Dissertations / Theses on the topic 'Indo-West Pacific'

It is often hypothesised that marine species with mobile planktonic phases are capable of widespread dispersal and may therefore be genetically homogenous throughout their distribution. Studies that have demonstrated positive correlation between duration of plankton phase and levels of gene flow reinforce the prediction that life history characteristics of marine species determine the potential extent of genetic and demographic connectivity throughout their distributions. This prediction has however been challenged by studies that have employed genetic markers highly sensitive to both historical and contemporary demographic changes. Disparities between dispersal potential and measured levels of gene flow have been demonstrated both among historically disconnected ocean basins and within semi-enclosed areas of strong hydraulic connectivity. These studies and others highlight a need for greater focus on factors that may influence population structure and distribution for marine species. In this thesis, I have examined genetic structure within and among populations of an estuarine species of mud crab Scylla serrata (Forskal, 1775) using a number of genetic markers and methods. The species is widely distributed throughout mangrove and estuarine habitats of the Indo - West Pacific (IWP); it is generally assumed that life-history characteristics of S. serrata promote high levels of population admixture and gene flow throughout its distribution. Alternatively, factors that have promoted population genetic structure for a variety of IWP marine species may also have affected S. serrata populations. By investigating genetic structure at several spatial scales of sampling, I was able to address a variety of hypotheses concerning the species distribution, dispersal, and genetic structure. Episodic changes to marine habitat and conditions experienced within the IWP during the Pleistocene may have affected genetic structure for a broad variety of marine taxa. The relative strength of this hypothesis may be assayed by comparative genetic studies of widespread IWP taxa with high dispersal capacity. In order to ascertain levels of historical and contemporary gene flow for S. serrata, I investigated the phylogeographic distribution of mitochondrial DNA haplotypes sampled throughout the species range. Adults were sampled from three west Indian ocean locations (N=21), six west Pacific sites (N=68), and two sites from northern eastern Australia (N=35). Temperature gradient gel electrophoresis and sequencing of 549 base pairs of the mitochondrial cytochrome oxidase I (COI) coding gene identified 18 distinct haplotypes. Apart from that seen in northern Australia, haplotype diversity was low (h < 0.36) at each of the locations. Total nucleotide diversity in the entire sample (excluding northern Australian locations) was also low (p = 0.09). Haplotypes clustered into two clades separated by approximately 2% sequence divergence. One clade was widespread throughout the IWP (clade 1) whereas the other was strictly confined to northern Australia (clade 2). Genealogical assessment of sequenced haplotypes relative to their distributions suggested that a historical radiation of clade 1 S. serrata throughout the IWP occurred rapidly and recently (<1Myr bp) from a west Pacific origin. The evidence of fixed unique haplotypes at the majority of locations suggested that contemporary maternal gene flow between trans-oceanic sites was limited. Contrary to reports for other widespread species of IWP taxa, there was no evidence of lengthy periods of regional separation between Indian from Pacific Ocean populations. However, results may indicate a separation of northern Australian crabs from other locations before and during the IWP radiation. I speculated that this isolation might have resulted in the formation of a new species of Scylla. Additional sampling of mud crabs from the Australian coastline allowed an examination of the diversity and distribution of clade 1 and 2 haplotypes among recently formed shelf-connected coastal locations, and across a historical bio-geographic barrier. Over 300 individuals were sampled from multiple locations within coastal regions (western, northern and eastern) of Australia and analysed for mutational differences at the COI gene. Analysis of molecular variance partitioned by sampling scale (Among regions, within regions, and within all locations) indicated mitochondrial haplotypes were structured regionally (P < 0.001), which contrasted with evidence of genetic panmixia within regions. Regional genetic structure broadly correlated with hydrological circulation, supporting the contention that release and transport of propagules away from the estuary may allow genetic connectivity among widespread shelf-connected S. serrata populations. That similar patterns of maternal gene flow were absent among trans-oceanic populations may indicate that the spatial scale of effective dispersal for this species is generally limited to areas of coastal shelf. The two clades of haplotypes were geographically separated either side of the Torres Strait, a narrow sea channel connecting the northern and eastern regions of coastal Australia. This pattern of historical genetic separation was concordant with a number of other marine species across northern Australia, and might indicate a shared history of vicariance induced by eustasy. Alternatively, differences in diversity and distribution of the clades may be evidence of two independent expansions of clade 1 and 2 crab populations into Australian regions following post-glacial estuary formation. Overall, despite evidence of genetic panmixia within extensive sections of the Australian distribution, there was also evidence of significant barriers to maternal gene flow with both shallow and deep regional phylogeographic assortment of mtDNA haplotypes. The presence of these barriers indicated both historical and contemporary factors have imposed limits to effective dispersal by this species among coastal habitats. A subset of the Australian sample (8 locations, N = 188) was also examined for variation at five microsatellite loci developed specifically here for S. serrata. I examined variation among samples at each of the loci to: a) independently verify regional structure among crab populations previously detected using the mtDNA analysis; b) test for evidence of co-distributed non-interbreeding stocks of S. serrata within Australian waters by examining samples for segregation of alleles within microsatellite loci concordant with the two mtDNA clades. The frequency and distribution of alleles for each of the highly polymorphic microsatellites were homogenous at all levels of sample partitioning and contrasted sharply with the instances of both weak and strong regional phylogeographic assortment of mtDNA haplotypes. These contrasting results between different genomic markers were examined in relation to the species life history, and to differences in mutational rate and inheritance of the genetic markers. Several hypotheses may explain the disparity, however it is most likely that rampant homoplasy and high rates of mutation at the microsatellite in conjunction with large Ne at locations may be concerted to delay equilibrium between genetic drift and migration among populations at these highly polymorphic nuclear markers. There was also no evidence that alleles at microsatellite loci were co-segregated with mtDNA clades and therefore no evidence of segregated breeding between the clades of crabs. Whether or not this result was also driven by homoplasy at the microsatellites remains unknown. Recently established mud crab populations (~ 3-4 years old) observed in a number of southwest Australian estuaries are almost 1000 kilometres south of their previously recorded distribution on the Western Australian coast. Colonisation of the southwest region may have occurred either by a natural range expansion from northwest Australian mud crab populations or by means of translocation from any number of mud crab sources within the Indo - West Pacific. I used mtDNA analysis to verify the species and determine the potential source population(s) of the colonists, by comparing sampled genetic material from the southwest (N = 32) against that previously described for the genus. I also compared levels of diversity at mtDNA and two microsatellite loci between the colonist and suspected source population(s) to qualitatively determine if the southwest populations experienced reductions in genetic diversity as a result of the colonisation process. All colonist samples had S. serrata mtDNA COI sequences identical to one previously described as both prevalent and endemic to northwest Australia. High levels of genetic diversity among source and colonist populations at two microsatellite loci contrasted to the mitochondrial locus which displayed an absence of variation among colonists compared to moderately diverse source populations. I argued that the southwest was recently colonised by large numbers of S. serrata propagules derived from the northwest of Australia, possibly due to an enhanced recruitment event coinciding with the reported strengthening of the Leeuwin Current during 1999. Contrasting levels of diversity among nuclear and mitochondrial loci may be attributed to a difference in response by the two genomes to the colonisation process. I predict that such differences may be generally prevalent among plankton-dispersed species. Finally, I discuss aspects of the species distribution and biogeography obtained as a composite of the various results and ideas expressed in this thesis. I propose that S. serrata populations in the IWP may have experienced several cycles of extinction and population retraction from temperate areas followed by subsequent periods of colonisation and rapid coastal expansion in response to the effects of glacial episodes on coastal habitats in the IWP. I propose that persistence of this species as remnant populations of clade 1 and 2 crabs at equatorial locations during low sea level stands provided source populations for later expansions by the species into a variety of coastal areas throughout the IWP. Further analysis is required to determine if mtDNA clade 1 and 2 crabs are non-interbreeding species of mud crab.

It is often hypothesised that marine species with mobile planktonic phases are capable of widespread dispersal and may therefore be genetically homogenous throughout their distribution. Studies that have demonstrated positive correlation between duration of plankton phase and levels of gene flow reinforce the prediction that life history characteristics of marine species determine the potential extent of genetic and demographic connectivity throughout their distributions. This prediction has however been challenged by studies that have employed genetic markers highly sensitive to both historical and contemporary demographic changes. Disparities between dispersal potential and measured levels of gene flow have been demonstrated both among historically disconnected ocean basins and within semi-enclosed areas of strong hydraulic connectivity. These studies and others highlight a need for greater focus on factors that may influence population structure and distribution for marine species. In this thesis, I have examined genetic structure within and among populations of an estuarine species of mud crab Scylla serrata (Forskal, 1775) using a number of genetic markers and methods. The species is widely distributed throughout mangrove and estuarine habitats of the Indo - West Pacific (IWP); it is generally assumed that life-history characteristics of S. serrata promote high levels of population admixture and gene flow throughout its distribution. Alternatively, factors that have promoted population genetic structure for a variety of IWP marine species may also have affected S. serrata populations. By investigating genetic structure at several spatial scales of sampling, I was able to address a variety of hypotheses concerning the species distribution, dispersal, and genetic structure. Episodic changes to marine habitat and conditions experienced within the IWP during the Pleistocene may have affected genetic structure for a broad variety of marine taxa. The relative strength of this hypothesis may be assayed by comparative genetic studies of widespread IWP taxa with high dispersal capacity. In order to ascertain levels of historical and contemporary gene flow for S. serrata, I investigated the phylogeographic distribution of mitochondrial DNA haplotypes sampled throughout the species range. Adults were sampled from three west Indian ocean locations (N=21), six west Pacific sites (N=68), and two sites from northern eastern Australia (N=35). Temperature gradient gel electrophoresis and sequencing of 549 base pairs of the mitochondrial cytochrome oxidase I (COI) coding gene identified 18 distinct haplotypes. Apart from that seen in northern Australia, haplotype diversity was low (h < 0.36) at each of the locations. Total nucleotide diversity in the entire sample (excluding northern Australian locations) was also low (p = 0.09). Haplotypes clustered into two clades separated by approximately 2% sequence divergence. One clade was widespread throughout the IWP (clade 1) whereas the other was strictly confined to northern Australia (clade 2). Genealogical assessment of sequenced haplotypes relative to their distributions suggested that a historical radiation of clade 1 S. serrata throughout the IWP occurred rapidly and recently (<1Myr bp) from a west Pacific origin. The evidence of fixed unique haplotypes at the majority of locations suggested that contemporary maternal gene flow between trans-oceanic sites was limited. Contrary to reports for other widespread species of IWP taxa, there was no evidence of lengthy periods of regional separation between Indian from Pacific Ocean populations. However, results may indicate a separation of northern Australian crabs from other locations before and during the IWP radiation. I speculated that this isolation might have resulted in the formation of a new species of Scylla. Additional sampling of mud crabs from the Australian coastline allowed an examination of the diversity and distribution of clade 1 and 2 haplotypes among recently formed shelf-connected coastal locations, and across a historical bio-geographic barrier. Over 300 individuals were sampled from multiple locations within coastal regions (western, northern and eastern) of Australia and analysed for mutational differences at the COI gene. Analysis of molecular variance partitioned by sampling scale (Among regions, within regions, and within all locations) indicated mitochondrial haplotypes were structured regionally (P < 0.001), which contrasted with evidence of genetic panmixia within regions. Regional genetic structure broadly correlated with hydrological circulation, supporting the contention that release and transport of propagules away from the estuary may allow genetic connectivity among widespread shelf-connected S. serrata populations. That similar patterns of maternal gene flow were absent among trans-oceanic populations may indicate that the spatial scale of effective dispersal for this species is generally limited to areas of coastal shelf. The two clades of haplotypes were geographically separated either side of the Torres Strait, a narrow sea channel connecting the northern and eastern regions of coastal Australia. This pattern of historical genetic separation was concordant with a number of other marine species across northern Australia, and might indicate a shared history of vicariance induced by eustasy. Alternatively, differences in diversity and distribution of the clades may be evidence of two independent expansions of clade 1 and 2 crab populations into Australian regions following post-glacial estuary formation. Overall, despite evidence of genetic panmixia within extensive sections of the Australian distribution, there was also evidence of significant barriers to maternal gene flow with both shallow and deep regional phylogeographic assortment of mtDNA haplotypes. The presence of these barriers indicated both historical and contemporary factors have imposed limits to effective dispersal by this species among coastal habitats. A subset of the Australian sample (8 locations, N = 188) was also examined for variation at five microsatellite loci developed specifically here for S. serrata. I examined variation among samples at each of the loci to: a) independently verify regional structure among crab populations previously detected using the mtDNA analysis; b) test for evidence of co-distributed non-interbreeding stocks of S. serrata within Australian waters by examining samples for segregation of alleles within microsatellite loci concordant with the two mtDNA clades. The frequency and distribution of alleles for each of the highly polymorphic microsatellites were homogenous at all levels of sample partitioning and contrasted sharply with the instances of both weak and strong regional phylogeographic assortment of mtDNA haplotypes. These contrasting results between different genomic markers were examined in relation to the species life history, and to differences in mutational rate and inheritance of the genetic markers. Several hypotheses may explain the disparity, however it is most likely that rampant homoplasy and high rates of mutation at the microsatellite in conjunction with large Ne at locations may be concerted to delay equilibrium between genetic drift and migration among populations at these highly polymorphic nuclear markers. There was also no evidence that alleles at microsatellite loci were co-segregated with mtDNA clades and therefore no evidence of segregated breeding between the clades of crabs. Whether or not this result was also driven by homoplasy at the microsatellites remains unknown. Recently established mud crab populations (~ 3-4 years old) observed in a number of southwest Australian estuaries are almost 1000 kilometres south of their previously recorded distribution on the Western Australian coast. Colonisation of the southwest region may have occurred either by a natural range expansion from northwest Australian mud crab populations or by means of translocation from any number of mud crab sources within the Indo - West Pacific. I used mtDNA analysis to verify the species and determine the potential source population(s) of the colonists, by comparing sampled genetic material from the southwest (N = 32) against that previously described for the genus. I also compared levels of diversity at mtDNA and two microsatellite loci between the colonist and suspected source population(s) to qualitatively determine if the southwest populations experienced reductions in genetic diversity as a result of the colonisation process. All colonist samples had S. serrata mtDNA COI sequences identical to one previously described as both prevalent and endemic to northwest Australia. High levels of genetic diversity among source and colonist populations at two microsatellite loci contrasted to the mitochondrial locus which displayed an absence of variation among colonists compared to moderately diverse source populations. I argued that the southwest was recently colonised by large numbers of S. serrata propagules derived from the northwest of Australia, possibly due to an enhanced recruitment event coinciding with the reported strengthening of the Leeuwin Current during 1999. Contrasting levels of diversity among nuclear and mitochondrial loci may be attributed to a difference in response by the two genomes to the colonisation process. I predict that such differences may be generally prevalent among plankton-dispersed species. Finally, I discuss aspects of the species distribution and biogeography obtained as a composite of the various results and ideas expressed in this thesis. I propose that S. serrata populations in the IWP may have experienced several cycles of extinction and population retraction from temperate areas followed by subsequent periods of colonisation and rapid coastal expansion in response to the effects of glacial episodes on coastal habitats in the IWP. I propose that persistence of this species as remnant populations of clade 1 and 2 crabs at equatorial locations during low sea level stands provided source populations for later expansions by the species into a variety of coastal areas throughout the IWP. Further analysis is required to determine if mtDNA clade 1 and 2 crabs are non-interbreeding species of mud crab.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Australian School of Environmental Studies
Full Text

Sesarmid crabs have important ecological roles in the mangroves of the Indo-west-Pacific biogeographic region. By processing large amount of leaf litter, these crabs retain organic matter in the mangroves, increase the rate of mineralisation, and fuel additional trophic links with the processed material. However, the dietary composition of the mangrove sesarmids is still a controversy. Gut content analyses suggest a dominant contribution of mangrove leaf litter in the crab diet but stable isotope data seem to support the assimilation of organic matter derived from the microphytobenthos but not mangrove litter. In addition, ability of the sesarmid crabs to obtain sufficient nutrition from mangrove litter, which is rich in structural carbon (cellulose) but poor in other nutrients such as nitrogen, has been questioned. The over-arching goal of this thesis was to fill these gaps of knowledge in detritivory of the mangrove sesarmids, using Parasesarma erythodactyla (Hess, 1865), the dominant shredder in sub-tropical Australian mangroves, as an animal model.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Griffith School of Environment
Science, Environment, Engineering and Technology
Full Text

Scylla serrata is a portunid crab which can attain a weight of over 2 kg and a carapace width exceeding 250 mm. It is distributed throughout the Indo-West Pacific extending down the east coast of Africa, and both the east and west coasts of Australia. In Australia it is commonly known as the mud crab because it occurs within muddy, mangrove-lined bays and estuaries. Mud crabs are generalist predators eating most small, slow moving animals which they can catch, but they are also vigorous scavengers. Being scavengers, they are readily caught in baited traps set by commercial and recreational fishers, and are the stock for these popular fisheries. Female crabs spawn offshore and larvae spend a period in the plankton where they develop into postlarvae or megalopae...
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Environment
Science, Environment, Engineering and Technology
Full Text

碩士
國立中山大學
海洋生物科技暨資源學系研究所
107
Seagrass, as marine angiosperms, plays an important role in coastal ecosystems. Understanding the population connectivity between geographic regions is important for their future restoration. Halophila ovalis is distributed in the Indo- West Pacific and can produce recruits through both asexual and sexual reproduction. The former uses rhizomatous rametes or rhizome fragments to disperse, the latter uses seeds to achieve the purpose of expanding their population. Since it’s fruits and seeds have negative buoyance and the seeds of H. ovalis could pass through the digestive tract of waterfowls and lead to higher germination rates than un-ingested controls. Therefore, biological vectors (i.e. migratory birds) may be a possible mechanism for long-distance dispersal. In this study, we collected 625 samples from 23 sites to understand the population connectivity of H. ovalis in the Indo-West Pacific. ITS and microsatellite loci were used to barcode and reveal the population connectivity pattern, respectively. According to the result, 432 samples of H. ovalis from 17 sites were used in this study. High level genetic diversity was found within 17 populations. The results of FST analysis showed that significant genetic differentiation was found among H. ovalis populations in the Indo- West Pacific. The results of STRUCTURE analysis showed that most of H. ovalis populations in the Indo- West Pacific possess unique genetic composition. Indicate that the gene flow between H. ovalis populations in the Indo- West Pacific is limited, therefore, long-distance dispersal by migratory birds is unlikely the main mechanism for shaping their connectivity pattern, and we suggest at least three cryptic species may occur within its distribution.

碩士
國立臺灣大學
漁業科學研究所
92
The Indo-West-Pacific region (IWP) hosts the highest marine biodiversity on earth. The concordance among different species can be used to deduct the common mechanism that forms the IWP marine biodiversity. Genetic variation of mitochondrial AT- rich region in the “living-fossil” horseshoe crab, Tachypleus tridentatus, were revealed for 82 individuals collected from 5 populations in 3 regions, including southern Burma coast of Andaman Sea (AB), Angsila in Gulf of Thailand (GT), and Kinmen (TK), Donwei (TD), Tehsiwei (TT) in Taiwan. Haplotype phylogeny constructed by neighbour-joining algorithm, the network derived from the minimum spanning network, and dating by fossil records demonstrated that a significantly deep divergence between the populations in Indian and Pacific Ocean, suggesting a pattern of Indian-Pacific tectonic plate divergence from late Oligocene to early Miocene (21-27 Ma). In addition, it also indicated that Taiwan population formed a significantly different clade from Gulf of Thailand divergence time indicates that South China Sea Basin might play an important role in retarding gene flow of between the T. tridentatus populations of southern and northern South China Sea from early Miocene to middle Miocene (17-21 Ma). The demography parameter and unimodal mismatch distribution indicates the sudden range expansion of T. tridentatus population in Gulf of Thailand and affected by sea level and habitat fluctuation during glaciations. The mismatch distribution indicated the bottleneck effect on Donwei population due to recent population size decline and inbreeding in this close bay. The implications of phylogeography and demography towards the T. tridentatus conservation in the IWP are also highlighted.

博士
臺灣大學
動物學研究所
98
Abstract The trichiurid fishes commonly called hairtails are important resources for various types of fisheries. Hairtails, being situated on the top of trophic pyramid, also play important roles in the demersal eco-systems. Due to highly specialized external appearance, the taxonomic status of hairtails is ambiguous as compared to the other fishes ranging from subfamily down to population levels. In this study, we used traditional measurements, geometric morphometrics and mitochondrial DNA as tool to reveal the phylogenetic relationships among genera, the species status of the genus Trichiurus and the population structure of T. japonicus in the western North Pacific. The phylogenetic trees among 9 genera showed that both Aphanopodinae and Trichiurinae are monophyletic groups, but not for Lepidopodinae. We suggest putting Eupleurogrammus and Tentoriceps to Trichiurinae, because they all shared with apomorph of reduced anal and caudal fins. In addition, Assurger and Evoxymetopon showed so closed relationship that they should combine into a complete genus. Similarly, due to closed relationship between Lepturacanthus and Trichiurus and paraphyly of Lepturacanthus, we also suggest that they belong to a same genus. The results from morphological and mitochondrial analyses showed that there are three valid species contained in the "T. lepturus" complex -- T. lepturus, T. japonicus and T. nanhaiensis. Traditional measurements showed that the ratio of measurements pairs were significant but overlapping. However, the shear (shape component, H) had fine resolution power to discriminate three species without overlapping. The first and second contributed of variables for the shear were represented body depth and preanal dorsal fin based length. Therefore, three species can be separated by using these two measurements compared to their total length. The phylogenetic relationships showed three distinct groups with no outliers. AMOVA showed that the major component of the variances concentrated among species (ΦCT = 0.967). The analyses of phylogeography of Trichiurus showed that all speciation events occurred around 8.5 million years ago in tropic waters among Indo-China, Sumatra and Borneo during the late Miocene. The high haplotype diversities (0.97-0.99) with moderate nucleotide diversities (0.005 - 0.009) might result from historical bottleneck and subsequently population expansion. Populations in the area were sub-structured into two groups of the SCS and pan-ECS (ECS+TS+YS), confirmed by AMOVA (ΦCT = 0.165). These results indicate that the TS served as a barrier, which interrupts mixture between populations in the ECS and SCS. However, intermittent gene flow were also traceable in the phylogenetic analyses, indicating that the SCS gained a small number of migrants from the TS. Limited larval dispersal ability across marine boundaries and monsoon-influenced flow patterns in the TS well explain a non-panmictic structuring. Coalescent theory estimated that the populations were subdivided during the middle Pleistocene glacial maxima, and expanded when the ice sheets retreated. Two management stocks are suggested for conservation purposes; i.e., the ECS (including the TS) and the SCS, to strengthen current fishery regulatory programs.

博士
國立臺灣師範大學
生命科學研究所
95
The colonization and differentiation of mangrove species are noticeably affected by geographic histories. The Indo-West Pacific (IWP) is the region that contains the most abundant and specious mangrove assemblages. The population of Ceriops tagal endemic in Southeast Asia, like that of many other mangrove species, was structured by the isolation of present Malay Peninsula and ancient Sundaland. I used maternally inherited chloroplast DNA, with which the effects of pollen dispersal could be excluded, to retrace the phylogeographic relationships among populations and dispersal route of propagules of C. tagal. In this dissertation, the Malay Peninsula was demonstrated to effectively isolate the gene flow of populations of C. tagal between the South China Sea (SCS) and the Bay of Bengal (BOB). During the glacials, the emergence of the Sunda Shelf connected the Borneo and the Malay Peninsula, forming a strict barrier named Sundaland. This caused populations within the SCS sharing common ancestral genotypes, and so was the situation in populations of the BOB water mass. The Gulf of Thailand (GOT) began to take shape 21 thousand years ago, and mangroves therefore started to retreat (or expand) to the coasts of the GOT. While populations in the GOT had frequent gene flow due to the tides and seashore currents, the independent demographic dynamics of each local population structured the whole GOT population. The closed gulf maintains the stable historical demography of whole GOT population and thus forms a classical metapopulation. The Kra Isthmus, the narrowest part of the Malay Peninsula, had been submerged under sea level before ca. 5 Mya, and this might lead to unhindered gene flow of mangroves between the SCS and the BOB. The divergent time of the SCS and BOB populations based on strict molecular clock is slightly underestimated when compared with the formation time of the Kra Isthmus. The long distance dispersal between the SCS and the BOB may be the cause of the underestimation of molecular clock. The most likely route for long distance dispersal across the land barrier is that via the Malacca Strait. The high gene flow between populations in the South Malay Peninsula and other areas in the past estimated by the coalescent-method provides an indirect evidence of Malacca Strait as the gate of dispersal. The isolation of populations in the two water masses during the glacials and the acceleration of gene flow due to sea-level rise during the interglacials might cause the high genetic diversity of mangroves in the IWP now. Moreover, while the periodic expansion and contraction of the SCS due to the sink and emergence of the Sundaland caused population expansion in the SCS, this situation never happened in the BOB, and population there maintained demographically stable. The population in the SCS may expand through colonization instead of local population growth because only few local populations were detected to expand. Thus, for conservation application, I suggest that the coasts of the Southeast Asia should be protected in order to provide steppingstone for the dispersal of mangroves.

碩士
國立海洋大學
海洋生物研究所
91
The purpose of this study is to analyze the patterns of biogeographical distribution of the coral reef fishes in Indo-west Pacific by using multivariate methods including clustering and ordination. The possible mechanisms of these patterns where also further discussed. In this study, we analysed the distributional data of Acanthuridae (73 species)、Pomacanthidae (54 species)、Pomacentrinae (59 species) and Chaetodon (75 species) among 16 locations in Indo-west Pacific. Further more, we examined the community structure of Chaetodon (75 species) among 49 locations, the correlations between species abundance and latitude/longitude, and the correlations between the historical factor (plate tectonics) and the ecological factors (currents, geographical distance, ocean-path distance). The result show that geographical distribution patterns of the coral reef fishes from16 sites can be divided into 3 geographical areas: (1) the north-west Pacific area, (2) the central-west pacific area, and (3) the west Indian ocean area. The geographical distribution pattern of the 75 species of Chaetodon examined from the 49 sites, however, can be divided into 8 geographical areas. The correlation between the biodiversity and the longitude appears to correspond with previous papers, but the latitude having no significant relation. This indicate that the temperature might not be so important to determine the distribution pattern of butterflyfish of Chaetodon. Using the Mentel test together with the Spearmans’ Rank correlation, this study discovered that the formation of the current distribution pattern of coral reef fishes has the greatest correlation with the ocean-path distance, following the geographical distance, then with the oceanic plates, and has the least correlation with the current ocean currents. This result might reveal that inshore coastal currents should have more influence on the dispersal of species than the off shore oceanic currents.

碩士
國立臺灣大學
海洋研究所
100
Dascyllus aruanus is distributed throughout the Indo-Pacific Ocean, from Red Sea and East Africa to French Polynesia, and from southern Japan to southeast Australia in West Pacific. The aims of this study were to reveal the phylogeographic relationship and population genetic diversity of D. aruanus in Indo-Pacific by using mtDNA cytochrome b (1040-bp) and 7 microsatellite loci. Totally, 260 individuals were collected from southern Taiwan, Raja Ampat (Indonesia), Okinawa (Japan), Paracel Island (China) and Dongsha Atoll in the South China Sea, New Caledonia, Gaohagan Island (Philippines), French Polynesia, Eilat in Red Sea and four locations around Madagascar. The phylogenetic tree of mtDNA showed that populations in Indian Ocean (Madagascar and Red Sea populations) formed a monophyletic group and the rest Pacific populations were mixed together. A strong genetic break between Indian and Pacific populations suggests that the Indo-Pacific barrier may play an important role in shaping their genetic structure. Among the 25 individuals collected from French Polynesia, 23 individuals formed a group with high bootstrap value, while the rest 2 individuals were mixed with other Pacific populations which might be due to rare dispersal events. The lower genetic diversity found in French Polynesia and Red Sea populations fit with the prediction of genetic diversity in peripheral populations. However, the other Pacific populations and four populations around Madagascar were characterized with higher genetic diversity which indicating that high and frequent gene flows may exist among local and regional populations.

博士
國立臺灣大學
海洋研究所
102
The Indo-West-Pacific region (IWP) hosts the highest marine biodiversity on earth. The concordance among different species can be used to deduct the common mechanism that forms the IWP marine biodiversity. The horseshoe crab is an ancient marine arthropod, which has a wide geographic distribution cross the IWP and a long evolutionary history and importance in costal ecosystem and economics. However, loss of habitats and population degradation urged the need to study genetic connectivity and population demography for conservation. In my PhD dissertation there are three aims to be addressed: (1) To apply with phylogeographic methods of three species of horseshoe crabs (Tachypleus tridentatus, T. gigas, and Carcinoscorpius rotundicauda) probing in the speciation mechanism of the colonization routes (Chapter 2). (2) To compare how the effect of paleoclimate and paleogeology change on historical demography between two species horseshoe crab, T. tridentatus in the northwestern Pacific and T. gigas in the Indo-Malay Archipelago (Chapter 3). (3) To transfer the pattern of the genetic connectivity into design of reserves network and other conservation actions for horseshoe crabs along East and northern South China Sea (Chapter 4). Phylogenetic relationship of three species of horseshoe crabs was revealed by mitochondrial (mt) COI, and AT-rich region. Based on dating Asian horseshoe crabs and Atlantic horseshoe crab (Limulus polyphemus) by fossil and biogeographic records of common ancestor and genetic variation of COI sequence, there were deep divergence at 24.7 ~33.6 million year ago (mya) between C. rotundicauda and two Tachypleus species, and 20.3~ 27.6 mya between T. gigas and T. tridentatus. The phylogenetic trees constructed by each marker all exhibited that only T. tridentatus had shallow genealogy relative to T. gigas. The deep divergent phylogeny of might be due to more isolation created by complicated sea basins and plate tectonic in Indo-Malay Archipelago than northwestern Pacific and also indicated the southern origin of Asian horseshoe crab according to the basal lineage in Indian Ocean. Pairwise difference (FST) also indicated that there was a significant differentiation between Indian and Pacific T. gigas populations. Genetic variation of mt AT-rich region was examined for genetic connectivity and demography of 114 T. tridentatus individuals from Mainland China coast and Taiwan Strait, and 296 individuals from Japan coast. There was gradual growth in effective population size of horseshoe crab in Mainland China and Taiwan Strait after Last Glacial Maxima during the past 35 thousands years ago by using Bayesian Skyline plot, while horseshoe crabs began to colonize after last minor glacial period to Japan (3500~4500 years ago). The extremely low of genetic diversity in most Japan populations could result from loss of genetic connectivity measured by FST from other populations in the northwestern Pacific. Based on genetic connectivity and historical demography in different spatial scale, it improve the measurement of the dispersal capacity of marine organism and realizing the risk and gain the information of conservation actions for those marine organism with lower dispersal capacity like horseshoe crab could sensitive to surfer from habitat degradation. A greater understanding of genetic connectivity could be used to realize the dispersal pattern and apply for reserve network design of T. tridentatus in East China Sea and north South China Sea. This dissertation also provides a conservation awareness to build a baseline for marine organisms, which are especially facing habitat deconstruction in the northwestern Pacific.

碩士
國立中興大學
生命科學院碩士在職專班
101
This study focused on the degree of diffence in gastric mills of fiddler crabs among and within subgenera and species, and whether these characters can be used for the taxonomy of fiddler crabs. The specimens used were collected from Indo-West Pacific region, including the subgenera Australuca, Austruca, Cranuca, Gelasimus, Paraleptuca and Tubuca. Other specimens of fiddler crabs outside the Indo-West Pacific, and other genera of the superfamily Ocypodoidea, were used for comparison. The morphology of urocardiac ossicle of stomach of these crabs was examined and described. The results showed that the urocardiac ossicles are very different among genera of the superfamily Ocypodoidea. There are various degrees of morphological differences among subgenera and species of Uca. For example, all species of the U. lactea-complex of Austruca, except U. lactea, have similar morphology of gastric mills. Regarding the difference within a species, different individuals within U. perplexa or U. formosensis still have similar gastric mills. It is suggested that the morphology of urocardiac ossicle of gastric mill should be useful in classification of some groups (subgenera and species) of Indo-West Pacific fiddler crabs.

碩士
國立臺灣大學
生態學與演化生物學研究所
99
Indo-Pacific humpback dolphin (Sousa chinensis) population that inhabits west coastal waters of Taiwan was estimated to number less than 100 individuals and is listed under the IUCN criteria as “Critically Endangered”. In this study, photo-identification mark-recapture techniques were applied to investigate their behavioral and reproductive dynamics. During a 4-year study period (2007-2010), 352 boat-based surveys were performed, resulting with over 60,000 photographs; 98 individuals were photo-catalogued, of which 22 were reproductively active females and 27 were calves. Hierarchical cluster analysis and multidimensional scaling revealed that the population consists of two communities, each with a moderately fluid pattern of geographic and social fidelity. Although the communities are not entirely discrete, their interactions are limited to "casual acquaintances” while modeled lagged identification rates suggest that “emigration and reimmigration” best describes their movement and ranging pattern. There seems to be further differences between individuals from both communities, including different percentage of coloration/age-stages and the number of mature females. Although some individuals can be seen in both communities, their heterogeneous movement pattern indicates that over a longer time scale they prefer a certain region which is their respective community range. The degree of separation between the two communities requires further investigation, but it seems to correspond with features of local habitat. It is also possible that the separation is a historically more recent event related to anthropogenic impacts, as there is an area of increased industrial activity located approximately in the middle between the two communities which might act as a human-caused barrier. The social behaviour might be performed as mate-searching behaviour, while the parturition happened throughout the year with a peak in spring and summer, resulted a crude birth rate of 0.064 ± s.d. 0.037. The mean survivorship and survival rate to Age 1 were estimated at 0.66 ± s.d. 0.20 and 0.78 ± s.d. 0.39, respectively; and the recruitment rate (at Age 1) was 0.090 ± s.d. 0.030 with calving interval approximating 3.52 ± s.d. 0.28 years with the weaning age at around 3-4 years old. Estimated suite of population parameters indicating a slow population growth rates highlight further the vulnerability and sensitive conservation status of Indo-Pacific humpback dolphins off Taiwan; indicating that informed conservation management plan is urgently needed.