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Supplementary material 3 from: Jażdżewska AM, Rewicz T, Mamos T, Wattier R, Bącela-Spychalska K, Grabowski M (2020) Cryptic diversity and mtDNA phylogeography of the invasive demon shrimp, Dikerogammarus haemobaphes (Eichwald, 1841), in Europe. NeoBiota 57: 53-86. https://doi.org/10.3897/neobiota.57.46699
Table S3
Cryptic genetic diversity and cytonuclear discordance characterize contact among Canada jay (Perisoreus canadensis) morphotypes in western North America
<p>Three distinct Canada jay (<em>Perisoreus canadensis</em>) morphotypes with easily recognizable plumage traits come into contact in western North America. Recent work demonstrated high genetic structure across the species' range; however, patterns of genetic variation in these contact zones remain unknown. We categorized 605 individuals into one of three morphotypes (Pacific, Rocky Mountain, and Boreal) based on plumage, and genotyped individuals at the mtDNA control region and 12 microsatellite loci to assess the extent of hybridization between morphotypes. Our data showed cryptic genetic diversity and high cytonuclear discordance among morphotypes within contact zones, which is likely the result of recent and historical admixture. The distributions of the Boreal and Pacific morphotypes each showed a strong association with a single, distinct genetic group, whereas the Rocky Mountain morphotype exhibited higher genetic diversity and was associated with multiple genotypes. Our analyses show the importance of considering both plumage and genetic traits when examining contact zones between closely related taxa. Finally, the data presented in this study reaffirm that the Pacific morphotype is distinct from the Boreal and Rocky Mountain morphotypes based on genetic, phenotypic, and ecological data, indicating that the Pacific morphotype should be re-elevated to a full species.</p>
Data from: Cryptic diversity and discordance in single-locus species delimitation methods within horned lizards (Phrynosomatidae: Phrynosoma)
Biodiversity reduction and loss continues to progress at an alarming rate, and thus there is widespread interest in utilizing rapid and efficient methods for quantifying and delimiting taxonomic diversity. Single-locus species-delimitation methods have become popular, in part due to the adoption of the DNA barcoding paradigm. These techniques can be broadly classified into tree-based and distance-based methods depending on whether species are delimited based on a constructed genealogy. Although the relative performance of these methods has been tested repeatedly with simulations, additional studies are needed to assess congruence with empirical data. We compiled a large data set of mitochondrial ND4 sequences from horned lizards (Phrynosoma) to elucidate congruence using four tree-based (single-threshold GMYC, multiple-threshold GMYC, bPTP, mPTP) and one distance-based (ABGD) species delimitation models. We were particularly interested in cases with highly uneven sampling and/or large differences in intraspecific diversity. Results showed a high degree of discordance among methods, with multiple-threshold GMYC and bPTP suggesting an unrealistically high number of species (29 and 26 species within the P. douglasii complex alone). The single-threshold GMYC model was the most conservative, likely a result of difficulty in locating the inflection point in the genealogies. mPTP and ABGD appeared to be the most stable across sampling regimes and suggested the presence of additional cryptic species that warrant further investigation. These results suggest that the mPTP model may be preferable in empirical data sets with highly uneven sampling or large differences in effective population sizes of species.
Data from: Nomenclature for the nameless: a proposal for an integrative molecular taxonomy of cryptic diversity exemplified by planktonic foraminifera
Investigations of biodiversity, biogeography and ecological processes rely on the identification of "species" as biologically significant, natural units of evolution. In this context, morpho-taxonomy only provides an adequate level of resolution if reproductive isolation matches morphological divergence. In many groups of organisms, morphologically defined species often disguise considerable genetic diversity, which may be indicative of the existence of cryptic species. The diversity hidden by morphological species can be disentangled through genetic surveys, which also provide access to data on the ecological distribution of genetically circumscribed units. These units can be identified by unique DNA sequence motifs and allow studies of evolutionary and ecological processes at different levels of divergence. However, the nomenclature of genetically circumscribed units within morphological species is not regulated and lacks stability. This represents a major obstacle to efforts to synthesize and communicate data on genetic diversity for multiple stakeholders. We have been confronted with such an obstacle in our work on planktonic foraminifera, where the stakeholder community is particularly diverse, involving geochemists, paleoceanographers, paleontologists and biologists, and the lack of stable nomenclature beyond the level of formal morphospecies prevents effective transfer of knowledge. To circumvent this problem, we have designed a stable, reproducible and flexible nomenclature system for genetically circumscribed units, analogous to the principles of a formal nomenclature system. Our system is based on the definition of unique DNA sequence motifs collocated within an individual, their typification (in analogy with holotypes), utilization of their hierarchical phylogenetic structure to define levels of divergence below that of the morphospecies, and a set of nomenclature rules assuring stability. The resulting molecular operational taxonomic units (MOTUs) remain outside the domain of current nomenclature codes, but are linked to formal morphospecies as regulated by the codes. Subsequently we show how this system can be applied to classify genetically defined units using the SSU rDNA marker in planktonic foraminifera and we highlight its potential use for other groups of organisms where similarly high levels of connectivity between molecular and formal taxonomies can be achieved.
Data from: The cryptic and the apparent reversed: lack of genetic differentiation within the morphologically diverse plexus of the planktonic foraminifer Globigerinoides sacculifer
Previous genetic studies of extant planktonic foraminifera have provided evidence that the traditional, strictly morphological definition of species in these organisms underestimates their biodiversity. Here, we report the first case where this pattern is reversed. The modern (sub)tropical species plexus Globigerinoides sacculifer is characterized by large morphological variability, which has led to the proliferation of taxonomic names attributed to morphological end-members within the plexus. In order to clarify the taxonomic status of its morphotypes and to investigate the genetic connectivity among its currently partly disjunct (sub)tropical populations, we carried out a global survey of two ribosomal RNA regions (SSU and ITS-1) in all recent morphotypes of the plexus collected throughout (sub)tropical surface waters of the global ocean. Unexpectedly, we find an extremely reduced genetic variation within the plexus and no correlation between genetic and morphological divergence, suggesting taxonomical overinterpretation. The genetic homogeneity within the morphospecies is unexpected, considering its partly disjunct range in the (sub)tropical Atlantic and Indo-Pacific and its old age (early Miocene). A sequence variant in the rapidly evolving ITS-1 region indicates the existence of an exclusively Atlantic haplotype, which suggests an episode of relatively recent (last glacial) isolation, followed by subsequent resumption of unidirectional gene flow from the Indo-Pacific into the Atlantic. This is the first example in planktonic foraminifera where the morphological variability in a morphospecies exceeds its rDNA genetic variability. Such evidence for inconsistent scaling of morphological and genetic diversity in planktonic foraminifera could complicate the interpretation of evolutionary patterns in their fossil record.
Data from: Coalescent-based species delimitation approach uncovers high cryptic diversity in the cosmopolitan lichen-forming fungal genus Protoparmelia (Lecanorales, Ascomycota)
Species recognition in lichen-forming fungi has been a challenge because of unsettled species concepts, few taxonomically relevant traits, and limitations of traditionally used morphological and chemical characters for identifying closely related species. Here we analyze species diversity in the cosmopolitan genus Protoparmelia s.l. The ~25 described species in this group occur across diverse habitats from the boreal -arctic/alpine to the tropics, but their relationship to each other remains unexplored. In this study, we inferred the phylogeny of 18 species currently assigned to this genus based on 160 specimens and six markers: mtSSU, nuLSU, ITS, RPB1, MCM7, and TSR1. We assessed the circumscription of species-level lineages in Protoparmelia s. str. using two coalescent-based species delimitation methods – BP&P and spedeSTEM. Our results suggest the presence of a tropical and an extra-tropical lineage, and eleven previously unrecognized distinct species-level lineages in Protoparmelia s. str. Several cryptic lineages were discovered as compared to phenotype-based species delimitation. Many of the putative species are supported by geographic evidence.
FIGURE 22 in Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status
FIGURE 22. Dorsal view of Aegla jundiai n. sp., female holotype (MZUSP 13493). Bar = 2.0 mm.
FIGURE 20 in Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status
FIGURE 20. Dorsal view of Aegla jaragua n. sp., male holotype (MZUSP 34376). Bar = 3.0 mm.
FIGURE 18 in Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status
FIGURE 18. Dorsal view of Aegla japi n. sp., male holotype (MZUSP 34374). Bar = 3.0 mm.
FIGURE 16 in Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status
FIGURE 16. Dorsal view of Aegla vanini n. sp., male holotype (MZUSP 34371). Bar = 3.0 mm.
FIGURE 1 in Three new species of leaflitter frogs from the upper Amazon forests: cryptic diversity within Pristimantis " ockendeni " (Anura: Strabomantidae) in Ecuador
FIGURE 1. Photograph of P. achuar holotype (QCAZ 25463) in life.
FIGURE 12 in Revision of the Australian Oenochroma vinaria Guenée, 1858 species-complex (Lepidoptera: Geometridae, Oenochrominae): DNA barcoding reveals cryptic diversity and assesses status of type specimen without dissection
FIGURE 12. Egg of Oenochroma barcodificata. sp. nov. freshly laid egg, scale bar 1 mm. (photo CY)
FIGURE 6 in Diversity of sponges (Porifera) from cryptic habitats on the Belize barrier reef near Carrie Bow Cay
FIGURE 6. Plakinastrella onkodes, spicules (SEM): a, diods; b, triods; c, calthrops.
FIGURE 15 in Diversity of sponges (Porifera) from cryptic habitats on the Belize barrier reef near Carrie Bow Cay
FIGURE 15. Cliona varians, spicules (SEM): a, tylostyles; b, spirasters and one amphiaster.
FIGURE 14 in Diversity of sponges (Porifera) from cryptic habitats on the Belize barrier reef near Carrie Bow Cay
FIGURE 14. Cliona schmidti, spicules (SEM): a, tylostyle; b, spirasters I; c, spirasters II.
FIGURE 12 in Cryptic diversity within the narrowly endemic Lerista wilkinsi group of north Queensland—two new species (Reptilia: Scincidae)
FIGURE 12. Lerista cinerea type locality, Cardigan Scrub, Warrawee Station, CQ (photo by A. Amey).
FIGURE 9 in Cryptic diversity within the narrowly endemic Lerista wilkinsi group of north Queensland—two new species (Reptilia: Scincidae)
FIGURE 9. Lerista hobsoni sp. nov. type locality, Rubbish Tip Rd, Pentland, CQ (photo by A. Amey).
FIGURE 10 in Cryptic diversity within the narrowly endemic Lerista wilkinsi group of north Queensland—two new species (Reptilia: Scincidae)
FIGURE 10. Lerista cinerea in life (QMJ93647, photo by S. K. Wilson).
FIGURE 3 in Cryptic diversity within the narrowly endemic Lerista wilkinsi group of north Queensland—two new species (Reptilia: Scincidae)
FIGURE 3. Lerista vanderduysi sp. nov. in life (QMJ77548, paratype, photo by S. K. Wilson).
FIGURE 20 in Cryptic diversity in the Azorean beetle genus Tarphius Erichson, 1845 (Coleoptera: Zopheridae): An integrative taxonomic approach with description of four new species
FIGURE 20. Habitus of Tarphius serranoi Borges. Scale 0.5 mm (Photo: Erno-Endre Gergely).
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