Pseudo-cryptic Speciation Research Articles

Integrative taxonomy in Syllis prolifera (Annelida, Syllidae): from a unique cosmopolitan species to a complex of pseudocryptic species.

Syllis prolifera (Syllidae, Syllinae) is an abundant species of marine annelids commonly found in warm to temperate waters worldwide. Although morphological variability occurs among populations, S. prolifera has long been considered a cosmopolitan species, widely distributed in coastal environments, including acidified and polluted areas. However, the increasing number of cases of cryptic and pseudocryptic speciation in several polychaete families in recent years has led us to question whether S. prolifera represents a single globally distributed taxon or is a species complex. To address this question, we conducted an integrative study, combining morphological, ecological and molecular data of 52 S. prolifera specimens collected in different localities across the western Mediterranean Sea and the Gulf of Cadiz. Our phylogenetic and species delimitation analyses that included two mitochondrial DNA markers (COI and 16S rRNA ) were congruent in not considering S. prolifera a unique entity. Five distinct lineages that can also be recognised by certain morphological and ecological traits were identified from these analyses instead. Overall, our study does not support the homogeneity of S. prolifera across the Mediterranean Sea, providing a new example of pseudocrypticism in marine invertebrates.

A stomach plate to divide them all: a phylogenetic reassessment of the family Tritoniidae (Nudibranchia: Cladobranchia)

Abstract The phylogeny of the family Tritoniidae has recently been studied with significant advances, but the relationships between genera are still controversial. In our study, we investigated the phylogeny of Tritoniidae using the most diverse taxon sampling possible. We applied an integrative approach based on new sequences of two mitochondrial genes (COI and 16S), a nuclear gene (H3) and morpho-anatomical characters. The monophyly of the family Tritoniidae was not recovered in our phylogenetic analyses. In view of our results, we propose a new rearrangement at the subfamily and genus levels. The plate-bearing genera are raised to the subfamily level as the monophyletic Marioniinae subfam. nov., formed by Marionia and the reinstated Marioniopsis. The remaining plate-less genera are raised to the subfamily level as the monophyletic Tritoniinae Lamarck, 1809. The genus Myrella is reinstated to assign the Antarctic and sub-Antarctic tritoniids. The taxonomic status of the monotypic Tritonidoxa is confirmed. Species delimitation analyses reveal a new large Marionia species from the Gulf of Cádiz (south-west Spain, Atlantic Ocean) and evidence for the pseudocryptic speciation of numerous Atlantic–Mediterranean and Indo-Pacific tritoniids. Finally, taxonomic notes are provided for several species according to the proposed rearrangement.

Molecular systematics of Crassiphycus and Hydropuntia (Gracilariales, Rhodophyta) with the description of poorly known taxa in the Western Atlantic Ocean

ABSTRACT This study builds on recent treatments of the marine red algal family Gracilariaceae (Gracilariales) focusing in detail on Hydropuntia and Crassiphycus. Species in these two genera often present identification problems due to high levels of morphologial similarity among genetically distinct species, and high levels of phenotypic plasticity, leading to pseudo-cryptic speciation and homoplasies. In order to resolve long standing problems, clarify some species concepts and better understand the evolution of the group, we performed phylogenetic analyses of all plastid rbcL DNA sequences available for known Hydropuntia and Crassiphycus species, including newly sequenced specimens. Our results revealed the presence of potentially undescribed species, the existence of strong phylogeographic patterns below and above the species level and helped re-delineate morphologically similar taxa. New detailed morphological descriptions for three common yet poorly known Western Atlantic species are provided: C. secundus, C. usneoides and H. rangiferina. H. rangiferina from the Indo-Pacific is a distinct species from the true H. rangiferina and represents a putative undescribed species. We also provide a time-calibrated phylogeny for the six genera in the Gracilariales to identify past geological and climatic processes associated with their origin and diversification.

The return of the clown: pseudocryptic speciation in the North Pacific clown nudibranch, Triopha catalinae (Cooper, 1863) sensu lato identified by integrative taxonomic approaches

The North Pacific nudibranch species Triopha catalinae (Cooper, 1863), also known as the clown nudibranch, includes two distinct morphotypes: the trans-Pacific morphotype, known from South Korea to Southern California, and the eastern Pacific-only morphotype from Southeast Alaska to Baja California. We tested the hypothesis that Triopha catalinae is a species complex by applying an integrative taxonomic approach that included (1) phylogenetic analyses of the mitochondrial 16S and COI, and the nuclear Histone H3 genes; (2) haplotype network analysis based on COI sequences; (3) Automatic Barcode Gap Discovery (ABGD) species delimitation analysis based on 16S and COI sequences; and (4) comparative internal and external morphological studies. Specimens of two morphotypes were found to be genetically distinct; they clustered into two well-supported clades in the phylogenetic analyses and two groups in the TCS haplotype network. Moreover, these two groups displayed morphological differences in the dorsal tubercles and radula structure: the trans-Pacific morphotype specimens possess relatively small and dendritic dorsal tubercles, two rows of arborescent tubercles on the dorso-lateral appendages of larger individuals, and radular formula 19–24 × (9–12.5–10.1.5–10.9–12). Specimens of the eastern Pacific-only morphotype have relatively large, conical or rounded dorsal tubercles, and radular formula 48–79 × (16–18.17–33.1.17–33.16–18). Finally, the ABGD analysis confirmed that these two morphotypes constitute different species. A review of the literature (including original descriptions) and available type material revealed that Triopha modesta Bergh, 1880 and T. catalinae are the valid names for the trans-Pacific and eastern Pacific-only morphotype, respectively.

Evolutionary history of species of the firefly subgenus Hotaria (Coleoptera, Lampyridae, Luciolinae, Luciola) inferred from DNA barcoding data

The firefly subgenus Hotaria sensu lato of the genus Luciola currently includes four morphospecies: L. (H.) parvula, L. (H.) unmunsana, L (H.) papariensis, and L. (H.) tsushimana. The latter three are taxonomically controversial based on both morphological and molecular data. We examined the phylogenetic relationships and evolutionary history of the species and related congeners using partial COI gene sequences (DNA barcoding). Our phylogenetic analyses consistently supported the monophyly of Hotaria sensu lato, but did not resolve the generic rank. The two types of L. (H.) parvula in Japan can be considered distinct species that arose by pseudocryptic speciation during the Miocene, with substantial genetic divergence (15.41%). Three morphospecies, L. (H.) unmunsana, L (H.) papariensis, and L. (H.) tsushimana, split into several polyphyletic or paraphyletic groups, forming entangled species groups. They are considered an incipient group that is distinguishable genetically but not morphologically, with evidence for recent allopatric speciation events corresponding to geologic events and sea-level changes during the Pliocene and Pleistocene. Group III of L. (H.) unmunsana collected from the Jeolla region is a new taxon.

Inferred pseudo-cryptic speciation in the coccolithophore species Braarudosphaera bigelowii (Gran and Braarud) during the Early Paleocene (Danian)

Abstract Pseudo-cryptic speciation occurs commonly in living oceanic plankton. In the coccolithophores, recent genetic studies have revealed that Braarudosphaera bigelowii has a number of unique genotypes that correlate well with pentalith size, indicating that this coccolithophore “species” actually contains multiple pseudo-cryptic taxa. In order to look for evidence of pseudo-cryptic speciation in the past, we measured the radii of 2800 B. bigelowii pentaliths from the Braarudosphaera-rich limestones that contain the GSSP for the Lower/Middle Paleocene (Danian/Selandian) boundary at Zumaia, Spain. Analysis of the radius measurements using the Expectation-Maximization algorithm yielded two size groups, herein termed form X (

Global phylogeography of Oithona similis s.l. (Crustacea, Copepoda, Oithonidae) – A cosmopolitan plankton species or a complex of cryptic lineages?

Traditionally, many small-sized copepod species are considered to be widespread, bipolar or cosmopolitan. However, these large-scale distribution patterns need to be re-examined in view of increasing evidence of cryptic and pseudo-cryptic speciation in pelagic copepods. Here, we present a phylogeographic study of Oithona similis s.l. populations from the Arctic Ocean, the Southern Ocean and its northern boundaries, the North Atlantic and the Mediterrranean Sea. O. similis s.l. is considered as one of the most abundant species in temperate to polar oceans and acts as an important link in the trophic network between the microbial loop and higher trophic levels such as fish larvae. Two gene fragments were analysed: the mitochondrial cytochrome oxidase c subunit I (COI), and the nuclear ribosomal 28 S genetic marker. Seven distinct, geographically delimitated, mitochondrial lineages could be identified, with divergences among the lineages ranging from 8 to 24%, thus representing most likely cryptic or pseudocryptic species within O. similis s.l. Four lineages were identified within or close to the borders of the Southern Ocean, one lineage in the Arctic Ocean and two lineages in the temperate Northern hemisphere. Surprisingly the Arctic lineage was more closely related to lineages from the Southern hemisphere than to the other lineages from the Northern hemisphere, suggesting that geographic proximity is a rather poor predictor of how closely related the clades are on a genetic level.

Molecular and phylogenetic characterization of Ostreopsis (Dinophyceae) and the description of a new species, Ostreopsis rhodesae sp. nov., from a subtropical Australian lagoon

Cryptic and pseudo-cryptic species are common amongst marine phytoplankton, and may cause misleading inferences of ecological and physiological data of plankton community studies. Deciphering the diversity and distribution of species of the benthic dinoflagellate Ostreopsis is one example, as there are many morphologically indistinct clades that differ greatly genetically and toxicologically from one another. In this study, a new species, Ostreopsis rhodesae from the southern Great Barrier Reef was described. While it initially appeared to be highly similar to several other Ostreopsis species, we found O. rhodesae can be distinguished based on the relative size of the second apical plate (2′), which is twice as long as the APC plate, and separates the third apical (3′) from the third precingular (3′′) plate. Phylogenetic trees based on the SSU, ITS/5.8S and D1-D2 and D8-D10 regions of the LSU rRNA were well supported, and showed a clear difference to other Ostreopsis clades. Compensatory base changes (CBCs) were identified in helices of the ITS2 between O. rhodesae and O. cf. ovata and O. cf. siamensis, which were also present in the same habitat. Fish gill cell lines were toxic to O. rhodesae, cell extracts but no palytoxin-like analogues were found in them. The findings highlight a case of pseudo-cryptic speciation, found in sympatry with closely related and morphologically similar species, but biologically and functionally distinct.

Evidence of cryptic and pseudocryptic speciation in Brachypodopsis baumi species complex (Acari, Hydrachnidia, Aturidae) from Borneo, with description of three new species

Abstract Water mites of the Brachypodopsis baumi species complex are confined to SE Asia, and up to now have been considered to belong to one species only. In the present study we used morphological data and DNA barcoding (556 bp of the mitochondrial gene cytochrome c oxidase subunit I, COI) to resolve taxonomic issues within the species complex from Borneo. The use of an integrative-taxonomy approach confirmed the identification of two “cryptic” species., i.e., Brachypodopsis crockerensis sp. nov. and B. kinabaluensis sp. nov. and one “pseudocryptic” species B. selampandei sp. nov. Based on phylogenetic analyses, Paraxanopsis truncata was transferred to the subgenus Brachypodopsis (s. s.). Brachypodopsis. gibberipalpis (Viets, 1935), a taxon previously synonymized with B. baumi, which is reinstated as a valid species.

Evidence of cryptic and pseudocryptic speciation in the Paracalanus parvus species complex (Crustacea, Copepoda, Calanoida)

IntroductionMany marine planktonic crustaceans such as copepods have been considered as widespread organisms. However, the growing evidence for cryptic and pseudo-cryptic speciation has emphasized the need of re-evaluating the status of copepod species complexes in molecular and morphological studies to get a clearer picture about pelagic marine species as evolutionary units and their distributions. This study analyses the molecular diversity of the ecologically important Paracalanus parvus species complex. Its seven currently recognized species are abundant and also often dominant in marine coastal regions worldwide from temperate to tropical oceans.ResultsCOI and Cytochrome b sequences of 160 specimens of the Paracalanus parvus complex from all oceans were obtained. Furthermore, 42 COI sequences from GenBank were added for the genetic analyses. Thirteen distinct molecular operational taxonomic units (MOTU) and two single sequences were revealed with cladistic analyses (Maximum Likelihood, Bayesian Inference), of which seven were identical with results from species delimitation methods (barcode gaps, ABDG, GMYC, Rosenberg’s P(AB)). In total, 10 to 12 putative species were detected and could be placed in three categories: (1) temperate geographically isolated, (2) warm-temperate to tropical wider spread and (3) circumglobal warm-water species.ConclusionsThe present study provides evidence of cryptic or pseudocryptic speciation in the Paracalanus parvus complex. One major insight is that the species Paracalanus parvus s.s. is not panmictic, but may be restricted in its distribution to the northeastern Atlantic.

High purity gamma amanitin isolation from Amanita phalloides mushroom

Cryptic and pseudo-cryptic species are common amongst marine phytoplankton, and may cause misleading inferences of ecological and physiological data of plankton community studies. Deciphering the diversity and distribution of species of the benthic dinoflagellate Ostreopsis is one example, as there are many morphologically indistinct clades that differ greatly genetically and toxicologically from one another. In this study, a new species, Ostreopsis rhodesae from the southern Great Barrier Reef was described. While it initially appeared to be highly similar to several other Ostreopsis species, we found O. rhodesae can be distinguished based on the relative size of the second apical plate (2′), which is twice as long as the APC plate, and separates the third apical (3′) from the third precingular (3′′) plate. Phylogenetic trees based on the SSU, ITS/5.8S and D1-D2 and D8-D10 regions of the LSU rRNA were well supported, and showed a clear difference to other Ostreopsis clades. Compensatory base changes (CBCs) were identified in helices of the ITS2 between O. rhodesae and O. cf. ovata and O. cf. siamensis, which were also present in the same habitat. Fish gill cell lines were toxic to O. rhodesae, cell extracts but no palytoxin-like analogues were found in them. The findings highlight a case of pseudo-cryptic speciation, found in sympatry with closely related and morphologically similar species, but biologically and functionally distinct.

Process length variation of the cyst of the dinoflagellate Protoceratium reticulatum in the North Pacific and Baltic‐Skagerrak region: calibration as an annual density proxy and first evidence of pseudo‐cryptic speciation

AbstractProcess length variation of cysts of the dinoflagellate Protoceratium reticulatum (Claparède et Lachmann) Bütschli in surface sediments from the North Pacific was investigated. The average process length showed a significant inverse relation to annual seawater density: σt annual = −0.8674 × average process length + 1029.3 (R2 = 0.84), with a standard error of 0.78 kg m−3. A sediment trap study from Effingham Inlet in British Columbia revealed the same relationship between average process length and local seawater density variations. In the Baltic–Skagerrak region, the average process length variation was related significantly to annual seawater density: σt annual = 3.5457 × average process length − 993.28 (R2 = 0.86), with a standard error of 3.09 kg m−3. These calibrations cannot be reconciled, which accentuates the regional character of the calibrations. This can be related to variations in molecular data (small subunit, long subunit and internal transcribed spacer sequences), which show the presence of several genotypes and the occurrence of pseudo‐cryptic speciation within this species. Copyright © 2012 John Wiley & Sons, Ltd.

329 Process length variation of the cyst of the dinoflagellate Protoceratium reticulatum in the North Pacific : a new density proxy and first evidence of pseudo-cryptic speciation

329 Process length variation of the cyst of the dinoflagellate Protoceratium reticulatum in the North Pacific : a new density proxy and first evidence of pseudo-cryptic speciation

Pseudocryptic speciation of Chrysochroa fulgidissima (Coleoptera: Buprestidae) with two new species from Korea, China and Vietnam

In the present study, the jewel beetle Chrysochroa fulgidissima was taxonomically reassessed based on molecular analyses of cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (16S) gene partial sequences, and morphological approaches, excluding the subspecies Chrysochroa fulgidissima adachii. Molecular (three data sets, COI, 16S, and COI + 16S in mtDNA) and morphological (quantitative and qualitative characters) evidence suggested that Ch. fulgidissima consists of four independent species found in seven geographical regions, namely Korea, Japan and Taiwan, China (GuangXi and Hainan) and Vietnam, and Okinawa Island. As a result of the large genetic divergences and subtle morphological differences amongst these populations, we were able to infer that the nominotypical subspecies, Chrysochroa fulgidissima fulgidissima, is divided into three pseudocryptic species that have undergone allopatric speciation events. Thus, we propose that the subspecies Chrysochroa fulgidissima alternans should be upgraded to valid specific status. We also provide a description of two new species, Chrysochroa coreana sp. nov. from Korea, and Chrysochroa pseudofulgidissima sp. nov. from China and Vietnam. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164, 71–98.

Morphological, genetic and mating diversity within the widespread bioindicator Nitzschia palea (Bacillariophyceae)

Trobajo R., Clavero E., Chepurnov V.A., Sabbe K., Mann D.G., Ishihara S. and Cox E.J. 2009. Morphological, genetic and mating diversity within the widespread bioindicator Nitzschia palea (Bacillariophyceae). Phycologia 48: 443–459. DOI: 10.2216/08-69.1.Nitzschia palea (Kützing) W. Smith is believed to be a widely distributed diatom and is common in various lotic and lentic freshwater habitats. However, it is also taxonomically problematic. As part of a multidisciplinary study of this diatom, 25 clones identified morphologically as N. palea were isolated from different freshwater habitats around the world (Belgium, Brazil, Egypt, India, Japan, Paraguay, Spain, Sri Lanka and the United Kingdom). Morphological and genetic diversity (using the hypervariable D1–D2 domains of LSU rDNA) were investigated, and an almost complete set of interclonal crossing experiments was carried out. Results indicate that N. palea is not a simple, homogeneous taxon and that N. palea will probably have to be split into three or more species. Molecular and mating groups do not separate along the traditional morphological boundaries among N. palea varieties, in particular between vars palea and debilis, two taxa that are commonly used to discriminate between different degrees of water pollution. At least two of the putative species within the N. palea complex appear to be geographically widespread. Because of the complexity of variation revealed by the LSU, mating and morphometric data, it is clear that further work, using extra genetic markers and new isolates, will be needed to determine the full extent of cryptic and pseudocryptic speciation in N. palea and to investigate whether the segregate species are ecologically differentiated and have value as indicators.

Pseudo-cryptic speciation in Braarudosphaera bigelowii (Gran and Braarud) Deflandre

Partial SSU rDNA sequences were obtained from 13 naturally collected cells of Braarudosphaera bigelowii obtained from various parts of seas surrounding Japan. Together with the two previously reported sequences, 15 specimens were classified into five SSU rDNA Genotypes I–V. Based on the side length of the pentaliths forming the coccosphere, these specimens were also classified into three size-morphotypes; Intermediate form-A, Intermediate form-B, and Large form. Genotypes of B. bigelowii were well correlated with size-morphotypes but not with sampling area. This result indicates that size differences in B. bigelowii are the results of speciation and not of intra-population variety. Therefore, Genotypes I and II (Intermediate form-A) and Genotypes IV and V (Large form) are regarded as pseudo-cryptic sibling species of typical B. bigelowii (Genotype III, Intermediate form-B), which corresponds to the original description of the species. From the SSU rDNA sequences, it is evident that Genotype V arose from Genotype IV, and Genotype IV originated from Genotype III. The specimens of Genotypes III–V showed size increase of pentaliths in accordance with their branching order. The consistency in the relationship between genotypes and size-morphotypes of living B. bigelowii-complex observed in this study suggests that inconsistency of size range of ‘ B. bigelowii’ pentaliths among different geological ages reported by palaeontological studies stems from additional pseudo-cryptic speciation in the lineage of ‘ B. bigelowii’ in the geological past.

Phylogenetic and morphometric differentiation reveal geographic radiation and pseudo-cryptic speciation in a mangrove crab from the Indo-West Pacific

The presence of boundaries to dispersal has been recently documented for many Indo-West Pacific (IWP) species with planktonic propagules and a widespread distribution. We studied the phylogeography of the mangrove crab Neosarmatium meinerti (Brachyura: Sesarmidae) and the phylogenetic relationship to its presumed sister species N. fourmanoiri in the IWP in order to compare intraspecific with interspecific diversity. Portions of the mitochondrial genes 16S and CoxI were sequenced for 23 specimens of N. meinerti and 5 N. fourmanoiri, while a fragment of the 28S was obtained for a subset of specimens. Genetic data are supplemented by morphometric and based on 37 adult males of N. meinerti and 9 males of N. fourmanoiri. The conserved nuclear 28S reveals the existence of a genetic break between the Indian and Pacific oceans. Otherwise, mitochondrial genes as well as morphometry clearly support the presence of a species complex within N. meinerti composed by four well structured and geographically defined lineages: East African coast; western Indian Ocean islands; South East Asia; and Australia.