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Smith ML, Wallace J, Tank DC, Sullivan J, Carstens BC. The role of multiple Pleistocene refugia in promoting diversification in the Pacific Northwest. Mol Ecol 2022; 31:4402-4416. [PMID: 35780485 DOI: 10.1111/mec.16595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/14/2022] [Accepted: 06/20/2022] [Indexed: 10/17/2022]
Abstract
Pleistocene glacial cycles drastically changed the distributions of taxa endemic to temperate rainforests in the Pacific Northwest, with many experiencing reduced habitat suitability during glacial periods. In this study, we investigate whether glacial cycles promoted intraspecific divergence and whether subsequent range changes led to secondary contact and gene flow. For seven invertebrate species endemic to the PNW, we estimated Species Distribution Models (SDMs) and projected them onto current and historical climate conditions to assess how habitat suitability changed during glacial cycles. Using single nucleotide polymorphism (SNP) data from these species, we assessed population genetic structure and used a machine-learning approach to compare models with and without gene flow between populations upon secondary contact after the Last Glacial Maximum (LGM). Finally, we estimated divergence times and rates of gene flow between populations. SDMs suggest that there was less suitable habitat in the North Cascades and Northern Rocky Mountains during glacial compared to interglacial periods, resulting in reduced habitat suitability and habitat fragmentation during the LGM. Our genomic data identify population structure in all taxa, and support gene flow upon secondary contact in five of the seven taxa. Parameter estimates suggest that population divergences date to the later Pleistocene for most populations. Our results support a role of refugial dynamics in driving intraspecific divergence in the Cascades Range. In these invertebrates, population structure often does not correspond to current biogeographic or environmental barriers. Rather, population structure may reflect refugial lineages that have since expanded their ranges, often leading to secondary contact between once isolated lineages.
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Affiliation(s)
- Megan L Smith
- Department of Evolution, Ecology & Organismal Biology, The Ohio State University, 318 W. 12th Avenue, 300 Aronoff Labs, Columbus, OH 43210-1293, USA
| | - Jessica Wallace
- Department of Evolution, Ecology & Organismal Biology, The Ohio State University, 318 W. 12th Avenue, 300 Aronoff Labs, Columbus, OH 43210-1293, USA
| | - David C Tank
- Department of Botany and Rocky Mountain Herbarium, University of Wyoming, 1000 E. University Ave., Laramie, WY 82071, USA.,Department of Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID 83844-3051, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID 83844-3051, USA
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID 83844-3051, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID 83844-3051, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology & Organismal Biology, The Ohio State University, 318 W. 12th Avenue, 300 Aronoff Labs, Columbus, OH 43210-1293, USA
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Ruffley M, Smith ML, Espíndola A, Turck DF, Mitchell N, Carstens B, Sullivan J, Tank DC. Genomic evidence of an ancient Inland Temperate Rainforest in the Pacific Northwest of North America. Mol Ecol 2022; 31:2985-3001. [PMID: 35322900 PMCID: PMC9322681 DOI: 10.1111/mec.16431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/15/2022] [Accepted: 02/21/2022] [Indexed: 12/02/2022]
Abstract
The disjunct temperate rainforests of the Pacific Northwest of North America (PNW) are characterized by late‐successional dominant tree species Thuja plicata (western redcedar) and Tsuga heterophylla (western hemlock). The demographic histories of these species, along with the PNW rainforest ecosystem in its entirety, have been heavily impacted by geological and climatic changes the PNW has experienced over the last 5 million years, including mountain orogeny and repeated Pleistocene glaciations. These environmental events have ultimately shaped the history of these species, with inland populations potentially being extirpated during the Pleistocene glaciations. Here, we collect genomic data for both species across their ranges to test multiple demographic models, each reflecting a different phylogeographical hypothesis on how the ecosystem‐dominating species may have responded to dramatic climatic change. Our results indicate that inland and coastal populations in both species diverged ~2.5 million years ago in the early Pleistocene and experienced decreases in population size during glacial cycles, with subsequent population expansion. Importantly, we found evidence for gene flow between coastal and inland populations during the mid‐Holocene. It is likely that intermittent migration in these species during this time has prevented allopatric speciation via genetic drift alone. In conclusion, our results from combining genomic data and demographic inference procedures establish that populations of the ecosystem dominants Thuja plicata and Tsuga heterophylla persisted in refugia located in both the coastal and inland regions of the PNW throughout the Pleistocene, with populations expanding and contracting in response to glacial cycles with occasional gene flow.
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Affiliation(s)
- Megan Ruffley
- Department of Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID, 83844-3051, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), 875 Perimeter Dr. MS 3051, Moscow, ID, 83844-3051, USA.,Department of Plant Biology, Carnegie Institution for Science, 260 Panama St, Stanford, CA, 94305, USA
| | - Megan L Smith
- Department of Evolution, Ecology, and Organismal Biology & Museum of Biological Diversity, The Ohio State University, 1315 Kinnear Rd, Columbus, OH, 43212, USA.,Department of Biology and Department of Computer Science, Indiana University, Bloomington, IN, 47405, USA
| | - Anahí Espíndola
- Department of Entomology, University of Maryland, 4291 Fieldhouse Dr, College Park, MD, 20742, USA
| | - Daniel F Turck
- Department of Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID, 83844-3051, USA.,Stillinger Herbarium, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID, 83844-3051, USA
| | - Niels Mitchell
- Department of Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID, 83844-3051, USA
| | - Bryan Carstens
- Department of Evolution, Ecology, and Organismal Biology & Museum of Biological Diversity, The Ohio State University, 1315 Kinnear Rd, Columbus, OH, 43212, USA
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID, 83844-3051, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), 875 Perimeter Dr. MS 3051, Moscow, ID, 83844-3051, USA
| | - David C Tank
- Department of Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID, 83844-3051, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), 875 Perimeter Dr. MS 3051, Moscow, ID, 83844-3051, USA.,Stillinger Herbarium, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID, 83844-3051, USA.,Department of Botany & Rocky Mountain Herbarium, University of Wyoming, 1000 E. University Ave, Laramie, WY, 82071, USA
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Stone BW, Wolfe AD. Phylogeographic analysis of shrubby beardtongues reveals range expansions during the Last Glacial Maximum and implicates the Klamath Mountains as a hotspot for hybridization. Mol Ecol 2021; 30:3826-3839. [PMID: 34013537 DOI: 10.1111/mec.15992] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 12/26/2022]
Abstract
Quaternary glacial cycles often altered species' geographic distributions, which in turn altered the geographic structure of species' genetic diversity. In many cases, glacial expansion forced species in temperate climates to contract their ranges and reside in small pockets of suitable habitat (refugia), where they were likely to interact closely with other species, setting the stage for potential gene exchange. These introgression events, in turn, would have degraded species boundaries, making the inference of phylogenetic relationships challenging. Using high-throughput sequence data, we employed a combination of species distribution models and hybridization tests to assess the effect of glaciation on the geographic distributions, phylogenetic relationships, and patterns of gene flow of five species of Penstemon subgenus Dasanthera, long-lived shrubby angiosperms distributed throughout the Pacific Northwest of North America. Surprisingly, we found that rather than reducing their ranges to small refugia, most Penstemon subgenus Dasanthera species experienced increased suitable habitat during the Last Glacial Maximum relative to the present day. We also found substantial evidence for gene exchange between species, with the bulk of introgression events occurring in or near the Klamath Mountains of southwestern Oregon and northwestern California. Subsequently, our phylogenetic inference reveals blurred taxonomic boundaries in the Klamath Mountains, where introgression is most prevalent. Our results question the classical paradigm of temperate species' responses to glaciation and highlight the importance of contextualizing phylogenetic inference with species' histories of introgression.
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Affiliation(s)
- Benjamin W Stone
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Andrea D Wolfe
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
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Cai R, Ané C. Assessing the fit of the multi-species network coalescent to multi-locus data. Bioinformatics 2021; 37:634-641. [PMID: 33027508 DOI: 10.1093/bioinformatics/btaa863] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/14/2020] [Accepted: 09/22/2020] [Indexed: 01/25/2023] Open
Abstract
MOTIVATION With growing genome-wide molecular datasets from next-generation sequencing, phylogenetic networks can be estimated using a variety of approaches. These phylogenetic networks include events like hybridization, gene flow or horizontal gene transfer explicitly. However, the most accurate network inference methods are computationally heavy. Methods that scale to larger datasets do not calculate a full likelihood, such that traditional likelihood-based tools for model selection are not applicable to decide how many past hybridization events best fit the data. We propose here a goodness-of-fit test to quantify the fit between data observed from genome-wide multi-locus data, and patterns expected under the multi-species coalescent model on a candidate phylogenetic network. RESULTS We identified weaknesses in the previously proposed TICR test, and proposed corrections. The performance of our new test was validated by simulations on real-world phylogenetic networks. Our test provides one of the first rigorous tools for model selection, to select the adequate network complexity for the data at hand. The test can also work for identifying poorly inferred areas on a network. AVAILABILITY AND IMPLEMENTATION Software for the goodness-of-fit test is available as a Julia package at https://github.com/cecileane/QuartetNetworkGoodnessFit.jl. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ruoyi Cai
- Department of Statistics, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Cécile Ané
- Department of Statistics, University of Wisconsin - Madison, Madison, WI 53706, USA.,Department of Botany, University of Wisconsin - Madison, Madison, WI 53706, USA
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Napier JD, Fernandez MC, de Lafontaine G, Hu FS. Ice-age persistence and genetic isolation of the disjunct distribution of larch in Alaska. Ecol Evol 2020; 10:1692-1702. [PMID: 32076544 PMCID: PMC7029070 DOI: 10.1002/ece3.6031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/18/2019] [Accepted: 01/06/2020] [Indexed: 01/07/2023] Open
Abstract
Larix laricina (eastern larch, tamarack) is a transcontinental North American conifer with a prominent disjunction in the Yukon isolating the Alaskan distribution from the rest of its range. We investigate whether in situ persistence during the last glacial maximum (LGM) or long-distance postglacial migration from south of the ice sheets resulted in the modern-day Alaskan distribution. We analyzed variation in three chloroplast DNA regions of 840 trees from a total of 69 populations (24 new sampling sites situated on both sides of the Yukon range disjunction pooled with 45 populations from a published source) and conducted ensemble species distribution modeling (SDM) throughout Canada and United States to hindcast the potential range of L. laricina during the LGM. We uncovered the genetic signature of a long-term isolation of larch populations in Alaska, identifying three endemic chlorotypes and low levels of genetic diversity. Range-wide analysis across North America revealed the presence of a distinct Alaskan lineage. Postglacial gene flow across the Yukon divide was unidirectional, from Alaska toward previously glaciated Canadian regions, and with no evidence of immigration into Alaska. Hindcast SDM indicates one of the broadest areas of past climate suitability for L. laricina existed in central Alaska, suggesting possible in situ persistence of larch in Alaska during the LGM. Our results provide the first unambiguous evidence for the long-term isolation of L. laricina in Alaska that extends beyond the last glacial period and into the present interglacial period. The lack of gene flow into Alaska along with the overall probability of larch occurrence in Alaska being currently lower than during the LGM suggests that modern-day Alaskan larch populations are isolated climate relicts of broader glacial distributions, and so are particularly vulnerable to current warming trends.
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Affiliation(s)
- Joseph D. Napier
- Department of Plant BiologyUniversity of IllinoisUrbanaILUSA
- Department of Integrative BiologyThe University of Texas at AustinAustinTXUSA
| | | | - Guillaume de Lafontaine
- Canada Research Chair in Integrative Biology of Northern FloraUniversité du Québec à RimouskiRimouskiQCCanada
| | - Feng Sheng Hu
- Department of Plant BiologyUniversity of IllinoisUrbanaILUSA
- Department of GeologyUniversity of IllinoisUrbanaILUSA
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Rankin AM, Wilke T, Lucid M, Leonard W, Espíndola A, Smith ML, Carstens BC, Sullivan J. Complex interplay of ancient vicariance and recent patterns of geographical speciation in north-western North American temperate rainforests explains the phylogeny of jumping slugs (Hemphillia spp.). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractThe history of the currently disjunct temperate rainforests of the Pacific Northwest of North America has shaped the evolution and diversity of endemics. This study focuses on how geological and climatic perturbations have driven speciation in the area by isolating lineages. We investigated the phylogenetic relationships and historical biogeography of the endemic jumping slugs (genus Hemphillia) using a multi-locus phylogeny. We evaluated the spatial distribution and divergence times of major lineages, generated ancestral area probabilities and inferred the biogeographical history of the genus. Our study revealed eight genetic lineages that formed three clades: one clade consisting of two Coast/Cascade lineages, and two reciprocally monophyletic clades that each contain a Coast/Cascade and two Rocky Mountains taxa. The results of the biogeographical analysis suggest that the ancestral range of the genus occupied Coast/Cascade habitats and then spread across into Northern Rocky Mountain interior habitats with subsequent fragmentations isolating coastal and inland lineages. Finally, there have been more recent speciation events among three lineage pairs that have shaped shallow structures of all clades. We add to our knowledge of the biogeographical history of the region in that we discovered diversification and speciation events that have occurred in ways more complex than previously thought.
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Affiliation(s)
- Andrew M Rankin
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Thomas Wilke
- Animal Ecology and Systematics, Justus Liebig University, Heinrich-Buff-Ring (IFZ), Giessen, Germany
| | - Michael Lucid
- Idaho Department of Fish and Game, Coeur d’Alene, ID, USA
| | | | - Anahí Espíndola
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Megan L Smith
- Department of Evolution, Ecology, & Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology, & Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, Moscow, ID, USA
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7
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Sullivan J, Smith ML, Espíndola A, Ruffley M, Rankin A, Tank D, Carstens B. Integrating life history traits into predictive phylogeography. Mol Ecol 2019; 28:2062-2073. [DOI: 10.1111/mec.15029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 01/04/2019] [Accepted: 01/16/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Jack Sullivan
- Department of Biological Sciences University of Idaho Moscow Idaho
- Institute for Bioinformatics and Evolutionary Studies University of Idaho Moscow Idaho
| | - Megan L. Smith
- Department of Ecology, Evolution and Organismal Biology The Ohio State University Columbus Ohio
| | - Anahí Espíndola
- Department of Biological Sciences University of Idaho Moscow Idaho
- Department of Entomology University of Maryland College Park Maryland
| | - Megan Ruffley
- Department of Biological Sciences University of Idaho Moscow Idaho
- Institute for Bioinformatics and Evolutionary Studies University of Idaho Moscow Idaho
| | - Andrew Rankin
- Department of Biological Sciences University of Idaho Moscow Idaho
- Institute for Bioinformatics and Evolutionary Studies University of Idaho Moscow Idaho
| | - David Tank
- Department of Biological Sciences University of Idaho Moscow Idaho
- Institute for Bioinformatics and Evolutionary Studies University of Idaho Moscow Idaho
| | - Bryan Carstens
- Department of Ecology, Evolution and Organismal Biology The Ohio State University Columbus Ohio
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