A comparative study of Ligophorus uruguayense and L. saladensis (Monogenea: Ancyrocephalidae) from Mugil liza (Teleostei: Mugilidae) in southern Brazil.

Representatives of Ligophorus Euzet et Suriano, 1977 were found on the gills of Mugil liza Valenciennes caught in southern Brazil. They were identified as Ligophorus uruguayense Failla Siquier et Ostrowski de Núñez, 2009 and Ligophorus saladensis Marcotegui et Martorelli, 2009, even though specific identification proved to be difficult due to inconsistencies in some diagnostic features reported for these two species. Therefore, a combined morphological and molecular approach was used to critically review the validity of these species, by means of phase contrast and confocal fluorescence microscopical examination of sclerotised hard parts, and assessing the genetic divergence between L. saladensis, L. uruguayense and their congeners using rDNA sequences. The main morphological differences between the two species relate to the shape of the accessory piece of the penis and the median process of the ventral bar. The accessory piece in L. uruguayense is shorter than in L. saladensis, has a cylindrical, convex upper lobe and straight lower lobe (vs with the distal tip of the lower lobe turning away from the upper lobe in the latter species). The ventral bar has a V-shaped anterior median part in L. uruguayense (vs U-shaped in L. saladensis). The two species are suggested to be part of a species complex together with L. mediterraneus Sarabeev, Balbuena et Euzet, 2005. We recommend to generalise such comparative assessment of species of Ligophorus for a reliable picture of the diversity and diversification mechanisms within the genus, and to make full use of its potential as an additional marker for mullet taxonomy and systematics.

A large-scale phylogeny of Synodontis (Mochokidae, Siluriformes) reveals the influence of geological events on continental diversity during the Cenozoic.

To explain the spatial variability of fish taxa at a large scale, two alternative proposals are usually evoked. In recent years, the debate has centred on the relative roles of present and historical processes in shaping biodiversity patterns. In Africa, attempts to understand the processes that determine the large scale distribution of fishes and exploration of historical contingencies have been under-investigated given that most of the phylogenetic studies focus on the history of the Great Lakes. Here, we explore phylogeographic events in the evolutionary history of Synodontis (Mohokidae, Siluriformes) over Africa during the Cenozoic focusing on the putative role of historical processes. We discuss how known geological events together with hydrographical changes contributed to shape Synodontis biogeographical history. Synodontis was chosen on the basis of its high diversity and distribution in Africa: it consists of approximately 120 species that are widely distributed in all hydrographic basins except the Maghreb and South Africa. We propose the most comprehensive phylogeny of this catfish genus. Our results provide support for the 'hydrogeological' hypothesis, which proposes that palaeohydrological changes linked with the geological context may have been the cause of diversification of freshwater fish deep in the Tertiary. More precisely, the two main geological structures that participated to shape the hydrographical network in Africa, namely the Central African Shear zone and the East African rift system, appear as strong drivers of Synodontis diversification and evolution.

Aphyosemion pamaense, a new killifish species (Cyprinodontiformes: Nothobranchiidae) from Cameroon.

Aphyosemion panaense sp. nov. is described from the Pama River, a small tributary of the Nyong, in the surroundings of Pama, Cameroon. It belongs to the subgenus Chromaphyosenion Radda, 1971 and is distinguished from its relatives by a unique/diagnostic combination of characters: orange unpaired fins, an anal fin without spots, an orange throat and purple to blue-grey flanks. The new species is also genetically differentiated from all the other Chromaphyosemion species as revealed by mtDNA (cytochrome b) analysis and characterised by a unique karyotype showing tentative sex chromosomes with 2n=35 chromosomes in males versus 2n=36 in females.

Description of a new species from Clarias maclareni and phylogenetical analysis of Quadriacanthus (Monogenea, Dactylogyridae) species transfers between clariid and non-clariid fish hosts in Cameroon.

Recently in Cameroon, two species belonging to Quadriacanthus: Q. anaspidoglanii Akoumba, Tombi & Bilong Bilong, 2017 and Q. euzeti Nack, Pariselle & Bilong Bilong, 2016 have been recorded on gill filaments of Notoglanidium macrostoma (Siluriformes, Claroteidae) in the Memou'ou River (Nyong Basin) and Papyrocranus afer (Osteoglossiformes, Notopteridae) in Lake Ossa, respectively. These records have been considered the result of lateral transfers from Clariidae to a Claroteidae host for the first case (parasitism of N. macrostoma by Q. anaspidoglanii) and from Clariidae or Bagridae to a Notopteridae host for the second (parasitism of P. afer by Q. euzeti). In this paper, the investigation of interspecific relationships among Quadriacanthus spp. parasitizing Clariidae, Bagridae, Claroteidae and Notopteridae in Cameroon resulted in the record of Q. anaspidoglanii from N. macrostoma, Q. euzeti from P. afer, a new record of Q. levequei Birgi, 1988 from Clarias jaensis in the Nyong River, and the description of Q. barombiensis n. sp. from Clarias maclareni in Lake Barombi Mbo. The newly identified species is characterized by having an accessory piece ending in one small hook and the median expansion of its dorsal bar with two filaments. Phylogenetic analysis based on 28S rDNA sequences confirms that the Quadriacanthus spp. parasitizing gill filaments of non-clariid hosts in Cameroon originate from lateral transfers from clariid fishes, and that Clariidae are ancestral hosts of these monogenean species.

Title: Description d'une nouvelle espèce parasite de Clarias maclareni et analyse phylogénétique des transferts d'espèces de Quadriacanthus (Monogenea, Dactylogyridae) entre poissons hôtes clariidés et non clariidés au Cameroun. Abstract: Récemment au Cameroun deux espèces appartenant à Quadriacanthus : Q. anaspidoglanii Akoumba, Tombi & Bilong Bilong, 2017 et Q. euzeti Nack, Pariselle & Bilong Bilong, 2016 ont été signalées, respectivement sur les filaments branchiaux de Notoglanidium macrostoma (Siluriformes, Claroteidae), dans la rivière Memou'ou (bassin du Nyong) et Papyrocranus afer (Osteoglossiformes, Notopteridae) dans le lac Ossa. Ces signalements ont été considérés comme le résultat de transferts latéraux de Clariidae vers un hôte Claroteidae pour le premier cas (parasitisme de N. macrostoma par Q. anaspidoglanii) et d'un Clariidae ou Bagridae vers un hôte Notopteridae pour le second (parasitisme de P. afer par Q. euzeti). Dans cet article, l'étude des relations interspécifiques entre Quadriacanthus spp. parasitant des Clariidae, Bagridae, Claroteidae et Notopteridae au Cameroun a abouti au signalement de Q. anaspidoglanii chez N. macrostoma, Q. euzeti chez P. afer, un nouveau signalement de Q. levequei Birgi, 1988 chez Clarias jaensis dans le fleuve Nyong, et à la description de Q. barombiensis n. sp. chez Clarias maclareni dans le lac Barombi Mbo. L'espèce nouvellement identifiée se caractérise par la présence d'une pièce accessoire se terminant par un petit crochet et l'expansion médiane de sa barre dorsale avec deux filaments. L'analyse phylogénétique basée sur les séquences d'ADNr 28S confirme que les Quadriacanthus spp. des filaments branchiaux parasitant des hôtes non-clariidés au Cameroun proviennent de transferts latéraux de poissons clariidés, et que les Clariidae sont bien les hôtes ancestraux de ces espèces de monogènes.

Parasites of Moroccan desert Coptodon guineensis (Pisces, Cichlidae): transition and resilience in a simplified hypersaline ecosystem.

Sebkha Imlili (Atlantic Sahara) is a salt flat with over 160 permanent holes of hypersaline water generated in the Holocene and inhabited by euryhaline organisms that are considered to be relics of the past, including the cichlid fish Coptodon guineensis. We surveyed the fish parasites four times over one year, to i) identify the parasites, and ii) determine possible seasonality in infection patterns. Over 60% of the fish were infected by one to three helminths: an acanthocephalan in the intestine and two digenean metacercariae in the kidney, spleen, liver, muscle, and mesenteries. The acanthocephalan Acanthogyrus (Acanthosentis) cf. tilapiae was identified morphologically and molecularly; only one digenean (the heterophyid Pygidiopsis genata) could be identified molecularly. Both identified parasites were present throughout the sampling periods; the unidentified metacercariae were present only in summer and fall. Mean intensities, but not prevalence of infection by the acanthocephalan, reflected a biannual pattern of transmission. Infection accrued with fish size, possibly due to cannibalism. Because the water holes include only a few invertebrates, the intermediate hosts of these parasites can be inferred to be the gastropod Ecrobia ventrosa for the digeneans and either the copepod Cletocamtpus retrogressus or the ostracod Cyprideis torosa for the acanthocephalan. This ecosystem appears stable and provides a window into the past, as the acanthocephalan likely switched from freshwater tilapia to C. guineensis when the Sebkha formed. However, this is a vulnerable environment where the survival of these parasites depends on interactions maintained among only very few hosts.

Title: Parasites de Coptodon guineensis (Pisces, Cichlidae) du désert marocain : transition et résilience dans un écosystème hypersalin simplifié. Abstract: La Sebkha d'Imlili est une sebkha (étendue désertique sableuse et salée) dans le Sahara Atlantique caractérisée par la présence de plus de 160 poches permanentes d'eau hypersaline qui sont apparues à l'Holocène et qui sont habitées par des organismes considérés comme des reliques du passé, dont un poisson cichlidé, Coptodon guineensis. Nous avons fait l'inventaire des parasites de ce poisson au cours des quatre saisons d'une année pour 1) identifier les parasites et 2) déterminer une éventuelle transmission saisonnière. Plus de 60 % des poissons étaient infestés par un à trois helminthes : un Acanthocéphale dans l'intestin et des métacercaires de deux espèces de Digène dans le rein, la rate, les muscles et le mésentère. L'Acanthocéphale Acanthogyrus (Acanthosentis) cf. tilapiae a été identifié morphologiquement et génétiquement mais seul un des deux Digènes (l'hétérophyidé Pygidiopsis genata) a pu être identifié par séquençage. Ces deux parasites étaient présents à chaque période d'étude, mais la métacercaire non identifiée était présente seulement en été et en automne. L'intensité moyenne de l'infestation par l'Acanthocéphale, mais pas sa prévalence, reflète une transmission biannuelle. L'infestation augmente avec la taille du poisson, peut-être à cause du cannibalisme. L'identité des hôtes intermédiaires de ces parasites peut être avancée parce que cet écosystème est simplifié et inclut seulement quelques invertébrés : pour les Digènes, le Gastéropode Ecrobia ventrosa, et pour l'Acanthocéphale, le Copépode Cletocamtpus retrogressus ou l'Ostracode Cyprideis torosa. Cet écosystème apparait stable et offre une vue sur le passé étant donné que l'Acanthocéphale a sans doute été transféré d'un tilapia d'eau douce quand la sebkha s'est formée. Cependant, c'est un environnement vulnérable où la survie de ces parasites dépend d'interactions entre très peu d'espèces hôtes.

Disentangling the taxonomy of the subfamily Rasborinae (Cypriniformes, Danionidae) in Sundaland using DNA barcodes.

Sundaland constitutes one of the largest and most threatened biodiversity hotspots; however, our understanding of its biodiversity is afflicted by knowledge gaps in taxonomy and distribution patterns. The subfamily Rasborinae is the most diversified group of freshwater fishes in Sundaland. Uncertainties in their taxonomy and systematics have constrained its use as a model in evolutionary studies. Here, we established a DNA barcode reference library of the Rasborinae in Sundaland to examine species boundaries and range distributions through DNA-based species delimitation methods. A checklist of the Rasborinae of Sundaland was compiled based on online catalogs and used to estimate the taxonomic coverage of the present study. We generated a total of 991 DNA barcodes from 189 sampling sites in Sundaland. Together with 106 previously published sequences, we subsequently assembled a reference library of 1097 sequences that covers 65 taxa, including 61 of the 79 known Rasborinae species of Sundaland. Our library indicates that Rasborinae species are defined by distinct molecular lineages that are captured by species delimitation methods. A large overlap between intraspecific and interspecific genetic distance is observed that can be explained by the large amounts of cryptic diversity as evidenced by the 166 Operational Taxonomic Units detected. Implications for the evolutionary dynamics of species diversification are discussed.

One-locus-several-primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies.

In diet metabarcoding analyses, insufficient taxonomic coverage of PCR primer sets generates false negatives that may dramatically distort biodiversity estimates. In this paper, we investigated the taxonomic coverage and complementarity of three cytochrome c oxidase subunit I gene (COI) primer sets based on in silico analyses and we conducted an in vivo evaluation using fecal and spider web samples from different invertivores, environments, and geographic locations. Our results underline the lack of predictability of both the coverage and complementarity of individual primer sets: (a) sharp discrepancies exist observed between in silico and in vivo analyses (to the detriment of in silico analyses); (b) both coverage and complementarity depend greatly on the predator and on the taxonomic level at which preys are considered; (c) primer sets' complementarity is the greatest at fine taxonomic levels (molecular operational taxonomic units [MOTUs] and variants). We then formalized the "one-locus-several-primer-sets" (OLSP) strategy, that is, the use of several primer sets that target the same locus (here the first part of the COI gene) and the same group of taxa (here invertebrates). The proximal aim of the OLSP strategy is to minimize false negatives by increasing total coverage through multiple primer sets. We illustrate that the OLSP strategy is especially relevant from this perspective since distinct variants within the same MOTUs were not equally detected across all primer sets. Furthermore, the OLSP strategy produces largely overlapping and comparable sequences, which cannot be achieved when targeting different loci. This facilitates the use of haplotypic diversity information contained within metabarcoding datasets, for example, for phylogeography and finer analyses of prey-predator interactions.

A euryhaline fish, lost in the desert: The unexpected metapopulation structure of Coptodon guineensis (Günther, 1862) in the Sebkha of Imlili.

Euryhaline Cichlid fish of the species Coptodon guineensis are present in different water holes situated in a dried depression in the desert in the extreme South of Morocco, the Sebkha of Imlili. A genetic survey of this population, using complete sequences of the ND2 gene (mtDNA) and sixteen microsatellite loci, revealed that the fish in the sebkha did not form a single population, but rather a metapopulation. This metapopulational structure may be regarded as good news from the point of view of the conservation of fish in the sebkha. Although small individual populations may have short, finite life spans, the metapopulation as a whole is more stable, because immigrants from one population are likely to re-colonize the habitat, left open by the extinction of another.

A phylogeny of Cichlidogyrus spp. (Monogenea, Dactylogyridea) clarifies a host-switch between fish families and reveals an adaptive component to attachment organ morphology of this parasite genus.

BACKGROUND: Parasite switches to new host species are of fundamental scientific interest and may be considered an important speciation mechanism. For numerous monogenean fish parasites, infecting different hosts is associated with morphological adaptations, in particular of the attachment organ (haptor). However, haptoral morphology in Cichlidogyrus spp. (Monogenea, Dactylogyridea), parasites of African cichlids, has been mainly linked to phylogenetic rather than to host constraints. Here we determined the position of Cichlidogyrus amieti, a parasite of species of Aphyosemion (Cyprinodontiformes, Nothobranchiidae) in the phylogeny of its congeners in order to infer its origin and assess the morphological changes associated with host-switching events. METHODS: The DNA of specimens of C. amieti isolated from Aphyosemion cameronense in Cameroon was sequenced and analyzed together with that of Cichlidogyrus spp. from cichlid hosts. In order to highlight the influence of the lateral transfer of C. amieti on the haptoral sclerotised parts we performed a Principal Component Analysis (PCA) to compare the attachment organ structure of C. amieti to that of congeners infecting cichlids. RESULTS: Cichlidogyrus amieti was found to be nested within a strongly supported clade of species described from Hemichromis spp. (i.e. C. longicirrus and C. dracolemma). This clade is located at a derived position of the tree, suggesting that C. amieti transferred from cichlids to Cyprinodontiformes and not inversely. The morphological similarity between features of their copulatory organs suggested that C. amieti shares a recent ancestor with C. dracolemma. It also indicates that in this case, these organs do not seem subjected to strong divergent selection pressure. On the other hand, there are substantial differences in haptoral morphology between C. amieti and all of its closely related congeners described from Hemichromis spp.. CONCLUSIONS: Our study provides new evidence supporting the hypothesis of the adaptive nature of haptor morphology. It demonstrates this adaptive component for the first time within Cichlidogyrus, the attachment organs of which were usually considered to be mainly phylogenetically constrained.

An important natural genetic resource of Oreochromis niloticus (Linnaeus, 1758) threatened by aquaculture activities in Loboi drainage, Kenya.

The need to improve food security in Africa through culture of tilapias has led to transfer of different species from their natural ranges causing negative impacts on wild fish genetic resources. Loboi swamp in Kenya is fed by three hot springs: Lake Bogoria Hotel, Chelaba and Turtle Springs, hosting natural populations of Oreochromis niloticus. The present study aimed at better genetic characterization of these threatened populations. Partial mtDNA sequences of the D-loop region and variations at 16 microsatellite loci were assessed in the three hot spring populations and compared with three other natural populations of O. niloticus in the region. Results obtained indicated that the hot spring populations had mitochondrial and nuclear genetic variability similar to or higher than the large closely related populations. This may be attributed to the perennial nature of the hot springs, which do not depend on rainfall but rather receive permanent water supply from deep aquifers. The study also revealed that gene flow between the three different hot spring populations was sufficiently low thus allowing their differentiation. This differentiation was unexpected considering the very close proximity of the springs to each other. It is possible that the swamp creates a barrier to free movement of fish from one spring to the other thereby diminishing gene flow. Finally, the most surprising and worrying results were that the three hot spring populations are introgressed by mtDNA genes of O. leucostictus, while microsatellite analysis suggested that some nuclear genes may also have crossed the species barrier. It is very likely that the recent intensification of aquaculture activities in the Loboi drainage may be responsible for these introgressions. Taking into account the importance of these new genetic resources, protection and management actions of the Loboi swamp should be accorded top priority to prevent the loss of these spring populations.

Local adaptation to altitude underlies divergent thermal physiology in tropical killifishes of the genus Aphyosemion.

In watersheds of equatorial West Africa, monophyletic groups of killifish species (genus Aphyosemion) occur in discrete altitudinal ranges, low altitude species (LA, sea level to ∼350 m) or high altitude species (HA, 350 to 900 m). We investigated the hypothesis that local adaptation to altitude by the LA and HA species would be revealed as divergent effects of temperature on their physiological energetics. Two species from each group (mass ∼350 mg) were acclimated to 19, 25 and 28°C, with 19 and 28°C estimated to be outside the thermal envelope for LA or HA, respectively, in the wild. Wild-caught animals (F0 generation) were compared with animals raised in captivity at 25°C (F1 generation) to investigate the contribution of adaptation versus plasticity. Temperature significantly increased routine metabolic rate in all groups and generations. However, LA and HA species differed in the effects of temperature on their ability to process a meal. At 25°C, the specific dynamic action (SDA) response was completed within 8 h in all groups, but acclimation to temperatures beyond the thermal envelope caused profound declines in SDA performance. At 19°C, the LA required ∼14 h to complete the SDA, whereas the HA required only ∼7 h. The opposite effect was observed at 28°C. This effect was evident in both F0 and F1. Reaction norms for effects of temperature on SDA therefore revealed a trade-off, with superior performance at warmer temperatures by LA being associated with inferior performance at cooler temperatures, and vice-versa in HA. The data indicate that divergent physiological responses to temperature in the LA and HA species reflect local adaptation to the thermal regime in their habitat, and that local adaptation to one thermal environment trades off against performance in another.

Functional microsatellite and possible selective sweep in natural populations of the black-chinned tilapia Sarotherodon melanotheron (Teleostei, Cichlidae).

The Prolactin I (PrlI) gene is a key locus involved in fish osmotic regulation. Two microsatellites, PrlI GT and PrlI AC, are present in the promoter region of this gene in tilapias. One of these microsatellite is associated to PrlI gene expression and growth rate. Aquaria reared individuals homozygous for long microsatellite alleles at the PrlI AC locus expressed less PrlI in fresh water than fishes with other genotypes. To assess the occurrence of selection acting on these microsatellites we carried out a survey of their variability compared with four others microsatellites in natural populations. Samples of two tilapia species were studied, Oreochromis niloticus (6 samples) a typically freshwater species inhabiting osmotically stable environments and Sarotherodon melanotheron (5 samples) a brackish water species obliged and able to adapt very rapidly to any salinity changes. For both species the different populations studied exhibited a high amount of differentiation (all F(st) value were statistically significant) at every loci. Only one locus, PrlI AC, was monomorphic for the same allele in all S. melanotheron populations. We have hypothesized that this outlier locus with its unique allele could have experienced a selective sweep that took place in the early stages of the species origin. S. melanotheron represents an example of adaptation (to fluctuant salinity environment) acting indirectly on gene product through its promoter.