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Dimitriou AC, Soares Campos-Filho I, Georgiou A, Taiti S, Sfenthourakis S. Intra-island patterns of cryptic diversity within an oceanic island: Insights from the differentiation of Schizidium Verhoeff, 1901 (Oniscidea, Armadillidiidae) within Cyprus, with descriptions of two new species. Mol Phylogenet Evol 2023; 187:107884. [PMID: 37467903 DOI: 10.1016/j.ympev.2023.107884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/11/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023]
Abstract
Cyprus is a Mediterranean island of volcanic origin isolated for at least 5.3 Myr from surrounding continental areas. The present study focuses on the diversification of the isopod genus Schizidium within the island, including also specimens from surrounding continental areas. The genus Schizidium sensu lato is probably non monophyletic, comprising 26 species distributed from Greece to Iran. Up to date the only representative of the genus reported from Cyprus was Schizidium fissum. Aiming to investigate the patterns of genetic diversity within the focal island, to evaluate the morphology-based taxonomy of the species in the genus, and at the same time to explore phylogenetic relationships with mainland populations, we applied genome-wide ddRADseq as well as Sanger sequencing targeting three mitochondrial (16S, COI and 12S) and the nuclear NaK loci. Results of phylogenetic analyses support the existence of two distinct epigean Schizidium clades with well-defined geographic boundaries that conform to the known paleogeography of Cyprus, plus one endogean clade with restricted distribution within the island. Genetic data and morphology corroborate the assignment of this latter endogean clade to a new species, Schizidium myrrae n. sp. The two epigean clades are also considered as distinct species, one corresponding to the known S. fissum at the eastern part of the island (Pentadaktylos massif) and the other to the newly described S. christosi n. sp. distributed along the western part of the island (Troodos massif). Even though detailed examination of many specimens could not retrieve any morphological differences among representatives of these two clades, clado-chronological analysis indicates a long isolation between them, estimated at ∼ 9 Mya, as well as the sharing of a common ancestor with S. tiberianum from Israel at ∼ 15 Mya. Hence, we can consider these epigean Schizidium species as one more case of cryptic diversity on Cyprus, exhibiting similar patterns with the recently described case in the genus Armadillo.
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Affiliation(s)
- Andreas C Dimitriou
- Department of Biological Sciences, University of Cyprus, Panepistimiou Ave. 1, 2109 Aglantzia, Nicosia, Cyprus.
| | | | - Anastasia Georgiou
- Department of Biological Sciences, University of Cyprus, Panepistimiou Ave. 1, 2109 Aglantzia, Nicosia, Cyprus
| | - Stefano Taiti
- Istituto di Ricerca sugli Ecosistemi Terrestri, Consiglio Nazionale delle Ricerche, Via Madonna del Piano 10, 50019 Sesto Fiorentino (Florence), Italy; Museo di Storia Naturale dell'Università di Firenze, Sezione di Zoologia "La Specola", Via Romana 17, 50125 Florence, Italy
| | - Spyros Sfenthourakis
- Department of Biological Sciences, University of Cyprus, Panepistimiou Ave. 1, 2109 Aglantzia, Nicosia, Cyprus
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Burbrink FT, Harrington SM, Bobo D, Myers EA. Considering admixture when producing draft genomes: an example in North American ratsnakes (Pantherophis alleghaniensis/Pantherophis obsoletus). G3 (BETHESDA, MD.) 2023; 13:jkad113. [PMID: 37228097 PMCID: PMC10411579 DOI: 10.1093/g3journal/jkad113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/24/2023] [Accepted: 05/04/2023] [Indexed: 05/27/2023]
Abstract
The number of reference genomes of snakes lags behind several other vertebrate groups (e.g. birds and mammals). However, in the last two years, a concerted effort by researchers from around the world has produced new genomes of snakes representing members from several new families. Here, we present a high-quality, annotated genome of the central ratsnake (Pantherophis alleghaniensis), a member of the most diverse snake lineage, Colubroidea. Pantherophis alleghaniensis is found in the central part of the Nearctic, east of the Mississippi River. This genome was sequenced using 10X Chromium synthetic long reads and polished using Illumina short reads. The final genome assembly had an N50 of 21.82 Mb and an L50 of 22 scaffolds with a maximum scaffold length of 82.078 Mb. The genome is composed of 49.24% repeat elements dominated by long interspersed elements. We annotated this genome using transcriptome assemblies from 14 tissue types and recovered 28,368 predicted proteins. Finally, we estimated admixture proportions between two species of ratsnakes and discovered that this specimen is an admixed individual containing genomes from the western (Pantherophis obsoletus) and central ratsnakes (P. alleghaniensis). We discuss the importance of considering interspecific admixture in downstream approaches for inferring demography and phylogeny.
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, New York, NY 10024, USA
| | - Sean M Harrington
- Department of Herpetology, American Museum of Natural History, New York, NY 10024, USA
- INBRE Data Science Core, University of Wyoming, Laramie, WY 82071, USA
| | - Dean Bobo
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Edward A Myers
- Department of Herpetology, American Museum of Natural History, New York, NY 10024, USA
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
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3
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Bruni G, Chiocchio A, Nascetti G, Cimmaruta R. Different patterns of introgression in a three species hybrid zone among European cave salamanders. Ecol Evol 2023; 13:e10437. [PMID: 37636870 PMCID: PMC10447881 DOI: 10.1002/ece3.10437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/29/2023] Open
Abstract
Hybrid zones occur where genetically distinct populations meet, mate and produce offspring with mixed ancestry. In Plethodontid salamanders, introgressive hybridization is a common phenomenon, where hybrids backcross with parental populations leading to the spread of new alleles into the parental genomes. Whereas many hybrid zones have been reported in American Plethodontid salamanders, only a single hybrid zone has been documented in European plethodontids so far, which is located at the Apuan Alps in the Italian Peninsula. Here, we describe a previously unreported hybrid zone in the Northern Apennines involving all the three Plethodontid salamander species inhabiting the Italian Peninsula. We found 21 new Speleomantes sites of occurrence, from a hitherto unexplored area located at the boundaries between three Speleomantes species ranges. Using mitochondrial (Cytb and ND2 genes) and nuclear markers (two diagnostic SNPs at the NCX1 gene), we revealed a three-way contact zone where all the three mainland species hybridize: S. strinatii, S. ambrosii and S. italicus. We observed a strong mitonuclear discordance, with mitochondrial markers showing a conspicuous geographic pattern, while diagnostic nuclear SNPs coexisted in both the same populations and individuals, providing evidence of hybridization in many possible combinations. The introgression is asymmetric, with S. italicus mitogenome usually associated with S. a. ambrosii and, to a lesser extent, to S. strinatii nuclear alleles. This finding confirms that Plethodontid are a group of choice to investigate hybridization mechanisms and suggests that behavioural, genetic and ecological components may concur in determining the direction and extent of introgression.
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Affiliation(s)
| | - Andrea Chiocchio
- Department of Ecological and Biological SciencesTuscia UniversityViterboItaly
| | - Giuseppe Nascetti
- Department of Ecological and Biological SciencesTuscia UniversityViterboItaly
| | - Roberta Cimmaruta
- Department of Ecological and Biological SciencesTuscia UniversityViterboItaly
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4
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Zhang K, Huang Y, Zhang Y, Liang R, Li Q, Li R, Zhao X, Bian C, Chen Y, Wu J, Shi Q, Lin L. A chromosome-level reference genome assembly of the Reeve's moray eel (Gymnothorax reevesii). Sci Data 2023; 10:501. [PMID: 37516767 PMCID: PMC10387071 DOI: 10.1038/s41597-023-02394-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/17/2023] [Indexed: 07/31/2023] Open
Abstract
Due to potentially hostile behaviors and elusive habitats, moray eels (Muraenidae) as one group of apex predators in coral reefs all across the globe have not been well investigated. Here, we constructed a chromosome-level genome assembly for the representative Reeve's moray eel (Gymnothorax reevesii). This haplotype genome assembly is 2.17 Gb in length, and 97.87% of the sequences are anchored into 21 chromosomes. It contains 56.34% repetitive sequences and 23,812 protein-coding genes, of which 96.77% are functionally annotated. This sequenced marine species in Anguilliformes makes a good complement to the genetic resource of eel genomes. It not only provides a genetic resource for in-depth studies of the Reeve's moray eel, but also enables deep-going genomic comparisons among various eels.
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Affiliation(s)
- Kai Zhang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou, 510225, China
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, 518081, China
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Yuxuan Zhang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou, 510225, China
| | - Rishen Liang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou, 510225, China
| | - Qingqing Li
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou, 510225, China
| | - Ruihan Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, 518081, China
| | - Xiaomeng Zhao
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, 518081, China
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, 518081, China
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Yongnan Chen
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou, 510225, China
| | - Jinhui Wu
- Agro-Tech Extension Center of Guangdong Province, Guangzhou, 510225, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, 518081, China.
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
| | - Li Lin
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China.
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou, 510225, China.
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5
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Everson KM, Donohue ME, Weisrock DW. A Pervasive History of Gene Flow in Madagascar's True Lemurs (Genus Eulemur). Genes (Basel) 2023; 14:1130. [PMID: 37372308 DOI: 10.3390/genes14061130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
In recent years, it has become widely accepted that interspecific gene flow is common across the Tree of Life. Questions remain about how species boundaries can be maintained in the face of high levels of gene flow and how phylogeneticists should account for reticulation in their analyses. The true lemurs of Madagascar (genus Eulemur, 12 species) provide a unique opportunity to explore these questions, as they form a recent radiation with at least five active hybrid zones. Here, we present new analyses of a mitochondrial dataset with hundreds of individuals in the genus Eulemur, as well as a nuclear dataset containing hundreds of genetic loci for a small number of individuals. Traditional coalescent-based phylogenetic analyses of both datasets reveal that not all recognized species are monophyletic. Using network-based approaches, we also find that a species tree containing between one and three ancient reticulations is supported by strong evidence. Together, these results suggest that hybridization has been a prominent feature of the genus Eulemur in both the past and present. We also recommend that greater taxonomic attention should be paid to this group so that geographic boundaries and conservation priorities can be better established.
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Affiliation(s)
- Kathryn M Everson
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Mariah E Donohue
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
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6
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Campos-Filho IS, Dimitriou AC, Taiti S, Sfenthourakis S. The genus Armadillo Latreille, 1802 (Oniscidea, Armadillidae) from Cyprus, with descriptions of two new species. Zootaxa 2023; 5270:67-91. [PMID: 37518177 DOI: 10.11646/zootaxa.5270.1.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Indexed: 08/01/2023]
Abstract
The present work aims to morphologically characterize the species of Armadillo from Cyprus. Moreover, two new species of the genus are described, A. konstantinoui sp. nov. from several places along the island, and A. karametae sp. nov. from Pafos region. The circum-Mediterranean species A. officinalis is also redescribed.
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Affiliation(s)
| | - Andreas C Dimitriou
- Department of Biological Sciences; University of Cyprus; Lefkosia (Nicosia); Cyprus..
| | - Stefano Taiti
- Istituto di Ricerca sugli Ecosistemi Terrestri; Consiglio Nazionale delle Ricerche; Sesto Fiorentino (Florence); Italy.; Museo di Storia Naturale; Sezione di Zoologia "La Specola"; Florence; Italy.,Department of Biological Sciences; University of Cyprus; Lefkosia (Nicosia); Cyprus..
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7
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Schöneberg Y, Winter S, Arribas O, Riccardo Di Nicola M, Master M, Benjamin Owens J, Rovatsos M, Wüster W, Janke A, Fritz U. Genomics reveals broad hybridization in deeply divergent Palearctic grass and water snakes (Natrix spp.). Mol Phylogenet Evol 2023; 184:107787. [PMID: 37080398 DOI: 10.1016/j.ympev.2023.107787] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/03/2023] [Accepted: 04/13/2023] [Indexed: 04/22/2023]
Abstract
Understanding speciation is one of the cornerstones of biological diversity research. Currently, speciation is often understood as a continuous process of divergence that continues until genetic or other incompatibilities minimize or prevent interbreeding. The Palearctic snake genus Natrix is an ideal group to study speciation, as it comprises taxa representing distinct stages of the speciation process, ranging from widely interbreeding parapatric taxa through parapatric species with very limited gene flow in narrow hybrid zones to widely sympatric species. To understand the evolution of reproductive isolation through time, we have sequenced the genomes of all five species within this genus and two additional subspecies. We used both long-read and short-read methods to sequence and de-novo-assemble two high-quality genomes (Natrix h. helvetica, Natrix n. natrix) to their 1.7 Gb length with a contig N50 of 4.6 Mbp and 1.5 Mbp, respectively, and used these as references to assemble the remaining short-read-based genomes. Our phylogenomic analyses yielded a well-supported dated phylogeny and evidence for a surprisingly complex history of interspecific gene flow, including between widely sympatric species. Furthermore, evidence for gene flow was also found for currently allopatric species pairs. Genetic exchange among these well-defined, distinct, and several million-year-old reptile species emphasizes that speciation and maintenance of species distinctness can occur despite continued genetic exchange.
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Affiliation(s)
- Yannis Schöneberg
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 9, 60325 Frankfurt am Main, Germany
| | - Sven Winter
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstraße 1, 1160 Vienna, Austria
| | - Oscar Arribas
- IES Castilla, Junta de Castilla, Castilla y León, 42003 Soria, Spain
| | | | - Maya Master
- Molecular Ecology and Evolution at Bangor (MEEB), School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor LL57 2UW, Wales, UK
| | - John Benjamin Owens
- Molecular Ecology and Evolution at Bangor (MEEB), School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor LL57 2UW, Wales, UK
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Praha 2, Czech Republic
| | - Wolfgang Wüster
- Molecular Ecology and Evolution at Bangor (MEEB), School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor LL57 2UW, Wales, UK
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 9, 60325 Frankfurt am Main, Germany; LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Uwe Fritz
- Senckenberg Dresden, Museum of Zoology, A. B. Meyer Building, 01109 Dresden, Germany.
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8
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Goymer A, Steele K, Jenkins F, Burgess G, Andrews L, Baumgartner N, Gubili C, Griffiths AM. For R-eel?! Investigating international sales of critically endangered species in freshwater eel products with DNA barcoding. Food Control 2023. [DOI: 10.1016/j.foodcont.2023.109752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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9
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Burbrink FT, Crother BI, Murray CM, Smith BT, Ruane S, Myers EA, Pyron RA. Empirical and philosophical problems with the subspecies rank. Ecol Evol 2022; 12:e9069. [PMID: 35845367 PMCID: PMC9271888 DOI: 10.1002/ece3.9069] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/01/2022] [Accepted: 06/10/2022] [Indexed: 11/12/2022] Open
Abstract
Species‐level taxonomy derives from empirical sources (data and techniques) that assess the existence of spatiotemporal evolutionary lineages via various species “concepts.” These concepts determine if observed lineages are independent given a particular methodology and ontology, which relates the metaphysical species concept to what “kind” of thing a species is in reality. Often, species concepts fail to link epistemology back to ontology. This lack of coherence is in part responsible for the persistence of the subspecies rank, which in modern usage often functions as a placeholder between the evolutionary events of divergence or collapse of incipient species. Thus, prospective events like lineages merging or diverging require information from unknowable future information. This is also conditioned on evidence that the lineage already has a detectably distinct evolutionary history. Ranking these lineages as subspecies can seem attractive given that many lineages do not exhibit intrinsic reproductive isolation. We argue that using subspecies is indefensible on philosophical and empirical grounds. Ontologically, the rank of subspecies is either identical to that of species or undefined in the context of evolutionary lineages representing spatiotemporally defined individuals. Some species concepts more inclined to consider subspecies, like the Biological Species Concept, are disconnected from evolutionary ontology and do not consider genealogy. Even if ontology is ignored, methods addressing reproductive isolation are often indirect and fail to capture the range of scenarios linking gene flow to species identity over space and time. The use of subspecies and reliance on reproductive isolation as a basis for an operational species concept can also conflict with ethical issues governing the protection of species. We provide a way forward for recognizing and naming species that links theoretical and operational species concepts regardless of the magnitude of reproductive isolation.
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology American Museum of Natural History New York New York USA
| | - Brian I Crother
- Department of Biological Sciences Southeastern Louisiana University Hammond Louisiana USA
| | - Christopher M Murray
- Department of Biological Sciences Southeastern Louisiana University Hammond Louisiana USA
| | - Brian Tilston Smith
- Department of Ornithology American Museum of Natural History New York New York USA
| | - Sara Ruane
- Life Sciences Section, Negaunee Integrative Research Center Field Museum of Natural History Chicago Illinois USA
| | - Edward A Myers
- Department of Herpetology American Museum of Natural History New York New York USA.,Department of Biological Sciences Clemson University Clemson South Carolina USA.,Department of Vertebrate Zoology Smithsonian Institution, National Museum of Natural History Washington District of Columbia USA
| | - Robert Alexander Pyron
- Department of Vertebrate Zoology Smithsonian Institution, National Museum of Natural History Washington District of Columbia USA.,Department of Biological Sciences The George Washington University Washington District of Columbia USA
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10
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Liu S, Tengstedt ANB, Jacobsen MW, Pujolar JM, Jónsson B, Lobón-Cervià J, Bernatchez L, Hansen MM. Genome-wide methylation in the panmictic European eel (Anguilla anguilla). Mol Ecol 2022; 31:4286-4306. [PMID: 35767387 DOI: 10.1111/mec.16586] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 11/30/2022]
Abstract
The role of methylation in adaptive, developmental and speciation processes has attracted considerable interest, but interpretation of results is complicated by diffuse boundaries between genetic and non-genetic variation. We studied whole genome genetic and methylation variation in the European eel, distributed from subarctic to subtropical environments, but with panmixia precluding genetically based local adaptation beyond single-generation responses. Overall methylation was 70.9%, with hypomethylation predominantly found in promoters and first exons. Redundancy analyses involving juvenile glass eels showed 0.06% and 0.03% of the variance at SNPs to be explained by localities and environmental variables, respectively, with GO terms of genes associated with outliers primarily involving neural system functioning. For CpGs 2.98% and 1.36% of variance was explained by localities and environmental variables. Differentially methylated regions particularly included genes involved in developmental processes, with hox clusters featuring prominently. Life stage (adult versus glass eels) was the most important source of inter-individual variation in methylation, likely reflecting both ageing and developmental processes. Demethylation of transposable elements relative to pure European eel was observed in European X American eel hybrids, possibly representing postzygotic barriers in this system characterized by prolonged speciation and ongoing gene flow. Whereas the genetic data are consistent with a role of single-generation selective responses, the methylation results underpin the importance of epigenetics in the life cycle of eels and suggests interactions between local environments, development and phenotypic variation mediated by methylation variation. Eels are remarkable by having retained eight hox clusters, and the results suggest important roles of methylation at hox genes for adaptive processes.
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Affiliation(s)
- Shenglin Liu
- Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Magnus W Jacobsen
- Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Jose Martin Pujolar
- Centre for Gelatinous Plankton Ecology and Evolution, National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Bjarni Jónsson
- North West Iceland Nature Center, Iceland.,The Icelandic Parliament, Reykjavík, Iceland
| | | | - Louis Bernatchez
- IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Québec, Canada
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11
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Population genetics reveals divergent lineages and ongoing hybridization in a declining migratory fish species complex. Heredity (Edinb) 2022; 129:137-151. [PMID: 35665777 PMCID: PMC9338086 DOI: 10.1038/s41437-022-00547-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 11/08/2022] Open
Abstract
Deciphering the effects of historical and recent demographic processes responsible for the spatial patterns of genetic diversity and structure is a key objective in evolutionary and conservation biology. Using population genetic analyses, we investigated the demographic history, the contemporary genetic diversity and structure, and the occurrence of hybridization and introgression of two species of anadromous fish with contrasting life history strategies and which have undergone recent demographic declines, the allis shad (Alosa alosa) and the twaite shad (Alosa fallax). We genotyped 706 individuals from 20 rivers and 5 sites at sea in Southern Europe at thirteen microsatellite markers. Genetic structure between populations was lower for the nearly semelparous species A. alosa, which disperses greater distances compared to the iteroparous species, A. fallax. Individuals caught at sea were assigned at the river level for A. fallax and at the region level for A. alosa. Using an approximate Bayesian computation framework, we inferred that the most likely long term historical divergence scenario between both species and lineages involved historical separation followed by secondary contact accompanied by strong population size decline. Accordingly, we found evidence for contemporary hybridization and bidirectional introgression due to gene flow between both species and lineages. Moreover, our results support the existence of at least one distinct species in the Mediterrannean sea: A. agone in Golfe du Lion area, and another divergent lineage in Corsica. Overall, our results shed light on the interplay between historical and recent demographic processes and life history strategies in shaping population genetic diversity and structure of closely related species. The recent demographic decline of these species' populations and their hybridization should be carefully considered while implementing conservation programs.
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12
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Musher LJ, Giakoumis M, Albert J, Del-Rio G, Rego M, Thom G, Aleixo A, Ribas CC, Brumfield RT, Smith BT, Cracraft J. River network rearrangements promote speciation in lowland Amazonian birds. SCIENCE ADVANCES 2022; 8:eabn1099. [PMID: 35394835 PMCID: PMC8993111 DOI: 10.1126/sciadv.abn1099] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Large Amazonian rivers impede dispersal for many species, but lowland river networks frequently rearrange, thereby altering the location and effectiveness of river barriers through time. These rearrangements may promote biotic diversification by facilitating episodic allopatry and secondary contact among populations. We sequenced genome-wide markers to evaluate the histories of divergence and introgression in six Amazonian avian species complexes. We first tested the assumption that rivers are barriers for these taxa and found that even relatively small rivers facilitate divergence. We then tested whether species diverged with gene flow and recovered reticulate histories for all species, including one potential case of hybrid speciation. Our results support the hypothesis that river rearrangements promote speciation and reveal that many rainforest taxa are micro-endemic, unrecognized, and thus threatened with imminent extinction. We propose that Amazonian hyper-diversity originates partly from fine-scale barrier displacement processes-including river dynamics-which allow small populations to differentiate and disperse into secondary contact.
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Affiliation(s)
- Lukas J. Musher
- Department of Ornithology, The Academy of Natural
Sciences of Drexel University, Philadelphia, PA 19103, USA
- Department of Ornithology, American Museum of Natural
History, New York, NY 10028, USA
- Corresponding author.
| | - Melina Giakoumis
- Department of Biology, City College of New York, New
York, NY 10031, USA
- Graduate Center, City University of New York, New
York, NY 10016, USA
| | - James Albert
- Department of Biology, University of Louisiana at
Lafayette, Lafayette, LA 70503, USA
| | - Glaucia Del-Rio
- Department of Biological Sciences, Louisiana State
University, Baton Rouge, LA 70803, USA
- Museum of Natural Science, Louisiana State
University, Baton Rouge, LA 70803, USA
| | - Marco Rego
- Department of Biological Sciences, Louisiana State
University, Baton Rouge, LA 70803, USA
- Museum of Natural Science, Louisiana State
University, Baton Rouge, LA 70803, USA
| | - Gregory Thom
- Department of Ornithology, American Museum of Natural
History, New York, NY 10028, USA
| | - Alexandre Aleixo
- Finnish Museum of Natural History of Helsinki,
University of Helsinki, Helsinki, Finland
- Museu Paraense Emílio Goeldi, Belém,
Brazil
- Instituto Tecnológico Vale, Belém,
Brazil
| | - Camila C. Ribas
- Instituto Nacional de Pesquisas da
Amazônia, INPA, Manaus, Brazil
| | - Robb T. Brumfield
- Department of Biological Sciences, Louisiana State
University, Baton Rouge, LA 70803, USA
- Museum of Natural Science, Louisiana State
University, Baton Rouge, LA 70803, USA
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural
History, New York, NY 10028, USA
| | - Joel Cracraft
- Department of Ornithology, American Museum of Natural
History, New York, NY 10028, USA
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13
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Pyron RA, O’Connell KA, Lemmon EM, Lemmon AR, Beamer DA. Candidate‐species delimitation in
Desmognathus
salamanders reveals gene flow across lineage boundaries, confounding phylogenetic estimation and clarifying hybrid zones. Ecol Evol 2022; 12:e8574. [PMID: 35222955 PMCID: PMC8848459 DOI: 10.1002/ece3.8574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 12/19/2022] Open
Abstract
Dusky Salamanders (genus Desmognathus) currently comprise only 22 described, extant species. However, recent mitochondrial and nuclear estimates indicate the presence of up to 49 candidate species based on ecogeographic sampling. Previous studies also suggest a complex history of hybridization between these lineages. Studies in other groups suggest that disregarding admixture may affect both phylogenetic inference and clustering‐based species delimitation. With a dataset comprising 233 Anchored Hybrid Enrichment (AHE) loci sequenced for 896 Desmognathus specimens from all 49 candidate species, we test three hypotheses regarding (i) species‐level diversity, (ii) hybridization and admixture, and (iii) misleading phylogenetic inference. Using phylogenetic and population‐clustering analyses considering gene flow, we find support for at least 47 candidate species in the phylogenomic dataset, some of which are newly characterized here while others represent combinations of previously named lineages that are collapsed in the current dataset. Within these, we observe significant phylogeographic structure, with up to 64 total geographic genetic lineages, many of which hybridize either narrowly at contact zones or extensively across ecological gradients. We find strong support for both recent admixture between terminal lineages and ancient hybridization across internal branches. This signal appears to distort concatenated phylogenetic inference, wherein more heavily admixed terminal specimens occupy apparently artifactual early‐diverging topological positions, occasionally to the extent of forming false clades of intermediate hybrids. Additional geographic and genetic sampling and more robust computational approaches will be needed to clarify taxonomy, and to reconstruct a network topology to display evolutionary relationships in a manner that is consistent with their complex history of reticulation.
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Affiliation(s)
- Robert Alexander Pyron
- Department of Biological Sciences The George Washington University Washington District of Columbia USA
- Division of Amphibians and Reptiles Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington District of Columbia USA
| | - Kyle A. O’Connell
- Department of Biological Sciences The George Washington University Washington District of Columbia USA
- Division of Amphibians and Reptiles Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington District of Columbia USA
- Global Genome Initiative National Museum of Natural History Smithsonian Institution Washington District of Columbia USA
- Biomedical Data Science Lab Deloitte Consulting LLP Arlington Virginia USA
| | | | - Alan R. Lemmon
- Department of Scientific Computing Florida State University Tallahassee Florida USA
| | - David A. Beamer
- Department of Natural Sciences Nash Community College Rocky Mount North Carolina USA
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14
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Matschiner M. Species Tree Inference with SNP Data. Methods Mol Biol 2022; 2512:23-44. [PMID: 35817997 DOI: 10.1007/978-1-0716-2429-6_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
While the inference of species trees from molecular sequences has become a common type of analysis in studies of species diversification, few programs so far allow for the use of single-nucleotide polymorphisms (SNPs) for the same purpose. In this book chapter, I discuss the use of the Bayesian program SNAPP, which infers the species tree by mathematically integrating over all possible genealogies at each SNP. In particular, I focus on a molecular clock model developed for SNAPP, allowing the inference of divergence times together with the species tree topology and the population size, directly from SNP datasets in variant call format. With the growing availability of SNP datasets for multiple closely related species, this approach is becoming increasingly relevant for the reconstruction of the temporal framework of recent species diversification.
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Affiliation(s)
- Michael Matschiner
- Department of Palaeontology and Museum, University of Zurich, Zurich, Switzerland.
- Natural History Museum, University of Oslo, Oslo, Norway.
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15
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Jacobs SJ, Grundler MC, Henriquez CL, Zapata F. An integrative genomic and phenomic analysis to investigate the nature of plant species in Escallonia (Escalloniaceae). Sci Rep 2021; 11:24013. [PMID: 34907249 PMCID: PMC8671583 DOI: 10.1038/s41598-021-03419-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 11/26/2021] [Indexed: 12/04/2022] Open
Abstract
What we mean by species and whether they have any biological reality has been debated since the early days of evolutionary biology. Some biologists even suggest that plant species are created by taxonomists as a subjective, artificial division of nature. However, the nature of plant species has been rarely tested critically with data while ignoring taxonomy. We integrate phenomic and genomic data collected across hundreds of individuals at a continental scale to investigate this question in Escallonia (Escalloniaceae), a group of plants which includes 40 taxonomic species (the species proposed by taxonomists). We first show that taxonomic species may be questionable as they match poorly to patterns of phenotypic and genetic variation displayed by individuals collected in nature. We then use explicit statistical methods for species delimitation designed for phenotypic and genomic data, and show that plant species do exist in Escallonia as an objective, discrete property of nature independent of taxonomy. We show that such species correspond poorly to current taxonomic species (\documentclass[12pt]{minimal}
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\begin{document}$$< 20\%$$\end{document}<20%) and that phenomic and genomic data seldom delimit congruent entities (\documentclass[12pt]{minimal}
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\begin{document}$$< 20\%$$\end{document}<20%). These discrepancies suggest that evolutionary forces additional to gene flow can maintain the cohesion of species. We propose that phenomic and genomic data analyzed on an equal footing build a broader perspective on the nature of plant species by helping delineate different ‘types of species’. Our results caution studies which take the accuracy of taxonomic species for granted and challenge the notion of plant species without empirical evidence. Note: A version of the complete manuscript in Spanish is available in the Supplemental Materials.
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Affiliation(s)
- Sarah J Jacobs
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA.,Department of Botany, California Academy of Sciences, San Francisco, CA, 94118, USA
| | - Michael C Grundler
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Claudia L Henriquez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Felipe Zapata
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA.
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16
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Nickel J, Schell T, Holtzem T, Thielsch A, Dennis SR, Schlick-Steiner BC, Steiner FM, Möst M, Pfenninger M, Schwenk K, Cordellier M. Hybridization Dynamics and Extensive Introgression in the Daphnia longispina Species Complex: New Insights from a High-Quality Daphnia galeata Reference Genome. Genome Biol Evol 2021; 13:6448229. [PMID: 34865004 PMCID: PMC8695838 DOI: 10.1093/gbe/evab267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2021] [Indexed: 01/02/2023] Open
Abstract
Hybridization and introgression are recognized as an important source of variation that influence adaptive processes; both phenomena are frequent in the genus Daphnia, a keystone zooplankton taxon in freshwater ecosystems that comprises several species complexes. To investigate genome-wide consequences of introgression between species, we provide here the first high-quality genome assembly for a member of the Daphnia longispina species complex, Daphnia galeata. We further resequenced 49 whole genomes of three species of the complex and their interspecific hybrids both from genotypes sampled in the water column and from single resting eggs extracted from sediment cores. Populations from habitats with diverse ecological conditions offered an opportunity to study the dynamics of hybridization linked to ecological changes and revealed a high prevalence of hybrids. Using phylogenetic and population genomic approaches, we provide first insights into the intra- and interspecific genome-wide variability in this species complex and identify regions of high divergence. Finally, we assess the length of ancestry tracts in hybrids to characterize introgression patterns across the genome. Our analyses uncover a complex history of hybridization and introgression reflecting multiple generations of hybridization and backcrossing in the Daphnia longispina species complex. Overall, this study and the new resources presented here pave the way for a better understanding of ancient and contemporary gene flow in the species complex and facilitate future studies on resting egg banks accumulating in lake sediment.
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Affiliation(s)
- Jana Nickel
- Institute of Zoology, Universität Hamburg, Germany
| | - Tilman Schell
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Tania Holtzem
- Department of Ecology, University of Innsbruck, Austria
| | - Anne Thielsch
- Molecular Ecology, Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
| | - Stuart R Dennis
- Department of Aquatic Ecology, EAWAG, Dübendorf, Switzerland
| | | | | | - Markus Möst
- Department of Ecology, University of Innsbruck, Austria
| | - Markus Pfenninger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany.,Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.,IoME, Gutenberg University, Mainz, Germany
| | - Klaus Schwenk
- Molecular Ecology, Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
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17
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Arntzen JW, Jehle R, Wielstra B. Genetic and morphological data demonstrate hybridization and backcrossing in a pair of salamanders at the far end of the speciation continuum. Evol Appl 2021; 14:2784-2793. [PMID: 34950229 PMCID: PMC8674889 DOI: 10.1111/eva.13312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 09/05/2021] [Accepted: 10/01/2021] [Indexed: 12/23/2022] Open
Abstract
Deeply diverged yet hybridizing species provide a system to investigate the final stages of the speciation process. We study a hybridizing pair of salamander species-the morphologically and genetically drastically different newts Triturus cristatus and T. marmoratus-with a panel of 32 nuclear and mitochondrial genetic markers. Morphologically identified hybrids are mostly of the F1 generation and mothered by T. cristatus. The sex ratio of the F1 hybrid class is reciprocally skewed, with a preponderance of females in T. cristatus-mothered hybrids and males in T. marmoratus-mothered hybrids. This amounts to the Haldane effect operating in one direction of the cross. Deeper generation hybrids are occasionally produced, possibly including F1 hybrid × backcross hybrid offspring. Interspecific gene flow is low, yet skewed toward T. cristatus. This asymmetry may be caused by hybrid zone movement, with the superseding species being predisposed to introgression. The persisting gene flow between deeply differentiated species supports the notion that full genetic isolation may be selected against. Conversely, published morphological data suggest that introgressive hybridization is detrimental, with digital malformations occurring more frequently in the area of sympatry. Finally, to assist field identification, both within the area of natural range overlap and concerning anthropogenic introductions elsewhere, we document the phenotypical variation of two generations of hybrids compared with both parental species. We suggest that fluctuating range boundaries, ecological segregation, cytonuclear incompatibilities and hybrid breakdown through Bateson-Dobzhansky-Muller incompatibilities all contribute to species integrity, despite incomplete isolation during secondary contact.
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Affiliation(s)
- Jan W. Arntzen
- Naturalis Biodiversity CenterLeidenThe Netherlands
- Institute of BiologyLeiden UniversityLeidenThe Netherlands
| | - Robert Jehle
- School of Science, Engineering and EnvironmentUniversity of SalfordSalfordUK
| | - Ben Wielstra
- Naturalis Biodiversity CenterLeidenThe Netherlands
- Institute of BiologyLeiden UniversityLeidenThe Netherlands
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18
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Myers EA, Mulcahy DG, Falk B, Johnson K, Carbi M, de Queiroz K. Interspecific Gene Flow and Mitochondrial Genome Capture During the Radiation of Jamaican Anolis Lizards (Squamata; Iguanidae). Syst Biol 2021; 71:501-511. [PMID: 34735007 DOI: 10.1093/sysbio/syab089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 11/12/2022] Open
Abstract
Gene flow and reticulation are increasingly recognized as important processes in the diversification of many taxonomic groups. With the increasing ease of collecting genomic data and the development of multispecies coalescent network approaches, such reticulations can be accounted for when inferring phylogeny and diversification. Caribbean Anolis lizards are a classic example of an adaptive radiation in which species have independently radiated on the islands of the Greater Antilles into the same ecomorph classes. Within the Jamaican radiation at least one species, A. opalinus, has been documented to be polyphyletic in its mitochondrial DNA, which could be the result of an ancient reticulation event or incomplete lineage sorting. Here we generate mtDNA and genotyping-by-sequencing (GBS) data and implement gene-tree, species-tree, and multispecies coalescent network methods to infer the diversification of this group. Our mtDNA gene-tree recovers the same relationships previously inferred for this group, which is strikingly different from the species-tree inferred from our GBS data. Posterior predictive simulations suggest that our genomic data violate commonly adopted assumptions of the multispecies coalescent model, so we use network approaches to infer phylogenetic relationships. The inferred network topology contains a reticulation event but does not explain the mtDNA polyphyly observed in this group, however coalescent simulations suggest that the observed mtDNA topology is likely the result of past introgression. How common a signature of gene flow and reticulation is across the radiation of Anolis is unknown; however, the reticulation events that we demonstrate here may have allowed for adaptive evolution, as has been suggested in other, more recent adaptive radiations.
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Affiliation(s)
- Edward A Myers
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Herpetology, The American Museum of Natural History, New York, NY, USA
| | - Daniel G Mulcahy
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Bryan Falk
- Division of Invertebrate Zoology, Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Kiyomi Johnson
- Science Research Mentoring Program, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - Marina Carbi
- Science Research Mentoring Program, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - Kevin de Queiroz
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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19
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Burbrink FT, Ruane S. Contemporary Philosophy and Methods for Studying Speciation and Delimiting Species. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/h2020073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Frank T. Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024; . Send reprint requests to this address
| | - Sara Ruane
- Earth and Environmental Sciences: Ecology and Evolution, Rutgers University–Newark, 195 University Avenue, Newark, New Jersey 07102
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20
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Myers EA. Genome-wide data reveal extensive gene flow during the diversification of the western rattlesnakes (Viperidae: Crotalinae: Crotalus). Mol Phylogenet Evol 2021; 165:107313. [PMID: 34537323 DOI: 10.1016/j.ympev.2021.107313] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 08/28/2021] [Accepted: 09/14/2021] [Indexed: 11/15/2022]
Abstract
Hybridization and introgression are important, but often overlooked processes when inferring phylogenies. When these processes are not accounted for and a strictly diverging phylogenetic model is applied to groups with a history of hybridization, phylogenetic inference and parameter estimation can be inaccurate. Recent developments in phylogenetic network approaches coupled with the increasing availability of genomic data allow inferences of reticulate evolutionary histories across the tree of life. The western rattlesnake species group (C. viridis species complex, C. mitchellii species complex, C. scutulutas, and C. tigris) is an iconic snake lineage that is widespread across western North America. This group is composed of several species complexes with unclear species limits, likely the result of ongoing gene flow among nascent lineages. Here I generate reduced representation genomic data and test for a history of reticulation within this group. I demonstrate that all species have undergone hybridization with at least one other lineage, suggesting introgression is widespread in this group. Topologies differ between phylogenies estimated under the multispecies coalescent and multispecies network coalescent methods, indicating that gene flow has obscured phylogenetic relationships within this group. These past introgression events are predominantly restricted to species that co-occur geographically. However, within species that have a history of introgression, this signature is detected regardless of specimen sampling across geography. Overall, my results suggest the accumulation of reproductive isolating barriers occurs slowly in rattlesnakes which likely leads to the difficulty in delimiting species, furthermore, the results of this study have implications for trait evolution in this group.
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Affiliation(s)
- Edward A Myers
- Department of Herpetology, American Museum of Natural History, New York, NY, USA; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
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21
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Leaché AD, Davis HR, Singhal S, Fujita MK, Lahti ME, Zamudio KR. Phylogenomic Assessment of Biodiversity Using a Reference-Based Taxonomy: An Example With Horned Lizards (Phrynosoma). Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.678110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Phylogenomic investigations of biodiversity facilitate the detection of fine-scale population genetic structure and the demographic histories of species and populations. However, determining whether or not the genetic divergence measured among populations reflects species-level differentiation remains a central challenge in species delimitation. One potential solution is to compare genetic divergence between putative new species with other closely related species, sometimes referred to as a reference-based taxonomy. To be described as a new species, a population should be at least as divergent as other species. Here, we develop a reference-based taxonomy for Horned Lizards (Phrynosoma; 17 species) using phylogenomic data (ddRADseq data) to provide a framework for delimiting species in the Greater Short-horned Lizard species complex (P. hernandesi). Previous species delimitation studies of this species complex have produced conflicting results, with morphological data suggesting that P. hernandesi consists of five species, whereas mitochondrial DNA support anywhere from 1 to 10 + species. To help address this conflict, we first estimated a time-calibrated species tree for P. hernandesi and close relatives using SNP data. These results support the paraphyly of P. hernandesi; we recommend the recognition of two species to promote a taxonomy that is consistent with species monophyly. There is strong evidence for three populations within P. hernandesi, and demographic modeling and admixture analyses suggest that these populations are not reproductively isolated, which is consistent with previous morphological analyses that suggest hybridization could be common. Finally, we characterize the population-species boundary by quantifying levels of genetic divergence for all 18 Phrynosoma species. Genetic divergence measures for western and southern populations of P. hernandesi failed to exceed those of other Phrynosoma species, but the relatively small population size estimated for the northern population causes it to appear as a relatively divergent species. These comparisons underscore the difficulties associated with putting a reference-based approach to species delimitation into practice. Nevertheless, the reference-based approach offers a promising framework for the consistent assessment of biodiversity within clades of organisms with similar life histories and ecological traits.
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22
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Esquerré D, Keogh JS, Demangel D, Morando M, Avila LJ, Sites JW, Ferri-Yáñez F, Leaché AD. Rapid radiation and rampant reticulation: Phylogenomics of South American Liolaemus lizards. Syst Biol 2021; 71:286-300. [PMID: 34259868 DOI: 10.1093/sysbio/syab058] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 01/09/2023] Open
Abstract
Understanding the factors that cause heterogeneity among gene trees can increase the accuracy of species trees. Discordant signals across the genome are commonly produced by incomplete lineage sorting (ILS) and introgression, which in turn can result in reticulate evolution. Species tree inference using the multispecies coalescent is designed to deal with ILS and is robust to low levels of introgression, but extensive introgression violates the fundamental assumption that relationships are strictly bifurcating. In this study, we explore the phylogenomics of the iconic Liolaemus subgenus of South American lizards, a group of over 100 species mostly distributed in and around the Andes mountains. Using mitochondrial DNA (mtDNA) and genome-wide restriction-site associated DNA sequencing (RADseq; nDNA hereafter), we inferred a time-calibrated mtDNA gene tree, nDNA species trees, and phylogenetic networks. We found high levels of discordance between mtDNA and nDNA, which we attribute in part to extensive ILS resulting from rapid diversification. These data also reveal extensive and deep introgression, which combined with rapid diversification, explain the high level of phylogenetic discordance. We discuss these findings in the context of Andean orogeny and glacial cycles that fragmented, expanded, and contracted species distributions. Finally, we use the new phylogeny to resolve long-standing taxonomic issues in one of the most studied lizard groups in the New World.
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Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | | | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC- CONICET), Puerto Madryn, Chubut, Argentina
| | - Luciano J Avila
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC- CONICET), Puerto Madryn, Chubut, Argentina
| | - Jack W Sites
- Department of Biology and M.L. Bean Life Science Museum, Brigham Young University, Provo, Utah, USA
| | - Francisco Ferri-Yáñez
- Departamento de Biogeografía y Cambio Global, Museo Nacional de Ciencias Naturales, CSIC & Laboratorio Internacional en Cambio Global CSIC-PUC (LINCGlobal), Calle José Gutiérrez Abascal, 2, 28006, Madrid, Spain
| | - Adam D Leaché
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, USA
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23
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Rautsaw RM, Schramer TD, Acuña R, Arick LN, DiMeo M, Mercier KP, Schrum M, Mason AJ, Margres MJ, Strickland JL, Parkinson CL. Genomic Adaptations to Salinity Resist Gene Flow in the Evolution of Floridian Watersnakes. Mol Biol Evol 2021; 38:745-760. [PMID: 33035326 PMCID: PMC7947766 DOI: 10.1093/molbev/msaa266] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The migration-selection balance often governs the evolution of lineages, and speciation with gene flow is now considered common across the tree of life. Ecological speciation is a process that can facilitate divergence despite gene flow due to strong selective pressures caused by ecological differences; however, the exact traits under selection are often unknown. The transition from freshwater to saltwater habitats provides strong selection targeting traits with osmoregulatory function. Several lineages of North American watersnakes (Nerodia spp.) are known to occur in saltwater habitat and represent a useful system for studying speciation by providing an opportunity to investigate gene flow and evaluate how species boundaries are maintained or degraded. We use double digest restriction-site associated DNA sequencing to characterize the migration-selection balance and test for evidence of ecological divergence within the Nerodia fasciata-clarkii complex in Florida. We find evidence of high intraspecific gene flow with a pattern of isolation-by-distance underlying subspecific lineages. However, we identify genetic structure indicative of reduced gene flow between inland and coastal lineages suggesting divergence due to isolation-by-environment. This pattern is consistent with observed environmental differences where the amount of admixture decreases with increased salinity. Furthermore, we identify significantly enriched terms related to osmoregulatory function among a set of candidate loci, including several genes that have been previously implicated in adaptation to salinity stress. Collectively, our results demonstrate that ecological differences, likely driven by salinity, cause strong divergent selection which promotes divergence in the N. fasciata-clarkii complex despite significant gene flow.
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Affiliation(s)
- Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC.,Department of Biology, University of Central Florida, Orlando, FL
| | | | - Rachel Acuña
- Department of Biology, University of Central Florida, Orlando, FL
| | - Lindsay N Arick
- Department of Biology, University of Central Florida, Orlando, FL
| | - Mark DiMeo
- Department of Biological Sciences, Clemson University, Clemson, SC.,Department of Biology, University of Central Florida, Orlando, FL
| | - Kathryn P Mercier
- Department of Biological Sciences, Clemson University, Clemson, SC.,Department of Biology, University of Central Florida, Orlando, FL.,Department of Biology, City College of New York, New York, NY.,PhD Program in Biology, The Graduate Center of the City University of New York, New York, NY
| | - Michael Schrum
- Department of Biology, University of Central Florida, Orlando, FL
| | - Andrew J Mason
- Department of Biological Sciences, Clemson University, Clemson, SC.,Department of Biology, University of Central Florida, Orlando, FL
| | - Mark J Margres
- Department of Biological Sciences, Clemson University, Clemson, SC.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA.,Department of Integrative Biology, University of South Florida, Tampa, FL
| | - Jason L Strickland
- Department of Biological Sciences, Clemson University, Clemson, SC.,Department of Biology, University of Central Florida, Orlando, FL.,Department of Biology, University of South Alabama, Mobile, AL
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC.,Department of Biology, University of Central Florida, Orlando, FL.,Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC
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24
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Kim D, Bauer BH, Near TJ. Introgression and Species Delimitation in the Longear Sunfish Lepomis megalotis (Teleostei: Percomorpha: Centrarchidae). Syst Biol 2021; 71:273-285. [PMID: 33944950 DOI: 10.1093/sysbio/syab029] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 04/20/2021] [Accepted: 04/27/2021] [Indexed: 11/14/2022] Open
Abstract
Introgression and hybridization are major impediments to genomic-based species delimitation because many implementations of the multispecies coalescent framework assume no gene flow among species. The sunfish genus Lepomis, one of the world's most popular groups of freshwater sport fish, has a complicated taxonomic history. The results of ddRAD phylogenomic analyses do not provide support for the current taxonomy that recognizes two species, L. megalotis and L. peltastes, in the L. megalotis complex. Instead, evidence from phylogenomics and phenotype warrants recognizing six relatively ancient evolutionary lineages in the complex. The introgressed and hybridizing populations in the L. megalotis complex are localized and appear to be the result of secondary contact or rare hybridization events between non-sister species. Segregating admixed populations from our multispecies coalescent analyses identifies six species with moderate to high genealogical divergence, whereas including admixed populations drives all but one lineage below the species threshold of genealogical divergence. Segregation of admixed individuals also helps reveal phenotypic distinctiveness among the six species in morphological traits used by ichthyologists to discover and delimit species over the last two centuries. Our protocols allow for the identification and accommodation of hybridization and introgression in species delimitation. Genomic-based species delimitation validated with multiple lines of evidence provides a path towards the discovery of new biodiversity and resolving long-standing taxonomic problems.
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Affiliation(s)
- Daemin Kim
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
| | - Bruce H Bauer
- David A. Etnier Ichthyological Collection, 515 Hesler Biology Building, University of Tennessee, Knoxville, TN 37996, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA.,Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
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Ferreira MS, Jones MR, Callahan CM, Farelo L, Tolesa Z, Suchentrunk F, Boursot P, Mills LS, Alves PC, Good JM, Melo-Ferreira J. The Legacy of Recurrent Introgression during the Radiation of Hares. Syst Biol 2021; 70:593-607. [PMID: 33263746 PMCID: PMC8048390 DOI: 10.1093/sysbio/syaa088] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 11/06/2020] [Accepted: 11/13/2020] [Indexed: 12/30/2022] Open
Abstract
Hybridization may often be an important source of adaptive variation, but the extent and long-term impacts of introgression have seldom been evaluated in the phylogenetic context of a radiation. Hares (Lepus) represent a widespread mammalian radiation of 32 extant species characterized by striking ecological adaptations and recurrent admixture. To understand the relevance of introgressive hybridization during the diversification of Lepus, we analyzed whole exome sequences (61.7 Mb) from 15 species of hares (1-4 individuals per species), spanning the global distribution of the genus, and two outgroups. We used a coalescent framework to infer species relationships and divergence times, despite extensive genealogical discordance. We found high levels of allele sharing among species and show that this reflects extensive incomplete lineage sorting and temporally layered hybridization. Our results revealed recurrent introgression at all stages along the Lepus radiation, including recent gene flow between extant species since the last glacial maximum but also pervasive ancient introgression occurring since near the origin of the hare lineages. We show that ancient hybridization between northern hemisphere species has resulted in shared variation of potential adaptive relevance to highly seasonal environments, including genes involved in circadian rhythm regulation, pigmentation, and thermoregulation. Our results illustrate how the genetic legacy of ancestral hybridization may persist across a radiation, leaving a long-lasting signature of shared genetic variation that may contribute to adaptation. [Adaptation; ancient introgression; hybridization; Lepus; phylogenomics.].
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Affiliation(s)
- Mafalda S Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Matthew R Jones
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Colin M Callahan
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Liliana Farelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Zelalem Tolesa
- Department of Biology, Hawassa University, Hawassa, Ethiopia
| | - Franz Suchentrunk
- Department for Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Pierre Boursot
- Institut des Sciences de l’Évolution Montpellier (ISEM), Université de Montpellier, CNRS, IRD, EPHE, France
| | - L Scott Mills
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, Montana, United States of America
- Office of Research and Creative Scholarship, University of Montana, Missoula, Montana, United States of America; Jeffrey M. Good and José Melo-Ferreira shared the senior authorship
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, Montana, United States of America
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, Montana, United States of America
| | - José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
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26
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Marini M, Pedrosa-Gerasmio IR, Santos MD, Shibuno T, Daryani A, Romana-Eguia MRR, Wibowo A. Genetic diversity, population structure and demographic history of the tropical eel Anguilla bicolor pacifica in Southeast Asia using mitochondrial DNA control region sequences. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01493] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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27
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Cerca J, Rivera-Colón AG, Ferreira MS, Ravinet M, Nowak MD, Catchen JM, Struck TH. Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species. PeerJ 2021; 9:e10896. [PMID: 33614296 PMCID: PMC7879940 DOI: 10.7717/peerj.10896] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/13/2021] [Indexed: 12/14/2022] Open
Abstract
Morphologically similar species, that is cryptic species, may be similar or quasi-similar owing to the deceleration of morphological evolution and stasis. While the factors underlying the deceleration of morphological evolution or stasis in cryptic species remain unknown, decades of research in the field of paleontology on punctuated equilibrium have originated clear hypotheses. Species are expected to remain morphologically identical in scenarios of shared genetic variation, such as hybridization and incomplete lineage sorting, or in scenarios where bottlenecks reduce genetic variation and constrain the evolution of morphology. Here, focusing on three morphologically similar Stygocapitella species, we employ a whole-genome amplification method (WGA) coupled with double-digestion restriction-site associated DNA sequencing (ddRAD) to reconstruct the evolutionary history of the species complex. We explore population structure, use population-level statistics to determine the degree of connectivity between populations and species, and determine the most likely demographic scenarios which generally reject for recent hybridization. We find that the combination of WGA and ddRAD allowed us to obtain genomic-level data from microscopic eukaryotes (∼1 millimetre) opening up opportunities for those working with population genomics and phylogenomics in such taxa. The three species share genetic variance, likely from incomplete lineage sorting and ancient admixture. We speculate that the degree of shared variation might underlie morphological similarity in the Atlantic species complex.
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Affiliation(s)
- José Cerca
- Department of Environmental Science, Policy, and Management, University of California, University of California, Berkeley, Berkeley, CA, United States of America
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Angel G. Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana Champaign, IL, United States of America
| | - Mafalda S. Ferreira
- Division of Biological Sciences, University of Montana, Missoula, MT, United States of America
- Departamento de Biologia, Universidade do Porto, Porto, Porto, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Porto, Porto, Portugal
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | | | - Julian M. Catchen
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana Champaign, IL, United States of America
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Guo X, Wang ZC, Wang S, Li HF, Suwannapoom C, Wang JX, Zhang C, Shao Y, Wang MS, Jiang RS. Genetic signature of hybridization between Chinese spot-billed ducks and domesticated ducks. Anim Genet 2020; 51:866-875. [PMID: 33020910 DOI: 10.1111/age.13002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 08/17/2020] [Accepted: 08/24/2020] [Indexed: 12/27/2022]
Abstract
In this study, we analyzed 93 whole genomes from Chinese spot-billed ducks (CSB), meat-type ducks (MET), and egg and dual purpose-type ducks (EDT) to characterize the genetic material flowing between the CSB and modern ducks. Using a frequency of shared identical-by-descent method, approximately 10.9 Mb introgression segments containing 140 genes were identified showing the signatures of introgression between CSB and EDT. Meanwhile, nearly 10.6 M introgression regions containing 149 genes were identified between CSB and MET. Based on the haplotypes tree of each segment, we found that the introgression between CSB and domesticated ducks was asymmetric with a high level of gene flow from domestic to CSB and a low level of migration in the opposite direction. Moreover, we identified several genes that were introgressions from CSB and showed the signature of positive selection, which may contribute to the breeding of modern ducks. Our results provide new insight into the evolution and breeding history of domestic ducks and may be useful for the future management of wild and domestic duck populations.
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Affiliation(s)
- X Guo
- College of Animal Science and Technology, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Z-C Wang
- College of Animal Science and Technology, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - S 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, 32 Jiaochang Dong Road, Kunming, Yunnan, 650223, China
| | - H-F Li
- Jiangsu Institute of Poultry Science, Chinese Academy of Agriculture Science, 58 cangjie Rode, Yangzhou, Jiangsu, 225125, China
| | - C Suwannapoom
- School of Agriculture and Natural Resources, University of Phayao, 19 Moo 2 Tambon Maeka, Amphur Muang, Phayao, 56000, Thailand
| | - J-X Wang
- College of Animal Science and Technology, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - C Zhang
- College of Animal Science and Technology, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Y Shao
- 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, 32 Jiaochang Dong Road, Kunming, Yunnan, 650223, China
| | - M-S Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, 1156 High St, Santa Cruz, CA, 95064, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 1156 High St, Santa Cruz, CA, 95064, USA
| | - R-S Jiang
- College of Animal Science and Technology, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
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29
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Chang YLK, Dall’Olmo G, Schabetsberger R. Tracking the marine migration routes of South Pacific silver eels. MARINE ECOLOGY PROGRESS SERIES 2020; 646:1-12. [PMID: 33364670 PMCID: PMC7116496 DOI: 10.3354/meps13398] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Three catadromous Pacific eels (2 Anguilla marmorata, 1 A. megastoma) from the Archipelago of Vanuatu were tagged with pop-up satellite archival transmitters and their migration tracks towards their presumed spawning area approximately 870 km northeast of the point of release were reconstructed in order to evaluate their movements in relation to oceanographic conditions. We used the timing of diel vertical migrations to derive the eels' positions. Two A. marmorata exhibited steep-angled turns resulting in a zig-zag migration path along the east-west axis, while one A. megastoma took a relatively straight course towards the presumed spawning area. They migrated with a speed over ground of 21-23 km day-1. In this region, the eastward flow of the South Equatorial Counter Current (SECC, ∼ 5-10°S) separates the westward flowing South Equatorial Current (SEC; ∼0-5°S and 10-18°S) into two branches. During shallower nighttime migration depths around 150 m eels crossed a variable flow field through the southern branch of the westward SEC with westward propagating mesoscale eddies and the eastward SECC, but stayed south of the stronger northern branch of SEC possibly increasing retention time of larvae within this area. The eels headed towards a tongue of high-salinity Subtropical Underwater (STUW) that may have provided cues for orientation. The eels did not move beyond a salinity front of 35.9-36.0 at a depth of 100-200 m, which may have provided cues for orientation towards the spawning area. These 3 tracks may represent the movements of mature silver eels all the way to where they spawn.
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Affiliation(s)
- Yu-Lin K. Chang
- Application Laboratory, Japan Agency of Marine-Earth Science and Technology, Yokohama, Japan
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