scholarly journals Genetic data of museum specimens allow for inferring evolutionary history of the cosmopolitan genusSirthenea(Heteroptera: Reduviidae)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6640
Author(s):  
Dominik Chłond ◽  
Natalia Sawka-Gądek ◽  
Dagmara Żyła
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Molecular Dating ◽  
Morphological Data ◽  
Cosmopolitan Distribution ◽  
History Of ◽  
Clock Analysis ◽  
Divergence Dates

Among the 30 known genera within subfamily Peiratinae, only the genusSirtheneahas a cosmopolitan distribution. The results of our studies are the first comprehensive analysis concerning one of the representatives of mentioned subfamily based on joint phylogenetic analyses of molecular and morphological data as well as molecular dating. A total of 32 species were included into the dataset with all known species of the genusSirthenea. Material of over 400 dry specimens was examined for the morphological part of this study. The cosmopolitan distribution ofSirtheneaand the inaccessibility of specimens preserved in alcohol required the extraction of DNA from the dried skeletal muscles of specimens deposited in 24 entomological collections. The oldest specimens used for the successful extraction and sequencing were collected more than 120 years ago in India. We performed Bayesian Inference analyses of molecular and morphological data separately, as well as combined analysis. The molecular and morphological data obtained during our research verify the correlation of the divergence dates of all knownSirtheneaspecies. Results of the relaxed molecular clock analysis of the molecular data show that, the genusSirtheneastarted diverging in the Late Cretaceous into two clades, which subsequently began to branch off in the Paleocene. Our results of phylogenetic analyses suggest that thefossula spongiosaand its development could be one of the most important morphological characters in the evolution of the genus, most likely associated with the ecological niche inhabited bySirthenearepresentatives. Confirmation of the results obtained in our studies is the reconciliation of the evolutionary history ofSirtheneawith the biogeographical processes that have shaped current global distribution of the genus.

scholarly journals Hagfish from the Cretaceous Tethys Sea and a reconciliation of the morphological–molecular conflict in early vertebrate phylogeny

2019 ◽  
Vol 116 (6) ◽  
pp. 2146-2151 ◽  
Author(s):  
Tetsuto Miyashita ◽  
Michael I. Coates ◽  
Robert Farrar ◽  
Peter Larson ◽  
Phillip L. Manning ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Morphological Data ◽  
Vertebrate Lineage ◽  
Crown Group ◽  
Tethys Sea ◽  
History Of ◽  
Animal Phylogeny ◽  
Early Late

Hagfish depart so much from other fishes anatomically that they were sometimes considered not fully vertebrate. They may represent: (i) an anatomically primitive outgroup of vertebrates (the morphology-based craniate hypothesis); or (ii) an anatomically degenerate vertebrate lineage sister to lampreys (the molecular-based cyclostome hypothesis). This systematic conundrum has become a prominent case of conflict between morphology- and molecular-based phylogenies. To date, the fossil record has offered few insights to this long-branch problem or the evolutionary history of hagfish in general, because unequivocal fossil members of the group are unknown. Here, we report an unequivocal fossil hagfish from the early Late Cretaceous of Lebanon. The soft tissue anatomy includes key attributes of living hagfish: cartilages of barbels, postcranial position of branchial apparatus, and chemical traces of slime glands. This indicates that the suite of characters unique to living hagfish appeared well before Cretaceous times. This new hagfish prompted a reevaluation of morphological characters for interrelationships among jawless vertebrates. By addressing nonindependence of characters, our phylogenetic analyses recovered hagfish and lampreys in a clade of cyclostomes (congruent with the cyclostome hypothesis) using only morphological data. This new phylogeny places the fossil taxon within the hagfish crown group, and resolved other putative fossil cyclostomes to the stem of either hagfish or lamprey crown groups. These results potentially resolve the morphological–molecular conflict at the base of the Vertebrata. Thus, assessment of character nonindependence may help reconcile morphological and molecular inferences for other major discords in animal phylogeny.

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 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.

scholarly journals Ancient DNA forces reconsideration of evolutionary history of Mediterranean pygmy elephantids

2006 ◽  
Vol 2 (3) ◽  
pp. 451-454 ◽  
Author(s):  
Nikos Poulakakis ◽  
Aris Parmakelis ◽  
Petros Lymberakis ◽  
Moysis Mylonas ◽  
Eleftherios Zouros ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Ancient Dna ◽  
Evolutionary History ◽  
Eastern Mediterranean ◽  
Multiple Displacement Amplification ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Mediterranean Islands ◽  
Amplification Method ◽  
History Of

During the Pleistocene pygmy elephantids, some only a quarter of their ancestors' size, were present on Mediterranean islands until about 10 000 years ago (y.a.). Using a new methodology for ancient DNA (aDNA) studies, the whole genomic multiple displacement amplification method, we were able to retrieve cytochrome b (cyt b ) DNA fragments from 4200 to 800 000 y.a. specimens from island and mainland samples, including pygmy and normal-sized forms. The short DNA sequence (43 bp) retrieved from the 800 000 y.a. sample is one of the oldest DNA fragment ever retrieved. Duplication of the experiments in two laboratories, the occurrence of three diagnostic sites and the results of the phylogenetic analyses strongly support its authenticity. Our results challenge the prevailing view that pygmy elephantids of the eastern Mediterranean originated exclusively from Elephas , suggesting independent histories of dwarfism and the presence of both pygmy mammoths and elephant-like taxa on these islands. Based on our molecular data, the origin of the Tilos and Cyprus elephantids from a lineage within the genus Elephas is confirmed, while the DNA sequence from the Cretan sample falls clearly within the mammoth clade. Thus, the name Mammuthus creticus rather than Elephas creticus , seems to be justified for this form. Our findings also suggest a need to re-evaluate the evolutionary history of the Sicilian/Maltese species, traditionally included in the genus Elephas .

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

Phytotaxa ◽  
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.

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 Paleogenomics illuminates the evolutionary history of the extinct Holocene “horned” crocodile of Madagascar, Voay robustus

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
E. Hekkala ◽  
J. Gatesy ◽  
A. Narechania ◽  
R. Meredith ◽  
M. Russello ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Molecular Data ◽  
Sister Group Relationship ◽  
Molecular Fossil ◽  
Close Relationship ◽  
History Of ◽  
Competing Hypotheses

AbstractAncient DNA is transforming our ability to reconstruct historical patterns and mechanisms shaping modern diversity and distributions. In particular, molecular data from extinct Holocene island faunas have revealed surprising biogeographic scenarios. Here, we recovered partial mitochondrial (mt) genomes for 1300–1400 year old specimens (n = 2) of the extinct “horned” crocodile, Voay robustus, collected from Holocene deposits in southwestern Madagascar. Phylogenetic analyses of partial mt genomes and tip-dated timetrees based on molecular, fossil, and stratigraphic data favor a sister group relationship between Voay and Crocodylus (true crocodiles). These well supported trees conflict with recent morphological systematic work that has consistently placed Voay within Osteolaeminae (dwarf crocodiles and kin) and provide evidence for likely homoplasy in crocodylian cranial anatomy and snout shape. The close relationship between Voay and Crocodylus lends additional context for understanding the biogeographic origins of these genera and refines competing hypotheses for the recent extinction of Voay from Madagascar.

scholarly journals Diversification patterns based on the largest morphological phylogenetic analysis of Pleurodira

2015 ◽  
Author(s):  
Gabriel S Ferreira ◽  
Juliana Sterli ◽  
Mario Bronzati Filho ◽  
Max C Langer
Keyword(s):  
Early Cretaceous ◽  
Late Cretaceous ◽  
Evolutionary History ◽  
Feeding Habits ◽  
Phylogenetic Analyses ◽  
Morphological Data ◽  
Phylogenetic Hypothesis ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
History Of

Background. Most studies on pleurodiran turtles are about the behavior and/or feeding habits analyzes, description of new taxa or specimens (both extinct and extant), or phylogenetic analyzes of one of its subclades with extant taxa: Chelidae, Pelomedusidae or Podocnemididae. With the exception of some molecular phylogenies, there are no phylogenetic analyses of extant and extinct representatives of Pleurodira including all of its lineages. A broader understanding of the evolutionary history of Pleurodira requires a phylogenetic hypothesis based on more extensive taxonomic and character samplings.Methods. We constructed a taxon-character matrix including 227 morphological characters and 87 taxa from all the Pleurodira lineages, plus one stem Pan-Pleurodira, Notoemys laticentralis, and one stem-Testudinata, Proganochelys quenstedti, as outgroups. The resulting matrix was analyzed using parsimony, Tree Bisection and Reconnection (TBR) algorithms, with 5000 replicates, and a hold of 20. The obtained strict consensus tree was used as the basis of a diversification analysis using topology-based methods. A nestedgrowing tree approach was employed to create a corresponding tree for different intervals of the geological history of the group. Six distinct time bins were created for periods in which members of Pleurodira occur: Early Cretaceous, Late Cretaceous, Paleocene, Eocene, Miocene, and Recent. Results. All main pleurodiran clades were recovered in the strict consensus tree, but with some changes in their relationship compared to previous analyses, e.g. the inclusiveness of both Pelomedusoides and Bothremydidae. The diversification analysis shows that, after the establishment of the two major lineages (i.e. Chelidae and Pelomedusoides) in the Early Cretaceous, these subgroups diversified in distinct rates along their evolutionary history. Two main diversification shifts were identified: one at the early evolution of Podocnemoidea, during the Late Cretaceous, and another during the Miocene, deep nested in the Podocnemididae clade. Discussion. The resulting strict consensus tree is the largest exclusive phylogenetic hypothesis for Pleurodira, including both extant and extinct taxa. Based on morphological data, it allows more inclusive inferences on the general morphological and diversification patterns of the group. The diversification pulses analysis suggests variation on the rates of diversification on the different pleurodiran clades. The first shift detected is related to the great radiation of Bothremydidae and Podocnemoidae in the Late Cretaceous; the second shift, detected in the Miocene, is related to a diversification within the Stereogenyina, a Podocnemididae clade. Ongoing analysis will determine which factors could enforce those different diversification rates in the evolution of Pleurodira.

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.

Cladistic relationships among higher groups of Heteroptera: congruence between morphological and molecular data sets

1993 ◽  
Vol 24 (2) ◽  
pp. 121-137 ◽  
Author(s):  
Ward C. Wheeler ◽  
Ranhy Bang ◽  
Randall T. Schuh
Keyword(s):  
Sister Group ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Sister Group Relationship ◽  
Molecular Evidence ◽  
Data Sets ◽  
Nuclear Rdna ◽  
History Of ◽  
Morphological And Molecular Data

AbstractThe monophyly of the 7 infraorders of Heteroptera and history of higher group concepts and interrelationships within the Heteroptera are briefly reviewed. Data from 31 morphological characters are combined with 669 bases of 18S nuclear rDNA for 29 taxa, including several outgroups to the Heteroptera, to produce a phylogeny based on the total available evidence. The molecular data alone and in conjunction with morphological data indicate that: the Homoptera are probably not monophyletic; the Auchenorrhyncha are the sister group of Coleorrhyncha + Heteroptera ; the Enicocephalomorpha are the sister group of remaining Heteroptera; the Dipsocoromorpha are the sister group of remaining Heteroptera; the Gerromorpha are the sister group of remaining Heteroptera; the Nepomorpha are the sister group of remaining Heteroptera; the Leptopodomorpha are the sister group of the Cimicomorpha + Pentatomomorpha. The molecular evidence corroborates the morphologically based theory of a sister group relationship between Aradoidea and trichophoran Pentatomomorpha. This scheme deviates from that previously published by Schuh, in which the Leptopodomorpha were treated as the sister group of the Nepomorpha.

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