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Michael A. Russello
Department of Biology University of British Columbia Kelowna BC Canada

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Original research
Published: 23 August 2021 in Ecology and Evolution
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Human-mediated habitat fragmentation in freshwater ecosystems can negatively impact genetic diversity, demography, and life history of native biota, while disrupting the behavior of species that are dependent on spatial connectivity to complete their life cycles. In the Alouette River system (British Columbia, Canada), dam construction in 1928 impacted passage of anadromous sockeye salmon (Oncorhynchus nerka), with the last records of migrants occurring in the 1930s. Since that time, O. nerka persisted as a resident population in Alouette Reservoir until experimental water releases beginning in 2005 created conditions for migration; two years later, returning migrants were observed for the first time in ~70 years, raising important basic and applied questions regarding life-history variation and population structure in this system. Here, we investigated the genetic distinctiveness and population history of Alouette Reservoir O. nerka using genome-wide SNP data (n = 7,709 loci) collected for resident and migrant individuals, as well as for neighboring anadromous sockeye salmon and resident kokanee populations within the Fraser River drainage (n = 312 individuals). Bayesian clustering and principal components analyses based on neutral loci revealed five distinct clusters, largely associated with geography, and clearly demonstrated that Alouette Reservoir resident and migrant individuals are genetically distinct from other O. nerka populations in the Fraser River drainage. At a finer level, there was no clear evidence for differentiation between Alouette Reservoir residents and migrants; although we detected eight high-confidence outlier loci, they all mapped to sex chromosomes suggesting that differences were likely due to uneven sex ratios rather than life history. Taken together, these data suggest that contemporary Alouette Reservoir O. nerka represents a landlocked sockeye salmon population, constituting the first reported instance of deep-water spawning behavior associated with this life-history form. This finding punctuates the need for reassessment of conservation status and supports ongoing fisheries management activities in Alouette Reservoir.

ACS Style

Farida Samad‐Zada; Brett T. van Poorten; Shannon Harris; Lyse Godbout; Michael A. Russello. Genome‐wide analysis reveals demographic and life‐history patterns associated with habitat modification in landlocked, deep‐spawning sockeye salmon ( Oncorhynchus nerka ). Ecology and Evolution 2021, 1 .

AMA Style

Farida Samad‐Zada, Brett T. van Poorten, Shannon Harris, Lyse Godbout, Michael A. Russello. Genome‐wide analysis reveals demographic and life‐history patterns associated with habitat modification in landlocked, deep‐spawning sockeye salmon ( Oncorhynchus nerka ). Ecology and Evolution. 2021; ():1.

Chicago/Turabian Style

Farida Samad‐Zada; Brett T. van Poorten; Shannon Harris; Lyse Godbout; Michael A. Russello. 2021. "Genome‐wide analysis reveals demographic and life‐history patterns associated with habitat modification in landlocked, deep‐spawning sockeye salmon ( Oncorhynchus nerka )." Ecology and Evolution , no. : 1.

Journal article
Published: 17 August 2021 in Diversity
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A key aspect in the conservation of endangered populations is understanding patterns of genetic variation and structure, which can provide managers with critical information to support evidence-based status assessments and management strategies. This is especially important for species with small wild and larger captive populations, as found in many endangered parrots. We used genotypic data to assess genetic variation and structure in wild and captive populations of two endangered parrots, the blue-throated macaw, Ara glaucogularis, of Bolivia, and the thick-billed parrot, Rhynchopsitta pachyrhyncha, of Mexico. In the blue-throated macaw, we found evidence of weak genetic differentiation between wild northern and southern subpopulations, and between wild and captive populations. In the thick-billed parrot we found no signal of differentiation between the Madera and Tutuaca breeding colonies or between wild and captive populations. Similar levels of genetic diversity were detected in the wild and captive populations of both species, with private alleles detected in captivity in both, and in the wild in the thick-billed parrot. We found genetic signatures of a bottleneck in the northern blue-throated macaw subpopulation, but no such signal was identified in any other subpopulation of either species. Our results suggest both species could potentially benefit from reintroduction of genetic variation found in captivity, and emphasize the need for genetic management of captive populations.

ACS Style

Carlos I. Campos; Melinda A. Martinez; Daniel Acosta; Jose A. Diaz-Luque; Igor Berkunsky; Nadine L. Lamberski; Javier Cruz-Nieto; Michael A. Russello; Timothy F. Wright. Genetic Diversity and Population Structure of Two Endangered Neotropical Parrots Inform In Situ and Ex Situ Conservation Strategies. Diversity 2021, 13, 386 .

AMA Style

Carlos I. Campos, Melinda A. Martinez, Daniel Acosta, Jose A. Diaz-Luque, Igor Berkunsky, Nadine L. Lamberski, Javier Cruz-Nieto, Michael A. Russello, Timothy F. Wright. Genetic Diversity and Population Structure of Two Endangered Neotropical Parrots Inform In Situ and Ex Situ Conservation Strategies. Diversity. 2021; 13 (8):386.

Chicago/Turabian Style

Carlos I. Campos; Melinda A. Martinez; Daniel Acosta; Jose A. Diaz-Luque; Igor Berkunsky; Nadine L. Lamberski; Javier Cruz-Nieto; Michael A. Russello; Timothy F. Wright. 2021. "Genetic Diversity and Population Structure of Two Endangered Neotropical Parrots Inform In Situ and Ex Situ Conservation Strategies." Diversity 13, no. 8: 386.

Author correction
Published: 25 May 2021 in Communications Biology
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E. Hekkala; J. Gatesy; A. Narechania; R. Meredith; M. Russello; M. L. Aardema; E. Jensen; S. Montanari; C. Brochu; M. Norell; G. Amato. Author Correction: Paleogenomics illuminates the evolutionary history of the extinct Holocene “horned” crocodile of Madagascar, Voay robustus. Communications Biology 2021, 4, 1 -1.

AMA Style

E. Hekkala, J. Gatesy, A. Narechania, R. Meredith, M. Russello, M. L. Aardema, E. Jensen, S. Montanari, C. Brochu, M. Norell, G. Amato. Author Correction: Paleogenomics illuminates the evolutionary history of the extinct Holocene “horned” crocodile of Madagascar, Voay robustus. Communications Biology. 2021; 4 (1):1-1.

Chicago/Turabian Style

E. Hekkala; J. Gatesy; A. Narechania; R. Meredith; M. Russello; M. L. Aardema; E. Jensen; S. Montanari; C. Brochu; M. Norell; G. Amato. 2021. "Author Correction: Paleogenomics illuminates the evolutionary history of the extinct Holocene “horned” crocodile of Madagascar, Voay robustus." Communications Biology 4, no. 1: 1-1.

Journal article
Published: 27 April 2021 in Communications Biology
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Ancient DNA is transforming our ability to reconstruct historical patterns and mechanisms shaping modern diversity and distributions. In particular, molecular data from extinct Holocene island faunas have revealed surprising biogeographic scenarios. Here, we recovered partial mitochondrial (mt) genomes for 1300–1400 year old specimens (n = 2) of the extinct “horned” crocodile, Voay robustus, collected from Holocene deposits in southwestern Madagascar. Phylogenetic analyses of partial mt genomes and tip-dated timetrees based on molecular, fossil, and stratigraphic data favor a sister group relationship between Voay and Crocodylus (true crocodiles). These well supported trees conflict with recent morphological systematic work that has consistently placed Voay within Osteolaeminae (dwarf crocodiles and kin) and provide evidence for likely homoplasy in crocodylian cranial anatomy and snout shape. The close relationship between Voay and Crocodylus lends additional context for understanding the biogeographic origins of these genera and refines competing hypotheses for the recent extinction of Voay from Madagascar.

ACS Style

E. Hekkala; J. Gatesy; A. Narechania; R. Meredith; M. Russello; M. L. Aardema; E. Jensen; S. Montanari; C. Brochu; M. Norell; G. Amato. Paleogenomics illuminates the evolutionary history of the extinct Holocene “horned” crocodile of Madagascar, Voay robustus. Communications Biology 2021, 4, 1 -11.

AMA Style

E. Hekkala, J. Gatesy, A. Narechania, R. Meredith, M. Russello, M. L. Aardema, E. Jensen, S. Montanari, C. Brochu, M. Norell, G. Amato. Paleogenomics illuminates the evolutionary history of the extinct Holocene “horned” crocodile of Madagascar, Voay robustus. Communications Biology. 2021; 4 (1):1-11.

Chicago/Turabian Style

E. Hekkala; J. Gatesy; A. Narechania; R. Meredith; M. Russello; M. L. Aardema; E. Jensen; S. Montanari; C. Brochu; M. Norell; G. Amato. 2021. "Paleogenomics illuminates the evolutionary history of the extinct Holocene “horned” crocodile of Madagascar, Voay robustus." Communications Biology 4, no. 1: 1-11.

Research article
Published: 22 October 2020 in Biological Invasions
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Brown rats (Rattus norvegicus) have commensally spread from northern China and Mongolia to become among the most invasive species on the planet. Understanding the proximate source(s) of invasion can inform biosecurity plans and eradication strategies for preventing or mitigating impacts to native biodiversity. The Haida Gwaii archipelago, located off the coast of British Columbia, Canada, is a significant nesting site for 1.5 million seabirds across 12 species, half of which are now threatened by brown rats. Local knowledge points to a European origin in the late 1800’s to early 1900’s, though the true source(s) and firm date(s) of invasion remain unknown. To fill these knowledge gaps, we analyzed genotypic data (16,598 SNPs) for 280 brown rats sampled throughout Haida Gwaii relative to a published global database of potential source populations. Principle component analysis and population assignment tests supported multiple potential invasion sources from Europe and North America. Likewise, demographic modelling best supported two invasions into the islands. The first invasion likely occurred in the early 1900’s into the south-central archipelago from Western Europe followed by a more recent invasion in the early 2000’s from Vancouver, British Columbia, into northern Haida Gwaii. The northern invasion of Haida Gwaii could also be indicative of contemporary gene flow between Haida Gwaii and the mainland, representing a significant biosecurity risk. Our results will inform management strategies for invasive rats in Haida Gwaii and serve as a guide for studies in other isolated systems worldwide.

ACS Style

Bryson M. F. Sjodin; Emily E. Puckett; Robyn L. Irvine; Jason Munshi-South; Michael A. Russello. Global origins of invasive brown rats (Rattus norvegicus) in the Haida Gwaii archipelago. Biological Invasions 2020, 23, 611 -623.

AMA Style

Bryson M. F. Sjodin, Emily E. Puckett, Robyn L. Irvine, Jason Munshi-South, Michael A. Russello. Global origins of invasive brown rats (Rattus norvegicus) in the Haida Gwaii archipelago. Biological Invasions. 2020; 23 (2):611-623.

Chicago/Turabian Style

Bryson M. F. Sjodin; Emily E. Puckett; Robyn L. Irvine; Jason Munshi-South; Michael A. Russello. 2020. "Global origins of invasive brown rats (Rattus norvegicus) in the Haida Gwaii archipelago." Biological Invasions 23, no. 2: 611-623.

Original article
Published: 21 September 2020 in Journal of Zoological Systematics and Evolutionary Research
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Galapagos giant tortoises (Chelonoidis spp.) are a group of large, long‐lived reptiles that includes 14 species, 11 of which are extant and threatened by human activities and introductions of non‐native species. Here, we evaluated the phylogenetic relationships of all extant and two extinct species (Chelonoidis abingdonii from the island of Pinta and Chelonoidis niger from the island of Floreana) using Bayesian and maximum likelihood analysis of complete or nearly complete mitochondrial genomes. We also provide an updated phylogeographic scenario of their colonization of the Galapagos Islands using chrono‐phylogenetic and biogeographic approaches. The resulting phylogenetic trees show three major groups of species: one from the southern, central, and western Galapagos Islands; the second from the northwestern islands; and the third group from the northern, central, and eastern Galapagos Islands. The time‐calibrated phylogenetic and ancestral area reconstructions generally align with the geologic ages of the islands. The divergence of the Galapagos giant tortoises from their South American ancestor likely occurred in the upper Miocene. Their diversification on the Galapagos adheres to the island progression rule, starting in the Pleistocene with the dispersal of the ancestral form from the two oldest islands (San Cristóbal and Española) to Santa Cruz, Santiago, and Pinta, followed by multiple colonizations from different sources within the archipelago. Our work provides an example of how to reconstruct the history of endangered taxa in spite of extinctions and human‐mediated dispersal events and provides a framework for evaluating the contribution of colonization and in situ speciation to the diversity of other Galapagos lineages.

ACS Style

Nikos Poulakakis; Joshua M. Miller; Evelyn L. Jensen; Luciano B. Beheregaray; Michael A. Russello; Scott Glaberman; Jeffrey Boore; Adalgisa Caccone. Colonization history of Galapagos giant tortoises: Insights from mitogenomes support the progression rule. Journal of Zoological Systematics and Evolutionary Research 2020, 58, 1262 -1275.

AMA Style

Nikos Poulakakis, Joshua M. Miller, Evelyn L. Jensen, Luciano B. Beheregaray, Michael A. Russello, Scott Glaberman, Jeffrey Boore, Adalgisa Caccone. Colonization history of Galapagos giant tortoises: Insights from mitogenomes support the progression rule. Journal of Zoological Systematics and Evolutionary Research. 2020; 58 (4):1262-1275.

Chicago/Turabian Style

Nikos Poulakakis; Joshua M. Miller; Evelyn L. Jensen; Luciano B. Beheregaray; Michael A. Russello; Scott Glaberman; Jeffrey Boore; Adalgisa Caccone. 2020. "Colonization history of Galapagos giant tortoises: Insights from mitogenomes support the progression rule." Journal of Zoological Systematics and Evolutionary Research 58, no. 4: 1262-1275.

Original research
Published: 09 July 2020 in Ecology and Evolution
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Recurring glacial cycles through the Quaternary period drastically altered the size and distribution of natural populations of North American flora and fauna. The “southerly refugia model” has been the longstanding framework for testing the effects of glaciation on contemporary genetic patterns; however, insights from ancient DNA have contributed to the reconstruction of more complex histories for some species. The American badger, Taxidea taxus , provides an interesting species for exploring the genetic legacy of glacial history, having been hypothesized to have postglacially emerged from a single, southerly refugium to recolonize northern latitudes. However, previous studies have lacked genetic sampling from areas where distinct glacial refugia have been hypothesized, including the Pacific Northwest and American Far North (Yukon, Alaska). In order to further investigate the phylogeographic history of American badgers, we collected mitochondrial DNA sequence data from ancient subfossil material collected within the historical range (Alaska, Yukon) and combined them with new and previously published data from across the species' contemporary distribution (n = 1,207). We reconstructed a mostly unresolved phylogenetic tree and star‐like haplotype network indicative of emergence from a largely panmictic glacial refugium and recent population expansion, the latter further punctuated by significantly negative Tajima's D and Fu's Fs values. Although directionality of migration cannot be unequivocally inferred, the moderate to high levels of genetic variation exhibited by American badgers, alongside the low frequency of haplotypes with indels in the Midwest, suggest a potential recolonization into central North America after the hypothesized ice‐free corridor reopened ~13,000 years ago. Overall, the expanded reconstruction of phylogeographic history of American badgers offers a broader understanding of contemporary range‐wide patterns and identifies unique genetic units that can likely be used to inform conservation of at‐risk populations at the northern periphery.

ACS Style

Brett M. Ford; Anna Cornellas; Jennifer A. Leonard; Richard D. Weir; Michael A. Russello. Spatiotemporal analyses suggest the role of glacial history and the ice‐free corridor in shaping American badger population genetic variation. Ecology and Evolution 2020, 10, 8345 -8357.

AMA Style

Brett M. Ford, Anna Cornellas, Jennifer A. Leonard, Richard D. Weir, Michael A. Russello. Spatiotemporal analyses suggest the role of glacial history and the ice‐free corridor in shaping American badger population genetic variation. Ecology and Evolution. 2020; 10 (15):8345-8357.

Chicago/Turabian Style

Brett M. Ford; Anna Cornellas; Jennifer A. Leonard; Richard D. Weir; Michael A. Russello. 2020. "Spatiotemporal analyses suggest the role of glacial history and the ice‐free corridor in shaping American badger population genetic variation." Ecology and Evolution 10, no. 15: 8345-8357.

Research article
Published: 18 June 2020 in PLOS ONE
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Invasive alien species (IAS) are among the main causes of global biodiversity loss. Invasive brown (Rattus norvegicus) and black (R. rattus) rats, in particular, are leading drivers of extinction on islands, especially in the case of seabirds where >50% of all extinctions have been attributed to rat predation. Eradication is the primary form of invasive rat management, yet this strategy has resulted in a ~10–38% failure rate on islands globally. Genetic tools can help inform IAS management, but such applications to date have been largely reactive, time-consuming, and costly. Here, we developed a Genotyping-in-Thousands by sequencing (GT-seq) panel for rapid species identification and population assignment of invasive brown and black rats (RapidRat) in Haida Gwaii, an archipelago comprising ~150 islands off the central coast of British Columbia, Canada. We constructed an optimized panel of 443 single nucleotide polymorphisms (SNPs) using previously generated double-digest restriction-site associated DNA (ddRAD) genotypic data (27,686 SNPs) from brown (n = 295) and black rats (n = 241) sampled throughout Haida Gwaii. The informativeness of this panel for identifying individuals to species and island of origin was validated relative to the ddRAD results; in all comparisons, admixture coefficients and population assignments estimated using RapidRat were consistent. To demonstrate application, 20 individuals from novel invasions of three islands (Agglomerate, Hotspring, Ramsay) were genotyped using RapidRat, all of which were confidently assigned (>98.5% probability) to Faraday and Murchison Islands as putative source populations. These results indicated that a previous eradication on Hotspring Island was conducted at an inappropriate geographic scale; future management should expand the eradication unit to include neighboring islands to prevent re-invasion. Overall, we demonstrated that RapidRat is an effective tool for managing invasive rat populations in Haida Gwaii and provided a clear framework for GT-seq panel development for informing biodiversity conservation in other systems.

ACS Style

Bryson M. F. Sjodin; Robyn L. Irvine; Michael A. Russello. RapidRat: Development, validation and application of a genotyping-by-sequencing panel for rapid biosecurity and invasive species management. PLOS ONE 2020, 15, e0234694 .

AMA Style

Bryson M. F. Sjodin, Robyn L. Irvine, Michael A. Russello. RapidRat: Development, validation and application of a genotyping-by-sequencing panel for rapid biosecurity and invasive species management. PLOS ONE. 2020; 15 (6):e0234694.

Chicago/Turabian Style

Bryson M. F. Sjodin; Robyn L. Irvine; Michael A. Russello. 2020. "RapidRat: Development, validation and application of a genotyping-by-sequencing panel for rapid biosecurity and invasive species management." PLOS ONE 15, no. 6: e0234694.

Original research
Published: 02 June 2020 in Ecology and Evolution
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Delineation of units below the species level is critical for prioritizing conservation actions for species at‐risk. Genetic studies play an important role in characterizing patterns of population connectivity and diversity to inform the designation of conservation units, especially for populations that are geographically isolated. The northernmost range margin of Western Rattlesnakes (Crotalus oreganus ) occurs in British Columbia, Canada, where it is federally classified as threatened and restricted to five geographic regions. In these areas, Western Rattlesnakes hibernate (den) communally, raising questions about connectivity within and between den complexes. At present, Western Rattlesnake conservation efforts are hindered by a complete lack of information on genetic structure and degree of isolation at multiple scales, from the den to the regional level. To fill this knowledge gap, we used Genotyping‐in‐Thousands by sequencing (GT‐seq) to genotype an optimized panel of 362 single nucleotide polymorphisms (SNPs) from individual samples (n = 461) collected across the snake's distribution in western Canada and neighboring Washington (USA). Hierarchical STRUCTURE analyses found evidence for population structure within and among the five geographic regions in BC, as well as in Washington. Within these regions, 11 genetically distinct complexes of dens were identified, with some regions having multiple complexes. No significant pattern of isolation‐by‐distance and generally low levels of migration were detected among den complexes across regions. Additionally, snakes within dens generally were more related than those among den complexes within a region, indicating limited movement. Overall, our results suggest that the single, recognized designatable unit for Western Rattlesnakes in Canada should be re‐assessed to proactively focus conservation efforts on preserving total genetic variation detected range‐wide. More broadly, our study demonstrates a novel application of GT‐seq for investigating patterns of diversity in wild populations at multiple scales to better inform conservation management.

ACS Style

Danielle A. Schmidt; Purnima Govindarajulu; Karl W. Larsen; Michael A. Russello. Genotyping‐in‐Thousands by sequencing reveals marked population structure in Western Rattlesnakes to inform conservation status. Ecology and Evolution 2020, 10, 7157 -7172.

AMA Style

Danielle A. Schmidt, Purnima Govindarajulu, Karl W. Larsen, Michael A. Russello. Genotyping‐in‐Thousands by sequencing reveals marked population structure in Western Rattlesnakes to inform conservation status. Ecology and Evolution. 2020; 10 (14):7157-7172.

Chicago/Turabian Style

Danielle A. Schmidt; Purnima Govindarajulu; Karl W. Larsen; Michael A. Russello. 2020. "Genotyping‐in‐Thousands by sequencing reveals marked population structure in Western Rattlesnakes to inform conservation status." Ecology and Evolution 10, no. 14: 7157-7172.

Editorial
Published: 17 March 2020 in Genes
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For more than thirty years, methods and theories from evolutionary biology, phylogenetics, population genetics and molecular biology have been used by conservation biologists to better understand threats to endangered species due to anthropogenic changes [...].

ACS Style

Michael Russello; George Amato; Robert DeSalle; Michael Knapp. Conservation Genetics and Genomics. Genes 2020, 11, 318 .

AMA Style

Michael Russello, George Amato, Robert DeSalle, Michael Knapp. Conservation Genetics and Genomics. Genes. 2020; 11 (3):318.

Chicago/Turabian Style

Michael Russello; George Amato; Robert DeSalle; Michael Knapp. 2020. "Conservation Genetics and Genomics." Genes 11, no. 3: 318.

Original article
Published: 16 December 2019 in Evolutionary Applications
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Invasive species have led to precipitous declines in biodiversity, especially in island systems. Brown (Rattus norvegicus) and black rats (R. rattus) are among the most invasive animals on the planet, with eradication being the primary tool for established island populations. The need for increased research for defining eradication units and monitoring outcomes has been highlighted as a means to maximize success. Haida Gwaii is an archipelago ~100 km off the northern coast of British Columbia, Canada that hosts globally significant breeding populations of seabirds that are at risk due to invasive rats. Here, we paired sampling of brown (n=287) and black (n=291) rats across the Haida Gwaii archipelago (British Columbia, Canada) with genotyping‐by‐sequencing (10,770‐27,686 SNPs) to investigate patterns of population connectivity and infer levels/direction of gene flow among invasive rat populations in Haida Gwaii. We reconstructed three regional clusters for both species (north, central, south), with proximate populations within regions being largely more related than those that were more distant, consistent with predictions from island biogeography theory. Population assignment of recently detected individuals post‐eradication on Faraday, Murchison, and the Bischof Islands revealed all were re‐invaders from Lyell Island, rather than being on‐island survivors. Based on these results, we identified six eradication units constituting single or clusters of islands that would limit the potential for re‐invasion, some of which will need to be combined with biosecurity measures. Overall, our results highlight the importance of targeted research prior to conducting eradications and demonstrates a framework for applying population genomics for guiding invasive species management in island systems.

ACS Style

Bryson M. F. Sjodin; Robyn L. Irvine; Adam T. Ford; Gregg R. Howald; Michael A. Russello. Rattuspopulation genomics across the Haida Gwaii archipelago provides a framework for guiding invasive species management. Evolutionary Applications 2019, 13, 889 -904.

AMA Style

Bryson M. F. Sjodin, Robyn L. Irvine, Adam T. Ford, Gregg R. Howald, Michael A. Russello. Rattuspopulation genomics across the Haida Gwaii archipelago provides a framework for guiding invasive species management. Evolutionary Applications. 2019; 13 (5):889-904.

Chicago/Turabian Style

Bryson M. F. Sjodin; Robyn L. Irvine; Adam T. Ford; Gregg R. Howald; Michael A. Russello. 2019. "Rattuspopulation genomics across the Haida Gwaii archipelago provides a framework for guiding invasive species management." Evolutionary Applications 13, no. 5: 889-904.

Journal article
Published: 23 September 2019 in Nature Climate Change
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Accounting for within-species variability in the relationship between occurrence and climate is essential to forecasting species’ responses to climate change. Few climate-vulnerability assessments explicitly consider intraspecific variation, and those that do typically assume that variability is best explained by genetic affinity. Here, we evaluate how well heterogeneity in responses to climate by a cold-adapted mammal, the American pika (Ochotona princeps), aligns with subdivisions of the geographic range by phylogenetic lineage, physiography, elevation or ecoregion. We find that variability in climate responses is most consistently explained by an ecoregional subdivision paired with background sites selected from a broad spatial extent indicative of long-term (millennial-scale) responses to climate. Our work challenges the common assumption that intraspecific variation in climate responses aligns with genetic affinity. Accounting for the appropriate context and scale of heterogeneity in species’ responses to climate will be critical for informing climate-adaptation management strategies at the local (spatial) extents at which such actions are typically implemented.

ACS Style

Adam B. Smith; Erik A. Beever; Aimee E. Kessler; Aaron N. Johnston; Chris Ray; Clinton W. Epps; Hayley C. Lanier; Rob C. Klinger; Thomas J. Rodhouse; Johanna Varner; John D. Perrine; Amy Seglund; L. Embere Hall; Kurt Galbreath; Chris MacGlover; Peter Billman; Gretchen Blatz; Jason Brewer; Jessica Castillo Vardaro; Anna D. Chalfoun; Gail Collins; April Craighead; Chris Curlis; Christopher Daly; Daniel F. Doak; Mitch East; Mark Edwards; Liesl Erb; Kristina A. Ernest; Brian Fauver; Kerry R. Foresman; Ken Goehring; Joan Hagar; Charles L. Hayes; Philippe Henry; Kimberly Hersey; Shannon L. Hilty; Jim Jacobson; Mackenzie R. Jeffress; Tom Manning; Amy Masching; Bryce Maxell; Rayo McCollough; Corrie McFarland; Eric Miskow; Toni Lyn Morelli; Lucas Moyer-Horner; Megan Mueller; Martin Nugent; Beth Pratt; Mary Rasmussen-Flores; Tom H. Rickman; Hillary Robison; Arthur Rodriguez; Karen Rowe; Kevin Rowe; Michael A. Russello; Vicki Saab; Angie Schmidt; Joseph A. E. Stewart; James N. Stuart; Leona K. Svancara; Will Thompson; Julie Timmins; Gregg Treinish; Matthew D. Waterhouse; Marie L. Westover; Jennifer Wilkening; Leah Yandow. Alternatives to genetic affinity as a context for within-species response to climate. Nature Climate Change 2019, 9, 787 -794.

AMA Style

Adam B. Smith, Erik A. Beever, Aimee E. Kessler, Aaron N. Johnston, Chris Ray, Clinton W. Epps, Hayley C. Lanier, Rob C. Klinger, Thomas J. Rodhouse, Johanna Varner, John D. Perrine, Amy Seglund, L. Embere Hall, Kurt Galbreath, Chris MacGlover, Peter Billman, Gretchen Blatz, Jason Brewer, Jessica Castillo Vardaro, Anna D. Chalfoun, Gail Collins, April Craighead, Chris Curlis, Christopher Daly, Daniel F. Doak, Mitch East, Mark Edwards, Liesl Erb, Kristina A. Ernest, Brian Fauver, Kerry R. Foresman, Ken Goehring, Joan Hagar, Charles L. Hayes, Philippe Henry, Kimberly Hersey, Shannon L. Hilty, Jim Jacobson, Mackenzie R. Jeffress, Tom Manning, Amy Masching, Bryce Maxell, Rayo McCollough, Corrie McFarland, Eric Miskow, Toni Lyn Morelli, Lucas Moyer-Horner, Megan Mueller, Martin Nugent, Beth Pratt, Mary Rasmussen-Flores, Tom H. Rickman, Hillary Robison, Arthur Rodriguez, Karen Rowe, Kevin Rowe, Michael A. Russello, Vicki Saab, Angie Schmidt, Joseph A. E. Stewart, James N. Stuart, Leona K. Svancara, Will Thompson, Julie Timmins, Gregg Treinish, Matthew D. Waterhouse, Marie L. Westover, Jennifer Wilkening, Leah Yandow. Alternatives to genetic affinity as a context for within-species response to climate. Nature Climate Change. 2019; 9 (10):787-794.

Chicago/Turabian Style

Adam B. Smith; Erik A. Beever; Aimee E. Kessler; Aaron N. Johnston; Chris Ray; Clinton W. Epps; Hayley C. Lanier; Rob C. Klinger; Thomas J. Rodhouse; Johanna Varner; John D. Perrine; Amy Seglund; L. Embere Hall; Kurt Galbreath; Chris MacGlover; Peter Billman; Gretchen Blatz; Jason Brewer; Jessica Castillo Vardaro; Anna D. Chalfoun; Gail Collins; April Craighead; Chris Curlis; Christopher Daly; Daniel F. Doak; Mitch East; Mark Edwards; Liesl Erb; Kristina A. Ernest; Brian Fauver; Kerry R. Foresman; Ken Goehring; Joan Hagar; Charles L. Hayes; Philippe Henry; Kimberly Hersey; Shannon L. Hilty; Jim Jacobson; Mackenzie R. Jeffress; Tom Manning; Amy Masching; Bryce Maxell; Rayo McCollough; Corrie McFarland; Eric Miskow; Toni Lyn Morelli; Lucas Moyer-Horner; Megan Mueller; Martin Nugent; Beth Pratt; Mary Rasmussen-Flores; Tom H. Rickman; Hillary Robison; Arthur Rodriguez; Karen Rowe; Kevin Rowe; Michael A. Russello; Vicki Saab; Angie Schmidt; Joseph A. E. Stewart; James N. Stuart; Leona K. Svancara; Will Thompson; Julie Timmins; Gregg Treinish; Matthew D. Waterhouse; Marie L. Westover; Jennifer Wilkening; Leah Yandow. 2019. "Alternatives to genetic affinity as a context for within-species response to climate." Nature Climate Change 9, no. 10: 787-794.

Resource article
Published: 04 September 2019 in Molecular Ecology Resources
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Minimally‐invasive sampling (MIS) is widespread in wildlife studies; however, its utility for massively parallel DNA sequencing (MPS) is limited. Poor sample quality and contamination by exogenous DNA can make MIS challenging to use with modern genotyping‐by‐sequencing approaches, which have been traditionally developed for high‐quality DNA sources. Given that MIS is often more appropriate in many contexts, there is a need to make such samples practical for harnessing MPS. Here, we test the ability for Genotyping‐in‐Thousands by sequencing (GT‐seq), a multiplex amplicon sequencing approach, to effectively genotype minimally‐invasive cloacal DNA samples collected from the Western Rattlesnake (Crotalus oreganus), a threatened species in British Columbia, Canada. As there was no previous genetic information for this species, an optimized panel of 362 SNPs was selected for use with GT‐seq from a de novo restriction‐site associated DNA sequencing (RADseq) assembly. Comparisons of genotypes generated within and among RADseq and GT‐seq for the same individuals found low rates of genotyping error (GT‐seq: 0.50%; RADseq: 0.80%) and discordance (2.57%), the latter likely due to the different genotype calling models employed. GT‐seq mean genotype discordance between blood and cloacal swab samples collected from the same individuals was also minimal (1.37%). Estimates of population diversity parameters were similar across GT‐seq and RADseq datasets, as were inferred patterns of population structure. Overall, GT‐seq can be effectively applied to low quality DNA samples, minimizing the inefficiencies presented by exogenous DNA typically found in minimally‐invasive samples and continuing the expansion of molecular ecology and conservation genetics in the genomics era. This article is protected by copyright. All rights reserved.

ACS Style

Danielle A. Schmidt; Nathan R. Campbell; Purnima Govindarajulu; Karl W. Larsen; Michael A. Russello. Genotyping‐in‐Thousands by sequencing (GT‐seq) panel development and application to minimally invasive DNA samples to support studies in molecular ecology. Molecular Ecology Resources 2019, 20, 114 -124.

AMA Style

Danielle A. Schmidt, Nathan R. Campbell, Purnima Govindarajulu, Karl W. Larsen, Michael A. Russello. Genotyping‐in‐Thousands by sequencing (GT‐seq) panel development and application to minimally invasive DNA samples to support studies in molecular ecology. Molecular Ecology Resources. 2019; 20 (1):114-124.

Chicago/Turabian Style

Danielle A. Schmidt; Nathan R. Campbell; Purnima Govindarajulu; Karl W. Larsen; Michael A. Russello. 2019. "Genotyping‐in‐Thousands by sequencing (GT‐seq) panel development and application to minimally invasive DNA samples to support studies in molecular ecology." Molecular Ecology Resources 20, no. 1: 114-124.

Review
Published: 26 August 2019 in Genes
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In this contribution, the aspects of reptile and amphibian speciation that emerged from research performed over the past decade are reviewed. First, this study assesses how patterns and processes of speciation depend on knowing the taxonomy of the group in question, and discuss how integrative taxonomy has contributed to speciation research in these groups. This study then reviews the research on different aspects of speciation in reptiles and amphibians, including biogeography and climatic niches, ecological speciation, the relationship between speciation rates and phenotypic traits, and genetics and genomics. Further, several case studies of speciation in reptiles and amphibians that exemplify many of these themes are discussed. These include studies of integrative taxonomy and biogeography in South American lizards, ecological speciation in European salamanders, speciation and phenotypic evolution in frogs and lizards. The final case study combines genomics and biogeography in tortoises. The field of amphibian and reptile speciation research has steadily moved forward from the assessment of geographic and ecological aspects, to incorporating other dimensions of speciation, such as genetic mechanisms and evolutionary forces. A higher degree of integration among all these dimensions emerges as a goal for future research.

ACS Style

Katharina C. Wollenberg Valero; Jonathon C. Marshall; Elizabeth Bastiaans; Adalgisa Caccone; Arley Camargo; Mariana Morando; Matthew L. Niemiller; Maciej Pabijan; Michael A. Russello; Barry Sinervo; Fernanda P. Werneck; Jr. Jack W. Sites; Jr.; John J. Wiens; Sebastian Steinfartz; Jack W. Sites; Wollenberg Valero. Patterns, Mechanisms and Genetics of Speciation in Reptiles and Amphibians. Genes 2019, 10, 646 .

AMA Style

Katharina C. Wollenberg Valero, Jonathon C. Marshall, Elizabeth Bastiaans, Adalgisa Caccone, Arley Camargo, Mariana Morando, Matthew L. Niemiller, Maciej Pabijan, Michael A. Russello, Barry Sinervo, Fernanda P. Werneck, Jr. Jack W. Sites, Jr., John J. Wiens, Sebastian Steinfartz, Jack W. Sites, Wollenberg Valero. Patterns, Mechanisms and Genetics of Speciation in Reptiles and Amphibians. Genes. 2019; 10 (9):646.

Chicago/Turabian Style

Katharina C. Wollenberg Valero; Jonathon C. Marshall; Elizabeth Bastiaans; Adalgisa Caccone; Arley Camargo; Mariana Morando; Matthew L. Niemiller; Maciej Pabijan; Michael A. Russello; Barry Sinervo; Fernanda P. Werneck; Jr. Jack W. Sites; Jr.; John J. Wiens; Sebastian Steinfartz; Jack W. Sites; Wollenberg Valero. 2019. "Patterns, Mechanisms and Genetics of Speciation in Reptiles and Amphibians." Genes 10, no. 9: 646.

Research article
Published: 07 May 2019 in Conservation Genetics
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Peripheral populations are often characterized by small population size and low genetic diversity, with many at risk of extirpation. These characteristics may be even more pronounced in human-modified landscapes that further reduce the resiliency of populations to environmental change. Situated at the northwestern edge of the species’ range, the western American badger (Taxidea taxus jeffersonii) is an endangered mammal in Canada, where it inhabits the interior grassland and open forest ecosystems of British Columbia (BC) and continues to be threatened by severe vehicle-induced mortality rates and other anthropogenic factors. Here, we collected mitochondrial DNA haplotypic and microsatellite genotypic data to investigate the extent and distribution of American badger genetic variation within and among sites in British Columbia, and relative to adjacent populations in the USA, including in Washington state. From these data, we reconstructed population structure and connectivity, and examined current designatable unit status. Patterns of genetic variation for American badgers in British Columbia were as expected for peripheral populations, including reduced genetic diversity, increased population differentiation, and evidence of demographic contraction. Furthermore, we found limited connectivity between regional populations in our study area and identified significant substructure isolating the most northwestern sampling unit (Cariboo), findings that starkly contrast with the high levels of gene flow observed between populations across the species’ range core. These results have important implications for current designatable unit status for western American badgers in British Columbia and emphasize the need for further population monitoring and mitigation of potential barriers to gene flow.

ACS Style

Brett M. Ford; Richard D. Weir; Jeffrey C. Lewis; Karl W. Larsen; Michael A. Russello. Fine-scale genetic structure and conservation status of American badgers at their northwestern range periphery. Conservation Genetics 2019, 20, 1023 -1034.

AMA Style

Brett M. Ford, Richard D. Weir, Jeffrey C. Lewis, Karl W. Larsen, Michael A. Russello. Fine-scale genetic structure and conservation status of American badgers at their northwestern range periphery. Conservation Genetics. 2019; 20 (5):1023-1034.

Chicago/Turabian Style

Brett M. Ford; Richard D. Weir; Jeffrey C. Lewis; Karl W. Larsen; Michael A. Russello. 2019. "Fine-scale genetic structure and conservation status of American badgers at their northwestern range periphery." Conservation Genetics 20, no. 5: 1023-1034.

Contributed paper
Published: 22 March 2019 in Conservation Biology
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Hybridization poses a major challenge for species conservation because it threatens both genetic integrity and adaptive potential. Yet, hybridization can occasionally offer unprecedented opportunity for species recovery if the genome of an extinct taxon is present among living hybrids such that selective breeding could re‐capture it. In this paper we explore the design elements for establishing a captive breeding program for Galapagos tortoises built around individuals with admixed ancestry involving an extinct species. The target individuals are hybrids between the extinct species from Floreana Island, Chelonoidis niger, and an extant species, C. becki, which were recently found in the endemic range of C. becki, Wolf Volcano (Isabela Island). We combined genotypic data from 35 tortoises with high ancestry from C. niger with forward‐in‐time simulations to explore captive breeding strategies that maximized overall genetic diversity and ancestry from C. niger while accommodating resource constraints, species biology, and the urgency to return tortoises to Floreana Island for facilitating ecosystem restoration. Our simulations indicate that overall genetic diversity can be maximized and substantial amounts of the C. niger genome can be captured within the resources available for selectively breeding tortoises in captivity, especially if captive‐bred offspring are released to the wild rather than used as additional breeders. Our study provides guidance on the inclusion of hybrids with genomic representation from extinct taxa into species restoration programs and informs the ongoing debate on the value of hybrids in biodiversity conservation. Article impact statement: Hybrid individuals provide invaluable genomic resources for captive breeding and restoration of an extinct Galapagos giant tortoise. This article is protected by copyright. All rights reserved

ACS Style

Maud C. Quinzin; Jonathan Sandoval-Castillo; Joshua M. Miller; Luciano B. Beheregaray; Michael A. Russello; Elizabeth A. Hunter; James P. Gibbs; Washington Tapia; Freddy Villalva; Adalgisa Caccone. Genetically informed captive breeding of hybrids of an extinct species of Galapagos tortoise. Conservation Biology 2019, 33, 1404 -1414.

AMA Style

Maud C. Quinzin, Jonathan Sandoval-Castillo, Joshua M. Miller, Luciano B. Beheregaray, Michael A. Russello, Elizabeth A. Hunter, James P. Gibbs, Washington Tapia, Freddy Villalva, Adalgisa Caccone. Genetically informed captive breeding of hybrids of an extinct species of Galapagos tortoise. Conservation Biology. 2019; 33 (6):1404-1414.

Chicago/Turabian Style

Maud C. Quinzin; Jonathan Sandoval-Castillo; Joshua M. Miller; Luciano B. Beheregaray; Michael A. Russello; Elizabeth A. Hunter; James P. Gibbs; Washington Tapia; Freddy Villalva; Adalgisa Caccone. 2019. "Genetically informed captive breeding of hybrids of an extinct species of Galapagos tortoise." Conservation Biology 33, no. 6: 1404-1414.

Journal article
Published: 03 December 2018 in Nature Ecology & Evolution
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Giant tortoises are among the longest-lived vertebrate animals and, as such, provide an excellent model to study traits like longevity and age-related diseases. However, genomic and molecular evolutionary information on giant tortoises is scarce. Here, we describe a global analysis of the genomes of Lonesome George-the iconic last member of Chelonoidis abingdonii-and the Aldabra giant tortoise (Aldabrachelys gigantea). Comparison of these genomes with those of related species, using both unsupervised and supervised analyses, led us to detect lineage-specific variants affecting DNA repair genes, inflammatory mediators and genes related to cancer development. Our study also hints at specific evolutionary strategies linked to increased lifespan, and expands our understanding of the genomic determinants of ageing. These new genome sequences also provide important resources to help the efforts for restoration of giant tortoise populations.

ACS Style

Víctor Quesada; Sandra Freitas-Rodríguez; Joshua Miller; José G. Pérez-Silva; Zi-Feng Jiang; Washington Tapia; Olaya Santiago-Fernández; Diana Campos-Iglesias; Lukas F. K. Kuderna; Maud Quinzin; Miguel G. Álvarez; Dido Carrero; Luciano B. Beheregaray; James P. Gibbs; Ylenia Chiari; Scott Glaberman; Claudio Ciofi; Miguel Araujo-Voces; Pablo Mayoral; Javier R. Arango; Isaac Tamargo-Gómez; David Roiz-Valle; María Pascual-Torner; Benjamin R. Evans; Danielle L. Edwards; Ryan C. Garrick; Michael A. Russello; Nikos Poulakakis; Stephen J. Gaughran; Danny O. Rueda; Gabriel Bretones; Tomàs Marquès-Bonet; Kevin P. White; Adalgisa Caccone; Carlos López-Otín. Giant tortoise genomes provide insights into longevity and age-related disease. Nature Ecology & Evolution 2018, 3, 87 -95.

AMA Style

Víctor Quesada, Sandra Freitas-Rodríguez, Joshua Miller, José G. Pérez-Silva, Zi-Feng Jiang, Washington Tapia, Olaya Santiago-Fernández, Diana Campos-Iglesias, Lukas F. K. Kuderna, Maud Quinzin, Miguel G. Álvarez, Dido Carrero, Luciano B. Beheregaray, James P. Gibbs, Ylenia Chiari, Scott Glaberman, Claudio Ciofi, Miguel Araujo-Voces, Pablo Mayoral, Javier R. Arango, Isaac Tamargo-Gómez, David Roiz-Valle, María Pascual-Torner, Benjamin R. Evans, Danielle L. Edwards, Ryan C. Garrick, Michael A. Russello, Nikos Poulakakis, Stephen J. Gaughran, Danny O. Rueda, Gabriel Bretones, Tomàs Marquès-Bonet, Kevin P. White, Adalgisa Caccone, Carlos López-Otín. Giant tortoise genomes provide insights into longevity and age-related disease. Nature Ecology & Evolution. 2018; 3 (1):87-95.

Chicago/Turabian Style

Víctor Quesada; Sandra Freitas-Rodríguez; Joshua Miller; José G. Pérez-Silva; Zi-Feng Jiang; Washington Tapia; Olaya Santiago-Fernández; Diana Campos-Iglesias; Lukas F. K. Kuderna; Maud Quinzin; Miguel G. Álvarez; Dido Carrero; Luciano B. Beheregaray; James P. Gibbs; Ylenia Chiari; Scott Glaberman; Claudio Ciofi; Miguel Araujo-Voces; Pablo Mayoral; Javier R. Arango; Isaac Tamargo-Gómez; David Roiz-Valle; María Pascual-Torner; Benjamin R. Evans; Danielle L. Edwards; Ryan C. Garrick; Michael A. Russello; Nikos Poulakakis; Stephen J. Gaughran; Danny O. Rueda; Gabriel Bretones; Tomàs Marquès-Bonet; Kevin P. White; Adalgisa Caccone; Carlos López-Otín. 2018. "Giant tortoise genomes provide insights into longevity and age-related disease." Nature Ecology & Evolution 3, no. 1: 87-95.

Journal article
Published: 12 November 2018 in PeerJ
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Four species of true crocodile (genusCrocodylus) have been described from the Americas. Three of these crocodile species exhibit non-overlapping distributions—Crocodylus intermediusin South America,C. moreletiialong the Caribbean coast of Mesoamerica, andC. rhombiferconfined to Cuba. The fourth,C. acutus, is narrowly sympatric with each of the other three species. In this study, we sampled 113 crocodiles acrossCrocodyluspopulations in Cuba, as well as exemplar populations in Belize and Florida (USA), and sequenced three regions of the mitochondrial genome (D-loop, cytochrome b, cytochrome oxidase I; 3,626 base pair long dataset) that overlapped with published data previously collected from Colombia, Jamaica, and the Cayman Islands. Phylogenetic analyses of these data revealed two, paraphyletic lineages ofC. acutus. One lineage, found in the continental Americas, is the sister taxon toC. intermedius, while the Greater Antillean lineage is most closely related toC. rhombifer. In addition to the paraphyly of the twoC. acutuslineages, we recovered a 5.4% estimate of Tamura-Nei genetic divergence between the Antillean and continental clades. The reconstructed paraphyly, distinct phylogenetic affinities and high genetic divergence between Antillean and continentalC. acutuspopulations are consistent with interspecific differentiation within the genus and suggest that the current taxon recognized asC. acutusis more likely a complex of cryptic species warranting a reassessment of current taxonomy. Moreover, the inclusion, for the first time, of samples from the western population of the American crocodile in Cuba revealed evidence for continental mtDNA haplotypes in the Antilles, suggesting this area may constitute a transition zone between distinct lineages ofC. acutus. Further study using nuclear character data is warranted to more fully characterize this cryptic diversity, resolve taxonomic uncertainty, and inform conservation planning in this system.

ACS Style

Yoamel Milián-García; Michael A. Russello; Jessica Castellanos-Labarcena; Martin Cichon; Vikas Kumar; Georgina Espinosa; Natalia Rossi; Frank Mazzotti; Evon Hekkala; George Amato; Axel Janke. Genetic evidence supports a distinct lineage of American crocodile (Crocodylus acutus) in the Greater Antilles. PeerJ 2018, 6, e5836 .

AMA Style

Yoamel Milián-García, Michael A. Russello, Jessica Castellanos-Labarcena, Martin Cichon, Vikas Kumar, Georgina Espinosa, Natalia Rossi, Frank Mazzotti, Evon Hekkala, George Amato, Axel Janke. Genetic evidence supports a distinct lineage of American crocodile (Crocodylus acutus) in the Greater Antilles. PeerJ. 2018; 6 ():e5836.

Chicago/Turabian Style

Yoamel Milián-García; Michael A. Russello; Jessica Castellanos-Labarcena; Martin Cichon; Vikas Kumar; Georgina Espinosa; Natalia Rossi; Frank Mazzotti; Evon Hekkala; George Amato; Axel Janke. 2018. "Genetic evidence supports a distinct lineage of American crocodile (Crocodylus acutus) in the Greater Antilles." PeerJ 6, no. : e5836.

Preprint
Published: 15 October 2018
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Speciation processes have long been inferred from phylogenetic, phylogeographic, and biogeographic pattern-driven perspectives. Now much current speciation research is attempting to more directly describe the underlying processes and mechanisms of divergence leading to speciation. Ideally, researchers should integrate both process- and pattern-based approaches for a more comprehensive understanding of speciation. To this end, a symposium was organized during the 7th World Congress of Herpetology in Canada with the goal of bringing leading experts together to share successful examples of these perspectives and to promote a more cohesive understanding of reptile and amphibian speciation. Here we present a joint paper of short and updated summaries of each of these contributions with the aim of providing a reference source and launching pad for students and researchers interested in speciation in amphibians and reptiles.

ACS Style

Jonathon C Marshall; Elizabeth Bastiaans; Adalgisa Caccone; Arley Camargo; Mariana Morando; Matthew L Niemiller; Maciej Pabijan; Michael A Russello; Barry Sinervo; Jr. Jack W Sites; Miguel Vences; Fernanda P Werneck; Katharina C Wollenberg Valero; Sebastian Steinfartz. Mechanisms of speciation in reptiles and amphibians: a synopsis. 2018, 1 .

AMA Style

Jonathon C Marshall, Elizabeth Bastiaans, Adalgisa Caccone, Arley Camargo, Mariana Morando, Matthew L Niemiller, Maciej Pabijan, Michael A Russello, Barry Sinervo, Jr. Jack W Sites, Miguel Vences, Fernanda P Werneck, Katharina C Wollenberg Valero, Sebastian Steinfartz. Mechanisms of speciation in reptiles and amphibians: a synopsis. . 2018; ():1.

Chicago/Turabian Style

Jonathon C Marshall; Elizabeth Bastiaans; Adalgisa Caccone; Arley Camargo; Mariana Morando; Matthew L Niemiller; Maciej Pabijan; Michael A Russello; Barry Sinervo; Jr. Jack W Sites; Miguel Vences; Fernanda P Werneck; Katharina C Wollenberg Valero; Sebastian Steinfartz. 2018. "Mechanisms of speciation in reptiles and amphibians: a synopsis." , no. : 1.

Journal article
Published: 11 September 2018 in Fisheries Research
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Molecular markers have been employed for monitoring fisheries re-stocking initiatives for decades, however, as such programs mature, traditional genetic markers may be ineffective at distinguishing more advanced introgression classes (e.g. backcrosses and F2 hybrids). Genome-wide single nucleotide polymorphisms (SNPs) can enable more accurate and cost-effective monitoring, but there is a need to evaluate the number of markers relative to their information content, especially in cases where native and re-introduced stocks have only recently diverged. This is the case with the anadromous sockeye salmon (Oncorhynchus nerka) stocking program in Skaha Lake that has seen successful stock establishment since commencement in 2004, but also hybridization with resident kokanee. Genetic monitoring to date has been unable to accurately assign hybrids beyond F1, which is a management need moving forward. Here, we conducted a simulation-based study to evaluate the accuracy and power of varying subsets of the data to assign individuals to advanced-generation hybrid classes. Using empirical data at 6339 variable SNPs previously collected from the reference populations, we simulated six introgression classes ranging from F1 to B3-backcrosses, using eight different datasets [100 random, 100 highest Fst, 300 random, 300 highest Fst, 1000 random, 1000 highest Fst, 23 outliers, 6326 non-outliers] and evaluated their performance using two different assignment algorithms (LEA and NEWHYBRIDS). As expected, greater number and divergence (high Fst) of markers yielded greater assignment accuracy. NEWHYBRIDS outperformed LEA in all comparisons except for the 6326 SNP panel. Overall, the 300 highest Fst SNP panel should provide the optimal balance of resolution and cost-effectiveness for monitoring introgression trends in Skaha Lake over the coming decade. Given the need for system-specific assessment of introgressive hybridization, we recommend similar simulation-based analyses for optimizing SNP panels for a given system and management question prior to commencing genetic monitoring.

ACS Style

Lucas Elliott; Michael A. Russello. SNP panels for differentiating advanced-generation hybrid classes in recently diverged stocks: A sensitivity analysis to inform monitoring of sockeye salmon re-stocking programs. Fisheries Research 2018, 208, 339 -345.

AMA Style

Lucas Elliott, Michael A. Russello. SNP panels for differentiating advanced-generation hybrid classes in recently diverged stocks: A sensitivity analysis to inform monitoring of sockeye salmon re-stocking programs. Fisheries Research. 2018; 208 ():339-345.

Chicago/Turabian Style

Lucas Elliott; Michael A. Russello. 2018. "SNP panels for differentiating advanced-generation hybrid classes in recently diverged stocks: A sensitivity analysis to inform monitoring of sockeye salmon re-stocking programs." Fisheries Research 208, no. : 339-345.