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List of works by Alan R. Lemmon

A Likelihood Framework for Estimating Phylogeographic History on a Continuous Landscape

scientific article (publication date: 14 August 2008)

A Passerine Bird's evolution corroborates the geologic history of the island of New Guinea

scientific article published in 2011

A combined approach of mitochondrial DNA and anchored nuclear phylogenomics sheds light on unrecognized diversity, phylogeny, and historical biogeography of the torrent frogs, genus Amolops (Anura: Ranidae)

scientific article published on 12 March 2020

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

scientific article

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

scientific article published in Nature

A deeper meaning for shallow‐level phylogenomic studies: nested anchored hybrid enrichment offers great promise for resolving the tiger moth tree of life (Lepidoptera: Erebidae: Arctiinae) ⬇️

scientific article

A genome-wide phylogeny of jumping spiders (Araneae, Salticidae), using anchored hybrid enrichment

scientific article

A high-throughput venom-gland transcriptome for the Eastern Diamondback Rattlesnake (Crotalus adamanteus) and evidence for pervasive positive selection across toxin classes

scientific article

A hybrid phylogenetic-phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification

scientific article

A new sectional classification of Lachenalia (Asparagaceae) based on a multilocus DNA phylogeny ⬇️

scientific article published on 26 February 2022

A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans

scientific article published on 01 April 2019

A phylogenomic framework, evolutionary timeline, and genomic resources for comparative studies of decapod crustaceans

A pilot study applying the plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae).

scientific article

An integrative phylogenomic approach illuminates the evolutionary history of Old World tree frogs (Anura: Rhacophoridae)

scientific article published on 24 December 2019

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics ⬇️

scientific article published on May 17, 2012

Anchored Hybrid Enrichment-Based Phylogenomics of Leafhoppers and Treehoppers (Hemiptera: Cicadomorpha: Membracoidea)

Anchored Phylogenomics of Angiosperms I: Assessing the Robustness of Phylogenetic Estimates

article

Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae)

scientific article

Anchored hybrid enrichment generated nuclear, plastid and mitochondrial markers resolve the Lepanthes horrida (Orchidaceae: Pleurothallidinae) species complex

scientific article published on 21 July 2018

Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L.

scientific article published on 19 January 2017

Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment

scientific article

Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes

scientific article published on 12 October 2015

Diversification in wild populations of the model organism Anolis carolinensis: A genome-wide phylogeographic investigation.

scientific article published on 17 October 2016

Drift, selection, and adaptive variation in small populations of a threatened rattlesnake

scientific article published on 17 June 2020

Editor’s Note: Phylogenomic Analysis of a Putative Missing Link Sparks Reinterpretation of Leech Evolution

scientific article published in 2019

Effectiveness of phylogenomic data and coalescent species-tree methods for resolving difficult nodes in the phylogeny of advanced snakes (Serpentes: Caenophidia).

scientific article

Environmental temperatures shape thermal physiology as well as diversification and genome-wide substitution rates in lizards

scientific article published on 09 September 2019

Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards

scientific article published on 11 April 2015

Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life

scientific article

Expression of concern: Phylogenomic Analysis of a Putative Missing Link Sparks Reinterpretation of Leech Evolution

scientific article published on 01 July 2019

Geological and climatic forces driving speciation in the continentally distributed trilling chorus frogs (Pseudacris).

scientific article

Golden Orbweavers Ignore Biological Rules: Phylogenomic and Comparative Analyses Unravel a Complex Evolution of Sexual Size Dimorphism.

scientific article published in July 2019

Hierarchical Hybrid Enrichment: Multi-tiered genomic data collection across evolutionary scales, with application to chorus frogs (Pseudacris)

scientific article published on 30 December 2019

High-Throughput Identification of Informative Nuclear Loci for Shallow-Scale Phylogenetics and Phylogeography ⬇️

scientific article published on May 18, 2012

Higher-Level Phylogeny and Reclassification of Lampyridae (Coleoptera: Elateroidea) ⬇️

Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics

scientific article

In the shadows: Phylogenomics and coalescent species delimitation unveil cryptic diversity in a Cerrado endemic lizard (Squamata: Tropidurus).

scientific article

Interrogating genomic-scale data for Squamata (lizards, snakes, and amphisbaenians) shows no support for key traditional morphological relationships

scientific article published on 24 September 2019

Methodological congruence in phylogenomic analyses with morphological support for teiid lizards (Sauria: Teiidae).

scientific article

Mitogenomes of two neotropical bird species and the multiple independent origin of mitochondrial gene orders in Passeriformes

scientific article published on 17 February 2018

Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes

scientific article published on 25 February 2019

Neutral and selective drivers of colour evolution in a widespread Australian passerine

article

New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset

scientific article

Off-target capture data, endosymbiont genes and morphology reveal a relict lineage that is sister to all other singing cicadas ⬇️

Out of Sight, Out of Mind: Widespread Nuclear and Plastid-Nuclear Discordance in the Flowering Plant Genus Polemonium (Polemoniaceae) Suggests Widespread Historical Gene Flow Despite Limited Nuclear Signal

scientific article published on 03 July 2020

Owlflies are derived antlions: anchored phylogenomics supports a new phylogeny and classification of Myrmeleontidae (Neuroptera)

Phylogenomic Analysis of a Putative Missing Link Sparks Reinterpretation of Leech Evolution

scientific article published on 01 July 2019

Phylogenomic data reveal reticulation and incongruence among mitochondrial candidate species in Dusky Salamanders (Desmognathus)

scientific article published on 03 February 2020

Phylogenomic data yield new and robust insights into the phylogeny and evolution of weevils

scientific article published on 26 December 2017

Phylogenomic support for evolutionary relationships of New World direct-developing frogs (Anura: Terraranae).

scientific article

Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life

scientific article published on 02 May 2020

Phylogenomics clarifies repeated evolutionary origins of inbreeding and fungus farming in bark beetles (Curculionidae, Scolytinae)

scientific article published on 31 May 2018

Phylogenomics of Ichneumonoidea (Hymenoptera) and implications for evolution of mode of parasitism and viral endogenization

scientific article published on 27 November 2020

Phylogenomics of monitor lizards and the role of competition in dictating body size disparity

scientific article published on 10 June 2020

Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes

scientific article published in Nature Communications

Phylogenomics, biogeography and morphometrics reveal rapid phenotypic evolution in pythons after crossing Wallace's line

scientific article published on 24 March 2020

Phylogenomics, biogeography and taxonomic revision of New Guinean pythons (Pythonidae, Leiopython) harvested for international trade

scientific article published on 17 September 2020

Phylogeny-based delimitation of species boundaries and contact zones in the trilling chorus frogs (Pseudacris).

scientific article published on 3 May 2007

Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus

scientific article published on 11 May 2020

Quantity, Not Quality: Rapid Adaptation in a Polygenic Trait Proceeded Exclusively through Expression Differentiation

scientific article published on 30 August 2017

Recalcitrant deep and shallow nodes in Aristolochia (Aristolochiaceae) illuminated using anchored hybrid enrichment

scientific article

Reinforcement and the genetics of hybrid incompatibilities

scientific article

Reinforcement in chorus frogs: lifetime fitness estimates including intrinsic natural selection and sexual selection against hybrids

scientific article published on 20 January 2010

Resolving Cypriniformes relationships using an anchored enrichment approach

scientific article

Resolving Rapid Radiations Within Angiosperm Families Using Anchored Phylogenomics

scientific article published on 4 May 2017

Resolving relationships among the megadiverse butterflies and moths with a novel pipeline for Anchored Phylogenomics

scientific article

Resolving the psyllid tree of life: phylogenomic analyses of the superfamily Psylloidea (Hemiptera)

Reticulate evolution in nuclear Middle America causes discordance in the phylogeny of palm‐pitvipers (Viperidae: Bothriechis ) ⬇️

Selection To Increase Expression, Not Sequence Diversity, Precedes Gene Family Origin and Expansion in Rattlesnake Venom

scientific article published on 5 May 2017

Speciation in the mountains and dispersal by rivers: Molecular phylogeny of Eulamprus water skinks and the biogeography of Eastern Australia

article

Species delimitation and systematics of the green pythons (Morelia viridis complex) of melanesia and Australia

scientific article published on 09 October 2019

Target Nuclear and Off-Target Plastid Hybrid Enrichment Data Inform a Range of Evolutionary Depths in the Orchid Genus Epidendrum

scientific article published on 01 January 2019

Targeted Sampling and Target Capture: Assessing Phylogeographic Concordance with Genome-wide Data

scientific article published on 01 November 2018

The Origins and Diversification of the Exceptionally Rich Gemsnakes (Colubroidea: Lamprophiidae: Pseudoxyrhophiinae) in Madagascar

scientific article published on 01 November 2019

The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales

scientific article published on 10 November 2020

The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference

scientific article

The impact of anchored phylogenomics and taxon sampling on phylogenetic inference in narrow-mouthed frogs (Anura, Microhylidae)

scientific article (publication date: 19 March 2015)

The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics.

scientific article

The importance of proper model assumption in bayesian phylogenetics

scientific article published in April 2004

The metapopulation genetic algorithm: An efficient solution for the problem of large phylogeny estimation

scientific article

The phylogeny and biogeography of Hakea (Proteaceae) reveals the role of biome shifts in a continental plant radiation

scientific article

The promises and pitfalls of next-generation sequencing data in phylogeography

scientific article published in October 2012

The venom-gland transcriptome of the eastern diamondback rattlesnake (Crotalus adamanteus)

scientific article

Tipping the scales: the migration-selection balance leans toward selection in snake venoms

scientific article published on 01 February 2019

Tracking temporal shifts in area, biomes, and pollinators in the radiation of Salvia (sages) across continents: leveraging anchored hybrid enrichment and targeted sequence data

scientific article published on 15 April 2019

Uncovering the genomic signature of ancient introgression between white oak lineages (Quercus)

scientific article published on 08 April 2019

Using phylogenomics to understand the link between biogeographic origins and regional diversification in ratsnakes

scientific article

When trees grow too long: investigating the causes of highly inaccurate bayesian branch-length estimates.

scientific article

Whole genome duplication potentiates inter-specific hybridisation and niche shifts in Australian burrowing frogs Neobatrachus

article published in 2019

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