1
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Overcast I, Noguerales V, Meramveliotakis E, Andújar C, Arribas P, Creedy TJ, Emerson BC, Vogler AP, Papadopoulou A, Morlon H. Inferring the ecological and evolutionary determinants of community genetic diversity. Mol Ecol 2023; 32:6093-6109. [PMID: 37221561 DOI: 10.1111/mec.16958] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 05/25/2023]
Abstract
Understanding the relative contributions of ecological and evolutionary processes to the structuring of ecological communities is needed to improve our ability to predict how communities may respond to future changes in an increasingly human-modified world. Metabarcoding methods make it possible to gather population genetic data for all species within a community, unlocking a new axis of data to potentially unveil the origins and maintenance of biodiversity at local scales. Here, we present a new eco-evolutionary simulation model for investigating community assembly dynamics using metabarcoding data. The model makes joint predictions of species abundance, genetic variation, trait distributions and phylogenetic relationships under a wide range of parameter settings (e.g. high speciation/low dispersal or vice versa) and across a range of community states, from pristine and unmodified to heavily disturbed. We first demonstrate that parameters governing metacommunity and local community processes leave detectable signatures in simulated biodiversity data axes. Next, using a simulation-based machine learning approach we show that neutral and non-neutral models are distinguishable and that reasonable estimates of several model parameters within the local community can be obtained using only community-scale genetic data, while phylogenetic information is required to estimate those describing metacommunity dynamics. Finally, we apply the model to soil microarthropod metabarcoding data from the Troodos mountains of Cyprus, where we find that communities in widespread forest habitats are structured by neutral processes, while high-elevation and isolated habitats act as an abiotic filter generating non-neutral community structure. We implement our model within the ibiogen R package, a package dedicated to the investigation of island, and more generally community-scale, biodiversity using community-scale genetic data.
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Affiliation(s)
- Isaac Overcast
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Department of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Víctor Noguerales
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Spain
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | | | - Carmelo Andújar
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Spain
| | - Paula Arribas
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Spain
| | - Thomas J Creedy
- Department of Life Sciences, Natural History Museum, London, UK
| | - Brent C Emerson
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Spain
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Anna Papadopoulou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Hélène Morlon
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
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2
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Smith ML, Wallace J, Tank DC, Sullivan J, Carstens BC. The role of multiple Pleistocene refugia in promoting diversification in the Pacific Northwest. Mol Ecol 2022; 31:4402-4416. [PMID: 35780485 DOI: 10.1111/mec.16595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/14/2022] [Accepted: 06/20/2022] [Indexed: 10/17/2022]
Abstract
Pleistocene glacial cycles drastically changed the distributions of taxa endemic to temperate rainforests in the Pacific Northwest, with many experiencing reduced habitat suitability during glacial periods. In this study, we investigate whether glacial cycles promoted intraspecific divergence and whether subsequent range changes led to secondary contact and gene flow. For seven invertebrate species endemic to the PNW, we estimated Species Distribution Models (SDMs) and projected them onto current and historical climate conditions to assess how habitat suitability changed during glacial cycles. Using single nucleotide polymorphism (SNP) data from these species, we assessed population genetic structure and used a machine-learning approach to compare models with and without gene flow between populations upon secondary contact after the Last Glacial Maximum (LGM). Finally, we estimated divergence times and rates of gene flow between populations. SDMs suggest that there was less suitable habitat in the North Cascades and Northern Rocky Mountains during glacial compared to interglacial periods, resulting in reduced habitat suitability and habitat fragmentation during the LGM. Our genomic data identify population structure in all taxa, and support gene flow upon secondary contact in five of the seven taxa. Parameter estimates suggest that population divergences date to the later Pleistocene for most populations. Our results support a role of refugial dynamics in driving intraspecific divergence in the Cascades Range. In these invertebrates, population structure often does not correspond to current biogeographic or environmental barriers. Rather, population structure may reflect refugial lineages that have since expanded their ranges, often leading to secondary contact between once isolated lineages.
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Affiliation(s)
- Megan L Smith
- Department of Evolution, Ecology & Organismal Biology, The Ohio State University, 318 W. 12th Avenue, 300 Aronoff Labs, Columbus, OH 43210-1293, USA
| | - Jessica Wallace
- Department of Evolution, Ecology & Organismal Biology, The Ohio State University, 318 W. 12th Avenue, 300 Aronoff Labs, Columbus, OH 43210-1293, USA
| | - David C Tank
- Department of Botany and Rocky Mountain Herbarium, University of Wyoming, 1000 E. University Ave., Laramie, WY 82071, USA.,Department of Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID 83844-3051, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID 83844-3051, USA
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID 83844-3051, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID 83844-3051, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology & Organismal Biology, The Ohio State University, 318 W. 12th Avenue, 300 Aronoff Labs, Columbus, OH 43210-1293, USA
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3
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Titus BM, Daly M. Population genomics for symbiotic anthozoans: can reduced representation approaches be used for taxa without reference genomes? Heredity (Edinb) 2022; 128:338-351. [PMID: 35418670 PMCID: PMC9076904 DOI: 10.1038/s41437-022-00531-3] [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: 09/09/2020] [Revised: 03/25/2022] [Accepted: 03/25/2022] [Indexed: 11/08/2022] Open
Abstract
Population genetic studies of symbiotic anthozoans have been historically challenging because their endosymbioses with dinoflagellates have impeded marker development. Genomic approaches like reduced representation sequencing alleviate marker development issues but produce anonymous loci, and without a reference genome, it is unknown which organism is contributing to the observed patterns. Alternative methods such as bait-capture sequencing targeting Ultra-Conserved Elements are now possible but costly. Thus, RADseq remains attractive, but how useful are these methods for symbiotic anthozoan taxa without a reference genome to separate anthozoan from algal sequences? We explore this through a case-study using a double-digest RADseq dataset for the sea anemone Bartholomea annulata. We assembled a holobiont dataset (3854 loci) for 101 individuals, then used a reference genome to create an aposymbiotic dataset (1402 loci). For both datasets, we investigated population structure and used coalescent simulations to estimate demography and population parameters. We demonstrate complete overlap in the spatial patterns of genetic diversity, demographic histories, and population parameter estimates for holobiont and aposymbiotic datasets. We hypothesize that the unique combination of anthozoan biology, diversity of the endosymbionts, and the manner in which assembly programs identify orthologous loci alleviates the need for reference genomes in some circumstances. We explore this hypothesis by assembling an additional 21 datasets using the assembly programs pyRAD and Stacks. We conclude that RADseq methods are more tractable for symbiotic anthozoans without reference genomes than previously realized.
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Affiliation(s)
- Benjamin M Titus
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA.
- Dauphin Island Sea Lab, Dauphin Island, AL, USA.
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA.
| | - Marymegan Daly
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
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4
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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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5
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Walton W, Stone GN, Lohse K. Discordant Pleistocene population size histories in a guild of hymenopteran parasitoids. Mol Ecol 2021; 30:4538-4550. [PMID: 34252238 DOI: 10.1111/mec.16074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 06/23/2021] [Accepted: 07/06/2021] [Indexed: 01/03/2023]
Abstract
Signatures of past changes in population size have been detected in genome-wide variation in many species. However, the causes of such demographic changes and the extent to which they are shared across co-distributed species remain poorly understood. During Pleistocene glacial maxima, many temperate European species were confined to southern refugia. While vicariance and range expansion processes associated with glacial cycles have been widely documented, it is unclear whether refugial populations of co-distributed species have experienced shared histories of population size change. We analyse whole-genome sequence data to reconstruct and compare demographic histories during the Quaternary for Iberian refuge populations in a single ecological guild (seven species of chalcid parasitoid wasps associated with oak cynipid galls). For four of these species, we find support for large changes in effective population size (Ne ) through the Pleistocene that coincide with major climate events. However, there is little evidence that the timing, direction and magnitude of demographic change are shared across species, suggesting that demographic histories in this guild are largely idiosyncratic, even at the scale of a single glacial refugium.
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Affiliation(s)
- William Walton
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Graham N Stone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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6
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Burbrink FT, Gehara M, McKelvy AD, Myers EA. Resolving spatial complexities of hybridization in the context of the gray zone of speciation in North American ratsnakes (Pantherophis obsoletus complex). Evolution 2021; 75:260-277. [PMID: 33346918 DOI: 10.1111/evo.14141] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 10/01/2020] [Accepted: 11/17/2020] [Indexed: 01/04/2023]
Abstract
Inferring the history of divergence between species in a framework that permits the presence of gene flow has been crucial for characterizing the "gray zone" of speciation, which is the period of time where lineages have diverged but have not yet achieved strict reproductive isolation. However, estimates of both divergence times and rates of gene flow often ignore spatial information, for example when considering the location and width of hybrid zones with respect to changes in the environment between lineages. Using population genomic data from the North American ratsnake complex (Pantherophis obsoletus), we connected phylogeographic estimates of lineage structure, migration, historical demography, and timing of divergence with hybrid zone dynamics. We examined the spatial context of diversification by linking migration and timing of divergence to the location and widths of hybrid zones. Artificial neural network approaches were applied to understand how landscape features and past climate have influenced population genetic structure among these lineages. We found that rates of migration between lineages were associated with the overall width of hybrid zones. Timing of divergence was not related to migration rate or hybrid zone width across species pairs but may be related to the number of alleles weakly introgressing through hybrid zones. This research underscores how incomplete reproductive isolation can be better understood by considering differential allelic introgression and the effects of historical and contemporary landscape features on the formation of lineages as well as overall genomic estimates of migration rates through time.
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology, The American Museum of Natural History, Central Park West and 79th Street, New York, New York, 10024
| | - Marcelo Gehara
- Department of Biological Sciences, Rutgers University Newark, 195 University Ave, Newark, New Jersey, 07102
| | - Alexander D McKelvy
- Department of Biology, The Graduate School and Center, City University of New York, New York, New York, 10016
| | - Edward A Myers
- Department of Herpetology, The American Museum of Natural History, Central Park West and 79th Street, New York, New York, 10024.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC
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7
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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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8
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Myers EA, McKelvy AD, Burbrink FT. Biogeographic barriers, Pleistocene refugia, and climatic gradients in the southeastern Nearctic drive diversification in cornsnakes (Pantherophis guttatus complex). Mol Ecol 2020; 29:797-811. [PMID: 31955477 DOI: 10.1111/mec.15358] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 12/21/2022]
Abstract
The southeastern Nearctic is a biodiversity hotspot that is also rich in cryptic species. Numerous hypotheses (e.g., vicariance, local adaptation, and Pleistocene speciation in glacial refugia) have been tested in an attempt to explain diversification and the observed pattern of extant biodiversity. However, previous phylogeographic studies have both supported and refuted these hypotheses. Therefore, while data support one or more of these diversification hypotheses, it is likely that taxa are forming within this region in species-specific ways. Here, we generate a genomic data set for the cornsnakes (Pantherophis guttatus complex), which are widespread across this region, spanning both biogeographic barriers and climatic gradients. We use phylogeographic model selection combined with hindcast ecological niche models to determine regions of habitat stability through time. This combined approach suggests that numerous drivers of population differentiation explain the current diversity of this group of snakes. The Mississippi River caused initial speciation in this species complex, with more recent divergence events linked to adaptations to ecological heterogeneity and allopatric Pleistocene refugia. Lastly, we discuss the taxonomy of this group and suggest there may be additional cryptic species in need of formal recognition.
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Affiliation(s)
- Edward A Myers
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Herpetology, The American Museum of Natural History, New York, NY, USA
| | - Alexander D McKelvy
- Department of Biology, The Graduate School and Center, City University of New York, New York, NY, USA
| | - Frank T Burbrink
- Department of Herpetology, The American Museum of Natural History, New York, NY, USA
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9
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Smith ML, Carstens BC. Process-based species delimitation leads to identification of more biologically relevant species. Evolution 2019; 74:216-229. [PMID: 31705650 DOI: 10.1111/evo.13878] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 10/08/2019] [Accepted: 10/12/2019] [Indexed: 12/23/2022]
Abstract
Most approaches to species delimitation to date have considered divergence-only models. Although these models are appropriate for allopatric speciation, their failure to incorporate many of the population-level processes that drive speciation, such as gene flow (e.g., in sympatric speciation), places an unnecessary limit on our collective understanding of the processes that produce biodiversity. To consider these processes while inferring species boundaries, we introduce the R-package delimitR and apply it to identify species boundaries in the reticulate taildropper slug (Prophysaon andersoni). Results suggest that secondary contact is an important mechanism driving speciation in this system. By considering process, we both avoid erroneous inferences that can be made when population-level processes such as secondary contact drive speciation but only divergence is considered, and gain insight into the process of speciation in terrestrial slugs. Further, we apply delimitR to three published empirical datasets and find results corroborating previous findings. Finally, we evaluate the performance of delimitR using simulation studies, and find that error rates are near zero when comparing models that include lineage divergence and gene flow for three populations with a modest number of Single Nucleotide Polymorphisms (SNPs; 1500) and moderate divergence times (<100,000 generations). When we apply delimitR to a complex model set (i.e., including divergence, gene flow, and population size changes), error rates are moderate (∼0.15; 10,000 SNPs), and, when present, misclassifications occur among highly similar models.
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Affiliation(s)
- Megan L Smith
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, 43210
| | - Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, 43210
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10
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Titus BM, Blischak PD, Daly M. Genomic signatures of sympatric speciation with historical and contemporary gene flow in a tropical anthozoan (Hexacorallia: Actiniaria). Mol Ecol 2019; 28:3572-3586. [PMID: 31233641 DOI: 10.1111/mec.15157] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 05/21/2019] [Accepted: 06/04/2019] [Indexed: 12/23/2022]
Abstract
Sympatric diversification is recognized to have played an important role in the evolution of biodiversity. However, an in situ sympatric origin for codistributed taxa is difficult to demonstrate because different evolutionary processes can lead to similar biogeographic outcomes, especially in ecosystems that can readily facilitate secondary contact due to a lack of hard barriers to dispersal. Here we use a genomic (ddRADseq), model-based approach to delimit a species complex of tropical sea anemones that are codistributed on coral reefs throughout the Tropical Western Atlantic. We use coalescent simulations in fastsimcoal2 and ordinary differential equations in Moments to test competing diversification scenarios that span the allopatric-sympatric continuum. Our results suggest that the corkscrew sea anemone Bartholomea annulata is a cryptic species complex whose members are codistributed throughout their range. Simulation and model selection analyses from both approaches suggest these lineages experienced historical and contemporary gene flow, supporting a sympatric origin, but an alternative secondary contact model receives appreciable model support in fastsimcoal2. Leveraging the genome of the closely related Exaiptasia diaphana, we identify five loci under divergent selection between cryptic B. annulata lineages that fall within mRNA transcripts or CDS regions. Our study provides a rare empirical, genomic example of sympatric speciation in a tropical anthozoan and the first range-wide molecular study of a tropical sea anemone, underscoring that anemone diversity is under-described in the tropics, and highlighting the need for additional systematic studies into these ecologically and economically important species.
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Affiliation(s)
- Benjamin M Titus
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Paul D Blischak
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA.,Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ, USA
| | - Marymegan Daly
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
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11
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Li H, Kong L, Wang K, Zhang S, Motokawa M, Wu Y, Wang W, Li Y. Molecular phylogeographic analyses and species delimitations reveal that Leopoldamys edwardsi (Rodentia: Muridae) is a species complex. Integr Zool 2019; 14:494-505. [PMID: 30688015 DOI: 10.1111/1749-4877.12378] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Leopoldamys edwardsi is a species with wide distribution ranges in southern China but is not discussed in studies on geographic variation and species differentiation. We used 2 mitochondrial (Cytb, CO1) and 3 nuclear (GHR, IRBP and RAG1) genes to clarify species phylogeography and geographical differentiation. Maximum likelihood (ML) and Bayesian phylogenetic inference (BI) trees consistently indicated that L. edwardsi is a species complex containing 3 main lineages with high Kimura-2-parameter (K2P) divergences (i.e. lineages LN , LS and LHN ) found in the northern and southern China and Hainan Island, respectively. The 3 species delimitation methods, automated barcoding gap discovery, Bayesian poisson tree process analysis and Bayesian phylogenetics and phylogeography, consistently supported the existence of cryptic species. Divergence times among the main lineages were inferred to be during the Pleistocene, with LHN /LS split at 1.33 Ma and LN /(LHN +LS ) at 2.61 Ma; the diversifications of L. edwardsi complex might be caused by the rapid uplifts of Tibetan Plateau, paleoclimate change and complex topography. The divergence between LHN and LS was probably related to the separation of Hainan Island from the mainland via the formation of the Qiongzhou Strait. Lineages LN and (LS +LHN ) likely diverged due to the Wuyi-Nanling mountain range forming a dispersal barrier. Our results suggested that L. edwardsi complex contains at least 3 distinct species: LHN represents L. hainanensis, endemic to Hainan Island and previously considered as a subspecies L. e. hainanensis; LS represents a cryptic species distributed throughout the southern Chinese continent; and LN represents the nominotypical species L. edwardsi.
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Affiliation(s)
- Haotian Li
- Marine College, Shandong University, Weihai, China
| | | | - Kaiyun Wang
- Institute of Ecology and Biodiversity, Shandong University, Jinan, China
| | - Shuping Zhang
- Institute of Ecology and Biodiversity, Shandong University, Jinan, China
| | | | - Yi Wu
- College of Life Science, Guangzhou University, Guangzhou, China
| | - Wenquan Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yuchun Li
- Marine College, Shandong University, Weihai, China
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12
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Massatti R, Prendeville HR, Larson S, Richardson BA, Waldron B, Kilkenny FF. Population history provides foundational knowledge for utilizing and developing native plant restoration materials. Evol Appl 2018; 11:2025-2039. [PMID: 30459846 PMCID: PMC6231468 DOI: 10.1111/eva.12704] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 08/21/2018] [Accepted: 08/26/2018] [Indexed: 01/14/2023] Open
Abstract
A species' population structure and history are critical pieces of information that can help guide the use of available native plant materials in restoration treatments and decide what new native plant materials should be developed to meet future restoration needs. In the western United States, Pseudoroegneria spicata (bluebunch wheatgrass; Poaceae) is an important component of grassland and shrubland plant communities and commonly used for restoration due to its drought resistance and competitiveness with exotic weeds. We used next-generation sequencing data to investigate the processes that shaped P. spicata's geographic pattern of genetic variation across the Intermountain West. Pseudoroegneria spicata's genetic diversity is partitioned into populations that likely differentiated since the Last Glacial Maximum. Adjacent populations display varying magnitudes of historical gene flow, with migration rates ranging from multiple migrants per generation to multiple generations per migrant. When considering the commercial germplasm sources available for restoration, genetic identities remain representative of the wildland localities from which germplasm sources were originally developed, and they maintain high levels of heterozygosity and nucleotide diversity. However, the commercial germplasm sources represent a small fraction of the overall genetic diversity of P. spicata in the Intermountain West. Given the low migration rates and long divergence times between some pairs of P. spicata populations, using commercial germplasm sources could facilitate undesirable restoration outcomes when used in certain geographic areas, even if the environment in which the commercial materials thrive is similar to that of the restoration site. As such, population structure and history can be used to provide guidance on what geographic areas may need additional native plant materials so that restoration efforts support species and community resilience and improve outcomes.
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Affiliation(s)
- Rob Massatti
- Southwest Biological Science CenterU.S. Geological SurveyFlagstaffArizona
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13
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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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14
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Bunnefeld L, Hearn J, Stone GN, Lohse K. Whole-genome data reveal the complex history of a diverse ecological community. Proc Natl Acad Sci U S A 2018; 115:E6507-E6515. [PMID: 29946026 PMCID: PMC6048486 DOI: 10.1073/pnas.1800334115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
How widespread ecological communities assemble remains a key question in ecology. Trophic interactions between widespread species may reflect a shared population history or ecological fitting of local pools of species with very different population histories. Which scenario applies is central to the stability of trophic associations and the potential for coevolution between species. Here we show how alternative community assembly hypotheses can be discriminated using whole-genome data for component species and provide a likelihood framework that overcomes current limitations in formal comparison of multispecies histories. We illustrate our approach by inferring the assembly history of a Western Palearctic community of insect herbivores and parasitoid natural enemies, trophic groups that together comprise 50% of terrestrial species. We reject models of codispersal from a shared origin and of delayed enemy pursuit of their herbivore hosts, arguing against herbivore attainment of "enemy-free space." The community-wide distribution of species expansion times is also incompatible with a random, neutral model of assembly. Instead, we reveal a complex assembly history of single- and multispecies range expansions through the Pleistocene from different directions and over a range of timescales. Our results suggest substantial turnover in species associations and argue against tight coevolution in this system. The approach we illustrate is widely applicable to natural communities of nonmodel species and makes it possible to reveal the historical backdrop against which natural selection acts.
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Affiliation(s)
- Lynsey Bunnefeld
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, Scotland;
- Biological & Environmental Sciences, University of Stirling, Stirling FK9 4LA, Scotland
| | - Jack Hearn
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, Scotland
| | - Graham N Stone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, Scotland
| | - Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, Scotland
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15
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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: 28] [Impact Index Per Article: 4.0] [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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