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Phylogeography of an endemic California silkmoth genus suggests the importance of an unheralded central California province in generating regional endemic biodiversity. Mol Phylogenet Evol 2021; 164:107256. [PMID: 34256128 DOI: 10.1016/j.ympev.2021.107256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 11/21/2022]
Abstract
The California Floristic province is a biodiversity hotspot. Understanding the phylogeographic patterns that exist in this diverse region is essential to understanding its evolution and for guiding conservation efforts. Calosaturnia is a charismatic silkmoth genus endemic to large portions of the region with three described species, C. mendocino, C. walterorum, and C. albofasciata. We sampled all three species from across their ranges, sequenced 1463 bp of mitochondrial COI and 1941 bp of nuclear DNA from three genes, and reconstructed phylogenetic relationships and estimated divergence times within the lineages. All three species show pronounced evidence of isolation and, in two cases, secondary reconnection. An unexpected monophyletic mtDNA lineage was found in the Central Coast region, in a region thought to represent an intergrade between C. mendocino and C. walterorum. Our genetic data also significantly revise previous hypotheses as to which species occur in which regions, suggesting that historical ecological changes around four Ma ago isolated some lineages, and a secondary isolation event two Ma ago led to isolation of populations both in the Central Coast region and the southern Sierra Nevada. Our results add to a currently under-appreciated pattern suggesting that coastal Central California is not a transition zone between Northern and Southern California Floristic Province faunas but rather its own unique, periodically isolated, biogeographic region. They also suggest cryptic diversity may be present in many other currently unrecognized groups. Additional research should focus on this central California region because many species may be highly restricted in range and in need of conservation attention.
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Jadin RC, Orlofske SA, Jezkova T, Blair C. Single-locus species delimitation and ecological niche modelling provide insights into the evolution, historical distribution and taxonomy of the Pacific chorus frogs. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Abstract
The Pacific chorus frogs are a complex of three wide-ranging species (i.e. Hyliola hypochondriaca, Hyliola regilla, Hyliola sierra) whose current taxonomy remains unresolved. We conducted species delimitation analyses of these taxa using fragments of the cytochrome b and 12S–16S mtDNA genes to assess the species diversity. Importantly, we included samples from new locations throughout the range to better understand species distributions and identify potential contact zones among clades. Our analyses revealed three slightly parapatric but distinct species-level clades. Molecular dating revealed that these species began diverging in the Pleistocene c. 1.4 Mya with H. hypochondriaca and H. sierra diverging more recently c. 0.8 Mya. We found that populations from western Montana and Idaho originated recently from populations to the southwest that belong to H. sierra, rather than from H. regilla populations directly to the west. Population sizes of each species expanded c. 130–80 Kya with H. hypochondriaca exhibiting a more pronounced expansion beginning c. 100 Kya than the more gradual expansion of the other two species. The climatic niche models suggest that distributions of the three species were similar during the last interglacial (LIG) as they are today. During the Last Glacial Maximum (LGM), H. hypochondriaca and H. sierra occupied a larger range than they do today whereas H. regilla occupied a smaller refugium, shifted south from the current distribution. This study highlights the continued effectiveness of utilizing single-locus data sets for species delimitation and biogeographic analyses.
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Affiliation(s)
- Robert C Jadin
- Department of Biology and Museum of Natural History, University of Wisconsin, Stevens Point, WI, USA
- Department of Biology, University of Wisconsin, Eau Claire, WI, USA
| | - Sarah A Orlofske
- Department of Biology and Museum of Natural History, University of Wisconsin, Stevens Point, WI, USA
| | - Tereza Jezkova
- Department of Biology, Miami University, Oxford, Ohio, USA
| | - Christopher Blair
- Department of Biological Sciences, New York City College of Technology, The City University of New York, Brooklyn, NY, USA
- Biology PhD Program, CUNY Graduate Center, New York, NY, USA
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Jockusch EL, Hansen RW, Fisher RN, Wake DB. Slender salamanders (genus Batrachoseps) reveal Southern California to be a center for the diversification, persistence, and introduction of salamander lineages. PeerJ 2020; 8:e9599. [PMID: 32864205 PMCID: PMC7430267 DOI: 10.7717/peerj.9599] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 07/02/2020] [Indexed: 11/20/2022] Open
Abstract
Background The southern California biodiversity hotspot has had a complex geological history, with both plate tectonic forces and sea level changes repeatedly reconfiguring the region, and likely driving both lineage splittings and extinctions. Here we investigate patterns of genetic divergence in two species of slender salamanders (Plethodontidae: Batrachoseps) in this region. The complex geological history in combination with several organismal traits led us to predict that these species harbor multiple ancient mitochondrial lineages endemic to southern California. These species belong to a clade characterized by fine-scale mitochondrial structure, which has been shown to track ancient splits. Both focal species, Batrachoseps major and B. nigriventris, are relatively widely distributed in southern California, and estimated to have persisted there across millions of years. Recently several extralimital populations of Batrachoseps were found in the San Joaquin Valley of California, a former desert area that has been extensively modified for agriculture. The origins of these populations are unknown, but based on morphology, they are hypothesized to result from human-mediated introductions of B. major. Methods We sequenced the mitochondrial gene cytochrome b from a geographically comprehensive sampling of the mitochondrial lineages of B. major and B. nigriventris that are endemic to southern California. We used phylogenetic analyses to characterize phylogeographic structure and identify mitochondrial contact zones. We also included the San Joaquin Valley samples to test whether they resulted from introductions. We used a bootstrap resampling approach to compare the strength of isolation-by-distance in both Batrachoseps species and four other salamander species with which they co-occur in southern California. Results The northern lineage of B. major harbors at least eight deeply differentiated, geographically cohesive mitochondrial subclades. We identify geographic contact between many of these mtDNA lineages and some biogeographic features that are concordant with lineage boundaries. Batrachoseps nigriventris also has multiple deeply differentiated clades within the region. Comparative analyses highlight the smaller spatial scales over which mitochondrial divergence accumulates in Batrachoseps relative to most other salamander species in southern California. The extralimital populations of Batrachoseps from the San Joaquin Valley are assigned to B. major and are shown to result from at least two independent introductions from different source populations. We also suggest that B. major on Catalina Island, where it is considered native, may be the result of an introduction. Some of the same traits that facilitate the build-up of deep phylogeographic structure in Batrachoseps likely also contribute to its propensity for introductions, and we anticipate that additional introduced populations will be discovered.
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Affiliation(s)
- Elizabeth L Jockusch
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA.,Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America
| | - Robert W Hansen
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America
| | - Robert N Fisher
- Western Ecological Research Center, San Diego Field Station, San Diego, CA, U.S. Geological Survey, United States of America
| | - David B Wake
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America.,Department of Integrative Biology, University of California, Berkeley, CA, United States of America
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Huang Y, Morrison GR, Brelsford A, Franklin J, Jolles DD, Keeley JE, Parker VT, Saavedra N, Sanders AC, Stoughton TR, Wahlert GA, Litt A. Subspecies differentiation in an enigmatic chaparral shrub species. AMERICAN JOURNAL OF BOTANY 2020; 107:923-940. [PMID: 32498125 DOI: 10.1002/ajb2.1496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 03/12/2020] [Indexed: 06/11/2023]
Abstract
PREMISE Delimiting biodiversity units is difficult in organisms in which differentiation is obscured by hybridization, plasticity, and other factors that blur phenotypic boundaries. Such work is more complicated when the focal units are subspecies, the definition of which has not been broadly explored in the era of modern genetic methods. Eastwood manzanita (Arctostaphylos glandulosa Eastw.) is a widely distributed and morphologically complex chaparral shrub species with much subspecific variation, which has proven challenging to categorize. Currently 10 subspecies are recognized, however, many of them are not geographically segregated, and morphological intermediates are common. Subspecies delimitation is of particular importance in this species because two of the subspecies are rare. The goal of this study was to apply an evolutionary definition of "subspecies" to characterize structure within Eastwood manzanita. METHODS We used publicly available geospatial environmental data and reduced-representation genome sequencing to characterize environmental and genetic differentiation among subspecies. In addition, we tested whether subspecies could be differentiated by environmentally associated genetic variation. RESULTS Our analyses do not show genetic differentiation among subspecies of Eastwood manzanita, with the exception of one of the two rare subspecies. In addition, our environmental analyses did not show ecological differentiation, though limitations of the analysis prevent strong conclusions. CONCLUSIONS Genetic structure within Eastwood manzanita does not correspond to current subspecies circumscriptions, but rather reflects geographic distribution. Our study suggests that subspecies concepts need to be reconsidered in long-lived plant species, especially in the age of next-generation sequencing.
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Affiliation(s)
- Yi Huang
- University of California, Riverside, Riverside, CA, 92521
| | | | - Alan Brelsford
- University of California, Riverside, Riverside, CA, 92521
| | - Janet Franklin
- University of California, Riverside, Riverside, CA, 92521
| | | | - Jon E Keeley
- U.S. Geological Survey Western Ecological Research Center, Three Rivers, CA, 93271
| | | | | | | | | | | | - Amy Litt
- University of California, Riverside, Riverside, CA, 92521
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Lavin BR, Wogan GOU, McGuire JA, Feldman CR. Phylogeography of the Northern Alligator Lizard (Squamata, Anguidae): Hidden diversity in a western endemic. ZOOL SCR 2018. [DOI: 10.1111/zsc.12294] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Brian R. Lavin
- Department of Biology; Sonoma State University; Rohnert Park California
| | - Guinevere O. U. Wogan
- Department of Environmental Science, Policy and Management and Museum of Vertebrate Zoology; University of California; Berkeley California
| | - Jimmy A. McGuire
- Department of Integrative Biology and Museum of Vertebrate Zoology; University of California; Berkeley California
| | - Chris R. Feldman
- Department of Biology and Program in Ecology, Evolution and Conservation Biology; University of Nevada; Reno Nevada
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Ortego J, Gugger PF, Sork VL. Genomic data reveal cryptic lineage diversification and introgression in Californian golden cup oaks (section Protobalanus). THE NEW PHYTOLOGIST 2018; 218:804-818. [PMID: 29274282 DOI: 10.1111/nph.14951] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/14/2017] [Indexed: 05/15/2023]
Abstract
Here we study hybridization, introgression and lineage diversification in the widely distributed canyon live oak (Quercus chrysolepis) and the relict island oak (Q. tomentella), two Californian golden cup oaks with an intriguing biogeographical history. We employed restriction-site-associated DNA sequencing and integrated phylogenomic and population genomic analyses to study hybridization and reconstruct the evolutionary past of these taxa. Our analyses revealed the presence of two cryptic lineages within Q. chrysolepis. One of these lineages shares its most recent common ancestor with Q. tomentella, supporting the paraphyly of Q. chrysolepis. The split of these lineages was estimated to take place during the late Pliocene or the early Pleistocene, a time corresponding well with the common presence of Q. tomentella in the fossil records of continental California. Analyses also revealed historical hybridization among lineages, high introgression from Q. tomentella into Q. chrysolepis in their current area of sympatry, and widespread admixture between the two lineages of Q. chrysolepis in contact zones. Our results support that the two lineages of Q. chrysolepis behave as a single functional species phenotypically and ecologically well differentiated from Q. tomentella, a situation that can be only accommodated considering hybridization and speciation as a continuum with diffuse limits.
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Affiliation(s)
- Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana, EBD-CSIC, Avda. Américo Vespucio 26, Seville, E-41092, Spain
| | - Paul F Gugger
- Appalachian Laboratory, University of Maryland Center for Environmental Science, 301 Braddock Road, Frostburg, MD, 21532, USA
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Box 957239, Los Angeles, CA, 90095, USA
- Institute of the Environment and Sustainability, University of California, Box 951496, Los Angeles, CA, 90095-1496, USA
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Richmond JQ, Wood DA, Westphal MF, Vandergast AG, Leaché AD, Saslaw LR, Butterfield HS, Fisher RN. Persistence of historical population structure in an endangered species despite near‐complete biome conversion in California's San Joaquin Desert. Mol Ecol 2017; 26:3618-3635. [DOI: 10.1111/mec.14125] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 01/24/2017] [Accepted: 03/13/2017] [Indexed: 01/06/2023]
Affiliation(s)
| | | | | | | | - Adam D. Leaché
- Department of Biology & Burke Museum of Natural History and Culture University of Washington Seattle WA USA
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Ortego J, Gugger PF, Sork VL. Impacts of human-induced environmental disturbances on hybridization between two ecologically differentiated Californian oak species. THE NEW PHYTOLOGIST 2017; 213:942-955. [PMID: 27621132 DOI: 10.1111/nph.14182] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/04/2016] [Indexed: 05/15/2023]
Abstract
Natural hybridization, which can be involved in local adaptation and in speciation processes, has been linked to different sources of anthropogenic disturbance. Here, we use genotypic data to study range-wide patterns of genetic admixture between the serpentine-soil specialist leather oak (Quercus durata) and the widespread Californian scrub oak (Quercus berberidifolia). First, we estimated hybridization rates and the direction of gene flow. Second, we tested the hypothesis that genetic admixture increases with different sources of environmental disturbance, namely anthropogenic destruction of natural habitats and wildfire frequency estimated from long-term records of fire occurrence. Our analyses indicate considerable rates of hybridization (> 25%), asymmetric gene flow from Q. durata into Q. berberidifolia, and a higher occurrence of hybrids in areas where both species live in close parapatry. In accordance with the environmental disturbance hypothesis, we found that genetic admixture increases with wildfire frequency, but we did not find a significant effect of other sources of human-induced habitat alteration (urbanization, land clearing for agriculture) or a suite of ecological factors (climate, elevation, soil type). Our findings highlight that wildfires constitute an important source of environmental disturbance, promoting hybridization between two ecologically well-differentiated native species.
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Affiliation(s)
- Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana, EBD-CSIC, Avda. Américo Vespucio s/n, E-41092, Seville, Spain
| | - Paul F Gugger
- Appalachian Laboratory, University of Maryland Center for Environmental Science, 301 Braddock Road, Frostburg, MD, 21532, USA
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Box 957239, Los Angeles, CA, 90095, USA
- Institute of the Environment and Sustainability, University of California, Box 951496, Los Angeles, CA, 90095-1496, USA
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Schierenbeck KA. Population-level genetic variation and climate change in a biodiversity hotspot. ANNALS OF BOTANY 2017; 119:215-228. [PMID: 28069633 PMCID: PMC5321061 DOI: 10.1093/aob/mcw214] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/19/2016] [Accepted: 09/19/2016] [Indexed: 05/06/2023]
Abstract
INTRODUCTION Estimated future climate scenarios can be used to predict where hotspots of endemism may occur over the next century, but life history, ecological and genetic traits will be important in informing the varying responses within myriad taxa. Essential to predicting the consequences of climate change to individual species will be an understanding of the factors that drive genetic structure within and among populations. Here, I review the factors that influence the genetic structure of plant species in California, but are applicable elsewhere; existing levels of genetic variation, life history and ecological characteristics will affect the ability of an individual taxon to persist in the presence of anthropogenic change. FACTORS INFLUENCING THE DISTRIBUTION OF GENETIC VARIATION Persistence in the face of climate change is likely determined by life history characteristics: dispersal ability, generation time, reproductive ability, degree of habitat specialization, plant-insect interactions, existing genetic diversity and availability of habitat or migration corridors. Existing levels of genetic diversity in plant populations vary based on a number of evolutionary scenarios that include endemism, expansion since the last glacial maximum, breeding system and current range sizes. REGIONAL PRIORITIES AND EXAMPLES A number of well-documented examples are provided from the California Floristic Province. Some predictions can be made for the responses of plant taxa to rapid environmental changes based on geographic position, evolutionary history, existing genetic variation, and ecological amplitude. CONCLUSIONS, SOLUTIONS AND RECOMMENDATIONS The prediction of how species will respond to climate change will require a synthesis drawing from population genetics, geography, palaeontology and ecology. The important integration of the historical factors that have shaped the distribution and existing genetic structure of California's plant taxa will enable us to predict and prioritize the conservation of species and areas most likely to be impacted by rapid climate change, human disturbance and invasive species.
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Affiliation(s)
- Kristina A Schierenbeck
- California State University, Chico Department of Biological Sciences, Chico, CA 95929-0515, USA
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Emata K, Hedin M. From the mountains to the coast and back again: Ancient biogeography in a radiation of short-range endemic harvestmen from California. Mol Phylogenet Evol 2016; 98:233-43. [DOI: 10.1016/j.ympev.2016.02.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 12/16/2015] [Accepted: 02/01/2016] [Indexed: 10/22/2022]
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Ortego J, Noguerales V, Gugger PF, Sork VL. Evolutionary and demographic history of the Californian scrub white oak species complex: an integrative approach. Mol Ecol 2015; 24:6188-208. [PMID: 26547661 DOI: 10.1111/mec.13457] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/30/2015] [Accepted: 11/03/2015] [Indexed: 01/17/2023]
Abstract
Understanding the factors promoting species formation is a major task in evolutionary research. Here, we employ an integrative approach to study the evolutionary history of the Californian scrub white oak species complex (genus Quercus). To infer the relative importance of geographical isolation and ecological divergence in driving the speciation process, we (i) analysed inter- and intraspecific patterns of genetic differentiation and employed an approximate Bayesian computation (ABC) framework to evaluate different plausible scenarios of species divergence. In a second step, we (ii) linked the inferred divergence pathways with current and past species distribution models (SDMs) and (iii) tested for niche differentiation and phylogenetic niche conservatism across taxa. ABC analyses showed that the most plausible scenario is the one considering the divergence of two main lineages followed by a more recent pulse of speciation. Genotypic data in conjunction with SDMs and niche differentiation analyses support that different factors (geography vs. environment) and modes of speciation (parapatry, allopatry and maybe sympatry) have played a role in the divergence process within this complex. We found no significant relationship between genetic differentiation and niche overlap, which probably reflects niche lability and/or that multiple factors, have contributed to speciation. Our study shows that different mechanisms can drive divergence even among closely related taxa representing early stages of species formation and exemplifies the importance of adopting integrative approaches to get a better understanding of the speciation process.
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Affiliation(s)
- Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana, EBD-CSIC, Avda. Américo Vespucio s/n, E-41092, Seville, Spain
| | - Víctor Noguerales
- Department of Integrative Ecology, Estación Biológica de Doñana, EBD-CSIC, Avda. Américo Vespucio s/n, E-41092, Seville, Spain
| | - Paul F Gugger
- Department of Ecology and Evolutionary Biology, University of California, Box 957239, Los Angeles, CA, 90095, USA
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Box 957239, Los Angeles, CA, 90095, USA.,Institute of the Environment and Sustainability, University of California, Box 951496, Los Angeles, CA, 90095-1496, USA
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Gottscho AD. Zoogeography of the San Andreas Fault system: Great Pacific Fracture Zones correspond with spatially concordant phylogeographic boundaries in western North America. Biol Rev Camb Philos Soc 2014; 91:235-54. [DOI: 10.1111/brv.12167] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 10/28/2014] [Accepted: 11/11/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Andrew D. Gottscho
- Department of Biology; San Diego State University; 5500 Campanile Drive San Diego CA 92182 U.S.A
- Department of Biology; University of California; Riverside CA 92521 U.S.A
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Sork VL, Werth S. Phylogeography of Ramalina menziesii, a widely distributed lichen-forming fungus in western North America. Mol Ecol 2014; 23:2326-39. [PMID: 24673777 DOI: 10.1111/mec.12735] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 03/13/2014] [Indexed: 11/28/2022]
Abstract
The complex topography and climate history of western North America offer a setting where lineage formation, accumulation and migration have led to elevated inter- and intraspecific biodiversity in many taxa. Here, we study Ramalina menziesii, an epiphytic lichenized fungus with a range encompassing major ecosystems from Baja California to Alaska to explore the predictions of two hypotheses: (i) that the widespread distribution of R. menziesii is due to a single migration episode from a single lineage and (ii) that the widespread distribution is due to the formation and persistence of multiple lineages structured throughout the species' range. To obtain evidence for these predictions, we first construct a phylogenetic tree and identify multiple lineages structured throughout the species' range--some ancient ones that are localized and other more recent lineages that are widely distributed. Second, we use an isolation with migration model to show that sets of ecoregion populations diverged from each other at different times, demonstrating the importance of historical and current barriers to gene flow. Third, we estimated migration rates among ecoregions and find that Baja California populations are relatively isolated, that inland California ecoregion populations do not send out emigrants and that migration out of California coastal and Pacific Northwest populations into inland California ecoregions is high. Such intraspecific geographical patterns of population persistence and dispersal both contribute to the wide range of this genetically diverse lichen fungus and provide insight into the evolutionary processes that enhance species diversity of the California Floristic Province.
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Affiliation(s)
- Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA, 90095-7239, USA; Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095-1496, USA
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Satler JD, Carstens BC, Hedin M. Multilocus species delimitation in a complex of morphologically conserved trapdoor spiders (mygalomorphae, antrodiaetidae, aliatypus). Syst Biol 2013; 62:805-23. [PMID: 23771888 DOI: 10.1093/sysbio/syt041] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Species are a fundamental unit for biological studies, yet no uniform guidelines exist for determining species limits in an objective manner. Given the large number of species concepts available, defining species can be both highly subjective and biased. Although morphology has been commonly used to determine species boundaries, the availability and prevalence of genetic data has allowed researchers to use such data to make inferences regarding species limits. Genetic data also have been used in the detection of cryptic species, where other lines of evidence (morphology in particular) may underestimate species diversity. In this study, we investigate species limits in a complex of morphologically conserved trapdoor spiders (Mygalomorphae, Antrodiaetidae, Aliatypus) from California. Multiple approaches were used to determine species boundaries in this highly genetically fragmented group, including both multilocus discovery and validation approaches (plus a chimeric approach). Additionally, we introduce a novel tree-based discovery approach using species trees. Results suggest that this complex includes multiple cryptic species, with two groupings consistently recovered across analyses. Due to incongruence across analyses for the remaining samples, we take a conservative approach and recognize a three species complex, and formally describe two new species (Aliatypus roxxiae, sp. nov. and Aliatypus starretti, sp. nov.). This study helps to clarify species limits in a genetically fragmented group and provides a framework for identifying and defining the cryptic lineage diversity that prevails in many organismal groups.
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Affiliation(s)
- Jordan D Satler
- Department of Evolution, Ecology and Organismal Biology, The Ohio University, Columbus, OH 43210, USA and Department of Biology, San Diego University, San Diego, CA 92182, USA
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Hedin M, Starrett J, Hayashi C. Crossing the uncrossable: novel trans-valley biogeographic patterns revealed in the genetic history of low-dispersal mygalomorph spiders (Antrodiaetidae,Antrodiaetus) from California. Mol Ecol 2012. [DOI: 10.1111/mec.12130] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Marshal Hedin
- Department of Biology; San Diego State University San Diego; San Diego CA 92182-4614 USA
| | - James Starrett
- Department of Biology; University of California; Riverside CA 92521 USA
| | - Cheryl Hayashi
- Department of Biology; University of California; Riverside CA 92521 USA
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Satler JD, Starrett J, Hayashi CY, Hedin M. Inferring species trees from gene trees in a radiation of California trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus). PLoS One 2011; 6:e25355. [PMID: 21966507 PMCID: PMC3180454 DOI: 10.1371/journal.pone.0025355] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 09/01/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The California Floristic Province is a biodiversity hotspot, reflecting a complex geologic history, strong selective gradients, and a heterogeneous landscape. These factors have led to high endemic diversity across many lifeforms within this region, including the richest diversity of mygalomorph spiders (tarantulas, trapdoor spiders, and kin) in North America. The trapdoor spider genus Aliatypus encompasses twelve described species, eleven of which are endemic to California. Several Aliatypus species show disjunct distributional patterns in California (some are found on both sides of the vast Central Valley), and the genus as a whole occupies an impressive variety of habitats. METHODOLOGY/PRINCIPAL FINDINGS We collected specimens from 89 populations representing all described species. DNA sequence data were collected from seven gene regions, including two newly developed for spider systematics. Bayesian inference (in individual gene tree and species tree approaches) recovered a general "3 clade" structure for the genus (A. gulosus, californicus group, erebus group), with three other phylogenetically isolated species differing slightly in position across different phylogenetic analyses. Because of extremely high intraspecific divergences in mitochondrial COI sequences, the relatively slowly evolving 28S rRNA gene was found to be more useful than mitochondrial data for identification of morphologically indistinguishable immatures. For multiple species spanning the Central Valley, explicit hypothesis testing suggests a lack of monophyly for regional populations (e.g., western Coast Range populations). Phylogenetic evidence clearly shows that syntopy is restricted to distant phylogenetic relatives, consistent with ecological niche conservatism. CONCLUSIONS/SIGNIFICANCE This study provides fundamental insight into a radiation of trapdoor spiders found in the biodiversity hotspot of California. Species relationships are clarified and undescribed lineages are discovered, with more geographic sampling likely to lead to additional species diversity. These dispersal-limited taxa provide novel insight into the biogeography and Earth history processes of California.
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Affiliation(s)
- Jordan D Satler
- Department of Biology, San Diego State University, San Diego, California, United States of America.
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Baldwin BG, Kalisz S, Armbruster WS. Phylogenetic perspectives on diversification, biogeography, and floral evolution of Collinsia and Tonella (Plantaginaceae). AMERICAN JOURNAL OF BOTANY 2011; 98:731-53. [PMID: 21613170 DOI: 10.3732/ajb.1000346] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
PREMISE OF THE STUDY Collinsia was the subject of classic biosystematic studies by Garber and colleagues and is increasingly investigated to address major evolutionary questions. Lack of phylogenetic data from more than one gene region and one taxonomic exemplar has left relationships, diversity, and phytogeography of Collinsia in question and has limited understanding of its diversification. METHODS Phylogenetic analyses representing 179 populations of Collinsia and closely related Tonella were conducted based on DNA sequences of nuclear ribosomal transcribed spacers, the single-copy nuclear gene CYCLOIDEA-1, and part of the chloroplast matK/trnK intron region to reexamine systematic hypotheses and extend understanding of the importance of floral characters, chromosome evolution, interfertility, crossability, hybridization, edaphic factors, and ecogeographic barriers to diversification in the group. KEY RESULTS Informal "sections" of Collinsia are artificial, although pedicel length and other traditional deep-level taxonomic characters are more conservative evolutionarily than flower size. Evolutionary loss of crossability and interfertility in Collinsia appears to be largely a byproduct of divergence. Although most taxa appear to have arisen by divergent evolution, multiple lines of evidence indicate a homoploid hybrid constitution of C. tinctoria, possibly explaining an occurrence of convergent chromosome evolution. Phylogeographic and cryptic diversity is extensive. CONCLUSIONS Diversity in Collinsia is greater than previously documented. Recently divergent lineages are often associated with distinct habitat (including soil) and geographic factors, different flower sizes, and contrasting chromosomal arrangements. Evidence for a hybrid constitution of diploid C. tinctoria is consistent with lack of strong intersterility barriers between closely related taxa.
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Affiliation(s)
- Bruce G Baldwin
- Jepson Herbarium and Department of Integrative Biology, 1001 Valley Life Sciences Building #2465, University of California, Berkeley, California 94720-2465, USA.
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POLIHRONAKIS MAXI, CATERINO MICHAELS, CHATZIMANOLIS STYLIANOS. Elucidating the phylogeographic structure among a mosaic of unisexual and bisexual populations of the weevil Geodercodes latipennis (Coleoptera: Curculionidae) in the Transverse Ranges of southern California. Biol J Linn Soc Lond 2010. [DOI: 10.1111/j.1095-8312.2010.01542.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Lind AJ, Spinks PQ, Fellers GM, Shaffer HB. Rangewide phylogeography and landscape genetics of the Western U.S. endemic frog Rana boylii (Ranidae): implications for the conservation of frogs and rivers. CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0138-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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MAREK PAULE. A revision of the Appalachian millipede genus Brachoria Chamberlin, 1939 (Polydesmida: Xystodesmidae: Apheloriini). Zool J Linn Soc 2010. [DOI: 10.1111/j.1096-3642.2010.00633.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Polihronakis M, Caterino MS. Contrasting patterns of phylogeographic relationships in sympatric sister species of ironclad beetles (Zopheridae: Phloeodes spp.) in California's Transverse Ranges. BMC Evol Biol 2010; 10:195. [PMID: 20573263 PMCID: PMC2904329 DOI: 10.1186/1471-2148-10-195] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Accepted: 06/24/2010] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Comparative phylogeography of sympatric sibling species provides an opportunity to isolate the effects of geography and demographics on the evolutionary history of two lineages over the same, known time scale. In the current study, we investigated the phylogeographic structure of two zopherid beetle species, Phloeodes diabolicus and P. plicatus, where their ranges overlap in California's Transverse Ranges. RESULTS Although P. diabolicus and P. plicatus share similar habitats with largely overlapping distributions, the results of this study revealed different evolutionary histories for each species since divergence from their most recent common ancestor. In general, P. plicatus had higher genetic diversity, and more among population isolation than P. diabolicus. The mismatch distributions indicated that one major difference between the two species was the timing of population expansion. This result was consistent with genetic patterns revealed by the Phist values and genetic diversity. Lastly, there were no parallel genetic breaks at similar geographic barriers between the species. CONCLUSIONS Our data revealed that differential demographics rather than geography were responsible for the genetic patterns of the two species.
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Affiliation(s)
- Maxi Polihronakis
- Department of Invertebrate Zoology, Santa Barbara Museum of Natural History, 2559 Puesta del Sol Rd, Santa Barbara, CA 93105 USA
| | - Michael S Caterino
- Department of Invertebrate Zoology, Santa Barbara Museum of Natural History, 2559 Puesta del Sol Rd, Santa Barbara, CA 93105 USA
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Feldman CR, Hoyer RF. A New Species of Snake in the Genus Contia (Squamata: Colubridae) from California and Oregon. COPEIA 2010. [DOI: 10.1643/ch-09-129] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Garrick RC, Sunnucks P, Dyer RJ. Nuclear gene phylogeography using PHASE: dealing with unresolved genotypes, lost alleles, and systematic bias in parameter estimation. BMC Evol Biol 2010; 10:118. [PMID: 20429950 PMCID: PMC2880299 DOI: 10.1186/1471-2148-10-118] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Accepted: 04/30/2010] [Indexed: 01/25/2023] Open
Abstract
Background A widely-used approach for screening nuclear DNA markers is to obtain sequence data and use bioinformatic algorithms to estimate which two alleles are present in heterozygous individuals. It is common practice to omit unresolved genotypes from downstream analyses, but the implications of this have not been investigated. We evaluated the haplotype reconstruction method implemented by PHASE in the context of phylogeographic applications. Empirical sequence datasets from five non-coding nuclear loci with gametic phase ascribed by molecular approaches were coupled with simulated datasets to investigate three key issues: (1) haplotype reconstruction error rates and the nature of inference errors, (2) dataset features and genotypic configurations that drive haplotype reconstruction uncertainty, and (3) impacts of omitting unresolved genotypes on levels of observed phylogenetic diversity and the accuracy of downstream phylogeographic analyses. Results We found that PHASE usually had very low false-positives (i.e., a low rate of confidently inferring haplotype pairs that were incorrect). The majority of genotypes that could not be resolved with high confidence included an allele occurring only once in a dataset, and genotypic configurations involving two low-frequency alleles were disproportionately represented in the pool of unresolved genotypes. The standard practice of omitting unresolved genotypes from downstream analyses can lead to considerable reductions in overall phylogenetic diversity that is skewed towards the loss of alleles with larger-than-average pairwise sequence divergences, and in turn, this causes systematic bias in estimates of important population genetic parameters. Conclusions A combination of experimental and computational approaches for resolving phase of segregating sites in phylogeographic applications is essential. We outline practical approaches to mitigating potential impacts of computational haplotype reconstruction on phylogeographic inferences. With targeted application of laboratory procedures that enable unambiguous phase determination via physical isolation of alleles from diploid PCR products, relatively little investment of time and effort is needed to overcome the observed biases.
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Affiliation(s)
- Ryan C Garrick
- Department of Biology, Virginia Commonwealth University, Richmond, 23284, USA.
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SPINKS PHILLIPQ, THOMSON ROBERTC, BRADLEY SHAFFER H. Nuclear gene phylogeography reveals the historical legacy of an ancient inland sea on lineages of the western pond turtle,Emys marmoratain California. Mol Ecol 2010; 19:542-56. [DOI: 10.1111/j.1365-294x.2009.04451.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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POLIHRONAKIS MAXI, CATERINO MICHAELS. Multilocus phylogeography of the flightless darkling beetle Nyctoporis carinata (Coleoptera: Tenebrionidae) in the California Floristic Province: deciphering an evolutionary mosaic. Biol J Linn Soc Lond 2010. [DOI: 10.1111/j.1095-8312.2009.01360.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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SHORT AEZ, CATERINO MS. On the validity of habitat as a predictor of genetic structure in aquatic systems: a comparative study using California water beetles. Mol Ecol 2009; 18:403-14. [DOI: 10.1111/j.1365-294x.2008.04039.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Kuchta SR, Parks DS, Wake DB. Pronounced phylogeographic structure on a small spatial scale: Geomorphological evolution and lineage history in the salamander ring species Ensatina eschscholtzii in central coastal California. Mol Phylogenet Evol 2009; 50:240-55. [DOI: 10.1016/j.ympev.2008.10.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2008] [Revised: 10/05/2008] [Accepted: 10/27/2008] [Indexed: 10/21/2022]
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Conroy CJ, Neuwald JL. Phylogeographic study of the California vole, Microtus californicus. J Mammal 2008. [DOI: 10.1644/07-mamm-a-189r1.1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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RICH KATHERINEA, THOMPSON JOHNN, FERNANDEZ CATHERINEC. Diverse historical processes shape deep phylogeographical divergence in the pollinating seed parasite Greya politella. Mol Ecol 2008; 17:2430-48. [DOI: 10.1111/j.1365-294x.2008.03754.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Caterino MS, Chatzimanolis S. Conservation genetics of three flightless beetle species in southern California. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9548-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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