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Phylogenetics

Molecular evolution of Drosophila Cdc6, an essential DNA replication-licensing gene, suggests an adaptive choice of replication origins

Wiggins BL, Malik HS.  2007.  Molecular evolution of Drosophila Cdc6, an essential DNA replication-licensing gene, suggests an adaptive choice of replication origins. Fly. 1(3):-163.

Darwin’s Phylogenetic Reasoning

Darwin claimed that similarity is evidence for common ancestry, and that adaptive similarities provide weaker evidence than neutral or deleterious similarities.  He also used phylogenetic trees to reason critically about adaptive hypotheses.  In this talk I'll analyze his bits of reasoning and describe frameworks for evaluating their correctness.

Species delimitation using Bayes factors: simulations and application to the Sceloporus scalaris species group (Squamata: Phrynosomatidae)

Grummer JA, Bryson RW, Reeder TW.  2014.  Species delimitation using Bayes factors: simulations and application to the Sceloporus scalaris species group (Squamata: Phrynosomatidae). Systematic biology. 63:119–133.

A new species of bunchgrass lizard (Squamata: Phrynosomatidae) from the southern sky islands of the Sierra Madre Occidental, Mexico

Grummer JA, Bryson RW.  2014.  A new species of bunchgrass lizard (Squamata: Phrynosomatidae) from the southern sky islands of the Sierra Madre Occidental, Mexico. Zootaxa. 3790:439–450.

Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing

Leaché AD, Chavez AS, Jones LN, Grummer JA, Gottscho AD, Linkem CW.  2015.  Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing. Genome biology and evolution. 7:706–719.

Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genus Sceloporus) in the southern Mexican highlands

Grummer JA, Calderón-Espinosa ML, de Oca ANieto-Mont, Smith EN, de la Cruz FRMéndez-, Leaché AD.  2015.  Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genus Sceloporus) in the southern Mexican highlands. Molecular ecology. 24:1523–1542.

Bayesian inference of species diffusion in the West African Agama agama species group (Reptilia, Agamidae)

Leaché AD, Grummer JA, Miller M, Krishnan S, Fujita MK, Böhme W, Schmitz A, Lebreton M, Ineich I, Chirio L et al..  2016.  Bayesian inference of species diffusion in the West African Agama agama species group (Reptilia, Agamidae). Systematics and Biodiversity. :1–12.

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