Canis lupus capture targets

Island populations are at heightened risk of inbreeding due to reduced
mating opportunities with unrelated conspecifics. Extensive inbreeding can
result in inbreeding depression (reduced fitness of individuals with
related parents). Alexander Archipelago wolves (Canis lupus ligoni) are a
geographically isolated subspecies that occur in the Southeast Alaskan
panhandle, USA and coastal British Columbia, Canada. Wolves on the Prince
of Wales Island complex (POW) in Southeast Alaska are expected to have
lower levels of resiliency because they are a small, insular population
that has experienced habitat fragmentation and cycles of moderate to heavy
harvest. To understand the extent of population structure and inbreeding
in Alexander Archipelago wolves, we designed a DNA hybridization capture
for wolves and sequenced captured DNA from 58 individuals sampled from
across Southeast Alaska during 2002–2016. Estimates of the proportion of
the genome in runs of homozygosity (FROH) regardless of run length
revealed that POW wolves were most inbred compared to wolves in other
areas of Southeast Alaska. Wolves on POW also had more long (≥10 Mb) runs
of homozygosity than the other populations we assessed, indicating more
frequent mating between individuals with recent common ancestors (1–10
generations ago). This pattern indicates a smaller population size for POW
wolves in the recent past compared to other Southeast Alaskan populations.
Wolves on POW exhibit an extent of inbreeding similar to that observed in
Isle Royale National Park wolves, a population that has exhibited severe
inbreeding depression. Our work demonstrates the utility of using genomic
capture data to infer individual inbreeding so that proactive management
(e.g. setting population targets and harvest quotas, curtailing habitat
alteration, etc.) can be considered to ensure the long-term sustainability
of small, isolated populations.

岛屿种群因难以与无亲缘关系的同种个体交配，近交风险显著升高。大范围近交可引发近交衰退（inbreeding depression，即双亲具亲缘关系的个体适合度降低）。亚历山大群岛狼（Canis lupus ligoni）是地理隔离的狼亚种，分布于美国阿拉斯加东南部狭长海岸带及加拿大不列颠哥伦比亚省沿海区域。位于阿拉斯加东南部的威尔士王子岛群（Prince of Wales Island Complex, POW）内的狼群，其种群恢复力被认为更低——这是由于该种群规模较小、处于岛屿隔离状态，且经历过生境破碎化与中度至高强度的猎捕周期。为明确亚历山大群岛狼的种群结构与近交程度，本研究开发了针对狼的DNA杂交捕获技术，并对2002至2016年间在阿拉斯加东南部全域采集的58份样本的捕获DNA完成测序。不计纯合子片段长度的基因组纯合度（FROH，即基因组中纯合子片段占比）估算结果显示，POW狼群的近交程度高于阿拉斯加东南部其他区域的狼群。相较于本研究评估的其他种群，POW狼群的长片段（≥10 Mb）纯合子片段数量更多，表明其1至10代内的近期亲缘个体交配事件更为频繁。该模式提示，相较阿拉斯加东南部其他狼群种群，POW狼群在近期的种群规模更小。POW狼群的近交程度与皇家岛国家公园的狼群种群相近，后者已出现严重的近交衰退现象。本研究证实了利用基因组捕获数据推断个体近交程度的实用性，据此可通过主动管理措施（如设定种群目标与猎捕配额、限制生境破坏等）保障小型隔离种群的长期存续。