scholarly journals Ignoring Heterozygous Sites Biases Phylogenomic Estimates of Divergence Times: Implications for the Evolutionary History of Microtus Voles

2013 ◽  
Vol 31 (4) ◽  
pp. 817-831 ◽  
Author(s):  
Heidi E.L. Lischer ◽  
Laurent Excoffier ◽  
Gerald Heckel
Keyword(s):  
Evolutionary History ◽  
Divergence Times ◽  
History Of ◽  
Microtus Voles

Towards resolving the evolutionary history of Caucasian pears (Pyrus, Rosaceae)-Phylogenetic relationships, divergence times and leaf trait evolution

2017 ◽  
Vol 56 (1) ◽  
pp. 35-47 ◽  
Author(s):  
Nadja Korotkova ◽  
Gerald Parolly ◽  
Anahit Khachatryan ◽  
Lusine Ghulikyan ◽  
Harutyun Sargsyan ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Divergence Times ◽  
Trait Evolution ◽  
Leaf Trait ◽  
History Of

scholarly journals Genome sequences reveal divergence times of malaria parasite lineages

Parasitology ◽  
2010 ◽  
Vol 138 (13) ◽  
pp. 1737-1749 ◽  
Author(s):  
JOANA C. SILVA ◽  
AMY EGAN ◽  
ROBERT FRIEDMAN ◽  
JAMES B. MUNRO ◽  
JANE M. CARLTON ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Common Ancestor ◽  
Orthologous Gene ◽  
The Other ◽  
Divergence Times ◽  
Last Common Ancestor ◽  
Genome Sequences ◽  
Malaria Parasites ◽  
Human Malaria ◽  
History Of

SUMMARYObjectiveThe evolutionary history of human malaria parasites (genus Plasmodium) has long been a subject of speculation and controversy. The complete genome sequences of the two most widespread human malaria parasites, P. falciparum and P. vivax, and of the monkey parasite P. knowlesi are now available, together with the draft genomes of the chimpanzee parasite P. reichenowi, three rodent parasites, P. yoelii yoelli, P. berghei and P. chabaudi chabaudi, and one avian parasite, P. gallinaceum.MethodsWe present here an analysis of 45 orthologous gene sequences across the eight species that resolves the relationships of major Plasmodium lineages, and provides the first comprehensive dating of the age of those groups.ResultsOur analyses support the hypothesis that the last common ancestor of P. falciparum and the chimpanzee parasite P. reichenowi occurred around the time of the human-chimpanzee divergence. P. falciparum infections of African apes are most likely derived from humans and not the other way around. On the other hand, P. vivax, split from the monkey parasite P. knowlesi in the much more distant past, during the time that encompasses the separation of the Great Apes and Old World Monkeys.ConclusionThe results support an ancient association between malaria parasites and their primate hosts, including humans.

Historical Biogeography of Holarctic Cymbiodyta Water Scavenger Beetles in the Times of Cenozoic Land Bridge Dispersal Routes

2019 ◽  
Vol 3 (5) ◽  
Author(s):  
Emmanuel F A Toussaint ◽  
Andrew E Z Short
Keyword(s):  
Evolutionary History ◽  
New Combination ◽  
Divergence Times ◽  
Range Estimation ◽  
Land Bridge ◽  
Palearctic Species ◽  
History Of ◽  
The Times ◽  
Ancestral Range Estimation

Abstract The genus Cymbiodyta Bedel, 1881 (Coleoptera: Hydrophilidae: Enochrinae) comprises 31 species distributed in both the Old and New World portions of the Holarctic realm. Although the species and taxonomy are relatively well known, the phylogenetic relationships among Cymbiodyta and the evolutionary history of the genus remain unexplored. To understand the systematics and evolution of this lineage, we sequenced five gene fragments for about half of the species in the genus, including most major morphological groups. We also estimated divergence times to test the hypothesis that Cymbiodyta beetles took advantage of the different land bridges connecting the Palearctic and Nearctic regions, that became subaerial in the Cretaceous and Paleocene. Our results recover the eastern Nearctic genus Helocombus Horn, 1890 nesting within Cymbiodyta. Therefore, we synonymize Helocombus syn. n. with Cymbiodyta, resulting in one new combination, Cymbiodyta bifidus (LeConte 1855) comb. n. Our dating analyses and ancestral range estimation support a Nearctic origin of Cymbiodyta in the late Cretaceous about 100 million year ago. The placement of the unique Palearctic species on a long branch as sister to the rest of the clade and the dating results cannot reject a role of the De Geer and/or Thulean routes in the colonization of the Palearctic region from the Nearctic; however, they do not support a role for Beringia in the more recent colonization of the Oriental region.

scholarly journals Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates

BMC Biology ◽  
2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Tiago R. Simões ◽  
Michael W. Caldwell ◽  
Stephanie E. Pierce
Keyword(s):  
Evolutionary History ◽  
Evolutionary Rates ◽  
Morphological Data ◽  
Divergence Times ◽  
Evolutionary Trees ◽  
Model Choice ◽  
Rates Of Evolution ◽  
History Of ◽  
Living Species ◽  
The Impact

Abstract Background The vast majority of all life that ever existed on earth is now extinct and several aspects of their evolutionary history can only be assessed by using morphological data from the fossil record. Sphenodontian reptiles are a classic example, having an evolutionary history of at least 230 million years, but currently represented by a single living species (Sphenodon punctatus). Hence, it is imperative to improve the development and implementation of probabilistic models to estimate evolutionary trees from morphological data (e.g., morphological clocks), which has direct benefits to understanding relationships and evolutionary patterns for both fossil and living species. However, the impact of model choice on morphology-only datasets has been poorly explored. Results Here, we investigate the impact of a wide array of model choices on the inference of evolutionary trees and macroevolutionary parameters (divergence times and evolutionary rates) using a new data matrix on sphenodontian reptiles. Specifically, we tested different clock models, clock partitioning, taxon sampling strategies, sampling for ancestors, and variations on the fossilized birth-death (FBD) tree model parameters through time. We find a strong impact on divergence times and background evolutionary rates when applying widely utilized approaches, such as allowing for ancestors in the tree and the inappropriate assumption of diversification parameters being constant through time. We compare those results with previous studies on the impact of model choice to molecular data analysis and provide suggestions for improving the implementation of morphological clocks. Optimal model combinations find the radiation of most major lineages of sphenodontians to be in the Triassic and a gradual but continuous drop in morphological rates of evolution across distinct regions of the phenotype throughout the history of the group. Conclusions We provide a new hypothesis of sphenodontian classification, along with detailed macroevolutionary patterns in the evolutionary history of the group. Importantly, we provide suggestions to avoid overestimated divergence times and biased parameter estimates using morphological clocks. Partitioning relaxed clocks offers methodological limitations, but those can be at least partially circumvented to reveal a detailed assessment of rates of evolution across the phenotype and tests of evolutionary mosaicism.

Elaborating the role of reflection and individual differences in the study of folk-economic beliefs

2018 ◽  
Vol 41 ◽  
Author(s):  
Kevin Arceneaux
Keyword(s):  
Decision Making ◽  
Individual Differences ◽  
Cognitive Processes ◽  
Evolutionary History ◽  
Behavioral Responses ◽  
History Of ◽  
Economic Beliefs

AbstractIntuitions guide decision-making, and looking to the evolutionary history of humans illuminates why some behavioral responses are more intuitive than others. Yet a place remains for cognitive processes to second-guess intuitive responses – that is, to be reflective – and individual differences abound in automatic, intuitive processing as well.

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