Impacts of Inference Method and Data set Filtering on Phylogenomic Resolution in a Rapid Radiation of Ground Squirrels (Xerinae: Marmotini) [0.03%]
推断方法和数据集过滤对地面松鼠(Xerinae：Marmotini，快速辐射谱系基因组分辨率的影响
Bryan S Mclean,Kayce C Bell,Julie M Allen et al.
Bryan S Mclean et al.
Phylogenomic data sets are illuminating many areas of the Tree of Life. However, the large size of these data sets alone may be insufficient to resolve problematic nodes in the most rapid evolutionary radiations, because inferences in zones...
Eli Levy Karin,Haim Ashkenazy,Jotun Hein et al.
Eli Levy Karin et al.
Classic alignment algorithms utilize scoring functions which maximize similarity or minimize edit distances. These scoring functions account for both insertion-deletion (indel) and substitution events. In contrast, alignments based on stoch...
Jamie R Oaks
Jamie R Oaks
A challenge to understanding biological diversification is accounting for community-scale processes that cause multiple, co-distributed lineages to co-speciate. Such processes predict non-independent, temporally clustered divergences across...
Pierre Barbera,Alexey M Kozlov,Lucas Czech et al.
Pierre Barbera et al.
Next generation sequencing (NGS) technologies have led to a ubiquity of molecular sequence data. This data avalanche is particularly challenging in metagenetics, which focuses on taxonomic identification of sequences obtained from diverse m...
Adam D Leaché,Tianqi Zhu,Bruce Rannala et al.
Adam D Leaché et al.
Recent simulation studies examining the performance of Bayesian species delimitation as implemented in the bpp program have suggested that bpp may detect population splits but not species divergences and that it tends to over-split when dat...
Model Selection and Parameter Inference in Phylogenetics Using Nested Sampling [0.03%]
利用嵌套采样进行系统发生模型选择和参数推断
Patricio Maturana Russel,Brendon J Brewer,Steffen Klaere et al.
Patricio Maturana Russel et al.
Bayesian inference methods rely on numerical algorithms for both model selection and parameter inference. In general, these algorithms require a high computational effort to yield reliable estimates. One of the major challenges in phylogene...
Phylodynamic Model Adequacy Using Posterior Predictive Simulations [0.03%]
用 posterior predictive simulations 检验 phylodynamic 模型的准确性
Sebastian Duchene,Remco Bouckaert,David A Duchene et al.
Sebastian Duchene et al.
Rapidly evolving pathogens, such as viruses and bacteria, accumulate genetic change at a similar timescale over which their epidemiological processes occur, such that, it is possible to make inferences about their infectious spread using ph...
Carolina L N Costa,Paula Lemos-Costa,Flavia M D Marquitti et al.
Carolina L N Costa et al.
Phylogenetic trees are representations of evolutionary relationships among species and contain signatures of the processes responsible for the speciation events they display. Inferring processes from tree properties, however, is challenging...
Optimal Rates for Phylogenetic Inference and Experimental Design in the Era of Genome-Scale Data Sets [0.03%]
基因组规模数据集时代的谱系推断和实验设计的最优速率
Alex Dornburg,Zhuo Su,Jeffrey P Townsend
Alex Dornburg
With the rise of genome-scale data sets, there has been a call for increased data scrutiny and careful selection of loci that are appropriate to use in an attempt to resolve a phylogenetic problem. Such loci should maximize phylogenetic inf...
Early Arrival and Climatically-Linked Geographic Expansion of New World Monkeys from Tiny African Ancestors [0.03%]
美洲猴气候相关地理扩张早期始于非洲小型祖先族群
Daniele Silvestro,Marcelo F Tejedor,Martha L Serrano-Serrano et al.
Daniele Silvestro et al.
New World Monkeys (NWM) (platyrrhines) are one of the most diverse groups of primates, occupying today a wide range of ecosystems in the American tropics and exhibiting large variations in ecology, morphology, and behavior. Although the rel...