Rozprawy doktorskie na temat „Atyidae”

The aim of this thesis is to use phylogenetic analyses of mitochondrial DNA to investigate the biogeography and evolutionary relationships within the freshwater shrimp family Atyidae in Australia at a nested series of scales, both geographic and systematic. At the largest scale, the relationships between Australian and Indo-West Pacific species were inferred using the two most common atyid genera in Australia, Caridina and Paratya. Most atyids are hypothesised to have colonised Australia from Southeast Asia, but Paratya may be a Gondwanan relict given its distribution. Australian Paratya all form a strong clade, with a sister relationship to species from Tasman Sea islands. Molecular clock estimates place all of the splits within Paratya after the break-up of Gondwana, with Australia being colonised once 3½-8½ million years ago. This transoceanic dispersal is conjectured to have taken place through oceanic currents because of the amphidromous life cycle of some taxa of Paratya. Caridina has a very different biogeographic history in Australia, as numerous Australian species have close evolutionary relationships with non-Australian taxa from locations throughout the region. This implies many colonisations to or from Australia over a long period, and thus highlights the surprising adeptness of freshwater shrimp in dispersal across ocean barriers and the unity of much of the region's freshwater biota. A number of potential species radiations within Australia were also identified. This agrees with patterns detected for a large number of Australian freshwater taxa, and implies a vicariant explanation due to the development of colder, dryer climates. The systematic relationships of the remaining two Australian surface genera (Caridinides, Australatya) and two subterranean genera (Parisia, Pycnisia) were also investigated. Australatya forms a strong clade with Pacific 'Atya-like' genera, and Caridinides falls within a clade containing Australian Caridina. The hypogean genera, Parisia and Pycnisia, form a strong clade in all analyses, implying an Australian subterranean speciation. The possibility of a relationship between Parisia/Pycnisia and some Australian Caridina species may have implications for the monophyly of the highly disjunct genus Parisia, as it may descend from local Caridina species and represent convergent morphologies. The common and speciose genus Caridina was used as a model taxon for analyses within Australia. At the medium scale, molecular taxonomic techniques were used to uncover cryptic species within a problematic east Australian species complex. At least five species were detected. Phylogeographic and population genetic analyses were carried out on each of these five cryptic species, which diverged from each other in the late Miocene/Pliocene. There were very large differences between the species in the scales of overall geographic distribution, intraspecific divergence and population structure. These were characterised as either: 1) species with large ranges, low intraspecific divergence, limited phylogeographic structuring (Caridina sp. D); 2) species with large ranges, high intraspecific divergence, a high level of phylogeographic structuring (sp. B); 3) species with a limited range, low intraspecific divergence, no phylogeographic structuring (sp. E); or 4) species with limited ranges, high intraspecific divergences, a high level of phylogeographic structuring (sp. A & C). These patterns reflect a combination of large-scale factors, such as landscape structure and climate change, and small-scale factors, such as species-specific tolerances to local conditions and differing dispersal capabilities. Life history variation (egg size) between species may be correlated with different dispersal abilities. Species with the smallest eggs have the least intraspecific divergence and largest distribution, while those with the biggest eggs have the most divergence and smallest distribution, with medium-sized egg species in between. At the smallest phylogeographic scale, C. sp. C from the sand dune islands of Moreton Bay in southeastern Queensland was further analysed. Two different lineages (C1, C2) were found which diverged from each other during the late Miocene/Pliocene and so are older than the current landscape in which they are found. Small-scale phylogeographic analyses within C1, C2 and a sympatric fish identified divergences dating to the Pleistocene (about 100-300 thousand years ago). This implies that ice age sea-level changes may have structured these populations, although there is little observable influence of the last glacial maximum (about 18 thousand years ago). This study has highlighted a number of taxonomic anomalies within the Atyidae. The detection of many cryptic species implies that biodiversity within freshwater invertebrates is higher than currently appreciated. The evolutionary and biogeographic relationships of Australian atyids have proved complex, with many taxa having their own individual histories. At the large Indo-Pacific scale, dispersal is most evident, but within Australia, both vicariance and dispersal have been responsible for structuring all taxa at every scale.

The aim of this thesis is to use phylogenetic analyses of mitochondrial DNA to investigate the biogeography and evolutionary relationships within the freshwater shrimp family Atyidae in Australia at a nested series of scales, both geographic and systematic. At the largest scale, the relationships between Australian and Indo-West Pacific species were inferred using the two most common atyid genera in Australia, Caridina and Paratya. Most atyids are hypothesised to have colonised Australia from Southeast Asia, but Paratya may be a Gondwanan relict given its distribution. Australian Paratya all form a strong clade, with a sister relationship to species from Tasman Sea islands. Molecular clock estimates place all of the splits within Paratya after the break-up of Gondwana, with Australia being colonised once 3½-8½ million years ago. This transoceanic dispersal is conjectured to have taken place through oceanic currents because of the amphidromous life cycle of some taxa of Paratya. Caridina has a very different biogeographic history in Australia, as numerous Australian species have close evolutionary relationships with non-Australian taxa from locations throughout the region. This implies many colonisations to or from Australia over a long period, and thus highlights the surprising adeptness of freshwater shrimp in dispersal across ocean barriers and the unity of much of the region's freshwater biota. A number of potential species radiations within Australia were also identified. This agrees with patterns detected for a large number of Australian freshwater taxa, and implies a vicariant explanation due to the development of colder, dryer climates. The systematic relationships of the remaining two Australian surface genera (Caridinides, Australatya) and two subterranean genera (Parisia, Pycnisia) were also investigated. Australatya forms a strong clade with Pacific 'Atya-like' genera, and Caridinides falls within a clade containing Australian Caridina. The hypogean genera, Parisia and Pycnisia, form a strong clade in all analyses, implying an Australian subterranean speciation. The possibility of a relationship between Parisia/Pycnisia and some Australian Caridina species may have implications for the monophyly of the highly disjunct genus Parisia, as it may descend from local Caridina species and represent convergent morphologies. The common and speciose genus Caridina was used as a model taxon for analyses within Australia. At the medium scale, molecular taxonomic techniques were used to uncover cryptic species within a problematic east Australian species complex. At least five species were detected. Phylogeographic and population genetic analyses were carried out on each of these five cryptic species, which diverged from each other in the late Miocene/Pliocene. There were very large differences between the species in the scales of overall geographic distribution, intraspecific divergence and population structure. These were characterised as either: 1) species with large ranges, low intraspecific divergence, limited phylogeographic structuring (Caridina sp. D); 2) species with large ranges, high intraspecific divergence, a high level of phylogeographic structuring (sp. B); 3) species with a limited range, low intraspecific divergence, no phylogeographic structuring (sp. E); or 4) species with limited ranges, high intraspecific divergences, a high level of phylogeographic structuring (sp. A & C). These patterns reflect a combination of large-scale factors, such as landscape structure and climate change, and small-scale factors, such as species-specific tolerances to local conditions and differing dispersal capabilities. Life history variation (egg size) between species may be correlated with different dispersal abilities. Species with the smallest eggs have the least intraspecific divergence and largest distribution, while those with the biggest eggs have the most divergence and smallest distribution, with medium-sized egg species in between. At the smallest phylogeographic scale, C. sp. C from the sand dune islands of Moreton Bay in southeastern Queensland was further analysed. Two different lineages (C1, C2) were found which diverged from each other during the late Miocene/Pliocene and so are older than the current landscape in which they are found. Small-scale phylogeographic analyses within C1, C2 and a sympatric fish identified divergences dating to the Pleistocene (about 100-300 thousand years ago). This implies that ice age sea-level changes may have structured these populations, although there is little observable influence of the last glacial maximum (about 18 thousand years ago). This study has highlighted a number of taxonomic anomalies within the Atyidae. The detection of many cryptic species implies that biodiversity within freshwater invertebrates is higher than currently appreciated. The evolutionary and biogeographic relationships of Australian atyids have proved complex, with many taxa having their own individual histories. At the large Indo-Pacific scale, dispersal is most evident, but within Australia, both vicariance and dispersal have been responsible for structuring all taxa at every scale.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Australian School of Environmental Studies
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Many species have been translocated from their native habitat into new environments. Some of these transfers have had negative impacts on the resident populations. Hybridization and introgression are some of the impacts that are associated with species incursions. These processes can potentially result in successful invasions and jeopardize the existence of native species and populations. It is thought that intraspecific hybridization can result in the loss of local adaptations and decrease adaptive divergence among populations. Understanding the factors affecting survival of the native species in altered landscapes is an important issue in species conservation. This study explores the processes that could lead to asymmetrical hybridization between two closely related lineages of freshwater shrimp Paratya australiensis. Selection pressure appears to be leading to extinction of one lineage in most of the sites adjacent to a pool where a translocation resulted in mixing of the two lineages (Hughes 2003). The aim of the thesis was to identify the processes and traits involved in the shaping of the current genetic structure of this shrimp following the translocation event; using genetic markers to identify what could have triggered the asymmetrical hybridization and almost complete extinction of the resident lineage. This is an ideal model system to study and understand interactions between recently (2-3 million years ago) diverged lineages. The translocated lineage 4 comes from Kilcoy Creek, which is at a higher altitude (cold temperatures) than Stony Creek, where the resident lineage 6 is situated (warm temperatures). The temperature differences and the fact that the two lineages were thought to have been isolated for 3million years, led to the expectation of some degree of reproductive isolation. Hughes et al. (2003) found that, after this translocation the reproductive isolation was asymmetrical, such that most of the males appeared to mate only with females from the introduced lineage 4. They noticed that lineage 4 was inducing lineage 6 to the edge of extinction in its local environment. This particular translocation event provides an ideal opportunity to test a number of hypotheses to explain asymmetrical hybridization. The sensory drive hypothesis focuses on how mating signals are effective for particular environments and may differ between environments (Endler, 1992). The second hypothesis proposed by Hughes et al. (2003), focuses on the fact that crosses between the resident females and translocated males lineages and vice versa may have differential viability.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Griffith School of Environment
Science, Environment, Engineering and Technology
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Esta dissertação compreende um estudo da sistemática e da distribuição geográfica dos camarões de água doce (Atyidae e Palaemonidae) existentes na rede fluvial do Estado do Rio de Janeiro. O presente estudo vem contribuir para o conhecimento de alguns aspectos ambientais ( salinidade, temperatura, declividade e oxigênio) os quais influenciam a distribuição destes animais. São considerados, também, os mecanismos de dispersão por eles utilizados. Este trabalho é constituído de uma introdução, uma parte sistemática, discussão, conclusões, referências bibliográficas, três quadros, cinco mapas e dez estampas das espécies estudadas. São apresentadas chaves de identificação para famílias e espécies, diagnoses das famílias e subfamílias, caracterização das espécies, tamanho, localidade tipo, distribuição geográfica, material examinado e observações. É registrada a ocorrência de uma espécie ainda não assinalada para a região, questionada a validade de uma espécie; e também são referidos fatores que influenciam a distribuição das espécies. As espécies são distribuídas de acordo com as unidades hidrográficas delimitadas pela SERLA (Superintendência Estadual de Rios e Lagos) em 1985.
Systematics and geographic distribution of freshwater shrimps (Atyidae and Palaemonidae) from the Rio de Janeiro fluvial system were studied. Some environmental factors (salinity, temperature, declivity and oxygen) influence upon species distribution. This dissertation contains an introduction, systematic part, discussion, conclusions, bibliography, three squares, five maps and ten plates corresponding to the species studied. Keys for classification of families and species, diagnosis of families and subfamilies are shown. Characterization, size, type locality, geographic distribution, material examined and notes for each species are mentioned. The occurrence of one species not yet recorded from the region is mentioned, the validity of one species is discussed, and reported factors which influence upon the species distribution. The species are distributed according to the hydrographic basins delimitated for SERLA (Superintendência Estadual de Rios e Lagos) in 1985.

Aquatic toxicity tests are increasingly being used in water resource management worldwide, and currently in South Africa, policy and legislation are being drafted to reflect this international trend. While standard toxicity test methods and test organisms are being considered to develop and set water quality guidelines and effluent discharge limits, it is not clear whether guidelines and discharge limits set using these standard test organisms will be sufficient to protect South Africa’s scarce water resources. As part of ongoing research to investigate the use of indigenous riverine organisms as toxicity test organisms a number of potential species have been identified, including the freshwater shrimp Caridina nilotica. For much of the history of aquatic toxicological data the bulk of the data has been generated by acute toxicity testing, based on short exposures and using mortality as the response end point. There are relatively few chronic, longterm tests with sub-lethal endpoints. However, it was recognized that information about longer exposure durations and non lethal response endpoints was needed, instead of mortality. Chronic tests can provide a more environmentally realistic measure of chemical toxicity than acute toxicity tests. Caridina nilotica has been identified as a potential standard toxicity test organism, as it is widely distributed, easy to find and it occurs in flowing waters. It is an indigenous species which can be easily cultured and maintained in the laboratory and is also ecologically important. Both adults and juveniles have been used successfully in acute toxicity tests at the Institute for Water Research (Rhodes University) and the ability to rear the organisms under laboratory conditions has allowed the development of chronic toxicity tests using C. nilotica. Chronic early life stage tests include continuous exposure of the early life stages, which are presumed to be the most sensitive for aquatic organisms. This study reports on the embryonic development of C. nilotica at the culture temperature of 24⁰C. Morphological developmental stages were monitored and measured and 7 developmental stages were identified. Based on the measurements of the features that were identified, toxicity tests using the reference chemicals sodium chloride (NaCl), sodium sulphate (Na₂SO₄) and cadmium chloride (CdCl₂) were undertaken to test the suitability of C. nilotica embryonic development for chronic toxicity tests for use in water resource management. The length, width, length:width ratios and area of the features decreased in size when exposed to the chemicals. The Lowest Observed Effect Concentration (LOEC) values were 2000mg/L for Na₂SO₄, 3000mg/L for NaCl and 0.31mg/L for CdCl₂. The No Observed Effect Concentration (NOEC) values were 1000mg/L for Na₂SO₄, 2000mg/L for NaCl and <0.31mg/L for CdCl₂. Further research on the teratogenic effects of single chemicals and industrial effluent on developing C. nilotica embryos needs to be undertaken in order to evaluate the described test protocol for use in water resource management.

Os camarões do gênero Atya Leach, 1816 são os maiores camarões da família Atyidae, sendo que as 13 espécies reconhecidas estão distribuídas em rios e riachos das regiões tropicais e subtropicais da América (vertentes atlântica e pacífica) e oeste da África. O primeiro relato de uma Atya ocorreu no séc. XVII e, desde então, novas espécies foram descritas e descrições prévias revisadas, produzindo um histórico de instabilidade e reclassificações. Embora ao longo do séc. XX revisões taxonômicas tenham estabilizado a sistemática do gênero, a variabilidade morfológica e distribuição geográfica trans-ístmica da espécie A. innocous gerou questionamentos. Além disso, mais recentemente trabalhos de filogenia molecular da família Atyidae que incluíram representantes de Atya suscitaram questões em relação à sistemática do gênero (possível não monofilia) e de algumas espécies como A. gabonensis, A. margaritacea e A. scabra. Visto que o uso de marcadores moleculares nunca foi empregado para a delimitação das espécies de Atya e que seu uso de forma complementar à morfologia poderia aperfeiçoar a sistemática do gênero, o objetivo do presente estudo foi avaliar por meio de dados moleculares as hipóteses taxonômicas das espécies A. gabonensis, A. innocous, A. margaritacea e A. scabra. Sequências dos genes mitocondriais 16S e Citocromo Oxidase I e gene nuclear Histona 3 foram geradas por meio de protocolos de extração e sequenciamento de DNA a partir do tecido de espécimes obtidos em empréstimos/doações. Potenciais espécies evidenciadas pelas análises de similaridade nucleotídicas (distâncias genéticas), compartilhamento de caracteres em um contexto evolutivo (reconstruções filogenéticas), Automatic Barcode Gap Discovery, Poisson Tree Processes e Generalized Mixed Yule Coalescence foram confrontadas com as hipóteses taxonômicas específicas atuais. A avaliação sistemática com dados moleculares aqui realizada, adicionalmente às informações morfológicas existentes na literatura sustentaram A. gabonensis como uma espécie de distribuição anfi-atlântica, mas não corroborou a hipótese de A. innocous como uma espécie trans-ístmica. Assim, o uso do nome A. innocous para as populações do Mar do Caribe e A. tenella para aquelas restritas ao Pacífico é sugerido. A espécie A. margaritacea, distribuída ao longo da costa pacífica da América foi considerada uma espécie válida e distinta de A. scabra, amplamente distribuída na vertente atlântica da América do Sul, África e Mar do Caribe. Contudo, é discutida a possibilidade de uma espécie críptica restrita no Golfo do México existir. Adicionalmente, o conhecimento existente e pertinente para futuros estudos de sistemática e taxonomia sobre os camarões do gênero Atya foram sumarizados e são apresentados.
The genus Atya Leach, 1816 shrimps are the largest of the Atyidae family, and the 13 acknowledge species are geographically distributed in rivers and stream in the tropical and subtropical regions of America (Atlantic and Pacific drainages) and West Africa. The first registry of an Atya was in the XVII century and since then new species were described and previous description revised in an eventful taxonomic historic. Although throughout the XX century taxonomic revisions stabilized the genus systematics, the morphological variability and the trans-isthmic geographic distribution of A. innocous caused questioning. Moreover, molecular phylogenetic studies that included Atya representatives raised doubt on the genus systematics (possibly non-monophyletism) and some species A. gabonensis A. margaritacea and A. scabra hypothesis. As molecular markers have never been used concerning Atya species delimitation complementary to the morphology and it could improve the genus systematics, the goal of this study was to evaluate with molecular markers the taxonomic hypothesis of the species A. gabonensis, A. innocous, A. margaritacea e A. scabra. Sequences of the mitochondrial genes 16S and Cytochrome Oxidase I and nuclear gene Histone 3 were generated by means of DNA extraction and sequence protocols from specimens obtained in loans/donations. Putative species evidenced by the analysis of nucleotide similarity (genetic distances), character sharing (phylogenetic reconstitutions), Automatic Barcode Gap Discovery, Poisson Tree Processes and Generalized Mixed Yule Coalescence were compared to the prevailing taxonomic hypothesis. The systematic evaluation with the molecular data of this study, in addition with the morphological information in the literature sustain A. gabonensis as an amphi-atlantic distributed species, but do not corroborated A. innocous hypothesis as an trans-isthmian species. In this sense, the use of A. innocous stricto sensu for the Caribbeans Sea populations and A. tenella to that restricted to the pacific drainage of America is suggested. Atya margaritacea, distributed along the pacific drainage of America, is considered a valid species distinct from A. scabra, widespread distributed in the Atlantic drainage of America and Africa, besides Caribbean Sea. However, the possibility of a cryptic species in the Gulf of Mexico population is discussed. Aditionally, the relevant knowledge to future systematic and taxonomy studies about the shrimps of the genus Atya were summarized and are shown.

Le macrofaune indigène des rivières insulaires caribéennes est constituée majoritairement d’espèces de poisson et de crustacé amphidromes. L’amphidromie est un cycle de vie caractérisé par la dévalaison des larves vers la mer suivi d’une dispersion larvaire marine, les juvéniles retournent en rivière pour grandir, y résider et se reproduire. Au cours de leurs migrations en rivière, ces individus rencontrent des perturbations de continuité écologique, telles que des barrages de hauteurs de chute variables. Ces ouvrages sont très largement répandus dans les rivières insulaires tropicales car ils permettent l’extraction de l’eau pour la production d’eau potable. Les objectifs de cette thèse ont été de caractériser leurs impacts sur la structure démographique et l’organisation trophique des populations de poissons et crustacés majoritaires aux Antilles et présentes sur l’ensemble du continuum de la rivière. Ce travail a été mené sur trois rivières de Guadeloupe afin d’analyser (1) la structure démographique de leurs populations et leur capacité à franchir les obstacles ; (2) la taille et le déplacement de leur niche trophique sous l’impact des obstacles à l’aide de l’analyse d’isotopes stables du carbone et de l’azote ; (3) l’évolution de la qualité nutritionnelle des sources de nourriture et la teneur en acides gras des consommateurs sur un gradient altitudinal grâce à des analyses lipidiques. Les résultats obtenus mettent en évidence (i) le rôle des embouchures comme lieu-clé assurant la résilience des milieux ; (ii) la qualité nutritionnelle des sources de nourritures comme l’un des éléments pouvant expliquer la montaison des espèces ; (iii) l’importance des transferts de matière allochtone de l’amont vers l’aval pour l’apport en acides gras essentiels ; (iv) le contexte environnemental au niveau de l’ouvrage déterminant les impacts démographiques et trophiques ; (v) des impacts trophiques visibles qui diffèrent en fonction des groupes fonctionnels, de leur place dans le réseau trophique et de la plasticité alimentaire des espèces
The native macrofauna of Caribbean island rivers consists mainly of amphidromous fish and crustacean species. Amphidromy is a life cycle characterized by the downstream migration of larvae towards the sea followed by a marine larval dispersion, juveniles return to the river to grow, reside and reproduce. During their migrations in rivers, these individuals encounter ecological continuity disturbances, such as dams with variable head heights. These dams are widespread in tropical island rivers because it enables the extraction of water for the production of drinking water. The objectives of this PhD were to determine their impacts on the demographic structure and trophic organization of the majority of fish and crustacean populations in the West Indies and present along the entire continuum of the river. This work was carried out on three rivers in Guadeloupe in order to analyze (1) the demographic structure of their population and their ability to overcome obstacles; (2) the size and shift of their trophic niche under the impact of obstacles using the analysis of stable isotopes of Carbon and Nitrogen; (3) the evolution of the nutritional quality of food sources and the fatty acid composition of consumers on an altitudinal gradient using lipid analysis. The results obtained highlight (i) the role of the rivermouth as a key place ensuring the resilience of environments; (ii) the nutritional quality of food sources as one of the driving forces that can explain the upstream migration of species; (iii) the importance of transfers of allochthonous material from upstream to downstream for the supply of essential fatty acids; (iv) the environmental context at the dam level determining demographic and trophic impacts; (v) visible trophic impacts that differ according to functional groups, their place in the food web and the food plasticity of the species

Les cours d’eau des îles tropicales abritent des organismes qui ont développé un cycle de vie diadrome, partagé entre une phase adulte en eau douce et une phase larvaire marine : l’amphidromie. Parmi ces organismes, dans la zone Indo-Pacifique, on trouve les crevettes du genre Caridina H. Milne Edwards, 1837. Avec plus de 300 espèces décrites, il s’agit du genre le plus diversifié de l’infra-ordre des Caridea, avec une systématique extrêmement confuse et compliquée. Au sein de ce genre, deux complexes d’espèces sont particulièrement bien représentés dans les systèmes insulaires de l’Indo-Pacifique, le complexe Caridina nilotica et le complexe C. weberi. Grâce au développement de nouvelles techniques de séquençage de nouvelles méthodes de taxonomie dite intégrative sont apparues, permettant de résoudre une partie des problèmes taxonomiques de ces groupes. L’objectif de la thèse était d’appliquer une approche de taxonomie intégrative aux espèces des complexes C. nilotica et C. weberi afin de clarifier leur systématique et, de fait, mieux appréhender leur biologie et fournir les outils aux gestionnaires pour mettre en place une meilleure conservation de ces espèces et de leurs milieux. Après avoir montré que certains caractères morphologiques traditionnellement utilisés pour décrire les espèces étaient influencés par l’environnement et donc fortement variables, l’étude de taxonomie intégrative a été conduite sur 92 espèces, permettant d’obtenir 1682 séquences auxquelles s’ajoutent 32 génomes mitochondriaux complets et 97 partiels, mettant en évidence 43 espèces nouvelles, certaines décrites au cours de la thèse. Les relations phylogénétiques entre les espèces des deux complexes ont été reconstruites à partir d’un grand jeu de données moléculaires, permettant de montrer que les complexes sont des groupes monophylétiques avec des différences en terme d’habitats occupés. Enfin, la faisabilité de l’étude sclérochronologique de l’amphidromie chez une espèce du complexe C. weberi (C. multidentata) a été testée sur la cuticule du pédoncule oculaire, avec une étude de l’ultrastructure de la cuticule, décrite pour la première fois chez cette espèce
Rivers of tropical islands harbor organisms that have developped a diadromous lifecycle, shared between a freshwater adult phase and a marine larval phase: amphidromy. Among these organisms, in the Indo-Pacific area are found shrimps of the genus Caridina H. Milne Edwards, 1837. With more than 300 described species it is the most speciose genus of the infra-order Caridea, with a most confused and complicated taxonomy. Within this genus, two species complexes are particularly well-represented in insular systems of the Indo-Pacific, the C. nilotica complex and the C. weberi complex. Thanks to the development of new sequencing techniques, new methods of integrative taxonomy appeared, allowing to resolve part of the taxonomic complexity of these taxa. The aim of the thesis was to apply an integrative taxonomy approach to species belonging to C. nilotica and C. weberi complexes in order to clarify their taxonomy and have a better understanding of their biology and provide tools to managers for establishing a better conservation of these species and their environments. After showing that some morphological characters traditionally used to describe species were influenced by the environment and so, highly variable, the integrative taxonomy was led on 92 species, allowing to obtain 1,682 sequences to which are added 32 complete and 97 partial mitochondrial genomes, highlighting 43 new species, some of them described during the thesis. Phylogenetic relationships among the species of the two complexes were reconstructed from a large molecular dataset, allowing to show that the complexes are monophyletic groups, with habitat differences. Finally, the feasibility of a sclerochronological study of amphidromy in a species of the C. weberi complex (C. multidentata) was tested on the eyestalk cuticle, with a study of the ultrastructure of the cuticle, described for the first time in this species

While the notion of species is central to our understanding of biological processes, it has been impossible to arrive at a consensus regarding a single, widely applicable or functional concept. This project provides insight into the progression through the speciation process by a widespread species of freshwater shrimp, Paratya australiensis. Using mate choice experiments and genetic analysis, multiple reproductive barriers were identified indicating strong divergence between two populations. These barriers are consistent with requirements for species separation under various species concepts, providing strong evidence to support taxonomic revision of this cryptic species complex.

The speciation debate in evolutionary science is long and protracted, evidenced by the multitude of concepts regarding species and speciation. Understanding the nature of species however, is of central importance in the study of biology and ecology. The purpose of this study was to investigate the genetic architecture of freshwater shrimp (Paratya australiensis) from two distinct lineages and of individuals across a known hybrid zone to gain insight into the process of speciation at the molecular level. The results of this study indicate that P. australiensis lineages sit in an advanced position along the speciation continuum, thus warranting taxonomic revision.

Freshwater ecosystems represent hotspots for the world’s total diversity and human well-being. However, they are also subjected to threats across the globe as a result of localised human activities, broad scale catchment clearance, climate change and invasive species. The increased degradation of freshwater habitats and their ecological functions as a consequence of these threats, at local and global scales, has led to significant freshwater problems for human existence and the world’s biodiversity. There is growing evidence that the loss of biodiversity is one of the most complex environmental issues facing the world; however, the importance of understanding species distribution patterns and the ecological differentiation among species that are reflected as species-specific responses or tolerances to environmental drivers is less well understood. In particular, when a morphological approach is used as a taxonomic tool for investigating species diversity and species level responses to environmental drivers, the diversity of responses hidden within species complexes may not be realized, and the conclusion of generality may mask specific cryptic species responses. In South-East Queensland, Australia, European occupation since the mid 1800’s has seen large scale clearing of native vegetation along streams and rivers in nearly all catchments. As a consequence of this land-use change catchment hydrology has been substantially altered, which, combined with the presence of dams and weirs, has resulted in a decline in water quality of streams in some catchments, which is of growing concern for conservation of species biodiversity. This study aimed to explore cryptic diversity in two species complexes of freshwater aytid shrimps common in South-East Queensland and elucidate species level responses to environmental variation that could explain their spatial distribution. This broad aim was met through three specific studies. First, using regional scale data of cryptic species diversity and water quality, the importance of species-specific responses to environmental conditions in determining spatial distribution patterns and environmental relationships of cryptic species in the Caridina indistincta and Paratya australiensis species complexes was examined. To accomplish this aim, DNA sequences were used to identify shrimp specimens from 89 sites in 17 catchments spanning the study area. In addition, an assessment of eight morphological traits was used to test whether these cryptic species could be morphologically identified. Use of these eight traits did allow species level identification, at least in South-East Queensland. However, caution is suggested in the use of these morphological traits for recognising species, due to the probability of morphological plasticity within a species across broad spatial scales. Ordination analysis of presence-absence data showed that the five cryptic species within the two species complexes showed spatially distinct distributions across streams in SEQ, with each cryptic species displaying different relationships with individual environmental variables. For species in the Caridina indistincta complex, C. indistincta sp. B was significantly associated with elevation, C. indistincta sp. D was significantly correlated with dissolved oxygen range, whilst, individuals of C. indistincta sp. A were negatively associated with elevation and dissolved oxygen range. This may indicate that C. indistincta sp. A tended to inhabit sites with low elevation and perhaps having a higher tolerance to a low range of dissolved oxygen. For the Paratya australiensis species complex, P. australiensis lineage 4 and 6 showed significant correlations with elevation and conductivity, respectively. The second broad aim of the study was to explore these spatial patterns at smaller geographical scales and with greater detail about water quality to understand and quantify the fundamental environmental factors (e.g., physical chemical water parameters and concentrations of heavy metals) that are potentially shaping the current distribution patterns and abundance of cryptic species within the two species complexes. To explore this aim, sediment samples from 22 sites in 13 catchments in SEQ were analysed to determine concentrations (mg/kg dry weight) of 11 heavy metals. Additionally, a number of water quality variables were measured in situ, including: elevation, stream width, stream temperature, dissolved oxygen, conductivity, pH, total dissolved solids, and turbidity. Also, a water sample was taken from each site for laboratory analysis of: Ammonium nitrogen (NH4-N), Dissolved oxidized nitrogen (Nitrate+Nitrite) (NOX-N), Total nitrogen (TN), Total kjeldahl nitrogen (TKN), Total kjeldahl phosphorus (TKP), Orthophosphate-P (PO4-P). Shrimps were collected from each site and identified to species using both morphology and DNA sequencing. The morphological identification of each adult individual (except juveniles which were genetically analysed) was used as a measure of absolute abundance and the genetic ‘checking’ of a set number of individuals in each sample was used to compute relative abundance. Redundancy analysis (RDA) showed that the spatial distribution and absolute and relative abundance of C. indistincta sp. D and sp. B were significantly positively influenced by elevation, while the relative abundance of P. australiensis Lin.6 was significantly positively affected by the concentration of manganese (Mn). Stream Total nitrogen (TN) was significantly positive driver of the spatial distribution and relative abundance of C. indistincta sp. A, while Orthophosphate-P (PO4-P) was significantly positive driver for the absolute and relative abundance of this species. Further analysis, this study confirms that P. australiensis Lin.6 was more tolerant of heavy metal concentrations compared with other cryptic species, as its distribution and absolute and relative abundance were significantly positively correlated with the concentrations of manganese, iron and cobalt. In contrast, C. indistincta sp. A was more sensitive to these metals than other study species. These results demonstrated that cryptic species of freshwater atyid shrimps of the C. indistincta and P. australiensis species complexes were different in their environmental requirements. As well, the cryptic species of both complexes were identified to have different associations with heavy metal concentrations, indicating that these species were different in their tolerance to toxicants. Finally, the third aim of the study was to further examine the differences in sensitivity to heavy metals (Copper and Zinc) among cryptic species of the two study complexes experimentally in the laboratory. Two cryptic species of each complex were used as study species, C. indistincta sp. A and sp. D and P. australiensis Lin.4 and Lin.6. The field studies showed differences among these species in their correlations with metal concentrations, and therefore they were seen as good candidate species for testing differences in the sensitivity to metal toxicants. Each cryptic species was exposed to six concentrations of each metal Cu or Zn using an acute (96-h) toxicity test. The results from this study were generally showed contrasting correlation between species and heavy metals; P. australiensis Lin.6 was the most tolerant species to both study metals, while C. indistincta sp. A was more sensitive to copper, and C. indistincta sp. D was more sensitive to Zn compared with the other tested species. Furthermore, the exposure of individuals of each species to the heavy metals caused changes in both their behaviour and their colour during exposure time. Overall, this study has shown cryptic species within broad species complexes can vary in their spatial distribution and their tolerance and response to water quality parameters. This highlights the advantage of using analyses of biotic and abiotic variables for ecological management and biodiversity conservation and the need to understand true species diversity when looking at species level responses to environmental degradation.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Environment and Sc
Science, Environment, Engineering and Technology
Full Text

The ecology of the protandrous freshwater shrimp, Australatya striolata (McCulloch and McNeill), was studied in two stream systems in north Queensland, in the context of its distribution in eastern Australia. The size frequency distributions of the populations studied were found to be bimodal, with the left mode consisting primarily of males, and the right mode of females. The modal size classes did not vary through time, although recruitment was found to be seasonal. The most likely mechanism for the maintenance of this bimodal distribution was a two-stage growth curve of an initial phase of relatively rapid growth of Juveniles followed by very slow growth of mature males, then a relatively rapid transition from male to female size followed by very slow growth of mature females. This explanation was well supported by a sigmoidal growth curve for individuals between the modal size classes, low levels of recruitment and negligible growth of tagged and caged males and females. Analysis of length frequency distributions through time also indicated very slow growth for mature males and females (1 mm in 870 days), and rapid growth of Juveniles (2-3 mm in 61 days). This growth pattern is possibly unique in the recorded literature. Breeding was seasonal and coincided with the summer wet season. Eggs were brooded and larvae released by the females in freshwater. The first larval stage was a zoea which was lecithotrophic and required salinities in excess of 20%. for further development. In lower salinities they could survive for up to 30 days on their yolk supplies. This was shown to be more than would be required for drift to the estuary (about 17 days in Yuccabine Creek and 8 days in Douglas Creek). The subsequent upstream migration of Juveniles required 12 to 18 months in the stream systems studied. A. striolata was shown to be primarily a filter feeder, but sweeping the substratum with the cheliped fan was used in periods of low stream flow. The predominant food was particulate organic matter, the abundance of which was not limiting for naturally occurring densities of shrimp. Predation and disease were shown to be minimal sources of mortality in the populations of adults studied, and the maintenance of near 1:1 sex ratios, despite the greater age of females, indicated high survival. The species was shown to be distributed in coastal streams from the Claudie River, Cape York Peninsular (12'45' S, 14312' E), to the Genoa River, Victoria (37°29' S, 149°35' E). The lowest observed altitude for adult populations tended to decrease with increasing latitude. The northern limit to the distribution was shown to be restricted by habitat availability. It is suggested that the observed differences in the size frequency distributions over the geographic range were due to different rates of recruitment. The adaptive significance of the life history of the species is discussed, with particular reference to the preference of adults for low order streams, and the advantages of the marine Larval stage.

博士
國立中山大學
海洋生物科技暨資源學系研究所
98
In this study, mtDNA was used to examine the phylogenetic and molecular relationships of the freshwater shrimp family Atyidae. The phylogeographical variations of two landlocked Caridina pseudodenticulata and Neocaridina denticulata were also discussed. Four genera and 32 species of the Atyidae were identified and divided into 6 groups. In addition to 14 previously recorded species, eight of them are new records, while another 10 species remain unconfirmed. The combination of morphological and molecular characteristics can effectively differentiate species within the family Atyidae. Analysis of demographic parameters indicates a recent population expansion of C. pseudodenticulata, but not for N. denticulata. The result of Bayesian skyline plot analysis implies that the expansion of C. pseudodenticulata began about 70,000 years ago, followed by a very recent rapid expansion approximately 4,000-6,000 years ago. Four major geographical regions of N. denticulata can be identified, including: (1) Southern Taiwan group; (2) Hualian group; (3) Northern Taiwan group; and (4) Ilan group. The study on the phylogenetic relationship of Atyidae in Taiwan could provide valuable information for future study of speciation and geological variation in tropical island.

碩士
國立東華大學
海洋生物多樣性及演化研究所
97
Monthly sampling of Caridina gracilipes was carried out from September 2006 to August 2008 at each of the two study sites: Lung-luan-tan Reservoir (landlocked) and Kangkou River (amphidromous). This study investigated two ecological types of C. gracilipes to understand the reproductive ecology of the shrimps inhabited different habitats. Total length and weight, carapace length, sex ratio, recruitment patterns, population dynamics, egg size and egg number were examined. We also constructed the molecular phylogenetic relationship of the species in Taiwan by using mitochondrial DNA COI gene. The results showed that the population density of the landlocked freshwater shrimps was larger than the amphidromous one, and so was the size. The sex ratio, male vs. female, was 1：1.1 in landlocked population, and 1：0.6 in amphidromous population, respectively. The reproduction of both populations was affected by water temperature and rainfall. Clutch size was smaller but the average egg size was larger in landlocked population as compared to amphidromous population, however the egg mass per female body weight was similar between the two populations, 15.9％ in landlocked and 16.4％ in amphidromous population, respectively. Females with eggs were found in most of the months, indicating a multiple ovulations. Analysis on length frequency distribution using computer package FiSAT, showed that the growth index of landlocked male was L∞＝4.2 mm, K＝0.98 year-1, φ=1.24, and L∞＝6.11 mm, K＝0.9 year-1, φ=1.53 for landlocked female; while the growth index was L∞＝4.85 mm, K＝0.87 year-1, φ=1.31 for amphidromous male, and L∞＝7.57 mm, K＝0.84 year-1, φ=1.68 for amphidromous female. This indicated that the growth rate of amphidromous was higher than the landlocked, while female growth rate was higher than male. We analyzed the DNA sequence from 27 specimens of C. gracilipes from different localities in Taiwan and concluded that the species can be divided into different groups. According to the high haplotype diversity and high nucleotide diversity and the results of Tajima’s D and Fu and Li’s D test, we suspected that the populations of C. gracilipes experienced bottleneck effect followed by population expansion event. NJ tree shows that the C. gracilipes populations in Taiwan can be divided into two groups, landlocked and amphidromous, with high support of bootstrap value, 100. All of the samples from different reservoirs are of the same type, however, the samples from rivers consist of both types. Based on the biological and molecular differences, we concluded that C. gracilipes in Taiwan might be in the process of population differentiation.

碩士
國立高雄海洋科技大學
水產養殖研究所
100
Caridina multidentata distributes from Japan, Taiwan to Madagascar. In Taiwan, it can be discovered at low attitude areas in Northern, Northeast, Eastern, Southern at low altitude area. In C.multidentata life history, with a female hatching migration from the river to an estuary, larval development in saltwater, and a return upriver migration by postlarvae (amphidromous migration). It’s not easy to increase the population size. Due to different and wan-wade influences. In this study measurements were done on the temporal and spatial distribution of reproductive C.multidentata in the Teng Stream, Taitung, Taiwan. Sampling of C.multidentata for this study took place at six sites along the Teng Stream for monthly a year (2010.12~2011.11). During these 12 months, 494 individuals were captured. The ratio of gender is 1:3.52 (female : male =140:354). Females (average carapace length (CL) = 8.43mm; maximum size(CL) =9.59mm ) were significantly larger than males(average CL =6.0mm; maximum size(CL) =7.94mm). The smallest mature size of female was 6.52mm. Many of the pre hatching females (with stage 2-3embryos) were observed with pre spawning ovaries (ovarian stage 2-3). This shows females were produced more than one brood during a breeding season. During the breeding season, females egg-carrying rate were correlated positively with temperature.