臺灣野豬和蘭嶼豬遺傳與形態之時空變異

豬隻馴化是人類跨入文明最重要的關鍵指標之一。家豬與野豬同種（Sus scrofa），且家豬由野豬馴化而來。透過長期的育種過程，馴化改變了野豬的遺傳與形態特徵。臺灣野豬（Sus scrofa taivanus）為臺灣特有亞種，雖然野豬在地馴化（in situ domestication）發生在東亞的許多馴化中心，但臺灣本地家豬－蘭嶼豬缺乏能夠直接證實馴化事件的考古學與遺傳證據，因此被認為是隱祕馴化（cryptic domestication）。為了釐清在臺灣發生的豬隻馴化事件，本論文擬研究同域之臺灣野豬和蘭嶼豬遺傳與形態之時空變異，建構臺灣潛在野豬馴化模型，並闡明臺灣野豬馴化模式。　　首先，桃園豬為最早自中國引入臺灣之家豬品種，為了釐清桃園豬與蘭嶼豬之間之親緣關係，本論文使用粒線體DNA序列與18對微衛星標記研究桃園豬族群之母系遺傳與遺傳多樣性，並利用遺傳分化指數評估桃園豬、亞洲型豬種與歐洲型豬種之族群分化。結果顯示，桃園豬族群中只存在一種基因單套型，且此基因單套型與中國長江型和華中型家豬品種群集，而與蘭嶼豬有所區分。此外，基於微衛星標記的多型性，族群內正近親係數（FIS）指出桃園豬保種族群遭受近親繁殖，高族群遺傳分化指數（FST）則顯示不同品種間之高度遺傳分化。非計量多元尺度分析（Non-metric multi-dimensional scaling）呈現7種品種間之清晰的幾何結構。因此，桃園豬母系起源於中國長江與華中地區，引入臺灣後，隔離飼養後造成遺傳分化。此外，桃園豬保種族群在粒線體及核基因組均喪失遺傳多樣性。　　其次，為了追溯蘭嶼豬之起源，本論文收集臺灣野豬、蘭嶼豬與菲律賓本地家豬，進行全面性之遺傳親緣關係研究。共計增幅345頭野豬與家豬之粒線體控制區序列全長，並加入206條亞洲各地區野豬序列進行後續分析。遺傳特徵和貝葉式親緣關係樹結果顯示，臺灣野豬中具有兩種遙遠親緣關係之不同血裔，分別命名為臺灣野豬裔（Formosan wild boar lineage）及蘭嶼臺灣野豬裔（Formosan wild boar with Lanyu sign lineage）。分子時鐘分析指出蘭嶼臺灣野豬裔與臺灣野豬裔大約在60萬年前分歧，蘭嶼臺灣野豬裔為東亞島嶼野豬中最早播遷至東亞島嶼，並隔離分歧出來。此外，結合親緣地理分析，本論文提出6個亞洲野豬冰河時期播遷事件，其中，至少有3起事件發生於東亞島嶼，隨後冰川退去形成的地理隔離，可能導致亞洲野豬亞種之異域分化。另一方面，蘭嶼豬和蘭嶼臺灣野豬裔相似之遺傳特徵與親緣獨特性，支持蘭嶼臺灣野豬裔為蘭嶼豬之野生祖先，此結果證實了臺灣潛在的豬隻在地馴化。最後，擁有蘭嶼臺灣野豬裔遺傳特徵之野豬和家豬遍布於臺灣、蘭嶼及菲律賓，呈現地理上之連續性分布，這樣的連續性分布可能意味著人類介入的豬隻播遷路線。　　再者，為了進一步確認蘭嶼豬於時間尺度上，何時開始存在於臺灣，故迫切需要一種在考古遺址中區分野豬和家豬的有效方法。本論文將建構一個骨測量和幾何形態測量分析的資料庫，能夠應用並準確區分野豬和家豬。共收集105個豬隻下顎骨樣本，包含68頭臺灣野豬及37頭蘭嶼豬，首先，藉由現生臺灣野豬與蘭嶼豬一系列下顎骨與牙齒形態測量，獲得其形態特徵，包含30項下顎骨測量值、22項前臼齒與臼齒頰舌徑及長度、6項第三大臼齒長寬與45個描繪第三大臼齒形狀之地標點。透過學生氏t檢定及主成分分析驗證臺灣野豬與蘭嶼豬之形態差異，並建立判別標準，結果顯示臺灣野豬與蘭嶼豬形態具顯著差異，不同之骨測量及幾何形態測量均能透過主成分分析有效鑑別臺灣野豬與蘭嶼豬。接著，收集橫跨4,000年，來自5個不同的考古遺址（恆春半島和南科園區遺址群），共計22個遺址出土豬牙樣本，應用這些樣本與現生形態資料庫比對，釐清各遺址之豬隻種屬，並確認蘭嶼豬存在於臺灣之時間。結合第三大臼齒大小與形狀分析結果，推斷至遲距今1,500年前，臺灣才開始有與蘭嶼豬形態相似牙齒的出現。　　綜上所述，本論文指出桃園豬母系起源於中國長江與華中地區，而與蘭嶼豬有所區分。此外，支持蘭嶼臺灣野豬裔為蘭嶼豬之野生祖先，並提出臺灣發生的豬隻在地馴化的想法。最後，建構了一系列現生臺灣野豬與蘭嶼豬的形態資料庫，此形態資料庫未來將有助於應用在現生樣本與遺址出土豬牙區分野豬和家豬上。

關鍵字

馴化；臺灣野豬；幾何形態測量法；蘭嶼豬；粒線體DNA ；骨測量法；親緣地理學

並列摘要

Pig domestication is one of the most important key indicators showing our entry into civilization. A long breeding progress mediated the changes of genetic and morphologic characteristics from wild boars to domestic pigs via domestication. Formosan wild boar (Sus scrofa taivanus, FWB) is an endemic subspecies in Taiwan. While in situ domestication of wild boar occurred at a number of domestication centers across East Asia, corroborating archeological and genetic evidence of pig domestication on Taiwan is lacking, leading to domestication being described as cryptic domestication. This characterization applies to Lanyu pig (LY) -- a domestic pig breed found on Taiwan. To better understand pig domestication, this study examines chronospatial variation of the genetics and morphology of sympatric FWB and domestic LY to build a model of potential wild boar domestication on Taiwan and elucidate wild-boar domestication patterns in the region. 　　Firstly, Taoyuan pig (TY) is a native Taiwan breed first introduced to Taiwan from China. To clarify the phylogenetic relationship between TY and LY, mitochondrial DNA sequences and 18 microsatellite markers were used to investigate maternal lineage and genetic diversity within the TY population. Population differentiation among TY, Asian type, and European type pig breeds was also evaluated using differentiation indices. Only one D-loop haplotype of the TY was found. It clustered with Lower Changjiang River Basin and Central China Type pig breeds, and was distincted from LY. Based on the polymorphism of microsatellite markers, a positive fixation index value (FIS) indicates that the conserved TY population suffers from inbreeding. In addition, high FST values were obtained, revealing high differentiation among these breeds. Non-metric multi-dimensional scaling showed a clear geometric structure among 7 breeds. Together these results indicate that maternally TY originated in the Lower Changjiang River Basin and Central China; however, since being introduced to Taiwan differentiation has occurred. In addition, TY has lost genetic diversity in both its mitochondrial and nuclear genomes. 　　Secondly, a comprehensive phylogenetic study of FWB and LY was conducted on animals sourced from Taiwan, Lanyu, and the Philippines to trace the origin of LY. Phylogenetic analyses were conducted using full mitochondrial control region sequences from 345 wild boar and domestic pigs. These were studied in concert with existing reports on 206 Asian wild boar. Genetic characteristics and Bayesian phylogenetic tree results identified 2 wild boar lineages of remote phylogenetic relationship. These were Formosan wild boar lineage (FWBL) and Formosan wild boar with Lanyu sign lineage (FWBLYL). Molecular clock analyses indicate FWBLYL diverged earlier than other insular East Asia wild boar, and show FWBLYL and FWBL diverged approximately 0.60 million years ago. This result supports boar of FWBLYL being the earliest wild boar to have spread and become isolated in insular East Asia. In addition, the study proposes 6 Asian wild boar dispersion routes during glacial periods. At least 3 of these events occurred in insular East Asia with subsequent geographical isolation after glacial recession. This isolation potentially led to allopatric differentiation of wild boar subspecies. Also, the similar genetic signature and phylogenetic uniqueness of LY to wild boar of FWBLYL suggests such wild boar were the wild ancestor of domestic LY. This result indicates potential in situ domestication occurring on Taiwan. Finally, pigs possessing FWBLYL’s genetic signatures were distributed continuously among Taiwan, Lanyu, and the Philippines. This pattern may signify human-mediated pig dispersal routes. 　　Thirdly, to further confirm the existence of LY on Taiwan in chronological scale, an effective method to distinguish wild boar and domestic pigs in archaeological sites is urgently needed. In this study, an applicable and accurate database based on osteometric measurements and geometric morphometric analysis was constructed. Mandibles of 68 FWB and 37 LY were collected. Thirty mandible measurements, 22 buccolingual measurements, 6 measurements of third molar size, and 45 landmarks depicted third molar shape were applied to obtain the morphological characteristics of FWB and LY. Student’s t-test and principal component analysis were performed to demonstrate the morphological difference of FWB and LY, and the results indicated three osteometric measurement methods and one geometric morphometric analysis showed the morphological distinguishability between FWB and LY. Twenty-two Sus teeth excavated from 5 different archaeological sites across nearly 4,000 years throughout Taiwan were applied to compare with modern morphological database to confirm the existence of LY in chronospatial scale. Both third molar size and shape analyses showed the morphology of LY type emerged at least about 1,500 YBP in archaeological Sus third molar. 　　In conclusion, this study indicates TY originated in the Lower Changjiang River Basin and Central China, and is distinct from LY. In addition, this study supports the idea that a domestication event occurring in Taiwan with the discovery that the wild ancestor of LY is common to certain FWB. Finally, a series of morphological database of modern FWB and LY were constructed. The database will be helpful in distinguishing between wild boar and domestic pigs in both modern specimens and archaeological Sus remains.