scholarly journals Investigating Morphological Complexes Using Informational Dissonance and Bayes Factors: A Case Study in Corbiculate Bees

2020 ◽  
Author(s):  
Diego S Porto ◽  
Eduardo A B Almeida ◽  
Matthew W Pennell
Keyword(s):  
Morphological Characters ◽  
Molecular Data ◽  
Bayes Factors ◽  
Morphological Data ◽  
Rate Variation ◽  
Phylogenetic Information ◽  
Gamma Distributions ◽  
A Genome ◽  
Starting Point ◽  
Corbiculate Bees

Abstract It is widely recognized that different regions of a genome often have different evolutionary histories and that ignoring this variation when estimating phylogenies can be misleading. However, the extent to which this is also true for morphological data is still largely unknown. Discordance among morphological traits might plausibly arise due to either variable convergent selection pressures or else phenomena such as hemiplasy. Here, we investigate patterns of discordance among 282 morphological characters, which we scored for 50 bee species particularly targeting corbiculate bees, a group that includes the well-known eusocial honeybees and bumblebees. As a starting point for selecting the most meaningful partitions in the data, we grouped characters as morphological modules, highly integrated trait complexes that as a result of developmental constraints or coordinated selection we expect to share an evolutionary history and trajectory. In order to assess conflict and coherence across and within these morphological modules, we used recently developed approaches for computing Bayesian phylogenetic information allied with model comparisons using Bayes factors. We found that despite considerable conflict among morphological complexes, accounting for among-character and among-partition rate variation with individual gamma distributions, rate multipliers, and linked branch lengths can lead to coherent phylogenetic inference using morphological data. We suggest that evaluating information content and dissonance among partitions is a useful step in estimating phylogenies from morphological data, just as it is with molecular data. Furthermore, we argue that adopting emerging approaches for investigating dissonance in genomic datasets may provide new insights into the integration and evolution of anatomical complexes. [Apidae; entropy; morphological modules; phenotypic integration; phylogenetic information.]

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.

Revision of Autolytinae (Syllidae: Polychaeta)

Zootaxa ◽  
2004 ◽  
Vol 680 (1) ◽  
pp. 1 ◽  
Author(s):  
ARNE NYGREN
Keyword(s):  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Nominal Species ◽  
Strict Consensus Tree ◽  
Incertae Sedis ◽  
Nomina Dubia ◽  
Morphological And Molecular Data ◽  
Combined Data

Autolytinae is revised based on available types, and newly collected specimens. Out of 170 nominal species, 18 are considered as incertae sedis, 43 are regarded as junior synonyms, and 25 are referred to as nomina dubia. The relationships of Autolytinae is assessed from 51 morphological characters and 211 states for 76 ingroup-taxa, and 460 molecular characters from mitochondrial 16S rDNA and nuclear 18S rDNA for 31 ingroup-taxa; outgroups include 12 non-autolytine syllid polychaetes. Two analyses are provided, one including morphological data only, and one with combined morphological and molecular data sets. The resulting strict consensus tree from the combined data is chosen for a reclassification. Three main clades are identified: Procerini trib. n., Autolytini Grube, 1850, and Epigamia gen. n. Proceraea Ehlers, 1864 and Myrianida Milne Edwards, 1845 are referred to as nomen protectum, while Scolopendra Slabber, 1781, Podonereis Blainville, 1818, Amytis Savigny, 1822, Polynice Savigny, 1822, and Nereisyllis Blainville, 1828 are considered

A revision of Australian species of Radula subg. Odontoradula

2013 ◽  
Vol 26 (6) ◽  
pp. 408 ◽  
Author(s):  
Matt A. M. Renner ◽  
Nicolas Devos ◽  
Elizabeth A. Brown ◽  
Matt J. von Konrat
Keyword(s):  
New Zealand ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
South Eastern ◽  
Chloroplast Markers ◽  
Molecular Divergence ◽  
Wet Tropics ◽  
Australian Flora ◽  
Morphological Differences

The current paper presents molecular data from three chloroplast markers (atpB–rbcL spacer, trnG G2 intron, trnL–trnF intron and spacer); morphological data, and geographic data to support the recognition of nine species belonging to Radula subg. Odontoradula in Australasia. R. ocellata, the subgeneric type from the Wet Tropics bioregion, is maintained as distinct from its sister species, R. pulchella, from south-eastern Australian rainforests; both species are Australian endemics. Reinstatement of R. allisonii from synonymy, under R. retroflexa, is supported by molecular data and morphological characters, including the absence of triradiate trigones on leaf-lobe cell walls, the apex of lobules on primary shoots not being turned outwards, the oblong-elliptic female bracts, and the perianths having a pronounced wing. Reinstatement of R. weymouthiana, from synonymy under R. retroflexa, is also supported by molecular data and morphological characters, including the presence of a single low dome-shaped papilla over each leaf-lobe cell, and the large imbricate lobules on primary shoots. R. weymouthiana occurs in Tasmania and New Zealand, whereas R. allisonii is a New Zealand endemic. Australian R. retroflexa exhibits differentiation into epiphytic and rheophytic morphs, interpreted as ecotypes. Australian individuals, comprising both epiphytic and rheophytic morphs, are monophyletic and nested within a clade containing individuals from other regions. R. novae-hollandiae is newly reported for the New Zealand Botanical Region, from Raoul Island in the Kermadecs. R. novae-hollandiae exhibits decoupling of morphological and molecular divergence, with Australian individuals forming two clades reflecting geography (a Wet Tropics bioregion clade and a south-eastern Rainforest clade). These clades exhibit equivalent levels of molecular divergence, as observed in R. pulchella and R. ocellata, but no morphological differences. Similar levels of molecular divergence were observed in trans-Tasman populations of R. tasmanica. The New Zealand endemic, R. plicata, is excluded from the Australian flora, and R. cuspidata replaces R. dentifolia for the New Zealand endemic species formerly known by both names.

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.

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.

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.

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

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.

scholarly journals Molecular and morphological data reveal three new cryptic species ofChiasmocleis(Mehely 1904) (Anura, Microhylidae) endemic to the Atlantic Forest, Brazil

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3005 ◽  
Author(s):  
Mauricio C. Forlani ◽  
João F.R. Tonini ◽  
Carlos A.G. Cruz ◽  
Hussam Zaher ◽  
Rafael O. de Sá
Keyword(s):  
New Species ◽  
Cryptic Species ◽  
Atlantic Forest ◽  
Morphological Characters ◽  
Molecular Data ◽  
Sao Paulo ◽  
Morphological Data ◽  
Congeneric Species ◽  
The Third ◽  
Coloration Patterns

Three new cryptic species ofChiasmocleisfrom the Atlantic Forest of Brazil are described. Two of these species occur in the northeastern states of Sergipe and Bahia, whereas the third species is found in the southeastern state of São Paulo. The new species can be distinguished from other congeneric species by the molecular data, as evidenced in the phylogeny, and by a combination of morphological characters including: size, foot webbing, dermal spines, and coloration patterns.Chiasmocleisspecies differ in osteological traits, therefore we also provide an osteological description of each new species and comparsions with data reported for other species in the genus.

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.

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