Justin C Bagley

Justin C Bagley
Jacksonville State University | JSU · Department of Biology

Ph.D., Integrative Biology
Recruiting grad students (MSc); publishing; teaching; working w/ state agencies (AL) to develop new fish projects.

About

56
Publications
95,204
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
570
Citations
Introduction
I am an ecologist and evolutionary biologist interested in molecular ecology, distributional ecology, and biodiversity science. I use genome-wide SNP & sequence capture data and ecological data to understand how historical/ecological processes shape biodiversity distributions in freshwater and terrestrial ecosystems. Current research: conservation genomics, phylogeography, phylogenomics, speciation/gene flow/local adaptation, and ENM prediction of species past, present, & future distributions.
Additional affiliations
August 2020 - October 2020
Jacksonville State University
Position
  • Professor (Assistant)
Description
  • Assistant Professor, Department of Biology, Jacksonville State University Research: Ecological and evolutionary genetics of plants and animals Courses taught: BY 101 (Introductory Biology I), BY 577 (Seminar in Systematics), BY 460 (Ichthyology)
October 2018 - August 2020
University of Missouri - St. Louis
Position
  • PostDoc Position
Description
  • Plant phylogenomics postdoc focused on phylogenomics, hybridization, and speciation in Andean bellflowers of the genus Burmeistera (family Campanulaceae).
April 2017 - October 2018
Virginia Commonwealth University
Position
  • PostDoc Position
Education
August 2008 - December 2014
Brigham Young University - Provo Main Campus
Field of study
  • Integrative Biology
January 2006 - April 2008
University of Alabama
Field of study
  • Biology
June 2002 - December 2004
University of Alabama
Field of study
  • Biology

Publications

Publications (56)
Article
Full-text available
http://onlinelibrary.wiley.com/doi/10.1111/brv.12076/abstract http://onlinelibrary.wiley.com/doi/10.1111/brv.12076/full Lower Central America (LCA) provides a geologically complex and dynamic, richly biodiverse model for studying the recent assembly and diversification of a Neotropical biota. Here, we review the growing literature of LCA phylogeog...
Article
Full-text available
Accurately delimiting species is fundamentally important for understanding species diversity and distributions and devising effective strategies to conserve biodiversity. However, species delimitation is problematic in many taxa, including 'non-adaptive radiations' containing morphologically cryptic lineages. Fortunately, coalescent-based species d...
Article
Full-text available
Interactions between extrinsic factors, such as disruptive selection, and intrinsic factors, such as genetic incompatibilities among loci, often contribute towards the maintenance of species boundaries. The relative roles of these factors in the establishment of reproductive isolation can be examined using species pairs characterized by gene flow t...
Preprint
Full-text available
Populus tremuloides is the widest-ranging tree species in North America, and an ecologically important component of mesic forest ecosystems displaced by the Pleistocene glaciations. Using phylogeographic analyses of genome-wide SNPs (34,796 SNPs, 183 individuals) and ecological niche modeling, we inferred population structure, admixture, and Pleist...
Article
Targeted sequence capture is a promising approach for large-scale phylogenomics. However, rapid evolutionary radiations pose significant challenges for phylogenetic inference (e.g. incomplete lineages sorting (ILS), phylogenetic noise), and the ability of targeted nuclear loci to resolve species trees despite such issues remains poorly studied. We...
Article
Full-text available
In the presently reported study, we estimated length–weight relation (LWRs) for seven species of freshwater fishes from Central America. Samples were collected using seines from 60 sites across Nicaragua, Costa Rica, and Panama during field expeditions conducted between 1997 and 2012. The fishes were preserved and transported to the lab, where thei...
Article
Anoura Gray, 1838 are Neotropical nectarivorous bats and the most speciose genus within the phyllostomid subfamily Glossophaginae. However, Anoura species limits remain debated, and phylogenetic relationships remain poorly known, because previous studies used limited Anoura taxon sampling or focused primarily on higher-level relationships. Here, we...
Article
We describe two new endemic Hypostomus species from central Brazil, which were previously identified as genetically distinct lineages in a recent genomic study that recommended their testing and potential description based on morphological data. A machine learning classification procedure (random forest) was used to investigate morphological variat...
Preprint
Full-text available
River capture is a geological process of potentially great importance in shaping the genetic diversity, distributions, and community composition of freshwater taxa. Using phylogeographic analyses of ddRAD-seq data from suckermouth armored catfish ( Hypostomus sp. 2) populations, we tested for predicted genetic effects of headwater river capture eve...
Article
Full-text available
Extant conifer species may be susceptible to rapid environmental change owing to their long generation times, but could also be resilient due to high levels of standing genetic diversity. Hybridisation between closely related species can increase genetic diversity and generate novel allelic combinations capable of fuelling adaptive evolution. Our s...
Article
Full-text available
Populus tremuloides is the widest‐ranging tree species in North America and an ecologically important component of mesic forest ecosystems displaced by the Pleistocene glaciations. Using phylogeographic analyses of genome‐wide SNPs (34,796 SNPs, 183 individuals) and ecological niche modeling, we inferred population structure, ploidy levels, admixtu...
Article
Full-text available
A lack of optimal gene combinations, as well as low levels of genetic diversity are often associated with the formation of species range margins. Conservation efforts rely on predictive modelling using abiotic variables and assessments of genetic diversity to determine target species and populations for controlled breeding, germplasm conservation a...
Article
Full-text available
The extraordinary species diversity of the Neotropical freshwater fish fauna is world renown. Yet, despite rich species diversity, taxonomic and genetic resources for its Cerrado ichthyofauna remain poorly developed. We provide a reference library of 149 DNA barcodes for 39 species/lineages of Cerrado headwater stream fishes from the Brazilian Dist...
Poster
Full-text available
Southwestern white pine (Pinus strobiformis; SWWP) is a native tree species threatened by the rapidly changing climate and a non-native tree disease (white pine blister rust). Our team of researchers studies the ecology and evolution of SWWP across its range in the United States and Mexico to find solutions for sustaining this tree. Genetic and env...
Article
Full-text available
We describe a new species of Enyalius endemic to the Brazilian Cerrado, based on morphological and molecular data sets. In the face of uncertain taxonomy among museum specimens of Enyalius, we used a novel analytical approach based on Gaussian mixture modeling for species assignments. We also used a machine-learning classification procedure (random...
Article
Full-text available
Most Neotropical frog and freshwater fish species sampled to date show phylogeographic breaks along the Pacific coast of the Isthmus of Panama, with lineages in Costa Rica and western Panama isolated from central Panama. We examine temporal patterns of diversification of taxa across this 'western Panama isthmus' (WPI) break to test hypotheses about...
Preprint
Full-text available
Populus tremuloides is the widest-ranging tree species in North America, and an ecologically important component of mesic forest ecosystems displaced by the Pleistocene glaciations. Using phylogeographic analyses of genome-wide SNPs (34,796 SNPs, 183 individuals) and ecological niche modeling, we inferred population structure, admixture, and Pleist...
Article
Full-text available
Catostomidae (“suckers”) is a diverse (76 species) and broadly distributed family of Holarctic freshwater fishes with a rich fossil record and a considerable number (∼35%) of threatened and imperiled species. We integrate DNA sequences (three mitochondrial genes, three nuclear genes), morphological data, and fossil information to infer sucker phylo...
Data
Appendix S1. Catostomidae fossils, fossil and external calibration age priors, and additional discussion of phylogenetic relationships within the Catostominae.
Data
Fig. S9. Probabilities of different character sets inferring the correct topology, a polytomy, or the incorrect topology (‘phylogenetic noise’) over the period of sucker subfamily divergence. The period investigated is the ‘subfamily divergence epoch’ (SDE; ∼63.16–34.37 Ma) in our time tree. The SDE defines an internode distance, t0, used in the pr...
Data
Fig. S3. MrBayes consensus tree derived from the morphology dataset.
Data
Fig. S5. MrBayes consensus tree derived from the nuclear IRBP dataset.
Data
Fig. S6. MrBayes consensus tree derived from the concatenated nDNA dataset.
Data
Fig. S7. Posterior density plots of BEAST ‘ucldStdev’ and ‘coefficient of variation’ statistics demonstrating significant among-lineage rate heterogeneity in the total-evidence dataset. Problematic mtDNA 1st and 3rd codon sites were excluded from the analysis.
Data
Table S1. Data subsets and corresponding DNA substitution models selected in PartitionFinder for the four-locus dataset. Model selection analyses using PartitionFinder v1.1.1 supported different best-fit models of DNA evolution for different data subsets (i.e. groups or ‘blocks’ of data, such as sites filtered by codon positions). When it was not p...
Data
Fig. S1. MrBayes consensus tree derived from the concatenated mtDNA dataset.
Data
Fig. S2. MrBayes consensus tree derived from the mtDNA + morphology dataset.
Data
Fig. S4. MrBayes consensus tree derived from the four-locus dataset.
Data
Fig. S8. Variation in substitution rates among sites. This figure plots variation in substitution rates among sites, based on posterior distributions of the gamma shape parameters (alpha estimates) assigned to different data subsets in BEAST (excluding problematic mtDNA 1stand 3rd codon position sites).
Preprint
Full-text available
Most Neotropical frog and freshwater fish species sampled to date show phylogeographic breaks along the Pacific coast of the Isthmus of Panama, with lineages in Costa Rica and western Panama isolated from central Panama. We examine temporal patterns of diversification of taxa across this ‘western Panama isthmus’ (WPI) break to test hypotheses about...
Preprint
Full-text available
Most Neotropical frog and freshwater fish species sampled to date show phylogeographic breaks along the Pacific coast of the Isthmus of Panama, with lineages in Costa Rica and western Panama isolated from central Panama. We examine temporal patterns of diversification of taxa across this ‘western Panama isthmus’ (WPI) break to test hypotheses about...
Preprint
Full-text available
Interactions between extrinsic factors, such as disruptive selection, and intrinsic factors, such as genetic incompatibilities among loci, can contribute to the maintenance of species boundaries. The relative roles of these factors in the establishment of reproductive isolation can be examined using species pairs characterized by gene flow througho...
Article
Full-text available
Background Estimating the variability in isolation times across co-distributed taxon pairs that may have experienced the same allopatric isolating mechanism is a core goal of comparative phylogeography. The use of hierarchical Approximate Bayesian Computation (ABC) and coalescent models to infer temporal dynamics of lineage co-diversification has b...
Article
Full-text available
The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009;...
Data
This plot is not part of the published stance but derives from it. The plot shows the number of authors by geographic region (courtesy of Dr. Diego Astua).
Article
We investigate phylogeographic patterns and delimit species boundaries within Amatitlania, a genus of CentralAmerican cichlid fishes. Phylogenetic analyses of mitochondrial DNA sequences from 318 individuals spanningthe geographical ranges of all three currently recognized Amatitlania species strongly supported one major clade,with a relatively dive...
Article
Viviparity, the bearing of live young, has evolved well over 100 times among squamate reptiles. This reproductive strategy is hypothesized to allow maternal control of the fetus’ thermal environment and thereby to increase the fitness of the parents and offspring. Two hypotheses have been posited to explain this phenomenon: (i) the cold-climate hyp...
Article
Full-text available
A central goal of comparative phylogeography is determining whether codistributed species experienced (1) concerted evolutionary responses to past geological and climatic events, indicated by congruent spatial and temporal patterns (“concerted-response hypothesis”); (2) independent responses, indicated by spatial incongruence (“independent-response...
Article
Full-text available
Climatic and sea-level fluctuations throughout the last Pleistocene glacial cycle (~130-0 ka) profoundly influenced present-day distributions and genetic diversity of Northern Hemisphere biotas by forcing range contractions in many species during the glacial advance and allowing expansion following glacial retreat ('expansion-contraction' model). E...
Article
Here is a link to my website! Just copy and paste it into your browser to learn more about my research interests, teaching, and blog. I look forward to seeing you and talking with you more on justinbagley.org. Note: It would be nice if ResearchGate permitted external links, html modifications, or other ways to customize one's profile. This is the...
Article
Full-text available
The freshwater fauna of Southern Australia is primarily restricted to the southwestern and southeastern corners of the continent, and is separated by a large, arid region that is inhospitable to this biota. This geographic phenomenon has attracted considerable interest from biogeographers looking to explain evolutionary diversification in this regi...
Data
Mean genetic divergences between western lineage populations of Galaxiella pusilla for cytochrome b calculated using p-distances. (DOC)
Data
Mean genetic divergences between populations of Galaxiella nigrostriata for cytochrome b calculated using p-distances. (DOC)
Data
Summary of genetic diversity of cytochrome b sequences sampled within Galaxiella pusilla populations and clades in this study. Locality numbers, the number of individuals sampled, number of haplotypes (H), haplotype diversity (Hd) with its standard deviations, nucleotide diversity (π) with its standard deviations, and the results of coalescent simu...
Data
Allozyme frequencies at all variable loci for the 22 sites surveyed for Galaxiella pusilla. Site codes follow Table 1. Frequencies of all but the rarer/rarest alleles are expressed as percentages and shown as superscripts (allowing the frequency of each rare allele to be calculated by subtraction from 100%). Maximum sample sizes per site are shown...
Data
Summary of pairwise comparisons of allele frequency between sites for Galaxiella pusilla east. Due to their small sample sizes, sites 16 and 20 were pooled with a geographically-proximate neighbour (sites 15 and 21 respectively). Lower triangle = number of loci displaying statistically-significant differences in allele frequency (P<0.05 after Bonfe...
Data
Summary of pairwise comparisons of allele frequency between sites for Galaxiella pusilla west. Site 9 was excluded from the analysis due to small sample size and lack of a geographically-proximate neighbour. Format as for Table S8. (DOC)
Data
Mean genetic divergences between species for cytochrome b calculated using p-distances. The last column represents mean within species divergences. (DOC)
Data
Mean genetic divergences between eastern lineage populations of Galaxiella pusilla for cytochrome b calculated using p-distances. (DOC)
Data
Mean genetic divergences between populations of Galaxiella munda for cytochrome b calculated using p-distances. (DOC)
Article
http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8312.2011.01720.x/full For groups of animals with limited or unstable taxonomic resolution, congeneric phylogeographical sampling represents a way to potentially increase resolution of species limits and internal branches during phylogenetic inference. We investigated species limits and whether the...

Questions

Questions (7)
Question
Specifically, what is a reasonable point estimate or distribution for the Ts:Tv ratio for plant nuclear DNA, 1) in general, 2) for conifers, and 3) more specifically for Pinaceae? I am looking through the literature for a value, or range of values, to use during simulations of DNA alignments in a study of pine trees. However, I would like to keep any information that the community can provide on this, for future reference during simulations or setting priors during Bayesian phylogenetic inference. A comparison of reasonable chloroplast vs. nuclear values would also be useful. Thanks ~J
Question
RAPiD Genomics (http://www.rapid-genomics.com) is a relatively new company in Florida (USA) that provides researchers a service to outsource genomics work for biology. Among a variety of other services including genotyping, genetic data analysis, bioinformatics, they do target capture to develop Ultraconserved Elements (UCE) data for model or non-model organisms. This is highly desirable data now in phylogeography and phylogenomics. I'm interested in getting the "inside scoop" from someone who's used them.
If you've done UCE work with RAPiD Genomics, please answer the following questions: 1) How was your experience? 2) How many samples did you run? 3) How many UCE loci did you get back? and 4) How much did it cost? I will plan to meet with one of their sales reps for more info, but I would like to hear from other biologists first. Thanks.
~J
Question
Science Careers has for the past couple of years offered the myIDP Individual Development Plan program (http://myidp.sciencecareers.org/) to help scientists assess their skills and identify how they will need to improve to make themselves competitive/suitable for particular science career paths.  I'm simply interested in two aspects of this program:  (1) whether and how many investigators in the Biological Sciences have completed the various assessments within the myIDP website (at least, as gauged from the sample of biologists in the ResearchGate community), and (2) whether they have found this to be useful for their careers.  In particular, did completing the myIDP program help you identify and/or hone your skills?  In your experience, has completing the myIDP program helped you obtain your current position or prepare for interviews?  Look forward to hearing back from people about this.
Question
Ecological niche modeling is increasingly important for understanding the factors that shape species distributions, as well as testing biogeographical hypotheses about species past, present, and future distributions as well as the role of ecology in speciation. However, most niche modeling work has focused on terrestrial and marine species (sound like conservation biology, in general?). I have previously used MAXENT to develop and project models of fish distributions, and the models we have published exhibited excellent predictive performance. And I am very interested in continuing to do so, particularly through coupling ENMs with phylogeographic analyses, and/or using them to inform phylogeographic hypotheses testing. However, I am skeptical of all models to some degree, and I am wanting to learn whether other techniques exist that would be more suitable for freshwater fish ecological niche modeling and paleoclimatic modeling, other than MAXENT (which is obviously most convenient for me). I am also interested in what the best data layers are for ENM analyses of freshwater habitats. I always want to learn more about these topics, so I figured I would ask here.
So, first, do such 'better' ENM models exist that could/should be used instead of or in combination with MAXENT? And, if so, what is required to run such other models, and how would the assumptions of these potentially 'better' models differ from those of MAXENT in different cases?
Second, it seems that a limitation of ecological niche modeling for freshwater taxa is a lack of sufficiently high resolution data layers for aquatic habitats. However, I am unsure about geospatial data repositories or resources for generating more suitable layers, and I would like specific advice about GIS procedures and data layers for making better data coverages. I am aware that some people are already doing this, but usually at very fine spatial scales. The broader community of ecologists and evolutionary biologists interested in fishes would therefore benefit much more from more comprehensive coverages.
FYI, I should indicate that I am not really interested in using masks over bioclimatic variables to restrict model output to the boundaries of stream and river networks, because many pilot analyses I have run on North American species suggest this does not add much or produce different results relative to running the models without such masks. So, I would prefer to avoid such discussion unless you know or can show me that doing so improves model performance. Thanks in advance for your replies. Take care.
Question
There are many metrics for measuring biodiversity in community ecology. It seems most diversity metrics are based on the spatially nested hierarchical organization of regional biotas. I am wanting your opinions about what the best metric is for measuring community diversity and comparing such patterns across scales. There are probably many squibbles about this, and some people might for example say that Shannon's index is irrelevant and shouldn't be reported. What do you think?
Question
In recent years, additive partitioning has surfaced as an important tool for understanding spatial and temporal scaling of biodiversity. However, I recently noticed that there seems to be some debate about this method. I want to know if additive partitioning is valid, and what the best way to go about such an analysis is. So, please offer any insights you have. My interest is primarily in freshwater organisms. Thus, I also have to say that I can't help but notice that there seem to be very few additive partitioning studies of freshwater taxa/communities in the literature. Why is this and is anyone doing any work on diversity partitioning using freshwater fishes?
Question
It is now standard practice to make not only your results, but also your data and metadata for a project freely accessible to the world. This is the best practice for the scientific enterprise, hands down. Personally, in addition to GenBank, I have had good experiences with TreeBASE in using their services to publish data (although formatting your datasets and getting everything right in their system can be a bit tricky). I want to know which database/repository do you prefer, particularly if you had to choose between Dryad or TreeBASE, for accessioning your phylogenetic results, DNA alignments, metadata, or analysis input files? In considering this question, you may want to give your opinion about which service is least expensive in time or funding, which online interface is nicest and easiest to use, which data types are accepted, or how difficult it is to format your files for upload. One thing that is not clear sometimes is whether you will have to pay a fee for Dryad services or not. Any opinions?

Network

Cited By

Projects

Projects (10)
Project
The long-term research goal of this project is to improve understanding of angiosperm diversification by uncovering the factors that have driven the recent, explosive radiations of Neotropical angiosperms with Andean-centered distributions. These clades are especially speciose, comprising over one-third of the plant diversity found in the Neotropics, and also tend to have highly specialized pollination systems. In this project, we study the process of speciation in the plant genus Burmeistera (Campanulaceae; ~130 described and undescribed species) by generating a species-level phylogeny to compare the contributions of pollination, gametic, and postzygotic barriers in maintaining species boundaries. Our central hypothesis is that post-pollination barriers have played the primary role in speciation, and that pollinator-mediated isolation only evolves secondarily in response to competition for pollination. Previous work shows a pattern of reproductive character displacement in pollen placement among sympatric Burmeistera, in that co-occurring species use different portions of bats’ bodies to transfer their pollen (Muchhala & Potts 2007). But did this pollinator isolation trigger speciation or follow it? We test this by 1) developing a species-level phylogeny of Burmeistera using a phylogenomic approach based on a recent targeted sequence capture approach, Hyb-Seq (Weitmier et al., 2014); 2) statistically testing the importance of pollinator isolation during speciation in Burmeistera, through phylogenetic comparative analyses of stamina column exsertion length (a marker of pollination syndrome (exsertion length), using the phylogeny from Goal 1; and 3) comparing gametic, postzygotic, and pollinator isolation as barriers to gene flow.