Species delimitation of the northeastern Anatolian Symphytum (Boraginaceae) taxa

Symphytum is regarded one of the most complicated genera in terms of the classification of its members among the Boraginaceae. In addition to different infrageneric classification methods, several species complex or aggregates have been proposed to deal with the taxonomical problem of genus members. Symphytum asperum aggregate was first introduced by Kurtto, who proposed six taxa within this aggregate. However, according to further studies by different researchers based on morphological data, total number of species of the complex was variable. The number of species was reduced to three, comprising S. asperum, S. savvalense, and S. sylvaticum, after the phylogenetic and morphological studies of Tarıkahya-Hacıoğlu and Erik. However, the taxonomical status of some of these species (i.e., S. savvalense and S. sylvaticum, and S. sepulcrale), which was assigned as a member of this complex by Kurtto, has been regarded as unresolved. To solve this uncertainty, different species delimitation methods were used, including statistical parsimony network analysis (TCS), generalized mixed Yule coalescent (GMYC), and Bayesian Phylogenetics and Phylogeography (BPP) of the ITS, trnL-F and trnS-G sequence data. In addition to members of this complex, S. ibericum, which is phylogenetically nested within the S. asperum aggregate, was also used. The TCS and GMYC analyses demonstrated more complicated clusters, whereas high posterior probabilities of BPP clusters were more compatible with the morphological data. In accordance with the morphological approach of Tarıkahya-Hacıoğlu and Erik, the species delimitation analyses based on molecular data support the recognition of S. asperum, S. ibericum, S. savvalense, and S. sylvaticum as different species.

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Species recognition and phylogeny of Thelotrema species in Australia (Ostropales, Ascomycota)

Australian Systematic Botany ◽

10.1071/sb07049 ◽

2008 ◽

Vol 21 (3) ◽

pp. 217 ◽

Cited By ~ 21

Author(s):

H. Thorsten Lumbsch ◽

Armin Mangold ◽

María P. Martín ◽

John A. Elix

Keyword(s):

Phylogenetic Trees ◽

Sequence Data ◽

Species Recognition ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Morphological Data ◽

Morphological Evidence ◽

Morphological Studies ◽

Morphological Differences ◽

Crustose Lichens

Species circumscriptions based on morphological data are difficult in crustose lichens with limited characters as they often show remarkable variability. An example is the genus Thelotrema s.str., a speciose genus of mostly tropical lichens. Morphological studies on Australian Thelotrema spp. were accompanied by a phylogenetic analysis of mt SSU rDNA sequence data of 19 species, including 25 newly obtained sequences. We performed maximum parsimony and Bayesian phylogenetic analyses of 50 samples, representing 25 species. Our results indicate that more species need to be accepted in Thelotrema than previously thought. Subtle morphological differences were found to be associated with independent lineages in the phylogenetic trees. Furthermore, monophyly of Thelotrema s.str. is strongly supported. On the basis of the corroboration of morphological evidence by molecular data, the new species Thelotrema capetribulense Mangold, T. crespoae Mangold, Lumbsch & Elix, T. oleosum Mangold, and T. pseudosubtile Mangold are described. The new combinations Chapsa phlyctidioides (Müll.Arg.) Mangold and Thelotrema defossum (Müll.Arg.) Mangold are proposed.

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Generic Delimitations and Relationships of the Cape Genera Capnophyllum, Dasispermum, and Sonderina, the North African Genera Krubera and Stoibrax, and a New Monotypic Genus of the Subfamily Apioideae (Apiaceae)

Systematic Botany ◽

10.1600/036364409789271218 ◽

2009 ◽

Vol 34 (3) ◽

pp. 580-594 ◽

Cited By ~ 13

Author(s):

Anthony R. Magee ◽

Ben-Erik van Wyk ◽

Patricia M. Tilney ◽

Stephen R. Downie

Keyword(s):

Sequence Data ◽

Molecular Data ◽

Morphological Data ◽

Data Sets ◽

Monotypic Genus ◽

North African ◽

African Species ◽

Dna Sequence Data ◽

The North ◽

Relationship Of

Generic circumscriptions and phylogenetic relationships of the Cape genera Capnophyllum, Dasispermum, and Sonderina are explored through parsimony and Bayesian inference analyses of nrDNA ITS and cpDNA rps16 intron sequences, morphology, and combined molecular and morphological data. The relationship of these genera with the North African genera Krubera and Stoibrax is also assessed. Analyses of both molecular data sets place Capnophyllum, Dasispermum, Sonderina, and the only southern African species of Stoibrax (S. capense) within the newly recognized Lefebvrea clade of tribe Tordylieae. Capnophyllum is strongly supported as monophyletic and is distantly related to Krubera. The monotypic genus Dasispermum and Stoibrax capense are embedded within a paraphyletic Sonderina. This complex is distantly related to the North African species of Stoibrax in tribe Apieae, in which the type species, Stoibrax dichotomum, occurs. Consequently, Dasispermum is expanded to include both Sonderina and Stoibrax capense. New combinations are formalized for Dasispermum capense, D. hispidum, D. humile, and D. tenue. An undescribed species from the Tanqua Karoo in South Africa is also closely related to Capnophyllum and the Dasispermum–Sonderina complex. The genus Scaraboides is described herein to accommodate the new species, S. manningii. This monotypic genus shares the dorsally compressed fruit and involute marginal wings with Capnophyllum, but is easily distinguished by its erect branching habit, green leaves, scabrous umbels, and fruit with indistinct median and lateral ribs, additional solitary vittae in each marginal wing, and parallel, closely spaced commissural vittae. Despite the marked fruit similarities with Capnophyllum, analyses of DNA sequence data place Scaraboides closer to the Dasispermum–Sonderina complex, with which it shares the erect habit, green (nonglaucous) leaves, and scabrous umbels.

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Species delimitation and nematode biodiversity: phylogenies rule

Nematology ◽

10.1163/15685410260438908 ◽

2002 ◽

Vol 4 (5) ◽

pp. 615-625 ◽

Cited By ~ 52

Author(s):

Steven Nadler

Keyword(s):

Species Delimitation ◽

Sequence Data ◽

Molecular Data ◽

Gene Trees ◽

California Sea Lions ◽

Separate Species ◽

Nucleotide Sequence Data ◽

Sea Lions ◽

Multiple Loci ◽

Fur Seals

AbstractPractitioners of nematode taxonomy have rarely been explicit about what species represent or how data are being used to delimit species prior to their description. This lack of explicitness reflects the broader species problem common to all biology: there is no universally accepted idea of what species are and, as a consequence, scientists disagree on how to go about finding species in nature. However, like other biologists, nematologists seem to agree that species are real and discrete units in nature, and that they result from descent with modification. This evolutionary perspective provides a conceptual framework for nematologists to view species as independent evolutionary lineages, and provides approaches for their delimitation. Specifically, species may be delimited scientifically by methods that can test the hypothesis of lineage independence. For sequence data, such hypothesis testing should be based on sampling many individual organisms for multiple loci to avoid mistaking tokogeny and gene trees as evidence of species. Evolutionary approaches to analysing data and delimiting species avoid the inherent pitfalls in approaches that use all observed sequence differences to define species through calculation of a genetic distance. To illustrate evolutionary species delimitation, molecular data are used to test the hypothesis that hookworms parasitic in northern fur seals and in California sea lions represent separate species. The advantages and potential caveats of employing nucleotide sequence data for species delimitation are discussed, and the merits of evolutionary approaches are contrasted to inherent problems in similarity-based methods.

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DNA Barcoding: Mixed results for big-headed flies (Diptera: Pipunculidae)

Zootaxa ◽

10.11646/zootaxa.1423.1.1 ◽

2007 ◽

Vol 1423 (1) ◽

pp. 1-26 ◽

Cited By ~ 20

Author(s):

JEFFREY H. SKEVINGTON ◽

CHRISTIAN KEHLMAIER ◽

GUNILLA STÅHLS

Keyword(s):

Dna Barcoding ◽

Sequence Data ◽

Phylogenetic Signal ◽

Morphological Characters ◽

Molecular Data ◽

Morphological Data ◽

Base Pairs ◽

Data Set ◽

Taxonomic Decision ◽

Morphological Species

Sequence data from 658 base pairs of mitochondrial cytochrome c oxidase I (cox1) were analysed for 28 described species of Pipunculidae (Diptera) in an effort to test the concept of DNA Barcoding on this family. Two recently revised but distantly related pipunculid lineages with presumed different evolutionary histories were used for the test (Clistoabdominalis Skevington, 2001 and Nephrocerus Zetterstedt, 1838). An effort was made to test the concept using sister taxa and morphologically similar sibling species swarms in these two genera. Morphological species concepts for Clistoabdominalis taxa were either supported by cox1 data or found to be too broad. Most of the discordance could be accounted for after reassessing morphological characters. In these cases, the molecular data were invaluable in assisting taxonomic decision-making. The radiation of Nearctic species of Nephrocerus could not be diagnosed using cox1. The ability of cox1 to recover phylogenetic signal was also tested on Clistoabdominalis. Morphological data for Clistoabdominalis were combined with the molecular data set. The pipunculid phylogeny from molecular data closely resembles the published phylogeny based on morphology. Partitioned Bremer support is used to localize areas of conflict between the datasets.

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Synonymization of the male-based ant genus Phaulomyrma (Hymenoptera, Formicidae) with Leptanilla based upon Bayesian total-evidence phylogenetic inference

10.1101/2020.08.28.272799 ◽

2020 ◽

Author(s):

Zachary H. Griebenow

Keyword(s):

Sequence Data ◽

Phylogenetic Inference ◽

Morphological Characters ◽

Molecular Data ◽

Total Evidence ◽

Morphological Data ◽

Systematic Revision ◽

Dna Sequence Data ◽

Evidence Framework ◽

Nuclear Loci

Abstract.Although molecular data have proven indispensable in confidently resolving the phylogeny of many clades across the tree of life, these data may be inaccessible for certain taxa. The resolution of taxonomy in the ant subfamily Leptanillinae is made problematic by the absence of DNA sequence data for leptanilline taxa that are known only from male specimens, including the monotypic genus Phaulomyrma Wheeler & Wheeler. Focusing upon the considerable diversity of undescribed male leptanilline morphospecies, the phylogeny of 35 putative morphospecies sampled from across the Leptanillinae, plus an outgroup, is inferred from 11 nuclear loci and 41 discrete male morphological characters using a Bayesian total-evidence framework, with Phaulomyrma represented by morphological data only. Based upon the results of this analysis Phaulomyrma is synonymized with Leptanilla Emery, and male-based diagnoses for Leptanilla that are grounded in phylogeny are provided, under both broad and narrow circumscriptions of that genus. This demonstrates the potential utility of a total-evidence approach in inferring the phylogeny of rare extant taxa for which molecular data are unavailable and begins a long-overdue systematic revision of the Leptanillinae that is focused on male material.

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DNA-barcoding of forensically important blow flies (Diptera: Calliphoridae) in the Caribbean Region

PeerJ ◽

10.7717/peerj.3516 ◽

2017 ◽

Vol 5 ◽

pp. e3516 ◽

Cited By ~ 13

Author(s):

Sohath Z. Yusseff-Vanegas ◽

Ingi Agnarsson

Keyword(s):

Dna Barcoding ◽

Species Delimitation ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Morphological Data ◽

Caribbean Region ◽

Reference Database ◽

Correct Identification ◽

Accurate Identification ◽

The Caribbean

Correct identification of forensically important insects, such as flies in the family Calliphoridae, is a crucial step for them to be used as evidence in legal investigations. Traditional identification based on morphology has been effective, but has some limitations when it comes to identifying immature stages of certain species. DNA-barcoding, using COI, has demonstrated potential for rapid and accurate identification of Calliphoridae, however, this gene does not reliably distinguish among some recently diverged species, raising questions about its use for delimitation of species of forensic importance. To facilitate DNA based identification of Calliphoridae in the Caribbean we developed a vouchered reference collection from across the region, and a DNA sequence database, and further added the nuclear ITS2 as a second marker to increase accuracy of identification through barcoding. We morphologically identified freshly collected specimens, did phylogenetic analyses and employed several species delimitation methods for a total of 468 individuals representing 19 described species. Our results show that combination of COI + ITS2 genes yields more accurate identification and diagnoses, and better agreement with morphological data, than the mitochondrial barcodes alone. All of our results from independent and concatenated trees and most of the species delimitation methods yield considerably higher diversity estimates than the distance based approach and morphology. Molecular data support at least 24 distinct clades within Calliphoridae in this study, recovering substantial geographic variation forLucilia eximia, Lucilia retroversa, Lucilia ricaandChloroprocta idioidea, probably indicating several cryptic species. In sum, our study demonstrates the importance of employing a second nuclear marker for barcoding analyses and species delimitation of calliphorids, and the power of molecular data in combination with a complete reference database to enable identification of taxonomically and geographically diverse insects of forensic importance.

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Evaluating methodologies for species delimitation: the mismatch between phenotypes and genotypes in lichenized fungi (Bryoria sect. Implexae, Parmeliaceae)

Persoonia - Molecular Phylogeny and Evolution of Fungi ◽

10.3767/persoonia.2019.42.04 ◽

2019 ◽

Vol 42 (1) ◽

pp. 75-100 ◽

Cited By ~ 11

Author(s):

C.G. Boluda ◽

V.J. Rico ◽

P.K. Divakar ◽

O. Nadyeina ◽

L. Myllys ◽

...

Keyword(s):

Dna Sequences ◽

Species Delimitation ◽

Sequence Data ◽

Species Recognition ◽

Phylogenetic Analyses ◽

Phylogenetic Reconstruction ◽

Haplotype Network ◽

Molecular Data ◽

Integrative Taxonomy ◽

Molecular Sequence Data

In many lichen-forming fungi, molecular phylogenetic analyses lead to the discovery of cryptic species within traditional morphospecies. However, in some cases, molecular sequence data also questions the separation of phenotypically characterised species. Here we apply an integrative taxonomy approach – including morphological, chemical, molecular, and distributional characters – to re-assess species boundaries in a traditionally speciose group of hair lichens, Bryoria sect. Implexae. We sampled multilocus sequence and microsatellite data from 142 specimens from a broad intercontinental distribution. Molecular data included DNA sequences of the standard fungal markers ITS, IGS, GAPDH, two newly tested loci (FRBi15 and FRBi16), and SSR frequencies from 18 microsatellite markers. Datasets were analysed with Bayesian and maximum likelihood phylogenetic reconstruction, phenogram reconstruction, STRUCTURE Bayesian clustering, principal coordinate analysis, haplotype network, and several different species delimitation analyses (ABGD, PTP, GMYC, and DISSECT). Additionally, past population demography and divergence times are estimated. The different approaches to species recognition do not support the monophyly of the 11 currently accepted morphospecies, and rather suggest the reduction of these to four phylogenetic species. Moreover, three of these are relatively recent in origin and cryptic, including phenotypically and chemically variable specimens. Issues regarding the integration of an evolutionary perspective into taxonomic conclusions in species complexes, which have undergone recent diversification, are discussed. The four accepted species, all epitypified by sequenced material, are Bryoria fuscescens, B. glabra, B. kockiana, and B. pseudofuscescens. Ten species rank names are reduced to synonymy. In the absence of molecular data, they can be recorded as the B. fuscescens complex. Intraspecific phenotype plasticity and factors affecting the speciation of different morphospecies in this group of Bryoria are outlined.

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DISTATIS: A Promising Framework to Integrate Distance Matrices in Molecular Phylogenetics.

Current Topics in Medicinal Chemistry ◽

10.2174/1568026621666210113164605 ◽

2021 ◽

Vol 21 ◽

Author(s):

Guillermin Agüero-Chapin ◽

Yuliana Jiménez ◽

Aminael Sánchez-Rodríguez ◽

Reinaldo Molina-Ruiz ◽

Oscar Vivanco ◽

...

Keyword(s):

Species Delimitation ◽

Phylogenetic Trees ◽

Molecular Phylogenetics ◽

Molecular Data ◽

Morphological Data ◽

Reproduction Mode ◽

Alignment Free ◽

Morphological Criteria ◽

Distance Matrices ◽

Ascospore Morphology

Background: Molecular phylogenetic algorithms frequently disagree with the approaches considering reproductive compatibility and morphological criteria for species delimitation. The question stems if the resulting species boundaries from molecular, reproductive and/or morphological data are definitively not reconcilable; or if the existing phylogenetic methods are not sensitive enough to agree morphological and genetic variation in species delimitation. Objectives : We propose to DISTATIS as an integrative framework to combine alignment-based (AB) and alignment-free (AF) distance matrices from ITS2 sequences/structures to shed light whether Gelasinospora and Neurospora are sister but independent genera? Methodology: We aimed at addressing this standing issue by harmonizing genus-specific classification based on their ascospore morphology and ITS2 molecular data. To validate our proposal, three phylogenetic approaches: i) traditional alignment-based, ii) alignment-free and iii) novel distance integrative (DI)-based were comparatively evaluated on a set of Gelasinospora and Neurospora species. All considered species have been extensively characterized at both the morphological and reproductive levels and there are known incongruences between their ascospore morphology and molecular data that hampers genus-specific delimitation. Results: Traditional AB phylogenetic analyses fail at resolving the Gelasinospora and Neurospora genera into independent monophyletic clades following ascospore morphology criteria. In contrast, AF and DI approaches produced phylogenetic trees that could properly delimit the expected monophyletic clades. Conclusions: The DI approach outperformed the AF one in the sense that it could also divide the Neurospora species according to their reproduction mode.

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Molecular phylogeny and systematic evaluation of the Caragana opulens species complex (Fabaceae, Papilionoideae) based on the molecular and morphological data

Phytotaxa ◽

10.11646/phytotaxa.478.2.1 ◽

2021 ◽

Vol 478 (2) ◽

pp. 179-200

Author(s):

SHABIR A. RATHER ◽

WANG SHU ◽

MAYANK DHAR DWIVEDI ◽

CHANG ZHAOYANG

Keyword(s):

Evolutionary History ◽

Sequence Data ◽

Morphological Characters ◽

Molecular Data ◽

Morphological Data ◽

Systematic Evaluation ◽

Morphological Variations ◽

Dna Sequence Data ◽

Different Populations ◽

Morphological And Molecular Data

In this study, we explored the evolutionary history and taxonomic treatment of the Caragana opulens complex taking information from morphological and molecular data. The complex consists of three species, C. opulens, C. licentiana and C. kansuensis. Moreover, the morphological characters currently used to differentiate the species present in the complex have been found insignificant and inconsistent and do not help diagnose the species. For the present study, we investigated its range and sampled 139 accessions from the different populations of the genus Caragana and 17 accessions of the complex. DNA sequence data from one nrDNA ITS and one cpDNA trnH-psbA loci were sequenced and analyzed using Maximum Likelihood and Bayesian methods. The resulting phylogenies were congruent in topologies. Based on morphological and molecular data, it is concluded that all three species of the complex are one of the same with significant morphological variations. Hence C. opulens is accepted as the correct name along with C. licentiana and C. kansuensis as synonyms.

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Corrigendum to: Phylogeny and biogeography of the ant subfamily Myrmeciinae (Hymenoptera : Formicidae)

Invertebrate Systematics ◽

10.1071/is02046_co ◽

2003 ◽

Vol 17 (4) ◽

pp. 605 ◽

Cited By ~ 1

Author(s):

Philip S. Ward ◽

Seán G. Brady

Keyword(s):

Sequence Data ◽

Strong Support ◽

Sister Group ◽

Molecular Data ◽

Morphological Data ◽

Recent Common Ancestor ◽

Bootstrap Support ◽

Data Set ◽

Molecular Sequence Data ◽

Most Recent Common Ancestor

We investigated phylogenetic relationships among the 'primitive' Australian ant genera Myrmecia and Nothomyrmecia (stat. rev.) and the Baltic amber fossil genus Prionomyrmex, using a combination of morphological and molecular data. Outgroups for the analysis included representatives from a variety of potential sister-groups, including five extant subfamilies of ants and one extinct group (Sphecomyrminae). Parsimony analysis of the morphological data provides strong support (~95% bootstrap proportions) for the monophyly of (1) genus Myrmecia, (2) genus Prionomyrmex, and (3) a clade containing those two genera plus Nothomyrmecia. A group comprising Nothomyrmecia and Prionomyrmex is also upheld (85% bootstrap support). Molecular sequence data (~2200 base pairs from the 18S and 28S ribosomal RNA genes) corroborate these findings for extant taxa, with Myrmecia and Nothomyrmecia appearing as sister-groups with ~100% bootstrap support under parsimony, neighbour-joining and maximum-likelihood analyses. Neither the molecular nor the morphological data set allows us to identify unambiguously the sister-group of (Myrmecia + (Nothomyrmecia + Prionomyrmex)). Rather, Myrmecia and relatives are part of an unresolved polytomy that encompasses most of the ant subfamilies. Taken as a whole, our results support the contention that many of the major lineages of ants – including a clade that later came to contain Myrmecia, Nothomyrmecia and Prionomyrmex – arose at around the same time during a bout of diversification in the middle or late Cretaceous. On the basis of Bayesian dating analysis, the estimated age of the most recent common ancestor of Myrmecia and Nothomyrmecia is 74 million years (95% confidence limits, 53–101�million years), a result consistent with the origin of the myrmeciine stem lineage in the Cretaceous. The ant subfamily Myrmeciinae is redefined to contain two tribes, Myrmeciini (genus Myrmecia) and Prionomyrmecini (Nothomyrmecia and Prionomyrmex). Phylogenetic analysis of the enigmatic Argentine fossils Ameghinoia and Polanskiella demonstrates that they are also members of the Myrmeciinae, probably more closely related to Prionomyrmecini than to Myrmeciini. Thus, the myrmeciine ants appear to be a formerly widespread group that retained many ancestral formicid characteristics and that became extinct everywhere except in the Australian region.

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