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With increasing human population, rising consumer demand, and intensification of industrial fishing, many valued fisheries are in decline. This review and synthesis explores how genetics informs classical fisheries management programs, especially in the context of managing declining fisheries resources. Discussing underlying principles and illustrative case studies drawn as possible from Southeast Asia, I focus upon application of genetics to: (1) define biologically based management units, (2) monitor the impacts of fisheries and fishery management actions, and (3) guide and evaluate fisheries restoration activities. Because overexploitation and declining fisheries arise from issues of economics, sociology, and politics, an effective approach to their solution must itself be interdisciplinary; application of genetic principles provides a valuable addition to such a holistic fisheries management program. Increasingly, progressive fisheries management agencies have in-house capabilities for genetic assessment and monitoring functions. Against this background, developing countries might seek to build their capacity for applied population genetics, either within fisheries management agencies or via scientific collaboration with research-oriented universities. While much progress has been achieved, the task of applying genetics to the effective management of declining fisheries is large and mostly before us.

1. Connectivity among stream fish populations allows for exchange of genetic material and helps maintain genetic diversity, adaptive potential and population stability over time. Changes in species demographics and population connectivity have the potential to permanently alter the genetic patterns of stream fish, although these changes through space and time are variable and understudied in small-bodied freshwater fish. 2. As a spatially widespread, common species of benthic freshwater fish, the variegate darter (Etheostoma variatum) is a model species for documenting how patterns of genetic structure and diversity respond to increasing isolation due to large dams and how scale of study may shape our understanding of these patterns. We sampled variegate darters from 34 sites across their range in the North American Ohio River basin and examined how patterns of genetic structure and diversity within and between populations responded to historical population changes and dams within and between populations. 3. Spatial scale and configuration of genetic structure varied across the eight identified populations, from tributaries within a watershed, to a single watershed, to multiple watersheds that encompass Ohio River mainstem habitats. This multiwatershed pattern of population structuring suggests genetic dispersal across large distances was and may continue to be common, although some populations remain isolated despite no apparent structural dispersal barriers. Populations with low effective population sizes and evidence of past population bottlenecks showed low allelic richness, but diversity patterns were not related to watershed size, a surrogate for habitat availability. Pairwise genetic differentiation (F-ST) increased with fluvial distance and was related to both historic and contemporary processes. Genetic diversity changes were influenced by underlying population size and stability, and while instream barriers were not strong determinants of genetic structuring or loss of genetic diversity, they reduce population connectivity and may impact long-term population persistence. 4. The broad spatial scale of this study demonstrated the large spatial extent of some variegate darter populations and indicated that dispersal is more extensive than expected given the movement patterns typically observed for small-bodied, benthic fish. Dam impacts depended on underlying population size and stability, with larger populations more resilient to genetic drift and allelic richness loss than smaller populations. 5. Other darters that inhabit large river habitats may show similar patterns in landscape-scale studies, and large river barriers may impact populations of small-bodied fish more than previously expected. Estimation of dispersal rates and behaviours is critical to conservation of imperilled riverine species such as darters. ; Virginia Department of Game and Inland Fisheries; U.S. Department of Agriculture Hatch ProgramUnited States Department of Agriculture (USDA); U.S. Department of Agriculture National Institute for Food and AgricultureUnited States Department of Agriculture (USDA); U.S. Geological SurveyUnited States Geological Survey; Virginia Tech; Virginia Department of Mines, Minerals, and Energy ; Virginia Department of Game and Inland Fisheries; U.S. Department of Agriculture Hatch Program; Virginia Department of Mines, Minerals, and Energy; U.S. Department of Agriculture National Institute for Food and Agriculture; U.S. Geological Survey; Virginia Tech ; Public domain authored by a U.S. government employee

The overall goal of the study was to evaluate effects of landscape features, barriers, on Brook Trout Salvelinus fontinalis population genetics and to identify a potential barrier height threshold where genetic diversity was reduced upstream of the barrier and differentiation and relatedness increase. We screened variation at eight microsatellite DNA loci within Brook Trout populations upstream and downstream of ten putative natural barriers ranging in height from 1.5 to 61 m to quantify allelic variation, differentiation (F-ST), individual assignment probability (Q), and relatedness (r(xy)). Average gene diversity per locus (H), differentiation (F-ST), and mean relatedness values (r(xy)) became significantly greater in relation to barrier height starting at 4 m according to piecewise linear regression. This potential barrier height threshold is greater than the barrier height criterion identified for Brook Trout based on physical criteria and jumping ability (0.74 m). The 4 m barrier-height criteria can be used to identify barrier sites where Brook Trout populations may be at risk due to reduced genetic diversity and increased relatedness. ; USDA Forest Service (Northern Research Station, Southern Research Station, and Region 9); Virginia Tech Department of Fish and Wildlife Conservation ; This study was funded by the USDA Forest Service (Northern Research Station, Southern Research Station, and Region 9) and the Virginia Tech Department of Fish and Wildlife Conservation. We thank K. Nislow for his feedback on this study and help with data analysis. We thank the U.S. Geological Survey, Conte Anadromous Fish Laboratory for providing laboratory facilities for processing fin clip samples. We thank B. Letcher, J. Coombs, P. Schueller, and G. Mendez for their help in the fish genetics laboratory. We thank J. Kuykendall and R. Stidham for logistical support. We also thank B. Flynn, C. B. Fox, A. Palmeri, J. Emmel, M. O'Melia; D. Belkoski, D. Hagedorn, J. Herrala, P. Lung, A. May, and M. Vincie for their hard work in the field. All procedures performed as a part of this research were performed in accordance with ethical standards approved by the Virginia Tech Animal Care and Use Committee. ; Public domain authored by a U.S. government employee

Understanding the reproductive biology of the endangered Epioblasma capsaeformis of the eastern United States is critical to conservation efforts at mussel hatcheries. We studied how males influenced gravidity among females held in captivity. Percent males (0%, 33%, 50%, and 67%) within a holding system was used as the predictor variable. Our response variables were percent females observed gravid, number of eggs and glochidia per gravid female, total eggs (sum of eggs and glochidia) per gravid female, and proportion of total eggs successfully fertilized and developed into glochidia. Mean percent of females gravid in the male treatments were 73%, 85%, 69%, and 60%, respectively, with no evidence that treatments differed significantly from one another. However, the treatment without males had significantly lower mean number of total eggs observed (4,533 vs. 5,868 to 7,330), with fewer viable glochidia (1,354 vs. 5,645 to 6,920). Most of the eggs in the treatment without males were unfertilized at experiment completion (3,179 vs. 206 to 410), with a much lower percentage of transformed glochidia (27% vs. 94 to 97%). Our study documents the important role that males play in fertilizing females for production of glochidia and that key reproductive processes occurred in captivity. ; U.S. Fish and Wildlife ServiceUS Fish & Wildlife Service [417689] ; This work was supported by the U.S. Fish and Wildlife Service [417689]. ; Public domain authored by a U.S. government employee

We assessed parentage within and among maternity colonies of northern long-eared bats (Myotis septentrionalis (Trouessart, 1897)) in north-central Kentucky, USA, from 2011 to 2013 to examine colony social structure, formation, and membership dynamics. We intensively sampled colonies in close and remote (>10 km) proximity before and after targeted day-roost removal. Colonies were not necessarily composed of closely related individuals, although natal philopatry was common. Adjacent colonies often contained maternally related individuals, indicating that some pups did disperse, albeit not far from their natal home range. Whereas some young had been sired by males also collected on site, most had not, as would be expected since the species mates in fall near hibernacula across a wider landscape. The number of parentages that we inferred among colonies, however, suggests that outside the maternity season, social groups may be relatively flexible and open. Analysis of microsatellite DNA data showed a low F-ST (0.011) and best fit to a model of one multilocus genotypic cluster across the study area. We observed high turnover in colony membership between years in all colonies, regardless of roost-removal treatment. Our results suggest that female northern long-eared bats exhibit fidelity to a general geographic area and complex, dynamic social-genetic structure. ; U.S. Army Environmental Quality and Installation Basic Research 6.1 program; Virginia Agricultural Experiment Station; U.S. Department of Agriculture National Institute of Food and AgricultureUnited States Department of Agriculture (USDA) ; This research was supported by the U.S. Army Environmental Quality and Installation Basic Research 6.1 program. The Kentucky Department of Fish and Wildlife Resources graciously provided field housing for this project. Additional funding was provided by the Virginia Agricultural Experiment Station and the U.S. Department of Agriculture National Institute of Food and Agriculture. The manuscript was improved by attending to the comments of the anonymous reviewers. The use of any trade, product, or firm names does not imply endorsement by the U.S. Government. ; Public domain authored by a U.S. government employee

Identification and conservation of genetic diversity within and among freshwater fish populations are important to better manage and conserve imperiled species. The Carolina Madtom Noturus furiosus is a small, nongame catfish that is endemic to the Tar and Neuse River basins of North Carolina. Genetic structure has not been studied in the species, and given recent population declines in both basins, identification of remaining genetic diversity within the species is vital for informing conservation efforts. To assess the status and trends of Carolina Madtom genetic structure, we analyzed genetic markers from 173 individuals to (1) define population genetic structure, (2) assess intra- and interbasin genetic differentiation in the Tar and Neuse River basins, and (3) present management implications to guide conservation efforts. Using 10 microsatellite primers developed for the related Yellowfin Madtom N. flavipinnis, we observed low genetic diversity in Carolina Madtoms. Genotype frequencies within samples were not in Hardy-Weinberg equilibrium, with a deficit of heterozygotes that could be due to family structure, inbreeding, or segregation of null alleles. Mean (+/- SD) M-ratios for the Tar River (0.414 +/- 0.117) and Neuse River (0.117 +/- 0.102) basin collections indicated that both populations have experienced recent demographic bottlenecks, with that in the Neuse River basin population being more severe. Effective population size estimates for the respective populations were small, on the order of tens of individuals, driving low genetic diversity within populations. However, the multilocus population differentiation metrics GST ' (mean +/- SE = 0.135 +/- 0.031) and D-EST (0.125 +/- 0.029) were significantly different from zero (P < 0.001), indicating significant genetic differentiation between the Tar and Neuse River basin populations. Our findings will inform managers on the status of genetic variation in the Carolina Madtom and will guide conservation toward protective listing and management decisions to maintain the viability of this important endemic species. ; NCWRC through the State Wildlife Grant Program; Virginia Agricultural Experiment Station under the U.S. Department of Agriculture's National Institute for Food and Agriculture; North Carolina State University; NCWRC; U.S. Geological SurveyUnited States Geological Survey; USFWSUS Fish & Wildlife Service; Wildlife Management Institute ; Published version ; Funding for this research was provided by the NCWRC through the State Wildlife Grant Program. We thank William Wood, Joseph McIver, Spencer Gardner, Tom Fox, Zoe Nichols, and Mike Walter for field and laboratory support. The manuscript was strengthened by attention to the comments of the anonymous peer reviewers. The participation of co-author Eric M. Hallerman was supported in part by the Virginia Agricultural Experiment Station under the U.S. Department of Agriculture's National Institute for Food and Agriculture. The North Carolina Cooperative Fish and Wildlife Research Unit is jointly supported by North Carolina State University, NCWRC, U.S. Geological Survey, USFWS, and Wildlife Management Institute. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government. There is no conflict of interest declared in this article. ; Public domain authored by a U.S. government employee

Walleye (Sander vitreus) is a popular sportfish threatened by overexploitation, habitat destruction, and loss of genetic integrity due to non-native walleye stocking. Previous studies have identified a genetically distinct lineage of walleye in the Mobile River Basin, but further work is needed to assess population structure and introgression among this southern lineage and northern populations. Here we generated 2782 genome-wide single nucleotide polymorphisms (SNPs) to characterize the genetic uniqueness of southern walleye. We also found strong evidence for a historical declining population trend with reduced genetic diversity and effective population size in a southern walleye population of conservation importance. A 68-SNP panel was developed for rapid identification of genetic integrity and hybrid classification among northern and southern walleye, enabling us to identify an anthropogenic hybrid zone resulting from the previous introduction of northern walleye into the Black Warrior River drainage, Alabama. Our results highlight the need for conservation management of southern walleye in the Mobile River Basin, with our 68-SNP assay already being implemented in ongoing stream survey and captive breeding programs. ; Alabama Department of Conservation and Natural Resources; Chinese Scholarship Council (CSC) award; Virginia Agricultural Experiment Station through the US Department of Agriculture Hatch Program ; This work was supported by funding to the Southeastern Fish Genetics Cooperative (E. Peatman, Director), particularly support from the Alabama Department of Conservation and Natural Resources. H.Z. was supported by the Chinese Scholarship Council (CSC) award. E.H. was supported in part by the Virginia Agricultural Experiment Station through the US Department of Agriculture Hatch Program. This is contribution No. 5079 from NOAA Pacific Marine Environmental Laboratory. We thank all those individuals who have provided walleye samples or assisted with sample collections. We thank Balaji Chattopadhyay for the assistance in our demography analysis and Matthew Neilson (USGS) for providing us walleye range shapefiles. All authors declare no conflict of interest. ; Public domain authored by a U.S. government employee