Phylogenetic relationships and divergence times of the family Araucariaceae based on the DNA sequences of eight genes

2009 ◽  
Vol 54 (15) ◽  
pp. 2648-2655 ◽  
Author(s):  
Nian Liu ◽  
Yong Zhu ◽  
ZongXian Wei ◽  
Jie Chen ◽  
QingBiao Wang ◽  
...  
Zootaxa ◽  
2018 ◽  
Vol 4486 (3) ◽  
pp. 311 ◽  
Author(s):  
SEBASTIAN HOFMAN ◽  
ALEKSANDRA RYSIEWSKA ◽  
ARTUR OSIKOWSKI ◽  
JOZEF GREGO ◽  
BORIS SKET ◽  
...  

The family Moitessieriidae includes minute dioecious gastropods exclusively inhabiting subterranean waters, including thermal ones. Only empty shells were collected in most species, the vast majority of them are described from their gross shell morphology alone. Several visits to a site are usually required to obtain at least some living individuals. High variability in shell morphology and the lack of diagnostic features, coupled with anticipated high levels of endemism, has resulted in a long list of nominal moitessierid species. Type specimens stored as empty shells omit unambiguous identification and delimitation of species boundaries. Due to inaccessibility of cave animals and consequent lack of material suitable for molecular analysis, the phylogenetic relationships, as well as the taxonomy of the family at genus/species level, are far from being understood. The anatomy of the family is also poorly known and provided only for a few taxa. The distinctness of the Moitessieriidae has sometimes been questioned, and their monophyly not proved. Twelve species of the Balkan Moitessieriidae are considered: two species of Paladilhiopsis, two species of Bythiospeum, six species of Iglica, Costellina turrita and Lanzaia bosnica. The shell morphology of each species, as well as the reproductive system of Paladilhiopsis and Iglica, were analysed. DNA sequences of nuclear histone H3, ribosomal 18S, ribosomal 28S and mitochondrial cytochrome oxidase subunit I (COI) were applied to infer phylogenetic relationships among the taxa. The sequences of Bythiospeum from GenBank have been used to infer relationships between Bythiospeum and Paladilhiopsis that were recently synonymized. Paladilhiopsis and Iglica are distinct, but closely related genera, as is the genus Bythiospeum, which does not occur in the Balkans. Its relationships with both former taxa remain unresolved. The Moitessieriidae are clearly distinct from all other families of the Truncatelloidea, however, their monophyly remains doubtful. 


Diversity ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 361
Author(s):  
Luis Mamani ◽  
Juan C. Chaparro ◽  
Claudio Correa ◽  
Consuelo Alarcón ◽  
Cinthya Y. Salas ◽  
...  

The family Gymnophthalmidae is one of the most speciose lineages of lizards in the Neotropical region. Despite recent phylogenetic studies, the species diversity of this family is unknown and thus, its phylogenetic relationships remain unclear and its taxonomy unstable. We analyzed four mitochondrial (12S, 16S, Cytb, ND4) and one nuclear (c-mos) DNA sequences of Pholidobolus anomalus, Cercosaura manicata boliviana and Cercosaura sp., using the maximum likelihood method to give insights into the phylogenetic relationships of these taxa within Cercosaurinae. Our results suggest that Pholidolus anomalus is nested within the clade of Cercosaura spp., that material we collected near Oxapampa belongs to a new species of Cercosaura, and that lizards identified as Cercosaura manicata boliviana belong to a separate lineage, possibly a new genus. We assign Pholidobolus anomalus to Cercosaura, redescribe the species, and designate a neotype to replace the lost holotype. In addition, we describe the new species of Cercosaura, and comment about the taxonomic status of “Cercosaura manicata boliviana”incertae sedis.


2000 ◽  
Vol 17 (4) ◽  
pp. 527-537 ◽  
Author(s):  
Masanao Honda ◽  
Hidetoshi Ota ◽  
Mari Kobayashi ◽  
Jarujin Nabhitabhata ◽  
Hoi-Sen Yong ◽  
...  

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5168 ◽  
Author(s):  
Justin C. Bagley ◽  
Richard L. Mayden ◽  
Phillip M. Harris

Catostomidae (“suckers”) is a diverse (76 species) and broadly distributed family of Holarctic freshwater fishes with a rich fossil record and a considerable number (∼35%) of threatened and imperiled species. We integrate DNA sequences (three mitochondrial genes, three nuclear genes), morphological data, and fossil information to infer sucker phylogenetic relationships and divergence times using Bayesian “total-evidence” methods, and then test hypotheses about the temporal diversification of the group. Our analyses resolved many nodes within subfamilies and clarified Catostominae relationships to be of the form ((Thoburniini, Moxostomatini), (Erimyzonini, Catostomini)). Patterns of subfamily relationships were incongruent, but mainly supported two placements of the Myxocyprininae; distinguishing these using Bayes factors lent strongest support to a model with Myxocyprininae sister to all remaining sucker lineages. We improved our Bayesian total-evidence dating analysis by excluding problematic characters, using a clock-partitioning scheme identified by Bayesian model selection, and employing a fossilized birth-death tree prior accommodating morphological data and fossils. The resulting chronogram showed that suckers evolved since the Late Cretaceous–Eocene, and that the Catostomini and Moxostomatini clades have accumulated species diversity since the early to mid-Miocene. These results agree with the fossil record and confirm previous hypotheses about dates for the origins of Catostomide and catostomine diversification, but reject previous molecular hypotheses about the timing of divergence of ictiobines, and between Asian–North American lineages. Overall, our findings from a synthesis of multiple data types enhance understanding of the phylogenetic relationships, taxonomic classification, and temporal diversification of suckers, while also highlighting practical methods for improving Bayesian divergence dating models by coupling phylogenetic informativeness profiling with relaxed-clock partitioning.


2000 ◽  
Vol 17 (4) ◽  
pp. 527-537 ◽  
Author(s):  
Masanao Honda ◽  
Hidetoshi Ota ◽  
Mari Kobayashi ◽  
Jarujin Nabhitabhata ◽  
Hoi-Sen Yong ◽  
...  

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1645-1656 ◽  
Author(s):  
Bruce Rannala ◽  
Ziheng Yang

Abstract The effective population sizes of ancestral as well as modern species are important parameters in models of population genetics and human evolution. The commonly used method for estimating ancestral population sizes, based on counting mismatches between the species tree and the inferred gene trees, is highly biased as it ignores uncertainties in gene tree reconstruction. In this article, we develop a Bayes method for simultaneous estimation of the species divergence times and current and ancestral population sizes. The method uses DNA sequence data from multiple loci and extracts information about conflicts among gene tree topologies and coalescent times to estimate ancestral population sizes. The topology of the species tree is assumed known. A Markov chain Monte Carlo algorithm is implemented to integrate over uncertain gene trees and branch lengths (or coalescence times) at each locus as well as species divergence times. The method can handle any species tree and allows different numbers of sequences at different loci. We apply the method to published noncoding DNA sequences from the human and the great apes. There are strong correlations between posterior estimates of speciation times and ancestral population sizes. With the use of an informative prior for the human-chimpanzee divergence date, the population size of the common ancestor of the two species is estimated to be ∼20,000, with a 95% credibility interval (8000, 40,000). Our estimates, however, are affected by model assumptions as well as data quality. We suggest that reliable estimates have yet to await more data and more realistic models.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Maria Alejandra Serna-Sánchez ◽  
Oscar A. Pérez-Escobar ◽  
Diego Bogarín ◽  
María Fernanda Torres-Jimenez ◽  
Astrid Catalina Alvarez-Yela ◽  
...  

AbstractRecent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth–death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.


Genome ◽  
2010 ◽  
Vol 53 (10) ◽  
pp. 769-777 ◽  
Author(s):  
Melanie Mehes-Smith ◽  
Paul Michael ◽  
Kabwe Nkongolo

Genome organization in the family Pinaceae is complex and largely unknown. The main purpose of the present study was to develop and physically map species-diagnostic and species-specific molecular markers in pine and spruce. Five RAPD (random amplified polymorphic DNA) and one ISSR (inter-simple sequence repeat) species-diagnostic or species-specific markers for Picea mariana , Picea rubens , Pinus strobus , or Pinus monticola were identified, cloned, and sequenced. In situ hybridization of these sequences to spruce and pine chromosomes showed the sequences to be present in high copy number and evenly distributed throughout the genome. The analysis of centromeric and telomeric regions revealed the absence of significant clustering of species-diagnostic and species-specific sequences in all the chromosomes of the four species studied. Both RAPD and ISSR markers showed similar patterns.


2002 ◽  
Vol 11 (2) ◽  
pp. 169-174 ◽  
Author(s):  
Peggy S. M. Hill ◽  
Cara Hoffart ◽  
Mark Buchheim

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