scholarly journals Phylogenetic analysis of ITS sequences suggests a Pliocene origin for the bipolar distribution of Scleranthus (Caryophyllaceae)

2003 ◽  
Vol 16 (3) ◽  
pp. 301 ◽  
Author(s):  
R. D. Smissen ◽  
P. J. Garnock-Jones ◽  
G. K. Chambers
Keyword(s):  
Sequence Data ◽  
Its Sequence ◽  
Data Sets ◽  
Long Distance Dispersal ◽  
Lineage Sorting ◽  
Long Distance ◽  
The Family ◽  
Alternative Hypotheses ◽  
Bipolar Distribution ◽  
Recent Origin

Scleranthus is a genus of about 12 species of herbaceous plants or subshrubs native to Eurasia and Australasia. Here Scleranthus is shown to consist of European and Australasian clades, which diverged within the last 10 million years. Biogeographic implications of this dating and alternative hypotheses explaining the disjunct north–south distribution of the genus, are discussed. The trans-Tasman distributions of S. biflorus and S. brockiei are of recent origin and therefore consistent with long-distance dispersal rather than vicariance explanations. Morphological and ITS sequence data sets are significantly incongruent and trees derived from them differ over relationships among Australasian species. Hybridisation and introgression or lineage sorting are invoked to explain this discordance. Within the family Caryophyllaceae, Scleranthus ITS2 sequences have greater similarity to sequences from representatives of the subfamilies Alsinoideae and Caryophylloideae than to sequences from representatives of the subfamily Paronychioideae.

First freshwater gastropod preserved in amber suggests long-distance dispersal during the Cretaceous Period

2021 ◽  
pp. 1-8
Author(s):  
Tingting Yu ◽  
Thomas A. Neubauer ◽  
Adrienne Jochum
Keyword(s):  
New Species ◽  
Freshwater Snail ◽  
Aquatic Biota ◽  
Long Distance Dispersal ◽  
Long Distance ◽  
Burmese Amber ◽  
Freshwater Gastropod ◽  
The Family ◽  
Cretaceous Period ◽  
Globally Distributed

Abstract Burmese amber continues to provide unique insights into the terrestrial biota inhabiting tropical equatorial forests during mid-Cretaceous time. In contrast to the large amount and great diversity of terrestrial species retrieved so far, aquatic biota constitute rare inclusions. Here we describe the first freshwater snail ever preserved in amber. The new species Galba prima sp. nov. belongs in the family Lymnaeidae, today a diverse and near globally distributed family. Its inclusion in terrestrial amber is probably a result of the amphibious lifestyle typical of modern representatives of the genus. The finding of a freshwater snail on the Burma Terrane, back then an island situated at some 1500 km from mainland Asia, has implications for the dispersal mechanisms of Mesozoic lymnaeids. The Cenomanian species precedes the evolution of waterfowl, which are today considered a main vector for long-distance dispersal. In their absence, we discuss several hypotheses to explain the disjunct occurrence of the new species.

scholarly journals A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis

2019 ◽  
Vol 37 (4) ◽  
pp. 1211-1223 ◽  
Author(s):  
Tomáš Flouri ◽  
Xiyun Jiao ◽  
Bruce Rannala ◽  
Ziheng Yang
Keyword(s):  
Gene Flow ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Mosquito Species ◽  
Phylogenomic Analysis ◽  
Data Sets ◽  
Lineage Sorting ◽  
Coalescent Model ◽  
Multispecies Coalescent

Abstract Recent analyses suggest that cross-species gene flow or introgression is common in nature, especially during species divergences. Genomic sequence data can be used to infer introgression events and to estimate the timing and intensity of introgression, providing an important means to advance our understanding of the role of gene flow in speciation. Here, we implement the multispecies-coalescent-with-introgression model, an extension of the multispecies-coalescent model to incorporate introgression, in our Bayesian Markov chain Monte Carlo program Bpp. The multispecies-coalescent-with-introgression model accommodates deep coalescence (or incomplete lineage sorting) and introgression and provides a natural framework for inference using genomic sequence data. Computer simulation confirms the good statistical properties of the method, although hundreds or thousands of loci are typically needed to estimate introgression probabilities reliably. Reanalysis of data sets from the purple cone spruce confirms the hypothesis of homoploid hybrid speciation. We estimated the introgression probability using the genomic sequence data from six mosquito species in the Anopheles gambiae species complex, which varies considerably across the genome, likely driven by differential selection against introgressed alleles.

Origin of Symphyotrichum anticostense (Asteraceae: Astereae), an endemic, high polyploid species of the Gulf of St. Lawrence region, based on morphological and nrDNA evidence

Botany ◽  
2022 ◽  
Author(s):  
Jamil Vaezi ◽  
Luc Brouillet
Keyword(s):  
New Brunswick ◽  
Multivariate Analyses ◽  
Sequence Data ◽  
Morphological Data ◽  
Its Sequence ◽  
Long Distance ◽  
High Polyploid ◽  
Geographic Origins ◽  
Anticosti Island ◽  
Rare Endemic

Symphyotrichum anticostense (Fernald) G.L.Nesom (Asteraceae: Astereae), a rare endemic of the Gulf of St. Lawrence region is a high allopolyploid (2n=10x=80). It has been hypothesized to be derived from the hybrid between tetraploid (2n=4x=32) individuals of S. boreale (Torr. & A.Gray) Löve & Löve and the hexaploid (2n=6x=48) S. novi-belgii (L.) G.L.Nesom. We investigated this hypothesis using morphological and molecular ITS-sequence data, and we tried to determine the potentially geographic origins of the taxon. Univariate morphological analyses show that 67.5% of the S. anticostense characters are parent-like, 43.5% from S. novi-belgii and 13% from S. boreale, the remainder not differing statistically from either parent; 23.5% are intermediate; and 9% transgressive. Multivariate analyses show that S. anticostense is intermediate between its putative parents. The molecular results support the morphological data, but due to the insufficient resolution among ribotypes on the tree, a more rapidly evolving marker will be needed to ascertain more reliably the origin of S. anticostense. Besides the hypothesis of genetic drift and allele fixation following long-distance dispersals, at least three independent geographic origins may be suggested for S. anticostense; Anticosti Island, Lake St. John, and Gaspé Peninsula-New Brunswick-Maine.

Molecular and Morphological evolution in the Physciaceae (Lecanorales, Lichenized Ascomycotina), with Special Emphasis on the Genus Rinodina

2001 ◽  
Vol 33 (1) ◽  
pp. 63-72 ◽  
Author(s):  
Martin Grube ◽  
Ulf Arup
Keyword(s):  
Sequence Data ◽  
Morphological Evolution ◽  
Chemical Compounds ◽  
Sister Group ◽  
Morphological Evidence ◽  
Its Sequence ◽  
The Family ◽  
Nuclear Its ◽  
Taxonomic Implications ◽  
Crustose Lichens

AbstractA phylogenetic hypothesis based on nuclear ITS sequence data is presented for the family Physciaceae based on various representatives of foliose and fruticose groups and a number of species selected from the crustose genera Rinodina and Buellia s.l. The analysis supports the monophyly of the Physcia- and the Buellia- groups. This is in agreement with existing morphological evidence, particularly ascus characters. The Physcia group in the analysis includes the genera Anaptychia, Heterodermia, Hyperphyscia, Mobergia, Phaeophyscia, Phaeorrhiza, Physcia, Physconia, Rinodina, and Rinodinella, while the Buellia group includes Amandinea, Buellia and Diploicia. The genera Physcia, Phaeophyscia, Phaeorrhiza and Rinodinella were well supported as monophyletic groups. The support for Physconia is low. Rinodina and Buellia are not supported as monophyletic genera. In agreement with ascus and ascospore characters, Buellia lindingeri is placed within the Rinodina group, close R. lecanorina. The genus Amandinea as currently circumscribed was not supported as a monophyletic group. The analysis confirms results from other lichen families that foliose members have evolved more than once from crustose lichens. Rinodina and Rinodinella species without chemical compounds in their thalli form the sister group to Phaeophyscia, and both groups form a monophyletic assemblage. A more detailed analysis of the Physcia group is presented. Whilst several of the foliose genera were well supported, there is only poor support for traditionally accepted crustose genera. The taxonomic implications of these findings are discussed.

PHYLOGENY, BIOGEOGRAPHY AND CHARACTER EVOLUTION OF DORSTENIA (MORACEAE)

2012 ◽  
Vol 69 (3) ◽  
pp. 413-440 ◽  
Author(s):  
T. M. Misiewicz ◽  
N. C. Zerega
Keyword(s):  
Maximum Likelihood ◽  
Life Form ◽  
Sequence Data ◽  
Morphological Characters ◽  
Molecular Dating ◽  
Its Sequence ◽  
The Family ◽  
Storage Organs ◽  
Woody Habit ◽  
Origin Hypothesis

Dorstenia, the second largest genus (105 species) within the Moraceae, is the only genus in the family with woody, herbaceous and succulent species. All but one species of Dorstenia are restricted to the Neotropics or Africa, and it is the only genus in the family with an almost equal transatlantic distribution. This work presents the first molecular phylogeny and the first evolutionary study to examine origin and diversification within the genus. We inferred the phylogeny with ITS sequence data using Bayesian and maximum likelihood approaches. We tracked the evolution of distinct morphological characters and tested for correlated evolution in multiple characters. Time and place of Dorstenia’s origin were estimated to test a post-Gondwanan versus a Gondwanan origin hypothesis using fossil calibrations, Bayesian molecular dating, and maximum likelihood-based ancestral range reconstructions. Our phylogenetic analysis supports the monophyly of Dorstenia; previous subgeneric classifications are polyphyletic and must be re-evaluated. Woody habit, phanerophytic life form, macrospermy, and lack of storage organs are ancestral traits found in African Dorstenia. Evolution of woodiness and macrospermy are correlated. Dorstenia appears to have originated in Africa, radiated into the Neotropics and subsequently re-colonised Africa. Whether or not the extant distribution is the result of vicariance or dispersal is equivocal.

A new family placement for Australian blue squill, Chamaescilla: Xanthorrhoeaceae (Hemerocallidoideae), not Asparagaceae

Phytotaxa ◽  
2016 ◽  
Vol 275 (2) ◽  
pp. 97 ◽  
Author(s):  
TODD G.B. McLAY ◽  
MICHAEL J. BAYLY
Keyword(s):  
Grain Shape ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Pollen Grain ◽  
Long Distance Dispersal ◽  
Long Distance ◽  
Dna Sequence Data ◽  
New Family ◽  
Australian Family

Chamaescilla is an endemic Australian genus, currently placed in the Asparagaceae, alongside other Australian endemic taxa in the tribe Lomandroideae. A recent molecular phylogeny indicated a relationship with another partly Australian family, the Xanthorrhoeaceae, but was not commented on by the authors. Here we added DNA sequence data for a single Chamaescilla specimen to an alignment representing all families in the Asparagales and performed parsimony and Bayesian phylogenetic analyses. Chamaescilla was strongly resolved as belonging to Xanthorrhoeaceae, subfamily Hemerocallidoideae, alongside two non-Australian members, Simethis and Hemerocallis in the hemerocallid clade. This position is corroborated by morphological characters, including pollen grain shape. We also produced an age-calibrated phylogeny and infer that the geographic distribution of the clade is the result of long distance dispersal between the Eocene and Miocene.

scholarly journals A taxonomic survey of monocotylar Apiaceae and the implications of their morphological diversity for their systematics and evolution

2019 ◽  
Vol 192 (3) ◽  
pp. 449-473
Author(s):  
Eugene V Kljuykov ◽  
Svetlana E Petrova ◽  
Galina V Degtjareva ◽  
Ekaterina A Zakharova ◽  
Tahir H Samigullin ◽  
...  
Keyword(s):  
Sequence Data ◽  
Parallel Evolution ◽  
Morphological Diversity ◽  
Evolutionary Significance ◽  
Its Sequence ◽  
Generic Level ◽  
Seedling Morphology ◽  
Potential Implication ◽  
New Findings ◽  
The Family

Abstract In Apiaceae, embryos of most species have two cotyledons, but some species are consistently monocotylar. Traditionally, the monocotyly has been considered as taxonomically important at the generic level, despite its presumably multiple origins in the family. In this study, a survey of the published literature and our new findings on cotyledon number, embryo and seedling morphology and nrDNA ITS sequence data are presented to provide modern insights into the taxonomic distribution and phylogenetic relationships of monocotylar taxa. A molecular phylogenetic tree representing much of the diversity of monocotylar Apiaceae was produced to re-evaluate the potential implication of monocotyly for systematics and to elucidate its evolutionary significance in the family. Our data document the presence of monocotylar seedlings in 59 species representing 15 genera, in three species and one genus (Postiella) of which monocotylar seedlings are reported for the first time. Analysis of ITS sequence data indicates that monocotyly in Apiaceae has arisen independently in at least seven different lineages encompassing five of 41 major clades of subfamily Apioideae, but not in early-diverging lineages. Parallel evolution has resulted in a remarkable morphological similarity in monocotylar embryo and seedling organization, especially in the proportion of the cotyledon length to the axis of the embryo and the multifunctional cotyledonary tube in the seedling. These features could be considered as adaptations to a geophilic life form, as all monocotylar species are perennial herbs with tuberous underground organs distributed mainly in the Ancient Mediterranean region. The single cotyledon in Apiaceae, as in most other monocotyledonous eudicots, could be interpreted as two united cotyledons (syncotyly), but further developmental studies are needed to test this hypothesis.

scholarly journals Cox2 community barcoding at Prince Edward Island reveals long-distance dispersal of a downy mildew species and potentially marine members of the Saprolegniaceae

2021 ◽  
Vol 20 (4) ◽  
pp. 509-516
Author(s):  
Julia A. F. Langer ◽  
Rahul Sharma ◽  
Bora Nam ◽  
Louis Hanic ◽  
Maarten Boersma ◽  
...  
Keyword(s):  
Prince Edward Island ◽  
Sequence Data ◽  
Marine Species ◽  
Global Ocean ◽  
Plankton Sample ◽  
Long Distance Dispersal ◽  
Long Distance ◽  
Marine Food Webs ◽  
Bona Fide ◽  
Globally Distributed

AbstractMarine oomycetes are highly diverse, globally distributed, and play key roles in marine food webs as decomposers, food source, and parasites. Despite their potential importance in global ocean ecosystems, marine oomycetes are comparatively little studied. Here, we tested if the primer pair cox2F_Hud and cox2-RC4, which is already well-established for phylogenetic investigations of terrestrial oomycetes, can also be used for high-throughput community barcoding. Community barcoding of a plankton sample from Brudenell River (Prince Edward Island, Canada), revealed six distinct oomycete OTU clusters. Two of these clusters corresponded to members of the Peronosporaceae—one could be assigned to Peronospora verna, an obligate biotrophic pathogen of the terrestrial plant Veronica serpyllifolia and related species, the other was closely related to Globisporangium rostratum. While the detection of the former in the sample is likely due to long-distance dispersal from the island, the latter might be a bona fide marine species, as several cultivable species of the Peronosporaceae are known to withstand high salt concentrations. Two OTU lineages could be assigned to the Saprolegniaceae. While these might represent marine species of the otherwise terrestrial genus, it is also conceivable that they were introduced on detritus from the island. Two additional OTU clusters were grouped with the early-diverging oomycete lineages but could not be assigned to a specific family. This reflects the current underrepresentation of cox2 sequence data which will hopefully improve with the increasing interest in marine oomycetes.

Phylogenomics Uncovers Confidence and Conflict in the Rapid Radiation of Australo-Papuan Rodents

2019 ◽  
Vol 69 (3) ◽  
pp. 431-444 ◽  
Author(s):  
Emily J Roycroft ◽  
Adnan Moussalli ◽  
Kevin C Rowe
Keyword(s):  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Signal ◽  
Strong Support ◽  
Bootstrap Support ◽  
Data Sets ◽  
Lineage Sorting ◽  
Nucleotide Sequence Data ◽  
Branch Support ◽  
Partitioning Strategy

Abstract The estimation of robust and accurate measures of branch support has proven challenging in the era of phylogenomics. In data sets of potentially millions of sites, bootstrap support for bifurcating relationships around very short internal branches can be inappropriately inflated. Such overestimation of branch support may be particularly problematic in rapid radiations, where phylogenetic signal is low and incomplete lineage sorting severe. Here, we explore this issue by comparing various branch support estimates under both concatenated and coalescent frameworks, in the recent radiation Australo-Papuan murine rodents (Muridae: Hydromyini). Using nucleotide sequence data from 1245 independent loci and several phylogenomic inference methods, we unequivocally resolve the majority of genus-level relationships within Hydromyini. However, at four nodes we recover inconsistency in branch support estimates both within and among concatenated and coalescent approaches. In most cases, concatenated likelihood approaches using standard fast bootstrap algorithms did not detect any uncertainty at these four nodes, regardless of partitioning strategy. However, we found this could be overcome with two-stage resampling, that is, across genes and sites within genes (using -bsam GENESITE in IQ-TREE). In addition, low confidence at recalcitrant nodes was recovered using UFBoot2, a recent revision to the bootstrap protocol in IQ-TREE, but this depended on partitioning strategy. Summary coalescent approaches also failed to detect uncertainty under some circumstances. For each of four recalcitrant nodes, an equivalent (or close to equivalent) number of genes were in strong support ($>$ 75% bootstrap) of both the primary and at least one alternative topological hypothesis, suggesting notable phylogenetic conflict among loci not detected using some standard branch support metrics. Recent debate has focused on the appropriateness of concatenated versus multigenealogical approaches to resolving species relationships, but less so on accurately estimating uncertainty in large data sets. Our results demonstrate the importance of employing multiple approaches when assessing confidence and highlight the need for greater attention to the development of robust measures of uncertainty in the era of phylogenomics.

MOLECULAR PHYLOGENY AND STRUCTURE PREDICTION OF RICE RFT1 PROTEIN

2016 ◽  
Vol 78 (2) ◽  
Author(s):  
Shahkila Mohd Arif ◽  
Abdulrahman Mahmoud Dogara ◽  
Nyuk Ling Ma ◽  
Mohd Shahir Shamsir Omar ◽  
Sepideh Parvizpour ◽  
...  
Keyword(s):  
Structure Prediction ◽  
Sequence Data ◽  
World Population ◽  
Data Sets ◽  
Important Species ◽  
The Family ◽  
Close Relationship ◽  
Protein Sequence Data ◽  
Flowering Time Gene ◽  
Mp Method

Rice is one of the most important species in the family of Poaceae. As one of the major crop that is consumed by world population, it is cultivated commercially in many parts of the world. Hence, the phylogeny study of this crop is crucial as a step for improvement of its breeding programs. Phylogenetic relationship among 12 rice cultivars that originated from two common sub-species; Indica and Japonica were inferred by comparing protein sequence data sets derived from its flowering time gene, namely RFT1 and analyzed using maximum parsimony (MP) method. The predicted structure of RFT1 protein was generated by I-TASSER server and analyzed using YASARA software. The result showed that the cultivars were classified into two major groups, where the first group (Japonica) evolved first followed by the second group (Indica). The findings suggested that some cultivars had a close relationship with each other even it is originates from different varieties. The relationships among these cultivars provide useful information for better understanding of molecular evolution process and designing good breeding program in order to generate new cultivar.

Sign in / Sign up

Export Citation Format

Share Document