Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

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Modern Applied Statistics With S

Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Integrative Genomics Viewer

The ranges of plants and animals are moving in response to recent changes in climate. As temperatures rise, ecosystems with 'nowhere to go', such as mountains, are considered to be more threatened. However, species survival may depend as much on keeping pace with moving climates as the climate's ultimate persistence. Here we present a new index of the velocity of temperature change (km yr(-1)), derived from spatial gradients ( degrees C km(-1)) and multimodel ensemble forecasts of rates of temperature increase ( degrees C yr(-1)) in the twenty-first century. This index represents the instantaneous local velocity along Earth's surface needed to maintain constant temperatures, and has a global mean of 0.42 km yr(-1) (A1B emission scenario). Owing to topographic effects, the velocity of temperature change is lowest in mountainous biomes such as tropical and subtropical coniferous forests (0.08 km yr(-1)), temperate coniferous forest, and montane grasslands. Velocities are highest in flooded grasslands (1.26 km yr(-1)), mangroves and deserts. High velocities suggest that the climates of only 8% of global protected areas have residence times exceeding 100 years. Small protected areas exacerbate the problem in Mediterranean-type and temperate coniferous forest biomes. Large protected areas may mitigate the problem in desert biomes. These results indicate management strategies for minimizing biodiversity loss from climate change. Montane landscapes may effectively shelter many species into the next century. Elsewhere, reduced emissions, a much expanded network of protected areas, or efforts to increase species movement may be necessary.

The velocity of climate change

Ribosomal ITS sequences and plant phylogenetic inference.

Regional phylogeographical studies involving co-distributed animal and plant species have been conducted for several areas, most notably for Europe and the Pacific Northwest of North America. Until recently, phylogeographical studies in unglaciated eastern North America have been largely limited to animals. As more studies emerge for diverse lineages (including plants), it seems timely to assess the phylogeography across this region: (i) comparing and contrasting the patterns seen in plants and animals; (ii) assessing the extent of pseudocongruence; and (iii) discussing the potential applications of regional phylogeography to issues in ecology, such as response to climatic change. Unglaciated eastern North America is a large, geologically and topographically complex area with the species examined having diverse distributions. Nonetheless, some recurrent patterns emerge: (i) maritime - Atlantic vs. Gulf Coast; (ii) Apalachicola River discontinuity; (iii) Tombigbee River discontinuity; (iv) the Appalachian Mountain discontinuity; (v) the Mississippi River discontinuity; and (vi) the Apalachicola River and Mississippi River discontinuities. Although initially documented in animals, most of these patterns are also apparent in plants, providing support for phylogeographical generalizations. These patterns may generally be attributable to isolation and differentiation during Pleistocene glaciation, but in some cases may be older (Pliocene). Molecular studies sometimes agree with longstanding hypotheses of glacial refugia, but also suggest additional possible refugia, such as the southern Appalachian Mountains and areas close to the Laurentide Ice Sheet. Many species exhibit distinct patterns that reflect the unique, rather than the shared, aspects of species' phylogeographical histories. Furthermore, similar modern phylogeographical patterns can result from different underlying causal factors operating at different times (i.e. pseudocongruence). One underemphasized component of pseudocongruence may result from the efforts of researchers to categorize patterns visually - similar patterns may, in fact, not fully coincide, and inferring agreement may obscure the actual patterns and lead to erroneous conclusions. Our modelling analyses indicate no clear spatial patterning and support the hypothesis that phylogeographical structure in diverse temperate taxa is complex and was not shaped by just a few barriers.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-294X.2006.03061.x

Comparative phylogeography of unglaciated eastern North America.

Recent models and analyses of paleoecological records suggest that tree populations are capable of rapid migration when climate warms. Fossil pollen is commonly interpreted as suggesting that the range of many temperate tree species expanded at rates of 100–1000 m/yr during the early Holocene. We used chloroplast DNA surveys to show that the geography of postglacial range expansion in two eastern North American tree species differs from that expected from pollen-based reconstructions and from patterns emerging from European molecular studies. Molecular evidence suggests that American beech (Fagus grandifolia) and red maple (Acer rubrum) persisted during the late glaciation as low-density populations, perhaps within 500 km of the Laurentide Ice Sheet. Because populations were closer to modern range limits than previously thought, postglacial migration rates may have been slower than those inferred from fossil pollen. Our estimated rates of <100 m/yr are consistent with model predictions based on life histo...

Molecular indicators of tree migration capacity under rapid climate change

http://ericlwalters.com/Manos_etal_1999.pdf

Phylogeny, Biogeography, and Processes of Molecular Differentiation in Quercus Subgenus Quercus (Fagaceae)

The angiosperm family Fagaceae is a central element of several distinct community types throughout the Northern Hemisphere and a prime candidate for modern biogeographic analysis. The rich fossil record for the family provides an unparalleled source to compare with modern distributions and evaluate hypotheses of origin, migration, and vicariance. We conducted separate phylogenetic analyses on genera with intercontinentally disjunct distributions using various noncoding regions of chloroplast and nuclear ribosomal DNA sequences. Analyses generally supported the (North \documentclass{aastex} \usepackage{amsbsy} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{bm} \usepackage{mathrsfs} \usepackage{pifont} \usepackage{stmaryrd} \usepackage{textcomp} \usepackage{portland,xspace} \usepackage{amsmath,amsxtra} \usepackage[OT2,OT1]{fontenc} \newcommand\cyr{ \renewcommand\rmdefault{wncyr} \renewcommand\sfdefault{wncyss} \renewcommand\encodingdefault{OT2} \normalfont \selectfont} \DeclareTextFontCommand{\textc...

https://www.jstor.org/stable/10.1086/323280

The Historical Biogeography of Fagaceae: Tracking the Tertiary History of Temperate and Subtropical Forests of the Northern Hemisphere

The family Fagaceae includes nine currently recognized genera and ca. 1000 species, making it one of the largest and most economically important groups within the order Fagales. In addition to wide variation in cupule and fruit morphology, polymorphism in pollination syndrome (wind vs. generalistic insect) also contributes to the uniqueness of the family. Phylogenetic relationships were examined using 179 accessions spanning the taxonomic breadth of the family, emphasizing tropical, subtropical, and relictual taxa. Nuclear ribosomal DNA sequences encoding the 5.8S rRNA gene and two flanking internal transcribed spacers (ITS) were used to evaluate phylogenetic hypotheses based on previous morphological cladistic analysis and intuitive schemes. Parsimony analyses rooted with Fagus supported two clades within the family, Trigonobalanus sensu lato and a large clade comprising Quercus and the castaneoid genera ( \documentclass{aastex} \usepackage{amsbsy} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{b...

https://www.jstor.org/stable/10.1086/322949

Paul S. Manos

Papers

Comparative phylogeography of unglaciated eastern North America.

Molecular indicators of tree migration capacity under rapid climate change

Phylogeny, Biogeography, and Processes of Molecular Differentiation in Quercus Subgenus Quercus (Fagaceae)

The Historical Biogeography of Fagaceae: Tracking the Tertiary History of Temperate and Subtropical Forests of the Northern Hemisphere

Systematics of Fagaceae: Phylogenetic tests of reproductive trait evolution