1
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Barraclough TG. Does selection favour the maintenance of porous species boundaries? J Evol Biol 2024; 37:616-627. [PMID: 38599591 DOI: 10.1093/jeb/voae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 03/01/2024] [Accepted: 03/05/2024] [Indexed: 04/12/2024]
Abstract
The endpoint of speciation has been viewed as complete isolation and the absence of gene flow between species. If the influx of genes from another species is maladaptive because species have different adaptations and genetic backgrounds, selection should favour the closing of species boundaries and zero gene flow, a process known as reinforcement. Recently, numerous cases of gene flow between species have been identified, many of which involved adaptive introgression of beneficial alleles. These cases could reflect transient states on the way to closed species boundaries or the result of declining strength or efficacy of selection for reinforcement as the level of gene flow approaches zero. An alternative hypothesis, however, is that selection favours porous species boundaries that allow beneficial alleles to cross, especially in changing environments. This perspective evaluates the conditions that would be needed for selection to favour porous species boundaries and the evidence for them. A contrast is made between hybridization in sexual eukaryotes and gene transfer via homologous recombination in bacteria. Current evidence is inconclusive on whether non-zero gene flow is favoured by selection. Studies are needed that quantify selection gradients on rates of gene flow and test for evolution towards intermediate values, especially experiments that manipulate conditions and track evolution for multiple generations. Estimation of gene flow networks for more clades and regional assemblages using emerging genome data will also allow the evolutionary determinants of interspecific gene flow to be better understood.
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2
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Yuhara T, Ohtsuki H, Hirota SK, Suyama Y, Urabe J. Contrasting population genetic structure of three semi-terrestrial brachyuran crabs on the coast of the Japanese archipelago. Ecol Evol 2024; 14:e11484. [PMID: 38846710 PMCID: PMC11154805 DOI: 10.1002/ece3.11484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 04/16/2024] [Accepted: 05/16/2024] [Indexed: 06/09/2024] Open
Abstract
Anthropogenic activities have reduced ecotones between the ocean and land, which is likely to threaten the population of brackish-water brachyuran crabs. To assess the current status of these crabs, we examine the population genetic structures of three semi-terrestrial brachyuran crabs widely distributed along the coast of the Japan and to clarify factors determining their genetic structures. We collected 184 Orisarma dehaani, 252 Chiromantes haematocheir, and 151 Helice tridens crabs from 36 localities of the Japanese archipelago. Genome-wide SNP data from these crabs were analyzed using MIG-seq. Bayesian clustering of STRUCTURE and DAPC analysis were used to identify genetically disturbed populations and to visualize genetic differentiation between local populations. Genetic population structure showed clear differentiation between populations on the Pacific coast of the Tohoku region and on other Japanese coasts in O. dehaani, but not in C. haematocheir or H. tridens. The inbreeding coefficient of O. dehaani was significantly higher on the Pacific coast of the Tohoku region compared to other Japanese coasts. C. haematocheir and H. tridens had homogeneous genetic structures along the Japanese coast, but showed genetic differentiation of a local population at their range limits. Thus, O. dehaani showed little gene flow and clear genetic differentiation between populations in the Tohoku Pacific region and those on other Japanese coasts due to ocean currents. Although such a regional differentiation was not found in C. haematocheir and H. tridens, one population of C. haematocheir was genetically isolated at the edge of its distribution range and likely vulnerable to environmental changes.
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Affiliation(s)
- Takeshi Yuhara
- Graduate School of Life SciencesTohoku UniversitySendaiMiyagiJapan
- Present address:
National Institute for Environmental StudiesTsukubaIbarakiJapan
| | - Hajime Ohtsuki
- Graduate School of Life SciencesTohoku UniversitySendaiMiyagiJapan
| | - Shun K. Hirota
- Graduate School of Agricultural SciencesTohoku UniversityOsakiMiyagiJapan
- Botanical GardensOsaka Metropolitan UniversityKatanoOsakaJapan
| | - Yoshihisa Suyama
- Graduate School of Agricultural SciencesTohoku UniversityOsakiMiyagiJapan
| | - Jotaro Urabe
- Graduate School of Life SciencesTohoku UniversitySendaiMiyagiJapan
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3
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Wooldridge B, Orland C, Enbody E, Escalona M, Mirchandani C, Corbett-Detig R, Kapp JD, Fletcher N, Cox-Ammann K, Raimondi P, Shapiro B. Limited genomic signatures of population collapse in the critically endangered black abalone (Haliotis cracherodii). Mol Ecol 2024:e17362. [PMID: 38682494 DOI: 10.1111/mec.17362] [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: 01/29/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 05/01/2024]
Abstract
The black abalone, Haliotis cracherodii, is a large, long-lived marine mollusc that inhabits rocky intertidal habitats along the coast of California and Mexico. In 1985, populations were impacted by a bacterial disease known as withering syndrome (WS) that wiped out >90% of individuals, leading to the closure of all U.S. black abalone fisheries since 1993. Current conservation strategies include restoring diminished populations by translocating healthy individuals. However, population collapse on this scale may have dramatically lowered genetic diversity and strengthened geographic differentiation, making translocation-based recovery contentious. Additionally, the current prevalence of WS remains unknown. To address these uncertainties, we sequenced and analysed the genomes of 133 black abalone individuals from across their present range. We observed no spatial genetic structure among black abalone, with the exception of a single chromosomal inversion that increases in frequency with latitude. Outside the inversion, genetic differentiation between sites is minimal and does not scale with either geographic distance or environmental dissimilarity. Genetic diversity appears uniformly high across the range. Demographic inference does indicate a severe population bottleneck beginning just 15 generations in the past, but this decline is short lived, with present-day size far exceeding the pre-bottleneck status quo. Finally, we find the bacterial agent of WS is equally present across the sampled range, but only in 10% of individuals. The lack of population genetic structure, uniform diversity and prevalence of WS bacteria indicates that translocation could be a valid and low-risk means of population restoration for black abalone species' recovery.
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Affiliation(s)
- Brock Wooldridge
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California, USA
| | - Chloé Orland
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Erik Enbody
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
| | - Cade Mirchandani
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, California, USA
| | - Joshua D Kapp
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Nathaniel Fletcher
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Karah Cox-Ammann
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Peter Raimondi
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Beth Shapiro
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, California, USA
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4
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Wooldridge B, Orland C, Enbody E, Escalona M, Mirchandani C, Corbett-Detig R, Kapp JD, Fletcher N, Ammann K, Raimondi P, Shapiro B. Limited genomic signatures of population collapse in the critically endangered black abalone ( Haliotis cracherodii). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.26.577275. [PMID: 38352393 PMCID: PMC10862700 DOI: 10.1101/2024.01.26.577275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
The black abalone, Haliotis cracherodii, is a large, long-lived marine mollusc that inhabits rocky intertidal habitats along the coast of California and Mexico. In 1985, populations were impacted by a bacterial disease known as withering syndrome (WS) that wiped out >90% of individuals, leading to the species' designation as critically endangered. Current conservation strategies include restoring diminished populations by translocating healthy individuals. However, population collapse on this scale may have dramatically lowered genetic diversity and strengthened geographic differentiation, making translocation-based recovery contentious. Additionally, the current prevalence of WS is unknown. To address these uncertainties, we sequenced and analyzed the genomes of 133 black abalone individuals from across their present range. We observed no spatial genetic structure among black abalone, with the exception of a single chromosomal inversion that increases in frequency with latitude. Genetic divergence between sites is minimal, and does not scale with either geographic distance or environmental dissimilarity. Genetic diversity appears uniformly high across the range. Despite this, however, demographic inference confirms a severe population bottleneck beginning around the time of WS onset, highlighting the temporal offset that may occur between a population collapse and its potential impact on genetic diversity. Finally, we find the bacterial agent of WS is equally present across the sampled range, but only in 10% of individuals. The lack of genetic structure, uniform diversity, and prevalence of WS bacteria indicates that translocation could be a valid and low-risk means of population restoration for black abalone species' recovery.
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Affiliation(s)
- Brock Wooldridge
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Chloé Orland
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Erik Enbody
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Cade Mirchandani
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Joshua D Kapp
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Nathaniel Fletcher
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Karah Ammann
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Peter Raimondi
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Beth Shapiro
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
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5
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Villegas LI, Ferretti L, Wiehe T, Waldvogel A, Schiffer PH. Parthenogenomics: Insights on mutation rates and nucleotide diversity in parthenogenetic Panagrolaimus nematodes. Ecol Evol 2024; 14:e10831. [PMID: 38192904 PMCID: PMC10771965 DOI: 10.1002/ece3.10831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 01/10/2024] Open
Abstract
Asexual reproduction is assumed to lead to the accumulation of deleterious mutations, and reduced heterozygosity due to the absence of recombination. Panagrolaimid nematode species display different modes of reproduction. Sexual reproduction with distinct males and females, asexual reproduction through parthenogenesis in the genus Panagrolaimus, and hermaphroditism in Propanagrolaimus. Here, we compared genomic features of free-living nematodes in populations and species isolated from geographically distant regions to study diversity, and genome-wide differentiation under different modes of reproduction. We firstly estimated genome-wide spontaneous mutation rates in a triploid parthenogenetic Panagrolaimus, and a diploid hermaphroditic Propanagrolaimus via long-term mutation accumulation lines. Secondly, we calculated population genetic parameters including nucleotide diversity, and fixation index (F ST) between populations of asexually and sexually reproducing nematodes. Thirdly, we used phylogenetic network methods on sexually and asexually reproducing Panagrolaimus populations to understand evolutionary relationships between them. The estimated mutation rate was slightly lower for the asexual population, as expected for taxa with this reproductive mode. Natural polyploid asexual populations revealed higher nucleotide diversity. Despite their common ancestor, a gene network revealed a high level of genetic differentiation among asexual populations. The elevated heterozygosity found in the triploid parthenogens could be explained by the third genome copy. Given their tendentially lower mutation rates it can be hypothesized that this is part of the mechanism to evade Muller's ratchet. Our findings in parthenogenetic triploid nematode populations seem to challenge common expectations of evolution under asexuality.
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Affiliation(s)
| | | | - Thomas Wiehe
- Institute for GeneticsUniversity of CologneKölnGermany
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6
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Glasenapp MR, Pogson GH. Extensive introgression among strongylocentrotid sea urchins revealed by phylogenomics. Ecol Evol 2023; 13:e10446. [PMID: 37636863 PMCID: PMC10451471 DOI: 10.1002/ece3.10446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/29/2023] Open
Abstract
Gametic isolation is thought to play an important role in the evolution of reproductive isolation in broadcast-spawning marine invertebrates. However, it is unclear whether gametic isolation commonly evolves early in the speciation process or only accumulates after other reproductive barriers are already in place. It is also unknown whether gametic isolation is an effective barrier to introgression following speciation. Here, we used whole-genome sequencing data and multiple complementary phylogenomic approaches to test whether the well-documented gametic incompatibilities among the strongylocentrotid sea urchins have limited introgression. We quantified phylogenetic discordance, inferred reticulate phylogenetic networks, and applied the Δ statistic using gene tree topologies reconstructed from multiple sequence alignments of protein-coding single-copy orthologs. In addition, we conducted ABBA-BABA tests on genome-wide single nucleotide variants and reconstructed a phylogeny of mitochondrial genomes. Our results revealed strong mito-nuclear discordance and considerable nonrandom gene tree discordance that cannot be explained by incomplete lineage sorting alone. Eight of the nine species examined demonstrated a history of introgression with at least one other species or ancestral lineage, indicating that introgression was common during the diversification of the strongylocentrotid urchins. There was strong support for introgression between four extant species pairs (Strongylocentrotus pallidus ⇔ S. droebachiensis, S. intermedius ⇔ S. pallidus, S. purpuratus ⇔ S. fragilis, and Mesocentrotus franciscanus ⇔ Pseudocentrotus depressus) and additional evidence for introgression on internal branches of the phylogeny. Our results suggest that the existing gametic incompatibilities among the strongylocentrotid urchin species have not been a complete barrier to hybridization and introgression following speciation. Their continued divergence in the face of widespread introgression indicates that other reproductive isolating barriers likely exist and may have been more critical in establishing reproductive isolation early in speciation.
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Affiliation(s)
- Matthew R. Glasenapp
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaSanta CruzCaliforniaUSA
| | - Grant H. Pogson
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaSanta CruzCaliforniaUSA
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7
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Hirase S, Sekino M, Hara M, Kikuchi K. Accumulation of gene copy number variations during the early phase of free-spawning abalone speciation. Ecol Evol 2023; 13:e9816. [PMID: 36818538 PMCID: PMC9936805 DOI: 10.1002/ece3.9816] [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: 08/02/2022] [Revised: 12/21/2022] [Accepted: 01/25/2023] [Indexed: 02/19/2023] Open
Abstract
The genetic basis of speciation in free-spawning marine invertebrates is poorly understood. Although gene copy number variations (GCNVs) and nucleotide variations possibly trigger the speciation of these organisms, empirical evidence for such a hypothesis is limited. In this study, we searched for genomic signatures of GCNVs that may contribute to the speciation of Western Pacific abalone species. Whole-genome sequencing data suggested the existence of significant amounts of GCNVs in closely related abalones, Haliotis discus and H. madaka, in the early phase of speciation. In addition, the degree of interspecies genetic differentiation in the genes where GCNVs were estimated was higher than that in other genes, suggesting that nucleotide divergence also accumulates in the genes with GCNVs. GCNVs in some genes were also detected in other related abalone species, suggesting that these GCNVs are derived from both ancestral and de novo mutations. Our findings suggest that GCNVs have been accumulated in the early phase of free-spawning abalone speciation.
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Affiliation(s)
- Shotaro Hirase
- Fisheries Laboratory, Graduate School of Agricultural and Life SciencesThe University of TokyoShizuokaJapan
| | - Masashi Sekino
- Bioinformatics and Biosciences Division, Fisheries Resources InstituteJapan Fisheries Research and Education AgencyYokohamaJapan
| | - Motoyuki Hara
- Tohoku Ecosystem‐Associated Marine SciencesTohoku UniversitySendaiJapan
| | - Kiyoshi Kikuchi
- Fisheries Laboratory, Graduate School of Agricultural and Life SciencesThe University of TokyoShizuokaJapan
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8
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Muto N, Kai Y. Allopatric origin, secondary contact and subsequent isolation of sympatric rockfishes (Sebastidae: Sebastes) in the north-western Pacific. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Understanding how speciation occurs is central to biology. Gene flow between diverging taxa is correlated with geography and other aspects of speciation; therefore, the examination of gene flow during divergence is a potent approach to understanding the nature of speciation. Here, we inferred the speciation process of the sympatric rockfishes Sebastes steindachneri and Sebastes wakiyai in the north-western Pacific and its marginal seas based on genome-wide single nucleotide polymorphism and mitochondrial DNA data. Model-based demographic inference showed that gene flow between the two species was absent in the initial and late stages of divergence and present only in the middle stage. Population expansion occurred before or during the period of gene flow. The estimated timings of the initial divergence and population expansion fell within the Pleistocene, during which the seas currently inhabited by the two species were repeatedly isolated and reconnected. Contemporary isolation was supported by the absence of hybrids and the shared mitochondrial DNA haplotypes. Our results suggest that the two species initially diverged in allopatry, followed by secondary contact and introgression and by the completion of reproductive isolation. Given that complete isolation following secondary contact has rarely been tested or documented in marine organisms, we highlight the importance of careful consideration of alternative divergence scenarios to be tested, which should take into account the geological and environmental settings.
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Affiliation(s)
- Nozomu Muto
- Department of Marine Biology and Sciences, School of Biological Sciences, Tokai University , 5-1-1-1 Minamisawa, Minami-Ku, Sapporo, Hokkaido 005-8601 , Japan
| | - Yoshiaki Kai
- Maizuru Fisheries Research Station, Field Science Education and Research Center, Kyoto University , Nagahama, Maizuru, Kyoto 625-0086 , Japan
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9
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Olivares‐Zambrano D, Daane J, Hyde J, Sandel MW, Aguilar A. Speciation genomics and the role of depth in the divergence of rockfishes (
Sebastes
) revealed through Pool‐seq analysis of enriched sequences. Ecol Evol 2022; 12:e9341. [PMID: 36188524 PMCID: PMC9502067 DOI: 10.1002/ece3.9341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/22/2022] [Accepted: 08/30/2022] [Indexed: 11/07/2022] Open
Abstract
Speciation in the marine environment is challenged by the wide geographic distribution of many taxa and potential for high rates of gene flow through larval dispersal mechanisms. Depth has recently been proposed as a potential driver of ecological divergence in fishes, and yet it is unclear how adaptation along these gradients' shapes genomic divergence. The genus Sebastes contains numerous species pairs that are depth‐segregated and can provide a better understanding of the mode and tempo of genomic diversification. Here, we present exome data on two species pairs of rockfishes that are depth‐segregated and have different degrees of divergence: S. chlorostictus–S. rosenblatti and S. crocotulus–S. miniatus. We were able to reliably identify “islands of divergence” in the species pair with more recent divergence (S. chlorostictus–S. rosenblatti) and discovered a number of genes associated with neurosensory function, suggesting a role for this pathway in the early speciation process. We also reconstructed demographic histories of divergence and found the best supported model was isolation followed by asymmetric secondary contact for both species pairs. These results suggest past ecological/geographic isolation followed by asymmetric secondary contact of deep to shallow species. Our results provide another example of using rockfish as a model for studying speciation and support the role of depth as an important mechanism for diversification in the marine environment.
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Affiliation(s)
- Daniel Olivares‐Zambrano
- Department of Biological SciencesCalifornia State University Los AngelesLos AngelesCaliforniaUSA
- Present address:
Department of Marine and Environmental BiologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Jacob Daane
- Department of Biology and BiochemistryUniversity of HoustonHoustonTexasUSA
| | - John Hyde
- National Oceanic and Atmospheric Administration, National Marine Fisheries ServiceNational Marine Fisheries ServiceSouthwest Fisheries Science CenterLa JollaCaliforniaUSA
| | - Michael W. Sandel
- Biological and Environmental SciencesUniversity of West AlabamaLivingstonAlabamaUSA
- Department of WIldlifeFisheries, and Aquaculture, Mississippi State UniversityMississippi StateMississippiUSA
| | - Andres Aguilar
- Department of Biological SciencesCalifornia State University Los AngelesLos AngelesCaliforniaUSA
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10
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Walton K, Scarsbrook L, Mitchell KJ, Verry AJF, Marshall BA, Rawlence NJ, Spencer HG. Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone. Mol Ecol Resour 2022; 23:118-130. [PMID: 35951485 PMCID: PMC10087340 DOI: 10.1111/1755-0998.13696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/15/2022] [Accepted: 08/08/2022] [Indexed: 11/28/2022]
Abstract
Natural history collections worldwide contain a plethora of mollusc shells. Recent studies have detailed the sequencing of DNA extracted from shells up to thousands of years old and from various taphonomic and preservational contexts. However, previous approaches have largely addressed methodological rather than evolutionary research questions. Here we report the generation of DNA sequence data from mollusc shells using such techniques, applied to Haliotis virginea Gmelin, 1791, a New Zealand abalone, in which morphological variation has led to the recognition of several forms and subspecies. We successfully recovered near-complete mitogenomes from 22 specimens including 12 dry-preserved shells up to 60 years old. We used a combination of palaeogenetic techniques that have not previously been applied to shell, including DNA extraction optimized for ultra-short fragments and hybridization-capture of single-stranded DNA libraries. Phylogenetic analyses revealed three major, well-supported clades comprising samples from: 1) the Three Kings Islands; 2) the Auckland, Chatham and Antipodes Islands; and 3) mainland New Zealand and Campbell Island. This phylogeographic structure does not correspond to the currently recognized forms. Critically, our non-reliance on freshly collected or ethanol-preserved samples enabled inclusion of topotypes of all recognized subspecies as well as additional difficult-to-sample populations. Broader application of these comparatively cost-effective and reliable methods to modern, historical, archaeological and palaeontological shell samples has the potential to revolutionize invertebrate genetic research.
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Affiliation(s)
- Kerry Walton
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Box 56, Dunedin 9054, PO, New Zealand
| | - Lachie Scarsbrook
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Box 56, Dunedin 9054, PO, New Zealand.,Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, 1 South Parks Road, OX1 3TG, University of Oxford, Oxford, United Kingdom
| | - Kieren J Mitchell
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Box 56, Dunedin 9054, PO, New Zealand
| | - Alexander J F Verry
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Box 56, Dunedin 9054, PO, New Zealand.,Centre for Anthropobiology and Genomics of Toulouse, CNRS UMR5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Bruce A Marshall
- Museum of New Zealand Te Papa Tongarewa, 169 Tory St, Te Aro, 6011, Wellington, New Zealand
| | - Nicolas J Rawlence
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Box 56, Dunedin 9054, PO, New Zealand
| | - Hamish G Spencer
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Box 56, Dunedin 9054, PO, New Zealand
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11
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Sato JJ, Yasuda K. Ancient rivers shaped the current genetic diversity of the wood mouse (Apodemus speciosus) on the islands of the Seto Inland Sea, Japan. ZOOLOGICAL LETTERS 2022; 8:9. [PMID: 35729644 PMCID: PMC9210816 DOI: 10.1186/s40851-022-00193-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
The current distributions of organisms have been shaped by both current and past geographical barriers. However, it remains unclear how past geographical factors-currently cryptic on the sea floor-affected the current distributions of terrestrial animals. Here, we examined the effects of currently cryptic ancient rivers on current genetic differentiation of the large Japanese wood mouse, Apodemus speciosus, which inhabits islands in the Seto Inland Sea, Japan. Genome-wide polymorphisms were identified by GRAS-Di (Genotyping by Random Amplicon Sequencing, Direct) analysis of 92 A. speciosus individuals. Maximum-likelihood analysis was performed with 94,142 single nucleotide polymorphisms (SNPs) identified by GRAS-Di analyses. Ancient rivers were visualized by Geographic Information System (GIS) channel analysis. Maximum-likelihood analysis showed strong support for the monophyly of each population in the islands in the Seto Inland Sea; it also showed close relationships between Innoshima-Ikuchijima, Ohmishima-Hakatajima-Oshima, Ohmishima-Hakatajima, Ohsakikamijima-Ohsakishimojima, Kamikamagarijima-Shimokamagarijima, and Kurahashijima-Etajima islands. The principal component analyses of the SNPs also supported these relationships. Furthermore, individuals from islands located on the east and west sides of the main stream of the ancient river were clustered on each side with strong support. These phylogenetic relationships were completely congruent with the paleogeographic relationships inferred from ancient rivers. In conclusion, the findings demonstrated that the current distribution of genetically distinct island lineages was shaped by ancient rivers that are currently submerged beneath the Seto Inland Sea, Japan.
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Affiliation(s)
- Jun J. Sato
- Laboratory of Zoology, Department of Biotechnology, Fukuyama University, Higashimura-cho, Aza, Sanzo, 985, Fukuyama, 729-0292 Japan
| | - Kouki Yasuda
- Laboratory of Zoology, Department of Biotechnology, Fukuyama University, Higashimura-cho, Aza, Sanzo, 985, Fukuyama, 729-0292 Japan
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12
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Saenz‐Agudelo P, Peluso L, Nespolo R, Broitman BR, Haye PA, Lardies MA. Population genomic analyses reveal hybridization and marked differences in genetic structure of
Scurria
limpet sister species with parapatric distributions across the South Eastern Pacific. Ecol Evol 2022; 12:e8888. [PMID: 35571762 PMCID: PMC9078047 DOI: 10.1002/ece3.8888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 03/30/2022] [Accepted: 04/08/2022] [Indexed: 11/08/2022] Open
Affiliation(s)
- Pablo Saenz‐Agudelo
- Instituto de Ciencias Ambientales y Evolutivas Universidad Austral de Chile Valdivia Chile
- ANID‐ Millennium Science Initiative Nucleus (NUTME) Las Cruces Chile
| | - Lívia Peluso
- Instituto de Ciencias Ambientales y Evolutivas Universidad Austral de Chile Valdivia Chile
- Doctorado en Ciencias Mención Ecología y Evolución Escuela de Graduados Facultad de Ciencias Universidad Austral de Chile Valdivia Chile
| | - Roberto Nespolo
- Instituto de Ciencias Ambientales y Evolutivas Universidad Austral de Chile Valdivia Chile
- ANID‐ Millennium Science Initiative Nucleus (LiLi) Valdivia Chile
- Center for Applied Ecology and Sustainability (CAPES) Santiago Chile
- Millennium Institute for Integrative Biology (iBio) Santiago Chile
| | - Bernardo R. Broitman
- Departamento de Ciencias Facultad de Artes Liberales Universidad Adolfo Ibañez Santiago Chile
- ANID‐ Millennium Science Initiative Nucleus UPWELL Santiago Chile
- Instituto Milenio en Socio‐Ecología Costera (SECOS) Santiago Chile
| | - Pilar A. Haye
- Instituto Milenio en Socio‐Ecología Costera (SECOS) Santiago Chile
- Departamento de Biología Marina Universidad Católica del Norte Coquimbo Chile
| | - Marco A. Lardies
- Departamento de Ciencias Facultad de Artes Liberales Universidad Adolfo Ibañez Santiago Chile
- Instituto Milenio en Socio‐Ecología Costera (SECOS) Santiago Chile
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13
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Gao W, Yu CX, Zhou WW, Zhang BL, Chambers EA, Dahn HA, Jin JQ, Murphy RW, Zhang YP, Che J. Species persistence with hybridization in toad-headed lizards driven by divergent selection and low recombination. Mol Biol Evol 2022; 39:6561330. [PMID: 35356979 PMCID: PMC9007161 DOI: 10.1093/molbev/msac064] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Speciation plays a central role in evolutionary studies, and particularly how reproductive isolation (RI) evolves. The origins and persistence of RI are distinct processes that require separate evaluations. Treating them separately clarifies the drivers of speciation and then it is possible to link the processes to understand large-scale patterns of diversity. Recent genomic studies have focused predominantly on how species or RI originate. However, we know little about how species persist in face of gene flow. Here, we evaluate a contact zone of two closely related toad-headed lizards (Phrynocephalus) using a chromosome-level genome assembly and population genomics. To some extent, recent asymmetric introgression from Phrynocephalus putjatai to P. vlangalii reduces their genomic differences. However, their highly divergent regions (HDRs) have heterogeneous distributions across the genomes. Functional gene annotation indicates that many genes within HDRs are involved in reproduction and RI. Compared with allopatric populations, contact areas exhibit recent divergent selection on the HDRs and a lower population recombination rate. Taken together, this implies that divergent selection and low genetic recombination help maintain RI. This study provides insights into the genomic mechanisms that drive RI and two species persistence in the face of gene flow during the late stage of speciation.
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Affiliation(s)
- Wei Gao
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Chuan-Xin Yu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Wei-Wei Zhou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - E Anne Chambers
- Department of Integrative Biology and Biodiversity Center, University of Texas at Austin, Austin, USA.,Department of Environmental Science, Policy, and Management, Univerity of California, Berkeley, USA
| | - Hollis A Dahn
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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14
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Liang S, Zhang X, Wei R. Ecological adaptation shaped the genetic structure of homoploid ferns against strong dispersal capacity. Mol Ecol 2022; 31:2679-2697. [DOI: 10.1111/mec.16420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 02/26/2022] [Accepted: 02/28/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Si‐Qi Liang
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany The Chinese Academy of Sciences Beijing 100093 China
- University of Chinese Academy of Sciences College of Life Sciences Beijing 100049 China
| | - Xian‐Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany The Chinese Academy of Sciences Beijing 100093 China
| | - Ran Wei
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany The Chinese Academy of Sciences Beijing 100093 China
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15
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Matsuyama T, Kiryu I, Inada M, Takano T, Matsuura Y, Kamaishi T. Susceptibility of Four Abalone Species, Haliotis gigantea, Haliotis discus discus, Haliotis discus hannai and Haliotis diversicolor, to Abalone asfa-like Virus. Viruses 2021; 13:v13112315. [PMID: 34835121 PMCID: PMC8621809 DOI: 10.3390/v13112315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/12/2021] [Accepted: 11/16/2021] [Indexed: 11/29/2022] Open
Abstract
Abalone amyotrophia is a viral disease that causes mass mortality of juvenile Haliotis discus and H. madaka. Although the cause of this disease has yet to be identified, we had previously postulated a novel virus with partial genome sequence similarity to that of African swine fever virus is the causative agent and proposed abalone asfa-like virus (AbALV) as a provisional name. In this study, three species of juvenile abalone (H. gigantea, H. discus discus, and H. diversicolor) and four species of adult abalone (the above three species plus H. discus hannai) were experimentally infected, and their susceptibility to AbALV was investigated by recording mortality, quantitatively determining viral load by PCR, and conducting immunohistological studies. In the infection test using 7-month-old animals, H. gigantea, which was previously reported to be insusceptible to the disease, showed multiplication of the virus to the same extent as in H. discus discus, resulting in mass mortality. H. discus discus at 7 months old showed abnormal cell masses, notches in the edge of the shell and brown pigmentation inside of the shell, which are histopathological and external features of this disease, while H. gigantea did not show any of these characteristics despite suffering high mortality. Adult abalones had low mortality and viral replication in all species; however, all three species, except H. diversicolor, became carriers of the virus. In immunohistological observations, cells positive for viral antigens were detected predominantly in the gills of juvenile H. discus discus and H. gigantea, and mass mortality was observed in these species. In H. diversicolor, neither juvenile nor adult mortality from infection occurred, and the AbALV genome was not increased by experimental infection through cohabitation or injection. Our results suggest that H. gigantea, H. discus discus and H. discus hannai are susceptible to AbALV, while H. diversicolor is not. These results confirmed that AbALV is the etiological agent of abalone amyotrophia.
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Affiliation(s)
- Tomomasa Matsuyama
- Research Center for Fish Diseases, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Minami-Ise 516-0193, Japan; (T.T.); (Y.M.); (T.K.)
- Correspondence:
| | - Ikunari Kiryu
- Diagnosis and Training Center for Fish Diseases, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Minami-Ise 516-0193, Japan; (I.K.); (M.I.)
| | - Mari Inada
- Diagnosis and Training Center for Fish Diseases, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Minami-Ise 516-0193, Japan; (I.K.); (M.I.)
| | - Tomokazu Takano
- Research Center for Fish Diseases, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Minami-Ise 516-0193, Japan; (T.T.); (Y.M.); (T.K.)
| | - Yuta Matsuura
- Research Center for Fish Diseases, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Minami-Ise 516-0193, Japan; (T.T.); (Y.M.); (T.K.)
| | - Takashi Kamaishi
- Research Center for Fish Diseases, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Minami-Ise 516-0193, Japan; (T.T.); (Y.M.); (T.K.)
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