scholarly journals Evolution of gliding in Southeast Asian geckos and other vertebrates is temporally congruent with dipterocarp forest development

2012 ◽  
Vol 8 (6) ◽  
pp. 994-997 ◽  
Author(s):  
Matthew P. Heinicke ◽  
Eli Greenbaum ◽  
Todd R. Jackman ◽  
Aaron M. Bauer
Keyword(s):  
Tropical Forests ◽  
Molecular Clock ◽  
Temporal Pattern ◽  
Sequence Data ◽  
Southeast Asian ◽  
Vertebrate Evolution ◽  
Divergence Times ◽  
Dipterocarp Forest ◽  
Time Period ◽  
Repeated Evolution

Gliding morphologies occur in diverse vertebrate lineages in Southeast Asian rainforests, including three gecko genera, plus frogs, snakes, agamid lizards and squirrels. It has been hypothesized that repeated evolution of gliding is related to the dominance of Asian rainforest tree floras by dipterocarps. For dipterocarps to have influenced the evolution of gliding in Southeast Asian vertebrates, gliding lineages must have Eocene or later origins. However, divergence times are not known for most lineages. To investigate the temporal pattern of Asian gliding vertebrate evolution, we performed phylogenetic and molecular clock analyses. New sequence data for geckos incorporate exemplars of each gliding genus ( Cosymbotus , Luperosaurus and Ptychozoon ), whereas analyses of other vertebrate lineages use existing sequence data. Stem ages of most gliding vertebrates, including all geckos, cluster in the time period when dipterocarps came to dominate Asian tropical forests. These results demonstrate that a gliding/dipterocarp correlation is temporally viable, and caution against the assumption of early origins for apomorphic taxa.

Molecular Phylogeny and Biogeography of the Tasmanian and New Zealand Mudfishes (Salmoniformes : Galaxiidae)

1997 ◽  
Vol 45 (1) ◽  
pp. 39 ◽  
Author(s):  
J. M. Waters ◽  
R. W. G. White
Keyword(s):  
New Zealand ◽  
Molecular Phylogeny ◽  
Molecular Clock ◽  
Convergent Evolution ◽  
Sequence Data ◽  
Mitochondrial Genes ◽  
Divergence Times ◽  
Marine Dispersal ◽  
Close Phylogenetic Relationship ◽  
Phylogenetic Affinities

The phylogenetic affinities of the diadromous Tasmanian mudfish, Galaxias cleaveri, have long been problematic. Some systematists have suggested that this species is closely related to the morphologically similar but non-diadromous New Zealand mudfish genus, Neochanna, while others argued that the similarities represent convergent evolution. Most recently, the Tasmanian mudfish was allocated to Neochanna on morphological grounds. The current paper presents sequence data from two mitochondrial genes that support this decision, revealing a close phylogenetic relationship between Tasmanian and New Zealand mudfish. Molecular clock calibrations are used to examine hypotheses of mudfish evolution and biogeography. Estimated divergence times are consistent with the suggestion that Neochanna burrowsius and N. apoda were separated by the uplift of New Zealand’s southern Alps about five million years ago. In addition, the divergence of the Tasmanian and New Zealand mudfish appears to postdate the rifting of Gondwana and is best explained by marine dispersal during the Pliocene.

scholarly journals Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution

2017 ◽  
Vol 284 (1857) ◽  
pp. 20170227 ◽  
Author(s):  
Rachel C. M. Warnock ◽  
Ziheng Yang ◽  
Philip C. J. Donoghue
Keyword(s):  
Molecular Clock ◽  
Sequence Data ◽  
Time Estimation ◽  
Divergence Times ◽  
Mechanistic Models ◽  
Sequence Evolution ◽  
High Coverage ◽  
Fossil Species ◽  
Fossil Preservation ◽  
Molecular Clock Dating

Molecular sequence data provide information about relative times only, and fossil-based age constraints are the ultimate source of information about absolute times in molecular clock dating analyses. Thus, fossil calibrations are critical to molecular clock dating, but competing methods are difficult to evaluate empirically because the true evolutionary time scale is never known. Here, we combine mechanistic models of fossil preservation and sequence evolution in simulations to evaluate different approaches to constructing fossil calibrations and their impact on Bayesian molecular clock dating, and the relative impact of fossil versus molecular sampling. We show that divergence time estimation is impacted by the model of fossil preservation, sampling intensity and tree shape. The addition of sequence data may improve molecular clock estimates, but accuracy and precision is dominated by the quality of the fossil calibrations. Posterior means and medians are poor representatives of true divergence times; posterior intervals provide a much more accurate estimate of divergence times, though they may be wide and often do not have high coverage probability. Our results highlight the importance of increased fossil sampling and improved statistical approaches to generating calibrations, which should incorporate the non-uniform nature of ecological and temporal fossil species distributions.

Molecular phylogeny and biogeography of the Tasmanian and New Zealand mudfishes (Salmoniformes : Galaxiidae)

1997 ◽  
Vol 45 (6) ◽  
pp. 671
Author(s):  
J. M. Waters ◽  
R. W. G. White
Keyword(s):  
New Zealand ◽  
Molecular Phylogeny ◽  
Molecular Clock ◽  
Convergent Evolution ◽  
Sequence Data ◽  
Mitochondrial Genes ◽  
Divergence Times ◽  
Marine Dispersal ◽  
Close Phylogenetic Relationship ◽  
Phylogenetic Affinities

The phylogenetic affinities of the diadromous Tasmanian mudfish, Galaxias cleaveri, have long been problematic. Some systematists have suggested that this species is closely related to the morphologically similar but non-diadromous New Zealand mudfish genus, Neochanna, while others argued that the similarities represent convergent evolution. Most recently, the Tasmanian mudfish was allocated to Neochanna on morphological grounds. The current paper presents sequence data from two mitochondrial genes that support this decision, revealing a close phylogenetic relationship between Tasmanian and New Zealand mudfish. Molecular clock calibrations are used to examine hypotheses of mudfish evolution and biogeography. Estimated divergence times are consistent with the suggestion that Neochanna burrowsius and N. apoda were separated by the uplift of New Zealand’s southern Alps about five million years ago. In addition, the divergence of the Tasmanian and New Zealand mudfish appears to postdate the rifting of Gondwana and is best explained by marine dispersal during the Pliocene.

scholarly journals Molecular clocks and the early evolution of metazoan nervous systems

2015 ◽  
Vol 370 (1684) ◽  
pp. 20150046 ◽  
Author(s):  
Gregory A. Wray
Keyword(s):  
Sensory Processing ◽  
Fossil Record ◽  
Sequence Data ◽  
Divergence Times ◽  
Molecular Clocks ◽  
Sense Organs ◽  
Animal Evolution ◽  
Nervous Systems ◽  
Nervous System Evolution ◽  
Fossil Records

The timing of early animal evolution remains poorly resolved, yet remains critical for understanding nervous system evolution. Methods for estimating divergence times from sequence data have improved considerably, providing a more refined understanding of key divergences. The best molecular estimates point to the origin of metazoans and bilaterians tens to hundreds of millions of years earlier than their first appearances in the fossil record. Both the molecular and fossil records are compatible, however, with the possibility of tiny, unskeletonized, low energy budget animals during the Proterozoic that had planktonic, benthic, or meiofaunal lifestyles. Such animals would likely have had relatively simple nervous systems equipped primarily to detect food, avoid inhospitable environments and locate mates. The appearance of the first macropredators during the Cambrian would have changed the selective landscape dramatically, likely driving the evolution of complex sense organs, sophisticated sensory processing systems, and diverse effector systems involved in capturing prey and avoiding predation.

scholarly journals Temporal Patterns of Sporulation Potential of Phomopsis viticola on Infected Grape Shoots, Canes, and Rachises

Plant Disease ◽  
2012 ◽  
Vol 96 (9) ◽  
pp. 1297-1302 ◽  
Author(s):  
D. J. Anco ◽  
L. V. Madden ◽  
M. A. Ellis
Keyword(s):  
Leaf Spot ◽  
Temporal Pattern ◽  
Growing Season ◽  
First Year ◽  
Bud Break ◽  
Optimal Conditions ◽  
Phomopsis Viticola ◽  
Time Period ◽  
Dormant Season ◽  
Vitis Spp

Phomopsis cane and leaf spot on Vitis spp. (grape) is currently understood to be monocyclic, with primary inoculum only being produced early in the growing season. However, of the few published studies pertaining to sporulation of Phomopsis viticola, none specifically examined rachises, and none were designed to determine when infected tissues become capable of sporulation. The objective of these studies was to determine when grape shoots, canes, and rachises infected with P. viticola develop the capacity to sporulate, and to determine the time period during which those tissues remain capable of sporulation. Starting in 2009 and 2010, infected first-year shoots and rachises were collected biweekly throughout the growing season, into the dormant season, and into the following growing season. Tissues were collected from ‘Catawba,’ ‘Concord,’ and ‘Reliance’ vineyards. Samples were observed for sporulation after 48 h of incubation in a moist chamber at 23°C; the magnitude of the conidia production under these optimal conditions was considered the sporulation potential. For infections that occurred in 2009 and 2010, the production of conidia was not observed until after harvest. In the year following infection, sporulation potential was found from about bud break until shortly after the end of bloom. There was a generally consistent temporal pattern to relative sporulation potential across sampled vineyards, years, and grape tissues (rachises and canes), described by a modified β model, with peak sporulation potential occurring around 16 May. These results confirmed that Phomopsis cane and leaf spot is a monocyclic disease and support control recommendations for use of fungicides in spring.

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