地理與生態因子在島嶼上黃芩屬物種的族群分化與快速種化上的效應
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2020
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Abstract
研究背景：
島嶼物種的快速種化可以由隨機的力量、遷徙拓殖、基因交流以及天擇等力量驅動。然而島嶼面積不大，頻繁的物種接觸導致的基因交流理應減少物種或族群分化，現今我們常以生態力量趨動的生態種化解釋之，因為生態因子如環境氣候異質性等使族群間有區域性適應阻擋部分基因組的基因交流，區域性適應影響的基因組週邊區域因連鎖而產生搭便車效應加強了該區段的基因交流阻隔，而漸漸的這些阻隔區域增加以到一定程度並完全種化，這些力量可以共同作用以加快島嶼物種的分化速度。研究具高特有種比例的物種有助了解這些力量在祖先物種拓殖入島嶼後加快分化速度的相對重要性。台灣產的黃芩屬特有種比例比起其他東亞及東南亞的鄰近島嶼或陸塊都高上許多，全部共8種，即有6種為特有種。過去的研究指出台灣產黃芩屬的多樣性來自至少三次的拓殖事件以及島嶼在地的快速種化。而台灣產的黃芩利用分子定年計算出的最早分歧時間不過50萬年內，其中被命名作indica group的印度黃芩、布烈氏黃芩、田代氏黃芩及南台灣黃芩形成單一分支且分歧時間短於20萬年內，被認為可能是其中一次拓殖事件後的在地快速種化。我們想以台灣產黃芩屬成員作材料切入生態種化如何與台灣高特有性之關聯性。
方法
我們使用了微衛星體基因型檢測作為快速變異的遺傳資料進行分析。並輔以溯祖理論分析法及演化模型選擇找出最適合解釋台灣產黃芩是否一如生態種化之預測分化早期有基因交流。並以環境因子與遺傳分化進行關聯性分析，了解遺傳變異或族群分化是否與環境因子有關。
結果
我們優先了解這群物種來檢測indica group是否主要來自單次的快速種化，以利後續設計實驗了解台灣產黃芩的快速種化之因。然而，依據溯祖理論IMa3分析，我們發現indica group在分歧時伴隨旺盛的基因交流，然而在使用貝氏歸群分析時卻顯示這些近期分歧且鄰域物佈的物種甚少種間遺傳混雜，顯示物種明顯分化，考量過去旺盛的基因交流及台灣島面積不大，物種易接觸，這麼短的分歧時間實難分化出這麼多特有種，我們藉分歧時有種間基因交流的情形，再依生態種化的概念，推論生態因子可能參與在這些快速種化的黃芩的物種維持與分化。我們挑選兩組共域/鄰域分佈的特有種，分別是田代氏與布烈氏黃芩組，以及向天盞與台北黃芩組來問答這個議題。我們利用以approximate Bayesian computation的方法進行溯祖模型選擇，發現田代氏黃芩與布烈氏黃芩有強烈的祖先性基因交流，然而現今已有明顯的分化及基因交流的阻斷。兩個物種的分化都可以由在地環境異質性及多環境因子組合的棲位分化來解釋。而向天盞及台北黃芩則展現不同的結果，不論是溯祖模擬模型選擇、群聚分析及單套形的樹形/網狀分析都無法清楚的區分特有的台北黃芩及廣布於東亞的向天盞。而可供區別的形態特徵如小堅果外衣紋路及葉型，在觀測後也證實僅是採集植物個體發育時期不同所致，並非可供物種區分的特徵。組合台北黃芩及向天盞的族群後發現族群間有明顯的遺傳結構，這些遺傳結構以廣義線性模型及座標軸分析等方法發現夏秋降雨量在族群的差異與族群遺傳分化有關。
結論
因此，無論是向天盞/台北黃芩組，或是布烈氏黃芩/田代氏黃芩組都發現明顯的族群尺度分化，這些分化都可以由氣候異質性及區域性適應解釋。換言之，氣候異質性及區域性適應均能促進台灣產黃芩屬成員讓族群分化，更可能加速種化以讓多樣性速率提升。
Background: Species diversification within an island can be invoked by stochastic process (eg. drift or geographic isolation), migration (or gene flow) and ecological factors (eg. divergent selection lead population differentiation). However, gene flow is often considered to homogenize the genetic component between populations or species as area of island may be so small that species may contact to each other. The ecological factors such as environment heterogeneity may lead local adaptation which can block gene flow in parts of the genome, and the hitchhiking effect may expand the isolation area of genome until the speciation complete. These processes are not mutually exclusive and may accelerate diversification rate of colonized species. Genus with high endemism in an island is therefore suitable for accessing the relative importance of both neutral and adaptive process on diversification of island species. The genus Scutellaria L. comprised eight species with six of them are endemic species, which is suitable for ecological speciation study. The endemism is almost the highest in East Asia. Previous studies revealed very recent divergence of these species (within 500 kilo years ago, kya) and at least three times colonization with subsequently radiation may invoke the high endemism of Taiwanese Scutellaria. Amongst them, S. indica, S. tashiroi, S. playfairii and S. austrotaiwanensis (hereafter: indica group) are the most monophyletic group in which relatively short divergent time (less than 200 kya). We aimed to ask whether the ecological species can be associated with rapid species diversification in Taiwanense Scutellaria. Methods We adopt microsatellite as our molecular marker due to its high mutation rate and variation. We also used coalescence analyses and evolutionary model choice to evaluate the magnitude of historical gene flow, so that we can check whether species divergence was accomplished with gene flow as expectation of ecological speciation. Results According to results of coalescence simulation using IMa3, highly historical gene flow can be found among members of indica group during divergence, but Bayesian clustering analysis revealed very few interspecific admixture, implying clear species divergence. Homogenizing genetic components between species can be often accived by historical gene flow. Therefore it is hard to believe that geographic factors along can lead to complete speciation in these rapid divergent Scutellaria. The historical gene flow often correlated to ecological speciation. Hence the ecological factors may also involve in these rapid divergent Scutelliara. We focus whether ecological factors can be associated with the divergence of the endemic Scutellaria in Taiwan. We adopt two sympatric or parapatric and morphological similar pair species as case, S. tashiroi/S. playfairii and S. barbata/S. taipeiensis, respectively, for understanding whether differentiation can be associated with neutral geographic distance or climatic driven local adaptation. We found that the clear divergence, local adaptation and niche differentiation can be found in former group even with consideration of geographic factors. Though gene flow can be detected with approximate Bayesian computation coalescence simulation analysis but differentiation in multidimensional hypervolume niches blocks the gene flow nowadays, indicating heterogeneity in environment drive divergence of S. tashiroi and S. playfairii. On the other hand, coalescence simulation, clustering analysis and tree/network analysis do not found the divergence between widespread species, S. barbata, and endemic S. taipeiensis. The distinct characters such as nutlet coat and leaf shape merely reflect different developmental stage or phenotypic plasticity. However, population level differentiation can be found to be associated with climatic factors such as Summer-Fall precipitation. Conclusions These two paired studies revealed that local adaptationdriven by environmental factors may lead population differentiation and may subsequently lead to rapid speciation.
Background: Species diversification within an island can be invoked by stochastic process (eg. drift or geographic isolation), migration (or gene flow) and ecological factors (eg. divergent selection lead population differentiation). However, gene flow is often considered to homogenize the genetic component between populations or species as area of island may be so small that species may contact to each other. The ecological factors such as environment heterogeneity may lead local adaptation which can block gene flow in parts of the genome, and the hitchhiking effect may expand the isolation area of genome until the speciation complete. These processes are not mutually exclusive and may accelerate diversification rate of colonized species. Genus with high endemism in an island is therefore suitable for accessing the relative importance of both neutral and adaptive process on diversification of island species. The genus Scutellaria L. comprised eight species with six of them are endemic species, which is suitable for ecological speciation study. The endemism is almost the highest in East Asia. Previous studies revealed very recent divergence of these species (within 500 kilo years ago, kya) and at least three times colonization with subsequently radiation may invoke the high endemism of Taiwanese Scutellaria. Amongst them, S. indica, S. tashiroi, S. playfairii and S. austrotaiwanensis (hereafter: indica group) are the most monophyletic group in which relatively short divergent time (less than 200 kya). We aimed to ask whether the ecological species can be associated with rapid species diversification in Taiwanense Scutellaria. Methods We adopt microsatellite as our molecular marker due to its high mutation rate and variation. We also used coalescence analyses and evolutionary model choice to evaluate the magnitude of historical gene flow, so that we can check whether species divergence was accomplished with gene flow as expectation of ecological speciation. Results According to results of coalescence simulation using IMa3, highly historical gene flow can be found among members of indica group during divergence, but Bayesian clustering analysis revealed very few interspecific admixture, implying clear species divergence. Homogenizing genetic components between species can be often accived by historical gene flow. Therefore it is hard to believe that geographic factors along can lead to complete speciation in these rapid divergent Scutellaria. The historical gene flow often correlated to ecological speciation. Hence the ecological factors may also involve in these rapid divergent Scutelliara. We focus whether ecological factors can be associated with the divergence of the endemic Scutellaria in Taiwan. We adopt two sympatric or parapatric and morphological similar pair species as case, S. tashiroi/S. playfairii and S. barbata/S. taipeiensis, respectively, for understanding whether differentiation can be associated with neutral geographic distance or climatic driven local adaptation. We found that the clear divergence, local adaptation and niche differentiation can be found in former group even with consideration of geographic factors. Though gene flow can be detected with approximate Bayesian computation coalescence simulation analysis but differentiation in multidimensional hypervolume niches blocks the gene flow nowadays, indicating heterogeneity in environment drive divergence of S. tashiroi and S. playfairii. On the other hand, coalescence simulation, clustering analysis and tree/network analysis do not found the divergence between widespread species, S. barbata, and endemic S. taipeiensis. The distinct characters such as nutlet coat and leaf shape merely reflect different developmental stage or phenotypic plasticity. However, population level differentiation can be found to be associated with climatic factors such as Summer-Fall precipitation. Conclusions These two paired studies revealed that local adaptationdriven by environmental factors may lead population differentiation and may subsequently lead to rapid speciation.
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Keywords
黃芩, 快速種化, 棲位模擬, ABC溯祖理論分析, Scutellaria, rapid speciation, niche modeling, ABC coalescence simulation