoria, the state of Canada’s Northern Atlantic cod (Gadus morhua) remains precarious. To test if recent stock growth was of endogenous or exogenous origin, we performed a whole genome scan (ddRAD) on 135 adults captured in 2015 at three offshore spawning locations spanning the range of the offshore stock along the northeastern Newfoundland and Labrador shelf (Hawke Channel, Notre Dame Channel and Bonavista Corridor), with an additional 105 adults from three more southern locations (St. Anns Bank, Browns Bank and Bay of Fundy). Population structure analysis using 5,077 single nucleotide polymorphisms (SNPs) detected a distinct genetic break off the coast of Nova Scotia near 45 °N. Gene flow between groups north and south of this divide appears to be limited despite the presence of several northern-type and admixed individuals present in the southern area. North of the genetic divide, allele frequencies of neutral loci were indicative of a panmictic population. Several outlier SNPs were found to be associated with ecologically relevant physical characteristics (visual pigments, fin development, response to hypoxia, and various metabolic processes), which may be indicative of different ecological niches.
Collections from the mesophytic zone off Bermuda reveal three species of Kallymeniaceae (Gigartinales, Rhodophyta) in genera with transoceanic distributions
(Wiley, 2018) Schneider, Craig, W.; Popolizio, Thea, R.; Saunders, Gary, W.
A molecular survey of red algae collected by technical divers and submersibles from 90 m in the mesophotic zone off the coast of Bermuda revealed three species assignable to the Kallymeniaceae. Two of the species are representative of recently described genera centered in the western Pacific in Australia and New Zealand, Austrokallymenia and Psaromenia and the third from the Mediterranean Sea and the eastern Atlantic, Nothokallymenia. A phylogenetic analysis of concatenated mitochondrial (COI-5P) and chloroplast (rbcL) genes, as well as morphological characteristics, revealed that two are shown to be new species with distant closest relatives (N. erosa and Psaromenia septentrionalis), while the third represents a deep water western Atlantic species now moved to an Australasian genus (A. westii).
Considering Fish as Recipients of Ecosystem Services Provides a Framework to Formally Link Baseline, Development, and Post-operational Monitoring Programs and Improve Aquatic Impact Assessments for Large Scale Developments
(Springer, 2022-05-21) Brown, Carolyn J. M.; Curry, R. Allen; Gray, Michelle A.; Lento, Jennifer; MacLatchy, Deborah L.; Monk, Wendy A.; Pavey, Scott A.; St-Hilaire, André; Wegscheider, Bernhard; Munkittrick, Kelly R.
In most countries, major development projects must satisfy an Environmental Impact Assessment (EIA) process that considers positive and negative aspects to determine if it meets environmental standards and appropriately mitigates or offsets negative impacts on the values being considered. The benefits of before-after-control-impact monitoring designs have been widely known for more than 30 years, but most development assessments fail to effectively link pre- and post-development monitoring in a meaningful way. Fish are a common component of EIA evaluation for both socioeconomic and scientific reasons. The Ecosystem Services (ES) concept was developed to describe the ecosystem attributes that benefit humans, and it offers the opportunity to develop a framework for EIA that is centred around the needs of and benefits from fish. Focusing an environmental monitoring framework on the critical needs of fish could serve to better align risk, development, and monitoring assessment processes. We define the ES that fish provide in the context of two common ES frameworks. To allow for linkages between environmental assessment and the ES concept, we describe critical ecosystem functions from a fish perspective to highlight potential monitoring targets that relate to fish abundance, diversity, health, and habitat. Finally, we suggest how this framing of a monitoring process can be used to better align aquatic monitoring programs across pre-development, development, and post-operational monitoring programs.
Detecting Alaria esculenta and Laminaria digitata (Laminariales, Phaeophyceae) gametophytes in red algae, with consideration of distribution patterns in the intertidal zone
(Taylor and Francis, 2019) Bringloe, Trevor, T.; Bartlett, Charlotte, A.B.; Bergeron, Emma, S.; Cripps, Katherine, S.A.; Daigle, Nicole, J.; Gallagher, Patrick, O.; Gallant, Alicia, D.; Giberson, Rachel, O.J.; Greenough, Simon, J.; Lamb, Jillian, M.; Leonard, Thomas, W.; MacKay, Jane, A.; McKenzie, Alexander, D.; Persaud, Shana, M.; Sheng, Tianqi; Stack Mills, Alexa, M.E.; Moore, Tanya, E.; Saunders, Gary, W.
Kelp ecology is heavily biased toward the conspicuous sporophyte stage, whereas understanding of the microscopic gametophyte remains limited. Given that kelp gametophytes are known to grow in/on other species of algae, we sought to determine if species-specific polymerase chain reaction could detect kelp gametophytes in situ from coextracted host DNA. Upon verifying our molecular results, we also assessed distributional patterns of the kelp gametophytes according to site, host species, and vertical placement in the intertidal zone. We sampled Chondrus crispus, Mastocarpus stellatus, and Palmaria palmata (Florideophyceae) at Wallace Cove, New Brunswick, Canada, on 13 September 2016, where kelp sporophytes were abundant, and at an adjacent location without obvious sporophyte presence, L'Etete, on 26 September 2016. Species-specific primers were used to assess the presence of Alaria esculenta and Laminaria digitata DNA from coextracted red algal DNA. We successfully amplified kelp DNA from the host tissue of each red algal species, indicating that gametophytes were present at Wallace Cove and L'Etete during the fall of 2016, with significantly less gametophyte presence at L'Etete. Although no significant differences in gametophyte presence occurred according to host species, P. palmata had significantly less gametophyte presence when sampled from its upper range in the intertidal. Microscopy and additional field observations confirmed the presence of brown endophytes in a variety of hosts, including C. crispus and P. palmata. Our study showcases a simple method for detecting kelp gametophytes, with our preliminary results demonstrating that the distributional and ecological range of kelp gametophytes is broader than that of the sporophytic counterparts.
DNA barcoding reveals multiple overlooked Australian species of the red algal order Rhodymeniales (Florideophyceae), with resurrection of Halopeltis J. Agardh and description of Pseudohalopeltis gen. nov.
(Canadian Science Publishing, 2010) Saunders, Gary, W.; McDonald, Brian
The DNA barcode (COI-5P) was used to investigate cryptic diversity among Rhodymenia spp. in southern Australia. Whereas eight species are currently recognized, we uncovered ca. 20 genetic species groups, phylogenetically assigned to four genera in two families. Procumbent specimens with molecular and anatomical signatures of the Fryeellaceae are assigned to Pseudohalopeltis tasmanensis gen. et sp. nov. Collections from Lord Howe Island recorded in the field as Rhodymenia/Fauchea sp. are assigned to the poorly known genus Microphyllum as Microphyllum robustum sp. nov. A cluster of species with distinct molecular and anatomical attributes is included in a resurrected Halopeltis J.G. Agardh, including Halopeltis australis (J. Agardh) comb. nov. (type species); Halopeltis austrina (Womersley) comb. nov.; Halopeltis cuneata (Harvey) comb. nov. [including Rhodymenia halymenioides (J. Agardh) Womersley]; Halopeltis gracilis sp. nov.; Halopeltis prostrata sp. nov.; and Halopeltis verrucosa (Womersley) comb. nov. Four additional species of Halopeltis from Lord Howe Island (LH1, LH2), Tasmania (TAS), and Western Australia are not characterized further. For Rhodymenia sensu stricto, similar levels of cryptic diversity were noted. Samples tentatively field-identified as “Rhodymenia sonderi,” but having affiliations to Rhodymenia rather than Halopeltis, are referred to Rhodymenia novahollandica sp. nov. Collections field-identified as R. obtusa are genetically distinct from that species and are assigned to Rhodymenia wilsonis (Sonder) comb. nov. Two highly divergent species currently identified as Rhodymenia leptophylla (LH from Lord Howe Island; TAS from Tasmania), as well as two additional cryptic previously unnamed taxa from South Australia (SA) and Victoria (VIC), are not characterized further.
Evidence for the introduction of the Asian red alga Neosiphonia japonica and its introgression with Neosiphonia harveyi (Ceramiales, Rhodophyta) in the Northwest Atlantic
(Wiley, 2015) Savoie, Amanda, M.; Saunders, Gary, W.
There is currently conflict in the literature on the taxonomic status of the reportedly cosmopolitan species Neosiphonia harveyi, a common red alga along the coast of Atlantic Canada and New England, USA. Neosiphonia harveyi sensu lato was assessed using three molecular markers: COI-5P, ITS and rbcL. All three markers clearly delimited three genetic species groups within N. harveyi sensu lato in this region, which we identified as N. harveyi, N. japonica and Polysiphonia akkeshiensis (here resurrected from synonymy with N. japonica). Although Neosiphonia harveyi is considered by some authors to be introduced to the Atlantic from the western Pacific, it was only confirmed from the North Atlantic suggesting it is native to this area. In contrast, Neosiphonia japonica was collected from only two sites in Rhode Island, USA, as well as from its reported native range in Asia (South Korea), which when combined with data in GenBank indicates that this species was introduced to the Northwest Atlantic. The GenBank data further indicate that N. japonica was also introduced to North Carolina, Spain, Australia and New Zealand. Despite the fact that all three markers clearly delimited N. harveyi and N. japonica as distinct genetic species groups, the ITS sequences for some N. harveyi individuals displayed mixed patterns and additivity indicating introgression of nuclear DNA from N. japonica into N. harveyi in the Northwest Atlantic. Introgression of DNA from an introduced species to a native species (i.e. ‘genetic pollution’) is one of the possible consequences of species introductions, and we believe this is the first documented evidence for this phenomenon in red algae.
Experimental Dissection of Metalloproteinase Inhibition-Mediated and Toxic Effects of Phenanthroline on Zebrafish Development
(MDPI AG, 2016) Crawford, Bryan D.; Ellis, Tonya R.
Metalloproteinases are zinc-dependent endopeptidases that function as primary effectors of tissue remodeling, cell-signaling, and many other roles. Their regulation is ferociously complex, and is exquisitely sensitive to their molecular milieu, making in vivo studies challenging. Phenanthroline (PhN) is an inexpensive, broad-spectrum inhibitor of metalloproteinases that functions by chelating the catalytic zinc ion, however its use in vivo has been limited due to suspected off-target effects. PhN is very similar in structure to phenanthrene (PhE), a well-studied poly aromatic hydrocarbon (PAH) known to cause toxicity in aquatic animals by activating the aryl hydrocarbon receptor (AhR). We show that zebrafish are more sensitive to PhN than PhE, and that PhN causes a superset of the effects caused by PhE. Morpholino knock-down of the AhR rescues the effects of PhN that are shared with PhE, suggesting these are due to PAH toxicity. The effects of PhN that are not shared with PhE (specifically disruption of neural crest development and angiogenesis) involve processes known to depend on metalloproteinase activity. Furthermore these PhN-specific effects are not rescued by AhR knock-down, suggesting that these are bona fide effects of metalloproteinase inhibition, and that PhN can be used as a broad spectrum metalloproteinase inhibitor for studies with zebrafish in vivo.
First evidence of White-footed Deer Mouse (Peromyscus leucopus) on mainland New Brunswick, Canada
(Ottawa Field-Naturalists’ Club, 2022-01-21) Huynh, Howard M.; McAlpine, Donald F.; Pavey, Scott A.
White-footed Deer Mouse (Peromyscus leucopus) and the closely related, and more northerly ranging, Deer Mouse (Peromyscus maniculatus) broadly overlap in distribution and are often difficult to distinguish from each other. Based on molecular genetic data (cytochrome b gene), we report two new distribution records for P. leucopus for New Brunswick, Canada, the first mainland localities for this species in the province. Previous sampling of Peromyscus in New Brunswick may have overlooked the presence of P. leucopus, possibly because the specimens collected were all assumed to be P. maniculatus. However, current detection in New Brunswick may be part of a broader recent northward range expansion documented to be underway in P. leucopus. Although our use of a single mitochondrial gene to identify P. leucopus does not eliminate the possibility that the New Brunswick specimens are of hybrid origin, our results support the presence of P. leuco-pus in New Brunswick and suggest more detailed analyses will be required to determine the nature of any genetic interaction between P. leucopus and P. maniculatus in the province. Recognition of morphologically cryptic Peromyscus in southern New Brunswick also emphasizes the need to incorporate comprehensive methods to ensure the correct identification of speci-mens of this genus in Maritime Canada. We also note the potential implications of this discovery with respect to the incidence of Lyme disease in New Brunswick.
Genomic population structure of Striped Bass (Morone saxatilis) from the Gulf of St. Lawrence to Cape Fear River
(Wiley Open Access, 2020-07-14) LeBlanc, Nathalie M.; Gahagan, Benjamin I.; Andrews, Samuel N.; Avery, Trevor S.; Puncher, Gregory N.; Reading, Benjamin J.; Buhariwalla, Colin F.; Curry, R. Allen; Whiteley, Andrew R.; Pavey, Scott A.
Striped Bass, Morone saxatilis (Walbaum, 1792), is an anadromous fish species that supports fisheries throughout North America and is native to the North American Atlantic Coast. Due to long coastal migrations that span multiple jurisdictions, a detailed understanding of population genomics is required to untangle demographic patterns, understand local adaptation, and characterize population movements. This study used 1,256 single nucleotide polymorphism (SNP) loci to investigate genetic structure of 477 Striped Bass sampled from 15 locations spanning the North American Atlantic coast from the Gulf of St. Lawrence, Canada, to the Cape Fear River, United States. We found striking differences in neutral divergence among Canadian sites, which were isolated from each other and US populations, compared with US populations that were much less isolated. Our SNP dataset was able to assign 99% of Striped Bass back to six reporting groups, a 39% improvement over previous genetic markers. Using this method, we found (a) evidence of admixture within Saint John River, indicating that migrants from the United States and from Shubenacadie River occasionally spawn in the Saint John River; (b) Striped Bass collected in the Mira River, Cape Breton, Canada, were found to be of both Miramichi River and US origin; (c) juveniles in the newly restored Kennebec River population had small and nonsignificant differences from the Hudson River; and (d) tributaries within the Chesapeake Bay showed a mixture of homogeny and small differences among each other. This study introduces new hypotheses about the dynamic zoogeography of Striped Bass at its northern range and has important implications for the local and international management of this species.
Hydrodynamic Model Setup for the Saint John River at Mactaquac
(Canadian Rivers Institute, 2016)

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