scholarly journals The phylogenetic significance of the morphology of the syrinx, hyoid and larynx, of the Southern Cassowary, Casuarius casuarius (Aves, Palaeognathae)

2019 ◽  
Author(s):  
Phoebe Louise McInerney ◽  
Michael S. Y. Lee ◽  
Alice M. Clement ◽  
Trevor H. Worthy
Keyword(s):  
Morphological Traits ◽  
Evolutionary History ◽  
Morphological Character ◽  
Phylogenetic Analyses ◽  
Molecular Evidence ◽  
Functional Roles ◽  
Phylogenetic Studies ◽  
Basal Clade ◽  
Casuarius Casuarius ◽  
Molecular Trees

Abstract Background: The Palaeognathae are a basal clade within Aves and include the large and flightless ratites and the smaller, volant tinamous. Although much research has been conducted on various aspects of palaeognath morphology, ecology, and evolutionary history, there are still areas which require investigation. This study aimed to fill gaps in our knowledge of the Southern Cassowary, Casuarius casuarius, for which information on the skeletal systems of the syrinx, hyoid and larynx is lacking - despite these structures having been recognised as performing key functional roles associated with vocalisation, respiration and feeding. Previous research into the syrinx and hyoid have also indicated these structures to be valuable for determining evolutionary relationships among neognath taxa, and thus suggest they would also be informative for palaeognath phylogenetic analyses, which still exhibits strong conflict between morphological and molecular trees. Results: The morphology of the syrinx, hyoid and larynx of C. casuarius is described from CT scans. The syrinx is of the simple tracheo-bronchial syrinx type, lacking specialised elements such as the pessulus; the hyoid is relatively short with longer ceratobranchials compared to epibranchials; and the larynx is comprised of entirely cartilaginous, standard avian anatomical elements including a concave, basin-like cricoid and fused cricoid wings. As in the larynx, both the syrinx and hyoid lack ossification and all three structures were most similar to Dromaius. We documented substantial variation across palaeognaths in the skeletal character states of the syrinx, hyoid, and larynx, using both the literature and novel observations (e.g. of C. casuarius). Notably, new synapomorphies linking Dinornithiformes and Tinamidae are identified, consistent with the molecular evidence for this clade. These shared morphological character traits include the ossification of the cricoid and arytenoid cartilages, and an additional cranial character, the articulation between the maxillary process of the nasal and the maxilla. Conclusion: Syrinx, hyoid and larynx characters of palaeognaths display greater concordance with molecular trees than do other morphological traits. These structures might therefore be less prone to homoplasy related to flightlessness and gigantism, compared to typical morphological traits emphasised in previous phylogenetic studies. Key Words: Palaeognathae, Cassowary, Syrinx, Hyoid, Larynx, Morphology, Phylogenetics, Optimisation

scholarly journals The phylogenetic significance of the morphology of the syrinx, hyoid and larynx, of the southern cassowary, Casuarius casuarius (Aves, Palaeognathae)

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Phoebe L. McInerney ◽  
Michael S. Y. Lee ◽  
Alice M. Clement ◽  
Trevor H. Worthy
Keyword(s):  
Morphological Traits ◽  
Evolutionary History ◽  
Morphological Character ◽  
Phylogenetic Analyses ◽  
Molecular Evidence ◽  
Functional Roles ◽  
Phylogenetic Studies ◽  
Basal Clade ◽  
Casuarius Casuarius ◽  
Molecular Trees

Abstract Background Palaeognathae is a basal clade within Aves and include the large and flightless ratites and the smaller, volant tinamous. Although much research has been conducted on various aspects of palaeognath morphology, ecology, and evolutionary history, there are still areas which require investigation. This study aimed to fill gaps in our knowledge of the Southern Cassowary, Casuarius casuarius, for which information on the skeletal systems of the syrinx, hyoid and larynx is lacking - despite these structures having been recognised as performing key functional roles associated with vocalisation, respiration and feeding. Previous research into the syrinx and hyoid have also indicated these structures to be valuable for determining evolutionary relationships among neognath taxa, and thus suggest they would also be informative for palaeognath phylogenetic analyses, which still exhibits strong conflict between morphological and molecular trees. Results The morphology of the syrinx, hyoid and larynx of C. casuarius is described from CT scans. The syrinx is of the simple tracheo-bronchial syrinx type, lacking specialised elements such as the pessulus; the hyoid is relatively short with longer ceratobranchials compared to epibranchials; and the larynx is comprised of entirely cartilaginous, standard avian anatomical elements including a concave, basin-like cricoid and fused cricoid wings. As in the larynx, both the syrinx and hyoid lack ossification and all three structures were most similar to Dromaius. We documented substantial variation across palaeognaths in the skeletal character states of the syrinx, hyoid, and larynx, using both the literature and novel observations (e.g. of C. casuarius). Notably, new synapomorphies linking Dinornithiformes and Tinamidae are identified, consistent with the molecular evidence for this clade. These shared morphological character traits include the ossification of the cricoid and arytenoid cartilages, and an additional cranial character, the articulation between the maxillary process of the nasal and the maxilla. Conclusion Syrinx, hyoid and larynx characters of palaeognaths display greater concordance with molecular trees than do other morphological traits. These structures might therefore be less prone to homoplasy related to flightlessness and gigantism, compared to typical morphological traits emphasised in previous phylogenetic studies.

scholarly journals The phylogenetic significance of the morphology of the syrinx, hyoid and larynx, of the Southern Cassowary, Casuarius casuarius (Aves, Palaeognathae)

2019 ◽  
Author(s):  
Phoebe Louise McInerney ◽  
Michael S. Y. Lee ◽  
Alice M. Clement ◽  
Trevor H. Worthy
Keyword(s):  
Evolutionary History ◽  
Morphological Character ◽  
Phylogenetic Analyses ◽  
Evolutionary Relationships ◽  
Functional Roles ◽  
Basal Clade ◽  
Data Topology ◽  
Combined Data ◽  
Casuarius Casuarius ◽  
Molecular Trees

Abstract The Palaeognathae are a basal clade within Aves and include the large and flightless ratites and the smaller, volant tinamous. Although much research has been conducted on various aspects of palaeognath morphology, ecology, and evolutionary history, there are still areas which require investigation. This study aimed to fill gaps in our knowledge of the Southern cassowary, Casuarius casuarius , for which information on the skeletal systems of the syrinx, hyoid and larynx is lacking despite these structures having been recognised as performing key functional roles associated with vocalisation, respiration and feeding. Previous research into the syrinx and hyoid have also indicated these structures to be valuable for determining evolutionary relationships among neognath taxa, and thus be informative for palaeognath phylogenetic analyses, which still exhibits strong conflict between morphological and molecular trees. We documented variation across palaeognaths in the skeletal character states of the syrinx, hyoid, and larynx, using both the literature and novel observations (e.g. of cassowary). Notably the molecular moa-tinamou clade was found to share morphological character traits including the ossification of the cricoid and arytenoid cartilages, and an additional cranial character, the articulation between the maxillary process of the nasal and the maxilla. These findings contributed to optimisation of syrinx, hyoid and larynx characters showing increased phylogenetic support for palaeognath relationships derived from a molecular and morphological combined-data topology.

scholarly journals The phylogenetic significance of the morphology of the syrinx, hyoid and larynx, of the Southern Cassowary, Casuarius casuarius (Aves, Palaeognathae)

2019 ◽  
Author(s):  
Phoebe Louise McInerney ◽  
Mike S. Y. Lee ◽  
Alice M. Clement ◽  
Trevor H. Worthy
Keyword(s):  
Morphological Traits ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Evolutionary Relationships ◽  
Functional Roles ◽  
Basal Clade ◽  
Shed Light ◽  
Shared Character ◽  
Casuarius Casuarius ◽  
Molecular Trees

Abstract The Palaeognathae are a basal clade within Aves and include the large and flightless ratites and the smaller, volant tinamous. Although much research has been conducted on various aspects of palaeognath morphology, ecology, and evolutionary history, there are still areas which require investigation. This study aimed to fill gaps in our knowledge of the Southern cassowary, Casuarius casuarius, for which information on the syrinx, hyoid and larynx is lacking despite these structures having been recognised as performing key functional roles associated with vocalisation, respiration and feeding. Previous research into the syrinx and hyoid have also indicated these structures to be valuable for determining evolutionary relationships among neognath taxa, and thus may also shed light on palaeognath phylogeny, which still exhibits strong conflict between morphological and molecular trees. We thus documented variation across palaeognaths in syringeal, hyoidal, and laryngeal character states, using both the literature and novel new observations (e.g. of cassowary). Notably the molecular moa-tinamou clade was found to share derived morphological traits including the ossification of the cricoid and arytenoid cartilages, and an additional cranial character, the articulation between the maxillary process of the nasal and the maxilla. Syringeal, hyoidal and laryngeal characters better optimised onto the topology resulting from phylogenetic analyses of a combined molecular and morphology analysis, than molecular-only or morphological-only trees. One primary factor for this support was the aforementioned shared character states between the moa and tinamou, also present in Lithornis and outgroup taxa.

The Phylogenetic Position of Crenea in the Lythraceae Based on Molecular Evidence, and the Transfer of Its Two Species to Ammannia

2021 ◽  
Vol 106 ◽  
pp. 325-339
Author(s):  
Shirley A. Graham ◽  
Peter W. Inglis ◽  
Taciana B. Cavalcanti
Keyword(s):  
Morphological Character ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Phylogenetic Position ◽  
Molecular Evidence ◽  
Monophyletic Lineage ◽  
The Family ◽  
Mangrove Vegetation ◽  
Molecular Phylogenetic ◽  
Globally Distributed

Crenea Aubl. (Lythraceae) is a ditypic genus of subshrubs occurring in mangrove vegetation on the coasts of northern South America. Phylogenetic analyses based on morphology have offered unresolved and conflicting phylogenetic positions for the genus in the family. This study presents the first molecular sequences for Crenea, from nrITS, rbcL, trnL, trnL-F, and matK regions. Molecular phylogenetic analyses find full support for Crenea within Ammannia L., a relationship not previously recognized. Ammannia is a globally distributed genus of terrestrial to amphibious herbs mostly occurring in freshwater marshes and wetlands. It was recently reconfigured based on phylogenetic evidence to include the genera Nesaea Comm. ex Kunth and Hionanthera A. Fern. & Diniz. The transfer of Crenea to Ammannia further extends the morphological, ecological, and biogeographical diversity of Ammannia and provides the final evidence defining Ammannia as a monophyletic lineage of the Lythraceae. A revised circumscription of Ammannia s.l. adds several new morphological character states and the first species in the genus restricted to mangrove vegetation. Two changes in taxonomic status are made: Ammannia maritima (Aubl.) S. A. Graham, P. W. Inglis, & T. B. Cavalc., comb. nov., and Ammannia patentinervius (Koehne) S. A. Graham, P. W. Inglis, & T. B. Cavalc., comb. nov. The new combinations are described, a list of exsiccatae examined is provided, and the effects of the reconfiguration to the morphology and biogeography of the genus are detailed.

scholarly journals The Culicidae (Diptera): a review of taxonomy, classification and phylogeny*

Zootaxa ◽  
2007 ◽  
Vol 1668 (1) ◽  
pp. 591-638 ◽  
Author(s):  
RALPH E. HARBACH
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Molecular Evidence ◽  
Traditional Classification ◽  
Phenetic Classification ◽  
Cladistic Analyses ◽  
Morphological And Molecular Data ◽  
Stable Classification

The taxonomy, classification and phylogeny of family Culicidae are reviewed. The application of explicit methods of phylogenetic analysis has revealed weaknesses in the traditional classification of mosquitoes, but little progress has been made to achieve a robust, stable classification that reflects evolutionary relationships. The current phenetic classification is discussed in view of phylogeny reconstructions based on cladistic analyses of morphological and molecular data. It is concluded that the generic and suprageneric relationships and the validity and monophyly of the generic and subgeneric groupings of Culicidae are in need of extensive reappraisal. If the classification is to reflect evolutionary history, changes to the nomenclature of mosquitoes are inevitable. There is strong morphological and molecular evidence that subfamily Anophelinae and tribes Aedini, Culicini and Sabethini of subfamily Culicinae are monophyletic, but the other taxonomic groupings are not demonstrably monophyletic or have not been subjected to phylogenetic analyses.

scholarly journals Finding Hidden Outliers to Promote the Consistency of Key Morphological Traits and Phylogeny in Dennstaedtiaceae

Taxonomy ◽  
2021 ◽  
Vol 1 (3) ◽  
pp. 256-265
Author(s):  
Ting Wang ◽  
Li Liu ◽  
Jun-Jie Luo ◽  
Yu-Feng Gu ◽  
Si-Si Chen ◽  
...  
Keyword(s):  
Morphological Traits ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Open Science ◽  
Systematic Classification ◽  
Spore Ornamentation ◽  
Shared Data ◽  
Phylogenetic Studies ◽  
Crucial Component ◽  
Molecular Phylogenetic

With the development of open science and technological innovation, using sharing data and molecular biology techniques in the study of taxonomy and systematics have become a crucial component of plants, which undoubtedly helps us discover more hidden outliers or deal with difficult taxa. In this paper, we take Dennstaedtia smithii as an example, based on sharing molecular database, virtual herbarium and plant photo bank, to clarify the outliers that have been hidden in Dennstaedtia and find the key morphological traits with consistent of molecular systematics. In molecular phylogenetic analyses, we used rbcL, rps4, psbA-trnH and trnL-F sequences from 5 new and 49 shared data; the results showed that Dennstaedtia smithii is nested within Microlepia rather than Dennstaedtia. We further studied the morphological characters based on the phylogeny result and found that D. smithii is distinguished from other species of Dennstaedtia by spore ornamentation and the unconnected of grooves between rachis and pinna rachis. According to morphological and molecular phylogenetic studies, our results supported that D. smithii should be a new member of Microlepia and renamed Microlepia smithii (Hook.) Y.H. Yan. Finding hidden outliers can promote the consistency of morphological and molecular phylogenetic results, and make the systematic classification more natural.

Molecular evidence confirms that Proctoeces humboldti and Proctoeces chilensis (Digenea: Fellodistomidae) are the same species

2010 ◽  
Vol 84 (4) ◽  
pp. 341-347 ◽  
Author(s):  
I.M. Valdivia ◽  
L. Cardenas ◽  
K. Gonzalez ◽  
D. Jofré ◽  
M. George-Nascimento ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genetic Information ◽  
Intestinal Parasite ◽  
Phylogenetic Analyses ◽  
Marine Organisms ◽  
Molecular Evidence ◽  
Rrna Gene ◽  
Taxonomic Identification ◽  
Ssu Rrna ◽  
Phylogenetic Studies

AbstractTwo species of Proctoeces Odhner, 1911 have been described in marine organisms from Chile: P. humboldti George-Nascimento & Quiroga (1983), parasitizing the gonads of keyhole limpets (Fissurella spp.), and P. chilensis Oliva (1984), an intestinal parasite of Sicyases sanguineus (Teleostei); both species were subsequently considered as P. lintoni Siddiqi & Cable (1960). To assist in the resolution of the taxonomic identification of Proctoeces species in marine organisms from Chile, phylogenetic studies using DNA sequences from the V4 region of the SSU rRNA gene were performed. Several specimens of P. lintoni were isolated from keyhole limpets (Fissurella spp.) and clingfish (S. sanguineus) from Bahia San Jorge (23°40′S) and Bahia Concepción (36°50′S). Phylogenetic analyses were conducted using three different approaches: a neighbour-joining (NJ), a maximum likelihood (ML) and Bayesian inference (BI). The phylogenetic analysis confirms that specimens of Proctoeces obtained from keyhole limpets and those specimens from the clingfish are in fact the same species. We prefer to consider our specimens as Proctoeces cf. lintoni, as the morphology of Proctoeces appears to be of doubtful value and genetic information about P. lintoni Siddiqi & Cable (1960) is not available. In addition, our results strongly suggest that there are at least three species in this genus.

scholarly journals Phylogenetic Analysis of the North American Beetle GenusTrichiotinus(Coleoptera: Scarabaeidae: Trichiinae)

2016 ◽  
Vol 2016 ◽  
pp. 1-9
Author(s):  
T. Keith Philips ◽  
Mark Callahan ◽  
Jesús Orozco ◽  
Naomi Rowland
Keyword(s):  
North American ◽  
Morphological Traits ◽  
Evolutionary History ◽  
Morphological Character ◽  
The Other ◽  
The North ◽  
Species Of Conservation Concern ◽  
History Of ◽  
Conservation Concern ◽  
East West

A hypothesized evolutionary history of the North American endemic trichiine scarab genusTrichiotinusis presented including all eight species and three outgroup taxa. Data from nineteen morphological traits and CO1 and 28S gene sequences were used to construct phylogenies using both parsimony and Bayesian algorithms. All results show thatTrichiotinusis monophyletic. The best supported topology shows that the basal speciesT. lunulatusis sister to the remaining taxa that form two clades, with four and three species each. The distribution of one lineage is relatively northern while the other is generally more southern. The ancestralTrichiotinuslineage arose from 23.8–14.9 mya, and east-west geographic partitioning of ancestral populations likely resulted in cladogenesis and new species creation, beginning as early as 10.6–6.2 mya and as recently as 1.2–0.7 mya. Morphological character evolution is also briefly discussed. The limited distribution ofT. rufobrunneusin Florida andT. viridansin the Midwest mainly due to urban development and widespread agriculture makes these two species of conservation concern.

scholarly journals Molecular phylogeny and evolutionary history ofMoricandiaDC (Brassicaceae)

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3964 ◽  
Author(s):  
Francisco Perfectti ◽  
José M. Gómez ◽  
Adela González-Megías ◽  
Mohamed Abdelaziz ◽  
Juan Lorite
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Internal Transcribed Spacers ◽  
Arid Environments ◽  
East Central ◽  
F Region ◽  
Phylogenetic Studies ◽  
Mediterranean Regions ◽  
Southern Mediterranean ◽  
African Clade

BackgroundThe phylogeny of tribe Brassiceae (Brassicaceae) has not yet been resolved because of its complex evolutionary history. This tribe comprises economically relevant species, including the genusMoricandiaDC. This genus is currently distributed in North Africa, Middle East, Central Asia and Southern Europe, where it is associated with arid and semi-arid environments. Although some species ofMoricandiahave been used in several phylogenetic studies, the phylogeny of this genus is not well established.MethodsHere we present a phylogenetic analysis of the genusMoricandiausing a nuclear (the internal transcribed spacers of the ribosomal DNA) and two plastidial regions (parts of the NADH dehydrogenase subunit F gene and thetrnT-trnF region). We also included in the analyses members of their sister genusRytidocarpusand from the close genusEruca.ResultsThe phylogenetic analyses showed a clear and robust phylogeny of the genusMoricandia. The Bayesian inference tree was concordant with the maximum likelihood and timing trees, with the plastidial and nuclear trees showing only minor discrepancies. The genusMoricandiaappears to be formed by two main lineages: the Iberian clade including three species, and the African clade including the four species inhabiting the Southern Mediterranean regions plusM. arvensis.DiscussionWe dated the main evolutionary events of this genus, showing that the origin of the Iberian clade probably occurred after a range expansion during the Messinian period, between 7.25 and 5.33 Ma. In that period, an extensive African-Iberian floral and faunal interchange occurred due to the existence of land bridges between Africa and Europa in what is, at present-days, the Strait of Gibraltar. We have demonstrated that a Spanish population previously ascribed toRytidocarpus moricandioidesis indeed aMoricandiaspecies, and we propose to name it asM. rytidocarpoidessp. nov. In addition, in all the phylogenetic analyses,M. foleyiappeared outside theMoricandialineage but within the genusEruca. Therefore,M. foleyishould be excluded from the genusMoricandiaand be ascribed, at least provisionally, to the genusEruca.

scholarly journals Nephromyces represents a diverse and novel lineage of the Apicomplexa that has retained apicoplasts

2019 ◽  
Author(s):  
Sergio A Muñoz-Gómez ◽  
Keira Durnin ◽  
Laura Eme ◽  
Christopher Paight ◽  
Christopher E Lane ◽  
...  
Keyword(s):  
Life Style ◽  
Metabolic Pathways ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Biosynthetic Pathways ◽  
History Of ◽  
Sea Squirts ◽  
Shed Light ◽  
Apicoplast Genome

Abstract A most interesting exception within the parasitic Apicomplexa is Nephromyces, an extracellular, probably mutualistic, endosymbiont found living inside molgulid ascidian tunicates (i.e., sea squirts). Even though Nephromyces is now known to be an apicomplexan, many other questions about its nature remain unanswered. To gain further insights into the biology and evolutionary history of this unusual apicomplexan, we aimed to (1) find the precise phylogenetic position of Nephromyces within the Apicomplexa, (2) search for the apicoplast genome of Nephromyces, and (3) infer the major metabolic pathways in the apicoplast of Nephromyces. To do this, we sequenced a metagenome and a metatranscriptome from the molgulid renal sac, the specialized habitat where Nephromyces thrives. Our phylogenetic analyses of conserved nucleus-encoded genes robustly suggest that Nephromyces is a novel lineage sister to the Hematozoa, which comprises both the Haemosporidia (e.g., Plasmodium) and the Piroplasmida (e.g., Babesia and Theileria). Furthermore, a survey of the renal sac metagenome revealed 13 small contigs that closely resemble the genomes of the non-photosynthetic reduced plastids, or apicoplasts, of other apicomplexans. We show that these apicoplast genomes correspond to a diverse set of most closely related but genetically divergent Nephromyces lineages that co-inhabit a single tunicate host. In addition, the apicoplast of Nephromyces appears to have retained all biosynthetic pathways inferred to have been ancestral to parasitic apicomplexans. Our results shed light on the evolutionary history of the only probably mutualistic apicomplexan known, Nephromyces, and provide context for a better understanding of its life style and intricate symbiosis.

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