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 Fish species diversity in headwaters streams of Paraguay and Paraná Basins

2007 ◽  
Vol 50 (6) ◽  
pp. 1033-1042 ◽  
Author(s):  
Yzel Rondon Súarez ◽  
Sabrina Bigatão Valério ◽  
Karina Keyla Tondado ◽  
Alexandro Cezar Florentino ◽  
Thiago Rota Alves Felipe ◽  
...  
Keyword(s):  
Species Richness ◽  
Species Diversity ◽  
Environmental Factors ◽  
Fish Species ◽  
Total Species Richness ◽  
Paraná Basin ◽  
Parana Basin ◽  
Number Of Individuals ◽  
Total Species ◽  
Fish Species Diversity

The influence of spatial, temporal and environmental factors on fish species diversity in headwater streams in Paraguay and Paraná basins, Brazil was examined. A total of 4,605 individuals were sampled, distributed in 60 species. The sampled streams in Paraná basin presented a larger total species richness (42) than Paraguay streams (40). However the estimated richness was larger in Paraguay basin (53) than Paraná streams (50). The streams of Paraná basin had a greater mean species richness and evenness, while more individuals per sample were found in the Paraguay basin. Difference between the sub-basins were found in the Paraguay basin, while for the basin of Paraná, richness and evenness vary significantly between the sub-basins, but the number of individuals varied seasonally. The most important environmental factors to species diversity and abundance were altitude, water temperature, stream width and stream depth for both the basins.

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.

Insight into species diversity of the Trichostrongylidae Leiper, 1912 (Nematoda: Strongylida) in ruminants

2015 ◽  
Vol 90 (6) ◽  
pp. 639-646 ◽  
Author(s):  
A. Wyrobisz ◽  
J. Kowal ◽  
P. Nosal
Keyword(s):  
Species Diversity ◽  
Cryptic Species ◽  
Species Identification ◽  
Parasitic Nematode ◽  
Molecular Evidence ◽  
Comparable Data ◽  
Current State ◽  
The Family ◽  
Species Distinction ◽  
Insight Into

AbstractThis paper focuses on the species diversity among the Trichostrongylidae Leiper, 1912 (Nematoda: Strongylida), and complexity of the family systematics. Polymorphism (subfamilies: Ostertagiinae, Cooperiinae and Haemonchinae), the presence of cryptic species (genus: Teladorsagia) and hybridization (genera: Cooperia, Haemonchus and Ostertagia) are presented and discussed, considering both morphological and molecular evidence. Some of these phenomena are common, nevertheless not sufficiently understood, which indicates the need for expanding the current state of knowledge thereof. Within the Trichostrongylidae, species distinction supported merely by morphological features is difficult, and requires confirmation by means of molecular methods. The parasitic nematode taxonomy is complicated mainly by the genus Teladorsagia, but complexity may also be expected among other Ostertagiinae (e.g. in the genera Ostertagia and Marshallagia). The data presented here show that the members of the Trichostrongylidae can significantly complicate unambiguous species identification. Hence, it is essential to consider the phenomena mentioned, to gather valid and comparable data on the biodiversity of this family.

scholarly journals SESGOS ASOCIADOS A CENSOS VISUALES DE PECES ARRECIFALES EN EL PACÍFICO ORIENTAL TROPICAL: IMPLICACIONES DEL USO DE TRANSECTOS SENCILLOS O DE TAMAÑO MIXTO, DE LA EXPERIENCIA DE LOS BUZOS Y DE LA ESTIMACIÓN DE LA TALLA

2016 ◽  
Vol 40 ◽  
Author(s):  
María Del Mar Palacios ◽  
Fernando A. Zapata
Keyword(s):  
Species Richness ◽  
Cryptic Species ◽  
Total Density ◽  
Size Estimation ◽  
Specific Density ◽  
Fish Size ◽  
Mobile Species ◽  
Total Species Richness ◽  
Accuracy And Precision ◽  
Total Species

Visual censuses on belt transects implemented to assess reef fish populations in the Eastern Tropical Pacific (ETP) vary greatly in the size of sampling units and census protocols. To examine the effects of such variation on estimates of species richness and density, and to help identify an appropriate (accurate, precise and efficient) protocol, we compared two belt transect methods: a single-size transect (one 30 x 2 m band) and a mixed-size transect (two bands, a 50 x 5 m band for large, mobile fishes, and a 50 x 1 m band for small or cryptic fishes). Three observers with different experience conducted 72 visual censuses on three fixed transects at El Arrecife coral formation in Malpelo Island, Colombia, following a factorial design to evaluate the effect of methods, observers and fish size estimation on the accuracy and precision of species richness and density estimates. Additionally, we examined the efficiency (cost in time in relation to the accuracy and precision) of each method. The Mixed Transect (MT) yielded more precise estimates of population and community parameters and more accurate estimates of species richness. However, it had a high implementation cost (25 min/census) and consistently underestimated total density and the density of species recorded in the 50 x 5 m transect (probably due to its greater band width and associated decrease in species detectability). The Single Transect (ST) was more cost-efficient (14 min/census) and produced more accurate estimates of total and specific density for most species (except cryptic or small ones). Both methods were biased by the estimation of fish size during the censuses and by observer inexperience, so they should be implemented under oceanographic conditions that facilitate carrying out visual censuses and by divers with prior training. Alternatively, random sampling can be performed independently of visual censuses to estimate size frequency distributions without affecting estimates of abundance and species richness. Given the generally poor visibility in the ETP and insufficient funding for research and monitoring projects, the ST protocol is more suitable for conducting surveys of multiple species. In addition to producing more accurate estimates of total and specific density for most species, the greater cost-efficiency of STs allows to increase the number of replicates and thus to improve the estimate of total species richness and the precision of all population and community estimates. However, due to the greater accuracy of the MT to assess total species richness and density of small and cryptic species, an alternative would be to use a MT of at least 30 m length, with a maximum width of 2 m for censusing large and mobile species, and of 1 m for small and cryptic species.

Molecular evidence for cryptic species among the Antarctic fish Trematomus bernacchii and Trematomus hansoni

1997 ◽  
Vol 9 (4) ◽  
pp. 381-385 ◽  
Author(s):  
Giacomo Bernardi ◽  
Usha Goswami
Keyword(s):  
Cryptic Species ◽  
Dna Sequences ◽  
Antarctic Fish ◽  
The Other ◽  
Molecular Evidence ◽  
Allozyme Analysis ◽  
Mcmurdo Sound ◽  
Trematomus Bernacchii ◽  
Colour Morphs ◽  
The Antarctic

The notothenid species Trematomus bernacchii has previously been shown, by allozyme analysis, to be a complex of two cryptic species, one of which being more closely related to T. hansoni than to the other T. bernacchii cryptic species. Two T. bernacchii colour morphs, “white blotch” and “brown”, at McMurdo Sound, may correspond to these cryptic species. In this study, we present mitochondrial DNA sequences of the 12S and 16S ribosomal regions for six “white blotch” morphs, eight “brown” morphs collected in McMurdo Sound, one individual collected off the Antarctic Peninsula, and two T. hansoni individuals from McMurdo Sound. These sequences were compared with those of T. bernacchii and T. hansoni in the literature. Based on 14 phylogenetically informative sequences, no differences were found between “white blotch” and “brown” morphs. Furthermore, only one substitution separated these sequences from the previously published T. hansoni sequence, while 10 substitutions separated them from the previously published T. bernacchii sequence. Misidentified specimens, and sequence misreadings may be at the origin of these discrepancies. However, the presence of cryptic species within T. bernacchii and T. hansoni is not ruled out.

scholarly journals Millipede and centipede assemblages on the northern and southern slopes of the lowland Altais, southwestern Siberia, Russia (Diplopoda, Chilopoda)

ZooKeys ◽  
2018 ◽  
Vol 741 ◽  
pp. 219-254 ◽  
Author(s):  
Pavel S. Nefediev ◽  
Gyulli Sh. Farzalieva ◽  
Ivan H. Tuf ◽  
Khozhiakbar Kh. Nedoev ◽  
Saparmurad T. Niyazov
Keyword(s):  
Species Richness ◽  
Species Diversity ◽  
Vertical Distribution ◽  
Age Structure ◽  
Seasonal Dynamics ◽  
Total Species Richness ◽  
Southwestern Siberia ◽  
First Time ◽  
Total Species ◽  
Specific Identity

The total species richness in the myriapod assemblages of the lowland Altais near Charyshskoe Village, Altai Province, southwestern Siberia, Russia is estimated to be at least 19 species from ten genera, eight families, five orders, and two classes. The following species are new to SW Siberia: Lithobius (Ezembius) ostiacorum Stuxberg, 1876,L. vagabundusStuxberg, 1876, and L. (Monotarsobius) nordenskioeldii Stuxberg, 1876, while L. (E.) proximus Sseliwanoff, 1880 and L. (M.) insolens Dányi & Tuf, 2012 are recorded for the first time from the Altai Province of Russia. A species ofStrigamiawhich is morphologically similar to Strigamia cf. transsilvanica (Verhoeff, 1928) has been found in the study area but its true specific identity is yet to be determined. The seasonal dynamics of myriapod assemblages in terms of the species diversity, density, sex-age structure, and vertical distribution along the soil profile have been studied with regard to the different slope exposures.

Species Diversity, Abundance and Habitat Distribution of Anurans in Mts. Palay-Palay Mataas-Na-Gulod Protected Landscape, Luzon Island, Philippines

2017 ◽  
Vol 10 ◽  
Keyword(s):  
Species Diversity ◽  
New Records ◽  
Management Plan ◽  
The Philippines ◽  
Sampling Time ◽  
Ecological Data ◽  
Total Species Richness ◽  
Transect Sampling ◽  
Total Species ◽  
Effective Conservation

Mt. Palay-Palay is Cavite’s only protected landscape and yet very few herpetological studies have been done in this area. Thus, the study aims to provide robust ecological data on different anuran species so that an effective conservation and management plan could be formulated. Five habitats were sampled using a combination of cruising transect, stratified random strip transect sampling, time-constrained searches, visual encounter survey (VES) and acoustic encounter survey (AES). A total of 1528 individuals belonging to 12 species was recorded from the study area. In addition to previous works, 2 Platymantis spp. were new records bringing the total species richness to 16. Of the 16 species, 10 (62.5%) are endemic to the Philippines. Among the species, Platymantis mimulus was the most abundant and also had the highest density of 174 frogs ha-1. Among the habitats riparian forests had highest species diversity, Mau Tao and Jackknife1 values which showed dependence of anurans on water. Of the 17 microhabitats, forest floor litter was the most occupied by anurans.

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.

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 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.

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