Pebbled places preferred by people and pipefish in a World Heritage protected area

Although the ecological impacts of recreational activities in clear tropical streams are occasionally acknowledged and addressed, frequently they remain unmanaged, despite the fact that such streams are highly sought-after destinations for leisure pursuits. Here, we provide a case study on the ecological characteristics of the Indo-Pacific freshwater pipefish Microphis leiaspis Bleeker, 1854, which is a habitat specialist with little available information aside from its reproductive biology and the downstream migration patterns of its larvae. Drawing from our collective experiences, we describe the distribution and habitat of Microphis leiaspis and examine the potential impacts of various small-scale human activities on its livelihood, including those occur- ring within protected areas. In particular, we document incidental observations of human disturbances to adult Microphis leiaspis habitat in clear freshwater streams located within the Australian Wet Tropics (AWT) World Heritage Area. Using these observations as a foundation, we conceptualize human interactions with this species in the AWT streams and more broadly across the tropical Indo-Pacific Ocean. Microphis leiaspis occurs in the lower-mid course of short-steep-coastal-streams, in association with pebble fields, where it feeds on microscop- ic benthic invertebrates. We observed three distinct human behaviours in the pipefish habitat within the AWT, including stone-stacking, the construction of boulder-cobble dams, and stone-skimming. Additionally, we report on other small-scale human activities that may potentially impact this pipefish species in streams across Pacific Island nations and select coastal regions of continents. Our recommendation is to promote a ‘leave no trace’ approach to the public, which can be effectively communicated by key individuals such as indigenous custodi- ans, national park managers, locals, and tourism operators. This approach aims to minimize rock movement by people, thereby aiding in the protection of diadromous pipefish and other aquatic species residing in short-steepcoastal-streams

Biodiversité, dispersion et histoire évolutive des syngnathidae (Teleostei) insulaires de la région Indo-Pacifique

The Syngnathidae family (seahorses, sea dragons and pipefishes) is represented by more than 300 species included in about fifty genera. The vast majority is distributed in tropical and temperate marine coastal waters. However, about thirty of them, are found in freshwater and mainly inhabit the rivers of the tropical islands of the Indo-Pacific region. These species face many anthropogenic pressures and are considered by some authors as the most threatened species of the family. Since their description, freshwater pipefish of the Nerophinae sub-family have known a complex taxonomic and nomenclatural history, the status of each species and genera has changed many times. Their taxonomy, only based on morphological criteria, was therefore imprecise and hindered any research on these organisms. The taxonomic revision by an integrative approach (morphological, molecular, geographical and ecological) of the freshwater species of the Nerophinae sub-family, previously distributed in 6 genera, has therefore allowed to group the thirty species within the same genus, Microphis Kaup, 1853. This work, led to recognize 31 valid species in the genus Microphis, including 2 new species as well as 2 revalidations of species. Once the taxonomy was clarified, we were able to study the ecology and the life cycle of several species, chosen for their more or less wide distributions: Microphis brachyurus (Bleeker, 1854) distributed from Sri Lanka to French Polynesia, Microphis nicoleae Haÿ et al., 2023 distributed from Papua New Guinae to Solomon Islands and Microphis cruentus Dawson & Fourmanoir, 1981, endemic to New-Caledonia. Microchemical analysis of their otoliths, using synchrotron-based scanning X-ray fluorescence confirmed for the first time an amphidromous life cycle for M. brachyurus and M. nicoleae and a facultative amphidromy for M. cruentus. In addition, hyper fine resolution provided by synchrotron-based methods allowed to explore in detail the complexity of otolith chemistry with implications for otolith sciences in general. Finally, with the preliminary phylogeographic analyzes of the species M. brachyurus and M. retzii, we were able to observe: (i) a structure into two distinct populations for M. brachyurus and (ii) a species complex for M. retzii in Southeast Asia. The simultaneous study of several species with close or even sympatric distributions is essential because although the biogeographical events they undergo are similar, the responses to these constraints vary. All these results of the PhD, with the taxonomic revision of genera and species, the understanding of their ecology and their dispersal are therefore of paramount importance for the conservation and protection of freshwater pipefish. They constitute a first essential basis for the implementation of management and conservation measures at local and regional scales.La famille des Syngnathidae (hippocampes, dragons des mers et syngnathes) est représentée par plus de 300 espèces reparties dans une cinquantaine de genres. La grande majorité est distribuée dans les eaux côtières marines tant tropicales que tempérées. Cependant, une trentaine d’entre elles, sont dulçaquicoles et peuplent les rivières des îles tropicales de la région Indo-Pacifique. Ces espèces font face à de nombreuses pressions anthropiques et sont d’ailleurs considérées par certains auteurs comme les espèces les plus menacées de la famille. Depuis leur description, les syngnathes d’eau douce de la sous famille des Nerophinae ont connu une histoire taxonomique et nomenclaturale complexe, l’appartenance aux différents genres et leur validité ayant changé de nombreuses fois au cours du temps. Leur taxonomie, basée uniquement sur des caractères morphologiques était donc imprécise et constituait un frein à toutes recherches sur ces organismes. La révision taxonomique par une approche intégrative (morphologique, moléculaire, géographique et écologique) des espèces dulçaquicoles de la sous-famille des Nerophinae, préalablement distribuées dans six genres, a permis de replacer la trentaine d’espèces au sein du même genre, Microphis Kaup, 1853. Ces travaux ont permis de valider 31 espèces dans le genre Microphis, incluant la description de deux nouvelles espèces et la revalidation de deux autres. Une fois la taxonomie clarifiée, nous avons pu étudier l’écologie et du cycle de vie de plusieurs espèces, choisies pour leurs répartitions géographiques plus ou moins larges : Microphis brachyurus (Bleeker, 1854) présente du Sri Lanka à la Polynésie française, Microphis nicoleae Haÿ et al., 2023 présente en Papouasie-Nouvelle-Guinée et aux îles Salomon et Microphis cruentus Dawson & Fourmanoir, 1981, endémique de Nouvelle-Calédonie. La microanalyse chimique de leurs otolithes, à l’aide du rayonnement synchrotron avec la fluorescence aux rayons X a confirmé un cycle de vie amphidrome pour M. brachyurus et M. nicoleae et une amphidromie facultative pour M. cruentus. De plus, la résolution très fine apporté par le rayonnement synchrotron a permis d’explorer plus en détail la complexité de la chimie de l’otolithe avec des implications dans le domaine de l’otolithométrie de manière générale. Enfin, avec les analyses phylogéographiques préliminaires des espèces M. brachyurus et M. retzii, nous avons pu constater : (i) une structuration en deux populations distinctes pour M. brachyurus et (ii) un complexe d’espèce pour M. retzii en Asie du Sud-Est. L’étude simultanée de plusieurs espèces aux aires de répartitions proches, voire même sympatriques est primordiale car bien que les évènements biogéographiques qu’elles subissent soient similaires, leurs réponses face à ces contraintes varient. L’ensemble des résultats de cette thèse avec la délimitation correcte des genres et des espèces, la compréhension de leur écologie et de leur dispersion sont donc d’une importance capitale pour la conservation et la protection des syngnathes dulçaquicoles. Ils constituent une première base essentielle pour la mise en place de plans de gestion et de conservation à une échelle locale mais aussi régionale

Biodiversité, dispersion et histoire évolutive des syngnathidae (Teleostei) insulaires de la région Indo-Pacifique

The Syngnathidae family (seahorses, sea dragons and pipefishes) is represented by more than 300 species included in about fifty genera. The vast majority is distributed in tropical and temperate marine coastal waters. However, about thirty of them, are found in freshwater and mainly inhabit the rivers of the tropical islands of the Indo-Pacific region. These species face many anthropogenic pressures and are considered by some authors as the most threatened species of the family. Since their description, freshwater pipefish of the Nerophinae sub-family have known a complex taxonomic and nomenclatural history, the status of each species and genera has changed many times. Their taxonomy, only based on morphological criteria, was therefore imprecise and hindered any research on these organisms. The taxonomic revision by an integrative approach (morphological, molecular, geographical and ecological) of the freshwater species of the Nerophinae sub-family, previously distributed in 6 genera, has therefore allowed to group the thirty species within the same genus, Microphis Kaup, 1853. This work, led to recognize 31 valid species in the genus Microphis, including 2 new species as well as 2 revalidations of species. Once the taxonomy was clarified, we were able to study the ecology and the life cycle of several species, chosen for their more or less wide distributions: Microphis brachyurus (Bleeker, 1854) distributed from Sri Lanka to French Polynesia, Microphis nicoleae Haÿ et al., 2023 distributed from Papua New Guinae to Solomon Islands and Microphis cruentus Dawson & Fourmanoir, 1981, endemic to New-Caledonia. Microchemical analysis of their otoliths, using synchrotron-based scanning X-ray fluorescence confirmed for the first time an amphidromous life cycle for M. brachyurus and M. nicoleae and a facultative amphidromy for M. cruentus. In addition, hyper fine resolution provided by synchrotron-based methods allowed to explore in detail the complexity of otolith chemistry with implications for otolith sciences in general. Finally, with the preliminary phylogeographic analyzes of the species M. brachyurus and M. retzii, we were able to observe: (i) a structure into two distinct populations for M. brachyurus and (ii) a species complex for M. retzii in Southeast Asia. The simultaneous study of several species with close or even sympatric distributions is essential because although the biogeographical events they undergo are similar, the responses to these constraints vary. All these results of the PhD, with the taxonomic revision of genera and species, the understanding of their ecology and their dispersal are therefore of paramount importance for the conservation and protection of freshwater pipefish. They constitute a first essential basis for the implementation of management and conservation measures at local and regional scales.La famille des Syngnathidae (hippocampes, dragons des mers et syngnathes) est représentée par plus de 300 espèces reparties dans une cinquantaine de genres. La grande majorité est distribuée dans les eaux côtières marines tant tropicales que tempérées. Cependant, une trentaine d’entre elles, sont dulçaquicoles et peuplent les rivières des îles tropicales de la région Indo-Pacifique. Ces espèces font face à de nombreuses pressions anthropiques et sont d’ailleurs considérées par certains auteurs comme les espèces les plus menacées de la famille. Depuis leur description, les syngnathes d’eau douce de la sous famille des Nerophinae ont connu une histoire taxonomique et nomenclaturale complexe, l’appartenance aux différents genres et leur validité ayant changé de nombreuses fois au cours du temps. Leur taxonomie, basée uniquement sur des caractères morphologiques était donc imprécise et constituait un frein à toutes recherches sur ces organismes. La révision taxonomique par une approche intégrative (morphologique, moléculaire, géographique et écologique) des espèces dulçaquicoles de la sous-famille des Nerophinae, préalablement distribuées dans six genres, a permis de replacer la trentaine d’espèces au sein du même genre, Microphis Kaup, 1853. Ces travaux ont permis de valider 31 espèces dans le genre Microphis, incluant la description de deux nouvelles espèces et la revalidation de deux autres. Une fois la taxonomie clarifiée, nous avons pu étudier l’écologie et du cycle de vie de plusieurs espèces, choisies pour leurs répartitions géographiques plus ou moins larges : Microphis brachyurus (Bleeker, 1854) présente du Sri Lanka à la Polynésie française, Microphis nicoleae Haÿ et al., 2023 présente en Papouasie-Nouvelle-Guinée et aux îles Salomon et Microphis cruentus Dawson & Fourmanoir, 1981, endémique de Nouvelle-Calédonie. La microanalyse chimique de leurs otolithes, à l’aide du rayonnement synchrotron avec la fluorescence aux rayons X a confirmé un cycle de vie amphidrome pour M. brachyurus et M. nicoleae et une amphidromie facultative pour M. cruentus. De plus, la résolution très fine apporté par le rayonnement synchrotron a permis d’explorer plus en détail la complexité de la chimie de l’otolithe avec des implications dans le domaine de l’otolithométrie de manière générale. Enfin, avec les analyses phylogéographiques préliminaires des espèces M. brachyurus et M. retzii, nous avons pu constater : (i) une structuration en deux populations distinctes pour M. brachyurus et (ii) un complexe d’espèce pour M. retzii en Asie du Sud-Est. L’étude simultanée de plusieurs espèces aux aires de répartitions proches, voire même sympatriques est primordiale car bien que les évènements biogéographiques qu’elles subissent soient similaires, leurs réponses face à ces contraintes varient. L’ensemble des résultats de cette thèse avec la délimitation correcte des genres et des espèces, la compréhension de leur écologie et de leur dispersion sont donc d’une importance capitale pour la conservation et la protection des syngnathes dulçaquicoles. Ils constituent une première base essentielle pour la mise en place de plans de gestion et de conservation à une échelle locale mais aussi régionale

Une nouvelle espèce de Coelonotus (teleostei : syngnathidae) d’eau douce de Papouasie-nouvelle- Guinée.

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Revision of the Genus Rhyacichthys Using Integrative Taxonomy

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Premier signalement d’Hippichthys albomaculosus Jen- kins & Mailautoka, 2010 (syngnathidae) en Nouvelle-Calédonie.

International audienceThree specimens of Hippichthys albomaculosus Jenkins and Mailautoka, 2010, only known from Fiji, were recently collected from the North Province of New Caledonia. Morphomeristic values confirm the identity of specimens. This study constitutes the first record of this species in New Caledonia and outside of its type locality.Trois spécimens d'Hippichthys albomaculosus Jenkins & Mailautoka, 2010, connu uniquement des Fidji, ont été récemment collectés dans la province Nord de la Nouvelle-Calédonie. Les valeurs morpho-méristiques confirment l'identité des spécimens. Cette étude constitue le premier signalement de cette espèce en Nouvelle-Calédonie et hors de sa localité type

Multiple introduction pathways of non-native Phoxinus minnows (Teleostei: Leuciscidae) in Corsica revealed by its hidden diversity and their parasites

International audienceAbstract The introduction of freshwater fish species is a leading cause of aquatic biodiversity erosion and can spread parasites to native populations. Hidden diversity evidenced by recent taxonomic revisions can add further complexity to the issue by rendering biological assessment data incomplete. The Eurasian minnows Phoxinus are one such example of cryptic diversity, with several described species being invasive. Current non-native fish populations in the small Mediterranean island of Corsica (France) are the result of successive waves of introductions, including several Phoxinus species. This study aims at determining which Phoxinus species were introduced to Corsica using the cytochrome oxidase subunit I barcoding marker, reconstructing their introduction routes and examining their parasite communities. The study found four species in Corsica: Phoxinus phoxinus and Phoxinus csikii mainly in the northernmost studied drainage basin and Phoxinus dragarum and Phoxinus septimaniae in the Tavignano drainage basin. P. phoxinus and P. csikii were most likely introduced through a live bait wholesaler while P. dragarum and P. septimaniae were probably introduced by recreational anglers bringing their bait from continental France. The molecular study of their Gyrodactylus (Platyhelminthes: Monogenea) parasites with the ITS marker allowed us to hypothesize inter-drainage basin secondary introduction routes for P. phoxinus and P. dragarum . In several sampling sites, Phoxinus minnows had black spot disease caused by encysted metacercariae of Digenea, likely Posthodiplostomum cuticola . These parasites were also found on the brown trout Salmo trutta in a locality where this patrimonial species co-occurs with Phoxinus minnows. Barcoding should be used in fish communities monitoring to help to accurately identify cryptic species

Needlepoint non-destructive internal tissue sampling for precious fish specimens

International audienceIn this paper, we describe a new non-damaging internal tissue sampling method for preserved collection of teleostean specimens. It was tested on freshwater pipefish, as external tissue sampling is made difficult by the lack of scales, the lack of pelvic fins, the atrophy of pectoral and anal fins. The internal tissue is detached by scratching the inside of the urogenital papilla with a fine metallic probe. 95% ethanol is injected using a fine syringe, and then sucked back into the syringe with the detached tissue. This protocol has been tested on 6 specimens from 5 species of pipefish. For each specimen DNA was extracted from the internal tissue, a caudal fin clip, and when possible, eggs sampled from the male brooding pouch. Partial Cytochrome c oxydase I (COI) was amplified and sequenced. For each specimen, the 582 bp long sequences obtained from the internal tissue, the fin clip and the eggs were identical. These results validate this non-damaging internal tissue sampling method, which leaves absolutely no trace on the specimen. Although this method was developed on pipefish, it could be applied to other teleostean, even precious museum collection specimens such as type specimens. The aim of this paper, using the example of freshwater pipefish, is to present this method, which aims at preserving precious collection specimens while still valorising them

Unmasking pipefish otolith using synchrotron-based scanning X-ray fluorescence

Abstract Scientists use otoliths to trace fish life history, especially fish migrations. Otoliths incorporate signatures of individual growth and environmental use. For many species, distinct increment patterns in the otolith are difficult to discern; thus, questions remain about crucial life history information. To unravel the history of such species, we use synchrotron-based scanning X-ray fluorescence. It allows the mapping of elements on the entire otolith at a high spatial resolution. It gives access to precise fish migration history by tagging landmark signature for environmental transition and it also characterises localised growth processes at a mineral level. Freshwater pipefish, which are of conservation concern, have otoliths that are small and fragile. Growth increments are impossible to identify and count; therefore, there is a major lack of knowledge about their life history. We confirm for the first time, by mapping strontium that the two tropical pipefish species studied are diadromous (transition freshwater/marine/freshwater). Mapping of other elements uncovered the existence of different migratory routes during the marine phase. Another major breakthrough is that we can chemically count growth increments solely based on sulphur signal as it is implicated in biomineralization processes. This novel method circumvents reader bias issues and enables age estimation even for otoliths with seemingly untraceable increments. The high spatial resolution elemental mapping methods push back limits of studies on life traits or stock characterisation