Taxonomy of the Haploporinae Nicoll, 1914 and Bunocotylinae Dollfus, 1950 (Digenea) from Mediterranean mullets (Teleostei): morphological and molecular approaches

The thesis aimed at developing a modern taxonomic framework of two major groups of mullet digeneans, the subfamily Bunocotylinae of the Hemiuridae and the subfamily Haploporinae of the Haploporidae, by combining morphological and molecular data. Saturnius is revised, three new species are described: S. minutus n. sp., S. dimitrovi n. sp. and S. overstreeti n. sp.; S. papernai is redescribed, a new diagnosis and a key to the species is provided. A taxonomic revision of the Mediterranean haploporid genera Haploporus, Dicrogaster, Forticulcita, Lecithobotrys and Saccocoelium was carried out. New generic diagnoses are provided for all genera. Haploporus and Lecithobotrys are considered monotypic Mediterranean genera and their type-species are redescribed. Dicrogaster perpusilla and D. contracta are redescribed and distinguished. A key to the valid species is given. Forticulcita gibsoni n. sp., is described. A key to Forticulcita spp. is presented. Saccocoelium obesum and S. tensum are redescribed. Three new species, Saccocoelium cephali n. sp., S. brayi n. sp. and S. currani n. sp., are described. A key to the recognised species is presented. Three new haploporine genera are established: Ragaia n. g. for R. lizae n. sp.; Pseudolecithobotrys n. g. and Pseudodicrogaster n. g. for Lecithobotrys stomachicola n. comb. and Dicrogaster japonica n. comb., respectively. A key to the ten recognised genera of the Haploporinae is presented. Molecular phylogenetic analyses are applied to evaluate the taxonomic framework of the Haploporinae based on morphology and its systematic position within the phylogeny of the Digenea. __________________________________________________________________________________________________ RESUMEN El propósito de esta tesis es desarrollar un marco taxonómico moderno para dos grupos mayoritarios de digénidos de mugílidos, la subfamilia Bunocotylinae, de la familia Hemiuridae y la subfamilia Haploporinae, de la familia Haploporidae; utilizando datos morfológicos y moleculares. El género Saturnius ha sido revisado y tres nuevas especies han sido descritas: S. minutus n. sp., S. dimitrovi n. sp. y S. overstreeti n. sp.; S. papernai ha sido redescrita, y una nueva diagnosis y una clave de identificación de las especies han sido presentadas. Se llevo a cabo la revisión taxonómica de los géneros de haplopóridos mediterráneos Haploporus, Dicrogaster, Forticulcita, Lecithobotrys y Saccocoelium. Se presentan nuevas diagnosis para cada género. Haploporus y Lecithobotrys han sido considerados géneros monotípicos mediterráneos y sus especies tipo han sido redescritas. Dicrogaster perpusilla y D. contracta se han redescrito y diferenciado, y una clave de identificación para todas las especies del género ha sido presentada. Se ha descrito Forticulcita gibsoni n. sp. y se presenta una clave de identificación para las especies de este género, Forticulcita. Saccocoelium obesum y S. tensum se han redescrito. Tres especies nuevas, Saccocoelium cephali n. sp., S. brayi n. sp. y S. currani n. sp., han sido descritas y se presenta una clave de identificación de las especies consideradas validas. Se han erigidos tres nuevos géneros de haploporinos: Ragaia n. g. para R. lizae n. sp.; Pseudolecithobotrys n. g. y Pseudodicrogaster n. g. para Lecithobotrys stomachicola n. comb. y Dicrogaster japonica n. comb., respectivamente. Se presenta una clave de identificación para los diez géneros de Haploporinae considerados válidos. Métodos de análisis filogenéticos moleculares han sido aplicados para evaluar el marco taxonómico de Haploporinae basado en la morfología, y su posición sistemática dentro de la filogenia de los digeneos

Evaluation of three methods for biomass estimation in small invertebrates, using three large disparate parasite species as model organisms

Invertebrate biomass is considered one of the main factors driving processes in ecosystems. It can be measured directly, primarily by weighing individuals, but more often indirect estimators are used. We developed two indirect and non-destructive approaches to estimate biomass of small invertebrates in a simple manner. The first one was based on clay modelling and the second one was based on image analysis implemented with open-source software. Furthermore, we tested the accuracy of the widely used geometric approximation method (third method). We applied these three different methods to three morphologically disparate model species, an acanthocephalan worm, a crustacean and a flatworm. To validate our indirect estimations and to test their accuracy, we weighed specimens of the three species and calculated their tissue densities. Additionally, we propose an uncomplicated technique to estimate thickness of individuals under a microscope, a required measurement for two of the three indirect methods tested. The indirect methods proposed in this paper provided the best approximation to direct measurements. Despite its wide use, the geometric approximation method showed the lowest accuracy. The approaches developed herein are timely because the recently increasing number of studies requiring reliable biomass estimates for small invertebrates to explain crucial processes in ecosystems

Beyond counting species : a new way to look at biodiversity

In modern ecology, the traditional diversity indices (usually of richness, abundance, and species evenness) have been highly revealing and useful for monitoring community and ecosystem processes. However, around two decades ago, a pioneering research team noticed that these indices did not completely resolve their open questions. Thus, they suggested changing the way biodiversity was measured. At its base, this new methodology considers the distance between species (in phylogenetic or functional terms) before subsequently applying the appropriate biodiversity indices. Including phylogenetic and functional elements in the evaluation of diversity allows us to approach the concept of biodiversity in a more comprehensive way

PACo: A Novel Procrustes Application to Cophylogenetic Analysis

We present Procrustean Approach to Cophylogeny (PACo), a novel statistical tool to test for congruence between phylogenetic trees, or between phylogenetic distance matrices of associated taxa. Unlike previous tests, PACo evaluates the dependence of one phylogeny upon the other. This makes it especially appropriate to test the classical coevolutionary model that assumes that parasites that spend part of their life in or on their hosts track the phylogeny of their hosts. The new method does not require fully resolved phylogenies and allows for multiple host-parasite associations. PACo produces a Procrustes superimposition plot enabling a graphical assessment of the fit of the parasite phylogeny onto the host phylogeny and a goodness-of-fit statistic, whose significance is established by randomization of the host-parasite association data. The contribution of each individual host-parasite association to the global fit is measured by means of jackknife estimation of their respective squared residuals and confidence intervals associated to each host-parasite link. We carried out different simulations to evaluate the performance of PACo in terms of Type I and Type II errors with respect to two similar published tests. In most instances, PACo performed at least as well as the other tests and showed higher overall statistical power. In addition, the jackknife estimation of squared residuals enabled more elaborate validations about the nature of individual links than the ParaFitLink1 test of the program ParaFit. In order to demonstrate how it can be used in real biological situations, we applied PACo to two published studies using a script written in the public-domain statistical software R

Phylogeography and cryptic species structure of a locally adapted parasite in New Zealand

The phylogeographic patterns of many taxa on New Zealand's South Island are characterized by disjunct distributions that have been attributed to Pleistocene climatic cycles and the formation of the Southern Alps. Pleistocene glaciation has been implicated in shaping the contemporary genetic differentiation between populations of the aquatic snail Potamopyrgus antipodarum. We investigated whether similar phylogeographic patterns exist for the snail's locally adapted trematode parasite, Atriophallophorus winterbourni. We found evidence for a barrier to gene-flow in sympatry between cryptic, but ecologically divergent species. When focusing on the most common of these species, disjunct geographic distributions are found for mitochondrial lineages that diverged during the Pleistocene. The boundary between these distributions is found in the central part of the South Island and is reinforced by low cross-alpine migration. Further support for a vicariant origin of the phylogeographic pattern was found when assessing nuclear multilocus SNP data. Nuclear and mitochondrial population differentiation was concordant in pattern, except for populations in a potential secondary contact zone. Additionally, we found larger than expected differentiation between nuclear- and mitochondrial-based empirical Bayes F>sub>ST estimates (global FST: 0.02 vs. 0.39 for nuclear and mitochondrial data, respectively). Population subdivision is theoretically expected to be stronger for mitochondrial genomes due to a smaller effective population size, but the strong difference here, together with mitonuclear discordance in a putative contact zone, is potentially indicative of divergent gene flow of nuclear and mitochondrial genomes

Occurrence of Dibothriocephalus latus in European perch from Alpine lakes, an important focus of diphyllobothriosis in Europe

The broad fish tapeworm Dibothriocephalus latus (syn. Diphyllobothrium latum) is one of the most common causative agents of human diphyllobothriosis, a significant fish-borne parasitic zoonosis. In Europe, the occurrence of D. latus has been repeatedly reported in lakes of the Alps region, the Baltic region, Fennoscandia and Russia. Regular detection of D. latus plerocercoids in fish coming from different subalpine lakes linked with ongoing D. latus infection in humans indicates that Alpine region is a rather specific area from the medical, epidemiological and ecological point of view. Results from the examination of 688 European perch (Perca fluviatilis) from six subalpine lakes in Switzerland, France and northern Italy (Lakes Geneva, Neuchâtel, Biel, Como, Maggiore and Iseo) confirmed the ongoing occurrence of D. latus in the Alps region. The detected prevalence of D. latus in the studied Alpine lakes (2% in Lake Neuchâtel; 37.5% in Lake Biel; 6.4% in Lake Geneva; 22.8% in Lake Iseo [2018]; 12.8% in Lake Iseo [2017]; 15.2% in Lake Como; 16.7% in Lake Maggiore) was compared with previously published data. In addition, the importance of the Alpine lakes region and data on the epidemiology and ecology of D. latus related to subalpine lakes were discussed

Determinants of parasite distribution in Arctic charr populations: catchment structure versus dispersal potential

Parasite distribution patterns in lotic catchments are driven by the combined influences of unidirectional water flow and the mobility of the most mobile host. However, the importance of such drivers in catchments dominated by lentic habitats are poorly understood. We examined parasite populations of Arctic charr Salvelinus alpinus from a series of linear-connected lakes in northern Norway to assess the generality of lotic-derived catchment-scale parasite assemblage patterns. Our results demonstrated that the abundance of most parasite taxa increased from the upper to lower catchment. Allogenic taxa (piscivorous birds as final host) were present throughout the entire catchment, whereas their autogenic counterparts (charr as final hosts) demonstrated restricted distributions, thus supporting the theory that the mobility of the most mobile host determines taxa-specific parasite distribution patterns. Overall, catchmentwide parasite abundance and distribution patterns in this lentic-dominated system were in accordance with those reported for lotic systems. Additionally, our study highlighted that upper catchment regions may be inadequate reservoirs to facilitate recolonization of parasite communities in the event of downstream environmental perturbations

Determinants of parasite distribution in Arctic charr populations: catchment structure versus dispersal potential

Parasite distribution patterns in lotic catchments are driven by the combined influences of unidirectional water flow and the mobility of the most mobile host. However, the importance of such drivers in catchments dominated by lentic habitats are poorly understood. We examined parasite populations of Arctic charr Salvelinus alpinus from a series of linear-connected lakes in northern Norway to assess the generality of lotic-derived catchment-scale parasite assemblage patterns. Our results demonstrated that the abundance of most parasite taxa increased from the upper to lower catchment. Allogenic taxa (piscivorous birds as final host) were present throughout the entire catchment, whereas their autogenic counterparts (charr as final hosts) demonstrated restricted distributions, thus supporting the theory that the mobility of the most mobile host determines taxa-specific parasite distribution patterns. Overall, catchmentwide parasite abundance and distribution patterns in this lentic-dominated system were in accordance with those reported for lotic systems. Additionally, our study highlighted that upper catchment regions may be inadequate reservoirs to facilitate recolonization of parasite communities in the event of downstream environmental perturbations

Temporal stability of polymorphic Arctic charr parasite communities reflects sustained divergent trophic niches

Polymorphic Arctic charr Salvelinus alpinus populations frequently display distinct differences in habitat use, diet, and parasite communities. Changes to the relative species densities and composition of the wider fish community have the potential to alter the habitat niche of sympatric Arctic charr populations. This study evaluated the temporal stability of the parasite community, diet, and stable isotopes (δ13C, δ15N) of three sympatric Arctic charr morphs (piscivore, benthivore, and planktivore) from Loch Rannoch, Scotland, in relation to changes to the fish community. All Arctic charr morphs displayed distinct differences in parasite communities, diet, and stable isotope signatures over time, despite the establishment of four new trophically transmitted parasite taxa, and increased fish and zooplankton consumption by the piscivorous and planktivore morphs, respectively. Native parasite prevalence also increased in all Arctic charr morphs. Overall, Loch Rannoch polymorphic Arctic charr morph populations have maintained their distinct trophic niches and parasite communities through time despite changes in the fish community. This result indicates that re-stocking a native fish species has the potential to induce shifts in the parasite community and diet of Arctic charr morphs

Molecular approaches to trematode systematics: 'best practice' and implications for future study

To date, morphological analysis has been the cornerstone to trematode systematics. However, since the late-1980s we have seen an increased integration of genetic data to overcome problems encountered when morphological data are considered in isolation. Here, we provide advice regarding the ‘best molecular practice’ for trematode taxonomy and systematic studies, in an attempt to help unify the field and provide a solid foundation to underpin future work. Emphasis is placed on defining the study goals and recommendations are made regarding sample preservation, extraction methods, and the submission of molecular vouchers. We advocate generating sequence data from all parasite species/host species/geographic location combinations and stress the importance of selecting two independently evolving loci (one ribosomal and one mitochondrial marker). We recommend that loci should be chosen to provide genetic variation suitable to address the question at hand and for which sufficient ‘useful’ comparative sequence data already exist. Quality control of the molecular data via using proof-reading Taq polymerase, sequencing PCR amplicons using both forward and reverse primers, ensuring that a minimum of 85% overlap exists when constructing consensus sequences, and checking electropherograms by eye is stressed. We advise that all genetic results are best interpreted using a holistic biological approach, which considers morphology, host identity, collection locality, and ecology. Finally, we consider what advances next-generation sequencing holds for trematode taxonomy and systematics