scholarly journals Modeling Phylogenetic Biome Shifts on a Planet with a Past

2020 ◽  
Vol 70 (1) ◽  
pp. 86-107
Author(s):  
Michael Landis ◽  
Erika J Edwards ◽  
Michael J Donoghue
Keyword(s):  
Spatial Distribution ◽  
Historical Biogeography ◽  
Deep Time ◽  
Mesic Forest ◽  
Ancestral States ◽  
Shift Model ◽  
Warm Temperate ◽  
Phylogenetic Models ◽  
Lineage Diversification ◽  
Biome Shift

Abstract The spatial distribution of biomes has changed considerably over deep time, so the geographical opportunity for an evolutionary lineage to shift into a new biome may depend on how the availability and connectivity of biomes has varied temporally. To better understand how lineages shift between biomes in space and time, we developed a phylogenetic biome shift model in which each lineage shifts between biomes and disperses between regions at rates that depend on the lineage’s biome affinity and location relative to the spatial distribution of biomes at any given time. To study the behavior of the biome shift model in an empirical setting, we developed a literature-based representation of paleobiome structure for three mesic forest biomes, six regions, and eight time strata, ranging from the Late Cretaceous (100 Ma) through the present. We then fitted the model to a time-calibrated phylogeny of 119 Viburnum species to compare how the results responded to various realistic or unrealistic assumptions about paleobiome structure. Ancestral biome estimates that account for paleobiome dynamics reconstructed a warm temperate (or tropical) origin of Viburnum, which is consistent with previous fossil-based estimates of ancestral biomes. Imposing unrealistic paleobiome distributions led to ancestral biome estimates that eliminated support for tropical origins, and instead inflated support for cold temperate ancestry throughout the warmer Paleocene and Eocene. The biome shift model we describe is applicable to the study of evolutionary systems beyond Viburnum, and the core mechanisms of our model are extensible to the design of richer phylogenetic models of historical biogeography and/or lineage diversification. We conclude that biome shift models that account for dynamic geographical opportunities are important for inferring ancestral biomes that are compatible with our understanding of Earth history.[Ancestral states; biome shifts; historical biogeography; niche conservatism; phylogenetics]

scholarly journals Modeling phylogenetic biome shifts on a planet with a past

2019 ◽  
Author(s):  
Michael J. Landis ◽  
Erika J. Edwards ◽  
Michael J. Donoghue
Keyword(s):  
Spatial Distribution ◽  
Late Cretaceous ◽  
Deep Time ◽  
The Core ◽  
Mesic Forest ◽  
Shift Model ◽  
Warm Temperate ◽  
Phylogenetic Models ◽  
Lineage Diversification ◽  
Biome Shift

AbstractThe spatial distribution of biomes has changed considerably over deep time, so the geographical opportunity for an evolutionary lineage to shift into a new biome may depend on how the availability and connectivity of biomes has varied temporally. To better understand how lineages shift between biomes in space and time, we developed a phylogenetic biome shift model in which each lineage shifts between biomes and disperses between regions at rates that depend on the lineage’s biome affinity and location relative to the spatiotemporal distribution of biomes at any given time. To study the behavior of the biome shift model in an empirical setting, we developed a literature-based representation of paleobiome structure for three mesic forest biomes, six regions, and eight time strata, ranging from the Late Cretaceous (100 Ma) through the present. We then fitted the model to a time-calibrated phylogeny of 119 Viburnum species to compare how the results responded to various realistic or unrealistic assumptions about paleobiome structure.Ancestral biome estimates that account for paleobiome dynamics reconstructed a warm temperate (or tropical) origin of Viburnum, which is consistent with previous fossil-based estimates of ancestral biomes. Imposing unrealistic paleobiome distributions led to ancestral biome estimates that eliminated support for tropical origins, and instead inflated support for cold temperate ancestry throughout the warmer Paleocene and Eocene. The biome shift model we describe is applicable to the study of evolutionary systems beyond Viburnum, and the core mechanisms of our model are extensible to the design of richer phylogenetic models of historical biogeography and/or lineage diversification. We conclude that biome shift models that account for dynamic geographical opportunities are important for inferring ancestral biomes that are compatible with our understanding of Earth history.

scholarly journals Fast and accurate estimation of species-specific diversification rates using data augmentation

2020 ◽  
Author(s):  
Odile Maliet ◽  
Hélène Morlon
Keyword(s):  
Data Augmentation ◽  
Computation Time ◽  
Accurate Estimation ◽  
Diversification Rates ◽  
Use Of Data ◽  
The Mean ◽  
Using Data ◽  
Species Specific ◽  
Shift Model ◽  
Phylogenetic Models

1AbstractDiversification rates vary across species as a response to various factors, including environmental conditions and species-specific features. Phylogenetic models that allow accounting for and quantifying this heterogeneity in diversification rates have proven particularly useful for understanding clades diversification. Recently, we introduced the cladogenetic diversification rate shift model (ClaDS), which allows inferring subtle rate variations across lineages. Here we present a new inference technique for this model that considerably reduces computation time through the use of data augmentation and provide an implementation of this method in Julia. In addition to drastically reducing computation time, this new inference approach provides a posterior distribution of the augmented data, that is the tree with extinct and unsampled lineages as well as associated diversification rates. In particular, this allows extracting the distribution through time of both the mean rate and the number of lineages. We assess the statistical performances of our approach using simulations and illustrate its application on the entire bird radiation.

Revisiting the diversity and distribution of the ophiuroids (Echinodermata: Ophiuroidea) from Peru

Zootaxa ◽  
2020 ◽  
Vol 4766 (4) ◽  
pp. 539-556
Author(s):  
REBECA GRANJA FERNÁNDEZ ◽  
YURI HOOKER
Keyword(s):  
Spatial Distribution ◽  
New Records ◽  
Transitional Zone ◽  
Eastern Pacific ◽  
Distribution Analysis ◽  
Deep Zone ◽  
Tropical Eastern Pacific ◽  
Southeastern Pacific ◽  
Warm Temperate ◽  
Pacific Area

While the Ophiuroidea of Peruvian waters have long been studied, there exists inconsistencies regarding taxonomy and spatial distribution records. Based on literature review and museum records, we provide an updated checklist of the ophiuroids accompanied by the first geographical distribution analysis. Peruvian waters host 36 species of Ophiuroidea (three doubtful), yet 15 previous records of species are considered invalid for the area. We recorded five new records of species for Peru: Amphiodia oerstedi, Diopederma daniana, Ophiocomella alexandri, Ophiolepis crassa, and Ophiophthalmus normani. Peruvian maritime area is divided into four areas: The Tropical Eastern Pacific area where 16 species of ophiuroids occur, the Transition Zone with 13 species, the Warm Temperate Southeastern Pacific with nine species, and the Deep Zone with 14 species. We found significant differences in species composition among areas (except among the Eastern Pacific and the Transitional Zone), and each of them is represented by particular species. According to the rarefaction curve, the inventory of ophiuroids for the country is not yet complete; therefore, we suggest performing more expeditions along the Peruvian waters focusing mainly on the deep zones which remain relatively unexplored to date. 

scholarly journals Uneven spatial sampling distorts reconstructions of Phanerozoic seawater temperature

Geology ◽  
2021 ◽  
Author(s):  
Lewis A. Jones ◽  
Kilian Eichenseer
Keyword(s):  
Spatial Distribution ◽  
Global Climate ◽  
Seawater Temperature ◽  
Spatial Sampling ◽  
Deep Time ◽  
Proxy Records ◽  
Spatial Coverage ◽  
Reconstructed Temperature ◽  
Gradient Based ◽  
Cooling Trend

Paleotemperature proxy records are widely used to reconstruct the global climate throughout the Phanerozoic and to test macroevolutionary hypotheses. However, the spatial distribution of these records varies through time. This is problematic because heat is unevenly distributed across Earth’s surface. Consequently, heterogeneous spatial sampling of proxy data has the potential to bias reconstructed temperature curves. We evaluated the spatiotemporal evolution of sampling using a compilation of Phanerozoic δ18O data. We tested the influence of variable spatial coverage on global estimates of paleotemperature by sampling a steep “modern-type” latitudinal temperature gradient and a flattened “Eocene-type” gradient, based on the spatial distribution of δ18O samples. We show that global paleotemperature is overestimated in ~70% of Phanerozoic stages. Perceived climatic trends for some intervals might be artifactually induced by shifts in paleolatitudinal sampling, with equatorward shifts in sampling concurring with warming trends, and poleward shifts concurring with cooling trends. Yet, the magnitude of some climatic perturbations might also be underestimated. For example, the observed Ordovician cooling trend may be underestimated due to an equatorward shift in sampling. Our findings suggest that while proxy records are vital for reconstructing Earth’s paleotemperature in deep time, consideration of the spatial nature of these data is crucial to improving these reconstructions.

scholarly journals Historical biogeography of early diverging termite lineages (Isoptera: Teletisoptera)

2021 ◽  
Author(s):  
Menglin Wang ◽  
Simon Hellemans ◽  
Jan Šobotník ◽  
Jigyasa Arora ◽  
Aleš Buček ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Continental Drift ◽  
Historical Biogeography ◽  
Rrna Genes ◽  
Recent Common Ancestor ◽  
Land Bridge ◽  
Most Recent Common Ancestor ◽  
The Family ◽  
The Common ◽  
Warm Temperate

AbstractTermites are social cockroaches distributed throughout warm temperate and tropical ecosystems. The ancestor of modern termites (crown-Isoptera) occurred during the earliest Cretaceous, approximately 140 million years ago, suggesting that both vicariance through continental drift and overseas dispersal may have shaped the distribution of early diverging termite lineages. We reconstruct the historical biogeography of three early diverging termite families – Stolotermitidae, Hodotermitidae, and Archotermopsidae – using the nuclear rRNA genes and mitochondrial genomes of 27 samples. Our analyses confirmed the monophyly of Stolotermitidae + Hodotermitidae + Archotermopsidae (clade Teletisoptera), with Stolotermitidae diverging from a monophyletic Hodotermitidae + Archotermopsidae approximately 100.3 Ma (94.3–110.4 Ma, 95% HPD), and with Archotermopsidae paraphyletic to a monophyletic Hodotermitidae. The Oriental Archotermopsis and the Nearctic Zootermopsis diverged 50.8 Ma (40.7–61.4 Ma, 95% HPD) before land connections between the Palearctic region and North America ceased to exist. The African Hodotermes + Microhodotermes diverged from Anacanthotermes, a genus found in Africa and Asia, 32.1 Ma (24.8–39.9 Ma, 95% HPD), and the most recent common ancestor of Anacanthotermes lived 10.7 Ma (7.3–14.3 Ma, 95% HPD), suggesting that Anacanthotermes dispersed to Asia using the land bridge connecting Africa and Eurasia ∼18–20 Ma. In contrast, the common ancestors of modern Porotermes and Stolotermes lived 20.2 Ma (15.7–25.1 Ma, 95% HPD) and 26.6 Ma (18.3–35.6 Ma, 95% HPD), respectively, indicating that the presence of these genera in South America, Africa, and Australia involved over-water dispersals. Our results suggest that early diverging termite lineages acquired their current distribution through a combination of over-water dispersals and dispersal via land bridges. We clarify the classification by resolving the paraphyly of Archotermopsidae, restricting the family to Archotermopsis and Zootermopsis, and elevating Hodotermopsinae (Hodotermopsis) as Hodotermopsidae (status novum).

Lithography below 100 nm

1983 ◽  
Vol 41 ◽  
pp. 96-99
Author(s):  
L. D. Jackel
Keyword(s):  
Spatial Distribution ◽  
Electron Beam ◽  
Electron Scattering ◽  
Electron Beam Lithography ◽  
Substrate Material ◽  
Local Electron ◽  
Electron Dose ◽  
Positive Resist ◽  
Exposure Process

Most production electron beam lithography systems can pattern minimum features a few tenths of a micron across. Linewidth in these systems is usually limited by the quality of the exposing beam and by electron scattering in the resist and substrate. By using a smaller spot along with exposure techniques that minimize scattering and its effects, laboratory e-beam lithography systems can now make features hundredths of a micron wide on standard substrate material. This talk will outline sane of these high- resolution e-beam lithography techniques.We first consider parameters of the exposure process that limit resolution in organic resists. For concreteness suppose that we have a “positive” resist in which exposing electrons break bonds in the resist molecules thus increasing the exposed resist's solubility in a developer. Ihe attainable resolution is obviously limited by the overall width of the exposing beam, but the spatial distribution of the beam intensity, the beam “profile” , also contributes to the resolution. Depending on the local electron dose, more or less resist bonds are broken resulting in slower or faster dissolution in the developer.

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