Lack of spatial and temporal genetic structure of Japanese eel (Anguilla japonica) populations

Japanese eel (Anguilla japonica) is an important food source in East Asia
whose population has dramatically declined since the 1970s. Despite past
analysis with DNA sequencing, microsatellite and isozyme methods,
management decisions remain hampered by contradictory findings. For
example, it remains unresolved whether Japanese eels are a single
panmictic population or whether they harbor significant substructure.
Accurate assessment of population genetic substructure, both spatial and
temporal, is essential for determining the relevant number of distinct
management units appropriate for this species. In the present study, we
assayed genetic variation genome-wide using Restriction Site Associated
DNA Sequencing (RAD-seq) technology to analyze the population genetic
structure of Japanese eels. For analysis of temporal isolation, five
“cohort” samples were collected yearly from 2005 to 2009 in the Yangtze
River Estuary. For analysis of spatial structure, five “arrival wave”
samples were collected in China in 2009, and two arrival wave samples were
collected in Japan in 2001. In each cohort of each arrival wave, five
individuals were collected for a total of 55 eels sampled. In total,
214,210 loci were identified from these individuals, 106,652 of which
satisfied quality checks and were retained for further analysis. There was
relatively little population differentiation between arrival waves and
cohorts collected either at different locations during the same year
(Fst = 0.077) or at the same location collected over subsequent years
(Fst = 0.082), and locations displayed no consistent
isolation-by-distance.

日本鳗鲡（Anguilla japonica）是东亚地区重要的食物来源，但其种群数量自20世纪70年代以来大幅下降。尽管以往采用DNA测序、微卫星（microsatellite）和同工酶（isozyme）方法进行过分析，但相互矛盾的研究结果仍阻碍着管理决策的制定。例如，日本鳗鲡属于单一随机交配种群（panmictic population）还是存在显著的种群亚结构，这一问题仍未解决。准确评估种群遗传亚结构的空间和时间特征，对于确定该物种适宜的不同管理单元（management units）数量至关重要。本研究采用限制性位点相关DNA测序技术（Restriction Site Associated DNA Sequencing, RAD-seq）对日本鳗鲡的种群遗传结构进行分析，以检测全基因组范围内的遗传变异。为分析时间隔离，2005年至2009年期间每年在长江口采集5个“世代”（cohort）样本；为分析空间结构，2009年在中国采集了5个“洄游波”（arrival wave）样本，2001年在日本采集了2个洄游波样本。每个洄游波的每个世代中采集5个个体，共取样55尾鳗鲡。从这些个体中共鉴定出214210个基因座（loci），其中106652个通过质量检测并保留用于后续分析。无论是同年不同地点采集的洄游波与世代之间，还是同一地点不同年份采集的样本之间，种群分化程度均相对较低（Fst分别为0.077和0.082），且各地点未表现出一致的距离隔离效应（isolation-by-distance）。