A. Storfer - Academia.edu (original) (raw)

Papers by A. Storfer

Research paper thumbnail of Spontaneous Tumor Regression in Tasmanian Devils Associated with RASL11A Activation

Genetics

Spontaneous tumor regression has been documented in a small proportion of human cancer patients, ... more Spontaneous tumor regression has been documented in a small proportion of human cancer patients, but the specific mechanisms underlying tumor regression without treatment are not well-understood. Tasmanian devils are threatened with extinction from a transmissible cancer due to universal susceptibility and a near 100% case fatality rate. In over 10,000 cases, fewer than 20 instances of natural tumor regression have been detected. Previous work in this system has focused on Tasmanian devil genetic variation associated with the regression phenotype. Here, we used comparative and functional genomics to identify tumor genetic variation associated with tumor regression. We show that a single point mutation in the 5' untranslated region of the putative tumor suppressor RASL11A significantly contributes to tumor regression. RASL11A was expressed in regressed tumors but silenced in wild-type, non-regressed tumors, consistent with RASL11A down-regulation in human cancers. Induced RASL11A...

Research paper thumbnail of Spontaneous tumor regression in Tasmanian devils associated with RASL11A activation

Genetics, 2020

Spontaneous tumor regression has been documented in a small proportion of human cancer patients, ... more Spontaneous tumor regression has been documented in a small proportion of human cancer patients, but the specific mechanisms underlying tumor regression without treatment are not well-understood. Tasmanian devils are threatened with extinction from a transmissible cancer due to universal susceptibility and a near 100% case fatality rate. In over 10,000 cases, fewer than 20 instances of natural tumor regression have been detected. Previous work in this system has focused on Tasmanian devil genetic variation associated with the regression phenotype. Here, we used comparative and functional genomics to identify tumor genetic variation associated with tumor regression. We show that a single point mutation in the 5' untranslated region of the putative tumor suppressor RASL11A significantly contributes to tumor regression. RASL11A was expressed in regressed tumors but silenced in wild-type, non-regressed tumors, consistent with RASL11A down-regulation in human cancers. Induced RASL11A...

Research paper thumbnail of The Impact of the “all-of-the-above” Option and Student Ability on Multiple Choice Tests

International Journal for the Scholarship of Teaching and Learning

Research paper thumbnail of Amphibian breeding phenology and reproductive outcome: an examination using terrestrial and aquatic sampling

Canadian Journal of Zoology

Worldwide amphibian declines highlight the need for programs that monitor species presence and tr... more Worldwide amphibian declines highlight the need for programs that monitor species presence and track population trends. We sampled larval amphibians with a box trap at 3-week intervals for 23 months in eight wetlands, and concurrently trapped adults and juveniles with drift fences, to examine spatiotemporal patterns of tadpole occurrence; explore relationships between breeding effort, tadpole abundance, and recruitment; and compare the efficacy of both methods in detecting species presence and reproductive outcome. Intermittent detection of species within and among wetlands suggested high mortality, followed by deposition of new eggs and tadpole cohorts. Breeding effort, tadpole abundance, and juvenile recruitment were generally not correlated. The reasons for this may include differential bias in detecting species or life stages between methods and high incidence of egg or tadpole mortality. Drift fences detected more species than box traps, but each provided insights regarding amp...

Research paper thumbnail of Comparative Genomics of an Emerging Amphibian Virus

G3: Genes|Genomes|Genetics, 2015

Ranaviruses, a genus of the Iridoviridae, are large double-stranded DNA viruses that infect cold-... more Ranaviruses, a genus of the Iridoviridae, are large double-stranded DNA viruses that infect cold-blooded vertebrates worldwide. Ranaviruses have caused severe epizootics in commercial frog and fish populations, and are currently classified as notifiable pathogens in international trade. Previous work shows that a ranavirus that infects tiger salamanders throughout Western North America (Ambystoma tigrinum virus, or ATV) is in high prevalence among salamanders in the fishing bait trade. Bait ATV strains have elevated virulence and are transported long distances by humans, providing widespread opportunities for pathogen pollution. We sequenced the genomes of 15 strains of ATV collected from tiger salamanders across western North America and performed phylogenetic and population genomic analyses and tests for recombination. We find that ATV forms a monophyletic clade within the rest of the Ranaviruses and that it likely emerged within the last several thousand years, before human activities influenced its spread. We also identify several genes under strong positive selection, some of which appear to be involved in viral virulence and/or host immune evasion. In addition, we provide support for the pathogen pollution hypothesis with evidence of recombination among ATV strains, and potential bait-endemic strain recombination. KEYWORDS Ranavirus Ambystoma tigrinum virus range expansion Emerging infectious diseases are increasingly appreciated as a leading health concern for humans, wildlife, and economically important agricultural populations (Daszak et al. 2000; Smith et al. 2009). Indeed, pathogens are now listed as a leading cause of species' declines and extinctions (De Castro and Bolker 2005; Smith et al. 2006). Ranaviruses, a genus of the Iridoviridae, are globally-distributed pathogens of amphibians, reptiles and commercial fish species (Chinchar 2002; Miller et al. 2011). These large, double-stranded DNA viruses are considered emerging due to increases in incidence and geographic range over the last 30 years (Daszak et al. 2000; Chinchar 2002; Miller et al. 2011). Ranaviruses are now classified as notifiable pathogens in international trade because of their effects on commercial and wildlife populations (Schloegel et al. 2010). Pathogen pollution is of particular concern, whereby non-native ranavirus strains are introduced into host populations with which they have no evolutionary history, potentially leading to large scale epizootics (Cunningham et al. 2003). Phylogenetic analyses provide several lines of evidence for host switching events among the 10 completely sequenced Ranavirus genomes (Jancovich et al. 2010; Abrams et al. 2013). These analyses suggest that TFV (tiger frog virus) and GIV (grouper iridovirus) are likely strains of the geographically-distant FV3 (frog virus 3) and SGIV (Singapore grouper iridovirus), respectively (Chinchar et al. 2011). In addition, strains isolated from different vertebrate classes, such as STIV (soft-shelled turtle iridovirus; Reptilia) and FV3 (Amphibia) are very similar in genome organization, and, like RGV (Lei et al. 2012), both have truncated versions of the viral homolog of eukaryotic translational initiation factor 2a [vIF-2a (Huang et al. 2009; Tan et al. 2004)]. Additional phylogenetic analyses, combined with comparisons of genomic organization, suggest that the most recent common ancestor of all ranaviruses was a strain that infected fish (Jancovich et al. 2010; Chinchar et al. 2011). Evidence of a fishamphibian host switch comes from the strong collinearity of EHNV (epizootic hematopoietic necrosis virus; isolated from rainbow trout) and ATV (Ambystoma tigrinum virus, isolated from salamanders). A possible mechanism for host switching among vertebrate classes was inferred from evidence of positive selection on 12 ranavirus genes; six of these genes were apparently acquired as a result of host switches (Abrams et al. 2013).

Research paper thumbnail of Current Status, Future Opportunities, and Remaining Challenges in Landscape Genetics

Research paper thumbnail of Introduction to Landscape Genetics - Concepts, Methods, Applications

Research paper thumbnail of Landscape genetics and genetic structure of the southern torrent salamander, Rhyacotriton variegatus

Conservation Genetics, 2014

Research paper thumbnail of A test of the central-marginal hypothesis using population genetics and ecological niche modelling in an endemic salamander (Ambystoma barbouri)

Molecular ecology, 2015

The central-marginal hypothesis (CMH) predicts that population size, genetic diversity and geneti... more The central-marginal hypothesis (CMH) predicts that population size, genetic diversity and genetic connectivity are highest at the core and decrease near the edges of species' geographic distributions. We provide a test of the CMH using three replicated core-to-edge transects that encompass nearly the entire geographic range of the endemic streamside salamander (Ambystoma barbouri). We confirmed that the mapped core of the distribution was the most suitable habitat using ecological niche modelling (ENM) and via genetic estimates of effective population sizes. As predicted by the CMH, we found statistical support for decreased genetic diversity, effective population size and genetic connectivity from core to edge in western and northern transects, yet not along a southern transect. Based on our niche model, habitat suitability is lower towards the southern range edge, presumably leading to conflicting core-to-edge genetic patterns. These results suggest that multiple processes ma...

Research paper thumbnail of Rangewide landscape genetics of an endemic Pacific northwestern salamander

Molecular Ecology, 2013

A species&amp... more A species' genetic structure often varies in response to ecological and landscape processes that differ throughout the species' geographic range, yet landscape genetics studies are rarely spatially replicated. The Cope's giant salamander (Dicamptodon copei) is a neotenic, dispersal-limited amphibian with a restricted geographic range in the Pacific northwestern USA. We investigated which landscape factors affect D. copei gene flow in three regions spanning the species' range, which vary in climate, landcover and degree of anthropogenic disturbance. Least cost paths and Circuitscape resistance analyses revealed that gene flow patterns vary across the species' range, with unique combinations of landscape variables affecting gene flow in different regions. Populations in the northern coastal portions of the range had relatively high gene flow, largely facilitated by stream and river networks. Near the southeastern edge of the species' range, gene flow was more restricted overall, with relatively less facilitation by streams and more limitation by heat load index and fragmented forest cover. These results suggested that the landscape is more difficult for individuals to disperse through at the southeastern edge of the species' range, with terrestrial habitat desiccation factors becoming more limiting to gene flow. We suggest that caution be used when attempting to extrapolate landscape genetic models and conservation measures from one portion of a species' range to another.

Research paper thumbnail of Current and historical drivers of landscape genetic structure differ in core and peripheral salamander populations

PloS one, 2012

With predicted decreases in genetic diversity and greater genetic differentiation at range periph... more With predicted decreases in genetic diversity and greater genetic differentiation at range peripheries relative to their cores, it can be difficult to distinguish between the roles of current disturbance versus historic processes in shaping contemporary genetic patterns. To address this problem, we test for differences in historic demography and landscape genetic structure of coastal giant salamanders (Dicamptodon tenebrosus) in two core regions (Washington State, United States) versus the species' northern peripheral region (British Columbia, Canada) where the species is listed as threatened. Coalescent-based demographic simulations were consistent with a pattern of post-glacial range expansion, with both ancestral and current estimates of effective population size being much larger within the core region relative to the periphery. However, contrary to predictions of recent human-induced population decline in the less genetically diverse peripheral region, there was no genetic ...

Research paper thumbnail of Ecopathology of Ranaviruses Infecting Amphibians

Viruses, 2011

Ranaviruses are capable of infecting amphibians from at least 14 families and over 70 individual ... more Ranaviruses are capable of infecting amphibians from at least 14 families and over 70 individual species. Ranaviruses infect multiple cell types, often culminating in organ necrosis and massive hemorrhaging. Subclinical infections have been documented, although their role in ranavirus persistence and emergence remains unclear. Water is an effective transmission medium for ranaviruses, and survival outside the host may be for significant duration. In aquatic communities, amphibians, reptiles and fish may serve as reservoirs. Controlled studies have shown that susceptibility to ranavirus infection and disease varies among amphibian species and developmental stages, and likely is impacted by host-pathogen coevolution, as well as, exogenous environmental factors. Field studies have demonstrated that the likelihood of epizootics is increased in areas of cattle grazing, where aquatic vegetation is sparse and water quality is poor. Translocation of infected amphibians through commercial trade (e.g., food, fish bait, pet industry) contributes to the spread of ranaviruses. Such introductions may be of particular concern, as several studies report that ranaviruses isolated from ranaculture, aquaculture, and bait facilities have greater virulence (i.e., ability to cause disease) than wild-type isolates. Future investigations should focus on the genetic basis for pathogen virulence and host susceptibility, ecological and anthropogenic mechanisms contributing to emergence, and vaccine development for use in captive populations and species reintroduction programs.

Research paper thumbnail of Comparative landscape genetics of two river frog species occurring at different elevations on Mount Kilimanjaro

Molecular Ecology, 2014

Estimating population connectivity and species&am... more Estimating population connectivity and species' abilities to disperse across the landscape is crucial for understanding the long-term persistence of species in changing environments. Surprisingly, few landscape genetic studies focused on tropical regions despite the alarming extinction rates within these ecosystems. Here, we compared the influence of landscape features on the distribution of genetic variation of an Afromontane frog, Amietia wittei, with that of its more broadly distributed lowland congener, Amietia angolensis, on Mt. Kilimanjaro, Tanzania. We predicted high gene flow in the montane species with movements enhanced through terrestrial habitats of the continuous rainforest. In contrast, dispersal might be restricted to aquatic corridors and reduced by anthropogenic disturbance in the lowland species. We found high gene flow in A. wittei relative to other montane amphibians. Nonetheless, gene flow was lower than in the lowland species which showed little population structure. Least-cost path analysis suggested that dispersal is facilitated by stream networks in both species, but different landscape features were identified to influence connectivity among populations. Contrary to a previous study, gene flow in the lowland species was negatively correlated with the presence of human settlements. Also, genetic subdivision in A. wittei did not coincide with specific physical barriers as in other landscape genetic studies, suggesting that factors other than topography may contribute to population divergence. Overall, these results highlight the importance of a comparative landscape genetic approach for assessing the influence of the landscape matrix on population connectivity, particularly because nonintuitive results can alter the course of conservation and management.

Research paper thumbnail of BioOne Online Journals - Evidence for Introgression in the

Research paper thumbnail of Quantitative genetics: a promising approach for the assessment of genetic variation in endangered species

Trends in Ecology & Evolution, 1996

genetic variation is correlated to the ability of a population to survive in a changing environme... more genetic variation is correlated to the ability of a population to survive in a changing environment can all dictate which tech

Research paper thumbnail of Correlations of Life-History and Distributional-Range Variation with Salamander Diversification Rates: Evidence for Species Selection

Systematic Biology, 2011

Evolutionary biologists have long debated the relative influence of species selection on evolutio... more Evolutionary biologists have long debated the relative influence of species selection on evolutionary patterns. As a test, we apply a statistical phylogenetic approach to evaluate the influence of traits related to species distribution and life-history characteristics on patterns of diversification in salamanders. We use independent contrasts to test traitmediated diversification while accommodating phylogenetic uncertainty in relationships among all salamander families. Using a neontological data set, we find several species-level traits to be variable, heritable, and associated with differential success (i.e., higher diversification rates) at higher taxonomic categories. Specifically, the macroecological trait of small geographic-range size is strongly correlated with a higher rate of net diversification. We further consider the role that plasticity in life-history traits appears to fulfill in macroevolutionary processes of lineage divergence and durability. We find that pedotypy-wherein some, but not all, organisms of a species mature in the gilled form without metamorphosing-is also associated with higher net diversification rate than is the absence of developmental plasticity. Often dismissed as an insignificant process in evolution, we provide direct evidence for the role of species selection in lineage diversification of salamanders. [Geographic range; heterochrony; pedomorphosis; pedomorphy; phylogenetic heritability; species sorting.]

Research paper thumbnail of New Microsatellite Markers for Examining Genetic Variation in Peripheral and Core Populations of the Coastal Giant Salamander (Dicamptodon tenebrosus)

PLoS ONE, 2010

The Coastal Giant Salamander (Dicamptodon tenebrosus) is classified as threatened at the northern... more The Coastal Giant Salamander (Dicamptodon tenebrosus) is classified as threatened at the northern periphery of its range in British Columbia (BC), Canada, primarily due to forestry practices and habitat fragmentation. Characterising dispersal behaviour and population connectivity is therefore a priority for this region, while genetic differentiation in core versus peripheral locations remains unstudied in this wide-ranging species. We present seven new polymorphic microsatellite markers for use in population genetic analyses of D. tenebrosus. We examine locus characteristics and genetic variation in 12 streams at the species' northern range limit in BC, and within two regions representing sub-peripheral (North Cascades) and core localities (South Cascades) in Washington State, United States. In BC, the number of alleles per locus ranged from 2-5 and observed heterozygosity ranged from 0.044-0.825. Genetic differentiation was highest between BC and the South Cascades, and intermediate between BC and the North Cascades. Across loci, mean allelic richness was similar across regions, while private allelic richness was highest in the core locality (corrected for sample size). These new microsatellite loci will be a valuable addition to existing markers for detailed landscape and population genetic analyses of D. tenebrosus across its range.

Research paper thumbnail of Newly developed polymorphic microsatellite markers for frogs of the genus Ascaphus

Molecular Ecology Resources, 2008

Thirteen polymorphic microsatellite loci were identified and developed for the coastal tailed fro... more Thirteen polymorphic microsatellite loci were identified and developed for the coastal tailed frog, Ascaphus truei, from sites within the Olympic Peninsula of Washington, USA. These tetranucleotide repeat loci were highly variable, averaging 19 alleles per locus and expected heterozygosity of 0.91. In addition, these loci cross-amplify in the sister species, Ascaphus montanus. These markers will prove useful in identifying fine-scale genetic structure, as well as provide insight into the evolution and conservation of this group across fragmented landscapes.

Research paper thumbnail of Polymorphic tetranucleotide microsatellites for Cope's giant salamander ( Dicamptodon copei ) and Pacific giant salamander ( Dicamptodon tenebrosus )

Molecular Ecology Resources, 2008

We present primers and amplification conditions for 15 microsatellite loci developed for the Cope... more We present primers and amplification conditions for 15 microsatellite loci developed for the Cope's giant salamander (Dicamptodon copei), 14 of which are tetranucleotide repeats. Cross-species amplification revealed 10 of these loci to also be polymorphic in the Pacific giant salamander (Dicamptodon tenebrosus). Several loci produced nonoverlapping allelic ranges between the two species and may be useful in species identification. These polymorphic microsatellite loci are potentially useful for future studies of population genetics in dicamptodontid salamanders.

Research paper thumbnail of Characterization of 10 microsatellite markers for the understorey Amazonian herb Heliconia acuminata

Molecular Ecology Resources, 2009

We characterized 10 microsatellite loci for the plant Heliconia acuminata from the Biological Dyn... more We characterized 10 microsatellite loci for the plant Heliconia acuminata from the Biological Dynamics of Forest Fragments Project (Manaus, Brazil). Markers were screened in 61 individuals from one population and were found to be polymorphic with an average of eight alleles per locus. We found moderate to high levels of polymorphic information content, and observed and expected heterozygosities. All 10 markers are suitable for spatial genetic structure and parentage analyses and will be used for understanding H. acuminata dynamics across a fragmented landscape.

Research paper thumbnail of Spontaneous Tumor Regression in Tasmanian Devils Associated with RASL11A Activation

Genetics

Spontaneous tumor regression has been documented in a small proportion of human cancer patients, ... more Spontaneous tumor regression has been documented in a small proportion of human cancer patients, but the specific mechanisms underlying tumor regression without treatment are not well-understood. Tasmanian devils are threatened with extinction from a transmissible cancer due to universal susceptibility and a near 100% case fatality rate. In over 10,000 cases, fewer than 20 instances of natural tumor regression have been detected. Previous work in this system has focused on Tasmanian devil genetic variation associated with the regression phenotype. Here, we used comparative and functional genomics to identify tumor genetic variation associated with tumor regression. We show that a single point mutation in the 5' untranslated region of the putative tumor suppressor RASL11A significantly contributes to tumor regression. RASL11A was expressed in regressed tumors but silenced in wild-type, non-regressed tumors, consistent with RASL11A down-regulation in human cancers. Induced RASL11A...

Research paper thumbnail of Spontaneous tumor regression in Tasmanian devils associated with RASL11A activation

Genetics, 2020

Spontaneous tumor regression has been documented in a small proportion of human cancer patients, ... more Spontaneous tumor regression has been documented in a small proportion of human cancer patients, but the specific mechanisms underlying tumor regression without treatment are not well-understood. Tasmanian devils are threatened with extinction from a transmissible cancer due to universal susceptibility and a near 100% case fatality rate. In over 10,000 cases, fewer than 20 instances of natural tumor regression have been detected. Previous work in this system has focused on Tasmanian devil genetic variation associated with the regression phenotype. Here, we used comparative and functional genomics to identify tumor genetic variation associated with tumor regression. We show that a single point mutation in the 5' untranslated region of the putative tumor suppressor RASL11A significantly contributes to tumor regression. RASL11A was expressed in regressed tumors but silenced in wild-type, non-regressed tumors, consistent with RASL11A down-regulation in human cancers. Induced RASL11A...

Research paper thumbnail of The Impact of the “all-of-the-above” Option and Student Ability on Multiple Choice Tests

International Journal for the Scholarship of Teaching and Learning

Research paper thumbnail of Amphibian breeding phenology and reproductive outcome: an examination using terrestrial and aquatic sampling

Canadian Journal of Zoology

Worldwide amphibian declines highlight the need for programs that monitor species presence and tr... more Worldwide amphibian declines highlight the need for programs that monitor species presence and track population trends. We sampled larval amphibians with a box trap at 3-week intervals for 23 months in eight wetlands, and concurrently trapped adults and juveniles with drift fences, to examine spatiotemporal patterns of tadpole occurrence; explore relationships between breeding effort, tadpole abundance, and recruitment; and compare the efficacy of both methods in detecting species presence and reproductive outcome. Intermittent detection of species within and among wetlands suggested high mortality, followed by deposition of new eggs and tadpole cohorts. Breeding effort, tadpole abundance, and juvenile recruitment were generally not correlated. The reasons for this may include differential bias in detecting species or life stages between methods and high incidence of egg or tadpole mortality. Drift fences detected more species than box traps, but each provided insights regarding amp...

Research paper thumbnail of Comparative Genomics of an Emerging Amphibian Virus

G3: Genes|Genomes|Genetics, 2015

Ranaviruses, a genus of the Iridoviridae, are large double-stranded DNA viruses that infect cold-... more Ranaviruses, a genus of the Iridoviridae, are large double-stranded DNA viruses that infect cold-blooded vertebrates worldwide. Ranaviruses have caused severe epizootics in commercial frog and fish populations, and are currently classified as notifiable pathogens in international trade. Previous work shows that a ranavirus that infects tiger salamanders throughout Western North America (Ambystoma tigrinum virus, or ATV) is in high prevalence among salamanders in the fishing bait trade. Bait ATV strains have elevated virulence and are transported long distances by humans, providing widespread opportunities for pathogen pollution. We sequenced the genomes of 15 strains of ATV collected from tiger salamanders across western North America and performed phylogenetic and population genomic analyses and tests for recombination. We find that ATV forms a monophyletic clade within the rest of the Ranaviruses and that it likely emerged within the last several thousand years, before human activities influenced its spread. We also identify several genes under strong positive selection, some of which appear to be involved in viral virulence and/or host immune evasion. In addition, we provide support for the pathogen pollution hypothesis with evidence of recombination among ATV strains, and potential bait-endemic strain recombination. KEYWORDS Ranavirus Ambystoma tigrinum virus range expansion Emerging infectious diseases are increasingly appreciated as a leading health concern for humans, wildlife, and economically important agricultural populations (Daszak et al. 2000; Smith et al. 2009). Indeed, pathogens are now listed as a leading cause of species' declines and extinctions (De Castro and Bolker 2005; Smith et al. 2006). Ranaviruses, a genus of the Iridoviridae, are globally-distributed pathogens of amphibians, reptiles and commercial fish species (Chinchar 2002; Miller et al. 2011). These large, double-stranded DNA viruses are considered emerging due to increases in incidence and geographic range over the last 30 years (Daszak et al. 2000; Chinchar 2002; Miller et al. 2011). Ranaviruses are now classified as notifiable pathogens in international trade because of their effects on commercial and wildlife populations (Schloegel et al. 2010). Pathogen pollution is of particular concern, whereby non-native ranavirus strains are introduced into host populations with which they have no evolutionary history, potentially leading to large scale epizootics (Cunningham et al. 2003). Phylogenetic analyses provide several lines of evidence for host switching events among the 10 completely sequenced Ranavirus genomes (Jancovich et al. 2010; Abrams et al. 2013). These analyses suggest that TFV (tiger frog virus) and GIV (grouper iridovirus) are likely strains of the geographically-distant FV3 (frog virus 3) and SGIV (Singapore grouper iridovirus), respectively (Chinchar et al. 2011). In addition, strains isolated from different vertebrate classes, such as STIV (soft-shelled turtle iridovirus; Reptilia) and FV3 (Amphibia) are very similar in genome organization, and, like RGV (Lei et al. 2012), both have truncated versions of the viral homolog of eukaryotic translational initiation factor 2a [vIF-2a (Huang et al. 2009; Tan et al. 2004)]. Additional phylogenetic analyses, combined with comparisons of genomic organization, suggest that the most recent common ancestor of all ranaviruses was a strain that infected fish (Jancovich et al. 2010; Chinchar et al. 2011). Evidence of a fishamphibian host switch comes from the strong collinearity of EHNV (epizootic hematopoietic necrosis virus; isolated from rainbow trout) and ATV (Ambystoma tigrinum virus, isolated from salamanders). A possible mechanism for host switching among vertebrate classes was inferred from evidence of positive selection on 12 ranavirus genes; six of these genes were apparently acquired as a result of host switches (Abrams et al. 2013).

Research paper thumbnail of Current Status, Future Opportunities, and Remaining Challenges in Landscape Genetics

Research paper thumbnail of Introduction to Landscape Genetics - Concepts, Methods, Applications

Research paper thumbnail of Landscape genetics and genetic structure of the southern torrent salamander, Rhyacotriton variegatus

Conservation Genetics, 2014

Research paper thumbnail of A test of the central-marginal hypothesis using population genetics and ecological niche modelling in an endemic salamander (Ambystoma barbouri)

Molecular ecology, 2015

The central-marginal hypothesis (CMH) predicts that population size, genetic diversity and geneti... more The central-marginal hypothesis (CMH) predicts that population size, genetic diversity and genetic connectivity are highest at the core and decrease near the edges of species' geographic distributions. We provide a test of the CMH using three replicated core-to-edge transects that encompass nearly the entire geographic range of the endemic streamside salamander (Ambystoma barbouri). We confirmed that the mapped core of the distribution was the most suitable habitat using ecological niche modelling (ENM) and via genetic estimates of effective population sizes. As predicted by the CMH, we found statistical support for decreased genetic diversity, effective population size and genetic connectivity from core to edge in western and northern transects, yet not along a southern transect. Based on our niche model, habitat suitability is lower towards the southern range edge, presumably leading to conflicting core-to-edge genetic patterns. These results suggest that multiple processes ma...

Research paper thumbnail of Rangewide landscape genetics of an endemic Pacific northwestern salamander

Molecular Ecology, 2013

A species&amp... more A species' genetic structure often varies in response to ecological and landscape processes that differ throughout the species' geographic range, yet landscape genetics studies are rarely spatially replicated. The Cope's giant salamander (Dicamptodon copei) is a neotenic, dispersal-limited amphibian with a restricted geographic range in the Pacific northwestern USA. We investigated which landscape factors affect D. copei gene flow in three regions spanning the species' range, which vary in climate, landcover and degree of anthropogenic disturbance. Least cost paths and Circuitscape resistance analyses revealed that gene flow patterns vary across the species' range, with unique combinations of landscape variables affecting gene flow in different regions. Populations in the northern coastal portions of the range had relatively high gene flow, largely facilitated by stream and river networks. Near the southeastern edge of the species' range, gene flow was more restricted overall, with relatively less facilitation by streams and more limitation by heat load index and fragmented forest cover. These results suggested that the landscape is more difficult for individuals to disperse through at the southeastern edge of the species' range, with terrestrial habitat desiccation factors becoming more limiting to gene flow. We suggest that caution be used when attempting to extrapolate landscape genetic models and conservation measures from one portion of a species' range to another.

Research paper thumbnail of Current and historical drivers of landscape genetic structure differ in core and peripheral salamander populations

PloS one, 2012

With predicted decreases in genetic diversity and greater genetic differentiation at range periph... more With predicted decreases in genetic diversity and greater genetic differentiation at range peripheries relative to their cores, it can be difficult to distinguish between the roles of current disturbance versus historic processes in shaping contemporary genetic patterns. To address this problem, we test for differences in historic demography and landscape genetic structure of coastal giant salamanders (Dicamptodon tenebrosus) in two core regions (Washington State, United States) versus the species' northern peripheral region (British Columbia, Canada) where the species is listed as threatened. Coalescent-based demographic simulations were consistent with a pattern of post-glacial range expansion, with both ancestral and current estimates of effective population size being much larger within the core region relative to the periphery. However, contrary to predictions of recent human-induced population decline in the less genetically diverse peripheral region, there was no genetic ...

Research paper thumbnail of Ecopathology of Ranaviruses Infecting Amphibians

Viruses, 2011

Ranaviruses are capable of infecting amphibians from at least 14 families and over 70 individual ... more Ranaviruses are capable of infecting amphibians from at least 14 families and over 70 individual species. Ranaviruses infect multiple cell types, often culminating in organ necrosis and massive hemorrhaging. Subclinical infections have been documented, although their role in ranavirus persistence and emergence remains unclear. Water is an effective transmission medium for ranaviruses, and survival outside the host may be for significant duration. In aquatic communities, amphibians, reptiles and fish may serve as reservoirs. Controlled studies have shown that susceptibility to ranavirus infection and disease varies among amphibian species and developmental stages, and likely is impacted by host-pathogen coevolution, as well as, exogenous environmental factors. Field studies have demonstrated that the likelihood of epizootics is increased in areas of cattle grazing, where aquatic vegetation is sparse and water quality is poor. Translocation of infected amphibians through commercial trade (e.g., food, fish bait, pet industry) contributes to the spread of ranaviruses. Such introductions may be of particular concern, as several studies report that ranaviruses isolated from ranaculture, aquaculture, and bait facilities have greater virulence (i.e., ability to cause disease) than wild-type isolates. Future investigations should focus on the genetic basis for pathogen virulence and host susceptibility, ecological and anthropogenic mechanisms contributing to emergence, and vaccine development for use in captive populations and species reintroduction programs.

Research paper thumbnail of Comparative landscape genetics of two river frog species occurring at different elevations on Mount Kilimanjaro

Molecular Ecology, 2014

Estimating population connectivity and species&am... more Estimating population connectivity and species' abilities to disperse across the landscape is crucial for understanding the long-term persistence of species in changing environments. Surprisingly, few landscape genetic studies focused on tropical regions despite the alarming extinction rates within these ecosystems. Here, we compared the influence of landscape features on the distribution of genetic variation of an Afromontane frog, Amietia wittei, with that of its more broadly distributed lowland congener, Amietia angolensis, on Mt. Kilimanjaro, Tanzania. We predicted high gene flow in the montane species with movements enhanced through terrestrial habitats of the continuous rainforest. In contrast, dispersal might be restricted to aquatic corridors and reduced by anthropogenic disturbance in the lowland species. We found high gene flow in A. wittei relative to other montane amphibians. Nonetheless, gene flow was lower than in the lowland species which showed little population structure. Least-cost path analysis suggested that dispersal is facilitated by stream networks in both species, but different landscape features were identified to influence connectivity among populations. Contrary to a previous study, gene flow in the lowland species was negatively correlated with the presence of human settlements. Also, genetic subdivision in A. wittei did not coincide with specific physical barriers as in other landscape genetic studies, suggesting that factors other than topography may contribute to population divergence. Overall, these results highlight the importance of a comparative landscape genetic approach for assessing the influence of the landscape matrix on population connectivity, particularly because nonintuitive results can alter the course of conservation and management.

Research paper thumbnail of BioOne Online Journals - Evidence for Introgression in the

Research paper thumbnail of Quantitative genetics: a promising approach for the assessment of genetic variation in endangered species

Trends in Ecology & Evolution, 1996

genetic variation is correlated to the ability of a population to survive in a changing environme... more genetic variation is correlated to the ability of a population to survive in a changing environment can all dictate which tech

Research paper thumbnail of Correlations of Life-History and Distributional-Range Variation with Salamander Diversification Rates: Evidence for Species Selection

Systematic Biology, 2011

Evolutionary biologists have long debated the relative influence of species selection on evolutio... more Evolutionary biologists have long debated the relative influence of species selection on evolutionary patterns. As a test, we apply a statistical phylogenetic approach to evaluate the influence of traits related to species distribution and life-history characteristics on patterns of diversification in salamanders. We use independent contrasts to test traitmediated diversification while accommodating phylogenetic uncertainty in relationships among all salamander families. Using a neontological data set, we find several species-level traits to be variable, heritable, and associated with differential success (i.e., higher diversification rates) at higher taxonomic categories. Specifically, the macroecological trait of small geographic-range size is strongly correlated with a higher rate of net diversification. We further consider the role that plasticity in life-history traits appears to fulfill in macroevolutionary processes of lineage divergence and durability. We find that pedotypy-wherein some, but not all, organisms of a species mature in the gilled form without metamorphosing-is also associated with higher net diversification rate than is the absence of developmental plasticity. Often dismissed as an insignificant process in evolution, we provide direct evidence for the role of species selection in lineage diversification of salamanders. [Geographic range; heterochrony; pedomorphosis; pedomorphy; phylogenetic heritability; species sorting.]

Research paper thumbnail of New Microsatellite Markers for Examining Genetic Variation in Peripheral and Core Populations of the Coastal Giant Salamander (Dicamptodon tenebrosus)

PLoS ONE, 2010

The Coastal Giant Salamander (Dicamptodon tenebrosus) is classified as threatened at the northern... more The Coastal Giant Salamander (Dicamptodon tenebrosus) is classified as threatened at the northern periphery of its range in British Columbia (BC), Canada, primarily due to forestry practices and habitat fragmentation. Characterising dispersal behaviour and population connectivity is therefore a priority for this region, while genetic differentiation in core versus peripheral locations remains unstudied in this wide-ranging species. We present seven new polymorphic microsatellite markers for use in population genetic analyses of D. tenebrosus. We examine locus characteristics and genetic variation in 12 streams at the species' northern range limit in BC, and within two regions representing sub-peripheral (North Cascades) and core localities (South Cascades) in Washington State, United States. In BC, the number of alleles per locus ranged from 2-5 and observed heterozygosity ranged from 0.044-0.825. Genetic differentiation was highest between BC and the South Cascades, and intermediate between BC and the North Cascades. Across loci, mean allelic richness was similar across regions, while private allelic richness was highest in the core locality (corrected for sample size). These new microsatellite loci will be a valuable addition to existing markers for detailed landscape and population genetic analyses of D. tenebrosus across its range.

Research paper thumbnail of Newly developed polymorphic microsatellite markers for frogs of the genus Ascaphus

Molecular Ecology Resources, 2008

Thirteen polymorphic microsatellite loci were identified and developed for the coastal tailed fro... more Thirteen polymorphic microsatellite loci were identified and developed for the coastal tailed frog, Ascaphus truei, from sites within the Olympic Peninsula of Washington, USA. These tetranucleotide repeat loci were highly variable, averaging 19 alleles per locus and expected heterozygosity of 0.91. In addition, these loci cross-amplify in the sister species, Ascaphus montanus. These markers will prove useful in identifying fine-scale genetic structure, as well as provide insight into the evolution and conservation of this group across fragmented landscapes.

Research paper thumbnail of Polymorphic tetranucleotide microsatellites for Cope's giant salamander ( Dicamptodon copei ) and Pacific giant salamander ( Dicamptodon tenebrosus )

Molecular Ecology Resources, 2008

We present primers and amplification conditions for 15 microsatellite loci developed for the Cope... more We present primers and amplification conditions for 15 microsatellite loci developed for the Cope's giant salamander (Dicamptodon copei), 14 of which are tetranucleotide repeats. Cross-species amplification revealed 10 of these loci to also be polymorphic in the Pacific giant salamander (Dicamptodon tenebrosus). Several loci produced nonoverlapping allelic ranges between the two species and may be useful in species identification. These polymorphic microsatellite loci are potentially useful for future studies of population genetics in dicamptodontid salamanders.

Research paper thumbnail of Characterization of 10 microsatellite markers for the understorey Amazonian herb Heliconia acuminata

Molecular Ecology Resources, 2009

We characterized 10 microsatellite loci for the plant Heliconia acuminata from the Biological Dyn... more We characterized 10 microsatellite loci for the plant Heliconia acuminata from the Biological Dynamics of Forest Fragments Project (Manaus, Brazil). Markers were screened in 61 individuals from one population and were found to be polymorphic with an average of eight alleles per locus. We found moderate to high levels of polymorphic information content, and observed and expected heterozygosities. All 10 markers are suitable for spatial genetic structure and parentage analyses and will be used for understanding H. acuminata dynamics across a fragmented landscape.