Phylogenomics and molecular species delimitation reveals great cryptic diversity of leaf-toed geckos (Phyllodactylidae: Phyllodactylus), ancient origins, and diversification in Mexico

2020 ◽  
Vol 150 ◽  
pp. 106880
Author(s):  
Tonatiuh Ramírez-Reyes ◽  
Christopher Blair ◽  
Oscar Flores-Villela ◽  
Daniel Piñero ◽  
Amy Lathrop ◽  
...  
Keyword(s):  
Molecular Species ◽  
Species Delimitation ◽  
Cryptic Diversity

scholarly journals Molecular Species Delimitation of Larks (Aves: Alaudidae), and Integrative Taxonomy of the Genus Calandrella, with the Description of a Range-Restricted African Relic Taxon

Diversity ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 428
Author(s):  
Martin Stervander ◽  
Bengt Hansson ◽  
Urban Olsson ◽  
Mark F. Hulme ◽  
Ulf Ottosson ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Molecular Species ◽  
Species Delimitation ◽  
Integrative Taxonomy ◽  
West African ◽  
Northwest Africa ◽  
Sub Saharan ◽  
Plateau State ◽  
Avian Family ◽  
Relic Population

Larks constitute an avian family of exceptional cryptic diversity and striking examples of convergent evolution. Therefore, traditional morphology-based taxonomy has recurrently failed to reflect evolutionary relationships. While taxonomy ideally should integrate morphology, vocalizations, behaviour, ecology, and genetics, this can be challenging for groups that span several continents including areas that are difficult to access. Here, we combine morphometrics and mitochondrial DNA to evaluate the taxonomy of Calandrella larks, with particular focus on the African C. cinerea and the Asian C. acutirostris complexes. We describe a new range-restricted West African taxon, Calandrella cinerea rufipecta ssp. nov. (type locality: Jos, Plateau State, Nigeria), with an isolated relic population 3000 km from its closest relative in the Rift Valley. We performed molecular species delimitation, employing coalescence-based multi-rate Poisson Tree Processes (mPTP) on cytochrome b sequences across 52 currently recognized lark species, including multiple taxa currently treated as subspecies. Three species-level splits were inferred within the genus Calandrella and another 13 across other genera, primarily among fragmented sub-Saharan taxa and taxa distributed from Northwest Africa to Arabia or East Africa. Previously unknown divergences date back as far as to the Miocene, indicating the presence of currently unrecognized species. However, we stress that taxonomic decisions should not be based on single datasets, such as mitochondrial DNA, although analyses of mitochondrial DNA can be a good indicator of taxa in need of further integrative taxonomic assessment.

scholarly journals Pond chironomid communities revealed by molecular species delimitation reflect eutrophication

2021 ◽  
Author(s):  
Kenzi Takamura ◽  
Ryuhei Ueno ◽  
Natsuko Ito Kondo ◽  
Kako Ohbayashi
Keyword(s):  
Molecular Species ◽  
Species Delimitation

scholarly journals Phylogeography and Molecular Species Delimitation of Pratylenchus capsici n. sp., a New Root-Lesion Nematode in Israel on Pepper (Capsicum annuum)

2019 ◽  
Vol 109 (5) ◽  
pp. 847-858 ◽  
Author(s):  
Xue Qing ◽  
Wim Bert ◽  
Abraham Gamliel ◽  
Patricia Bucki ◽  
Svetlana Duvrinin ◽  
...  
Keyword(s):  
New Species ◽  
Capsicum Annuum ◽  
Molecular Species ◽  
Species Delimitation ◽  
Chenopodium Album ◽  
Haplotype Diversity ◽  
Small Scale ◽  
Growing Seasons ◽  
Contemporary Gene Flow ◽  
A New Species

Root-lesion nematodes of the genus Pratylenchus parasitize the roots of numerous plants and can cause severe damage and yield loss. Here, we report on a new species, Pratylenchus capsici n. sp., from the Arava rift, Israel, which was characterized by integrative methods, including detailed morphology, molecular phylogeny, population genetics, and phylogeography. This species is widely spread across the Arava rift, causing significant infection in pepper (Capsicum annuum) roots and inhibiting plant growth. Both morphological and molecular species delimitation support the recovered species as a new species. We found high cytochrome oxidase subunit I haplotype diversity, and phylogeography analysis suggests that contemporary gene flow is prevented among different agricultural farms, while population dispersal from weeds (Chenopodium album and Sonchus oleraceus) to pepper occurs on a relatively small scale. Our results suggest that weeds are an important reservoir for the dispersal of P. capsici n. sp., either as the original nematode source or at least in maintaining the population between growing seasons.

scholarly journals In the shadows: Phylogenomics and coalescent species delimitation unveil cryptic diversity in a Cerrado endemic lizard (Squamata: Tropidurus)

2017 ◽  
Vol 107 ◽  
pp. 455-465 ◽  
Author(s):  
Fabricius M.C.B. Domingos ◽  
Guarino R. Colli ◽  
Alan Lemmon ◽  
Emily Moriarty Lemmon ◽  
Luciano B. Beheregaray
Keyword(s):  
Species Delimitation ◽  
Cryptic Diversity

scholarly journals Establishment of six new Rhabdoblatta species (Blattodea, Blaberidae, Epilamprinae) from China

ZooKeys ◽  
2019 ◽  
Vol 851 ◽  
pp. 27-69
Author(s):  
Rong Yang ◽  
Zhenzhen Wang ◽  
Yanshuang Zhou ◽  
Zongqing Wang ◽  
Yanli Che
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Molecular Species ◽  
Species Delimitation ◽  
Female Genitalia ◽  
Morphological Data ◽  
Coi Sequences ◽  
First Time

This study examined 504 Rhabdoblatta specimens sampled from China, of which, 86 Rhabdoblatta specimens were used for COI sequencing. A phylogenetic analysis using the ML method and MOTUs estimations by ABGD and GMYC based on COI sequences was performed. Eighteen Rhabdoblatta species were identified when these data were combined with morphological data. Six new species were established among these samples, i.e., Rh.similsinuatasp. n., Rh.densimaculatasp. n., Rh.gyroflexasp. n., Rh.chaulformissp. n., Rh.maculatasp. n., and Rh.ecarinatasp. n. For the first time, females including female genitalia of 14 known Rhabdoblatta species are described worldwide. Our study shows that combining molecular species delimitation methods with morphological data helps to delimit species and understand cockroach biodiversity.

Extensive cryptic diversity of giant clams (Cardiidae: Tridacninae) revealed by DNA-sequence-based species delimitation approaches with new data from Hainan Island, South China Sea

2020 ◽  
Vol 86 (1) ◽  
pp. 56-63 ◽  
Author(s):  
Jun Liu ◽  
Dan Cui ◽  
Hui Wang ◽  
Jiawei Chen ◽  
Helu Liu ◽  
...  
Keyword(s):  
South China Sea ◽  
South China ◽  
Species Delimitation ◽  
Strong Support ◽  
Hainan Island ◽  
The Philippines ◽  
Nominal Species ◽  
Cryptic Diversity ◽  
China Sea ◽  
Giant Clams

Abstract Accurate species delimitation is important, especially for endangered species. As one of the most conspicuous bivalve taxa, giant clams are threatened throughout their geographic range. Many phylogeographic studies have revealed strong population structure among giant clams in the Indo-Pacific, suggesting cryptic diversity within these species. However, less attention has been paid to their identification and delimitation. In this study, we assembled a comprehensive dataset of mitochondrial cytochrome c oxidase subunit I (COI) sequences for Tridacna species, focusing on new sequences from Hainan Island in the South China Sea and previously published ones from Japan, Taiwan, Singapore, the Philippines, Indonesia, Australia, the Solomon Islands and the Red Sea. Three nominal species, Tridacna crocea, T. squamosa and T. noae, were recognized at Hainan Island on the basis of distance-based DNA barcoding, with mean interspecific K2P distances of 10.6–24.7% for seven Tridacna species (T. crocea, T. squamosa, T. noae, T. maxima, T. mbalavuana, T. derasa and T. gigas). The most abundant species, T. noae, represents the first record of this species from Hainan Island. Using a combination of phylogenetic and DNA-based species delimitation analyses (automatic barcode gap discovery, generalized mixed Yule coalescent and Bayesian Poisson tree processes), we found strong support for a total of 13 operational taxonomic units (OTUs) for the seven nominal Tridacna species. These results, coupled with the fact that each OTU occupies different regions in the Indo-Pacific, strongly suggest multiple cryptic species of giant clams. Our findings point to the need for taxonomic revisionary work on giant clams throughout the Indo-Pacific; such work will have important conservation implications.

scholarly journals Hidden biodiversity revealed by integrated morphology and genetic species delimitation of spring dwelling water mite species (Acari, Parasitengona: Hydrachnidia)

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Lucas Blattner ◽  
Reinhard Gerecke ◽  
Stefanie von Fumetti
Keyword(s):  
Species Identification ◽  
Molecular Species ◽  
Species Delimitation ◽  
Mite Species ◽  
Water Mites ◽  
Water Mite ◽  
Barcoding Gap ◽  
Molecular Species Identification ◽  
True Diversity ◽  
Genetic Species

Abstract Background Water mites are among the most diverse organisms inhabiting freshwater habitats and are considered as substantial part of the species communities in springs. As parasites, Hydrachnidia influence other invertebrates and play an important role in aquatic ecosystems. In Europe, 137 species are known to appear solely in or near springheads. New species are described frequently, especially with the help of molecular species identification and delimitation methods. The aim of this study was to verify the mainly morphology-based taxonomic knowledge of spring-inhabiting water mites of central Europe and to build a genetic species identification library. Methods We sampled 65 crenobiontic species across the central Alps and tested the suitability of mitochondrial (cox1) and nuclear (28S) markers for species delimitation and identification purposes. To investigate both markers, distance- and phylogeny-based approaches were applied. The presence of a barcoding gap was tested by using the automated barcoding gap discovery tool and intra- and interspecific genetic distances were investigated. Furthermore, we analyzed phylogenetic relationships between different taxonomic levels. Results A high degree of hidden diversity was observed. Seven taxa, morphologically identified as Bandakia concreta Thor, 1913, Hygrobates norvegicus (Thor, 1897), Ljania bipapillata Thor, 1898, Partnunia steinmanni Walter, 1906, Wandesia racovitzai Gledhill, 1970, Wandesia thori Schechtel, 1912 and Zschokkea oblonga Koenike, 1892, showed high intraspecific cox1 distances and each consisted of more than one phylogenetic clade. A clear intraspecific threshold between 5.6–6.0% K2P distance is suitable for species identification purposes. The monophyly of Hydrachnidia and the main superfamilies is evident with different species clearly separated into distinct clades. cox1 separates water mite species but is unsuitable for resolving higher taxonomic levels. Conclusions Water mite species richness in springs is higher than has been suggested based on morphological species identification alone and further research is needed to evaluate the true diversity. The standard molecular species identification marker cox1 can be used to identify species but should be complemented by a nuclear marker, e.g. 28S, to resolve taxonomic relationships. Our results contribute to the taxonomical knowledge on spring inhabiting Hydrachnida, which is indispensable for the development and implementation of modern environment assessment methods, e.g. metabarcoding, in spring ecology.

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