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Barton N. Limits to species' range: the tension between local and global adaptation. J Evol Biol 2024; 37:605-615. [PMID: 38683160 DOI: 10.1093/jeb/voae052] [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: 11/18/2023] [Revised: 04/02/2024] [Accepted: 05/08/2024] [Indexed: 05/01/2024]
Abstract
We know that heritable variation is abundant, and that selection causes all but the smallest populations to rapidly shift beyond their original trait distribution. So then, what limits the range of a species? There are physical constraints and also population genetic limits to the effectiveness of selection, ultimately set by population size. Global adaptation, where the same genotype is favoured over the whole range, is most efficient when based on a multitude of weakly selected alleles and is effective even when local demes are small, provided that there is some gene flow. In contrast, local adaptation is sensitive to gene flow and may require alleles with substantial effect. How can populations combine the advantages of large effective size with the ability to specialise into local niches? To what extent does reproductive isolation help resolve this tension? I address these questions using eco-evolutionary models of polygenic adaptation, contrasting discrete demes with continuousspace.
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Affiliation(s)
- Nicholas Barton
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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2
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Hartley GA, Frankenberg SR, Robinson NM, MacDonald AJ, Hamede RK, Burridge CP, Jones ME, Faulkner T, Shute H, Rose K, Brewster R, O'Neill RJ, Renfree MB, Pask AJ, Feigin CY. Genome of the endangered eastern quoll (Dasyurus viverrinus) reveals signatures of historical decline and pelage color evolution. Commun Biol 2024; 7:636. [PMID: 38796620 PMCID: PMC11128018 DOI: 10.1038/s42003-024-06251-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/26/2024] [Indexed: 05/28/2024] Open
Abstract
The eastern quoll (Dasyurus viverrinus) is an endangered marsupial native to Australia. Since the extirpation of its mainland populations in the 20th century, wild eastern quolls have been restricted to two islands at the southern end of their historical range. Eastern quolls are the subject of captive breeding programs and attempts have been made to re-establish a population in mainland Australia. However, few resources currently exist to guide the genetic management of this species. Here, we generated a reference genome for the eastern quoll with gene annotations supported by multi-tissue transcriptomes. Our assembly is among the most complete marsupial genomes currently available. Using this assembly, we infer the species' demographic history, identifying potential evidence of a long-term decline beginning in the late Pleistocene. Finally, we identify a deletion at the ASIP locus that likely underpins pelage color differences between the eastern quoll and the closely related Tasmanian devil (Sarcophilus harrisii).
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Affiliation(s)
- Gabrielle A Hartley
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA
| | | | - Natasha M Robinson
- Fenner School of Environment & Society, Australian National University, Canberra, ACT, 2601, Australia
| | - Anna J MacDonald
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
- Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kingston, TAS, 7050, Australia
| | - Rodrigo K Hamede
- School of Natural Sciences, University of Tasmania, Hobart, TAS, 7005, Australia
| | | | - Menna E Jones
- School of Natural Sciences, University of Tasmania, Hobart, TAS, 7005, Australia
| | - Tim Faulkner
- Australian Reptile Park & Aussie Ark, Somersby, NSW, 2250, Australia
| | - Hayley Shute
- Australian Reptile Park & Aussie Ark, Somersby, NSW, 2250, Australia
| | - Karrie Rose
- Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Mosman, NSW, 2088, Australia
| | - Rob Brewster
- WWF-Australia, PO Box 528, Sydney, NSW, 2001, Australia
| | - Rachel J O'Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Andrew J Pask
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Department of Sciences, Museums Victoria, Carlton, VIC, 3053, Australia
| | - Charles Y Feigin
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia.
- Department of Environment and Genetics, La Trobe University, Bundoora, VIC, 3086, Australia.
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3
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Barrett LH, Fraga D, Lehtinen RM. The Genetic Basis of Melanism in Abert's Squirrel ( Sciurus aberti). Animals (Basel) 2024; 14:648. [PMID: 38396615 PMCID: PMC10885973 DOI: 10.3390/ani14040648] [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: 01/10/2024] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
Melanism is widespread in different taxa and has been hypothesized to provide adaptive benefits in certain environments. Melanism is typically caused by mutations in one of two regulatory genes: the Melanocortin 1 Receptor (MC1R) or the Agouti Signaling Protein (ASIP). Melanism has repeatedly evolved among tree squirrels and their relatives (tribe Sciurini) in at least 12 different species based on our review of the literature. The causal mutations for melanism have been characterized in two species so far. This study examines Abert's Squirrel (Sciurus aberti), which has a melanistic morph whose genetic basis has not yet been established. We sequenced the MC1R and ASIP genes for five wild-type and seven melanistic S. aberti individuals to search for melanism-associated mutations. A novel single base pair mutation in the ASIP gene, unique to S. aberti, was found to be associated with melanism in the species, indicating that melanism in S. aberti evolved independently from other tree squirrels and thus represents an example of convergent evolution. The independent evolution of melanism in this species suggests that there is an adaptive advantage to the melanistic phenotype. The geographic range and habitat of S. aberti suggest possible benefits associated with thermoregulation, post-forest-fire camouflage, or other untested hypotheses.
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Affiliation(s)
| | | | - Richard M. Lehtinen
- Biology Department, 931 College Mall, The College of Wooster, Wooster, OH 44691, USA; (L.H.B.); (D.F.)
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Branney AB, Abernathy HN, Conner LM, Garrison E, Cherry MJ. Photographic documentation of melanism in bobcats ( Lynx rufus) in the Greater Everglades. Ecol Evol 2024; 14:e10754. [PMID: 38235409 PMCID: PMC10791593 DOI: 10.1002/ece3.10754] [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: 07/31/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 01/19/2024] Open
Abstract
We document the presence of bobcats (Lynx rufus) that demonstrate melanism in the Greater Everglades. The South Florida landscape is driven by a myriad of disturbance regimes particularly that of short fire intervals. We monitored 180 camera traps for 3 years and obtained 9503 photographs of bobcats 25 (<0.5%) of these detections included melanistic individuals. Our observations and historical accounts suggest melanism is a phenotype that persists, albeit it at an exceedingly low frequency, in bobcats in the region. While we do not know if the expression of melanism conferred a fitness benefit in our system, the vegetation structure that was characterized by frequently burned uplands and low-light and densely vegetated swamps produced conditions that may render a benefit from melanism through enhanced crypsis. The investigation of rare phenomenon in ecology is important yet difficult within a given field study, but reporting novel observations, like melanism in bobcats, allows for science to gain insight across studies that would not be otherwise possible.
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Affiliation(s)
- Aidan B. Branney
- Caesar Kleberg Wildlife Research InstituteTexas A&M University‐KingsvilleKingsvilleTexasUSA
- Present address:
California Department of Fish and WildlifeRancho CardovaCaliforniaUSA
| | - Heather N. Abernathy
- Haub School of Environment and Natural ResourcesUniversity of WyomingLaramieWyomingUSA
| | | | - Elina Garrison
- Florida Fish and Wildlife Conservation CommissionGainesvilleFloridaUSA
| | - Michael J. Cherry
- Caesar Kleberg Wildlife Research InstituteTexas A&M University‐KingsvilleKingsvilleTexasUSA
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5
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Zakoh K, Fujiwara K, Takada T, Osada N, Suzuki H. Genealogical characterization of regional populations and dorsal coat color variation in the house mouse Mus musculus from Asia based on haplotype structure analysis of a gene-rich region harboring Mc1r. Genes Genet Syst 2023; 98:73-87. [PMID: 37558462 DOI: 10.1266/ggs.22-00157] [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: 08/11/2023] Open
Abstract
We analyzed 196 haplotype sequences from a gene-rich region (250 kb) that includes Mc1r, a gene involved in coat color regulation, to gain insight into the evolution of coat color variation in subspecies of the house mouse Mus musculus. Phylogenetic networks revealed haplotype groups from the major subspecies of M. m. castaneus (CAS), M. m. domesticus (DOM), and M. m. musculus (MUS). Using haplotype sequences assigned to each of CAS and MUS through phylogenetic analysis, we proposed migration routes associated with prehistoric humans from west to east across Eurasia. Comparing nucleotide diversity among subspecies-specific haplotypes in different geographic areas showed a marked reduction during migration, particularly in MUS-derived haplotypes from Korea and Japan, suggesting intensive population bottlenecks during migration. We found that a C>T polymorphism at site 302 (c.302C>T) in the Mc1r coding region correlated with a darkening of dorsal fur color in both CAS and MUS. However, C/C homozygous mice in MUS showed marked variation in lightness, indicating the possibility of another genetic determinant that affects the lightness of dorsal fur color. Detailed sequence comparisons of haplotypes revealed that short fragments assigned to DOM were embedded in CAS-assigned fragments, indicating ancient introgression between subspecies. The estimated age of c.302C>T also supports the hypothesis that genetic interaction between subspecies occurred in ancient times. This suggests that the genome of M. musculus evolved through gene flow between subspecies over an extended period before the movement of the species in conjunction with prehistoric humans.
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Affiliation(s)
- Kazuhiro Zakoh
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University
| | - Kazumichi Fujiwara
- Graduate School of Information Science and Technology, Hokkaido University
| | - Toyoyuki Takada
- Integrated Bioresource Information Division, RIKEN BioResource Research Center
| | - Naoki Osada
- Graduate School of Information Science and Technology, Hokkaido University
| | - Hitoshi Suzuki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University
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Elkin J, Martin A, Courtier-Orgogozo V, Santos ME. Analysis of the genetic loci of pigment pattern evolution in vertebrates. Biol Rev Camb Philos Soc 2023; 98:1250-1277. [PMID: 37017088 DOI: 10.1111/brv.12952] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 04/06/2023]
Abstract
Vertebrate pigmentation patterns are amongst the best characterised model systems for studying the genetic basis of adaptive evolution. The wealth of available data on the genetic basis for pigmentation evolution allows for analysis of trends and quantitative testing of evolutionary hypotheses. We employed Gephebase, a database of genetic variants associated with natural and domesticated trait variation, to examine trends in how cis-regulatory and coding mutations contribute to vertebrate pigmentation phenotypes, as well as factors that favour one mutation type over the other. We found that studies with lower ascertainment bias identified higher proportions of cis-regulatory mutations, and that cis-regulatory mutations were more common amongst animals harbouring a higher number of pigment cell classes. We classified pigmentation traits firstly according to their physiological basis and secondly according to whether they affect colour or pattern, and identified that carotenoid-based pigmentation and variation in pattern boundaries are preferentially associated with cis-regulatory change. We also classified genes according to their developmental, cellular, and molecular functions. We found a greater proportion of cis-regulatory mutations in genes implicated in upstream developmental processes compared to those involved in downstream cellular functions, and that ligands were associated with a higher proportion of cis-regulatory mutations than their respective receptors. Based on these trends, we discuss future directions for research in vertebrate pigmentation evolution.
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Affiliation(s)
- Joel Elkin
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, 800 22nd St. NW, Suite 6000, Washington, DC, 20052, USA
| | | | - M Emília Santos
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
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Sooriyabandara MGC, Bandaranayake AU, Hathurusinghe HABM, Jayasundara SM, Marasinghe MSRRP, Prasad GAT, Abeywardana VPMK, Pinidiya MA, Nilanthi RMR, Bandaranayake PCG. A unique single nucleotide polymorphism in Agouti Signalling Protein (ASIP) gene changes coat colour of Sri Lankan leopard (Panthera pardus kotiya) to dark black. PLoS One 2023; 18:e0269967. [PMID: 37440497 PMCID: PMC10343082 DOI: 10.1371/journal.pone.0269967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/13/2023] [Indexed: 07/15/2023] Open
Abstract
The Sri Lankan leopard (Panthera pardus kotiya) is an endangered subspecies restricted to isolated and fragmented populations in Sri Lanka. Among them, melanistic leopards have been recorded on a few occasions. Literature suggests the evolution of melanism several times in the Felidae family, with three species having distinct mutations. Nevertheless, the mutations or other variations in the remaining species, including Sri Lankan melanistic leopard, are unknown. We used reference-based assembled nuclear genomes of Sri Lankan wild type and melanistic leopards and de novo assembled mitogenomes of the same to investigate the genetic basis, adaptive significance, and evolutionary history of the Sri Lankan melanistic leopard. Interestingly, we identified a single nucleotide polymorphism in exon-4 Sri Lankan melanistic leopard, which may completely ablate Agouti Signalling Protein (ASIP) function. The wild type leopards in Sri Lanka did not carry this mutation, suggesting the cause for the occurrence of melanistic leopords in the population. Comparative analysis of existing genomic data in the literature suggests it as a P. p. kotiya specific mutation and a novel mutation in the ASIP-gene of the Felidae family, contributing to naturally occurring colour polymorphism. Our data suggested the coalescence time of Sri Lankan leopards at ~0.5 million years, sisters to the Panthera pardus lineage. The genetic diversity was low in Sri Lankan leopards. Further, the P. p. kotiya melanistic leopard is a different morphotype of the P. p. kotiya wildtype leopard resulting from the mutation in the ASIP-gene. The ability of black leopards to camouflage, along with the likelihood of recurrence and transfer to future generations, suggests that this rare mutation could be environment-adaptable.
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Affiliation(s)
| | - A. U. Bandaranayake
- Department of Computer Engineering, Faculty of Engineering, University of Peradeniya, Peradeniya, Sri Lanka
| | - H. A. B. M. Hathurusinghe
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
| | - S. M. Jayasundara
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
| | | | - G. A. T. Prasad
- Department of Wildlife Conservation, Battaramulla, Sri Lanka
| | | | - M. A. Pinidiya
- Department of Wildlife Conservation, Battaramulla, Sri Lanka
| | | | - P. C. G. Bandaranayake
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
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8
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Cotts L, Slifkin JP, Moratelli R, Gonçalves L, Rocha-Barbosa O. Multiple colors in anteaters: review and description of chromatic disorders in Tamandua (Xenarthra: Pilosa) with reports of new and rare coat colorations. ZOOLOGIA 2023. [DOI: 10.1590/s1984-4689.v40.e22034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
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9
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Chaturvedi S, Gompert Z, Feder JL, Osborne OG, Muschick M, Riesch R, Soria-Carrasco V, Nosil P. Climatic similarity and genomic background shape the extent of parallel adaptation in Timema stick insects. Nat Ecol Evol 2022; 6:1952-1964. [PMID: 36280782 PMCID: PMC7613875 DOI: 10.1038/s41559-022-01909-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 09/13/2022] [Indexed: 12/15/2022]
Abstract
Evolution can repeat itself, resulting in parallel adaptations in independent lineages occupying similar environments. Moreover, parallel evolution sometimes, but not always, uses the same genes. Two main hypotheses have been put forth to explain the probability and extent of parallel evolution. First, parallel evolution is more likely when shared ecologies result in similar patterns of natural selection in different taxa. Second, parallelism is more likely when genomes are similar because of shared standing variation and similar mutational effects in closely related genomes. Here we combine ecological, genomic, experimental and phenotypic data with Bayesian modelling and randomization tests to quantify the degree of parallelism and its relationship with ecology and genetics. Our results show that the extent to which genomic regions associated with climate are parallel among species of Timema stick insects is shaped collectively by shared ecology and genomic background. Specifically, the extent of genomic parallelism decays with divergence in climatic conditions (that is, habitat or ecological similarity) and genomic similarity. Moreover, we find that climate-associated loci are likely subject to selection in a field experiment, overlap with genetic regions associated with cuticular hydrocarbon traits and are not strongly shaped by introgression between species. Our findings shed light on when evolution is most expected to repeat itself.
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Affiliation(s)
- Samridhi Chaturvedi
- Department of Integrative Biology, University of California, Berkeley, CA, USA.
- Department of Biology and Ecology Center, Utah State University, Logan, UT, USA.
| | - Zachariah Gompert
- Department of Biology and Ecology Center, Utah State University, Logan, UT, USA.
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Owen G Osborne
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, UK
| | - Moritz Muschick
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Rüdiger Riesch
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | | | - Patrik Nosil
- Department of Biology and Ecology Center, Utah State University, Logan, UT, USA
- CEFE, Univ. Montpellier, CNRS, EPHE, IRD, Univ. Paul Valéry Montpellier 3, Montpellier, France
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10
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Campagna L, Mo Z, Siepel A, Uy JAC. Selective sweeps on different pigmentation genes mediate convergent evolution of island melanism in two incipient bird species. PLoS Genet 2022; 18:e1010474. [PMID: 36318577 PMCID: PMC9624418 DOI: 10.1371/journal.pgen.1010474] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/12/2022] [Indexed: 11/19/2022] Open
Abstract
Insular organisms often evolve predictable phenotypes, like flightlessness, extreme body sizes, or increased melanin deposition. The evolutionary forces and molecular targets mediating these patterns remain mostly unknown. Here we study the Chestnut-bellied Monarch (Monarcha castaneiventris) from the Solomon Islands, a complex of closely related subspecies in the early stages of speciation. On the large island of Makira M. c. megarhynchus has a chestnut belly, whereas on the small satellite islands of Ugi, and Santa Ana and Santa Catalina (SA/SC) M. c. ugiensis is entirely iridescent blue-black (i.e., melanic). Melanism has likely evolved twice, as the Ugi and SA/SC populations were established independently. To investigate the genetic basis of melanism on each island we generated whole genome sequence data from all three populations. Non-synonymous mutations at the MC1R pigmentation gene are associated with melanism on SA/SC, while ASIP, an antagonistic ligand of MC1R, is associated with melanism on Ugi. Both genes show evidence of selective sweeps in traditional summary statistics and statistics derived from the ancestral recombination graph (ARG). Using the ARG in combination with machine learning, we inferred selection strength, timing of onset and allele frequency trajectories. MC1R shows evidence of a recent, strong, soft selective sweep. The region including ASIP shows more complex signatures; however, we find evidence for sweeps in mutations near ASIP, which are comparatively older than those on MC1R and have been under relatively strong selection. Overall, our study shows convergent melanism results from selective sweeps at independent molecular targets, evolving in taxa where coloration likely mediates reproductive isolation with the neighboring chestnut-bellied subspecies. Chestnut-bellied Monarchs (Monarcha castaneiventris ugiensis) from two archipelagos in the Solomon Islands have evolved entirely black plumage from a chestnut ancestor (Monarcha castaneiventris megarhynchus), a phenomenon known as island melanism. We obtain and analyze whole genome sequences using traditional summary statistics and new methods that combine inference of the ancestral recombination graph with machine learning. We find multiple lines of evidence for independent selective sweeps on the MC1R and ASIP genes, a receptor/ligand pair which regulates the production of melanin. Melanism on each archipelago is mediated by mutations in one of these two genes. Mutations in and around MC1R underwent a recent soft sweep experiencing strong selection on the islands of Santa Ana and Santa Catalina, whereas selection was also strong but comparatively older for ASIP on the island of Ugi. We show how melanism originated under positive selection on independent molecular targets, evolving convergently in taxa where coloration mediates reproductive isolation.
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Affiliation(s)
- Leonardo Campagna
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, New York, United States of America
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
- * E-mail: (LC); (JACU)
| | - Ziyi Mo
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - J. Albert C. Uy
- Department of Biology, University of Rochester, Rochester, New York, United States of America
- * E-mail: (LC); (JACU)
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11
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An enhancer of Agouti contributes to parallel evolution of cryptically colored beach mice. Proc Natl Acad Sci U S A 2022; 119:e2202862119. [PMID: 35776547 PMCID: PMC9271204 DOI: 10.1073/pnas.2202862119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Identifying the genetic basis of repeatedly evolved traits provides a way to reconstruct their evolutionary history and ultimately investigate the predictability of evolution. Here, we focus on the oldfield mouse (Peromyscus polionotus), which occurs in the southeastern United States, where it exhibits considerable color variation. Dorsal coats range from dark brown in mainland mice to near white in mice inhabiting sandy beaches; this light pelage has evolved independently on Florida's Gulf and Atlantic coasts as camouflage from predators. To facilitate genomic analyses, we first generated a chromosome-level genome assembly of Peromyscus polionotus subgriseus. Next, in a uniquely variable mainland population (Peromyscus polionotus albifrons), we scored 23 pigment traits and performed targeted resequencing in 168 mice. We find that pigment variation is strongly associated with an ∼2-kb region ∼5 kb upstream of the Agouti signaling protein coding region. Using a reporter-gene assay, we demonstrate that this regulatory region contains an enhancer that drives expression in the dermis of mouse embryos during the establishment of pigment prepatterns. Moreover, extended tracts of homozygosity in this Agouti region indicate that the light allele experienced recent and strong positive selection. Notably, this same light allele appears fixed in both Gulf and Atlantic coast beach mice, despite these populations being separated by >1,000 km. Together, our results suggest that this identified Agouti enhancer allele has been maintained in mainland populations as standing genetic variation and from there, has spread to and been selected in two independent beach mouse lineages, thereby facilitating their rapid and parallel evolution.
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12
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Takeishi T, Fujiwara K, Osada N, Mita A, Takada T, Shiroishi T, Suzuki H. Phylogeographic study using nuclear genome sequences of <i>Asip</i> to infer the origins of ventral fur color variation in the house mouse <i>Mus musculus</i>. Genes Genet Syst 2021; 96:271-284. [DOI: 10.1266/ggs.21-00075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Toki Takeishi
- Laboratory of Ecology and Genetics Graduate School of Environmental Science, Hokkaido University
| | - Kazumichi Fujiwara
- Graduate School of Information Science and Technology, Hokkaido University
| | - Naoki Osada
- Graduate School of Information Science and Technology, Hokkaido University
| | | | - Toyoyuki Takada
- Integrated Bioresource Information Division, RIKEN BioResource Research Center
| | | | - Hitoshi Suzuki
- Laboratory of Ecology and Genetics Graduate School of Environmental Science, Hokkaido University
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13
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Newell C, Walker H, Caro T. Pig pigmentation: testing Gloger’s rule. J Mammal 2021. [DOI: 10.1093/jmammal/gyab090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Comparative studies indicate that several mammalian clades obey Gloger’s rule in that they exhibit darker coloration in humid warm climates, although the mechanisms responsible for this association still are poorly understood. We surveyed external appearances of a single species, the feral pig (Sus scrofa), shot at 48 hunting lodges across North America and matched these to potential abiotic drivers, namely: relative humidity, temperature, precipitation, and ultraviolet (UV) radiation, and to biotic factors of habitat shade and predation pressure. We found that darker animals occupy locations of greater precipitation and warmer temperatures, as expected from Gloger’s rule. The recent range expansion of S. scrofa implies selection for pelage coloration has occurred very rapidly. Separating pelage coloration into eumelanin- and phaeomelanin-based pigmentation, we found more pronounced eumelanin-based pelage in areas of higher rainfall and temperatures and UV radiation, whereas pelage phaeomelanin is related to cool dry climates with lower UV radiation. This implies that humidity or UV protection but not crypsis are the mechanisms underlying Gloger’s rule in this species and the factors driving eumelanin and phaeomelanin expression in mammalian pelage are different, reinforcing new interpretations of this venerable rule.
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Affiliation(s)
- Caroline Newell
- Department of Wildlife, Fish and Conservation Biology, University of California Davis, Davis, CA 95616, USA
| | - Hannah Walker
- Wildlife Biology Program, University of Montana, Missoula, MT 59812, USA
| | - Tim Caro
- Department of Wildlife, Fish and Conservation Biology, University of California Davis, Davis, CA 95616, USA
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, United Kingdom
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14
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Kokita T, Ueno K, Yamasaki YY, Matsuda M, Tabata R, Nagano AJ, Mishina T, Watanabe K. Gudgeon fish with and without genetically determined countershading coexist in heterogeneous littoral environments of an ancient lake. Ecol Evol 2021; 11:13283-13294. [PMID: 34646469 PMCID: PMC8495823 DOI: 10.1002/ece3.8050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/02/2021] [Accepted: 08/09/2021] [Indexed: 11/16/2022] Open
Abstract
Countershading, characterized by a darker dorsal surface and lighter ventral surface, is common among many animals. This dorsoventral pigment polarity is often thought to be adaptive coloration for camouflage. By contrast, noncountershaded (melanistic) morphs often occur within a species due to genetic color polymorphism in terrestrial animals. However, the polymorphism with either countershaded or melanistic morphs is poorly known in wild aquatic animals. This study explored the genetic nature of diverged color morphs of a lineage of gudgeon fish (genus Sarcocheilichthys) in the ancient Lake Biwa and propose this system as a novel model for testing hypotheses of functional aspects of countershading and its loss in aquatic environments. This system harbors two color morphs that have been treated taxonomically as separate species; Sarcocheilichthys variegatus microoculus which occurs throughout the littoral zone and Sarcocheilichthys biwaensis which occurs in and around rocky areas. First, we confirmed that the divergence of dorsoventral color patterns between the two morphs is under strict genetic control at the levels of chromatophore distribution and melanin-related gene expression under common garden rearing. The former morph displayed sharp countershading coloration, whereas the latter morph exhibited a strong tendency toward its loss. The crossing results indicated that this divergence was likely controlled by a single locus in a two-allele Mendelian inheritance pattern. Furthermore, our population genomic and genome-wide association study analyses detected no genome-wide divergence between the two morphs, except for one region near a locus that may be associated with the color divergence. Thus, these morphs are either in a state of intraspecific color polymorphism or two incipient species. Evolutionary forces underlying this polymorphism appear to be associated with heterogeneous littoral environments in this lake. Future ecological genomic research will provide insight into adaptive functions of this widespread coloration, including the eco-evolutionary drivers of its loss, in the aquatic world.
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Affiliation(s)
- Tomoyuki Kokita
- Faculty of Marine Science and TechnologyFukui Prefectural UniversityObamaJapan
| | - Kohtaro Ueno
- Faculty of Marine Science and TechnologyFukui Prefectural UniversityObamaJapan
| | | | | | | | - Atsushi J. Nagano
- Faculty of AgricultureRyukoku UniversityOtsuJapan
- Institute for Advanced BiosciencesKeio UniversityTsuruokaJapan
| | - Tappei Mishina
- Laboratory for Chromosome SegregationRIKEN Center for Biosystems Dynamics ResearchKobeJapan
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15
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Corbett-Detig RB, Russell SL, Nielsen R, Losos J. Phenotypic Convergence Is Not Mirrored at the Protein Level in a Lizard Adaptive Radiation. Mol Biol Evol 2021; 37:1604-1614. [PMID: 32027369 DOI: 10.1093/molbev/msaa028] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
There are many compelling examples of molecular convergence at individual genes. However, the prevalence and the relative importance of adaptive genome-wide convergence remain largely unknown. Many recent works have reported striking examples of excess genome-wide convergence, but some of these studies have been called into question because of the use of inappropriate null models. Here, we sequenced and compared the genomes of 12 species of anole lizards that have independently converged on suites of adaptive behavioral and morphological traits. Despite extensive searches for a genome-wide signature of molecular convergence, we found no evidence supporting molecular convergence at specific amino acids either at individual genes or at genome-wide comparisons; we also uncovered no evidence supporting an excess of adaptive convergence in the rates of amino acid substitutions within genes. Our findings indicate that comprehensive phenotypic convergence is not mirrored at genome-wide protein-coding levels in anoles, and therefore, that adaptive phenotypic convergence is likely not constrained by the evolution of many specific protein sequences or structures.
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Affiliation(s)
- Russell B Corbett-Detig
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA.,Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA
| | - Shelbi L Russell
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA.,Centre for GeoGenetics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan Losos
- Department of Biology and Living Earth Collaborative, Washington University, Saint Louis, MO
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16
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Liang D, Zhao P, Si J, Fang L, Pairo-Castineira E, Hu X, Xu Q, Hou Y, Gong Y, Liang Z, Tian B, Mao H, Yindee M, Faruque MO, Kongvongxay S, Khamphoumee S, Liu GE, Wu DD, Barker JSF, Han J, Zhang Y. Genomic Analysis Revealed a Convergent Evolution of LINE-1 in Coat Color: A Case Study in Water Buffaloes (Bubalus bubalis). Mol Biol Evol 2021; 38:1122-1136. [PMID: 33212507 PMCID: PMC7947781 DOI: 10.1093/molbev/msaa279] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Visible pigmentation phenotypes can be used to explore the regulation of gene expression and the evolution of coat color patterns in animals. Here, we performed whole-genome and RNA sequencing and applied genome-wide association study, comparative population genomics and biological experiments to show that the 2,809-bp-long LINE-1 insertion in the ASIP (agouti signaling protein) gene is the causative mutation for the white coat phenotype in swamp buffalo (Bubalus bubalis). This LINE-1 insertion (3' truncated and containing only 5' UTR) functions as a strong proximal promoter that leads to a 10-fold increase in the transcription of ASIP in white buffalo skin. The 165 bp of 5' UTR transcribed from the LINE-1 is spliced into the first coding exon of ASIP, resulting in a chimeric transcript. The increased expression of ASIP prevents melanocyte maturation, leading to the absence of pigment in white buffalo skin and hairs. Phylogenetic analyses indicate that the white buffalo-specific ASIP allele originated from a recent genetic transposition event in swamp buffalo. Interestingly, as a similar LINE-1 insertion has been identified in the cattle ASIP gene, we discuss the convergent mechanism of coat color evolution in the Bovini tribe.
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Affiliation(s)
- Dong Liang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of MOAR, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Pengju Zhao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of MOAR, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jingfang Si
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of MOAR, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lingzhao Fang
- Medical Research Council Human Genetics Unit at the Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Erola Pairo-Castineira
- Medical Research Council Human Genetics Unit at the Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Xiaoxiang Hu
- State Key Laboratory of AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qing Xu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Yali Hou
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yu Gong
- Guizhou Domestic Animal Genetic Resources Management Station, Guiyang, China
| | - Zhengwen Liang
- Agriculture and Rural Affairs Bureau of Fenggang County, Zunyi, China
| | - Bing Tian
- Animal Disease Prevention and Control Station of Zunyi City, Zunyi, China
| | - Huaming Mao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Marnoch Yindee
- Akkhararatchakumari Veterinary College (AVC), Walailak University, Nakorn Si Thammarat, Thailand
| | - Md Omar Faruque
- Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Siton Kongvongxay
- Livestock Research Center, National Agriculture and Forestry Research Institute, Ministry of Agriculture and Forestry, Vientiane, Lao PDR
| | - Souksamlane Khamphoumee
- Livestock Research Center, National Agriculture and Forestry Research Institute, Ministry of Agriculture and Forestry, Vientiane, Lao PDR
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD
| | - Dong-Dong Wu
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - James Stuart F Barker
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Jianlin Han
- International Livestock Research Institute (ILRI), Nairobi, Kenya
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yi Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of MOAR, College of Animal Science and Technology, China Agricultural University, Beijing, China
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17
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Abstract
The diversity of mammalian coat colors, and their potential adaptive significance, have long fascinated scientists as well as the general public. The recent decades have seen substantial improvement in our understanding of their genetic bases and evolutionary relevance, revealing novel insights into the complex interplay of forces that influence these phenotypes. At the same time, many aspects remain poorly known, hampering a comprehensive understanding of these phenomena. Here we review the current state of this field and indicate topics that should be the focus of additional research. We devote particular attention to two aspects of mammalian pigmentation, melanism and pattern formation, highlighting recent advances and outstanding challenges, and proposing novel syntheses of available information. For both specific areas, and for pigmentation in general, we attempt to lay out recommendations for establishing novel model systems and integrated research programs that target the genetics and evolution of these phenotypes throughout the Mammalia.
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Affiliation(s)
- Eduardo Eizirik
- Laboratory of Genomics and Molecular Biology, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul 90619-900, Brazil;
| | - Fernanda J Trindade
- Laboratory of Genomics and Molecular Biology, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul 90619-900, Brazil;
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18
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Chong VK, Stinchcombe JR. Evaluating Population Genomic Candidate Genes Underlying Flowering Time in Arabidopsis thaliana Using T-DNA Insertion Lines. J Hered 2020; 110:445-454. [PMID: 31158286 DOI: 10.1093/jhered/esz026] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 04/16/2019] [Indexed: 12/14/2022] Open
Abstract
Population genomic scans have emerged as a powerful tool to detect regions of the genome that are potential targets of selection. Despite the success of genomic scans in identifying novel lists of loci potentially underlying adaptation, few studies proceed to validate the function of these candidate genes. In this study, we used transfer-DNA (T-DNA) insertion lines to evaluate the effects of 27 candidate genes on flowering time in North American accessions of Arabidopsis thaliana. We compared the flowering time of T-DNA insertion lines that knock out the function of a candidate gene obtained from population genomic studies to a wild type under long- and short-day conditions. We also did the same for a collection of randomly chosen genes that had not been identified as candidates. We validated the well-known effect of long-day conditions in accelerating flowering time and found that gene disruption caused by insertional mutagenesis tends to delay flowering. Surprisingly, we found that knockouts in random genes were just as likely to produce significant phenotypic effects as knockouts in candidate genes. T-DNA insertions at a handful of candidate genes that had previously been identified as outlier loci showed significant delays in flowering time under both long and short days, suggesting that they are promising candidates for future investigation.
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Affiliation(s)
- Veronica K Chong
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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19
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Jones MR, Mills LS, Jensen JD, Good JM. Convergent evolution of seasonal camouflage in response to reduced snow cover across the snowshoe hare range*. Evolution 2020; 74:2033-2045. [DOI: 10.1111/evo.13976] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/26/2020] [Accepted: 04/02/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Matthew R. Jones
- Division of Biological Sciences University of Montana Missoula Montana 59812
| | - L. Scott Mills
- Wildlife Biology Program University of Montana Missoula Montana 59812
- Office of Research and Creative Scholarship University of Montana Missoula Montana 59812
| | - Jeffrey D. Jensen
- School of Life Sciences Arizona State University Tempe Arizona 85281
| | - Jeffrey M. Good
- Division of Biological Sciences University of Montana Missoula Montana 59812
- Wildlife Biology Program University of Montana Missoula Montana 59812
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20
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Abstract
The generation of variation is paramount for the action of natural selection. Although biologists are now moving beyond the idea that random mutation provides the sole source of variation for adaptive evolution, we still assume that variation occurs randomly. In this review, we discuss an alternative view for how phenotypic plasticity, which has become well accepted as a source of phenotypic variation within evolutionary biology, can generate nonrandom variation. Although phenotypic plasticity is often defined as a property of a genotype, we argue that it needs to be considered more explicitly as a property of developmental systems involving more than the genotype. We provide examples of where plasticity could be initiating developmental bias, either through direct active responses to similar stimuli across populations or as the result of programmed variation within developmental systems. Such biased variation can echo past adaptations that reflect the evolutionary history of a lineage but can also serve to initiate evolution when environments change. Such adaptive programs can remain latent for millions of years and allow development to harbor an array of complex adaptations that can initiate new bouts of evolution. Specifically, we address how ideas such as the flexible stem hypothesis and cryptic genetic variation overlap, how modularity among traits can direct the outcomes of plasticity, and how the structure of developmental signaling pathways is limited to a few outcomes. We highlight key questions throughout and conclude by providing suggestions for future research that can address how plasticity initiates and harbors developmental bias.
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Affiliation(s)
- Kevin J. Parsons
- Institute of Biodiversity, Animal Health, and Comparative MedicineUniversity of GlasgowGlasgowUK
| | - Kirsty McWhinnie
- Institute of Biodiversity, Animal Health, and Comparative MedicineUniversity of GlasgowGlasgowUK
| | - Natalie Pilakouta
- Institute of Biodiversity, Animal Health, and Comparative MedicineUniversity of GlasgowGlasgowUK
| | - Lynsey Walker
- Institute of Biodiversity, Animal Health, and Comparative MedicineUniversity of GlasgowGlasgowUK
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21
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Ríos-Alvear G, Cadena-Ortiz H. Records of melanistic Tamandua tetradactyla (Pilosa, Myrmecophagidae) from Ecuador. NEOTROPICAL BIOLOGY AND CONSERVATION 2019. [DOI: 10.3897/neotropical.14.e37714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In Ecuador, the presence of melanistic individuals of Southern Tamandua Tamandua tetradactyla Linnaeus (1758) has been recognized but there has not been a formal report written about it. Neither has there been one on the observations or the collected specimens in museums. We present six records of melanism in Tamandua tetradactyla from southern Ecuador and discuss other records in wildlife and from museum collections. Half of the records are recent photographic ones (2018), and the other three are museum specimens collected between 2009 and 2016. Our report of melanistic individuals suggests that dark coloration varieties are frequent mutations in the region. This report can be useful to promote conservation initiatives, based on the Southern Tamandua as a potential flagship-species.
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22
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McRobie HR, Moncrief ND, Mundy NI. Multiple origins of melanism in two species of North American tree squirrel (Sciurus). BMC Evol Biol 2019; 19:140. [PMID: 31296164 PMCID: PMC6625063 DOI: 10.1186/s12862-019-1471-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 06/30/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND While our understanding of the genetic basis of convergent evolution has improved there are still many uncertainties. Here we investigate the repeated evolution of dark colouration (melanism) in eastern fox squirrels (Sciurus niger; hereafter "fox squirrels") and eastern gray squirrels (S. carolinensis; hereafter "gray squirrels"). RESULTS We show that convergent evolution of melanism has arisen by independent genetic mechanisms in two populations of the fox squirrel. In a western population, melanism is associated with a 24 bp deletion in the melanocortin-1-receptor gene (MC1RΔ24 allele), whereas in a south-eastern population, melanism is associated with a point substitution in the agouti signalling protein gene causing a Gly121Cys mutation. The MC1R∆24 allele is also associated with melanism in gray squirrels, and, remarkably, all the MC1R∆24 haplotypes are identical in the two species. Evolutionary analyses show that the MC1R∆24 haplotype is more closely related to other MC1R haplotypes in the fox squirrel than in the gray squirrel. Modelling supports the possibility of gene flow between the two species. CONCLUSIONS The presence of the MC1R∆24 allele and melanism in gray squirrels is likely due to introgression from fox squirrels, although we cannot completely rule out alternative hypotheses including introgression from gray squirrels to fox squirrels, or an ancestral polymorphism. Convergent melanism in these two species of tree squirrels has evolved by at least two and probably three different evolutionary routes.
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Affiliation(s)
- Helen R McRobie
- School of Life Sciences, Anglia Ruskin University, Cambridge, CB1 1PT, UK.
| | - Nancy D Moncrief
- Virginia Museum of Natural History, Martinsville, VA, 24112, USA
| | - Nicholas I Mundy
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
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23
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Krohn AR, Diepeveen ET, Bi K, Rosenblum EB. Local adaptation does not lead to genome-wide differentiation in lava flow lizards. Ecol Evol 2019; 9:6810-6820. [PMID: 31380017 PMCID: PMC6662252 DOI: 10.1002/ece3.5231] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 04/11/2019] [Accepted: 04/15/2019] [Indexed: 11/09/2022] Open
Abstract
Adaptation can occur with or without genome-wide differentiation. If adaptive loci are linked to traits involved in reproductive isolation, genome-wide divergence is likely, and speciation is possible. However, adaptation can also lead to phenotypic differentiation without genome-wide divergence if levels of ongoing gene flow are high. Here, we use the replicated occurrence of melanism in lava flow lizards to assess the relationship between local adaptation and genome-wide differentiation. We compare patterns of phenotypic and genomic divergence among lava flow and nonlava populations for three lizard species and three lava flows in the Chihuahuan Desert. We find that local phenotypic adaptation (melanism) is not typically accompanied by genome-wide differentiation. Specifically, lava populations do not generally exhibit greater divergence from nonlava populations than expected by geography alone, regardless of whether the lava formation is 5,000 or 760,000 years old. We also infer that gene flow between lava and nonlava populations is ongoing in all lava populations surveyed. Recent work in the isolation by environment and ecological speciation literature suggests that environmentally driven genome-wide differentiation is common in nature. However, local adaptation may often simply be local adaptation rather than an early stage of ecological speciation.
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Affiliation(s)
- Alexander R. Krohn
- Department of Environmental Science, Policy and ManagementUniversity of California, BerkeleyBerkeleyCalifornia
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCalifornia
| | - Eveline T. Diepeveen
- Department of Bionanoscience, Kavli Institute of NanoScience, Faculty of Applied SciencesDelft University of TechnologyDelftThe Netherlands
| | - Ke Bi
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCalifornia
- Computational Genomics Resource Laboratory (CGRL), California Institute for Quantitative Biosciences (QB3)University of California, BerkeleyBerkeleyCalifornia
| | - Erica Bree Rosenblum
- Department of Environmental Science, Policy and ManagementUniversity of California, BerkeleyBerkeleyCalifornia
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCalifornia
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24
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van der Geer AAE. Effect of isolation on coat colour polymorphism of Polynesian rats in Island Southeast Asia and the Pacific. PeerJ 2019; 7:e6894. [PMID: 31119086 PMCID: PMC6511229 DOI: 10.7717/peerj.6894] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 04/02/2019] [Indexed: 01/03/2023] Open
Abstract
Populations of vertebrate species introduced onto islands regularly develop similar phenotypic changes, e.g., larger or smaller body size, shortened limbs, duller coats, as well as behavioural changes such as increased tameness and reduced flight-initiation distance. These changes overlap in part with those associated with the 'domestication syndrome', especially tameness and changes in coat patterns, and might indicate a similar neural crest involvement in the concurrent development of multiple phenotypic traits. Here I examine long-term data on free-living populations of wild Polynesian rats from seven mainland countries and 117 islands (n = 3,034), covering the species' native and introduced range. Mainland populations showed no aberrant coat patterns, with the exception of one albino, whereas aberrant coat patterns were found in 12 island populations. Observed coat colour polymorphisms consisted of leucistic (including singular white patches), melanistic (darkly pigmented) and piebald (mixed) coat patterns. After isolation for at least seven centuries, wild Polynesian rat populations on islands seem to exhibit a trend towards a higher incidence of aberrant coat patterns. These phenotypic changes are here explained as a neutral, non-adaptive process, likely part of the 'domestication syndrome' (via the commensal pathway of domestication), in combination with genetic drift, little or no gene flow between the islands and/or the mainland and a relaxed selection (as a result of the weakening or removal of competitor/predator pressure) under commensality.
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25
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Construction of MC1R and ASIP Eukaryotic Expression Vector and its Regulation of Plumage Color in Japanese Quail ( Coturnix japonica). J Poult Sci 2019; 56:84-90. [PMID: 32055201 PMCID: PMC7005409 DOI: 10.2141/jpsa.0180058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The Japanese quail expresses polymorphism in plumage colors, including black, yellow, white, wild-type (maroon), and various intermediate colors through hybridization of quail with different plumage colors. The expression levels of MC1R and ASIP play important roles in the regulation of plumage colors in birds. In this study, the eukaryotic expression vector of pcDNA 3.1 + was used to analyze the effects of forced expression of MC1R and ASIP on the plumage colors of Japanese quail embryos. The constructed eukaryotic expression vectors of pcDNA 3.1 (+)-MC1R and pcDNA 3.1(+)-ASIP were transfected into wild-type Japanese quail embryos by Lipofectamine™ 2000 liposome at 6 days of incubation. After 3 days, the embryos were collected to analyze the plumage colors and the expression levels of MC1R, ASIP, and DCT genes in skin tissue. Forced expression of the MC1R gene by transfection of the pcDNA 3.1(+)-MC1R vector led to hyperpigmentation (similar to black plumage), whereas forced expression of the ASIP gene by transfection of the pcDNA 3.1(+)-ASIP vector led to hypopigmentation (similar to white plumage) in wild-type quail embryos. Two kinds of ASIP alternative splicing (ASIP1 and ASIP2) were found in Japanese quail, which did not have a significant effect on the plumage color or the main motifs of the ASIP protein. This study indicated that the black plumage color may be caused by increased production of MC1R and the white plumage color may be caused by increased production of ASIP in Japanese quail.
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26
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Bosch J, Mestre J, Baiges C, Martínez JE, Calvo JF, Jiménez‐Franco MV. Colour plumage polymorphism in the Booted Eagle: inheritance pattern and temporal stability of the morph frequencies. J Zool (1987) 2019. [DOI: 10.1111/jzo.12666] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- J. Bosch
- Cra. de Navarcles 43, Santpedor Barcelona Spain
| | - J. Mestre
- Departament de Territori i Sostenibilitat Parc Natural dels Ports Tarragona Spain
| | - C. Baiges
- Departament de Territori i Sostenibilitat Parc Natural dels Ports Tarragona Spain
| | - J. E. Martínez
- Departamento de Ecología e Hidrología Universidad de Murcia Murcia Spain
- Bonelli′s Eagle Study and Conservation Group Murcia Spain
| | - J. F. Calvo
- Departamento de Ecología e Hidrología Universidad de Murcia Murcia Spain
| | - M. V. Jiménez‐Franco
- Departamento de Biología Aplicada Universidad Miguel Hernández Elche, Alicante Spain
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27
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Pfeifer SP, Laurent S, Sousa VC, Linnen CR, Foll M, Excoffier L, Hoekstra HE, Jensen JD. The Evolutionary History of Nebraska Deer Mice: Local Adaptation in the Face of Strong Gene Flow. Mol Biol Evol 2019; 35:792-806. [PMID: 29346646 PMCID: PMC5905656 DOI: 10.1093/molbev/msy004] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The interplay of gene flow, genetic drift, and local selective pressure is a dynamic process that has been well studied from a theoretical perspective over the last century. Wright and Haldane laid the foundation for expectations under an island-continent model, demonstrating that an island-specific beneficial allele may be maintained locally if the selection coefficient is larger than the rate of migration of the ancestral allele from the continent. Subsequent extensions of this model have provided considerably more insight. Yet, connecting theoretical results with empirical data has proven challenging, owing to a lack of information on the relationship between genotype, phenotype, and fitness. Here, we examine the demographic and selective history of deer mice in and around the Nebraska Sand Hills, a system in which variation at the Agouti locus affects cryptic coloration that in turn affects the survival of mice in their local habitat. We first genotyped 250 individuals from 11 sites along a transect spanning the Sand Hills at 660,000 single nucleotide polymorphisms across the genome. Using these genomic data, we found that deer mice first colonized the Sand Hills following the last glacial period. Subsequent high rates of gene flow have served to homogenize the majority of the genome between populations on and off the Sand Hills, with the exception of the Agouti pigmentation locus. Furthermore, mutations at this locus are strongly associated with the pigment traits that are strongly correlated with local soil coloration and thus responsible for cryptic coloration.
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Affiliation(s)
- Susanne P Pfeifer
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,School of Life Sciences, Center for Evolution & Medicine, Arizona State University, Tempe, AZ
| | - Stefan Laurent
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Vitor C Sousa
- Institute of Ecology & Evolution, University of Berne, Berne, Switzerland.,Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | | | - Matthieu Foll
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Laurent Excoffier
- Institute of Ecology & Evolution, University of Berne, Berne, Switzerland
| | - Hopi E Hoekstra
- Department of Organismic & Evolutionary Biology and Molecular & Cellular Biology, Museum of Comparative Zoology, Howard Hughes Medical Institute, Harvard University, Cambridge, MA
| | - Jeffrey D Jensen
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,School of Life Sciences, Center for Evolution & Medicine, Arizona State University, Tempe, AZ
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28
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Sakuma Y, Matsunami M, Takada T, Suzuki H. Multiple Conserved Elements Structuring Inverted Repeats in the Mammalian Coat Color-Related Gene Asip. Zoolog Sci 2019; 36:23-30. [PMID: 31116535 DOI: 10.2108/zs180081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 09/17/2018] [Indexed: 11/17/2022]
Abstract
In the agouti signaling gene protein (Asip) of the house mouse (Mus musculus), inverted repeat (IR) arrays are known to exist in a non-coding region adjacent to the ventral-specific promoter region and the accompanying two exons (exons 1A and 1A'), which are around 100 kb upstream from the amino acid coding regions of exons 2, 3, and 4. To determine the gene structure of mammalian Asip and to elucidate trends in its evolution, non-coding sequences of six rodent (mouse, rat, Chinese hamster, squirrel, guinea pig, and naked mole rat) and three non-rodent (rabbit, human, and cow) species were retrieved from databases and compared. Our homology search analyses revealed the presence of three to five highly conserved non-coding elements (CNE). These CNEs were found to form IRs in rodents and lagomorphs. Combinations of IRs were further shown to build symmetric, long IR arrays. Intra- and inter-specific comparisons of the sequences of three universal CNEs showed homogeneity between CNE pairs within species. This implies that certain evolutionary constraints maintained the IR structure in the rodent and rabbit species.
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Affiliation(s)
- Yuki Sakuma
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
| | - Masatoshi Matsunami
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan, .,Graduate School of Medicine, University of the Ryukyus, Nishihara-cho 903-0215, Japan,
| | - Toyoyuki Takada
- Mammalian Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hitoshi Suzuki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
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Barrett RDH, Laurent S, Mallarino R, Pfeifer SP, Xu CCY, Foll M, Wakamatsu K, Duke-Cohan JS, Jensen JD, Hoekstra HE. Linking a mutation to survival in wild mice. Science 2019; 363:499-504. [DOI: 10.1126/science.aav3824] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/06/2018] [Indexed: 12/19/2022]
Abstract
Adaptive evolution in new or changing environments can be difficult to predict because the functional connections between genotype, phenotype, and fitness are complex. Here, we make these explicit connections by combining field and laboratory experiments in wild mice. We first directly estimate natural selection on pigmentation traits and an underlying pigment locus, Agouti, by using experimental enclosures of mice on different soil colors. Next, we show how a mutation in Agouti associated with survival causes lighter coat color through changes in its protein binding properties. Together, our findings demonstrate how a sequence variant alters phenotype and then reveal the ensuing ecological consequences that drive changes in population allele frequency, thereby illuminating the process of evolution by natural selection.
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30
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Eliason CM, Clarke JA. Metabolic physiology explains macroevolutionary trends in the melanic colour system across amniotes. Proc Biol Sci 2018; 285:20182014. [PMID: 30963907 PMCID: PMC6304050 DOI: 10.1098/rspb.2018.2014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/21/2018] [Indexed: 11/12/2022] Open
Abstract
Metabolism links organisms to their environment through its effects on thermoregulation, feeding behaviour and energetics. Genes involved in metabolic processes have known pleiotropic effects on some melanic colour traits. Understanding links between physiology and melanic colour is critical for understanding the role of, and potential constraints on, colour production. Despite considerable variation in metabolic rates and presumed ancestral melanic coloration in vertebrates, few studies have looked at a potential relationship between these two systems in a comparative framework. Here, we test the hypothesis that changes in melanosome shape in integumentary structures track metabolic rate variation across amniotes. Using multivariate comparative analyses and incorporating both extant and fossil taxa, we find significantly faster rates of melanosome shape evolution in taxa with high metabolic rates, as well as both colour- and clade-specific differences in the relationship between metabolic rate and melanosome shape. Phylogenetic tests recover an expansion in melanosome morphospace in maniraptoran dinosaurs, as well as rate shifts within birds (in songbirds) and mammals. These findings indicate another core phenotype influenced by metabolic changes in vertebrates. They also provide a framework for testing clade-specific gene expression patterns in the melanocortin system and may improve colour reconstructions in extinct taxa.
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Affiliation(s)
- Chad M. Eliason
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA
- Jackson School of Geosciences, University of Texas at Austin, Austin, TX, USA
| | - Julia A. Clarke
- Jackson School of Geosciences, University of Texas at Austin, Austin, TX, USA
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31
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Whitney JL, Bowen BW, Karl SA. Flickers of speciation: Sympatric colour morphs of the arc-eye hawkfish, Paracirrhites arcatus, reveal key elements of divergence with gene flow. Mol Ecol 2018; 27:1479-1493. [PMID: 29420860 DOI: 10.1111/mec.14527] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 01/01/2023]
Abstract
One of the primary challenges of evolutionary research is to identify ecological factors that favour reproductive isolation. Therefore, studying partially isolated taxa has the potential to provide novel insight into the mechanisms of evolutionary divergence. Our study utilizes an adaptive colour polymorphism in the arc-eye hawkfish (Paracirrhites arcatus) to explore the evolution of reproductive barriers in the absence of geographic isolation. Dark and light morphs are ecologically partitioned into basaltic and coral microhabitats a few metres apart. To test whether ecological barriers have reduced gene flow among dark and light phenotypes, we evaluated genetic variation at 30 microsatellite loci and a nuclear exon (Mc1r) associated with melanistic coloration. We report low, but significant microsatellite differentiation among colour morphs and stronger divergence in the coding region of Mc1r indicating signatures of selection. Critically, we observed greater genetic divergence between colour morphs on the same reefs than that between the same morphs in different geographic locations. We hypothesize that adaptation to the contrasting microhabitats is overriding gene flow and is responsible for the partial reproductive isolation observed between sympatric colour morphs. Combined with complementary studies of hawkfish ecology and behaviour, these genetic results indicate an ecological barrier to gene flow initiated by habitat selection and enhanced by assortative mating. Hence, the arc-eye hawkfish fulfil theoretical expectations for the earliest phase of speciation with gene flow.
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Affiliation(s)
- Jonathan L Whitney
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| | - Stephen A Karl
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
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32
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Sasamori S, Wiewel AS, Thomson VA, Kobayashi M, Nakata K, Suzuki H. Potential Causative Mutation for Melanism in Rats Identified in the Agouti Signaling Protein Gene (Asip) of the Rattus rattus Species Complex on Okinawa Island, Japan. Zoolog Sci 2017; 34:513-522. [PMID: 29219041 DOI: 10.2108/zs170027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The occurrence of black fur, or melanism, in many mammalian species is known to be linked to DNA sequence variation in the agouti signaling protein (Asip) gene, which is a major determinant of eumelanin and pheomelanin pigments in coat color. We investigated 38 agouti (i.e., banded wildtype) and four melanistic Rattus rattus species complex (RrC) lineage II specimens from Okinawa Island, Ryukyu Islands, Japan, for genetic variation in three exons and associated flanking regions in the Asip gene. On Okinawa, a predicted loss-of-function mutation caused by a cysteine to serine amino acid change at p.124C>S (c.370T>A) in the highly conserved functional domain of Asip was found in melanistic rats, but was absent in agouti specimens, suggesting that the p.124C>S mutation is responsible for the observed melanism. Phylogeographic analysis found that Asip sequences from Okinawan RrC lineage II, including both agouti and melanistic specimens, differed from: 1) both agouti and melanistic RrC lineage I from Otaru, Hokkaido, Japan, and 2) agouti RrC lineages I and II from South Australia. This suggests the possibility of in-situ mutation of the Asip gene, either within the RrC lineage II population on Okinawa or in an unsampled RrC lineage II population with biogeographic links to Okinawa, although incomplete lineage sorting could not be ruled out.
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Affiliation(s)
- Shoichi Sasamori
- 1 Division of Bioscience, Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Andrew S Wiewel
- 2 School of Biological Sciences, University of Adelaide, North Terrace, Adelaide SA 5005, Australia
| | - Vicki A Thomson
- 2 School of Biological Sciences, University of Adelaide, North Terrace, Adelaide SA 5005, Australia
| | - Motoko Kobayashi
- 1 Division of Bioscience, Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Katsushi Nakata
- 3 Yambaru Wildlife Conservation Center, Ministry of the Environment, Kunigami-son, Okinawa 905-1413, Japan
| | - Hitoshi Suzuki
- 1 Division of Bioscience, Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
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Uy JAC, Cooper EA, Cutie S, Concannon MR, Poelstra JW, Moyle RG, Filardi CE. Mutations in different pigmentation genes are associated with parallel melanism in island flycatchers. Proc Biol Sci 2017; 283:rspb.2016.0731. [PMID: 27412275 DOI: 10.1098/rspb.2016.0731] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/21/2016] [Indexed: 12/17/2022] Open
Abstract
The independent evolution of similar traits across multiple taxa provides some of the most compelling evidence of natural selection. Little is known, however, about the genetic basis of these convergent or parallel traits: are they mediated by identical or different mutations in the same genes, or unique mutations in different genes? Using a combination of candidate gene and reduced representation genomic sequencing approaches, we explore the genetic basis of and the evolutionary processes that mediate similar plumage colour shared by isolated populations of the Monarcha castaneiventris flycatcher of the Solomon Islands. A genome-wide association study (GWAS) that explicitly controlled for population structure revealed that mutations in known pigmentation genes are the best predictors of parallel plumage colour. That is, entirely black or melanic birds from one small island share an amino acid substitution in the melanocortin-1 receptor (MC1R), whereas similarly melanic birds from another small island over 100 km away share an amino acid substitution in a predicted binding site of agouti signalling protein (ASIP). A third larger island, which separates the two melanic populations, is inhabited by birds with chestnut bellies that lack the melanic MC1R and ASIP allelic variants. Formal FST outlier tests corroborated the results of the GWAS and suggested that strong, directional selection drives the near fixation of the MC1R and ASIP variants across islands. Our results, therefore, suggest that selection acting on different mutations with large phenotypic effects can drive the evolution of parallel melanism, despite the relatively small population size on islands.
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Affiliation(s)
- J Albert C Uy
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
| | - Elizabeth A Cooper
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Stephen Cutie
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
| | - Moira R Concannon
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Jelmer W Poelstra
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Robert G Moyle
- Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| | - Christopher E Filardi
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY 10024, USA
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34
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Bourgeois YXC, Delahaie B, Gautier M, Lhuillier E, Malé PJG, Bertrand JAM, Cornuault J, Wakamatsu K, Bouchez O, Mould C, Bruxaux J, Holota H, Milá B, Thébaud C. A novel locus on chromosome 1 underlies the evolution of a melanic plumage polymorphism in a wild songbird. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160805. [PMID: 28386436 PMCID: PMC5367300 DOI: 10.1098/rsos.160805] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/12/2017] [Indexed: 06/07/2023]
Abstract
Understanding the mechanisms responsible for phenotypic diversification within and among species ultimately rests with linking naturally occurring mutations to functionally and ecologically significant traits. Colour polymorphisms are of great interest in this context because discrete colour patterns within a population are often controlled by just a few genes in a common environment. We investigated how and why phenotypic diversity arose and persists in the Zosterops borbonicus white-eye of Reunion (Mascarene archipelago), a colour polymorphic songbird in which all highland populations contain individuals belonging to either a brown or a grey plumage morph. Using extensive phenotypic and genomic data, we demonstrate that this melanin-based colour polymorphism is controlled by a single locus on chromosome 1 with two large-effect alleles, which was not previously described as affecting hair or feather colour. Differences between colour morphs appear to rely upon complex cis-regulatory variation that either prevents the synthesis of pheomelanin in grey feathers, or increases its production in brown ones. We used coalescent analyses to show that, from a 'brown' ancestral population, the dominant 'grey' allele spread quickly once it arose from a new mutation. Since colour morphs are always found in mixture, this implies that the selected allele does not go to fixation, but instead reaches an intermediate frequency, as would be expected under balancing selection.
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Affiliation(s)
- Yann X. C. Bourgeois
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Boris Delahaie
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Mathieu Gautier
- INRA, UMR 1062 CBGP (INRA, IRD, Cirad, Montpellier SupAgro), Campus de Baillarguet, 34988 Montferrier-sur-Lez, France
| | - Emeline Lhuillier
- INRA, GeT-PlaGe, Genotoul, 24 chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan, France
- INRA, UAR1209, 24 chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan, France
| | - Pierre-Jean G. Malé
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Joris A. M. Bertrand
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Josselin Cornuault
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Kazumasa Wakamatsu
- Department of Chemistry, Fujita Health University, School of Health Sciences, Toyoake Aichi 470-1192, Japan
| | - Olivier Bouchez
- INRA, GeT-PlaGe, Genotoul, 24 chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan, France
- GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, 24 chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan, France
| | - Claire Mould
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Jade Bruxaux
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Hélène Holota
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), 28006 Madrid, Spain
| | - Christophe Thébaud
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
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35
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Holcová-Gazárková A, Kryštufek B, Adamík P. Anomalous coat colour in the fat dormouse (Glis glis): a review with new records. MAMMALIA 2017. [DOI: 10.1515/mammalia-2016-0122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractWe reviewed the available records on aberrantly coloured fat dormice
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36
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Roberts RB, Moore EC, Kocher TD. An allelic series at pax7a is associated with colour polymorphism diversity in Lake Malawi cichlid fish. Mol Ecol 2017; 26:2625-2639. [PMID: 28027432 DOI: 10.1111/mec.13975] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 11/04/2016] [Accepted: 11/18/2016] [Indexed: 01/01/2023]
Abstract
Despite long-standing interest in the evolution and maintenance of discrete phenotypic polymorphisms, the molecular genetic basis of such polymorphism in the wild is largely unknown. Female sex-associated blotched colour polymorphisms found in cichlids of Lake Malawi, East Africa, represent a highly successful polymorphic phenotype, found and maintained in four genera across the geographic expanse of the lake. Previously, we identified an association with an allelic variant of the paired-box transcription factor gene pax7a and blotched colour morphs in Lake Malawi cichlid fishes. Although a diverse range of blotched phenotypes are present in Lake Malawi cichlid species, they all appeared to result from an allele of pax7a that produces increased levels of transcript. Here, we examine the developmental and genetic basis of variation among blotched morphs. First, we confirm that pax7a-associated blotch morphs result primarily from modulation of melanophore development and survival. From laboratory crosses and natural population studies, we identify at least three alleles of pax7a associated with discrete subtypes of blotched morphs, in addition to the ancestral pax7a allele. Genotypes at pax7a support initial evolution of a novel pax7a allele to produce the blotched class of morphs, followed by subsequent evolution of that pax7a blotched allele to produce additional alleles associated with discrete colour morphs. Variant alleles of pax7a produce different levels of pax7a transcript, correlating with pigmentation phenotype at the cellular level. This naturally selected allelic series should serve as a case study for understanding the molecular genetic control of pax7a expression and the evolution of sex-associated alleles.
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Affiliation(s)
- Reade B Roberts
- Department of Biological Sciences, North Carolina State University, 3510 Thomas Hall, Raleigh, NC, 27695, USA
| | - Emily C Moore
- Keck Center for Behavioral Biology, North Carolina State University, 3510 Thomas Hall, Raleigh, NC, 27695, USA
| | - Thomas D Kocher
- Department of Biology, University of Maryland, 1210 Biology-Psychology Building, College Park, MD, 20742, USA
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37
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Eanes WF. New views on the selection acting on genetic polymorphism in central metabolic genes. Ann N Y Acad Sci 2016; 1389:108-123. [PMID: 27859384 DOI: 10.1111/nyas.13285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 09/20/2016] [Accepted: 09/29/2016] [Indexed: 12/14/2022]
Abstract
Studies of the polymorphism of central metabolic genes as a source of fitness variation in natural populations date back to the discovery of allozymes in the 1960s. The unique features of these genes and their enzymes and our knowledge base greatly facilitates the systems-level study of this group. The expectation that pathway flux control is central to understanding the molecular evolution of genes is discussed, as well as studies that attempt to place gene-specific molecular evolution and polymorphism into a context of pathway and network architecture. There is an increasingly complex picture of the metabolic genes assuming additional roles beyond their textbook anabolic and catabolic reactions. In particular, this review emphasizes the potential role of these genes as part of the energy-sensing machinery. It is underscored that the concentrations of key cellular metabolites are the reflections of cellular energy status and nutritional input. These metabolites are the top-down signaling messengers that set signaling through signaling pathways that are involved in energy economy. I propose that the polymorphisms in central metabolic genes shift metabolite concentrations and in that fashion act as genetic modifiers of the energy-state coupling to the transcriptional networks that affect physiological trade-offs with significant fitness consequences.
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Affiliation(s)
- Walter F Eanes
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York
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38
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Hoban S, Kelley JL, Lotterhos KE, Antolin MF, Bradburd G, Lowry DB, Poss ML, Reed LK, Storfer A, Whitlock MC. Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions. Am Nat 2016; 188:379-97. [PMID: 27622873 PMCID: PMC5457800 DOI: 10.1086/688018] [Citation(s) in RCA: 431] [Impact Index Per Article: 53.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Uncovering the genetic and evolutionary basis of local adaptation is a major focus of evolutionary biology. The recent development of cost-effective methods for obtaining high-quality genome-scale data makes it possible to identify some of the loci responsible for adaptive differences among populations. Two basic approaches for identifying putatively locally adaptive loci have been developed and are broadly used: one that identifies loci with unusually high genetic differentiation among populations (differentiation outlier methods) and one that searches for correlations between local population allele frequencies and local environments (genetic-environment association methods). Here, we review the promises and challenges of these genome scan methods, including correcting for the confounding influence of a species' demographic history, biases caused by missing aspects of the genome, matching scales of environmental data with population structure, and other statistical considerations. In each case, we make suggestions for best practices for maximizing the accuracy and efficiency of genome scans to detect the underlying genetic basis of local adaptation. With attention to their current limitations, genome scan methods can be an important tool in finding the genetic basis of adaptive evolutionary change.
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Affiliation(s)
- Sean Hoban
- Morton Arboretum, Lisle, Illinois 60532; and National Institute for Mathematical and Biological Synthesis (NIMBioS), Knoxville, Tennessee 37966
| | - Joanna L. Kelley
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
| | - Katie E. Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, Massachusetts 01908
| | - Michael F. Antolin
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523
| | - Gideon Bradburd
- Museum of Vertebrate Zoology and Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720
| | - David B. Lowry
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Mary L. Poss
- Department of Biology and Veterinary and Biomedical Sciences, Penn State University, University Park, Pennsylvania 16802
| | - Laura K. Reed
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35406
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
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Mallarino R, Linden TA, Linnen CR, Hoekstra HE. The role of isoforms in the evolution of cryptic coloration inPeromyscusmice. Mol Ecol 2016; 26:245-258. [DOI: 10.1111/mec.13663] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 04/12/2016] [Accepted: 04/17/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Ricardo Mallarino
- Departments of Organismic & Evolutionary Biology and Molecular & Cellular Biology; Museum of Comparative Zoology; Howard Hughes Medical Institute; Harvard University; 26 Oxford Street Cambridge MA 02138 USA
| | - Tess A. Linden
- Departments of Organismic & Evolutionary Biology and Molecular & Cellular Biology; Museum of Comparative Zoology; Howard Hughes Medical Institute; Harvard University; 26 Oxford Street Cambridge MA 02138 USA
| | - Catherine R. Linnen
- Department of Biology; University of Kentucky; 675 Rose Street Lexington KY 40506 USA
| | - Hopi E. Hoekstra
- Departments of Organismic & Evolutionary Biology and Molecular & Cellular Biology; Museum of Comparative Zoology; Howard Hughes Medical Institute; Harvard University; 26 Oxford Street Cambridge MA 02138 USA
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40
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Erickson PA, Glazer AM, Killingbeck EE, Agoglia RM, Baek J, Carsanaro SM, Lee AM, Cleves PA, Schluter D, Miller CT. Partially repeatable genetic basis of benthic adaptation in threespine sticklebacks. Evolution 2016; 70:887-902. [PMID: 26947264 DOI: 10.1111/evo.12897] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 02/10/2016] [Accepted: 02/23/2016] [Indexed: 12/13/2022]
Abstract
The extent to which convergent adaptation to similar ecological niches occurs by a predictable genetic basis remains a fundamental question in biology. Threespine stickleback fish have undergone an adaptive radiation in which ancestral oceanic populations repeatedly colonized and adapted to freshwater habitats. In multiple lakes in British Columbia, two different freshwater ecotypes have evolved: a deep-bodied benthic form adapted to forage near the lake substrate, and a narrow-bodied limnetic form adapted to forage in open water. Here, we use genome-wide linkage mapping in marine × benthic F2 genetic crosses to test the extent of shared genomic regions underlying benthic adaptation in three benthic populations. We identify at least 100 Quantitative Trait Loci (QTL) harboring genes influencing skeletal morphology. The majority of QTL (57%) are unique to one cross. However, four genomic regions affecting eight craniofacial and armor phenotypes are found in all three benthic populations. We find that QTL are clustered in the genome and overlapping QTL regions are enriched for genomic signatures of natural selection. These findings suggest that benthic adaptation has occurred via both parallel and nonparallel genetic changes.
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Affiliation(s)
- Priscilla A Erickson
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720
| | - Andrew M Glazer
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720
| | - Emily E Killingbeck
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720
| | - Rachel M Agoglia
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720
| | - Jiyeon Baek
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720
| | - Sara M Carsanaro
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720
| | - Anthony M Lee
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720
| | - Phillip A Cleves
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720
| | - Dolph Schluter
- Biodiversity Research Centre and Zoology Department, University of British Columbia, Vancouver, British Columbia, Canada
| | - Craig T Miller
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720.
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Bourgeois YXC, Bertrand JAM, Delahaie B, Cornuault J, Duval T, Milá B, Thébaud C. Candidate Gene Analysis Suggests Untapped Genetic Complexity in Melanin-Based Pigmentation in Birds. J Hered 2016; 107:327-35. [PMID: 26995742 DOI: 10.1093/jhered/esw017] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 03/15/2016] [Indexed: 12/22/2022] Open
Abstract
Studies on melanin-based color variation in a context of natural selection have provided a wealth of information on the link between phenotypic and genetic variation. Here, we evaluated associations between melanic plumage patterns and genetic polymorphism in the Réunion grey white-eye (Zosterops borbonicus), a species in which mutations on MC1R do not seem to play any role in explaining melanic variation. This species exhibits 5 plumage color variants that can be grouped into 3 color forms which occupy discrete geographic regions in the lowlands of Réunion, and a fourth high-elevation form which comprises 2 color morphs (grey and brown) and represents a true color polymorphism. We conducted a comprehensive survey of sequence variation in 96 individuals at a series of 7 candidate genes other than MC1R that have been previously shown to influence melanin-based color patterns in vertebrates, including genes that have rarely been studied in a wild bird species before: POMC, Agouti, TYR, TYRP1, DCT, Corin, and SLC24A5 Of these 7 genes, 2 (Corin and TYRP1) displayed an interesting shift in allele frequencies between lowland and highland forms and a departure from mutation-drift equilibrium consistent with balancing selection in the polymorphic highland form only. Sequence variation at Agouti, a gene frequently involved in melanin-based pigmentation patterning, was not associated with color forms or morphs. Thus, we suggest that functionally important changes in loci other than those classically studied are involved in the color polymorphism exhibited by the Réunion grey white-eye and possibly many other nonmodel species.
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Affiliation(s)
- Yann X C Bourgeois
- From the Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, Université Paul Sabatier, Toulouse 3-Centre National de la Recherche Scientifique (CNRS)-École Nationale de Formation Agronomique (ENFA), 118 route de Narbonne, F-31062 Toulouse, France (Bourgeois, Bertrand, Delahaie, Cornuault, and Thébaud); Hémisphères, BP 438, 98822 Poindimié, Nouvelle-Calédonie (Duval); and Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), José Gutiérrez Abascal 2, Madrid E-28006, Spain (Milá).
| | - Joris A M Bertrand
- From the Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, Université Paul Sabatier, Toulouse 3-Centre National de la Recherche Scientifique (CNRS)-École Nationale de Formation Agronomique (ENFA), 118 route de Narbonne, F-31062 Toulouse, France (Bourgeois, Bertrand, Delahaie, Cornuault, and Thébaud); Hémisphères, BP 438, 98822 Poindimié, Nouvelle-Calédonie (Duval); and Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), José Gutiérrez Abascal 2, Madrid E-28006, Spain (Milá)
| | - Boris Delahaie
- From the Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, Université Paul Sabatier, Toulouse 3-Centre National de la Recherche Scientifique (CNRS)-École Nationale de Formation Agronomique (ENFA), 118 route de Narbonne, F-31062 Toulouse, France (Bourgeois, Bertrand, Delahaie, Cornuault, and Thébaud); Hémisphères, BP 438, 98822 Poindimié, Nouvelle-Calédonie (Duval); and Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), José Gutiérrez Abascal 2, Madrid E-28006, Spain (Milá)
| | - Josselin Cornuault
- From the Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, Université Paul Sabatier, Toulouse 3-Centre National de la Recherche Scientifique (CNRS)-École Nationale de Formation Agronomique (ENFA), 118 route de Narbonne, F-31062 Toulouse, France (Bourgeois, Bertrand, Delahaie, Cornuault, and Thébaud); Hémisphères, BP 438, 98822 Poindimié, Nouvelle-Calédonie (Duval); and Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), José Gutiérrez Abascal 2, Madrid E-28006, Spain (Milá)
| | - Thomas Duval
- From the Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, Université Paul Sabatier, Toulouse 3-Centre National de la Recherche Scientifique (CNRS)-École Nationale de Formation Agronomique (ENFA), 118 route de Narbonne, F-31062 Toulouse, France (Bourgeois, Bertrand, Delahaie, Cornuault, and Thébaud); Hémisphères, BP 438, 98822 Poindimié, Nouvelle-Calédonie (Duval); and Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), José Gutiérrez Abascal 2, Madrid E-28006, Spain (Milá)
| | - Borja Milá
- From the Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, Université Paul Sabatier, Toulouse 3-Centre National de la Recherche Scientifique (CNRS)-École Nationale de Formation Agronomique (ENFA), 118 route de Narbonne, F-31062 Toulouse, France (Bourgeois, Bertrand, Delahaie, Cornuault, and Thébaud); Hémisphères, BP 438, 98822 Poindimié, Nouvelle-Calédonie (Duval); and Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), José Gutiérrez Abascal 2, Madrid E-28006, Spain (Milá)
| | - Christophe Thébaud
- From the Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, Université Paul Sabatier, Toulouse 3-Centre National de la Recherche Scientifique (CNRS)-École Nationale de Formation Agronomique (ENFA), 118 route de Narbonne, F-31062 Toulouse, France (Bourgeois, Bertrand, Delahaie, Cornuault, and Thébaud); Hémisphères, BP 438, 98822 Poindimié, Nouvelle-Calédonie (Duval); and Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), José Gutiérrez Abascal 2, Madrid E-28006, Spain (Milá)
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42
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Ralph PL, Coop G. Convergent Evolution During Local Adaptation to Patchy Landscapes. PLoS Genet 2015; 11:e1005630. [PMID: 26571125 PMCID: PMC4646681 DOI: 10.1371/journal.pgen.1005630] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 10/07/2015] [Indexed: 11/18/2022] Open
Abstract
Species often encounter, and adapt to, many patches of similar environmental conditions across their range. Such adaptation can occur through convergent evolution if different alleles arise in different patches, or through the spread of shared alleles by migration acting to synchronize adaptation across the species. The tension between the two reflects the constraint imposed on evolution by the underlying genetic architecture versus how effectively selection and geographic isolation act to inhibit the geographic spread of locally adapted alleles. This paper studies the balance between these two routes to adaptation in a model of continuous environments with patchy selection pressures. We address the following questions: How long does it take for a novel allele to appear in a patch where it is locally adapted through mutation? Or, through migration from another, already adapted patch? Which is more likely to occur, as a function of distance between the patches? What population genetic signal is left by the spread of migrant alleles? To answer these questions we examine the family structure underlying migration-selection equilibrium surrounding an already adapted patch, treating those rare families that reach new patches as spatial branching processes. A main result is that patches further apart than a critical distance will likely evolve independent locally adapted alleles; this distance is proportional to the spatial scale of selection ([Formula: see text], where σ is the dispersal distance and sm is the selective disadvantage of these alleles between patches), and depends linearly on log(sm/μ), where μ is the mutation rate. This provides a way to understand the role of geographic separation between patches in promoting convergent adaptation and the genomic signals it leaves behind. We illustrate these ideas using the convergent evolution of cryptic coloration in the rock pocket mouse, Chaetodipus intermedius, as an empirical example.
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Affiliation(s)
- Peter L. Ralph
- Computational Biology and Bioinformatics, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
| | - Graham Coop
- Evolution and Ecology, University of California, Davis, Davis, California, United States of America
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43
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Alterations in Mc1r gene expression are associated with regressive pigmentation in Astyanax cavefish. Dev Genes Evol 2015; 225:367-75. [PMID: 26462499 DOI: 10.1007/s00427-015-0517-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 09/08/2015] [Indexed: 12/16/2022]
Abstract
Diverse changes in coloration across distant taxa are mediated through alterations in certain highly conserved pigmentation genes. Among these genes, Mc1r is a frequent target for mutation, and many documented alterations involve coding sequence changes. We investigated whether regulatory mutations in Mc1r may also contribute to pigmentation loss in the blind Mexican cavefish, Astyanax mexicanus. This species comprises multiple independent cave populations that have evolved reduced (or absent) melanic pigmentation as a consequence of living in darkness for millions of generations. Among the most salient cave-associated traits, complete absence (albinism) or reduced levels of pigmentation (brown) have long been the focus of degenerative pigmentation research in Astyanax. These two Mendelian traits have been linked to specific coding mutations in Oca2 (albinism) and Mc1r (brown). However, four of the seven caves harboring the brown phenotype exhibit unaffected coding sequences compared to surface fish. Thus, diverse genetic changes involving the same genes likely impact reduced pigmentation among cavefish populations. Using both sequence and expression analyses, we show that certain cave-dwelling populations harboring the brown mutation have substantial alterations to the putative Mc1r cis-regulatory region. Several of these sequence mutations in the Mc1r 5' region were present across multiple, independent cave populations. This study suggests that pigmentation reduction in Astyanax cavefish evolves through a combination of both coding and cis-regulatory mutations. Moreover, this study represents one of the first attempts to identify regulatory alterations linked to regressive changes in cave-dwelling populations of A. mexicanus.
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44
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Radke DW, Lee C. Adaptive potential of genomic structural variation in human and mammalian evolution. Brief Funct Genomics 2015; 14:358-68. [PMID: 26003631 DOI: 10.1093/bfgp/elv019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Because phenotypic innovations must be genetically heritable for biological evolution to proceed, it is natural to consider new mutation events as well as standing genetic variation as sources for their birth. Previous research has identified a number of single-nucleotide polymorphisms that underlie a subset of adaptive traits in organisms. However, another well-known class of variation, genomic structural variation, could have even greater potential to produce adaptive phenotypes, due to the variety of possible types of alterations (deletions, insertions, duplications, among others) at different genomic positions and with variable lengths. It is from these dramatic genomic alterations, and selection on their phenotypic consequences, that adaptations leading to biological diversification could be derived. In this review, using studies in humans and other mammals, we highlight examples of how phenotypic variation from structural variants might become adaptive in populations and potentially enable biological diversification. Phenotypic change arising from structural variants will be described according to their immediate effect on organismal metabolic processes, immunological response and physical features. Study of population dynamics of segregating structural variation can therefore provide a window into understanding current and historical biological diversification.
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45
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Pardo-Diaz C, Salazar C, Jiggins CD. Towards the identification of the loci of adaptive evolution. Methods Ecol Evol 2015; 6:445-464. [PMID: 25937885 PMCID: PMC4409029 DOI: 10.1111/2041-210x.12324] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 11/28/2014] [Indexed: 12/17/2022]
Abstract
1. Establishing the genetic and molecular basis underlying adaptive traits is one of the major goals of evolutionary geneticists in order to understand the connection between genotype and phenotype and elucidate the mechanisms of evolutionary change. Despite considerable effort to address this question, there remain relatively few systems in which the genes shaping adaptations have been identified. 2. Here, we review the experimental tools that have been applied to document the molecular basis underlying evolution in several natural systems, in order to highlight their benefits, limitations and suitability. In most cases, a combination of DNA, RNA and functional methodologies with field experiments will be needed to uncover the genes and mechanisms shaping adaptation in nature.
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Affiliation(s)
- Carolina Pardo-Diaz
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del RosarioCarrera 24 No 63C-69, Bogotá 111221, Colombia
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del RosarioCarrera 24 No 63C-69, Bogotá 111221, Colombia
| | - Chris D Jiggins
- Department of Zoology, University of CambridgeDowning Street, Cambridge, CB2 3EJ, UK
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46
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Ciesielski TH, Pendergrass SA, White MJ, Kodaman N, Sobota RS, Huang M, Bartlett J, Li J, Pan Q, Gui J, Selleck SB, Amos CI, Ritchie MD, Moore JH, Williams SM. Diverse convergent evidence in the genetic analysis of complex disease: coordinating omic, informatic, and experimental evidence to better identify and validate risk factors. BioData Min 2014; 7:10. [PMID: 25071867 PMCID: PMC4112852 DOI: 10.1186/1756-0381-7-10] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 06/08/2014] [Indexed: 11/10/2022] Open
Abstract
In omic research, such as genome wide association studies, researchers seek to repeat their results in other datasets to reduce false positive findings and thus provide evidence for the existence of true associations. Unfortunately this standard validation approach cannot completely eliminate false positive conclusions, and it can also mask many true associations that might otherwise advance our understanding of pathology. These issues beg the question: How can we increase the amount of knowledge gained from high throughput genetic data? To address this challenge, we present an approach that complements standard statistical validation methods by drawing attention to both potential false negative and false positive conclusions, as well as providing broad information for directing future research. The Diverse Convergent Evidence approach (DiCE) we propose integrates information from multiple sources (omics, informatics, and laboratory experiments) to estimate the strength of the available corroborating evidence supporting a given association. This process is designed to yield an evidence metric that has utility when etiologic heterogeneity, variable risk factor frequencies, and a variety of observational data imperfections might lead to false conclusions. We provide proof of principle examples in which DiCE identified strong evidence for associations that have established biological importance, when standard validation methods alone did not provide support. If used as an adjunct to standard validation methods this approach can leverage multiple distinct data types to improve genetic risk factor discovery/validation, promote effective science communication, and guide future research directions.
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Affiliation(s)
- Timothy H Ciesielski
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.,Institute for Quantitative Biomedical Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Sarah A Pendergrass
- Center for Systems Genomics, Pennsylvania State University, University Park, PA 16802, USA.,Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Marquitta J White
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.,Institute for Quantitative Biomedical Sciences, Dartmouth College, Hanover, NH 03755, USA.,Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232-0700, USA
| | - Nuri Kodaman
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.,Institute for Quantitative Biomedical Sciences, Dartmouth College, Hanover, NH 03755, USA.,Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232-0700, USA
| | - Rafal S Sobota
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.,Institute for Quantitative Biomedical Sciences, Dartmouth College, Hanover, NH 03755, USA.,Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232-0700, USA
| | - Minjun Huang
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Jacquelaine Bartlett
- Institute for Quantitative Biomedical Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Jing Li
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Qinxin Pan
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Jiang Gui
- Institute for Quantitative Biomedical Sciences, Dartmouth College, Hanover, NH 03755, USA.,Community and Family Medicine, Section of Biostatistics & Epidemiology, Geisel School of Medicine, Hanover, NH 03766, USA
| | - Scott B Selleck
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Christopher I Amos
- Institute for Quantitative Biomedical Sciences, Dartmouth College, Hanover, NH 03755, USA.,Community and Family Medicine, Section of Biostatistics & Epidemiology, Geisel School of Medicine, Hanover, NH 03766, USA
| | - Marylyn D Ritchie
- Center for Systems Genomics, Pennsylvania State University, University Park, PA 16802, USA.,Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Jason H Moore
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.,Institute for Quantitative Biomedical Sciences, Dartmouth College, Hanover, NH 03755, USA.,Community and Family Medicine, Section of Biostatistics & Epidemiology, Geisel School of Medicine, Hanover, NH 03766, USA
| | - Scott M Williams
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.,Institute for Quantitative Biomedical Sciences, Dartmouth College, Hanover, NH 03755, USA
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47
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Affiliation(s)
- Jessica A. Bolker
- Department of Biological Sciences; University of New Hampshire; Durham NH 03824 USA
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48
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Derelle R, Kondrashov FA, Arkhipov VY, Corbel H, Frantz A, Gasparini J, Jacquin L, Jacob G, Thibault S, Baudry E. Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene (MC1R). BMC Res Notes 2013; 6:310. [PMID: 23915680 PMCID: PMC3750627 DOI: 10.1186/1756-0500-6-310] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 07/22/2013] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Genetic variation at the melanocortin-1 receptor (MC1R) gene is correlated with melanin color variation in many birds. Feral pigeons (Columba livia) show two major melanin-based colorations: a red coloration due to pheomelanic pigment and a black coloration due to eumelanic pigment. Furthermore, within each color type, feral pigeons display continuous variation in the amount of melanin pigment present in the feathers, with individuals varying from pure white to a full dark melanic color. Coloration is highly heritable and it has been suggested that it is under natural or sexual selection, or both. Our objective was to investigate whether MC1R allelic variants are associated with plumage color in feral pigeons. FINDINGS We sequenced 888 bp of the coding sequence of MC1R among pigeons varying both in the type, eumelanin or pheomelanin, and the amount of melanin in their feathers. We detected 10 non-synonymous substitutions and 2 synonymous substitution but none of them were associated with a plumage type. It remains possible that non-synonymous substitutions that influence coloration are present in the short MC1R fragment that we did not sequence but this seems unlikely because we analyzed the entire functionally important region of the gene. CONCLUSIONS Our results show that color differences among feral pigeons are probably not attributable to amino acid variation at the MC1R locus. Therefore, variation in regulatory regions of MC1R or variation in other genes may be responsible for the color polymorphism of feral pigeons.
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49
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Singaravelan N, Raz S, Tzur S, Belifante S, Pavlicek T, Beiles A, Ito S, Wakamatsu K, Nevo E. Adaptation of pelage color and pigment variations in Israeli subterranean blind mole rats, Spalax ehrenbergi [corrected]. PLoS One 2013; 8:e69346. [PMID: 23935991 PMCID: PMC3723903 DOI: 10.1371/journal.pone.0069346] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Accepted: 06/08/2013] [Indexed: 11/19/2022] Open
Abstract
Background Concealing coloration in rodents is well established. However, only a few studies examined how soil color, pelage color, hair-melanin content, and genetics (i.e., the causal chain) synergize to configure it. This study investigates the causal chain of dorsal coloration in Israeli subterranean blind mole rats, Spalax ehrenbergi. Methods We examined pelage coloration of 128 adult animals from 11 populations belonging to four species of Spalax ehrenbergi superspecies (Spalax galili, Spalax golani, Spalax carmeli, and Spalax judaei) and the corresponding coloration of soil samples from the collection sites using a digital colorimeter. Additionally, we quantified hair-melanin contents of 67 animals using HPLC and sequenced the MC1R gene in 68 individuals from all four mole rat species. Results Due to high variability of soil colors, the correlation between soil and pelage color coordinates was weak and significant only between soil hue and pelage lightness. Multiple stepwise forward regression revealed that soil lightness was significantly associated with all pelage color variables. Pelage color lightness among the four species increased with the higher southward aridity in accordance to Gloger's rule (darker in humid habitats and lighter in arid habitats). Darker and lighter pelage colors are associated with darker basalt and terra rossa, and lighter rendzina soils, respectively. Despite soil lightness varying significantly, pelage lightness and eumelanin converged among populations living in similar soil types. Partial sequencing of the MC1R gene identified three allelic variants, two of which were predominant in northern species (S. galili and S. golani), and the third was exclusive to southern species (S. carmeli and S. judaei), which might have caused the differences found in pheomelanin/eumelanin ratio. Conclusion/Significance Darker dorsal pelage in darker basalt and terra rossa soils in the north and lighter pelage in rendzina and loess soils in the south reflect the combined results of crypsis and thermoregulatory function following Gloger's rule.
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Affiliation(s)
- Natarajan Singaravelan
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa, Israel
- Bommanampalayam, Coimbatore, Tamil Nadu, India
- * E-mail:
| | - Shmuel Raz
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa, Israel
| | - Shay Tzur
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa, Israel
| | - Shirli Belifante
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa, Israel
| | - Tomas Pavlicek
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa, Israel
| | - Avigdor Beiles
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa, Israel
| | - Shosuke Ito
- Department of Chemistry, Fujita Health University School of Health Sciences Toyoake, Aichi, Japan
| | - Kazumasa Wakamatsu
- Department of Chemistry, Fujita Health University School of Health Sciences Toyoake, Aichi, Japan
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa, Israel
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50
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Chandramohan B, Renieri C, La Manna V, La Terza A. The alpaca agouti gene: Genomic locus, transcripts and causative mutations of eumelanic and pheomelanic coat color. Gene 2013; 521:303-10. [DOI: 10.1016/j.gene.2013.03.060] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 02/01/2013] [Accepted: 03/16/2013] [Indexed: 12/01/2022]
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