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Folk RA, Gaynor ML, Engle-Wrye NJ, O’Meara BC, Soltis PS, Soltis DE, Guralnick RP, Smith SA, Grady CJ, Okuyama Y. Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method. Syst Biol 2023; 72:856-873. [PMID: 37073863 PMCID: PMC10405357 DOI: 10.1093/sysbio/syad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 03/23/2023] [Accepted: 04/17/2023] [Indexed: 04/20/2023] Open
Abstract
Applications of molecular phylogenetic approaches have uncovered evidence of hybridization across numerous clades of life, yet the environmental factors responsible for driving opportunities for hybridization remain obscure. Verbal models implicating geographic range shifts that brought species together during the Pleistocene have often been invoked, but quantitative tests using paleoclimatic data are needed to validate these models. Here, we produce a phylogeny for Heuchereae, a clade of 15 genera and 83 species in Saxifragaceae, with complete sampling of recognized species, using 277 nuclear loci and nearly complete chloroplast genomes. We then employ an improved framework with a coalescent simulation approach to test and confirm previous hybridization hypotheses and identify one new intergeneric hybridization event. Focusing on the North American distribution of Heuchereae, we introduce and implement a newly developed approach to reconstruct potential past distributions for ancestral lineages across all species in the clade and across a paleoclimatic record extending from the late Pliocene. Time calibration based on both nuclear and chloroplast trees recovers a mid- to late-Pleistocene date for most inferred hybridization events, a timeframe concomitant with repeated geographic range restriction into overlapping refugia. Our results indicate an important role for past episodes of climate change, and the contrasting responses of species with differing ecological strategies, in generating novel patterns of range contact among plant communities and therefore new opportunities for hybridization. The new ancestral niche method flexibly models the shape of niche while incorporating diverse sources of uncertainty and will be an important addition to the current comparative methods toolkit. [Ancestral niche reconstruction; hybridization; paleoclimate; pleistocene.].
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Affiliation(s)
- Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Michelle L Gaynor
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Nicholas J Engle-Wrye
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Brian C O’Meara
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, USA
| | - Robert P Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Charles J Grady
- Biodiversity Institute, University of Kansas, Lawrence, KS, 66045, USA
| | - Yudai Okuyama
- Tsukuba Botanical Garden, National Museum of Nature and Science, Tsukuba, Japan
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Scott R, Resetarits WJ. Spatially explicit habitat selection: Testing contagion and the ideal free distribution with Culex mosquitoes. Am Nat 2022; 200:675-690. [DOI: 10.1086/721009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Resetarits WJ, Pintar MR, Bohenek JR. Complex multi‐predator effects on demographic habitat selection and community assembly in colonizing aquatic insects. ECOL MONOGR 2021. [DOI: 10.1002/ecm.1474] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- William J. Resetarits
- Department of Biology Centers for Water and Wetlands Resources, and Conservation and Biodiversity Research The University of Mississippi University Mississippi 38677‐1848 USA
| | - Matthew R. Pintar
- Department of Biology Centers for Water and Wetlands Resources, and Conservation and Biodiversity Research The University of Mississippi University Mississippi 38677‐1848 USA
| | - Jason R. Bohenek
- Department of Biology Centers for Water and Wetlands Resources, and Conservation and Biodiversity Research The University of Mississippi University Mississippi 38677‐1848 USA
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Resetarits WJ. Between a rock and a hard place: Ovipositing treefrogs navigate complex trade‐offs in the landscape of patch quality. Ecosphere 2021. [DOI: 10.1002/ecs2.3524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- William J. Resetarits
- Department of Biology and Centers for Water and Wetlands Resources, and Biodiversity and Conservation Research University of Mississippi University Mississippi38677USA
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Du H, Liu M, Zhang S, Liu F, Zhang Z, Kong X. Lineage Divergence of Dendrolimus punctatus in Southern China Based on Mitochondrial Genome. Front Genet 2020; 11:65. [PMID: 32153637 PMCID: PMC7045034 DOI: 10.3389/fgene.2020.00065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/20/2020] [Indexed: 12/12/2022] Open
Abstract
In southern China, the masson pine caterpillar, Dendrolimus punctatus, has caused serious damage to the Pinus massoniana (Lamb.) pine forests. Here, the whole mitochondrial DNA (mtDNA) was employed to analyze the population evolution of D. punctatus and to understand the process underlying its current phylogenetic pattern. D. punctatus populations within its distribution range in China were categorized into five subgroups: central and eastern China (CEC), southwestern China (SWC), Yibin in Sichuan (SC), Baise in Guangxi (GX), and Luoding in Guangdong (GD), with a high level of haplotype diversity and nucleotide diversity among them. The genetic distances between subgroups are relatively large; however, the genetic distances between populations within the CEC subgroup were relatively small, suggesting that many populations were closely related in this subgroup. The mantel test showed that geographic distance had an important impact on the genetic distance of different geographic populations (r = 0.3633, P < 0.001). The neutrality tests, Bayesian skyline plot, and haplotype network showed that D. punctatus experienced a population expansion around 100,000 years ago. The divergence times of GX/SC, SWC, GD, and CEC were 0.347, 0.236, 0.200, and 0.110 million years ago, respectively. The SWC, CEC, and GD subgroups might have evolved from GX or SC subgroups. The population genetic structure of D. punctatus was closely related to its host tree species, geographic distance among populations, the weak flight capacity, and many eco-environment conditions.
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Affiliation(s)
- Huicong Du
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Man Liu
- Guizhou Institute of Biology, Guizhou Academy of Sciences, Guiyang, China
| | - Sufang Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Fu Liu
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Zhen Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Xiangbo Kong
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
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Li J, Jin Q, Zhu G, Jiang C, Zhang A. Phylogeography of Dendrolimus punctatus (Lepidoptera: Lasiocampidae): Population differentiation and last glacial maximum survival. Ecol Evol 2019; 9:7480-7496. [PMID: 31346417 PMCID: PMC6635939 DOI: 10.1002/ece3.5278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 04/12/2019] [Accepted: 04/15/2019] [Indexed: 11/10/2022] Open
Abstract
Although the Masson pine moth, Dendrolimus punctatus, is one of the most destructive forest pest insects and is an endemic condition in China, we still do not fully understand the patterns of how its distribution range varies in response to Quaternary climatic oscillations. Here, we sequenced one maternally inherited mitochondrial gene (COI) and biparentally inherited nuclear data (ITS1 and ITS2) among 23 natural populations across the entire range of the species in China. A total of 51 mitotypes and 38 ribotypes were separately obtained using mtDNA and ITS1 data. Furthermore, significant phylogeographical structure (N ST > G ST, p < 0.01) were detected. The spatial distribution of mitotypes implied that two distinct groups existed in the species: one in the southwest distribution, including 10 locations, and the other located in the northeast region of China. It is suggested, therefore, that each group was derived from ancestors that occupied different isolated refugia during previous periods, possibly last glacial maximum. Mismatch distribution and Bayesian population dynamics analysis suggested the population size underwent sudden expansion, which is consistent with the results of ecological niche modeling. As a typical phytophagous insect, the history of population expansion was in accordance with the host plants, providing abundant food resources and habitat. Intraspecific success rate of barcoding identification was lower than interspecific ones, indicating a level of difficulty in barcoding individuals from different populations. However, it still provides an early insight into the pattern of genetic diversity within a species. OPEN RESEARCH BADGES This article has been awarded an Open Data and Open Materials. All materials and data are publicly accessible via the Open Science Framework at https://doi.org/10.5061/dryad.2df87g2. Learn more about the Open Practices badges from the Center for Open Science: https://osf.io/tvyxz/wiki.
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Affiliation(s)
- Jing Li
- College of Life SciencesCapital Normal UniversityBeijingChina
| | - Qian Jin
- College of Life SciencesCapital Normal UniversityBeijingChina
- Suqian Institute of Agricultural SciencesJiangsu Academy of Agricultural SciencesSuqianChina
| | - Geng‐ping Zhu
- College of Life SciencesTianjin Normal UniversityTianjinChina
| | - Chong Jiang
- College of Life SciencesCapital Normal UniversityBeijingChina
| | - Ai‐bing Zhang
- College of Life SciencesCapital Normal UniversityBeijingChina
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Extreme diversification of floral volatiles within and among species of Lithophragma (Saxifragaceae). Proc Natl Acad Sci U S A 2019; 116:4406-4415. [PMID: 30765532 DOI: 10.1073/pnas.1809007116] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
A major challenge in evolutionary biology is to understand how complex traits of multiple functions have diversified and codiversified across interacting lineages and geographic ranges. We evaluate intra- and interspecific variation in floral scent, which is a complex trait of documented importance for mutualistic and antagonistic interactions between plants, pollinators, and herbivores. We performed a large-scale, phylogenetically structured study of an entire plant genus (Lithophragma, Saxifragaceae), of which several species are coevolving with specialized pollinating floral parasites of the moth genus Greya (Prodoxidae). We sampled 94 Lithophragma populations distributed across all 12 recognized Lithophragma species and subspecies, and four populations of related saxifragaceous species. Our results reveal an unusually high diversity of floral volatiles among populations, species, and clades within the genus. Moreover, we found unexpectedly major changes at each of these levels in the biosynthetic pathways used by local populations in their floral scents. Finally, we detected significant, but variable, genus- and species-level patterns of ecological convergence in the floral scent signal, including an impact of the presence and absence of two pollinating Greya moth species. We propose that one potential key to understanding floral scent variation in this hypervariable genus is its geographically diverse interactions with the obligate specialized Greya moths and, in some species and sites, more generalized copollinators.
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Friberg M, Waters MT, Thompson JN. Nutrient availability affects floral scent much less than other floral and vegetative traits in Lithophragma bolanderi. ANNALS OF BOTANY 2017; 120:471-478. [PMID: 28655187 PMCID: PMC5591434 DOI: 10.1093/aob/mcx069] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 01/09/2017] [Indexed: 05/29/2023]
Abstract
Background and Aims Many plant-pollinator interactions are mediated by floral scents that can vary among species, among populations within species and even among individuals within populations. This variation could be innate and unaffected by the environment, but, because many floral volatiles have amino-acid precursors, scent variation also could be affected by differences in nutrient availability among environments. In plants that have coevolved with specific pollinators, natural selection is likely to favour low phenotypic plasticity in floral scent even under different conditions of nutrient availability if particular scents or scent combinations are important for attracting local pollinators. Methods Clonal pairs of multiple seed-families of two Lithophragma bolanderi (Saxifragaceae) populations were subjected to a high and a low nutrient treatment. These plants are pollinated primarily by host-specific Greya moths. It was evaluated how nutrient treatment affected variation in floral scent relative to other vegetative and reproductive traits. Key Results Floral scent strength (the per-flower emission rate) and composition were unaffected by nutrient treatment, but low-nutrient plants produced fewer and lighter leaves, fewer scapes and fewer flowers than high-nutrient plants. The results held in both populations, which differed greatly in the number and composition of floral scents produced. Conclusions The results reveal a strong genetic component both to scent composition and emission level, and partly contrasts with the only previous study that has assessed the susceptibility of floral volatile signals to variation in the abundance of nutrients. These results, and the tight coevolutionary relationship between Lithophragma plants and their specialized Greya moth pollinators, indicate that reproductive traits important to coevolving interactions, such as the floral scent of L. bolanderi, may be locally specialized and more canalized than other traits important for plant fitness.
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Affiliation(s)
- Magne Friberg
- Uppsala University, Department of Plant Ecology and Evolution, Evolutionary Biology Centre, EBC, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Mia T Waters
- University of California, Santa Cruz, Department of Ecology and Evolutionary Biology, Santa Cruz, CA, USA
| | - John N Thompson
- University of California, Santa Cruz, Department of Ecology and Evolutionary Biology, Santa Cruz, CA, USA
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Thompson JN, Schwind C, Friberg M. Diversification of Trait Combinations in Coevolving Plant and Insect Lineages. Am Nat 2017; 190:171-184. [PMID: 28731801 DOI: 10.1086/692164] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Closely related species often have similar traits and sometimes interact with the same species. A crucial problem in evolutionary ecology is therefore to understand how coevolving species diverge when they interact with a set of closely related species from another lineage rather than with a single species. We evaluated geographic differences in the floral morphology of all woodland star plant species (Lithophragma, Saxifragaceae) that are pollinated by Greya (Prodoxidae) moths. Flowers of each woodland star species differed depending on whether plants interact locally with one, two, or no pollinating moth species. Plants of one species grown in six different environments showed few differences in floral traits, suggesting that the geographic differences are not due significantly to trait plasticity. Greya moth populations also showed significant geographic divergence in morphology, depending on the local host and on whether the moth species co-occurred locally. Divergence in the plants and the moths involved shifts in combinations of partially correlated traits, rather than any one trait. The results indicate that the geographic mosaic of coevolution can be amplified as coevolving lineages diversify into separate species and come together in different combinations in different ecosystems.
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