Award Abstract # 1441634
Collaborative Research: VertLife Terrestrial: A complete, global assembly of phylogenetic, trait, spatial and environment characteristics for a model clade
NSF Org: |
DEB
Division Of Environmental Biology
|
Recipient: |
LOUISIANA STATE UNIVERSITY
|
Initial Amendment Date:
|
September 8, 2014 |
Latest Amendment Date:
|
February 14, 2017 |
Award Number: |
1441634 |
Award Instrument: |
Standard Grant |
Program Manager: |
Katharina Dittmar
kdittmar@nsf.gov
(703)292-7799
DEB
Division Of Environmental Biology
BIO
Directorate for Biological Sciences
|
Start Date: |
October 1, 2014 |
End Date: |
September 30, 2020 (Estimated) |
Total Intended Award
Amount: |
$356,938.00 |
Total Awarded Amount to
Date: |
$371,638.00 |
Funds Obligated to Date:
|
FY 2014 = $356,938.00
FY 2016 = $7,300.00
FY 2017 = $7,400.00
|
History of Investigator:
|
-
Jacob
Esselstyn
(Principal Investigator)
esselstyn@lsu.edu
|
Recipient Sponsored Research
Office: |
Louisiana State University
202 HIMES HALL
BATON ROUGE
LA
US
70803-0001
(225)578-2760
|
Sponsor Congressional
District: |
06
|
Primary Place of
Performance: |
Louisiana State University & Agricultural and Mechanical College
119 Foster Hall
Baton Rouge
LA
US
70803-2701
|
Primary Place of
Performance Congressional District: |
06
|
Unique Entity Identifier
(UEI): |
ECQEYCHRNKJ4
|
Parent UEI: |
|
NSF Program(s): |
GoLife, Systematics & Biodiversity Sci
|
Primary Program Source:
|
01001415DB NSF RESEARCH & RELATED ACTIVIT
01001617DB NSF RESEARCH & RELATED ACTIVIT
01001718DB NSF RESEARCH & RELATED ACTIVIT
|
Program Reference
Code(s): |
6133,
7689,
9169,
9178,
9251,
EGCH
|
Program Element Code(s):
|
613300,
737400
|
Award Agency Code: |
4900
|
Fund Agency Code: |
4900
|
Assistance Listing
Number(s): |
47.074
|
ABSTRACT

Terrestrial vertebrates (Tetrapoda) include our own species and represent one of the great and diverse evolutionary radiations that intersect with humans' everyday lives. The four tetrapod classes - birds, mammals, amphibians and reptiles - together comprise ca. 33,000 species, include life histories ranging from aquatic, subterranean, and arboreal to aerial, cover a variety of trophic strategies, and harbor some of the most stunning ecological adaptations. Tetrapods play a significant role in providing diverse ecological functions, and they are vital to biodiversity monitoring efforts. However, significant knowledge gaps remain in the evolutionary relationships, distributions of ecologically important traits, and distributions of species. The project will undertake concerted assembling efforts that will yield near species-level completeness of key evolutionary and ecological attributes thereby establishing a global model system for macroevolution, macroecology, comparative biology and global change research. The compiled trait and spatial data will provide a vital backbone for rigorous conservation monitoring and prioritization. The online analysis and visualization tools will extend successful, existing projects and will be built to be directly usable for other taxa and other Genealogy of Life (GoLife) projects.
Massive parallel sequencing methods will be used to collect new multi-locus genetic information for ca. 4,000 species currently lacking such data. These data will be used to derive a dated posterior tree set that includes all tetrapod species and captures remaining uncertainty. The posterior tree set will be used to calculate evolutionary distinctness and a variety of tree metrics. Together with key collaborators the researchers will compile morphological, ecological and life history trait data for dozens of variables and additionally benefit from phylogenetic imputation to predict missing values. A new tool incorporated into the existing Map of Life infrastructure will link existing species distributional datasets to global environmental data layers and provide broad-scale niche characteristics for all vertebrates together with estimates of uncertainty. Further integration will link these products to online phylogeny visualization tools to allow map- and tree-based discovery and download. Finally, the project will demonstrate the utility of the integrated layers through example biogeographic, conservation and comparative analyses that will highlight the advance in inference and in predictive conservation use arising from near-complete and unbiased global data. The research will also provide online visualizations and tutorials, a museum exhibit developed around the products, a workshop based on VertLife infrastructure, and undergraduate and graduate summer internships.
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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(Showing: 1 - 10 of 38)
(Showing: 1 - 38 of 38)
Demos, Terrence C and Achmadi, Anang S and Handika, Heru and Rowe, Kevin C and Esselstyn, Jacob A
"A new species of shrew (Soricomorpha: Crocidura) from Java, Indonesia: possible character displacement despite interspecific gene flow"
Journal of Mammalogy
, v.98
, 2017
, p.183--193
Eldridge RA, Achmadi AS, Giarla TC, Rowe KC, Esselstyn JA
"Geographic isolation and elevational gradients promote lineage diversification in an endemic shrew on Sulawesi"
Molecular Phylogenetics and Evolution
, v.118
, 2018
, p.306
10.1016/j.ympev.2017.09.018
Eldridge, R.A., Achmadi, A.S., Giarla, T.C., Rowe, K.C., Esselstyn, J.A.
"Geographic isolation and elevational gradients promote lineage diversification in an endemic shrew on Sulawesi"
Molecular Phylogenetics and Evolution
, 2017
10.1016/j.ympev.2017.09.018
Eldridge, RA, AS Achmadi, TC Giarla, KC Rowe, JA Esselstyn
"Geographic isolation and elevational gradients promote lineage diversification in an endemic shrew on Sulawesi"
Molecular Phylogenetics and Evolution
, v.118
, 2018
, p.306
10.1016/j.ympev.2017.09.018
Eldridge, Ryan A and Achmadi, Anang S and Giarla, Thomas C and Rowe, Kevin C and Esselstyn, Jacob A
"Geographic isolation and elevational gradients promote diversification in an endemic shrew on Sulawesi"
Molecular phylogenetics and evolution
, v.118
, 2018
, p.306--317
Esselstyn JA, Achmadi AS, Handika H, Giarla TC, Rowe KC
"A new climbing shrew from Sulawesi highlights the tangled taxonomy of an endemic radiation"
Journal of Mammalogy
, v.100
, 2019
, p.1713
10.1093/jmammal/gyz077
Esselstyn, JA, CH Oliveros, MT Swanson, BC Faircloth
"Investigating difficult nodes in the placental mammal tree with expanded taxon sampling and thousands of ultraconserved elements"
Genome Biology and Evolution
, v.9
, 2017
, p.2308
10.1093/gbe/evx168
Esselstyn, Jacob A. and Achmadi, Anang S. and Handika, Heru and Swanson, Mark T. and Giarla, Thomas C. and Rowe, Kevin C.
"Fourteen new, endemic species of shrew (genus Crocidura) from Sulawesi reveal a spectacular island radiation"
Bulletin of the American Museum of Natural History
, v.454
, 2021
Citation
Details
Esselstyn, Jacob A and Achmadi, Anang S and Handika, Heru C and Giarla, Thomas C and Rowe, Kevin and Powell, Roger
"A new climbing shrew from Sulawesi highlights the tangled taxonomy of an endemic radiation"
Journal of Mammalogy
, v.100
, 2019
10.1093/jmammal/gyz077
Citation
Details
Esselstyn, Jacob A and Oliveros, Carl H and Swanson, Mark T and Faircloth, Brant C
"Investigating difficult nodes in the placental mammal tree with expanded taxon sampling and thousands of ultraconserved elements"
Genome Biology and Evolution
, v.9
, 2017
, p.2308--232
Esselstyn JA, Oliveros CH, Swanson MT, Faircloth BC
"Investigating difficult nodes in the placental mammal tree with expanded taxon sampling and thousands of ultraconserved elements"
Genome Biology and Evolution
, v.9
, 2017
, p.2308
10.1093/gbe/evx168
Esselstyn, J.A., Oliveros, C.H., Swanson, M.T., Faircloth, B.C.
"Investigating difficult nodes in the placental mammal tree with expanded taxon sampling and thousands of ultraconserved elements"
Genome Biology and Evolution
, v.9
, 2017
, p.2308
10.1093/gbe/evx168
Giarla TC, Maher SP, Achmadi AS, Moore MK, Swanson MT, Rowe KC, Esselstyn JA
"Isolation by marine barriers and climate explain areas of endemism in an island rodent"
Journal of Biogeography
, v.45
, 2018
, p.2053
10.1111/jbi.13392
Giarla, TC, SP Maher, AS Achmadi, MK Moore, MT Swanson, KC Rowe, JA Esselstyn
"Isolation by marine barriers and climate explain areas of endemism in an island rodent"
Journal of Biogeography
, v.45
, 2018
, p.2053
10.1111/jbi.13392
Giarla, Thomas C and Maher, Sean P and Achmadi, Anang S and Moore, Meagan K and Swanson, Mark T and Rowe, Kevin C and Esselstyn, Jacob A
"Isolation by marine barriers and climate explain areas of endemism in an island rodent"
Journal of Biogeography
, v.45
, 2018
, p.2053--206
Handika, Heru, Achmadi, Anang S., Esselstyn, Jacob A., Rowe, Kevin C.
"Molecular and morphological systematics of the Bunomys division (Rodentia: Muridae), an endemic radiation on Sulawesi"
Zoologica Scripta
, 2020
10.1111/zsc.12469
Handika, Heru and Achmadi, Anang S. and Esselstyn, Jacob A. and Rowe, Kevin C.
"Molecular and morphological systematics of the Bunomys division (Rodentia: Muridae), an endemic radiation on Sulawesi"
Zoologica Scripta
, v.50
, 2020
https://doi.org/10.1111/zsc.12460
Citation
Details
Hernández-Canchola, Giovani and León-Paniagua, Livia and Esselstyn, Jacob A.
"Mitochondrial DNA indicates paraphyletic relationships of disjunct populations in the Neotoma mexicana species group"
Therya
, v.12
, 2021
https://doi.org/10.12933/therya-21-1082
Citation
Details
Hutterer R, Balete DS, Giarla TC, Heaney LR, Esselstyn JA
"A new genus and species of shrew (Mammalia: Soricidae) from Palawan Island, Philippines"
Journal of Mammalogy
, v.99
, 2018
, p.518
10.1093/jmammaly/gyy041
Hutterer, R, DS Balete, TC Giarla, LR Heaney, JA Esselstyn
"A new genus and species of shrew (Mammalia: Soricidae) from Palawan Island, Philippines"
Journal of Mammalogy
, v.99
, 2018
, p.518
10.1093/jmammaly/gyy041
Martinez Q, Lebrun R, Achmadi AS, Esselstyn JA, Evans AR, Heaney LR, Miguez RP, Rowe KC, Fabre P-H
"Convergent evolution of an extreme dietary specialization, the olfactory system of worm-eating rodents"
Scientific Reports
, v.8
, 2018
, p.17806
10.1038/s41598-018-35827-0
Martinez, Quentin and Lebrun, Renaud and Achmadi, Anang S and Esselstyn, Jacob A and Evans, Alistair R and Heaney, Lawrence R and Miguez, Roberto Portela and Rowe, Kevin C and Fabre, Pierre-Henri
"Convergent evolution of an extreme dietary specialisation, the olfactory system of worm-eating rodents"
Scientific reports
, v.8
, 2018
, p.1--13
Nations JA, Heaney LR, Demos TC, Achmadi AS, Rowe KC, Esselstyn JA
"A simple skeletal measure effectively predicts climbing behaviour in a diverse clade of small mammals"
Biological Journal of the Linnean Society
, v.128
, 2019
, p.323
10.1093/biolinnean/blz085
Nations, Jonathan A and Heaney, Lawrence R and Demos, Terrence C and Achmadi, Anang S and Rowe, Kevin C and Esselstyn, Jacob A
"A simple skeletal measurement effectively predicts climbing behaviour in a diverse clade of small mammals"
Biological Journal of the Linnean Society
, v.128
, 2019
, p.323--336
Nations, Jonathan A. and Heaney, Lawrence R. and Demos, Terrence C. and Achmadi, Anang S. and Rowe, Kevin C. and Esselstyn, Jacob A.
"A simple skeletal measurement effectively predicts climbing behaviour in a diverse clade of small mammals"
Biological Journal of the Linnean Society
, 2019
https://doi.org/10.1093/biolinnean/blz085
Citation
Details
Nations, Jonathan A. and Mount, Genevieve G. and Morere, Sara M. and Achmadi, Anang S. and Rowe, Kevin C. and Esselstyn, Jacob A.
"Locomotory mode transitions alter phenotypic evolution and lineage diversification in an ecologically rich clade of mammals"
Evolution
, v.75
, 2021
https://doi.org/10.1111/evo.14156
Citation
Details
Nations, Jonathan A and Mursyid, Ahmad and Busta, Ryski Darma and Adrian, Sah Putra and Handika, Heru and Achmadi, Anang S and Esselstyn, Jacob A and others
"The first report of albinism in a Sundaland endemic rodent"
Mammalia
, v.1
, 2020
Rowe KC, Achmadi AS, Fabre P-H, Schenk JJ, Steppan SJ, Esselstyn JA
"Oceanic islands of Wallacea as a source for dispersal and diversification of murine rodents"
Journal of Biogeography
, 2019
10.1111/jbi.13720
Rowe, Kevin C and Achmadi, Anang S and Fabre, Pierre-Henri and Schenk, John J and Steppan, Scott J and Esselstyn, Jacob A
"Oceanic islands of Wallacea as a source for dispersal and diversification of murine rodents"
Journal of Biogeography
, v.46
, 2019
, p.2752--276
Rowe, Kevin_C and Achmadi, Anang_S and Fabre, PierreHenri and Schenk, John_J and Steppan, Scott_J and Esselstyn, Jacob_A
"Oceanic islands of Wallacea as a source for dispersal and diversification of murine rodents"
Journal of Biogeography
, v.46
, 2019
https://doi.org/10.1111/jbi.13720
Citation
Details
Swanson, Mark T and Oliveros, Carl H and Esselstyn, Jacob A
"A phylogenomic rodent tree reveals the repeated evolution of masseter architectures"
Proceedings of the Royal Society B
, v.286
, 2019
, p.20190672
Swanson, Mark T. and Oliveros, Carl H. and Esselstyn, Jacob A.
"A phylogenomic rodent tree reveals the repeated evolution of masseter architectures"
Proceedings of the Royal Society B: Biological Sciences
, v.286
, 2019
10.1098/rspb.2019.0672
Citation
Details
Swanson MT, Oliveros CH, Esselstyn JA
"A phylogenomic rodent tree reveals the repeated evolution of masseter architectures"
Proceedings of the Royal Society, B, Biological Sciences
, v.286
, 2019
10.1098/rspb.2019.0672
Upham, Nathan S and Esselstyn, Jacob A and Jetz, Walter
"Ecological causes of uneven diversification and richness in the mammal tree of life"
bioRxiv
, 2019
, p.504803
Upham, Nathan S and Esselstyn, Jacob A and Jetz, Walter
"Ecological causes of uneven speciation and species richness in mammals"
BioRxiv
, 2020
, p.504803
Upham, Nathan S. and Esselstyn, Jacob A. and Jetz, Walter
"Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation"
PLOS Biology
, v.17
, 2019
https://doi.org/10.1371/journal.pbio.3000494
Citation
Details
Upham NS, Esselstyn JA, Jetz W
"Ecological causes of uneven diversification and richness in the mammal tree of life"
BioRxiv
, v.50483
, 2018
Upham NS, Esselstyn JA, Jetz W
"Inferring the mammal tree: species-level sets of phylogenies for questions in ecology, evolution, and conservation"
PLoS Biology
, v.17
, 2019
, p.e3000494
10.1371/journal.pbio.3000494
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(Showing: 1 - 38 of 38)
PROJECT OUTCOMES REPORT

Disclaimer
This Project Outcomes Report for the General Public is displayed verbatim as submitted by the
Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or
recommendations expressed in this Report are those of the PI and do not necessarily reflect the
views of the National Science Foundation; NSF has not approved or endorsed its content.
The primary goal of this project was to develop publicly available resources for understanding the evolutionary history of mammals. The major reason we lacked comprehensive estimates of the relationships among species is that researchers had never obtained any genetic sequences from approximately one of every six living mammal species. As such, all prior estimates of evolutionary relationships among mammals have been incomplete. To advance our understanding of mammalian diversity and evolutionary history, we used all publicly available DNA sequences to provide as-comprehensive-as-possible estimates of evolutionary relationships, and we obtained DNA sequences of approximately 600 species of mammals that had never been sequenced. These data and analyses provided new perspectives on the branching pattern and timing of mammalian diversification, including greater resolution among major clades of mammals. Our analyses also revealed extensive variation among mammals in recent rates of diversification, highlighting the ecological factors that promote diversity. The results are now publicly available and have been incorporated into the OneZoom tree of life explorer. Numerous researchers are using our results to test their own hypotheses related to trait evolution, biogeography, and other aspects of mammalian biodiversity.
In addition, data collected for this project made substantial contributions to our efforts to document and describe new species of mammals, to improve available information on the geographic ranges of individual mammal species, and to better understand the ecogeographic conditions that promote diversification in mammals. To date, this grant has supported 13 peer-reviewed publications, with more anticipated.
Throughout this project, junior researchers gained experience in a variety of research areas, including next generation DNA sequencing techniques, comparative genomics, field research on mammals, curation of natural history collections, project management, experimental design, and presentation of research findings. Junior researchers included seven undergraduate students, five graduate students, and five post-doctoral researchers.
Last Modified: 11/12/2020
Modified by: Jacob A Esselstyn
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