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.

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 DNA barcoding uncovers cryptic diversity in 50% of deep-sea Antarctic polychaetes

2016 ◽  
Vol 3 (11) ◽  
pp. 160432 ◽  
Author(s):  
Madeleine J. Brasier ◽  
Helena Wiklund ◽  
Lenka Neal ◽  
Rachel Jeffreys ◽  
Katrin Linse ◽  
...  
Keyword(s):  
Species Diversity ◽  
Cryptic Species ◽  
Dna Sequences ◽  
Cryptic Diversity ◽  
Polychaete Species ◽  
Total Species Richness ◽  
Antarctic Benthos ◽  
The Antarctic ◽  
Total Species ◽  
Insight Into

The Antarctic marine environment is a diverse ecosystem currently experiencing some of the fastest rates of climatic change. The documentation and management of these changes requires accurate estimates of species diversity. Recently, there has been an increased recognition of the abundance and importance of cryptic species, i.e. those that are morphologically identical but genetically distinct. This article presents the largest genetic investigation into the prevalence of cryptic polychaete species within the deep Antarctic benthos to date. We uncover cryptic diversity in 50% of the 15 morphospecies targeted through the comparison of mitochondrial DNA sequences, as well as 10 previously overlooked morphospecies, increasing the total species richness in the sample by 233%. Our ability to describe universal rules for the detection of cryptic species within polychaetes, or normalization to expected number of species based on genetic data is prevented by taxon-specific differences in phylogenetic outputs and genetic variation between and within potential cryptic species. These data provide the foundation for biogeographic and functional analysis that will provide insight into the drivers of species diversity and its role in ecosystem function.

scholarly journals High levels of cryptic species diversity uncovered in Amazonian frogs

2011 ◽  
Vol 279 (1734) ◽  
pp. 1806-1814 ◽  
Author(s):  
W. Chris Funk ◽  
Marcel Caminer ◽  
Santiago R. Ron
Keyword(s):  
Species Richness ◽  
Species Diversity ◽  
Cryptic Species ◽  
Amazon Basin ◽  
Nuclear Dna ◽  
Cryptic Diversity ◽  
Undescribed Species ◽  
Tropical Regions ◽  
The Poor ◽  
Poor Understanding

One of the greatest challenges for biodiversity conservation is the poor understanding of species diversity. Molecular methods have dramatically improved our ability to uncover cryptic species, but the magnitude of cryptic diversity remains unknown, particularly in diverse tropical regions such as the Amazon Basin. Uncovering cryptic diversity in amphibians is particularly pressing because amphibians are going extinct globally at an alarming rate. Here, we use an integrative analysis of two independent Amazonian frog clades, Engystomops toadlets and Hypsiboas treefrogs, to test whether species richness is underestimated and, if so, by how much. We sampled intensively in six countries with a focus in Ecuador ( Engystomops : 252 individuals from 36 localities; Hypsiboas : 208 individuals from 65 localities) and combined mitochondrial DNA, nuclear DNA, morphological, and bioacoustic data to detect cryptic species. We found that in both clades, species richness was severely underestimated, with more undescribed species than described species. In Engystomops , the two currently recognized species are actually five to seven species (a 150–250% increase in species richness); in Hypsiboas , two recognized species represent six to nine species (a 200–350% increase). Our results suggest that Amazonian frog biodiversity is much more severely underestimated than previously thought.

Two new and potentially highly threatened Megophrys Horned frogs (Amphibia: Megophryidae) from Indochina’s highest mountains

Zootaxa ◽  
2018 ◽  
Vol 4508 (3) ◽  
pp. 301 ◽  
Author(s):  
BENJAMIN TAPLEY ◽  
TIMOTHY CUTAJAR ◽  
STEPHEN MAHONY ◽  
CHUNG THANH NGUYEN ◽  
VINH QUANG DAU ◽  
...  
Keyword(s):  
New Species ◽  
Species Diversity ◽  
Southeast Asia ◽  
Cryptic Species ◽  
Habitat Degradation ◽  
Distinct Species ◽  
High Elevation ◽  
Species Level ◽  
Two New Species ◽  
Isthmus Of Kra

Megophrys are a group of morphologically conserved, primarily forest-dependent frogs known to harbour cryptic species diversity. In this study, we examined populations of small-sized Megophrys from mid- and high elevation locations in the Hoang Lien Range, northern Vietnam. On the basis of morphological, molecular and bioacoustic data, individuals of these populations differed from all species of Megophrys known from mainland Southeast Asia north of the Isthmus of Kra and from neighbouring provinces in China. Further, the newly collected specimens formed two distinct species-level groups. We herein describe two new species, Megophrys fansipanensis sp. nov. and Megophrys hoanglienensis sp. nov. Both new species are range restricted and likely to be highly threatened by habitat degradation. These discoveries highlight the importance of the Hoang Lien Range for Vietnam’s amphibian diversity.  

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.

Overview of Xanthoparmelia taxa from South Korea including the description of two new species (Parmeliaceae, Ascomycota)

Phytotaxa ◽  
2014 ◽  
Vol 181 (2) ◽  
pp. 96 ◽  
Author(s):  
Udeni Jayalal ◽  
Pradeep K Divakar ◽  
Santosh Joshi ◽  
Soon Ok Oh ◽  
Jung A Kim ◽  
...  
Keyword(s):  
New Species ◽  
South Korea ◽  
Dna Sequences ◽  
Usnic Acid ◽  
Lower Surface ◽  
Species Boundaries ◽  
Future Studies ◽  
Two New Species ◽  
Traditional Taxonomy ◽  
Natural Groups

In the genus Xanthoparmelia, species boundaries are based on morphological and chemical features such as the presence and/or absence of secondary metabolites, diagnostic reproductive structures, isidia morphology, and color of lower surface. Two new species of Xanthoparmelia are described from South Korea, X. kolriana with cylindrical isidia containing atranorin and salazinic acid as major components in the medulla together with cortical usnic acid, while X. volcanicola is characterised by a red coloured medulla, and subglobose isidia. The characteristics of Xanthoparmelia species and their distribution in South Korea are outlined and an identification key given. Additionally, we used ITS ribosomal DNA sequences to assess the monophyly of Xanthoparmelia species from South Korea. Our results reveal that traditionally circumscribed species were not recovered as monophyletic clades. Further, we here show that ITS is insufficient to estimate a well-supported phylogenetic hypothesis, but suggests that traditional taxonomy may not reflect natural groups. This communication provides an important framework for future studies assessing species boundaries in Xanthoparmelia species in South Korea.

scholarly journals Cryptic diversity and range extension in the big-eyed bat genus Chiroderma (Chiroptera, Phyllostomidae)

ZooKeys ◽  
2020 ◽  
Vol 918 ◽  
pp. 41-63 ◽  
Author(s):  
Burton K. Lim ◽  
Livia O. Loureiro ◽  
Guilherme S.T. Garbino
Keyword(s):  
Systematic Review ◽  
Species Diversity ◽  
Cryptic Species ◽  
Endemic Species ◽  
Detailed Examination ◽  
Lesser Antilles ◽  
Cryptic Diversity ◽  
Species Status ◽  
The Caribbean ◽  
First Time

Since the last systematic review of Chiroderma (big-eyed bats) more than two decades ago, we report on biodiversity surveys that expand the distribution and species diversity of this Neotropical genus. The Caribbean endemic species Chiroderma improvisum is documented for the first time from Nevis in the northern Lesser Antilles. A broader geographic sampling for a molecular analysis identifies a paraphyletic relationship in Chiroderma trinitatum with respect to Chiroderma doriae. Cis-Andean populations of C. trinitatum are most closely related to the morphologically distinctive and allopatrically distributed C. doriae in the Cerrado and Atlantic Forest of Brazil and Paraguay. The sister taxon to this grouping includes trans-Andean populations of C. trinitatum, which we recommend to elevate to species status as C. gorgasi. This is an example of a cryptic species because C. gorgasi was previously considered morphologically similar to C. trinitatum, but more detailed examination revealed that it lacks a posterolabial accessory cusp on the lower second premolar and has a narrower breadth of the braincase. We provide an amended description of Chiroderma gorgasi.

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.

scholarly journals Cryptic diversity in the subgenus Oxyphortica (Diptera, Drosophilidae, Stegana)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12347
Author(s):  
Ya-Lian Wang ◽  
Nan-Nan Wang ◽  
Yuan Zhang ◽  
Shun-Chern Tsaur ◽  
Hong-Wei Chen
Keyword(s):  
New Species ◽  
Species Delimitation ◽  
Southwest China ◽  
Morphological Characteristics ◽  
Mitochondrial Genes ◽  
Species Boundaries ◽  
Molecular Evidence ◽  
Hengduan Mountains ◽  
Cryptic Diversity ◽  
Barcode Gap

Phylogenetic relationships of the subgenus Oxyphortica were reconstructed based on two mitochondrial genes (COI and ND2). The results revealed the paraphyly of Oxyphortica and supported high levels of cryptic diversity within this subgenus. By integrating morphological characteristics and molecular evidence, we identified 17 new species as members of Oxyphortica: S. (O.) amphigya sp. nov., S. (O.) armillata sp. nov., S. (O.) ashima sp. nov., S. (O.) bawo sp. nov., S. (O.) crypta sp. nov., S. (O.) gelea sp. nov., S. (O.) hengduanmontana sp. nov., S. (O.) jinmingi sp. nov., S. (O.) mengbalanaxi sp. nov., S. (O.) mouig sp. nov., S. (O.) setipes sp. nov., S. (O.) shangrila sp. nov., S. (O.) tsauri sp. nov., S. (O.) valleculata sp. nov., S. (O.) wanhei sp. nov., S. (O.) yangjin sp. nov. and S. (O.) hypophaia sp. nov. To test the early morphological identifications and confirm the species boundaries, different species delimitation methods, including Automatic Barcode Gap Discovery (ABGD) and Bayesian Phylogenetics and Phylogeography (BP&P), were used, together with traditional distance. All species boundaries were clearly defined. As Oxyphortica species are mainly distributed across Southwest China (e.g., 20 spp. from the Hengduan Mountains), the complex climate and topographic landforms of the area may be responsible for the high levels of species diversity and endemism.

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