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List of works by Lacey Knowles

A matter of phylogenetic scale: Distinguishing incomplete lineage sorting from lateral gene transfer as the cause of gene tree discord in recent versus deep diversification histories

scientific article published on 01 March 2018

Applying species-tree analyses to deep phylogenetic histories: challenges and potential suggested from a survey of empirical phylogenetic studies

scientific article

Author Correction: Decimated little brown bats show potential for adaptive change

scientific article published on 24 March 2020

Bayesian species delimitation combining multiple genes and traits in a unified framework.

scientific article published on 16 January 2015

Breaking out of biogeographical modules: range expansion and taxon cycles in the hyperdiverse ant genus Pheidole

scientific article

Calibrating divergence times on species trees versus gene trees: implications for speciation history of Aphelocoma jays.

scientific article

Colonization from divergent ancestors: glaciation signatures on contemporary patterns of genomic variation in Collared Pikas (Ochotona collaris).

scientific article

Common barriers, but temporal dissonance: Genomic tests suggest ecological and paleo-landscape sieves structure a coastal riverine fish community

scientific article published on 11 February 2020

Conceptual and empirical bridges between micro- and macroevolution

scientific article published in 2023

Conflict between direct and indirect benefits of female choice in desert Drosophila

scientific article published on February 2007

Contrasting support for alternative models of genomic variation based on microhabitat preference: species-specific effects of climate change in alpine sedges

scientific article

Coupling Genetic and Ecological-Niche Models to Examine How Past Population Distributions Contribute to Divergence

scientific article (publication date: June 2007)

Decimated little brown bats show potential for adaptive change

scientific article published on 20 February 2020

Delimiting species without monophyletic gene trees

scientific article (publication date: December 2007)

Differences in Quaternary co-divergence reveals community-wide diversification in the mountains of southwest China varied among species

scientific article published on 06 January 2021

Disentangling the effects of historic vs. contemporary landscape structure on population genetic divergence

scientific article

Dispersal barriers and opportunities drive multiple levels of phylogeographic concordance in the Southern Alps of New Zealand

scientific article published on 29 September 2020

Diversification History of Clown Tree Frogs in Neotropical Rainforests (Anura, Hylidae, Dendropsophus leucophyllatus group)

scientific article published on 05 June 2020

Do estimated and actual species phylogenies match? Evaluation of East African cichlid radiations

scientific article

Does niche divergence accompany allopatric divergence in Aphelocoma jays as predicted under ecological speciation? Insights from tests with niche models.

scientific article

Ecological niche models in phylogeographic studies: applications, advances and precautions

scientific article

Ecological selection as the cause and sexual differentiation as the consequence of species divergence? ⬇️

scientific article published on January 7, 2013

Effects of missing data on species tree estimation under the coalescent ⬇️

scientific article published on June 13, 2013

Effects of vicariant barriers, habitat stability, population isolation and environmental features on species divergence in the south-western Australian coastal reptile community.

scientific article

Embracing heterogeneity: Building the Tree of Life and the future of phylogenomics

Embracing heterogeneity: Building the Tree of Life and the future of phylogenomics

Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics

scientific article published on 14 February 2019

Estimating a geographically explicit model of population divergence

scientific article

Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers

scientific article

Estimating species trees: methods of phylogenetic analysis when there is incongruence across genes

scientific article published on 17 September 2009

Evidence for overdominant selection maintaining X-linked fitness variation in Drosophila melanogaster

scientific article published in July 2006

Exploring the consequences of postmating-prezygotic interactions between the sexes

scientific article published on 01 August 2004

Exploring the population genetic consequences of the colonization process with spatio-temporally explicit models: insights from coupled ecological, demographic and genetic models in montane grasshoppers

scientific article

Full modeling versus summarizing gene-tree uncertainty: Method choice and species-tree accuracy ⬇️

scientific article published on July 23, 2012

Functional connectivity in sympatric spiny rats reflects different dimensions of Amazonian forest‐association

scientific article published in 2021

Genealogical portraits of speciation in montane grasshoppers (genus Melanoplus) from the sky islands of the Rocky Mountains

scientific article published in February 2001

Genome‐wide DNA and phenotypic information supports recent colonization of South American grasslands by Correndera Pipit (Aves, Motacillidae)

scientific article published in 2021

Genomic evidence of survival near ice sheet margins for some, but not all, North American trees

article

Genomic insights into the origin of trans‐Mediterranean disjunct distributions

scientific article published in 2020

Genomic signatures of paleodrainages in a freshwater fish along the southeastern coast of Brazil: genetic structure reflects past riverine properties

scientific article published on 2 August 2017

Genomic tests of the species-pump hypothesis: Recent island connectivity cycles drive population divergence but not speciation in Caribbean crickets across the Virgin Islands

scientific article published on 8 May 2015

Geographic distributions, phenotypes, and phylogenetic relationships of Phalloceros (Cyprinodontiformes: Poeciliidae): Insights about diversification among sympatric species pools

scientific article published on 07 December 2018

Geographical isolation versus dispersal: Relictual alpine grasshoppers support a model of interglacial diversification with limited hybridization

scientific article published in 2021

Glacial refugia, recolonization patterns and diversification forces in Alpine-endemic Megabunus harvestmen.

scientific article

Global phylogenetic structure of the hyperdiverse ant genus Pheidole reveals the repeated evolution of macroecological patterns

scientific article

Habitat corridors facilitate genetic resilience irrespective of species dispersal abilities or population sizes

scientific article

How low can you go? The effects of mutation rate on the accuracy of species-tree estimation

scientific article

INSIGHT INTO SPECIATION FROM HISTORICAL DEMOGRAPHY IN THE PHYTOPHAGOUS BEETLE GENUS OPHRAELLA.

scientific article published on December 1999

Identifying targets of selection in mosaic genomes with machine learning: applications in Anopheles gambiae for detecting sites within locally adapted chromosomal inversions

scientific article

Importance of genetic drift during Pleistocene divergence as revealed by analyses of genomic variation

scientific article

Incorporating interspecific interactions into phylogeographic models: A case study with Californian oaks

scientific article published on 13 July 2020

Integrative taxonomy of the lizards Cercosaura ocellata species complex (Reptilia: Gymnophthalmidae)

scientific article published in 2018

Integrative testing of how environments from the past to the present shape genetic structure across landscapes

scientific article published on 5 June 2013

Intergenomic conflict revealed by patterns of sex-biased gene expression

scientific article published in September 2005

Is Recombination a Problem for Species-Tree Analyses? ⬇️

scientific article published on January 2, 2012

Linking micro- and macroevolutionary perspectives to evaluate the role of Quaternary sea-level oscillations in island diversification

scientific article published on 26 October 2017

Localized versus generalist phenotypes in a broadly distributed tropical mammal: how is intraspecific variation distributed across disparate environments? ⬇️

scientific article published on July 31, 2013

Machine Learning Biogeographic Processes from Biotic Patterns: A New Trait-Dependent Dispersal and Diversification Model with Model Choice By Simulation-Trained Discriminant Analysis

scientific article published on 28 December 2015

Machine Learning Biogeographic Processes from Biotic Patterns: A New Trait-Dependent Dispersal and Diversification Model with Model-Choice By Simulation-Trained Discriminant Analysis

article

Macroevolutionary integration of phenotypes within and across ant worker castes

scientific article published on 18 August 2020

Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design

scientific article

Microevolutionary processes impact macroevolutionary patterns

scientific article published on 10 August 2018

Microhabitat differences impact phylogeographic concordance of codistributed species: genomic evidence in montane sedges (Carex L.) from the Rocky Mountains

scientific article published on 21 August 2014

Molecular evidence of a peripatric origin for two sympatric species of field crickets (Gryllus rubens and G. texensis) revealed from coalescent simulations and population genetic tests.

scientific article

Multispecies coalescent delimits structure, not species

scientific article

Museum epigenomics: Characterizing cytosine methylation in historic museum specimens

scientific article published on 04 November 2019

Museum specimens and phylogenies elucidate ecology's role in coevolutionary associations between mites and their bee hosts

scientific article

New species boundaries and the diversification history of marsh rat taxa clarifies historical connections among ecologically and geographically distinct wetlands of South America

scientific article published on 20 October 2020

Occupancy spectrum distribution: application for coalescence simulation with generic mergers

scientific article published on 12 February 2020

Paternity analyses in wild-caught and laboratory-reared Caribbean cricket females reveal the influence of mating environment on post-copulatory sexual selection

scientific article published on 8 September 2015

Phylogenetic Analysis of Montane Grasshoppers from Western North America (Genus Melanoplus, Acrididae: Melanoplinae)

article

Rapid adaptation with gene flow via a reservoir of chromosomal inversion variation?

article

Recombination rate and protein evolution in yeast

scientific article

Repeated Parallel Evolution of Minimal rRNAs Revealed from Detailed Comparative Analysis ⬇️

scientific article published on March 21, 2011

Riverscape properties contribute to the origin and structure of a hybrid zone in a Neotropical freshwater fish

scientific article published on 09 August 2020

STEM: species tree estimation using maximum likelihood for gene trees under coalescence

scientific article published on 10 February 2009

Sexually antagonistic coevolution of a postmating-prezygotic reproductive character in desert Drosophila

scientific article published on 10 July 2001

Shifting distributions and speciation: species divergence during rapid climate change.

scientific article

Similar but different: Revealing the relative roles of species‐traits versus biome properties structuring genetic variation in South American marsh rats

scientific article published on 26 February 2019

Socially Parasitic Ants Evolve a Mosaic of Host-Matching and Parasitic Morphological Traits

scientific article published on 21 July 2020

Sources of Error Inherent in Species-Tree Estimation: Impact of Mutational and Coalescent Effects on Accuracy and Implications for Choosing among Different Methods ⬇️

scientific article published on September 10, 2010

Spatially explicit models of dynamic histories: examination of the genetic consequences of Pleistocene glaciation and recent climate change on the American Pika ⬇️

scientific article published on June 15, 2012

Species detection and individual assignment in species delimitation: can integrative data increase efficacy?

scientific article published on 8 January 2014

Species-specific responses to island connectivity cycles: refined models for testing phylogeographic concordance across a Mediterranean Pleistocene Aggregate Island Complex.

scientific article published on 8 July 2015

Statistical phylogeography

scientific article

TESTS OF INBREEDING EFFECTS ON HOST-SHIFT POTENTIAL IN THE PHYTOPHAGOUS BEETLE OPHRAELLA COMMUNA.

scientific article published on April 1999

Terrestrial species adapted to sea dispersal: differences in propagule dispersal of two Caribbean mangroves

article

Testing the effect of palaeodrainages versus habitat stability on genetic divergence in riverine systems: study of a Neotropical fish of the Brazilian coastal Atlantic Forest

article

Testing which axes of species differentiation underlie covariance of phylogeographic similarity among montane sedge species

scientific article published on 02 January 2021

Tests of phenotypic and genetic concordance and their application to the conservation of Panamanian golden frogs (Anura, Bufonidae)

scientific article (publication date: August 2007)

Tests of species-specific models reveal the importance of drought in postglacial range shifts of a Mediterranean-climate tree: insights from integrative distributional, demographic and coalescent modelling and ABC model selection.

scientific article

The Species versus Subspecies Conundrum: Quantitative Delimitation from Integrating Multiple Data Types within a Single Bayesian Approach in Hercules Beetles

scientific article published on 16 December 2015

The architecture of river networks can drive the evolutionary dynamics of aquatic populations

scientific article published on 17 February 2016

The historical context of contemporary climatic adaptation: a case study in the climatically dynamic and environmentally complex southwestern United States

scientific article published on 23 January 2020

The mechanisms of morph determination in the amphipod Jassa: implications for the evolution of alternative male phenotypes

scientific article

Toward a paradigm shift in comparative phylogeography driven by trait-based hypotheses

scientific article

Trait-Dependent Biogeography: (Re)Integrating Biology into Probabilistic Historical Biogeographical Models

scientific article published on 20 April 2018

Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences

scientific article

Upstream analyses create problems with DNA-based species delimitation

scientific article published on 20 December 2013

Using gradient Forest to predict climate response and adaptation in Cork oak

scientific article published in 2021

Utilizing RADseq data for phylogenetic analysis of challenging taxonomic groups: A case study in Carex sect. Racemosae

scientific article published on 5 February 2016

What is the danger of the anomaly zone for empirical phylogenetics?

scientific article

Why does a method that fails continue to be used?

scientific article

Widespread geographical distribution of mitochondrial haplotypes in rock-dwelling cichlid fishes from Lake Tanganyika

scientific article published on 01 June 1996

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