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"Copepoda - classification"
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Genome architecture evolution in an invasive copepod species complex
Chromosomal fusions are hypothesized to facilitate evolutionary adaptation, but empirical evidence has been scarce. Here, we analyze chromosome-level genome sequences of three sibling species within the copepod
Eurytemora affinis
species complex, known for its remarkable ability to rapidly colonize new habitats. Genomes of this species complex show expansions of ion transport-related gene families, likely related to adaptation to various environmental salinities. Among three genetically distinct sibling species, we discover notable patterns of chromosomal evolution, with chromosomal fusions observed in two different sibling species. As a result of these chromosomal fusions, functionally linked ion transport-related genes located near the telomeres become joined near the newly formed centromeres, where recombination is low. Notably, for the highly invasive
E. carolleeae
and to a lesser extent for
E. gulfia
, the ancient chromosomal fusion sites, especially the centromeres, are significantly enriched with contemporary signatures of selection between saline and freshwater populations. This study uncovers intriguing patterns of genome architecture evolution with potentially important implications for mechanisms of adaptive evolution in response to rapid environmental change.
Chromosomal fusions are hypothesized to promote adaptation, but direct evidence has been scarce. By analyzing chromosome-level genomes of three invasive copepod sibling species, this study shows that ancient fusions reshaped genome architecture and continue to impact contemporary selection responses.
Journal Article
MIG-seq: an effective PCR-based method for genome-wide single-nucleotide polymorphism genotyping using the next-generation sequencing platform
Restriction-enzyme (RE)-based next-generation sequencing methods have revolutionized marker-assisted genetic studies; however, the use of REs has limited their widespread adoption, especially in field samples with low-quality DNA and/or small quantities of DNA. Here, we developed a PCR-based procedure to construct reduced representation libraries without RE digestion steps, representing
de novo
single-nucleotide polymorphism discovery and its genotyping using next-generation sequencing. Using multiplexed inter-simple sequence repeat (ISSR) primers, thousands of genome-wide regions were amplified effectively from a wide variety of genomes, without prior genetic information. We demonstrated: 1) Mendelian gametic segregation of the discovered variants; 2) reproducibility of genotyping by checking its applicability for individual identification; and 3) applicability in a wide variety of species by checking standard population genetic analysis. This approach, called multiplexed ISSR genotyping by sequencing, should be applicable to many marker-assisted genetic studies with a wide range of DNA qualities and quantities.
Journal Article
Taxonomic Resolutions Based on 18S rRNA Genes: A Case Study of Subclass Copepoda
Biodiversity studies are commonly conducted using 18S rRNA genes. In this study, we compared the inter-species divergence of variable regions (V1-9) within the copepod 18S rRNA gene, and tested their taxonomic resolutions at different taxonomic levels. Our results indicate that the 18S rRNA gene is a good molecular marker for the study of copepod biodiversity, and our conclusions are as follows: 1) 18S rRNA genes are highly conserved intra-species (intra-species similarities are close to 100%); and could aid in species-level analyses, but with some limitations; 2) nearly-whole-length sequences and some partial regions (around V2, V4, and V9) of the 18S rRNA gene can be used to discriminate between samples at both the family and order levels (with a success rate of about 80%); 3) compared with other regions, V9 has a higher resolution at the genus level (with an identification success rate of about 80%); and 4) V7 is most divergent in length, and would be a good candidate marker for the phylogenetic study of Acartia species. This study also evaluated the correlation between similarity thresholds and the accuracy of using nuclear 18S rRNA genes for the classification of organisms in the subclass Copepoda. We suggest that sample identification accuracy should be considered when a molecular sequence divergence threshold is used for taxonomic identification, and that the lowest similarity threshold should be determined based on a pre-designated level of acceptable accuracy.
Journal Article
The Copepoda mitogenome as a dynamic evolutionary landscape
Copepods are an extraordinarily diverse group that exhibit a broad spectrum of morphological, physiological, life-history traits, and habitat specializations. Despite their ecological, evolutionary, and economic importance, molecular resources are scarce, limiting our understanding of their diversification and adaptation. We analysed the evolution of copepod mitogenomes at different phylogenetic scales using 19 complete mitogenomes deposited in GenBank along with five de novo assemblies from species of the genus Leptodiaptomus from Central Mexico. All five new mitogenomes are circularized and include all canonical metazoan coding regions but differ in the composition and size of non-coding regions (NCRs). The mitochondrial genomes of the four populations of the L. sicilis-group are the largest reported to date in Copepoda (>36,000 bp). The NCRs of Leptodiaptomus spp. contain repeated regions, pseudogenes, long palindromes with secondary structures, and open reading frames, although much of their content is still unexplained. Gene ordering in Copepoda is highly dynamic, and even gene blocks highly conserved across metazoans are either absent or occur at a low frequency. In Calanoida, the NCRs have expanded considerably, whereas in podoplean clades (Cyclopoida, Harpacticoida, and Siphonostomatoida), they remain similar to the hypothetical ancestral state. While some genes display evident signatures of purifying selection, most exhibit evidence of positive selection across all branches of the phylogeny. These findings offer a basis for further research on the molecular mechanisms driving copepod adaptation and diversification, as well as for refining predictions of their responses to environmental change.
Journal Article
Molecular Phylogeny and Revision of Copepod Orders (Crustacea: Copepoda)
For the first time, the phylogenetic relationships between representatives of all 10 copepod orders have been investigated using 28S and 18S rRNA, Histone H3 protein and COI mtDNA. The monophyly of Copepoda (including Platycopioida Fosshagen, 1985) is demonstrated for the first time using molecular data. Maxillopoda is rejected, as it is a polyphyletic group. The monophyly of the major subgroups of Copepoda, including Progymnoplea Lang, 1948 (=Platycopioida); Neocopepoda Huys and Boxshall, 1991; Gymnoplea Giesbrecht, 1892 (=Calanoida Sars, 1903); and Podoplea Giesbrecht, 1892, are supported in this study. Seven copepod orders are monophyletic, including Platycopioida, Calanoida, Misophrioida Gurney, 1933; Monstrilloida Sars, 1901; Siphonostomatoida Burmeister, 1834; Gelyelloida Huys, 1988; and Mormonilloida Boxshall, 1979. Misophrioida (=Propodoplea Lang, 1948) is the most basal Podoplean order. The order Cyclopoida Burmeister, 1835, is paraphyletic and now encompasses Poecilostomatoida Thorell, 1859, as a sister to the family Schminkepinellidae Martinez Arbizu, 2006. Within Harpacticoida Sars, 1903, both sections, Polyarthra Lang, 1948, and Oligoarthra Lang, 1948, are monophyletic, but not sister groups. The order Canuelloida is proposed while maintaining the order Harpacticoida s. str. (Oligoarthra). Cyclopoida, Harpacticoida and Cyclopinidae are redefined, while Canuelloida ordo. nov., Smirnovipinidae fam. nov. and Cyclopicinidae fam. nov are proposed as new taxa.
Journal Article
Exploring South Africa's hidden marine parasite diversity: two new marine Ergasilus species (Copepoda: Cyclopoida: Ergasilidae) from the Evileye blaasop, Amblyrhynchote honckenii (Bloch)
Marine parasites remain understudied in South Africa with little information available on their diversity and the effects these parasites may have on their hosts. This is especially true for parasitic copepods within the family Ergasilidae. Among the 4 genera known in Africa, Ergasilus Nordmann, 1832 is the most speciose with 19 reported species. However, this represents only 12% (19/163) of the global diversity. Furthermore, only 5 known African species are reported from marine environments, and only 1 is reported from the South African coastline. Given the rich biodiversity along this coastline, a high marine parasite diversity could be expected from these shores. As a case study, the Evileye blaasop, Amblyrhynchote honckenii (Bloch), a marine and brackish fish species, was screened for parasites along the South African coastline. This resulted in the discovery of 2 species of Ergasilus new to science ( Ergasilus arenalbus n. sp. and Ergasilus chintensis n. sp.), which makes them the second and third ergasilid species reported for tetraodontid pufferfishes worldwide. Although genetically distinct, the 2 newly described species clustered in the same subclade within the Ergasilidae based on 18S rDNA, 28S rDNA and COI mtDNA phylogenies. The newly described species differ morphologically from each other, and their respective congeners based on the size and armature of the antenna; body segmentation; and general ornamentation throughout the entire body. The addition of these 2 new species from a single host species indicates that South Africa's marine fishes contain most probably a hidden parasitic copepod diversity that is worth exploring.
Journal Article
Phylogeography of Pennella (Copepoda: Siphonostomatoida: Pennellidae) indicates interoceanic dispersal mediated by cetacean and fish hosts
Copepods of the genus Pennella parasitize a wide range of marine animals, including cetaceans, teleosts, and cephalopods worldwide. Their taxonomy is unclear, as there is incongruence between morphological and genetic data and incomplete species coverage. This study provides new morphological and genetic (COI) data from 23 specimens of Pennella cf. filosa (syn. P. balaenoptera) from western Mediterranean whales and a swordfish. First, their position in the phylogeny of Pennella was assessed and species delimitation revisited using all available Pennella COI sequences (n = 189), obtained from Mediterranean and north Pacific specimens from 18 host species (including multiple cetaceans and teleosts). Second, it was investigated whether the geographic location, degree of host vagility, or host taxonomic identity help explain genetic differentiation. Five distinct haplotype groups with varying genetic divergence were distinguished. Although the presence of sibling species cannot be ruled out, species delimitation methods could not find interspecific genetic differences, leaving the taxonomy of the genus unresolved. The observed genetic differentiation could not be attributed to geography or host type. This suggests that members of the genus Pennella show low specificity for definitive hosts and interoceanic dispersal mediated by some vagile definitive hosts. The use of more genetic markers for addressing these questions in the future is encouraged.
Journal Article
Integrating DNA metabarcoding and morphological analysis improves marine zooplankton biodiversity assessment
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.
Journal Article
Morphological and molecular diversity patterns of the genus Tropodiaptomus Kiefer, 1932 (Copepoda, Calanoida, Diaptomidae) in Thailand
Tropodiaptomus
is one of the most specious genera in the family Diaptomidae, but it is often rare in terms of distribution and abundance. Moreover,
Tropodiaptomus
species show a noteworthy variability in some of the morphological characters considered of prime importance in diaptomid taxonomy, and the presence of cryptic or pseudocryptic species is likely. Thus, through a geographically-wide sampling in Thailand, we aimed to investigate the local diversity of the genus and to compare the morphological and molecular diversity pattern based on mitochondrial and nuclear genes sequences. DNA taxonomy was also implemented in order to check whether the
Tropodiaptomus
lineages were independent species according to the “evolutionary genetic species concept”. Six
Tropodiaptomus
morphospecies were found, three of which are putative species new to Science pending a formal description. The finding of such a high incidence of undescribed species stresses the existence of a significant “Linnean shortfall” affecting Thai diaptomids. The molecular results showed that most of the studied species could be identified consistently with their morphology-based taxonomy. However,
Tropodiaptomus vicinus
and
T
. cf.
lanaonus
showed a high level of genetic diversity, suggesting that traditional morphological techniques might be inadequate for correctly assessing their taxonomical status.
Journal Article