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

2008 ◽  
Vol 21 (3) ◽  
pp. 217 ◽  
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.

Species delimitation of the northeastern Anatolian Symphytum (Boraginaceae) taxa

Phytotaxa ◽  
2021 ◽  
Vol 516 (3) ◽  
Author(s):  
KURTULUŞ ÖZGİŞİ ◽  
BURCU TARIKAHYA-HACIOĞLU
Keyword(s):  
Species Delimitation ◽  
Sequence Data ◽  
Molecular Data ◽  
Morphological Data ◽  
Infrageneric Classification ◽  
Number Of Species ◽  
Morphological Studies ◽  
Statistical Parsimony ◽  
Taxonomical Status ◽  
Parsimony Network Analysis

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.

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

2019 ◽  
Vol 42 (1) ◽  
pp. 75-100 ◽  
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.

The formerly enigmatic Unidentiidae in the limelight again: a new species of the genus Unidentia from Thailand (Gastropoda: Nudibranchia)

Zootaxa ◽  
2019 ◽  
Vol 4551 (5) ◽  
pp. 556 ◽  
Author(s):  
TATIANA KORSHUNOVA ◽  
RAHUL MEHROTRA ◽  
SPENCER ARNOLD ◽  
KENNET LUNDIN ◽  
BERNARD PICTON ◽  
...  
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Morphological Data ◽  
Sea Slugs ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Morphological Differences ◽  
First Time ◽  
A New Species

An integrative molecular and morphological study is presented for the family Unidentiidae. Molecular phylogenetic analyses were conducted with the inclusion of all previous and newly obtained molecular data for the family Unidentiidae Millen & Hermosillo 2012. A new species of the genus Unidentia Millen & Hermosillo 2012, U. aliciae sp. nov., is described from Thailand as part of an inventory of sea slugs at Koh Tao. All up-to-date available morphological data for the species of the genus Unidentia is for the first time summarized. Morphological differences among the different species of Unidentia are clarified showing that every species has its own distinguishable morphological traits. According to the new molecular and morphological data, the family Unidentiidae is re-confirmed as a well-supported taxon of the aeolidacean nudibranchs. The taxonomy and phylogeny of the Aeolidacea in the light of the family Unidentiidae is briefly discussed and necessity of a fine-scale and narrowly-defined taxa approach instead of a ‘‘superlumping’’ one is highlighted. 

Integration of morphological and molecular data sets in estimating fungal phytogenies

1995 ◽  
Vol 73 (S1) ◽  
pp. 649-659 ◽  
Author(s):  
François Lutzoni ◽  
Rytas Vilgalys
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Molecular Data ◽  
Morphological Data ◽  
Homogeneity Test ◽  
Data Sets ◽  
Data Set ◽  
Sampling Statistics ◽  
Combined Data

To provide a clearer picture of fungal species relationships, increased efforts are being made to include both molecular and morphological data sets in phylogenetic studies. This general practice in systematics has raised many unresolved questions and controversies regarding how to best integrate the phylogenetic information revealed by morphological and molecular characters. This is because phylogenetic trees derived using different data sets are rarely identical. Such discrepancies can be due to sampling error, to the use of an inappropriate evolutionary model for a given data set, or to different phylogenetic histories between the organisms and the molecule. Methods have been developed recently to test for heterogeneity among data sets, although none of these methods have been subjected to simulation studies. In this paper we compare three tests: a protocol described by Rodrigo et al., an adapted version of Faith's T-PTP test, and Kishino and Hasegawa's likelihood test. These tests were empirically compared using seven lichenized and nonlichenized Omphalina species and the related species Arrhenia lobata (Basidiomycota, Agaricales) for which nrDNA large subunit sequences and morphological data were gathered. The results of these three tests were inconsistent, Rodrigo's test being the only one suggesting that the two data sets could be combined. One of the three most parsimonious trees obtained from the combined data set with eight species is totally congruent with the relationships among the same eight species in an analysis restricted to the same portion of the nrDNA large subunit but extended to 26 species of Omphalina and related genera. Therefore, the results from phylogenetic analyses of this large molecular data set converged on one of the three most parsimonious topologies generated by the combined data set analysis. This topology was not recovered from either data set when analysed separately. This suggests that Rodrigo's homogeneity test might be better suited than the two other tests for determining if trees obtained from different data sets are sampling statistics of the same phylogenetic history. Key words: data sets heterogeneity, homogeneity test, lichen phylogeny, Omphalina, ribosomal DNA.

Affinities of four freshwater putative “Chantransia” stages (Rhodophyta) in Southern China from molecular and morphological data

Phytotaxa ◽  
2020 ◽  
Vol 441 (1) ◽  
pp. 47-59
Author(s):  
JIN-FEN HAN ◽  
FANG-RU NAN ◽  
JIA FENG ◽  
JUN-PING LV ◽  
QI LIU ◽  
...  
Keyword(s):  
Yunnan Province ◽  
Sequence Data ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Morphological Description

Four putative “Chantransia” isolates were collected from four locations in Hubei and Yunnan Provinces, China. Morphological analyses were conducted on all isolates. Two specimens (HB26 and YN2) fit the morphological description of A. pygmaea, while the other two isolates (YN1 and YN3) varied in morphology, but were within the circumscription of Audouinella hermannii. Due to the fact that the morphological characters of the “Chantransia” stages of order Batrachospermales and the species of genus Audouinella are too similar to be distinguished, a molecular analysis was performed to clarify the phylogenetic position of these four isolates based on rbcL and psbA sequences. Two “pygmaea” specimens collected from Jiugong Mountain, Hubei Province (HB26) and Shimen Gorge, Yunnan Province (YN2), such as S. jiugongshanensis and S. shimenxiaensis, are proposed primarily based on the DNA sequence data generated in this study. The description of these two new species provides more molecular data for phylogenetic analysis of the genus Sheathia. In addition to these newly described species, the results strongly support that those “hermannii” isolates (YN1 and YN3) collected from Yunnan Province were the “Chantransia” of S. arcuata. However, their gametophyte stages have not been found, meaning that critical diagnostic morphological features were unavailable and molecular methods were the only means for ascertaining their phylogenetic position. Considering the extensive application of the rbcL and psbA genes in phylogenetic analyses of freshwater red algae, we recommend using these two genes to identify species when no morphological characteristics are available.

scholarly journals Integrative taxonomy of the new millipede genus Coxobolellus, gen. nov. (Diplopoda : Spirobolida : Pseudospirobolellidae), with descriptions of ten new species

2020 ◽  
Author(s):  
Piyatida Pimvichai ◽  
Henrik Enghoff ◽  
Somsak Panha ◽  
Thierry Backeljau
Keyword(s):  
New Species ◽  
New Genus ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Sequence Divergence ◽  
Morphological Characters ◽  
Integrative Taxonomy ◽  
Morphological Data ◽  
Morphological Evidence ◽  
Morphological Differences

Pseudospirobolellidae is a poorly known family of spirobolidan millipedes with only two genera and five described species. Yet, the descriptive taxonomy and molecular systematics of this group have been largely neglected. Therefore, the present work presents an integrative taxonomic study of new pseudospirobolellid taxa in Thailand. To this end, two mitochondrial gene fragments (COI and 16S rRNA) combined with morphological characters were used to define the genus Coxobolellus, gen. nov. with 10 new species, viz. C. albiceps, sp. nov., C. compactogonus, sp. nov., C. fuscus, sp. nov., C. nodosus, sp. nov., C. serratus, sp. nov., C. simplex, sp. nov., C. tenebris, sp. nov., C. tigris, sp. nov., C. transversalis, sp. nov. and C. valvatus, sp. nov. The interspecific COI sequence divergences among the new species ranged from 6 to 15%. The intergeneric COI sequence divergence between species of Coxobolellus, gen. nov., Benoitolus birgitae and Pseudospirobolellus sp. ranged from 20 to 23%. Three major morphological differences separate Coxobolellus, gen. nov. from Benoitolus and Pseudospirobolellus, namely (1) the protruding process on the 3rd (and 4th) coxae on male legs, (2) the posterior gonopod telopodite divided into two parts, and (3) a conspicuous opening pore at the mesal margin at the end of the coxal part of the posterior gonopod. Thus, the new genus is well supported by both mtDNA and morphological evidence, while the delimitation of the 10 new species is supported by the congruence between mtDNA and morphological data. Yet, with respect to the relationships of Benoitolus birgitae, morphological data suggest a similarity with Coxobolellus, gen. nov. and Pseudospirobolellus, whereas mtDNA data place this species in the Pachybolidae. Further phylogenetic analyses are needed to explore this apparent incongruence and test the monophyly of Pseudospirobolellidae.

scholarly journals Phylogenetic and morphological studies in Xylodon (Hymenochaetales, Basidiomycota) with the addition of four new species

MycoKeys ◽  
2019 ◽  
Vol 47 ◽  
pp. 97-137 ◽  
Author(s):  
Janett Riebesehl ◽  
Eugene Yurchenko ◽  
Karen K. Nakasone ◽  
Ewald Langer
Keyword(s):  
New Species ◽  
New Zealand ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Its Region ◽  
Morphological Data ◽  
Similar Species ◽  
New Combinations ◽  
Line Drawings ◽  
Morphological Studies

Xylodon (Hymenochaetales, Basidiomycota) is the largest segregate genus of Hyphodontia s.l. Based on molecular and morphological data, 77 species are accepted in Xylodon to date. Phylogenetic analyses of ITS and 28S sequences, including 38 new ITS and 20 28S sequences of Xylodon species, revealed four species new to science. The new taxa X.exilis, X.filicinus, X.follis and X.pseudolanatus from Taiwan, Nepal, Réunion, Belize, and USA are described and illustrated. In addition, species concepts for Odontiavesiculosa from New Zealand and Xylodonlanatus from U.S.A. are revised and the new name X.vesiculosus is proposed. Phylogenetic analyses of the ITS region placed X.spathulatus, X.bubalinus and X.chinensis in a strongly supported clade and demonstrated that they are conspecific. Palifer and Odontiopsis are synonymised under Xylodon based on morphological and sequence data. The following new combinations are proposed: X.erikssonii, X.gamundiae, X.hjortstamii, X.hyphodontinus, X.septocystidiatus and X.verecundus. Line drawings of X.cystidiatus, X.hyphodontinus, X.lanatus and X.vesiculosus, as well as photographs of X.raduloides basidiomata, are provided. A key to X.lanatus and similar species is presented.

Taxonomic status of Velinoides Matsumura (Hemiptera: Reduviidae: Harpactorinae) inferred from mitochondrial and nuclear genes

Zootaxa ◽  
2009 ◽  
Vol 2080 (1) ◽  
pp. 55-68 ◽  
Author(s):  
HUI LIU ◽  
PING ZHAO ◽  
SHUJUAN LI ◽  
WANZHI CAI
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Gene Segment ◽  
Nuclear Gene ◽  
Taxonomic Status ◽  
Sister Group ◽  
Molecular Data ◽  
28S Rrna ◽  
Minimum Evolution ◽  
Morphological Studies

In this study, we used three mitochondrial genes (cyt b, COI, and 16S rRNA) and one nuclear gene (28S rRNA) to evaluate the current taxonomic status of the genus Velinoides erected by Matsumura. Phylogenetic analyses of genes using maximum parsimony, maximum likelihood, and minimum evolution resulted in different phylogenetic trees. However, the combined dataset analysis revealed better phylogenetic relationships. The constructed phylogenies appeared to be largely congruent with morphological studies. Results based on the molecular data strongly supported that the C. dilatatus, the type species of Velinoides, was the sister group to all other species of the genus Coranus Curtis. Incorporation with the morphological and cytogenetic characteristics, we proposed that Velinoides is of subgeneric status, the genus Coranus Curtis should be divided into two subgenera, Velinoides Matsumura and Coranus Curtis. Our phylogenetic results suggested that the 28S rDNA gene segment alone might not be an optimal molecular marker for the phylogeny of the genus Coranus Curtis.

scholarly journals Assessing bivalve phylogeny using Deep Learning and Computer Vision approaches

2021 ◽  
Author(s):  
Steffen Kiel
Keyword(s):  
Computer Vision ◽  
Deep Learning ◽  
Phylogenetic Relationships ◽  
Convergent Evolution ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Morphological Data ◽  
Future Directions ◽  
Classification Tasks

ABSTRACTPhylogenetic analyses using morphological data currently require hand-crafted character matrices, limiting the number of taxa that can be included. Here I explore how Deep Learning and Computer Vision approaches typically applied to image classification tasks, may be used to infer phylogenetic relationships among bivalves. A convolutional neural network (CNN) was trained on thousands of images showing species of 75 bivalve families. The predictions of the CNN on a large number of bivalve images are then interpreted as an indication of how similar these bivalves are to each other, are averaged by the families to which the species belonged, and visualized in a cluster diagram. In this cluster diagram, significantly more families clustered with members of their subclasses than expected by chance, confirming the feasibility of the approach. To address the issue of convergent evolution, two further CNNs were trained, on the same images but grouped by the orders and subclasses to which the species belonged. Combining predictions for the same images but on different taxonomic levels improved the inferred phylogenetic relationships also of families that the CNNs had not been trained on. Finally, this combined tree is merged with five published phylogenetic trees into a supertree, representing the largest single phylogeny of the Bivalvia to date, encompassing 128 families, including six exclusively fossil families and nine extant families for which presently no molecular data are available. Issues inherent to the approach and suggestions for future directions are discussed.

scholarly journals What do ossification sequences tell us about the origin of extant amphibians?

2018 ◽  
Author(s):  
Michel Laurin ◽  
Océane Lapauze ◽  
David Marjanović
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Information Criterion ◽  
Molecular Data ◽  
Molecular Dating ◽  
Morphological Data ◽  
Monophyletic Origin ◽  
Paleozoic Tetrapods ◽  
Ossification Sequences ◽  
Ossification Sequence

AbstractThe origin of extant amphibians has been studied using several sources of data and methods, including phylogenetic analyses of morphological data, molecular dating, stratigraphic data, and integration of ossification sequence data, but a consensus about their affinities with other Paleozoic tetrapods has failed to emerge. We have compiled five datasets to assess the relative support for six competing hypotheses about the origin of extant amphibians: a monophyletic origin among temnospondyls, a monophyletic origin among lepospondyls, a diphyletic origin among both temnospondyls and lepospondyls, a diphyletic origin among temnospondyls alone, and two variants of a triphyletic origin, in which anurans and urodeles come from different temnospondyl taxa while caecilians come from lepospondyls and are either closer to anurans and urodeles or to amniotes. Our datasets comprise ossification sequences of up to 107 terminal taxa and up to eight cranial bones, and up to 65 terminal taxa and up to seven appendicular bones, respectively. Among extinct taxa, only two or three temnospondyl can be analyzed simultaneously for cranial data, but this is not an insuperable problem because each of the six tested hypotheses implies a different position of temnospondyls and caecilians relative to other sampled taxa. For appendicular data, more extinct taxa can be analyzed, including some lepospondyls and the finned tetrapodomorph Eusthenopteron, in addition to temnospondyls. The data are analyzed through maximum likelihood, and the AICc (corrected Akaike Information Criterion) weights of the six hypotheses allow us to assess their relative support. By an unexpectedly large margin, our analyses of the cranial data support a monophyletic origin among lepospondyls; a monophyletic origin among temnospondyls, the current near-consensus, is a distant second. All other hypotheses are exceedingly unlikely according to our data. Surprisingly, analysis of the appendicular data supports triphyly of extant amphibians within a clade that unites lepospondyls and temnospondyls, contrary to all phylogenies based on molecular data and recent trees based on paleontological data, but this conclusion is not very robust.

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