Pronounced Genetic Structure in a Highly Mobile Coral Reef Fish, Caesio Cuning, in the Coral Triangle

The redbelly yellowtail fusilier, Caesio cuning, has a tropical Indo-West Pacific range that straddles the Coral Triangle, a region of dynamic geological history and the highest marine biodiversity on the planet. Previous genetic studies in the Coral Triangle indicate the presence of regional limits to connectivity across this region. However, these have focused almost exclusively on benthic reef dwelling species. Schooling, reef-associated fusiliers (Perciformes: Caesionidae) account for a sizable portion of the annual reef catch in the Coral Triangle, yet to date, there have been no in depth studies on the population structure of fusiliers or other mid-water, reef-associated planktivores across this region. We evaluated the genetic population structure of C. cuning using a 382bp segment of the mitochondrial control region amplified from over 620 fish sampled from 33 localities across the Philippines and Indonesia. Phylogeographic analysis showed that individuals sampled from sites in western Sumatra belong to a distinct Indian-Ocean lineage, resulting in pronounced regional structure between western Sumatra and the rest of the Coral Triangle (ΦCT = 0.4796, p \u3c 0.0043). We measured additional significant population structure between central Southeast Asia and eastern Indonesia (ΦCT = 0.0450, 36 p \u3c 0.0002). These data in conjunction with spatial analyses indicate that there are two major lineages of C. cuning and at least three distinct management units across the region. The location of genetic breaks as well as the distribution of divergent haplotypes across our sampling range suggests that current oceanographic patterns could be contributing to observed patterns of structure

Pronounced Genetic Structure in a Highly Mobile Coral Reef Fish, Caesio cuning, in the Coral Triangle

The redbelly yellowtail fusilier Caesio cuning has a tropical Indo-West Pacific range that straddles the Coral Triangle, a region of dynamic geological history and the highest marine biodiversity on the planet. Previous genetic studies in the Coral Triangle indicate the presence of multiple limits to connectivity. However, these studies have focused almost exclusively on benthic, reef-dwelling species. Schooling, reef-associated fusiliers (Perciformes: Caesionidae) account for a sizable portion of the annual reef catch in the Coral Triangle, yet to date, there have been no indepth studies on the population structure of fusiliers or other mid-water, reef-associated planktivores across this region. We evaluated the genetic population structure of C. cuning using a 382 bp segment of the mitochondrial control region amplified from over 620 fish sampled from 33 localities across the Philippines and Indonesia. Phylogeographic analysis showed that individuals sampled from sites in western Sumatra belong to a distinct Indian Ocean lineage, resulting in pronounced regional structure between western Sumatra and the rest of the Coral Triangle (φCT = 0.4796, p \u3c 0.004). We found additional significant population structure between central Southeast Asia and eastern Indonesia (φCT = 0.0450, p \u3c 0.001). These data in conjunction with spatial analyses indicate that there are 2 major lineages of C. cuning and at least 3 distinct management units across the region. The location of genetic breaks as well as the distribution of divergent haplotypes across our sampling range suggests that current oceanographic patterns could be contributing to observed patterns of structure

Cryptic Lineages and a Population Damned to Incipient Extinction? Insights into the Genetic Structure of a Mekong River Catfish

An understanding of the genetic composition of populations across management boundaries is vital to developing successful strategies for sustaining biodiversity and food resources. This is especially important in ecosystems where habitat fragmentation has altered baseline patterns of gene flow, dividing natural populations into smaller sub-populations and increasing potential loss of genetic variation through genetic drift. River systems can be highly fragmented by dams built for flow regulation and hydropower. We used reduced-representation sequencing to examine genomic patterns in an exploited catfish, Hemibagrus spilopterus, in a hotspot of biodiversity and hydropower development- the Mekong River basin. Our results revealed the presence of two highly-divergent coexisting genetic lineages which may be cryptic species. Within the lineage with the greatest sample sizes, pairwise FST values, principal components analysis, and a STRUCTURE analysis all suggest that long-distance migration is not common across the Lower Mekong Basin, even in areas where flood-pulse hydrology has limited genetic divergence. In tributaries, effective population size estimates were at least an order of magnitude lower than in the Mekong mainstream indicating these populations may be more vulnerable to perturbations such as human-induced fragmentation. Fish isolated upstream of several dams in one tributary exhibited particularly low genetic diversity, high amounts of relatedness, and a level of inbreeding (GIS = 0.51) that has been associated with inbreeding depression in other outcrossing species. Our results highlight the importance of assessing genetic structure and diversity in riverine fisheries populations across proposed dam development sites for the preservation of these critically-important resources

A translational polarization rotator

We explore a free-space polarization modulator in which a variable phase is introduced between the right- and left-handed circular polarization components and used to rotate the linear polarization of the outgoing beam relative to that of the incoming beam. In this device, the polarization states are separated by a circular polarizer that consists of a quarter-wave plate in combination with a wire grid. A movable mirror is positioned behind and parallel to the circular polarizer. As the polarizer-mirror distance is changed, an incident linear polarization will be rotated through an angle that is proportional to the introduced phase delay.We demonstrate a prototype device that modulates Stokes Q and U over a 20% bandwidth, from 77 to 94 GHz. © 2012 Optical Society of America

Dispersive currents explain patterns of population connectivity in an ecologically and economically important fish

Abstract How to identify the drivers of population connectivity remains a fundamental question in ecology and evolution. Answering this question can be challenging in aquatic environments where dynamic lake and ocean currents coupled with high levels of dispersal and gene flow can decrease the utility of modern population genetic tools. To address this challenge, we used RAD‐Seq to genotype 959 yellow perch (Perca flavescens), a species with an ~40‐day pelagic larval duration (PLD), collected from 20 sites circumscribing Lake Michigan. We also developed a novel, integrative approach that couples detailed biophysical models with eco‐genetic agent‐based models to generate “predictive” values of genetic differentiation. By comparing predictive and empirical values of genetic differentiation, we estimated the relative contributions for known drivers of population connectivity (e.g., currents, behavior, PLD). For the main basin populations (i.e., the largest contiguous portion of the lake), we found that high gene flow led to low overall levels of genetic differentiation among populations (FST = 0.003). By far the best predictors of genetic differentiation were connectivity matrices that were derived from periods of time when there were strong and highly dispersive currents. Thus, these highly dispersive currents are driving the patterns of population connectivity in the main basin. We also found that populations from the northern and southern main basin are slightly divergent from one another, while those from Green Bay and the main basin are highly divergent (FST = 0.11). By integrating biophysical and eco‐genetic models with genome‐wide data, we illustrate that the drivers of population connectivity can be identified in high gene flow systems

Population genomics of the peripheral freshwater fish Polynemus melanochir (Perciformes, Polynemidae) in a changing Mekong Delta

The Mekong River is a vital fisheries resource supporting millions of people in mainland Southeast Asia. However, numerous threats have the potential to negatively impact fish populations in this region including overfishing, pollution, climate change and increased urban, agriculture and upstream hydropower development. Although a few studies have examined the population genetic structure of fishes within the upper Mekong River, no known studies have explored that of fishes within the Mekong Delta (MD). Here, we examine the population structure of an important food fish within the MD, Polynemus melanochir, using a panel of 1735 single nucleotide polymorphisms (SNPs) generated by restriction site-associated DNA (RAD) sequencing across eight locations on the Tien (Mekong) and Hau (Bassac) Rivers in Vietnam. Pairwise FST values, principal component analysis and Structure analysis all indicate high levels of gene flow among the sites sampled across the MD. In contrast to the lack of genetic structure, high levels of relatedness were found, including 26 putatively related pairs, as well as an effective population size (Ne) of less than 500 across the MD. While panmixia indicates that fragmentation of this population is not presently an important threat, a low Ne estimate suggests this species may not be resilient to long-term environmental changes in the MD. The reliance on P. melanochir as a food resource may be contingent on management and mitigation of low effective population sizes

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

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 bio-diversityloss crisis

Results of the collaborative Lake Ontario bloater restoration stocking and assessment, 2012–2020

Bloater, Coregonus hoyi, are deepwater planktivores native to the Laurentian Great Lakes and Lake Nipigon. Interpretations of commercial fishery time series suggest they were common in Lake Ontario through the early 1900s but by the 1950s were no longer captured by commercial fishers. Annual bottom trawl surveys that began in 1978 and sampled extensively across putative bloater habitat only yielded one individual (1983), suggesting that the species had been locally extirpated. In 2012, a multiagency restoration program stocked bloater into Lake Ontario from gametes collected in Lake Michigan. From 2012 to 2020, 1,028,191 bloater were stocked into Lake Ontario. Bottom trawl surveys first detected stocked fish in 2015, and through 2020 ten bloater have been caught (total length mean = 129 mm, s.d. = 44 mm, range: 96–240 mm). Hatchery applied marks and genetic analyses confirmed the species identification and identified stocking location for some individuals. Trawl capture locations and acoustic telemetry suggested that stocked fish dispersed throughout the main lake within months or sooner, and stocking and depth distribution was similar to historic distributions in Lake Ontario and other Great Lakes. Predicted bloater trawl catches, based on modeled population abundance and trawl survey efficiency, were similar to observed catches, suggesting that post-stocking survival is less than 20% and contemporary bottom trawl surveys can quantify bloater abundance at low densities and track restoration