Dissertations / Theses on the topic 'Fish Taxonomy'

Thesis: S.M. in Science Writing, Massachusetts Institute of Technology, Department of Humanities, Graduate Program in Science Writing, 2014.
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 23-24).
In today's increasingly digitized, data-driven world, the "old ways" of doing things, especially science, are quickly abandoned in favor of newer, ostensibly better methods. One such discipline is the ancient study of taxonomy, the discovery and organization of life on Earth. New techniques like DNA sequencing are allowing taxonomists to gain insight into the tangled web of relationships between species (among the Acanthomorph fish, for example). But is the newest, shiniest toy always the best? Are we in danger of losing vital information about the world if we abandon the thousands of years of cumulative human knowledge to gather dust in basements? This thesis explores the current crossroads at which taxonomy finds itself, and offers a solution to preserve the past while diving headlong into the future.
by Lindsay Kirlin Brownell.
S.M. in Science Writing

It is estimated that less than ten percent of the world's species have been discovered and described. The main reason for the slow pace of new species description is that the science of taxonomy, as traditionally practiced, can be very laborious: taxonomists have to manually gather and analyze data from large numbers of specimens and identify the smallest subset of external body characters that uniquely diagnoses the new species as distinct from all its known relatives. The pace of data gathering and analysis can be greatly increased by the information technology. In this paper, we propose a content-based image retrieval system for taxonomic research. The system can identify representative body shape characters of known species based on digitized landmarks and provide statistical clues for assisting taxonomists to identify new species or subspecies. The experiments on a taxonomic problem involving species of suckers in the genera Carpiodes demonstrate promising results.

Thesis (PhD)--University of Stellenbosch, 2005.
ENGLISH ABSTRACT: The fossiliferous Waaipoort Formation (Witteberg Group, Cape Supergroup), Ganikobis Formation (Dwyka Group, Karoo Supergroup) and Whitehill Formation (Ecca Group, Karoo Supergroup) span a protracted period interrupted by a +-45Ma glacial event. This Late Carboniferous glacial event resulted in a prolonged hiatus in sedimentation as well as significant erosion in many southern continents of Gondwana. This study demonstrates how the glacial episode affected faunal composition and changes in palaeoecology in southern Gondwana across this time period. The Waaipoort shows the highest overall faunal diversity with relatively high palaeoniscoid diversity within Ganikobis and Whitehill Formations. This study is unique in correlating Early Carboniferous - Early Permian fish fauna of South Africa and Namibia specifically, as well as other parts of southern Gondwana, and includes maps of possible fish migration routes. This study attempts to refine the body of disjointed knowledge on the taxonomy and distribution of the fish fauna surrounding this period in southern Gondwana. Three new Waaipoort taxa are recognised, and several reassigned. Earlier work on Late Carboniferous fish from Southern Africa has been updated herein to incorporate recent collections. This has allowed the recognition of up to 15 new palaeonoscoid taxa, some of which are endemic to this region. Several new taxa are recognised within the Whitehill Formation fish fauna and a new lectotype for Palaeoniscum. capensis is presented. Detailed taphonomic and sedimentological studies (with 6 lithologs) of fossil localities visited in this broad-based study verify the correlation, and impart information often lost or ignored in pure palaeontological studies on the palaeoecology or palaeoenvironment of the fauna. Systematic relationships discussed here also serve to strengthen the palaeobiogeographical correlations between the Gondwanan continents.
AFRIKAANSE OPSOMMING: Die fossie1draende Waaipoort Formasie (Witteberg Groep, Kaap Supergroep), Ganikobis Formasie (Dwyka Groep, Karoo Supergroep) en Whitehill Formasie (Ecca Groep, Karoo Supergroep) strek oor 'n uitgebreide tydvak wat 'n periode van vergletsering van ongeveer 45 miljoen jaar insluit. Hierdie Laat Karboon ystyd het sedimentasieprosesse lank onderbreek en beduidende erosie in baie van die suidelike kontinente van Gondwana veroorsaak. Die huidige studie toon hoe die vergletsering die faunistiese samestelling en veranderings in die paleo-ekologie van suidelike Gondwana beinvloed het. In totaal toon die Waaipoort die grootste faunistiese diversiteit, terwyl 'n relatief hoe diversiteit ook onder die Palaeoniscoidei van die Ganikobis en Whitehill Formasies voorkom. Hierdie studie is uniek insoverre dit spesifiek data oor die Vroee Karboon - Vroee Perm visfauna van Suid-Afrika en Namibie, asook ander gebiede van suidelike Gondwana korrelleer en kaarte van moontlike migrasieroetes insluit. Die navorsing poog om die groot hoeveelheid losstaande inligting oor die taksonomie en verspreiding van die visfauna in suidelike Gondwana te verwerk en te verfyn. Drie nuwe taksa is uit die Waaipoort geidentifiseer en 'n verdere aantal is geherklassifiseer. Vroeer navorsing oor die Laat Karboon-visse van Suider-Afrika is bygewerk in die lig van resente versamelings. Dit het die herkenning van tot 15 nuwe taksa onder die Palaeoniscoidei, waarvan sommige endemies aan hierdie streek is, moontlik gemaak. 'n Aantal nuwe taksa word onder die visfauna van die Whitehill Formasie aangeteken, saam met 'n nuwe lektotipe van Palaeoniscum capensis. Gedetailleerde tafonomiese en sedimentologiese analises van die vindplekke wat tydens hierdie studie ondersoek is en wat 6 vertikale profiele insluit, ondersteun hierdie korrelasie. Sodoende stel dit inligting beskikbaar wat dikwels gedurende suiwer paleontologiese studies oor die paleo-ekologie of paleo-omgewing van die fauna verlore sou gaan of geignoreer sou word. Die sistematiese verwantskappe wat hier bespreek word dien ook om die paleobiogeografiese ooreenkomste tussen die Gondwana-kontinente te versterk.

Correct species identification is fundamental to all areas of biology, but particularly the policy related areas of conservation and fisheries management. To enable guidelines to be developed for environmental management and conservation, such identifications need links to studies of the evolutionary history, biological factors and environmental influences driving species divergence and population dynamics for the target species. This study concerns two genera of gadiform fish, Muraenolepis and Macrourus, found in southern temperate and Antarctic waters, with a single species, Macrourus berglax, present in the North Atlantic. With similar distribution patterns to toothfish species, Dissostichus eleginoides and D. mawsoni, they are a major food source and by-catch of the toothfish fishery. Both are slow growing and long lived, with different evolutionary histories, life expectancies and strategies for reproduction. For both genera, the accuracy of morphological keys, number of described species and their distribution is under debate. This study has identified specimens to species level using both morphological and genetic techniques, redefining the range for morphological features and taxonomic keys. For Muraenolepis, this has clarified confusion over Mu. marmoratus and Mu. microps being a single species, confirmed some mis-identification from sexual dimorphism and provided genetic evidence for the recently described species Mu. evseenkoi. For Macrourus, this work has identified a new species, now named Ma. caml, and found that Ma. holotrachys and Ma. berglax are genetically identical, raising the question of bipolar distribution or recent divergence. The low level of genetic variation within both species suggests a recent evolution and expansion into Antarctic waters. Similar geographic species limits imply common processes influencing divergence, with the oceanographic fronts as potential barriers. Further investigation of niche overlap and fine scale population structure are required to fully understand the processes driving speciation and provide the underlying data required for fisheries management.

This research was initiated in 2001 with the overall objective of providing scientific information relevant to the sustainable management of South African Umbrina species. Previously there was confusion over the identity and distribution of Umbrina species in South African waters and very little was known of their life histories, population dynamics and stock status. Morphological comparison of a large number of South African Umbrina (n = 369) with specimens from the type locality (Canary Islands) confirmed the identity of South African U canariensis Valenciennes, 1843, and allowed for an expanded description of the species. However, differences between specimens of U ronchus Valenciennes, 1843 and those of the second South African species, lead to the resurrection of U robinson; Gilchrist and Thompson 1908, as a valid name for this species. Spatial analysis of South African specimens collected with a variety of gear revealed U robinsoni to be a shallow water species found from the surf-zone to 40 m depth that is targeted by recreational shore anglers and spear fishers, whilst U canariensis occurs predominantly from 40-100m depth and is predominately landed as a by-catch in the inshore trawl fishery. Although both species occur throughout the South African eastern seaboard, U canariensis is most common west of the Kei River, where the continental shelf is wider.

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The species of the genus Hemibrycon Günther (1864) are reviewed and redescribed based on their type series and additional specimens. Hemibrycon is hypothesized to be monophyletic and related to Clade A genera sensu Malabarba & Weitzman (2003) based on the analysis of 123 characters including 45 taxa. A total of 21 species are recognized in Hemibrycon, including five new species. Hemibrycon n. sp. 1 from the upper río Ucayali drainage, Peru; Hemibrycon n. sp. 2 from small rivers of the Caribbean Sea coastal drainages of Colombia; Hemibrycon n. sp. 3 and Hemibrycon n. sp. 4 from the middle río Magdalena basin, Colombia, and Hemibrycon n. sp. 5 from the upper río Madre de Dios, Peru. These species are distinguished among themselves mainly in the color pattern and number of branched anal-fin rays, lateral line scales, and maxillary teeth. The known geographical distribution of the genus is enlarged reaching the lower rio Tocantins basin, Brazil, with the occurrence of H. surinamensis in this area, the first record of the species for that country. The taxonomic status of Bryconamericus decurrens and Hemibrycon orcesi is discussed. New synonymies are proposed for some species of Hemibrycon: H. coxeyi is a junior synonym of H. polyodon, H. carrilloi is a junior synonym of H. dariensis, and H. guppyi is a junior synonym of H. taeniurus. An identification key to the examined species of Hemibrycon is provided.
As espécies do gênero Hemibrycon Günther (1864) são revisadas e redescritas com base na análise do material tipo e exemplares adicionais. Hemibrycon é considerado monofilético e relacionado ao Clado A sensu Malabarba & Weitzman (2003) com base na análise de 123 caracteres e 45 táxons. No total, 21 espécies de Hemibrycon são reconhecidas, incluindo cinco novas espécies. Hemibrycon n. sp. 1 da bacia superior do río Ucayali, Peru; Hemibrycon n. sp. 2 de pequenos rios de drenagens costeiras do Mar do Caribe, Colômbia; Hemibrycon n. sp. 3 e Hemibrycon n. sp. 4 da porção média da bacia do río Magdalena, Colômbia, e Hemibrycon n. sp. 5 da bacia superior do río Madre de Dios, Peru. Estas espécies distinguem-se, principalmente, pelo padrão de colorido e número de raios ramificados da nadadeira anal, de escamas da linha lateral e de dentes no maxilar. A área de distribuição do gênero é ampliada para a bacia do baixo rio Tocantins, Brasil, com a ocorrência de H. surinamensis nessa bacia, sendo o primeiro registro da espécie para este país. A posição taxonômica de Bryconamericus decurrens e Hemibrycon orcesi é discutida. Novos sinônimos são propostos para algumas espécies de Hemibrycon: H. coxeyi é sinônimo júnior de H. polyodon, H. carrilloi é sinônimo júnior de H. dariensis e H. guppyi é sinônimo júnior de H. taeniurus. É fornecida uma chave de identificação para as espécies examinadas de Hemibrycon.

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As esp?cies do g?nero Hemibrycon G?nther (1864) s?o revisadas e redescritas com base na an?lise do material tipo e exemplares adicionais. Hemibrycon ? considerado monofil?tico e relacionado ao Clado A sensu Malabarba & Weitzman (2003) com base na an?lise de 123 caracteres e 45 t?xons. No total, 21 esp?cies de Hemibrycon s?o reconhecidas, incluindo cinco novas esp?cies. Hemibrycon n. sp. 1 da bacia superior do r?o Ucayali, Peru; Hemibrycon n. sp. 2 de pequenos rios de drenagens costeiras do Mar do Caribe, Col?mbia; Hemibrycon n. sp. 3 e Hemibrycon n. sp. 4 da por??o m?dia da bacia do r?o Magdalena, Col?mbia, e Hemibrycon n. sp. 5 da bacia superior do r?o Madre de Dios, Peru. Estas esp?cies distinguem-se, principalmente, pelo padr?o de colorido e n?mero de raios ramificados da nadadeira anal, de escamas da linha lateral e de dentes no maxilar. A ?rea de distribui??o do g?nero ? ampliada para a bacia do baixo rio Tocantins, Brasil, com a ocorr?ncia de H. surinamensis nessa bacia, sendo o primeiro registro da esp?cie para este pa?s. A posi??o taxon?mica de Bryconamericus decurrens e Hemibrycon orcesi ? discutida. Novos sin?nimos s?o propostos para algumas esp?cies de Hemibrycon: H. coxeyi ? sin?nimo j?nior de H. polyodon, H. carrilloi ? sin?nimo j?nior de H. dariensis e H. guppyi ? sin?nimo j?nior de H. taeniurus. ? fornecida uma chave de identifica??o para as esp?cies examinadas de Hemibrycon.

The zebra sea bream, Diplodus cervinus (Sparidae) is an inshore fish comprised of two boreal subspecies from the Gulf of Oman and the Mediterranean / north eastern Atlantic and one austral subspecies from South Africa and southern Angola. The assumption of a single austral subspecies has, however, been questioned due to mounting molecular and morphological evidence suggesting that the cool Benguela current is a vicariant barrier that has separated many synonymous inshore fish species between South Africa and southern Angola. The aims of this thesis are to conduct a comparative morphological analysis of Diplodus cervinus in southern Angola and South Africa in order to classify the southern Angolan population and then to conduct a life history assessment to assess the life history impact of allopatry on this species between the two regions. Results of the morphological findings of the present study (ANOSIM, p < 0.05, Rmeristic = 0.42) and (Rmorphometric = 0.30) along with a concurrent molecular study (FST = 0.4 – 0.6), identified significant divergence between specimens from South Africa (n = 25) and southern Angola (n = 37) and supported stock separation and possibly sub-speciation, depending on the classification criteria utilised. While samples from the two boreal subspecies were not available for the comparative morphological or molecular analysis, comparisons of the colouration patterns between the three subspecies, suggested similarity between the southern Angola and the northern Atlantic / Mediterranean populations. In contrast, the colouration patterns between the southern Angolan and South African specimens differed substantially, further supporting the morphological and molecular results. The distinct morphological divergence between the southern Angolan and South African populations was not reflected within the life history traits of both populations. A combination of methods, including length/age frequency analyses, adult sex ratios and histological analysis was used to determine that this species is a rudimentary hermaphrodite in southern Angola. Peak spawning season was observed between June and July. The overall sex ratio (M: F) was 1:1.52 with females dominating smaller younger size classes and 50% maturity was attained at 210 mm FL and 4.6 years. Females [L(t) = 287.5(1-e⁻°·¹⁸⁽t⁻²·⁸⁴⁾)] grew significantly faster (LRT, p < 0.05) than males [L(t) = 380.19(1-e⁻°·°⁶⁽t⁻⁷·¹²⁾)]. The higher maximum age of the southern Angolan population of D. cervinus (43 years) was older than that of South African individuals sampled in the tsitsikamma national park. The similarities in the life history of the two austral populations are probably a consequence of similar selective pressures in the similar warmtemperate habitats. Evidence to support the above comments was found in the feeding study which showed that the South African and Angolan populations were almost identical, with both populations feeding primarily on amphipods and polychaete worms throughout ontogeny. In contrast, the diet of their boreal conspecifics from the Mediterranean was different, where larger individuals tended to select larger, and more robust, prey items. The life history differences observed between the boreal and austral populations can be attributed to either sampling bias or environmental factors. Sampling biases included the use of different age and growth estimation techniques, while the environmental factors would include differential selective pressures most likely driven by different resource availability and exploitation. The present study provides crucial baseline life history information of a potentially exploitable species off southern Angola as well as information on the life history plasticity of the species. Unfortunately, the current lack of uniformity in the methods used to estimate life history parameters between studies conducted on the boreal and austral populations have complicated our understanding of the evolution of various life history trends in sparid fish. From a management perspective however, the results from the present study can be used to propose management strategies for an emerging trap fishery in southern Angola. Using a balanced exploitation fishery approach (harvesting up to the size-at-100% maturity), the size of the fish traps entrance was calculated based the morphological information from this and other small sparid species that are targeted and was estimated to be 62 mm.

The blacktail, Diplodus capensis, is an inshore sparid fish distributed from Mozambique to Angola. This species forms an important component of coastal fisheries within its distribution, one being the subsistence handline fishery in southern Angola. With this fishery being critically important to the livelihoods of local communities, a biological study and stock assessment was conducted to provide information for the management of this species in southern Angola. However, with molecular evidence suggesting that the Benguela current may have separated the southern African populations of many inshore fish species over two million years ago, a morphological, taxonomic analysis was considered necessary to first investigate whether there was evidence for allopatry in this species. A total of 46 morphometric measurements and 18 counts were carried out on specimens collected from various locations in southern Angola and South Africa. Results were analysed using multi-dimensional scaling (MDS) and the significance of clusters was tested using analysis of similarities (ANOSIM). Biological samples of D. capensis were collected monthly from an unexploited area from April 2008 to March 2009. Additional biological samples were collected from the subsistence fishers in an exploited area during May, June and December 2009. Standard biological laboratory techniques were employed for the lifehistory comparison between the exploited and unexploited area. A per-recruit analysis was conducted using the life-history parameters from both areas in order to assess the current status of the subsistence fishery and to investigate the potential short-falls of the per-recruit assessment approach. The morphometric comparison showed that there was not sufficient evidence for speciation between the southern Angolan and South African populations of D. capensis. There was, however, sufficient morphological evidence to suggest that these populations are separate stocks. This indicated that the existing reference points on which the management of the South African population is based are unsuitable for the Angolan population. Diplodus capensis in southern Angola is omnivorous, feeding predominantly on algae, barnacles and mussels. An ontogenetic shift from algae to barnacles and mussels was correlated with allometric growth patterns in their feeding apparatus. This species is a rudimentary hermaphrodite in southern Angola with peak spawning in June and July. The overall sex ratio (M: F) was 1: 4.7 in the unexploited area and 50% maturity was attained at 149.5mm FL and five years. Diplodus capensis in southern Angola exhibits very slow growth with the maximum age observed being 31 years (validated using mark recapture of chemically injected fish). Females [L(t) = 419.5(1-e⁻°·°⁴⁵⁽t⁻³·⁴ ⁾)] grew significantly faster (LRT, p < 0.05) than males [L(t) = 297.4(1-e⁻°·°⁷⁷⁽t⁻²·⁷⁾)], and females dominated the larger size classes and older age classes. In the exploited area, the length and age frequencies were severely truncated, the maximum observed age was greatly reduced (17 years) and the sex ratio was less female biased at 1: 2.2. Although there was no evidence for a physiological response to exploitation through alterations in growth or size/age at sexual maturity between the two areas, there was an increase in the proportion of small females in the exploited area, which may have been a compensatory response for the loss of large females. A combination of an underestimate of longevity, different estimates of the Von Bertalanffy growth parameters and overestimates of the natural mortality rate in the exploited population resulted in a 92% underestimate of the pristine spawner biomass-per-recruit (SBR) value. An assessment based on the actual pristine SBR estimate from the unexploited area revealed that the subsistence fishery had actually reduced D. capensis to 20% of its pristine SBR levels and highlighted the value of pre-exploitation life-history information for the application of per-recruit models. This study has shown that D. capensis in southern Angola displays life-history characteristics that render it susceptible to overexploitation, even at low levels of fishing pressure. The current lack of infrastructure and enforcement capacity in the fisheries department of Angola renders traditional linefish regulatory tools, such as size limits, bag limits and closed seasons, inappropriate. Therefore, suitably designed marine protected areas are recommended as the best management option for this species.

This study investigated the epidemiology and taxonomy of Diplostomuni species in the deeper parts of the eye (DPE) of roach Rutilus rutilus (L. ), perch Perca fluviatilis L., ruffe Gymnocephalus cernua (L. ) and gwyniad Coregonus lavaretus (L. ) at Llyn Tegid, North Wales, and in the cranium of catfish Clarias gariepinus (Burchell, 1822) and the vitreous humour of Oreochromis species at Mindu dam and river Ruvu, Tanzania. At Llyn Tegid, two species of Diplostomum metacercariae, large and small forms, coexisted in DPE of perch, ruffe and gwyniad but only one, large forms, occurred in roach. Large forms were distinguished by their large size, oval body tapering at both ends and pseudosuckers at the level of the oral sucker. Small forms were distinguished by their smaller size, oval body with parallel sides and pseudosuckers occurring below the level of the oral sucker. The taxonomy of the two forms was not resolved even after obtaining adults from chickens. Tentatively, small forms keyed close to D. gasterostei Williams, 1966 and large forms to D. volvens Nordmann, 1832. Inadequate identification manuals and remarkable similarity between Diplostonlum species confounded identification. Mean intensity of metacercariae was highest in ruffe and lowest in perch and increased with host size in all hosts. Factors responsible for differences in mean intensity between hosts were discussed. There was no seasonality of occurrence. Recruitment occurred from May - November correlating with water temperatures. Immature metacercariae occurred throughout the period of investigation. Metacercariae were overdispersed in all three hosts. At Mindu and Ruvu two species were present, D. sp. X (1,2) in the cranium of catfish and D. sp. Y in the vitreous humour of Oreochromis sp. D. sp. X (1,2) were distinguished by their elongate body, oval calcareous corpuscles and long hindbody. D. sp. Y were distinguished by a vestigial ventral sucker, glandular Brandes organ, short hindbody and spherical calcareous corpuscles. D. sp. X (1,2) were identified as D. mashonense Beverley - Burton, 1963. Adults cultured in chickens confirmed identification. D. sp. X (1,2) developed to ovigerous adults within 24h. Percent recovery of adults from chickens declined with days p. i. Miracidia developed in eggs in six days. D. sp. Y is considered an undescribed taxon. Prevalence and mean intensity of D. sp. Y in Oreochromis sp. were low and did not fluctuate seasonally. Prevalence of D. mashonense in catfish was similar at Mindu and Ruvu and exhibited no seasonal fluctuations. Mean intensity of D. mashonense in catfish of Mindu fluctuated seasonally, increased with host size and was higher than in catfish from Ruvu. Causes of high intensity and seasonal changes at Mindu were discussed. D. mashonense was overdispersed in catfish at both localities but only data from Mindu fitted the negative binomial model. Small samples and the dynamism of forces creating overdispersion were considered responsible for the situation at Ruvu. Using SEM ciliated-pit and dome-shaped papillae were observed on the surface of metacercariae and adults of D. mashonense . Ciliated-pit papillae occurred only on metacercariae. Dome-shaped papillae, in adults and metacercariae, were aggregated on suckers, excretory and genital atria. Spines were multipointed in adults but single pointed in metacercariae.

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Milton Valente
A família Loricariidae compreende o maior número de espécies descritas de cascudinhos com aproximadamente 872 espécies válidas, sendo a maior família da ictiofauna mundial. A subfamília Hypoptopomatinae composta por 20 gêneros e 136 espécies é reconhecida como monofilética. Entretanto, a monofilia do gênero Parotocinclus, (Lehmann, 2006) vem sendo contestada. Estudos filogenéticos afirmam que Parotocinclus ocupa uma posição mais basal dentro tribo Otothyrini. Em uma hipótese mais recente da filogenia da subfamília, não foi encontrado suporte para apoiar o monofiletismo da tribo Otothyrini, e Parotocinclus foi reconhecido como um gênero agrupando um complexo de espécies altamente polifilético. Atualmente, Parotocinclus agrupa 28 espécies válidas. Parotocinclus maculicauda (Steindachner, 1877) (espécie tipo do gênero) é encontrada nos rios costeiros desde Santa Catarina até o Espírito Santo. Caracteriza-se pela presença de placas ósseas, cintura peitoral exposta suportando odontódeos, nadadeira adiposa presente e nadadeira dorsal e peitoral um pouco avermelhada. Apresenta dimorfismo sexual, machos com papila genital visível e uma projeção de pele na base do espinho na nadadeira pélvica. O esqueleto de P. maculicauda apresenta alto grau de fusão e redução de tamanho em muitas estruturas ósseas. A análise de caracteres externos e internos e, sua comparação entre as diferentes espécies de Loricariideos, assim como a configuração dos ossos e músculos associados à cintura peitoral e ao crânio, são considerados no levantamento de caracteres morfológicos informativos a diferentes níveis dentro da família Loricariidae.
The family Loricariidae comprises the largest number of described species of catfishes with approximately 872 valid species , the largest family of world fish fauna. The Hypoptopomatinae subfamily comprises 20 genera and 136 species are recognized as monophyletic . However , the monophyly of the genus Parotocinclus, is being challenged . Phylogenetic studies claim that Parotocinclus occupies a more basal position within Otothyrini tribe. In a more recent hypothesis of the phylogeny of the subfamily, was not found support for the monophyly of Otothyrini tribe and Parotocinclus was recognized as a genera gathering a complex of highly polyphyletic species. Currently , Parotocinclus joins 28 valid species. Parotocinclus maculicauda (type species of the genus) is found in coastal rivers from Santa Catarina to the Espirito Santo states . It is characterized by the presence of bony plates, pectoral girdle exposed supporting odontodes , the presence of adipose fin and dorsal and pectoral fins slightly reddish . Was sexually dimorphic, males with visible genital papilla, a projection of skin at the base of the spine in the pelvic fin. The skeleton of P. maculicauda presents a high degree of mergers and downsizing in many bony structures. The analysis of external and internal characters and their comparison between different loricaiid species, as well as the configuration of the bones and associated pectoral girdle and skull muscles, are considered in the survey of morphological information at different levels within the family Loricariidae.m

Environmental gradients structure ichthyofaunal communities longitudinally along river networks via the selective filtering of species’ traits. In many instances, these environmental influences have created distinct zones of co-occurring fish species. Zonation studies have most often been conducted with taxonomic data (species x site matrices), but the increasing availability of functional trait data creates an opportunity to build more rigorous understanding of species’ co-occurrence patterns. Notably, zonation studies that use taxonomic data may not reveal the same patterns as studies based on trait data. In this study, we tested for distinct ichthyofaunal zonation in James River Basin, VA using a combination of historical (1950-1987) and contemporary fish occurrence records (1986-2016) that were aggregated within 12-digit hydrologic units (HU). Zonation tests were performed separately for taxonomic data and functional trait data, using a combination of non-metric multidimensional scaling and k-means cluster analysis. We detected three distinct taxonomic zones and three functional trait zones within the James River Basin. In addition, through identifying that taxonomic dissimilarity between HUs was strongly correlated with functional dissimilarity, these zonation patterns were determined to not be significantly different.

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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
O gênero Moenkhausia ainda se encontra alocado como incertae sedis na família Characidae, com 88 espécies válidas. Moenkhausia oligolepis foi investigada com o intuito de verificar se esta representa uma única espécie ou um complexo de espécies, buscando assim esclarecer questões taxonômicas sobre o gênero. Além de M. oligolepis analisamos as espécies M. sanctaefilomenae, M. forestii e M. australe, pois observamos que estas são mais similares entre si quando comparadas as outras espécies do grupo “complexo Moenkhausia oligolepis/M. sanctaefilomenae”. Sendo assim, estamos considerando essas quatro espécies como o grupo “Moenkhausia oligolepis”. Foram analisados, através de dados morfométricos e merísticos, 321 lotes, totalizando 1522 espécimes disponíveis em coleções ictiológicas brasileiras e estrangeiras. A partir de nossas analises, foram identificadas e propostas duas novas espécies, distribuídas nas bacias dos rios Tapajós (Moenkhausia sp. n.1) e Guaporé (Moenkhausia sp. n.2). Nossos resultados não suportam a hipótese proposta por Benine et al. (2009), de que Moenkhausia oligolepis represente um complexo de espécies, uma vez que não foram detectados caracteres morfológicos diagnósticos justificando a separação e descrição tradicional entre os táxons dos rios Amazonas, Araguaia e Paraguai. Aqui, apontamos as variações morfológicas populacionais de M. oligolepis, como também discussões sobre sua distribuição e a sua relação com algumas espécies do complexo Moenkhausia oligolepis/M. sanctaefilomenae. As redescrições de M. australe e M. sanctaefilomenae são apresentadas com comentários, e ampliamos a distribuição de M. forestii para o rio Mamoré.
The genus Moenkhausia remaining as incertae sedis in the Characidae, with 88 valid species. Moenkhausia oligolepis was investigated in order to verify if it represents a single species or a complex, with the intention to illuminate taxonomic issues about the genus. Beside to M. oligolepis we analyzed the species M. sanctaefilomenae, M. forestii and M. australe, because we observed that these species are more similar to each other when compared to the other species of the group "Moenkhausia oligolepis / M. sanctaefilomenae complex ". Therefore, we are considering these four species as the group "Moenkhausia oligolepis". 321 lots were analyzed through morphometric and meristic data, totaling 1522 specimens available in Brazilian and foreign ichthyological collections. From our analyzes, two new species were identified and proposed, distributed in the rivers Tapajós (Moenkhausia sp. n.1) and Guaporé (Moenkhausia sp. n.2) basins. Our results do not support the hypothesis that Moenkhausia oligolepis is a species complex as proposed by Benine et al. (2009), since no morphological diagnostic characters were observed justifying the separation and traditional description among the taxa of the rivers Amazonas, Araguaia and Paraguay basins. Here we point out the population morphological variations of M. oligolepis, as well as discussions about their distribution and their relationship with some species of the Moenkhausia oligolepis / M. sanctaefilomenae complex. The redescriptions of M. australe and M. sanctaefilomenae are presented with comments and we have extended a distribution of M. forestii to the Mamoré River.

Die Arbeit verfolgt das Ziel, eine Übersicht über die bei verschiedenen Süßwasserfischarten festgestellten Myxosporidien zu geben. Aus Gewässern der DDR-Bezirke Potsdam, Berlin, Frankfurt (Oder), Cottbus und Dresden wurden 1.850 Fische (1.015 Karpfen, 258 Regenbogenforellen, 143 Silberkarpfen, 104 Plötzen sowie weitere 22 Fischarten in geringer Zahl untersucht. Es wurden 40 Myxosporidienarten folgender taxonomischer Gruppen nachgewiesen: Myxidiidae (7), Sphaerosporidae (6), Chloromyxidae (4) und Myxobolidae (23). In der Arbeit sind Maße, Fotos und Zeichnungen der Parasiten enthalten. Es wurden Angaben über die Taxonomie, Organspezifität, Saisondynamik, Epizootiologie und Auswirkungen auf die Fischgesundheit gemacht. Es erfolgte ein Vergleich mit früheren Arbeiten in der DDR auf diesem Gebiet. Der Artenbestand an Myxosporidien konnte um 39 Arten erweitert werden. Anhand faunistischer Arbeiten aus benachbarten Ländern wurden die Bedeutung und Perspektiven zum Auftreten von Myxosporidiosen in der DDR herausgestellt.
This work aims to give an overview about the detected Myxosporeans in different species of freshwater fishes. From inland waters of the GDR districts Potsdam, Berlin, Frankfurt (Oder), Cottbus and Dresden 1.850 fishes (1.015 carps, 258 rainbow trouts, 143 silver carps, 104 roach and more 22 Fish species in small numbers were studied. 40 Myxosporean species of following taxonomic groups were detected: Myxidiidae (7), Sphaerosporidae (6), Chloromyxidae (4) und Myxobolidae (23). In this work are presented dimensions, photos and drawings of the parasites. Details are given on taxonomy, organ specificity, season dynamics, epizootiology and the impact on fish health A comparison with previous work in the GDR on this subject was carried out. The species inventory on Myxosporidia could be extended to 39 species. Based on faunal work from neighboring countries the importance and prospects for occurrence of Myxosporidiosis in the GDR were highlighted.

Multiple dimensions of biodiversity within and across producer and consumer guilds in the food web affect an ecosystem’s functionality and stability. Tropical and subtropical aquatic ecosystems, which are extremely diverse, have received much less attention than terrestrial ecosystems in regards to the effects of biodiversity on ecosystem functioning. We conducted a field experiment that tested for effects of macrophyte functional diversity on diversity and stability of associated fish assemblages in floodplain lakes of the Upper Paraná River floodplain, Brazil. Three levels of macrophyte functional diversity were maintained through time in five floodplain lakes and response variables included various components of fish taxonomic and functional diversity and stability. Components of functional diversity of fish assemblages were quantified using a suite of ecomorphological traits that relate to foraging and habitat use. Response variables primarily distinguished macrophyte treatments from the control. Macrophyte treatments had, on average, double the number of species and total abundance than the control treatment, but only limited effects on stability. The high diversity treatment was essentially nested within the low diversity for assemblage structure and had similar or even slightly lower levels of species richness and abundance in most cases. Gymnotiformes and young-of-year were diverse and relatively abundant in macrophyte treatments contributing to the large differences in diversity between macrophyte and control treatments. Higher fish diversity in structured habitats compared to more homogenous habitats is likely associated with increased ecomorphological diversity to exploit heterogeneous microhabitats and resources provided by the macrophytes.

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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
Pimelodidae is a family of fishes of South America, and although several taxonomic and molecular studies have been conducted, the phylogenetic relationships among the genera are not still fully understood. In order to provide data to assist in the understanding of the relationships within this family, cytogenetic studies were performed in two species of Iheringichthys and seven species of Pimelodus from three river systems. The specimens were collected in the Piquiri River, Upper Paraná River basin; in the Iguaçu River, downstream to the Iguaçu Falls in the Middle Paraná River basin; in the Iguaçu River, Lower Iguaçu River basin and in the Ijuí River, Upper Uruguay River basin. The analysis showed the presence of 2n=56 chromosomes for all species, corroborating the hypothesis of this basal diploid number for the family. The AgNORs, confirmed by 18S rDNA-FISH, were localized in the terminal position on long arm of a chromosome pair for all analyzed species, which has been reported for all species of Pimelodidae and may indicate a basal trait for the family. The heterochromatin distribution pattern found herein is similar to those described for other Pimelodidae, and allowed us to differentiate most of the species, becoming an important marker. The location of 5S rDNA sequences in Iheringichthys species allowed their differentiation, and can be used as a taxonomic marker. In Pimelodus species, it was verified a variation in the number and position of 5S rDNA sites. In P. britskii and P. maculates, sites of 5S rDNA and 18S were found in synteny, which may indicate a derived condition for these species, considering that they are the only for pimelodids species till now studied that have this feature. The results of this study provided data that contribute to the knowledge of the evolutionary history of the species for Pimelodidae; establishing phylogenetic relationships and assisting in the identification of these species.
Pimelodidae é uma família de peixes da região Neotropical, e embora vários estudos taxonômicos e moleculares tenham sido realizados, as relações filogenéticas entre seus gêneros ainda não são totalmente compreendidas. Com o intuito de fornecer dados para auxiliar no entendimento das relações dentro desta família, foram realizados estudos citogenéticos em duas espécies de Iheringichthys e em sete espécies de Pimelodus de três sistemas hidrográficos. Os exemplares foram coletados no rio Piquiri, Bacia do Alto rio Paraná; no rio Iguaçu, jusante às Cataratas do Iguaçu na Bacia do Médio rio Paraná; no rio Iguaçu, Bacia do Baixo rio Iguaçu e no rio Ijuí, Bacia do Alto rio Uruguai. As análises mostraram a presença de 2n=56 cromossomos em todas as espécies, reforçando a hipótese de número diplóide basal para a família. As AgRONs, confirmadas pela FISH-DNAr 18S, foram localizadas na região terminal do braço longo de um par de cromossomos em todas as espécies estudadas, sendo que posição terminal desta região é observada em todas as espécies de Pimelodidae e pode indicar um caracter basal da família. O padrão de distribuição de heterocromatina encontrado é semelhante ao observado em outros Pimelodidae, e permitiu diferenciar a maioria das espécies, sendo um importante marcador. A localização das sequências de DNAr 5S nas espécies de Iheringichthys permitiu diferenciá-las, podendo ser utilizado como marcador taxonômico. Em Pimelodus, variação quanto ao número e posição de sítios do DNAr 5S foi observada. Em P. britskii e P. maculatus os sítios de DNAr 5S e 18S foram localizados em sintenia, o que pode indicar uma condição derivada para estas espécies, visto que são as únicas espécies de Pimelodidae que apresentam esta característica até o momento. Os resultados do presente estudo fornecem dados que contribuem para o conhecimento da história evolutiva das espécies de Pimelodidae, permitem estabelecer relações filogenéticas e auxiliam na identificação destas espécies.

Orientador: Marlene Tiduko Ueta
Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: O pacu Piaractus mesopotamicus (Holmberg, 1887) é uma das principais espécies de importância econômica no Brasil. Peixe nativo da Bacia dos rios Paraná e Paraguai é uma das espécies mais comuns em pisciculturas. Mixosporídeos e monogêneas são parasitos de alta prevalência e causam danos em cultivos comerciais, tornando importante seu estudo detalhado. Neste estudo foram examinados 278 especimens de P. mesopotamicus de vários tamanhos, no período de Fevereiro de 2008 a Julho de 2010, coletados nos tanques do Centro de Pesquisa e Conservação de Peixes Continentais - CEPTA/ Instituto Chico Mendes de Conservação da Biodiversidade - ICMBio, Pirassununga, SP e em pisciculturas particulares da mesma região. Os parasitos identificados foram os mixosporídeos Henneguya piaractus (Martins & Souza, 1997) e Myxobolus colossomatis (Molnár & Békési, 2007) e os monogêneas Anacanthorus penilabiatus (Boeger, Husak & Martins, 1995), Mymarothecium viatorum (Boeger, Piasecki & Sobecka, 2002) e Dactylogyridae sp1 (não identificada). Análises ultraestruturais mostraram em Henneguya piaractus uma fina camada granular entre o plasmódio e as células do hospedeiro, uma única parede no plasmódio com numerosos canais de pinocitose. Myxobolus colossomatis apresentou uma camada plasmodial com numerosa atividade fagocítica em comunicação com as células do hospedeiro. A histopatologia apresentou hiperplasia nas lamelas branquiais em peixes altamente infectados e deformação das lamelas em relação a cistos de H. piaractus. A microscopia eletrônica de varredura mostrou para A. penilabiatus tegumento relativamente liso e microvilosidades nas regiões adesivas. Mymarothecium viatorum apresentou na superfície de seu tegumento, projeções similares a escamas com variações tipo microvilosidades. Análises moleculares utilizando marcadores ribossomais para mixosporídeos e monogeneas (porção18S) posicionaram as espécies em árvores filogenéticas. A descrição do genoma mitocondrial parcial de A. penilabiatus é apresentada
Abstract: The freshwater fish Piaractus mesopotamicus (Holmberg, 1887), popularly known as "pacu", is one of the most economically important species of fish in Brazil. The fish is endemic to the Paraná-Paraguay river basin, and is one of the species that is most cultivated in fish farms. A detailed study of Myxosporea and Monogenea is important, due to their high prevalence and the damage they cause in commercial fish farms. A total of 278 specimens of P. mesopotamicus were examined from February 2008 to July 2010, collected in fish ponds at the Centro de Pesquisa e Conservação de Peixes Continentais (CEPTA), Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio), in the city of Pirassununga, in the state of Sao Paulo, and in other commercial fish farms nearby. The main parasites found were the myxosporeans Henneguya piaractus (Martins & Souza, 1997) and Myxobolus colossomatis (Molnár & Békési, 2007) and the monogeneans Anacanthorus penilabiatus (Boeger, Husak & Martins, 1995), Mymarothecium viatorum (Boeger, Piasecki & Sobecka, 2002) and Dactylogyridae sp1 (not identified). Ultrastructural analysis of H. piaractus showed a thin layer of granular material between the plasmodial wall and the host cells. The single plasmodial wall was connected to a plasmodial ectoplasm zone through numerous and extensive pinocytotic canals. Myxobolus colossomatis showed a plasmodial ectoplasm zone with numerous and extensive phagocytic activity, and numerous projections in the direction of the host cells. Histopathological data showed hyperplasia in the lamellae in highly infected fish and deformation of the lamellae regarding cysts of H. piaractus. Scanning electron microscopy found that A. penilabiatus had a relatively smooth tegument and microvilli in the adhesive regions. However, the M. viatorum tegument showed that the top surface had variations similar to scales. Molecular analysis, using ribosomal markers for myxosporeans and monogeneans (18S rDNA) positioned the species in phylogenetic trees. The partial mitochondrial genome of A. penilabiatus is also recorded
Doutorado
Parasitologia
Doutor em Parasitologia

Orientador: Edson Aparecido Adriano
Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: Parasitos do filo Myxozoa são cosmopolitas, infectam peixes em diversas regiões e estão entre os mais importantes patógenos de peixes, tanto em ambiente natural, como em sistemas de criação, onde podem causar prejuízos importantes. Este trabalho teve por objetivo o estudo da interação parasito-hospedeiro em infecções de peixes do gênero Pseudoplatystoma, pintado (Pseudoplatystoma corruscans), cachara (Pseudoplatystoma fasciatum) e o híbrido (pintado x cachara), causadas por parasitos do filo Myxozoa. Os peixes estudados foram oriundos de ambiente natural, Pantanal Mato-Grossense e de sistemas de criação, pisciculturas dos Estados de São Paulo e do Mato Grosso do Sul. Durante este trabalho foi possível estudar e descrever duas novas espécies de Henneguya infectando Pseudoplatystoma spp. Henneguya sp. 1 foi descrito infectando pintado híbrido de sistemas de criação nos Estados de São Paulo e Mato Grosso e as respectivas prevalências foram 100 e 36, 7%. Devido à intensidade de infecção, com vários plasmódios em um mesmo filamento, o desenvolvimento do parasito produziu importante redução de área do epitélio branquial. A análise ultra-estrutural revelou uma única parede plasmodial ligada à zona do ectoplasma por vários canais de pinocitose. A outra espécie (Henneguya sp. 2) foi encontrado infectando simultaneamente brânquia de exemplares de pintado e cachara obtidos em ambiente natural, no Pantanal Mato-Grossense. A prevalência foi de 17,1% para ambas espécies de peixes examinados. A análise histopatológica revelou o desenvolvimento do parasito no tecido conectivo sub-epitelial do filamento branquial, estando os plasmódios envolvidos por uma cápsula de tecido conectivo. O plasmódio produziu uma leve compressão dos tecidos adjacentes, mas nenhum infiltrado inflamatório foi observado no sítio da infecção. A análise ultra-estrutural mostrou uma única parede plasmodial conectada com o ectoplasma através de numerosos canais de pinocitose.
Abstract: Myxozoa are cosmopolitan parasites and are among the most important pathogens of wild and cultivated fish. The aim of the present study was to investigate the host-parasite interaction in fish of the genus Pseudoplatystoma infected by Myxozoan parasites: the spotted sorubim (Pseudoplatystoma corruscans), barred sorubim (Pseudoplatystoma fasciatum) and a hybrid of the two species. Specimens were obtained from the natural environment in the Mato Grosso wetlands and fish farms in the states of São Paulo and Mato Grosso do Sul, Brazil. Two news species of Henneguya were described infecting Pseudoplatystoma ssp. Henneguya sp.1 was described infecting the hybrid on fish farms in the states of São Paulo and Mato Grosso do Sul (Brazil), with a prevalence of 100 and 36.7%, respectively. Due to the intensity of the infection, with several plasmodia in a single gill filament, the development of the parasite caused an important reduction in the area of functional epithelium. The ultrastructural analysis revealed a single plasmodial wall connected to the ectoplasma zone through several pinocytotic canals. Henneguya sp.2 was found infecting the gills of both the spotted and barred sorubim caught in the natural wetland environment. The prevalence was 17.1% in both species of fish. The histopathological analysis revealed that the parasite develops in the sub-epithelial connective tissue of the gill filaments and the plasmodium is surrounded by a capsule of connective tissue. The plasmodia caused slight compression of the adjacent tissues, but no inflammatory infiltrate was observed at the infection site. The ultrastructural analysis revealed a single plasmodial wall connected to the ectoplasma zone through numerous pinocytotic canals.
Mestrado
Parasitologia
Mestre em Parasitologia

Comprendre les mécanismes d'assemblages des communautés est l'une des principales questions en écologie et biogéographie. Elle est également essentielle pour prédire les conséquences des changements globaux sur la distribution future de la biodiversité. Les communautés écologiques sont la résultante de facteurs interagissant à plusieurs échelles spatiales et temporelles. En outre, ces processus peuvent affecter différemment les composantes taxonomique, fonctionnelle et phylogénétique de la biodiversité. Nous étudions ici les processus écologiques qui structurent les communautés de poissons de récif, l'un des assemblages de vertébrés les plus diversifié sur Terre. Les facettes taxonomique et fonctionnelle de ces assemblages ont été étudiées au travers de plusieurs échelles spatiales. Nos objectifs sont (i) d'identifier les facteurs structurant les assemblages de poissons de récif à différentes échelles (du régional au local), (ii) d'évaluer dans quelles mesures les processus structurant les groupes taxonomiques et fonctionnels sont consistants entre eux et (iii) de comprendre la distribution de la rareté fonctionnelle dans les assemblages de poissons de récif. Deux bases de données ont été utilisées : (1) une base de données sur les caractéristiques fonctionnelles et les distributions globales de plus de 6000 espèces de poissons dans six régions biogéographiques ; (2) un ensemble de données comprenant les occurrences de 1 474 espèces de poissons sur 9 681 échantillons obtenus le long de transects (comptages visuels en scaphandre autonome) de 40m² à travers 252 sites dans plusieurs régions biogéographiques. Dans l'océan Atlantique, la structure taxonomique et fonctionnelle des communautés de poissons a une signature biogéographique, avec une différence marquée entre les espèces des récifs biogènes riches (dans les Caraïbes et composée des petites espèces) et les régions périphériques dominées par des espèces plus grandes. L'environnement joue également un rôle important dans la structuration des assemblages dans d'autres domaines biogéographiques. Alors que la composition taxonomique des communautés est principalement liée à l'isolement des récifs, la structure fonctionnelle est influencée par la disponibilité de l'habitat à l'échelle locale. Encore une fois, il y a une plus grande contribution des petites espèces dans les sites les plus riches alors que les grandes espèces dominent en périphérie, suite à la plus forte capacité de colonisation des grandes espèces. Les assemblages présentent des structures fonctionnels emboîtées. Plus précisément les sites pauvres en diversité fonctionnelle, ici mesurée en nombre d'entités fonctionnelles différentes, sont des sous-ensembles des sites riches. Cette structure résulte de l'interaction entre les capacités de dispersion/colonisation des espèces et/ou des besoins en ressources, ainsi que des gradients d'isolement et de surface. Malgré la présence de groupes fonctionnels essentiels et de redondance dans les assemblages de poissons, la majorité des espèces dans les communautés sont rares. De plus, les espèces rares occupent une large proportion de la gamme de traits fonctionnels et effectuent souvent des fonctions uniques. Selon les scénarios simulant la perte d'espèces rares (de 8 à plus de 200 espèces rares / moyenne : 78,2 ± 62), il y aurait une perte élevée - 80 % dans un seul site - de la diversité fonctionnelle. Nos résultats révèlent que les processus au sein d'un domaine biogéographique sont responsables d'une structuration taxonomique et fonctionnelle. De plus, le rôle essentiel de la capacité de colonisation de l'espèce met en évidence l'importance de la connectivité pour le maintien de la structure fonctionnelle des communautés de poissons de récif. Enfin, la contribution des espèces rares à la diversité fonctionnelle montre que ces taxons doivent être protégés afin de maintenir l'ensemble des fonctions et services des écosystèmes
Understanding the mechanisms of community assembly is one of the main questions in ecology and biogeography, and is essential for predicting the implications of future biodiversity loss. It is known that an array of processes operating at different spatial and temporal scales interact to produce ecological communities. These processes may affect differently the multiple components of communities: the taxonomic, functional and phylogenetic components. Here we investigate the patterns and processes structuring one of the most diverse vertebrate assemblages on Earth: reef fishes. Reef fish assemblages were assessed across multiple spatial scales, under a taxonomic and functional perspective. Our main objectives included: (i) the identification of determinants of structure in reef fish assemblages across scales (regional to local); (ii) assessing to which extent the processes behind assemblage structures are consistent for taxonomic and functional groups; (iii) understanding the patterns of functional rarity in reef fish assemblages at a global scale. Two databases were utilized: (1) an extensive database on the functional traits and the global distributions of over 6,000 reef fish species across six marine biogeographic regions; (2) a dataset comprising the occurrences of 1,474 fish species over 9,681 underwater visual transects of 40m2 across 252 sites, also throughout the major biogeographic regions. Within the Atlantic Ocean, the taxonomic and functional structure of reef fish assemblages exhibit a biogeographic fingerprint, with a marked discrimination between species rich biogenic reefs – primarily in the Caribbean, where communities were dominated by small invertebrate feeders – and poorer peripheral regions dominated by larger species with more diverse diets. At the regional scale, both historical events and environmental characteristics (coral reefs vs. periphery) have played a role in structuring both components of assemblages. The role of environment features also holds for the structure of assemblages in other biogeographic realms (i.e. Indo-Pacific and Tropical Eastern Pacific). While the taxonomic composition of assemblages is mainly related to reef isolation, the functional structure is influenced by local habitat availability. Again, there is a greater contribution of small-bodied species in the most species-rich locations; and large-bodied species prevailing in peripheral assemblages, a pattern related to species' colonization capacity. Reef fish assemblages across most regions depicted significantly functional nested structures, attributed to functional redundancy – different species constitute a number of key functional entities. The nested structure results from the interaction between species' dispersal/colonization capabilities and/or resource requirements, with isolation and area gradients. Despite the existence of key functional groups and redundancy, the majority of species are rare (low abundance or occupancy). Also, rare species fulfil much of the range of functional traits within reef fish communities and often perform unique roles. Under scenarios of rare species loss (from 8 to over 200 rare species/ mean: 78.2±62) there would be high functional diversity erosion in the majority of reef fish communities, this level reaching up to 80% of functional diversity in one location. However the extent to which these functional groups actually contribute to ecosystem functioning is unknown. Our results reveal that within-realm processes, such as evolutionary histories, have shaped the taxonomic and functional structure of assemblages in each realm. Moreover, the key role of species' colonization capacity highlights the importance of connectivity to the maintenance of the functional structure across reef fish communities. Finally, the contribution of rare species to functional diversity indicates that protecting these taxa is essential to maintain ecosystem functioning and services in reef fish communities

Primers for 10 polymorphic DNA microsatellite loci were developed and characterized for the endangered oyster mussel Epioblasma capsaeformis from the Clinch River, TN. Microsatellite loci also were amplified for individuals collected from the following additional populations or species: (1) E. capsaeformis from Duck River, TN; (2) E. florentina walkeri from Indian Creek, upper Clinch River, VA; (3) E. florentina walkeri from Big South Fork Cumberland River, TN; and (4) E. torulosa rangiana from Allegheny River, PA. Allelic diversity ranged from 9-20 alleles/locus, and averaged 13.6/locus for all 5 populations investigated. Average expected heterozygosity (HE) per locus ranged from 0.78-0.92, and averaged 0.86. A genetic characterization of extant populations of E. capsaeformis and E. florentina walkeri was conducted to assess taxonomic validity and to resolve conservation issues related to recovery planning. These mussel species exhibit pronounced phenotypic variation, and are difficult to characterize phylogenetically using DNA sequences. Monophyletic lineages, congruent with phenotypic variation among species, were obtained only after extensive analysis of combined mitochondrial (1378 bp of 16S, cytochrome-b, ND1) and nuclear (515 bp of ITS-1) DNA sequences. In contrast, analysis of variation at 10 hyper variable DNA microsatellite loci showed moderate to highly divergent populations based on FST values, which ranged from 0.12-0.39. Quantitative genetic variation was observed in fish host specificity, with transformation success of glochidia of E. capsaeformis significantly greater (p<0.05) on the greenside darter Etheostoma blennioides, and that of E. f. walkeri significantly greater (p<0.05) on the fantail darter E. flabellare. Lengths of glochidia differed significantly (p<0.001) between species, with sizes ranging from 241-272 mm. Underwater photographs of mantle-pads and micro-lures of female mussels documented fixed phenotypic variation between species. The texture and color of the mantle-pad of E. capsaeformis is smooth and bluish-white, while that of E. f. walkeri is pustuled and brown, with tan mottling. Based on extensive molecular, morphological, and life history data, a population of E. capsaeformis from the Duck River, TN is described and proposed as a separate species, and a population of E. f. walkeri from the upper Clinch River, VA is described and proposed as a separate subspecies. Genetic management guidelines were developed to assess taxonomic status, genetic variation of donor-recipient populations targeted for augmentation, and field and laboratory protocols to maximize genetically effective population size, minimize genetic changes in captive-reared progeny, and prevent the release of juvenile mussels into non-native drainages. A pragmatic approach to species recovery is advocated; one that incorporates the principles of conservation genetics into breeding programs, but prioritizes the immediate demographic needs of critically endangered mussel species.
Master of Science

Les écosystèmes naturels subissent des impacts anthropiques croissants qui altèrent la diversité des communautés biologiques. Les cours d'eau amazoniens abritent une biodiversité unique et conséquente, mais sont confrontés à des taux de déforestation sans précédent. Il est donc urgent de comprendre comment l'anthropisation affecte la biodiversité dans ces écosystèmes. Ce travail propose une approche en écologie des communautés pour définir comment l'anthropisation affecte les patrons de diversité, mais aussi les processus écologiques qui façonnent les communautés de poissons. Une méthode d'échantillonnage non-invasive, l'ADN environnemental (ADNe), a été utilisée pour inventorier les communautés de poissons dans les ruisseaux et les grands fleuves en Guyane française. Des surfaces déforestées ont été cartographiées à partir de données spatiales pour créer une variable de déforestation globale qui intègre les effets de l'urbanisation, l'agriculture et l'exploitation aurifère et forestière. Ce travail a, premièrement, permis d'optimiser et valider l'utilisation de l'ADNe pour évaluer l'impact humain sur les écosystèmes riches en espèces, tels que les rivières tropicales. La méthode a montré une reproductibilité élevée, ainsi qu'une capacité à distinguer les communautés de poissons, les habitats et les sites perturbés des sites non perturbés. De plus, nous avons montré que la déforestation affecte la biodiversité au-delà des effets locaux et avons mis en évidence un effet étendu de la déforestation sur la biodiversité en aval. Cet impact lointain a provoqué un déclin de plus de 30% de la diversité taxonomique et fonctionnelle des communautés de poissons qui habitent les fleuves. Cependant, cette perturbation n'a pas été déterminante sur les processus écologiques qui façonnent les communautés de poissons, ni sur la composition des traits. Dans les petits ruisseaux, la déforestation a entraîné des modifications dans la composition spécifique, sans diminuer le nombre d'espèces ni la richesse fonctionnelle. Ces altérations ont été induites par un rôle prépondérant des filtres environnementaux sur l'assemblage des communautés. En conséquence, les espèces étaient moins uniformément réparties dans l'espace fonctionnel, laissant des traits liés au compartiment benthique et au régime phytophage sous-représentés alors que les espèces pélagiques et détritivores étaient surreprésentées. Nos résultats montrent la complexité des réponses de la biodiversité à la déforestation. Outre des réponses dépendantes de l'habitat, la déforestation a modifié la biodiversité des communautés de poissons d'eau douce à travers différentes facettes. Finalement, ce travail a souligné la vulnérabilité de la faune tropicale à des légers changements environnementaux, même dans des régions relativement bien préservées, comme la Guyane Française
Natural ecosystems are facing increasing anthropogenic impacts that alter the diversity of biological communities. Amazonian rivers and streams shelter a unique and vast biodiversity. Yet, they are facing unprecedented deforestation levels due to human activities, such as mining, logging and agriculture. It is therefore urgent to deeply understand how human impacts affect biological communities in these ecosystems. The majority of studies addressing this issue were conducted in small streams and documented changes on species composition, but not responses on local species richness. This work proposes a community ecology approach, in which the connected nature of freshwater ecosystems is considered, to define how deforestation affects diversity patterns, but also the ecological processes shaping fish communities. Environmental DNA (eDNA), a non-invasive sampling method was used to equally sampling fish communities in streams and rivers across French Guiana. Deforested surfaces from spatial data were extracted to create a global deforestation variable that integrates the effects of urbanization, agriculture, gold-mining and logging. This work has optimized and validated the use of eDNA to assess the effects of human activities on species-rich ecosystems, such as tropical streams and rivers. The method showed high replicability, as well as the ability to distinguish local fish communities, habitats and disturbed sites from pristine sites. Moreover, we show that deforestation affected fish biodiversity beyond local effects and reveal an extended effect of distant upstream deforestation on downstream fish biodiversity. Distant and low-intensity deforestation caused a decline of over 30% in taxonomic and functional richness of riverine fish communities. Nonetheless, this perturbation was not determinant on the ecological processes shaping fish communities in rivers nor on the trait composition, which were more influenced by the upstream-downstream gradient than by the deforestation gradient. In stream communities, deforestation leads to changes in species composition, without a significant decrease in species or functional richness. These alterations were mediated by environmental filtering which was reinforced in highly deforested sites. As a result, species were less evenly distributed within the functional space, leaving the traits related to the benthic and phytophagous guild underrepresented while overrepresented by pelagic detritivorous. Our findings strongly support the complexity of deforestation impacts on Amazonian biodiversity. Besides, context-dependent responses, the diversity of freshwater fish communities responded to deforestation in a multifaceted way. This work underlined the vulnerability of tropical fauna to slight environmental changes, even in relatively well-preserved region, such as French Guiana

Pendant longtemps, la biodiversité était caractérisée uniquement par sa diversité taxonomique, c'est-à-dire par le nombre et la composition en espèces des assemblages. Cependant, de récentes études montrent que la biodiversité ne peut être résumée uniquement à cette composante, car elle ne prend pas en compte les caractéristiques écologiques des espèces. Pour cela, la diversité fonctionnelle est un outil permettant de considérer les traits fonctionnels des espèces. Peu d'études à larges échelles ont décrit cette facette de la biodiversité et son lien avec la diversité taxonomique. L'objectif de cette thèse est donc de 1) décrire et comprendre la distribution de la diversité fonctionnelle des assemblages de poissons d'eau douce à l'échelle globale et de 2) quantifier les conséquences des activités humaines sur cette facette. Pour cela, nous avons construit une base de données de traits fonctionnels de plus de 9000 espèces de poissons d'eau douce. Nous avons mis en évidence que la diversité fonctionnelle mondiale est distribuée de façon très hétérogène. Elle est essentiellement concentrée dans les bassins Néotropicaux, contrastant avec des zones taxonomiquement riches mais fonctionnellement redondantes comme l'Afrique ou l'Asie. Ces patrons pouvaient être expliqués par une diversification fonctionnelle de certains ordres de poissons Néotropicaux. À l'échelle des bassins versants, nous avons montré une faible, mais significative, influence des variables environnementales en particulier des variables historiques pour expliquer l'hétérogénéité des patrons de diversité fonctionnel des bassins versants. Nous avons également montré que les activités humaines, sous l'effet des introductions d'espèces, ont contribué à modifier considérablement les patrons de diversité fonctionnelle par rapport aux changements de diversité taxonomique. Ces changements mettent en évidence la nécessité de prendre en compte les conséquences des espèces non-natives sur le fonctionnement des écosystèmes. Dans ce travail de thèse, nous avons ainsi démontré que la diversité fonctionnelle est une facette complémentaire à la diversité taxonomique chez des poissons d'eau douce. Ces résultats contribuent à enrichir les connaissances de la structure des assemblages et peuvent avoir des implications en termes de gestion de la biodiversité
For a long time, biodiversity was characterised solely by its taxonomic diversity, i.e. the number and species composition of assemblages. However, recent studies show that biodiversity cannot be summed up solely by this component as it does not take into account the ecological characteristics of species. For this, functional diversity is a tool for considering the functional traits of species. Few large-scale studies have described this facet of biodiversity and its link with taxonomic diversity. The aim of this thesis is therefore to 1) describe and understand the distribution of functional diversity of freshwater fish assemblages on a global scale and 2) quantify the consequences of human activities on this facet. For this purpose, we have built a database of functional traits of more than 9000 species of freshwater fish. We have shown that the world's functional diversity is very heterogeneously distributed. It is essentially concentrated in the Neotropical basins, contrasting with taxonomically rich but functionally redundant areas such as Africa or Asia. These patterns could be explained by a functional diversification of certain orders of Neotropical fish. At the watershed scale, we showed a weak, but significant, influence of environmental variables, in particular historical variables, to explain the heterogeneity of the functional diversity patterns of watersheds. We have also shown that human activities, under the effect of species introductions, have contributed to a significant change in functional diversity patterns compared to changes in taxonomic diversity. These changes highlight the need to take into account the consequences of non-native species on ecosystem functioning. In this thesis work, we have thus demonstrated that functional diversity is a complementary facet of taxonomic diversity in freshwater fish. These results contribute to knowledge of the structure of assemblages and may have implications in terms of biodiversity management

Globally most of the conventional fish stocks have reached a state of optimum exploitation or even over-exploitation; efficient utilization of non-conventional resources is necessary to meet the supply-demand gap for protein supply. Mesopelagic fishes can be considered as one such promising resource for the future, if appropriate harvest and post-harvest technologies are developed. Increasing human population and increasing demand for cheaper food fishes has made myctophids a possible potential resource for future exploitation and utilization. Earlier studies indicated the abundance of Diaphus spp. in the eastern and northeastern Arabian Sea. The present study also indicates the dominance of Diaphus spp. in the deep sea trawling grounds of south west coast of India.

Deep-sea fishes are one of the very interesting groups of animals that live in the darkness that is below the epipelagic or photic zone of the ocean. The deep-sea ecosystem is the largest habitat on Earth, covering 300 x106 km 2 that comprise about 63% of the earth’s surface, and is the main reservoir of global biodiversity (Smith et al., 2008). However, the deep-sea is the least productive part of the oceans, although some high biomass concentrations of fishes are found on the topographic features like seamounts, mid-oceanic ridges and continental slopes (Norse et al., 2012). Deep-sea fishes can be placed into mesopelagic, bathypelagic and benthopelagic categories, depending upon their depth preferences. Mesopelagic and bathypelagic species are true pelagic fishes, generally of small size even at their adult stage and unlikely to be exploited on a commercial scale (Valinassab et al., 2007). Lantern fishes (Myctophidae) and cyclothonids (Gonostomatidae) are the common mesopelagic fishes that live below the photic zone extending to 1000 m depth and they, along with bathypelagic fishes that live below 1000 m, are highly adapted to live in an environment where food is scarce. The deep-sea fishes from mesopelagic and bathypelagic depths have many unique and interesting adaptations for living in the extreme deep-sea environment.

Samples of fishes of the family Balistidae were collecfed regularly from landings of hook and line and trawl at Tuticorin and Kanyakumari along southeast coast of India; Vizhinjam and Colachel along southwest coast oflndia during August 1998 to October 2000. Specimens of a few species were collected from trawl, trap, spear, gill net and hook and line landings of Mumbai, Veraval, Chennai, Mandapam and Kelakarai and Minicoy Island (Lakshadweep) were also analysed for this work. Specimens in the collections of Zoological Survey of India (ZSI), Kolkatta and those in the reference collection Museum of the Central Marine Fisheries Research Institute (CMFRI) at Cochin and Mandapam were also examined. 2. The morphological characters like teeth, nasal apertures, gi ll rakers were studied. 3. Based on the shape of the first and second teeth of the upper and lower jaw, fi ve types have been identi fied. 4. The anterior nasal aperture has different shapes, which is species specific but the posterior aperture is similar in all species. Based on the shape of the anterior nasal aperture five types have been identified. S. The outer most branchial arch possesses gill rakers. Based on its shape they are divided into five types. 6. The pattern of arrangement of scales and its eternal morphology was studied. 7. Scales on body and caudal peduncle are diamond shaped, were as scales on cheek are rhomboid, rectangular, square or triangular occurring in different combinations. Scales on abdomen are rhomboid or rectangular or square with round edges. 8. The arrangement of scales on body, abdomen and caudal peduncle were similar between the species. 218

There are three recognized species of Siphateles from the Great Basin; S. alvordensis, S. boraxobius and the tui chub, S. bicolor. One species, S. boraxobius, is endangered and one population of tui chub at Hutton Spring is threatened. Despite several morphological and molecular studies, the taxonomy and relationships of tui chubs are unclear. A recurrent theme in prior studies has been the possibility of translocation of tui chubs, especially into Summer Lake Basin, and probably by bait bucket introductions. I approached this problem by using cytochrome b (cyt b) sequences to define clades and constructed a neighbor-joining tree to examine relationships. Developmental ontogeny and adult meristic characters were used to corroborate clades, and microsatellites (nDNA) used to explore the possibility of hybridization among Summer Lake Basin fish and those from surrounding basins. The cyt b tree recovered a basal polytomy containing a western clade from Sycan Marsh, an eastern clade from the Alvord Basin, and S. bicolor. The Sycan Marsh clade was represented by two fish and requires additional research. Within the Alvord Basin, S. boraxobius and S. alvordensis were well corroborated by morphological characters but sequence divergence was only 0.37%. There were three major clades in S. bicolor – a basal S. newarkensis clade in Nevada, an Oregon Lakes S. bicolor clade, and, sister to it, a disjunct S. obesa clade in Nevada and the Oregon Lakes. In the Oregon Lakes, there were two clades within S. bicolor: S. thalassinus was sister to the remaining S. bicolor and there were two clades within S. obesus: S. oregonensis was sister to a "Summer Lake Basin" clade. There was some morphological corroboration for S. oregonensis, but no corroboration for the others. Clades were geographically disjunct or not confined to single basins. The S. oregonensis clade was sister to a Nevada polytomy and historical evidence implicates that at least one population of S. oregonensis in XL Spring was introduced in the late 1800's. Average sequence divergence with the Nevada clade, 0.62 - 0.88%, did not seem to support possible Miocene or Pliocene vicariance scenarios. Elsewhere, the S. thalassinus clade was found outside of Goose Lake in Summer Lake Basin and the "Summer Lake Basin" clade was found in Goose Lake Basin. Clustering of three microsatellite loci did not match cyt b clades, rather, individuals clustered based on sample location, suggesting that the cyt b patterns were due to introgression. In Summer Lake Basin, evidence of poisoning and subsequent transplants was consistent with these observations. These results suggest the presence of three or four tui chub taxa in the Oregon Lakes and Alvord Basin, however translocation and subsequent introgression appear to have been common in many populations, and will prove challenging for taxonomists and conservation managers.
Graduation date: 2013

The burgeoning world population has prompted mankind to. exploit new and varied avenues for acquiring food. The sea is often seen as a vast and endless source of food for mankind. The f.ishery resources of the sea have been exploited by man from time immemorial and the recent rapid strides in technology have enabled him to utilise the vast and deep expanses of the oceans effectively. The total annual world fish production is estimated as 92.86 million tonnes in 1999. Of this, production from marine fisheries alone accounted for 84.6 million tonnes (FAO, 1999). India ranks eighth (FAO, 1999) in the total fish production in the world. With its long coastline of 8129 km and an extensive Exclusive Economic Zone of 2.02 million sq km, with an estimated fishery resources potential of 3.9 million tonnes (Anon, 2000), the importance of the marine fisheries sector in the national economy, food security and employment generation need not be overemphasised. In the 3651 fishing villages situated along the coastline, about one million people are employed full time in marine capture fisheries. The fish ing sector dominated by small scale and semi industrial operations, support several ancillary industries such as boat building yards, processing plants etc (Devaraj and Vivekanandan, 1999). Marine fisheries operations have grown from a subsistence level carried out almost exclusively by the traditional fishermen in the preindependence days, to that of a capital-intensive industry requiring close monitoring and management for their sustainability. In the course of the past over five decades of independence, the average annual marine fish production increased from six lakh tonnes in the fifties to the current level of 2.72 mt in 2000. The mechanisation of indigenous artisanal fishing craft and the introduction of modern gear materials during the fifties, introduction of synthetic gear materials during the sixties, advent of purse seining and the motorisation of artisanal craft in the seventies and the substantial growth of motorised artisanal craft operating ring-seines in the eighties were some of the factors contributing to the phenomenal growth of the fisheries sector (Devaraj et al., 1997).

Fish larvae are particularly sensitive to a number of factors and, since larval survival may directly influence future abundances of adult stocks, understanding how larval survival and populational fluctuations affects the yearly recruitment strength and spatial distribution of populations becomes of key importance. The main objectives of this research were to perform a taxonomic characterization of the ichthyoplankton collected along the Cacheu river, assess its biodiversity and how it fluctuates with environmental variability. To achieve this, we performed a taxonomical identification and quantification of fish larvae, down to the lowest possible taxonomic level, collected from zooplankton sampling tows at four stations along the Cacheu river, in the Republic of Guinea-Bissau (RGB). With the abundance data gathered from this, we assessed the biodiversity within the estuary and how environmental factors (i.e.: depth, O2 saturation, salinity, and temperature) drove each taxon’s distribution along the stream. Our results have shown that there seems to be no correlation between the variation of larval abundance and that of the environmental factors. However, the overall abundance was observed to decrease with depth, increase from upstream to downstream and to have different distributions in each season. We found 10 taxa in our samples: Atherinidae (no previous records of presence in the area), Carangidae, Clupeidae, Congridae, Gobiidae, Mugilidae, Syngnathidae, Clupeiformes, Heterosomata (Pleuronectiformes), and Elops. Overall, Gobiidae larvae represented the majority of the fish larvae identified, followed by Clupeidae and Carangidae. The relative difference in abundances between Clupeidae and Carangidae is in accordance with two previous studies undertaken off the coast of the RGB, however the predominance of Gobiidae is not, which may be due to the sampling environment of the present study being estuarine whereas in both previous studies it was marine. This appears to be the first study regarding taxonomic characterization of ichthyoplankton (more specifically, fish larvae) within an estuarine environment, in the RGB, and may thusly be of significance in aiding the characterization of the biodiversity of the Cacheu river, providing a baseline reference for future taxonomic studies within it.
As larvas de peixe são particularmente sensíveis a vários factores e, como a sobrevivência larvar pode influenciar directamente as futuras abundâncias dos stocks adultos, torna-se particularmente importante compreender como a sobrevivência larvar e as flutuações populacionais afectam a força do recrutamento anual e a distribuição espacial de populações. Os principais objectivos deste estudo foram a caracterização taxonómica do ictioplâncton do rio Cacheu, a aferição da sua biodiversidade e de como esta varia com a variabilidade ambiental. Para este propósito, procedeu-se à identificação taxonómica e quantificação de larvas de peixe, até ao nível taxonómico mais baixo possível, capturadas em amostragens de zooplâncton realizadas em quatro estações de amostragem ao longo do rio Cacheu, na República da Guiné-Bissau (RGB). Com os dados de abundância recolhidos, foi aferida a biodiversidade dentro do estuário e a forma como os factores ambientais (i.e.: profundidade, saturação de O2, salinidade e temperatura) impulsionaram a distribuição de cada táxon ao longo do curso de água. Os resultados demonstraram que parece não haver uma correlação entre a variação da abundância larvar e a dos factores ambientais. No entanto, observou-se que a abundância geral diminui com a profundidade, aumenta de montante para jusante e tem distribuições diferentes em cada estação do ano. Foram encontrados 10 taxa: Atherinidae (sem registos prévios de presença nesta zona), Carangidae, Clupeidae, Congridae, Gobiidae, Mugilidae, Syngnathidae, Clupeiformes, Heterosomata (Pleuronectiformes) e Elops. No geral, as larvas de Gobiidae representam a maioria das larvas de peixe identificadas, seguidas por Clupeidae e Carangidae. A diferença relativa de abundâncias entre Clupeidae e Carangidae está em concordância com dois estudos anteriores, levados a cabo ao largo da costa da RGB, mas a predominância de Gobiidae não, o que pode dever-se ao facto de o meio de amostragem deste estudo ser estuarino, enquanto em ambos os estudos anteriores o meio era marinho. Este parece ser o primeiro estudo dedicado à caracterização taxonómica de ictioplâncton (ou mais concretamente, larvas de peixe) dentro de um ambiente estuarino na RGB e poderá assim ter importância no auxílio da caracterização da biodiversidade do rio Cacheu, fornecendo uma base de referência para futuros estudos taxonómicos neste rio.
Mestrado em Biologia Marinha Aplicada

The genus Pelasgus (Cyprinidae) is endemic to the southern part of the Balkan Peninsula and includes seven species. In this work, a multilocus approach has been applied to study phylogenetic relationships between the species and their populations and to revise their distribution areas. 180 specimens from 47 localities from 30 river drainages were analyzed, comprehensively covering the distribution range of the genus. Moreover, samples from type localities of all species were included in the analyses. Mitochondrial (cytochrome b) and nuclear markers (the first intron of ribosomal protein S7, recombination activating gene RAG1 and rhodopsin) were used. Existence of seven well supported lineages was revealed based on cytochrome b, which is the most variable marker. These lineages correspond to P. laconicus, P. marathonicus, P. minutus, P. stymphalicus, P. thesproticus, P. prespensis and Pelasgus sp. The most variable nuclear marker was first intron of S7, which provides almost the same results as cytochrome b, revealing six well supported lineages, whereas RAG1 and rhodopsin appear to be less informative, revealing only four well supported clades. These markers did not separate several species (P. marathonicus, P. stymphalicus, P. thesproticus, and Pelasgus sp.) due to low variability of the markers...

The fossiliferous sediments of the Hueso and Tapiado formations exposed in the Vallecito Creek-Fish Creek section (VCFC) of the Anza-Borrego Desert (ABD) span the boundary between Blancan and Irvingtonian North American Land Mammal 'Ages.' Historically, the determination of the Blancan-Irvingtonian (B-I) boundary in the VCFC proved problematic. A new study to determine the B-I boundary in the VCFC revealed data inaccuracies in both published works and curatorial records of the mammal and other vertebrate fossils from the ABD. Most individual inaccuracies were minor, but an accumulation of over 50 years of multiple inaccuracies had significant effects on local and regional biostratigraphic and biochronologic correlations. A detailed investigation of the inaccurate data resulted in recognition of 17 types of error, with at least five sources. The two most prominent sources of error are those derived from publication and curation protocols. Examination of over 150 publications and in-house faunal lists produced over 830 taxonomic names and format variants, for 110 mammalian taxa identified from the ABD and VCFC. Approximately 50% of the taxonomic identifications were previously published without voucher catalogue numbers or fossil descriptions. A critical review of the taxonomic assignments resulted in an updated faunal list of ABD terrestrial Mammalia, including 110 taxonomic names, 66 unqualified genera, and 46 unqualified species. A supplemental list of 'retired' taxa includes 178 previously published or listed taxonomic names and format variants. The 4.5 km sequence of originally superposed sediments within VCFC is now tilted at 23 degrees and exposed in plan view. This exposure was captured in both aerial photos and satellite imagery. GIS layers of the Geomagnetic Polarity Time Scale and individual collecting localities are readily superposed onto the stratigraphic images. When united with the faunal database, GIS maps of biostratigraphic data facilitate detection and correction of data errors. Resulting corrected maps show highest and lowest stratigraphic occurrences of taxa, as well as geographic clustering of taxonomic groups, outlining possible paleohabitats. As a result of data improvement and GIS display, the local B-I boundary currently is best estimated by the presence of Ovibovini at >1.42 Ma.
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Despite the increases in the intensity and frequency of disturbances on coral reefs in the Red Sea over the past decade, patterns of variability in fish communities are still poorly understood. This study aims to contribute to a better understanding of how fish communities vary along multiple spatial scales (10-100’ of kilometers) and to provide a baseline for future comparisons, fundamental to assess responses to climate change and other disturbances. Coral reefs along the Saudi Arabian Red Sea coast were surveyed from 2017 to 2019. The reefs ranged from 28° N to 18 °N and were categorized according their geographical location and grouped within three regions, namely north (24-28.5°N; 12 reefs), central (20.4-22.3°N; 11 reefs), and south (18.5-21.2°N; 30 reefs). The quantification of spatial patterns was conducted based on both taxonomic- and trait-based approaches. Considering the dependence of fish communities on the benthic habitat the relationship between different attributes of the fish assemblages and coral cover was also investigated. A consistent pattern of separation between assemblages of the northern and central region from the ones in the south was observed in nearshore reefs but was not evident for offshore reefs. The southern region supported higher densities, biomass, and species richness than the other two regions. The analysis showed that transect and reef scales contributed to the greatest variation in fish communities, suggesting higher levels of variability within small spatial scales. Several parameters of the fish community (total species, total density, total biomass, total functional entities, functional richness, functional redundancy) were positively correlated to coral cover, particularly in the northern region. Responses were not consistent across the Red Sea basin, suggesting that management plans should be regionally based. This study can be helpful to design management strategies as it provides a current baseline from both taxonomic and trait perspectives for Red Sea reefs that can be used to evaluate future changes due to natural and human-based disturbances.

Tese de mestrado em Ecologia Marinha, apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2016
Os estuários são áreas de transição entre os rios e os mares, extremamente importantes para as comunidades de peixes, que utilizam os estuários para se alimentarem, como áreas de viveiro e como parte das suas rotas de migração. Devido à alta produtividade que é característica dos estuários e à elevada importância económica das suas espécies, as áreas estuarinas têm sido altamente exploradas pelo Homem. Esta sobre-exploração juntamente com as alterações climáticas, fazem dos estuários um dos ecossistemas mais ameaçados a nível global. A biodiversidade é um recurso natural valioso, quer a nível económico como cultural, e é também um excelente indicador ecológico. É também um conceito muito vasto, que engloba três vertentes (taxonómica, funcional e filogenética). O principal objetivo deste trabalho foi investigar a variabilidade espacial, sazonal e temporal das comunidades de peixes do estuário do Mondego, bem como a influência das variáveis ambientais na comunidade de peixes. Para cumprir este objetivo, utilizámos uma série temporal, com amostragens periódicas efetuadas no estuário, entre 2003 e 2013, com informações sobre a riqueza específica, as respetivas abundâncias de cada espécie em cada sessão de amostragem e os valores das variáveis ambientais (temperatura, salinidade, oxigénio, curso de água, precipitação e o índice North Atlantic Oscilation (NAO). Cada espécie foi classificada a nível taxonómico e de acordo com cinco características funcionais (preferência de salinidade, mobilidade, dieta, modo de alimentação e tamanho máximo) e dois genes mitocondriais (16s e COI). Para investigar as alterações nas comunidades de peixes do estuário, foram utilizados diversos índices de cada vertente da diversidade (taxonómica – riqueza específica, Shannon-Wiener, Simpson e Pielou; funcional – espécies funcionalmente únicas, riqueza funcional, equitabilidade funcional, divergência funcional, dispersão funcional e índice de Rao; e filogenética – índice de Rao e distância mínima entre pares de espécies). Para além disso, foi feita uma comparação direta entre as três vertentes da diversidade, utilizando o índice de Rao, uma vez que este índice permite fazer uma comparação entre vertentes distintas. Em relação às variáveis ambientais, os nossos resultados estão de acordo com outros estudos já realizados, onde a salinidade (relação direta), a temperatura (relação direta) e o caudal de água doce (relação inversa), foram os fatores que mais influenciam as comunidades de peixes. Para além disto, os nossos resultados, destacam a estabilidade das comunidades de peixes do estuário do Mondego, uma vez que não existiram diminuições de diversidade em nenhuma das três vertentes (com exceção da riqueza funcional, que está provavelmente relacionado com o desaparecimento de várias espécies de água doce devido a um aumento da salinidade), apesar de variações sazonais ao nível das abundâncias das espécies e de alguma variação entre anos em vários índices. As variações sazonais ao nível da equitabilidade (que aconteceram no verão), poderão estar relacionadas com a biologia reprodutiva das espécies e com as migrações associadas à reprodução das mesmas, uma vez que os juvenis da maior parte dos peixes que utilizam este estuário como área de viveiro, atingem densidades muito elevadas no estuário na primavera/verão. Verificou-se também um gradiente espacial (provavelmente causado pela salinidade), de montante a jusante, com as riquezas específica e funcional, mais elevadas a jusante e mais baixas a montante enquanto que a equitabilidade das espécies mais baixa a jusante e mais elevada na zona central do estuário. Relativamente à diversidade filogenética, não foi notório um gradiente espacial, uma vez que existiu uma diversidade filogenética maior a montante e a jusante do estuário e menor na zona central, o que poderá estar relacionado com uma maior diversidade característica das zonas marinhas e dulçaquícolas adjacentes ao estuário do que na área estuarina.
Estuaries are transitional areas, with high importance for numerous fish species which use estuaries as nursery, migration, feeding and spawning grounds. Due to their location, high productivity and economic importance of their species, estuaries have been highly explored by humans, which together with climate change, makes estuaries highly threatened ecosystems worldwide. Biodiversity is a natural valuable resource at both economic and cultural levels and a useful ecological indicator. It is a wide concept that includes multiple dimensions (taxonomic, functional and phylogenetic). The main goal of this study was to assess inter-annual, seasonal and spatial changes in biodiversity of the fish assemblage of the Mondego estuary and links with environmental variables. To do so, we used a time series with periodic sampling between 2003 and 2013 reporting fish species richness and abundance, and environmental variables (temperature, salinity, oxygen, runoff, precipitation and the North Atlantic Oscilation (NAO) index. Each species was classified taxonomically, and also based on five functional traits (salinity preference, mobility, diet, feeding mode and maximum body length) and on two mitochondrial genes (16s and COI). To investigate changes regarding the fish assemblages, we used several diversity indices (taxonomic – species richness, Shannon-Wiener, Simpson and Pielou’s evenness; functional – functionally singular species, functional richness, functional evenness, functional divergence, functional dispersion and functional Rao’s Quadratic Entropy; and phylogenetic – phylogenetic Rao’s Quadratic Entropy and mean pairwise distance). Moreover, to allow direct comparisons between diversity dimensions we used Rao’s Quadratic Entropy. Regarding environmental variables, our results are in agreement with previous studies, where salinity (direct relationship), temperature (direct relationship) and river runoff (inverse relationship) were the factors with higher influence on the fish assemblages. Moreover, our results highlight the stability of the fish assemblages in the Mondego estuary, with no linear changes in biodiversity facets throughout the study period (with the exception of slight loss of functional richness, which is probably related with the disappearance of freshwater species due to an increase in salinity), despite seasonal variation in taxonomic evenness and inter-annual variation in many indices. Seasonal variations in taxonomic evenness (which occurred in summer) may be explained by the reproductive biology of fishes and the associated recruitment patterns and spawning migrations, since juveniles of most of the fishes that use this estuary as a nursery area attain high densities inside the estuary during spring/summer. There was a spatial gradient (probably caused by salinity) from upstream to downstream of the estuary, with species and functional richness higher downstream and lower upstream whilst evenness was lower downstream and higher in middle areas. Phylogenetic diversity was lower in middle areas than upstream and downstream, which is probably related to higher diversity that exists in the freshwater and marine adventitious areas than in estuarine areas.

Plusieurs études à grande échelle ont identifié la modification ou la perte d’habitats comme menace principale à la conservation des communautés de poissons d’eau douce. Au Canada, « aucune perte nette dans la capacité productive des habitats » (NNL) est le principe directeur de la politique de gestion des habitats du ministère des Pêches et Océans. Le respect du NNL implique l’avancement des connaissances au niveau des relations entre les poissons et leurs habitats, de même que des outils pour quantifier l’impact de la modification des habitats sur les poissons. Les modèles d’utilisation de l’habitat des poissons (FHUM) sont des outils qui permettent d’améliorer nos connaissances des relations poissons – habitat, de prédire la distribution des espèces, mais aussi leurs densités, biomasses ou abondances, sur la base des caractéristiques de l’environnement. L’objectif général de mon mémoire est d’améliorer la performance des FHUM pour les rivières des basses Laurentides, en suggérant des perfectionnements au niveau de 2 aspects cruciaux de l’élaboration de tels modèles : la description précise de la communauté de poissons et l’utilisation de modèles statistiques efficaces. Dans un premier chapitre, j’évalue la performance relative de la pêcheuse électrique et de l’échantillonnage en visuel (plongée de surface) pour estimer les abondances des combinaisons d’espèces et de classes de taille des poissons en rivière. J’évalue aussi l’effet des conditions environnementales sur les différences potentielles entre les communautés observées par ces 2 méthodes d’échantillonnage. Pour ce faire, 10 sections de rivière de 20 m de longueur ont été échantillonnées à l’aide de ces 2 méthodes alors qu’elles étaient fermées par des filets de blocage. 3 plongeurs performèrent l’échantillonnage en visuel en se déplaçant de l’aval vers l’amont des sections, tout en dénombrant les espèces et classes de taille. Par la suite, nous avons fait 3 passages de pêcheuse électrique et les abondances furent estimées grâce à un modèle restreint de maximum de vraisemblance, basé sur la diminution des abondances observées. De plus grandes abondances de poissons furent observées en visuel qu’avec la pêcheuse électrique à tous les sites. La richesse spécifique observée en visuel était plus élevée (6/10) ou égale (4/10) à celle observée avec la pêcheuse électrique. Les différences entre les communautés de poissons observées à l’aide de ces 2 méthodes ne purent être reliées aux conditions environnementales. Les résultats de cette expérience sont contraires à ceux de toutes les études comparant ces 2 méthodes d’échantillonnage, lesquels suggèrent une supériorité de la pêcheuse électrique. Les conditions environnementales de notre expérience étaient distinctes de celles observées dans les autres études (absence d’arbres tombés dans l’eau, très peu de substrats grossiers), mais la différence la plus marquante était en terme de communauté de poissons observée (dominance des cyprinidés et des centrarchidés plutôt que des salmonidés). Je termine ce chapitre en suggérant que les caractéristiques comportementales favorisant l’évitement de la capture (formation de bancs) et facilitant l’observation en visuel (curiosité) sont responsables de la supériorité de la plongée de surface pour échantillonner les communautés dans les rivières des basses Laurentides. Dans un deuxième chapitre, je développe des FHUM pour des communautés de poissons de rivière ayant plusieurs espèces. Dans le but de simplifier la modélisation de telles communautés et d’améliorer notre compréhension des relations poissons – habitat, j’utilise les concepts de guilde écologique et de filtre environnemental pour explorer les relations entre les guildes formées sur la bases de différents types de traits (reproducteurs, taxonomiques, éco-morphologiques et alimentaires) et les conditions environnementales locales à l’échelle du méso-habitat. Les modèles d’habitats basés sur les guildes reproductrices ont clairement surpassé les autres modèles, parce que l’habitat de fraie reflète l’habitat de préférence en dehors de la période de reproduction. J’ai également utilisé l’approche inverse, c’est à dire définir des guildes d’utilisation de l’habitat et les mettre en relation avec les traits des espèces. Les traits reliés à l’alimentation des poissons ont semblés être les meilleurs pour expliquer l’appartenance aux groupes d’utilisation de l’habitat, mais le modèle utilisé ne représentait pas bien la relation entre les groupes. La validation de notre modèle basé sur les guildes reproductrices avec un jeu de données indépendant pourrait confirmer notre découverte, laquelle représente une manière prometteuse de modéliser les relations poissons – environnement dans des communautés de poissons complexes. En conclusion, mon mémoire suggère d’importantes améliorations aux FHUM pour les communautés de poissons des basses Laurentides, en suggérant de prendre en compte les caractéristiques biologiques des cours d’eau dans le choix d’une méthode d’échantillonnage, et également en utilisant une méthode prometteuse pour simplifier les FHUM de communautés de poissons complexes : les guildes reproductrices.
Many large scale studies have identified habitat modification or habitat losses as primary threats for the conservation of freshwater fish communities. In Canada, No Net Loss (NNL) of the productive capacity of habitats is the guiding principle of the Department of Fisheries and Oceans’ policy for the management of fish habitat. To respect NNL, a better understanding of fish-habitat relationships is required, as well as tools to quantify the impact of habitat modifications on fish. Fish habitat use models (FHUM) are tools that can improve our understanding of fish-habitat relationships, predict species occurrences, densities or biomass on the basis of habitat descriptors and quantify habitat requirements. They consist in relationships between biological descriptors of fish and habitat descriptors. The general objective of my thesis is to improve the performance of FHUM for the lower Laurentian streams by suggesting refinements on 2 crucial aspects in the development of these models: a precise description of the fish community and the use of efficient statistical models. In the first chapter, I evaluate the relative performance of electrofishing and visual surveys (snorkeling) for estimating the abundance of combinations of fish species and size classes in rivers. I also assessed the effect of environmental conditions on potential differences between the results obtained using these two sampling methods. Sampling sites consisted in 10 river sections of 20 m in length distributed in the Laurentian region of Québec. Both methods were used while sections were blocked. Three snorkelers that swam the river sections upstream while identifying and counting fish of each species and size-classes performed visual surveys. Three-pass electrofishing was performed and abundances were estimated with a maximum likelihood depletion model. Greater abundances of fish were observed by snorkeling than by electrofishing at all sites. Snorkeling species richness was higher (6/10) or equal (4/10) to electrofishing richness. Differences in the fish communities observed by both sampling methods were not related to environmental conditions. The results of our work are therefore contrary to that of most published studies that suggested the superiority of electrofishing on visual surveys. Compared to the conditions found in previous studies, our sampling sites had different environmental characteristics (no fallen trees, insignificant cover of large cobble and boulder) but the most striking dissimilarity was in terms of fish communities (dominance of cyprinids and centrarchids instead of salmonids). Behavioural characteristics favouring capture avoidance (schooling) and facilitating underwater observation (curiosity) may be responsible for the superiority of visual surveys in our study rivers. Survey methods should be selected based on fish community composition. In the second chapter, I develop FHUM for complex stream fish communities. In order to simplify the modelling of such communities, as well as improve our understanding of fish – habitat relationships, I used the ecological guild concept and the niche filtering hypothesis to explore the relationships between guilds based on different types of traits (eco-morphological, reproductive, alimentary and taxonomic) and local environmental descriptors, at the coarse meso-habitat scale. Reproductive guilds led to FHUM that clearly outperformed the other 3 approaches, because of the close relationship between preferred spawning grounds and non spawning habitat preferences, and also because reproductive traits are linked to habitat characteristics at the reach or coarse mesohabitat scale. We also defined guilds based on habitat-use and related them to species traits. Traits related to the feeding biology of fishes seemed to be the best at explaining the habitat-use guilds, but our model did not correctly represent the among-guild relationships. Validation of our reproductive trait model on an independent dataset would confirm our finding, which represents a promising way of modelling fish - habitat relationships in complex fish communities. In conclusion, my thesis suggests important improvements to FHUM models in the Laurentian streams by giving new insights on the choice of a sampling method that take into account the biological characteristics of the streams targeted, and by using a promising way of simplifying FHUM for species rich communities: reproductive guilds.