1
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Rakotoarivelo AR, Rambuda T, Taron UH, Stalder G, O'Donoghue P, Robovský J, Hartmann S, Hofreiter M, Moodley Y. Complex patterns of gene flow and convergence in the evolutionary history of the spiral-horned antelopes (Tragelaphini). Mol Phylogenet Evol 2024; 198:108131. [PMID: 38909875 DOI: 10.1016/j.ympev.2024.108131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 05/19/2024] [Accepted: 06/15/2024] [Indexed: 06/25/2024]
Abstract
The Tragelaphini, also known as spiral-horned antelope, is a phenotypically diverse mammalian tribe comprising a single genus, Tragelaphus. The evolutionary history of this tribe has attracted the attention of taxonomists and molecular geneticists for decades because its diversity is characterised by conflicts between morphological and molecular data as well as between mitochondrial, nuclear and chromosomal DNA. These inconsistencies point to a complex history of ecological diversification, coupled by either phenotypic convergence or introgression. Therefore, to unravel the phylogenetic relationships among spiral-horned antelopes, and to further investigate the role of divergence and gene flow in trait evolution, we sequenced genomes for all nine accepted species of the genus Tragelaphus, including a genome each for the highly divergent bushbuck lineages (T. s. scriptus and T. s. sylvaticus). We successfully reconstructed the Tragelaphus species tree, providing genome-level support for the early Pliocene divergence and monophyly of the nyala (T. angasii) and lesser kudu (T. imberbis), the monophyly of the two eland species (T. oryx and T. derbianus) and, importantly, the monophyly of kéwel (T. s. scriptus) and imbabala (T. s. sylvaticus) bushbuck. We found strong evidence for gene flow in at least four of eight nodes on the species tree. Among the six phenotypic traits assessed here, only habitat type mapped onto the species tree without homoplasy, showing that trait evolution was the result of complex patterns of divergence, introgression and convergent evolution.
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Affiliation(s)
- Andrinajoro R Rakotoarivelo
- Department of Biological Sciences, University of Venda, Private Bag X5050, Thohoyandou 0950, Republic of South Africa; Department of Zoology and Entomology, University of the Free State: QwaQwa Campus, Private Bag X13, Phuthaditjhaba 9866, Republic of South Africa
| | - Thabelo Rambuda
- Department of Biological Sciences, University of Venda, Private Bag X5050, Thohoyandou 0950, Republic of South Africa; Department of Genetics, University of Pretoria, Private Bag X20, Hatfield 0028, Republic of South Africa
| | - Ulrike H Taron
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Gabrielle Stalder
- Department of Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, University of Veterinary Medicine, Savoyenstraße 1, A-1160 Wien, Austria
| | | | - Jan Robovský
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 1760, 37005 České Budějovice, Czech Republic
| | - Stefanie Hartmann
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Yoshan Moodley
- Department of Biological Sciences, University of Venda, Private Bag X5050, Thohoyandou 0950, Republic of South Africa.
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2
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Long Z, Rieseberg LH. Documenting homoploid hybrid speciation. Mol Ecol 2024:e17412. [PMID: 38780141 DOI: 10.1111/mec.17412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/11/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
Homoploid hybrid speciation is challenging to document because hybridization can lead to outcomes other than speciation. Thus, some authors have argued that establishment of homoploid hybrid speciation should include evidence that reproductive barriers isolating the hybrid neo-species from its parental species were derived from hybridization. While this criterion is difficult to satisfy, several recent papers have successfully employed a common pipeline to identify candidate genes underlying such barriers and (in one case) to validate their function. We describe this pipeline, its application to several plant and animal species and what we have learned about homoploid hybrid speciation as a consequence. We argue that - given the ubiquity of admixture and the polygenic basis of reproductive isolation - homoploid hybrid speciation could be much more common and more protracted than suggested by earlier conceptual arguments and theoretical studies.
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Affiliation(s)
- Zhiqin Long
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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3
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Jia Y, Liu ML, López-Pujol J, Jia RW, Kou YX, Yue M, Guan TX, Li ZH. The hybridization origin of the Chinese endemic herb genus Notopterygium (Apiaceae): Evidence from population genomics and ecological niche analysis. Mol Phylogenet Evol 2023; 182:107736. [PMID: 36805473 DOI: 10.1016/j.ympev.2023.107736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/03/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023]
Abstract
Hybridization is recognized as a major force in species evolution and biodiversity formation, generally leading to the origin and differentiation of new species. Multiple hybridization events cannot easily be reconstructed, yet they offer the potential to study a number of evolutionary processes. Here, we used nuclear expressed sequence tag-simple sequence repeat and large-scale single nucleotide polymorphism variation data, combined with niche analysis, to investigate the putative independent hybridization events in Notopterygium, a group of perennial herb plants endemic to China. Population genomic analysis indicated that the four studied species are genetically well-delimited and that N. forrestii and N. oviforme have originated by hybridization. According to Approximate Bayesian Computation, the best-fit model involved the formation of N. forrestii from the crossing of N. franchetii and N. incisum, with N. forrestii further backcrossing to N. franchetii to form N. oviforme. The niche analyses indicated that niche divergence [likely triggered by the regional climate changes, particularly the intensification of East Asian winter monsoon, and tectonic movements (affecting both Qinghai-Tibetan Plateau and Qinling Mountains)] may have promoted and maintained the reproductive isolation among hybrid species. N. forrestii shows ecological specialization with respect to their parental species, whereas N. oviforme has completely shifted its niche. These results suggested that the climate and environmental factors together triggered the two-step hybridization of the East Asia herb plants. Our study also emphasizes the power of genome-wide SNPs for investigating suspected cases of hybridization, particularly unravelling old hybridization events.
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Affiliation(s)
- Yun Jia
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China; Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi'an 710061, Shaanxi, China
| | - Mi-Li Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Jordi López-Pujol
- Botanic Institute of Barcelona (IBB), CSIC-Ajuntament de Barcelona, Barcelona 08038, Catalonia, Spain; Escuela de Ciencias Ambientales, Universidad Espíritu Santo (UEES), Samborondón 091650, Ecuador
| | - Rui-Wen Jia
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Yi-Xuan Kou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China; Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi'an 710061, Shaanxi, China
| | - Tian-Xia Guan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China; Key Laboratory of Hexi Corridor Resources Utilization of Gansu, College of Life Sciences and Engineering, Hexi University, Zhangye 734000, Gansu, China.
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China.
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4
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Dai C, Feng P. Multiple concordant cytonuclear divergences and potential hybrid speciation within a species complex in Asia. Mol Phylogenet Evol 2023; 180:107709. [PMID: 36657627 DOI: 10.1016/j.ympev.2023.107709] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/29/2022] [Accepted: 01/12/2023] [Indexed: 01/19/2023]
Abstract
Various environmental factors impact the distribution, population structure, demography and evolutionary trajectory of a bird species, leading to genetic and morphological divergences between populations across its distribution. The Paradoxornis webbianus species complex is found throughout much of East Asia, where its geographically distinct populations exhibit dramatic morphological variation. This has resulted in a hotly debated taxonomy. This study intended to identify genetic divergence patterns and their underlying contributing factors for this species complex. We collected 243 birds, whose data was combined with those available in GenBank to perform phylogeographic analyses using one mitochondrial and six nuclear loci. Six mitochondrial clades were observed in the species complex, while individual-based Bayesian clustering using nuclear markers showed multiple congruent breaks. Overall, the six molecular lineages could be recognized as independent species under the lineage species concept in view of genetic divergence, clade-specific morphological changes and distribution: P. webbianus, P. w. bulomachus, P. alphonsianus, P. a. ganluoensis, P. brunneus brunneus and P. b. ricketti. The estimated divergence times range from 0.46 to 3.36 million years ago, suggesting it was likely impacted by paleoclimatic changes. Interestingly, P. alphonsianus carries two divergent mitochondrial lineages shared with P. webbianus and P. a. ganluoensis, respectively, and analyses based on nuclear loci found a similar pattern. We discussed the various hypotheses for this pattern and argued that P. alphonsianus was likely the result of hybridization between P. webbianus and P. a. ganluoensis. Further data on genome, transcriptome and breeding ecology are needed to address the hypothesis of hybrid speciation and its underlying mechanisms.
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Affiliation(s)
- Chuanyin Dai
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin 541006, China; Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin 541006, China.
| | - Ping Feng
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin 541006, China; Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin 541006, China
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5
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Shepherd LD, Miskelly CM, Bulgarella M, Tennyson AJD. Genomic analyses of fairy and fulmar prions (Procellariidae: Pachyptila spp.) reveals parallel evolution of bill morphology, and multiple species. PLoS One 2022; 17:e0275102. [PMID: 36166411 PMCID: PMC9514608 DOI: 10.1371/journal.pone.0275102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/11/2022] [Indexed: 11/18/2022] Open
Abstract
Prions are small petrels that are abundant around the Southern Ocean. Here we use mitochondrial DNA (COI and cytochrome b) and nuclear reduced representation sequencing (ddRADseq) to examine the relationships within and between fairy (Pachyptila turtur) and fulmar (P. crassirostris) prions from across their distributions. We found that neither species was recovered as monophyletic, and that at least three species were represented. Furthermore, we detected several genetic lineages that are also morphologically distinct occurring in near sympatry at two locations (Snares Islands and Chatham Islands). The factors that have driven diversification in the fairy/fulmar prion complex are unclear but may include philopatry, differences in foraging distribution during breeding, differences in non-breeding distributions and breeding habitat characteristics. The observed distribution of genetic variation in the fairy/fulmar prion complex is consistent with population expansion from ice-free Last Glacial Maximum refugia into previously glaciated areas.
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Affiliation(s)
- Lara D. Shepherd
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
- * E-mail:
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6
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Independent evolution of intermediate bill widths in a seabird clade. Mol Genet Genomics 2021; 297:183-198. [PMID: 34921614 PMCID: PMC8803701 DOI: 10.1007/s00438-021-01845-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/28/2021] [Indexed: 10/29/2022]
Abstract
Interspecific introgression can occur between species that evolve rapidly within an adaptive radiation. Pachyptila petrels differ in bill size and are characterised by incomplete reproductive isolation, leading to interspecific gene flow. Salvin's prion (Pachyptila salvini), whose bill width is intermediate between broad-billed (P. vittata) and Antarctic (P. desolata) prions, evolved through homoploid hybrid speciation. MacGillivray's prion (P. macgillivrayi), known from a single population on St Paul (Indian Ocean), has a bill width intermediate between salvini and vittata and could also be the product of interspecies introgression or hybrid speciation. Recently, another prion population phenotypically similar to macgillivrayi was discovered on Gough (Atlantic Ocean), where it breeds 3 months later than vittata. The similarity in bill width between the medium-billed birds on Gough and macgillivrayi suggest that they could be closely related. In this study, we used genetic and morphological data to infer the phylogenetic position and evolutionary history of P. macgillivrayi and the Gough medium-billed prion relative other Pachyptila taxa, to determine whether species with medium bill widths evolved through common ancestry or convergence. We found that Gough medium-billed prions belong to the same evolutionary lineage as macgillivrayi, representing a new population of MacGillivray's prion that originated through a colonisation event from St Paul. We show that macgillivrayi's medium bill width evolved through divergence (genetic drift) and independently from that of salvini, which evolved through hybridisation (gene flow). This represents the independent convergence towards a similarly medium-billed phenotype. The newly discovered MacGillivray's prion population on Gough is of utmost conservation relevance, as the relict macgillivrayi population in the Indian Ocean is very small.
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7
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Päckert M. No hybrid snowcocks in the Altai-Hyper-variable markers can be problematic for phylogenetic inference. Ecol Evol 2021; 11:16354-16364. [PMID: 34824832 PMCID: PMC8601899 DOI: 10.1002/ece3.8199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/24/2021] [Accepted: 09/10/2021] [Indexed: 11/10/2022] Open
Abstract
A recent article in Ecology and Evolution featured the discovery of hybrid snowcocks (Tetraogallus) and speculated on the hybrid origin of an extant species (T. altaicus). Comprehensive re-analyses of original data from the latter paper reliably refute the phylogenetic hypothesis taken as firm evidence of a past hybridization event in these birds. The new re-analyses showed that there is no evidence of hybridization in these snowcocks from the data available so far.
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Affiliation(s)
- Martin Päckert
- Senckenberg Natural History Collections Museum of Zoology Dresden Germany
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8
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Ferrer Obiol J, James HF, Chesser RT, Bretagnolle V, González-Solís J, Rozas J, Riutort M, Welch AJ. Integrating Sequence Capture and Restriction Site-Associated DNA Sequencing to Resolve Recent Radiations of Pelagic Seabirds. Syst Biol 2021; 70:976-996. [PMID: 33512506 PMCID: PMC8357341 DOI: 10.1093/sysbio/syaa101] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 11/13/2020] [Accepted: 12/15/2020] [Indexed: 01/01/2023] Open
Abstract
The diversification of modern birds has been shaped by a number of radiations. Rapid diversification events make reconstructing the evolutionary relationships among taxa challenging due to the convoluted effects of incomplete lineage sorting (ILS) and introgression. Phylogenomic data sets have the potential to detect patterns of phylogenetic incongruence, and to address their causes. However, the footprints of ILS and introgression on sequence data can vary between different phylogenomic markers at different phylogenetic scales depending on factors such as their evolutionary rates or their selection pressures. We show that combining phylogenomic markers that evolve at different rates, such as paired-end double-digest restriction site-associated DNA (PE-ddRAD) and ultraconserved elements (UCEs), allows a comprehensive exploration of the causes of phylogenetic discordance associated with short internodes at different timescales. We used thousands of UCE and PE-ddRAD markers to produce the first well-resolved phylogeny of shearwaters, a group of medium-sized pelagic seabirds that are among the most phylogenetically controversial and endangered bird groups. We found that phylogenomic conflict was mainly derived from high levels of ILS due to rapid speciation events. We also documented a case of introgression, despite the high philopatry of shearwaters to their breeding sites, which typically limits gene flow. We integrated state-of-the-art concatenated and coalescent-based approaches to expand on previous comparisons of UCE and RAD-Seq data sets for phylogenetics, divergence time estimation, and inference of introgression, and we propose a strategy to optimize RAD-Seq data for phylogenetic analyses. Our results highlight the usefulness of combining phylogenomic markers evolving at different rates to understand the causes of phylogenetic discordance at different timescales. [Aves; incomplete lineage sorting; introgression; PE-ddRAD-Seq; phylogenomics; radiations; shearwaters; UCEs.].
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Affiliation(s)
- Joan Ferrer Obiol
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain
| | - Helen F James
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - R Terry Chesser
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- U.S. Geological Survey, Patuxent Wildlife Research Center, Laurel, MD, USA
| | - Vincent Bretagnolle
- Centre d’Études Biologiques de Chizé, CNRS & La Rochelle Université, 79360, Villiers en Bois, France
| | - Jacob González-Solís
- Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain
| | - Marta Riutort
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain
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9
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Pavón-Vázquez CJ, Brennan IG, Keogh JS. A Comprehensive Approach to Detect Hybridization Sheds Light on the Evolution of Earth's Largest Lizards. Syst Biol 2021; 70:877-890. [PMID: 33512509 DOI: 10.1093/sysbio/syaa102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 11/14/2022] Open
Abstract
Hybridization between species occurs more frequently in vertebrates than traditionally thought but distinguishing ancient hybridization from other phenomena that generate similar evolutionary patterns remains challenging. Here, we used a comprehensive workflow to discover evidence of ancient hybridization between the Komodo dragon (Varanus komodoensis) from Indonesia and a common ancestor of an Australian group of monitor lizards known colloquially as sand monitors. Our data comprises >300 nuclear loci, mitochondrial genomes, phenotypic data, fossil and contemporary records, and past/present climatic data. We show that the four sand monitor species share more nuclear alleles with V. komodoensis than expected given a bifurcating phylogeny, likely as a result of hybridization between the latter species and a common ancestor of sand monitors. Sand monitors display phenotypes that are intermediate between their closest relatives and V. komodoensis. Biogeographic analyses suggest that V. komodoensis and ancestral sand monitors co-occurred in northern Australia. In agreement with the fossil record, this provides further evidence that the Komodo dragon once inhabited the Australian continent. Our study shows how different sources of evidence can be used to thoroughly characterize evolutionary histories that deviate from a treelike pattern, that hybridization can have long-lasting effects on phenotypes and that detecting hybridization can improve our understanding of evolutionary and biogeographic patterns.
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Affiliation(s)
- Carlos J Pavón-Vázquez
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Ian G Brennan
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
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10
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Lopes F, Oliveira LR, Kessler A, Beux Y, Crespo E, Cárdenas-Alayza S, Majluf P, Sepúlveda M, Brownell RL, Franco-Trecu V, Páez-Rosas D, Chaves J, Loch C, Robertson BC, Acevedo-Whitehouse K, Elorriaga-Verplancken FR, Kirkman SP, Peart CR, Wolf JBW, Bonatto SL. Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere. Syst Biol 2020; 70:786-802. [PMID: 33367817 DOI: 10.1093/sysbio/syaa099] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/02/2020] [Accepted: 12/08/2020] [Indexed: 12/25/2022] Open
Abstract
The phylogeny and systematics of fur seals and sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount of molecular data. However, only a few phylogenetic relationships have reached acceptance because of strong gene-tree species tree discordance. Divergence times estimates in the group also vary largely between studies. These uncertainties impeded the understanding of the biogeographical history of the group, such as when and how trans-equatorial dispersal and subsequent speciation events occurred. Here, we used high-coverage genome-wide sequencing for 14 of the 15 species of Otariidae to elucidate the phylogeny of the family and its bearing on the taxonomy and biogeographical history. Despite extreme topological discordance among gene trees, we found a fully supported species tree that agrees with the few well-accepted relationships and establishes monophyly of the genus Arctocephalus. Our data support a relatively recent trans-hemispheric dispersal at the base of a southern clade, which rapidly diversified into six major lineages between 3 and 2.5 Ma. Otaria diverged first, followed by Phocarctos and then four major lineages within Arctocephalus. However, we found Zalophus to be nonmonophyletic, with California (Zalophus californianus) and Steller sea lions (Eumetopias jubatus) grouping closer than the Galapagos sea lion (Zalophus wollebaeki) with evidence for introgression between the two genera. Overall, the high degree of genealogical discordance was best explained by incomplete lineage sorting resulting from quasi-simultaneous speciation within the southern clade with introgresssion playing a subordinate role in explaining the incongruence among and within prior phylogenetic studies of the family. [Hybridization; ILS; phylogenomics; Pleistocene; Pliocene; monophyly.].
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Affiliation(s)
- Fernando Lopes
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900 Porto Alegre, RS, Brazil.,Laboratório de Ecologia de Mamíferos, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, Brazil
| | - Larissa R Oliveira
- Laboratório de Ecologia de Mamíferos, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, Brazil.,GEMARS, Grupo de Estudos de Mamíferos Aquáticos do Rio Grande do Sul, 95560-000 Torres, RS, Brazil
| | - Amanda Kessler
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900 Porto Alegre, RS, Brazil
| | - Yago Beux
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900 Porto Alegre, RS, Brazil
| | - Enrique Crespo
- Centro Nacional Patagónico - CENPAT, CONICET, Puerto Madryn, Argentina
| | - Susana Cárdenas-Alayza
- Centro para la Sostenibilidad Ambiental, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Patricia Majluf
- Centro para la Sostenibilidad Ambiental, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Maritza Sepúlveda
- Centro de Investigación y Gestión de Recursos Naturales (CIGREN), Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
| | - Robert L Brownell
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration, NOAA, La Jolla, USA
| | - Valentina Franco-Trecu
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Diego Páez-Rosas
- Colegio de Ciencias Biológicas y Ambientales, COCIBA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Jaime Chaves
- Colegio de Ciencias Biológicas y Ambientales, COCIBA, Universidad San Francisco de Quito, Quito, Ecuador.,Department of Biology, San Francisco State University, 1800 Holloway Ave, San Francisco, CA, USA
| | - Carolina Loch
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
| | | | - Karina Acevedo-Whitehouse
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Universidad Autónoma de Querétaro, Querétaro, Mexico
| | | | - Stephen P Kirkman
- Department of Environmental Affairs, Oceans and Coasts, Cape Town, South Africa
| | - Claire R Peart
- Department Biologie II, Division of Evolutionary Biology, Ludwig-Maximilians-Universität München, Münich, Germany
| | - Jochen B W Wolf
- Department Biologie II, Division of Evolutionary Biology, Ludwig-Maximilians-Universität München, Münich, Germany
| | - Sandro L Bonatto
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900 Porto Alegre, RS, Brazil
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11
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Lukhtanov VA, Dincă V, Friberg M, Vila R, Wiklund C. Incomplete Sterility of Chromosomal Hybrids: Implications for Karyotype Evolution and Homoploid Hybrid Speciation. Front Genet 2020; 11:583827. [PMID: 33193715 PMCID: PMC7594530 DOI: 10.3389/fgene.2020.583827] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/14/2020] [Indexed: 11/17/2022] Open
Abstract
Heterozygotes for major chromosomal rearrangements such as fusions and fissions are expected to display a high level of sterility due to problems during meiosis. However, some species, especially plants and animals with holocentric chromosomes, are known to tolerate chromosomal heterozygosity even for multiple rearrangements. Here, we studied male meiotic chromosome behavior in four hybrid generations (F1–F4) between two chromosomal races of the Wood White butterfly Leptidea sinapis differentiated by at least 24 chromosomal fusions/fissions. Previous work showed that these hybrids were fertile, although their fertility was reduced as compared to crosses within chromosomal races. We demonstrate that (i) F1 hybrids are highly heterozygous with nearly all chromosomes participating in the formation of trivalents at the first meiotic division, and (ii) that from F1 to F4 the number of trivalents decreases and the number of bivalents increases. We argue that the observed process of chromosome sorting would, if continued, result in a new homozygous chromosomal race, i.e., in a new karyotype with intermediate chromosome number and, possibly, in a new incipient homoploid hybrid species. We also discuss the segregational model of karyotype evolution and the chromosomal model of homoploid hybrid speciation.
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Affiliation(s)
- Vladimir A Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Saint Petersburg, Russia
| | - Vlad Dincă
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland.,Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Magne Friberg
- Biodiversity Unit, Department of Biology, Lund University, Lund, Sweden
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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Ramos R, Paiva VH, Zajková Z, Precheur C, Fagundes AI, Jodice PGR, Mackin W, Zino F, Bretagnolle V, González-Solís J. Spatial ecology of closely related taxa: the case of the little shearwater complex in the North Atlantic Ocean. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Seabirds inhabiting vast water masses provide numerous examples where opposing phenomena, such as natal and breeding philopatry vs. vagility have dug cryptic taxonomic boundaries among closely related taxa. The taxonomy of little shearwaters of the North Atlantic Ocean (Little–Audubon’s shearwater complex, Puffinus assimilis–lherminieri) still remains unclear, and complementary information on non-breeding distributions and at-sea behaviour becomes essential to unravel divergent local adaptations to specific habitats. Using miniaturized light-level geolocators from seven study areas in the North Atlantic, we evaluate the spatial and habitat segregation, estimate the timing of their key life-cycle events and describe the at-sea behaviour of three taxa of these little shearwaters year-round to distinguish ecological patterns and specializations that could ultimately unravel potential lineage divergences. We also assess morphometric data from birds that were breeding at each study area to further discuss potential adaptations to specific habitats. Our results show that, while birds from different taxa segregated in space and habitats, they share ecological plasticity, similar annual phenology and diel foraging behaviour. These ecological inconsistencies, while defining the evolutionary stressors faced by these taxa, do not suggest the existence of three Evolutionary Significant Units. However, they confirm the recent evolutionary divergence among the three little shearwaters of the North Atlantic.
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Affiliation(s)
- Raül Ramos
- Institut de Recerca de la Biodiversitat (IRBio) and Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Av Diagonal, Barcelona, Spain
| | - Vitor H Paiva
- University of Coimbra, MARE - Marine and Environmental Sciences Centre, Department of Life Sciences, Calçada Martim de Freitas, Coimbra, Portugal
| | - Zuzana Zajková
- Institut de Recerca de la Biodiversitat (IRBio) and Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Av Diagonal, Barcelona, Spain
- Centre for Advanced Studies of Blanes (CEAB-CSIC), Accés Cala St. Francesc 14, Blanes, Spain
| | - Carine Precheur
- CEBC, UMR, CNRS & Université de La Rochelle, Villiers en Bois, France
- Laboratoire Biologie marine (EA926), Université des Antilles, Pointe-à-Pitre, Guadeloupe, France
| | - Ana Isabel Fagundes
- Portuguese Society for the Study of Birds (SPEA), Avenida Columbano Bordalo Pinheiro, Lisboa, Portugal
| | - Patrick G R Jodice
- US Geological Survey, South Carolina Cooperative Fish & Wildlife Research Unit, Clemson University, SC 29634 Clemson, South Carolina, USA
| | | | - Francis Zino
- Freira Conservation Project (FCP), Avenida do Infante, Funchal, Madeira, Portugal
| | | | - Jacob González-Solís
- Institut de Recerca de la Biodiversitat (IRBio) and Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Av Diagonal, Barcelona, Spain
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Quillfeldt P, Weimerskirch H, Delord K, Cherel Y. Niche switching and leapfrog foraging: movement ecology of sympatric petrels during the early breeding season. MOVEMENT ECOLOGY 2020; 8:23. [PMID: 32514358 PMCID: PMC7260822 DOI: 10.1186/s40462-020-00212-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The timing of events in the early part of the breeding season is crucially important for successful reproduction. Long-lived animals that migrate large distances independently of each other meet at the breeding sites to re-establish their pair bonds and coordinate their breeding duties with their partners. METHODS Using miniature light-geolocation and immersion data together with blood stable isotopes, we studied the early breeding season in Thin-billed prions Pachyptila belcheri, Antarctic prions P. desolata and Blue petrels Halobaena caerulea breeding at Kerguelen Islands in the Indian Ocean. These three species exhibit differences in their winter habitat and timing of migration, moult and breeding. We hypothesised that these differences would influence their behaviour during the early breeding season. RESULTS In line with our hypothesis, we found clear differences not only in the timing of colony attendance, but also in the time budgets while at sea and in habitat use. Both early breeding Blue petrels and late breeding Antarctic prions spent about 8 h per day in flight and 15 h foraging. In comparison, Thin-billed prions, which breed in mid-summer, spent less time (5 h daily) in flight and more time (18 h daily) foraging, thus maximizing the time spent foraging during the longest daylight days of the year. While the ecological habitat parameters (sea temperature, wind, productivity) of Thin-billed prions and Blue petrels were relatively stable throughout the year, Antarctic prions showed clear niche switching, caused by leapfrogging between the northernmost winter distribution to the southernmost distribution during the early breeding season. Blood stable isotopes confirmed the habitat switch between the inter-breeding and early breeding periods and highlighted trophic segregation with Blue petrels feeding more on fish and Antarctic petrels more on crustaceans during the early breeding period. CONCLUSION We found that the three sympatric petrel species segregated in time and space, both in the winter and the early breeding season. The interplay of timing and distribution meant that the three species show the full range of migratory strategies, from niche-tracking Blue petrels to niche-switching Antarctic prions. The latitudinal distribution resembled the leapfrogging of terrestrial avian migrant species or populations.
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Affiliation(s)
- Petra Quillfeldt
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
| | - Henri Weimerskirch
- Centre d’Etudes Biologiques de Chizé, UMR 7372 du CNRS-La Rochelle Université, 79360 Villiers-en-Bois, France
| | - Karine Delord
- Centre d’Etudes Biologiques de Chizé, UMR 7372 du CNRS-La Rochelle Université, 79360 Villiers-en-Bois, France
| | - Yves Cherel
- Centre d’Etudes Biologiques de Chizé, UMR 7372 du CNRS-La Rochelle Université, 79360 Villiers-en-Bois, France
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