Anthropogenic activities such as mining pose a putative threat to deep-sea ecosystems and baseline studies of key indicator species are required to assess future loss of biodiversity. We examined population genetic structure, connectivity, cryptic diversity and phylogeography of the deep-sea scavenging amphipod, Abyssorchomene distinctus, using DNA sequence data (mitochondrial COI and nuclear 28S genes) from 373 specimens collected from six abyssal basins. We observed a striking absence of cryptic diversity, suggesting a single, widely distributed species in the Pacific and Indian Ocean. A single event of population expansion across distances up to 24,000 km is further supported by a main ancestral haplotype in the star-like shaped COI haplotype network, a skewed nucleotide mismatch distribution and deviations from evolutionary neutrality tests. In the Pacific, A. distinctus showed weak genetic population structure and low differentiation between the basins of the Clarion-Clipperton Zone and the DISCOL Experimental Area, suggesting a possible higher chance of recovery from deep-sea mining impacts. However, since our data indicate a single recent historic population expansion event, A. distinctus populations will likely be affected to unknown extents, as the exact drivers shaping distribution and dispersion of A. distinctus are still unclear.
... This is the first true confirmation of V. gracilis outside of the Atlantic Ocean, adding it to the growing number of deep-sea amphipod species with pan-oceanic distributions (e.g. Hirondellea dubia Dahl, 1959, Weston & Jamieson, 2022Paralicella tenuipes Chevreux, 1908, Jażdżewska et al., 2021aEurythenes gryllus, Havermans et al., 2013; Abyssorchomene distinctus (Birstein & Vinogradov, 1960), Dupont et al., 2024;Rhachotropis abyssalis Lörz, 2010, Lörz et al., 2023. ...
... Population genetics studies offer the means to investigate patterns of genetic connectivity and diversity; however, the logistical difficulties of deep-sea sampling combined with often low sample numbers, make connectivity studies of abyssal invertebrates challenging (Taylor and Roterman 2017). Available population genetics studies of abyssal Amphipoda have shown some species to have limited genetic differentiation across multiple ocean basins, with haplotype networks of Abyssorchomene distinctus suggesting a single population expansion event across distances up to 24 000 km (Dupont et al. 2024). Long range dispersal in the abyss is suggested to be facilitated by abyssal currents, such as the Pacific Arctic Intermediate Water across the Pacific Ocean (Havermans 2016). ...
Valettietta Lincoln & Thurston, 1983 (Amphipoda: Alicelloidea) is an infrequently sampled genus of scavenging amphipod, with a known bathymetric range from 17–5467 m encompassing a variety of habitats from anchialine caves to abyssal plains. Molecular systematics studies have uncovered cryptic speciation in specimens collected from the abyssal Pacific, highlighting uncertainty in the description of Valettietta anacantha (Birstein & Vinogradov, 1963). Here, we apply an integrative taxonomic approach and describe two new species, Valettietta trottarum sp. nov. and Valettietta synchlys sp. nov., collected at abyssal depths in the Clarion-Clipperton Zone, Pacific Ocean. Both species can be distinguished by characters of the gnathopods, uropod 3, and the inner plate of the maxilliped. Further, molecular phylogenetic analyses of two mitochondrial (16S rDNA and COI) and two nuclear (Histone 3 and 28S rRNA) regions found both new species to form well-supported clades and allowed us to re-identify previously published records based on genetic species delimitation. The biogeography of Valettietta is discussed in light of these re-evaluated records, and a new taxonomic key to the genus is provided. These new taxa highlight the strength of applying an integrated taxonomic approach to uncover biodiversity, which is critical in regions being explored for potential industrial purposes.
The Clarion-Clipperton Zone (CCZ) situated in the central east Pacific holds major portions of manganese nodule deposits and is therefore subject to intense exploration for future deep-sea mining. However, mining rises multiple concerns. Among others about its direct or indirect impact on abyssal environment. The more, proper evaluation of deep-sea protection plans to be applied there is still hindered by insufficient knowledge of the abyssal fauna diversity and their assemblages. Amphipoda are speciose and abundant in all marine habitats and were proven to be important food source for higher trophic levels. These crustaceans are brooders with no planktonic larval stage, so migration of species depend only on swimming capacities of adult animals. In the CCZ macrofauna-sized and relatively mobile, epibenthic Amphipoda, not collected with commonly used box corers or multicorers, remained unstudied. The present work aims to fill in this gap in knowledge by: 1) characterizing the diversity of amphipods across the CCZ and one Area of Particular Environmental Interest (APEI), 2) studying the amphipod species distribution and assemblages as well as 3) inferring the connectivity between eastern and western parts of the CCZ and other deep-sea regions. The material was collected with epibenthic sledge from three contractor zones (UK, Singapore, Germany) and from APEI-06. Specimens were sorted into families and preferably morphospecies and subjected to cytochrome c oxidase subunit I gene (COI) barcoding. Within total of 708 individuals 23 known and one undescribed families were identified. The barcoding allowed to obtain 581 sequences that were ascribed to 207 Molecular Operational Taxonomic Units (MOTUs). The families that dominated barcoded material in terms of abundance and species richness were: Pardaliscidae (123 ind., 44 MOTUs), Eusiridae (122 ind., 32 MOTUs) and Synopiidae (74 ind., 31 MOTUs). Only 17 known species were identified; another 48 are considered as new to science. Almost 70% of MOTUs were singletons or doubletons and 186 MOTUs were unique for the present study. The remaining 21 taxa appeared to be broadly distributed. Among the MOTUs recorded only in the CCZ majority was distributed within 400 km distance. Just six species reached or exceeded 1000 km distance of occurrence. Additionally only one species was shared between contractor areas and the studied APEI that was supposed to be preserved area representative for the mining zones. The cluster analysis of the fauna collected during three expeditions to the German contractor areas revealed almost no similarity between the West and East part of the CCZ. Additionally, within the eastern part of the studied region geographic proximity appeared to have no influence on station clustering. The study confirmed low abundance and high species richness of deep-sea amphipod fauna of the CCZ and their highly variable assemblages. Moreover, it has shown weak connectivity between eastern and western parts of the region as well as between the contractor zones, APEIs and other deep-sea regions of the World. All the above suggest high vulnerability of the assemblages studied and, with the present state of knowledge, weak representativeness of Areas of Particular Environmental Interest for the mining zones. In order to better understand the deep-sea biodiversity and develop Regional Environmental Management Plans for the whole CCZ area two main recommendations are to be made: 1) to conduct more intensive sampling program of APEIs parallel to monitoring studies of contractor zones with the goal to better assess their usefulness as reservoirs of biodiversity for the mining areas, 2) to include the epibenthic sledge among standard gears used for sampling in order to avoid missing important part of deep-sea fauna in the monitoring studies.
The deepest marine ecosystem, the hadal zone, hosts endemic biodiversity resulting from geographic isolation and environmental selection pressures. However, the pan-ocean distribution of some fauna challenges the concept that the hadal zone is a series of isolated island-like habitats. Whether this remains true at the population genomic level is untested. We investigated phylogeographic patterns of the amphipod, Bathycallisoma schellenbergi, from 12 hadal features across the Pacific, Atlantic, Indian, and Southern oceans and analyzed genome-wide single-nucleotide polymorphism markers and two mitochondrial regions. Despite a cosmopolitan distribution, populations were highly restricted to individual features with only limited gene flow between topographically connected features. This lack of connectivity suggests that populations are on separate evolutionary trajectories, with evidence of potential cryptic speciation at the Atacama Trench. Together, this global study demonstrates that the shallower ocean floor separating hadal features poses strong barriers to dispersal, driving genetic isolation and creating pockets of diversity to conserve.
The hadal zone (depths > 6,000 m) comprises isolated features that host high degrees of endemism, with species inhabiting only a single feature or a group of adjacent features. The amphipod, Hirondellea dubia is an abundant scavenger at the hadal depths of the Kermadec, Tonga, and New Hebrides trenches in the Southwest Pacific Ocean, particularly at depths > 9,500 m. However, several records have hinted that H. dubia may not be restricted to the Southwest Pacific nor be exclusively hadal. Here, we present new records of H. dubia recovered by baited landers deployed to five hadal trenches during three expeditions and assess the geographic and vertical distribution of this species. To rule out the possibility of cryptic diversity, morphological taxonomy was paired with two mitochondrial markers (16S and COI) to test for species boundaries among the new and published molecular data using four delineation approaches (ABGD, CD-HIT, GMYC, and bPTP). We found H. dubia to be a single species and not restricted to the Southwest Pacific or hadal depths. This species’ geographic range extends from the Southwest Pacific to the Mariana Trench (Northwest Pacific), the Clarion-Clipperton Zone (Central Pacific), the South Sandwich Trench (Southern), and the Puerto Rico Trench (North Atlantic). This amphipod’s vertical range spans over half of the ocean’s total depth, between 4,700 and 10,817 m. This study presents an extraordinary geographic range extension to a species long considered endemic to a cluster of three Southwest Pacific trenches and shows a pan-oceanic distribution across extremely isolated hadal features.
Hydrothermal vent areas have drawn increasing interest since they were discovered in 1977. Because of chemoautotrophic bacteria, they possess high abundances of vent endemic species as well as many non-vent species around the fields. During the survey conducted by the Bundesanstalt für Geowissenschaften und Rohstoffe (Federal Institute for Geosciences and Natural Resources, BGR) to identify inactive polymetallic sulfide deposits along Central and Southeast Indian Ridges, the INDEX project studied the scavenging amphipod community at three newly discovered hydrothermal fields. A sample consisting of 463 representatives of Amphipoda (Malacostraca: Crustacea) was collected by means of baited traps in active and inactive vents of three different sites and subsequently studied by both morphological and genetic methods. Molecular methods included the analysis of two mitochondrial (cytochrome c oxidase subunit I [COI] and 16S rRNA) and one nuclear (18S rRNA) genes. By six delimitation methods, 22 molecular operational taxonomic units (MOTUs) belonging to 12 genera and 10 families were defined. The existence of potential species complexes was noted for the representatives of the genus Paralicella. The inactive site, where 19 species were found, showed higher species richness than did the active one, where only 10 taxa were recorded. Seven genera, Ambasiopsis, Cleonardo, Eurythenes, Parandania, Pseudonesimus, Tectovalopsis, and Valettiopsis, were observed only at inactive sites, whereas Haptocallisoma, was collected exclusively at active ones. The species Abyssorchomene distinctus (Birstein and Vinogradov, 1960), Hirondellea brevicaudata Chevreux, 1910, and Hirondellea guyoti Barnard and Ingram, 1990, have been previously reported from vent sites in the Atlantic or Pacific oceans. The present study provides the first report of Eurythenes magellanicus (H. Milne Edwards, 1848) and five other already described species in the Indian Ocean. The addition of 356 sequences strongly increases the number of amphipod barcodes in reference databases and provides for the first time COI barcodes for Cleonardo neuvillei Chevreux, 1908, Haptocallisoma abyssi (Oldevig, 1959), Hirondellea guyoti, Tectovalopsis fusilus Barnard and Ingram, 1990, and the genera Haptocallisoma, Pseudonesimus, and Valettiopsis.
In the age of global climate change and biodiversity loss there is an urgent need to provide effective and robust tools for diversity monitoring. One of the promising techniques for species identification is the use of DNA barcoding, that in Metazoa utilizes the so called 'gold-standard' gene of cytochrome c oxidase (COI). However, the success of this method relies on the existence of trustworthy barcode libraries of the species. The Barcode of Life Data System (BOLD) aims to provide barcodes for all existing organisms, and is complemented by the Barcode Index Number (BIN) system serving as a tool for potential species recognition. Here we provide an analysis of all public COI sequences available in BOLD of the diverse and ubiquitous crustacean order Amphipoda, to identify the barcode library gaps and provide recommendations for future barcoding studies. Our gap analysis of 25,702 records has shown that although 3,835 BINs (indicating putative species) were recognised by BOLD, only 10% of known amphipod species are represented by barcodes. We have identified almost equal contribution of both records (sequences) and BINs associated with freshwater and with marine realms. Three quarters of records have a complete species-level identification provided, while BINs have just 50%. Large disproportions between identification levels of BINs coming from freshwaters and the marine environment were observed, with three quarters of the former possessing a species name, and less than 40% for the latter. Moreover, the majority of BINs are represented by a very low number of sequences rendering them unreliable according to the quality control system. The geographical coverage is poor with vast areas of Africa, South America and the open ocean acting as ''white gaps''. Several, of the most species rich and highly abundant families of Amphipoda (e.g., Phoxocephalidae, Ampeliscidae, Caprellidae), have very poor representation in the BOLD barcode library. As a result of our study we recommend stronger effort in identification of already recognised BINs, prioritising the studies of families that are known to be important and abundant components of particular communities, and targeted sampling programs for taxa coming from geographical regions with the least knowledge.
Paralicella tenuipes Chevreux, 1908 and Paralicella caperesca Shulenberger & Barnard, 1976 are known as widely distributed deep-sea scavenging amphipods. Some recent studies based on genetic data indicated the presence of high intraspecific variation of P. caperesca suggesting it is a species complex. Based on published molecular data from the Pacific and Indian oceans and new material obtained from North and South Atlantic, we integrated the knowledge on the intraspecific variation and species distribution of the two nominal taxa. The study included analysis of three genes (COI, 16S rRNA, 28S rRNA) and revealed the existence of a single Molecular Operational Taxonomic Unit (MOTU) within P. tenuipes and six different MOTUs forming P. caperesca. The distribution pattern of the recognized lineages varied with three (P. tenuipes, MOTU 1 and MOTU 5 of P. caperesca) being widely distributed. There was evidence of contemporary population connectivity expressed by the share of the same COI haplotypes by individuals from very distant localities. At the same time no signal of recent demographic changes was observed within the studied taxa. The time-calibrated phylogeny suggested the emergence of species to be at the time of Mesozoic/Cenozoic transition that may be associated with global changes of the ocean circulation and deep sea water cooling.
Recently, there has been a resurgent interest in the exploration of deep-sea mineral deposits, particularly polymetallic nodules in the Clarion-Clipperton Zone (CCZ), central Pacific. Accurate environmental impact assessment is critical to the effective management of a new industry and depends on a sound understanding of species taxonomy, biogeography, and connectivity across a range of scales. Connectivity is a particularly important parameter in determining ecosystem resilience, as it helps to define the ability of a system to recover post-impact. Scavenging amphipods in the superfamilies Alicelloidea Lowry and De Broyer, 2008 and Lysianassoidea Dana, 1849 contribute to a unique and abundant scavenging community in abyssal ecosystems. They are relatively easy to sample and in recent years have become the target of several molecular and taxonomic studies, but are poorly studied in the CCZ. Here, a molecular approach is used to identify and delimit species, and to investigate evolutionary relationships of scavenging amphipods from both abyssal plain and deep (>3000 m) seamount habitats in three APEIs (Areas of Particular Environmental Interest, i.e., designated conservation areas) in the western CCZ. A total of 17 different morphospecies of scavenging amphipods were identified, which include at least 30 genetic species delimited by a fragment of the cytochrome c oxidase subunit I (COI) barcode gene. The scavenging communities sampled in the western CCZ included the most common species (Abyssorchomene gerulicorbis (Shulenberger and Barnard, 1976), A. chevreuxi (Stebbing, 1906), Paralicella caperesca Shulenberger and Barnard, 1976, and P. tenuipes Chevreux, 1908) reported for other ocean basins. Only four morphospecies, representing five genetic species, were shared between APEIs 1, 4, and 7. The two abyssal plain sites at APEIs 4 and 7 were dominated by two and three of the most common scavenging species, respectively, while the APEI 1 seamount site was dominated by two species potentially new to science that appeared to be endemic to the site. The presence of common species in all sites and high genetic diversity, yet little geographic structuring, indicate connectivity over evolutionary time scales between the areas, which span about 1500 km. Similar to recent studies, the differences in amphipod assemblages found between the seamount and abyssal sites suggest that ecological conditions on seamounts generate distinct community compositions.
The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular evolution. Here, we describe new additions that make MEGA a more comprehensive tool for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. Methods for estimating divergence times and confidence intervals are implemented to use probability densities for calibration constraints for node-dating and sequence sampling dates for tip-dating analyses, which will be supported by new options for tagging sequences with spatiotemporal sampling information, an expanded interactive Node Calibrations Editor, and an extended Tree Explorer to display timetrees. We have now added a Bayesian method for estimating neutral evolutionary probabilities of alleles in a species using multispecies sequence alignments and a machine learning method to test for the autocorrelation of evolutionary rates in phylogenies. The computer memory requirements for the maximum likelihood analysis are reduced significantly through reprogramming, and the graphical user interface (GUI) has been made more responsive and interactive for very big datasets. These enhancements will improve the user experience, quality of results, and the pace of biological discovery. Natively compiled GUI and command-line versions of MEGA11 are available for Microsoft Windows, Linux, and macOS from www.megasoftware.net.
The Clarion-Clipperton Zone (CCZ), located in the abyssal equatorial Pacific, has been subject to intensive international exploration for polymetallic nodule mining over the last four decades. Many studies have investigated the potential effects of mining on deep-sea ecosystems and highlighted the importance of defining environmental baseline conditions occurring at potential mining sites. However, current information on biodiversity and species distributions in the CCZ is still scarce and hampers the ability to effectively manage and reduce the potential impacts of mining activities. As part of the regulatory regimes adopted by the International Seabed Authority, concession holders are required to conduct an environmental impact assessment and gather baseline data on biodiversity and community structure in relation to their license areas. In the present study, we used an integrative molecular and morphological approach to assess species richness and genetic variation of deep-sea scavenging amphipods collected in two nodule-mining exploration areas (UK-1 and OMS-1 areas) and one Area of Particular Environmental Interest (APEI-6) in the eastern part of the CCZ. We analyzed the DNA sequences of the cytochrome c oxidase subunit I gene of 645 specimens belonging to ten distinct morphospecies. Molecular data uncover potential cryptic diversity in two investigated species, morphologically identified as Paralicella caperesca Shulenberger & Barnard, 1976 and Valettietta cf. anacantha (Birstein & Vinogradov, 1963). Our study highlights the importance of using molecular tools in conjunction with traditional morphological methods for modern biodiversity assessment studies, particularly to evaluate morphologically similar individuals and incomplete specimens. The results of this study can help determine species identity and ranges, information which can feed into environmental management.
Phyllochaetopterus (Annelida: Chaetopteridae) is a diverse genus of tube-dwelling polychaetes found in a wide range of marine environments from subtidal to abyssal depths, including chemosynthesis-based ecosystems. The Shinkai Seep Field (SSF) is a serpentinite-hosted system in the Mariana Trench, where the deepest-known Phyllochaetopterus polychaetes inhabit the surfaces of brucite/carbonate chimneys. Despite all specimens collected from SSF being morphologically consistent with P. polus originally described from a deep-sea hot vent on the Mid-Atlantic Ridge, molecular barcoding using the mitochondrial cytochrome c oxidase subunit I (COI) gene revealed at least three cryptic lineages, none of which corresponded to P. polus. Phylogenetic reconstruction recovered P. polus embedded among the three SSF lineages, confirming their close relationship. These results warrant careful examination of Phyllochaetopterus from other regions using integrative taxonomy in order to understand its true diversity and pinpoint further taxonomically informative morphological characters.
![A Population genetic parameters of Abyssorchomene distinctus. All samples include populations from both, the Indian and Pacific Ocean for COI, and only Pacific Ocean for 28S. The Pacific Ocean includes the two basins CCZ and DEA. Number of samples, number of polymorphic sites and haplotypes, estimated haplotype (h) and nucleotide diversities (pi) and results of neutrality tests (Fu’s Fs statistic and Tajima’s D diversity) are shown. Significant values (*P < 0.05, ***P < 0.001) are indicated in bold. B Genetic population structure (ΦST, Phi-statistic) and partitioning of genetic variance of Abyssorchomene distinctus analysed with a standard AMOVA. For COI, the analysis was designed with three hierarchical levels to depict different geographic scales. Level 1 compares genetic data from the Pacific Ocean group versus the Indian Ocean group, level 2 compares data of each basin groups in each ocean and level 3 compares data between each station groups from the same basins. For 28S, two hierarchical levels to depict different geographic scales. Level 1 compares data from the CCZ basin group versus the DEA basin group within the Pacific Ocean and, level 2 compares data between each station groups from the same basins. Significant (*P < 0.05, **P < 0.01, ***P < 0.001) fixation indexes [i.e. amongst groups (ΦCT), amongst populations within groups (ΦSC), and amongst populations (ΦST)] are indicated in bold. nc non-computable. C Population differentiation between stations within the CCZ basin, analysed with a standard AMOVA in the COI dataset. Results are shown as ФST pairwise differences and range between 0 (low) and 1 (high differentiation). Eight stations are compared in the matrix. Statistically significant differentiations (*P < 0.05) are indicated in bold. D Population differentiation between stations within the CCZ basin, analysed with a standard AMOVA in the 28S dataset. Results are shown as ФST pairwise differences and range between 0 (low) and 1 (high differentiation). Six stations are compared. Statistically significant differentiations (*P < 0.05) are indicated in bold](https://www.researchgate.net/profile/Deborah-Dupont/publication/377808226/figure/fig4/AS:11431281236592185@1713233142815/A-Population-genetic-parameters-of-Abyssorchomene-distinctus-All-samples-include_Q320.jpg)
