Identifying Origins and Pathways of Spread of Zebra Mussels using Genetics and Genomics

Identifying Origins and Pathways of Spread of Zebra Mussels using Genetics and Genomics Michael McCartney and Sophie Mallez MN AIS Research Center (MAISRC) University of Minnesota, St. Paul Upper Midwest Invasive Species Conference LaCrosse WI October 17th, 2016

North American invasion Several introductions to the Great Lakes in ship ballast water 2011: Brown and Stepien Appeared in Lake St Clair (1988: arrow) Through navigable waters (Great Lakes and Mississippi Basins, Hudson and Susquehanna Rivers) they reached Louisiana to the south, Quebec and New York to the east, Oklahoma and Minnesota to the west in 5 years!

Spread to inland lakes: much slower, less predictable In Minnesota Introduced in 1989, in Lake Superior Upper Mississippi and St Croix Rivers: early 1990 s First natural inland lake infested in 2003: Ossawinnamakee A long lag, 10 years longer than other US states. Now invasion rate of inland lakes is very high Data sources: US Geological Survey (NAS: 2014) MnDNR (2015)

Minnesota s rate of new inland invasions is now among the highest in the US From Mallez and McCartney (in review) We have the time, the will, and the resources to slow spread and prevent infestation of many prized water bodies! Prevention works, but must be targeted by Studying transport pathways (boats, docks, lifts ) both on the map and to understand the vectors Using genetics and genomics to directly pinpoint invasion sources and determine routes

Hypotheses for inland spread in MN Longer lag Prevention success Slow dispersal from Miss/St Croix Rivers, into inland hub lakes Post-2008 increase Secondary spread from inland hub(s) (e.g. Mille Lacs Lake)

Invasion genetics and genomics DNA markers to track invasion paths, both past and present DNA markers Variable (ie. polymorphic) genes or DNA fragments whose chromosomal location is known Distinguishes individuals Allows their assignment to population-of-origin

Genetic markers for zebra mussel Microsatellite markers Repeated motifs GTTAGTCCAGAGAG.AGAGAGTTCGATCT Polymorphic numerous alleles Genotyping of 9 microsatellite markers Obtained from the literature Optimized for this study

Waterbodies sampled 2014-2016 Sampling throughout Minnesota (and nearby regions) 59 sites - 35 water bodies 1747 individuals

Waterbodies sampled 2014-2016 Sampling throughout Minnesota (and nearby regions) 59 sites - 35 water bodies 1747 individuals Detroit Lakes area (9 lakes)

Analyzing the invasion in Minnesota 1747 individuals genotyped at 9 microsatellite markers 35 lakes, 3 river systems Several lakes (e.g. Gull, Mille Lacs, Minnetonka, Prior, Pelican, Superior); Mississippi & St. Croix Rivers at multiple sites Each brand of analysis targets a different invasion process: - Analysis of genetic diversity = Number of individuals introduced, severity and duration of bottleneck when lakes were colonized - Analysis of genetic structure/clustering = Genetic differences between lakes set up by unique histories - Analysis of invasion models = Origins and routes of introduction. Contrast of detailed scenarios to describe invasion history. Most lessons for management are generated here.

Analysis of genetic diversity * Mille Lacs Lake Prior Lake 8 lakes in Alexandria area Moderate founder effects due to bottlenecks Broad pattern: large numbers of mussels and/or larvae cause infestations

Analysis of genetic structure/clustering Mille Lacs Prior Alexandria area Brainerd area K = 2 K = 3 K = 4 K = 5 K = 6 K = 7 K = 8 Some well-defined genetic clusters distinguish important lake infestations

Analysis of invasion models Comparisons of scenarios of invasion Approximate Bayesian Computation Selection of the most likely scenario of invasion based on probabilities Focus on distinguishable lakes Super-spreader lakes Clustered invasion Mille Lacs Lake Prior Lake Alexandria-area Lakes

Analysis of invasion models Super-spreader lakes Mille Lacs Lake A source for spread to other inland lakes infested later (post-2005)? Successive invasion scenario Independent invasion scenario Gull Lake Gull Lake Mille Lacs Lake Mille Lacs Lake X Mille Lacs Mille Lake Lacs Lake

Analysis of invasion models Super-spreader lakes Mille Lacs Lake A source for spread to other inland lakes infested later (post-2005)? Successive invasion scenario Independent invasion scenario Gull Lake Gull Lake Posterior P = 0.89 Mille Lacs Lake Mille Lacs Lake X Mille Lacs Lake The answer No was strongly preferred for 10 of 11 lakes (Prior is ambiguous) (Posterior Probabilities from 0.86 to 0.99) Mille Lacs Lake did not infest Carlos, LeHomme Dieu, Darling, Gull, Pelican (Otter Tail), Minnetonka, Xmas, Pike (St. Louis), Bass, Sand (Itasca)

Where are we going with this? Expanded sampling of water bodies, both in MN and throughout the Upper Mississippi and Great Lakes Basins To examine, more comprehensively the causes of clustered invasions To obtain several more recently-infested lakes to increase confidence in results for hubs Mille Lacs was heavily infested only 2009 Minnetonka 2010

Where are we going with this? New lakes sampled in 2016 for Mille Lacs analyses Alexandria was this large cluster founded from Mille Lacs? Brainerd Lakes: geographically proximate to Mille Lacs Many new infestations 2009 or later Alexandria Lakes Region Brainerd Lakes Region AIS-infested ZM ZM-infested Sampled Mille Lacs Lake

Where are we going with this? New lakes sampled in 2016 for Mille Lacs analyses Pelican Rapids/Detroit Lakes Region Lakes (e.g. Cass) that are next stop destinations for boaters Cass/Winnie Region

Analysis of invasion models Super-spreader lakes Mille Lacs Lake A source for spread to other inland lakes infested later (post-2005)? Successive invasion scenario Independent invasion scenario Gull Lake Gull Lake Posterior P = 0.89 Mille Lacs Lake Mille Lacs Lake X Mille Lacs Lake The answer No was strongly preferred for 26 of 27lakes tested so far (Prior Lake is ambiguous)

Analysis of invasion models Super-spreader lakes Mille Lacs Lake A source for spread to other inland lakes infested later (post-2005)? Independent invasion scenario Gull Lake Posterior P = 0.89 X Mille Lacs Lake Mille Lacs Lake did not infest Alexandria Region Lakes: Brophy, Cowdrey, Darling, Carlos, Irene, Miltona, Ida, Victoria, Geneva, LeHomme Dieu, Mary, Maple; Brainerd Region Lakes: Gilbert, Gull, Round, Rice, North Long, Cross, Lower Hay, Ossie, Pelican (Crow Wing); also Minnetonka, Christmas, Pike (St. Louis), Bass, or Sand (Itasca)

The Zebra Mussel Genome Project We sequenced the zebra mussel genome using Illumina short read technology 100s of millions of fragments, each 50-300 base pairs Piled up and stitched together using bioinformatics We used this draft genome to help genotype Single Nucleotide Polymorphism (SNP) markers 5,000 to 200,000 markers per mussel! Genotyped using Sequence Based Genotyping (SBG) new technology at UMGC These thousands of variable SNP markers provide higher resolution for studying sources and pathways of spread

Coord. 2 Genomic Markers for Studying Spread 24 mussels from Minnetonka and 24 mussels from Gull Lake (2 putative super spreader lakes) Genotyped with 9 microsatellite markers (left panel) Genotyped with > 5,500 genomic (SNP) markers (right panel) Analyzed the same way (Principal Component Analysis) to examine genetic differences between lakes Lake Minnetonka Gull Lake Coord. 1

Time Time Higher genetic resolution = more complex scenario testing = more targeted management Lake Michigan Upper Miss Scenario I: Successive invasions inland Mille Lacs Minne tonka Management: target boat traffic between inland lakes Lake Michigan Scenario II: Chronic reintroductions Mille Lacs Minne tonka Management: increase surveillance of chronic sources (e.g, Mississippi boat ramps, or sources out of state)

Analyses of super spreader lakes (Mille Lacs, Prior) have so far indicated a surprising lack of contribution to spread We continue to analyze lakes infested post-2009 for better confidence

Lake Michigan Management implications? Upper Miss Mille Lacs Watercraft inspection of boats departing Mille Lacs may be working Invasions are not following patterns of transport of trailered boats (veligers in residual water, mostly) Lakes infested post-2009

Lake Michigan Management implications? Upper Miss Mille Lacs Time is now to consider other pathways (docks, lifts, transport of resident boats from marinas on St. Croix/UMR) How to better monitor and intercept these less frequent but high risk events? Lakes infested post-2009 www.marinedocklift.com www.nps.gov

Thanks to UMN: Grace Van Susteren, Sarah Peterson, Maxwell Kleinhaus, Melody Truong for collecting help and lab support UM Genomics Center: Kenneth Beckman, Daryl Gohl, Shea Anderson, Aaron Becker for molecular biology; John Garbe for informatics NPS: Byron Karns, Michelle Prosser for field support on St. Croix & Mississippi MnDNR: Dan Swanson, Rich Rezanka, Keegan Lund for field support and advice on collecting MN waters USGS: Mary-Anne Evans for collections in western Lake Erie Clear Water Fund, ENRTF for funding