Cryptic diversity of the mangrove-associated alga Bostrychia (Rhodomelaceae, Rhodophyta) from Thailand

2016 ◽  
Vol 59 (5) ◽  
Author(s):  
Jantana Saengkaew ◽  
Narongrit Muangmai ◽  
Giuseppe C. Zuccarello
Keyword(s):  
Cryptic Species ◽  
Cryptic Diversity ◽  
Algal Diversity ◽  
Molecular Approaches

AbstractAlgal diversity has been extensively investigated using combinations of morphological and molecular approaches. These combined approaches are especially relevant for organisms where cryptic species are known to exist.

An updated look at the uneven distribution of cryptic diversity among parasitic helminths

2017 ◽  
Vol 92 (2) ◽  
pp. 197-202 ◽  
Author(s):  
G. Pérez-Ponce de León ◽  
R. Poulin
Keyword(s):  
Cryptic Species ◽  
Dna Sequences ◽  
Meta Analysis ◽  
Parasitic Nematodes ◽  
Trematode Species ◽  
Sampling Effort ◽  
Separate Analysis ◽  
Cryptic Diversity ◽  
Parasite Diversity ◽  
Parasitic Helminths

AbstractCryptic parasite diversity is a major issue for taxonomy and systematics, and for attempts to control diseases of humans, domestic animals and wildlife. Here, we re-examine an earlier report that, after correcting for sampling effort, more cryptic species of trematodes are found per published study than for other helminth taxa. We performed a meta-analysis of 110 studies that used DNA sequences to search for cryptic species in parasitic helminth taxa. After correcting for study effort and accounting for the biogeographical region of origins, we found that more cryptic species tend to be uncovered among trematodes, and fewer among cestodes and animal-parasitic nematodes, than in other helminth groups. However, this pattern was only apparent when we included only studies using nuclear markers in the analysis; it was not seen in a separate analysis based only on mitochondrial markers. We propose that the greater occurrence of cryptic diversity among trematodes may be due to some of their unique features, such as their mode of reproduction or frequent lack of hard morphological structures, or to the way in which trematode species are described. Whatever the reason, the high frequency of cryptic species among trematodes has huge implications for estimates of parasite diversity and for future taxonomic research.

scholarly journals Molecular approaches uncover cryptic diversity in intertidalLigiaisopods (Crustacea, Isopoda, Ligiidae) across the southern Africa coastline

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4658 ◽  
Author(s):  
Taylor M. Greenan ◽  
Charles L. Griffiths ◽  
Carlos A. Santamaria
Keyword(s):  
Southern Africa ◽  
Open Water ◽  
Biological Traits ◽  
Cryptic Diversity ◽  
Nuclear Markers ◽  
Molecular Approaches ◽  
Kwazulu Natal ◽  
The World ◽  
Mitochondrial And Nuclear Markers

Recent phylogeographic studies along the coastline of southern Africa have uncovered cryptic diversity in several coastal invertebrates, including direct developing crustaceans in the superorder Peracarida. These findings indicating the possible existence of additional cryptic diversity in other yet to be studied peracarids, particularly those known to harbor said cryptic diversity in other regions of the world. Isopods in the genusLigiaare one such taxon. They inhabit patchy rocky beaches, are direct developers, avoid the open water, and exhibit other biological traits that severely constrain their dispersal potential (e.g., poor desiccation resistance). These traits are thought to have led to long-term isolation of populations, and allopatric diversification inLigiaspecies around the world; however,Ligiaspecies in southern Africa, where three endemicLigiaspecies of uncertain validity are known to exist, remain unstudied to date. In this study, we used mitochondrial and nuclear markers to characterizeLigiacollected in 18 localities from Namibia to the KwaZulu-Natal region of South Africa. We report the presence of cryptic lineages withinLigiaspecies in the region that suggest the need for taxonomic reevaluation of these isopod species.

Fungal taxonomy and nomenclature

2018 ◽  
pp. 8-16
Author(s):  
Andrew M. Borman
Keyword(s):  
Cryptic Species ◽  
Structural Features ◽  
Fungal Taxonomy ◽  
New Genera ◽  
Molecular Approaches ◽  
Dual Nomenclature ◽  
Fungal Identification ◽  
Phenotypic Features ◽  
Genetic Entity

This chapter summarizes historical and modern approaches to fungal taxonomy, the current taxonomic standing of medically important fungi, and the implications for fungal nomenclature following the recent Amsterdam Declaration on Fungal Nomenclature, which prohibits dual nomenclature. Fungi comprise an entire kingdom, containing an estimated 1–10 million species. Traditionally, fungal identification was based on examination of morphological and phenotypic features, including the type of sexual spores they form and method of formation, and structural features of their asexual spores. Thus, many fungi have been described and named independently several times, based on either their sexual or asexual stages, resulting in a single genetic entity having multiple names. Recent molecular approaches to fungal identification have led to profound changes in fungal nomenclature and taxonomy. Certain phyla have now been disbanded, cryptic species have been identified via molecular approaches, and long-recognized species have been transferred to new genera, based on genotypic comparisons.

DNA barcoding Australian macroinvertebrates for monitoring programs: benefits and current short comings

2016 ◽  
Vol 67 (3) ◽  
pp. 380 ◽  
Author(s):  
Michael Shackleton ◽  
Gavin N. Rees
Keyword(s):  
Cryptic Species ◽  
Dna Barcoding ◽  
Sequence Data ◽  
Aquatic Environments ◽  
Molecular Approaches ◽  
Monitoring Programs ◽  
Online Databases ◽  
Murray Darling Basin ◽  
Freshwater Fauna ◽  
Australian Freshwater

Identification of macroinvertebrates is a key component of monitoring programs that seek to understand the condition of aquatic environments. Classical identification approaches underpin such programs, but molecular approaches are gaining recognition as valuable ways to identify organisms for research and monitoring programs. We applied DNA barcoding data to specimens collected as part of monitoring programs in the Murray–Darling Basin, to investigate the possible informational benefits these data may provide. We also tested the performances of two online DNA databases in assigning taxon names to our sequence data. We found that relying on the online databases to determine species identifications was currently problematic for the Australian freshwater fauna because of a lack of available sequence data. However, we also found that collecting and applying barcode data to our monitoring programs gave considerable informational benefits by providing greater resolution of specimen identity, highlighting the presence of potential cryptic species, providing information on larval and adult associations, demonstrating instances where misidentification had occurred though classical approaches, and providing conformation of the performance of diagnostic characters currently used in keys to determine species identities.

A combination of molecular and morphological approaches resolves species in the taxonomically difficult genus Procladius Skuse (Diptera: Chironomidae) despite high intra-specific morphological variation

2011 ◽  
Vol 101 (5) ◽  
pp. 505-519 ◽  
Author(s):  
M.E. Carew ◽  
S.E. Marshall ◽  
A.A. Hoffmann
Keyword(s):  
Cryptic Species ◽  
Morphological Variation ◽  
Nuclear Gene ◽  
Pupal Stage ◽  
Mitochondrial Genes ◽  
Pollution Monitoring ◽  
Species Variation ◽  
Molecular Approaches ◽  
Difficult Genus ◽  
Morphological Criteria

AbstractMolecular approaches for identifying aquatic macroinvertebrate species are increasingly being used but there is ongoing debate about the number of DNA markers needed to differentiate species accurately. Here, we use two mitochondrial genes (cytochrome oxidase I, cytochrome b) and a nuclear gene (carbamoylphosphate synthetase) to differentiate species variation within the taxonomically challenging chironomid genus Procladius from southern Australia, a genus which is important for pollution monitoring. The mitochondrial genes indicated cryptic species that were subsequently linked to morphological variation at the larval and pupal stage. Two species previously described based on morphological criteria were linked to molecular markers, and there was evidence for additional cryptic species. Each genetic marker provided different information, highlighting the importance of considering multiple genes when dissecting taxonomically difficult groups, particularly those used in pollution monitoring.

scholarly journals Taxonomic distribution of cryptic diversity among metazoans: not so homogeneous after all

2016 ◽  
Vol 12 (8) ◽  
pp. 20160371 ◽  
Author(s):  
Gerardo Pérez-Ponce de León ◽  
Robert Poulin
Keyword(s):  
Invasive Species ◽  
Species Richness ◽  
Cryptic Species ◽  
Biodiversity Conservation ◽  
Research Effort ◽  
Cryptic Diversity ◽  
Taxonomic Distribution ◽  
Extensive Survey ◽  
Taxonomic Groups

Cryptic diversity plagues estimates of biodiversity, conservation efforts and attempts to control diseases and invasive species. Here, we re-visit a decade-old assessment of whether or not cryptic species are homogeneously reported among higher metazoan taxa. We compiled information from an extensive survey of the literature to recover all reports of cryptic species among metazoans. After correcting for currently known species richness and research effort per taxon, we find that cryptic species are over-reported in some taxa and under-reported in others. Although several taxa showing either a lack or an excess of reported cryptic species were poorly studied invertebrate groups, we found that cryptic species were over-reported in amphibians, reptiles and crustaceans, all relatively well-studied groups. The observed heterogeneity in the distribution of reported cryptic species may reflect taxon-specific properties affecting either the propensity for cryptic species to be formed or their likelihood of being detected by conventional taxonomy. Either way, the implications of cryptic diversity may not apply equally across all taxonomic groups.

scholarly journals Molecular Approaches to Identify Cryptic Species and Polymorphic Species within a Complex Community of Fig Wasps

PLoS ONE ◽  
2010 ◽  
Vol 5 (11) ◽  
pp. e15067 ◽  
Author(s):  
Jin-Hua Xiao ◽  
Ning-Xin Wang ◽  
Yan-Wei Li ◽  
Robert W. Murphy ◽  
Dong-Guang Wan ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Fig Wasps ◽  
Molecular Approaches ◽  
Polymorphic Species

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 Interstitial Annelida

Diversity ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 77
Author(s):  
Katrine Worsaae ◽  
Alexandra Kerbl ◽  
Maikon Di Domenico ◽  
Brett C. Gonzalez ◽  
Nicolas Bekkouche ◽  
...  
Keyword(s):  
Morphological Traits ◽  
Life Forms ◽  
Cryptic Diversity ◽  
Special Issue ◽  
Number Of Species ◽  
Molecular Approaches ◽  
High Degree ◽  
Ciliary Locomotion

Members of the following marine annelid families are found almost exclusively in the interstitial environment and are highly adapted to move between sand grains, relying mostly on ciliary locomotion: Apharyngtidae n. fam., Dinophilidae, Diurodrilidae, Nerillidae, Lobatocerebridae, Parergodrilidae, Polygordiidae, Protodrilidae, Protodriloididae, Psammodrilidae and Saccocirridae. This article provides a review of the evolution, systematics, and diversity of these families, with the exception of Parergodrilidae, which was detailed in the review of Orbiniida by Meca, Zhadan, and Struck within this Special Issue. While several of the discussed families have previously only been known by a few described species, recent surveys inclusive of molecular approaches have increased the number of species, showing that all of the aforementioned families exhibit a high degree of cryptic diversity shadowed by a limited number of recognizable morphological traits. This is a challenge for studies of the evolution, taxonomy, and diversity of interstitial families as well as for their identification and incorporation into ecological surveys. By compiling a comprehensive and updated review on these interstitial families, we hope to promote new studies on their intriguing evolutionary histories, adapted life forms and high and hidden diversity.

Avian taxonomy in turmoil: The 7-point rule is poorly reproducible and may overlook substantial cryptic diversity

The Auk ◽  
2021 ◽  
Author(s):  
Frank E Rheindt ◽  
Elize Y X Ng
Keyword(s):  
Cryptic Species ◽  
Scoring System ◽  
Red List ◽  
The Other ◽  
Cryptic Diversity ◽  
High Reproducibility ◽  
Indonesian Archipelago ◽  
Other Hand ◽  
Detailed Assessment

Abstract The ornithological world has 4 global checklists (as of early 2020). While 3 follow the results of peer-reviewed research at varying pace and conservatism, the HBW/BirdLife checklist, which is adopted by the global Red List authority, has implemented Tobias et al.’s (2010) 7-point scoring system to overhaul global ornithological treatment. Critically received in some academic quarters, this scoring system is lauded by other ornithologists for its simplicity and reproducibility, a claim that remains to be tested. We subjected 26 ornithologists to a set of 48 bird skins belonging to 20 controversial taxonomic complexes and observed a wide variance in scoring results, in most cases straddling anywhere from far below to above the species threshold of the 7-point rule and casting doubt on claims of high reproducibility. For a detailed assessment of genuine taxonomic discord, we compared the taxonomic coverage of the avifauna of the Indonesian Archipelago (comprising ~1,400 species) between the HBW/BirdLife checklist, other major authorities, and the peer-reviewed literature. We detected that controversial treatments supported by the 7-point rule but at odds with the peer-reviewed literature predominantly refer to lumps, not splits, which are the usual subject of modern taxonomic quarrels. Notably, the method tends to unite morphologically (and sometimes vocally) cryptic forms into single larger species because of its inability to accommodate molecular and massive bioacoustic datasets that would indicate otherwise. On the other hand, the 7-point rule has produced numerous novel proposals for splits that may or may not be corroborated by future peer-reviewed inquiry. We recommend the 7-point rule as one of the multiple unofficial exploratory tools to flag cases of potentially cryptic species requiring further inquiry, but we advise against its adoption by other taxonomic authorities and the ornithological community.

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