The redbelly yellowtail fusilier, Caesio cuning, has a tropical Indo-West Pacific range 21 that straddles the Coral Triangle, a region of dynamic geological history and the highest 22 marine biodiversity on the planet. Previous genetic studies in the Coral Triangle indicate 23 the presence of regional limits to connectivity across this region. However, these have 24 focused almost exclusively on benthic reef dwelling species. Schooling, reef-associated 25 fusiliers (Perciformes: Caesionidae) account for a sizable portion of the annual reef catch 26 in the Coral Triangle, yet to date, there have been no in depth studies on the population 27 structure of fusiliers or other mid-water, reef-associated planktivores across this region. 28 We evaluated the genetic population structure of C. cuning using a 382bp segment of the 29 mitochondrial control region amplified from over 620 fish sampled from 33 localities 30 across the Philippines and Indonesia. Phylogeographic analysis showed that individuals 31 sampled from sites in western Sumatra belong to a distinct Indian-Ocean lineage, 32 resulting in pronounced regional structure between western Sumatra and the rest of the 33 Coral Triangle (Φ CT = 0.4796, p < 0.0043). We measured additional significant 34 population structure between central Southeast Asia and eastern Indonesia (Φ CT = 0.0450, 35 p < 0.0002). These data in conjunction with spatial analyses indicate that there are two 36 major lineages of C. cuning and at least three distinct management units across the 37 region. The location of genetic breaks as well as the distribution of divergent haplotypes 38 across our sampling range suggests that current oceanographic patterns could be 39 contributing to observed patterns of structure. 40 41 42 Keywords: connectivity, gene flow, isolation by distance, coral reef fish, artisanal 43 fisheries, Coral Triangle 44 Johannes 2002; Sale 2006). Because dispersive larvae are the primary means of 92 demographic and genetic connectivity among most populations, understanding patterns of 93 larval dispersal has been identified as one of the most critical gaps in developing effective 94 reserve networks (Sale et al. 2005). Although genetic connectivity is not equivalent to 95 demographic connectivity, genetic methods can be of use in guiding conservation 96 planning in marine ecosystems (Palumbi 2003). By identifying regions that are 97 genetically and demographically independent, conservation planners can partition large 98 marine ecosystems into smaller, more tractable management areas for which networks of 99 marine reserves can be designed (Green and Mous 2004). This approach has been 100 specifically proposed as a management mechanism in the Coral Triangle (Carpenter et al. 101 2011). 102 Schooling, reef-associated fusiliers (Perciformes: Caesionidae) are planktivores 103 found feeding at the reef face and account for a sizable portion of harvested reef species 104 in the Coral Triangle. They are caught via a variety of methods including hand-line, fish 105 traps, trawls, d...

Effective resource management depends on our ability to partition diversity into biologically meaningful units. Recent evolutionary divergence, however, can often lead to ambiguity in morphological and genetic differentiation, complicating the delineation of valid conservation units. Such is the case with the "coregonine problem," where recent postglacial radiations of coregonines into lacustrine habitats resulted in the evolution of numerous species flocks, often with ambiguous taxonomy. The application of genomics methods is beginning to shed light on this problem and the evolutionary mechanisms underlying divergence in these ecologically and economically important fishes. Here, we used restriction site-associated DNA (RAD) S U PP O RTI N G I N FO R M ATI O N Additional supporting information may be found online in the Supporting Information section. How to cite this article: Ackiss AS, Larson WA, Stott W. Genotyping-by-sequencing illuminates high levels of divergence among sympatric forms of coregonines in the Laurentian Great Lakes.

Effective resource management depends on our ability to partition diversity into biologically meaningful units. Recent evolutionary divergence, however, can often lead to ambiguity in morphological and genetic differentiation, complicating the delineation of valid conservation units. Such is the case with the “coregonine problem,” where recent post-glacial radiations of coregonines into lacustrine habitats resulted in the evolution of numerous species flocks, often with ambiguous taxonomy. The application of genomics methods is beginning to shed light on this problem and the evolutionary mechanisms underlying divergence in these ecologically and economically important fishes. Here, we used restriction site-associated DNA (RAD) sequencing to examine genetic diversity and differentiation among sympatric species in theCoregonus artedicomplex in the Apostle Islands of Lake Superior, the largest lake in the Laurentian Great Lakes. Using 29,068 SNPs, we were not only able to clearly distinguish the three most common forms for the first time, but putative hybrids and potentially mis-identified specimens as well. Assignment rates to form with our RAD data were 93-100% with the only mis-assignments arising from putative F1 hybrids, an improvement from 62-77% using microsatellites. Estimates of pairwise differentiation (FST: 0.045-0.056) were large given the detection of hybrids, suggesting that hybridization among forms may not be successful beyond the F1 state. We also used a newly builtC. artedilinkage map to look for islands of adaptive genetic divergence among forms and found widespread differentiation across the genome, a pattern indicative of long-term drift, suggesting that these forms have been reproductively isolated for a substantial amount of time. The results of this study provide valuable information that can be applied to develop well-informed management strategies and stress the importance of re-evaluating conservation units with genomic tools to ensure they accurately reflect species diversity.

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.

No abstract