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Doronina L, Hughes GM, Moreno-Santillan D, Lawless C, Lonergan T, Ryan L, Jebb D, Kirilenko BM, Korstian JM, Dávalos LM, Vernes SC, Myers EW, Teeling EC, Hiller M, Jermiin LS, Schmitz J, Springer MS, Ray DA. Contradictory Phylogenetic Signals in the Laurasiatheria Anomaly Zone. Genes (Basel) 2022; 13:766. [PMID: 35627151 PMCID: PMC9141728 DOI: 10.3390/genes13050766] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/12/2022] [Accepted: 04/21/2022] [Indexed: 02/04/2023] Open
Abstract
Relationships among laurasiatherian clades represent one of the most highly disputed topics in mammalian phylogeny. In this study, we attempt to disentangle laurasiatherian interordinal relationships using two independent genome-level approaches: (1) quantifying retrotransposon presence/absence patterns, and (2) comparisons of exon datasets at the levels of nucleotides and amino acids. The two approaches revealed contradictory phylogenetic signals, possibly due to a high level of ancestral incomplete lineage sorting. The positions of Eulipotyphla and Chiroptera as the first and second earliest divergences were consistent across the approaches. However, the phylogenetic relationships of Perissodactyla, Cetartiodactyla, and Ferae, were contradictory. While retrotransposon insertion analyses suggest a clade with Cetartiodactyla and Ferae, the exon dataset favoured Cetartiodactyla and Perissodactyla. Future analyses of hitherto unsampled laurasiatherian lineages and synergistic analyses of retrotransposon insertions, exon and conserved intron/intergenic sequences might unravel the conflicting patterns of relationships in this major mammalian clade.
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Affiliation(s)
- Liliya Doronina
- Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany;
| | - Graham M. Hughes
- School of Biology and Environmental Science, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland; (C.L.); (T.L.); (L.R.); (E.C.T.); (L.S.J.)
| | - Diana Moreno-Santillan
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA; (D.M.-S.); (J.M.K.)
- Department of Integrative Biology, University of California, Berkeley, CA 92697, USA
| | - Colleen Lawless
- School of Biology and Environmental Science, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland; (C.L.); (T.L.); (L.R.); (E.C.T.); (L.S.J.)
| | - Tadhg Lonergan
- School of Biology and Environmental Science, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland; (C.L.); (T.L.); (L.R.); (E.C.T.); (L.S.J.)
| | - Louise Ryan
- School of Biology and Environmental Science, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland; (C.L.); (T.L.); (L.R.); (E.C.T.); (L.S.J.)
| | - David Jebb
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; (D.J.); (E.W.M.)
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Bogdan M. Kirilenko
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany; (B.M.K.); (M.H.)
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Faculty of Biosciences, Goethe-University, 60438 Frankfurt, Germany
| | - Jennifer M. Korstian
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA; (D.M.-S.); (J.M.K.)
| | - Liliana M. Dávalos
- Department of Ecology and Evolution and Consortium for Inter—Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY 11794, USA;
| | - Sonja C. Vernes
- School of Biology, The University of St Andrews, St Andrews KY16 9ST, UK;
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, 6525 Nijmegen, The Netherlands
| | - Eugene W. Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; (D.J.); (E.W.M.)
- Faculty of Computer Science, Technical University Dresden, 01307 Dresden, Germany
- The Okinawa Institute of Science and Technology, Okinawa 904-0495, Japan
| | - Emma C. Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland; (C.L.); (T.L.); (L.R.); (E.C.T.); (L.S.J.)
| | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany; (B.M.K.); (M.H.)
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Faculty of Biosciences, Goethe-University, 60438 Frankfurt, Germany
| | - Lars S. Jermiin
- School of Biology and Environmental Science, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland; (C.L.); (T.L.); (L.R.); (E.C.T.); (L.S.J.)
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
- Earth Institute, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Jürgen Schmitz
- Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany;
| | - Mark S. Springer
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, CA 92521, USA;
| | - David A. Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA; (D.M.-S.); (J.M.K.)
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Allio R, Tilak MK, Scornavacca C, Avenant NL, Kitchener AC, Corre E, Nabholz B, Delsuc F. High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox. eLife 2021; 10:e63167. [PMID: 33599612 PMCID: PMC7963486 DOI: 10.7554/elife.63167] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/16/2021] [Indexed: 12/26/2022] Open
Abstract
In a context of ongoing biodiversity erosion, obtaining genomic resources from wildlife is essential for conservation. The thousands of yearly mammalian roadkill provide a useful source material for genomic surveys. To illustrate the potential of this underexploited resource, we used roadkill samples to study the genomic diversity of the bat-eared fox (Otocyon megalotis) and the aardwolf (Proteles cristatus), both having subspecies with similar disjunct distributions in Eastern and Southern Africa. First, we obtained reference genomes with high contiguity and gene completeness by combining Nanopore long reads and Illumina short reads. Then, we showed that the two subspecies of aardwolf might warrant species status (P. cristatus and P. septentrionalis) by comparing their genome-wide genetic differentiation to pairs of well-defined species across Carnivora with a new Genetic Differentiation index (GDI) based on only a few resequenced individuals. Finally, we obtained a genome-scale Carnivora phylogeny including the new aardwolf species.
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Affiliation(s)
- Rémi Allio
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Marie-Ka Tilak
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Celine Scornavacca
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Nico L Avenant
- National Museum and Centre for Environmental Management, University of the Free StateBloemfonteinSouth Africa
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums ScotlandEdinburghUnited Kingdom
| | - Erwan Corre
- CNRS, Sorbonne Université, CNRS, ABiMS, Station Biologique de RoscoffRoscoffFrance
| | - Benoit Nabholz
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
- Institut Universitaire de France (IUF)ParisFrance
| | - Frédéric Delsuc
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
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3
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Abstract
To effectively analyze the increasing amounts of available genomic data, improved comparative analytical tools that are accessible to and applicable by a broad scientific community are essential. We built the “2-n-way” software suite to provide a fundamental and innovative processing framework for revealing and comparing inserted elements among various genomes. The suite comprises two user-friendly web-based modules. The 2-way module generates pairwise whole-genome alignments of target and query species. The resulting genome coordinates of blocks (matching sequences) and gaps (missing sequences) from multiple 2-ways are then transferred to the n-way module and sorted into projects, in which user-defined coordinates from reference species are projected to the block/gap coordinates of orthologous loci in query species to provide comparative information about presence (blocks) or absence (gaps) patterns of targeted elements over many entire genomes and phylogroups. Thus, the 2-n-way software suite is ideal for performing multidirectional, non-ascertainment-biased screenings to extract all possible presence/absence data of user-relevant elements in orthologous sequences. To highlight its applicability and versatility, we used 2-n-way to expose approximately 100 lost introns in vertebrates, analyzed thousands of potential phylogenetically informative bat and whale retrotransposons, and novel human exons as well as thousands of human polymorphic retrotransposons.
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4
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Watson DG, Pomeroy PP, Al-Tannak NF, Kennedy MW. Stockpiling by pups and self-sacrifice by their fasting mothers observed in birth to weaning serum metabolomes of Atlantic grey seals. Sci Rep 2020; 10:7465. [PMID: 32366923 PMCID: PMC7198541 DOI: 10.1038/s41598-020-64488-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 04/15/2020] [Indexed: 12/23/2022] Open
Abstract
During the uniquely short lactations of true seals, pups acquire a greater proportion of maternal body resources, at a greater rate, than in any other group of mammals. Mothers in many species enter a period of anorexia but must preserve sufficient reserves to fuel hunting and thermoregulation for return to cold seas. Moreover, pups may undergo a period of development after weaning during which they have no maternal care or nutrition. This nutritionally closed system presents a potentially extreme case of conflict between maternal survival and adequate provisioning of offspring, likely presenting strains on their metabolisms. We examined the serum metabolomes of five mother and pup pairs of Atlantic grey seals, Halichoerus grypus, from birth to weaning. Changes with time were particularly evident in pups, with indications of strain in the fat and energy metabolisms of both. Crucially, pups accumulate certain compounds to levels that are dramatically greater than in mothers. These include compounds that pups cannot synthesise themselves, such as pyridoxine/vitamin B6, taurine, some essential amino acids, and a conditionally essential amino acid and its precursor. Fasting mothers therefore appear to mediate stockpiling of critical metabolites in their pups, potentially depleting their own reserves and prompting cessation of lactation.
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Affiliation(s)
- David G Watson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, Scotland, UK.
| | - Patrick P Pomeroy
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, St Andrews, Fife, Scotland, United Kingdom
| | - Naser F Al-Tannak
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, Scotland, UK.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kuwait University, P.O. Box 23924, Safat, 13110, Kuwait City, Kuwait
| | - Malcolm W Kennedy
- Institute of Biodiversity, Animal Health & Comparative Medicine, Graham Kerr Building, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK.
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5
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Paterson RS, Rybczynski N, Kohno N, Maddin HC. A Total Evidence Phylogenetic Analysis of Pinniped Phylogeny and the Possibility of Parallel Evolution Within a Monophyletic Framework. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2019.00457] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Cloutier A, Sackton TB, Grayson P, Clamp M, Baker AJ, Edwards SV. Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone. Syst Biol 2019; 68:937-955. [PMID: 31135914 PMCID: PMC6857515 DOI: 10.1093/sysbio/syz019] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/06/2019] [Accepted: 04/09/2019] [Indexed: 01/17/2023] Open
Abstract
Palaeognathae represent one of the two basal lineages in modern birds, and comprise the volant (flighted) tinamous and the flightless ratites. Resolving palaeognath phylogenetic relationships has historically proved difficult, and short internal branches separating major palaeognath lineages in previous molecular phylogenies suggest that extensive incomplete lineage sorting (ILS) might have accompanied a rapid ancient divergence. Here, we investigate palaeognath relationships using genome-wide data sets of three types of noncoding nuclear markers, together totaling 20,850 loci and over 41 million base pairs of aligned sequence data. We recover a fully resolved topology placing rheas as the sister to kiwi and emu + cassowary that is congruent across marker types for two species tree methods (MP-EST and ASTRAL-II). This topology is corroborated by patterns of insertions for 4274 CR1 retroelements identified from multispecies whole-genome screening, and is robustly supported by phylogenomic subsampling analyses, with MP-EST demonstrating particularly consistent performance across subsampling replicates as compared to ASTRAL. In contrast, analyses of concatenated data supermatrices recover rheas as the sister to all other nonostrich palaeognaths, an alternative that lacks retroelement support and shows inconsistent behavior under subsampling approaches. While statistically supporting the species tree topology, conflicting patterns of retroelement insertions also occur and imply high amounts of ILS across short successive internal branches, consistent with observed patterns of gene tree heterogeneity. Coalescent simulations and topology tests indicate that the majority of observed topological incongruence among gene trees is consistent with coalescent variation rather than arising from gene tree estimation error alone, and estimated branch lengths for short successive internodes in the inferred species tree fall within the theoretical range encompassing the anomaly zone. Distributions of empirical gene trees confirm that the most common gene tree topology for each marker type differs from the species tree, signifying the existence of an empirical anomaly zone in palaeognaths.
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Affiliation(s)
- Alison Cloutier
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Department of Ornithology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Timothy B Sackton
- Informatics Group, Harvard University, 28 Oxford Street, Cambridge, MA 02138, USA
| | - Phil Grayson
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Department of Ornithology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Michele Clamp
- Informatics Group, Harvard University, 28 Oxford Street, Cambridge, MA 02138, USA
| | - Allan J Baker
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, Ontario M5S 3B2, Canada
- Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, Ontario M5S 2C6, Canada
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Department of Ornithology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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Composition of the canid auditory bulla and a new look at the evolution of carnivoran entotympanics. ORG DIVERS EVOL 2019. [DOI: 10.1007/s13127-019-00395-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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8
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Sparwel M, Doronina L, Churakov G, Stegemann A, Brosius J, Robinson TJ, Schmitz J. The Volcano Rabbit in the Phylogenetic Network of Lagomorphs. Genome Biol Evol 2019; 11:11-16. [PMID: 30476046 PMCID: PMC6319600 DOI: 10.1093/gbe/evy257] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2018] [Indexed: 11/13/2022] Open
Abstract
The order Lagomorpha unifies pikas (Ochotonidae) and the hares plus rabbits (Leporidae). Phylogenetic reconstructions of the species within Leporidae based on traditional morphological or molecular sequence data provide support for conflicting hypotheses. The retroposon presence/absence patterns analyzed in this study revealed strong support for the broadly accepted splitting of lagomorphs into ochotonids and leporids with Pronolagus as the first divergence in the leporid tree. Furthermore, the retroposon presence/absence patterns nested the rare volcano rabbit, Romerolagus diazi, within an unresolved network of deeper leporid relationships and provide the first homoplasy-free image of incomplete lineage sorting and/or ancestral hybridization/introgression in rapidly radiated Leporidae. At the same time, the strongest retroposon presence/absence signal supports the volcano rabbit as a separate branch between the Pronolagus junction and a unified cluster of the remaining leporids.
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Affiliation(s)
| | - Liliya Doronina
- Institute of Experimental Pathology (ZMBE), University of Münster, Germany
| | - Gennady Churakov
- Institute of Experimental Pathology (ZMBE), University of Münster, Germany
| | - Anja Stegemann
- Institute of Experimental Pathology (ZMBE), University of Münster, Germany
| | - Jürgen Brosius
- Institute of Experimental Pathology (ZMBE), University of Münster, Germany.,Brandenburg Medical School (MHB), Neuruppin, Germany
| | - Terence J Robinson
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, South Africa
| | - Jürgen Schmitz
- Institute of Experimental Pathology (ZMBE), University of Münster, Germany
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9
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Peng C, Niu L, Deng J, Yu J, Zhang X, Zhou C, Xing J, Li J. Can-SINE dynamics in the giant panda and three other Caniformia genomes. Mob DNA 2018; 9:32. [PMID: 30455747 PMCID: PMC6230240 DOI: 10.1186/s13100-018-0137-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 11/01/2018] [Indexed: 11/10/2022] Open
Abstract
Background Although repeat sequences constitute about 37% of carnivore genomes, the characteristics and distribution of repeat sequences among carnivore genomes have not been fully investigated. Based on the updated Repbase library, we re-annotated transposable elements (TEs) in four Caniformia genomes (giant panda, polar bear, domestic dog, and domestic ferret) and performed a systematic, genome-wide comparison focusing on the Carnivora-specific SINE family, Can-SINEs. Results We found the majority of young recently integrated transposable elements are LINEs and SINEs in carnivore genomes. In particular, SINEC1_AMe, SINEC1B_AMe and SINEC_C1 are the top three most abundant Can-SINE subfamilies in the panda and polar bear genomes. Transposition in transposition analysis indicates that SINEC1_AMe and SINEC1B_AMe are the most active subfamilies in the panda and the polar bear genomes. SINEC2A1_CF and SINEC1A_CF subfamilies show a higher retrotransposition activity in the dog genome, and MVB2 subfamily is the most active Can-SINE in the ferret genome. As the giant panda is an endangered icon species, we then focused on the identification of panda specific Can-SINEs. With the panda-associated two-way genome alignments, we identified 250 putative panda-specific (PPS) elements (139 SINEC1_AMes and 111 SINEC1B_AMes) that inserted in the panda genome but were absent at the orthologous regions of the other three genomes. Further investigation of these PPS elements allowed us to identify a new Can-SINE subfamily, the SINEC1_AMe2, which was distinguishable from the current SINEC1_AMe consensus by four non-CpG sites. SINEC1_AMe2 has a high copy number (> 100,000) in the panda and polar bear genomes and the vast majority (> 96%) of the SINEC1_AMe2 elements have divergence rates less than 10% in both genomes. Conclusions Our results suggest that Can-SINEs show lineage-specific retransposition activity in the four genomes and have an important impact on the genomic landscape of different Caniformia lineages. Combining these observations with results from the COSEG, Network, and target site duplication analysis, we suggest that SINEC1_AMe2 is a young mobile element subfamily and currently active in both the panda and polar bear genomes.
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Affiliation(s)
- Changjun Peng
- 1Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life and Sciences, University of Sichuan, Chengdu, China
| | - Lili Niu
- Sichuan Wild Animal Research Institute, Chengdu Zoo, Chengdu, China
| | - Jiabo Deng
- Sichuan Wild Animal Research Institute, Chengdu Zoo, Chengdu, China
| | - Jianqiu Yu
- Sichuan Wild Animal Research Institute, Chengdu Zoo, Chengdu, China
| | - Xueyan Zhang
- 1Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life and Sciences, University of Sichuan, Chengdu, China
| | - Chuang Zhou
- 3Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan China
| | - Jinchuan Xing
- 4Department of Genetics, Human Genetic Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ USA
| | - Jing Li
- 1Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life and Sciences, University of Sichuan, Chengdu, China
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10
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Dodt WG, Gallus S, Phillips MJ, Nilsson MA. Resolving kangaroo phylogeny and overcoming retrotransposon ascertainment bias. Sci Rep 2017; 7:16811. [PMID: 29196678 PMCID: PMC5711953 DOI: 10.1038/s41598-017-16148-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 10/26/2017] [Indexed: 01/31/2023] Open
Abstract
Reconstructing phylogeny from retrotransposon insertions is often limited by access to only a single reference genome, whereby support for clades that do not include the reference taxon cannot be directly observed. Here we have developed a new statistical framework that accounts for this ascertainment bias, allowing us to employ phylogenetically powerful retrotransposon markers to explore the radiation of the largest living marsupials, the kangaroos and wallabies of the genera Macropus and Wallabia. An exhaustive in silico screening of the tammar wallaby (Macropus eugenii) reference genome followed by experimental screening revealed 29 phylogenetically informative retrotransposon markers belonging to a family of endogenous retroviruses. We identified robust support for the enigmatic swamp wallaby (Wallabia bicolor) falling within a paraphyletic genus, Macropus. Our statistical approach provides a means to test for incomplete lineage sorting and introgression/hybridization in the presence of the ascertainment bias. Using retrotransposons as “molecular fossils”, we reveal one of the most complex patterns of hemiplasy yet identified, during the rapid diversification of kangaroos and wallabies. Ancestral state reconstruction incorporating the new retrotransposon phylogenetic information reveals multiple independent ecological shifts among kangaroos into more open habitats, coinciding with the Pliocene onset of increased aridification in Australia from ~3.6 million years ago.
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Affiliation(s)
- William G Dodt
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology (QUT), 2 George Street, Brisbane, Australia.
| | - Susanne Gallus
- Senckenberg Biodiversity and Climate Research Centre (BiK-F) Frankfurt, Senckenberg Gesellschaft fuer Naturforschung, Senckenberganlage 25, Frankfurt am Main, Germany
| | - Matthew J Phillips
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology (QUT), 2 George Street, Brisbane, Australia.
| | - Maria A Nilsson
- Senckenberg Biodiversity and Climate Research Centre (BiK-F) Frankfurt, Senckenberg Gesellschaft fuer Naturforschung, Senckenberganlage 25, Frankfurt am Main, Germany.
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11
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Doronina L, Churakov G, Kuritzin A, Shi J, Baertsch R, Clawson H, Schmitz J. Speciation network in Laurasiatheria: retrophylogenomic signals. Genome Res 2017; 27:997-1003. [PMID: 28298429 PMCID: PMC5453332 DOI: 10.1101/gr.210948.116] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 02/23/2017] [Indexed: 11/24/2022]
Abstract
Rapid species radiation due to adaptive changes or occupation of new ecospaces challenges our understanding of ancestral speciation and the relationships of modern species. At the molecular level, rapid radiation with successive speciations over short time periods-too short to fix polymorphic alleles-is described as incomplete lineage sorting. Incomplete lineage sorting leads to random fixation of genetic markers and hence, random signals of relationships in phylogenetic reconstructions. The situation is further complicated when you consider that the genome is a mosaic of ancestral and modern incompletely sorted sequence blocks that leads to reconstructed affiliations to one or the other relative, depending on the fixation of their shared ancestral polymorphic alleles. The laurasiatherian relationships among Chiroptera, Perissodactyla, Cetartiodactyla, and Carnivora present a prime example for such enigmatic affiliations. We performed whole-genome screenings for phylogenetically diagnostic retrotransposon insertions involving the representatives bat (Chiroptera), horse (Perissodactyla), cow (Cetartiodactyla), and dog (Carnivora), and extracted among 162,000 preselected cases 102 virtually homoplasy-free, phylogenetically informative retroelements to draw a complete picture of the highly complex evolutionary relations within Laurasiatheria. All possible evolutionary scenarios received considerable retrotransposon support, leaving us with a network of affiliations. However, the Cetartiodactyla-Carnivora relationship as well as the basal position of Chiroptera and an ancestral laurasiatherian hybridization process did exhibit some very clear, distinct signals. The significant accordance of retrotransposon presence/absence patterns and flanking nucleotide changes suggest an important influence of mosaic genome structures in the reconstruction of species histories.
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Affiliation(s)
- Liliya Doronina
- Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany
| | - Gennady Churakov
- Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Andrej Kuritzin
- Department of System Analysis, Saint Petersburg State Institute of Technology, 190013 St. Petersburg, Russia
| | - Jingjing Shi
- Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany
| | - Robert Baertsch
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Hiram Clawson
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Jürgen Schmitz
- Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany
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12
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Doronina L, Matzke A, Churakov G, Stoll M, Huge A, Schmitz J. The Beaver's Phylogenetic Lineage Illuminated by Retroposon Reads. Sci Rep 2017; 7:43562. [PMID: 28256552 PMCID: PMC5335264 DOI: 10.1038/srep43562] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/25/2017] [Indexed: 11/18/2022] Open
Abstract
Solving problematic phylogenetic relationships often requires high quality genome data. However, for many organisms such data are still not available. Among rodents, the phylogenetic position of the beaver has always attracted special interest. The arrangement of the beaver's masseter (jaw-closer) muscle once suggested a strong affinity to some sciurid rodents (e.g., squirrels), placing them in the Sciuromorpha suborder. Modern molecular data, however, suggested a closer relationship of beaver to the representatives of the mouse-related clade, but significant data from virtually homoplasy-free markers (for example retroposon insertions) for the exact position of the beaver have not been available. We derived a gross genome assembly from deposited genomic Illumina paired-end reads and extracted thousands of potential phylogenetically informative retroposon markers using the new bioinformatics coordinate extractor fastCOEX, enabling us to evaluate different hypotheses for the phylogenetic position of the beaver. Comparative results provided significant support for a clear relationship between beavers (Castoridae) and kangaroo rat-related species (Geomyoidea) (p < 0.0015, six markers, no conflicting data) within a significantly supported mouse-related clade (including Myodonta, Anomaluromorpha, and Castorimorpha) (p < 0.0015, six markers, no conflicting data).
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Affiliation(s)
- Liliya Doronina
- Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany
| | - Andreas Matzke
- Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany
| | - Gennady Churakov
- Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Monika Stoll
- Core Facility Genomics, Medical Faculty, University of Münster, Münster, Germany
| | - Andreas Huge
- Core Facility Genomics, Medical Faculty, University of Münster, Münster, Germany
| | - Jürgen Schmitz
- Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany
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Kuritzin A, Kischka T, Schmitz J, Churakov G. Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data. PLoS Comput Biol 2016; 12:e1004812. [PMID: 26967525 PMCID: PMC4788455 DOI: 10.1371/journal.pcbi.1004812] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 02/13/2016] [Indexed: 01/25/2023] Open
Abstract
Ancient retroposon insertions can be used as virtually homoplasy-free markers to reconstruct the phylogenetic history of species. Inherited, orthologous insertions in related species offer reliable signals of a common origin of the given species. One prerequisite for such a phylogenetically informative insertion is that the inserted element was fixed in the ancestral population before speciation; if not, polymorphically inserted elements may lead to random distributions of presence/absence states during speciation and possibly to apparently conflicting reconstructions of their ancestry. Fortunately, such misleading fixed cases are relatively rare but nevertheless, need to be considered. Here, we present novel, comprehensive statistical models applicable for (1) analyzing any pattern of rare genomic changes, (2) testing and differentiating conflicting phylogenetic reconstructions based on rare genomic changes caused by incomplete lineage sorting or/and ancestral hybridization, and (3) differentiating between search strategies involving genome information from one or several lineages. When the new statistics are applied, in non-conflicting cases a minimum of three elements present in both of two species and absent in a third group are considered significant support (p<0.05) for the branching of the third from the other two, if all three of the given species are screened equally for genome or experimental data. Five elements are necessary for significant support (p<0.05) if a diagnostic locus derived from only one of three species is screened, and no conflicting markers are detected. Most potentially conflicting patterns can be evaluated for their significance and ancestral hybridization can be distinguished from incomplete lineage sorting by considering symmetric or asymmetric distribution of rare genomic changes among possible tree configurations. Additionally, we provide an R-application to make the new KKSC insertion significance test available for the scientific community at http://retrogenomics.uni-muenster.de:3838/KKSC_significance_test/. The presence/absence patterns of transposed elements, so called jumping genes, provide invaluable information about evolution. Unfortunately, there is still no clear all-encompassing analysis of the statistical significance of insertion patterns, and the single existing model of insertion data is no longer sufficient for the emerging genomic era. Here, we have provided a comprehensive statistical framework for testing the significance of support for phylogenetic hypotheses derived from genome-level presence/absence data such as retroposon insertions and for evaluating such data for different evolutionary scenarios, including polytomy, incomplete lineage sorting, and ancestral hybridization. This statistical framework is especially important for high-throughput applications of current and upcoming genome projects due to its treatment of unlimited numbers of testable markers, and is embedded in a user-friendly R-application available to the scientific community online. Finally, a reliable, adaptable calculation for the significance of support for phylogenetic trees derived from retroposon presence/absence data is now available.
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Affiliation(s)
- Andrej Kuritzin
- Department of System Analysis, Saint Petersburg State Institute of Technology, St. Petersburg, Russia
| | - Tabea Kischka
- Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
| | - Jürgen Schmitz
- Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany
- * E-mail: (JS); (GC)
| | - Gennady Churakov
- Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany
- Institute of Evolution and Biodiversity, University of Münster, Münster, Germany
- * E-mail: (JS); (GC)
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Nilsson MA. The devil is in the details: Transposable element analysis of the Tasmanian devil genome. Mob Genet Elements 2015; 6:e1119926. [PMID: 27066301 DOI: 10.1080/2159256x.2015.1119926] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 11/10/2015] [Indexed: 10/22/2022] Open
Abstract
The third marsupial genome was sequenced from the Tasmanian devil (Sarcophilus harrisii), a species that currently is driven to extinction by a rare transmissible cancer. The transposable element (TE) landscape of the Tasmanian devil genome revealed that the main driver of retrotransposition the Long INterspersed Element 1 (LINE1) seem to have become inactivated during the past 12 million years. Strangely, the Short INterspersed Elements (SINE), that normally hijacks the LINE1 retrotransposition system, became inactive prior to LINE1 at around 30 million years ago. The SINE inactivation was in vitro verified in several species. Here I discuss that the apparent LINE1 inactivation might be caused by a genome assembly artifact. The repetitive fraction of any genome is highly complex to assemble and the observed problems are not unique to the Tasmanian devil genome.
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Affiliation(s)
- Maria A Nilsson
- Senckenberg Biodiversity and Climate Research Center, Senckenberg Gesellschaft für Naturforschung , Frankfurt am Main, Germany
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15
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Kuramoto T, Nishihara H, Watanabe M, Okada N. Determining the Position of Storks on the Phylogenetic Tree of Waterbirds by Retroposon Insertion Analysis. Genome Biol Evol 2015; 7:3180-9. [PMID: 26527652 PMCID: PMC4700946 DOI: 10.1093/gbe/evv213] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Despite many studies on avian phylogenetics in recent decades that used morphology, mitochondrial genomes, and/or nuclear genes, the phylogenetic positions of several birds (e.g., storks) remain unsettled. In addition to the aforementioned approaches, analysis of retroposon insertions, which are nearly homoplasy-free phylogenetic markers, has also been used in avian phylogenetics. However, the first step in the analysis of retroposon insertions, that is, isolation of retroposons from genomic libraries, is a costly and time-consuming procedure. Therefore, we developed a high-throughput and cost-effective protocol to collect retroposon insertion information based on next-generation sequencing technology, which we call here the STRONG (Screening of Transposons Obtained by Next Generation Sequencing) method, and applied it to 3 waterbird species, for which we identified 35,470 loci containing chicken repeat 1 retroposons (CR1). Our analysis of the presence/absence of 30 CR1 insertions demonstrated the intra- and interordinal phylogenetic relationships in the waterbird assemblage, namely 1) Loons diverged first among the waterbirds, 2) penguins (Sphenisciformes) and petrels (Procellariiformes) diverged next, and 3) among the remaining families of waterbirds traditionally classified in Ciconiiformes/Pelecaniformes, storks (Ciconiidae) diverged first. Furthermore, our genome-scale, in silico retroposon analysis based on published genome data uncovered a complex divergence history among pelican, heron, and ibis lineages, presumably involving ancient interspecies hybridization between the heron and ibis lineages. Thus, our retroposon-based waterbird phylogeny and the established phylogenetic position of storks will help to understand the evolutionary processes of aquatic adaptation and related morphological convergent evolution.
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Affiliation(s)
- Tae Kuramoto
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Hidenori Nishihara
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Maiko Watanabe
- Division of Microbiology, National Institute of Health Sciences, Setagaya, Tokyo, Japan
| | - Norihiro Okada
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan Foundation for Advancement of International Science, Tsukuba, Ibaraki, Japan Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
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