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Herrera ND, Bell KC, Callahan CM, Nordquist E, Sarver BAJ, Sullivan J, Demboski JR, Good JM. Genomic resolution of cryptic species diversity in chipmunks. Evolution 2022; 76:2004-2019. [PMID: 35778920 DOI: 10.1111/evo.14546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 01/22/2023]
Abstract
Discovery of cryptic species is essential to understand the process of speciation and assessing the impacts of anthropogenic stressors. Here, we used genomic data to test for cryptic species diversity within an ecologically well-known radiation of North American rodents, western chipmunks (Tamias). We assembled a de novo reference genome for a single species (Tamias minimus) combined with new and published targeted sequence-capture data for 21,551 autosomal and 493 X-linked loci sampled from 121 individuals spanning 22 species. We identified at least two cryptic lineages corresponding with an isolated subspecies of least chipmunk (T. minimus grisescens) and with a restricted subspecies of the yellow-pine chipmunk (Tamias amoenus cratericus) known only from around the extensive Craters of the Moon lava flow. Additional population-level sequence data revealed that the so-called Crater chipmunk is a distinct species that is abundant throughout the coniferous forests of southern Idaho. This cryptic lineage does not appear to be most closely related to the ecologically and phenotypically similar yellow-pine chipmunk but does show evidence for recurrent hybridization with this and other species.
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Affiliation(s)
- Nathanael D Herrera
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Kayce C Bell
- Natural History Museum of Los Angeles County, Los Angeles, California, USA
| | - Colin M Callahan
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Erin Nordquist
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Brice A J Sarver
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, Idaho, USA
| | - John R Demboski
- Department of Zoology, Denver Museum of Nature & Sciences, Denver, Colorado, USA
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA.,Wildlife Biology Program, University of Montana, Missoula, Montana, USA
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Sarver BAJ, Herrera ND, Sneddon D, Hunter SS, Settles ML, Kronenberg Z, Demboski JR, Good JM, Sullivan J. Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias). Syst Biol 2021; 70:908-921. [PMID: 33410870 DOI: 10.1093/sysbio/syaa085] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/18/2022] Open
Abstract
Evidence from natural systems suggests that hybridization between animal species is more common than traditionally thought, but the overall contribution of introgression to standing genetic variation within species remains unclear for most animal systems. Here, we use targeted exon-capture to sequence thousands of nuclear loci and complete mitochondrial genomes from closely related chipmunk species in the Tamias quadrivittatus group that are distributed across the Great Basin and the central and southern Rocky Mountains of North America. This recent radiation includes six overlapping, ecologically distinct species (T. canipes, T. cinereicollis, T. dorsalis, T. quadrivittatus, T. rufus, and T. umbrinus) that show evidence for widespread introgression across species boundaries. Such evidence has historically been derived from a handful of markers, typically focused on mitochondrial loci, to describe patterns of introgression; consequently, the extent of introgression of nuclear genes is less well characterized. We conducted a series of phylogenomic and species-tree analyses to resolve the phylogeny of six species in this group. In addition, we performed several population genomic analyses to characterize nuclear genomes and infer coancestry among individuals. Furthermore, we used emerging quartets-based approaches to simultaneously infer the species tree (SVDquartets) and identify introgression (HyDe). We found that, in spite of rampant introgression of mitochondrial genomes between some species pairs (and sometimes involving up to three species), there appears to be little to no evidence for nuclear introgression. These findings mirror other genomic results where complete mitochondrial capture has occurred between chipmunk species in the absence of appreciable nuclear gene flow. The underlying causes of recurrent massive cytonuclear discordance remain unresolved in this group but mitochondrial DNA appears highly misleading of population histories as a whole. Collectively, it appears that chipmunk species boundaries are largely impermeable to nuclear gene flow and that hybridization, while pervasive with respect to mtDNA, has likely played a relatively minor role in the evolutionary history of this group.
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Affiliation(s)
- Brice A J Sarver
- Department of Biological Sciences, University of Idaho, Moscow, Idaho.,Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow Idaho
| | | | - David Sneddon
- Department of Biological Sciences, University of Idaho, Moscow, Idaho
| | - Samuel S Hunter
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow Idaho.,UC-Davis Genome Center, Davis, California
| | | | | | - John R Demboski
- Department of Zoology, Denver Museum of Nature & Sciences, Denver, Colorado
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, Montana.,Wildlife Biology Program, University of Montana, Missoula, Montana
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, Idaho.,Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow Idaho
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Tambur AR, Herrera ND, Haarberg KMK, Cusick MF, Gordon RA, Leventhal JR, Friedewald JJ, Glotz D. Assessing Antibody Strength: Comparison of MFI, C1q, and Titer Information. Am J Transplant 2015; 15:2421-30. [PMID: 25930984 DOI: 10.1111/ajt.13295] [Citation(s) in RCA: 200] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/09/2015] [Accepted: 02/28/2015] [Indexed: 02/06/2023]
Abstract
The presence of donor-specific HLA antibodies before or after transplantation may have different implications based on the antibody strength. Yet, current approaches do not provide information regarding the true antibody strength as defined by antigen-antibody dissociation rate. To assess currently available methods, we compared between neat mean fluorescence intensity (MFI) values, C1q MFI values, ethylenediaminetetraacetic acid (EDTA)-treated samples, as well as titration studies and peak MFI values of over 7000 Luminex-based single-antigen HLA antibody data points. Our results indicate that neat MFI values do not always accurately depict antibody strength. We further showed that EDTA treatment (6%) does not always remove all inhibitory factors compared with C1q or titration studies. In this study of patients presenting with multiple antibody specificities, a prozone effect was observed in 71% of the cohort (usually not affecting all antibody specificities within a single serum sample, though). Similar to titration studies, the C1q assay was able to address the issue of potential inhibition; however, its limitation is its low sensitivity and inability to detect the presence of weak antibodies. Titration studies are the only method among the approaches used in this study to provide information suggesting antigen-antibody dissociation rates and are, therefore, likely to provide better indication of true antibody strength.
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Affiliation(s)
- A R Tambur
- Transplant Immunology Laboratory, Northwestern University Feinberg School of Medicine, Chicago, IL.,Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - N D Herrera
- Transplant Immunology Laboratory, Northwestern University Feinberg School of Medicine, Chicago, IL.,Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - K M K Haarberg
- Transplant Immunology Laboratory, Northwestern University Feinberg School of Medicine, Chicago, IL.,Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - M F Cusick
- Transplant Immunology Laboratory, Northwestern University Feinberg School of Medicine, Chicago, IL.,Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - R A Gordon
- Division of Cardiology, Northwestern University Feinberg School of Medicine, Chicago, IL.,Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - J R Leventhal
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL.,Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - J J Friedewald
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - D Glotz
- Nephrology and Transplantation Service, Hôpital Saint-Louis, Paris, France
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Herrera ND, Ter Poorten JJ, Bieler R, Mikkelsen PM, Strong EE, Jablonski D, Steppan SJ. Molecular phylogenetics and historical biogeography amid shifting continents in the cockles and giant clams (Bivalvia: Cardiidae). Mol Phylogenet Evol 2015; 93:94-106. [PMID: 26234273 DOI: 10.1016/j.ympev.2015.07.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 07/02/2015] [Accepted: 07/18/2015] [Indexed: 10/23/2022]
Abstract
Reconstructing historical biogeography of the marine realm is complicated by indistinct barriers and, over deeper time scales, a dynamic landscape shaped by plate tectonics. Here we present the most extensive examination of model-based historical biogeography among marine invertebrates to date. We conducted the largest phylogenetic and molecular clock analyses to date for the bivalve family Cardiidae (cockles and giant clams) with three unlinked loci for 110 species representing 37 of the 50 genera. Ancestral ranges were reconstructed using the dispersal-extinction-cladogenesis (DEC) method with a time-stratified paleogeographic model wherein dispersal rates varied with shifting tectonics. Results were compared to previous classifications and the extensive paleontological record. Six of the eight prior subfamily groupings were found to be para- or polyphyletic. Cardiidae originated and subsequently diversified in the tropical Indo-Pacific starting in the Late Triassic. Eastern Atlantic species were mainly derived from the tropical Indo-Mediterranean region via the Tethys Sea. In contrast, the western Atlantic fauna was derived from Indo-Pacific clades. Our phylogenetic results demonstrated greater concordance with geography than did previous phylogenies based on morphology. Time-stratifying the DEC reconstruction improved the fit and was highly consistent with paleo-ocean currents and paleogeography. Lastly, combining molecular phylogenetics with a rich and well-documented fossil record allowed us to test the accuracy and precision of biogeographic range reconstructions.
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Affiliation(s)
- Nathanael D Herrera
- Department of Biological Science, Florida State University, Tallahassee, FL 32304, United States.
| | - Jan Johan Ter Poorten
- Naturalis Biodiversity Center, P.O. Box 9517, Leiden, Netherlands; Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, United States.
| | - Rüdiger Bieler
- Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, United States.
| | - Paula M Mikkelsen
- Paleontological Research Institution, and Department of Earth and Atmospheric Sciences, Cornell University, Ithaca, NY 14850, United States.
| | - Ellen E Strong
- Smithsonian Institution, National Museum of Natural History, Washington, DC 20013, United States.
| | - David Jablonski
- Department of Geophysical Sciences, University of Chicago, Chicago, IL 60637, United States.
| | - Scott J Steppan
- Department of Biological Science, Florida State University, Tallahassee, FL 32304, United States
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