I am working with collaborators in Brazil, the U.S., and Mexico to complete genetic data analyses and manuscripts from two postdoctoral research fellowships. This slideshow presents a brief overview of the two main funded research projects that I am involved in.
Project Overview: Ecological & Evolutionary Genetics of Southwestern White Pi...Justin C. Bagley
Provides a brief overview of our project on the ecological and evolutionary genetics of southwestern white pine (SWWP), an alpine white pine distributed in the sky-islands of the North American desert southwest.
Association mapping identifies loci for canopy coverage in diverse soybean ge...Avjinder (Avi) Kaler
Rapid establishment of canopy coverage decreases
soil evaporation relative to transpiration improves
water use efficiency and light interception, and increases
soybean competitiveness against weeds.
Project Overview: Ecological & Evolutionary Genetics of Southwestern White Pi...Justin C. Bagley
Provides a brief overview of our project on the ecological and evolutionary genetics of southwestern white pine (SWWP), an alpine white pine distributed in the sky-islands of the North American desert southwest.
Association mapping identifies loci for canopy coverage in diverse soybean ge...Avjinder (Avi) Kaler
Rapid establishment of canopy coverage decreases
soil evaporation relative to transpiration improves
water use efficiency and light interception, and increases
soybean competitiveness against weeds.
Genome Wide SNP Analysis for Inferring the Population Structure and Genetic H...Hong ChangBum
Study of genome-wide SNPs, mitochondrial DNA and Y-chromosomal DNA variation can provide a valuable information about the population structure and peopling of human populations. To explain a genetic homogeneity of Koreans and population structure of Koreans and the East Asian populations, we analyzed 153 individuals from the Korea and 77 individuals from the East Asia at 46,559 common single-nucleotide polymorphic loci. The 137 CHB and 113 JPT individuals at 25,769 common SNPs from the International HapMap project were further analyzed to reveal the population structure of the East Asians. Principal Component analyses (PCA) and population differentiation ( ) are examined. In the PCA test, the Jeju individuals were slightly different from other Koreans but their values were not significant. This reflect the genetic homogeneity of Korea population. In general, all the individual samples studied here were clustered into subset of ethnic origin according to their geographical location except Mongolians. Whole genome sequencing of Koreans and other population genome by next generation sequencing technology will provide great opportunity to understand the population expansion and peopling of Korea better.
Biodiversity conservation in fragmented landscapesMarco Pautasso
Biodiversity conservation in fragmented landscapes, the importance of habitat and landscape connectivity, resilience to abrupt climate changes, roadless areas, protected areas
My talk on genome-wide selection components analysis in a fish with male pregnancy (the Gulf pipefish, Syngnathus scovelli) from the Evolution 2017 meeting. Video of presentation available https://www.youtube.com/watch?v=gOdv99wF_TY
Population genomics reveals multiple drivers of population differentiationSarah Flanagan
My presentation at the Evolution 2016 meeting in Austin, TX about using ddRAD-seq to identify the effects of genetic drift, sexual selection, and local adaptation on the genome of 12 populations of Syngnathus scovelli, the Gulf pipefish. #Evol2016
Evaluating fodder quality in sorghum RIL population under contrasting water r...ICRISAT
Drought (midseason or terminal)is a regular and recurring event in arid and semi-arid land, affected by approximately 30% of the world total area and are in habited by 20% of the total world population. The reduction in crop production and yield caused by drought has direct effecton livelihood of farmers(and their families)that inturn affects the yield from livestock (draft capacity/milching).Sorghum is a dual purpose drought resilient crop cultivated in Africa and Asia.
Genomic aided selection for crop improvementtanvic2
In last Several years novel genetic and genomics approaches are expended. Genetics and genomics have greatly enhanced our understanding of the structural and functional aspects of plant genomes.
33. N. L. Roberts, A. M. Piotrowski, J. F. McManus, L. D. Keig.docxgilbertkpeters11344
33. N. L. Roberts, A. M. Piotrowski, J. F. McManus, L. D. Keigwin,
Science 327, 75–78 (2010).
34. W. Broecker, A. E. Putnam, Quat. Sci. Rev. 57, 17–25
(2012).
35. Y.-J. Wang et al., Science 294, 2345–2348 (2001).
36. K. A. Allen et al., Quat. Sci. Rev. 122, 180–191 (2015).
37. Z. Liu et al., Science 325, 310–314 (2009).
38. P. Köhler, G. Knorr, E. Bard, Nat. Commun. 5, 5520 (2014).
39. K. Matsumoto, Geophys. Res. Lett. 34, L20605 (2007).
40. J. Southon, A. L. Noronha, H. Cheng, R. L. Edwards, Y. J. Wang,
Quat. Sci. Rev. 33, 32–41 (2012).
41. K. K. Andersen et al.North Greenland Ice Core Project
members, Nature 431, 147–151 (2004).
ACKNOWLEDGMENTS
This study was funded by the European Research Council, the
Philip Leverhulme Trust, the U.S. National Science Foundation
(grants 0636787, 0944474, 0902957, and 1234664), and a Marie
Curie Reintegration Grant. All the data reported in this paper are
available in the supplementary materials. We acknowledge the
crew and science parties of RRS James Cook cruise JC094 and RV
Nathaniel B. Palmer cruise NBP1103 who made this study possible.
We also thank J. F. McManus and K. R. Hendry for the helpful
comments during the preparation of this manuscript and
C. D. Coath, C. A. Taylor, S. Lucas, and C. Bertrand for help with
sample preparation and analyses. Comments from two anonymous
reviewers helped to improve the manuscript, inspiring us to look at
the deglacial ventilation and circulation events from a more
broadened view.
SUPPLEMENTARY MATERIALS
www.sciencemag.org/content/349/6255/1537/suppl/DC1
Materials and Methods
Supplementary Text
Figs. S1 to S6
Tables S1 to S4
References (42–54)
20 May 2015; accepted 27 August 2015
10.1126/science.aac6159
EVOLUTIONARY ECOLOGY
Functional mismatch in a bumble bee
pollination mutualism under
climate change
Nicole E. Miller-Struttmann,1,2* Jennifer C. Geib,3 James D. Franklin,2 Peter G. Kevan,4
Ricardo M. Holdo,2 Diane Ebert-May,5 Austin M. Lynn,2 Jessica A. Kettenbach,2,6
Elizabeth Hedrick,7 Candace Galen2
Ecological partnerships, or mutualisms, are globally widespread, sustaining agriculture and
biodiversity. Mutualisms evolve through the matching of functional traits between partners,
such as tongue length of pollinators and flower tube depth of plants. Long-tongued pollinators
specialize on flowers with deep corolla tubes, whereas shorter-tongued pollinators generalize
across tube lengths. Losses of functional guilds because of shifts in global climate may disrupt
mutualisms and threaten partner species. We found that in two alpine bumble bee species,
decreases in tongue length have evolved over 40 years. Co-occurring flowers have not become
shallower, nor are small-flowered plants more prolific. We argue that declining floral resources
because of warmer summers have favored generalist foraging, leading to a mismatch between
shorter-tongued bees and the longer-tubed plants they once pollinated.
L
ong-tongued bumble bees have coevolved
to pollinate pla.
Effects of density on spacing patterns and habitat associations of a Neotropi...Nicole Angeli
Presentation at Ecological Society of America, August 2013. Minneapolis, USA. –Oral Paper
Angeli, N. F., K. Lips, G. V. DiRenzo, and A. Cunha. “Effects of density on spacing patterns
and habitat associations in the Neotropical Glassfrog Espadarana prosoblepon.”
Genome Wide SNP Analysis for Inferring the Population Structure and Genetic H...Hong ChangBum
Study of genome-wide SNPs, mitochondrial DNA and Y-chromosomal DNA variation can provide a valuable information about the population structure and peopling of human populations. To explain a genetic homogeneity of Koreans and population structure of Koreans and the East Asian populations, we analyzed 153 individuals from the Korea and 77 individuals from the East Asia at 46,559 common single-nucleotide polymorphic loci. The 137 CHB and 113 JPT individuals at 25,769 common SNPs from the International HapMap project were further analyzed to reveal the population structure of the East Asians. Principal Component analyses (PCA) and population differentiation ( ) are examined. In the PCA test, the Jeju individuals were slightly different from other Koreans but their values were not significant. This reflect the genetic homogeneity of Korea population. In general, all the individual samples studied here were clustered into subset of ethnic origin according to their geographical location except Mongolians. Whole genome sequencing of Koreans and other population genome by next generation sequencing technology will provide great opportunity to understand the population expansion and peopling of Korea better.
Biodiversity conservation in fragmented landscapesMarco Pautasso
Biodiversity conservation in fragmented landscapes, the importance of habitat and landscape connectivity, resilience to abrupt climate changes, roadless areas, protected areas
My talk on genome-wide selection components analysis in a fish with male pregnancy (the Gulf pipefish, Syngnathus scovelli) from the Evolution 2017 meeting. Video of presentation available https://www.youtube.com/watch?v=gOdv99wF_TY
Population genomics reveals multiple drivers of population differentiationSarah Flanagan
My presentation at the Evolution 2016 meeting in Austin, TX about using ddRAD-seq to identify the effects of genetic drift, sexual selection, and local adaptation on the genome of 12 populations of Syngnathus scovelli, the Gulf pipefish. #Evol2016
Evaluating fodder quality in sorghum RIL population under contrasting water r...ICRISAT
Drought (midseason or terminal)is a regular and recurring event in arid and semi-arid land, affected by approximately 30% of the world total area and are in habited by 20% of the total world population. The reduction in crop production and yield caused by drought has direct effecton livelihood of farmers(and their families)that inturn affects the yield from livestock (draft capacity/milching).Sorghum is a dual purpose drought resilient crop cultivated in Africa and Asia.
Genomic aided selection for crop improvementtanvic2
In last Several years novel genetic and genomics approaches are expended. Genetics and genomics have greatly enhanced our understanding of the structural and functional aspects of plant genomes.
33. N. L. Roberts, A. M. Piotrowski, J. F. McManus, L. D. Keig.docxgilbertkpeters11344
33. N. L. Roberts, A. M. Piotrowski, J. F. McManus, L. D. Keigwin,
Science 327, 75–78 (2010).
34. W. Broecker, A. E. Putnam, Quat. Sci. Rev. 57, 17–25
(2012).
35. Y.-J. Wang et al., Science 294, 2345–2348 (2001).
36. K. A. Allen et al., Quat. Sci. Rev. 122, 180–191 (2015).
37. Z. Liu et al., Science 325, 310–314 (2009).
38. P. Köhler, G. Knorr, E. Bard, Nat. Commun. 5, 5520 (2014).
39. K. Matsumoto, Geophys. Res. Lett. 34, L20605 (2007).
40. J. Southon, A. L. Noronha, H. Cheng, R. L. Edwards, Y. J. Wang,
Quat. Sci. Rev. 33, 32–41 (2012).
41. K. K. Andersen et al.North Greenland Ice Core Project
members, Nature 431, 147–151 (2004).
ACKNOWLEDGMENTS
This study was funded by the European Research Council, the
Philip Leverhulme Trust, the U.S. National Science Foundation
(grants 0636787, 0944474, 0902957, and 1234664), and a Marie
Curie Reintegration Grant. All the data reported in this paper are
available in the supplementary materials. We acknowledge the
crew and science parties of RRS James Cook cruise JC094 and RV
Nathaniel B. Palmer cruise NBP1103 who made this study possible.
We also thank J. F. McManus and K. R. Hendry for the helpful
comments during the preparation of this manuscript and
C. D. Coath, C. A. Taylor, S. Lucas, and C. Bertrand for help with
sample preparation and analyses. Comments from two anonymous
reviewers helped to improve the manuscript, inspiring us to look at
the deglacial ventilation and circulation events from a more
broadened view.
SUPPLEMENTARY MATERIALS
www.sciencemag.org/content/349/6255/1537/suppl/DC1
Materials and Methods
Supplementary Text
Figs. S1 to S6
Tables S1 to S4
References (42–54)
20 May 2015; accepted 27 August 2015
10.1126/science.aac6159
EVOLUTIONARY ECOLOGY
Functional mismatch in a bumble bee
pollination mutualism under
climate change
Nicole E. Miller-Struttmann,1,2* Jennifer C. Geib,3 James D. Franklin,2 Peter G. Kevan,4
Ricardo M. Holdo,2 Diane Ebert-May,5 Austin M. Lynn,2 Jessica A. Kettenbach,2,6
Elizabeth Hedrick,7 Candace Galen2
Ecological partnerships, or mutualisms, are globally widespread, sustaining agriculture and
biodiversity. Mutualisms evolve through the matching of functional traits between partners,
such as tongue length of pollinators and flower tube depth of plants. Long-tongued pollinators
specialize on flowers with deep corolla tubes, whereas shorter-tongued pollinators generalize
across tube lengths. Losses of functional guilds because of shifts in global climate may disrupt
mutualisms and threaten partner species. We found that in two alpine bumble bee species,
decreases in tongue length have evolved over 40 years. Co-occurring flowers have not become
shallower, nor are small-flowered plants more prolific. We argue that declining floral resources
because of warmer summers have favored generalist foraging, leading to a mismatch between
shorter-tongued bees and the longer-tubed plants they once pollinated.
L
ong-tongued bumble bees have coevolved
to pollinate pla.
Effects of density on spacing patterns and habitat associations of a Neotropi...Nicole Angeli
Presentation at Ecological Society of America, August 2013. Minneapolis, USA. –Oral Paper
Angeli, N. F., K. Lips, G. V. DiRenzo, and A. Cunha. “Effects of density on spacing patterns
and habitat associations in the Neotropical Glassfrog Espadarana prosoblepon.”
Macro ecology is a subfield of ecology concerned with large spatial and/or temporal scales, focusing on using statistical models to identify emergent properties in species traits (e.g., body size), geographic ranges, local abundance, and diversity to understand the general ecological and evolutionary forces that influence these patterns
Landscape ecology is a subfield of ecology concerned with the reciprocal interactions between spatial patterns and ecological processes at a range of spatial scales. The appropriate spatial scale to quantify the influence of landscape on biodiversity is generally conceptualised in terms of the particular species, communities, or ecological processes of interest.
Species richness, bird macroecology, landscape pathology, network epidemiology. Ants and people: a test of two mechanisms behind the large-scale human-biodiversity correlation for Formicidae in Europe. Aphid biodiversity is correlated with human population in European countries. Plant health and global change – some implications forlandscape management
"Keeping up with the plant destroyers." My talk at The Royal Society, 7 March...Sophien Kamoun
Tackling emerging threats to animal health, food security and ecosystem resilience, The Royal Society, Monday 7 – Tuesday 8 March 2016. https://royalsociety.org/events/2016/03/emerging-fungal-threats/
The climbing vine kudzu, a member of the leguminous
pea family (Fabaceae), was introduced into the USA
from its native Asia in the 1800s. It was initially lauded
for efficacy in erosion control along highways and as a
high-quality grazing crop for livestock. P. montana var.
lobata has since become a truculent invasive, spreading
via vegetative runners and seed dispersal. Seven
million acres of the American southeast are now
plagued by this vine.
My talk at BASF Science Symposium: sustainable food chain - from field to table, Jun 23-24, 2015, Chicago.
Notes and acknowledgements at http://kamounlab.tumblr.com/post/122151022390/plant-pathology-in-the-post-genomics-era
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
insect taxonomy importance systematics and classification
Current Projects Summary
1. Current Projects Summary
Dr. Justin C. Bagley
Postdoctoral Scholar
Virginia Commonwealth University
Universidade de Brasília
2. Current Projects Summary
I am working with collaborators in Brazil, the
U.S., and Mexico to complete genetic data
analyses and manuscripts from two
postdoctoral research fellowships.
The following slides briefly describe the two
funded projects:
justinbagley.org
3. 1. Ecological & Evolutionary Genomics of
Southwestern White Pine (Pinus
strobiformis)
justinbagley.org
4. This project constitutes the VCU/
Eckert Lab portion of a broader ~$4
million NSF MacroSystem Biology
grant to study the ecological and
evolutionary processes influencing
the distribution, genetic diversity,
adaptive evolution, and persistence of
southwestern white pine (Pinus
strobiformis) in the face of ongoing
climate change and an encroaching
fungal pathogen, white pine blister
rust (Cronartia ribicola).
Southwestern White Pine (SWWP) Genomics
Sub-projects:
• Ecological speciation (demography, niche divergence) in SWWP
• Adaptation across a longitudinal climatic gradient
• Adaptation to challenging environments, i.e. high elevations
P. strobiformis
5. Southwestern White Pine (SWWP) Genomics
Andrew J. Eckert Justin C. Bagley Mitra Menon
Team
PI, Team Leader Postdoc PhD Student
6. • Southwestern white pine is an alpine
species that occurs across a range of
moderate to higher elevations in
disjunct population scattered across
the North American desert southwest,
from the southern Rockies to the Sierra
Madre Occidental of northern Mexico.
• Our NAU, UNAM, and USDAFS
collaborators sampled SWWP and
limber pine (P. flexilis; LP) from
throughout their ranges, and we have
been tasked with genotyping samples
using genome-wide ddRAD-seq data
and inferring genomic signatures of
selection, adaptation, and demographic
processes in SWWP and LP across the
range of each species sampled (Fig. 1).
Southwestern White Pine (SWWP) Genomics
justinbagley.org
Figure 1
7. SWWP Population Genomics poster (JCB)
Evolution 2017, Portland, OR
NP
= 13,764,973
NC
= 2,596,228
MA
MPF
MFP
M4
T1
= 11.36
T2
= 2.29
Time(Ma)
P. strobiformis
core periphery
P. flexilis
NF
= 764,816
NAF
= 1,890,795
MA
= 6.91
migration rates:
MFP
= 4.35
MPF
= 8.81
θ= Neref
=
2,596,228
Model Ln composite
likelihood
k AIC ΔAICi
M1 −883.143112 6 1778.29 65.44
M2 −886.227416 7 1786.45 73.60
M3 −888.003307 7 1790.01 77.16
M4 −847.424540 9 1712.85 0.00
M5 −885.428135 9 1788.86 76.01
M6 −883.949484 10 1787.90 75.05
M7 −892.210862 9 1806.42 93.57
M8 −869.824520 14 1757.65 44.80
M9 −884.511096 11 1791.02 78.17
M10 −902.279445 9 1828.56 115.71
M11 −922.814525 11 1873.63 160.78
Model Model
description
Predicted pattern of
gene flow
Tension zone
(Barton and
Hewitt 1985)
Reduction in hybrid fitness due
to lack of genomic
cohesiveness and absence of a
different niche available for
hybrids
Secondary contact
between divergent
parental lineages (no
ancient migration)
Bounded hybrid
superiority
(Moore 1977;
Gross and
Rieseberg 2005)
Restricted gene flow between
diverging lineages due to a)
positive epistasis, or b) because
these loci facilitate adaptation
to novel environmental
conditions
Little to no
contemporary gene flow
between lineages (with
or without ancient
migration)
M10
M11
M9
NF
NP
NC NF
NP
NC
NF
NP
NC
MAh
MA
MFPh
MFP
MCP
MPC
MFPh
MFP
MCP
MPC
MAh
MA
M5
M6
M1
M2
M4
T1
T1
T2
T2
TimeTime
P. strobiformis
core periphery P. flexilis
M3
M7
M8
T1
T2
Time
NF
NP
NC
NF
NP
NC
NF
NP
NC
NF
NP
NC
NF
NP
NC
NF
NP
NC
NF
NP
NC
NF
NP
NC
MPF
MFP
MA
MA
MPF
MFP
MA
MPF
MFP
MCP
MPC
MPF
MFP
MCP
MPC
MCP
MPC MAh
MA
NAF NAF
NAF
NAF
NAF
NAF
NAF
NAF
NAF
NAF
NAF
MCP
MPC
MA
Acknowledgments
Research was supported by NSF grants EF-1442486 (AJE),
EF-1442456 (H. Lintz), and EF-1442597 (KW), and computational
resources from VCU’s Center for High Performance Computing
and the Brigham Young University Fulton Supercomputing Lab.
Introduction
Understanding speciation, including processes leading to
lineage divergence and the origin and maintenance of
reproductive barriers, is a fundamental goal of evolutionary
biology (Losos et al. 2013). As populations move across a fitness
landscape, they form different ecotypes resulting in shifts in
allele frequency correlated with environmental differences.
Given sufficient time or strong diversifying selection, ecotypes
can develop reproductive isolation, forming ecologically
differentiated species via ecological speciation (Schluter &
Conte 2009). Two models explain the maintenance of species
boundaries during ecological speciation predict varying
demographic scenarios, with different genomic signatures,
especially patterns of gene flow (Table 1).
Materials and Methods
We sampled P. strobiformis across its geographical range, and
P. flexilis mainly from the southern periphery and center of its
range (Fig. 1). We extracted whole genomic DNA then prepared
five ddRAD-seq libraries (Peterson et al. 2012) each containing
up to 96 multiplexed samples. Libraries were sequenced on an
Illumina HiSeq 2500, and read processing, and SNP filtering and
genotyping, were performed in DDOCENT (Puritz et al. 2014).
To infer the timing and influence of demographic processes
shaping divergence of the focal species plus two intraspecific
genetic lineages within P. strobiformis (geographical range
‘core’ and ‘periphery’ lineages), we conducted demographic
modeling analyses using ∂A∂I v1.7 (Gutenkunst et al. 2009). To
avoid issues with linkage disequilibrium, we ran ∂A∂I on 1 SNP
per RAD tag drawn from a reduced subset of 10,053 SNPs (out
of 51,633 SNPs total). We compared a ‘pure divergence’ model
(M1) against 10 alternative demographic models (M2–M11)
representing different speciation scenarios with varying timing
and directionality of ancient versus contemporary gene flow
(Fig. 2). Models M8–M11 were similar
Conclusions
Our results support a pattern of P. strobiformis–P. flexilis
speciation with gene flow, as well as low–moderate ongoing
gene flow broadly consistent with predictions of the bounded
hybrid superiority model. Incorporating genomic islands of
differentiation through parameterizing heterogeneous
migration also produced much worse models with essentially
no weight of evidence compared with the best ∂A∂I model
(Table 2). Thus, while genomic islands of differentiation are
possible in a tension zone experiencing gene flow, they seem
unlikely to have formed in this system through differential
divergence or introgression of loci. This is consistent with
numbers of migrants per generation (Mij) estimated in ∂A∂I,
which are not strongly asymmetric between lineages at T1 or T2
(Fig. 3).
These findings are also consistent with biogeography
studies of the desert southwest suggesting that montane ‘sky-
island’ forest ecosystems expanded along lower elevations
during glacial periods such as the Last Glacial Maximum (LGM),
providing opportunities for gene flow between presently
isolated montane lineages (e.g. Knowles 2000; Mastretta-Yanes
et al. 2015, refs. therein). Boreal forest trees of the Mexican
Highlands including our focal taxa may have been more likely
to experience continuous gene flow, rather than post-glacial
secondary contact, as lineages were repeatedly connected as
cold and humid habitats expanded during Pleistocene glacial
periods, as indicated by climate models and phylogeographic
data (e.g. reviewed in Mastretta-Yanes et al. 2015).
Population genomics supports speciation with gene flow, not genomic islands of differentiation, in
sky-island populations of southwestern white pine
Justin C. Bagley,1,2,* Mitra Menon,1,3 Christopher Friedline,1 Amy Whipple4, Anna Schoettle5, Alejandro L. Sáenz6, Christian A. Wehenkel6,
Daniel McGarvey7, Lluvia H. Flores-Renteria8, Richard Sneizko5, Sam Cushman5, Kristen Waring9, and Andrew J. Eckert1
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Benkman, C. W., R. P. Balda, and C. C. Smith. 1984. Ecology 65:632–642.
Burnham, K. P., and D. R. Anderson. 2002. Model Selection and Multimodal
Inference: A Practical Information Theoretic Approach, 2nd Edn. Springer-
Verlag, New York.
Christe, C., K. N. Stölting, M. Paris, C. Fraїsse, N. Bierne, and C. Lexer. 2017. Mol. Ecol.
26:59–76.
De La Torre, A. R., T. Wang, B. Jaquish, and S. N. Aitken. 2014. New Phytol. 201:687–
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Gross, B. L., and L. H. Rieseberg. 2005. J. Hered. 96:241–252.
Gutenkunst, R. N., R. D. Hernandez, S. H. Williamson, and C. D. Bustamante. 2009.
PLoS Genetics 5:e1000695.
Knowles, L. L. 2000. Evolution 54:1337–1348.
Lackey, A. C. R., and J. W. Boughman. 2017. Evolution 71: 357–372.
Lindtke, D., and C. A. Buerkle. 2015. Evolution 69:1987–2004.
Losos, J. B., S. J. Arnold, G. Bejerano, E. D. Brodie, D. Hibbett, H. E. Hoekstra, et al.
2013. PLoS Biol. 11.
Mastretta-Yanes, A., A. Moreno-Letelier, D. Piñero, T. H. Jorgensen, and B. C.
Emerson. 2015. J. Biogeogr. 42:1586-1600.
Moore, W. S. 1977. Q. Rev. Biol. 52:263–277.
Moreno-Letelier, A., and T. G. Barraclough. 2015. Evol. Ecol. 29:733–748.
Moreno-Letelier, A., A. Ortíz-Medrano, and D. Piñero. 2013. PLoS One 8:e78228.
Puritz, J. B., C. M. Hollenbeck, and J. R. Gold. 2014. PeerJ 2:e431.
Schluter, D., and G. L. Conte. 2009. Proc. Natl. Acad. Sci. 106:9955–9962.
Tine, M., H. Kuhl, P.-A. Gagnaire, B. Louro, E. Desmarais, R. S. T. Martins, et al. 2014.
Nature Comm. 5:5770.
Fig. 2. Schematics and parameter details for each of the 11
demographic models of the divergence of P. strobiformis core
and periphery lineages and P. flexilis run in our ∂A∂I analysis.
Parameters include divergence times (Ti), population sizes (Ni),
homogeneous migration rates (Mij) and heterogeneous
migration rates (Mijh).
Results
The best-supported demographic model identified during AIC
model selection (i.e. with highest information content) was M4,
a model of symmetric ancient migration between ancestral P.
strobiformis and P. flexilis lineages, followed by contemporary
gene flow only between the P. strobiformis periphery lineage
and P. flexilis (Table 2; Figs 2 and 3). This model was supported
by a very distinct minimum AIC score that was better than that
of all other ∂A∂I models by a margin of at least 44.8 information
units (ΔAICi = 44.8), indicating other models, including all island
of differentiation models, were unlikely. Models with ΔAICi > 10
have no support and fail to explain any substantial variation in
the data (Burnham and Anderson 2002). Converted parameter
estimates indicated that the two species diverged ~11.36
million years ago (Ma) in the Miocene, but that intraspecific
lineages within P. strobiformis diverged at T2 at ~2.29 Ma in the
early Pleistocene (Fig. 3). Also, P. strobiformis periphery had the
largest population size estimate (NP), while P. flexilis was
inferred to have experienced a reduction in population size (NF)
through time.
Fig. 3. The best-supported ∂A∂I model plotted with
optimized values of divergence time estimates (Ti) in units
of millions of years ago (Ma), converted reference effective
population size (θ; after conversion, Neref), lineage
population sizes (Ni), and migration rates (Mij).
Abbreviations: C, core; F, P. flexilis; P, periphery.
For further information
Please contact jcbagley vcu.edu, follow JBagz1 on
Twitter, and visit www.justinbagley.org. The QR code at
right links to an online, PDF version of this poster.
1 Department of Biology, Virginia Commonwealth University, Richmond, VA 23284, 2 Departamento de Zoologia, Universidade de Brasília, 70910-900 Brasília, DF, Brazil, 3 Integrative Life Sciences, Virginia Commonwealth University, Richmond,
VA 23284, 4 Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 36011, 5 USDA Forest Service, 6 Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, 34120 Durango, México,
7 Center for Environmental Studies, Virginia Commonwealth University, Richmond, VA 23284, 8 Department of Biology, San Diego State University, San Diego, CA 92182, 9 School of Forestry, Northern Arizona University, Flagstaff, AZ 36011.
*E-mail correspondence: jcbagley vcu.edu.
Fig. 1. Growth form and
geographical distributions of
the focal taxa. Southwestern
white pine (SWWP), Pinus
strobiformis (a); limber pine
(LP), P. flexilis (b). Panel c shows
species ranges and sampling
sites.
(a) (b)
(c)
to the others, except they modeled ancient migration or P.
strobiformis periphery–P. flexilis migration as ‘heterogeneous
migration’, with neutrally evolving loci experiencing differential
migration rates relative to those in GIDs (Fig. 2). We ran 10
replicate runs of each model in ∂A∂I, using a 200 × 220 × 240
grid space and the nonlinear BFGS optimization routine. We
specified heterogeneous migration parameters using Python
code from Tine et al. (2014). We conducted model selection
using Akaike information criterion (AIC) and ΔAICi (AICmodel i −
AICbest model) scores (Burnham and Anderson 2002) calculated
using results from the best replicate (highest composite
likelihood) for each model. We converted parameter estimates
from the single best-supported model (minimum AIC) using
equations in Gutenkunst et al. (2009), a per-site mutation rate
(μ) calculated from the 7.28 × 10−10 substitutions/site/year rate
estimated for Pinaceae by De La Torre et al. (2014) using 42
single-copy nuclear loci, and a generation time (g) of 50 years.
Universidade de
Brasília
Table 2. Model likelihoods and AIC model selection results
for the single best replicate ∂A∂I run of each model, with the
best-supported model (minimum AIC) shown in boldface.
If selection is strong and remains constant, then loci
contributing to initial ecological divergence may become
associated with mate recognition and form coadapted gene
complexes with reduced recombination, thereby generating
‘genomic islands of differentiation’ (GID; Christe et al. 2017;
Lindtke & Buerkle 2015). However, this pattern is only expected
under the tension zone model, or where adaptation occurs
from de novo mutations (Lackey & Boughman 2017).
Here, we test the above predictions on the prevalence of
gene flow during species formation in two species of North
American pine trees, Pinus strobiformis and P. flexilis, that are
broadly distributed across the desert southwest, with a narrow
range of sympatry in the southern Rocky Mountains (Fig. 1).
These taxa exhibit few morphological or reproductive
differences (e.g. Benkman et al. 1984) and are probably locally
adapted to varying climate across their ranges. Moreno-Letelier
Table 1. Two models for the maintenance of species boundaries
during ecological speciation.
et al. (2013) and Moreno-Letelier & Barraclough (2015) provided
the first evidence of ecological divergence in these two species
based on species distribution models and differentiation at
climate-associated candidate genes. We use demographic
modeling on genome-wide single nucleotide polymorphism
(SNP) data to infer demographic changes, migration rates, and
divergence times of these taxa, and to test the two models of
ecological speciation discussed above.
@ @
@
8. 2. Comparative phylogeography and
phylogenetic community structure of
freshwater fishes of the Cerrado
justinbagley.org
9. This project is funded by a Young Talent Fellowship grant from the Brazil’s CNPq,
as well as ancillary funding (e.g. Fundação CAPES) and represents a collaboration
between researchers at the University of Brasília (UnB), State University of São
Paulo (UNESP), and Federal University of Amazonas (UFAM), led by Justin Bagley.
The overarching aim of the project is to use comparative phylogeography and
community phylogenetics to understand the influence of ecological and historical
factors (such as river capture) on the genetic diversity and community
composition of the headwater stream fish assemblage.
Comparative Biogeography of Cerrado Stream Fish
Communities
Sub-projects:
• Single species and comparative ddRAD-seq phylogeography to test
genetic predictions of river capture in single fish species
• Molecular-based community phylogenetics analyses of regional fish
communities
12. Comparative Biogeography of Cerrado Stream Fish
Communities
Example focal species
Hypostomus sp. 2, Loricariidae
• Small range
• Endemic to PTSF study area
• Ongoing taxonomic description
Photo credit: P. Aquino
(center, top); I. Pinheiro
(bottom left).
13. Bioinformatics pipelines and analysis scripts
pyRAD /
ipyrad
.fastq file
millions of
raw NGS reads
18x
sh/bash shell
fastSTRUCTURE RAxML
18x
Assembly
characteristics
18x
• Plots of treespace
• Variance-based sensitivity analysis
• Parameter importance analysis
18x
HypJCB309
HypJCB97
HypJCB124
HypJCB134
HypJCB42
HypJCB64
HypJCB62
HypJCB22
HypJCB253
HypJCB50
HypJCB49
HypJCB20
HypJCB17
HypJCB11
HypJCB44
HypJCB265
HypJCB15
HypJCB47
HypJCB13
HypJCB18
HypJCB46
HypJCB51
HypJCB63
HypJCB152
HypJCB150
HypJCB149
HypJCB156
HypJCB163
HypJCB168
HypJCB201
HypJCB65
HypJCB161
HypJCB167
HypJCB66
HypJCB254
HypJCB100
HypJCB226
HypJCB99
HypJCB148
HypJCB123
HypJCB98
HypJCB310
./gene_trees/p_rad_pO20_md4_clust75−275loci_RAxML_best.tre
0.005
PDFs PDFs
Best
K
RF dist
Geodesic dist
e.g. sensitivity
• Developing variety of scripts for
population genomics / phylogenomics
analyses, e.g. RAPFX (RADseq
Assembly Parameter FX tool for basic
performance & sensitivity analyses).