scholarly journals Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi

1999 ◽  
Vol 266 (1415) ◽  
pp. 163-171 ◽  
Author(s):  
Daniel Y.-C. Wang ◽  
Sudhir Kumar ◽  
S. Blair Hedges
Keyword(s):  
Divergence Time ◽  
Early History ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Animal Phyla ◽  
History Of

scholarly journals Morphological and molecular phylogenetic analyses of Zepedanulus ishikawai (Arachnida: Opiliones: Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago

2021 ◽  
pp. 1-28
Author(s):  
Yoshimasa Kumekawa ◽  
Haruka Fujimoto ◽  
Osamu Miura ◽  
Ryo Arakawa ◽  
Jun Yokoyama ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Morphological Characters ◽  
Ryukyu Archipelago ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Polymerase Chain

Abstract Harvestmen (Arachnida: Opiliones) are soil animals with extremely low dispersal abilities that experienced allopatric differentiation. To clarify the morphological and phylogenetic differentiation of the endemic harvestman Zepedanulus ishikawai (Suzuki, 1971) (Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago, we conducted molecular phylogenetic analyses and divergence time estimates based on CO1 and 16S rRNA sequences of mtDNA, the 28S rRNA sequence of nrDNA, and the external morphology. A phylogenetic tree based on mtDNA sequences indicated that individuals of Z. ishikawai were monophyletic and were divided into clade I and clade II. This was supported by the nrDNA phylogenetic tree. Although clades I and II were distributed sympatrically on all three islands examined (Ishigaki, Iriomote, and Yonaguni), heterogeneity could not be detected by polymerase chain reaction–restriction fragment length polymorphism of nrDNA, indicating that clades I and II do not have a history of hybridisation. Also, several morphological characters differed significantly between individuals of clade I and clade II. The longstanding isolation of the southern Ryukyus from the surrounding islands enabled estimation of the original morphological characters of both clades of Z. ishikawai.

scholarly journals Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes

2020 ◽  
Author(s):  
Alexandre Hassanin ◽  
Géraldine Véron ◽  
Anne Ropiquet ◽  
Bettine Jansen van Vuuren ◽  
Alexis Lécu ◽  
...  
Keyword(s):  
Divergence Time ◽  
Mitochondrial Genomes ◽  
Fossil Calibration ◽  
Divergence Time Estimates ◽  
Early Eocene Climatic Optimum ◽  
Time Estimates ◽  
History Of ◽  
Nucleotide Divergence ◽  
Final Alignment ◽  
Complete Mitochondrial Genomes

AbstractThe order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversifications are still a matter of debate.Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of Carnivora. We assembled 51 new mitogenomes from 13 families, and aligned them with available mitogenomes by selecting only those showing more than 1% of nucleotide divergence and excluding those suspected to be of low-quality or from misidentified taxa. Our final alignment included 220 taxa representing 2,442 mitogenomes. Our analyses led to a robust resolution of suprafamilial and intrafamilial relationships. We identified 22 fossil calibration points to estimate a molecular timescale for carnivorans. According to our divergence time estimates, crown carnivorans appeared during or just after the Early Eocene Climatic Optimum; all major groups of Caniformia (Cynoidea/Arctoidea; Ursidae; Musteloidea/Pinnipedia) diverged from each other during the Eocene, while all major groups of Feliformia (Nandiniidae; Feloidea; Viverroidea) diversified more recently during the Oligocene, with a basal divergence of Nandinia at the Eocene/Oligocene transition; intrafamilial divergences occurred during the Miocene, except for the Procyonidae, as Potos separated from other genera during the Oligocene.

scholarly journals Mountains as Islands: Species Delimitation and Evolutionary History of the Ant-Loving Beetle Genus Panabachia (Coleoptera, Staphylinidae) from the Northern Andes

Insects ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 64
Author(s):  
Sofía Muñoz-Tobar ◽  
Michael Caterino
Keyword(s):  
Species Delimitation ◽  
Divergence Time ◽  
Morphological Characters ◽  
Protein Coding ◽  
Widespread Species ◽  
Mitochondrial Coi ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Putative Species ◽  
History Of

The ant-loving beetle genus Panabachia Park 1942 is a poorly studied beetle lineage from the new world tropics. We recently collected Panabachia from several previously unrecorded locations in the páramo biome of the high Ecuadorian Andes, with males exhibiting great morphological variation in the distribution of the foveae and depressions in the pronotum, as well as aspects of the male genitalia. Here, we employ phylogenetic and species delimitation methods with mitochondrial (COI) and nuclear protein-coding (wingless) gene sequences to examine the concordance of morphological characters and geography with hypothesized species boundaries. Three methods of species delimitation (bPTP, GMYC and Stacey) were used to estimate the number of species, and divergence times between putative species using molecular clock calibration. Phylogenetic analysis revealed two parallel radiations, and species delimitation analyses suggest there are between 17 and 22 putative species. Based on clade support and concordance across species delimitation methods we hypothesize 17 distinct clusters, with allopatric speciation consistent with most geographic patterns. Additionally, a widespread species appears to be present in northern páramo sites, and some sister species sympatry may indicate other diversification processes have operated on certain lineages of Panabachia. Divergence time estimates suggest that Panabachia originated in the Miocene, but most species analyzed diverged during the Pliocene and Pleistocene (5.3–0.11 Mya), contemporaneous with the evolution of páramo plant species.

Evolutionary history of trypanosomes from South American caiman (Caiman yacare) and African crocodiles inferred by phylogenetic analyses using SSU rDNA and gGAPDH genes

Parasitology ◽  
2008 ◽  
Vol 136 (1) ◽  
pp. 55-65 ◽  
Author(s):  
L. B. VIOLA ◽  
R. S. ALMEIDA ◽  
R. C. FERREIRA ◽  
M. CAMPANER ◽  
C. S. A. TAKATA ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Ssu Rdna ◽  
Tsetse Flies ◽  
South American ◽  
Data Set ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
History Of ◽  
Brazilian Pantanal

SUMMARYIn this study, using a combined data set of SSU rDNA and gGAPDH gene sequences, we provide phylogenetic evidence that supports clustering of crocodilian trypanosomes from the Brazilian Caiman yacare (Alligatoridae) and Trypanosoma grayi, a species that circulates between African crocodiles (Crocodilydae) and tsetse flies. In a survey of trypanosomes in Caiman yacare from the Brazilian Pantanal, the prevalence of trypanosome infection was 35% as determined by microhaematocrit and haemoculture, and 9 cultures were obtained. The morphology of trypomastigotes from caiman blood and tissue imprints was compared with those described for other crocodilian trypanosomes. Differences in morphology and growth behaviour of caiman trypanosomes were corroborated by molecular polymorphism that revealed 2 genotypes. Eight isolates were ascribed to genotype Cay01 and 1 to genotype Cay02. Phylogenetic inferences based on concatenated SSU rDNA and gGAPDH sequences showed that caiman isolates are closely related to T. grayi, constituting a well-supported monophyletic assemblage (clade T. grayi). Divergence time estimates based on clade composition, and biogeographical and geological events were used to discuss the relationships between the evolutionary histories of crocodilian trypanosomes and their hosts.

scholarly journals Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0240770
Author(s):  
Alexandre Hassanin ◽  
Géraldine Veron ◽  
Anne Ropiquet ◽  
Bettine Jansen van Vuuren ◽  
Alexis Lécu ◽  
...  
Keyword(s):  
Divergence Time ◽  
Mitochondrial Genomes ◽  
Fossil Calibration ◽  
Divergence Time Estimates ◽  
Early Eocene Climatic Optimum ◽  
Time Estimates ◽  
History Of ◽  
Nucleotide Divergence ◽  
Final Alignment ◽  
Complete Mitochondrial Genomes

The order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversification of members of the order are still a matter of debate. Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of Carnivora. We assembled 51 new mitogenomes from 13 families, and aligned them with available mitogenomes by selecting only those showing more than 1% of nucleotide divergence and excluding those suspected to be of low-quality or from misidentified taxa. Our final alignment included 220 taxa representing 2,442 mitogenomes. Our analyses led to a robust resolution of suprafamilial and intrafamilial relationships. We identified 21 fossil calibration points to estimate a molecular timescale for carnivorans. According to our divergence time estimates, crown carnivorans appeared during or just after the Early Eocene Climatic Optimum; all major groups of Caniformia (Cynoidea/Arctoidea; Ursidae; Musteloidea/Pinnipedia) diverged from each other during the Eocene, while all major groups of Feliformia (Nandiniidae; Feloidea; Viverroidea) diversified more recently during the Oligocene, with a basal divergence of Nandinia at the Eocene/Oligocene transition; intrafamilial divergences occurred during the Miocene, except for the Procyonidae, as Potos separated from other genera during the Oligocene.

Insights into the Evolutionary History of the Hawaiian Bidens (Asteraceae) Adaptive Radiation Revealed Through Phylogenomics

2020 ◽  
Vol 111 (1) ◽  
pp. 119-137 ◽  
Author(s):  
Matthew L Knope ◽  
M Renee Bellinger ◽  
Erin M Datlof ◽  
Timothy J Gallaher ◽  
Melissa A Johnson
Keyword(s):  
Adaptive Radiation ◽  
Incomplete Lineage Sorting ◽  
Divergence Time ◽  
Lineage Sorting ◽  
Crown Group ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Biogeographic History ◽  
History Of ◽  
Phylogenomic Analyses

Abstract Hawaiian plant radiations often result in lineages with exceptionally high species richness and extreme morphological and ecological differentiation. However, they typically display low levels of genetic variation, hindering the use of classic DNA markers to resolve their evolutionary histories. Here we utilize a phylogenomic approach to generate the first generally well-resolved phylogenetic hypothesis for the evolution of the Hawaiian Bidens (Asteraceae) adaptive radiation, including refined initial colonization and divergence time estimates. We sequenced the chloroplast genome (plastome) and nuclear ribosomal complex for 18 of the 19 endemic species of Hawaiian Bidens and 4 outgroup species. Phylogenomic analyses based on the concatenated dataset (plastome and nuclear) resulted in identical Bayesian and Maximum Likelihood trees with high statistical support at most nodes. Estimates from dating analyses were similar across datasets, with the crown group emerging ~1.76–1.82 Mya. Biogeographic analyses based on the nuclear and concatenated datasets indicated that colonization within the Hawaiian Islands generally followed the progression rule with 67–80% of colonization events from older to younger islands, while only 53% of events followed the progression rule in the plastome analysis. We find strong evidence for nuclear-plastome conflict indicating a potentially important role for hybridization in the evolution of the group. However, incomplete lineage sorting cannot be ruled out due to the small number of independent loci analyzed. This study contributes new insights into species relationships and the biogeographic history of the explosive Hawaiian Bidens adaptive radiation.

Molecular phylogeny and divergence time estimates of Penaeid Shrimp Lineages (Decapoda: Penaeidae)

Zootaxa ◽  
2009 ◽  
Vol 2107 (1) ◽  
pp. 41-52 ◽  
Author(s):  
CAROLINA M VOLOCH ◽  
PABLO R FREIRE ◽  
CLAUDIA A M RUSSO
Keyword(s):  
Fossil Record ◽  
Divergence Time ◽  
Penaeid Shrimp ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Global Clock ◽  
Late Tertiary ◽  
The Family ◽  
Molecular Studies ◽  
Triassic Period

Fossil record of penaeids indicates that the family exists since the Triassic period, but extant genera appeared only recently in Tertiary strata. Molecular based divergence time estimates on the matter of penaeid radiation were never properly addressed, due to shortcomings of the global molecular clock assumptions. Here, we studied the diversification patterns of the family, uncovering, more specifically, a correlation between fossil and extant Penaeid fauna. For this, we have used a Bayesian framework that does not assume a global clock. Our results suggest that Penaeid genera originated between 20 million years ago and 43 million years ago, much earlier than expected by previous molecular studies. Altogether, these results promptly discard late Tertiary or even Quaternary hypotheses that presumed a major glaciations influence on the diversification patterns of the family.

scholarly journals Out of the Neotropics: Late Cretaceous colonization of Australasia by American arthropods

2012 ◽  
Vol 279 (1742) ◽  
pp. 3501-3509 ◽  
Author(s):  
Prashant P. Sharma ◽  
Gonzalo Giribet
Keyword(s):  
Late Cretaceous ◽  
Divergence Time ◽  
Disjunct Distribution ◽  
Continental Margins ◽  
Divergence Time Estimates ◽  
Evolutionary Origins ◽  
Source Regions ◽  
Time Estimates ◽  
Fiji Islands ◽  
The Pacific

The origins of tropical southwest Pacific diversity are traditionally attributed to southeast Asia or Australia. Oceanic and fragment islands are typically colonized by lineages from adjacent continental margins, resulting in attrition of diversity with distance from the mainland. Here, we show that an exceptional tropical family of harvestmen with a trans-Pacific disjunct distribution has its origin in the Neotropics. We found in a multi-locus phylogenetic analysis that the opilionid family Zalmoxidae, which is distributed in tropical forests on both sides of the Pacific, is a monophyletic entity with basal lineages endemic to Amazonia and Mesoamerica. Indo-Pacific Zalmoxidae constitute a nested clade, indicating a single colonization event. Lineages endemic to putative source regions, including Australia and New Guinea, constitute derived groups. Divergence time estimates and probabilistic ancestral area reconstructions support a Neotropical origin of the group, and a Late Cretaceous ( ca 82 Ma) colonization of Australasia out of the Fiji Islands and/or Borneo, which are consistent with a transoceanic dispersal event. Our results suggest that the endemic diversity within traditionally defined zoogeographic boundaries might have more complex evolutionary origins than previously envisioned.

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