2015年1月20日 星期二

[研討會報告CP12] 蝸居東部的隱藏種:以婚姻平權為名的彩虹大臍蝸牛

[研討會名稱] 2015動物行為暨生態學研討會

[發表型式] 壁報展示

[摘要]

蝸居東部的隱藏種:以婚姻平權為名的彩虹大臍蝸牛
Cryptic landsnail species in eastern Taiwan, Aegista diversifamilia

黃致維1、李彥錚2、林思民1、巫文隆2
1國立臺灣師範大學生命科學系
2中央研究院生物多樣性研究中心

臺灣大臍蝸牛Aegista subchinensis (Möllendorff, 1884)在以往被認為廣布於臺灣全島。2003年,李彥錚博士首次注意到東、西部的臺灣大臍蝸牛族群有形態分化。初步研究透過三個DNA片段(粒線體COI、16S和核ITS2基因)重建臺灣大臍蝸牛東、西部族群和近緣種(日本石垣島的A. vermis [Reeve, 1852]和宮古島的A. oculus [Pfeiffer, 1850])的親緣關係,並以殼形態分析臺灣大臍蝸牛東、西部族群,確立臺灣東部的大臍蝸牛族群應視為一物種,命名為彩虹大臍蝸牛A. diversifamilia,以向世界各國與臺灣為婚姻平權的努力致敬。根據三個DNA片段重建之親緣關係樹顯示臺灣大臍蝸牛和彩虹大臍蝸牛為姊妹種,而四物種間的bootstrap支持度均低,無法釐清種間的親緣關係。新增九個核基因片段(共十二個基因片段)重建之物種演化樹(species tree),則顯示彩虹大臍蝸牛和宮古島的A. oculus為姊妹種。

關鍵字:八重山群島、大臍蝸牛、柄眼目、扁蝸牛、軟體動物

蝸居東部的隱藏種:以婚姻平權為名的彩虹大臍蝸牛


[研討會報告CP02] 東亞地區山椒蝸牛科 (軟體動物門:腹足綱) 之親緣關係、 親緣地理和地景遺傳學研究

[研討會名稱] 2009 年台大師大生態演化聯合學術發表會

[發表型式] 壁報展示

[摘要]

東亞地區山椒蝸牛科 (軟體動物門:腹足綱) 之親緣關係、親緣地理和地景遺傳學研究

黃致維1、林思民1、巫文隆2
1臺灣師範大學生命科學系
2中央研究院生物多樣性研究中心

親緣地理學兼顧種內演化過程與地理分布模式,為一整合性之研究學門。複雜的地理環境與地質歷史,造就台灣的高度生物多樣性。山椒蝸牛科 (Assimineidae) 廣布於南極洲以外的各大陸,且為高度物種多樣性的兩棲性蝸牛,沿海、河口、淡水和陸域環境均有不同山椒蝸牛種類棲息。目前的山椒蝸牛科的分類仍以形態與解剖構造為主,許多物種的分類近年來有大幅度變動且有許多新種發表,因此山椒蝸牛科的親緣關係亟待進一步釐清。東亞地區的山椒蝸牛科由於擁有豐富的物種多樣性,而成為絕佳的研究材料,可探討其起源、親緣關係和親緣地理學。本研究將針對以下主題:(1) 東亞地區的山椒蝸牛之親緣關係與台灣的山椒蝸牛物種來源;(2) 台灣的陸域和河口的山椒蝸牛物種之比較親緣地理;(3) 台灣山椒蝸牛 (Assiminea taiwanensis) 的地景遺傳,探討不同地景特徵對其族群遺傳之影響。用於親緣關係分析的東亞地區山椒蝸牛物種將採集或交換自韓國、日本、台灣、中國和菲律賓;親緣地理分析的部份,依照台灣的主要水系和山脈進行採集;台灣山椒蝸牛的地景遺傳分析,將針對其模式產地和台北盆地,依據不同的棲地類型進行採集。利用酚-氯仿法進行DNA粗萃取。以粒線體去氧核醣核酸 (COI, CYTB, ND1, 12S and 16S rRNA) 作為分子特徵,以最大概似法 (maximum likelihood) 和貝氏法 (Bayesian method) 重建山椒蝸牛科之親緣關係;並利用分子變方分析 (AMOVA) 和單基因型網狀脈絡圖 (haplotype network) 等方法分析親緣地理。東亞地區的山椒蝸牛科之親緣關係和台灣山椒蝸牛的地景遺傳研究將於未來釐清;本研究預期台灣的山椒蝸牛科動物相和親緣地理,可能是由擴散和地理割裂事件共同影響所形成。

關鍵字:山椒蝸牛科、地景遺傳學 、腹足綱、親緣關係、親緣地理學

東亞地區山椒蝸牛科 (軟體動物門:腹足綱) 之親緣關係、親緣地理和地景遺傳學研究


[研討會報告CP01] 應用粒線體COI片段探討台灣的河殼菜蛤族群遺傳結構

[研討會名稱] 2009 年動物行為暨生態學術聯合年會

[發表型式] 口頭報告

[摘要]

應用粒線體COI片段探討台灣的河殼菜蛤族群遺傳結構 Population Genetic Structure of Limnoperna fortunei (Dunker 1856) in Taiwan Based on Sequences of Mitochondrial Cytochrome C Oxidase Subunit I

黃致維1,2、姜鈴3
1台灣師範大學生命科學系博士班研究生
2中央研究院生物多樣性研究中心 軟體動物研究室
3彰化師範大學生物學系 助理教授

原生於亞洲大陸的淡水雙殼貝河殼菜蛤 Limnoperna fortunei (Dunker, 1856) 先後入侵至香港、台灣、日本、阿根廷、烏拉圭、巴拉圭,巴西和玻利維亞。河殼菜蛤在台灣的確定族群,先後發現於台北縣新店溪直潭壩、南投縣日月潭和桃園縣石門水庫。為釐清台灣3個水系間河殼菜蛤的族群關係,本研究應用粒線體COI片段的501個核苷酸序列,分析台灣、日本和阿根廷6個水系共326隻個體,21個變異點區分出17種單基因型。台灣 (Hd = 0.233, π = 0.000275) 和阿根廷 (Hd = 0.378, π = 0.000253) 的河殼菜蛤族群之遺傳多樣性偏低,且mismatch analysis呈現單一高峰,顯示為單次引入,且有明顯奠基者效應 (founder effect);而日本的遺傳多樣性很高 (Hd = 0.895, π = 0.00097) 和2 ~ 3個高峰的mismatch distribution,推測是多次引入所造成。H1為3國共有單基因型,推測H1可能為原生地廣布的單基因型;三個國家各有其獨特的單基因型:台灣 (H2 ~ H4)、日本 (H5 ~ H15) 和阿根廷 (H16和H 17),顯示3國的河殼菜蛤均為不同來源。除了台灣和日本的河殼菜蛤族群有明顯分化的單基因型之外,大部分單基因型間僅相差一個鹼基變異,使NJ、MP、ML、Baysien analysis和MJ network的分析結果,無法釐清多數單基因型的親緣關係。河殼菜蛤在台灣發現的3水系—新店溪、大漢溪和日月潭水系的族群遺傳多樣性均低;3個水系族群之間,至少共有2種單基因型 (H1>80 %和H2),應為奠基者效應所造成。3水系間的平均遺傳距離 (0.259 % ~ 0.387 %) 和FST值 (0.032 ~ 0.0490),顯示台灣3水系族群關係相近,推測可能是單次引入至某一水系再被引入至另外2水系,而河殼菜蛤於台灣水系間的擴散,可能透過工程船或休閒船引入至另一水域。

關鍵字:河殼菜蛤 Limnoperna fortunei、族群遺傳結構 Population genetic structure、新店溪 Shindian River、石門水庫 Shihmen Reservoir、日月潭 Sun Moon Lake

2015年1月15日 星期四

[發表研究SP02] 臺灣大臍蝸牛的東部隱藏種--彩虹大臍蝸牛 Aegista diversifamilia

分布於臺灣東部的新種--彩虹大臍蝸牛 Aegista diversifamilia
圖片採用創用CC授權 4.0版,圖片作者:黃致維 Chih-Wei Huang 

[關於此研究]

西元1884年,科學文獻首度描述臺灣大臍蝸牛Aegista subchinensis。以往,對於此種蝸牛的認知是分布於臺灣全島。然而,李彥錚博士於2003年出版的蝸牛圖鑑提及,中央山脈東部的臺灣大臍蝸牛比西部族群還大。此研究中,我們分析臺灣大臍蝸牛的東、西部族群的外殼形狀、外殼可測量形質和生殖腺特徵,加上粒線體COI、16S和核ITS2基因片段分析近緣種間的親緣關係,確認臺灣大臍蝸牛的東部族群為演化顯著單元,而命名為新種:彩虹大臍蝸牛 Aegista diversifamilia。此研究已於2014年發表在線上公開取閱(open access)的期刊Zookeys


[本文開始] 原始文獻連結在此

根據多個基因重建之親緣關係和形態證據,修訂臺灣大臍蝸牛Aegista subchinensis (Möllendorff, 1884)(柄眼目:扁蝸牛科)的分類和描述臺灣東部Aegista屬的一個新種
Taxonomic revision of Aegista subchinensis (Möllendorff, 1884) (Stylommatophora, Bradybaenidae) and a description of a new species of Aegista from eastern Taiwan based on multilocus phylogeny and comparative morphology

作者:黃致維Chih-Wei Huang 1、李彥錚Yen-Chen Lee 2、林思民Si-Min Lin 1、巫文隆 Wen-Lung Wu 2
1 國立臺灣師範大學生命科學系
Department of Life Science, National Taiwan Normal University, No. 88, Sec. 4, Tingzhou Rd., Wenshan Dist., 11677, Taipei, TAIWAN, R.O.C.
2 中央研究院生物多樣性研究中心
Biodiversity Research Center, Academia Sinica, No. 128 Academia Road Sec. 2, Nankang Dist., 11529, Taipei, TAIWAN, R.O.C.

通訊作者 Corresponding author
黃致維Chih-Wei Huang (limnoperna@gmail.com)
巫文隆 Wen-Lung Wu (malacolg@gate.sinica.edu.tw)

學術編輯 Academic editor:Menno Schilthuizen

收稿日期:2014年4月23日 | 接受日期:2014年9月7日 | 發表日期:2014年10月13日
Received: 23 Apr 2014 | Approved: 07 Sep 2014 | Published: 13 Oct 2014


摘要 Abstract

臺灣大臍蝸牛Aegista subchinensis (Möllendorff, 1884)是廣布臺灣且有形態變異的特有種蝸牛。此研究以三個基因片段(粒線體COI、16S和核基因ITS2)重建臺灣大臍蝸牛與其近緣種A. vermis (Reeve, 1852) and A. oculus (Pfeiffer, 1850)之親緣關係並推估種間的遺傳分化程度。根據親緣關係和形態分析,顯示現在認知的臺灣大臍蝸牛裡有隱藏種(新種)。新種名為彩虹大臍蝸牛A. diversifamilia,其與臺灣大臍蝸牛的區別為,彩虹大臍蝸牛的殼直徑、殼口、殼頂夾角較大,臍孔較寬,殼形較為低矮。彩虹大臍蝸牛和臺灣大臍蝸牛的分布以蘭陽溪為界。

Aegista subchinensis (Möllendorff, 1884) is a widely distributed land snail species with morphological variation and endemic to Taiwan. Three genetic markers (partial sequence of the mitochondrial cytochrome c oxidase subunit I [COI], the 16S rDNA and the nuclear internal transcribed spacer 2 [ITS2]) were analysed to infer phylogenetic relationships and genetic divergence of closely related species of the genus Aegista, A. vermis (Reeve, 1852) and A. oculus (Pfeiffer, 1850). A new species from A. subchinensis has been recognized on the basis of phylogenetic and morphological evidences. The nominal new species, A. diversifamilia sp. n. is distinguished from A. subchinensis (Möllendorff, 1884) by its larger shell size, aperture and apex angle; wider umbilicus and flatter shell shape. The northernmost distribution of A. diversifamilia sp. n. is limited by the Lanyang River, which is presumed to mark the geographic barrier between A. diversifamilia sp. n. and A. subchinensis.


關鍵字 Keywords
柄眼目 Stylommatophora、大蝸牛超科 Helicoidea、南琉球群島 Southern Ryukyu Islands、八重山群島 Yaeyama Islands、新種 new species



相關媒體報導

中文媒體
泛科學PanSci  以婚姻平權為名的蝸牛新種:彩虹大臍蝸牛
地球圖輯隊  挺婚姻平權 台灣學者將蝸牛命名「彩虹」
國家地理雜誌  新發表物種「彩虹大臍蝸牛」,支持多元成家
果殼網  【论文故事】新种蜗牛,倡导同性婚姻权利

英文媒體
ScienceDaily  A new land snail species named for equal marriage rights (這篇是原始新聞稿)
BBC  Hermaphrodite snail named after marriage equality
The Gardian  New species of snail named in celebration of same-sex marriage
TECH TIMES  New species of snail named in honor of same-sex marriage: Say hello to Aegista diversifamilia
IFLScience  New Species Of Snail Named For Marriage Equality

2014年十大年度新種報導
TIME  Top 10 New Species
Mongabay  the top new animal discoveries of 2014
IFLScience  Top 10 New Species of 2014
ABCDNet  Top new species of 2014 in Asia


2014年10月1日 星期三

[發表研究SP01] Molluscan fauna of Gueishan Island, Taiwan 台灣的龜山島的軟體動物相

[發表研究]相關文章的說明

基於知識共享和自己的研究自己分享之理念,未來將會把我個人發表的相關研究,以中英對照的方式呈現在部落格上,並搭配簡短的說明,試圖讓非科學專業的讀者也能夠理解。這算是對我自己的一個交代,也算是對漫長的學習研究階段作個摘要。


[關於此研究]

此研究以資料文章(data paper)的形式發表於線上公開取閱(open access)的期刊Zookeys。呼應全球生物多樣性資訊機構(Global Biodiversity Information Facility,縮寫GBIF)提倡,將埋藏於研究室的珍貴調查資料發表,使得生物多樣性資料得以永存且可被引用。


[本文開始] 原始文獻連結在此

台灣的龜山島的軟體動物相 Molluscan fauna of Gueishan Island, Taiwan

作者:黃致維Chih-Wei Huang 1,2、熊大維Ta-Wei Hsiung 2、林思民Si-Min Lin 1、巫文隆 Wen-Lung Wu 2
1 國立臺灣師範大學生命科學系
Department of Life Science, National Taiwan Normal University, No. 88, Sec. 4, Tingzhou Rd., Wenshan Dist., 11677, Taipei, TAIWAN, R.O.C.
2 中央研究院生物多樣性研究中心
Biodiversity Research Center, Academia Sinica, No. 128 Academia Road Sec. 2, Nankang Dist., 11529, Taipei, TAIWAN, R.O.C.

通訊作者 Corresponding author:巫文隆 Wen-Lung Wu (malacolg@gate.sinica.edu.tw)

學術編輯 Academic editor:V. Chavan

收稿日期:2012年10月26日 | 接受日期:2013年1月14日 | 發表日期:2013年1月24日
Received 26 October 2012 | Accepted 14 January 2013 | Published 24 January 2013


摘要 Abstract

此資料彙整龜山島(台灣唯一的活火山島嶼)軟體動物調查的歷年研究文獻和2011-2012年間的田野調查,提供龜山島目前已知的軟體動物物種分布與名錄。文獻回顧包括發表於1934-2003年間的七篇研究,累積紀錄37科61屬112種軟體動物。根據我們的田野調查,共發現23科28屬34種軟體動物,其中14種是龜山島新記錄:大駝石鱉Liolophura japonica雜斑蓮花青螺 Lottia luchuana黑肋蜑螺Nerita costata蘭富蜑螺Nerita rumphii、烏來芝麻蝸牛Diplommatina suganikeiensis波紋玉黍螺Littoraria undulata、台灣山椒蝸牛Solenomphala taiwanensis、山椒蝸牛未知種Assiminea sp.花松螺Siphonaria laciniosa盤蜷Laevapex nipponica八丈島罌粟蝸牛Carychium hachijoensis、台灣椎實蝸牛Succinea erythrophana鬼牙細煙管蝸牛Zaptyx crassilamellata細錐蝸牛Allopeas pyrgula。龜山島的軟體動物總計有45科71屬126種。以上資料已透過GBIF發布,並彙整至台灣貝類資料庫

This dataset records the occurrence and inventory of molluscan fauna on Gueishan Island, the only active volcanic island in Taiwan, based on the literature survey and field investigation conducted between 2011 and 2012. The literature review involved seven studies published from 1934 to 2003, which collectively reported 112 species from 61 genera and 37 families of Mollusca on Gueishan Island. Through our field investigation, we identified 34 species from 28 genera and 23 families. Fourteen of these species were new records on Gueishan Island: Liolophura japonica, Lottia luchuana, Nerita costata, Nerita rumphii, Diplommatina suganikeiensis, Littoraria undulata, Solenomphala taiwanensis, Assiminea sp., Siphonaria laciniosa, Laevapex nipponica, Carychium hachijoensis, Succinea erythrophana, Zaptyx crassilamellata, and Allopeas pyrgula. In Total, there are 126 species from 71 genera and 45 families of Mollusca on Gueishan Island. These data have been published through GBIF [http://taibif.org.tw/ipt/resource.do?r=gueishan_island] and integrated into the Taiwan Malacofauna Database (http://shell.sinica.edu.tw/).

關鍵字 Keywords
軟體動物 Mollusca、腹足綱 Gastropoda、雙殼綱 Bivalvia、頭足綱 Cephalopoda、多板綱 Polyplacophora、台灣 Taiwan、龜山島 Gueishan Island

計畫詳情 Project details

計畫名稱龜山島軟體動物相調查
Project title: Investigation of molluscan fauna of Gueishan Island, Taiwan.

人員黃致維(鑑定、資料蒐集、資料管理、資料發布)、熊大維(鑑定、資料蒐集、資料管理)、李彥錚(鑑定)、林思民(計畫指導)、巫文隆(計畫指導、資料管理)
Personnel: Chih-Wei Huang (collection identifier, data collector, data manager, data publisher), Ta-Wei Hsiung (collection identifier, data collector, data manager), Yen-Chen Lee (collection identifier), Si-Min Lin (Project Director), Wen-Lung Wu (Project Director, data manager).

經費來源中央研究院、行政院國家科技委員會、行政院農委會林務局
Funding: Academia Sinica; National Science Council, Executive Yuan, R.O.C.(Taiwan); Forest Bureau, Council of Agriculture, Executive Yuan, R.O.C.(Taiwan).

研究區域描述龜山島位於距離台灣本島約10公里處。龜山島是由165萬年前的火山活動所形成,經歷多次火山噴發,最近一次噴發是在2萬年前(Juang et al. 2011),龜山島被認為是台灣附近唯一的活火山島。龜山島的陸域面積約2.85平方公里,最高海拔為398公尺。島上有兩座湖泊,淡鹹水的龜首湖(Head Lake)和淡水的龜尾湖(Tail Lake)(圖一)。大約在19世紀中期,島上開始有人類拓殖而形成小聚落,直到西元1977年,因軍事需要而將所有居民搬遷至台灣本島。直到西元2000年,龜山島由東北角暨宜蘭海岸國家風景區管理處管理,島上的動物相才開始有系統化的調查,並開放觀光遊客登島。

Study area descriptions/descriptor: Gueishan Island is located about 10 km from Taiwan. The island was formed via volcanic activity about 1.65 Ma ago and experienced multiple volcanic eruption events until 20 ka ago (Juang et al. 2011). It is considered the only active volcanic island near Taiwan. The land area of the island is about 2.85 km2, and the highest peak of the island is 398 meters above sea level. There are two lakes on the island, one of which consist of brackish water (Head Lake) and the other of freshwater (Tail Lake) (Figure 1). Humans colonized Gueishan Island in mid-19th century, by forming a small village. Later in 1977, all residents were moved back to Taiwan due to military requirements for the island. The fauna of this island were not investigated systematically until 2000, when the island came under the management of the Northeast and Yilan Coast National Scenic Area Administration, Tourism Bureau, MOTC and was open to tourists.

研究描述棲息於島嶼上物種,因為族群數量小且資源有限,容易面臨滅絕。島嶼的物種數則是遷入物種和滅絕物種的動態平衡結果。火山島的生物相會因為火山噴發而全數滅絕後,自鄰近地區擴散拓殖而來,因而成為島嶼生物地理學的有趣研究案例。龜山島上的生物可能經歷過數次的火山噴發滅絕後,於冰河時期海平面下降時,再度自台灣本島擴散拓殖而來。人類活動可能在有意或無意間,提供軟體動物拓殖的機會。以往的龜山島軟體動物調查,並未針對陸棲軟體動物進行廣泛的調查。我們搜尋各種文獻報告資料庫,以彙整前人於龜山島地區的軟體動物調查結果,除此之外,也在2011-2012年間,進行龜山島的海生、淡水和陸生軟體動物調查,以期建立龜山島的軟體動物清單。我們同時考量地形與棲地類型,特別針對以往研究所忽略的陸生軟體動物,進行調查。根據文獻回顧與我們的田野調查結果,龜山島軟體動物共有45科71屬126種。此研究提供龜山島生物多樣性的基礎資料。

Design description: Island species are vulnerable to extinction due to their relatively small population size and limited access to resources. The number of species on an island represents a dynamic equilibrium between immigration and extinction. Volcanic islands provide particularly interesting cases of island biogeography, in that their biota is erased by volcanic activity and recolonized from neighboring regions. Species on Gueishan Island may have under gone several cycles of extinction after volcanic eruption, followed by recolonization from Taiwan when the sea-level dropped during glacial periods. Human activity may also have provided opportunities for colonization of mollusks, either intentionally or accidentally. Investigations of molluscan fauna have been previously conducted on Gueishan Island, but these did not involve a comprehensive examination of land snails. We performed a literature survey using diverse databases, in order to collect previously identified reports on molluscan fauna of Gueishan Island. In addition, we performed field sampling of mollusks in marine, freshwater and terrestrial environments during 2011 and 2012 to establish the inventory of molluscan fauna of Gueishan Island. We considered both the topography of the island and the habitats of mollusks during our field investigation. We focused on the terrestrial environment, as the majority of the earlier investigations examined non-terrestrial habitats. In total, our literature survey and field investigation identified 126 species from 71 genera and 45 families of Mollusca on Gueishan Island. This dataset provides basic information on the island’s biodiversity.

分類群涵蓋範圍此資料包括45科71屬126種軟體動物(表一),棲息於龜山島的海洋、淡水或陸生環境。包括腹足綱(物種數佔調查結果的88.10%)、雙殼綱(8.73%)、頭足綱(1.59%)和多板綱(1.59%)。物種數最多的前五個科分別為寶螺科(20種,15.87%)、鐘螺科(13種,10.32%)、骨螺科(11種,8.73%)、蜑螺科(8種,6.35%)和玉黍螺科(5 種,3.97%)(圖二)。

Taxonomic coverage
General taxonomic coverage description: The coverage of this dataset includes 126 species from 71 genera and 45 families of Mollusks of marine, freshwater and terrestrial environments on Gueishan Island (Table 1). It includes Class Gastropoda (88.10%), Class Bivalvia (8.73%), Class Cephalopoda (1.59%), and Class Polyplacophora (1.59%). The top five representative families are Cypraeidae (20 species, 15.87%), Trochidae (13 species, 10.32%), Muricidae (11 species, 8.73%), Neritidae (8 species, 6.35%), and Littorinidae (5 species, 3.97%) (Figure 2).

分類階層 Taxonomic ranks

動物門 Phylum: Mollusca
綱 Class: Bivalvia, Cephalopoda, Gastropoda, Polyplacophora
目 Order: Arcoida, Caenogastropoda, Heterobranchia, Neoloricata, Neritimorpha, Octopoda, Ostreoida, Patellogastropoda, Pterioida, Unionoida, Veneroida, Vetigastropoda
科 Family: Achatinidae, Aplysiidae, Arcidae,  Argonautidae,  Assimineidae, Bradybaenidae, Bursidae, Camaenidae,  Cardiidae, Chitonidae, Clausiliidae, Columbellidae, Conidae, Corbiculidae, Cypraeidae, Diplommatinidae, Ellobiidae, Fasciolariidae,  Haliotidae, Littorinidae, Lottiidae, Muricidae, Nassariidae, Neritidae, Octopodidae, Ostreidae, Ovulidae, Patellidae, Pectinidae, Philomycidae, Phyllidiidae, Planaxidae, Planorbidae, Potamididae,  Pteriidae, Ranellidae, Siphonariidae, Subulinidae, Succineidae, Thiaridae, Trochidae, Turbinellidae, Turbinidae, Unionidae, Veronicellidae
屬 Genus: Achatina, Acusta, Aegista, Allopeas, Aplysia, Argonauta, Assiminea, Astralium, Barbatia, Batillaria, Bradybaena, Bursa, Calliostoma, Calpurnus, Carychium, Cellana, Chicoreus, Chlamys, Chlorostoma, Collisella, Coniglobus, Conus, Corbicula, Crassostrea, Cristaria, Cymatium, Cypraea, Diplommatina, Dolabrifera, Drupa, Ergalatax, Haliotis, Laevapex, Liolophura, Littoraria, Lottia, Lunella, Mancinella, Meghimatium, Monodonta, Morula, Nassarius, Nerita, Nodilittorina, Notoacmea, Octopus, Ovula, Patella, Peristernia, Phyllidia, Pinctada, Planaxis, Pteria, Purpura, Pyrene, Saccostrea, Siphonaria, Solenomphala, Stomatella, Succinea, Tarebia, Tectus, Telasco, Tenguella, Thais, Thiara, Tridacna, Trochus, Vaginulus, Vasum, Zaptyx.

空間涵蓋範圍 Spatial coverage
General spatial coverage: The spatial coverage of the literature and our field investigation ranged from a latitude of 24°49'48"N to 24°51'0"N and a longitude of 121°55'48"E to 121°57'36"E. It includes the marine, intertidal, freshwater and terrestrial environment of Gueishan Island, Taiwan (Figure 1)
Coordinates: 24°49'48"N and 24°51'0"N Latitude; 121°55'48"E and 121°57'36"E Longitude

時間涵蓋範圍 Temporal coverage
1934–2012.

方法 Methods

採樣描述 Sampling description

文獻搜尋:針對以下資料庫,搜尋龜山島軟體動物調查的相關出版品,包括期刊、計畫報告、博碩士論文與書籍:(1)臺灣博碩士論文知識加值系統(此資料庫囊括1956年以來的博碩士論文,未查詢到本研究可用資訊);(2)全國圖書書目資訊網(此資料庫整合國家圖書館與其他74座圖書館的國內出版品與部分的政府研究報告,搜尋到三筆相關資料(Wu 2002, National Museum of Marine Biology and Aquarium 2003, Hwang and Lee 2003);(3)政府研究資訊系統(此資料庫收錄1993年以來的政府研究計畫,未查詢到本研究可用資訊);(4)Google學術搜尋(此資料庫廣括各種來源,從期刊、書籍到網頁,查詢到兩筆期刊資料(Chen and Fu 2007, Lee and Chen 2010));(5)台灣貝類資料庫(該資料庫包含台灣軟體動物的分類資訊、物種分布和相關文獻,查詢到六筆相關資料(Lee and Wu 1998, Jung and Lai 1999, Wu 2002, National Museum of Marine Biology and Aquarium 2003, Hwang and Lee 2003, Chen and Fu 2007))。另外,從Wu (2002)一書的參考文獻,找到三筆相關文獻(Hayasaka and Tan 1934, Kuroda 1938, Kuroda 1941)。總計搜尋到10筆可用的文獻資料,其中三筆文獻是描述龜山島附近海域漁船捕獲的軟體動物,並未紀錄詳細的採樣地理資訊,因而排除不納入此物種清單(Lee and Wu 1998, Chen and Fu 2007, Lee and Chen 2010)。其餘的七篇文獻,用於建置物種清單,包括採集點、採集者、學名等資訊,彙整記錄於Microsoft EXCEL 2010。上述提及的所有文獻,皆可在國家圖書館和國立臺灣圖書館調閱。

Literature survey: We searched for publications (including journals, project reports, theses and books) associated with the molluscan fauna of Gueishan Island from the following databases: (1) the National Digital Library of Theses and Dissertations in Taiwan (this contains details of theses and dissertations published since 1956, but did not contain publications relevant to this study); (2) the National Bibliographic Information Network (this catalog integrates information from National Central Library and 74 other libraries containing all publications with a Taiwan ISBN and selected government project reports; three publications (Wu 2002, National Museum of Marine Biology and Aquarium 2003, Hwang and Lee 2003) from this database met our requirement); (3) the Government Research Bulletin (this contains government project reports made since 1993, but did not contain reports relevant to this study); (4) Google Scholar (this contains a wide range of resources, from journals and books to webpages, and it provided two relevant journal articles (Chen and Fu 2007, Lee and Chen 2010)); (5) The Taiwan Malacofauna Database (this database contains taxonomy, distribution and references of all mollusks occurred in Taiwan, and provided six relevant publications (Lee and Wu 1998, Jung and Lai 1999, Wu 2002, National Museum of Marine Biology and Aquarium 2003, Hwang and Lee 2003, Chen and Fu 2007)). In addition, three relevant publications (Hayasaka and Tan 1934, Kuroda 1938, Kuroda 1941) were identified from citations in Wu (2002). In total, we identified ten relevant publications. Three of these publications (Lee and Wu 1998, Chen and Fu 2007, Lee and Chen 2010) were excluded because they described specimens acquired from fishing ports that had been captured by shrimp fishing or bottom trawling boats near Gueishan Island, without information of the precise sampling location. The seven remaining publications were used to establish the occurrence and inventory data. Sampling sites, names of collectors and the scientific name of each species were recorded using Microsoft EXCEL 2010. All of the publications mentioned above can be accessed in the National Central Library and the National Taiwan Library.

田野調查本研究同時考量龜山島的地形與棲地類型進行調查。潮間帶、淡水和陸域環境,以肉眼搜尋軟體動物(圖一)。海水退潮時,檢視海邊的岩石、港口的人造物表面是否有附著軟體動物。針對淡水環境的龜尾湖,檢視周邊的水下或水邊的落葉和石頭等底質。陸域環境,包括龜尾湖步道、401高地步道和北岸步道,檢視樹葉枝幹、枯枝落葉堆、石頭底部、朽木等。我們蝸牛活動較活躍的雨後、清晨和夜間進行調查。每個物種至少採集一個空殼或活體,以作為存證標本。活體標本帶回實驗室後,冷凍於攝氏-80度,隨後轉置於95%酒精溶液,以利於長期保存。

Field Sampling: The topology of Gueishan Island and the types of mollusk habitat were considered for field investigation. Visual search was conducted for mollusks in intertidal, freshwater and terrestrial environments (Figure 1). The surface of rocks on the coastline and man-made concrete structures in port were searched for marine mollusks during low tide. Leaf litter and rocks under or near water around Tail Lake (the only freshwater habitat on island) were inspected for freshwater mollusks. We inspected from leaves, trunks, leaves litter, rocks and rotten woods for land snails along three trails: one trail around Tail Lake, another leads to the highest peak (401 Highland) on the island, and the other leads to the northern part of the island. We surveyed for land snails during their active periods: during and after rainfall, early morning, and night. At least one living individual or dead shells of each species was collected as voucher specimens. Living organisms were brought back to laboratory, fixed via freezing in a -80°C freezer, and subsequently transferred to 95% ethanol for long term preservation.

資料品質描述以Garmin GPSmap 60CSx衛星定位儀測量,當誤差範圍小於10公尺時,記錄該採集點的經度、緯度和海拔,座標採用WGS84系統。採集回來的標本,分別由黃致維和熊大維鑑定。文獻回顧搜尋到的七篇文獻,缺乏清晰的物種照片或其他物種描述資訊。鑑定物種是依據以下台灣軟體動物相關文獻:Pace (1973)、Lai (1990, 1998)、Lee and Chen (2003)、Wu and Lee (2005)和Hsieh et al. (2006)。初步認定的龜山島新紀錄的物種,另由中央研究院生物多樣性研究中心的博士後研究員,李彥錚博士再次鑑定。十四種龜山島新紀錄種,皆有分布於臺灣,是龜山島以往調查沒有記錄到的物種。所有物種的學名,均透過台灣貝類資料庫和World Register of Marine Species資料庫比對確認。

Quality control description: Latitude, longitude and altitude of sampling sites were recorded using Garmin GPSmap 60CSx with uncertainty of less than 10 meters. Sampling sites were georeferenced (WGS84). All the specimens collected during the field investigation were identified independently by Huang and Hsiung. Seven earlier studies described the mollucan fauna of Gueishan Island, but these publications lack clear photos or other information for identifying specimens. Species identification was performed using the following guide books and publications about Taiwan malacofauna: Pace (1973), Lai (1990, 1998), Lee and Chen (2003), Wu and Lee (2005), and Hsieh et al. (2006). Newly recorded species were further confirmed by Dr. Yen-Chen Lee, a Mollusca specialist and postdoctoral researcher in the Biodiversity Research Center, Academia Sinica. Fourteen new recorded species were found to be native to Taiwan but previously unreported on Gueishan Island. The scientific names of all mollusks were checked against the Taiwan Malacofauna Database and World Register of Marine Species.

資料來源 Data resources
本研究資料儲存於GBIF
The data underpinning the analysis reported in this paper are deposited at GBIF, the Global Biodiversity Information Facility, http://taibif.org.tw/ipt/resource.do?r=gueishan_island

資料集 Datasets
資料集描述此資料彙整七篇龜山島軟體動物相的文獻(Hayasaka and Tan 1934, Kuroda 1938, Kuroda 1941, Jung and Lai 1999, Wu 2002, National Museum of Marine Biology and Aquarium 2003, Hwang and Lee 2003)與田野調查的結果。資料包括調查日期、分類資訊、地理座標、海拔、棲地類型、採集者姓名、調查方式和文獻紀錄。根據發表於1934-2003年的文獻,紀錄37科61屬112種。我們在2011-2012年的田野調查,共記錄到23科28屬34種,其中14種為龜山島新紀錄種。彙整文獻紀錄和田野調查結果,龜山島軟體動物相共記錄有45科71屬126種,14種龜山島新紀錄種為棲息於海邊的大駝石鱉Liolophura japonica雜斑蓮花青螺 Lottia luchuana花松螺Siphonaria laciniosa黑肋蜑螺Nerita costata蘭富蜑螺Nerita rumphii波紋玉黍螺Littoraria undulata;採集自淡水環境,龜尾湖的山椒蝸牛未知種Assiminea sp.盤蜷Laevapex nipponica;採集自陸域環境的台灣山椒蝸牛Solenomphala taiwanensis烏來芝麻蝸牛Diplommatina suganikeiensis八丈島罌粟蝸牛Carychium hachijoensis鬼牙細煙管蝸牛Zaptyx crassilamellata、細錐蝸牛Allopeas pyrgula台灣椎實蝸牛Succinea erythrophana。此資料提供龜山島的生物多樣性與生物地理的基礎資料。此資料將由中央研究院生物多樣性研究中心的軟體動物學研究室維護。

Dataset description: This dataset incorporates seven publications (Hayasaka and Tan 1934, Kuroda 1938, Kuroda 1941, Jung and Lai 1999, Wu 2002, National Museum of Marine Biology and Aquarium 2003, Hwang and Lee 2003) associated with the molluscan fauna of Gueishan Island and field investigation results. The dataset includes sampling date, taxonomy information, GPS location, elevation, type of habitat, name of collector, method of collection, and literature record. Based on the literature published during the period between 1934 and 2003, 112 species from 61 genera and 37 families of Mollusca were recorded on Gueishan Island. Of the 34 species from 28 genera and 23 families identified during our 2011-2012 field investigation, fourteen species were new records on Gueishan Island. In total, our literature survey and field investigation documents 126 species from 71 genera and 45 families of Mollusca on Gueishan Island. The fourteen newly recorded species are: Liolophura japonica (Lischke, 1873), Lottia luchuana (Pilsbry, 1901), Siphonaria laciniosa (Linnaeus, 1758), Nerita costata Gmelin, 1791, Nerita rumphii Recluz, 1841, and Littoraria undulata (Gray, 1839), which were sampled from the marine environment; Assiminea sp. and Laevapex nipponica (Kuroda, 1947), which were discovered in a freshwater environment, Tail Lake; and Solenomphala taiwanensis (Habe, 1942), Diplommatina suganikeiensis (Pilsbry & Hirase, 1905), Carychium hachijoensis Pilsbry, 1902, Zaptyx crassilamellata Kuroda, 1941, Allopeas pyrgula (Schmacker & Boettger, 1891), and Succinea erythrophana Ancey, 1883 discovered in the terrestrial environment. This dataset provide basic information for the island’s biodiversity and biogeography. This dataset will be maintained by the Malacology Lab, Biodiversity Research Center, Academia Sinica.

Object name: Darwin Core Archive Molluscan fauna of Gueishan Island, Taiwan

Character encoding: UTF-8

Format name: Darwin Core Archive format

Format version: 1.0

Distribution: http://taibif.org.tw/ipt/archive.do?r=gueishan_island

Publication date of data: 2012-12-21

Language: English

Licenses of use: This work is licensed under a Creative Commons CCZero 1.0 License http://creativecommons.org/publicdomain/zero/1.0/legalcode

Metadata language: English

Date of metadata creation: 2012-09-21

Hierarchy level: Dataset

致謝 Acknowledgements
感謝宜蘭縣政府和東北角暨宜蘭海岸國家風景區管理處核准龜山島的調查。田野調查工作,要感謝頭城漁會,中央研究院生物多樣性研究中心軟體動物學研究室全體人員、國立臺灣師範大學生命科學系草魚研究室全體人員的協助。感謝Duncan Wright博士與兩位匿名審稿者,提供意見而使此文更加完整。

We would like to thank Yilan County Government and Northeast and Yilan Coast National Scenic Area Administration, Tourism Bureau, MOTC for approval of field investigation on Gueishan Island. Fieldwork was made possible by the assistance of Toucheng Fishermen’s Association, all members of the Malacology Laboratory (Biodiversity Research Center, Academia Sinica) and all members of the Laboratory of Grass Lizard and Fish (Department of Life Science, National Taiwan Normal University). We would like to thank Dr. Duncan Wright as well as two anonymous reviewers for helpful comments which greatly improved the manuscript.

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2014年2月12日 星期三

重建族群歷史波動的方法:skyline-plot


以前不懂事的時候,參考著年代久遠的文獻,想找到利用DNA序列來推估某生物的歷史族群波動(historical population demography)的方法。早期會用neutrality test的正負值或是mismatch distribution analysis的波峰分布和數值來推斷,該生物族群過去是否經歷過族群擴張或衰減,雖然有其理論依據,但這些方法太過簡化,而無法貼近實際上可能更複雜的歷史族群波動。

近年來發展出考量參數較多且較有彈性的skyline-plot方法,先根據DNA序列alignment演算出序列的演化譜系(genealogy),再依據演化譜系推算出的族群波動歷史。Ho and Shapiro發表於2011年的一篇review,提供當時已有的skyline-plot方法的採樣策略、方法原理和準確度評估。分析兩種族群擴張情況產生的模擬序列,結果顯示Bayesian skyline plot方法的結果比較貼近模擬的族群波動。然而大多skyline-plot方法只能分析單一序列片段,由於不同的演化歷史會有差異,且以單一序列重建演化譜系的偏差較大,近年來更發展出可分析多個序列片段的extended bayesian skyline plot(文中未分析準確度),可減少重建演化譜系的偏差,理論上是更加準確。

完整內容請參考 Skyline-plot methods for estimating demographic history from nucleotide sequences

節錄轉載【2013回顧 PNAS十個細菌小故事】噬菌體:免疫系統最前線?

先感謝PanSci平台的創立,讓大眾能接觸到更多科學故事與觀點。前陣子讀到陳俊堯老師發表於的文章【2013回顧】PNAS 十個細菌小故事(),噬菌體的研究讓我聯想到,同樣很會分泌黏液的軟體動物,或許也有對抗細菌的功能,先筆記起來。


以下節錄自陳俊堯老師發表於PanSci的文章【2013回顧】PNAS 十個細菌小故事

噬菌體:免疫系統最前線?

你一定知道,想要對付敵手的進攻,把它怕的東西抓來守大門就對了。

這篇研究講的就是這一個道理,可是它卻發生在一個我完全沒想到情境上。這實在是個太大膽的推論,忍不住要跟大家分享。故事起因於一群海洋病毒學家發現了一個現象:在海洋動物的黏液裡,有大量的噬菌體的基因出現。進一步比對發現從海葵多毛類到魚類人類都有這個現象。他們回實驗室用能分泌黏液的人類細胞株進行測試,發現這些細胞果然可以留住比較多的 T4 噬菌體。

為什麼呢?動物的黏液被認為只要用來對付外界微生物的屏障,為什麼和獵殺細菌的噬菌體有關?難道這樣可以用來對抗細菌的進攻嗎?他們在這些能分泌黏液的細胞上先加 T4 噬菌體附著在黏液裡,再加入大腸桿菌,結果發現因為噬菌體的關係,成功留在動物細胞上的細菌數量顯著變少。

這群研究人員證實了噬菌體可以利用外鞘蛋白裡 hoc 基因產物裡的類抗體區段(Ig-like domain)來和人類黏液蛋白(mucin)結合。接著他們遍尋前人的基因資料庫,發現類抗體區段的基因真的在各種黏液樣本裡出現的機率比較高。這下假設清楚了:動物黏液裡有大量黏液蛋白,而噬菌體的外鞘上有類抗體區段可以和黏液蛋白結合而被拉住。噬菌體長得像登月小艇,外鞘蛋白裡包著 DNA,用尾部感染細菌。黏液拉住了噬菌體的頭,把尾部朝向外面的敵人。如果有細菌膽敢進攻,一定會先接觸到噬菌體的尾部而被攻擊。雖然這個假設還有一些不確定的地方(請看這篇解析),不過看起來是個相當可行的假設。我們動物是不是利用黏液來收編噬菌體,當做免疫系統的傭兵呢?

研究原文

Barr JJ, Auro R, Furlan M, Whiteson KL, Erb ML, Pogliano J, Stotland A, Wolkowicz R, Cutting AS, Doran KS, Salamon P, Youle M, Rohwer F. Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc Natl Acad Sci U S A. 2013 Jun 25;110(26):10771-6. doi: 10.1073/pnas.1305923110.

2011年9月8日 星期四

地球上到底有多少生物?


地球上(on Earth)到底(on earth)有多少種生物?當外星人飄來地球時,生物學家恐怕也無法回答這麼簡單的問題!即使連研究相當透徹的哺乳動物和鳥類,分類學家每年都持續發現與描述新的物種!

以往推測總物種數有兩類方法,一類是請分類學家評估可能還有多少物種待發現;另一類方法是根據已詳細調查區域的物種數量,外推至全球的總物種數。根據不同的方法推算,科學家認為地球上可能有三百萬到一億種生物。然而,這些方法有許多假設與限制,使得推算的總物種數差異甚大。

Camilo Mora博士主導的研究,應用生物分類階層(生物課本裡學過的界門綱目科屬種)的數量趨勢,推估地球的總物種數平均為870萬種(740萬-1000萬種)。例如某動物門=10綱=100目 =1000科=10000屬=100000種,不同類群的分類階層數量有相似的趨勢,且高階分類(屬以上的分類階層)相對於種(species)較穩定,因此可推估得到較可信的總物種數。Mora博士等人也提及包括對於物種的定義,高階分類的變動,分類學家研究努力量等,都是會造成總物種數低估的可能原因。

自從林奈提出以二名法命名物種以來,經歷約250年的分類學研究,人類已描述約120萬種生物。僅佔海洋生物的9%,陸域淡水域生物的14%。如果以過去20年來的動物新種發表速率推算(平均每年發表6200種新種,平均每位分類學家一生平均發表24.8種新種),需要30.3萬名分類學家,以1200年的時間才能描述完地球上所有動物新種。但因為人類嚴重改變地球生態系,使得現代的物種滅絕速率是自然情況下的100-1000倍,將會有非常多的生物,在我們認識牠之前,就消失在地球上了!

備註:
1. 該研究參考的陸域淡水域生物分類階層數量是根據Species 2000資料庫,此資料庫的目標是完整收錄目前已知的生物物種名。但是根據我比較熟悉的幾個軟體動物類群,超過1000種物種的煙管蝸牛科(Clausiliidae)卻未列入該資料庫,超過1000種的扁蝸牛科(Bradybaenidae)只列入17種,顯然全球總物種數是低估的!
2. 該研究報告也特別提到,分類學家曾經計算過,描述一個新種的平均花費是48500美元(包括野外採集與實驗室分析的設備、交通費、分類學家薪資等),以1美元兌換臺幣29元換算,等於約臺幣140萬元。描述完地球上所有的動物,約需3640億美元!

延伸閱讀:
原始發表文獻-How Many Species Are There on Earth and in the Ocean?
PLoS Biology專文導讀-Why Worry about How Many Species and Their Loss?
ScienceDaily相關報導-How Many Species On Earth? About 8.7 Million, New Estimate Says

本文亦發表於生態演化文獻閱讀俱樂部 以及 PanSci 泛科學 網站

十億年前,我還沒登陸,只到淡水而已!


生物從海洋演化至淡水環境,或是演化至陸域環境,會面臨全然不同的物理化學狀況,例如細胞滲透壓調節的改變、支撐身體重量的能力或構造、減少水分喪失的機制等等。科學家認為地球上的生命,是由棲息於海洋的生物逐漸演化至陸域環境,而至少在前寒武紀(約5.42億年前),陸地上可能就有各式各樣的生物生存。然而生物的演化難道如同教科書所寫的那麼簡單嗎?

Strother等人發表於Nature(2011年4月13日線上搶鮮版)的研究認為,他們找到目前最早棲息於非海洋環境的真核生物化石。Strother等人從廣佈於蘇格蘭西北部,一種統稱為Torridonian的沉積岩中尋找到大量的多細胞生物化石,大約10億年前,此地不是海洋也不是陸地,而是淡水湖!他們應用各種化學分析方法,推論這些棲息於淡水環境的多細胞生物已經具備細胞核構造,還有粒線體和葉綠體(具有細胞核和粒線體等膜狀胞器的生物,稱為真核生物)。Strother等人認為這是目前已知最早的地球生物演化至非海洋環境的直接證據。

可惜臺灣的科學新聞再次過度簡化報導,化石不僅被說成從Torridonian湖底採得,連十億年前的多細胞生物都從海底直接登陸。還要全然相信沒有參考文獻的科學新聞嗎?請各位記者們多打幾個字,提供新聞原始來源吧!

延伸閱讀:
過度簡化報導–科學家找到生物早期登陸化石
原始發表論文–Earth’s earliest non-marine eukaryotes
比較貼近論文真相的報導–Complex life hit freshwater early
生物登陸的些微扭曲報導–Palaeobiologists uncover how sun and sex on land emerged earlier than thought 以及 Loch Fossils Show Life Harnessed Sun and Sex Early on

以上亦刊登於 PanSci 泛科學 網站

用尺量出的雄性生殖力?


針對老鼠與其他哺乳動物的研究發現,肛門到生殖器的長度(anogenital distance,AGD)和胎兒在母親子宮內暴露於雄激素的程度有所關聯,且和雄性的精子量與濃度有相關。然而有些環境荷爾蒙會導致胎兒器官的發育產生變化,使得發育完成的個體有較短的AGD。

AGD是否也能應用於人類,評估雄性的生殖力?Mendiola等人招募了126位自願參與研究的男性紐約客,測量AGDAS(肛門到陰囊下方)、AGDAP(肛門到陰莖基部)的距離和精液體積、精子數量、活動精子比例與正常形態精子比例(正常狀況下,還是會有許多畸形的精子出現)的相關性。分析結果顯示只有AGDAS的距離和精子數量、活動精子比例與正常形態精子比例有達到統計上的顯著,但相關程度並不高!由於生殖能力不完全只決定於精子數量,還有其他因素(例如射程距離、精子泳動能力等),且此研究僅分析126位紐約客,無法代表所有西方人,更不一定適用於東方人!

臺灣媒體發布的中文新聞卻有誤導之嫌,來自中央社的報導說"肛門尿道距離 決定男性生殖力",然而事實上應該是肛門到陰囊下方的距離,和男性生殖力有相關性,而非決定性!

誤導報導:
肛門尿道距離 決定男性生殖力
不看大小 肛門尿道距離決定男性生殖力
肛門到生殖器距離 決定男性生育力

延伸閱讀:
Shorter Anogenital Distance Predicts Poorer Semen Quality in Young Men in Rochester, New York

以上亦刊登於 PanSci 泛科學 網站