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Digital images of the posterior prosome and urosome of P. piseki – P. gracilis animals from four genetic clades. Animals from (A) clade A, (B) clade C, (C) clade G, and (D) clade E are shown in ventral and right lateral views. By traditional morphological criteria, animals in (A), (B), and (C) would be identified as P. piseki and the animal in (D) would be identified as P. gracilis. Note that clade A and C both have a large black pigment spot at the copulatory pore, as well as a marked groove on the left side of the genital double-somite near the posterior margin (marked by an arrow), which was included in the original species description for P. piseki (Farran 1929). Clade G (panel C) also has a large black spot at the copulatory pore, but the spot is located at the posterior edge of the genital boss, and appears as a right-left oval rather than round in shape. Animals from this clade apparently lack the marked groove on the left side of the genital double-somite (absence visible at the black arrow). Finally, animals in clades E and B have genital characters that appear ‘gracilian’ (P. gracilis-like), as shown in panel D on a clade E specimen.
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Although holoplankton are ocean drifters and exhibit high dispersal potential, a number of studies on single species are finding highly divergent genetic clades. These cryptic species complexes are important to discover and describe, as identification of common marine species is fundamental to understanding ecosystem dynamics. Here we investigate t...
Citations
... Another critical limitation of morphological identification is the challenge posed by cryptic speciation in copepods 8,[23][24][25][26] . Cryptic species, which are morphologically similar but genetically distinct, may be overlooked, potentially leading to underestimations of biodiversity and misinterpretation of ecological patterns [27][28][29][30] . This was particularly evident in our study for closely related species pairs, such as Acartia hudsonica and A. omorii, where misidentification could result in incorrect ecological interpretations due to their differing habitat preferences. ...
Marine copepod communities play crucial roles in ocean ecosystems. However, their accurate assessment remains challenging due to taxonomic complexities. This study combines morphological and DNA metabarcoding approaches to evaluate copepod diversity and community structure in the northern East China Sea. Zooplankton samples were collected from 10 stations along a coastal-offshore gradient in August 2019. Morphological analysis identified 34 species from 25 genera, while DNA metabarcoding detected 31 species from 20 genera. Both methods revealed distinct coastal and offshore assemblages, with Paracalanus parvus s.l. as the dominant species across all stations. A significant positive correlation was found between morphology-based individual counts and metabarcoding sequence reads (Spearman’s Rho = 0.58, p < 0.001), improving at the genus level (Rho = 0.70, p < 0.001). Redundancy analysis revealed that salinity, temperature, and phytoplankton density significantly influenced copepod distribution. Although both approaches captured similar broad-scale patterns, they provided complementary insights into community structure. Morphological identification was more effective for detecting Cyclopoida diversity, whereas DNA metabarcoding had greater sensitivity for specific Calanoid species. This study underscores the value of integrating traditional and molecular methods for marine biodiversity assessment, especially in the context of global environmental changes.
... Another critical limitation of morphological identi cation is the challenge posed by cryptic speciation in copepods 8, [23][24][25][26] . Cryptic species, which are morphologically similar but genetically distinct, may be overlooked, potentially leading to underestimations of biodiversity and misinterpretation of ecological patterns [27][28][29][30] . This was particularly evident in our study for closely related species pairs, such as Acartia hudsonica and A. omorii, where misidenti cation could result in incorrect ecological interpretations due to their differing habitat preferences. ...
Marine copepod communities play crucial roles in ocean ecosystems. However, their accurate assessment remains challenging due to taxonomic complexities. This study combines morphological and DNA metabarcoding approaches to evaluate copepod diversity and community structure in the northern East China Sea. Zooplankton samples were collected from 10 stations along a coastal-offshore gradient in August 2019. Morphological analysis identified 34 species from 25 genera, while DNA metabarcoding detected 31 species from 20 genera. Both methods revealed distinct coastal and offshore assemblages, with Paracalanus parvus s.l. as the dominant species across all stations. A significant positive correlation was found between morphology-based individual counts and metabarcoding sequence reads (Spearman’s Rho = 0.58, p < 0.001), improving at the genus level ( Rho = 0.70, p < 0.001). Redundancy analysis revealed that salinity, temperature, and phytoplankton density significantly influenced copepod distribution. Although both approaches captured similar broad-scale patterns, they provided complementary insights into community structure. Morphological identification was more effective for detecting Cyclopoida diversity, whereas DNA metabarcoding had greater sensitivity for specific Calanoid species. This study underscores the value of integrating traditional and molecular methods for marine biodiversity assessment, especially in the context of global environmental changes.
... Cryptic diversity has been previously suggested in widespread and vagile taxa-those that are less affected by barriers. This includes both non-migratory and migratory bird species (Irwin et al., 2011;Lohman et al., 2010), planktonic marine copepods (Halbert et al., 2013), and marine and freshwater bony and cartilaginous fishes (D'Aloia et al., 2017;Fahmi et al., 2021;Neilson & Stepien, 2009). For example, migratory populations of the Wilson's warbler (a bird) exhibit strong genetic differentiation, perhaps reflecting differences in migratory patterns (Irwin et al., 2011). ...
Identification of taxonomically cryptic species is essential for the effective conservation of biodiversity. Freshwater‐limited organisms tend to be genetically isolated by drainage boundaries, and thus may be expected to show substantial cryptic phylogenetic and taxonomic diversity. By comparison, populations of diadromous taxa, that migrate between freshwater and marine environments, are expected to show less genetic differentiation. Here we test for cryptic diversity in Australasian populations (both diadromous and non‐diadromous) of two widespread Southern Hemisphere fish species, Galaxias brevipinnis and Galaxias maculatus. Both mtDNA and nuclear markers reveal putative cryptic species within these taxa. The substantial diversity detected within G. brevipinnis may be explained by its strong climbing ability which allows it to form isolated inland populations. In island populations, G. brevipinnis similarly show deeper genetic divergence than those of G. maculatus, which may be explained by the greater abundance of G. maculatus larvae in the sea allowing more ongoing dispersal. Our study highlights that even widespread, ‘high‐dispersal’ species can harbour substantial cryptic diversity and therefore warrant increased taxonomic and conservation attention.
... Many conventional and emerging approaches can bolster existing means to estimate the extent of knowledge gaps and shifts in taxonomic expertise of these groups, such as statistical modeling (Dorazio et al., 2006;Cai et al., 2023;Benedetti et al., 2023). Moreover, the full scope of species richness and diversity patterns may have been historically underestimated due to factors such as crypticity (McManus and Katz, 2009;Halbert et al., 2013). Challenges also arise when molecular tools alone are insufficient for accurate species descriptions, which has been documented in the literature (Zamani et al., 2022), indicating the need for a multifaceted approach to biodiversity assessment (McManus and Katz, 2009). ...
Freshwater ecosystems provide essential services for human well-being, with their conservation success reliant on the precise quantification of biodiversity. Diplostraca (= Cladocera) and Copepoda are diverse groups of microcrustaceans in aquatic ecosystems, important for a multitude of these services. We examined biodiversity trends of these groups utilising a comprehensive dataset, approximately 2341 studies, spanning from the early 19th Century to the present day, aiming at predicting the total number of microcrustacean species that will have been described by 2100. Descriptions increased until the 1900s, surged, and then declined after 1975. The predictive models indicate that by the year 2100, an additional 16–68% of cladoceran species and 37–126% of copepod species are likely to be identified, representing a significant portion of currently unrealised biodiversity. Eighteen prolific authors contributed to a quarter of these descriptions, with the rest spread among numerous authorities. Based on our extrapolation, the total number of microcrustacean species could potentially exceed 6114 by 2050 and 9046 by 2100, notwithstanding extinctions. These findings, which point to a significant amount of unrealised biodiversity, underscore the need to refine biodiversity estimates beyond conventional expert opinion. Such accuracy is crucial for addressing the underappreciated scale of the current biodiversity crisis.
... With the increased availability of powerful genetic tools, there has been growing evidence for cryptic species complexes in the open ocean, contrary to historical expectations that many pelagic species would have circumglobal, panmictic populations (Norris, 2000;van der Spoel & Heyman, 1983). The majority of circumglobal planktonic species examined with genetic data have been found to harbour cryptic diversity, with examples ranging from diatoms (Casteleyn et al., 2010;Whittaker & Rynearson, 2017) to copepods (Andrews et al., 2014;Cornils et al., 2017;Halbert et al., 2013;Hirai et al., 2015) and other calcifying plankton, including gastropods (Burridge et al., 2019;Wall-Palmer et al., 2018), foraminifers (Darling et al., 2004;De Vargas et al., 1999;Kucera & Darling, 2002) and coccolithophores (Filatov et al., 2021;Sáez et al., 2003). Therefore, an important step for understanding the capacity of plankton to adapt to future environmental change is to assess the spatial distribution of genetic variation and potential for gene flow across their species ranges (Bell, 2013;Harvey et al., 2014;Manno et al., 2017;Munday et al., 2013;Poloczanska et al., 2016;Sunday et al., 2014). ...
Little is known about when and how planktonic species arise and persist in the open ocean without apparent dispersal barriers. Pteropods are planktonic snails with thin shells susceptible to dissolution that are used as bio-indicators of ocean acidification. However, distinct evolutionary units respond to acidification differently and defining species boundaries is therefore crucial for predicting the impact of changing ocean conditions. In this global population genomic study of the shelled pteropod Limacina bulimoides, we combined genetic (759,000 single nucleotide polymorphisms) and morphometric data from 161 individuals, revealing three major genetic lineages (FST = 0.29 to 0.41): an 'Atlantic lineage' sampled across the Atlantic, an 'Indo-Pacific lineage' sampled in the North Pacific and Indian Ocean, and a 'Pacific lineage' sampled in the North and South Pacific. A time-calibrated phylogeny suggests that the lineages diverged about one million years ago, with estimated effective population size remaining high (~10 million) throughout Pleistocene glacial cycles. We do not observe any signatures of recent hybridisation, even in areas of sympatry in the North Pacific. While the lineages are reproductively isolated, they are morphologically cryptic, with overlapping shell shape and shell colour distributions. Despite showing that the circumglobal L. bulimoides consists of multiple species with smaller ranges than initially thought, we found that these pteropods still possess high levels of genetic variability. Our study adds to the growing evidence that speciation is often overlooked in the open ocean, and suggests the presence of distinct biological species within many other currently defined circumglobal planktonic species.
... Even if this species number could be an overestimation, it is a clear signal of a potential cripticity in these genera. Interestengly, putative species delimitated within the same morpho-molecular data correspond to different geographical areas of sampling, suggesting a mechanism of allopatric speciation, across varied pelagic habitats, as observed by Halbert et al. (2013) and Blanco-Bercial et al. (2014). ...
Zooplankton molecular analyses allow for accurate species identification with a proper molecular signature, complementing classic phenotypic-based taxonomy (α taxonomy). For the first time in the Mediterranean Sea, cytochrome oxidase I (COI) gene sequences of calanoid copepods were associated with morphological identification, HD and SEM images, using a fully integrated approach to assess taxonomic diversity. Such method was applied to selected species, generating consensus sequences from the Gulf of Naples (Central Tyrrhenian Sea, Western Mediterranean Sea) also including reference barcodes of three target species (Nannocalanus minor, Pleuromamma gracilis and the non-indigenous species (NIS) Pseudodiaptomus marinus) that are new for the Mediterranean area. The new barcodes were selected including: dominant and rare species; species that were originally described in the study area as type locality, but lacking a molecular description; emergent NIS and potential species complex. The integration between morphological and molecular identification by tree placement, using species-specific highly conserved oligonucleotides, also provided new and high-quality references of the most common and abundant copepod genera and species in the Mediterranean Sea. Our regional reference library was then integrated and analyzed with global data reference available on BOLD database to explore the presence of potential cryptic species and biogeographic patterns and links among geographically distant populations of copepods. Overall, this study provides valuable insight into the actual copepod taxonomic diversity and contributes to building baseline knowledge to monitor coastal biodiversity in neritic areas worldwide, where copepods are of paramount ecological importance, paving the way for future metabarcoding studies.
... Recent genetic studies have revealed that several zooplankton species with a circumglobal distribution are composed of cryptic species complexes or clades (Halbert et al. 2013, Hirai et al. 2015. Copepod species within the genus Pleuromamma exhibit distinct spatial structuring of the populations across major oceanic gyres (Goetze 2011) and show high levels of genetic variability between populations (Goetze et al. 2017). ...
... Because of their ubiquity, they have been the focus of numerous population genetic studies exploring the level of genetic and molecular diversity within this group. High genetic diversity was observed for P. piseki, P. gracilis (Halbert et al. 2013) and P. xiphias (Goetze et al. 2017) with phylogenetic analyses revealing distinct genetic lineages with diverse biogeographic distributions. Up to 18 strongly supported sub-populations were found within these species alone, making this group the most genetically diverse oceanic group of copepods known. ...
Niche conservatism is the hypothesis that a species' niche remains stable in space and time. This concept is central to understanding phenomena ranging from the role of climate change impacts on species biogeography to community dynamics. Marine zooplankton have been used as indicators of global change in the ocean, and niche conservatism is usually assumed for these organisms due to their high dispersal capacity, which may limit the development of local adaptations. However, recent evidence suggests that several zooplankton species with a circumglobal distribution are comprised of several cryptic species complexes, but it is unknown if the niches of cryptic species complexes have remained conserved or if they have diverged. Habitat management based on niche modelling would be strengthened by better understanding patterns of niche conservation or divergence, as the usual assumption that species have fixed environmental niches may be misleading. We assess the niche differences for 15 copepod species with populations in the North Atlantic, Southern Ocean and Australia. Pairwise differences in the realised niches were computed for each species using two complementary analyses. Our analysis indicates that global‐scale niche modelling of zooplankton cannot assume niche conservatism across all lineages and future studies should look to incorporate phylogenetic information to improve future niche estimates.
... Interestingly, an analysis targeting two species, Eucalanus hyalinus and Eucalanus spinifer globally presented a basin-scale differentiation of the two species, with subtle differences and species-specific biogeography and connectivity (Goetze, 2005). The same team repeated the same approach with Pleuromamma piseki and Pleuromamma gracilis and also showed that the mCOI analysis differed from morphological definitions (Halbert et al., 2013). In parallel, they also discriminated several clades inside these species, with some clades being widely distributed and others more local, with a general basin-scale structure. ...
Marine plankton constitute an ecosystem regrouping species of micro-organisms of a high diversity, from bacteria to jellyfishes, which wander across the currents. These organisms play an essential role in several Earth's biogeochemical cycles (carbon, oxygen, nitrate...) and in the oceanic trophic chain. Anthropogenic climate changes are set to create important upheavals in oceans, such as acidification and global warming. It is thus crucial to understand plankton populations as a whole. Recently, progress of molecular tools and high-throughput sequencing technologies allowed a deeper study of plankton's diversity, biogeography and connectivity.Population genomics is a vast domain that focuses on genetic relations between populations, species evolution and their causes. This field can offer new perspectives to understand plankton species in relation with their environment. Nevertheless, the lack of references (genomes, transcriptomes) in databases is a heavy obstacle. Following this, the Tara Oceans project, that gathered meta-omic data from hundreds of samples and locations, enabled to adopt a new and global approach.During my thesis, my goal was to exploit Tara Oceans data to improve our knowledge on population structures of plankton and to understand the impact of environmental factors. The first step was to develop a new tool to allow to identify, without references, metavariants species (MVS) via metagenomic reads. MVS are thought as the representation of species polymorphism. With the aim to adopt a global view of plankton differentiation, I applied this method to Tara samples from the Atlantic and Austral Oceans and Mediterranean Sea. By studying MVSs, I showed that population structures of plankton were mainly explained by marine currents, temperature and salinity, and was characterized by a mosaic pattern. Finally, by focusing on polar populations of the copepod Oithona similis and by integrating Tara metagenomic and metatranscriptomic data, I identified loci under selection that presented a relative expression particularly different from their genomic abundance, opening new perspectives to study acclimation and adaptation of plankton.
... ring, bongo, midwater trawl). These have been previously described for most of the oceanographic cruises listed here [11,[50][51][52][53][54]. Collection techniques for cruises SO255, KOK1703 and AMT27 have not been previously published and we describe them here. ...
Background:
The aragonite shelled, planktonic gastropod family Atlantidae (shelled heteropods) is likely to be one of the first groups to be impacted by imminent ocean changes, including ocean warming and ocean acidification. With a fossil record spanning at least 100 Ma, atlantids have experienced and survived global-scale ocean changes and extinction events in the past. However, the diversification patterns and tempo of evolution in this family are largely unknown.
Results:
Based on a concatenated maximum likelihood phylogeny of three genes (cytochrome c oxidase subunit 1 mitochondrial DNA, 28S and 18S ribosomal rRNA) we show that the three extant genera of the family Atlantidae, Atlanta, Protatlanta and Oxygyrus, form monophyletic groups. The genus Atlanta is split into two groups, one exhibiting smaller, well ornamented shells, and the other having larger, less ornamented shells. The fossil record, in combination with a fossil-calibrated phylogeny, suggests that large scale atlantid extinction was accompanied by considerable and rapid diversification over the last 25 Ma, potentially driven by vicariance events.
Conclusions:
Now confronted with a rapidly changing modern ocean, the ability of atlantids to survive past global change crises gives some optimism that they may be able to persist through the Anthropocene.
... ring, bongo, midwater trawl). These have been previously described for most of the oceanographic cruises listed here [31,[50][51][52][53][54]. ...
Background: The aragonite shelled, planktonic gastropod family Atlantidae (shelled heteropods) is likely to be one of the first groups to be impacted by imminent ocean changes, including ocean warming and ocean acidification. With a fossil record spanning at least 100 Million years (Ma), atlantids have experienced and survived global-scale ocean changes and extinction events in the past. However, the diversification patterns and tempo of evolution in this family are largely unknown.
Results: Based on a concatenated maximum likelihood phylogeny of three genes (cytochrome c oxidase subunit 1 mitochondrial DNA, 28S and 18S ribosomal rRNA) we show that the three extant genera of the family Atlantidae, Atlanta, Protatlanta and Oxygyrus, form monophyletic groups. The genus Atlanta is split into two groups, one exhibiting smaller, well ornamented shells, and the other having larger, less ornamented shells. The fossil record, in combination with a fossil-calibrated phylogeny, suggests that large scale atlantid extinction was accompanied by considerable and rapid diversification over the last 25 Ma, potentially driven by vicariance events.
Conclusions: Now confronted with a rapidly changing modern ocean, the ability of atlantids to survive past global change crises gives some optimism that they may be able to persist through the Anthropocene.
