雖然目前一般認為新鼠海豚屬(Neophocaena)為一包含三個亞種的單種屬，但新鼠海豚屬內的分類仍存在一些爭議。江豚(“Neophocaena phocaenoides”)是嚴重遭受人類活動干擾的小型鯨類，目前被列入華盛頓公約的「附錄一」中。談到保育，最首要的是要有明確的「保育單元(units)」。存在東海南端(包括台灣海峽)的江豚，其分類地位在過去型態研究上呈現爭議的現象。本研究，根據4個微衛星體的分析，認為此地區的江豚應屬於”北方亞種”。本研究比較了夏等人的研究中關於”長江亞種”的基因型(genotype)數據，有三群非常相異的基因群存在新鼠海豚屬，此三群分別是:（1）存在南中國海及台灣海峽的W-type群，依據背脊型態特徵被認為是”指名亞種(N. p. phocaenoides)”；（2）存在長江中下游的VN-type群，認為是”長江亞種(N. p. asiaeorientalis)”；（3）存在黃海、東海、台灣海峽及南中國海北端的IN-type + UN-type 群，認為是”北方亞種(N. p. sunameri)”。根據11個微衛星體的分析， IN-type + UN-type 群和W-type群皆無群內分化的現象。W-type 群和 IN-type + UN-type 群在馬祖地區有部分共域的現象，這是一個研究其分類地位的機會。由於發現在馬祖地區的W-type 群和 UN-type 群，在型態上並沒有中間型的個體存在，且在11個微衛星體基因座的分析顯示，兩群之間也沒有雜交的個體。根據E.O.Wiley 的定義，認為W-type 群和 IN-type + UN-type 群應該是兩個種的分類地位。此外，依據Crandall 等人對演化顯著單元 (ESU)的定義，本篇研究認為在新鼠海豚屬內應該存在三個演化顯著單元（ESUs）。

Although the Neophocaena is currently thought to be monotypic (“Neophocaena phocaenoides”) with three “subspecies”, the taxonomy of this genus still remains uncertainty. The finless porpoise (“Neophocaena phocaenoides”) is one of the small cetacean species under threats from human activities. At present, finless porpoise is listed in Appendix I of Convention on International Trade in Endangered Species of Wild Flora and Fauna (CITES). For conservation issue, it is important to define appropriate and unambiguous “units”. In this study, I intended to settle the taxonomic status of the specimens of finless porpoise from the southern part of the East China Sea (including the Taiwan Strait) in which the status has been under debate. Results from this study, indicated that they should belong to “N. p. sunameri”. Comparing the genotypes of the microsatellite of additional individuals of the “N. p. asiaeorientalis” belonging to the VN-type group given in Xia and coworkers report with our data, three distinguished genetic groups were revealed: (1) the group occurring in the Taiwan Strait (i.e., the W-type group, currently recognized as “N. p. phocaenoides”); (2) the group occurred in the Yangtze Rive (i.e., the VN-type group, currently recognized as “N. p. asiaeorientalis”); (3) the group occurred in the Yellow Sea and the Taiwan strait (i.e., the IN-type + UN-type group, currently recognized as “N. p. sunameri”). Population differentiation was absent not only within the W-type group but also within the IN-type +UN-type group. I tried to detect the taxonomy of the two parapatric groups in where the W-type and IN-type +UN-type groups are co-exit sympatrically. No specimens with intermediate character state of the width of the dorsal denticles (i. e., hybrids) were presented in Matsu Islands on the Chinese coast where the W-type and UN-type groups were sympatric. Hybrid individual exhibiting the hybrid states of the 11 microsatellite loci between these two groups was also not found. According to E.O. Wiley’s criteria for recognizing species, these two groups are eligible to be considered separate species. Based on Crandall and his coworkers’ criteria of evolutionarily significant unit (ESU), the three groups, the W-type, IN-type +UN-type and VN-type groups, should be treated as three distinct ESUs.

Table of contents
Acknowledgements .……….………….……….……….……….……………..….…..i
Abstract in Chinese .……….………….……….……….……….……………..….…..iii
Abstract…….……….……….………. …….………….….……….…………………iv
Table of Contents ……….………..………….……….……….…………………….. vi
Table legends .….…………….………….……….……….…………………….... .…vii
Figure legends .…………….……….……….……….………………………………viii
Table of appendix………….……….……….……….…………………………………ix
Introduction…….……….……….…….…….…….……….……….…………………1
Materials and methods…….……….……….……….………..……….………………7
Results……….……….……….…………….……….……….……………………....13
Discussion……….…….…………….……….……….……….………………..……18
References……….……….…………….……….……….……….…………..………26

Table legends
Table 1. Primers and core sequences of the seven microsatellite loci developed from finless porpoise (Neophocaena phocaenoides) ……….……….….………….…31
Table 2. Estimates of the number of alleles per locus (A), allelic richness (AR), observed heterozygosity (HO), expected heterozygosity (HE), and Hardy-Weinberg exact test (HW) for 4 microsatellite loci in the IN-type +UN-type group, W-type group, and VN-type group of finless porpoise ……….……….……………. .….…. .32
Table 3. Estimates of the number of alleles per locus (A), allelic richness (AR), observed heterozygosity (HO), expected heterozygosity (HE), and Hardy-Weinberg exact test (HW) for 11 microsatellite loci in the IN-type +UN-type group, and W-type group of finless porpoise ……….……….……………………….…. .…. .….….33
Table 4. Pairwise estimates of Fst (Wright 1987; below diagonal) and Rst (Slatkin 1995; above diagonal) for the IN-type +UN-type group, the W-type group and the VN-type group using 4 microsatellite loci………….………………….. .…. .….34
Table 5. Estimate of the number of migrants per generation (Nm) among the IN-type +UN-type group, the W-type group and the VN-type group of finless porpoise ….……….…………………………………………….…….... .…. .…35
Table 6. Estimate of the number of female migrants per generation (Nefmf) among the IN-type +UN-type group, the W-type group and the VN-type group of finless porpoise. (modified from Yang et al. 2002 )……….…. .…. ………..….…. .….36
Table 7. Evolutionarily significant units (ESUs) of the finless porpoise were defined on the basis of genetic and ecological exchangeability. ..….…………. ….………. 37

Figure legends
Figure 1. Distribution of sample collection.…….………………….………..……….…38
Figure 2. Subdivision of groups of Neophocaena species from the Yangtze River and the western Pacific coastal waters.…….……….……….……….……..……………39
Figure 3.Subdivision of groups within the same dorsal-ridge form of finless porpoise ...40
Figure 4 Allele frequencies and size distributions of 4 microsatellite loci in the W-type, IN-type + UN-type and VN-type groups of finless porpoises.…….…….………41
Figure 5. Allele frequency distributions of 11 microsatellite loci.…………….……... ...42
Figure 6. Number of monthly samples of the W-type and UN-type groups of finless porpoises in Matsu Islands from 1994 to 2006…….……….………….…..……44
Figure 7. Number of monthly samples of the W-type and UN-type groups of finless porpoises in Fujian, China from 1994 to 1996 and 1999 …….………...……….45

Table of appendix
Appendix 1. Primers and core sequences of the seven microsatellite loci developed from other cetacean species……………………………………..…………………46
Appendix 2. Categories of population distinctiveness based on rejection (+) or failure to reject (-) the null hypotheses (HO) of genetic and ecological exchangeability, for both recent and historical timeframes……………………………………47
Appendix 3. Typical chromatogram for 11 microsatellite loci. …….…….………..……48
Appendix 4. Genotypes of the 22 Yangtze finless porpoise (the VN-type group) given by Xia et al. (2005) ..……………………………………………………...….…50

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