Inferring Speciation Rates From Phylogenies

Nee, Sean

doi:10.1554/0014-3820(2001)055[0661:isrfp]2.0.co;2

Cited by 202 publications

(97 citation statements)

References 24 publications

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“…5). A resolved phylogeny is important for answering a variety of questions in evolutionary biology, including estimating speciation rates (e.g., Nee 2001), inferring rates of morphological evolution (e.g., Pennell and Harmon 2013), and characterizing patterns of molecular evolution (e.g., Zhang et al. 2005).…”

Section: Discussionmentioning

confidence: 99%

Phylogenomic Insights into Mouse Evolution Using a Pseudoreference Approach

Sarver

Keeble

Cosart

et al. 2017

Genome Biology and Evolution

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Comparative genomic studies are now possible across a broad range of evolutionary timescales, but the generation and analysis of genomic data across many different species still present a number of challenges. The most sophisticated genotyping and down-stream analytical frameworks are still predominantly based on comparisons to high-quality reference genomes. However, established genomic resources are often limited within a given group of species, necessitating comparisons to divergent reference genomes that could restrict or bias comparisons across a phylogenetic sample. Here, we develop a scalable pseudoreference approach to iteratively incorporate sample-specific variation into a genome reference and reduce the effects of systematic mapping bias in downstream analyses. To characterize this framework, we used targeted capture to sequence whole exomes (∼54 Mbp) in 12 lineages (ten species) of mice spanning the Mus radiation. We generated whole exome pseudoreferences for all species and show that this iterative reference-based approach improved basic genomic analyses that depend on mapping accuracy while preserving the associated annotations of the mouse reference genome. We then use these pseudoreferences to resolve evolutionary relationships among these lineages while accounting for phylogenetic discordance across the genome, contributing an important resource for comparative studies in the mouse system. We also describe patterns of genomic introgression among lineages and compare our results to previous studies. Our general approach can be applied to whole or partitioned genomic data and is easily portable to any system with sufficient genomic resources, providing a useful framework for phylogenomic studies in mice and other taxa.

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Section: Discussionmentioning

confidence: 99%

Phylogenomic Insights into Mouse Evolution Using a Pseudoreference Approach

Sarver

Keeble

Cosart

et al. 2017

Genome Biology and Evolution

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“…The models were compared according to the Akaike information criterion (AIC). To visualize the variation of diversification rates with time, the rates were calculated within overlapping periods of 400 thousand years using yuleWindow function [75] and compared with the δ 18 O curve [76], which is a good climate proxy. For the comparison and better visualization of climate oscillations, we calculated the variance in the δ 18 O records within the same overlapping periods.…”

Section: Methodsmentioning

confidence: 99%

Evolutionary history and phylogeographic relationships of shrews from Sorex araneus group

et al. 2017

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Shrews of the Sorex genus are an evolutionarily successful group that includes more than 77 species widely distributed in Eurasia and North America. The genus is one of the rare cases where karyotypic changes reflect well the evolutionary relationships among its species. The taxa showing the greatest variation in karyotype are usually classified into the Sorex araneus group. Its evolution was associated with chromosomal rearrangements, which could have promoted fast diversification of this group into many chromosomal races and species. These processes were additionally complicated by introgressions of mitochondrial DNA, which made the evolutionary history of this group quite complex and difficult to infer. To tackle the problem, we performed multi-method phylogenetic analyses based on mitochondrial cytochrome b that is considered a good molecular marker available for many representatives of Sorex. The results were compared with phylogenies based on chromosomal rearrangement data and put into temporal and spatial context using molecular dating and historical biogeography methods. We complemented the study with the estimation of diversification rates within the S. araneus group as well as comparing the results with paleontological records and climatic oscillations within the last 4 million years. Based on the gathered data, we proposed a hypothetical scenario for the evolution and geographic dispersion of species belonging to the S. araneus group. The shrews began to diversify about 2.7 million years ago in Eurasia and then migrated at least twice to North America. The evolution of shrews was driven by Pleistocene glacial and interglacial cycles, which increased their speciation rate and the emergence of new lineages. The migrations of populations were accompanied by introgressions of mitochondrial DNA into native shrews and occurred at least twice.

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“…Such observations, combined especially with the rapid rise of molecular phylogenetics, have stimulated the development of methods and tools to extract information about diversifi cation rates from phylogenies. These range from tree-balance measures that variously test for asymmetry in the partitioning of species diversity across a tree (e.g., Agapow and Purvis, 2002 ;Purvis et al, 2002 ;Chan and Moore, 2005 ;Holman, 2005 ), to methods that combine both topological and temporal information to infer speciation and extinction parameters (e.g., Nee et al, 1992 ;Magall ó n and Sanderson, 2001 ;Nee, 2001 ;Rabosky and Lovette, 2008 ;Alfaro et al, 2009 ;Moore and Donoghue, 2009 ).…”

Section: Identifying Major Radiations In a Phylogenetic Treementioning

confidence: 99%

Understanding angiosperm diversification using small and large phylogenetic trees

Smith

Beaulieu

Stamatakis

et al. 2011

American J of Botany

165

155

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How will the emerging possibility of inferring ultra-large phylogenies influence our ability to identify shifts in diversification rate? For several large angiosperm clades (Angiospermae, Monocotyledonae, Orchidaceae, Poaceae, Eudicotyledonae, Fabaceae, and Asteraceae), we explore this issue by contrasting two approaches: (1) using small backbone trees with an inferred number of extant species assigned to each terminal clade and (2) using a mega-phylogeny of 55473 seed plant species represented in GenBank. The mega-phylogeny approach assumes that the sample of species in GenBank is at least roughly proportional to the actual species diversity of different lineages, as appears to be the case for many major angiosperm lineages. Using both approaches, we found that diversification rate shifts are not directly associated with the major named clades examined here, with the sole exception of Fabaceae in the GenBank mega-phylogeny. These agreements are encouraging and may support a generality about angiosperm evolution: major shifts in diversification may not be directly associated with major named clades, but rather with clades that are nested not far within these groups. An alternative explanation is that there have been increased extinction rates in early-diverging lineages within these clades. Based on our mega-phylogeny, the shifts in diversification appear to be distributed quite evenly throughout the angiosperms. Mega-phylogenetic studies of diversification hold great promise for revealing new patterns, but we will need to focus more attention on properly specifying null expectation.

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Inferring Speciation Rates From Phylogenies

Cited by 202 publications

References 24 publications

Phylogenomic Insights into Mouse Evolution Using a Pseudoreference Approach

Phylogenomic Insights into Mouse Evolution Using a Pseudoreference Approach

Evolutionary history and phylogeographic relationships of shrews from Sorex araneus group

Understanding angiosperm diversification using small and large phylogenetic trees

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