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 Semiaquilegia danxiashanensis (Ranunculaceae), a new species from Danxia Shan in Guangdong, southern China

Phytotaxa ◽  
2019 ◽  
Vol 405 (1) ◽  
pp. 1 ◽  
Author(s):  
JIAN-JUN ZHOU ◽  
ZHANG-PING HUANG ◽  
JIA-HUI LI ◽  
SCOTT HODGES ◽  
WEI-SHENG DENG ◽  
...  
Keyword(s):  
New Species ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Separate Species ◽  
F Region ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
Nuclear Its ◽  
A New Species ◽  
Northern Guangdong

Based on morphological and molecular phylogenetic studies, Semiaquilegia danxiashanensis, a new species from Danxia Shan in northern Guangdong, southern China, is described and illustrated. This species is easily distinguishable from each of other three known species in the genus by characters of the flowers and fruits. In addition, molecular phylogenetic analyses of both the nuclear ITS and the plastid trnL-F region strongly supported S. danxiashanensis as a separate species from other species of Semiaquilegia. We provide a detailed morphological and habitat description, distribution, as well as colour photographs and illustrations of the new species.

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 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.

scholarly journals The first mitochondrial genome of the genus Exhippolysmata (Decapoda: Caridea: Lysmatidae), with gene rearrangements and phylogenetic associations in Caridea

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ying-ying Ye ◽  
Jing Miao ◽  
Ya-hong Guo ◽  
Li Gong ◽  
Li-hua Jiang ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Bootstrap Support ◽  
Trna Genes ◽  
Gene Rearrangements ◽  
Phylogenetic Studies ◽  
Gc Skew ◽  
Strong Bootstrap Support

AbstractThe complete mitochondrial genome (mitogenome) of animals can provide useful information for evolutionary and phylogenetic analyses. The mitogenome of the genus Exhippolysmata (i.e., Exhippolysmata ensirostris) was sequenced and annotated for the first time, its phylogenetic relationship with selected members from the infraorder Caridea was investigated. The 16,350 bp mitogenome contains the entire set of 37 common genes. The mitogenome composition was highly A + T biased at 64.43% with positive AT skew (0.009) and negative GC skew (− 0.199). All tRNA genes in the E. ensirostris mitogenome had a typical cloverleaf secondary structure, except for trnS1 (AGN), which appeared to lack the dihydrouridine arm. The gene order in the E. ensirostris mitogenome was rearranged compared with those of ancestral decapod taxa, the gene order of trnL2-cox2 changed to cox2-trnL2. The tandem duplication-random loss model is the most likely mechanism for the observed gene rearrangement of E. ensirostris. The ML and BI phylogenetic analyses place all Caridea species into one group with strong bootstrap support. The family Lysmatidae is most closely related to Alpheidae and Palaemonidae. These results will help to better understand the gene rearrangements and evolutionary position of E. ensirostris and lay a foundation for further phylogenetic studies of Caridea.

Akamboja gen. nov., a new genus of railroad-worm beetle endemic to the Atlantic Rainforest, with five new species (Coleoptera: Phengodidae, Mastinocerinae)

Zootaxa ◽  
2017 ◽  
Vol 4306 (4) ◽  
pp. 501 ◽  
Author(s):  
ANDRÉ SILVA ROZA ◽  
HINGRID YARA SOUZA QUINTINO ◽  
JOSÉ RICARDO MIRAS MERMUDES ◽  
LUIZ FELIPE LIMA DA SILVEIRA
Keyword(s):  
New Species ◽  
Evolutionary History ◽  
New Genus ◽  
Landscape Heterogeneity ◽  
Atlantic Rainforest ◽  
Disjunct Distribution ◽  
Key To Species ◽  
Diagnostic Features ◽  
Mountain Ranges ◽  
Phylogenetic Studies

The Atlantic Rainforest is a hotspot of biodiversity, housing several endemic species. Environmental stasis through broad time scales, vast latitudinal extension and landscape heterogeneity are thought to contribute in explaining the greater species richness of this biome. Unfortunately, it is threatened mainly due to anthropic-driven habitat loss. Ectotherms of low-mobility, such as tropical, small soft-bodied railroad-worms, may be especially threatened by anthropogenic climate changes. Many of such species have narrow climatic niches and therefore might become extinct before we know them. Here we describe a new genus endemic of the Atlantic Rainforest mountain ranges, and five spatially disjunct new species. Akamboja gen. nov. is unique by its ten-segmented antenna, IV to VIII with two short symmetrical branches, branches of antennomere IX fused in a singular flabellum, slightly depressed medially; elytron short, surpassing the second to fourth abdominal segment (depending on species); first tarsomere of anterior leg with a ventral comb; claws with six long and asymmetrical teeth; aedeagus with patch of bristles at paramere apex. We provide a key to species as well as illustrations for the diagnostic features. We highlight that Akamboja cleidae sp. nov., as defined here, has a disjunct distribution and its populations are surrounded by an unsuitable environmental matrix, thus are probably reproductively isolated. Future phylogenetic studies should address the evolutionary history and delimitation of this taxon. We also provide a key to genera of Mastinocerinae with ten antennomeres, including Akamboja gen. nov. 

scholarly journals Optimal markers for the identification ofColletotrichumspecies

2019 ◽  
Author(s):  
Willie Anderson dos Santos Vieira ◽  
Priscila Alves Bezerra ◽  
Anthony Carlos da Silva ◽  
Josiene Silva Veloso ◽  
Marcos Paz Saraiva Câmara ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Species Complex ◽  
Plant Pathogens ◽  
Phylogenetic Signal ◽  
Intergenic Spacer ◽  
Internal Transcribed Spacers ◽  
Type Locus ◽  
Phylogenetic Studies ◽  
Fungal Plant Pathogens ◽  
Species Complexes

ABSTRACTColletotrichumis among the most important genera of fungal plant pathogens. Molecular phylogenetic studies over the last decade have resulted in a much better understanding of the evolutionary relationships and species boundaries within the genus. There are now approximately 200 species accepted, most of which are distributed among 13 species complexes. Given their prominence on agricultural crops around the world, rapid identification of a large collection ofColletotrichumisolates is routinely needed by plant pathologists, regulatory officials, and fungal biologists. However, there is no agreement on the best molecular markers to discriminate species in each species complex. Here we calculate the barcode gap distance and intra/inter-specific distance overlap to evaluate each of the most commonly applied molecular markers for their utility as a barcode for species identification. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone-3 (HIS3), DNA lyase (APN2), intergenic spacer between DNA lyase and the mating-type locusMAT1-2-1 (APN2/MAT-IGS), and intergenic spacer between GAPDH and a hypothetical protein (GAP2-IGS) have the properties of good barcodes, whereas sequences of actin (ACT), chitin synthase (CHS-1) and nuclear rDNA internal transcribed spacers (nrITS) are not able to distinguish most species. Finally, we assessed the utility of these markers for phylogenetic studies using phylogenetic informativeness profiling, the genealogical sorting index (GSI), and Bayesian concordance analyses (BCA). Although GAPDH, HIS3 and β-tubulin (TUB2) were frequently among the best markers, there was not a single set of markers that were best for all species complexes. Eliminating markers with low phylogenetic signal tends to decrease uncertainty in the topology, regardless of species complex, and leads to a larger proportion of markers that support each lineage in the Bayesian concordance analyses. Finally, we reconstruct the phylogeny of each species complex using a minimal set of phylogenetic markers with the strongest phylogenetic signal and find the majority of species are strongly supported as monophyletic.

scholarly journals A test statistic to quantify treelikeness in phylogenetics

2021 ◽  
Author(s):  
Caitlin Cherryh ◽  
Bui Quang Minh ◽  
Rob Lanfear
Keyword(s):  
Evolutionary History ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Phylogenetic Network ◽  
Parametric Bootstrap ◽  
Lineage Sorting ◽  
Test Statistic ◽  
Sequence Alignments ◽  
Wide Range ◽  
History Of

AbstractMost phylogenetic analyses assume that the evolutionary history of an alignment (either that of a single locus, or of multiple concatenated loci) can be described by a single bifurcating tree, the so-called the treelikeness assumption. Treelikeness can be violated by biological events such as recombination, introgression, or incomplete lineage sorting, and by systematic errors in phylogenetic analyses. The incorrect assumption of treelikeness may then mislead phylogenetic inferences. To quantify and test for treelikeness in alignments, we develop a test statistic which we call the tree proportion. This statistic quantifies the proportion of the edge weights in a phylogenetic network that are represented in a bifurcating phylogenetic tree of the same alignment. We extend this statistic to a statistical test of treelikeness using a parametric bootstrap. We use extensive simulations to compare tree proportion to a range of related approaches. We show that tree proportion successfully identifies non-treelikeness in a wide range of simulation scenarios, and discuss its strengths and weaknesses compared to other approaches. The power of the tree-proportion test to reject non-treelike alignments can be lower than some other approaches, but these approaches tend to be limited in their scope and/or the ease with which they can be interpreted. Our recommendation is to test treelikeness of sequence alignments with both tree proportion and mosaic methods such as 3Seq. The scripts necessary to replicate this study are available at https://github.com/caitlinch/treelikeness

scholarly journals The genus Microniphargus (Crustacea, Amphipoda): evidence for three lineages distributed across northwestern Europe and transfer from Niphargidae to Pseudoniphargidae

2021 ◽  
Vol 151 ◽  
Author(s):  
Dieter Weber ◽  
Fabio Stoch ◽  
Lee R.F.D. Knight ◽  
Claire Chauveau ◽  
Jean-François Flot
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Phylogenetic Analyses ◽  
Ribosomal Gene ◽  
Phylogenetic Position ◽  
Mitochondrial Cytochrome ◽  
Monotypic Genus ◽  
Centre Of Origin ◽  
Phylogenetic Studies ◽  
The Family

Microniphargus leruthi Schellenberg, 1934 (Amphipoda: Niphargidae) was first described based on samples collected in Belgium and placed in a monotypic genus within the family Niphargidae. However, some details of its morphology as well as recent phylogenetic studies suggest that Microniphargus may be more closely related to Pseudoniphargus (Amphipoda: Pseudoniphargidae) than to Niphargus. Moreover, M. leruthi ranges over 1,469 km from Ireland to Germany, which is striking since only a few niphargids have confirmed ranges in excess of 200 km. To find out the phylogenetic position of M. leruthi and check whether it may be a complex of cryptic species, we collected material from Ireland, England and Belgium then sequenced fragments of the mitochondrial cytochrome c oxidase subunit 1 gene as well as of the nuclear 28S ribosomal gene. Phylogenetic analyses of both markers confirm that Microniphargus is closer to Pseudoniphargus than to Niphargus, leading us to reallocate Microniphargus to Pseudoniphargidae. We also identify three congruent mito-nuclear lineages present respectively in Ireland, in both Belgium and England, and in England only (with the latter found in sympatry at one location), suggesting that M. leruthi is a complex of at least three species with a putative centre of origin in England.

scholarly journals Morphometric and phylogenetic analyses of the Paleozoic Subulitoidea (Gastropoda)

1992 ◽  
Vol 6 ◽  
pp. 93-93
Author(s):  
Douglas H. Erwin
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Temporal Trends ◽  
Thin Sections ◽  
Middle Ordovician ◽  
Shell Form ◽  
External Shell ◽  
Morphometric Analyses ◽  
Angular Measurements ◽  
Permian Mass Extinction

The gastropod superfamily Subulitoidea first appeared during the Early-Middle Ordovician gastropod radiation, seemingly from within the pleurotomarid family Lophospiridea, and persisted with low diversity and generally low abundance through the Paleozoic. One species survived the end-Permian mass extinction, but like many other Paleozoic remnants, the clade became extinct in the mid-Triassic. Many members of the clade are homeomorphic with later ‘neogastropods' and have frequently been fingered as the ancestors of these later, predatory gastropods. There is however, no direct evidence for an ancestor-descendent relationship. Addressing this possibility and understanding of the systematics and evolutionary history of the clade has been complicated by relatively simple shell form and apparent paucity of shell characters. The strength of the morphological and probable ecologic similarities between subulitids and ‘neogastropods' raises the question why this clade was unable to capitalize on their position as perhaps the only predatory gastropods during the Paleozoic. Such questions of evolutionary history are best addressed within the context of a combination of morphometric and phylogenetic analyses which may resolve the systematic questions and reveal something of the evolutionary relationships of the clade.Morphometric analyses were performed on some 40 specimens covering the 13 described genera (and several undescribed forms). Both linear and angular measurements of external shell form and internal structure from axial thin sections were measured and apertures were analyzed using elliptical Fourier analysis (EFA). The number of specimens analyzed was intentionally limited because of difficulties obtaining specimens with sufficient preservation of the aperture. The results demonstrate the necessity, for this clade at least, of including a more complex description of apertural morphology than simple maximum length and width. Principle component analyses of the EFA data distinguishes complexity of the columellar folds along the first axis and basal rounding along the second - both biologically meaningful aspects of apertural form. Moreover, the occupation of a taxon-specific apertural space defined by the PCA increases through the Paleozoic. Further, the analyses suggest that the two traditionally recognized subfamilies of the Subulitidae (Ordovician-Devonian and Devonian-Triassic) each exhibit increased variance in the occupation of morphologic space, but additional data is required to confirm this pattern and determine if any temporal trends exist.Analyzing patterns of occupation of morphologic space requires a rigorously constructed phylogeny. A cladistic (parsimony) analysis of the superfamily was performed using 16 taxa and over 30 discrete morphologic characters. The resulting cladograms were plotted within the taxon-specific morphospaces produced by the morphometric analyses.

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