Population Genomics Training for the Next Generation of Conservation Geneticists: ConGen 2018 Workshop

Stahlke, Amanda R.; Bell, Donavan; Dhendup, Tashi; Kern, Brooke; Pannoni, Samuel; Robinson, Zachary L.; Strait, Jeffrey; Smith, Seth; Hand, Brian K.; Hohenlohe, Paul A.; Luikart, Gordon

doi:10.1093/jhered/esaa001

Cited by 3 publications

(2 citation statements)

References 86 publications

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“…First, raw sequencing reads of each library were filtered for PCR duplicates using clone_filter. Then reads were de-multiplexed by individual barcode and re-oriented using the --bestrad flag in process_radtags, allowing for 3 mismatches and discarding reads with low-quality scores (Catchen, Hohenlohe, Bassham, Amores, & Cresko, 2013; Rochette et al, 2019; Stahlke et al, 2020). Each processed sample was then aligned to our D. carinulata draft genome using the --very_sensitive flag of bowtie2 version 2.2.9 (Langmead & Salzberg, 2012), and sorted with SAMtools version 1.9 (Li et al, 2009).…”

Section: Methodsmentioning

confidence: 99%

Hybridization and range expansion in tamarisk beetles (Diorhabda spp.) introduced to North America for classical biological control

Stahlke

Bitume

Özsoy

et al. 2021

Preprint

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With the global rise of human-mediated translocations and invasions, it is critical to understand the genomic consequences of hybridization and mechanisms of range expansion. Conventional wisdom is that high genetic drift and loss of genetic diversity due to repeated founder effects will constrain introduced species. However, reduced genetic variation can be countered by behavioral aspects and admixture with other distinct populations. As planned invasions, classical biological control (biocontrol) agents present important opportunities to understand the mechanisms of establishment and spread in a novel environment. The ability of biocontrol agents to spread and adapt, and their effects on local ecosystems, depends on genomic variation and the consequences of admixture in novel environments. Here we use a biocontrol system to examine the genome-wide outcomes of introduction, spread, and hybridization in four cryptic species of a biocontrol agent, the tamarisk beetle (Diorhabda carinata, D. carinulata, D. elongata, and D. sublineata), introduced from six localities across Eurasia to control the invasive shrub tamarisk (Tamarix spp.) in western North America. We assembled a de novo draft reference genome and applied RADseq to over 500 individuals from laboratory cultures, the native ranges, and across the introduced range. Despite evidence of a substantial genetic bottleneck among D. carinulata in N. America, populations continue to establish and spread, possibly due to aggregation behavior. We found that D. carinata, D. elongata, and D. sublineata hybridize in the field to varying extents, with D. carinata x D. sublineata hybrids being the most abundant. Genetic diversity was greater at sites with hybrids, highlighting potential for increased ability to adapt and expand. Our results demonstrate the complex patterns of genomic variation that can result from introduction of multiple ecotypes or species for biocontrol, and the importance of understanding them to predict and manage the effects of biocontrol agents in novel ecosystems.

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Section: Methodsmentioning

confidence: 99%

Hybridization and range expansion in tamarisk beetles (Diorhabda spp.) introduced to North America for classical biological control

Stahlke

Bitume

Özsoy

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…First, raw sequencing reads of each library were filtered for PCR duplicates using clone_filter. Then, reads were demultiplexed by individual barcode and re-oriented using the --bestrad flag in pro-cess_radtags, allowing for 3 mismatches and discarding reads with low-quality scores (Catchen et al, 2013;Rochette et al, 2019;Stahlke et al, 2020). Each processed sample was then aligned to our D. carinulata draft genome using the --very_sensitive flag of bowtie2 version 2.2.9 (Langmead & Salzberg, 2012), and sorted with SAMtools version 1.9 (Li et al, 2009).…”

Section: Sampling and Individual Genotyping Across The Native Range I...mentioning

confidence: 99%

Hybridization and range expansion in tamarisk beetles (Diorhabda spp.) introduced to North America for classical biological control

Stahlke

Bitume

Özsoy

et al. 2021

Evolutionary Applications

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With the global rise of human‐mediated translocations and invasions, it is critical to understand the genomic consequences of hybridization and mechanisms of range expansion. Conventional wisdom is that high genetic drift and loss of genetic diversity due to repeated founder effects will constrain introduced species. However, reduced genetic variation can be countered by behavioral aspects and admixture with other distinct populations. As planned invasions, classical biological control (biocontrol) agents present important opportunities to understand the mechanisms of establishment and spread in a novel environment. The ability of biocontrol agents to spread and adapt, and their effects on local ecosystems, depends on genomic variation and the consequences of admixture in novel environments. Here, we use a biocontrol system to examine the genome‐wide outcomes of introduction, spread, and hybridization in four cryptic species of a biocontrol agent, the tamarisk beetle (Diorhabda carinata, D. carinulata, D. elongata, and D. sublineata), introduced from six localities across Eurasia to control the invasive shrub tamarisk (Tamarix spp.) in western North America. We assembled a de novo draft reference genome and applied RADseq to over 500 individuals across laboratory cultures, the native ranges, and the introduced range. Despite evidence of a substantial genetic bottleneck among D. carinulata in N. America, populations continue to establish and spread, possibly due to aggregation behavior. We found that D. carinata, D. elongata, and D. sublineata hybridize in the field to varying extents, with D. carinata × D. sublineata hybrids being the most abundant. Genetic diversity was greater at sites with hybrids, highlighting potential for increased ability to adapt and expand. Our results demonstrate the complex patterns of genomic variation that can result from introduction of multiple ecotypes or species for biocontrol, and the importance of understanding them to predict and manage the effects of biocontrol agents in novel ecosystems.

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Big Data in Conservation Genomics: Boosting Skills, Hedging Bets, and Staying Current in the Field

Schweizer

Saarman

Ramstad

et al. 2021

Journal of Heredity

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A current challenge in the fields of evolutionary, ecological, and conservation genomics is balancing production of large-scale datasets with additional training often required to handle such datasets. Thus, there is an increasing need for conservation geneticists to continually learn and train to stay up-to-date through avenues such as symposia, meetings, and workshops. The ConGen meeting is a near-annual workshop that strives to guide participants in understanding population genetics principles, study design, data processing, analysis, interpretation, and applications to real-world conservation issues. Each year of ConGen gathers a diverse set of instructors, students, and resulting lectures, hands-on sessions, and discussions. Here, we summarize key lessons learned from the 2019 meeting and more recent updates to the field with a focus on big data in conservation genomics. First, we highlight classical and contemporary issues in study design that are especially relevant to working with big datasets, including the intricacies of data filtering. We next emphasize the importance of building analytical skills and simulating data, and how these skills have applications within and outside of conservation genetics careers. We also highlight recent technological advances and novel applications to conservation of wild populations. Finally, we provide data and recommendations to support ongoing efforts by ConGen organizers and instructors -- and beyond -- to increase participation of underrepresented minorities in conservation and eco-evolutionary sciences. The future success of conservation genetics requires both continual training in handling big data and a diverse group of people and approaches to tackle key issues including the global biodiversity-loss crisis.

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Population Genomics Training for the Next Generation of Conservation Geneticists: ConGen 2018 Workshop

Cited by 3 publications

References 86 publications

Hybridization and range expansion in tamarisk beetles (Diorhabda spp.) introduced to North America for classical biological control

Hybridization and range expansion in tamarisk beetles (Diorhabda spp.) introduced to North America for classical biological control

Hybridization and range expansion in tamarisk beetles (Diorhabda spp.) introduced to North America for classical biological control

Big Data in Conservation Genomics: Boosting Skills, Hedging Bets, and Staying Current in the Field

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