scholarly journals The phylogenetic conundrum of Lutzia (Diptera: Culicidae: Culicini): a cautionary account of conflict and support

2015 ◽  
Vol 46 (3) ◽  
pp. 269-290 ◽  
Author(s):  
Ian J. Kitching ◽  
C. Lorna Culverwell ◽  
Ralph E. Harbach
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Set ◽  
Generic Status ◽  
Strong Signal ◽  
Phylogenetic Studies ◽  
Data Support

Lutzia Theobald was reduced to a subgenus of Culex in 1932 and was treated as such until it was restored to its original generic status in 2003, based mainly on modifications of the larvae for predation. Previous phylogenetic studies based on morphological and molecular data have provided conflicting support for the generic status of Lutzia: analyses of morphological data support the generic status whereas analyses based on DNA sequences do not. Our previous phylogenetic analyses of Culicini (based on 169 morphological characters and 86 species representing the four genera and 26 subgenera of Culicini, most informal group taxa of subgenus Culex and five outgroup species from other tribes) seemed to indicate a conflict between adult and larval morphological data. Hence, we conducted a series of comparative and data exclusion analyses to determine whether the alternative positions of Lutzia are due to conflicting signal or to a lack of strong signal. We found that separate and combined analyses of adult and larval data support different patterns of relationships between Lutzia and other Culicini. However, the majority of conflicting clades are poorly supported and once these are removed from consideration, most of the topological disparity disappears, along with much of the resolution, suggesting that morphology alone does not have sufficiently strong signal to resolve the position of Lutzia. We critically examine the results of other phylogenetic studies of culicinine relationships and conclude that no morphological or molecular data set analysed in any study conducted to date has adequate signal to place Lutzia unequivocally with regard to other taxa in Culicini. Phylogenetic relationships observed thus far suggest that Lutzia is placed within Culex but further data and extended taxon sampling are required to confirm its position relative to Culex.

Taxonomy and phylogeny of Nitella (Charophyceae, Characeae) from Brazil with emphasis on the midwest and southeast regions

Phytotaxa ◽  
2018 ◽  
Vol 356 (3) ◽  
pp. 181
Author(s):  
FABIO RENATO BORGES ◽  
ORLANDO NECCHI JR
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Molecular Evidence ◽  
Type Specimens ◽  
Brazilian Studies ◽  
Two Populations ◽  
Section Level

The genus Nitella is the most species-rich within the Charales. Brazilian studies on the genus are relatively scarce and consist of floristic surveys, lacking modern and more precise information. This investigation applied scanning electron microscopy to analyze the oospore wall and molecular data associated with traditional morphological characters to analyze forty-two populations of Nitella from the midwest and southeast regions of Brazil. Forty-two new sequences of rbcL, twelve of ITS1 and twenty-three of ITS2 were generated for the five species recognized in this study: Nitella acuminata A. Braun ex Wallman, Nitella axillaris A. Braun, Nitella elegans B. P. Pal, Nitella flagellifera J. Groves & G. O. Allen and Nitella microcarpa A. Braun.. Phylogenetic analyses of sequences of these three markers were congruent in that they grouped our species with others from different countries to form five clades. Our results on ultrastrucure of the oospore wall were consistent with previous studies for the same species from other regions of the world. The data reinforced the conclusion that the use of ornamentation of oospore wall may be extremely useful for the construction of a natural system for Characeae at section level. Molecular evidence, reinforced by morphological data, for the Brazilian material analyzed suggests that Nitella subglomerata A. Braun and Nitella gollmeriana A. Braun could be synonymys of Nitella acuminata; and Nitella axilliformis K. Imahori appears to be the same as Nitella axillaris. However, no formal proposition was made considering that type specimens were not analyzed and these observations were based on a relatively small number of samples strictly from Brazil. We showed that even among geographically distant populations, such as from other continents, of some Nitella species, the degree of identity among DNA sequences was high.

scholarly journals The effects of fossil taxa, hypothetical predicted ancestors, and a molecular scaffold on pseudoextinction analyses of extant placental orders

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0257338
Author(s):  
Peggy L. Brady ◽  
Mark S. Springer
Keyword(s):  
Molecular Phylogenetics ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Ancestral State ◽  
Molecular Scaffolds ◽  
Data Set ◽  
Molecular Scaffold ◽  
Hypothetical Ancestor

Pseudoextinction analyses, which simulate extinction in extant taxa, use molecular phylogenetics to assess the accuracy of morphological phylogenetics. Previous pseudoextinction analyses have shown a failure of morphological phylogenetics to place some individual placental orders in the correct superordinal clade. Recent work suggests that the inclusion of hypothetical ancestors of extant placental clades, estimated by ancestral state reconstructions of morphological characters, may increase the accuracy of morphological phylogenetic analyses. However, these studies reconstructed direct hypothetical ancestors for each extant taxon based on a well-corroborated molecular phylogeny, which is not possible for extinct taxa that lack molecular data. It remains to be determined if pseudoextinct taxa, and by proxy extinct taxa, can be accurately placed when their immediate hypothetical ancestors are unknown. To investigate this, we employed molecular scaffolds with the largest available morphological data set for placental mammals. Each placental order was sequentially treated as pseudoextinct by exempting it from the molecular scaffold and recoding soft morphological characters as missing for all its constituent species. For each pseudoextinct data set, we omitted the pseudoextinct taxon and performed a parsimony ancestral state reconstruction to obtain hypothetical predicted ancestors. Each pseudoextinct order was then evaluated in seven parsimony analyses that employed combinations of fossil taxa, hypothetical predicted ancestors, and a molecular scaffold. In treatments that included fossils, hypothetical predicted ancestors, and a molecular scaffold, only 8 of 19 pseudoextinct placental orders (42%) retained the same interordinal placement as on the molecular scaffold. In treatments that included hypothetical predicted ancestors but not fossils or a scaffold, only four placental orders (21%) were recovered in positions that are congruent with the scaffold. These results indicate that hypothetical predicted ancestors do not increase the accuracy of pseudoextinct taxon placement when the immediate hypothetical ancestor of the taxon is unknown. Hypothetical predicted ancestors are not a panacea for morphological phylogenetics.

scholarly journals Disentangling relationships among eastern Mediterranean Cymbalaria including description of a novel species from the southern Peloponnese (Greece)

2021 ◽  
Vol 307 (2) ◽  
Author(s):  
Pau Carnicero ◽  
Núria Garcia-Jacas ◽  
Llorenç Sáez ◽  
Theophanis Constantinidis ◽  
Mercè Galbany-Casals
Keyword(s):  
Eastern Mediterranean ◽  
Phylogenetic Analyses ◽  
Taxonomic Revision ◽  
Distribution Patterns ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Long Distance ◽  
Aegean Islands ◽  
Molecular Phylogenetic

AbstractThe eastern Mediterranean basin hosts a remarkably high plant diversity. Historical connections between currently isolated areas across the Aegean region and long-distance dispersal events have been invoked to explain current distribution patterns of species. According to most recent treatments, at least two Cymbalaria species occur in this area, Cymbalaria microcalyx and C. longipes. The former comprises several intraspecific taxa, treated at different ranks by different authors based on morphological data, evidencing the need of a taxonomic revision. Additionally, some populations of C. microcalyx show exclusive morphological characters that do not match any described taxon. Here, we aim to shed light on the systematics of eastern Mediterranean Cymbalaria and to propose a classification informed by various sources of evidence. We performed molecular phylogenetic analyses using ITS, 3’ETS, ndhF and rpl32-trnL sequences and estimated the ploidy level of some taxa performing relative genome size measures. Molecular data combined with morphology support the division of traditionally delimited C. microcalyx into C. acutiloba, C. microcalyx and C. minor, corresponding to well-delimited nrDNA lineages. Furthermore, we propose to combine C. microcalyx subsp. paradoxa at the species level. A group of specimens previously thought to belong to Cymbalaria microcalyx constitute a well-defined phylogenetic and morphological entity and are described here as a new species, Cymbalaria spetae. Cymbalaria longipes is non-monophyletic, but characterized by being glabrous and diploid, unlike other eastern species. The nrDNA data suggest at least two dispersals from the mainland to the Aegean Islands, potentially facilitated by marine regressions.

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

Zootaxa ◽  
2007 ◽  
Vol 1423 (1) ◽  
pp. 1-26 ◽  
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.

Monophyly of Verbascum (Scrophularieae : Scrophulariaceae): evidence from nuclear and plastid phylogenetic analyses

2014 ◽  
Vol 62 (8) ◽  
pp. 638 ◽  
Author(s):  
Farrokh Ghahremaninejad ◽  
Mehrshid Riahi ◽  
Melina Babaei ◽  
Faride Attar ◽  
Lütfi Behçet ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Nrdna Its ◽  
Starting Point ◽  
High Species Diversity ◽  
Phylogenetic Estimation

Verbascum is one of the main genera of Scrophulariaceae, but delimitation and phylogenetic relationships of this genus are unclear and have not yet been studied using DNA sequences. Here, using four selected molecular markers (nrDNA ITS and the plastid spacers trnS/G, psbA-trnH and trnY/T), we present a phylogeny of Verbascum and test previous infrageneric taxonomic hypotheses as well as its monophyly with respect to Scrophularia. We additionally discuss morphological variation and the utility of morphological characters as predictors of phylogenetic relationships. Our results show that while molecular data unambiguously support the circumscription of Verbascum inferred from morphology, they prove to be of limited utility in resolving infrageneric relationships, suggesting that Verbascum ‘s high species diversity is due to rapid and recent radiation. Our work provides phylogenetic estimation of the genus Verbascum using molecular data and can serve as a starting point for future investigations of Verbascum and relatives.

The greenhouse thrips, Heliothrips haemorrhoidalis, and its generic relationships within the subfamily Panchaetothripinae (Thysanoptera: Thripidae)

2001 ◽  
Vol 32 (2) ◽  
pp. 205-216 ◽  
Author(s):  
John W.H. Trueman ◽  
Rita Marullo ◽  
Laurence A. Mound
Keyword(s):  
Sister Group ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Sister Group Relationship ◽  
Pest Species ◽  
Data Set ◽  
Weak Support ◽  
Heliothrips Haemorrhoidalis ◽  
Generic Relationships

AbstractThe subfamily Panchaetothripinae, comprising 35 genera and 98 species, includes several pest species of which the most notorious is the greenhouse thrips, Heliothrips haemorrhoidalis. In an attempt to establish the sister-group of Heliothrips, the relationships of this genus to 31 of the other genera in the subfamily were examined cladistically, using 35 parsimony-informative morphological characters. The analysis indicated that there was no support for two of the three tribes into which this subfamily is customarily arranged, the Monilothripini and the Panchaetothripini, but weak support for the tribe Tryphactothripini. No clear sister-group relationship could be identified for the New World genus Heliothrips, although it grouped with three old world genera Australothrips, Retithrips and Rhipiphorothrips. It is concluded that a morphological data set is not capable of producing a robust phylogeny of the Panchaetothripinae, and that the subject requires re-examination using molecular data.

Taxonomy and phylogeny of Chara (Charophyceae, Characeae) from Brazil with emphasis on the midwest and southeast regions

Phytotaxa ◽  
2017 ◽  
Vol 302 (2) ◽  
pp. 101 ◽  
Author(s):  
FABIO RENATO BORGES ◽  
ORLANDO NECCHI JR
Keyword(s):  
Molecular Markers ◽  
Maximum Likelihood ◽  
Dna Sequences ◽  
American Studies ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
South American ◽  
Bayesian Analyses ◽  
Sem Analyses

South American studies on the genus Chara are relatively scarce, most consisting of floristic surveys and using only traditional morphological characters. This study is a first approach to the systematics of the genus Chara applying modern techniques (DNA sequences and oospore SEM analyses) in addition to the alpha-taxonomy investigations that have been conducted in Brazil. Twelve populations of Chara were analyzed from the midwest and southeast regions of Brazil. Sequences of three molecular markers were applied to infer phylogenies. The ultrastructure of the oospore wall and currently used morphological characters were analyzed for Chara populations. Maximum likelihood and Bayesian analyses of sequences of rbcL, ITS2, and matK were congruent in that they grouped the species in six clades, each representing one species: Chara braunii C.C. Gmelin, C. foliolosa C.L.Willdenow, C. guairensis R.Bicudo, C. haitensis M.P.J.F. Turpin, C. hydropitys H. Reichenbach and C. rusbyana M. Howe. Morphological characters, including ultrastructure of oospore wall, provided good evidences to characterize each species. Molecular data supported the recent view that some traditional infra-generic taxa (e.g. subgenus Charopsis and subsection Willdenowia) are not supported in phylogenetic analyses, whereas some species (e.g. C. foliolosa, C. haitensis, C. hydropitys and C. rusbyana previously considered as varieties and forms of C. zeylanica) were consistently distinguished in the analyses for the three molecular markers.

scholarly journals ULASAN Kajian Filogenetika Molekuler dan Peranannya dalam Menyediakan Informasi Dasar untuk Meningkatkan Kualitas Sumber Genetik Anggrek

2016 ◽  
Vol 4 (1) ◽  
pp. 35 ◽  
Author(s):  
Topik Hidayat ◽  
Adi Pancoro
Keyword(s):  
Dna Sequences ◽  
Molecular Phylogenetics ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Biochemical Properties ◽  
Intergeneric Hybrids ◽  
Basic Knowledge ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
Ornamental Crops

<p>Early information<br />resulted from molecular phylogenetic studies of many important<br />ornamental crops is often less attention to many<br />growers and farmers. Phylogenetics is one of the most preferable<br />method in systematics to reconstruct evolutionary<br />relationships of groups of biological organisms in order to<br />understand their biodiversities. This has been revolutionized<br />by DNA sequences data. In this method, a group of organisms<br />that shares many identical characteristics are considered<br />to be closely related; deriving from a common<br />ancestor and is assumed to have similar genetic patterns<br />and biochemical properties. By these basic principles,<br />molecular phylogenetics plays important roles in revealing a<br />basic knowledge on pattern of relationships to which<br />genetic resources can be improved. Over the past decade,<br />botanists have done several thousand phylogenetic analyses<br />based on molecular data of economically and horticulturally<br />important crops. Orchids are the best example for this.<br />There is no doubt that most orchid plants had played roles in<br />horticulture and hybridization. At present, many infrageneric<br />and intergeneric hybrids are available commercially. Successful<br />hybridization can be achieved if two or more individual<br />plants understudy are closely related in respect to their<br />genetics and evolution.</p>

scholarly journals Craniodental morphology and phylogeny of marsupials

2021 ◽  
Author(s):  
Robin M. D. Beck ◽  
Robert Voss ◽  
Sharon Jansa
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Future Research ◽  
Data Types ◽  
Wide Range ◽  
Morphological And Molecular Data ◽  
Dense Sampling

The current literature on marsupial phylogenetics includes numerous studies based on analyses of morphological data with relatively limited sampling of Recent and fossil taxa, and many studies based on analyses of molecular data that include a dense sampling of Recent taxa, but relatively few that combine both data types. Another dichotomy in the marsupial phylogenetic literature is between studies that focus on New World taxa, others that focus on Sahulian taxa. To date, there has been no attempt to assess the phylogenetic relationships of the global marsupial fauna, based on combined analyses of morphology and molecular sequences, for a dense sampling of Recent and fossil taxa. For this report, we compiled morphological and molecular data from an unprecedented number of Recent and fossil marsupials. Our morphological data consist of 180 craniodental characters that we scored for 97 species representing every currently recognized Recent genus, 42 additional ingroup (crown-clade marsupial) taxa represented by well-preserved fossils, and 5 outgroups (non-marsupial metatherians). Our molecular data comprise 24.5 kb of DNA sequences from whole-mitochondrial genomes and six nuclear loci (APOB, BRCA1, GHR, RAG1, RBP3 and VWF) for 97 marsupial terminals (the same Recent taxa scored for craniodental morphology) and several placental and monotreme outgroups. The results of separate and combined analyses of these data using a wide range of phylogenetic methods support many currently accepted hypotheses of ingroup (marsupial) relationships, but they also underscore the difficulty of placing fossils with key missing data (e.g., †Evolestes), and the unique difficulty of placing others that exhibit mosaics of plesiomorphic and autapomorphic traits (e.g., †Yalkaparidon). Unique contributions of our study are (1) critical discussions and illustrations of marsupial craniodental morphology, including descriptions and illustrations of some features never previously coded for phylogenetic analysis; (2) critical assessments of relative support for many suprageneric clades; (3) estimates of divergence times derived from tip-and-node dating based on uniquely taxon-dense analyses; and (4) a revised, higher-order classification of marsupials accompanied by lists of supporting craniodental synapomorphies. Far from the last word on these topics, this report lays the foundation for future research that may be enabled by the discovery of new fossil taxa, better-preserved material of previously described taxa, novel morphological characters, and improved methods of phylogenetic analysis.

Disentangling the taxonomy of the Galactia-Camptosema- Collaea complex with new generic circumscriptions in the Galactia clade (Leguminosae, Diocleae)

Neodiversity ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 56-94
Author(s):  
Luciano P. Queiroz ◽  
◽  
Ana C.S. Oliveira ◽  
Cristiane Snak
Keyword(s):  
Maximum Parsimony ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
New Genera ◽  
Genus Level ◽  
Phylogenetic Studies ◽  
Taxonomic History ◽  
Molecular Phylogenetic

The Galactia clade is one of three major lineages of the papilionoid legume tribe Diocleae. It comprises eight genera and approximately 140 species almost entirely restricted to the Americas. Establishing stable generic boundaries within this clade has been a challenge because of its tortuous taxonomic history and the broad polyphyly of the genera of the so-called Galactia-Camptosema-Collaea complex. Previous molecular phylogenetic studies revealed some well-supported lineages, but did not advance towards any new taxonomic arrangements. We carried out maximum parsimony and Bayesian phylogenetic analyses of a combined dataset including our previously published multilocus molecular data (nrITS and ETS and plastid trnK/matK and trnT-Y regions) and 82 morphological characters. The resulting topologies largely concur with those previously reported based on molecular data only, where Camptosema and Galactia appear as broadly polyphyletic, with species scattered among five (Camptosema) and seven (Galactia) of the twelve lineages that are newly recognized here at genus level. We are therefore proposing the following new taxonomic rearrangements within the Galactia clade: descriptions of the new genera Caetangil, Cerradicola, Mantiqueira, and Nanogalactia; resurrection of Betencourtia; and the subsuming of Neorudolphia into Rhodopis and of Camptosema sect. Macropetalum into Cratylia.

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