General Mixed Yule Coalescent Model Research Articles

Violins we see, species we don’t… Species delimitation of the spider genus Loxosceles Heineken & Lowe (Araneae: Sicariidae) from North America using morphological and molecular evidence

In modern systematics, different sources of evidence are commonly used for the discovery, identification, and delimitation of species, especially when morphology fails to delineate between species or in underestimated species complexes or cryptic species. In this study, morphological data and two DNA barcoding markers—cytochrome c oxidase subunit I (COI) and internal transcribed spacer 2 (ITS2)—were used to delimit species in the spider genus Loxosceles from North America. The molecular species delimitation analyses were carried out using three different methods under the corrected p-distance Neighbor-Joining (NJ) criteria: 1) Assemble Species by Automatic Partitioning (ASAP), 2) General Mixed Yule Coalescent model (GMYC), and 3) Bayesian Poisson Tree Processes (bPTP). The analyses incorporated 192 terminals corresponding to 43 putative species of Loxosceles, of which 15 are newly recognized herein, as putative new species, based on morphology and congruence between molecular methods with COI. The average intraspecific genetic distance (p-distance) was <2%, whereas the average interspecific genetic distance was 15.6%. The GMYC and bPTP molecular methods recovered 65-79 and 69 species respectively, overestimating the diversity in comparison with morphology, whereas the ASAP method delimited 60 species. The morphology of primary sexual structures (males palps and female seminal receptacles) was congruent with most of the molecular methods mainly with COI, showing that they are robust characters for identification at the species level. For species delimitation COI was more informative than ITS2. The diversity of Loxosceles species is still underestimated for North America, particularly in Mexico which holds the highest diversity of this genus worldwide.

Species delimitation and molecular phylogeny of the grasshopper subfamily Gomphocerinae (Orthoptera: Acrididae) from Algeria based on mitochondrial and nuclear DNA markers

Gomphocerinae grasshoppers (Orthoptera: Acrididae) are generally characterised by their polymorphism and cryptic diversity, which can be confusing when relying on morphological identification alone. DNA taxonomy serves as a powerful molecular tool for species identification and biodiversity assessment. In the context of zoogeography and the biodiversity conservation of animal resources in ecosystems, DNA barcoding data for Algerian Gomphocerinae fauna remains limited in global databases, despite their agroeconomic and environmental importance. Therefore, in this study, we collected various species of this subfamily from the Biskra region in Algeria and conducted DNA barcoding analysis, employing different molecular species delimitation methods (the automatic barcode gap discovery, assemble species by automatic partitioning, single-threshold general mixed Yule coalescent model, Bayesian Poisson tree process and multi-rate Poisson tree process methods), as well as phylogenetic analyses (maximum-likelihood and Bayesian inference) based on two molecular markers (COI and ITS). The results of the 163 newly generated sequences demonstrated that DNA barcoding technology is highly efficient and valuable for species identification in the subfamily Gomphocerinae, showing strong congruence with morphological evidence for 12 species, including eight species that were sequenced for the first time. This study also reported a new record of the genus Stenohippus Uvarov, 1926 in Algeria, comprising two species. Additionally, taxonomic revision allowed the species Dociostaurus biskrensis Moussi & Petit, 2014, to be transferred to the genus Stenohippus. Molecular tree analyses revealed the phylogenetic positions of the newly sequenced species within the subfamily Gomphocerinae and provided insights into their evolutionary relationships. These new data serve as a starting point for future research in other geographical areas, enabling a better understanding of the biodiversity of this insect group in Algeria.

To be or not to be… Integrative taxonomy and species delimitation in the daddy long-legs spiders of the genus Physocyclus (Araneae, Pholcidae) using DNA barcoding and morphology.

Integrative taxonomy is crucial for discovery, recognition, and species delimitation, especially in underestimated species complex or cryptic species, by incorporating different sources of evidence to construct rigorous species hypotheses. The spider genus Physocyclus Simon, 1893 (Pholcidae, Arteminae) is composed of 37 species, mainly from North America. In this study, traditional morphology was compared with three DNA barcoding markers regarding their utility in species delimitation within the genus: 1) Cytochrome c Oxidase subunit 1 (CO1), 2) Internal Transcribed Spacer 2 (ITS2), and 3) Ribosomal large subunit (28S). The molecular species delimitation analyses were carried out using four methods under the corrected p-distances Neighbor-Joining (NJ) criteria: 1) Automatic Barcode Gap Discovery (ABGD), 2) Assemble Species by Automatic Partitioning (ASAP), 3) General Mixed Yule Coalescent model (GMYC), and 4) Bayesian Poisson Tree Processes (bPTP). The analyses incorporated 75 terminals from 22 putative species of Physocyclus. The average intraspecific genetic distance (p-distance) was found to be < 2%, whereas the average interspecific genetic distance was 20.6%. The ABGD, ASAP, and GMYC methods were the most congruent, delimiting 26 or 27 species, while the bPTP method delimited 33 species. The use of traditional morphology for species delimitation was congruent with most molecular methods, with the male palp, male chelicerae, and female genitalia shown to be robust characters that support species-level identification. The barcoding with CO1 and 28S had better resolution for species delimitation in comparison with ITS2. The concatenated matrix and traditional morphology were found to be more robust and informative for species delimitation within Physocyclus.

COI mtDNA barcoding and morphology for the description of a new species of ricinuleid of the genus Pseudocellus (Arachnida: Ricinulei: Ricinoididae) from El Triunfo Biosphere Reserve, Chiapas, Mexico

A new species of epigean ricinuleid of the genus Pseudocellus Platnick, 1980 from El Triunfo Biosphere Reserve, Chiapas, Mexico is described. DNA barcoding utilizing mitochondrial cytochrome c oxidase subunit 1 (CO1) and morphology were used for species delimitation. Molecular analyses and species delimitation included four methods: 1) General Mixed Yule Coalescent model (GMYC), 2) Automatic Barcode Gap Discovery (ABGD), 3) Bayesian Poisson Tree Process (bPTP), and 4) Assemble Species by Automatic Partitioning (ASAP). All molecular methods and morphology were consistent in delimiting and recognizing the new species described herein. The average interspecific genetic distance (p-distance) among analyzed species of Pseudocellus was 11.6%. The species is described based on adult males and females: Pseudocellus giribeti sp. nov. This is the seventh species described from Chiapas, which holds the highest number of ricinuleids species for the country. The total number of described species of Pseudocellus from Mexico increases to 21, having the highest species diversity of known ricinuleids worldwide.

A DNA barcode library for mangrove gastropods and crabs of Hong Kong and the Greater Bay Area reveals an unexpected faunal diversity associated with the intertidal forests of Southern China

BackgroundMangroves are tropical and subtropical intertidal forests colonising sheltered coasts across the world. They host a unique faunal community, dominated by brachyuran crabs and gastropods. These invertebrates strongly contribute to the functionality of the entire forest. The reliable assessment of mangrove faunal diversity is, thus, a crucial step for efficient management and conservation plans, but it is hindered by difficulties in species identification. Here we provide a verified DNA barcode library for brachyuran crabs and gastropods inhabiting the mangroves of the Greater Bay Area, Southern China. In particular, we collected and morphologically identified 1100 specimens of mangrove associated brachyuran crabs and gastropods. The partial sequences of the mtDNA cytochrome oxidase subunit I gene were obtained from 275 specimens. Barcode sequences were then used to delineate Molecular Operational Taxonomic Units (MOTUs), employing three different delimitation methods: the automatic barcode gap discovery (ABGD) method, the general mixed Yule coalescent (GMYC) model and a Bayesian implementation of the Poisson tree processes (bPTP) model.ResultsBy integrating DNA barcodes with morphology, we identified 44 gastropod species and 58 brachyuran species associated with Hong Kong mangroves, with five and seven new records, for gastropods and crabs, respectively, for the Greater Bay Area. The delineation of MOTUs based on barcode sequences revealed a strong congruence between morphological and molecular identification for both taxa, showing the high reliability of the barcode library.ConclusionsThis study provides the first reference barcode library for mangrove-associated macrobenthic fauna in the Greater Bay Area and represents a reliable tool to management and conservation plans. Our molecular analyses resolved long lasting taxonomic misidentifications and inconsistencies and updated the knowledge on the geographical distribution of Asian mangrove associated fauna, ultimately highlighting a level of biodiversity higher than previously thought for Southern China.

DNA Barcoding of Penaeidae (Decapoda; Crustacea): Non-Distance-Based Species Delimitation of the Most Economically Important Shrimp Family

The Penaeidae family includes some of the most economic and ecological important marine shrimp, comprising hundreds of species. Despite this importance and diversity, the taxonomic classification for penaeid shrimp has constantly been revised, and issues related to the species identification are common. In this study, we implemented DNA barcoding analyses in addition to single-gene species delimitation analyses in order to identify molecular operational taxonomy units (MOTUs) and to generate robust molecular information for penaeid shrimp based on the cytochrome oxidase subunit I (COI) mitochondrial gene. Our final data set includes COI sequences from 112 taxa distributed in 23 genera of penaeids. We employed the general mixed Yule coalescent (GMYC) model, the Poisson tree processes (PTP), and the Bayesian PTP model (bPTP) for MOTUs delimitation. Intraspecific and interspecific genetic distances were also calculated. Our findings evidenced a high level of hidden diversity, showing 143 MOTUs, with 27 nominal species not agreeing with the genetic delimitation obtained here. These data represent potential new species or highly structured populations, showing the importance of including a non-distance-based species delimitation approach in biodiversity studies. The results raised by this study shed light on the Penaeidae biodiversity, addressing important issues about taxonomy and mislabeling in databases and contributing to a better comprehension of the group, which can certainly help management policies for shrimp fishery activity in addition to conservation programs.

Species Delimitation of Southeast Pacific Angel Sharks (Squatina spp.) Reveals Hidden Diversity through DNA Barcoding

Angel sharks are distributed worldwide in tropical to subtropical waters. Across the Eastern Pacific Ocean (EPO), two valid species are reported: The Pacific angelshark Squatina californica and the Chilean angelshark Squatina armata; however, there is still uncertainty about their geographic distribution, mainly along the northern Peru coast where the species have been reported to be sympatric. The aim of this study is to describe the genetic differences between the genus Squatina from the EPO, including samples from northern Peru, and using DNA barcoding and three species delimitation models: Poisson tree processes (PTP) model, Bayesian implementation of the PTP (bPTP) model and the general mixed Yule coalescent (GMYC) model. The three approaches summarized 19 nominal Squatina species in 23 consensus Molecular Taxonomic Units (MOTU). Only 16 of them were in accordance with taxonomic identifications. From the EPO, four Squatina MOTUs were identified, one from North America (S. californica USA/Mexico) and three sampled in northern Peru, S. californica Peru, S. armata and Squatina sp. (a potential new species). This study contributes to the management and conservation policies of angel sharks in Peru, suggesting the presence of an undescribed species inhabiting the northern Peruvian coast. The use of molecular approaches, such as DNA barcoding, has the potential to quickly flag undescribed species in poorly studied regions, including the Southeast Pacific, within groups of ecologically and economically important groups like angel sharks.

P2C2M.GMYC: An R package for assessing the utility of the Generalized Mixed Yule Coalescent model

Abstract In clades that contain large numbers of undescribed species, DNA barcoding methods can serve as a first pass at identifying species limits. The General Mixed Yule Coalescent (GMYC) approach to species delimitation is accurate under certain conditions that are difficult to verify in the very clades for which the GMYC holds the greatest appeal. To circumvent this challenge, we have developed an R package for assessing how well the statistical model implemented in the GMYC fits empirical data. Our approach uses either a parametric bootstrap or a posterior predictive simulation to evaluate model fit. Computational requirements are modest for our package, and most analyses can be completed within minutes to an hour on a typical laptop, depending on whether a user selects a maximum likelihood or Bayesian framework. Results of simulation testing indicate that our approach is effective for assessing the utility of the GMYC model and suggest that it should be included in the analytical pipeline whenever researchers apply the GMYC to clades with unknown species boundaries.

Description of a new species of Loxosceles Heineken &amp; Lowe (Araneae, Sicariidae) recluse spiders from Hidalgo, Mexico, under integrative taxonomy: morphological and DNA barcoding data (CO1 + ITS2)

Based on an integrative taxonomic approach, a new species of the genus Loxosceles Heineken &amp; Lowe, 1832, is described from the state of Hidalgo, Mexico. Loxosceles tolantongo sp. nov. is described based on DNA barcoding using cytochrome c oxidase subunit 1 (CO1) and internal transcribed spacer 2 (ITS2), and morphology. For species delimitation, four molecular methods were implemented: 1) corrected p-distances under neighbor joining (NJ); 2) automatic barcode gap discovery (ABGD); 3) general mixed yule coalescent model (GMYC) and 4) Bayesian Poisson tree processes (bPTP). The new species morphologically resembles L. jaca, another species from Hidalgo, but there are morphological differences mainly in the tibiae of the male palp, the seminal receptacles of the females and also the high genetic p-distances. CO1 was more informative than ITS2 for the genetic separation; however, both concatenated genes (CO1 + ITS2) present robust evidence for species delimitation. Loxosceles tolantongo sp. nov. is considered a unique species for four reasons: 1) it can be diagnosed and distinguished by morphological characters (of the male palps mainly, but also of the seminal receptacles of the females); 2) the genetic p-distances with CO1 were high (&gt;10%); 3) the molecular species delimitation methods were congruent under CO1 and CO1 + ITS2; and 4) under CO1 and CO1 + ITS2, the new species is a putative sister group of L. jaca + L. tenango.

COI mtDNA barcoding and morphology for species delimitation in the spider genus Ixchela Huber (Araneae: Pholcidae), with the description of two new species from Mexico.

The spider genus Ixchela Huber 2000, is comprised of 22 species distributed from north-eastern Mexico to Central America, including the two new species described herein from Mexico: Ixchela panchovillai sp. nov. and Ixchela zapatai sp. nov., both from the state of Oaxaca and described for both sexes. DNA barcoding utilizing mitochondrial cytochrome c oxidase subunit 1 (COI) and morphology were used for species delimitation. Molecular analyses and species delimitation included four methods: 1) corrected p-distances under neighbor-joining (NJ), 2) general mixed yule coalescent model (GMYC), 3) automatic barcode gap discovery (ABGD), and 4) Poisson tree processes (bPTP). All molecular methods and morphology were consistent in delimiting and recognizing the two new species describing herein. The average inter-specific genetic distance (p-distance) within the genus Ixchela is 12%. Ixchela panchovillai sp. nov. is closely related in the NJ analysis with I. placida, with an average p-distance of 7.9%, whereas I. zapatai sp. nov. is closely related to I. taxco, with an average p-distance of 8.4% between both species. Additionally, identification keys for males and females of the genus Ixchela are presented.

Under an integrative taxonomic approach: the description of a new species of the genus Loxosceles (Araneae, Sicariidae) from Mexico City

A new species of the spider genus Loxosceles Heineken & Lowe, 1832, Loxosceles tenochtitlan Valdez-Mondragón & Navarro-Rodríguez, sp. nov., is described based on adult male and female specimens from the states of Mexico City, Estado de Mexico and Tlaxcala. Integrative taxonomy including traditional morphology, geometric and lineal morphology, and molecules (DNA barcodes of cytochrome c oxidase subunit 1 (CO1) and internal transcribed spacer 2 (ITS2)), were used as evidence to delimit the new species. Four methods were used for molecular analyses and species delimitation: 1) corrected p-distances under neighbor joining (NJ), 2) automatic barcode gap discovery (ABGD), 3) general mixed yule coalescent model (GMYC), and 4) poisson tree processes (bPTP). All molecular methods, traditional, geometric and lineal morphology were consistent in delimiting and recognizing the new species. Loxosceles tenochtitlansp. nov. is closely related to L. misteca based on molecular data. Although both species are morphologically similar, the average p-distance from CO1 data was 13.8% and 4.2% for ITS2 data. The molecular species delimitation methods recovered well-supported monophyletic clusters for samples of L. tenochtitlansp. nov. from Mexico City + Tlaxcala and for samples of L. misteca from Guerrero. Loxosceles tenochtitlansp. nov. is considered a unique species for three reasons: (1) it can be distinguished by morphological characters (genitalic and somatic); (2) the four different molecular species delimitation methods were congruent to separate both species; and (3) there is variation in leg I length of males between both species, with the males of L. misteca having longer legs than males of L. tenochtitlansp. nov., also morphometrically, the shape of tibiae of the palp between males of both species is different.

Historical museum collections clarify the evolutionary history of cryptic species radiation in the world's largest amphibians.

Inaccurate taxonomic assessment of threatened populations can hinder conservation prioritization and management, with human‐mediated population movements obscuring biogeographic patterns and confounding reconstructions of evolutionary history. Giant salamanders were formerly distributed widely across China, and are interpreted as a single species, Andrias davidianus. Previous phylogenetic studies have identified distinct Chinese giant salamander lineages but were unable to associate these consistently with different landscapes, probably because population structure has been modified by human‐mediated translocations for recent commercial farming. We investigated the evolutionary history and relationships of allopatric Chinese giant salamander populations with Next‐Generation Sequencing methods, using historical museum specimens and late 20th‐century samples, and retrieved partial or near‐complete mitogenomes for 17 individuals. Samples from populations unlikely to have been affected by translocations form three clades from separate regions of China, spatially congruent with isolation by either major river drainages or mountain ranges. Pliocene–Pleistocene divergences for these clades are consistent with topographic modification of southern China associated with uplift of the Qinghai‐Tibet Plateau. General Mixed Yule Coalescent model analysis indicates that these clades represent separate species: Andrias davidianus (Blanchard, 1871) (northern Yangtze/Sichuan), Andrias sligoi (Boulenger, 1924) (Pearl/Nanling), and an undescribed species (Huangshan). Andrias sligoi is possibly the world's largest amphibian. Inclusion of additional reportedly wild samples from areas of known giant salamander exploitation and movement leads to increasing loss of biogeographic signal. Wild Chinese giant salamander populations are now critically depleted or extirpated, and conservation actions should be updated to recognize the existence of multiple species.

Hidden species diversity in Pachyhynobius: A multiple approaches species delimitation with mitogenomes

The lack of distinct morphological features of cryptic species is a hard problem for taxonomy, especially when the taxa are closely related with considerable amounts of ancestral polymorphism. Lately, intensive coalescent-based analyses involving multiple loci have become the preferred method to assess the extent of genetic distinctiveness in otherwise phenotypically similar populations. Previously, phylogenetic studies on Pachyhynobius shangchengensis uncovered five extremely deeply divergent clades, which suggested that this species may be a cryptic species complex. In this study, we used the complete mitochondrial genome data and samples from the entire range of stout salamander (Pachyhynobius), as well as publicly available mitochondrial genomes to assess species boundaries within this genus using a suite of diverse methodologies (e.g. general mixed Yule coalescent model, Automatic Barcode Gap Discovery). The phylogenetic relationships recovered two major groups within P. shangchengensis, with one group formed by four of the six extant populations and corresponding to the central and eastern range of the Dabie mountains, while the other group encompassed two other lineages in the north west of the Dabie mountain range. The species delimitation comparison within Pachyhynobius supported the presence of recognized species within the genus, and consensus was observed across methods for the existence of up to five cryptic species within what has been traditionally considered to be P. shangchengensis. While this implies the existence of four taxa in addition to the described P. shangchengensis species, morphological data and life history information are further required to contribute to the species definition. The observed pattern of genetic variation is likely the outcome of a discontinuous habitat combined with niche conservatism, which produced the sky-island effect observed in Pachyhynobius, and which led to formation of a hidden species diversity in this genus.

A new Epeorus (Caucasiron) (Ephemeroptera: Heptageniidae) species from Turkey based on molecular and morphological evidence.

Epeorus (Caucasiron) turcicus sp. nov. is described based on larvae from NE Turkey. The new species can be distinguished from other Caucasiron by a unique combination of several diagnostic characters: the presence of a rounded hypodermal medial femur spot, colouration of abdominal terga and sterna, narrow gill plate VII, fine hair-like setae on the surface of abdominal terga, and absence of postero-lateral projections on tergum X. In addition to morphological analysis, two single-locus analytical approaches are employed for delimiting the new species using COI sequences (Automatic Barcode Gap Discovery, ABGD; and General Mixed Yule Coalescent Model, GMYC). Both approaches unambiguously recognized E. (C.) turcicus sp. nov. as a distinct species. Our molecular dataset contains all Caucasiron species occurring in the Caucasus and the delimitation of individual species mostly follows the morphologically defined species. This study confirms the suitability of the GMYC approach for species delimitation within Caucasiron.

Diversifying into the branches: Species boundaries in African green and bush snakes, Philothamnus (Serpentes: Colubridae)

The African green and bush snakes of the genus Philothamnus currently comprises 21 species and three subspecies and occurs throughout sub-Saharan Africa. The genus has been the subject of previous taxonomic revisions based on traditional morphological characters and limited genetic assessment, and may not reflect their evolutionary history. Indeed, previous findings based on phylogenetics show discordant results of interspecific relationships and question the monophyly of the genus, although taxon sampling has been limited to date. We investigated phylogenetic affinities within Philothamnus with more inclusive genetic and geographical sampling, with the aim of better understanding their evolutionary history, so that future taxonomic revision of Philothamnus can be better informed. Species relationships were examined within a phylogenetic context and sampling included 133 ingroup samples from 16 taxa. Phylogenies were constructed in Bayesian and likelihood frameworks using three mitochondrial (16S, cyt b and ND4) and two nuclear (c-mos and RAG1) markers. Competing hypotheses relating to the monophyly of the genus were tested with a Shimodaira-Hasegawa test. To examine species boundaries, Bayesian General Mixed Yule-Coalescent Model and multi-rate Poisson Tree Processes analyses were conducted. In addition, a barcoding approach was used to further clarify species-level relationships by comparing frequency distributions between intra- and interspecific sequence divergence. The genus was recovered as monophyletic; however, species-delimitation results suggest that the current taxonomy does not reflect the evolutionary history of this group. For example, Philothamnus s. semivariegatus is paraphyletic, with at least four distinct clades. Philothamnus carinatus consists of two cryptic (sister) lineages from Central and West Africa that are deeply divergent, suggesting a long history of isolation between those regions. Furthermore, the subspecies P. n. natalensis and P. n. occidentalis show strong support for species-level divergence, which reflects their morphological and ecological differences. Accordingly, we elevate P. occidentalisnov. comb. to a full species. A fully informed taxonomic revision of these taxa will require additional morphological and ecological data for corroboration, but it seems that the morphological characters (e.g. scalation, dentition) used to describe these species to date are labile within and between species. This most likely has clouded our understanding of the species boundaries within the genus. Our phylogeny and species-delimitation analyses should provide a sounder framework for taxonomy, but may also prove useful toward understanding the morphological adaptations of these species to their respective habitats.

A hyper-diverse genus of acanthocephalans revealed by tree-based and non-tree-based species delimitation methods: Ten cryptic species of Neoechinorhynchus in Middle American freshwater fishes

The genus Neoechinorhynchus represents a hyper-diverse group of acanthocephalans, parasites of fresh and brackish water fish and freshwater turtles, with approximately 116 species described worldwide. Forty-nine species have been recorded in the Americas, nine of them in Middle America. Even though species delimitation methods using DNA sequences have been rarely used for parasitic helminths, the genetic library for species of Neoechinorhynchus has grown in the past few years, enhancing the possibility of using these methods for inferring evolutionary relationships and for establishing more robust species boundaries. In this study, we used non-tree-based and tree-based methods through a coalescent approach to explore the species limits of specimens of Neoechinorhynchus collected in 57 localities across Middle America. We sequenced a large number of individuals to build a comprehensive dataset for three genes: the mitochondrial cytochrome c oxidase subunit I (352 individuals), the internal transcribed spacers (330 individuals), and the D2 + D3 domains of the large subunit (278 individuals). Several species delimitation methods were implemented, i.e., Automatic Barcode Gap Discovery (ABGD), General Mixed Yule-Coalescent Model (GMYC), Bayesian species delimitation (BPP) and species tree (∗BEAST). Additionally, we conducted a detailed morphological study of the diagnostic traits associated with the proboscis of 184 males and 169 females. Overall, our analyses allowed us to validate nine nominal species of Neoechinorhynchus and to identify 10 additional genetic lineages herein regarded as candidate species. This unexpected genetic diversity and the lack of reliable morphological traits show that the genus Neoechinorhynchus includes a group of cryptic species, at least in Middle America.

Genetic and Morphological Analyses Demonstrate That Schizolecis guntheri (Siluriformes: Loricariidae) Is Likely to Be a Species Complex.

Schizolecis is a monotypic genus of Siluriformes widely distributed throughout isolated coastal drainages of southeastern Brazil. Previous studies have shown that fish groups found in isolated river basins tend to differentiate over time in the absence of gene flow, resulting in allopatric speciation. In this study, we used partial sequences of the mitochondrial gene COI with the analysis of the General Mixed Yule Coalescent model (GMYC) and the Automatic Barcode Gap Discovery (ABGD) for single locus species delimitation, and a Principal Component Analysis (PCA) of external morphology to test the hypothesis that Schizolecis guntheri is a complex of species. We analyzed 94 samples of S. guntheri for GMYC and ABGD, and 82 samples for PCA from 22 coastal rivers draining to the Atlantic in southeastern Brazil from the Paraná State to the north of the Rio de Janeiro State. As a result, the GMYC model and the ABGD delimited five operational taxonomy units (OTUs – a nomenclature referred to in the present study of the possible new species delimited for the genetic analysis), a much higher number compared to the traditional alfa taxonomy that only recognizes S. guntheri across the isolated coastal rivers of Brazil. Furthermore, the PCA analysis suggests that S. guntheri is highly variable in aspects of external body proportions, including dorsal-fin spine length, pectoral-fin spine length, pelvic-fin spine length, lower caudal-fin spine length, caudal peduncle depth, anal width and mandibular ramus length. However, no exclusive character was found among the isolated populations that could be used to describe a new species of Schizolecis. Therefore, we can conclude, based on our results of PCA contrasting with the results of GMYC and ABGD, that S. guntheri represents a complex of species.

Phylogenetic relationships and molecular delimitation of CulicoidesLatreille (Diptera: Ceratopogonidae) species in the Afrotropical region: interest for the subgenus Avaritia

AbstractPhylogenetic relationships of Culicoides species of the Afrotropical region are problematic as different authors disagree on the placement of species into specific subgenera or groups. In this study we sequenced two mitochondrial (COI and 16S rDNA) and two nuclear (CAD and 28S rDNA) gene fragments to reconstruct phylogenetic relationships within the Avaritia, Remmia and Synhelea subgenera and the Milnei, Neavei and Similis groups of Culicoides using both Bayesian inference and maximum‐likelihood approaches. Based on phylogenetic trees, we used the bGMYC (Bayesian General Mixed Yule Coalescent model) and the PTP (Bayesian Poisson Tree Processes) to investigate species boundaries. All species relationships within the studied subgenera and groups were well‐supported by using morphological characters and molecular analyses. The subgenus Avaritia includes (i) all of the species of the Imicola group, as well as the putative new species, C. sp. #22, and we confirmed the monophyly of this group; (ii) the Dasyops group includes C. kanagai and C. sp. #54 Meiswinkel (new species), shown to be monophyletic; (iii) the C. sp. #20 belongs to the Orientalis group; (iv) C. grahamii, C. gulbenkiani and C. kibatiensis. Our results also show that subgenus Remmia is monophyletic. Relationships of species of the Milnei group were well‐supported and demonstrate the monophyly of this group. Borkent's classification for Similis group is confirmed. In addition, C. neavei and C. ovalis (Neavei group) are placed in the subgenus Synhelea.

Sequence-based species delineation and molecular phylogenetics of the transitional Nearctic–Neotropical grasshopper genus Taeniopoda (Orthoptera, Romaleidae)

Taeniopoda is a genus of grasshoppers currently represented by 12 species distributed from southern USA to Panama, with most of them occurring along the transitional Nearctic–Neotropical region in central and southern Mexico. Despite being a small group of conspicuous, colourful species, the systematics of Taeniopoda has been largely neglected, including its phylogenetic affinity with the morphologically similar, monotypic genus Romalea. Here, we assessed the species limits in 11 of the species of Teniopoda based on two mitochondrial (mt) markers (COI, cyt b). Phylogenetic relationships were reconstructed adding two nuclear gene markers (28S, H3). A relaxed molecular clock analysis was performed based on the mt markers. We detected nuclear mt paralogues (numts) and the probable introgression of T. tamaulipensis mtDNA in specimens of T. eques from central Mexico. Between six and 14 species of Taeniopoda were delimited by the sequence-based approaches performed (COI divergence with thresholds of 1 and 2%; General Mixed Yule-Coalescent (GMYC) model). The GMYC and 1% threshold analyses with COI were more congruent with the currently recognized morphology-based taxonomy with 10 and 11 putative species, respectively. Four of these species were regarded as ‘stable’, since they were supported by at least one of the molecular analyses and by diagnostic morphological features. The species-based phylogeny recovered Taeniopoda as paraphyletic with respect to the monotypic genus Romalea. Three morphologically and geographically congruent major clades were recovered, two with species having a considerably elevated pronotal crest and one with its members having it less elevated. The origin and subsequent diversification of Taeniopoda were estimated to occur from the mid and late Miocene to Pliocene, respectively. The current species diversity in Taeniopoda was estimated to occur during the Pleistocene, which was probably influenced by the climatic oscillations that occurred during this period and the uplift of mountain ranges in Central America.

Resolving the Melampsora epitea complex

ABSTRACTMelampsora epitea (Pucciniales, Basidiomycota) has been widely known as the main rust pathogen on willows, but its species boundary has been extremely confusing. Melampsora epitea was often confused with several morphologically similar species, such as M. arctica, M. humilis, and M. epiphylla. Recent DNA-based studies using specimens from North America and Europe suggested that M. epitea was a complex of several phylogenetic species. In this study, we examined the species boundary of M. epitea based on rDNA phylogeny and the general mixed Yule coalescent (GMYC) model from 534 specimens. Twelve distinct species corresponding to 10 known species and 2 new species were recognized from East Asian specimens. We also evaluated the association of morphological characteristics, geographic origins, and host ranges with phylogenetic relationships. Our results revealed that several previously overlooked morphological characters in uredinial and telial stages were informative in delimiting M. epitea and allied species. Two novel species, M. salicis-futurae and M. salicis-triandrae, are described and compared with closely related species. A lectotype for M. epitea and epitypes for M. epitea, M. epiphylla, and M. humilis are designated to stabilize the use of names.