DNA-based approaches uncover cryptic diversity in the European Lepidocyrtus lanuginosus species group (Collembola: Entomobryidae)

2019 ◽  
Author(s):  
Bing Zhang ◽  
Ting-Wen Chen ◽  
Eduardo Mateos ◽  
Stefan Scheu ◽  
Ina Schaefer
Keyword(s):  
Cryptic Species ◽  
Species Delimitation ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Full Range ◽  
Accurate Determination ◽  
Nuclear Gene ◽  
Species Group ◽  
Species Boundaries ◽  
Cryptic Diversity

DNA sequence data and phylogenies are useful tools for species delimitation, especially in taxa comprising cryptic species. The Lepidocyrtus lanuginosus species group (Collembola: Entomobryidae) comprises three morphospecies and distinct cryptic species. We applied three DNA-based methods to delimit species boundaries in the L. lanuginosus species group across central and southern Europe. Using cytochrome c oxidase subunit I and II, we identified gaps of genetic distances that indicate species boundaries and found 10 and 9 distinct genetic lineages in L. cyaneus and L. lanuginosus, respectively. The nuclear gene elongation factor 1-α delimited 89% of the lineages but 28S rDNA (D1–2 domain) was too conserved for this purpose. The phylogenetic trees showed that L. cyaneus and L. lanuginosus are polyphyletic, suggesting that body colour is insufficient for delimiting species in the L. lanuginosus species group. Our study challenges the current morphology-based species delimitation in the L. lanuginosus species group and suggests that molecular approaches are needed for fast and accurate determination of Collembola species in both taxonomic and ecological studies. Overall, the results suggest that wide geographic sampling combined with molecular phylogenetic approaches is needed to delimit species and to understand the full range of cryptic diversity in Collembola.

scholarly journals Cryptic Species Diversity and Phylogenetic Relationship in the Rust Genus Chrysomyxa from China

2022 ◽  
Vol 8 (1) ◽  
pp. 83
Author(s):  
Rui Wang ◽  
Clement K. M. Tsui ◽  
Chongjuan You
Keyword(s):  
Species Diversity ◽  
Cryptic Species ◽  
Species Delimitation ◽  
Fungal Pathogens ◽  
Economic Losses ◽  
Species Boundaries ◽  
Cryptic Diversity ◽  
Future Studies ◽  
Rust Diseases ◽  
Two New Species

Chrysomyxa rusts are fungal pathogens widely distributed in the Northern hemisphere, causing spruce needle and cone rust diseases, and they are responsible for significant economic losses in China. Taxonomic delimitation and precise species identification are difficult within this genus because some characters often overlap in several species. Adequate species delimitation, enhanced by the use of DNA-based methodologies, will help to establish well-supported species boundaries and enable the identification of cryptic species. Here, we explore the cryptic species diversity in the rust genus Chrysomyxa from China. Species delimitation analyses are conducted using a distance-based method (ABGD) and three tree-based methods (GMYC, bPTP, and mPTP) based on combined LSU and ITS sequences of over 60 specimens. Although there is some incongruence among species delimitation methods, two new species and three putative cryptic species are identified. The key to 20 Chrysomyxa species distributed in China is presented. These results suggest that a significant level of undiscovered cryptic diversity is likely to be found in Chrysomyxa from China. Future studies should consider multiple analytical methods when dealing with multi-locus datasets.

scholarly journals On the Species Delimitation of the Maddenia Group of Prunus (Rosaceae): Evidence From Plastome and Nuclear Sequences and Morphology

2021 ◽  
Vol 12 ◽  
Author(s):  
Na Su ◽  
Bin-bin Liu ◽  
Jun-ru Wang ◽  
Ru-chang Tong ◽  
Chen Ren ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Phylogenetic Network ◽  
Single Copy ◽  
Morphological Evidence ◽  
Molecular Evidence ◽  
Variable Regions ◽  
Dna Sequence Data

The recognition, identification, and differentiation of closely related plant species present significant and notorious challenges to taxonomists. The Maddenia group of Prunus, which comprises four to seven species, is an example of a group in which species delimitation and phylogenetic reconstruction have been difficult, due to the lack of clear morphological distinctions, limited sampling, and low informativeness of molecular evidence. Thus, the precise number of species in the group and the relationships among them remain unclear. Here, we used genome skimming to generate the DNA sequence data for 22 samples, including 17 Maddenia individuals and five outgroups in Amygdaloideae of Rosaceae, from which we assembled the plastome and 446 single-copy nuclear (SCN) genes for each sample. The phylogenetic relationships of the Maddenia group were then reconstructed using both concatenated and coalescent-based methods. We also identified eight highly variable regions and detected simple sequence repeats (SSRs) and repeat sequences in the Maddenia species plastomes. The phylogenetic analysis based on the complete plastomes strongly supported three main subclades in the Maddenia group of Prunus, while five subclades were recognized based on the nuclear tree. The phylogenetic network analysis detected six hybridization events. Integrating the nuclear and morphological evidence, we proposed to recognize five species within the Maddenia group, i.e., Prunus fujianensis, P. himalayana, P. gongshanensis, P. hypoleuca, and P. hypoxantha. Within this group, the first three species are well-supported, while the gene flow occurring throughout the Maddenia group seems to be especially frequent between P. hypoleuca and P. hypoxantha, eroding the barrier between them. The phylogenetic trees based on eight concatenated hypervariable regions had a similar topology with the complete plastomes, showing their potential as molecular markers and effective barcodes for further phylogeographic studies on Maddenia.

Species delimitation in trematodes using DNA sequences: Middle-American Clinostomum as a case study

Parasitology ◽  
2016 ◽  
Vol 143 (13) ◽  
pp. 1773-1789 ◽  
Author(s):  
GERARDO PÉREZ-PONCE DE LEÓN ◽  
MARTÍN GARCÍA-VARELA ◽  
CARLOS D. PINACHO-PINACHO ◽  
ANA L. SERENO-URIBE ◽  
ROBERT POULIN
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Species Delimitation ◽  
Nuclear Gene ◽  
Species Tree ◽  
Coi Gene ◽  
Complex Life Cycle ◽  
Species Boundaries ◽  
Intermediate Hosts ◽  
Putative Species

SUMMARYThe recent development of genetic methods allows the delineation of species boundaries, especially in organisms where morphological characters are not reliable to differentiate species. However, few empirical studies have used these tools to delineate species among parasitic metazoans. Here we investigate the species boundaries of Clinostomum, a cosmopolitan trematode genus with complex life cycle. We sequenced a mitochondrial [cytochrome c oxidase subunit I (COI)] gene for multiple individuals (adults and metacercariae) from Middle-America. Bayesian phylogenetic analysis of the COI uncovered five reciprocally monophyletic clades. COI sequences were then explored using the Automatic Barcode Gap Discovery to identify putative species; this species delimitation method recognized six species. A subsample was sequenced for a nuclear gene (ITS1, 5·8S, ITS2), and a concatenated phylogenetic analysis was performed through Bayesian inference. The species delimitation of Middle-American Clinostomum was finally validated using a multispecies coalescent analysis (species tree). In total, five putative species are recognized among our samples. Mapping the second intermediate hosts (fish) onto the species tree suggests that metacercariae of these five species exhibit some level of host specificity towards their fish intermediate host (at the family level), irrespective of geographical distribution.

scholarly journals Phylogenetic, population genetic, and morphological analyses reveal evidence for one species of Eastern Indigo Snake (Drymarchon couperi)

2018 ◽  
Author(s):  
Brian Folt ◽  
Javan Bauder ◽  
Stephen Spear ◽  
Dirk Stevenson ◽  
Michelle Hoffman ◽  
...  
Keyword(s):  
Gene Flow ◽  
Species Delimitation ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Nuclear Gene ◽  
Large Species ◽  
High Dispersal ◽  
Contemporary Gene Flow ◽  
Eastern Indigo Snake

AbstractAccurate species delimitation and description are necessary to guide effective conservation management of imperiled species. The Eastern Indigo Snake (Drymarchon couperi) is a large species in North America that is federally-protected as Threatened under the Endangered Species Act. Recently, two associated studies hypothesized that Drymarchon couperi is two species. Here, we use diverse approaches to test the two-species hypothesis for D. couperi. Our analyses reveal that (1) phylogenetic reconstruction in previous studies was based entirely on variance of mitochondrial DNA sequence data, (2) microsatellite data demonstrate significant population admixture and nuclear gene flow between mitochondrial lineages, and (3) morphological analyses recover a single diagnosable species. Our results are inconsistent with the two-species hypothesis, thus we reject it and formally place Drymarchon kolpobasileus into synonymy with D. couperi. We suggest inconsistent patterns between mitochondrial and nuclear DNA may be driven by high dispersal of males relative to females. We caution against species delimitation exercises when one or few loci are used without evaluation of contemporary gene flow, particularly species with strong sex-biased dispersal (e.g., squamates) and/or when results have implications for ongoing conservation efforts.

scholarly journals RAD sequencing enables unprecedented phylogenetic resolution and objective species delimitation in recalcitrant divergent taxa

2015 ◽  
Author(s):  
Santiago Herrera ◽  
Timothy M. Shank
Keyword(s):  
Species Delimitation ◽  
Sequence Data ◽  
Conclusive Evidence ◽  
Species Boundaries ◽  
Effective Population ◽  
Dna Sequence Data ◽  
Genome Wide ◽  
Phylogenetic Resolution ◽  
Specific Factors ◽  
Morphological Species

Species delimitation is problematic in many taxa due to the difficulty of evaluating predictions from species delimitation hypotheses, which chiefly relay on subjective interpretations of morphological observations and/or DNA sequence data. This problem is exacerbated in recalcitrant taxa for which genetic resources are scarce and inadequate to resolve questions regarding evolutionary relationships and uniqueness. In this case study we demonstrate the empirical utility of restriction site associated DNA sequencing (RAD-seq) by unambiguously resolving phylogenetic relationships among recalcitrant octocoral taxa with divergences greater than 80 million years. We objectively infer robust species boundaries in the genusParagorgia, which contains some of the most important ecosystem engineers in the deep-sea, by testing alternative taxonomy-guided or unguided species delimitation hypotheses using the Bayes factors delimitation method (BFD*) with genome-wide single nucleotide polymorphism data. We present conclusive evidence rejecting the current morphological species delimitation model for the genusParagorgiaand indicating the presence of cryptic species boundaries associated with environmental variables. We argue that the suitability limits of RAD-seq for phylogenetic inferences in divergent taxa cannot be assessed in terms of absolute time, but depend on taxon-specific factors such as mutation rate, generation time and effective population size. We show that classic morphological taxonomy can greatly benefit from integrative approaches that provide objective tests to species delimitation hypothesis. Our results pave the way for addressing further questions in biogeography, species ranges, community ecology, population dynamics, conservation, and evolution in octocorals and other marine taxa.

scholarly journals Molecular taxonomy of endemic coastal Ligia isopods from the Hawaiian Islands: re-description of L. hawaiensis and description of seven novel cryptic species

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7531
Author(s):  
Carlos A. Santamaria
Keyword(s):  
Cryptic Species ◽  
Species Delimitation ◽  
Molecular Taxonomy ◽  
Hawaiian Islands ◽  
Nuclear Gene ◽  
Morphological Differentiation ◽  
Taxonomic Revision ◽  
Hawaiian Archipelago ◽  
Genetic Lineages ◽  
Molecular Characters

Past phylogeographic work has shown Ligia hawaiensis, a coastal isopod species endemic to the Hawaiian Islands, to be a paraphyletic complex of several highly genetically divergent yet morphologically cryptic lineages. Despite the need for a taxonomic revision of this species, the lack of morphological differentiation has proven an impediment to formally describe new Ligia species in the region. Molecular characters and species delimitation approaches have been successfully used to formally describe cryptic species in other crustacean taxa, suggesting they may aid taxonomic revisions of L. hawaiensis. Herein, various distance- and tree-based molecular species delimitation approaches are applied on a concatenated dataset comprised of both mitochondrial and nuclear gene sequences of L. hawaiensis and L. perkinsi, a terrestrial species endemic to the Hawaiian archipelago. Results of these analyses informed a taxonomic revision leading to the redescription of L. hawaiensis and the description of seven new cryptic species on the basis of molecular characters: L. dante, L. eleluensis, L. honu, L. kamehameha, L. mauinuiensis, L. pele, and L. rolliensis. These coastal Ligia species from the Hawaiian archipelago appear to be largely limited to single islands, where they appear largely constrained to volcanic rift zones suggesting allopatric events at local scales may drive diversification for poorly dispersing organisms in the Hawaiian coastlines. Additional work remains needed to fully assess the role of said events; however, the description of these novel species underscore their potential to aid in studies of local diversification of marine organisms in Hawai‘i. Lastly, this represents the first application of molecular taxonomic approaches to formally describe genetic lineages found in Ligia isopods as species, underscoring the promise these methods hold to taxonomic revisions in other species in the genus shown to harbor cryptic genetic lineages.

Phylogeny of Trematomus (Notothenioidei: Nototheniidae) inferred from mitochondrial and nuclear gene sequences

2009 ◽  
Vol 21 (6) ◽  
pp. 565-570 ◽  
Author(s):  
Kristen L. Kuhn ◽  
Thomas J. Near
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Single Copy ◽  
Morphological Characters ◽  
Mitochondrial Genes ◽  
Phylogenetic Resolution

AbstractThe biota of Antarctica is amazingly rich and highly endemic. The phylogenetics of notothenioid fishes has been extensively investigated through analyses of morphological characters, DNA sequences from mitochondrial genes, and single copy nuclear genes. These phylogenetic analyses have produced reasonably similar phylogenetic trees of notothenioids, however a number of phylogenetic questions remain. The nototheniid clade Trematomus is an example of a group where phylogenetic relationships remain unresolved. In this paper we revisit the phylogenetic relationships of Trematomus using both increased taxon sampling and an expanded dataset which includes DNA sequences from two mitochondrial genes (ND2 and 16S rRNA) and one single-copy nuclear gene (RPS7). The Bayesian phylogeny resulting from the analysis of the combined mitochondrial and nuclear gene datasets was well resolved and contained more interspecific nodes supported with significant Bayesian posteriors than either the mitochondrial or nuclear gene phylogenies alone. This demonstrates that the addition of nuclear gene sequence data to mitochondrial data can enhance phylogenetic resolution and increase node support. Additionally, the results of the combined mitochondrial and nuclear Bayesian analyses provide further support for the inclusion of species previously classified as Pagothenia and Cryothenia in Trematomus.

scholarly journals A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals

2019 ◽  
Author(s):  
Andrea M. Quattrini ◽  
Tiana Wu ◽  
Keryea Soong ◽  
Ming-Shiou Jeng ◽  
Yehuda Benayahu ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Species Delimitation ◽  
Incomplete Lineage Sorting ◽  
Dna Barcode ◽  
Species Boundaries ◽  
Future Research ◽  
Species Trees ◽  
Lineage Sorting ◽  
Evolutionary Diversification

AbstractBackgroundOur ability to investigate processes shaping the evolutionary diversification of corals (Cnidaria: Anthozoa) is limited by a lack of understanding of species boundaries. Discerning species has been challenging due to a multitude of factors, including homoplasious and plastic morphological characters and the use of molecular markers that are either not informative or have not completely sorted. Hybridization can also blur species boundaries by leading to incongruence between morphology and genetics. We used traditional DNA barcoding and restriction-site associated DNA sequencing combined with coalescence-based and allele-frequency methods to elucidate species boundaries and simultaneously examine the potential role of hybridization in a speciose genus of octocoral, Sinularia.ResultsSpecies delimitations using two widely used DNA barcode markers, mtMutS and 28S rDNA, were incongruent with one another and with the morphospecies identifications, likely due to incomplete lineage sorting. In contrast, 12 of the 15 morphospecies examined formed well-supported monophyletic clades in both concatenated RAxML phylogenies and SNAPP species trees of >6,000 RADSeq loci. DAPC and Structure analyses also supported morphospecies assignments, but indicated the potential for two additional cryptic species. Three morphologically distinct species pairs could not, however, be distinguished genetically. ABBA-BABA tests demonstrated significant admixture between some of those species, suggesting that hybridization may confound species delimitation in Sinularia.ConclusionsA genomic approach can help to guide species delimitation while simultaneously elucidating the processes generating diversity in corals. Results support the hypothesis that hybridization is an important mechanism in the evolution of Anthozoa, including octocorals, and future research should examine the contribution of this mechanism in generating diversity across the coral tree of life.

scholarly journals Phylogeny and Taxonomy on Cryptic Species of Forked Ferns of Asia

2021 ◽  
Vol 12 ◽  
Author(s):  
Zuoying Wei ◽  
Zengqiang Xia ◽  
Jiangping Shu ◽  
Hui Shang ◽  
Stephen J. Maxwell ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Morphological Variation ◽  
Divergence Time ◽  
Distinct Species ◽  
Species Boundaries ◽  
New Combinations ◽  
Cryptic Diversity ◽  
Chloroplast Gene ◽  
Morphological Comparison ◽  
Molecular Phylogenetic

Cryptic species comprise two or more taxa that are grounded under a single name because they are more-or-less indistinguishable morphologically. These species are potentially important for detailed assessments of biodiversity, but there now appear to be many more cryptic species than previously estimated. One taxonomic group likely to contain many cryptic species is Dicranopteris, a genus of forked ferns that occurs commonly along roadsides in Asia. The genus has a complex taxonomical history, and D. linearis has been particularly challenging with many intra-specific taxa dubiously erected to accommodate morphological variation that lacks clear discontinuities. To resolve species boundaries within Dicranopteris, we applied a molecular phylogenetic approach as complementary to morphology. Specifically, we used five chloroplast gene regions (rbcL, atpB, rps4, matK, and trnL-trnF) to generate a well-resolved phylogeny based on 37 samples representing 13 taxa of Dicranopteris, spanning the major distributional area in Asia. The results showed that Dicranopteris consists of ten highly supported clades, and D. linearis is polyphyletic, suggesting cryptic diversity within the species. Further through morphological comparison, we certainly erected Dicranopteris austrosinensis Y.H. Yan & Z.Y. Wei sp. nov. and Dicranopteris baliensis Y.H. Yan & Z.Y. Wei sp. nov. as distinct species and proposed five new combinations. We also inferred that the extant diversity of the genus Dicranopteris may result from relatively recent diversification in the Miocene based on divergence time dating. Overall, our study not only provided additional insights on the Gleicheniaceae tree of life, but also served as a case of integrating molecular and morphological approaches to elucidate cryptic diversity in taxonomically difficult groups.

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