A multilocus phylogeny of the genus Sarcohyla (Anura: Hylidae), and an investigation of species boundaries using statistical species delimitation

2018 ◽  
Vol 118 ◽  
pp. 184-193 ◽  
Author(s):  
Itzue W. Caviedes-Solis ◽  
Adrián Nieto-Montes de Oca
Mycologia ◽  
2012 ◽  
Vol 104 (6) ◽  
pp. 1369-1380 ◽  
Author(s):  
Yuko Ota ◽  
Takashi Yamanaka ◽  
Hitoshi Murata ◽  
Hitoshi Neda ◽  
Akira Ohta ◽  
...  

2021 ◽  
Author(s):  
Yann Spöri ◽  
Fabio Stoch ◽  
Simon Dellicour ◽  
C. William Birky ◽  
Jean-François Flot

K/θ is a method to delineate species that rests on the calculation of the ratio between the average distance K separating two putative species-level clades and the genetic diversity θ of these clades. Although this method is explicitly rooted in population genetic theory, it was never benchmarked due to the absence of a program allowing automated analyses. For the same reason, its application by hand was limited to small datasets of a few tens of sequences. We present an automatic implementation of the K/θ method, dubbed KoT (short for "K over Theta"), that takes as input a FASTA file, builds a neighbour-joining tree, and returns putative species boundaries based on a user-specified K/θ threshold. This automatic implementation avoids errors and makes it possible to apply the method to datasets comprising many sequences, as well as to test easily the impact of choosing different K/θ threshold ratios. KoT is implemented in Haxe, with a javascript webserver interface freely available at https://eeg-ebe.github.io/KoT/ .


2018 ◽  
Vol 68 (3) ◽  
pp. 441-459 ◽  
Author(s):  
Jonas Eberle ◽  
Erika Bazzato ◽  
Silvia Fabrizi ◽  
Michele Rossini ◽  
Mariastella Colomba ◽  
...  

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Chyi Yin Gwee ◽  
James A. Eaton ◽  
Elize Y. X. Ng ◽  
Frank E. Rheindt

Abstract Background The taxonomy of the Collared Owlet (Glaucidium brodiei) species complex is confused owing to great individual variation in plumage colouration seemingly unrelated to their distribution. Although generally recognised as a single species, vocal differences among the subspecies have been noted by field recordists. However, there is no study assessing the vocal differences among these four subspecies. Methods We obtained 76 sound recordings of the G. brodiei species complex comprising all four subspecies. We conducted bioacoustic examinations using principal component analysis and the Isler criterion to quantitatively test species boundaries within the G. brodiei complex. In addition, we compared plumage colouration among 13 specimens of the G. brodiei complex deposited at the Natural History Museum at Tring, UK and the Lee Kong Chian Natural History Museum, Singapore to ascertain the presence of plumage differences across taxa. Results We found the Bornean and Sumatran populations vocally similar to each other, but distinctly different from the mainland and Taiwan populations. The vocal pattern seems to corroborate plumage distinctions in the colouration of neck collars: the Bornean and Sumatran taxa share a white neck collar, whereas the continental and Taiwan taxa share a rufous neck collar. Conclusions We propose the taxonomic elevation of the Sumatran and Bornean populations to species level as Sunda Owlet G. sylvaticum, with one subspecies on Sumatra (G. s. sylvaticum) and Borneo (G. s. borneense) each. Our study corroborates the importance of bioacoustics in ascertaining species boundaries in non-passerines, and emphasises the significance of incorporating multiple species delimitation approaches when making taxonomic decisions.


PLoS ONE ◽  
2015 ◽  
Vol 10 (4) ◽  
pp. e0121139 ◽  
Author(s):  
Justin C. Bagley ◽  
Fernando Alda ◽  
M. Florencia Breitman ◽  
Eldredge Bermingham ◽  
Eric P. van den Berghe ◽  
...  

2018 ◽  
Vol 125 ◽  
pp. 177-187 ◽  
Author(s):  
Panayiota Kotsakiozi ◽  
Daniel Jablonski ◽  
Çetin Ilgaz ◽  
Yusuf Kumlutaş ◽  
Aziz Avcı ◽  
...  

2018 ◽  
Vol 57 (6) ◽  
pp. 781-789 ◽  
Author(s):  
Ivan M Pchelin ◽  
Daniil V Azarov ◽  
Maria A Churina ◽  
Sergey G Scherbak ◽  
Svetlana V Apalko ◽  
...  

AbstractThe fungi Trichophyton mentagrophytes and T. interdigitale are closely related species, causing superficial infections in humans and other mammals. The status of these taxa is a field of long-lasting debates. To clarify their phylogenetic relationships within the genus Trichophyton and sharpen the species boundaries, we performed sequencing of four T. mentagrophytes genomes and also evaluated three previously published multilocus data sets. We performed computational species delimitation analysis on all available in GenBank internal transcribed spacer region (ITS) sequences of Trichophyton spp. Phylogenomic data, phylogenetic network, and species delimitation analyses implied that T. mentagrophytes and T. interdigitale belong to the same phylogenetic species. However, we argue that taxonomic status quo should be retained, from the perspective of epidemiological data and the principle of taxonomic stability. Since there is a correlation between ITS genotype and epidemiological source of an isolate, restriction of T. interdigitale to purely anthropophilic ITS genotypes seems to be reasonable.


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