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Fonseca EM, Pope NS, Peterman WE, Werneck FP, Colli GR, Carstens BC. Genetic structure and landscape effects on gene flow in the Neotropical lizard Norops brasiliensis (Squamata: Dactyloidae). Heredity (Edinb) 2024; 132:284-295. [PMID: 38575800 PMCID: PMC11166928 DOI: 10.1038/s41437-024-00682-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024] Open
Abstract
One key research goal of evolutionary biology is to understand the origin and maintenance of genetic variation. In the Cerrado, the South American savanna located primarily in the Central Brazilian Plateau, many hypotheses have been proposed to explain how landscape features (e.g., geographic distance, river barriers, topographic compartmentalization, and historical climatic fluctuations) have promoted genetic structure by mediating gene flow. Here, we asked whether these landscape features have influenced the genetic structure and differentiation in the lizard species Norops brasiliensis (Squamata: Dactyloidae). To achieve our goal, we used a genetic clustering analysis and estimate an effective migration surface to assess genetic structure in the focal species. Optimized isolation-by-resistance models and a simulation-based approach combined with machine learning (convolutional neural network; CNN) were then used to infer current and historical effects on population genetic structure through 12 unique landscape models. We recovered five geographically distributed populations that are separated by regions of lower-than-expected gene flow. The results of the CNN showed that geographic distance is the sole predictor of genetic variation in N. brasiliensis, and that slope, rivers, and historical climate had no discernible influence on gene flow. Our novel CNN approach was accurate (89.5%) in differentiating each landscape model. CNN and other machine learning approaches are still largely unexplored in landscape genetics studies, representing promising avenues for future research with increasingly accessible genomic datasets.
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Affiliation(s)
- Emanuel M Fonseca
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Nathaniel S Pope
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - William E Peterman
- School of Environment and Natural Resources, The Ohio State University, Columbus, OH, USA
| | - Fernanda P Werneck
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Brazil
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA.
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2
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Dantas-Queiroz MV, Hurbath F, de Russo Godoy FM, Lanna FM, Versieux LM, Palma-Silva C. Comparative phylogeography reveals the demographic patterns of neotropical ancient mountain species. Mol Ecol 2023. [PMID: 36934376 DOI: 10.1111/mec.16929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 03/20/2023]
Abstract
Mountains are renowned for their bountiful biodiversity. Explanations on the origin of such abundant life are usually regarded to their orogenic history. However, ancient mountain systems with geological stability also exhibit astounding levels of number of species and endemism, as illustrated by the Brazilian Quartzitic Mountains (BQM) in Eastern South America. Thus, cycles of climatic changes over the last couple million years are usually assumed to play an important role in the origin of mountainous biota. These climatic oscillations potentially isolated and reconnected adjacent populations, a phenomenon known as flickering connectivity, accelerating speciation events due to range fragmentation, dispersion, secondary contact, and hybridization. To evaluate the role of the climatic fluctuations on the diversification of the BQM biota, we estimated the ancient demography of distinct endemic species of animals and plants using hierarchical approximate Bayesian computation analysis and Ecological Niche Modelling. Additionally, we evaluated if climatic oscillations have driven a genetic spatial congruence in the genetic structure of codistributed species from the Espinhaço Range, one of the main BQM areas. Our results show that the majority of plant lineages underwent a synchronous expansion over the Last Glacial Maximum (LGM, c. 21 thousand years ago), although we could not obtain a clear demographic pattern for the animal lineages. We also obtained a signal of a congruent phylogeographic break between lineages endemic to the Espinhaço Range, suggesting how ancient climatic oscillations might have driven the evolutionary history of the Espinhaço's biota.
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Affiliation(s)
- Marcos Vinicius Dantas-Queiroz
- Programa de Pós-Graduação em Biologia Vegetal, Universidade Estadual Paulista (UNESP), São Paulo, Brazil
- Department of Evolutionary Plant Biology, Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, Czech Republic
| | - Fernanda Hurbath
- Universidade do Estado de Minas Gerais - Unidade Passos, Av. Juca Stockler, 1130, bairro Belo Horizonte, Passos, Brazil
| | - Fernanda Maria de Russo Godoy
- Programa de Pós-Graduação em Biotecnologia e Biodiversidade, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Flávia Mol Lanna
- Department of Evolution, Ecology and Organismal Biology. Museum of Biological Diversity, The Ohio State University, Columbus, Ohio, USA
| | - Leonardo M Versieux
- Departamento de Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Clarisse Palma-Silva
- Programa de Pós-Graduação em Biologia Vegetal, Universidade Estadual Paulista (UNESP), São Paulo, Brazil
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
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3
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Martins NT, Macagnan LB, Cassano V, Gurgel CFD. Brazilian marine phylogeography: A literature synthesis and analysis of barriers. Mol Ecol 2022; 31:5423-5439. [PMID: 36073087 DOI: 10.1111/mec.16684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 08/15/2022] [Accepted: 08/30/2022] [Indexed: 12/24/2022]
Abstract
In the last 30 years a plethora of phylogeography studies have been published targeting Brazilian marine species. To date, several historical and extant physical and ecological processes have been identified as drivers of allopatric, sympatric and parapatric population genetic differentiation detected along the Brazilian coast. Examples of extant physical barriers include the split of the South Equatorial Current into the Brazil and North Brazil boundary currents, the mouth of major rivers (e.g., Amazon, São Francisco and Doce rivers) and coastal upwellings. Examples of historical barriers include the Vitória-Trindade seamount chain promoting genetic differentiation during periods of glacial maxima and lower sea levels. Examples of ecological speciation include adaptations to different substrata, resource use and reproductive biology. We used published data to build data sets and generalized additive models to identify patterns of spatial phylogeographical concordance across multiple taxa and markers. Our results identify Cape São Roque as the most dominant extant barrier to gene flow along the Brazilian coast, followed by the Vitória-Trindade seamount chain and Cape Santa Marta. Cape Santa Marta is the northern winter limit of the Rio da Plata plume and is intermittently influenced by the Malvinas Current. This study provides a novel explicit quantitative approach to comparative phylogeography that recognizes four Brazilian phylogeographical regions delimited by processes associated with barriers to gene flow.
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Affiliation(s)
- Nuno T Martins
- Departamento de Botânica, Universidade de São Paulo, Instituto de Biociências, São Paulo, São Paulo, Brazil
| | - Leonardo B Macagnan
- NUPEM - Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Valéria Cassano
- Departamento de Botânica, Universidade de São Paulo, Instituto de Biociências, São Paulo, São Paulo, Brazil
| | - Carlos Frederico D Gurgel
- NUPEM - Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
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4
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Pelletier TA, Parsons DJ, Decker SK, Crouch S, Franz E, Ohrstrom J, Carstens BC. phylogatR: Phylogeographic data aggregation and repurposing. Mol Ecol Resour 2022; 22:2830-2842. [PMID: 35748425 PMCID: PMC9796472 DOI: 10.1111/1755-0998.13673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/10/2022] [Accepted: 06/07/2022] [Indexed: 01/01/2023]
Abstract
Patterns of genetic diversity within species contain information the history of that species, including how they have responded to historical climate change and how easily the organism is able to disperse across its habitat. More than 40,000 phylogeographic and population genetic investigations have been published to date, each collecting genetic data from hundreds of samples. Despite these millions of data points, meta-analyses are challenging because the synthesis of results across hundreds of studies, each using different methods and forms of analysis, is a daunting and time-consuming task. It is more efficient to proceed by repurposing existing data and using automated data analysis. To facilitate data repurposing, we created a database (phylogatR) that aggregates data from different sources and conducts automated multiple sequence alignments and data curation to provide users with nearly ready-to-analyse sets of data for thousands of species. Two types of scientific research will be made easier by phylogatR: large meta-analyses of thousands of species that can address classic questions in evolutionary biology and ecology, and student- or citizen- science based investigations that will introduce a broad range of people to the analysis of genetic data. phylogatR enhances the value of existing data via the creation of software and web-based tools that enable these data to be recycled and reanalysed and increase accessibility to big data for research laboratories and classroom instructors with limited computational expertise and resources.
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Affiliation(s)
| | - Danielle J. Parsons
- Department of Evolution, Ecology, and Organismal BiologyThe Ohio State UniversityColumbusOhioUSA,Museum of Biological DiversityThe Ohio State UniversityColumbusOhioUSA
| | - Sydney K. Decker
- Department of Evolution, Ecology, and Organismal BiologyThe Ohio State UniversityColumbusOhioUSA,Museum of Biological DiversityThe Ohio State UniversityColumbusOhioUSA
| | | | - Eric Franz
- Ohio Supercomputer CenterColumbusOhioUSA
| | | | - Bryan C. Carstens
- Department of Evolution, Ecology, and Organismal BiologyThe Ohio State UniversityColumbusOhioUSA,Museum of Biological DiversityThe Ohio State UniversityColumbusOhioUSA
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5
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Myburgh AM, Daniels SR. Between the Cape Fold Mountains and the deep blue sea: Comparative phylogeography of selected codistributed ectotherms reveals asynchronous cladogenesis. Evol Appl 2022; 15:1967-1987. [DOI: 10.1111/eva.13493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
| | - Savel Regan Daniels
- Department of Botany & Zoology University of Stellenbosch Stellenbosch South Africa
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6
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Heil JA, Wolock CJ, Pierce NE, Pringle A, Bittleston LS. Sarracenia pitcher plant-associated microbial communities differ primarily by host species across a longitudinal gradient. Environ Microbiol 2022; 24:3500-3516. [PMID: 35384233 DOI: 10.1111/1462-2920.15993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 03/18/2022] [Accepted: 03/31/2022] [Indexed: 11/27/2022]
Abstract
Plant-associated microbial communities can profoundly affect plant health and success, and research is still uncovering factors driving the assembly of these communities. Here, we examine how geography versus host species affect microbial community structure and differential abundances of individual taxa. We use metabarcoding to characterize the bacteria and eukaryotes associated with five, often co-occurring species of Sarracenia pitcher plants (Sarraceniaceae) and three natural hybrids along the longitudinal gradient of the U.S. Gulf Coast, as well as samples from S. purpurea in Massachusetts. To tease apart the effects of geography versus host species, we focus first on sites with co-occurring species and then on species located across different sites. Our analyses show that bacterial and eukaryotic community structures are clearly and consistently influenced by host species identity, with geographic factors also playing a role. Naturally-occurring hybrids appear to also host unique communities, that are in some ways intermediate between their parent species. We see significant effects of geography (site and longitude), but these generally explain less of the variation among pitcher communities. Overall, in Sarracenia pitchers, host plant phenotype significantly affects the pitcher microbiomes and other associated organisms. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jacob A Heil
- Department of Biological Sciences, Boise State University
| | | | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology, Harvard University
| | - Anne Pringle
- Departments of Botany and Bacteriology, University of Wisconsin-Madison
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7
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Bittleston LS, Benson EL, Bernardin JR, Pierce NE. Characterization and Comparison of Convergence Among Cephalotus follicularis Pitcher Plant-Associated Communities With Those of Nepenthes and Sarracenia Found Worldwide. FRONTIERS IN PLANT SCIENCE 2022; 13:887635. [PMID: 35734258 PMCID: PMC9207445 DOI: 10.3389/fpls.2022.887635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/13/2022] [Indexed: 05/09/2023]
Abstract
The Albany pitcher plant, Cephalotus follicularis, has evolved cup-shaped leaves and a carnivorous habit completely independently from other lineages of pitcher plants. It is the only species in the family Cephalotaceae and is restricted to a small region of Western Australia. Here, we used metabarcoding to characterize the bacterial and eukaryotic communities living in C. follicularis pitchers at two different sites. Bacterial and eukaryotic communities were correlated in both richness and composition; however, the factors associated with richness were not the same across bacteria and eukaryotes, with bacterial richness differing with fluid color, and eukaryotic richness differing with the concentration of DNA extracted from the fluid, a measure roughly related to biomass. For turnover in composition, the variation in both bacterial and eukaryotic communities primarily differed with fluid acidity, fluid color, and sampling site. We compared C. follicularis-associated community diversity with that of Australian Nepenthes mirabilis, as well as a global comparison of Southeast Asian Nepenthes and North American Sarracenia. Our results showed similarity in richness with communities from other pitcher plants, and specific bacterial taxa shared among all three independent lineages of pitcher plants. Overall, we saw convergence in richness and particular clades colonizing pitcher plants around the world, suggesting that these highly specialized habitats select for certain numbers and types of inhabitants.
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Affiliation(s)
- Leonora S. Bittleston
- Department of Biological Sciences, Boise State University, Boise, ID, United States
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
- *Correspondence: Leonora S. Bittleston,
| | - Elizabeth L. Benson
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Jessica R. Bernardin
- Department of Biological Sciences, Boise State University, Boise, ID, United States
| | - Naomi E. Pierce
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
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8
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Lado P, Smith ML, Carstens BC, Klompen H. Population genetic structure and demographic history of the lone star tick, Amblyomma americanum (Ixodida: Ixodidae): New evidence supporting old records. Mol Ecol 2020; 29:2810-2823. [PMID: 32574413 DOI: 10.1111/mec.15524] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 01/25/2023]
Abstract
Range expansions are a potential outcome of changes in habitat suitability, which commonly result as a consequence of climate change. Hypotheses on such changes in the geographic distribution of a certain species can be evaluated using population genetic structure and demography. In this study we explore the population genetic structure, genetic variability, demographic history of, and habitat suitability for Amblyomma americanum, a North American tick species that is a known vector of several pathogenic microorganisms. We used a double digestion restriction site-associated DNA sequencing technique (dd-RAD seq) and discovered 8,181 independent single nucleotide polymorphisms (SNPs) in 189 ticks from across the geographic range of the species. Genetic diversity was low, particularly when considering the broad geographic range of this species. The edge populations were less diverse than populations belonging to the historic range, possibly indicative of a range expansion, but this hypothesis was not statistically supported by a test based on genetic data. Nonetheless, moderate levels of population structure and substructure were detected between geographic regions. For New England, demographic and species distribution models support a scenario where A. americanum was present in more northern locations in the past, underwent a bottleneck, and subsequently recovered. These results are consistent with a hypothesis that this species is re-establishing in this area, rather than one focused on range expansion from the south. This hypothesis is consistent with old records describing the presence of A. americanum in the northeastern US in the early colonial period.
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Affiliation(s)
- Paula Lado
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Megan L Smith
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Hans Klompen
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
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9
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Victoriano PF, Muñoz-Ramírez CP, Canales-Aguirre CB, Jara A, Vera-Escalona I, Burgos-Careaga T, Muñoz-Mendoza C, Habit EM. Contrasting evolutionary responses in two co-distributed species of Galaxias (Pisces, Galaxiidae) in a river from the glaciated range in Southern Chile. ROYAL SOCIETY OPEN SCIENCE 2020; 7:200632. [PMID: 32874654 PMCID: PMC7428232 DOI: 10.1098/rsos.200632] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/10/2020] [Indexed: 05/05/2023]
Abstract
Life-history traits are among the most important factors affecting population abundance and genetic diversity of species. Here, we analysed the genetic patterns of two Galaxias species with different life-history traits to investigate how these biological differences impacted their evolution in the Valdivia River basin, Southern Chile. We analysed mitochondrial DNA (mtDNA) sequences from 225 individuals of Galaxias maculatus and 136 of G. platei to compare patterns of genetic diversity, structure and demographic growth across the basin. Galaxias maculatus presented higher genetic diversity and higher genetic structure than G. platei. Demographic analyses showed G. maculatus kept a higher population size over time, with a signal of demographic expansion in the last 250 kyr. Whereas Galaxias platei, exhibited lower, but constant population size over time. Furthermore, haplotype networks revealed higher lineage diversity in G. maculatus with a tendency to occupy different areas of the basin. Coalescent simulations ruled out that genetic differences between species could be explained by stochastic processes (genetic drift), suggesting species-specific biological differences as responsible for the observed genetic differences. We discuss how differences in life-history traits and past glaciations interact to shape the evolutionary history of the two Galaxias species.
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Affiliation(s)
- P. F. Victoriano
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
- Authors for correspondence: P. F. Victoriano e-mail:
| | - C. P. Muñoz-Ramírez
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Chile
- Departamento de Ecología, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Concepción, Chile
- Centro de Investigación en Biodiversidad y Ambientes Sustentables (CIBAS), Universidad Católica de la Santísima Concepción, Concepción, Chile
- Authors for correspondence: C. P. Muñoz-Ramírez e-mail:
| | - C. B. Canales-Aguirre
- Centro i∼mar, Universidad de Los Lagos, Camino Chinquihue Km 7, Puerto Montt, Chile
- Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - A. Jara
- Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - I. Vera-Escalona
- Departamento de Ecología, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Concepción, Chile
- Centro de Investigación en Biodiversidad y Ambientes Sustentables (CIBAS), Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - T. Burgos-Careaga
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - C. Muñoz-Mendoza
- Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - E. M. Habit
- Unidad de Sistemas Acuáticos, Centro de Ciencias Ambientales Eula-Chile, Universidad de Concepción, Concepcion, Chile
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10
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Xue AT, Hickerson MJ. Comparative phylogeographic inference with genome‐wide data from aggregated population pairs. Evolution 2020; 74:808-830. [DOI: 10.1111/evo.13945] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/24/2020] [Accepted: 01/29/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Alexander T. Xue
- Subprogram in Ecology, Evolutionary Biology, and Behavior, Department of BiologyGraduate Center of City University of New York New York NY 10016
- Subprogram in Ecology, Evolutionary Biology, and Behavior, Department of BiologyCity College of City University of New York New York NY 10031
- Human Genetics Institute of New Jersey and Department of GeneticsRutgers University Piscataway NJ 08854
- Simons Center for Quantitative BiologyCold Spring Harbor Laboratory Cold Spring Harbor NY 11724
| | - Michael J. Hickerson
- Subprogram in Ecology, Evolutionary Biology, and Behavior, Department of BiologyGraduate Center of City University of New York New York NY 10016
- Subprogram in Ecology, Evolutionary Biology, and Behavior, Department of BiologyCity College of City University of New York New York NY 10031
- Division of Invertebrate ZoologyAmerican Museum of Natural History New York NY 10024
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11
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Rincon-Sandoval M, Betancur-R R, Maldonado-Ocampo JA. Comparative phylogeography of trans-Andean freshwater fishes based on genome-wide nuclear and mitochondrial markers. Mol Ecol 2019; 28:1096-1115. [PMID: 30714250 DOI: 10.1111/mec.15036] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/17/2019] [Accepted: 01/23/2019] [Indexed: 01/06/2023]
Abstract
The Neotropical region represents one of the greatest biodiversity hot spots on earth. Despite its unparalleled biodiversity, regional comparative phylogeographic studies are still scarce, with most focusing on model clades (e.g. birds) and typically examining a handful of loci. Here, we apply a genome-wide comparative phylogeographic approach to test hypotheses of codiversification of freshwater fishes in the trans-Andean region. Using target capture methods, we examined exon data for over 1,000 loci combined with complete mitochondrial genomes to study the phylogeographic history of five primary fish species (>150 individuals) collected from eight major river basins in Northwestern South America and Lower Central America. To assess their patterns of genetic structure, we inferred genealogical concordance taking into account all major aspects of phylogeography (within loci, across multiple genes, across species and among biogeographic provinces). Based on phylogeographic concordance factors, we tested four a priori biogeographic hypotheses, finding support for three of them and uncovering a novel, unexpected pattern of codiversification. The four emerging inter-riverine patterns are as follows: (a) Tuira + Atrato, (b) Ranchería + Catatumbo, (c) Magdalena system and (d) Sinú + Atrato. These patterns are interpreted as shared responses to the complex uplifting and orogenic processes that modified or sundered watersheds, allowing codiversification and speciation over geological time. We also find evidence of cryptic speciation in one of the species examined and instances of mitochondrial introgression in others. These results help further our knowledge of the historical geographic factors shaping the outstanding biodiversity of the Neotropics.
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Affiliation(s)
- Melissa Rincon-Sandoval
- Laboratorio de Ictiología, Unidad de Ecología y Sistemática (UNESIS), Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia.,Department of Biology, University of Puerto Rico, San Juan, Puerto Rico
| | - Ricardo Betancur-R
- Department of Biology, University of Puerto Rico, San Juan, Puerto Rico.,Department of Biology, The University of Oklahoma, Norman, Oklahoma
| | - Javier A Maldonado-Ocampo
- Laboratorio de Ictiología, Unidad de Ecología y Sistemática (UNESIS), Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
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12
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Derkarabetian S, Castillo S, Koo PK, Ovchinnikov S, Hedin M. A demonstration of unsupervised machine learning in species delimitation. Mol Phylogenet Evol 2019; 139:106562. [PMID: 31323334 PMCID: PMC6880864 DOI: 10.1016/j.ympev.2019.106562] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 07/03/2019] [Accepted: 07/15/2019] [Indexed: 01/13/2023]
Abstract
One major challenge to delimiting species with genetic data is successfully differentiating population structure from species-level divergence, an issue exacerbated in taxa inhabiting naturally fragmented habitats. Many fields of science are now using machine learning, and in evolutionary biology supervised machine learning has recently been used to infer species boundaries. These supervised methods require training data with associated labels. Conversely, unsupervised machine learning (UML) uses inherent data structure and does not require user-specified training labels, potentially providing more objectivity in species delimitation. In the context of integrative taxonomy, we demonstrate the utility of three UML approaches (random forests, variational autoencoders, t-distributed stochastic neighbor embedding) for species delimitation in an arachnid taxon with high population genetic structure (Opiliones, Laniatores, Metanonychus). We find that UML approaches successfully cluster samples according to species-level divergences and not high levels of population structure, while model-based validation methods severely over-split putative species. UML offers intuitive data visualization in two-dimensional space, the ability to accommodate various data types, and has potential in many areas of systematic and evolutionary biology. We argue that machine learning methods are ideally suited for species delimitation and may perform well in many natural systems and across taxa with diverse biological characteristics.
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Affiliation(s)
- Shahan Derkarabetian
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, United States; Department of Biology, San Diego State University, San Diego, CA 92182, United States; Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA 92521, United States.
| | - Stephanie Castillo
- Department of Biology, San Diego State University, San Diego, CA 92182, United States; Department of Entomology, University of California, Riverside, Riverside, CA 92521, United States
| | - Peter K Koo
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, United States
| | - Sergey Ovchinnikov
- Center for Systems Biology, Harvard University, Cambridge, MA 02138, United States
| | - Marshal Hedin
- Department of Biology, San Diego State University, San Diego, CA 92182, United States
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13
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Adams RH, Schield DR, Castoe TA. Recent Advances in the Inference of Gene Flow from Population Genomic Data. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s40610-019-00120-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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14
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Antonelli A, Ariza M, Albert J, Andermann T, Azevedo J, Bacon C, Faurby S, Guedes T, Hoorn C, Lohmann LG, Matos-Maraví P, Ritter CD, Sanmartín I, Silvestro D, Tejedor M, ter Steege H, Tuomisto H, Werneck FP, Zizka A, Edwards SV. Conceptual and empirical advances in Neotropical biodiversity research. PeerJ 2018; 6:e5644. [PMID: 30310740 PMCID: PMC6174874 DOI: 10.7717/peerj.5644] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 08/27/2018] [Indexed: 01/23/2023] Open
Abstract
The unparalleled biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in recent years in our understanding of the origin and diversification of many Neotropical taxa and biotic regions, many questions remain to be answered. Additional biological and geological data are still needed, as well as methodological advances that are capable of bridging these research fields. In this review, aimed primarily at advanced students and early-career scientists, we introduce the concept of "trans-disciplinary biogeography," which refers to the integration of data from multiple areas of research in biology (e.g., community ecology, phylogeography, systematics, historical biogeography) and Earth and the physical sciences (e.g., geology, climatology, palaeontology), as a means to reconstruct the giant puzzle of Neotropical biodiversity and evolution in space and time. We caution against extrapolating results derived from the study of one or a few taxa to convey general scenarios of Neotropical evolution and landscape formation. We urge more coordination and integration of data and ideas among disciplines, transcending their traditional boundaries, as a basis for advancing tomorrow's ground-breaking research. Our review highlights the great opportunities for studying the Neotropical biota to understand the evolution of life.
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Affiliation(s)
- Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Gothenburg Botanical Garden, Gothenburg, Sweden
- Department of Organismic Biology and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - María Ariza
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Laboratory Ecologie et Biologie des Interactions, Team “Ecologie, Evolution, Symbiose”, Université de Poitiers, Poitiers, France
| | - James Albert
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, USA
| | - Tobias Andermann
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Josué Azevedo
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Christine Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Søren Faurby
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Thais Guedes
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Federal University of São Paulo, Diadema, Brazil
- Museum of Zoology, University of São Paulo, São Paulo, Brazil
| | - Carina Hoorn
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
- Universidad Regional Amazonica IKIAM, Napo, Ecuador
| | - Lúcia G. Lohmann
- Instituto de Biociências, Departamento de Botânica, Universidade de São Paulo, São Paulo, Brazil
- Integrative Biology, University of California, Berkeley, CA, USA
| | - Pável Matos-Maraví
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Camila D. Ritter
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | | | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marcelo Tejedor
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Instituto Patagónico de Geología y Paleontología, Puerto Madryn, Guatemala
| | - Hans ter Steege
- Naturalis Biodiversity Center, Leiden, Netherlands
- Systems Ecology, Free University, Amsterdam, Netherlands
| | - Hanna Tuomisto
- Department of Biology, University of Turku, Turku, Finland
| | | | - Alexander Zizka
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Scott V. Edwards
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Department of Organismic Biology and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
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15
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Bell KC, Demboski JR, Cook JA. Sympatric Parasites Have Similar Host-Associated, but Asynchronous, Patterns of Diversification. Am Nat 2018; 192:E106-E119. [DOI: 10.1086/698300] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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16
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Bittleston LS, Wolock CJ, Yahya BE, Chan XY, Chan KG, Pierce NE, Pringle A. Convergence between the microcosms of Southeast Asian and North American pitcher plants. eLife 2018; 7:36741. [PMID: 30152327 PMCID: PMC6130972 DOI: 10.7554/elife.36741] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 08/08/2018] [Indexed: 01/11/2023] Open
Abstract
The ‘pitchers’ of carnivorous pitcher plants are exquisite examples of convergent evolution. An open question is whether the living communities housed in pitchers also converge in structure or function. Using samples from more than 330 field-collected pitchers of eight species of Southeast Asian Nepenthes and six species of North American Sarracenia, we demonstrate that the pitcher microcosms, or miniature ecosystems with complex communities, are strikingly similar. Compared to communities from surrounding habitats, pitcher communities house fewer species. While communities associated with the two genera contain different microbial organisms and arthropods, the species are predominantly from the same phylogenetic clades. Microbiomes from both genera are enriched in degradation pathways and have high abundances of key degradation enzymes. Moreover, in a manipulative field experiment, Nepenthes pitchers placed in a North American bog assembled Sarracenia-like communities. An understanding of the convergent interactions in pitcher microcosms facilitates identification of selective pressures shaping the communities. The ecosystems found across the Earth, including in forests, lakes and prairies, consist of communities of plants, animals and microbes. How these organisms interact with each other determines which ones grow and thrive. We still do not understand how communities form: why different species exist where they do, and what enables them to survive in different locations. This knowledge is particularly limited with regard to communities of microbes because they are hard to see and count. Pitcher plants are an ideal system for studying how communities and ecosystems assemble. The pitcher-shaped leaves of these plants each contain small aquatic communities of microbes and arthropods (including insects and mites) that can be relatively easily studied. Because unrelated groups of plants have evolved pitchers at different times and on different continents, these communities can also be used to explore how evolutionary history and the current environment determine which species thrive in a particular location. Bittleston et al. sampled the DNA of the communities living within 330 pitchers from various North American and Southeast Asian pitcher plant species. This revealed that very distantly related plants on opposite sides of the planet have pitchers that host similar communities, with the organisms found in one pitcher plant often closely related to the organisms found in others. The genes within the community’s DNA also shared many functions, with the majority of shared genes devoted to digesting captured insect prey. Bittleston et al. also relocated pitcher plants from Southeast Asia to grow alongside North American species and found the same microbes and arthropods colonizing both groups, indicating that the different types of pitchers present a similar habitat. Overall, the results of the experiments performed by Bittleston et al. suggest that certain kinds of interactions between species (such as between the pitcher plants and their microbes) can evolve independently in different parts of the world. Researchers can use these interactions to learn more about how communities and ecosystems form. With a greater understanding of the Earth’s ecosystems, it will be easier to protect them and predict how they will fare as global conditions change.
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Affiliation(s)
- Leonora S Bittleston
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.,Museum of Comparative Zoology, Harvard University, Cambridge, United States
| | - Charles J Wolock
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.,Museum of Comparative Zoology, Harvard University, Cambridge, United States
| | - Bakhtiar E Yahya
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | - Xin Yue Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.,International Genome Centre, Jiangsu University, Zhenjiang, China
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.,Museum of Comparative Zoology, Harvard University, Cambridge, United States
| | - Anne Pringle
- Departments of Botany and Bacteriology, University of Wisconsin-Madison, Wisconsin, United States
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17
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Barrow LN, Lemmon AR, Lemmon EM. Targeted Sampling and Target Capture: Assessing Phylogeographic Concordance with Genome-wide Data. Syst Biol 2018; 67:979-996. [DOI: 10.1093/sysbio/syy021] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 03/15/2018] [Indexed: 01/09/2023] Open
Affiliation(s)
- Lisa N Barrow
- Department of Biology, Museum of Southwestern Biology, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131-0001, USA
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4120, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, USA
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18
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Besnard G, Terral JF, Cornille A. On the origins and domestication of the olive: a review and perspectives. ANNALS OF BOTANY 2018; 121:385-403. [PMID: 29293871 PMCID: PMC5838823 DOI: 10.1093/aob/mcx145] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/12/2017] [Indexed: 05/18/2023]
Abstract
Background Unravelling domestication processes is crucial for understanding how species respond to anthropogenic pressures, forecasting crop responses to future global changes and improving breeding programmes. Domestication processes for clonally propagated perennials differ markedly from those for seed-propagated annual crops, mostly due to long generation times, clonal propagation and recurrent admixture with local forms, leading to a limited number of generations of selection from wild ancestors. However, additional case studies are required to document this process more fully. Scope The olive is an iconic species in Mediterranean cultural history. Its multiple uses and omnipresence in traditional agrosystems have made this species an economic pillar and cornerstone of Mediterranean agriculture. However, major questions about the domestication history of the olive remain unanswered. New paleobotanical, archeological, historical and molecular data have recently accumulated for olive, making it timely to carry out a critical re-evaluation of the biogeography of wild olives and the history of their cultivation. We review here the chronological history of wild olives and discuss the questions that remain unanswered, or even unasked, about their domestication history in the Mediterranean Basin. We argue that more detailed ecological genomics studies of wild and cultivated olives are crucial to improve our understanding of olive domestication. Multidisciplinary research integrating genomics, metagenomics and community ecology will make it possible to decipher the evolutionary ecology of one of the most iconic domesticated fruit trees worldwide. Conclusion The olive is a relevant model for improving our knowledge of domestication processes in clonally propagated perennial crops, particularly those of the Mediterranean Basin. Future studies on the ecological and genomic shifts linked to domestication in olive and its associated community will provide insight into the phenotypic and molecular bases of crop adaptation to human uses.
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Affiliation(s)
- Guillaume Besnard
- CNRS-UPS-ENSFEA-IRD, EDB, UMR 5174, Université Paul Sabatier, Toulouse Cedex , France
| | - Jean-Frédéric Terral
- ISEM, UMR 5554, CNRS-Université de Montpellier-IRD-EPHE, Equipe Dynamique de la Biodiversité, Anthropo-écologie, Montpellier Cedex, France
- International Associated Laboratory (LIA, CNRS) EVOLea, Zürich, Switzerland
| | - Amandine Cornille
- Center for Adaptation to a Changing Environment, ETH Zürich, Zürich, Switzerland
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
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19
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Liang HY, Feng ZP, Pei B, Li Y, Yang XT. Demographic expansion of two Tamarix species along the Yellow River caused by geological events and climate change in the Pleistocene. Sci Rep 2018; 8:60. [PMID: 29311687 PMCID: PMC5758526 DOI: 10.1038/s41598-017-19034-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 12/20/2017] [Indexed: 11/13/2022] Open
Abstract
The geological events and climatic fluctuations during the Pleistocene played important roles in shaping patterns of species distribution. However, few studies have evaluated the patterns of species distribution that were influenced by the Yellow River. The present work analyzed the demography of two endemic tree species that are widely distributed along the Yellow River, Tamarix austromongolica and Tamarix chinensis, to understand the role of the Yellow River and Pleistocene climate in shaping their distribution patterns. The most common chlorotype, chlorotype 1, was found in all populations, and its divergence time could be dated back to 0.19 million years ago (Ma). This dating coincides well with the formation of the modern Yellow River and the timing of Marine Isotope Stages 5e-6 (MIS 5e-6). Bayesian reconstructions along with models of paleodistribution revealed that these two species experienced a demographic expansion in population size during the Quaternary period. Approximate Bayesian computation analyses supported a scenario of expansion approximately from the upper to lower reaches of the Yellow River. Our results provide support for the roles of the Yellow River and the Pleistocene climate in driving demographic expansion of the populations of T. austromongolica and T. chinensis. These findings are useful for understanding the effects of geological events and past climatic fluctuations on species distribution patterns.
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Affiliation(s)
- Hong-Yan Liang
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China.,Sanmenxia Polytechnic, Sanmenxia, 472000, China
| | - Zhi-Pei Feng
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Bing Pei
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yong Li
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xi-Tian Yang
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China.
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20
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Mueller UG, Ishak HD, Bruschi SM, Smith CC, Herman JJ, Solomon SE, Mikheyev AS, Rabeling C, Scott JJ, Cooper M, Rodrigues A, Ortiz A, Brandão CRF, Lattke JE, Pagnocca FC, Rehner SA, Schultz TR, Vasconcelos HL, Adams RMM, Bollazzi M, Clark RM, Himler AG, LaPolla JS, Leal IR, Johnson RA, Roces F, Sosa-Calvo J, Wirth R, Bacci M. Biogeography of mutualistic fungi cultivated by leafcutter ants. Mol Ecol 2017; 26:6921-6937. [PMID: 29134724 DOI: 10.1111/mec.14431] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/19/2017] [Accepted: 10/04/2017] [Indexed: 01/03/2023]
Abstract
Leafcutter ants propagate co-evolving fungi for food. The nearly 50 species of leafcutter ants (Atta, Acromyrmex) range from Argentina to the United States, with the greatest species diversity in southern South America. We elucidate the biogeography of fungi cultivated by leafcutter ants using DNA sequence and microsatellite-marker analyses of 474 cultivars collected across the leafcutter range. Fungal cultivars belong to two clades (Clade-A and Clade-B). The dominant and widespread Clade-A cultivars form three genotype clusters, with their relative prevalence corresponding to southern South America, northern South America, Central and North America. Admixture between Clade-A populations supports genetic exchange within a single species, Leucocoprinus gongylophorus. Some leafcutter species that cut grass as fungicultural substrate are specialized to cultivate Clade-B fungi, whereas leafcutters preferring dicot plants appear specialized on Clade-A fungi. Cultivar sharing between sympatric leafcutter species occurs frequently such that cultivars of Atta are not distinct from those of Acromyrmex. Leafcutters specialized on Clade-B fungi occur only in South America. Diversity of Clade-A fungi is greatest in South America, but minimal in Central and North America. Maximum cultivar diversity in South America is predicted by the Kusnezov-Fowler hypothesis that leafcutter ants originated in subtropical South America and only dicot-specialized leafcutter ants migrated out of South America, but the cultivar diversity becomes also compatible with a recently proposed hypothesis of a Central American origin by postulating that leafcutter ants acquired novel cultivars many times from other nonleafcutter fungus-growing ants during their migrations from Central America across South America. We evaluate these biogeographic hypotheses in the light of estimated dates for the origins of leafcutter ants and their cultivars.
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Affiliation(s)
- Ulrich G Mueller
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Heather D Ishak
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Sofia M Bruschi
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.,Centro de Estudos de Insetos Sociais, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil
| | - Chad C Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Jacob J Herman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Scott E Solomon
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.,Centro de Estudos de Insetos Sociais, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil.,Department of Ecology & Evolutionary Biology, Rice University, Houston, TX, USA
| | - Alexander S Mikheyev
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.,Okinawa Institute of Science & Technology, Kunigami, Okinawa, Japan
| | - Christian Rabeling
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.,School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Jarrod J Scott
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Michael Cooper
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Andre Rodrigues
- Centro de Estudos de Insetos Sociais, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil
| | - Adriana Ortiz
- Universidad Nacional de Colombia, Medellin, Colombia
| | | | - John E Lattke
- Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Brazil
| | - Fernando C Pagnocca
- Centro de Estudos de Insetos Sociais, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil
| | - Stephen A Rehner
- Mycology and Nematology Genomic Diversity and Biology Laboratory, Beltsville, MD, USA
| | - Ted R Schultz
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | | | - Rachelle M M Adams
- Department of Evolution, Ecology & Organismal Biology, Museum of Biological Diversity, Columbus, OH, USA
| | - Martin Bollazzi
- Section of Entomology, Universidad de la República, Montevideo, Uruguay
| | - Rebecca M Clark
- Integrative Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Anna G Himler
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.,Department of Biology, College of Idaho, Caldwell, ID, USA
| | - John S LaPolla
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Biological Sciences, Towson University, Towson, MD, USA
| | - Inara R Leal
- Departamento de Botânica, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Robert A Johnson
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Flavio Roces
- Department of Behavioral Physiology and Sociobiology, Biozentrum, University of Würzburg, Würzburg, Germany
| | | | - Rainer Wirth
- Department of Plant Ecology and Systematics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Maurício Bacci
- Centro de Estudos de Insetos Sociais, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil
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21
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Overcast I, Bagley JC, Hickerson MJ. Strategies for improving approximate Bayesian computation tests for synchronous diversification. BMC Evol Biol 2017; 17:203. [PMID: 28836959 PMCID: PMC5571621 DOI: 10.1186/s12862-017-1052-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/14/2017] [Indexed: 11/22/2022] Open
Abstract
Background Estimating the variability in isolation times across co-distributed taxon pairs that may have experienced the same allopatric isolating mechanism is a core goal of comparative phylogeography. The use of hierarchical Approximate Bayesian Computation (ABC) and coalescent models to infer temporal dynamics of lineage co-diversification has been a contentious topic in recent years. Key issues that remain unresolved include the choice of an appropriate prior on the number of co-divergence events (Ψ), as well as the optimal strategies for data summarization. Methods Through simulation-based cross validation we explore the impact of the strategy for sorting summary statistics and the choice of prior on Ψ on the estimation of co-divergence variability. We also introduce a new setting (β) that can potentially improve estimation of Ψ by enforcing a minimal temporal difference between pulses of co-divergence. We apply this new method to three empirical datasets: one dataset each of co-distributed taxon pairs of Panamanian frogs and freshwater fishes, and a large set of Neotropical butterfly sister-taxon pairs. Results We demonstrate that the choice of prior on Ψ has little impact on inference, but that sorting summary statistics yields substantially more reliable estimates of co-divergence variability despite violations of assumptions about exchangeability. We find the implementation of β improves estimation of Ψ, with improvement being most dramatic given larger numbers of taxon pairs. We find equivocal support for synchronous co-divergence for both of the Panamanian groups, but we find considerable support for asynchronous divergence among the Neotropical butterflies. Conclusions Our simulation experiments demonstrate that using sorted summary statistics results in improved estimates of the variability in divergence times, whereas the choice of hyperprior on Ψ has negligible effect. Additionally, we demonstrate that estimating the number of pulses of co-divergence across co-distributed taxon-pairs is improved by applying a flexible buffering regime over divergence times. This improves the correlation between Ψ and the true variability in isolation times and allows for more meaningful interpretation of this hyperparameter. This will allow for more accurate identification of the number of temporally distinct pulses of co-divergence that generated the diversification pattern of a given regional assemblage of sister-taxon-pairs. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-1052-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Isaac Overcast
- Biology Department, City College of New York, New York, NY, 10031, USA. .,The Graduate Center, City University of New York, New York, NY, 10016, USA.
| | - Justin C Bagley
- Departamento de Zoologia, Universidade de Brasília, Brasília, DF, 70910-900, Brazil.,Departamento de Zoologia e Botânica, IBiLCE, Universidade Estadual Paulista, São José do Rio Preto, SP, 15054-000, Brazil
| | - Michael J Hickerson
- Biology Department, City College of New York, New York, NY, 10031, USA.,The Graduate Center, City University of New York, New York, NY, 10016, USA
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22
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Chua VL, Smith BT, Burner RC, Rahman MA, Lakim M, Prawiradilaga DM, Moyle RG, Sheldon FH. Evolutionary and ecological forces influencing population diversification in Bornean montane passerines. Mol Phylogenet Evol 2017; 113:139-149. [PMID: 28545973 DOI: 10.1016/j.ympev.2017.05.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 04/28/2017] [Accepted: 05/16/2017] [Indexed: 01/05/2023]
Abstract
The mountains of Borneo are well known for their high endemicity and historical role in preserving Southeast Asian rainforest biodiversity, but the diversification of populations inhabiting these mountains is poorly studied. Here we examine the genetic structure of 12 Bornean montane passerines by comparing complete mtDNA ND2 gene sequences of populations spanning the island. Maximum likelihood and Bayesian phylogenetic trees and haplotype networks are examined for common patterns that might signal important historical events or boundaries to dispersal. Morphological and ecological characteristics of each species are also examined using phylogenetic generalized least-squares (PGLS) for correlation with population structure. Populations in only four of the 12 species are subdivided into distinct clades or haplotype groups. Although this subdivision occurred at about the same time in each species (ca. 0.6-0.7Ma), the spatial positioning of the genetic break differs among the species. In two species, northeastern populations are genetically divergent from populations elsewhere on the island. In the other two species, populations in the main Bornean mountain chain, including the northeast, are distinct from those on two isolated peaks in northwestern Borneo. We suggest different historical forces played a role in shaping these two distributions, despite commonality in timing. PGLS analysis showed that only a single characteristic-hand-wing index-is correlated with population structure. Birds with longer wings, and hence potentially more dispersal power, have less population structure. To understand historical forces influencing montane population structure on Borneo, future studies must compare populations across the entirety of Sundaland.
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Affiliation(s)
- Vivien L Chua
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York 10024, USA
| | - Ryan C Burner
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Mustafa Abdul Rahman
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - Maklarin Lakim
- Sabah Parks, P.O. Box 10626, 88806 Kota Kinabalu, Sabah, Malaysia
| | - Dewi M Prawiradilaga
- Division of Zoology, Research Centre for Biology-LIPI, Jl. Raya Bogor km. 46, Cibinong-Bogor 16911, Indonesia
| | - Robert G Moyle
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| | - Frederick H Sheldon
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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23
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Satler JD, Carstens BC. Do ecological communities disperse across biogeographic barriers as a unit? Mol Ecol 2017; 26:3533-3545. [DOI: 10.1111/mec.14137] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 03/13/2017] [Accepted: 03/29/2017] [Indexed: 01/15/2023]
Affiliation(s)
- Jordan D. Satler
- Department of Evolution, Ecology and Organismal BiologyThe Ohio State University Columbus OH USA
- Department of Ecology, Evolution, and Organismal Biology Iowa State University Ames IA USA
| | - Bryan C. Carstens
- Department of Evolution, Ecology and Organismal BiologyThe Ohio State University Columbus OH USA
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24
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Wallace LE, Wheeler GL, McGlaughlin ME, Bresowar G, Helenurm K. Phylogeography and genetic structure of endemic Acmispon argophyllus and A. dendroideus (Fabaceae) across the California Channel Islands. AMERICAN JOURNAL OF BOTANY 2017; 104:743-756. [PMID: 28526725 DOI: 10.3732/ajb.1600429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 04/06/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY Taxa inhabiting the California Channel Islands exhibit variation in their degree of isolation, but few studies have considered patterns across the entire archipelago. We studied phylogeography of insular Acmispon argophyllus and A. dendroideus to determine whether infraspecific taxa are genetically divergent and to elucidate patterns of diversification across these islands. METHODS DNA sequences were collected from nuclear (ADH) and plastid genomes (rpL16, ndhA, psbD-trnT) from >450 samples on the Channel Islands and California. We estimated population genetic diversity and structure, phylogenetic patterns among populations, and migration rates, and tested for population growth. KEY RESULTS Populations of northern island A. argophyllus var. niveus are genetically distinct from conspecific populations on southern islands. On the southern islands, A. argophyllus var. argenteus populations on Santa Catalina are phylogenetically distinct from populations of var. argenteus and var. adsurgens on the other southern islands. For A. dendroideus, we found the varieties to be monophyletic. Populations of A. dendroideus var. traskiae on San Clemente are genetically differentiated from other conspecific populations, whereas populations on the northern islands and Santa Catalina show varying degrees of gene flow. Evidence of population growth was found in both species. CONCLUSIONS Oceanic barriers between islands have had a strong influence on population genetic structure in both Acmispon species, although the species have differing phylogeographic patterns. This study provides a contrasting pattern of dispersal on a near island system that does not follow a strict stepping-stone model, commonly found on isolated island systems.
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Affiliation(s)
- Lisa E Wallace
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - Gregory L Wheeler
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - Mitchell E McGlaughlin
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado 80639, USA
| | - Gerald Bresowar
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado 80639, USA
| | - Kaius Helenurm
- Department of Biology, University of South Dakota, Vermillion, South Dakota 57069, USA
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25
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Oswald JA, Overcast I, Mauck WM, Andersen MJ, Smith BT. Isolation with asymmetric gene flow during the nonsynchronous divergence of dry forest birds. Mol Ecol 2017; 26:1386-1400. [PMID: 28100029 DOI: 10.1111/mec.14013] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/30/2016] [Accepted: 12/29/2016] [Indexed: 01/17/2023]
Abstract
Dry forest bird communities in South America are often fragmented by intervening mountains and rainforests, generating high local endemism. The historical assembly of dry forest communities likely results from dynamic processes linked to numerous population histories among codistributed species. Nevertheless, species may diversify in the same way through time if landscape and environmental features, or species ecologies, similarly structure populations. Here we tested whether six co-distributed taxon pairs that occur in the dry forests of the Tumbes and Marañón Valley of northwestern South America show concordant patterns and modes of diversification. We employed a genome reduction technique, double-digest restriction site-associated DNA sequencing, and obtained 4407-7186 genomewide SNPs. We estimated demographic history in each taxon pair and inferred that all pairs had the same best-fit demographic model: isolation with asymmetric gene flow from the Tumbes into the Marañón Valley, suggesting a common diversification mode. Overall, we also observed congruence in effective population size (Ne ) patterns where ancestral Ne were 2.9-11.0× larger than present-day Marañón Valley populations and 0.3-2.0× larger than Tumbesian populations. Present-day Marañón Valley Ne was smaller than Tumbes. In contrast, we found simultaneous population isolation due to a single event to be unlikely as taxon pairs diverged over an extended period of time (0.1-2.9 Ma) with multiple nonoverlapping divergence periods. Our results show that even when populations of codistributed species asynchronously diverge, the mode of their differentiation can remain conserved over millions of years. Divergence by allopatric isolation due to barrier formation does not explain the mode of differentiation between these two bird assemblages; rather, migration of individuals occurred before and after geographic isolation.
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Affiliation(s)
- Jessica A Oswald
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611-7800, USA.,Museum of Natural Science, Louisiana State University, 119 Foster Hall, Baton Rouge, LA, 70803, USA
| | - Isaac Overcast
- Subprogram in Ecology, Evolution and Behavior, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - William M Mauck
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
| | - Michael J Andersen
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.,Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
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