台灣特有種招潮蟹遺傳結構的研究
摘要
臺灣旱招潮為臺灣西部沿海潮間帶特有且瀕危的招潮蟹,棲息於破碎的海岸環境,且成體擴散能力極低。儘管如此,該物種仍展現出意料之外的高遺傳多樣性與基因交流。為了探討維繫此連通性的機制,我們結合全基因體單核苷酸多型(SNP)資料與水動力模型,以模擬幼體擴散對成體遺傳結構的影響。遺傳分析顯示強烈的自我補充、高度連通性及低遺傳分化。幼體漂流模擬結果與臺灣海峽南北向主要海流一致,顯示臺灣海峽的海流在基因流動中扮演關鍵角色。進一步將颱風事件納入模型後,結果顯示特定路徑的颱風可顯著增加幼體漂流距離。因為颱風在干擾成體棲地的同時也提供了幼體長距離擴散的機會,這種由颱風促成的擴散似乎能緩衝棲地破碎化的影響,並維持樣點間的遺傳連通性。然而,隨著氣候變遷可能改變颱風的頻率、強度與季節性,若此類擴散機會減少,可能會加劇族群間的遺傳隔離以及連通性下降。因此極端天氣事件在維持具浮游幼生階段的物種基因交流上相當重要,將颱風引發的物理過程應納入海洋保育策略中,極端氣候驅動的海洋環境變化預測,以及如何影響動態海岸棲地物種的長期存續,對維持族群連通性與復原力至關重要。
方法與執行步驟
Samples of Xeruca formosensis were collected from eight representative coastal wetland sites along the west coast of Taiwan, spanning the latitudinal range of the species from north to south as follows: Tamsui River, New Taipei City (TS: 25.172707, 121.406110), Xiangshan, Hsinchu City (XS: 24.786325, 120.909901), Gaomei, Taichung City (GM: 24.309685, 120.546957), Shengang, Changhua County (SG: 24.167326, 120.460932), Mailiao, Yunlin County (ML: 23.837211, 120.224266), Bazhang Estuary, Chiayi County (BZ: 23.326654, 120.115387), Qigu Zengwen Estuary, Tainan City (QG: 23.055399, 120.061944), and Gaoping Estuary, Kaohsiung City (GP: 22.478405, 120.415706). Sampling was conducted during low tide within three days before and after the spring tide in order to maximize accessibility to intertidal habitats and to standardize larval recruitment conditions among sites. At each locality, approximately 10 to 15 adult individuals were randomly captured by hand or small dip nets and temporarily stored in aerated containers. All specimens were transported to the laboratory on the same day to minimize stress, and a single walking leg from each individual was excised for DNA extraction before the crab was released back to its original capture location. Genomic DNA was isolated using a standard protocol and quantified for quality and concentration. We employed a double-digest RAD-sequencing (ddRAD) approach to obtain genome-wide SNPs. Genomic DNA was digested with selected restriction enzymes to generate sticky-ended fragments suitable for adaptor ligation. P1 and P2 adaptors incorporated individual or population-specific barcode sequences, Illumina PCR primer sites, and a protector sequence to avoid re-digestion. Enzyme choice and ligation conditions followed previously established protocols but were optimized for X. formosensis based on pilot tests. Sequencing was performed on an Illumina platform, and raw reads were demultiplexed by barcode using the process_radtags function in Stacks. After quality filtering, samples with excessive missing data or extreme divergence were excluded. High-quality loci were then assembled de novo and genotyped using ustacks, cstacks, gstacks, and sstacks modules within the Stacks pipeline. To examine larval dispersal, we used the Connectivity Modeling System (CMS), which is based on a Lagrangian particle-tracking framework and integrates a hydrodynamic model, an Individual-Based Model (IBM), and 11 sub-modules describing larval–ocean interactions. Oceanographic data were obtained from the Hybrid Coordinate Ocean Model (HYCOM) via the OPeNDAP data format, which provides a horizontal resolution of approximately 4 × 4 km for the domain spanning 116–122°E and 21–26°N. Coastal habitat grids delineating each sampling site were derived from the official coastal zone boundary dataset released by the National Land Administration of Taiwan on 8 April 2022. The IBM was parameterized according to larval traits, spawning location and timing, survival rates, vertical behavior, and pelagic larval duration documented for X. formosensis and closely related species. These parameters determined larval release schedules, vertical swimming responses, and settlement competency in the model, enabling realistic simulation of both passive and active dispersal processes
創新作為與跨域合作
This study presents an innovative cross-disciplinary framework that combines long-term oceanographic modeling with high-resolution molecular approaches to elucidate the mechanisms driving genetic connectivity in X. formosensis. We first used a 10-year hydrodynamic model of Taiwan Strait to simulate larval dispersal trajectories and settlement probabilities across fragmented coastal habitats. These dispersal simulations were then integrated with population genomic data from adult fiddler crabs to examine how larval transport processes influence observed gene flow and population structure at a fine spatial scale. Building on this baseline, we further assessed the effects of typhoon events by incorporating storm-driven hydrodynamic disturbances into the larval dispersal model. This integrated approach, linking physical oceanography, molecular ecology, and climate science, provides novel insights into how long-term ocean currents and episodic extreme weather events interact to shape genetic diversity and connectivity. Our findings also offer practical guidance for conserving coastal species under increasing climate variability.
預期成果與貢獻
Our results showed thatX. formosensis is capable of maintaining genetic connectivity among geographically separated populations through the exchange of a limited number of migrants (Fig 2). However, this connectivity is inherently fragile and highly susceptible to disruption. Simulation outcomes indicate that while frequent typhoon events can severely damage or eliminate adult intertidal habitats, they also enhance larval dispersal by extending zoeal drift distances (Fig 3). This increased dispersal provides larvae with a greater opportunity to maintain gene flow among populations, suggesting that typhoons can simultaneously act as both ecological disturbances and mechanisms for connectivity (Fig 4). Under projected climate change scenarios, which anticipate a reduction in typhoon frequency alongside increasing storm intensity, the conditions that facilitate larval dispersal may become less frequent. When combined with ongoing habitat loss from coastal development, these environmental changes are likely to constrain gene exchange and increase the risk of population isolation. Once genetic connectivity is compromised, the endemic X. formosensis may face rapid demographic decline and an elevated risk of extinction. Despite these insights, the ecology and behavior of the larval stage remain poorly understood, highlighting the need to clarify dispersal mechanisms to better interpret adult genetic structure and forecast population resilience.
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