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Croft L, Matheson P, Flemming C, Butterworth NJ, McGaughran A. Population structure and interspecific hybridisation of two invasive blowflies (Diptera: Calliphoridae) following replicated incursions into New Zealand. Ecol Evol 2024; 14:e10832. [PMID: 38192906 PMCID: PMC10772223 DOI: 10.1002/ece3.10832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 01/10/2024] Open
Abstract
Rates of biological invasion are increasing globally, with associated negative effects on native biodiversity and ecosystem services. Among other genetic processes, hybridisation can facilitate invasion by producing new combinations of genetic variation that increase adaptive potential and associated population fitness. Yet the role of hybridisation (and resulting gene flow) in biological invasion in invertebrate species is under-studied. Calliphora hilli and Calliphora stygia are blowflies proposed to have invaded New Zealand separately from Australia between 1779 and 1841, and are now widespread throughout the country. Here, we analysed genome-wide single nucleotide polymorphisms (SNPs), generating genotyping-by-sequencing data for 154 individuals collected from 24 populations across New Zealand and Australia to assess the extent of gene flow and hybridisation occurring within and between these blowflies and to better understand their overall population structure. We found that New Zealand populations of both species had weak genetic structure, suggesting high gene flow and an absence of dispersal limitations across the country. We also found evidence that interspecific hybridisation is occurring in the wild between C. hilli and C. stygia in both the native and invasive ranges, and that intraspecific admixture is occurring among populations at appreciable rates. Collectively, these findings provide new insights into the population structure of these two invasive invertebrates and highlight the potential importance of hybridisation and gene flow in biological invasion.
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Affiliation(s)
- Lilly Croft
- Te Aka Mātuatua – School of ScienceUniversity of WaikatoHamiltonNew Zealand
| | - Paige Matheson
- Te Aka Mātuatua – School of ScienceUniversity of WaikatoHamiltonNew Zealand
| | - Chloe Flemming
- Te Aka Mātuatua – School of ScienceUniversity of WaikatoHamiltonNew Zealand
| | | | - Angela McGaughran
- Te Aka Mātuatua – School of ScienceUniversity of WaikatoHamiltonNew Zealand
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Sethuraman A, Nunziata SO, Jones A, Obrycki J, Weisrock DW. Go west: Population genomics reveals unexpected population fluctuations and little gene flow in Western hemisphere populations of the predatory lady beetle, Hippodamia convergens. Evol Appl 2024; 17:e13631. [PMID: 38283604 PMCID: PMC10810170 DOI: 10.1111/eva.13631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 11/22/2023] [Accepted: 11/30/2023] [Indexed: 01/30/2024] Open
Abstract
Hippodamia convergens-the convergent lady beetle, has been used extensively in augmentative biological control of aphids, thrips, and whiteflies across its native range in North America, and was introduced into South America in the 1950s. Overwintering H. convergens populations from its native western range in the United States are commercially collected and released across its current range in the eastern USA, with little knowledge of the effectiveness of its augmentative biological control. Here we use a novel ddRADseq-based SNP/haplotype discovery approach to estimate its range-wide population diversity, differentiation, and recent evolutionary history. Our results indicate (1) significant population differentiation among eastern USA, western USA, and South American populations of H. convergens, with (2) little to no detectable recent admixture between them, despite repeated population augmentation, and (3) continued recent population size expansion across its range. These results contradict previous findings using microsatellite markers. In light of these new findings, the implications for the effectiveness of augmentative biological control using H. convergens are discussed. Additionally, because quantifying the non-target effects of augmentative biological control is a difficult problem in migratory beetles, our results could serve as a cornerstone in improving and predicting the efficacy of future releases of H. convergens across its range.
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Affiliation(s)
- Arun Sethuraman
- Department of BiologySan Diego State UniversitySan DiegoCaliforniaUSA
| | - Schyler O. Nunziata
- Department of BiologyUniversity of KentuckyLexingtonKentuckyUSA
- Present address:
United States Department of AgricultureWashingtonDCUSA
| | - Angela Jones
- Department of BiologyUniversity of KentuckyLexingtonKentuckyUSA
- Present address:
Duke UniversityDurhamNorth CarolinaUSA
| | - John Obrycki
- Department of EntomologyUniversity of KentuckyLexingtonKentuckyUSA
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Meziere Z, Popovic I, Prata K, Ryan I, Pandolfi J, Riginos C. Exploring coral speciation: Multiple sympatric Stylophora pistillata taxa along a divergence continuum on the Great Barrier Reef. Evol Appl 2024; 17:e13644. [PMID: 38283599 PMCID: PMC10818133 DOI: 10.1111/eva.13644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/30/2024] Open
Abstract
Understanding how biodiversity originates and is maintained are fundamental challenge in evolutionary biology. Speciation is a continuous process and progression along this continuum depends on the interplay between evolutionary forces driving divergence and forces promoting genetic homogenisation. Coral reefs are broadly connected yet highly heterogeneous ecosystems, and divergence with gene flow at small spatial scales might therefore be common. Genomic studies are increasingly revealing the existence of closely related and sympatric taxa within taxonomic coral species, but the extent to which these taxa might still be exchanging genes and sharing environmental niches is unclear. In this study, we sampled extensively across diverse habitats at multiple reefs of the Great Barrier Reef (GBR) and comprehensively examined genome-wide diversity and divergence histories within and among taxa of the Stylophora pistillata species complex. S. pistillata is one of the most abundant and well-studied coral species, yet we discovered five distinct taxa, with wide geographic ranges and extensive sympatry. Demographic modelling showed that speciation events have occurred with gene flow and that taxa are at different stages along a divergence continuum. We found significant correlations between genetic divergence and specific environmental variables, suggesting that niche partitioning may have played a role in speciation and that S. pistillata taxa might be differentially adapted to different environments. Conservation actions rely on estimates of species richness, population sizes and species ranges, which are biased if divergent taxa are lumped together. As coral reefs are rapidly degrading due to climate change, our study highlights the importance of recognising evolutionarily distinct and differentially adapted coral taxa to improve conservation and restoration efforts aiming at protecting coral genetic diversity.
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Affiliation(s)
- Zoe Meziere
- School of the EnvironmentThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Iva Popovic
- School of the EnvironmentThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Katharine Prata
- School of the EnvironmentThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Isobel Ryan
- School of the EnvironmentThe University of QueenslandSt. LuciaQueenslandAustralia
| | - John Pandolfi
- School of the EnvironmentThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Cynthia Riginos
- School of the EnvironmentThe University of QueenslandSt. LuciaQueenslandAustralia
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Pyron RA, Kakkera A, Beamer DA, O'Connell KA. Discerning structure versus speciation in phylogeographic analysis of Seepage Salamanders (Desmognathus aeneus) using demography, environment, geography, and phenotype. Mol Ecol 2024; 33:e17219. [PMID: 38015012 DOI: 10.1111/mec.17219] [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: 08/04/2023] [Revised: 10/26/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023]
Abstract
Numerous mechanisms can drive speciation, including isolation by adaptation, distance, and environment. These forces can promote genetic and phenotypic differentiation of local populations, the formation of phylogeographic lineages, and ultimately, completed speciation. However, conceptually similar mechanisms may also result in stabilizing rather than diversifying selection, leading to lineage integration and the long-term persistence of population structure within genetically cohesive species. Processes that drive the formation and maintenance of geographic genetic diversity while facilitating high rates of migration and limiting phenotypic differentiation may thereby result in population genetic structure that is not accompanied by reproductive isolation. We suggest that this framework can be applied more broadly to address the classic dilemma of "structure" versus "species" when evaluating phylogeographic diversity, unifying population genetics, species delimitation, and the underlying study of speciation. We demonstrate one such instance in the Seepage Salamander (Desmognathus aeneus) from the southeastern United States. Recent studies estimated up to 6.3% mitochondrial divergence and four phylogenomic lineages with broad admixture across geographic hybrid zones, which could potentially represent distinct species supported by our species-delimitation analyses. However, while limited dispersal promotes substantial isolation by distance, microhabitat specificity appears to yield stabilizing selection on a single, uniform, ecologically mediated phenotype. As a result, climatic cycles promote recurrent contact between lineages and repeated instances of high migration through time. Subsequent hybridization is apparently not counteracted by adaptive differentiation limiting introgression, leaving a single unified species with deeply divergent phylogeographic lineages that nonetheless do not appear to represent incipient species.
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Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Anvith Kakkera
- Thomas Jefferson High School for Science and Technology, Alexandria, Virginia, USA
| | - David A Beamer
- Office of Research, Economic Development and Engagement, East Carolina University, Greenville, North Carolina, USA
| | - Kyle A O'Connell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
- Deloitte Consulting LLP, Health and Data AI, Arlington, Virginia, USA
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Chan KO, Mulcahy DG, Anuar S. The Artefactual Branch Effect and Phylogenetic Conflict: Species Delimitation with Gene Flow in Mangrove Pit Vipers (Trimeresurus purpureomaculatus-erythrurus Complex). Syst Biol 2023; 72:1209-1219. [PMID: 37478480 DOI: 10.1093/sysbio/syad043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/19/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023] Open
Abstract
Mangrove pit vipers of the Trimeresurus purpureomaculatus-erythrurus complex are the only species of viper known to naturally inhabit mangroves. Despite serving integral ecological functions in mangrove ecosystems, the evolutionary history, distribution, and species boundaries of mangrove pit vipers remain poorly understood, partly due to overlapping distributions, confusing phenotypic variations, and the lack of focused studies. Here, we present the first genomic study on mangrove pit vipers and introduce a robust hypothesis-driven species delimitation framework that considers gene flow and phylogenetic uncertainty in conjunction with a novel application of a new class of speciation-based delimitation model implemented through the program Delineate. Our results showed that gene flow produced phylogenetic conflict in our focal species and substantiates the artefactual branch effect where highly admixed populations appear as divergent nonmonophyletic lineages arranged in a stepwise manner at the basal position of clades. Despite the confounding effects of gene flow, we were able to obtain unequivocal support for the recognition of a new species based on the intersection and congruence of multiple lines of evidence. This study demonstrates that an integrative hypothesis-driven approach predicated on the consideration of multiple plausible evolutionary histories, population structure/differentiation, gene flow, and the implementation of a speciation-based delimitation model can effectively delimit species in the presence of gene flow and phylogenetic conflict.
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Affiliation(s)
- Kin Onn Chan
- Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Singapore
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Gelugor, Penang, Malaysia
| | - Daniel G Mulcahy
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
| | - Shahrul Anuar
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Gelugor, Penang, Malaysia
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56
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Guilliams CM, Hasenstab-Lehman KE. Conservation Genetics of the Endangered Lompoc Yerba Santa ( Eriodictyon capitatum Eastw., Namaceae), including Phylogenomic Insights into the Evolution of Eriodictyon. PLANTS (BASEL, SWITZERLAND) 2023; 13:90. [PMID: 38202398 PMCID: PMC10780715 DOI: 10.3390/plants13010090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024]
Abstract
Eriodictyon capitatum (Namaceae) is a narrowly distributed shrub endemic to western Santa Barbara County, where it is known from only 10 extant California Natural Diversity Database element occurrences (EOs). Owing to low numbers of plants in nature, a limited overall extent, and multiple current threats, E. capitatum is listed as Endangered under the Federal Endangered Species Act and as Rare under the California Native Plant Protection Act. In the present study, high-throughput DNA sequence data were analyzed to investigate genetic diversity within and among all accessible EOs; to determine the extent of genetic isolation among EOs; to examine clonality within EOs; and to examine the taxonomic circumscriptions of E. capitatum, E. altissimum, E. angustifolium, and E. californicum through phylogenomic analysis. Population genetic analyses of E. capitatum reveal a pattern of strong genetic differentiation by location/EO. The clonality assessment shows that certain small EOs may support relatively few multilocus genotypes. The phylogenomic analyses strongly support the present-day taxonomic circumscriptions of both E. altissimum and E. capitatum, showing them to be reciprocally monophyletic and sister with strong support. Taken together, these results paint a picture of an evolutionarily and morphologically distinct species known from relatively few, genetically isolated stations.
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Barcenas-Peña A, Divakar PK, Crespo A, Nuñez-Zapata J, Lumbsch HT, Grewe F. Reference-Based Restriction-Site-Associated DNA Sequencing Data Are Useful for Species Delineation in a Recently Diverged Asexually Reproducing Species Complex (Parmeliaceae, Ascomycota). J Fungi (Basel) 2023; 9:1180. [PMID: 38132781 PMCID: PMC10744373 DOI: 10.3390/jof9121180] [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: 10/30/2023] [Revised: 12/01/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
Cryptic species are common in lichen-forming fungi and have been reported from different genera in the most speciose family, Parmeliaceae. Herein, we address species delimitation in a group of mainly asexually reproducing Parmelina species. The morphologically distinct P. pastillifera was previously found nested within a morphologically circumscribed P. tiliacea based on several loci. However, these studies demonstrated a relatively high genetic diversity within P. tiliacea sensu lato. Here, we revisit the species delimitation in the group by analyzing single-nucleotide polymorphisms (SNPs) through genome-wide assessment using Restriction-Site-Associated sequencing and population genomic methods. Our data support previous studies and provide further insight into the phylogenetic relationships of the four clades found within the complex. Based on the evidence suggesting a lack of gene flow among the clades, we recognize the four clades as distinct species, P. pastillifera and P. tiliacea sensu stricto, and two new species, P. clandestina sp. nov. and P. mediterranea sp. nov.
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Affiliation(s)
- Alejandrina Barcenas-Peña
- The Grainger Bioinformatics Center & Negaunee Integrative Research Center, Collections, Conservation and Research Division, The Field Museum, Chicago, IL 60605, USA; (H.T.L.); (F.G.)
| | - Pradeep K. Divakar
- Department of Pharmacology, Pharmacognosy and Botany (DU Botany), Faculty of Pharmacy, Plaza de Ramón y Cajal s/n, Universidad Complutense, 28040 Madrid, Spain; (P.K.D.); (A.C.); (J.N.-Z.)
| | - Ana Crespo
- Department of Pharmacology, Pharmacognosy and Botany (DU Botany), Faculty of Pharmacy, Plaza de Ramón y Cajal s/n, Universidad Complutense, 28040 Madrid, Spain; (P.K.D.); (A.C.); (J.N.-Z.)
| | - Jano Nuñez-Zapata
- Department of Pharmacology, Pharmacognosy and Botany (DU Botany), Faculty of Pharmacy, Plaza de Ramón y Cajal s/n, Universidad Complutense, 28040 Madrid, Spain; (P.K.D.); (A.C.); (J.N.-Z.)
| | - H. Thorsten Lumbsch
- The Grainger Bioinformatics Center & Negaunee Integrative Research Center, Collections, Conservation and Research Division, The Field Museum, Chicago, IL 60605, USA; (H.T.L.); (F.G.)
| | - Felix Grewe
- The Grainger Bioinformatics Center & Negaunee Integrative Research Center, Collections, Conservation and Research Division, The Field Museum, Chicago, IL 60605, USA; (H.T.L.); (F.G.)
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58
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Zbinden ZD, Douglas MR, Chafin TK, Douglas ME. Riverscape community genomics: A comparative analytical approach to identify common drivers of spatial structure. Mol Ecol 2023; 32:6743-6765. [PMID: 36461662 DOI: 10.1111/mec.16806] [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: 07/26/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/04/2022]
Abstract
Genetic differentiation among local groups of individuals, that is, genetic β-diversity, is a key component of population persistence related to connectivity and isolation. However, most genetic investigations of natural populations focus on a single species, overlooking opportunities for multispecies conservation plans to benefit entire communities in an ecosystem. We present an approach to evaluate genetic β-diversity within and among many species and demonstrate how this riverscape community genomics approach can be applied to identify common drivers of genetic structure. Our study evaluated genetic β-diversity in 31 co-distributed native stream fishes sampled from 75 sites across the White River Basin (Ozarks, USA) using SNP genotyping (ddRAD). Despite variance among species in the degree of genetic divergence, general spatial patterns were identified corresponding to river network architecture. Most species (N = 24) were partitioned into discrete subpopulations (K = 2-7). We used partial redundancy analysis to compare species-specific genetic β-diversity across four models of genetic structure: Isolation by distance (IBD), isolation by barrier (IBB), isolation by stream hierarchy (IBH), and isolation by environment (IBE). A significant proportion of intraspecific genetic variation was explained by IBH (x̄ = 62%), with the remaining models generally redundant. We found evidence for consistent spatial modularity in that gene flow is higher within rather than between hierarchical units (i.e., catchments, watersheds, basins), supporting the generalization of the stream hierarchy model. We discuss our conclusions regarding conservation and management and identify the 8-digit hydrologic unit (HUC) as the most relevant spatial scale for managing genetic diversity across riverine networks.
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Affiliation(s)
- Zachery D Zbinden
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
| | - Marlis R Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
| | - Tyler K Chafin
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
- Biomathematics and Statistics Scotland, Edinburgh, UK
| | - Michael E Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
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Duckett DJ, Calder K, Sullivan J, Tank DC, Carstens BC. Reduced representation approaches produce similar results to whole genome sequencing for some common phylogeographic analyses. PLoS One 2023; 18:e0291941. [PMID: 38032899 PMCID: PMC10688678 DOI: 10.1371/journal.pone.0291941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 09/09/2023] [Indexed: 12/02/2023] Open
Abstract
When designing phylogeographic investigations researchers can choose to collect many different types of molecular markers, including mitochondrial genes or genomes, SNPs from reduced representation protocols, large sequence capture data sets, and even whole genomes. Given that the statistical power and accuracy of various analyses are expected to differ depending on both the type of marker and the amount of data collected, an exploration of the variance across methodological results as a function of marker type should provide valuable information to researchers. Here we collect mitochondrial Cytochrome b sequences, whole mitochondrial genomes, single nucleotide polymorphisms (SNP)s isolated using a genotype by sequencing (GBS) protocol, sequences from ultraconserved elements, and low-coverage nuclear genomes from the North American water vole (Microtus richardsoni). We estimate genetic distances, population genetic structure, and historical demography using data from each of these datasets and compare the results across markers. As anticipated, the results exhibit differences across marker types, particularly in terms of the resolution offered by different analyses. A cost-benefit analysis indicates that SNPs collected using a GBS protocol are the most cost-effective molecular marker, with inferences that mirror those collected from the whole genome data at a fraction of the cost per sample.
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Affiliation(s)
- Drew J. Duckett
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, United States of America
| | - Kailee Calder
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States of America
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States of America
| | - David C. Tank
- Department of Botany, University of Wyoming, Laramie, WY, United States of America
| | - Bryan C. Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, United States of America
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Piatkowski B, Weston DJ, Aguero B, Duffy A, Imwattana K, Healey AL, Schmutz J, Shaw AJ. Divergent selection and climate adaptation fuel genomic differentiation between sister species of Sphagnum (peat moss). ANNALS OF BOTANY 2023; 132:499-512. [PMID: 37478307 PMCID: PMC10666999 DOI: 10.1093/aob/mcad104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/24/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND AND AIMS New plant species can evolve through the reinforcement of reproductive isolation via local adaptation along habitat gradients. Peat mosses (Sphagnaceae) are an emerging model system for the study of evolutionary genomics and have well-documented niche differentiation among species. Recent molecular studies have demonstrated that the globally distributed species Sphagnum magellanicum is a complex of morphologically cryptic lineages that are phylogenetically and ecologically distinct. Here, we describe the architecture of genomic differentiation between two sister species in this complex known from eastern North America: the northern S. diabolicum and the largely southern S. magniae. METHODS We sampled plant populations from across a latitudinal gradient in eastern North America and performed whole genome and restriction-site associated DNA sequencing. These sequencing data were then analyzed computationally. KEY RESULTS Using sliding-window population genetic analyses we find that differentiation is concentrated within 'islands' of the genome spanning up to 400 kb that are characterized by elevated genetic divergence, suppressed recombination, reduced nucleotide diversity and increased rates of non-synonymous substitution. Sequence variants that are significantly associated with genetic structure and bioclimatic variables occur within genes that have functional enrichment for biological processes including abiotic stress response, photoperiodism and hormone-mediated signalling. Demographic modelling demonstrates that these two species diverged no more than 225 000 generations ago with secondary contact occurring where their ranges overlap. CONCLUSIONS We suggest that this heterogeneity of genomic differentiation is a result of linked selection and reflects the role of local adaptation to contrasting climatic zones in driving speciation. This research provides insight into the process of speciation in a group of ecologically important plants and strengthens our predictive understanding of how plant populations will respond as Earth's climate rapidly changes.
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Affiliation(s)
- Bryan Piatkowski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Blanka Aguero
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Aaron Duffy
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Karn Imwattana
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Adam L Healey
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - A Jonathan Shaw
- Department of Biology, Duke University, Durham, NC 27708, USA
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61
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Wang WY, Yamada A. Scrutinising an inscrutable bark-nesting ant: Exploring cryptic diversity in the Rhopalomastix javana (Hymenoptera: Formicidae) complex using DNA barcodes, genome-wide MIG-seq and geometric morphometrics. PeerJ 2023; 11:e16416. [PMID: 38025712 PMCID: PMC10657568 DOI: 10.7717/peerj.16416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Overlooking cryptic species diversity has grave implications on assessments of climate change impacts on biodiversity, ecosystems and organismal populations. Discriminating between cryptic species has long been challenging even for seasoned taxonomists, as interspecies morphological differences are often indiscernible by visual observation. Multi-disciplinary methods involving genetic analyses in conjunction with quantitative morphological data, should therefore be used to investigate boundaries between cryptic species. We adopted an integrated approach combining analyses of mitochondrial COI barcodes, a genome-wide dataset obtained via multiplexed inter-simple sequence repeats (ISSRs) genotyping by sequencing (MIG-seq), and geometric morphometrics to investigate species divergences in the inscrutable Rhopalomastix javana species complex. Objective clustering of COI suggested five putative molecular species units divergent from each other by thresholds within 4.2-10.6% uncorrected pairwise distance. Phylogenetic analyses based on concatenated MIG-seq data also recovered and strongly supported the monophyly of five major lineages in agreement with COI clusters. Co-ancestry analyses based on MIG-seq data using fineRADstructure resolved variable patterns of admixture linked to geography, and potential genetic drift within some putative species. Geometric morphometric analyses of specimen images further detected statistically significant differences in at least one of three anatomical aspects (Head, Meso, Profile) between all pairs of putative species. Head shape (full-face view) was determined to be the most informative character for species diagnosis, with relatively high classification accuracy. Thin-plate spline deformation grids highlighted areas of high variation between species in each shape for deeper taxonomic scrutiny. The presence of species from multiple distinct lineages existing in near-sympatry firmly demonstrates that R. javana comprises more than one closely-related species, but exact species boundaries are difficult to ascertain. Differences in elevation and its associated abiotic effects on ant adaptations and reproductive phenology may contribute to restricting gene flow and maintaining species boundaries between sympatric populations of the R. javana complex. We further assess the advantages and limitations of geometric morphometrics as a taxonomic tool. Despite its drawbacks, our combined approach has helped draw important insights on cryptic diversity in R. javana, and also identified gaps of knowledge that await address. Results from this study will inform and prime future in-depth taxonomic investigation on the R. javana complex, including formal descriptions and establishment of the five putative species.
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Affiliation(s)
- Wendy Y. Wang
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore
| | - Aiki Yamada
- Systematic Zoology Laboratory, Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
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62
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Ruiz Mondragón KY, Klimova A, Aguirre-Planter E, Valiente-Banuet A, Lira R, Sanchez-de la Vega G, Eguiarte LE. Differences in the genomic diversity, structure, and inbreeding patterns in wild and managed populations of Agave potatorum Zucc. used in the production of Tobalá mezcal in Southern Mexico. PLoS One 2023; 18:e0294534. [PMID: 37972146 PMCID: PMC10653438 DOI: 10.1371/journal.pone.0294534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
Agave potatorum Zucc. locally known as Tobalá, is an important species for mezcal production. It is a perennial species that takes 10 to 15 years to reach reproductive age. Because of high demand of Tobalá mezcal and the slow maturation of the plants, its wild populations have been under intense anthropogenic pressure. The main objective of this study was to estimate the genome-wide diversity in A. potatorum and determine if the type of management has had any effect on its diversity, inbreeding and structure. We analyzed 174 individuals (105 wild, 42 cultivated and 27 from nurseries) from 34 sites with a reduced representation genomic method (ddRADseq), using 14,875 SNPs. The diversity measured as expected heterozygosity was higher in the nursery and wild plants than in cultivated samples. We did not find private alleles in the cultivated and nursery plants, which indicates that the individuals under management recently derived from wild populations, which was supported by higher gene flow estimated from wild populations to the managed plants. We found low but positive levels of inbreeding (FIS = 0.082), probably related to isolation of the populations. We detected low genetic differentiation among populations (FST = 0.0796), with positive and significant isolation by distance. The population genetic structure in the species seems to be related to elevation and ecology, with higher gene flow among populations in less fragmented areas. We detected an outlier locus related to the recognition of pollen, which is also relevant to self-incompatibility protein (SI). Due to seed harvest and long generation time, the loss of diversity in A. potatorum has been gradual and artificial selection and incipient management have not yet caused drastic differences between cultivated and wild plants. Also, we described an agroecological alternative to the uncontrolled extraction of wild individuals.
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Affiliation(s)
- Karen Y. Ruiz Mondragón
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Anastasia Klimova
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Erika Aguirre-Planter
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Alfonso Valiente-Banuet
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
| | - Rafael Lira
- Laboratorio de Recursos Naturales, Unidad de Biotecnología y Prototipos (UBIPRO), Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Estado de México, México
| | - Guillermo Sanchez-de la Vega
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
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Kagawa O, Hirota SK, Saito T, Uchida S, Watanabe H, Miyazoe R, Yamaguchi T, Matsuno T, Araki K, Wakasugi H, Suzuki S, Kobayashi G, Miyazaki H, Suyama Y, Hanyuda T, Chiba S. Host-Shift Speciation Proceeded with Gene Flow in Algae Covering Shells. Am Nat 2023; 202:721-732. [PMID: 37963116 DOI: 10.1086/726221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
AbstractHost shifts represent the advancement of a novel niche and often lead to speciation in symbionts. However, its mechanisms are not well understood. Here, we focused on the alga Pseudocladophora conchopheria growing on the shells of intertidal snails. Previous surveys have shown that the alga has host specificity-only attaching to the shell of Lunella correensis-but we discovered that the alga attaches to the shells of multiple sympatric snails. A genome-wide single-nucleotide polymorphism analysis (MIG-seq) was performed to determine whether host-associated speciation occurred in the algae. As a result, there was no gene flow or limited gene flow among the algae from different hosts, and some algae were genetically differentiated among hosts. In addition, the demographic estimate revealed that speciation with gene flow occurred between the algae from different hosts. Therefore, these results support the idea that host-shift speciation gradually proceeded with gene flow in the algae, providing insight into the early evolution of host shifts.
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64
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Reichard M, Koblmüller S, Blažek R, Zimmermann H, Katongo C, Bryjová A, Bryja J. Lack of host specialization despite selective host use in brood parasitic cuckoo catfish. Mol Ecol 2023; 32:6070-6082. [PMID: 37861460 DOI: 10.1111/mec.17173] [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: 06/28/2023] [Revised: 09/30/2023] [Accepted: 10/09/2023] [Indexed: 10/21/2023]
Abstract
Host-parasite dynamics involve coevolutionary arms races, which may lead to host specialization and ensuing diversification. Our general understanding of the evolution of host specialization in brood parasites is compromised by a restricted focus on bird and insect lineages. The cuckoo catfish (Synodontis multipunctatus) is an obligate parasite of parental care of mouthbrooding cichlids in Lake Tanganyika. Given the ecological and taxonomic diversity of mouthbrooding cichlids in the lake, we hypothesized the existence of sympatric host-specific lineages in the cuckoo catfish. In a sample of 779 broods from 20 cichlid species, we found four species parasitized by cuckoo catfish (with prevalence of parasitism of 2%-18%). All parasitized cichlids were from the tribe Tropheini, maternal mouthbrooders that spawn over a substrate (rather than in open water). Phylogenetic analysis based on genomic (ddRAD sequencing) and mitochondrial (Dloop) data from cuckoo catfish embryos showed an absence of host-specific lineages. This was corroborated by analyses of genetic structure and co-ancestry matrix. Within host species, parasitism was not associated with any individual characteristic we recorded (parent size, water depth), but was costly as parasitized parents carried smaller clutches of their own offspring. We conclude that the cuckoo catfish is an intermediate generalist and discuss costs, benefits and constraints of host specialization in this species and brood parasites in general.
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Affiliation(s)
- Martin Reichard
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | | | - Radim Blažek
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Holger Zimmermann
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Institute of Biology, University of Graz, Graz, Austria
| | - Cyprian Katongo
- Department of Biological Sciences, University of Zambia, Lusaka, Zambia
| | - Anna Bryjová
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Josef Bryja
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
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Ramirez JL, Machado CB, de Mello Affonso PRA, Galetti PM. Speciation in Coastal Basins Driven by Staggered Headwater Captures: Dispersal of a Species Complex, Leporinus bahiensis, as Revealed by Genome-wide SNP Data. Syst Biol 2023; 72:973-983. [PMID: 37260367 PMCID: PMC10627554 DOI: 10.1093/sysbio/syad034] [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: 03/03/2022] [Revised: 05/22/2023] [Accepted: 05/30/2023] [Indexed: 06/02/2023] Open
Abstract
Past sea level changes and geological instability along watershed boundaries have largely influenced fish distribution across coastal basins, either by dispersal via palaeodrainages now submerged or by headwater captures, respectively. Accordingly, the South American Atlantic coast encompasses several small and isolated drainages that share a similar species composition, representing a suitable model to infer historical processes. Leporinus bahiensis is a freshwater fish species widespread along adjacent coastal basins over narrow continental shelf with no evidence of palaeodrainage connections at low sea level periods. Therefore, this study aimed to reconstruct its evolutionary history to infer the role of headwater captures in the dispersal process. To accomplish this, we employed molecular-level phylogenetic and population structure analyses based on Sanger sequences (5 genes) and genome-wide SNP data. Phylogenetic trees based on Sanger data were inconclusive, but SNPs data did support the monophyletic status of L. bahiensis. Both COI and SNP data revealed structured populations according to each hydrographic basin. Species delimitation analyses revealed from 3 (COI) to 5 (multilocus approach) MOTUs, corresponding to the sampled basins. An intricate biogeographic scenario was inferred and supported by Approximate Bayesian Computation (ABC) analysis. Specifically, a staggered pattern was revealed and characterized by sequential headwater captures from basins adjacent to upland drainages into small coastal basins at different periods. These headwater captures resulted in dispersal throughout contiguous coastal basins, followed by deep genetic divergence among lineages. To decipher such recent divergences, as herein represented by L. bahiensis populations, we used genome-wide SNPs data. Indeed, the combined use of genome-wide SNPs data and ABC method allowed us to reconstruct the evolutionary history and speciation of L. bahiensis. This framework might be useful in disentangling the diversification process in other neotropical fishes subject to a reticulate geological history.
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Affiliation(s)
- Jorge L Ramirez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
- Museo de Historia Natural de la Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Carolina B Machado
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | | | - Pedro M Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
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Rees M, Neaves LE, Lewis GP, de Lima HC, Gagnon E. Phylogenomic and morphological data reveal hidden patterns of diversity in the national tree of Brazil, Paubrasilia echinata. AMERICAN JOURNAL OF BOTANY 2023; 110:e16241. [PMID: 37672601 DOI: 10.1002/ajb2.16241] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 09/08/2023]
Abstract
PREMISE Paubrasilia echinata (common names, pau brasil, brazilwood) is the national tree of Brazil and an endangered species endemic to the Brazilian Atlantic Forest. Over its wide distribution of 2000 km, its leaflets morphology exhibits extensive plasticity. Three morphotypes are commonly identified based on leaf size, but it is unclear if they represent distinct taxa or a single polymorphic species. This study aims to clarify the taxonomic position of the three morphotypes to inform conservation decisions. METHODS A morphometric study of leaf characters of herbarium specimens was coupled with genetic analyses using genotype-by-sequencing data. We used maximum-likelihood and coalescent methods to evaluate the phylogenetic and population structure of the species. We compared these with a morphological dendrogram built from hierarchical clustering. RESULTS Two of the three morphotypes formed separately evolving lineages, the third morphotype formed two geographically separate lineages, and northern trees with intermediate leaf morphology formed a separate fifth lineage. Leaflet size varied by over 35-fold, and although morphological clustering generally matched the genetic patterns, there were some overlaps, highlighting the cryptic diversity within this group. CONCLUSIONS Our genetic and morphological results provide some evidence that cultivated trees from different states in Brazil seem to have a limited genetic origin and do not reflect the broader genetic and geographical diversity of the species. As a result, more care is likely needed to preserve the overall genomic diversity of this endangered and iconic species.
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Affiliation(s)
- Mathew Rees
- Tropical Diversity, Royal Botanic Garden Edinburgh, Edinburgh, EH5 3LR, UK
- School of GeoSciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Linda E Neaves
- Tropical Diversity, Royal Botanic Garden Edinburgh, Edinburgh, EH5 3LR, UK
- Fenner School of Environment & Society, Australian National University, Australian Capital Territory, Australia
| | - Gwilym P Lewis
- Accelerated Taxonomy Department, Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK
| | - Haroldo C de Lima
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rua Pacheco Leão, 915, Rio de Janeiro, RJ, 22460-030, Brazil
- Instituto Nacional da Mata Atlântica/INMA-MCTI, Av. José Ruschi, 4, Centro, Santa Teresa, Espírito Santo, Brazil
| | - Edeline Gagnon
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, 85352, Freising-Weihenstephan, Germany
- Department of Integrative BIology, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
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67
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San Jose M, Doorenweerd C, Geib S, Barr N, Dupuis JR, Leblanc L, Kauwe A, Morris KY, Rubinoff D. Interspecific gene flow obscures phylogenetic relationships in an important insect pest species complex. Mol Phylogenet Evol 2023; 188:107892. [PMID: 37524217 DOI: 10.1016/j.ympev.2023.107892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/07/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023]
Abstract
As genomic data proliferates, the prevalence of post-speciation gene flow is making species boundaries and relationships increasingly ambiguous. Although current approaches inferring fully bifurcating phylogenies based on concatenated datasets provide simple and robust answers to many species relationships, they may be inaccurate because the models ignore inter-specific gene flow and incomplete lineage sorting. To examine the potential error resulting from ignoring gene flow, we generated both a RAD-seq and a 500 protein-coding loci highly multiplexed amplicon (HiMAP) dataset for a monophyletic group of 12 species defined as the Bactrocera dorsalis sensu lato clade. With some of the world's worst agricultural pests, the taxonomy of the B. dorsalis s.l. clade is important for trade and quarantines. However, taxonomic confusion confounds resolution due to intra- and interspecific phenotypic variation and convergence, mitochondrial introgression across half of the species, and viable hybrids. We compared the topological convergence of our datasets using concatenated phylogenetic and various multispecies coalescent approaches, some of which account for gene flow. All analyses agreed on species delimitation, but there was incongruence between species relationships. Under concatenation, both datasets suggest identical species relationships with mostly high statistical support. However, multispecies coalescent and multispecies network approaches suggest markedly different hypotheses and detected significant gene flow. We suggest that the network approaches are likely more accurate because gene flow violates the assumptions of the concatenated phylogenetic analyses, but the data-reductive requirements of network approaches resulted in reduced statistical support and could not unambiguously resolve gene flow directions. Our study highlights the importance of testing for gene flow, particularly with phylogenomic datasets, even when concatenated approaches receive high statistical support.
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Affiliation(s)
- Michael San Jose
- University of Hawaii, College of Tropical Agriculture and Human Resources, Department of Plant and Environmental Protection Sciences, Entomology Section, 3050 Maile Way, Honolulu, HI, 96822-2231, USA.
| | - Camiel Doorenweerd
- University of Hawaii, College of Tropical Agriculture and Human Resources, Department of Plant and Environmental Protection Sciences, Entomology Section, 3050 Maile Way, Honolulu, HI, 96822-2231, USA
| | - Scott Geib
- Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye U.S. Pacific Basin Agricultural Center, USDA Agricultural Research Services, Hilo, HI, USA
| | - Norman Barr
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Plant Protection and Quarantine, Science & Technology, Insect Management and Molecular Diagnostics Laboratory, 22675 N. Moorefield Road, Edinburg, TX 78541, USA
| | - Julian R Dupuis
- University of Kentucky, Department of Entomology, S225 Ag Science Center North, 1100 South Limestone, Lexington, KY, 40546-0091, USA
| | - Luc Leblanc
- University of Idaho, Department of Entomology, Plant Pathology and Nematology, 875 Perimeter Drive, MS2329, Moscow, ID, 83844-2329, USA
| | - Angela Kauwe
- Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye U.S. Pacific Basin Agricultural Center, USDA Agricultural Research Services, Hilo, HI, USA
| | - Kimberley Y Morris
- University of Hawaii, College of Tropical Agriculture and Human Resources, Department of Plant and Environmental Protection Sciences, Entomology Section, 3050 Maile Way, Honolulu, HI, 96822-2231, USA; Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye U.S. Pacific Basin Agricultural Center, USDA Agricultural Research Services, Hilo, HI, USA
| | - Daniel Rubinoff
- University of Hawaii, College of Tropical Agriculture and Human Resources, Department of Plant and Environmental Protection Sciences, Entomology Section, 3050 Maile Way, Honolulu, HI, 96822-2231, USA
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Arana A, Esteves J, Ramírez R, Galetti PM, Pérez Z J, Ramirez JL. Population genomics reveals how 5 ka of human occupancy led the Lima leaf-toed gecko (Phyllodactylus sentosus) to the brink of extinction. Sci Rep 2023; 13:18465. [PMID: 37891335 PMCID: PMC10611785 DOI: 10.1038/s41598-023-45715-x] [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: 03/01/2023] [Accepted: 10/23/2023] [Indexed: 10/29/2023] Open
Abstract
Small species with high home fidelity, high ecological specialization or low vagility are particularly prone to suffer from habitat modification and fragmentation. The Lima leaf-toed gecko (Phyllodactylus sentosus) is a critically endangered Peruvian species that shelters mostly in pre-Incan archeological areas called huacas, where the original environmental conditions are maintained. We used genotyping by sequencing to understand the population genomic history of P. sentosus. We found low genetic diversity (He 0.0406-0.134 and nucleotide diversity 0.0812-0.145) and deviations of the observed heterozygosity relative to the expected heterozygosity in some populations (Fis - 0.0202 to 0.0187). In all analyses, a clear population structuring was observed that cannot be explained by isolation by distance alone. Also, low levels of historical gene flow were observed between most populations, which decreased as shown in contemporary migration rate analysis. Demographic inference suggests these populations experienced bottleneck events during the last 5 ka. These results indicate that habitat modification since pre-Incan civilizations severely affected these populations, which currently face even more drastic urbanization threats. Finally, our predictions show that this species could become extinct in a decade without further intervention, which calls for urgent conservation actions being undertaken.
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Affiliation(s)
- Alejandra Arana
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Juan Esteves
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Rina Ramírez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Pedro M Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
| | - José Pérez Z
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Jorge L Ramirez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru.
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Zhang C, Meng R, Meng Y, Guo BL, Liu QR, Nie ZL. Parallel evolution, atavism, and extensive introgression explain the radiation of Epimedium sect. Diphyllon (Berberidaceae) in southern East Asia. FRONTIERS IN PLANT SCIENCE 2023; 14:1234148. [PMID: 37915504 PMCID: PMC10616310 DOI: 10.3389/fpls.2023.1234148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023]
Abstract
East Asia is the richest region of plant biodiversity in the northern temperate zone, and its radiation provides key insights for understanding rapid speciation, including evolutionary patterns and processes. However, it is challenging to investigate the recent evolutionary radiation among plants because of the lack of genetic divergence, phenotypic convergence, and interspecific gene flow. Epimedium sect. Diphyllon is a rarely studied plant lineage endemic to East Asia, especially highly diversified in its southern part. In this study, we report a robust phylogenomic analysis based on genotyping-by-sequencing data of this lineage. The results revealed a clear biogeographic pattern for Epimedium sect. Diphyllon with recognition into two major clades corresponding to the Sino-Himalayan and Sino-Japanese subkingdoms of East Asian Flora and rapid diversification of the extant species dated to the Pleistocene. Evolutionary radiation of Epimedium sect. Diphyllon is characterized by recent and predominant parallel evolution and atavism between the two subkingdom regions, with extensive reticulating hybridization within each region during the course of diversification in southern East Asia. A parallel-atavism-introgression hypothesis is referred to in explaining the radiation of plant diversity in southern East Asia, which represents a potential model for the rapid diversification of plants under global climate cooling in the late Tertiary. Our study advances our understanding of the evolutionary processes of plant radiation in East Asia as well as in other biodiversity hotspot regions.
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Affiliation(s)
- Cheng Zhang
- Key Laboratory of Biodiversity Science and Ecological Engineering of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
- College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Ran Meng
- College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Ying Meng
- College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Bao-Lin Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Quan-Ru Liu
- Key Laboratory of Biodiversity Science and Ecological Engineering of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Ze-Long Nie
- College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
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70
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Villa-Machío I, Heuertz M, Álvarez I, Nieto Feliner G. Demography-driven and adaptive introgression in a hybrid zone of the Armeria syngameon. Mol Ecol 2023. [PMID: 37837272 DOI: 10.1111/mec.17167] [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: 07/18/2022] [Revised: 09/30/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023]
Abstract
Syngameons represent networks of otherwise distinct species connected by limited gene exchange. Although most studies have focused on how species maintain their cohesiveness despite gene flow, there are additional relevant questions regarding the evolutionary dynamics of syngameons and their drivers, as well as the success of their members and the network as a whole. Using a ddRADseq approach, we analysed the genetic structure, genomic clines and demographic history of a coastal hybrid zone involving two species of the Armeria (Plumbaginaceae) syngameon in southern Spain. We inferred that a peripheral population of the sand dune-adapted A. pungens diverged from the rest of the conspecific populations and subsequently hybridized with a locally more abundant pinewood congener, A. macrophylla. Both species display extensive plastid DNA haplotype sharing. Genomic cline analysis identified bidirectional introgression, but more outlier loci with excess A. pungens than A. macrophylla ancestry, suggesting the possibility of selection for A. pungens alleles. This is consistent with the finding that the A. pungens phenotype is selected for in open habitats, and with the strong correlation found between ancestry and phenotype. Taken together, our analyses suggest an intriguing scenario in which bidirectional introgression may, on the one hand, help to avoid reduced levels of genetic diversity due to the small size and isolated location of the A. pungens range-edge population, thereby minimizing demographic risks of stochastic extinction. On the other hand, the data also suggest that introgression into A. macrophylla may allow individuals to grow in open, highly irradiated, deep sandy, salt-exposed habitats.
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Affiliation(s)
- Irene Villa-Machío
- Department of Biodiversity and Conservation, Real Jardín Botánico (RJB), CSIC, Madrid, Spain
| | | | - Inés Álvarez
- Department of Biodiversity and Conservation, Real Jardín Botánico (RJB), CSIC, Madrid, Spain
| | - Gonzalo Nieto Feliner
- Department of Biodiversity and Conservation, Real Jardín Botánico (RJB), CSIC, Madrid, Spain
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71
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Márquez-Corro JI, Martín-Bravo S, Blanco-Pastor JL, Luceño M, Escudero M. The holocentric chromosome microevolution: From phylogeographic patterns to genomic associations with environmental gradients. Mol Ecol 2023. [PMID: 37795678 DOI: 10.1111/mec.17156] [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: 06/13/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/06/2023]
Abstract
Geographic isolation and chromosome evolution are two of the major drivers of diversification in eukaryotes in general, and specifically, in plants. On one hand, range shifts induced by Pleistocene glacial oscillations deeply shaped the evolutionary trajectories of species in the Northern Hemisphere. On the other hand, karyotype variability within species or species complexes may have adaptive potential as different karyotypes may represent different recombination rates and linkage groups that may be associated with locally adapted genes or supergenes. Organisms with holocentric chromosomes are ideal to study the link between local adaptation and chromosome evolution, due to their high cytogenetic variability, especially when it seems to be related to environmental variation. Here, we integrate the study of the phylogeography, chromosomal evolution and ecological requirements of a plant species complex distributed in the Western Euro-Mediterranean region (Carex gr. laevigata, Cyperaceae). We aim to clarify the relative influence of these factors on population differentiation and ultimately on speciation. We obtained a well-resolved RADseq phylogeny that sheds light on the phylogeographic patterns of molecular and chromosome number variation, which are compatible with south-to-north postglacial migration. In addition, landscape genomics analyses identified candidate loci for local adaptation, and also strong significant associations between the karyotype and the environment. We conclude that karyotype distribution in C. gr. laevigata has been constrained by both range shift dynamics and local adaptation. Our study demonstrates that chromosome evolution may be responsible, at least partially, for microevolutionary patterns of population differentiation and adaptation in Carex.
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Affiliation(s)
- José Ignacio Márquez-Corro
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Seville, Spain
- Jodrell Laboratory, Department of Trait Diversity and Function, Royal Botanic Gardens, Kew, Richmond, UK
| | - Santiago Martín-Bravo
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Seville, Spain
| | - José Luis Blanco-Pastor
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Seville, Spain
- Departamento de Biología, IVAGRO, Universidad de Cádiz, Campus de Excelencia Internacional Agroalimentario (CeiA3), Cádiz, Spain
| | - Modesto Luceño
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Seville, Spain
| | - Marcial Escudero
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Seville, Spain
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Kim TH, Kim S, Park W, Woo KS, Lee K, Chung MN, Lee YH, Lee HU, Lee KH, Nam SS, Jo H, Lee JD. Genome-wide association study to identify novel loci and genes for Fusarium root rot resistance in sweet potato using genotyping-by-sequencing. FRONTIERS IN PLANT SCIENCE 2023; 14:1251157. [PMID: 37860237 PMCID: PMC10584150 DOI: 10.3389/fpls.2023.1251157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/15/2023] [Indexed: 10/21/2023]
Abstract
Fusarium root rot, caused by Fusarium solani, is a major post-harvest disease in sweet potatoes (Ipomoea batatas (L.) Lam.). An effective strategy for controlling this disease is the development of resistant varieties. In this study, a genome-wide association study (GWAS) was conducted on 96 sweet potato genotypes to identify novel candidate loci and dissect the genetic basis of Fusarium root rot resistance. Genotyping was performed using genotyping-by-sequencing (GBS), and 44,255 SNPs were identified after filtering. The genotypes (n = 96) were evaluated through resistance tests in 2021 and 2022, separately and combined. The GWAS identified two significant SNP markers (LG3_22903756 and LG4_2449919) on chromosomes 3 and 4 associated with Fusarium root rot resistance, respectively. Lesion length showed significant differences between homozygous A and G alleles of LG3_22903756, which can potentially be used to develop molecular markers for selecting accessions resistant to Fusarium root rot. Expression analysis of 11 putative genes flanking the significant SNPs revealed the alteration in the expression of nine genes, indicating their possible involvement in Fusarium root rot resistance. The results of this study will aid in the marker-assisted selection and functional analysis of candidate genes for Fusarium root rot resistance in sweet potatoes.
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Affiliation(s)
- Tae Hwa Kim
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Sujung Kim
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Won Park
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Koan Sik Woo
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Keunpyo Lee
- International Technology Cooperation Center, Technology Cooperation Bureau, Rural Development Administration, Jeonju, Republic of Korea
| | - Mi Nam Chung
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Young Hoon Lee
- Planning and Coordination Division, National Institute of Crop Science, Rural Development Administration, Jeonju, Republic of Korea
| | - Hyeong-Un Lee
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Kyo Hwui Lee
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Sang-Sik Nam
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Hyun Jo
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jeong-Dong Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
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73
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Shaw AJ, Duffy AM, Nieto-Lugilde M, Aguero B, Schuette S, Robinson S, Loveland J, Hicks KA, Weston D, Piatkowski B, Kolton M, Koska JE, Healey AL. Clonality, local population structure and gametophyte sex ratios in cryptic species of the Sphagnum magellanicum complex. ANNALS OF BOTANY 2023; 132:77-94. [PMID: 37417448 PMCID: PMC10550268 DOI: 10.1093/aob/mcad077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/06/2023] [Indexed: 07/08/2023]
Abstract
BACKGROUND AND AIMS Sphagnum (peatmoss) comprises a moss (Bryophyta) clade with ~300-500 species. The genus has unparalleled ecological importance because Sphagnum-dominated peatlands store almost a third of the terrestrial carbon pool and peatmosses engineer the formation and microtopography of peatlands. Genomic resources for Sphagnum are being actively expanded, but many aspects of their biology are still poorly known. Among these are the degree to which Sphagnum species reproduce asexually, and the relative frequencies of male and female gametophytes in these haploid-dominant plants. We assess clonality and gametophyte sex ratios and test hypotheses about the local-scale distribution of clones and sexes in four North American species of the S. magellanicum complex. These four species are difficult to distinguish morphologically and are very closely related. We also assess microbial communities associated with Sphagnum host plant clones and sexes at two sites. METHODS Four hundred and five samples of the four species, representing 57 populations, were subjected to restriction site-associated DNA sequencing (RADseq). Analyses of population structure and clonality based on the molecular data utilized both phylogenetic and phenetic approaches. Multi-locus genotypes (genets) were identified using the RADseq data. Sexes of sampled ramets were determined using a molecular approach that utilized coverage of loci on the sex chromosomes after the method was validated using a sample of plants that expressed sex phenotypically. Sex ratios were estimated for each species, and populations within species. Difference in fitness between genets was estimated as the numbers of ramets each genet comprised. Degrees of clonality [numbers of genets/numbers of ramets (samples)] within species, among sites, and between gametophyte sexes were estimated. Sex ratios were estimated for each species, and populations within species. Sphagnum-associated microbial communities were assessed at two sites in relation to Sphagnum clonality and sex. KEY RESULTS All four species appear to engage in a mixture of sexual and asexual (clonal) reproduction. A single ramet represents most genets but two to eight ramets were dsumbers ansd text etected for some genets. Only one genet is represented by ramets in multiple populations; all other genets are restricted to a single population. Within populations ramets of individual genets are spatially clustered, suggesting limited dispersal even within peatlands. Sex ratios are male-biased in S. diabolicum but female-biased in the other three species, although significantly so only in S. divinum. Neither species nor males/females differ in levels of clonal propagation. At St Regis Lake (NY) and Franklin Bog (VT), microbial community composition is strongly differentiated between the sites, but differences between species, genets and sexes were not detected. Within S. divinum, however, female gametophytes harboured two to three times the number of microbial taxa as males. CONCLUSIONS These four Sphagnum species all exhibit similar reproductive patterns that result from a mixture of sexual and asexual reproduction. The spatial patterns of clonally replicated ramets of genets suggest that these species fall between the so-called phalanx patterns, where genets abut one another but do not extensively mix because of limited ramet fragmentation, and the guerrilla patterns, where extensive genet fragmentation and dispersal result in greater mixing of different genets. Although sex ratios in bryophytes are most often female-biased, both male and female biases occur in this complex of closely related species. The association of far greater microbial diversity for female gametophytes in S. divinum, which has a female-biased sex ratio, suggests additional research to determine if levels of microbial diversity are consistently correlated with differing patterns of sex ratio biases.
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Affiliation(s)
- A Jonathan Shaw
- Department of Biology & L. E. Anderson Bryophyte Herbarium, Duke University, Durham, NC, 27708, USA
| | - Aaron M Duffy
- Department of Biology & L. E. Anderson Bryophyte Herbarium, Duke University, Durham, NC, 27708, USA
| | - Marta Nieto-Lugilde
- Department of Biology & L. E. Anderson Bryophyte Herbarium, Duke University, Durham, NC, 27708, USA
| | - Blanka Aguero
- Department of Biology & L. E. Anderson Bryophyte Herbarium, Duke University, Durham, NC, 27708, USA
| | - Scott Schuette
- Pennsylvania Natural Heritage Program, Western Pennsylvania Conservancy, Pittsburgh, PA, 15222, USA
| | - Sean Robinson
- Department of Biology, SUNY Oneonta, Oneonta, NY, 13820, USA
| | - James Loveland
- Department of Biology, Kenyon College, Gambier, OH 43022, USA
| | - Karen A Hicks
- Department of Biology, Kenyon College, Gambier, OH 43022, USA
| | - David Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Bryan Piatkowski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Max Kolton
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, 8499000, Israel
| | - Joel E Koska
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Adam L Healey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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74
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Mascarenhas R, Meirelles PM, Batalha-Filho H. Urbanization drives adaptive evolution in a Neotropical bird. Curr Zool 2023; 69:607-619. [PMID: 37637315 PMCID: PMC10449428 DOI: 10.1093/cz/zoac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 08/16/2022] [Indexed: 08/29/2023] Open
Abstract
Urbanization has dramatic impacts on natural habitats and such changes may potentially drive local adaptation of urban populations. Behavioral change has been specifically shown to facilitate the fast adaptation of birds to changing environments, but few studies have investigated the genetic mechanisms of this process. Such investigations could provide insights into questions about both evolutionary theory and management of urban populations. In this study, we investigated whether local adaptation has occurred in urban populations of a Neotropical bird species, Coereba flaveola, specifically addressing whether observed behavioral adaptations are correlated to genetic signatures of natural selection. To answer this question, we sampled 24 individuals in urban and rural environments, and searched for selected loci through a genome-scan approach based on RADseq genomic data, generated and assembled using a reference genome for the species. We recovered 46 loci as putative selection outliers, and 30 of them were identified as associated with biological processes possibly related to urban adaptation, such as the regulation of energetic metabolism, regulation of genetic expression, and changes in the immunological system. Moreover, genes involved in the development of the nervous system showed signatures of selection, suggesting a link between behavioral and genetic adaptations. Our findings, in conjunction with similar results in previous studies, support the idea that cities provide a similar selective pressure on urban populations and that behavioral plasticity may be enhanced through genetic changes in urban populations.
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Affiliation(s)
- Rilquer Mascarenhas
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, 40170-115 Salvador, Bahia, Brazil
| | - Pedro Milet Meirelles
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, 40170-115 Salvador, Bahia, Brazil
| | - Henrique Batalha-Filho
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, 40170-115 Salvador, Bahia, Brazil
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75
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Giakoumis M, Pinilla-Buitrago GE, Musher LJ, Wares JP, Baird SJE, Hickerson MJ. Evidence of introgression, ecological divergence and adaptation in Asterias sea stars. Mol Ecol 2023; 32:5541-5557. [PMID: 37691604 DOI: 10.1111/mec.17118] [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: 06/24/2022] [Revised: 07/29/2023] [Accepted: 08/09/2023] [Indexed: 09/12/2023]
Abstract
Hybrid zones are important windows into the evolutionary dynamics of populations, revealing how processes like introgression and adaptation structure population genomic variation. Importantly, they are useful for understanding speciation and how species respond to their environments. Here, we investigate two closely related sea star species, Asterias rubens and A. forbesi, distributed along rocky European and North American coastlines of the North Atlantic, and use genome-wide molecular markers to infer the distribution of genomic variation within and between species in this group. Using genomic data and environmental niche modelling, we document hybridization occurring between northern New England and the southern Canadian Maritimes. We investigate the factors that maintain this hybrid zone, as well as the environmental variables that putatively drive selection within and between species. We find that the two species differ in their environmental niche breadth; Asterias forbesi displays a relatively narrow environmental niche while conversely, A. rubens has a wider niche breadth. Species distribution models accurately predict hybrids to occur within environmental niche overlap, thereby suggesting environmental selection plays an important role in the maintenance of the hybrid zone. Our results imply that the distribution of genomic variation in North Atlantic sea stars is influenced by the environment, which will be crucial to consider as the climate changes.
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Affiliation(s)
- Melina Giakoumis
- The Graduate Center, The City University of New York, New York, New York City, USA
- The City College of New York, New York, New York City, USA
- The American Museum of Natural History, New York, New York City, USA
| | - Gonzalo E Pinilla-Buitrago
- The Graduate Center, The City University of New York, New York, New York City, USA
- The City College of New York, New York, New York City, USA
| | - Lukas J Musher
- The Academy of Natural Sciences of Drexel University, Pennsylvania, Philadelphia, USA
| | - John P Wares
- Odum School of Ecology and Department of Genetics, University of Georgia, Georgia, Athens, USA
| | - Stuart J E Baird
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czechia
| | - Michael J Hickerson
- The Graduate Center, The City University of New York, New York, New York City, USA
- The City College of New York, New York, New York City, USA
- The American Museum of Natural History, New York, New York City, USA
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76
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Hopper KR. Reduced-representation libraries in insect genetics. CURRENT OPINION IN INSECT SCIENCE 2023; 59:101084. [PMID: 37442341 DOI: 10.1016/j.cois.2023.101084] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 05/04/2023] [Accepted: 07/06/2023] [Indexed: 07/15/2023]
Abstract
Genotyping-by-sequencing of reduced-representation libraries has ushered in an era where genome-wide data can be gotten for any species. Here, I review research on this topic during the last two years, report meta-analysis of the results, and discuss analysis methods and issues. Scanning the literature from 2021 to 2022 identified 21 papers, the majority of which were on population differences, including local adaptation and migration, but several papers were on genetic maps and their use in assembly scaffolding or analysis of quantitative trait loci, on the origin of incursions of pest insects, or on infection rates of a pathogen in a disease vector. The research reviewed includes 33 species from 25 families and 11 orders. Meta-analysis showed that less than 16%, and most often, less than 1% of the genome was implicated in local adaptation and that the number of adaptive loci correlated with genetic divergence among populations.
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Affiliation(s)
- Keith R Hopper
- Beneficial Insect Introductions Research Unit, ARS, USDA, Newark, DE, United States.
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Sromek L, Ylinen E, Kunnasranta M, Maduna SN, Sinisalo T, Michell CT, Kovacs KM, Lydersen C, Ieshko E, Andrievskaya E, Alexeev V, Leidenberger S, Hagen SB, Nyman T. Loss of species and genetic diversity during colonization: Insights from acanthocephalan parasites in northern European seals. Ecol Evol 2023; 13:e10608. [PMID: 37869427 PMCID: PMC10585441 DOI: 10.1002/ece3.10608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/24/2023] Open
Abstract
Studies on host-parasite systems that have experienced distributional shifts, range fragmentation, and population declines in the past can provide information regarding how parasite community richness and genetic diversity will change as a result of anthropogenic environmental changes in the future. Here, we studied how sequential postglacial colonization, shifts in habitat, and reduced host population sizes have influenced species richness and genetic diversity of Corynosoma (Acanthocephala: Polymorphidae) parasites in northern European marine, brackish, and freshwater seal populations. We collected Corynosoma population samples from Arctic, Baltic, Ladoga, and Saimaa ringed seal subspecies and Baltic gray seals, and then applied COI barcoding and triple-enzyme restriction-site associated DNA (3RAD) sequencing to delimit species, clarify their distributions and community structures, and elucidate patterns of intraspecific gene flow and genetic diversity. Our results showed that Corynosoma species diversity reflected host colonization histories and population sizes, with four species being present in the Arctic, three in the Baltic Sea, two in Lake Ladoga, and only one in Lake Saimaa. We found statistically significant population-genetic differentiation within all three Corynosoma species that occur in more than one seal (sub)species. Genetic diversity tended to be high in Corynosoma populations originating from Arctic ringed seals and low in the landlocked populations. Our results indicate that acanthocephalan communities in landlocked seal populations are impoverished with respect to both species and intraspecific genetic diversity. Interestingly, the loss of genetic diversity within Corynosoma species seems to have been less drastic than in their seal hosts, possibly due to their large local effective population sizes resulting from high infection intensities and effective intra-host population mixing. Our study highlights the utility of genomic methods in investigations of community composition and genetic diversity of understudied parasites.
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Affiliation(s)
- Ludmila Sromek
- Department of Marine Ecosystems Functioning, Institute of OceanographyUniversity of GdanskGdyniaPoland
| | - Eeva Ylinen
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandJoensuuFinland
| | - Mervi Kunnasranta
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandJoensuuFinland
- Natural Resources Institute FinlandJoensuuFinland
| | - Simo N. Maduna
- Department of Ecosystem in the Barents RegionNorwegian Institute of Bioeconomy ResearchSvanvikNorway
| | - Tuula Sinisalo
- Department of Biological and Environmental SciencesUniversity of JyväskyläJyväskyläFinland
| | - Craig T. Michell
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandJoensuuFinland
- Red Sea Research CenterKing Abdullah University of Science and TechnologyJeddahSaudi Arabia
| | | | | | - Evgeny Ieshko
- Institute of Biology, Karelian Research CentreRussian Academy of SciencesPetrozavodskRussia
| | | | | | - Sonja Leidenberger
- Department of Biology and Bioinformatics, School of BioscienceUniversity of SkövdeSkövdeSweden
| | - Snorre B. Hagen
- Department of Ecosystem in the Barents RegionNorwegian Institute of Bioeconomy ResearchSvanvikNorway
| | - Tommi Nyman
- Department of Ecosystem in the Barents RegionNorwegian Institute of Bioeconomy ResearchSvanvikNorway
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Ramírez-Reyes T, Armendáriz-Toledano F, Rodríguez LGC. Rearranging and completing the puzzle: Phylogenomic analysis of bark beetles Dendroctonus reveals new hypotheses about genus diversification. Mol Phylogenet Evol 2023; 187:107885. [PMID: 37467902 DOI: 10.1016/j.ympev.2023.107885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/07/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023]
Abstract
Studies carried out on bark beetles within Dendroctonus have been extensive and revealed diverse information in different areas of their natural history, taxonomy, evolution, and interactions, among others. Despite these efforts, phylogenetic hypotheses have remained obscured mainly due to limited information analyzed (taxonomic, gene sampling, or both) in studies focused on obtaining evolutionary hypotheses for this genus. With the aim of filling these gaps in the evolutionary history for Dendroctonus, we analyzed ∼1800 loci mapped to a reference genome obtained for 20 of the 21 species recognized to date, minimizing the impact of missing information and improving the assumption of orthology in a phylogenomic framework. We obtained congruent phylogenetic topologies from two phylogenomic inference strategies: loci concatenation (ML framework) and a multispecies coalescent model (MSC) through the analysis of site pattern frequencies (SNPs). Dendroctonus is composed of two major clades (A and B), each containing five and four subclades, respectively. According to our divergence dating analysis, the MRCA for Dendroctonus dates back to the early Eocene, while the MRCA for each major clade diverged in the mid-Eocene. Interestingly, most of the speciation events of extant species occurred during the Miocene, which could be correlated with the diversification of pine trees (Pinus). The MRCA for Dendroctonus inhabited large regions of North America, with all ancestors and descendants of clade A having diversified within this region. The Mexican Transition Zone is important in the diversification processes for the majority of clade A species. For clade B, we identified two important colonization events to the Old World from America: the first in the early Oligocene from the Arctic to Asia (via Beringia), and the second during the Miocene from the Arctic-Western-Alleghany region to Europe and Siberia (also via Beringia). Our genomic analyses also supported the existence of hidden structured lineages within the frontalis complex, and also that D. beckeri represent a lineage independent from D. valens, as previously suggested. The information presented here updates the knowledge concerning the diversification of a genus with remarkable ecological and economic importance.
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Affiliation(s)
- Tonatiuh Ramírez-Reyes
- Instituto de Biología, Departamento de Zoología, Colección Nacional de Insectos, Universidad Nacional Autónoma de México, Circuito Zona Deportiva S/N, C.U., Coyoacán, 04510 Ciudad de México, Mexico; Facultad de Ciencias Forestales, Universidad Autónoma de Nuevo León, Carretera Nacional 85, Km. 145, 67700 Linares, Nuevo León, Mexico
| | - Francisco Armendáriz-Toledano
- Instituto de Biología, Departamento de Zoología, Colección Nacional de Insectos, Universidad Nacional Autónoma de México, Circuito Zona Deportiva S/N, C.U., Coyoacán, 04510 Ciudad de México, Mexico.
| | - Luis Gerardo Cuéllar Rodríguez
- Facultad de Ciencias Forestales, Universidad Autónoma de Nuevo León, Carretera Nacional 85, Km. 145, 67700 Linares, Nuevo León, Mexico
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Dimitriou AC, Soares Campos-Filho I, Georgiou A, Taiti S, Sfenthourakis S. Intra-island patterns of cryptic diversity within an oceanic island: Insights from the differentiation of Schizidium Verhoeff, 1901 (Oniscidea, Armadillidiidae) within Cyprus, with descriptions of two new species. Mol Phylogenet Evol 2023; 187:107884. [PMID: 37467903 DOI: 10.1016/j.ympev.2023.107884] [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: 02/21/2023] [Revised: 07/11/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023]
Abstract
Cyprus is a Mediterranean island of volcanic origin isolated for at least 5.3 Myr from surrounding continental areas. The present study focuses on the diversification of the isopod genus Schizidium within the island, including also specimens from surrounding continental areas. The genus Schizidium sensu lato is probably non monophyletic, comprising 26 species distributed from Greece to Iran. Up to date the only representative of the genus reported from Cyprus was Schizidium fissum. Aiming to investigate the patterns of genetic diversity within the focal island, to evaluate the morphology-based taxonomy of the species in the genus, and at the same time to explore phylogenetic relationships with mainland populations, we applied genome-wide ddRADseq as well as Sanger sequencing targeting three mitochondrial (16S, COI and 12S) and the nuclear NaK loci. Results of phylogenetic analyses support the existence of two distinct epigean Schizidium clades with well-defined geographic boundaries that conform to the known paleogeography of Cyprus, plus one endogean clade with restricted distribution within the island. Genetic data and morphology corroborate the assignment of this latter endogean clade to a new species, Schizidium myrrae n. sp. The two epigean clades are also considered as distinct species, one corresponding to the known S. fissum at the eastern part of the island (Pentadaktylos massif) and the other to the newly described S. christosi n. sp. distributed along the western part of the island (Troodos massif). Even though detailed examination of many specimens could not retrieve any morphological differences among representatives of these two clades, clado-chronological analysis indicates a long isolation between them, estimated at ∼ 9 Mya, as well as the sharing of a common ancestor with S. tiberianum from Israel at ∼ 15 Mya. Hence, we can consider these epigean Schizidium species as one more case of cryptic diversity on Cyprus, exhibiting similar patterns with the recently described case in the genus Armadillo.
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Affiliation(s)
- Andreas C Dimitriou
- Department of Biological Sciences, University of Cyprus, Panepistimiou Ave. 1, 2109 Aglantzia, Nicosia, Cyprus.
| | | | - Anastasia Georgiou
- Department of Biological Sciences, University of Cyprus, Panepistimiou Ave. 1, 2109 Aglantzia, Nicosia, Cyprus
| | - Stefano Taiti
- Istituto di Ricerca sugli Ecosistemi Terrestri, Consiglio Nazionale delle Ricerche, Via Madonna del Piano 10, 50019 Sesto Fiorentino (Florence), Italy; Museo di Storia Naturale dell'Università di Firenze, Sezione di Zoologia "La Specola", Via Romana 17, 50125 Florence, Italy
| | - Spyros Sfenthourakis
- Department of Biological Sciences, University of Cyprus, Panepistimiou Ave. 1, 2109 Aglantzia, Nicosia, Cyprus
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80
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Wang Y, Wang C, Hong W, Tian S, Lu Q, Wang BJ, Jin H, Zhuoma N, Lu X, Zhao H. Genomic analysis of Tibetan ground tits identifies molecular adaptations associated with cooperative breeding. Curr Zool 2023; 69:620-630. [PMID: 37637321 PMCID: PMC10449426 DOI: 10.1093/cz/zoac067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/16/2022] [Indexed: 08/29/2023] Open
Abstract
Cooperative breeding is a sophisticated altruistic social behavior that helps social animals to adapt to harsh environments. The Tibetan ground tit, Pseudopodoces humilis, is a high-altitude bird endemic to the Tibetan plateau. Recently, it has become an exciting system for studying the evolution of facultative cooperative breeding. To test for molecular adaptations associated with cooperative breeding, we resequenced the whole genome of ground tits from 6 wild populations that display remarkable variation in the frequency of cooperative breeding. Population structure analyses showed that the 6 populations were divided into 4 lineages, which is congruent with the major geographical distribution of the sampling sites. Using genome-wide selective sweep analysis, we identified putative positively selected genes (PSGs) in groups of tits that displayed high and low cooperative breeding rates. The total number of PSGs varied from 146 to 722 in high cooperative breeding rate populations, and from 272 to 752 in low cooperative breeding rate populations. Functional enrichment analysis of these PSGs identified several significantly enriched ontologies related to oxytocin signaling, estrogen signaling, and insulin secretion. PSGs involved in these functional ontologies suggest that molecular adaptations in hormonal regulation may have played important roles in shaping the evolution of cooperative breeding in the ground tit. Taken together, our study provides candidate genes and functional ontologies involved in molecular adaptations associated with cooperative breeding in Tibetan ground tits, and calls for a better understanding of the genetic roles in the evolution of cooperative breeding.
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Affiliation(s)
- Yi Wang
- Department of Ecology, Tibetan Centre for Ecology and Conservation at Wuhan University—Tibet University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Chen Wang
- Department of Ecology, Tibetan Centre for Ecology and Conservation at Wuhan University—Tibet University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wei Hong
- Department of Ecology, Tibetan Centre for Ecology and Conservation at Wuhan University—Tibet University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Shilin Tian
- Department of Ecology, Tibetan Centre for Ecology and Conservation at Wuhan University—Tibet University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Qin Lu
- Department of Ecology, Tibetan Centre for Ecology and Conservation at Wuhan University—Tibet University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Bing-Jun Wang
- Department of Ecology, Tibetan Centre for Ecology and Conservation at Wuhan University—Tibet University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Huaiming Jin
- Research Center for Ecology, College of Science, Tibet University, Lhasa 850000, China
| | - Nima Zhuoma
- Research Center for Ecology, College of Science, Tibet University, Lhasa 850000, China
| | - Xin Lu
- Department of Ecology, Tibetan Centre for Ecology and Conservation at Wuhan University—Tibet University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Huabin Zhao
- Department of Ecology, Tibetan Centre for Ecology and Conservation at Wuhan University—Tibet University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Research Center for Ecology, College of Science, Tibet University, Lhasa 850000, China
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81
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Cervantes CR, Montes JR, Rosas U, Arias S. Phylogenetic discordance and integrative species delimitation in the Mammillaria haageana species complex (Cactaceae). Mol Phylogenet Evol 2023; 187:107891. [PMID: 37517507 DOI: 10.1016/j.ympev.2023.107891] [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: 04/24/2023] [Revised: 06/15/2023] [Accepted: 07/26/2023] [Indexed: 08/01/2023]
Abstract
Species complexes consist of very close phylogenetic relatives, where morphological similarities make it difficult to distinguish between them using traditional taxonomic methods. Here, we focused on the long-standing challenge of species delimitation in the Mammillaria haageana complex, a group that presents great morphological diversity that makes its taxonomy a puzzle. Our work integrates genomic, morphological, and ecological data to establish the taxonomic limits in the M. haageana complex, and we also studied the evolutionary relationships with the remainder of the M. ser. Supertextae species. Our genetic analyses, as well as morphological and ecological evidence, led us to propose that the M. haageana complex is made up of six distinct entities (M. acultzingensis, M. conspicua, M. haageana, M. lanigera, M. meissneri, and M. san-angelensis), mainly as a result of ecological speciation. A recent taxonomic proposal considered these taxa as a single species; therefore, we propose their recognition at the species level. Our results also show a high level of incomplete lineage sorting rather than reticulation, which is especially likely in recently diverged species such as those comprising M. ser. Supertextae. The species hypotheses proposed here may be useful in future extinction risk assessments and conservation strategies.
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Affiliation(s)
- Cristian R Cervantes
- Unidad de Síntesis en Sistemática y Evolución, Instituto de Biología, Circuito Exterior s.n., Ciudad Universitaria, Ciudad de México 04510, México; Posgrado en Ciencias Biológicas, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, México.
| | - José-Rubén Montes
- Posgrado en Ciencias Biológicas, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, México
| | - Ulises Rosas
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito Exterior, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, México
| | - Salvador Arias
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito Exterior, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, México
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82
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Lajmi A, Glinka F, Privman E. Optimizing ddRAD sequencing for population genomic studies with ddgRADer. Mol Ecol Resour 2023. [PMID: 37732396 DOI: 10.1111/1755-0998.13870] [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: 10/27/2022] [Revised: 08/04/2023] [Accepted: 08/31/2023] [Indexed: 09/22/2023]
Abstract
Double-digest Restriction-site Associated DNA sequencing (ddRADseq) is widely used to generate genomic data for non-model organisms in evolutionary and ecological studies. Along with affordable paired-end sequencing, this method makes population genomic analyses more accessible. However, multiple factors should be considered when designing a ddRADseq experiment, which can be challenging for new users. The generated data often suffer from substantial read overlaps and adaptor contamination, severely reducing sequencing efficiency and affecting data quality. Here, we analyse diverse datasets from the literature and carry out controlled experiments to understand the effects of enzyme choice and size selection on sequencing efficiency. The empirical data reveal that size selection is imprecise and has limited efficacy. In certain scenarios, a substantial proportion of short fragments pass below the lower size-selection cut-off resulting in low sequencing efficiency. However, enzyme choice can considerably mitigate inadvertent inclusion of these shorter fragments. A simple model based on these experiments is implemented to predict the number of genomic fragments generated after digestion and size selection, number of SNPs genotyped, number of samples that can be multiplexed and the expected sequencing efficiency. We developed ddgRADer - http://ddgrader.haifa.ac.il/ - a user-friendly webtool and incorporated these calculations to aid in ddRADseq experimental design while optimizing sequencing efficiency. This tool can also be used for single enzyme protocols such as Genotyping-by-Sequencing. Given user-defined study goals, ddgRADer recommends enzyme pairs and allows users to compare and choose enzymes and size-selection criteria. ddgRADer improves the accessibility and ease of designing ddRADseq experiments and increases the probability of success of the first population genomic study conducted in labs with no prior experience in genomics.
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Affiliation(s)
- Aparna Lajmi
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Felix Glinka
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Eyal Privman
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
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83
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Wessinger CA, Katzer AM, Hime PM, Rausher MD, Kelly JK, Hileman LC. A few essential genetic loci distinguish Penstemon species with flowers adapted to pollination by bees or hummingbirds. PLoS Biol 2023; 21:e3002294. [PMID: 37769035 PMCID: PMC10538765 DOI: 10.1371/journal.pbio.3002294] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 08/11/2023] [Indexed: 09/30/2023] Open
Abstract
In the formation of species, adaptation by natural selection generates distinct combinations of traits that function well together. The maintenance of adaptive trait combinations in the face of gene flow depends on the strength and nature of selection acting on the underlying genetic loci. Floral pollination syndromes exemplify the evolution of trait combinations adaptive for particular pollinators. The North American wildflower genus Penstemon displays remarkable floral syndrome convergence, with at least 20 separate lineages that have evolved from ancestral bee pollination syndrome (wide blue-purple flowers that present a landing platform for bees and small amounts of nectar) to hummingbird pollination syndrome (bright red narrowly tubular flowers offering copious nectar). Related taxa that differ in floral syndrome offer an attractive opportunity to examine the genomic basis of complex trait divergence. In this study, we characterized genomic divergence among 229 individuals from a Penstemon species complex that includes both bee and hummingbird floral syndromes. Field plants are easily classified into species based on phenotypic differences and hybrids displaying intermediate floral syndromes are rare. Despite unambiguous phenotypic differences, genome-wide differentiation between species is minimal. Hummingbird-adapted populations are more genetically similar to nearby bee-adapted populations than to geographically distant hummingbird-adapted populations, in terms of genome-wide dXY. However, a small number of genetic loci are strongly differentiated between species. These approximately 20 "species-diagnostic loci," which appear to have nearly fixed differences between pollination syndromes, are sprinkled throughout the genome in high recombination regions. Several map closely to previously established floral trait quantitative trait loci (QTLs). The striking difference between the diagnostic loci and the genome as whole suggests strong selection to maintain distinct combinations of traits, but with sufficient gene flow to homogenize the genomic background. A surprisingly small number of alleles confer phenotypic differences that form the basis of species identity in this species complex.
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Affiliation(s)
- Carolyn A. Wessinger
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
| | - Amanda M. Katzer
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Paul M. Hime
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, United States of America
| | - Mark D. Rausher
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - John K. Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Lena C. Hileman
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
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84
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Chen X, Cornille A, An N, Xing L, Ma J, Zhao C, Wang Y, Han M, Zhang D. The East Asian wild apples, Malus baccata (L.) Borkh and Malus hupehensis (Pamp.) Rehder., are additional contributors to the genomes of cultivated European and Chinese varieties. Mol Ecol 2023; 32:5125-5139. [PMID: 35510734 DOI: 10.1111/mec.16485] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 04/09/2022] [Accepted: 04/17/2022] [Indexed: 11/29/2022]
Abstract
The domestication process in long-lived plant perennials differs dramatically from that of annuals, with a huge amount of genetic exchange between crop and wild populations. Though apple is a major fruit crop grown worldwide, the contribution of wild apple species to the genetic makeup of the cultivated apple genome remains a topic of intense study. We used population genomics approaches to investigate the contributions of several wild apple species to European and Chinese rootstock and dessert genomes, with a focus on the extent of wild-crop gene flow. Population genetic structure inferences revealed that the East Asian wild apples, Malus baccata (L.) Borkh and M. hupehensis (Pamp.), form a single panmictic group, and that the European dessert and rootstock apples form a specific gene pool whereas the Chinese dessert and rootstock apples were a mixture of three wild gene pools, suggesting different evolutionary histories of European and Chinese apple varieties. Coalescent-based inferences and gene flow estimates indicated that M. baccata - M. hupehensis contributed to the genome of both European and Chinese cultivated apples through wild-to-crop introgressions, and not as an initial contributor as previously supposed. We also confirmed the contribution through wild-to-crop introgressions of Malus sylvestris Mill. to the cultivated apple genome. Apple tree domestication is therefore one example in woody perennials that involved gene flow from several wild species from multiple geographical areas. This study provides an example of a complex protracted process of domestication in long-lived plant perennials, and is a starting point for apple breeding programmes.
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Affiliation(s)
- Xilong Chen
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Gif-sur-Yvette, France
| | - Amandine Cornille
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Gif-sur-Yvette, France
| | - Na An
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Libo Xing
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Juanjuan Ma
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Caiping Zhao
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Yibin Wang
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Mingyu Han
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Dong Zhang
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
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85
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Holmes IA, Monagan IV, Westphal MF, Johnson PJ, Rabosky ARD. Parsing variance by marker type: Testing biogeographic hypotheses and differential contribution of historical processes to population structure in a desert lizard. Mol Ecol 2023; 32:4880-4897. [PMID: 37466017 PMCID: PMC10530499 DOI: 10.1111/mec.17076] [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: 10/10/2021] [Revised: 06/19/2023] [Accepted: 07/04/2023] [Indexed: 07/20/2023]
Abstract
A fundamental goal of population genetic studies is to identify historical biogeographic patterns and understand the processes that generate them. However, localized demographic events can skew population genetic inference. Assessing populations with multiple types of genetic markers, each with unique mutation rates and responses to changes in population size, can help to identify potentially confounding population-specific demographic processes. Here, we compared population structure and connectivity inferred from microsatellites and restriction site-associated DNA loci among 17 populations of an arid-specialist lizard, the desert night lizard, Xantusia vigilis, in central California to test among historical processes structuring population genetic diversity. We found that both marker types yielded generally concordant insights into population genetic structure including a major phylogenetic break maintained between two populations separated by less than 10 km, suggesting that either marker type could be used to understand generalized demographic patterns across the region for management purposes. However, we also found that the effects of demography on marker discordance could be used to elucidate population histories and distinguish among competing biogeographic hypotheses. Our results suggest that comparisons of within-population diversity across marker types provide powerful opportunities for leveraging marker discordance, particularly for understanding the creation and maintenance of contact zones among clades.
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Affiliation(s)
- Iris A. Holmes
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI USA
- Cornell Institute of Host Microbe Interactions and Disease and Department of Microbiology, Cornell University, Ithaca, NY 14853 USA
| | - Ivan V. Monagan
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI USA
- Department of Ecology, Evolution, and Environmental Biology, Columbia University and American Museum of Natural History, NY, USA
| | | | | | - Alison R. Davis Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI USA
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA USA
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86
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Méndez-Cea B, García-García I, Linares JC, Gallego FJ. Warming appears as the main risk of non-adaptedness for western Mediterranean relict fir forests under expected climate change scenarios. FRONTIERS IN PLANT SCIENCE 2023; 14:1155441. [PMID: 37636100 PMCID: PMC10451094 DOI: 10.3389/fpls.2023.1155441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 07/19/2023] [Indexed: 08/29/2023]
Abstract
Circum-Mediterranean firs are considered among the most drought-sensitive species to climate change. Understanding the genetic basis of trees' adaptive capacity and intra-specific variability to drought avoidance is mandatory to define conservation measures, thus potentially preventing their extinction. We focus here on Abies pinsapo and Abies marocana, both relict tree species, endemic from south Spain and north Morocco, respectively. A total of 607 samples were collected from eight nuclei: six from Spanish fir and two from Moroccan fir. A genotyping by sequencing technique called double digestion restriction site-associated DNA sequencing (ddRAD-seq) was performed to obtain a genetic matrix based on single-nucleotide polymorphisms (SNPs). This matrix was utilized to study the genetic structure of A. pinsapo populations and to carry out selection signature studies. In order to understand how Spanish fir and Moroccan fir cope with climate change, genotype-environment associations (GEAs) were identified. Further, the vulnerability of these species to climate variations was estimated by the risk of non-adaptedness (RONA). The filtering of the de novo assembly of A. pinsapo provided 3,982 SNPs from 504 out of 509 trees sequenced. Principal component analysis (PCA) genetically separated Grazalema from the rest of the Spanish populations. However, FST values showed significant differences among the sampling points. We found 51 loci potentially under selection. Homolog sequences were found for some proteins related to abiotic stress response, such as dehydration-responsive element binding transcription factor, regulation of abscisic acid signaling, and methylation pathway. A total of 15 associations with 11 different loci were observed in the GEA studies, with the maximum temperature of the warmest month being the variable with the highest number of associated loci. This temperature sensitivity was also supported by the risk of non-adaptedness, which yielded a higher risk for both A. pinsapo and A. marocana under the high emission scenario (Representative Concentration Pathway (RCP) 8.5). This study sheds light on the response to climate change of these two endemic species.
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Affiliation(s)
- Belén Méndez-Cea
- Dpto. Genética, Fisiología y Microbiología, Unidad Docente de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Isabel García-García
- Dpto. Genética, Fisiología y Microbiología, Unidad Docente de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Juan Carlos Linares
- Dpto. Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Sevilla, Spain
| | - Francisco Javier Gallego
- Dpto. Genética, Fisiología y Microbiología, Unidad Docente de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, Madrid, Spain
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87
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Ortiz D, Pekár S, Bilat J, Shafaie S, Alvarez N, Gauthier J. Dynamic evolution of size and colour in the highly specialized Zodarion ant-eating spiders. Proc Biol Sci 2023; 290:20230797. [PMID: 37554037 PMCID: PMC10410226 DOI: 10.1098/rspb.2023.0797] [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: 04/05/2023] [Accepted: 07/17/2023] [Indexed: 08/10/2023] Open
Abstract
Ecological specialists constitute relevant case studies for understanding the mechanisms, potential and limitations of evolution. The species-rich and strictly myrmecophagous spiders of the genus Zodarion show diversified defence mechanisms, including myrmecomorphy of different ant species and nocturnality. Through Hybridization Capture Using RAD Probes (hyRAD), a phylogenomic technique designed for sequencing poorly preserved specimens, we reconstructed a phylogeny of Zodarion using 52 (approx. a third of the nominal) species that cover its phylogenetic and distributional diversity. We then estimated the evolution of body size and colour, traits that have diversified noticeably and are linked to defence mechanisms, across the group. Our genomic matrix of 300 loci led to a well-supported phylogenetic hypothesis that uncovered two main clades inside Zodarion. Ancestral state estimation revealed the highly dynamic evolution of body size and colour across the group, with multiple transitions and convergences in both traits, which we propose is likely indicative of multiple transitions in ant specialization across the genus. Our study will allow the informed targeted selection of Zodarion taxa of special interest for research into the group's remarkable adaptations to ant specialization. It also exemplifies the utility of hyRAD for phylogenetic studies using museum material.
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Affiliation(s)
- David Ortiz
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Julia Bilat
- Geneva Natural History Museum, Geneva, Switzerland
| | - Sepideh Shafaie
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
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88
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Harigai W, Saito A, Zemmoto C, Karasawa S, Yokoi T, Nagano AJ, Suzuki H, Yamamoto M. History of the terrestrial isopod genus Ligidium in Japan based on phylogeographic analysis. BMC Ecol Evol 2023; 23:38. [PMID: 37550609 PMCID: PMC10405464 DOI: 10.1186/s12862-023-02144-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 07/26/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Phylogeographical approaches explain the genetic diversity of local organisms in the context of their geological and geographic environments. Thus, genetic diversity can be a proxy for geological history. Here we propose a genus of woodland isopod, Ligidium, as a marker of geological history in relation to orogeny and the Quaternary glacial cycle. RESULTS Mitochondrial analysis of 721 individuals from 97 sites across Japan revealed phylogenetic divergence between the northeastern and southwestern Japan arcs. It also showed repeated population expansions in northeastern Japan in response to Quaternary glacial and interglacial cycles. Genome-wide analysis of 83 selected individuals revealed multiple genetic nuclear clusters. The genomic groupings were consistent with the local geographic distribution, indicating that the Ligidium phylogeny reflects its regional history. CONCLUSION Ligidium DNA sequence analysis can provide insight into the geological, geographical, and paleoenvironmental history of the studied region.
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Affiliation(s)
- Wakana Harigai
- Graduate School of Environmental Science, Hokkaido University, Kita-Ku, Sapporo, 060-0810, Japan.
- Present address: Department of Child Development and Molecular Brain Science, United Graduate School of Child Development, Osaka University, Suita, 565-0871, Japan.
| | - Aya Saito
- Department of Earth and Planetary Sciences, Faculty of Science, Hokkaido University, Kita-Ku, Sapporo, 060-0810, Japan
| | - Chika Zemmoto
- Department of Earth and Planetary Sciences, Faculty of Science, Hokkaido University, Kita-Ku, Sapporo, 060-0810, Japan
| | - Shigenori Karasawa
- Faculty of Agriculture, Tottori University, 4-101, Koyama-Cho Minami, Tottori, 680-8553, Japan
| | - Touta Yokoi
- Faculty of Agriculture, Tottori University, 4-101, Koyama-Cho Minami, Tottori, 680-8553, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan
| | - Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University, Kita-Ku, Sapporo, 060-0810, Japan
- Faculty of Environmental Earth Science, Hokkaido University, Kita-Ku, Sapporo, 060-0810, Japan
| | - Masanobu Yamamoto
- Graduate School of Environmental Science, Hokkaido University, Kita-Ku, Sapporo, 060-0810, Japan
- Faculty of Environmental Earth Science, Hokkaido University, Kita-Ku, Sapporo, 060-0810, Japan
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89
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Sánchez KI, Diaz Huesa EG, Breitman MF, Avila LJ, Sites JW, Morando M. Complex Patterns of Diversification in the Gray Zone of Speciation: Model-Based Approaches Applied to Patagonian Liolaemid Lizards (Squamata: Liolaemus kingii clade). Syst Biol 2023; 72:739-752. [PMID: 37097104 DOI: 10.1093/sysbio/syad019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 03/28/2023] [Accepted: 04/11/2023] [Indexed: 04/26/2023] Open
Abstract
In this study we detangled the evolutionary history of the Patagonian lizard clade Liolaemus kingii, coupling dense geographic sampling and novel computational analytical approaches. We analyzed nuclear and mitochondrial data (restriction site-associated DNA sequencing and cytochrome b) to hypothesize and evaluate species limits, phylogenetic relationships, and demographic histories. We complemented these analyses with posterior predictive simulations to assess the fit of the genomic data to the multispecies coalescent model. We also employed a novel approach to time-calibrate a phylogenetic network. Our results show several instances of mito-nuclear discordance and consistent support for a reticulated history, supporting the view that the complex evolutionary history of the kingii clade is characterized by extensive gene flow and rapid diversification events. We discuss our findings in the contexts of the "gray zone" of speciation, phylogeographic patterns in the Patagonian region, and taxonomic outcomes. [Model adequacy; multispecies coalescent; multispecies network coalescent; phylogenomics; species delimitation.].
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Affiliation(s)
- Kevin I Sánchez
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Puerto Madryn, U9120ACD, Argentina
| | - Emilce G Diaz Huesa
- Instituto de Diversidad y Evolución Austral, Consejo Nacional de Investigaciones Científicas y Técnicas (IDEAus-CONICET), Puerto Madryn, U9120ACD, Argentina
| | - María F Breitman
- Department of Biology and Environmental Science, Auburn University at Montgomery, Montgomery, 36117, USA
| | - Luciano J Avila
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Puerto Madryn, U9120ACD, Argentina
| | - Jack W Sites
- Department of Biology, Austin Peay State University, Clarksville, 37044, USA
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Puerto Madryn, U9120ACD, Argentina
- Universidad Nacional de la Patagonia San Juan Bosco (UNPSJB), Puerto Madryn, U9120ACD, Argentina
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90
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Gallego-García N, Vargas-Ramírez M, Shaffer HB. The importance of cryptic diversity in the conservation of wide-ranging species: The red-footed tortoise Chelonoidis carbonarius in Colombia. Mol Ecol 2023; 32:4531-4545. [PMID: 37340598 DOI: 10.1111/mec.17052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 05/23/2023] [Accepted: 06/07/2023] [Indexed: 06/22/2023]
Abstract
Wide-ranging species are seldom considered conservation priorities, yet they have the potential to harbour genetically deeply differentiated units across environments or ecological barriers, including some that warrant taxonomic recognition. Documenting such cryptic genetic diversity is especially important for wide-ranging species that are in decline, as they may comprise a set of even more endangered lineages or species with small distributions. However, studies of wide-ranging species, particularly when they cross political borders, are extremely challenging. One approach to overcoming these challenges is to conduct detailed local analyses in combination with less detailed, range-wide studies. We used this approach with the red-footed tortoise (Chelonoidis carbonarius), a threatened species likely to contain cryptic diversity given its vast range and the distinctive ecoregions that it inhabits. Previous single-gene molecular studies indicated the presence of at least five lineages, two of which occur in different ecoregions separated by the Andes within Colombia. We used a comprehensive genomic analysis to test the hypothesis of cryptic diversity within the single jurisdiction of Colombia. We used a combination of restriction-site-associated DNA sequencing and environmental niche modelling to provide three independent lines of evidence that support the presence of important cryptic diversity that may deserve taxonomic recognition: allopatric reproductive isolation, local adaptation and ecological divergence. We also provide a fine-scale genetic map with the distribution of conservation units in Colombia. As we complete ongoing range-wide analyses and make taxonomic adjustments, we recommend that the two lineages in Colombia be treated as separate units for conservation purposes.
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Affiliation(s)
- Natalia Gallego-García
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, USA
| | - Mario Vargas-Ramírez
- Biodiversidad y Conservación Genética, Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, USA
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91
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Klimova A, Ruiz Mondragón KY, Aguirre-Planter E, Valiente A, Lira R, Eguiarte LE. Genomic analysis unveils reduced genetic variability but increased proportion of heterozygotic genotypes of the intensively managed mezcal agave, Agave angustifolia. AMERICAN JOURNAL OF BOTANY 2023; 110:e16216. [PMID: 37478873 DOI: 10.1002/ajb2.16216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 07/23/2023]
Abstract
PREMISE The central Oaxaca Basin has a century-long history of agave cultivation and is hypothesized to be the region of origin of other cultivated crops. Widely cultivated for mezcal production, the perennial crop known as "espadín" is putatively derived from wild Agave angustifolia. Nevertheless, little is known about its genetic relationship to the wild A. angustifolia or how the decades-long clonal propagation has affected its genetics. METHODS Using restriction-site-associated DNA sequencing and over 8000 single-nucleotide polymorphisms, we studied aspects of the population genomics of wild and cultivated A. angustifolia in Puebla and Oaxaca, Mexico. We assessed patterns of genetic diversity, inbreeding, distribution of genetic variation, and differentiation among and within wild populations and plantations. RESULTS Genetic differentiation between wild and cultivated plants was strong, and both gene pools harbored multiple unique alleles. Nevertheless, we found several cultivated individuals with high genetic affinity with wild samples. Higher heterozygosity was observed in the cultivated individuals, while in total, they harbored considerably fewer alleles and presented higher linkage disequilibrium compared to the wild plants. Independently of geographic distance among sampled plantations, the genetic relatedness of the cultivated plants was high, suggesting a common origin and prevalent role of clonal propagation. CONCLUSIONS The considerable heterozygosity found in espadín is contained within a network of highly related individuals, displaying high linkage disequilibrium generated by decades of clonal propagation and possibly by the accumulation of somatic mutations. Wild A. angustifolia, on the other hand, represents a significant genetic diversity reservoir that should be carefully studied and conserved.
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Affiliation(s)
- Anastasia Klimova
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Karen Y Ruiz Mondragón
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Erika Aguirre-Planter
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Alfonso Valiente
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Rafael Lira
- Laboratorio de Recursos Naturales, Unidad de Biotecnología y Prototipos (UBIPRO), Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Luis E Eguiarte
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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92
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Burbrink FT, Ruane S, Rabibisoa N, Raselimanana AP, Raxworthy CJ, Kuhn A. Speciation rates are unrelated to the formation of population structure in Malagasy gemsnakes. Ecol Evol 2023; 13:e10344. [PMID: 37529593 PMCID: PMC10375368 DOI: 10.1002/ece3.10344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 06/07/2023] [Accepted: 06/30/2023] [Indexed: 08/03/2023] Open
Abstract
Speciation rates vary substantially across the tree of life. These rates should be linked to the rate at which population structure forms if a continuum between micro and macroevolutionary patterns exists. Previous studies examining the link between speciation rates and the degree of population formation in clades have been shown to be either correlated or uncorrelated depending on the group, but no study has yet examined the relationship between speciation rates and population structure in a young group that is constrained spatially to a single-island system. We examine this correlation in 109 gemsnakes (Pseudoxyrhophiidae) endemic to Madagascar and originating in the early Miocene, which helps control for extinction variation across time and space. We find no relationship between rates of speciation and the formation rates of population structure over space in 33 species of gemsnakes. Rates of speciation show low variation, yet population structure varies widely across species, indicating that speciation rates and population structure are disconnected. We suspect this is largely due to the persistence of some lineages not susceptible to extinction. Importantly, we discuss how delimiting populations versus species may contribute to problems understanding the continuum between shallow and deep evolutionary processes.
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Affiliation(s)
- Frank T. Burbrink
- Department of HerpetologyAmerican Museum of Natural HistoryNew York CityNew YorkUSA
| | - Sara Ruane
- Life Sciences Section, Negaunee Integrative Research CenterField Museum of Natural HistoryChicagoIllinoisUSA
| | - Nirhy Rabibisoa
- Sciences de la Vie et de l'Environnement, Faculté des Sciences, de Technologies et de l'EnvironnementUniversité de MahajangaMahajangaMadagascar
| | - Achille P. Raselimanana
- Zoologie et Biodiversité Animale, Faculté des SciencesUniversité d'AntananarivoAntananarivoMadagascar
| | | | - Arianna Kuhn
- Department of HerpetologyAmerican Museum of Natural HistoryNew York CityNew YorkUSA
- Virginia Museum of Natural HistoryMartinsvilleVirginiaUSA
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93
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García-García I, Méndez-Cea B, González de Andrés E, Gazol A, Sánchez-Salguero R, Manso-Martínez D, Horreo JL, Camarero JJ, Linares JC, Gallego FJ. Climate and Soil Microsite Conditions Determine Local Adaptation in Declining Silver Fir Forests. PLANTS (BASEL, SWITZERLAND) 2023; 12:2607. [PMID: 37514222 PMCID: PMC10384727 DOI: 10.3390/plants12142607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/15/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023]
Abstract
Ongoing climatic change is threatening the survival of drought-sensitive tree species, such as silver fir (Abies alba). Drought-induced dieback had been previously explored in this conifer, although the role played by tree-level genetic diversity and its relationship with growth patterns and soil microsite conditions remained elusive. We used double digest restriction-site-associated DNA sequencing (ddRADseq) to describe different genetic characteristics of five silver fir forests in the Spanish Pyrenees, including declining and non-declining trees. Single nucleotide polymorphisms (SNPs) were used to investigate the relationships between genetics, dieback, intraspecific trait variation (functional dendrophenotypic traits and leaf traits), local bioclimatic conditions, and rhizosphere soil properties. While there were no noticeable genetic differences between declining and non-declining trees, genome-environment associations with selection signatures were abundant, suggesting a strong influence of climate, soil physicochemical properties, and soil microbial diversity on local adaptation. These results provide novel insights into how genetics and diverse environmental factors are interrelated and highlight the need to incorporate genetic data into silver fir forest dieback studies to gain a better understanding of local adaptation.
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Affiliation(s)
- Isabel García-García
- Departamento de Genética, Fisiología y Microbiología, Unidad de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Belén Méndez-Cea
- Departamento de Genética, Fisiología y Microbiología, Unidad de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | | | - Antonio Gazol
- Instituto Pirenaico de Ecología (IPE-CSIC), 50059 Zaragoza, Spain
| | - Raúl Sánchez-Salguero
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - David Manso-Martínez
- Departamento de Genética, Fisiología y Microbiología, Unidad de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Jose Luis Horreo
- Departamento de Genética, Fisiología y Microbiología, Unidad de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - J Julio Camarero
- Instituto Pirenaico de Ecología (IPE-CSIC), 50059 Zaragoza, Spain
| | - Juan Carlos Linares
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Francisco Javier Gallego
- Departamento de Genética, Fisiología y Microbiología, Unidad de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
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94
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Carscadden KA, Doak DF, Oldfather MF, Emery NC. Demographic responses of hybridizing cinquefoils to changing climate in the Colorado Rocky Mountains. Ecol Evol 2023; 13:e10097. [PMID: 37449020 PMCID: PMC10336340 DOI: 10.1002/ece3.10097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/27/2023] [Indexed: 07/18/2023] Open
Abstract
Hybridization between taxa generates new pools of genetic variation that can lead to different environmental responses and demographic trajectories over time than seen in parental lineages. The potential for hybrids to have novel environmental tolerances may be increasingly important in mountainous regions, which are rapidly warming and drying due to climate change. Demographic analysis makes it possible to quantify within- and among-species responses to variation in climate and to predict population growth rates as those conditions change. We estimated vital rates and population growth in 13 natural populations of two cinquefoil taxa (Potentilla hippiana and P. pulcherrima) and their hybrid across elevation gradients in the Southern Rockies. Using three consecutive years of environmental and demographic data, we compared the demographic responses of hybrid and parental taxa to environmental variation across space and time. All three taxa had lower predicted population growth rates under warm, dry conditions. However, the magnitude of these responses varied among taxa and populations. Hybrids had consistently lower predicted population growth rates than P. hippiana. In contrast, hybrid performance relative to P. pulcherrima varied with population and climate, with the hybrid maintaining relatively stable growth rates while populations of P. pulcherrima shrank under warm, dry conditions. Our findings demonstrate that hybrids in this system are neither intrinsically unfit nor universally more vigorous than parents, suggesting that the demographic consequences of hybridization are context-dependent. Our results also imply that shifts to warmer and drier conditions could have particularly negative repercussions for P. pulcherrima, which is currently the most abundant taxon in the study area, possibly as a legacy of more favorable historical climates. More broadly, the distributions of these long-lived taxa are lagging behind their demographic trajectories, such that the currently less common P. hippiana could become the most abundant of the Potentilla taxa as this region continues to warm and dry.
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Affiliation(s)
- Kelly A. Carscadden
- Department of Ecology and Evolutionary BiologyUniversity of Colorado BoulderBoulderColoradoUSA
| | - Daniel F. Doak
- Department of Environmental StudiesUniversity of Colorado BoulderBoulderColoradoUSA
| | - Meagan F. Oldfather
- Department of Ecology and Evolutionary BiologyUniversity of Colorado BoulderBoulderColoradoUSA
| | - Nancy C. Emery
- Department of Ecology and Evolutionary BiologyUniversity of Colorado BoulderBoulderColoradoUSA
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95
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Dong X, Zhang H, Zhu X, Wang K, Xue H, Ye Z, Zheng C, Bu W. Mitochondrial introgression and mito-nuclear discordance obscured the closely related species boundaries in Cletus Stål from China (Heteroptera: Coreidae). Mol Phylogenet Evol 2023; 184:107802. [PMID: 37221926 DOI: 10.1016/j.ympev.2023.107802] [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: 11/08/2022] [Revised: 04/07/2023] [Accepted: 04/18/2023] [Indexed: 05/25/2023]
Abstract
Accurate taxonomy and delimitation are of great importance for pest control strategies and management programs. Here, we focus on Cletus (Insecta: Hemiptera: Coreidae), which includes many crop pests. The species boundaries still conflict and only cytochrome c oxidase subunit I (COI) barcoding has been previously used for molecular studies. We generated new mitochondrial genome and nuclear genome-wide SNPs to explore the species boundaries of 46 Cletus samples from China using multiple species delimitation approaches. All results recovered a monophyly with high support, except for two closely related species in clade I - C. punctiger and C. graminis. Mitochondrial data demonstrated admixture in clade I, while genome-wide SNPs unambiguously identified two separate species, which were confirmed by morphological classification. Inconsistent nuclear and mitochondrial data indicated mito-nuclear discordance. Mitochondrial introgression is the most likely explanation, and more extensive sampling and more comprehensive data are needed to ascertain a pattern. Accurate species delimitation will shed light on species status; thus, an accurate taxonomy is of particular concern, as there is a pressing need to implement precise control of agricultural pests and to perform further research on diversification.
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Affiliation(s)
- Xue Dong
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Haiguang Zhang
- College of Life Science, Linyi University, Linyi 276000, China
| | - Xiuxiu Zhu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Kaibin Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Huaijun Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Chenguang Zheng
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
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96
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Su N, Hodel RG, Wang X, Wang JR, Xie SY, Gui CX, Zhang L, Chang ZY, Zhao L, Potter D, Wen J. Molecular phylogeny and inflorescence evolution of Prunus (Rosaceae) based on RAD-seq and genome skimming analyses. PLANT DIVERSITY 2023; 45:397-408. [PMID: 37601549 PMCID: PMC10435964 DOI: 10.1016/j.pld.2023.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 08/22/2023]
Abstract
Prunus is an economically important genus widely distributed in the temperate Northern Hemisphere. Previous studies on the genus using a variety of loci yielded conflicting phylogenetic hypotheses. Here, we generated nuclear reduced representation sequencing data and plastid genomes for 36 Prunus individuals and two outgroups. Both nuclear and plastome data recovered a well-resolved phylogeny. The species were divided into three main clades corresponding to their inflorescence types, - the racemose group, the solitary-flower group and the corymbose group - with the latter two sister to one another. Prunus was inferred to have diversified initially in the Late Cretaceous around 67.32 million years ago. The diversification of the three major clades began between the Paleocene and Miocene, suggesting that paleoclimatic events were an important driving force for Prunus diversification. Ancestral state reconstructions revealed that the most recent common ancestor of Prunus had racemose inflorescences, and the solitary-flower and corymb inflorescence types were derived by reduction of flower number and suppression of the rachis, respectively. We also tested the hybrid origin hypothesis of the racemose group proposed in previous studies. Prunus has undergone extensive hybridization events, although it is difficult to identify conclusively specific instances of hybridization when using SNP data, especially deep in the phylogeny. Our study provides well-resolved nuclear and plastid phylogenies of Prunus, reveals substantial cytonuclear discord at shallow scales, and sheds new light on inflorescence evolution in this economically important lineage.
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Affiliation(s)
- Na Su
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Richard G.J. Hodel
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Xi Wang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Jun-Ru Wang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Si-Yu Xie
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Chao-Xia Gui
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Ling Zhang
- College of Life Sciences, Tarim University, Alaer 843300, China
| | - Zhao-Yang Chang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Liang Zhao
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Daniel Potter
- Department of Plant Sciences, MS2, University of California, Davis, CA 95616, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA
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97
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Gijsbers JC, Englebert N, Prata KE, Pichon M, Dinesen Z, Brunner R, Eyal G, González-Zapata FL, Kahng SE, Latijnhouwers KRW, Muir P, Radice VZ, Sánchez JA, Vermeij MJA, Hoegh-Guldberg O, Jacobs SJ, Bongaerts P. Global phylogenomic assessment of Leptoseris and Agaricia reveals substantial undescribed diversity at mesophotic depths. BMC Biol 2023; 21:147. [PMID: 37365558 DOI: 10.1186/s12915-023-01630-1] [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: 09/22/2022] [Accepted: 05/23/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Mesophotic coral communities are increasingly gaining attention for the unique biological diversity they host, exemplified by the numerous mesophotic fish species that continue to be discovered. In contrast, many of the photosynthetic scleractinian corals observed at mesophotic depths are assumed to be depth-generalists, with very few species characterised as mesophotic-specialists. This presumed lack of a specialised community remains largely untested, as phylogenetic studies on corals have rarely included mesophotic samples and have long suffered from resolution issues associated with traditional sequence markers. RESULTS Here, we used reduced-representation genome sequencing to conduct a phylogenomic assessment of the two dominant mesophotic genera of plating corals in the Indo-Pacific and Western Atlantic, respectively, Leptoseris and Agaricia. While these genome-wide phylogenies broadly corroborated the morphological taxonomy, they also exposed deep divergences within the two genera and undescribed diversity across the current taxonomic species. Five of the eight focal species consisted of at least two sympatric and genetically distinct lineages, which were consistently detected across different methods. CONCLUSIONS The repeated observation of genetically divergent lineages associated with mesophotic depths highlights that there may be many more mesophotic-specialist coral species than currently acknowledged and that an urgent assessment of this largely unstudied biological diversity is warranted.
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Affiliation(s)
- J C Gijsbers
- California Academy of Sciences, San Francisco, CA, 94118, USA.
| | - N Englebert
- Global Change Institute, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - K E Prata
- California Academy of Sciences, San Francisco, CA, 94118, USA
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - M Pichon
- Biodiversity Section, Queensland Museum, Townsville, 4810, Australia
| | - Z Dinesen
- Centre for Biodiversity and Conservation Science, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - R Brunner
- Global Change Institute, The University of Queensland, St Lucia, QLD, 4072, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - G Eyal
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
- ARC Centre of Excellence for Coral Reef Studies, The University of Queensland, St Lucia, QLD, 4072, Australia
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002, Ramat Gan, Israel
| | - F L González-Zapata
- Laboratorio de Biología Molecular Marina (BIOMMAR), Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de Los Andes, 111711, Bogotá, Colombia
| | - S E Kahng
- Department of Oceanography, University of Hawaii at Manoa, 1000 Pope Road, Honolulu, HI, 96822, USA
| | - K R W Latijnhouwers
- CARMABI Foundation, Piscaderabaai Z/N, PO Box 2090, Willemstad, Curaçao
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 700, 1098 XH, Amsterdam, The Netherlands
| | - P Muir
- Global Change Institute, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - V Z Radice
- Global Change Institute, The University of Queensland, St Lucia, QLD, 4072, Australia
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, 23529, USA
| | - J A Sánchez
- Laboratorio de Biología Molecular Marina (BIOMMAR), Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de Los Andes, 111711, Bogotá, Colombia
| | - M J A Vermeij
- CARMABI Foundation, Piscaderabaai Z/N, PO Box 2090, Willemstad, Curaçao
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 700, 1098 XH, Amsterdam, The Netherlands
| | - O Hoegh-Guldberg
- Global Change Institute, The University of Queensland, St Lucia, QLD, 4072, Australia
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
- ARC Centre of Excellence for Coral Reef Studies, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - S J Jacobs
- California Academy of Sciences, San Francisco, CA, 94118, USA
| | - P Bongaerts
- California Academy of Sciences, San Francisco, CA, 94118, USA.
- Global Change Institute, The University of Queensland, St Lucia, QLD, 4072, Australia.
- CARMABI Foundation, Piscaderabaai Z/N, PO Box 2090, Willemstad, Curaçao.
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98
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Ren CQ, Zhang DQ, Liu XY, Zhang JQ. Genomic data provide a robust phylogeny backbone for Rhodiola L. (Crassulaceae) and reveal extensive reticulate evolution during its rapid radiation. Mol Phylogenet Evol 2023:107863. [PMID: 37329933 DOI: 10.1016/j.ympev.2023.107863] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/19/2023]
Abstract
The Tibetan Plateau and adjacent mountain regions (TP; including the Tibetan Plateau, Himalaya, Hengduan Mountains and Mountains of Central Asia) harbor great biodiversity, some lineages on which may have undergone rapid radiations. However, only a few studies have investigated the evolutionary pattern of such diversification in depth using genomic data. In this study, we reconstructed a robust phylogeny backbone of Rhodiola, a lineage that may have undergone rapid radiation in the TP, using Genotyping-by-sequencing data, and conducted a series of gene flow and diversification analyses. The concatenation and coalescent-based methods yield similar tree topologies, and five well-supported clades were revealed. Potential gene flow and introgression events were detected, both between species from different major clades and closely related species, suggesting pervasive hybridization and introgression. An initial rapid and later slowdown of the diversification rate was revealed, indicating niche filling. Molecular dating and correlation analyses showed that the uplift of TP and global cooling in the mid-Miocene might have played an important role in promoting the rapid radiation of Rhodiola. Our work demonstrates that gene flow and introgression might be an important contributor to rapid radiation possibly by quickly reassembling old genetic variation into new combinations.
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Affiliation(s)
- Chun-Qian Ren
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China; Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, Shaanxi Normal University, Xi'an 710119, China
| | - Dan-Qing Zhang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China; Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, Shaanxi Normal University, Xi'an 710119, China
| | - Xiao-Ying Liu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China; Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, Shaanxi Normal University, Xi'an 710119, China
| | - Jian-Qiang Zhang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China; Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, Shaanxi Normal University, Xi'an 710119, China.
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99
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Arantes ÍC, Vasconcellos MM, Smith ML, Garrick RC, Colli GR, Noonan BP. Species limits and diversification of the Dendropsophus rubicundulus subgroup (Anura, Hylidae) in Neotropical savannas. Mol Phylogenet Evol 2023:107843. [PMID: 37286064 DOI: 10.1016/j.ympev.2023.107843] [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: 05/23/2022] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/09/2023]
Abstract
Understanding the processes that generate and maintain biodiversity at and below the species level is a central goal of evolutionary biology. Here we explore the spatial and temporal drivers of diversification of the treefrog subgroup Dendropsophus rubicundulus, a subgroup of the D. microcephalus species group, over periods of pronounced geological and climatic changes in the Neotropical savannas that they inhabit. This subgroup currently comprises 11 recognized species distributed across the Brazilian and Bolivian savannas, but the taxonomy has been in a state of flux, necessitating reexamination. Using newly generated single nucleotide polymorphism (SNP) data from restriction-site associated DNA sequencing (RADseq) and mitochondrial 16S sequence data for ∼150 specimens, we inferred phylogenetic relationships, tested species limits using a model-based approach, and estimated divergence times to gain insights into the geographic and climatic events that affected the diversification of this subgroup. Our results recognized at least nine species: D. anataliasiasi, D. araguaya, D. cerradensis, D. elianeae, D. jimi, D. rubicundulus, D. tritaeniatus, D. rozenmani, and D. sanborni. Although we did not collect SNP data for the latter two species, they are likely distinct based on mitochondrial data. In addition, we found genetic structure within the widespread species D. rubicundulus, which comprises three allopatric lineages connected by gene flow upon secondary contact. We also found evidence of population structure and perhaps undescribed diversity in D. elianeae, which warrants further study. The D. rubicundulus subgroup is estimated to have originated in the Late Miocene (∼5.45 million years ago), with diversification continuing through the Pliocene and Early Pleistocene, followed by the most recent divergence of D. rubicundulus lineages in the Middle Pleistocene. The epeirogenic uplift followed by erosion and denudation of the central Brazilian plateau throughout the Pliocene and Pleistocene, in combination with the increasing frequency and amplitude of climatic fluctuations during the Pleistocene, was important for generating and structuring diversity at or below the species level in the D. rubicundulus subgroup.
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Affiliation(s)
- Ísis C Arantes
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA.
| | - Mariana M Vasconcellos
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 05508-090, Brazil
| | - Megan L Smith
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
| | - Ryan C Garrick
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, 70910-900 Brasília, Distrito Federal, Brazil
| | - Brice P Noonan
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA
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Cantley JT, Jordon-Thaden IE, Roche MD, Hayes D, Kate S, Martine CT. A Foundational Population Genetics Investigation of the Sexual Systems of Solanum (Solanaceae) in the Australian Monsoon Tropics Suggests Dioecious Taxa May Benefit from Increased Genetic Admixture via Obligate Outcrossing. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112200. [PMID: 37299179 DOI: 10.3390/plants12112200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/21/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023]
Abstract
Solanum section Leptostemonum is an ideal lineage to test the theoretical framework regarding proposed evolutionary benefits of outcrossing sexual systems in comparison to cosexuality. Theoretically, non-cosexual taxa should support more genetic diversity within populations, experience less inbreeding, and have less genetic structure due to a restricted ability to self-fertilize. However, many confounding factors present challenges for a confident inference that inherent differences in sexual systems influence observed genetic patterns among populations. This study provides a foundational baseline of the population genetics of several species of different sexual systems with the aim of generating hypotheses of any factor-including sexual system-that influences genetic patterns. Importantly, results indicate that dioecious S. asymmetriphyllum maintains less genetic structure and greater admixture among populations than cosexual S. raphiotes at the same three locations where they co-occur. This suggests that when certain conditions are met, the evolution of dioecy may have proceeded as a means to avoid genetic consequences of self-compatibility and may support hypotheses of benefits gained through differential resource allocation partitioned across sexes. Arguably, the most significant finding of this study is that all taxa are strongly inbred, possibly reflective of a shared response to recent climate shifts, such as the increased frequency and intensity of the region's fire regime.
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Affiliation(s)
- Jason T Cantley
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
- Biology Department, Bucknell University, Lewisburg, PA 17837, USA
| | - Ingrid E Jordon-Thaden
- Biology Department, Bucknell University, Lewisburg, PA 17837, USA
- Department of Botany, University of Wisconsin Madison, Madison, WI 53706, USA
| | - Morgan D Roche
- Biology Department, Bucknell University, Lewisburg, PA 17837, USA
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Daniel Hayes
- Biology Department, Bucknell University, Lewisburg, PA 17837, USA
| | - Stephanie Kate
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
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