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Tapondjou Nkonmeneck WP, Allen KE, Hime PM, Knipp KN, Kameni MM, Tchassem AM, Gonwouo LN, Brown RM. Diversification and historical demography of Rhampholeon spectrum in West-Central Africa. PLoS One 2022; 17:e0277107. [PMID: 36525408 PMCID: PMC9757597 DOI: 10.1371/journal.pone.0277107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 10/19/2022] [Indexed: 12/23/2022] Open
Abstract
Pygmy Chameleons of the genus Rhampholeon represent a moderately diverse, geographically circumscribed radiation, with most species (18 out of 19 extant taxa) limited to East Africa. The one exception is Rhampholeon spectrum, a species restricted to West-Central African rainforests. We set out to characterize the geographic basis of genetic variation in this disjunctly distributed Rhampholeon species using a combination of multilocus Sanger data and genomic sequences to explore population structure and range-wide phylogeographic patterns. We also employed demographic analyses and niche modeling to distinguish between alternate explanations to contextualize the impact of past geological and climatic events on the present-day distribution of intraspecific genetic variation. Phylogenetic analyses suggest that R. spectrum is a complex of five geographically delimited populations grouped into two major clades (montane vs. lowland). We found pronounced population structure suggesting that divergence and, potentially, speciation began between the late Miocene and the Pleistocene. Sea level changes during the Pleistocene climatic oscillations resulted in allopatric divergence associated with dispersal over an ocean channel barrier and colonization of Bioko Island. Demographic inferences and range stability mapping each support diversification models with secondary contact due to population contraction in lowland and montane refugia during the interglacial period. Allopatric divergence, congruent with isolation caused by geologic uplift of the East African rift system, the "descent into the Icehouse," and aridification of sub-Saharan Africa during the Eocene-Oligocene are identified as the key events explaining the population divergence between R. spectrum and its closely related sister clade from the Eastern Arc Mountains. Our results unveil cryptic genetic diversity in R. spectrum, suggesting the possibility of a species complex distributed across the Lower Guinean Forest and the Island of Bioko. We highlight the major element of species diversification that modelled today's diversity and distributions in most West-Central African vertebrates.
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Affiliation(s)
- Walter Paulin Tapondjou Nkonmeneck
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| | - Kaitlin E. Allen
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| | - Paul M. Hime
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| | - Kristen N. Knipp
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| | - Marina M. Kameni
- Laboratory of Zoology, Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon
| | - Arnaud M. Tchassem
- Laboratory of Zoology, Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon
| | - LeGrand N. Gonwouo
- Laboratory of Zoology, Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon
| | - Rafe M. Brown
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
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2
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Grismer JL, Escalona M, Miller C, Beraut E, Fairbairn CW, Marimuthu MPA, Nguyen O, Toffelmier E, Wang IJ, Shaffer HB. Reference genome of the rubber boa, Charina bottae (Serpentes: Boidae). J Hered 2022; 113:641-648. [PMID: 36056886 PMCID: PMC9709994 DOI: 10.1093/jhered/esac048] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
The rubber boa, Charina bottae is a semi-fossorial, cold-temperature adapted snake that ranges across the wetter and cooler ecoregions of the California Floristic Province. The rubber boa is 1 of 2 species in the family Boidae native to California and currently has 2 recognized subspecies, the Northern rubber boa C. bottae bottae and the Southern rubber boa C. bottae umbratica. Recent genomic work on C. bottae indicates that these 2 subspecies are collectively composed of 4 divergent lineages that separated during the late Miocene. Analysis of habitat suitability indicates that C. bottae umbratica montane sky-island populations from southern California will lose the majority of their habit over the next 70 yr, and is listed as Threatened under the California Endangered Species Act. Here, we report a new, chromosome-level assembly of C. bottae bottae as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises 289 scaffolds covering 1,804,944,895 bp, has a contig N50 of 37.3 Mb, a scaffold N50 of 97 Mb, and BUSCO completeness score of 96.3%, and represents the first reference genome for the Boidae snake family. This genome will enable studies of genetic differentiation and connectivity among C. bottae bottae and C. bottae umbratica populations across California and help manage locally endemic lineages as they confront challenges from human-induced climate warming, droughts, and wildfires across California.
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Affiliation(s)
- Jesse L Grismer
- Department of Biology, La Sierra University, Riverside, CA, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Courtney Miller
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Colin W Fairbairn
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA, United States
| | - Erin Toffelmier
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States
| | - H Bradley Shaffer
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, United States
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3
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Grismer J, Scott P, Toffelmier E, Hinds B, Klabacka R, Stewart G, White V, Oaks J, Bradley Shaffer H. Genomic data reveal local endemism in Southern California Rubber Boas (Serpentes: Boidae, Charina) and the critical need for enhanced conservation actions. Mol Phylogenet Evol 2022; 174:107542. [PMID: 35690376 DOI: 10.1016/j.ympev.2022.107542] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 05/25/2022] [Accepted: 05/31/2022] [Indexed: 10/18/2022]
Abstract
The mountains of southern California represent unique, isolated ecosystems that support distinct high-elevation habitats found nowhere else in the area. Analyses of several moisture-dependent species across these sky-islands indicate they exist as locally endemic lineages that occur across these fragmented mountains ranges. The Rubber Boa is a semi-fossorial snake species that is widely distributed in the cooler and more moist ecoregions regions of western North America, including isolated populations across southern California mountain ranges. We developed a genomic and ecological dataset to examine genetic diversity within Rubber Boas and to determine if the endemic Southern Rubber Boa represents a distinct lineage. We quantified current and future habitat suitability under a range of climate change scenarios, and discuss the possible environmental threats facing these unique montane isolates. Our results support four major lineages within Rubber Boas, with genetic breaks that are consistent with biogeographic boundaries observed in other co-distributed, cool-temperature, moisture adapted species. Our data support previous studies that the Southern Rubber Boa is an independent evolutionary unit and now includes multiple locally endemic sky-island populations, restricted to isolated mountain tops and ranges across southern California. Analyses of future habitat suitability indicate that many of these sky-island populations will lose most of their suitable habitat over the next 70 years given predicted increases in drought, rising temperatures, and wildfires. Collectively these data emphasize the critical conservation needs of these montane ecosystems in southern California under current and projected climate change conditions.
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Affiliation(s)
- Jesse Grismer
- Department of Ecology and Evolutionary Biology, La Kretz Center for Californian Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA; Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL 36849, USA; Department of Biology, La Sierra University, Riverside, CA 92515, USA.
| | - Peter Scott
- Department of Ecology and Evolutionary Biology, La Kretz Center for Californian Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA; Department of Life, Earth, and Environmental Sciences, West Texas A&M University, Canyon, TX 79016, USA
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, La Kretz Center for Californian Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Brian Hinds
- Department of Biology, La Sierra University, Riverside, CA 92515, USA
| | - Randy Klabacka
- Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL 36849, USA
| | - Glenn Stewart
- Department of Biological Sciences, California State Polytechnic University, Pomona, CA 91768, USA
| | - Virginia White
- Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL 36849, USA
| | - Jamie Oaks
- Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL 36849, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, La Kretz Center for Californian Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
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4
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Wang Z, Pierce NE. Fine-scale genome-wide signature of Pleistocene glaciation in Thitarodes moths (Lepidoptera: Hepialidae), host of Ophiocordyceps fungus in the Hengduan Mountains. Mol Ecol 2022; 32:2695-2714. [PMID: 35377501 DOI: 10.1111/mec.16457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 02/12/2022] [Accepted: 03/21/2022] [Indexed: 11/28/2022]
Abstract
The Hengduan Mountains region is a biodiversity hotspot known for its topologically complex, deep valleys and high mountains. While landscape and glacial refugia have been evoked to explain patterns of inter-species divergence, the accumulation of intra-species (i.e. population level) genetic divergence across the mountain-valley landscape in this region has received less attention. We used genome-wide restriction site-associated DNA sequencing (RADseq) to reveal signatures of Pleistocene glaciation in populations of Thitarodes shambalaensis (Lepidoptera: Hepialidae), the host moth of parasitic Ophiocordyceps sinensis (Hypocreales: Ophiocordycipitaceae) or "caterpillar fungus" endemic to the glacier of eastern Mt. Gongga. We used moraine history along the glacier valleys to model the distribution and environmental barriers to gene flow across populations of T. shambalaensis. We found that moth populations separated by less than 10 km exhibited valley-based population genetic clustering and isolation-by-distance (IBD), while gene flow among populations was best explained by models using information about their distributions at the local last glacial maximum (LGML , 58 kya), not their contemporary distribution. Maximum likelihood lineage history among populations, and among subpopulations as little as 500 meters apart, recapitulated glaciation history across the landscape. We also found signals of isolated population expansion following the retreat of LGML glaciers. These results reveal the fine-scale, long-term historical influence of landscape and glaciation on the genetic structuring of populations of an endangered and economically important insect species. Similar mechanisms, given enough time and continued isolation, could explain the contribution of glacier refugia to the generation of species diversity among the Hengduan Mountains.
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Affiliation(s)
- Zhengyang Wang
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Naomi E Pierce
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
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5
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Allen KE, Greenbaum E, Hime PM, Tapondjou N. WP, Sterkhova VV, Kusamba C, Rödel M, Penner J, Peterson AT, Brown RM. Rivers, not refugia, drove diversification in arboreal, sub-Saharan African snakes. Ecol Evol 2021; 11:6133-6152. [PMID: 34141208 PMCID: PMC8207163 DOI: 10.1002/ece3.7429] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/12/2021] [Accepted: 02/18/2021] [Indexed: 12/26/2022] Open
Abstract
The relative roles of rivers versus refugia in shaping the high levels of species diversity in tropical rainforests have been widely debated for decades. Only recently has it become possible to take an integrative approach to test predictions derived from these hypotheses using genomic sequencing and paleo-species distribution modeling. Herein, we tested the predictions of the classic river, refuge, and river-refuge hypotheses on diversification in the arboreal sub-Saharan African snake genus Toxicodryas. We used dated phylogeographic inferences, population clustering analyses, demographic model selection, and paleo-distribution modeling to conduct a phylogenomic and historical demographic analysis of this genus. Our results revealed significant population genetic structure within both Toxicodryas species, corresponding geographically to river barriers and divergence times from the mid-Miocene to Pliocene. Our demographic analyses supported the interpretation that rivers are indications of strong barriers to gene flow among populations since their divergence. Additionally, we found no support for a major contraction of suitable habitat during the last glacial maximum, allowing us to reject both the refuge and river-refuge hypotheses in favor of the river-barrier hypothesis. Based on conservative interpretations of our species delimitation analyses with the Sanger and ddRAD data sets, two new cryptic species are identified from east-central Africa. This study highlights the complexity of diversification dynamics in the African tropics and the advantages of integrative approaches to studying speciation in tropical regions.
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Affiliation(s)
- Kaitlin E. Allen
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Eli Greenbaum
- Department of Biological SciencesUniversity of Texas at El PasoEl PasoTXUSA
| | - Paul M. Hime
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Walter P. Tapondjou N.
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Viktoria V. Sterkhova
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Chifundera Kusamba
- Laboratoire d’Hérpétologie, Département de BiologieCentre de Recherche en Sciences NaturellesLwiroDemocratic Republic of Congo
| | - Mark‐Oliver Rödel
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Johannes Penner
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
- Chair of Wildlife Ecology and ManagementUniversity of FreiburgFreiburgGermany
| | - A. Townsend Peterson
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Rafe M. Brown
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
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6
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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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7
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Firneno TJ, O'Neill JR, Portik DM, Emery AH, Townsend JH, Fujita MK. Finding complexity in complexes: Assessing the causes of mitonuclear discordance in a problematic species complex of Mesoamerican toads. Mol Ecol 2020; 29:3543-3559. [PMID: 32500624 DOI: 10.1111/mec.15496] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/18/2020] [Accepted: 05/26/2020] [Indexed: 12/22/2022]
Abstract
Mitonuclear discordance is a frequently encountered pattern in phylogeographic studies and occurs when mitochondrial and nuclear DNA display conflicting signals. Discordance among these genetic markers can be caused by several factors including confounded taxonomies, gene flow, and incomplete lineage sorting. In this study, we present a strong case of mitonuclear discordance in a species complex of toads (Bufonidae: Incilius coccifer complex) found in the Chortís Block of Central America. To determine the cause of mitonuclear discordance in this complex, we used spatially explicit genetic data to test species limits and relationships, characterize demographic history, and quantify gene flow. We found extensive mitonuclear discordance among the three recognized species within this group, especially in populations within the Chortís Highlands of Honduras. Our data reveal nuclear introgression within the Chortís Highlands populations that was most probably driven by cyclical range expansions due to climatic fluctuations. Though we determined introgression occurred within the nuclear genome, our data suggest that it is not the key factor in driving mitonuclear discordance in the entire species complex. Rather, due to a lack of discernible geographic pattern between mitochondrial and nuclear DNA, as well as a relatively recent divergence time of this complex, we concluded that mitonuclear discordance has been caused by incomplete lineage sorting. Our study provides a framework to test sources of mitonuclear discordance and highlights the importance of using multiple marker types to test species boundaries in cryptic species.
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Affiliation(s)
- Thomas J Firneno
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Justin R O'Neill
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA, USA
| | | | - Alyson H Emery
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Josiah H Townsend
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA, USA.,Centro Zamorano de Biodiversidad, Departamento de Ambiente y Desarrollo, Escuela Agrícola Panamericana Zamorano, Municipalidad de San Antonio de Oriente, Francisco Morazán, Honduras
| | - Matthew K Fujita
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas at Arlington, Arlington, TX, USA
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Naser-Khdour S, Minh BQ, Zhang W, Stone EA, Lanfear R. The Prevalence and Impact of Model Violations in Phylogenetic Analysis. Genome Biol Evol 2019; 11:3341-3352. [PMID: 31536115 PMCID: PMC6893154 DOI: 10.1093/gbe/evz193] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2019] [Indexed: 12/24/2022] Open
Abstract
In phylogenetic inference, we commonly use models of substitution which assume that sequence evolution is stationary, reversible, and homogeneous (SRH). Although the use of such models is often criticized, the extent of SRH violations and their effects on phylogenetic inference of tree topologies and edge lengths are not well understood. Here, we introduce and apply the maximal matched-pairs tests of homogeneity to assess the scale and impact of SRH model violations on 3,572 partitions from 35 published phylogenetic data sets. We show that roughly one-quarter of all the partitions we analyzed (23.5%) reject the SRH assumptions, and that for 25% of data sets, tree topologies inferred from all partitions differ significantly from topologies inferred using the subset of partitions that do not reject the SRH assumptions. This proportion increases when comparing trees inferred using the subset of partitions that rejects the SRH assumptions, to those inferred from partitions that do not reject the SRH assumptions. These results suggest that the extent and effects of model violation in phylogenetics may be substantial. They highlight the importance of testing for model violations and possibly excluding partitions that violate models prior to tree reconstruction. Our results also suggest that further effort in developing models that do not require SRH assumptions could lead to large improvements in the accuracy of phylogenomic inference. The scripts necessary to perform the analysis are available in https://github.com/roblanf/SRHtests, and the new tests we describe are available as a new option in IQ-TREE (http://www.iqtree.org).
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Affiliation(s)
- Suha Naser-Khdour
- Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Bui Quang Minh
- Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
- Research School of Computer Science, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Wenqi Zhang
- Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Eric A Stone
- Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Robert Lanfear
- Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
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9
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Habitat preference differentiates the Holocene range dynamics but not barrier effects on two sympatric, congeneric trees (Tristaniopsis, Myrtaceae). Heredity (Edinb) 2019; 123:532-548. [PMID: 31243348 DOI: 10.1038/s41437-019-0243-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 05/25/2019] [Accepted: 05/29/2019] [Indexed: 11/08/2022] Open
Abstract
Niche partitioning can lead to differences in the range dynamics of plant species through its impacts on habitat availability, dispersal, or selection for traits that affect colonization and persistence. We investigated whether niche partitioning into upland and riparian habitats differentiates the range dynamics of two closely related and sympatric eastern Australian trees: the mountain water gum (Tristaniopsis collina) and the water gum (T. laurina). Using genomic data from SNP genotyping of 480 samples, we assessed the impact of biogeographic barriers and tested for signals of range expansion. Circuit theory was used to model isolation-by-resistance across three palaeo-environment scenarios: the Last Glacial Maximum, the Holocene Climate Optimum and present-day (1950-2014). Both trees showed similar genetic structure across historically dry barriers, despite evidence of significant environmental niche differentiation and different post-glacial habitat shifts. Tristaniopsis collina exhibits the signature of serial founder effects consistent with recent or rapid range expansion, whilst T. laurina has genetic patterns consistent with long-term persistence in geographically isolated populations despite occupying a broader bioclimatic niche. We found the minor influence of isolation-by-resistance on both species, though other unknown factors appear to shape genetic variation. We postulate that specialized recruitment traits (adapted to flood-disturbance regimes) rather than habitat availability limited post-glacial range expansion in T. laurina. Our findings indicate that niche breadth does not always facilitate range expansion through colonization and migration across barriers, though it can promote long-term persistence in situ.
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10
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Vasconcellos MM, Colli GR, Weber JN, Ortiz EM, Rodrigues MT, Cannatella DC. Isolation by instability: Historical climate change shapes population structure and genomic divergence of treefrogs in the Neotropical Cerrado savanna. Mol Ecol 2019; 28:1748-1764. [DOI: 10.1111/mec.15045] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 01/17/2019] [Accepted: 01/23/2019] [Indexed: 12/30/2022]
Affiliation(s)
| | - Guarino R. Colli
- Departamento de Zoologia Universidade de Brasília Brasília Brazil
| | - Jesse N. Weber
- Department of Biological Sciences University of Alaska Anchorage Anchorage, Alaska
| | - Edgardo M. Ortiz
- Department of Integrative Biology The University of Texas at Austin Austin Texas
- Plant Biodiversity Research Department of Ecology and Ecosystem Management Technical University of Munich Freising Germany
| | - Miguel T. Rodrigues
- Departamento de Zoologia, Instituto de Biociências Universidade de São Paulo São Paulo Brazil
| | - David C. Cannatella
- Department of Integrative Biology The University of Texas at Austin Austin Texas
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11
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Licona-Vera Y, Ornelas JF, Wethington S, Bryan KB. Pleistocene range expansions promote divergence with gene flow between migratory and sedentary populations of Calothorax hummingbirds. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Yuyini Licona-Vera
- Departamento de Biología Evolutiva, Instituto de Ecología, AC, Xalapa, Veracruz, Mexico
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12
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Soares LE, Goetze M, Zanella CM, Bered F. Genetic diversity and population structure of Vriesea reitzii (Bromeliaceae), a species from the Southern Brazilian Highlands. Genet Mol Biol 2018; 41:308-317. [PMID: 29583153 PMCID: PMC5913716 DOI: 10.1590/1678-4685-gmb-2017-0062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/22/2017] [Indexed: 12/01/2022] Open
Abstract
The Southern Brazilian Highlands are composed by a mosaic of Mixed Ombrophilous Forest (MOF) and grassland formations, an interesting landscape for the study of population structure. We analyzed the genetic diversity within and among populations of the MOF-endemic bromeliad Vriesea reitzii by genotyping seven nuclear microsatellite loci in 187 individuals from six populations. We characterized levels of genetic diversity and assessed the genetic structure among populations. Vriesea reitzii populations showed high levels of genetic variation (number of alleles 28 - 43, allelic richness 3.589 - 5.531) and moderate levels of genetic differentiation (FST = 0.123, RST = 0.096). The high levels of genetic diversity may be explained by species life-history traits, such as habit and mating system. The moderate structure may be a product of the combination of ancient and contemporary gene flow, resulting from the expansion of the forest in the Holocene, and/or due to facilitated dispersal mediated by the MOF’s mosaic landscape. The genetic results indicated no imminent threat to this bromeliad. However, the species is highly associated with the MOF, putting landscape conservation at the center of conservation efforts for the species’ maintenance.
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Affiliation(s)
- Luis Eduardo Soares
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil.,Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Márcia Goetze
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Camila M Zanella
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil.,The John Bingham Laboratory, National Institute of Agricultural Botany (NIAB), Cambridge, UK
| | - Fernanda Bered
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
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13
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Richart CH, Chichester LF, Boyer B, Pearce TA. Rediscovery of the southern California endemic American Keeled Slug Anadenulus cockerelli (Hemphill, 1890) after a 68-year hiatus. J NAT HIST 2018. [DOI: 10.1080/00222933.2018.1447700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Casey H. Richart
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Brendan Boyer
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Timothy A. Pearce
- Section of Mollusks, Carnegie Museum of Natural History, Pittsburgh, PA, USA
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14
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Portik DM, Leaché AD, Rivera D, Barej MF, Burger M, Hirschfeld M, Rödel M, Blackburn DC, Fujita MK. Evaluating mechanisms of diversification in a Guineo‐Congolian tropical forest frog using demographic model selection. Mol Ecol 2017; 26:5245-5263. [DOI: 10.1111/mec.14266] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 07/17/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Daniel M. Portik
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Adam D. Leaché
- Department of Biology University of Washington Seattle WA USA
- Burke Museum of Natural History and Culture University of Washington Seattle WA USA
| | - Danielle Rivera
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Michael F. Barej
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
| | - Marius Burger
- African Amphibian Conservation Research Group Unit for Environmental Sciences and Management North‐West University Potchefstroom South Africa
- Flora Fauna & Man Ecological Services Ltd. Tortola British Virgin Island
| | - Mareike Hirschfeld
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
| | - Mark‐Oliver Rödel
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
| | - David C. Blackburn
- Florida Museum of Natural History University of Florida Gainesville FL USA
| | - Matthew K. Fujita
- Amphibian and Reptile Diversity Research Center The University of Texas at Arlington Arlington TX USA
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15
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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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16
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Derkarabetian S, Burns M, Starrett J, Hedin M. Population genomic evidence for multiple Pliocene refugia in a montane‐restricted harvestman (Arachnida, Opiliones,
Sclerobunus robustus
) from the southwestern United States. Mol Ecol 2016; 25:4611-31. [DOI: 10.1111/mec.13789] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 07/11/2016] [Accepted: 07/19/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Shahan Derkarabetian
- Department of Biology San Diego State University 5500 Campanile Dr. San Diego CA 92182‐4614 USA
- Department of Biology University of California Riverside Riverside CA 92521 USA
| | - Mercedes Burns
- Department of Biology San Diego State University 5500 Campanile Dr. San Diego CA 92182‐4614 USA
| | - James Starrett
- Department of Biology San Diego State University 5500 Campanile Dr. San Diego CA 92182‐4614 USA
| | - Marshal Hedin
- Department of Biology San Diego State University 5500 Campanile Dr. San Diego CA 92182‐4614 USA
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17
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Bryson RW, Savary WE, Zellmer AJ, Bury RB, McCormack JE. Genomic data reveal ancient microendemism in forest scorpions across the California Floristic Province. Mol Ecol 2016; 25:3731-51. [DOI: 10.1111/mec.13707] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 05/03/2016] [Indexed: 01/16/2023]
Affiliation(s)
- Robert W. Bryson
- Department of Biology and Burke Museum of Natural History and Culture; University of Washington; Box 351800 Seattle WA 98195-1800 USA
| | - Warren E. Savary
- Department of Entomology; California Academy of Sciences; 55 Music Concourse Drive, Golden Gate Park San Francisco CA 94118 USA
| | - Amanda J. Zellmer
- Department of Biology; Occidental College; 1600 Campus Road Los Angeles CA 90041 USA
| | | | - John E. McCormack
- Department of Biology; Occidental College; 1600 Campus Road Los Angeles CA 90041 USA
- Moore Laboratory of Zoology; Occidental College; 1600 Campus Road Los Angeles CA 90041 USA
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18
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Pinto CM, Soto-Centeno JA, Núñez Quiroz ÁM, Ferreyra N, Delgado-Espinoza F, Stahl PW, Tirira DG. Archaeology, biogeography, and mammalogy do not provide evidence for tarukas (Cervidae:
Hippocamelus antisensis
) in Ecuador. J Mammal 2015. [DOI: 10.1093/jmammal/gyv151] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Knowing whether a species has been extirpated, or if it ever inhabited a specific geographic area, has direct importance for planning conservation activities. The taruka ( Hippocamelus antisensis ) is one of the largest Neotropical mammals; it is distributed in the central Andes, and there are published records of this species in Ecuador. Recently, missing museum specimens have cast doubts on the validity of these Ecuadorian records. Here, we examine whether the taruka ever inhabited Ecuador by analyzing multiple sources of information. Our approach consists of 3 components: 1) we surveyed archaeological collections and literature for any biological remains and cultural artifacts that may represent tarukas, 2) we searched mammal collections for specimens reported in publications, and 3) we generated ecological niche models (ENMs) of current and past climates to determine whether Ecuador offers suitable habitats for the taruka. Our results suggest that the taruka never inhabited Ecuador. We did not find any reliable supporting evidence in the form of specimens nor convincing literature reports. Furthermore, ENMs revealed that Ecuador has not supported suitable climates for the taruka. We suggest that published records of taruka in Ecuador may have been due to improper identifications of specimens. The methods used here may also prove useful in determining the presence of species that are either thought to be extinct, or suspected to be recently introduced into a new geographic area.
Conocer si una especie ha sido extirpada, o si alguna vez habitó un área geográfica específica, tiene importancia directa para la planificación de actividades de conservación. La Taruka ( Hippocamelus antisensis ) es uno de los mamíferos Neotropicales más grandes; se distribuye en los Andes centrales, y existen registros publicados de esta especie en Ecuador. Recientemente, ha habido dudas sobre la validez de los registros ecuatorianos porque los especímenes testigo se han perdido. Aquí examinamos si la taruka alguna vez habitó Ecuador, analizando múltiples fuentes de información. Nuestro enfoque metodológico consistió de 3 componentes: 1) examen de colecciones y literatura arqueológica para detectar restos biológicos o artefactos culturales que puedan representar tarukas, 2) búsqueda en colecciones mastozoológicas especímenes reportados en publicaciones; y 3) generación de modelos de nicho ecológico con climas pasados y presentes para determinar si Ecuador ofrece ambientes adecuados para la taruka. Nuestros resultados sugieren que la taruka nunca ha habitado Ecuador. No encontramos ninguna evidencia confiable en la forma de especímenes o reportes convincentes en la literatura. Además, los modelos de nicho ecológico revelaron que Ecuador no ha presentado las preferencias climáticas de la taruka. Sugerimos que los registros publicados de la taruka en Ecuador pueden ser el producto de la identificación errónea de especímenes. Las metodologías usadas en este trabajo pueden resultar útiles para investigar la presencia de especies que se creen extintas, o que se sospecha que son introducciones recientes a nuevas áreas geográficas.
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Ortego J, Bonal R, Muñoz A, Espelta JM. Living on the edge: the role of geography and environment in structuring genetic variation in the southernmost populations of a tropical oak. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:676-683. [PMID: 25284378 DOI: 10.1111/plb.12272] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 09/26/2014] [Indexed: 06/03/2023]
Abstract
Understanding the factors determining genetic diversity and structure in peripheral populations is a long-standing goal of evolutionary biogeography, yet little empirical information is available for tropical species. In this study, we combine information from nuclear microsatellite markers and niche modelling to analyse the factors structuring genetic variation across the southernmost populations of the tropical oak Quercus segoviensis. First, we tested the hypothesis that genetic variability decreases with population isolation and increases with local habitat suitability and stability since the Last Glacial Maximum (LGM). Second, we employed a recently developed multiple matrix regression with randomisation (MMRR) approach to study the factors associated with genetic divergence among the studied populations and test the relative contribution of environmental and geographic isolation to contemporary patterns of genetic differentiation. We found that genetic diversity was negatively correlated with average genetic differentiation with other populations, indicating that isolation and limited gene flow have contributed to erode genetic variability in some populations. Considering the relatively small size of the study area (<120 km), analyses of genetic structure indicate a remarkable inter-population genetic differentiation. Environmental dissimilarity and differences in current and past climate niche suitability and their additive effects were not associated with genetic differentiation after controlling for geographic distance, indicating that local climate does not contribute to explain spatial patterns of genetic structure. Overall, our data indicate that geographic isolation, but not current or past climate, is the main factor determining contemporary patterns of genetic diversity and structure within the southernmost peripheral populations of this tropical oak.
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Affiliation(s)
- J Ortego
- Conservation and Evolutionary Genetics Group, Department of Integrative Ecology, Estación Biológica de Doñana, Seville, Spain; Grupo de Investigación de la Biodiversidad Genética y Cultural, Instituto de Investigación en Recursos Cinegéticos, Ciudad Real, Spain
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20
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An B, Zhang L, Liu N, Wang Y. Refugia persistence of Qinghai-Tibetan plateau by the cold-tolerant bird Tetraogallus tibetanus (Galliformes: Phasianidae). PLoS One 2015; 10:e0121118. [PMID: 25822918 PMCID: PMC4378977 DOI: 10.1371/journal.pone.0121118] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/10/2015] [Indexed: 11/19/2022] Open
Abstract
Most of the temperate species are expected to have moved to lower altitudes during the glacial periods of the Quaternary. Here we tested this hypothesis in a cold-tolerant avian species Tibetan snowcock (Tetraogallus tibetanus) using two segments of mitochondrial gene (a 705bp Cytochrome-b; abbrev. Cyt-b and an 854 bp Control Region; abbrev. CR) and eight microsatellite loci by characterizing population differentiation and gene flow across its range. Combined (Cyt-b + CR) datasets detected several partially lineages with poor support. Microsatellite data, however, identified two distinct lineages congruent with the geographically separated western and central regions of Qinghai-Tibetan Plateau (QTP). The phylogeographic patterns that we observed might be explained by a combination of vicariance events that led to local isolation of T. tibetanus during warm periods and range expansions and population intermixing during cold periods. The results of this study add to our knowledge of population differentiation and connectivity in high altitude mountain ecosystems.
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Affiliation(s)
- Bei An
- School of Basic Medicine Sciences, Lanzhou University, Lanzhou, China
| | - Lixun Zhang
- School of Life Sciences, Lanzhou University, Lanzhou, China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou, China
- * E-mail: (LZ); (NL)
| | - Naifa Liu
- School of Life Sciences, Lanzhou University, Lanzhou, China
- * E-mail: (LZ); (NL)
| | - Ying Wang
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, Shandong, China
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21
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Abstract
Partitioning is a commonly used method in phylogenetics that aims to accommodate variation in substitution patterns among sites. Despite its popularity, there have been few systematic studies of its effects on phylogenetic inference, and there have been no studies that compare the effects of different approaches to partitioning across many empirical data sets. In this study, we applied four commonly used approaches to partitioning to each of 34 empirical data sets, and then compared the resulting tree topologies, branch-lengths, and bootstrap support estimated using each approach. We find that the choice of partitioning scheme often affects tree topology, particularly when partitioning is omitted. Most notably, we find occasional instances where the use of a suboptimal partitioning scheme produces highly supported but incorrect nodes in the tree. Branch-lengths and bootstrap support are also affected by the choice of partitioning scheme, sometimes dramatically so. We discuss the reasons for these effects and make some suggestions for best practice.
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Affiliation(s)
- David Kainer
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Robert Lanfear
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT, Australia National Evolutionary Synthesis Center, Durham, NC Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
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22
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Erratum. Mol Ecol 2014; 23:5645. [DOI: 10.1111/mec.12974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Engler JO, Balkenhol N, Filz KJ, Habel JC, Rödder D. Comparative landscape genetics of three closely related sympatric Hesperid butterflies with diverging ecological traits. PLoS One 2014; 9:e106526. [PMID: 25184414 PMCID: PMC4153614 DOI: 10.1371/journal.pone.0106526] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 08/07/2014] [Indexed: 12/02/2022] Open
Abstract
To understand how landscape characteristics affect gene flow in species with diverging ecological traits, it is important to analyze taxonomically related sympatric species in the same landscape using identical methods. Here, we present such a comparative landscape genetic study involving three closely related Hesperid butterflies of the genus Thymelicus that represent a gradient of diverging ecological traits. We analyzed landscape effects on their gene flow by deriving inter-population connectivity estimates based on different species distribution models (SDMs), which were calculated from multiple landscape parameters. We then used SDM output maps to calculate circuit-theoretic connectivity estimates and statistically compared these estimates to actual genetic differentiation in each species. We based our inferences on two different analytical methods and two metrics of genetic differentiation. Results indicate that land use patterns influence population connectivity in the least mobile specialist T. acteon. In contrast, populations of the highly mobile generalist T. lineola were panmictic, lacking any landscape related effect on genetic differentiation. In the species with ecological traits in between those of the congeners, T. sylvestris, climate has a strong impact on inter-population connectivity. However, the relative importance of different landscape factors for connectivity varies when using different metrics of genetic differentiation in this species. Our results show that closely related species representing a gradient of ecological traits also show genetic structures and landscape genetic relationships that gradually change from a geographical macro- to micro-scale. Thus, the type and magnitude of landscape effects on gene flow can differ strongly even among closely related species inhabiting the same landscape, and depend on their relative degree of specialization. In addition, the use of different genetic differentiation metrics makes it possible to detect recent changes in the relative importance of landscape factors affecting gene flow, which likely change as a result of contemporary habitat alterations.
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Affiliation(s)
- Jan O. Engler
- Zoological Research Museum Alexander Koenig, Bonn, Germany
- Department of Wildlife Sciences, University of Göttingen, Göttingen, Germany
- * E-mail:
| | - Niko Balkenhol
- Department of Wildlife Sciences, University of Göttingen, Göttingen, Germany
| | - Katharina J. Filz
- Department of Biogeography, Trier University, Trier, Germany
- Museum of Natural History Dortmund, Dortmund, Germany
| | - Jan C. Habel
- Department of Ecology and Ecosystemmanagement, Technical University Munich, Freising-Weihenstephan, Germany
| | - Dennis Rödder
- Zoological Research Museum Alexander Koenig, Bonn, Germany
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24
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Streicher JW, Devitt TJ, Goldberg CS, Malone JH, Blackmon H, Fujita MK. Diversification and asymmetrical gene flow across time and space: lineage sorting and hybridization in polytypic barking frogs. Mol Ecol 2014; 23:3273-91. [DOI: 10.1111/mec.12814] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 05/20/2014] [Accepted: 05/23/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Jeffrey W. Streicher
- Department of Biology; The University of Texas at Arlington; Arlington TX 76010 USA
| | - Thomas J. Devitt
- Department of Integrative Biology; The University of Texas at Austin; Austin TX 78712 USA
| | - Caren S. Goldberg
- Fish and Wildlife Sciences; University of Idaho; Moscow ID 83844 USA
| | - John H. Malone
- Department of Molecular and Cell Biology; University of Connecticut; Storrs CT 06269 USA
| | - Heath Blackmon
- Department of Biology; The University of Texas at Arlington; Arlington TX 76010 USA
| | - Matthew K. Fujita
- Department of Biology; The University of Texas at Arlington; Arlington TX 76010 USA
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25
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Soare TW, Kumar A, Naish KA, O'Donnell S. Genetic evidence for landscape effects on dispersal in the army ant Eciton burchellii. Mol Ecol 2013; 23:96-109. [PMID: 24372755 DOI: 10.1111/mec.12573] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 09/30/2013] [Accepted: 10/15/2013] [Indexed: 11/29/2022]
Abstract
Inhibited dispersal, leading to reduced gene flow, threatens populations with inbreeding depression and local extinction. Fragmentation may be especially detrimental to social insects because inhibited gene flow has important consequences for cooperation and competition within and among colonies. Army ants have winged males and permanently wingless queens; these traits imply male-biased dispersal. However, army ant colonies are obligately nomadic and have the potential to traverse landscapes. Eciton burchellii, the most regularly nomadic army ant, is a forest interior species: colony raiding activities are limited in the absence of forest cover. To examine whether nomadism and landscape (forest clearing and elevation) affect population genetic structure in a montane E. burchellii population, we reconstructed queen and male genotypes from 25 colonies at seven polymorphic microsatellite loci. Pairwise genetic distances among individuals were compared to pairwise geographical and resistance distances using regressions with permutations, partial Mantel tests and random forests analyses. Although there was no significant spatial genetic structure in queens or males in montane forest, dispersal may be male-biased. We found significant isolation by landscape resistance for queens based on land cover (forest clearing), but not on elevation. Summed colony emigrations over the lifetime of the queen may contribute to gene flow in this species and forest clearing impedes these movements and subsequent gene dispersal. Further forest cover removal may increasingly inhibit Eciton burchellii colony dispersal. We recommend maintaining habitat connectivity in tropical forests to promote population persistence for this keystone species.
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Affiliation(s)
- Thomas W Soare
- Animal Behavior Program, Department of Psychology, University of Washington, Seattle, WA 98195, USA
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26
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Velo-Antón G, Parra JL, Parra-Olea G, Zamudio KR. Tracking climate change in a dispersal-limited species: reduced spatial and genetic connectivity in a montane salamander. Mol Ecol 2013; 22:3261-78. [PMID: 23710831 DOI: 10.1111/mec.12310] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 02/18/2013] [Accepted: 02/26/2013] [Indexed: 11/29/2022]
Abstract
Tropical montane taxa are often locally adapted to very specific climatic conditions, contributing to their lower dispersal potential across complex landscapes. Climate and landscape features in montane regions affect population genetic structure in predictable ways, yet few empirical studies quantify the effects of both factors in shaping genetic structure of montane-adapted taxa. Here, we considered temporal and spatial variability in climate to explain contemporary genetic differentiation between populations of the montane salamander, Pseudoeurycea leprosa. Specifically, we used ecological niche modelling (ENM) and measured spatial connectivity and gene flow (using both mtDNA and microsatellite markers) across extant populations of P. leprosa in the Trans-Mexican Volcanic Belt (TVB). Our results indicate significant spatial and genetic isolation among populations, but we cannot distinguish between isolation by distance over time or current landscape barriers as mechanisms shaping population genetic divergences. Combining ecological niche modelling, spatial connectivity analyses, and historical and contemporary genetic signatures from different classes of genetic markers allows for inference of historical evolutionary processes and predictions of the impacts future climate change will have on the genetic diversity of montane taxa with low dispersal rates. Pseudoeurycea leprosa is one montane species among many endemic to this region and thus is a case study for the continued persistence of spatially and genetically isolated populations in the highly biodiverse TVB of central Mexico.
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Affiliation(s)
- G Velo-Antón
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
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