51
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Schreiber D, Pfenninger M. Genomic divergence landscape in recurrently hybridizing Chironomus sister taxa suggests stable steady state between mutual gene flow and isolation. Evol Lett 2021; 5:86-100. [PMID: 33552538 PMCID: PMC7857304 DOI: 10.1002/evl3.204] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/11/2020] [Accepted: 10/19/2020] [Indexed: 12/30/2022] Open
Abstract
Divergence is mostly viewed as a progressive process often initiated by selection targeting individual loci, ultimately resulting in ever increasing genomic isolation due to linkage. However, recent studies show that this process may stall at intermediate stable equilibrium states without achieving complete genomic isolation. We tested the extent of genomic isolation between two recurrently hybridizing nonbiting midge sister taxa, Chironomus riparius and Chironomus piger, by analyzing the divergence landscape. Using a principal component-based method, we estimated that only about 28.44% of the genomes were mutually isolated, whereas the rest was still exchanged. The divergence landscape was fragmented into isolated regions of on average 30 kb, distributed throughout the genome. Selection and divergence time strongly influenced lengths of isolated regions, whereas local recombination rate only had minor impact. Comparison of divergence time distributions obtained from several coalescence-simulated divergence scenarios with the observed divergence time estimates in an approximate Bayesian computation framework favored a short and concluded divergence event in the past. Most divergence happened during a short time span about 4.5 million generations ago, followed by a stable equilibrium between mutual gene flow through ongoing hybridization for the larger part of the genome and isolation in some regions due to rapid purifying selection of introgression, supported by high effective population sizes and recombination rates.
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Affiliation(s)
- Dennis Schreiber
- Department of Molecular EcologySenckenberg Biodiversity and Climate Research CentreFrankfurt am Main60325Germany
- Institute for Molecular and Organismic EvolutionJohannes Gutenberg UniversityMainz55128Germany
| | - Markus Pfenninger
- Department of Molecular EcologySenckenberg Biodiversity and Climate Research CentreFrankfurt am Main60325Germany
- Institute for Molecular and Organismic EvolutionJohannes Gutenberg UniversityMainz55128Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am Main60325Germany
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52
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Lai WL, Chew J, Gatherer D, Ngoprasert D, Rahman S, Ayub Q, Kannan A, Vaughan E, Wong ST, Kulaimi NAM, Ratnayeke S. Mitochondrial DNA Profiling Reveals Two Lineages of Sun Bears in East and West Malaysia. J Hered 2021; 112:214-220. [PMID: 33439997 DOI: 10.1093/jhered/esab004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/12/2021] [Indexed: 11/13/2022] Open
Abstract
Sun bear populations are fragmented and at risk from habitat loss and exploitation for body parts. These threats are made worse by significant gaps in knowledge of sun bear population genetic diversity, population connectivity, and taxonomically significant management units. Using a complete sun bear mitochondrial genome, we developed a set of mitochondrial markers to assess haplotype variation and the evolutionary history of sun bears from Peninsular (West) Malaysia and Sabah (East Malaysia). Genetic samples from 28 sun bears from Peninsular Malaysia, 36 from Sabah, and 18 from Thailand were amplified with primers targeting a 1800 bp region of the mitochondrial genome including the complete mitochondrial control region and adjacent genes. Sequences were analyzed using phylogenetic methods. We identified 51 mitochondrial haplotypes among 82 sun bears. Phylogenetic and network analyses provided strong support for a deep split between Malaysian sun bears and sun bears in East Thailand and Yunnan province in China. The Malaysian lineage was further subdivided into two clades: Peninsular Malaysian and Malaysian Borneo (Sabah). Sun bears from Thailand occurred in both Sabah and Peninsular Malaysian clades. Our study supports recent findings that sun bears from Sundaland form a distinct clade from those in China and Indochina with Thailand possessing lineages from the three clades. Importantly, we demonstrate a more recent and clear genetic delineation between sun bears from the Malay Peninsula and Sabah indicating historical barriers to gene flow within the Sundaic region.
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Affiliation(s)
- Wai-Ling Lai
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Selangor Darul Ehsan, Malaysia
| | - Jactty Chew
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Selangor Darul Ehsan, Malaysia
| | - Derek Gatherer
- Division of Biomedical & Life Sciences, Faculty of Health & Medicine, Lancaster University, Lancaster, UK
| | - Dusit Ngoprasert
- Conservation Ecology Program, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Sadequr Rahman
- Monash University Malaysia Genomics Facility, School of Science, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan, Malaysia.,Tropical Medicine and Biology Multidisplinary Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Qasim Ayub
- Monash University Malaysia Genomics Facility, School of Science, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan, Malaysia.,Tropical Medicine and Biology Multidisplinary Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Adrian Kannan
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Selangor Darul Ehsan, Malaysia
| | - Eleanor Vaughan
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Selangor Darul Ehsan, Malaysia
| | - Siew Te Wong
- Bornean Sun Bear Conservation Centre, Sandakan, Sabah, Malaysia
| | - Noor Azleen Mohd Kulaimi
- and National Wildlife Forensic Laboratory (NWFL), Ex-situ Conservation Division, Department of Wildlife and National Parks (DWNP), Kuala Lumpur, Malaysia
| | - Shyamala Ratnayeke
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Selangor Darul Ehsan, Malaysia
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53
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Kong S, Kubatko LS. Comparative Performance of Popular Methods for Hybrid Detection using Genomic Data. Syst Biol 2021; 70:891-907. [PMID: 33404632 DOI: 10.1093/sysbio/syaa092] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 11/13/2020] [Indexed: 11/13/2022] Open
Abstract
Interspecific hybridization is an important evolutionary phenomenon that generates genetic variability in a population and fosters species diversity in nature. The availability of large genome scale datasets has revolutionized hybridization studies to shift from the observation of the presence or absence of hybrids to the investigation of the genomic constitution of hybrids and their genome-specific evolutionary dynamics. Although a handful of methods have been proposed in an attempt to identify hybrids, accurate detection of hybridization from genomic data remains a challenging task. In addition to methods that infer phylogenetic networks or that utilize pairwise divergence, site pattern frequency based and population genetic clustering approaches are popularly used in practice, though the performance of these methods under different hybridization scenarios has not been extensively examined. Here, we use simulated data to comparatively evaluate the performance of four tools that are commonly used to infer hybridization events: the site pattern frequency based methods HyDe and the D-statistic (i.e., the ABBA-BABA test) and the population clustering approaches structure and ADMIXTURE. We consider single hybridization scenarios that vary in the time of hybridization and the amount of incomplete lineage sorting (ILS) for different proportions of parental contributions (γ); introgressive hybridization; multiple hybridization scenarios; and a mixture of ancestral and recent hybridization scenarios. We focus on the statistical power to detect hybridization and the false discovery rate (FDR) for comparisons of the D-statistic and HyDe, and the accuracy of the estimates of γ as measured by the mean squared error for HyDe, structure, and ADMIXTURE. Both HyDe and the D-statistic are powerful for detecting hybridization in all scenarios except those with high ILS, although the D-statistic often has an unacceptably high FDR. The estimates of γ in HyDe are impressively robust and accurate whereas structure and ADMIXTURE sometimes fail to identify hybrids, particularly when the proportional parental contributions are asymmetric (i.e., when γ is close to 0). Moreover, the posterior distribution estimated using structure exhibits multimodality in many scenarios, making interpretation difficult. Our results provide guidance in selecting appropriate methods for identifying hybrid populations from genomic data.
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Affiliation(s)
- Sungsik Kong
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Laura S Kubatko
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA.,Department of Statistics, The Ohio State University, Columbus, OH, USA
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54
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Seifert B. The Gene and Gene Expression (GAGE) Species Concept: An Universal Approach for All Eukaryotic Organisms. Syst Biol 2021; 69:1033-1038. [PMID: 32298447 DOI: 10.1093/sysbio/syaa032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 03/20/2020] [Accepted: 04/07/2020] [Indexed: 12/31/2022] Open
Abstract
The Gene and Gene Expression (GAGE) species concept, a new version of the Pragmatic Species Concept of Seifert (2014), is proposed as a concept applicable to any described recent or fossil eukaryotic organism independent from its mode of reproduction or evolutionary history. In addition to presenting the concept as such, the article also provides practical recommendations for taxonomists when delimiting species and describing taxa. The wording of the new concept contains a heading core sentence plus five attached sentences addressing essential conditions for its translation into a sound taxonomic practice: "Species are separable clusters that have passed a threshold of evolutionary divergence and are exclusively defined by nuclear DNA sequences and/or their expression products. Nuclear DNA sequences and their expression products are different character systems but have a highly correlated indicative function. Character systems with the least risk of epigenetic or ontogenetic modification have superior indicative value when conflicts between character systems of integrative studies arise. All character systems have to be described by an adequate numerics allowing cluster formation and determination of thresholds. Thresholds for each character system should be fixed by consensus among the experts under the principle of avoiding oversplitting or lumping. Clusters must not be the expression of intraspecific polymorphism." Recognizing the distortions and conflicts caused to taxonomy through barcoding or through assessment on the basis of association with other organisms, the GAGE species concept strongly downgrades the use of cytoplasmic DNA of endosymbiotic origin (mtDNA, cpDNA) or DNA of closely associated microbes (e.g., Wolbachia bacteria) for final taxonomic decision-making. Recognizing the distortion of phylogenies by the high frequency of reticulate evolution, it is argued that delimiting and naming species has to be separated from constructing bifurcating phylogenetic trees. [Cytoplasmic DNA; lumping; nuclear DNA; numeric taxonomy; oversplitting; reticulate evolution.].
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Affiliation(s)
- Bernhard Seifert
- Department of Zoology, Senckenberg Museum of Natural History Görlitz, Am Museum 1, D-02826 Görlitz, Germany
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55
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Duchen P, Salamin N. A Cautionary Note on the Use of Genotype Callers in Phylogenomics. Syst Biol 2020; 70:844-854. [PMID: 33084875 PMCID: PMC8208803 DOI: 10.1093/sysbio/syaa081] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/02/2020] [Accepted: 10/02/2020] [Indexed: 12/13/2022] Open
Abstract
Next-generation-sequencing genotype callers are commonly used in studies to call variants from newly sequenced species. However, due to the current availability of genomic resources, it is still common practice to use only one reference genome for a given genus, or even one reference for an entire clade of a higher taxon. The problem with traditional genotype callers, such as the one from GATK, is that they are optimized for variant calling at the population level. However, when these callers are used at the phylogenetic level, the consequences for downstream analyses can be substantial. Here, we performed simulations to compare the performance between the genotype callers of GATK and ATLAS, and present their differences at various phylogenetic scales. We show that the genotype caller of GATK substantially underestimates the number of variants at the phylogenetic level, but not at the population level. We also found that the accuracy of heterozygote calls declines with increasing distance to the reference genome. We quantified this decline and found that it is very sharp in GATK, while ATLAS maintains high accuracy even at moderately divergent species from the reference. We further suggest that efforts should be taken towards acquiring more reference genomes per species, before pursuing high-scale phylogenomic studies. [ATLAS; efficiency of SNP calling; GATK; heterozygote calling; next-generation sequencing; reference genome; variant calling.]
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Affiliation(s)
- Pablo Duchen
- Department of Computational Biology, University of Lausanne, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, Quartier Sorge, 1015 Lausanne, Switzerland
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56
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Linck E, Freeman BG, Dumbacher JP. Speciation and gene flow across an elevational gradient in New Guinea kingfishers. J Evol Biol 2020; 33:1643-1652. [PMID: 32916016 DOI: 10.1111/jeb.13698] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/24/2020] [Accepted: 08/29/2020] [Indexed: 01/01/2023]
Abstract
Closely related species with parapatric elevational ranges are ubiquitous in tropical mountains worldwide. The gradient speciation hypothesis proposes that these series are the result of in situ ecological speciation driven by divergent selection across elevation. Direct tests of this scenario have been hampered by the difficulty inferring the geographic arrangement of populations at the time of divergence. In cichlids, sticklebacks and Timema stick insects, support for ecological speciation driven by other selective pressures has come from demonstrating parallel speciation, where divergence proceeds independently across replicated environmental gradients. Here, we take advantage of the unique geography of the island of New Guinea to test for parallel gradient speciation in replicated populations of Syma kingfishers that show extremely subtle differentiation across elevation and between historically isolated mountain ranges. We find that currently described high-elevation and low-elevation species have reciprocally monophyletic gene trees and form nuclear DNA clusters, rejecting this hypothesis. However, demographic modelling suggests selection has likely maintained species boundaries in the face of gene flow following secondary contact. We compile evidence from the published literature to show that although in situ gradient speciation in labile organisms such as birds appears rare, divergent selection and post-speciation gene flow may be an underappreciated force in the origin of elevational series and tropical beta diversity along mountain slopes.
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Affiliation(s)
- Ethan Linck
- Department of Biology & Burke Museum of Natural History & Culture, University of Washington, Seattle, WA, USA
| | - Benjamin G Freeman
- Beaty Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - John P Dumbacher
- Ornithology & Mammalogy, California Academy of Sciences, San Francisco, CA, USA
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57
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Chan KO, Hutter CR, Wood PL, Grismer LL, Das I, Brown RM. Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex. Mol Ecol 2020; 29:3970-3987. [PMID: 32808335 DOI: 10.1111/mec.15603] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 07/29/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023]
Abstract
Most new cryptic species are described using conventional tree- and distance-based species delimitation methods (SDMs), which rely on phylogenetic arrangements and measures of genetic divergence. However, although numerous factors such as population structure and gene flow are known to confound phylogenetic inference and species delimitation, the influence of these processes is not frequently evaluated. Using large numbers of exons, introns, and ultraconserved elements obtained using the FrogCap sequence-capture protocol, we compared conventional SDMs with more robust genomic analyses that assess population structure and gene flow to characterize species boundaries in a Southeast Asian frog complex (Pulchrana picturata). Our results showed that gene flow and introgression can produce phylogenetic patterns and levels of divergence that resemble distinct species (up to 10% divergence in mitochondrial DNA). Hybrid populations were inferred as independent (singleton) clades that were highly divergent from adjacent populations (7%-10%) and unusually similar (<3%) to allopatric populations. Such anomalous patterns are not uncommon in Southeast Asian amphibians, which brings into question whether the high levels of cryptic diversity observed in other amphibian groups reflect distinct cryptic species-or, instead, highly admixed and structured metapopulation lineages. Our results also provide an alternative explanation to the conundrum of divergent (sometimes nonsister) sympatric lineages-a pattern that has been celebrated as indicative of true cryptic speciation. Based on these findings, we recommend that species delimitation of continuously distributed "cryptic" groups should not rely solely on conventional SDMs, but should necessarily examine population structure and gene flow to avoid taxonomic inflation.
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Affiliation(s)
- Kin O Chan
- Lee Kong Chian National History Museum, Faculty of Science, National University of Singapore, Singapore
| | - Carl R Hutter
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.,Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Perry L Wood
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.,Department of Biological Sciences & Museum of Natural History, Auburn University, Auburn, AL, USA
| | - L L Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, Riverside, CA, USA
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
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58
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Ruiz-García M, Arias Vásquez JY, Restrepo H, Cáceres-Martínez CH, Shostell JM. The genetic structure of the spectacled bear (Tremarctos ornatus; Ursidae, Carnivora) in Colombia by means of mitochondrial and microsatellite markers. J Mammal 2020. [DOI: 10.1093/jmammal/gyaa082] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
AbstractThe spectacled bear (Ursidae: Tremarctos ornatus) is an emblematic umbrella species and one of the top carnivores in the Andean mountains. It is also listed as vulnerable by IUCN and as endangered by CITES. We analyzed the genetic structure of this species in nine geographical regions representing the three Andean Cordilleras in Colombia. We sequenced six mitochondrial genes in 115 spectacled bears; a subset of these specimens (n = 61) were genotyped at seven nuclear microsatellites. We addressed three objectives: 1) determine the genetic diversity and historical demographic changes of the spectacled bear in Colombia; 2) determine phylogeographic patterns of genetic divergence among spectacled bear populations in Colombia; and 3) estimate the levels of gene flow among different regions of Colombia. Our analyses show evidence of high mitochondrial genetic diversity in spectacled bears, both in Colombia as well as in each of the nine regions, most particularly Norte de Santander, Nariño, and Antioquia-Córdoba. In addition, we detected population expansion in Colombia that occurred around 24,000 years ago, followed by a population decrease during the last 7,000 years, and a sudden expansion in the last 300 years. Phylogenetic analyses showed few well-supported clades, with some haplotypes detected in all the departments and Colombian Andean Cordilleras, and other haplotypes restricted to certain geographical areas (Antioquia, Norte de Santander, Cundinamarca, and Nariño). We detected significant genetic heterogeneity among some departments and among the three Colombian Andean Cordilleras for both mitochondrial and nuclear genes. Nevertheless, the moderate levels of gene flow estimated from FST statistics suggest that geographical barriers have not been definitive obstacles to the dispersion of the spectacled bear throughout Colombia. Despite these gene flow estimates, significant spatial autocorrelation was detected for spectacled bear in Colombia, where two kinds of spatial patterns were discovered: genetic patches of 144 km of diameter, and isolation by distance among bears separated from 578 to 800 km. The two most northern spectacled bear populations of Colombia (Norte de Santander and Antioquia) also were the two most differentiated. Their distinctiveness may qualify them as distinct Management Units (MUs) in the context of conservation policies for the spectacled bear in Colombia.
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Affiliation(s)
- Manuel Ruiz-García
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá D.C., Colombia
| | - Jessica Yanina Arias Vásquez
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá D.C., Colombia
| | | | - Carlos Herney Cáceres-Martínez
- Grupo de Investigación en Ecología y Conservación de Fauna Silvestre, Universidad Nacional de Colombia, sede Medellín, Colombia
| | - Joseph Mark Shostell
- Math, Science and Technology Department, University of Minnesota Crookston, Crookston, MN, USA
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59
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Samaniego Castruita JA, Westbury MV, Lorenzen ED. Analyses of key genes involved in Arctic adaptation in polar bears suggest selection on both standing variation and de novo mutations played an important role. BMC Genomics 2020; 21:543. [PMID: 32758141 PMCID: PMC7430819 DOI: 10.1186/s12864-020-06940-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/22/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Polar bears are uniquely adapted to an Arctic existence. Since their relatively recent divergence from their closest living relative, brown bears, less than 500,000 years ago, the species has evolved an array of novel traits suited to its Arctic lifestyle. Previous studies sought to uncover the genomic underpinnings of these unique characteristics, and disclosed the genes showing the strongest signal of positive selection in the polar bear lineage. Here, we survey a comprehensive dataset of 109 polar bear and 33 brown bear genomes to investigate the genomic variants within these top genes present in each species. Specifically, we investigate whether fixed homozygous variants in polar bears derived from selection on standing variation in the ancestral gene pool or on de novo mutation in the polar bear lineage. RESULTS We find that a large number of sites fixed in polar bears are biallelic in brown bears, suggesting selection on standing variation. Moreover, we uncover sites in which polar bears are fixed for a derived allele while brown bears are fixed for the ancestral allele, which we suggest may be a signal of de novo mutation in the polar bear lineage. CONCLUSIONS Our findings suggest that, among other mechanisms, natural selection acting on changes in genes derived from a combination of variation already in the ancestral gene pool, and from de novo missense mutations in the polar bear lineage, may have enabled the rapid adaptation of polar bears to their new Arctic environment.
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60
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Taylor RS, Manseau M, Horn RL, Keobouasone S, Golding GB, Wilson PJ. The role of introgression and ecotypic parallelism in delineating intraspecific conservation units. Mol Ecol 2020; 29:2793-2809. [PMID: 32567754 PMCID: PMC7496186 DOI: 10.1111/mec.15522] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/04/2020] [Accepted: 06/15/2020] [Indexed: 01/03/2023]
Abstract
Parallel evolution can occur through selection on novel mutations, standing genetic variation or adaptive introgression. Uncovering parallelism and introgressed populations can complicate management of threatened species as parallelism may have influenced conservation unit designations and admixed populations are not generally considered under legislations. We examined high coverage whole-genome sequences of 30 caribou (Rangifer tarandus) from across North America and Greenland, representing divergent intraspecific lineages, to investigate parallelism and levels of introgression contributing to the formation of ecotypes. Caribou are split into four subspecies and 11 extant conservation units, known as designatable units (DUs), in Canada. Using genomes from all four subspecies and six DUs, we undertake demographic reconstruction and confirm two previously inferred instances of parallel evolution in the woodland subspecies and uncover an additional instance of parallelism of the eastern migratory ecotype. Detailed investigations reveal introgression in the woodland subspecies, with introgressed regions found spread throughout the genomes encompassing both neutral and functional sites. Our investigations using whole genomes highlight the difficulties in unequivocally demonstrating parallelism through adaptive introgression in nonmodel species with complex demographic histories, with standing variation and introgression both potentially involved. Additionally, the impact of parallelism and introgression on conservation policy for management units needs to be considered in general, and the caribou designations will need amending in light of our results. Uncovering and decoupling parallelism and differential patterns of introgression will become prevalent with the availability of comprehensive genomic data from nonmodel species, and we highlight the need to incorporate this into conservation unit designations.
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Affiliation(s)
| | - Micheline Manseau
- Biology DepartmentTrent UniversityPeterboroughONCanada
- Landscape Science and Technology DivisionEnvironment and Climate Change CanadaOttawaONCanada
| | - Rebekah L. Horn
- Biology DepartmentTrent UniversityPeterboroughONCanada
- Columbia River Inter‐Tribal Fish CommissionHagermanIDUSA
| | - Sonesinh Keobouasone
- Landscape Science and Technology DivisionEnvironment and Climate Change CanadaOttawaONCanada
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61
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Montgomery RA, Carr M, Booher CR, Pointer AM, Mitchell BM, Smith N, Calnan K, Montgomery GM, Ogada M, Kramer DB. Characteristics that make trophy hunting of giant pandas inconceivable. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2020; 34:915-924. [PMID: 31916271 PMCID: PMC7522670 DOI: 10.1111/cobi.13458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 12/10/2019] [Accepted: 01/01/2020] [Indexed: 06/10/2023]
Abstract
In November 1928, Theodore Jr. and Kermit Roosevelt led an expedition to China with the expressed purpose of being the first Westerners to kill the giant panda (Ailuropoda melanoleuca). The expedition lasted 8 months and resulted in the brothers shooting a giant panda in the mountains of Sichuan Province. Given the concurrent attention in the popular press describing this celebrated expedition, the giant panda was poised to be trophy hunted much like other large mammals around the world. Today, however, the killing of giant pandas, even for the generation of conservation revenue, is unthinkable for reasons related to the species itself and the context, in time and space, in which the species was popularized in the West. We found that the giant panda's status as a conservation symbol, exceptional charisma and gentle disposition, rarity, value as a nonconsumptive ecotourism attraction, and endemism are integral to the explanation of why the species is not trophy hunted. We compared these intrinsic and extrinsic characteristics with 20 of the most common trophy-hunted mammals to determine whether the principles applying to giant pandas are generalizable to other species. Although certain characteristics of the 20 trophy-hunted mammals aligned with the giant panda, many did not. Charisma, economic value, and endemism, in particular, were comparatively unique to the giant panda. Our analysis suggests that, at present, exceptional characteristics may be necessary for certain mammals to be excepted from trophy hunting. However, because discourse relating to the role of trophy hunting in supporting conservation outcomes is dynamic in both science and society, we suspect these valuations will also change in future.
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Affiliation(s)
- Robert A. Montgomery
- Department of Fisheries and WildlifeMichigan State University480 Wilson Road, 13 Natural Resources BuildingEast LansingMI48824U.S.A.
| | - Madeline Carr
- Department of Fisheries and WildlifeMichigan State University480 Wilson Road, 13 Natural Resources BuildingEast LansingMI48824U.S.A.
| | - Charlie R. Booher
- Department of Fisheries and WildlifeMichigan State University480 Wilson Road, 13 Natural Resources BuildingEast LansingMI48824U.S.A.
- College of Social SciencesMichigan State University509 E. Circle Drive, Berkey HallEast LansingMI48824U.S.A.
| | - Abigail M. Pointer
- Department of Fisheries and WildlifeMichigan State University480 Wilson Road, 13 Natural Resources BuildingEast LansingMI48824U.S.A.
| | - Brendan M. Mitchell
- Department of Fisheries and WildlifeMichigan State University480 Wilson Road, 13 Natural Resources BuildingEast LansingMI48824U.S.A.
| | - Natalie Smith
- James Madison CollegeMichigan State University842 Chestnut Rd Room S369LEast LansingMI48825U.S.A.
| | - Keegan Calnan
- Department of Fisheries and WildlifeMichigan State University480 Wilson Road, 13 Natural Resources BuildingEast LansingMI48824U.S.A.
| | - Georgina M. Montgomery
- Lyman Briggs CollegeMichigan State University919 E Shaw LnEast LansingMI48825U.S.A.
- Department of HistoryMichigan State University506 E. Circle DrEast LansingMI48824U.S.A.
| | - Mordecai Ogada
- Department of HistoryMichigan State University506 E. Circle DrEast LansingMI48824U.S.A.
- Conservation Solutions AfrikaMuthaiga Estate P.O. Box 880–10400NanyukiKenya
| | - Daniel B. Kramer
- Department of Fisheries and WildlifeMichigan State University480 Wilson Road, 13 Natural Resources BuildingEast LansingMI48824U.S.A.
- James Madison CollegeMichigan State University842 Chestnut Rd Room S369LEast LansingMI48825U.S.A.
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62
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Love Stowell SM, Gagne RB, McWhirter D, Edwards W, Ernest HB. Bighorn Sheep Genetic Structure in Wyoming Reflects Geography and Management. J Wildl Manage 2020. [DOI: 10.1002/jwmg.21882] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Sierra M. Love Stowell
- Wildlife Genomics & Disease Ecology Lab, Department of Veterinary SciencesUniversity of Wyoming 1174 Snowy Range Rd Laramie WY 82070 USA
| | - Roderick B. Gagne
- Wildlife Genomics & Disease Ecology Lab, Department of Veterinary SciencesUniversity of Wyoming 1174 Snowy Range Rd Laramie WY 82070 USA
| | - Doug McWhirter
- Wyoming Game and Fish DepartmentJackson Regional Office 420 N Cache St Jackson WY 830001 USA
| | - William Edwards
- Wyoming Game and Fish DepartmentWildlife Health Laboratory 1174 Snowy Range Rd Laramie WY 82070 USA
| | - Holly B. Ernest
- Wildlife Genomics & Disease Ecology Lab, Department of Veterinary SciencesUniversity of Wyoming 1174 Snowy Range Rd Laramie WY 82070 USA
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63
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Marin J, Achaz G, Crombach A, Lambert A. The genomic view of diversification. J Evol Biol 2020; 33:1387-1404. [PMID: 32654283 DOI: 10.1111/jeb.13677] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 05/11/2020] [Accepted: 06/17/2020] [Indexed: 11/29/2022]
Abstract
The process of species diversification is traditionally summarized by a single tree, the species tree, whose reconstruction from molecular data is hindered by frequent conflicts between gene genealogies. Here, we argue that instead of seeing these conflicts as nuisances, we can exploit them to inform the diversification process itself. We adopt a gene-based view of diversification to model the ubiquitous presence of gene flow between diverging lineages, one of the most important processes explaining disagreements among gene trees. We propose a new framework for modelling the joint evolution of gene and species lineages relaxing the hierarchy between the species tree and gene trees inherent to the standard view, as embodied in a popular model known as the multispecies coalescent (MSC). We implement this framework in two alternative models called the gene-based diversification models (GBD): (a) GBD-forward following all evolving genomes through time and (b) GBD-backward based on coalescent theory. They feature four parameters tuning colonization, gene flow, genetic drift and genetic differentiation. We propose an inference method based on differences between gene trees. Applied to two empirical data sets prone to gene flow, we find better support for the GBD-backward model than for the MSC model. Along with the increasing awareness of the extent of gene flow, this work shows the importance of considering the richer signal contained in genomic histories, rather than in the mere species tree, to better apprehend the complex evolutionary history of species.
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Affiliation(s)
- Julie Marin
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, PSL Research University, Paris, France
| | - Guillaume Achaz
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, PSL Research University, Paris, France.,Institut de Systématique, Évolution, Biodiversité (ISYEB), MNHN, CNRS, EPHE, Sorbonne Université, Paris, France.,UMR 7206 Eco-anthropologie, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Université de Paris, Paris, France
| | - Anton Crombach
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, PSL Research University, Paris, France.,Inria, Lyon Antenne La Doua, Villeurbanne, France.,INSA-Lyon, LIRIS, UMR 5205, Université de Lyon, Villeurbanne, France
| | - Amaury Lambert
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, PSL Research University, Paris, France.,Laboratoire de Probabilités, Statistique et Modélisation (LPSM), CNRS UMR 8001, Sorbonne Université, Paris, France
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64
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Jiangzuo Q, Flynn JJ. The Earliest Ursine Bear Demonstrates the Origin of Plant-Dominated Omnivory in Carnivora. iScience 2020; 23:101235. [PMID: 32559731 PMCID: PMC7303987 DOI: 10.1016/j.isci.2020.101235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 04/26/2020] [Accepted: 05/29/2020] [Indexed: 11/26/2022] Open
Abstract
In Carnivora, increases in body size often lead to dietary specialization toward hypercarnivory. Ursine bears (Tremarctos and Ursus), however, are the only omnivorous Carnivora that evolved large body sizes (i.e., >50 kg). Traits contributing to their gigantism, and how those traits evolved, have never been studied. Here we propose that special dental characters of Ursinae (parallel buccal and lingual ridges) permit a sagittally oriented mastication associated with increasing emphasis on plant foods. This pattern can be traced back to a new early diverging bear of plant-dominated omnivorous diet, Aurorarctos tirawa gen. et sp. nov. from the late Middle Miocene of North America, which was supported as the earliest known ursine bear by phylogenetic analysis. The anatomical transition to increased masticatory efficiency, probably together with the ability to hibernate, helped bears break prior ecological limitations on body size and led to the evolution of a distinctive lineage of herbivorous-omnivorous, large-bodied Carnivora.
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Affiliation(s)
- Qigao Jiangzuo
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China; Division of Paleontology, American Museum of Natural History, New York 10024, USA.
| | - John J Flynn
- Division of Paleontology, American Museum of Natural History, New York 10024, USA
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65
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Korniienko Y, Nguyen L, Baumgartner S, Vater M, Tiedemann R, Kirschbaum F. Intragenus F1-hybrids of African weakly electric fish (Mormyridae: Campylomormyrus tamandua ♂ × C. compressirostris ♀) are fertile. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2020; 206:571-585. [PMID: 32468077 PMCID: PMC8520511 DOI: 10.1007/s00359-020-01425-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 05/01/2020] [Accepted: 05/16/2020] [Indexed: 11/25/2022]
Abstract
Hybridization is widespread in fish and constitutes an important mechanism in fish speciation. There is, however, little knowledge about hybridization in mormyrids. F1-interspecies hybrids between Campylomormyrus tamandua ♂ × C. compressirostris ♀ were investigated concerning: (1) fertility; (2) survival of F2-fish and (3) new gene combinations in the F2-generation concerning the structure of the electric organ and features of the electric organ discharge. These F1-hybrids achieved sexual maturity at about 12–13.5 cm total length. A breeding group comprising six males and 13 females spawned 28 times naturally proving these F1-fish to be fertile. On average 228 eggs were spawned, the average fertilization rate was 47.8%. Eggs started to hatch 70–72 h after fertilization, average hatching rate was 95.6%. Average mortality rate during embryonic development amounted to 2.3%. Average malformation rate during the free embryonic stage was 27.7%. Exogenous feeding started on day 11. In total, we raised 353 normally developed larvae all of which died consecutively, the oldest specimen reaching an age of 5 months. During survival, the activities of the larval and adult electric organs were recorded and the structure of the adult electric organ was investigated histologically.
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Affiliation(s)
- Yevheniia Korniienko
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Unit of Biology and Ecology of Fishes, Humboldt University of Berlin, Philippstr. 13, Haus 16, 10115, Berlin, Germany
| | - Linh Nguyen
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Unit of Biology and Ecology of Fishes, Humboldt University of Berlin, Philippstr. 13, Haus 16, 10115, Berlin, Germany
- Institute of Biochemistry and Biology, Unit of Evolutionary Biology/Systematic Zoology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Haus 26, 14476, Potsdam, Germany
| | - Stephanie Baumgartner
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Unit of Biology and Ecology of Fishes, Humboldt University of Berlin, Philippstr. 13, Haus 16, 10115, Berlin, Germany
| | - Marianne Vater
- Institute of Biochemistry and Biology, Unit of General Zoology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Haus 26, 14476, Potsdam, Germany
| | - Ralph Tiedemann
- Institute of Biochemistry and Biology, Unit of Evolutionary Biology/Systematic Zoology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Haus 26, 14476, Potsdam, Germany
| | - Frank Kirschbaum
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Unit of Biology and Ecology of Fishes, Humboldt University of Berlin, Philippstr. 13, Haus 16, 10115, Berlin, Germany.
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66
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Ruiz-García M, Castellanos A, Arias-Vásquez JY, Shostell JM. Genetics of the Andean bear ( Tremarctos ornatus; Ursidae, Carnivora) in Ecuador: when the Andean Cordilleras are not an Obstacle. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:190-208. [PMID: 32468901 DOI: 10.1080/24701394.2020.1769088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
One of the top carnivores in the Andean mountains is the Andean bear (Tremarctos ornatus, Ursidae), the only bear in South America. This is a flagship and key umbrella species in Ecuador because its conservation has a positive impact on the conservation of many other species in the Andes. But to preserve, first one must know the genetic characteristics of a species, among other things. For this, we analyzed six mitochondrial genes and seven nuclear DNA microsatellites of 108 Andean bear specimens sampled throughout Ecuador. We adopted three strategies for analyzing the data: by Province, by Region (north vs south), and by Cordillera. Four main results were obtained. First, the mitochondrial genetic diversity levels were elevated, but there were no differences in genetic diversity by Province or by Cordillera. By Regions, southern Ecuador had higher genetic diversity levels than to northern Ecuador. The genetic diversity for the microsatellites was only medium for the Andean bear at this country. Second, there was clear and significant evidence of female population expansions, for the overall sample, by Province, Region, and Cordillera. This population expansion was determined to have occurred in the time interval of 30,000-20,000 years ago (YA), during the last phase of the Pleistocene. We detected a population decrease to have occurred more recently, within the last 5000 years. It continued until about 300-200 YA when a population increase was again detected. Third, there were, practically, no phylogeographic pattern nor genetic differentiation among Andean bear populations in Ecuador by Province or by Cordillera for either mitochondrial or microsatellite markers. There was a little more genetic differentiation between northern and southern areas. Fourth, there was no trace of significant spatial genetic structure for the Andean bear in Ecuador in agreement with the genetic differentiation analyses. This shows that the Andean Cordilleras in this country did not present an obstacle to the dispersion of this species. Therefore, all of the Andean bear specimens in Ecuador should be treated as a unique Management Unit (MU) for conservation purposes, differently to that determined for other countries as Colombia.
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Affiliation(s)
- Manuel Ruiz-García
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia.,Instituto Nacional de Biodiversidad (INABIO), Quito, Ecuador
| | - Armando Castellanos
- Instituto Nacional de Biodiversidad (INABIO), Quito, Ecuador.,Andean Bear Foundation, Quito, Ecuador
| | - Jessica Yanina Arias-Vásquez
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Joseph Mark Shostell
- Math, Science and Technology Department, University of Minnesota Crookston, Crookston, MN, USA
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67
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Zhu C, Xu W, Li J, Liu C, Hu M, Yuan Y, Yuan K, Zhang Y, Song X, Han J, Cui X. Draft Genome Assembly for the Tibetan Black Bear ( Ursus thibetanus thibetanus). Front Genet 2020; 11:231. [PMID: 32300354 PMCID: PMC7142260 DOI: 10.3389/fgene.2020.00231] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/26/2020] [Indexed: 12/17/2022] Open
Affiliation(s)
- Chenglong Zhu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Wenjie Xu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Jianchuan Li
- Department of Animal Resources, Tibet Plateau Institute of Biology, Lhasa, China
| | - Chang Liu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Mingliang Hu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yuan Yuan
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Ke Yuan
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yijiuling Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Xingzhi Song
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Jin Han
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Xinxin Cui
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
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68
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Jiao X, Flouri T, Rannala B, Yang Z. The Impact of Cross-Species Gene Flow on Species Tree Estimation. Syst Biol 2020; 69:830-847. [DOI: 10.1093/sysbio/syaa001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 11/12/2019] [Accepted: 01/15/2020] [Indexed: 12/26/2022] Open
Abstract
Abstract
Recent analyses of genomic sequence data suggest cross-species gene flow is common in both plants and animals, posing challenges to species tree estimation. We examine the levels of gene flow needed to mislead species tree estimation with three species and either episodic introgressive hybridization or continuous migration between an outgroup and one ingroup species. Several species tree estimation methods are examined, including the majority-vote method based on the most common gene tree topology (with either the true or reconstructed gene trees used), the UPGMA method based on the average sequence distances (or average coalescent times) between species, and the full-likelihood method based on multilocus sequence data. Our results suggest that the majority-vote method based on gene tree topologies is more robust to gene flow than the UPGMA method based on coalescent times and both are more robust than likelihood assuming a multispecies coalescent (MSC) model with no cross-species gene flow. Comparison of the continuous migration model with the episodic introgression model suggests that a small amount of gene flow per generation can cause drastic changes to the genetic history of the species and mislead species tree methods, especially if the species diverged through radiative speciation events. Estimates of parameters under the MSC with gene flow suggest that African mosquito species in the Anopheles gambiae species complex constitute such an example of extreme impact of gene flow on species phylogeny. [IM; introgression; migration; MSci; multispecies coalescent; species tree.]
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Affiliation(s)
- Xiyun Jiao
- Department of Genetics, University College London, Gower Street, London WC1E 6BT, UK
| | - Tomáš Flouri
- Department of Genetics, University College London, Gower Street, London WC1E 6BT, UK
| | - Bruce Rannala
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Ziheng Yang
- Department of Genetics, University College London, Gower Street, London WC1E 6BT, UK
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69
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Duckett DJ, Pelletier TA, Carstens BC. Identifying model violations under the multispecies coalescent model using P2C2M.SNAPP. PeerJ 2020; 8:e8271. [PMID: 31949994 PMCID: PMC6956792 DOI: 10.7717/peerj.8271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 11/22/2019] [Indexed: 11/20/2022] Open
Abstract
Phylogenetic estimation under the multispecies coalescent model (MSCM) assumes all incongruence among loci is caused by incomplete lineage sorting. Therefore, applying the MSCM to datasets that contain incongruence that is caused by other processes, such as gene flow, can lead to biased phylogeny estimates. To identify possible bias when using the MSCM, we present P2C2M.SNAPP. P2C2M.SNAPP is an R package that identifies model violations using posterior predictive simulation. P2C2M.SNAPP uses the posterior distribution of species trees output by the software package SNAPP to simulate posterior predictive datasets under the MSCM, and then uses summary statistics to compare either the empirical data or the posterior distribution to the posterior predictive distribution to identify model violations. In simulation testing, P2C2M.SNAPP correctly classified up to 83% of datasets (depending on the summary statistic used) as to whether or not they violated the MSCM model. P2C2M.SNAPP represents a user-friendly way for researchers to perform posterior predictive model checks when using the popular SNAPP phylogenetic estimation program. It is freely available as an R package, along with additional program details and tutorials.
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Affiliation(s)
- Drew J Duckett
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | | | - Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
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70
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Battey CJ. Evidence of linked selection on the Z chromosome of hybridizing hummingbirds. Evolution 2020; 74:725-739. [PMID: 31859363 DOI: 10.1111/evo.13888] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 10/01/2019] [Accepted: 11/12/2019] [Indexed: 12/25/2022]
Abstract
Levels of genetic differentiation vary widely along the genomes of recently diverged species. What processes cause this variation? Here, I analyze geographic population structure and genome-wide patterns of variation in the Rufous, Allen's, and Calliope Hummingbirds (Selasphorus rufus/Selasphorus sasin/Selasphorus calliope) and assess evidence that linked selection on the Z chromosome drives patterns of genetic differentiation in a pair of hybridizing species. Demographic models, introgression tests, and genotype clustering analyses support a reticulate evolutionary history consistent with divergence during the late Pleistocene followed by gene flow across migrant Rufous and Allen's Hummingbirds during the Holocene. Relative genetic differentiation ( F s t ) is elevated, and within-population diversity (π) is depressed on the Z chromosome in all interspecific comparisons. The ratio of Z to autosomal within-population diversity is much lower than that expected from population size effects alone, and Tajima's D is depressed on the Z chromosome in S. rufus and S. calliope. These results suggest that conserved structural features of the genome play a prominent role in shaping genetic differentiation through the early stages of speciation in northern Selasphorus hummingbirds, and that the Z chromosome is a likely site of genes underlying behavioral and morphological variation in the group.
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Affiliation(s)
- Christopher J Battey
- Department of Biology, University of Washington, Seattle, Washington, 97403-1201.,Current Address: Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403
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71
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Barlow A, Hartmann S, Gonzalez J, Hofreiter M, Paijmans JLA. Consensify: A Method for Generating Pseudohaploid Genome Sequences from Palaeogenomic Datasets with Reduced Error Rates. Genes (Basel) 2020; 11:E50. [PMID: 31906474 PMCID: PMC7017230 DOI: 10.3390/genes11010050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/24/2019] [Accepted: 12/27/2019] [Indexed: 11/16/2022] Open
Abstract
A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.
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72
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Admixture in Mammals and How to Understand Its Functional Implications. Bioessays 2019; 41:e1900123. [DOI: 10.1002/bies.201900123] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/03/2019] [Indexed: 12/13/2022]
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73
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Sienkiewicz T, Sergiel A, Huber D, Maślak R, Wrzosek M, Podgórski P, Reljić S, Paśko Ł. The Brain Anatomy of the Brown Bear (Carnivora, Ursus arctos L., 1758) Compared to That of Other Carnivorans: A Cross-Sectional Study Using MRI. Front Neuroanat 2019; 13:79. [PMID: 31555102 PMCID: PMC6727829 DOI: 10.3389/fnana.2019.00079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 07/18/2019] [Indexed: 11/13/2022] Open
Abstract
In this study, we aimed to provide a neuroanatomy atlas derived from cross-sectional and magnetic resonance imaging (MRI) of the encephalon of the brown bear (Ursus arctos). A postmortem brain analysis using magnetic resonance imaging (MRI - 1,5T; a high-resolution submillimeter three-dimensional T1-3D FFE) and cross-sectional macroscopic anatomy methods revealed major embryological and anatomical subdivisions of the encephalon, including the ventricular system. Most of the internal structures were comparably identifiable in both methods. The tractus olfactorius medialis, corpus subthalamicum, brachium colliculi rostralis, fasciculus longitudinalis medialis, nuclei vestibulares, velum medullare rostrale, nucleus fastigii, fasciculi cuneatus et gracilis were identified entirely by cross-sectional macroscopic analysis. However, the glandula pinealis, lemniscus lateralis and nuclei rhaphe were visualized only with MRI. Gross neuroanatomic analysis provided information about sulci and gyri of the cerebral hemispheres, components of the vermis and cerebellar hemispheres, and relative size and morphology of constituents of the rhinencephalon and cerebellum constituents. Similarities and discrepancies in identification of structures provided by both methods, as well as hallmarks of the structures facilitating identification using these methods are discussed. Finally, we compare the brown bear encephalon with other carnivores and discuss most of the identified structures compared to those of the domestic dog, the domestic cat, Ursidae and Mustelidae families and Pinnipedia clade.
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Affiliation(s)
- Tomasz Sienkiewicz
- Department of Evolutionary Biology and Conservation of Vertebrates, Institute of Environmental Biology, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | - Agnieszka Sergiel
- Department of Wildlife Conservation, Institute of Nature Conservation, Polish Academy of Sciences, Krakow, Poland
| | - Djuro Huber
- Department of Biology, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Robert Maślak
- Department of Evolutionary Biology and Conservation of Vertebrates, Institute of Environmental Biology, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | - Marcin Wrzosek
- Department of Internal Medicine and Clinic of Diseases for Horses, Dogs and Cats, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Przemysław Podgórski
- Department of General Radiology, Interventional Radiology and Neuroradiology, Faculty of Postgraduate Medical Training, Wrocław Medical University, Wrocław, Poland
| | - Slaven Reljić
- Department of Biology, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Łukasz Paśko
- Department of Evolutionary Biology and Conservation of Vertebrates, Institute of Environmental Biology, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
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74
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Tumendemberel O, Zedrosser A, Proctor MF, Reynolds HV, Adams JR, Sullivan JM, Jacobs SJ, Khorloojav T, Tserenbataa T, Batmunkh M, Swenson JE, Waits LP. Phylogeography, genetic diversity, and connectivity of brown bear populations in Central Asia. PLoS One 2019; 14:e0220746. [PMID: 31408475 PMCID: PMC6692007 DOI: 10.1371/journal.pone.0220746] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/22/2019] [Indexed: 11/28/2022] Open
Abstract
Knowledge of genetic diversity and population structure is critical for conservation and management planning at the population level within a species' range. Many brown bear populations in Central Asia are small and geographically isolated, yet their phylogeographic relationships, genetic diversity, and contemporary connectivity are poorly understood. To address this knowledge gap, we collected brown bear samples from the Gobi Desert (n = 2360), Altai, Sayan, Khentii, and Ikh Khyangan mountains of Mongolia (n = 79), and Deosai National Park in the Himalayan Mountain Range of Pakistan (n = 5) and generated 927 base pairs of mitochondrial DNA (mtDNA) sequence data and genotypes at 13 nuclear DNA microsatellite loci. We documented high levels of mtDNA and nDNA diversity in the brown bear populations of northern Mongolia (Altai, Sayan, Buteeliin nuruu and Khentii), but substantially lower diversity in brown bear populations in the Gobi Desert and Himalayas of Pakistan. We detected 3 brown bear mtDNA phylogeographic groups among bears of the region, with clade 3a1 in Sayan, Khentii, and Buteeliin nuruu mountains, clade 3b in Altai, Sayan, Buteeliin nuruu, Khentii, and Ikh Khyangan, and clade 6 in Gobi and Pakistan. Our results also clarified the phylogenetic relationships and divergence times with other brown bear mtDNA clades around the world. The nDNA genetic structure analyses revealed distinctiveness of Gobi bears and different population subdivisions compared to mtDNA results. For example, genetic distance for nDNA microsatellite loci between the bears in Gobi and Altai (FST = 0.147) was less than that of the Gobi and Pakistan (FST = 0.308) suggesting more recent male-mediated nuclear gene flow between Gobi and Altai than between Gobi and the Pakistan bears. Our results provide valuable information for conservation and management of bears in this understudied region of Central Asia and highlight the need for special protection and additional research on Gobi brown bears.
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Affiliation(s)
- Odbayar Tumendemberel
- Department of Natural Science and Environmental Health, University of South-Eastern Norway, Bø i Telemark, Norway
| | - Andreas Zedrosser
- Department of Natural Science and Environmental Health, University of South-Eastern Norway, Bø i Telemark, Norway
| | | | | | - Jennifer R. Adams
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Jack M. Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Sarah J. Jacobs
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Tumennasan Khorloojav
- Genetics Laboratory, Institute of General and Experimental Biology, Mongolian Academy of Sciences, Ulaanbaatar, Mongolia
| | - Tuya Tserenbataa
- Sunshine Village Complex, Bayanzurkh District, Ulaanbaatar, Mongolia
| | - Mijiddorj Batmunkh
- Mongolian-Chinese Joint Molecular Biology Laboratory, Ulaanbaatar, Mongolia
| | - Jon E. Swenson
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, Idaho, United States of America
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75
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Speciation, gene flow, and seasonal migration in Catharus thrushes (Aves:Turdidae). Mol Phylogenet Evol 2019; 139:106564. [PMID: 31330265 DOI: 10.1016/j.ympev.2019.106564] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/16/2019] [Accepted: 07/16/2019] [Indexed: 10/26/2022]
Abstract
New World thrushes in the genus Catharus are small, insectivorous or omnivorous birds that have been used to explore several important questions in avian evolution, including the evolution of seasonal migration and plumage variation. Within Catharus, members of a clade of obligate long-distance migrants (C. fuscescens, C. minimus, and C. bicknelli) have also been used in the development of heteropatric speciation theory, a divergence process in which migratory lineages (which might occur in allopatry or sympatry during portions of their annual cycle) diverge despite low levels of gene flow. However, research on Catharus relationships has thus far been restricted to the use of small genetic datasets, which provide limited resolution of both phylogenetic and demographic histories. We used a large, multi-locus dataset from loci containing ultraconserved elements (UCEs) to study the demographic histories of the migratory C. fuscescens-minimus-bicknelli clade and to resolve the phylogeny of the migratory species of Catharus. Our dataset included more than 2000 loci and over 1700 variable genotyped sites, and analyses supported our prediction of divergence with gene flow in the fully migratory clade, with significant gene flow among all three species. Our phylogeny of the genus differs from past work in its placement of C. ustulatus, and further analyses suggest historic gene flow throughout the genus, producing genetically reticulate (or network) phylogenies. This raises questions about trait origins and suggests that seasonal migration and the resulting migratory condition of heteropatry is likely to promote hybridization not only during pairwise divergence and speciation, but also among non-sisters.
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76
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Ackermann RR, Arnold ML, Baiz MD, Cahill JA, Cortés-Ortiz L, Evans BJ, Grant BR, Grant PR, Hallgrimsson B, Humphreys RA, Jolly CJ, Malukiewicz J, Percival CJ, Ritzman TB, Roos C, Roseman CC, Schroeder L, Smith FH, Warren KA, Wayne RK, Zinner D. Hybridization in human evolution: Insights from other organisms. Evol Anthropol 2019; 28:189-209. [PMID: 31222847 PMCID: PMC6980311 DOI: 10.1002/evan.21787] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 01/30/2019] [Accepted: 04/30/2019] [Indexed: 12/14/2022]
Abstract
During the late Pleistocene, isolated lineages of hominins exchanged genes thus influencing genomic variation in humans in both the past and present. However, the dynamics of this genetic exchange and associated phenotypic consequences through time remain poorly understood. Gene exchange across divergent lineages can result in myriad outcomes arising from these dynamics and the environmental conditions under which it occurs. Here we draw from our collective research across various organisms, illustrating some of the ways in which gene exchange can structure genomic/phenotypic diversity within/among species. We present a range of examples relevant to questions about the evolution of hominins. These examples are not meant to be exhaustive, but rather illustrative of the diverse evolutionary causes/consequences of hybridization, highlighting potential drivers of human evolution in the context of hybridization including: influences on adaptive evolution, climate change, developmental systems, sex-differences in behavior, Haldane's rule and the large X-effect, and transgressive phenotypic variation.
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Affiliation(s)
- Rebecca R. Ackermann
- Department of Archaeology, University of Cape Town, Rondebosch, South Africa
- Human Evolution Research Institute, University of Cape Town, Rondebosch, South Africa
| | | | - Marcella D. Baiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - James A. Cahill
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California
| | - Liliana Cortés-Ortiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - Ben J. Evans
- Biology Department, Life Sciences Building, McMaster University, Hamilton, Canada
| | - B. Rosemary Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey
| | - Peter R. Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey
| | - Benedikt Hallgrimsson
- Department of Cell Biology and Anatomy and the Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Robyn A. Humphreys
- Department of Archaeology, University of Cape Town, Rondebosch, South Africa
- Human Evolution Research Institute, University of Cape Town, Rondebosch, South Africa
| | - Clifford J. Jolly
- Center for the Study of Human Origins, Department of Anthropology, New York University, and NYCEP, New York, New York
| | - Joanna Malukiewicz
- Biodesign Institute, Arizona State University, Tempe, Arizona
- Federal University of Vicosa, Department of Animal Biology, Brazil
| | - Christopher J. Percival
- Department of Cell Biology and Anatomy and the Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
- Department of Anthropology, Stony Brook University, New York
| | - Terrence B. Ritzman
- Department of Archaeology, University of Cape Town, Rondebosch, South Africa
- Human Evolution Research Institute, University of Cape Town, Rondebosch, South Africa
- Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri
- Department of Anthropology, Washington University, St. Louis, Missouri
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center (DPZ), Leibniz Institute for Primate Research, Göttingen, Germany
| | - Charles C. Roseman
- Department of Animal Biology, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Lauren Schroeder
- Human Evolution Research Institute, University of Cape Town, Rondebosch, South Africa
- Department of Anthropology, University of Toronto Mississauga, Mississauga, Canada
| | - Fred H. Smith
- Department of Sociology and Anthropology, Illinois State University, Normal, Illinois
| | - Kerryn A. Warren
- Department of Archaeology, University of Cape Town, Rondebosch, South Africa
- Human Evolution Research Institute, University of Cape Town, Rondebosch, South Africa
| | | | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center (DPZ), Leibniz Institute for Primate Research, Göttingen, Germany
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77
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Polar bear evolution is marked by rapid changes in gene copy number in response to dietary shift. Proc Natl Acad Sci U S A 2019; 116:13446-13451. [PMID: 31209046 DOI: 10.1073/pnas.1901093116] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Polar bear (Ursus maritimus) and brown bear (Ursus arctos) are recently diverged species that inhabit vastly differing habitats. Thus, analysis of the polar bear and brown bear genomes represents a unique opportunity to investigate the evolutionary mechanisms and genetic underpinnings of rapid ecological adaptation in mammals. Copy number (CN) differences in genomic regions between closely related species can underlie adaptive phenotypes and this form of genetic variation has not been explored in the context of polar bear evolution. Here, we analyzed the CN profiles of 17 polar bears, 9 brown bears, and 2 black bears (Ursus americanus). We identified an average of 318 genes per individual that showed evidence of CN variation (CNV). Nearly 200 genes displayed species-specific CN differences between polar bear and brown bear species. Principal component analysis of gene CN provides strong evidence that CNV evolved rapidly in the polar bear lineage and mainly resulted in CN loss. Olfactory receptors composed 47% of CN differentiated genes, with the majority of these genes being at lower CN in the polar bear. Additionally, we found significantly fewer copies of several genes involved in fatty acid metabolism as well as AMY1B, the salivary amylase-encoding gene in the polar bear. These results suggest that natural selection shaped patterns of CNV in response to the transition from an omnivorous to primarily carnivorous diet during polar bear evolution. Our analyses of CNV shed light on the genomic underpinnings of ecological adaptation during polar bear evolution.
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78
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Delsuc F, Kuch M, Gibb GC, Karpinski E, Hackenberger D, Szpak P, Martínez JG, Mead JI, McDonald HG, MacPhee RDE, Billet G, Hautier L, Poinar HN. Ancient Mitogenomes Reveal the Evolutionary History and Biogeography of Sloths. Curr Biol 2019; 29:2031-2042.e6. [PMID: 31178321 DOI: 10.1016/j.cub.2019.05.043] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/18/2019] [Accepted: 05/15/2019] [Indexed: 12/20/2022]
Abstract
Living sloths represent two distinct lineages of small-sized mammals that independently evolved arboreality from terrestrial ancestors. The six extant species are the survivors of an evolutionary radiation marked by the extinction of large terrestrial forms at the end of the Quaternary. Until now, sloth evolutionary history has mainly been reconstructed from phylogenetic analyses of morphological characters. Here, we used ancient DNA methods to successfully sequence 10 extinct sloth mitogenomes encompassing all major lineages. This includes the iconic continental ground sloths Megatherium, Megalonyx, Mylodon, and Nothrotheriops and the smaller endemic Caribbean sloths Parocnus and Acratocnus. Phylogenetic analyses identify eight distinct lineages grouped in three well-supported clades, whose interrelationships are markedly incongruent with the currently accepted morphological topology. We show that recently extinct Caribbean sloths have a single origin but comprise two highly divergent lineages that are not directly related to living two-fingered sloths, which instead group with Mylodon. Moreover, living three-fingered sloths do not represent the sister group to all other sloths but are nested within a clade of extinct ground sloths including Megatherium, Megalonyx, and Nothrotheriops. Molecular dating also reveals that the eight newly recognized sloth families all originated between 36 and 28 million years ago (mya). The early divergence of recently extinct Caribbean sloths around 35 mya is consistent with the debated GAARlandia hypothesis postulating the existence at that time of a biogeographic connection between northern South America and the Greater Antilles. This new molecular phylogeny has major implications for reinterpreting sloth morphological evolution, biogeography, and diversification history.
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Affiliation(s)
- Frédéric Delsuc
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France.
| | - Melanie Kuch
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Gillian C Gibb
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France; Wildlife and Ecology Group, School of Agriculture and Environment, Massey University, Centennial Drive, Hokowhitu, Palmerston North 4410, New Zealand
| | - Emil Karpinski
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Dirk Hackenberger
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Paul Szpak
- Department of Anthropology, Trent University, 1600 West Bank Drive, Peterborough, ON K9L 0G2, Canada
| | - Jorge G Martínez
- Instituto Superior de Estudios Sociales, CONICET-Instituto de Arqueología y Museo, Universidad Nacional de Tucumán, San Martín 1545, CP4000 San Miguel de Tucumán, Argentina
| | - Jim I Mead
- The Mammoth Site, Hot Springs, Hot Springs, SD 57747, USA; East Tennessee State University Natural History Museum, 1212 Suncrest Drive, Johnson City, TN 37615, USA
| | - H Gregory McDonald
- Bureau of Land Management, Utah State Office, 440 West 200 South #500, Salt Lake City, UT 84101, USA
| | - Ross D E MacPhee
- Division of Vertebrate Zoology/Mammalogy, American Museum of Natural History, Central Park West & 79th Street, New York, NY 10024, USA
| | - Guillaume Billet
- Centre de Recherche en Paléontologie - Paris (CR2P), UMR CNRS 7207, Sorbonne Université, Muséum National d'Histoire Naturelle, 57 Rue Cuvier, 75005 Paris, France
| | - Lionel Hautier
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France; Mammal Section, Life Sciences, Vertebrate Division, The Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada.
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79
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Lambert SM, Streicher JW, Fisher‐Reid MC, Méndez de la Cruz FR, Martínez‐Méndez N, García-Vázquez UO, Nieto Montes de Oca A, Wiens JJ. Inferring introgression using RADseq and
D
FOIL
: Power and pitfalls revealed in a case study of spiny lizards (
Sceloporus
). Mol Ecol Resour 2019; 19:818-837. [DOI: 10.1111/1755-0998.12972] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 10/26/2018] [Indexed: 02/03/2023]
Affiliation(s)
- Shea M. Lambert
- Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona
| | - Jeffrey W. Streicher
- Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona
- Department of Life Sciences The Natural History Museum London UK
| | - M. Caitlin Fisher‐Reid
- Department of Biological Sciences Bridgewater State University Bridgewater Massachusetts
| | - Fausto R. Méndez de la Cruz
- Laboratorio de Herpetología, Instituto de Biología Universidad Nacional Autónoma de México Mexico City Mexico
| | - Norberto Martínez‐Méndez
- Laboratorio de Bioconservación y Manejo, Departamento de Zoología Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional Mexico City Mexico
| | - Uri Omar García-Vázquez
- Unidad Multidisciplinaria de Investigación, Facultad de Estudios Superiores Zaragoza Universidad Nacional Autónoma de México Mexico City Mexico
| | - Adrián Nieto Montes de Oca
- Departamento de Biología Evolutiva, Facultad de Ciencias Universidad Nacional Autónoma de México Mexico City Mexico
| | - John J. Wiens
- Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona
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80
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Zarza E, Reynoso VH, Faria CMA, Emerson BC. Introgressive hybridization in a Spiny-Tailed Iguana, Ctenosaura pectinata, and its implications for taxonomy and conservation. PeerJ 2019; 7:e6744. [PMID: 31065455 PMCID: PMC6485205 DOI: 10.7717/peerj.6744] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 03/05/2019] [Indexed: 11/30/2022] Open
Abstract
Introgression, the transmission of genetic material of one taxon into another through hybridization, can have various evolutionary outcomes. Previous studies have detected signs of introgression between western populations of the Mexican endemic and threatened spiny-tailed iguana, Ctenosaura pectinata. However, the extent of this phenomenon along the geographic distribution of the species is unknown. Here, we use multilocus data together with detailed geographic sampling to (1) define genotypic clusters within C. pectinata; (2) evaluate geographic concordance between maternally and biparentally inherited markers; (3) examine levels of introgression between genotypic clusters, and (4) suggest taxonomic modifications in light of this information. Applying clustering methods to genotypes of 341 individuals from 49 localities of C. pectinata and the closely related C. acanthura, we inferred the existence of five genotypic clusters. Contact zones between genotypic clusters with signatures of interbreeding were detected, showing different levels of geographic discordance with mtDNA lineages. In northern localities, mtDNA and microsatellites exhibit concordant distributions, supporting the resurrection of C. brachylopha. Similar concordance is observed along the distribution of C. acanthura, confirming its unique taxonomic identity. Genetic and geographic concordance is also observed for populations within southwestern Mexico, where the recognition of a new species awaits in depth taxonomic revision. In contrast, in western localities a striking pattern of discordance was detected where up to six mtDNA lineages co-occur with only two genotypic clusters. Given that the type specimen originated from this area, we suggest that individuals from western Mexico keep the name C. pectinata. Our results have profound implications for conservation, management, and forensics of Mexican iguanas.
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Affiliation(s)
- Eugenia Zarza
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.,Grupo Académico de Biotecnología Ambiental, El Colegio de la Frontera Sur, Unidad Tapachula, Tapachula, Chiapas, Mexico.,CONACYT, Ciudad de México, Mexico
| | - Víctor H Reynoso
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Christiana M A Faria
- School of Biological Sciences, University of East Anglia, Norwich, UK.,Current Affiliation: Departamento de Biologia, Universidade Federal do Ceará, Campus do Pici, Fortaleza, Ceará, Brasil
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), C/Astrofísico Francisco Sánchez 3, La Laguna, Tenerife, Canary Islands, Spain
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81
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Arnaudo ME, Toledo N, Soibelzon L, Bona P. Phylogenetic signal analysis in the basicranium of Ursidae (Carnivora, Mammalia). PeerJ 2019; 7:e6597. [PMID: 30891368 PMCID: PMC6422017 DOI: 10.7717/peerj.6597] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 02/09/2019] [Indexed: 11/29/2022] Open
Abstract
Ursidae is a monophyletic group comprised of three subfamilies: Tremarctinae, Ursinae and Ailuropodinae, all of which have a rich geographical distribution. The phylogenetic relationships within the Ursidae group have been underexamined, especially regarding morphological traits such as the basicranium. Importantly, the basicranium is a highly complex region that covers a small portion of the skull, combining both structural and functional aspects that determine its morphology. Phylogenetic hypotheses of the Ursidae (including Tremarctinae) have been made based on morphological characters that considers skull, mandible and teeth features, while specific characters of the auditory region and basicranium have not been taken into account. To do this, we analyse the shape and size macroevolution of the basicranium of Ursidae, testing its morphological disparity in a phylogenetic context, which is quantified by means of the phylogenetic signal. We investigated phylogenetical autocorrelation by shape (depicted by Principal Components Analysis scores from previous published analyses) and basicranium size (depicted by centroid size, CS) using an orthonormal decomposition analysis and Abouheif C mean. The main advantages of these methods are that they rely exclusively on cladogram topology and do not require branch-length estimates. Also, an optimisation of the ancestral nodes was performed using TNT 1.5 software. In relation to the phylogenetic signal, both methods showed similar results: the presence of autocorrelation was detected in PC1 and PC2, while in PC3, PC4 and PC5 and in the size of the basicranium (CS), the absence of autocorrelation occurred. The most significant nodes (where there is autocorrelation) are the basal nodes 'Ursidae' and 'Ursinae-Tremarctinae'. Within this last group, distinctive basicranium morphology is observed, being more conservative in Tremarctinae than in Ursinae. The differences between these subfamilies could be related to historical events involving varying food and environmental preferences. The high phylogenetic signal in the node Tremarctinae probably indicates that the basicranium configuration of these bears was obtained early in their evolutionary history. Finally, our results of the basicranium and skull length ratios indicate that in Tremarctinae, the basicranium size was not determined by phylogeny but instead by other factors, such as adaptive responses to climatic changes and competition with other carnivores.
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Affiliation(s)
- María Eugenia Arnaudo
- División de Paleontología Vertebrados, Facultad de Ciencias Naturales y Museo-UNLP, La Plata, Buenos Aires, Argentina
- CONICET, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Néstor Toledo
- CONICET, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- División Paleontología Vertebrados, Unidades de Investigación Anexo Museo, Facultad de Ciencias Naturales y Museo-UNLP, La Plata, Buenos Aires, Argentina
| | - Leopoldo Soibelzon
- CONICET, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- Laboratorio de Morfología Evolutiva y Desarrollo (MORPHOS)-División de Paleontología Vertebrados, Facultad de Ciencias Naturales y Museo-UNLP, La Plata, Buenos Aires, Argentina
| | - Paula Bona
- CONICET, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- División Paleontología Vertebrados, Unidades de Investigación Anexo Museo, Facultad de Ciencias Naturales y Museo-UNLP, La Plata, Buenos Aires, Argentina
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82
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Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization. BIOINFORMATICS AND PHYLOGENETICS 2019. [DOI: 10.1007/978-3-030-10837-3_13] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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83
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Savriama Y, Valtonen M, Kammonen JI, Rastas P, Smolander OP, Lyyski A, Häkkinen TJ, Corfe IJ, Gerber S, Salazar-Ciudad I, Paulin L, Holm L, Löytynoja A, Auvinen P, Jernvall J. Bracketing phenogenotypic limits of mammalian hybridization. ROYAL SOCIETY OPEN SCIENCE 2018; 5:180903. [PMID: 30564397 PMCID: PMC6281900 DOI: 10.1098/rsos.180903] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 10/29/2018] [Indexed: 05/09/2023]
Abstract
An increasing number of mammalian species have been shown to have a history of hybridization and introgression based on genetic analyses. Only relatively few fossils, however, preserve genetic material, and morphology must be used to identify the species and determine whether morphologically intermediate fossils could represent hybrids. Because dental and cranial fossils are typically the key body parts studied in mammalian palaeontology, here we bracket the potential for phenotypically extreme hybridizations by examining uniquely preserved cranio-dental material of a captive hybrid between grey and ringed seals. We analysed how distinct these species are genetically and morphologically, how easy it is to identify the hybrids using morphology and whether comparable hybridizations happen in the wild. We show that the genetic distance between these species is more than twice the modern human-Neanderthal distance, but still within that of morphologically similar species pairs known to hybridize. By contrast, morphological and developmental analyses show grey and ringed seals to be highly disparate, and that the hybrid is a predictable intermediate. Genetic analyses of the parent populations reveal introgression in the wild, suggesting that grey-ringed seal hybridization is not limited to captivity. Taken together, we postulate that there is considerable potential for mammalian hybridization between phenotypically disparate taxa.
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Affiliation(s)
- Yoland Savriama
- Developmental Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
| | - Mia Valtonen
- Developmental Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
- Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 111, 80101 Joensuu, Finland
| | - Juhana I. Kammonen
- Genome Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
| | - Pasi Rastas
- Genome Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
| | - Olli-Pekka Smolander
- Genome Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
| | - Annina Lyyski
- Genome Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
| | - Teemu J. Häkkinen
- Developmental Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
| | - Ian J. Corfe
- Developmental Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
| | - Sylvain Gerber
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, 45 rue Buffon, CP 50, 75005 Paris, France
| | - Isaac Salazar-Ciudad
- Developmental Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Lars Paulin
- Genome Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
| | - Liisa Holm
- Genome Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
| | - Ari Löytynoja
- Genome Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
- Authors for correspondence: Ari Löytynoja e-mail:
| | - Petri Auvinen
- Genome Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
- Authors for correspondence: Petri Auvinen e-mail:
| | - Jukka Jernvall
- Developmental Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
- Authors for correspondence: Jukka Jernvall e-mail:
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84
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Lee JM, Song HJ, Park SI, Lee YM, Jeong SY, Cho TO, Kim JH, Choi HG, Choi CG, Nelson WA, Fredericq S, Bhattacharya D, Yoon HS. Mitochondrial and Plastid Genomes from Coralline Red Algae Provide Insights into the Incongruent Evolutionary Histories of Organelles. Genome Biol Evol 2018; 10:2961-2972. [PMID: 30364957 PMCID: PMC6279150 DOI: 10.1093/gbe/evy222] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2018] [Indexed: 11/14/2022] Open
Abstract
Mitochondria and plastids are generally uniparentally inherited and have a conserved gene content over hundreds of millions of years, which makes them potentially useful phylogenetic markers. Organelle single gene-based trees have long been the basis for elucidating interspecies relationships that inform taxonomy. More recently, high-throughput genome sequencing has enabled the construction of massive organelle genome databases from diverse eukaryotes, and these have been used to infer species relationships in deep evolutionary time. Here, we test the idea that despite their expected utility, conflicting phylogenetic signal may exist in mitochondrial and plastid genomes from the anciently diverged coralline red algae (Rhodophyta). We generated complete organelle genome data from five coralline red algae (Lithothamnion sp., Neogoniolithon spectabile, Renouxia sp., Rhodogorgon sp., and Synarthrophyton chejuensis) for comparative analysis with existing organelle genome data from two other species (Calliarthron tuberculosum and Sporolithon durum). We find strong evidence for incongruent phylogenetic signal from both organelle genomes that may be explained by incomplete lineage sorting that has maintained anciently derived gene copies or other molecular evolutionary processes such as hybridization or gene flow during the evolutionary history of coralline red algae.
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Affiliation(s)
- Jun Mo Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Hae Jung Song
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Seung In Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Yu Min Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - So Young Jeong
- Department of Marine Life Science, Chosun University, Gwangju, Korea
| | - Tae Oh Cho
- Department of Marine Life Science, Chosun University, Gwangju, Korea
| | - Ji Hee Kim
- Division of Life Sciences, Korea Polar Research Institute, KOPRI, Incheon, Korea
| | - Han-Gu Choi
- Division of Life Sciences, Korea Polar Research Institute, KOPRI, Incheon, Korea
| | - Chang Geun Choi
- Department of Ecological Engineering, Pukyong National University, Busan, Korea
| | - Wendy A Nelson
- National Institute for Water and Atmospheric Research, Wellington, New Zealand.,School of Biological Sciences, University of Auckland, New Zealand
| | - Suzanne Fredericq
- Biology Department, University of Louisiana at Lafayette, Lafayette, Louisiana
| | | | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
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85
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Abstract
Most phylogenies are typically represented as purely bifurcating. However, as genomic data have become more common in phylogenetic studies, it is not unusual to find reticulation among terminal lineages or among internal nodes (deep time reticulation; DTR). In these situations, gene flow must have happened in the same or adjacent geographic areas for these DTRs to have occurred and therefore biogeographic reconstruction should provide similar area estimates for parental nodes, provided extinction or dispersal has not eroded these patterns. We examine the phylogeny of the widely distributed New World kingsnakes (Lampropeltis), determine if DTR is present in this group, and estimate the ancestral area for reticulation. Importantly, we develop a new method that uses coalescent simulations in a machine learning framework to show conclusively that this phylogeny is best represented as reticulating at deeper time. Using joint probabilities of ancestral area reconstructions on the bifurcating parental lineages from the reticulating node, we show that this reticulation likely occurred in northwestern Mexico/southwestern US, and subsequently, led to the diversification of the Mexican kingsnakes. This region has been previously identified as an area important for understanding speciation and secondary contact with gene flow in snakes and other squamates. This research shows that phylogenetic reticulation is common, even in well-studied groups, and that the geographic scope of ancient hybridization is recoverable.
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology, The American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
| | - Marcelo Gehara
- Department of Herpetology, The American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
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86
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Nilsson MA, Zheng Y, Kumar V, Phillips MJ, Janke A. Speciation Generates Mosaic Genomes in Kangaroos. Genome Biol Evol 2018; 10:33-44. [PMID: 29182740 PMCID: PMC5758907 DOI: 10.1093/gbe/evx245] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2017] [Indexed: 12/22/2022] Open
Abstract
The iconic Australasian kangaroos and wallabies represent a successful marsupial radiation. However, the evolutionary relationship within the two genera, Macropus and Wallabia, is controversial: mitochondrial and nuclear genes, and morphological data have produced conflicting scenarios regarding the phylogenetic relationships, which in turn impact the classification and taxonomy. We sequenced and analyzed the genomes of 11 kangaroos to investigate the evolutionary cause of the observed phylogenetic conflict. A multilocus coalescent analysis using ∼14,900 genome fragments, each 10 kb long, significantly resolved the species relationships between and among the sister-genera Macropus and Wallabia. The phylogenomic approach reconstructed the swamp wallaby (Wallabia) as nested inside Macropus, making this genus paraphyletic. However, the phylogenomic analyses indicate multiple conflicting phylogenetic signals in the swamp wallaby genome. This is interpreted as at least one introgression event between the ancestor of the genus Wallabia and a now extinct ghost lineage outside the genus Macropus. Additional phylogenetic signals must therefore be caused by incomplete lineage sorting and/or introgression, but available statistical methods cannot convincingly disentangle the two processes. In addition, the relationships inside the Macropus subgenus M. (Notamacropus) represent a hard polytomy. Thus, the relationships between tammar, red-necked, agile, and parma wallabies remain unresolvable even with whole-genome data. Even if most methods resolve bifurcating trees from genomic data, hard polytomies, incomplete lineage sorting, and introgression complicate the interpretation of the phylogeny and thus taxonomy.
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Affiliation(s)
- Maria A Nilsson
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Yichen Zheng
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Vikas Kumar
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Matthew J Phillips
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany.,Institute for Ecology, Evolution & Diversity, Biologicum, Goethe University Frankfurt, Frankfurt am Main, Germany
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87
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Gopalakrishnan S, Sinding MHS, Ramos-Madrigal J, Niemann J, Samaniego Castruita JA, Vieira FG, Carøe C, Montero MDM, Kuderna L, Serres A, González-Basallote VM, Liu YH, Wang GD, Marques-Bonet T, Mirarab S, Fernandes C, Gaubert P, Koepfli KP, Budd J, Rueness EK, Sillero C, Heide-Jørgensen MP, Petersen B, Sicheritz-Ponten T, Bachmann L, Wiig Ø, Hansen AJ, Gilbert MTP. Interspecific Gene Flow Shaped the Evolution of the Genus Canis. Curr Biol 2018; 28:3441-3449.e5. [PMID: 30344120 PMCID: PMC6224481 DOI: 10.1016/j.cub.2018.08.041] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 04/30/2018] [Accepted: 08/16/2018] [Indexed: 12/30/2022]
Abstract
The evolutionary history of the wolf-like canids of the genus Canis has been heavily debated, especially regarding the number of distinct species and their relationships at the population and species level [1-6]. We assembled a dataset of 48 resequenced genomes spanning all members of the genus Canis except the black-backed and side-striped jackals, encompassing the global diversity of seven extant canid lineages. This includes eight new genomes, including the first resequenced Ethiopian wolf (Canis simensis), one dhole (Cuon alpinus), two East African hunting dogs (Lycaon pictus), two Eurasian golden jackals (Canis aureus), and two Middle Eastern gray wolves (Canis lupus). The relationships between the Ethiopian wolf, African golden wolf, and golden jackal were resolved. We highlight the role of interspecific hybridization in the evolution of this charismatic group. Specifically, we find gene flow between the ancestors of the dhole and African hunting dog and admixture between the gray wolf, coyote (Canis latrans), golden jackal, and African golden wolf. Additionally, we report gene flow from gray and Ethiopian wolves to the African golden wolf, suggesting that the African golden wolf originated through hybridization between these species. Finally, we hypothesize that coyotes and gray wolves carry genetic material derived from a "ghost" basal canid lineage.
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Affiliation(s)
- Shyam Gopalakrishnan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - Mikkel-Holger S Sinding
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; Natural History Museum, University of Oslo, Oslo, Norway; The Qimmeq Project, University of Greenland, Nuussuaq, Greenland; University of Greenland, Manuutoq 1, Nuuk, Greenland
| | - Jazmín Ramos-Madrigal
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Niemann
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Jose A Samaniego Castruita
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Filipe G Vieira
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Christian Carøe
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Lukas Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | - Aitor Serres
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | | | - Yan-Hu Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan, China
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California, San Diego, San Diego, CA, USA
| | - Carlos Fernandes
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Philippe Gaubert
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UM-CNRS-IRD-EPHE, Université de Montpellier, Montpellier, France
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA; Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 41A Sredniy Prospekt, St. Petersburg 199034, Russia
| | - Jane Budd
- Breeding Centre for Endangered Arabian Wildlife, Sharjah, United Arab Emirates
| | - Eli Knispel Rueness
- Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Claudio Sillero
- Wildlife Conservation Research Unit, Zoology, University of Oxford, Tubney House, Tubney OX13 5QL, UK; IUCN SSC Canid Specialist Group, Oxford, UK
| | - Mads Peter Heide-Jørgensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
| | - Bent Petersen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Thomas Sicheritz-Ponten
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Lutz Bachmann
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Øystein Wiig
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Anders J Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; The Qimmeq Project, University of Greenland, Nuussuaq, Greenland; University of Greenland, Manuutoq 1, Nuuk, Greenland
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; Norwegian University of Science and Technology, University Museum, Trondheim, Norway
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88
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Winter S, Fennessy J, Janke A. Limited introgression supports division of giraffe into four species. Ecol Evol 2018; 8:10156-10165. [PMID: 30397455 PMCID: PMC6206193 DOI: 10.1002/ece3.4490] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 08/06/2018] [Accepted: 08/07/2018] [Indexed: 01/17/2023] Open
Abstract
All giraffe (Giraffa) were previously assigned to a single species (G. camelopardalis) and nine subspecies. However, multi-locus analyses of all subspecies have shown that there are four genetically distinct clades and suggest four giraffe species. This conclusion might not be fully accepted due to limited data and lack of explicit gene flow analyses. Here, we present an extended study based on 21 independent nuclear loci from 137 individuals. Explicit gene flow analyses identify less than one migrant per generation, including between the closely related northern and reticulated giraffe. Thus, gene flow analyses and population genetics of the extended dataset confirm four genetically distinct giraffe clades and support four independent giraffe species. The new findings support a revision of the IUCN classification of giraffe taxonomy. Three of the four species are threatened with extinction, and mostly occurring in politically unstable regions, and as such, require the highest conservation support possible.
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Affiliation(s)
- Sven Winter
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
- Institute for Ecology, Evolution and DiversityGoethe UniversityFrankfurt am MainGermany
| | | | - Axel Janke
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
- Institute for Ecology, Evolution and DiversityGoethe UniversityFrankfurt am MainGermany
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89
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Pratas D, Hosseini M, Grilo G, Pinho AJ, Silva RM, Caetano T, Carneiro J, Pereira F. Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard. Genes (Basel) 2018; 9:E445. [PMID: 30200636 PMCID: PMC6162538 DOI: 10.3390/genes9090445] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/03/2018] [Accepted: 09/03/2018] [Indexed: 12/17/2022] Open
Abstract
The sequencing of ancient DNA samples provides a novel way to find, characterize, and distinguish exogenous genomes of endogenous targets. After sequencing, computational composition analysis enables filtering of undesired sources in the focal organism, with the purpose of improving the quality of assemblies and subsequent data analysis. More importantly, such analysis allows extinct and extant species to be identified without requiring a specific or new sequencing run. However, the identification of exogenous organisms is a complex task, given the nature and degradation of the samples, and the evident necessity of using efficient computational tools, which rely on algorithms that are both fast and highly sensitive. In this work, we relied on a fast and highly sensitive tool, FALCON-meta, which measures similarity against whole-genome reference databases, to analyse the metagenomic composition of an ancient polar bear (Ursus maritimus) jawbone fossil. The fossil was collected in Svalbard, Norway, and has an estimated age of 110,000 to 130,000 years. The FASTQ samples contained 349 GB of nonamplified shotgun sequencing data. We identified and localized, relative to the FASTQ samples, the genomes with significant similarities to reference microbial genomes, including those of viruses, bacteria, and archaea, and to fungal, mitochondrial, and plastidial sequences. Among other striking features, we found significant similarities between modern-human, some bacterial and viral sequences (contamination) and the organelle sequences of wild carrot and tomato relative to the whole samples. For each exogenous candidate, we ran a damage pattern analysis, which in addition to revealing shallow levels of damage in the plant candidates, identified the source as contamination.
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Affiliation(s)
- Diogo Pratas
- Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Morteza Hosseini
- Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, 3810-193 Aveiro, Portugal.
- Department of Electronics, Telecommunications and Informatics, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Gonçalo Grilo
- Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, 3810-193 Aveiro, Portugal.
- Department of Electronics, Telecommunications and Informatics, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Armando J Pinho
- Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, 3810-193 Aveiro, Portugal.
- Department of Electronics, Telecommunications and Informatics, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Raquel M Silva
- Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, 3810-193 Aveiro, Portugal.
- Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal.
- Institute for Biomedicine, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Tânia Caetano
- Department of Biology, University of Aveiro, University of Aveiro, 3810-193 Aveiro, Portugal.
- Centre for Environmental and Marine Studies, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - João Carneiro
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Matosinhos, Portugal.
| | - Filipe Pereira
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Matosinhos, Portugal.
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90
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Barlow A, Cahill JA, Hartmann S, Theunert C, Xenikoudakis G, Fortes GG, Paijmans JLA, Rabeder G, Frischauf C, Grandal-d'Anglade A, García-Vázquez A, Murtskhvaladze M, Saarma U, Anijalg P, Skrbinšek T, Bertorelle G, Gasparian B, Bar-Oz G, Pinhasi R, Slatkin M, Dalén L, Shapiro B, Hofreiter M. Partial genomic survival of cave bears in living brown bears. Nat Ecol Evol 2018; 2:1563-1570. [PMID: 30150744 DOI: 10.1038/s41559-018-0654-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/27/2018] [Indexed: 02/06/2023]
Abstract
Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the directionality and relative timing of gene flow. We find that segments of cave bear DNA still persist in the genomes of living brown bears, with cave bears contributing 0.9 to 2.4% of the genomes of all brown bears investigated. Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species.
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Affiliation(s)
- Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
| | - James A Cahill
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Stefanie Hartmann
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Christoph Theunert
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA.,Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Gloria G Fortes
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.,Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | | | - Gernot Rabeder
- Institute of Palaeontology, University of Vienna, Vienna, Austria
| | | | | | - Ana García-Vázquez
- Instituto Universitario de Xeoloxía, Universidade da Coruña, A Coruña, Spain
| | | | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Peeter Anijalg
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Tomaž Skrbinšek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Boris Gasparian
- Institute of Archaeology and Ethnography, National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia
| | - Guy Bar-Oz
- Zinman Institute of Archaeology, University of Haifa, Haifa, Israel
| | - Ron Pinhasi
- Earth Institute, University College Dublin, Dublin, Ireland.,Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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91
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Shanker K, Vijayakumar SP, Ganeshaiah KN. Unpacking the species conundrum: philosophy, practice and a way forward. J Genet 2018; 96:413-430. [PMID: 28761006 DOI: 10.1007/s12041-017-0800-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The history of ecology and evolutionary biology is rife with attempts to define and delimit species. However, there has been confusion between concepts and criteria, which has led to discussion, debate, and conflict, eventually leading to lack of consistency in delimitation. Here, we provide a broad review of species concepts, a clarification of category versus concept, an account of the general lineage concept (GLC), and finally a way forward for species discovery and delimitation. Historically, species were considered as varieties bound together by reproduction. After over 200 years of uncertainty, Mayr attempted to bring coherence to the definition of species through the biological species concept (BSC). This has, however, received much criticism, and the last half century has spawned at least 20 other concepts. A central philosophical problem is that concepts treat species as 'individuals' while the criteria for categorization treats them as 'classes'. While not getting away from this problem entirely, the GLC attempts to provide a framework where lineage divergence is influenced by a number of different factors (and correlated to different traits) which relate to the different species concepts. We also introduce an 'inclusive' probabilistic approach for understanding and delimiting species. Finally, we provide aWallacean (geography related) approach to the Linnaean problem of identifying and delimiting species, particularly for cases of allopatric divergence, and map this to the GLC. Going one step further, we take a morphometric terrain approach to visualizing and understanding differences between lineages. In summary, we argue that while generalized frameworks may work well for concepts of what species are, plurality and 'inclusive' probabilistic approaches may work best for delimitation.
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Affiliation(s)
- Kartik Shanker
- Centre for Ecological Sciences, Indian Institute of Science, Bengaluru 560 012, India.
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92
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Ancient DNA from Giant Panda (Ailuropoda melanoleuca) of South-Western China Reveals Genetic Diversity Loss during the Holocene. Genes (Basel) 2018; 9:genes9040198. [PMID: 29642393 PMCID: PMC5924540 DOI: 10.3390/genes9040198] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 02/02/2023] Open
Abstract
The giant panda was widely distributed in China and south-eastern Asia during the middle to late Pleistocene, prior to its habitat becoming rapidly reduced in the Holocene. While conservation reserves have been established and population numbers of the giant panda have recently increased, the interpretation of its genetic diversity remains controversial. Previous analyses, surprisingly, have indicated relatively high levels of genetic diversity raising issues concerning the efficiency and usefulness of reintroducing individuals from captive populations. However, due to a lack of DNA data from fossil specimens, it is unknown whether genetic diversity was even higher prior to the most recent population decline. We amplified complete cytb and 12s rRNA, partial 16s rRNA and ND1, and control region sequences from the mitochondrial genomes of two Holocene panda specimens. We estimated genetic diversity and population demography by analyzing the ancient mitochondrial DNA sequences alongside those from modern giant pandas, as well as from other members of the bear family (Ursidae). Phylogenetic analyses show that one of the ancient haplotypes is sister to all sampled modern pandas and the second ancient individual is nested among the modern haplotypes, suggesting that genetic diversity may indeed have been higher earlier during the Holocene. Bayesian skyline plot analysis supports this view and indicates a slight decline in female effective population size starting around 6000 years B.P., followed by a recovery around 2000 years ago. Therefore, while the genetic diversity of the giant panda has been affected by recent habitat contraction, it still harbors substantial genetic diversity. Moreover, while its still low population numbers require continued conservation efforts, there seem to be no immediate threats from the perspective of genetic evolutionary potential.
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93
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Árnason Ú, Lammers F, Kumar V, Nilsson MA, Janke A. Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow. SCIENCE ADVANCES 2018; 4:eaap9873. [PMID: 29632892 PMCID: PMC5884691 DOI: 10.1126/sciadv.aap9873] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 02/15/2018] [Indexed: 05/24/2023]
Abstract
Reconstructing the evolution of baleen whales (Mysticeti) has been problematic because morphological and genetic analyses have produced different scenarios. This might be caused by genomic admixture that may have taken place among some rorquals. We present the genomes of six whales, including the blue whale (Balaenoptera musculus), to reconstruct a species tree of baleen whales and to identify phylogenetic conflicts. Evolutionary multilocus analyses of 34,192 genome fragments reveal a fast radiation of rorquals at 10.5 to 7.5 million years ago coinciding with oceanic circulation shifts. The evolutionarily enigmatic gray whale (Eschrichtius robustus) is placed among rorquals, and the blue whale genome shows a high degree of heterozygosity. The nearly equal frequency of conflicting gene trees suggests that speciation of rorqual evolution occurred under gene flow, which is best depicted by evolutionary networks. Especially in marine environments, sympatric speciation might be common; our results raise questions about how genetic divergence can be established.
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Affiliation(s)
- Úlfur Árnason
- Department of Brain Surgery, Faculty of Medicine, University of Lund, Lund, Sweden
| | - Fritjof Lammers
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Goethe University Frankfurt, Institute for Ecology, Evolution and Diversity, Biologicum, Max-von-Laue-Straße 13, 60439 Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany
| | - Vikas Kumar
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Maria A. Nilsson
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Goethe University Frankfurt, Institute for Ecology, Evolution and Diversity, Biologicum, Max-von-Laue-Straße 13, 60439 Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany
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94
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Cahill JA, Heintzman PD, Harris K, Teasdale MD, Kapp J, Soares AER, Stirling I, Bradley D, Edwards CJ, Graim K, Kisleika AA, Malev AV, Monaghan N, Green RE, Shapiro B. Genomic Evidence of Widespread Admixture from Polar Bears into Brown Bears during the Last Ice Age. Mol Biol Evol 2018; 35:1120-1129. [DOI: 10.1093/molbev/msy018] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- James A Cahill
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA
| | - Peter D Heintzman
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA
- Tromsø University Museum, UiT – The Arctic University of Norway, Tromsø, Norway
| | - Kelley Harris
- Department of Genetics, Stanford University, Stanford, CA
| | - Matthew D Teasdale
- Smurfit Institute of Genetics, Dublin 2, Ireland
- BioArCh, University of York, York, United Kingdom
| | - Joshua Kapp
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA
| | - Andre E R Soares
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA
| | - Ian Stirling
- Wildlife Research Division, Department of Environment, c/o Department of Biological Sciences, University of Alberta, Edmonton, AB
- Department of Biological Sciences, University of Alberta, Edmonton, AB
| | | | - Ceiridwen J Edwards
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, United Kingdom
| | - Kiley Graim
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, NJ
- Flatiron Institute, Simons Foundation, New York, NY
| | | | | | - Nigel Monaghan
- National Museum of Ireland – Natural History, Dublin, Ireland
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA
- UCSC Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA
- UCSC Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA
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95
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Morales AE, Carstens BC. Evidence that Myotis lucifugus “Subspecies” are Five Nonsister Species, Despite Gene Flow. Syst Biol 2018; 67:756-769. [DOI: 10.1093/sysbio/syy010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 02/10/2018] [Indexed: 12/13/2022] Open
Affiliation(s)
- Ariadna E Morales
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210, USA
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96
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Zheng Y, Janke A. Gene flow analysis method, the D-statistic, is robust in a wide parameter space. BMC Bioinformatics 2018; 19:10. [PMID: 29310567 PMCID: PMC5759368 DOI: 10.1186/s12859-017-2002-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 12/18/2017] [Indexed: 01/13/2023] Open
Abstract
Background We evaluated the sensitivity of the D-statistic, a parsimony-like method widely used to detect gene flow between closely related species. This method has been applied to a variety of taxa with a wide range of divergence times. However, its parameter space and thus its applicability to a wide taxonomic range has not been systematically studied. Divergence time, population size, time of gene flow, distance of outgroup and number of loci were examined in a sensitivity analysis. Result The sensitivity study shows that the primary determinant of the D-statistic is the relative population size, i.e. the population size scaled by the number of generations since divergence. This is consistent with the fact that the main confounding factor in gene flow detection is incomplete lineage sorting by diluting the signal. The sensitivity of the D-statistic is also affected by the direction of gene flow, size and number of loci. In addition, we examined the ability of the f-statistics, \documentclass[12pt]{minimal}
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\begin{document}$$ {\widehat{f}}_{hom} $$\end{document}f^hom, to estimate the fraction of a genome affected by gene flow; while these statistics are difficult to implement to practical questions in biology due to lack of knowledge of when the gene flow happened, they can be used to compare datasets with identical or similar demographic background. Conclusions The D-statistic, as a method to detect gene flow, is robust against a wide range of genetic distances (divergence times) but it is sensitive to population size. The D-statistic should only be applied with critical reservation to taxa where population sizes are large relative to branch lengths in generations. Electronic supplementary material The online version of this article (10.1186/s12859-017-2002-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yichen Zheng
- Biodiversität und Klima Forschungszentrum, Senckenberg Gesellschaft für Naturforschung, 60325, Frankfurt, Germany.
| | - Axel Janke
- Biodiversität und Klima Forschungszentrum, Senckenberg Gesellschaft für Naturforschung, 60325, Frankfurt, Germany
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97
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Wang X, Rybczynski N, Harington CR, White SC, Tedford RH. A basal ursine bear (Protarctos abstrusus) from the Pliocene High Arctic reveals Eurasian affinities and a diet rich in fermentable sugars. Sci Rep 2017; 7:17722. [PMID: 29255278 PMCID: PMC5735171 DOI: 10.1038/s41598-017-17657-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 11/24/2017] [Indexed: 11/09/2022] Open
Abstract
The skeletal remains of a small bear (Protarctos abstrusus) were collected at the Beaver Pond fossil site in the High Arctic (Ellesmere I., Nunavut). This mid-Pliocene deposit has also yielded 12 other mammals and the remains of a boreal-forest community. Phylogenetic analysis reveals this bear to be basal to modern bears. It appears to represent an immigration event from Asia, leaving no living North American descendants. The dentition shows only modest specialization for herbivory, consistent with its basal position within Ursinae. However, the appearance of dental caries suggest a diet high in fermentable-carbohydrates. Fossil plants remains, including diverse berries, suggests that, like modern northern black bears, P. abstrusus may have exploited a high-sugar diet in the fall to promote fat accumulation and facilitate hibernation. A tendency toward a sugar-rich diet appears to have arisen early in Ursinae, and may have played a role in allowing ursine lineages to occupy cold habitats.
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Affiliation(s)
- Xiaoming Wang
- Department of Vertebrate Paleontology, Natural History Museum of Los Angeles County, 900 Exposition Blvd, Los Angeles, CA, 90007, United States. .,Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China. .,Division of Paleontology, American Museum of Natural History, Central Park West at 79th Street, New York, New York, 10024, United States.
| | - Natalia Rybczynski
- Palaeobiology, Canadian Museum of Nature, PO Box 3443 STN "D", Ottawa, Ontario, K1P 6P4, Canada.,Department of Biology & Department of Earth Sciences, Carleton University, 1125 Colonel By Dr, Ottawa, ON K1S 5B6, Canada
| | - C Richard Harington
- Palaeobiology, Canadian Museum of Nature, PO Box 3443 STN "D", Ottawa, Ontario, K1P 6P4, Canada
| | - Stuart C White
- School of Dentistry, University of California, Los Angeles, 10833 Le Conte Ave., Los Angeles, California, 90095, United States
| | - Richard H Tedford
- Division of Paleontology, American Museum of Natural History, Central Park West at 79th Street, New York, New York, 10024, United States
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98
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Schmickl R, Marburger S, Bray S, Yant L. Hybrids and horizontal transfer: introgression allows adaptive allele discovery. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5453-5470. [PMID: 29096001 DOI: 10.1093/jxb/erx297] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Evolution has devised countless remarkable solutions to diverse challenges. Understanding the mechanistic basis of these solutions provides insights into how biological systems can be subtly tweaked without maladaptive consequences. The knowledge gained from illuminating these mechanisms is equally important to our understanding of fundamental evolutionary mechanisms as it is to our hopes of developing truly rational plant breeding and synthetic biology. In particular, modern population genomic approaches are proving very powerful in the detection of candidate alleles for mediating consequential adaptations that can be tested functionally. Especially striking are signals gained from contexts involving genetic transfers between populations, closely related species, or indeed between kingdoms. Here we discuss two major classes of these scenarios, adaptive introgression and horizontal gene flow, illustrating discoveries made across kingdoms.
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Affiliation(s)
- Roswitha Schmickl
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague, Czech Republic
| | - Sarah Marburger
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sian Bray
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Levi Yant
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
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99
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Myers EA, Burgoon JL, Ray JM, Martínez-Gómez JE, Matías-Ferrer N, Mulcahy DG, Burbrink FT. Coalescent Species Tree Inference of Coluber and Masticophis. COPEIA 2017. [DOI: 10.1643/ch-16-552] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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100
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Lammers F, Gallus S, Janke A, Nilsson MA. Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable Element Insertions in Low-Coverage Genomes. Genome Biol Evol 2017; 9:2862-2878. [PMID: 28985298 PMCID: PMC5737362 DOI: 10.1093/gbe/evx170] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2017] [Indexed: 12/15/2022] Open
Abstract
Phylogenetic reconstruction from transposable elements (TEs) offers an additional perspective to study evolutionary processes. However, detecting phylogenetically informative TE insertions requires tedious experimental work, limiting the power of phylogenetic inference. Here, we analyzed the genomes of seven bear species using high-throughput sequencing data to detect thousands of TE insertions. The newly developed pipeline for TE detection called TeddyPi (TE detection and discovery for Phylogenetic Inference) identified 150,513 high-quality TE insertions in the genomes of ursine and tremarctine bears. By integrating different TE insertion callers and using a stringent filtering approach, the TeddyPi pipeline produced highly reliable TE insertion calls, which were confirmed by extensive in vitro validation experiments. Analysis of single nucleotide substitutions in the flanking regions of the TEs shows that these substitutions correlate with the phylogenetic signal from the TE insertions. Our phylogenomic analyses show that TEs are a major driver of genomic variation in bears and enabled phylogenetic reconstruction of a well-resolved species tree, despite strong signals for incomplete lineage sorting and introgression. The analyses show that the Asiatic black, sun, and sloth bear form a monophyletic clade, in which phylogenetic incongruence originates from incomplete lineage sorting. TeddyPi is open source and can be adapted to various TE and structural variation callers. The pipeline makes it possible to confidently extract thousands of TE insertions even from low-coverage genomes (∼10×) of nonmodel organisms. This opens new possibilities for biologists to study phylogenies and evolutionary processes as well as rates and patterns of (retro-)transposition and structural variation.
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Affiliation(s)
- Fritjof Lammers
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- Institute for Ecology, Evolution & Diversity, Biologicum, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Susanne Gallus
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- Institute for Ecology, Evolution & Diversity, Biologicum, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Maria A. Nilsson
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
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