scholarly journals Cryptic diversity in vertebrates: molecular data double estimates of species diversity in a radiation of Australian lizards ( Diplodactylus , Gekkota)

2009 ◽  
Vol 276 (1664) ◽  
pp. 2001-2007 ◽  
Author(s):  
Paul M. Oliver ◽  
Mark Adams ◽  
Michael S.Y. Lee ◽  
Mark N. Hutchinson ◽  
Paul Doughty
Keyword(s):  
Species Diversity ◽  
Molecular Data ◽  
Nominal Species ◽  
Cryptic Diversity ◽  
Industrialized Countries ◽  
Taxonomic Impediment ◽  
Species Complexes ◽  
Developed Nations ◽  
Diversity Estimates ◽  
Conservation And Management

A major problem for biodiversity conservation and management is that a significant portion of species diversity remains undocumented (the ‘taxonomic impediment’). This problem is widely acknowledged to be dire among invertebrates and in developing countries; here, we demonstrate that it can be acute even in conspicuous animals (reptiles) and in developed nations (Australia). A survey of mtDNA, allozyme and chromosomal variation in the Australian gecko, genus Diplodactylus , increases overall species diversity estimates from 13 to 29. Four nominal species each actually represent multi-species complexes; three of these species complexes are not even monophyletic. The high proportion of cryptic species discovered emphasizes the importance of continuing detailed assessments of species diversity, even in apparently well-known taxa from industrialized countries.

scholarly journals Updating species diversity of Colletotrichum, with a phylogenomic overview

2022 ◽  
Author(s):  
F. Liu ◽  
Z.Y. Ma ◽  
L.W. Hou ◽  
Y.Z. Diao ◽  
W.P. Wu ◽  
...  
Keyword(s):  
Species Diversity ◽  
Plant Pathogens ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Single Copy ◽  
Molecular Data ◽  
Human Pathogens ◽  
Species Complexes ◽  
Backbone Tree ◽  
The Uk

The genus Colletotrichum includes important plant pathogens, endophytes, saprobes and human pathogens. Even though the polyphasic approach has facilitated Colletotrichum species identification, knowledge of the overall species diversity and host distribution is largely incomplete. To address this, we examined 952 Colletotrichum strains isolated from plants representing 322 species from 248 genera, or air and soil samples, from 87 locations in China, as well as 56 strains from Saudi Arabia, Thailand, Turkey, and the UK. Based on morphological characteristics and multi-locus phylogenetic analyses, the strains were assigned to 107 species, including 30 new species described in this paper and 18 new records for China. The currently most comprehensive backbone tree of Colletotrichum, comprising 16 species complexes (including a newly introduced C. bambusicola species complex) and 15 singleton species, is provided. Based on these analyses, 280 species with available molecular data are accepted in this genus, of which 139 have been reported in China, accounting for 49.6 % of the species. Colletotrichum siamense, C. karsti, C. fructicola, C. truncatum, C. fioriniae, and C. gloeosporioides were the most commonly detected species in China, as well as the species with the broadest host range. By contrast, 76 species were currently found to be associated with a single plant species or genus in China. To date, 33 Colletotrichum species have been exclusively reported as endophytes. Furthermore, we generated and assembled whole-genome sequences of the 30 new and a further 18 known species. The most comprehensive genome tree comprising 94 Colletotrichum species based on 1 893 single-copy orthologous genes was hence generated, with all nodes, except four, supported by 100 % bootstrap values. Collectively, this study represents the most comprehensive investigation of Colletotrichum diversity and host occurrence to date, and greatly enhances our understanding of the diversity and phylogenetic relationships in this genus.

scholarly journals Molecular and morphological systematics of Bursatella leachii de Blainville, 1817 and Stylocheilus striatus Quoy & Gaimard, 1832 reveal cryptic diversity in pantropically distributed taxa (Mollusca : Gastropoda : Heterobranchia)

2020 ◽  
Author(s):  
Enrico Bazzicalupo ◽  
Fabio Crocetta ◽  
Terrence M. Gosliner ◽  
Véronique Berteaux-Lecellier ◽  
Yolanda E. Camacho-García ◽  
...  
Keyword(s):  
Nominal Species ◽  
Western Pacific Ocean ◽  
Cryptic Diversity ◽  
Western Atlantic ◽  
Sea Hare ◽  
Species Complexes ◽  
Sea Slugs ◽  
Bursatella Leachii ◽  
Pacific Species ◽  
Stylocheilus Striatus

The ragged sea hare (Bursatella leachii) and the long-tailed sea hare (Stylocheilus striatus) are two widely distributed species of benthic heterobranch sea slugs. In this paper, integrative taxonomic analyses have been conducted to detect possible cryptic diversity. Our results revealed that both nominal species are actually species complexes, consisting of five genetically distinct taxa. Two of them belong to the genus Bursatella and three to the genus Stylocheilus. The name B. leachii is retained for a widely distributed species, present in the Atlantic, the Mediterranean, and parts of the Indo-Pacific region. The name B. ocelligera is resurrected for the other species, restricted to the Indo-Pacific and co-occurring with B. leachii in that area. With the present data, it is not possible to test whether B. leachii and B. ocelligera have evolved allopatrically in the Atlantic and Indo-Pacific or sympatrically in the latter. Bursatella leachii has been able to maintain gene flow between the Atlantic and the Indo-Pacific Oceans, possibly because of a combined effect of the Agulhas Leakage process and the ability to survive the colder waters of South Africa. On the contrary, the three species of Stylocheilus are allopatric; the name S. striatus is retained for an Indo-Pacific species, while the names S. polyomma and S. rickettsi are resurrected for species inhabiting the Western Atlantic and the Eastern Pacific respectively. Finally, the discovery of a museum specimen mistakenly identified as B. leachii, but bearing a shell in its adult form, led to the resurrection of the genus Phycophila, previously synonymised with Aplysia. Phycophila euchlora, the only species described to date, is distributed in the Central and Western Pacific Ocean.

Unraveling the species diversity and relationships in the Leptodactylus mystaceus complex (Anura: Leptodactylidae), with the description of three new Brazilian species

Zootaxa ◽  
2020 ◽  
Vol 4779 (2) ◽  
pp. 151-189 ◽  
Author(s):  
LEANDRO A. DA SILVA ◽  
FELIPE M. MAGALHÃES ◽  
HANS THOMASSEN ◽  
FELIPE S. F. LEITE ◽  
ADRIAN A. GARDA ◽  
...  
Keyword(s):  
Species Diversity ◽  
Dna Sequences ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Species Discrimination ◽  
Nominal Species ◽  
South American ◽  
Geographic Ranges ◽  
The Andes ◽  
Three New Species

Members of the Leptodactylus mystaceus species complex are widely distributed in forests and open formations of South America east of the Andes. Species of the complex are morphologically similar or indistinguishable among each other, but acoustic data have been the cornerstone for species discrimination across their geographic ranges. In this paper, we re-examine the monophyly, species diversity, and relationships in the L. mystaceus complex on the basis of morphology, coloration, acoustics, and DNA sequences. Morphological and color patterns originally used to the allocation of species to the L. mystaceus complex are also reassessed. Our results revealed three new species from the Brazilian Atlantic Forest and Cerrado, which are named and described herein, based mainly on acoustic and molecular data. Populations assigned to the lineage widely distributed across the South American Dry Diagonal (DD), reported in this study as L. cf. mystaceus, is likely paraphyletic with respect to the nominal species (Amazonian lineage), but additional data are still needed to address the taxonomic status of the DD lineage. 

scholarly journals DNA barcode library for European Gelechiidae (Lepidoptera) suggests greatly underestimated species diversity

ZooKeys ◽  
2020 ◽  
Vol 921 ◽  
pp. 141-157 ◽  
Author(s):  
Peter Huemer ◽  
Ole Karsholt ◽  
Leif Aarvik ◽  
Kai Berggren ◽  
Oleksiy Bidzilya ◽  
...  
Keyword(s):  
Species Diversity ◽  
Dna Barcode ◽  
Species Level ◽  
Coi Gene ◽  
Species Discrimination ◽  
Nominal Species ◽  
Nearest Neighbour ◽  
Cryptic Diversity ◽  
Dna Barcodes ◽  
First Time

For the first time, a nearly complete barcode library for European Gelechiidae is provided. DNA barcode sequences (COI gene – cytochrome c oxidase 1) from 751 out of 865 nominal species, belonging to 105 genera, were successfully recovered. A total of 741 species represented by specimens with sequences ≥ 500bp and an additional ten species represented by specimens with shorter sequences were used to produce 53 NJ trees. Intraspecific barcode divergence averaged only 0.54% whereas distance to the Nearest-Neighbour species averaged 5.58%. Of these, 710 species possessed unique DNA barcodes, but 31 species could not be reliably discriminated because of barcode sharing or partial barcode overlap. Species discrimination based on the Barcode Index System (BIN) was successful for 668 out of 723 species which clustered from minimum one to maximum 22 unique BINs. Fifty-five species shared a BIN with up to four species and identification from DNA barcode data is uncertain. Finally, 65 clusters with a unique BIN remained unidentified to species level. These putative taxa, as well as 114 nominal species with more than one BIN, suggest the presence of considerable cryptic diversity, cases which should be examined in future revisionary studies.

Integrative taxonomy of giant crested Eusirus in the Southern Ocean, including the description of a new species (Crustacea: Amphipoda: Eusiridae)

2020 ◽  
Author(s):  
Marie L Verheye ◽  
Cédric D’Udekem D’Acoz
Keyword(s):  
New Species ◽  
Species Diversity ◽  
Morphological Analysis ◽  
Integrative Taxonomy ◽  
Putative Species ◽  
Species Complexes ◽  
Statistical Parsimony ◽  
Bayesian Implementation ◽  
A New Species ◽  
Giant Species

Abstract Among Antarctic amphipods of the genus Eusirus, a highly distinctive clade of giant species is characterized by a dorsal, blade-shaped tooth on pereionites 5–7 and pleonites 1–3. This lineage, herein named ‘crested Eusirus’, includes two potential species complexes, the Eusirus perdentatus and Eusirus giganteus complexes, in addition to the more distinctive Eusirus propeperdentatus. Molecular phylogenies and statistical parsimony networks (COI, CytB and ITS2) of crested Eusirus are herein reconstructed. This study aims to formally revise species diversity within crested Eusirus by applying several species delimitation methods (Bayesian implementation of the Poisson tree processes model, general mixed Yule coalescent, multi-rate Poisson tree processes and automatic barcode gap discovery) on the resulting phylogenies. In addition, results from the DNA-based methods are benchmarked against a detailed morphological analysis of all available specimens of the E. perdentatus complex. Our results indicate that species diversity of crested Eusirus is underestimated. Overall, DNA-based methods suggest that the E. perdentatus complex is composed of three putative species and that the E. giganteus complex includes four or five putative species. The morphological analysis of available specimens from the E. perdentatus complex corroborates molecular results by identifying two differentiable species, the genuine E. perdentatus and a new species, herein described as Eusirus pontomedon sp. nov.

Species diversity of Onchidiidae (Eupulmonata: Heterobranchia) on the mainland of China based on molecular data

2013 ◽  
Vol 34 (1) ◽  
pp. 62-70 ◽  
Author(s):  
Bianna Sun ◽  
Cheng Chen ◽  
Heding Shen ◽  
Kunxia Zhang ◽  
Na Zhou ◽  
...  
Keyword(s):  
Species Diversity ◽  
Molecular Data ◽  
The Mainland Of China

scholarly journals Old and new challenges in using species diversity for assessing biodiversity

2011 ◽  
Vol 366 (1576) ◽  
pp. 2426-2437 ◽  
Author(s):  
Alessandro Chiarucci ◽  
Giovanni Bacaro ◽  
Samuel M. Scheiner
Keyword(s):  
Species Diversity ◽  
Quantitative Measurement ◽  
Phylogenetic Distance ◽  
Existing Problems ◽  
Species Abundances ◽  
Species Lists ◽  
Assessment And Monitoring ◽  
New Challenges ◽  
Patterns And Processes ◽  
Conservation And Management

Although the maintenance of diversity of living systems is critical for ecosystem functioning, the accelerating pace of global change is threatening its preservation. Standardized methods for biodiversity assessment and monitoring are needed. Species diversity is one of the most widely adopted metrics for assessing patterns and processes of biodiversity, at both ecological and biogeographic scales. However, those perspectives differ because of the types of data that can be feasibly collected, resulting in differences in the questions that can be addressed. Despite a theoretical consensus on diversity metrics, standardized methods for its measurement are lacking, especially at the scales needed to monitor biodiversity for conservation and management purposes. We review the conceptual framework for species diversity, examine common metrics, and explore their use for biodiversity conservation and management. Key differences in diversity measures at ecological and biogeographic scales are the completeness of species lists and the ability to include information on species abundances. We analyse the major pitfalls and problems with quantitative measurement of species diversity, look at the use of weighting measures by phylogenetic distance, discuss potential solutions and propose a research agenda to solve the major existing problems.

scholarly journals The role of climatic and geological events in generating diversity in Ethiopian grass frogs (genus Ptychadena )

2017 ◽  
Vol 4 (8) ◽  
pp. 170021 ◽  
Author(s):  
Megan L. Smith ◽  
Brice P. Noonan ◽  
Timothy J. Colston
Keyword(s):  
Habitat Complexity ◽  
Molecular Data ◽  
Cryptic Diversity ◽  
Horn Of Africa ◽  
Climatic Fluctuations ◽  
Divergence Dating ◽  
Evolutionary Radiation ◽  
Novel Taxa ◽  
Climatic History

Ethiopia is a world biodiversity hotspot and harbours levels of biotic endemism unmatched in the Horn of Africa, largely due to topographic—and thus habitat—complexity, which results from a very active geological and climatic history. Among Ethiopian vertebrate fauna, amphibians harbour the highest levels of endemism, making amphibians a compelling system for the exploration of the impacts of Ethiopia's complex abiotic history on biotic diversification. Grass frogs of the genus Ptychadena are notably diverse in Ethiopia, where they have undergone an evolutionary radiation. We used molecular data and expanded taxon sampling to test for cryptic diversity and to explore diversification patterns in both the highland radiation and two widespread lowland Ptychadena . Species delimitation results support the presence of nine highland species and four lowland species in our dataset, and divergence dating suggests that both geologic events and climatic fluctuations played a complex and confounded role in the diversification of Ptychadena in Ethiopia. We rectify the taxonomy of the endemic P. neumanni species complex, elevating one formally synonymized name and describing three novel taxa. Finally, we describe two novel lowland Ptychadena species that occur in Ethiopia and may be more broadly distributed.

scholarly journals Seasonal Changes In Species Diversity And Dominance Structure In Communities Of Oribatid Mites (Sarcoptiformes, Oribatei) In Megalopolis Green Areas

2014 ◽  
Vol 48 (1) ◽  
pp. 3-10 ◽  
Author(s):  
O. S. Shevchenko ◽  
L. A. Kolodochka
Keyword(s):  
Species Diversity ◽  
Seasonal Changes ◽  
Oribatid Mites ◽  
Seasonal Fluctuations ◽  
Species Complexes ◽  
Dominance Structure ◽  
Green Areas ◽  
Different Parts

Abstract Species complexes of oribatid mites in soil and litter in 10 plots in green areas of different parts of Kyiv city in April-September 2011 were studied. In total, 107 species of 76 genera of 44 families of oribatids were found. Trends of seasonal fluctuations of species diversity and dominance structure of oribatids in studied plots were assessed.

scholarly journals SPECIES COMPLEXES OF THE ORIBATID MITES (SARCOPTIFORMES, ORIBATEI) IN SOILS OF URBAN STREET LAWNS WITH DIFFERENT POLLUTION RATES

2013 ◽  
Vol 47 (6) ◽  
pp. 49-52 ◽  
Author(s):  
O. S. Shevchenko ◽  
L. A. Kolodochka
Keyword(s):  
Species Diversity ◽  
Soil Pollution ◽  
Oribatid Mites ◽  
Urban Street ◽  
Total Soil ◽  
Species Complexes

Abstract Species complexes of oribatid mites at six plots on the street lawns in one of Kyiv districts are studied. In total 27 species of 26 genera and 19 families of oribatid mites are found. Direct correlation between oribatid species diversity and the level of total soil pollution is not shown.

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