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All issues No 427 (2026) Knowl. Manag. Aquat. Ecosyst., 427 (2026) 4 Full HTML
Issue
Knowl. Manag. Aquat. Ecosyst.
Number 427, 2026
Multidisciplinary solutions for conservation
Article Number 4
Number of page(s) 10
DOI https://doi.org/10.1051/kmae/2025032
Published online 02 February 2026

© V. de Mazancourt et al., Published by EDP Sciences 2026

Licence Creative CommonsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License CC-BY-ND (https://creativecommons.org/licenses/by-nd/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. If you remix, transform, or build upon the material, you may not distribute the modified material.

1 Introduction

Freshwater ecosystems are experiencing an unprecedented biodiversity crisis, with species disappearing at a rate far exceeding that of terrestrial and marine environments (Sayer et al., 2025). Habitat destruction, pollution, climate change, and the introduction of invasive species are among the major drivers of this decline. Dams and water diversions disrupt hydrological connectivity, while deforestation and agricultural expansion degrade water quality (Dudgeon, 2019). Freshwater species, particularly those with restricted ranges, are highly vulnerable to these disturbances. Among the most affected are insular freshwater taxa, whose small, isolated populations are exceptionally sensitive to habitat alterations and biological invasions (Dudgeon et al., 2006; Strayer and Dudgeon, 2010).

The Mascarene Archipelago, located east of Madagascar in the Indian Ocean, comprises Réunion Island (a French overseas department) and the sovereign state of Mauritius, which includes the islands of Mauritius and Rodrigues. Like many tropical oceanic islands, the Mascarenes host a highly endemic freshwater fauna, shaped by long-term isolation and limited colonization events (Keith et al., 2006). However, island species are particularly susceptible to anthropogenic pressures, and the Mascarenes have already witnessed the loss of several iconic endemic species, such as the dodo (Raphus cucullatus (Linnaeus, 1758)) in Mauritius and the Réunion giant tortoise (Cylindraspis indica (Schneider, 1783)) (Fernández-Palacios et al., 2021). The next potential addition to this list of extinct species may be Macrobrachium hirtimanus (Olivier, 1811), a freshwater shrimp endemic to the Mascarene Islands notable for its unique morphology among regional congeners, particularly its large, spine-covered chelae.

Originally described as Palaemon hirtimanus by Olivier (1811) from specimens collected during the Baudin expedition, the species was later transferred to the genus Macrobrachium by Holthuis (1950). Its distribution was initially thought to extend to the Malay Archipelago due to confusion with M. lepidactyloides (De Man, 1892), but Holthuis (1952) later reinstated it as a distinct species restricted to the Mascarenes. Historical records indicate that M. hirtimanus was already rare by the late 20th century. Starmühlner (1977, 1979) failed to report it during his hydrobiological surveys, and Kiener and Duchochois (1981) collected specimens from only four rivers of Réunion Island in 1980. The species has not been recorded since these observations, while another species, M. lepidactylus (Hilgendorf, 1879), was first reported in the region in the 1990s (Keith and Vigneux, 2000).

The disappearance of M. hirtimanus aligns with the introduction or expansion of M. lepidactylus, an African/Malagasy species that occupies similar habitats. The two species have never been documented in synchronous sympatry, raising the question of whether M. hirtimanus was competitively displaced. Invasive Macrobrachium species have been implicated in the decline of native freshwater crustaceans elsewhere, such as Macrobrachium lar in Pacific islands (De Grave et al., 2015). Additionally, habitat destruction and poaching have likely contributed to the decline of M. hirtimanus, as observed in other insular freshwater decapods (Keith et al., 1999).

Determining the extinction status of M. hirtimanus is crucial for conservation planning. If the species persists in undetected populations, targeted conservation actions could be implemented, including habitat protection and control of invasive species. Conversely, confirming its extinction would reinforce the need for stricter biodiversity management policies in the Mascarenes, particularly regarding invasive species monitoring. Advances in environmental DNA (eDNA) analysis provide an opportunity to detect rare or cryptic species that elude conventional sampling methods, as demonstrated in recent rediscoveries of presumed-extinct amphibians (Lopes et al., 2021). The generation of DNA reference sequences from museum specimens of M. hirtimanus could thus facilitate future eDNA surveys, improving the capacity to monitor freshwater biodiversity in the Mascarenes.

Integrative taxonomy is a powerful tool to differentiate between species when a single dataset proves to be unsatisfactory. This approach has been successful to solve taxonomical problems in freshwater shrimps (de Mazancourt et al., 2018, 2019a) and especially in the genus Macrobrachium (Castelin et al., 2017; Chow et al., 2022). However, in order to use DNA to characterise the species, it is better to work with fresh (i.e., recent enough) specimens that have been correctly preserved. In our case, the problem is that the most recent specimens at our disposal – those collected by Kiener in 1980 – have reportedly been fixated in formalin, which prevents sequencing. The next most recent specimens available are those reported by Roux (1934) collected in 1926 and preserved in ethanol. As DNA tends to degrade with time, it will be difficult to obtain sequences from them through regular PCR and Sanger sequencing as it is usually done for DNA barcoding.

Recent advances in sequencing methods that do not require a PCR step have become increasingly accessible, enabling the recovery of diagnostic sequences from challenging samples (Burrell et al., 2015; Raxworthy et al., 2021). In this study, we apply Next Generation Sequencing (NGS) technology to retrieve mitochondrial DNA sequences from historical museum specimens of M. hirtimanus. NGS methods, such as the Illumina platform used here, theoretically allow for the analysis of the full mitochondrial genome (>18 kb). However, due to the fragmented state of DNA in old specimens, the results are likely incomplete, with only barcode regions of the mitogenome, such as the COI and 16S markers, being recoverable. These fragments, though limited, are sufficient for comparing the obtained sequences with barcode reference databases to confirm the identification of the samples.

We compiled a list of available M. hirtimanus specimens from historical museum collections and selected several from the Muséum national d’Histoire naturelle for sequencing, which was successful. The comparison of the sequences obtained from these historical specimens with those of co-occurring Macrobrachium species will help clarify whether M. hirtimanus and M. lepidactylus are distinct species or conspecific.

Additionally, this study provides reference sequences for future eDNA-based detection efforts, which could assist in determining the current conservation status of these species. By integrating historical collections, molecular tools, and emerging biodiversity monitoring techniques, this research highlights the importance of these approaches in assessing the conservation status of endangered freshwater taxa.

2 Materials and methods

2.1 Specimens sampling

Specimens of M. hirtimanus were searched in various museum collections worldwide based on published records, through public databases and requests to curators. Four large male specimens from the MNHN collection were selected, including two from Mauritius and two from La Réunion to account for the intra-specific diversity across the range of the species.

2.2 DNA extraction

Muscular tissue from pleopods of the fifth pair was sampled on four specimens of M. hirtimanus preserved in 70-96% ethanol in the collections of the MNHN: (1) MNHN-IU-2021-8795: Mauritius, Bambous, coll. P. Carié, Feb. 1912; (2) MNHN-IU-2021-8796: Mauritius, coll. J.-R. Quoy & J.-P. Gaimard, 1818 (probably) (Fig. 1C); (3) MNHN-IU-2021-8798 and (4) MNHN-IU-2021-8799: Réunion, Rivière des Marsouins, coll. G. Petit, 1926.

These samples were extracted with a QIAmp DNA Mini Kit, frequently used when working on dry or ethanol-preserved tissues with low DNA concentration (see for example Keith and Mennesson, 2020) and forensics. The protocol was modified to increase DNA yields from degraded tissue samples from historical specimens as followed: Step n°1 unchanged, we used step n°2a (cut up to 25 mg of tissue), step n°3 the incubation was at 50°C, step n°4 unchanged, we used step n°5b by adding 400 μl Buffer AL, step n°6 with 400 μl ethanol, steps n°7, 8, 9 and 10 unchanged (Keith and Mennesson, 2020). For the elution step, we used 50 μl Buffer AE (50% AE – 50% water) and incubated at room temperature for 5 min. Since DNA was expected to be degraded and thus fragmented, extracts were quantified using a Qubit fluorimeter (Thermo and a Fragment Analyzer with similar results for both methods). This however cannot ensure the quality of the extracts (number/size of fragments, coverage, contamination, etc.) which can only be assessed after sequencing in our case.

thumbnail Fig. 1

Macrobrachium hirtimanus (Olivier, 1811). A: Drawing of the type specimen from the Paris Museum by Latreille (1818). B: The only known photograph of living specimens taken by Kiener (Kiener and Duchochois, 1981) enhanced and colorized. Also the last living individuals known to have been collected. C: One of the four specimens sequenced for the present study (MNHN-IU-2021-8796).

2.3 Sequencing

DNA of the four specimens of M. hirtimanus was sequenced using shotgun-sequencing method with a NovaSeq 6000 SP Reagent Kit (300 cycles) at the the iGenSeq core facility, at the Institut du Cerveau et de la Moëlle (ICM, Paris). Shotgun libraries prepared by the third-party laboratory following their own protocol adapted to the kit and sequencer chosen were then sequenced on an Illumina® NovaSeq 6000 sequencer following manufacturer’s instructions. Filtering for quality and trimming of the reads was performed by the ICM following their own pipeline before sending us the final results.

2.4 Reads mapping

Reads were mapped against the complete mitochondrial genome of M. bullatum (NC_027602, Gan et al., 2015) used as a reference with the “map to reference” feature implemented in Geneious Prime software (v. 2023.0.1, Biomatters Ltd.) leaving parameters as default. All NGS data was deposited in GenBank (accession number PRJNA1378948).

2.5 Phylogenetic analyses

DNA sequences of the 16S rRNA and COI gene were extracted from the consensus sequence where coverage was sufficient on the barcode regions using the consensus extraction feature implemented in Geneious Prime v. 2023.0.1. Sequences extracted were aligned using Muscle algorithm (Edgar, 2004) implemented in MEGA11 software (Tamura et al., 2021) with other sequences either retrieved from GenBank (published by Aznar-Cormano et al., 2015; Castelin et al., 2013; 2017; Chen et al., 2007; Hernawati et al., 2020; Liu et al., 2007 and Zimmermann, 2009) or newly produced (see de Mazancourt et al., 2024 for the protocol followed). These sequences from GenBank represent the three other species of Macrobrachium known to occur on Réunion Island (namely M. australe, M. lar and M. lepidactylus) with the addition of M. lepidactyloides that used to be synonymized with M. hirtimanus and Palaemon debilis as the outgroup. All newly produced sequences were deposited in GenBank (Tab. 2).

Neighbor-Joining phylogenetic analyses were performed on both alignments using Geneious.

3 Results

3.1 Specimens sampling

Only a handful of occurrences have been reported for M. hirtimanus: from Mauritius by White (1847), Milne-Edwards (1869), Sharp (1893) and Ward (1942), from Réunion Island by Roux (1934), Holthuis (1952) and Kiener and Duchochois (1981), and Rodrigues by Miers (1879). By inquiring the collections cited and some others, we could locate around 70 specimens extant in collections worldwide, collected as early as 1818 (by J.-R. Quoy & J.-P. Gaimard) and as late as 1980 (by Kiener). The lots of specimens are listed in Table 1.

Table 1

List of the specimens of Macrobrachium hirtimanus found in various collections worldwide.

Table 2

List of the sequences included in the molecular analyses.

3.2 DNA extraction

All four specimens included in the study contained DNA. Quantifications using a Qubit fluorimeter gave the following results: 0.858 ng/μL for specimen 1, 0.220 for specimen 2, 0.230 for specimen 3 and 0.192 for specimen 4.

3.3 Sequencing

Two sequencing runs were generated for each specimen, yielding between 48M and 59M reads per run. Reads could be mapped to the reference mitogenome of M. bullatum for all four specimens of M. hirtimanus, with 1,415 reads for specimen 1, 695 for specimen 2, 836 for specimen 3 and 423 for specimen 4. Coverage was low overall and uneven, with similar peaks across all four specimens, the most notable one being around the 16S rRNA region (Fig. 2).

Nevertheless, coverage was sufficient to get the full length of the 16S barcode fragment (514 bp) for all four specimens and a partial COI barcode fragment (261 bp) for specimen 3 only.

thumbnail Fig. 2

Coverage graph of the number of reads mapped to each nucleotide position of the reference mitochondrial genome for each of the four specimens sequenced.

3.4 Phylogenetic analysis

Phylogenetic analyses of both markers showed that M. hirtimanus is distinct from all the other species occurring in the Mascarenes and from M. lepidactyloides (Figs. 3 and 4). In 16S, all four specimens of M. hirtimanus clustered together in a strongly supported group (bootstrap of 99.9%) well separated from the other species (pairwise p-distances of 10.2‒11.4% for 16S and 19.5% for COI to M. lepidactyloides, its closest relative).

thumbnail Fig. 3

Neighbor-Joining tree based on the 16S alignment.
thumbnail Fig. 4

Neighbor-Joining tree based on the COI alignment.

4 Discussion

The sequences produced in the present study are a first step towards answering the questions raised previously. M. hirtimanus is indeed a valid species, being clearly distinct both morphologically and genetically from the other Macrobrachium occurring in the area and from M. lepidactyloides, which used to be considered its junior synonym.

Despite numerous surveys since 1980 using traditional sampling methods (hand net and electro-fishing) on Reunion Island during which M. hirtimanus could not be found, it is not yet certain whether the species is extinct globally, locally, or even at all. The newly produced sequences will be useful as a reference for eDNA studies in the Mascarenes (see Zieritz et al., 2022 for instance). This type of survey might detect traces of this species in the rivers of the Mascarenes, which would suggest its recent presence, as it was the case with a presumed extinct species of frog from Brazil (Lopes et al., 2021) or could confirm its absence, allowing to update the status of M. hirtimanus for the IUCN Red List to extinct.

In any case, it is undeniable that the species has become extremely rare, if not extinct as no verified specimen has been caught since 1980, a regression seemingly concomitant with the establishment of M. lepidactylus in the area.

In 1991, one of us (GM) caught a specimen of Macrobrachium identified by L. B. Holthuis as M. patsa (Coutière, 1899) in the “rivière des Roches” on Réunion Island. During this prospection by electric fishing no specimen of M. hirtimanus was caught. We now consider this specimen to be an immature M. lepidactylus. Later, Keith and Vigneux (2000) report their finding of adult specimens of the same species during prospections made in November 1998. In his book on the fauna of Mauritius, F. Staub (1993) illustrates his entry about M. hirtimanus with a colour photograph of an adult male individual that can clearly be identified as M. lepidactylus. These occurrences suggest that M. lepidactylus was already established in the Mascarenes by the early 1990s, while M. hirtimanus was last seen in 1980 (Kiener and Duchochois, 1981).

M. lepidactylus naturally occurs in East and South-East Africa, and Madagascar (Holthuis, 1980), living in well-oxygenated, flowing waters all along the river courses (Keith and Vigneux, 2000). It is unlikely for this species to have been introduced by man in the Mascarenes given its minor commercial interest (Holthuis, 1980). Since it is an amphidromous species (Keith et al., 2006) and due to the relative proximity of Madagascar, one can expect M. lepidactylus to reach Réunion and Mauritius Islands by natural means with post-larvae born in rivers of Madagascar recruiting in estuaries of these islands, drifting along favourable oceanic currents, as for other amphidromous species of the area (see de Mazancourt et al., 2023; Keith and Mennesson, 2023).

However, why was it not present there before the 1990s? M. hirtimanus occupies the same habitat as M. lepidactylus (Kiener pers. comm. in Keith and Vigneux, 2000), which suggests that both species compete for the same ecological niche. Reduction in populations of M. hirtimanus in the 1980s due to poaching might have allowed juveniles of M. lepidactylus to settle in favourable habitats where the presence of the well-established endemic species previously prevented it. Biological or ecological reasons explaining how M. lepidactylus might have outcompeted M. hirtimanus (e.g., more aggressive behaviour, life history traits, etc.) are yet to be found due to the lack of data on both species. This pattern is indeed very common in insular systems where ecologically plastic invasive species often supplant their endemic counterparts (Russell et al., 2017).

Compared to their marine counterparts, freshwater shrimps indeed face many threats specific to their inland habitat and migratory behaviour (see De Grave et al., 2015; de Mazancourt et al., 2021). In the case of M. hirtimanus, poaching has been the main explanation (Keith and Vigneux, 2000; De Grave, 2013) along with the degradation of its habitat (Keith et al., 1999; Keith, 2002; De Grave, 2013). Similarly, Caridina natalensis De Man, 1908, another freshwater shrimp native to the Mascarenes may be under threat of extirpation as it has become very rare on Réunion Island (de Mazancourt et al., 2019b) probably because of habitat degradation. On the other hand, old reports of a freshwater crab identified as Potamon bouvieri Rathbun, 1904 from Mauritius (Rathbun, 1904; Jehangeer, 1984) and Réunion (Kiener and Duchochois, 1981) should be investigated further as this species may also be extinct, if not just extremely rare.

Acknowledgments

This work was funded by the Direction de l'environnement, de l'aménagement et du logement (DEAL) of La Réunion with support of the IRD. The authors would like to thank Laure Corbari and Paula Martin-Lefèvre (respectively Curator and Collection Manager of the Crustacean collection at MNHN, Paris), Paul Callomon (Collection Manager of Malacology and General Invertebrates at the Academy of Natural Sciences of Drexel University, Philadelphia), and Roberta Tota (Technician of the Section of Zoology at the Museo Regionale di Scienze Naturali, Turin) for providing data about specimens of M. hirtimanus in various collections. This work benefited from equipment and services from the iGenSeq core facility, at ICM. We wish to thank an anonymous reviewer for the helpful comments that helped improving the manuscript.

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Cite this article as: de Mazancourt V, Mennesson M, Marquet G, Valade P, Keith P. 2026. NGS data from historical museum collections help to clarify the conservation status of endangered or supposedly extinct species: the case of the Mascarene endemic freshwater shrimp Macrobrachium hirtimanus (Olivier, 1811). Knowl. Manag. Aquat. Ecosyst. 427, 4. https://doi.org/10.1051/kmae/2025032.

All Tables

Table 1

List of the specimens of Macrobrachium hirtimanus found in various collections worldwide.

In the text
Table 2

List of the sequences included in the molecular analyses.

In the text

All Figures

thumbnail Fig. 1

Macrobrachium hirtimanus (Olivier, 1811). A: Drawing of the type specimen from the Paris Museum by Latreille (1818). B: The only known photograph of living specimens taken by Kiener (Kiener and Duchochois, 1981) enhanced and colorized. Also the last living individuals known to have been collected. C: One of the four specimens sequenced for the present study (MNHN-IU-2021-8796).
In the text
thumbnail Fig. 2

Coverage graph of the number of reads mapped to each nucleotide position of the reference mitochondrial genome for each of the four specimens sequenced.
In the text
thumbnail Fig. 3

Neighbor-Joining tree based on the 16S alignment.
In the text
thumbnail Fig. 4

Neighbor-Joining tree based on the COI alignment.
In the text

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