1
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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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2
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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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3
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Tensen L, Fischer K. Heterozygosity is low where rare color variants in wild carnivores prevail. Ecol Evol 2024; 14:e10881. [PMID: 38327687 PMCID: PMC10847885 DOI: 10.1002/ece3.10881] [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] [Accepted: 12/04/2023] [Indexed: 02/09/2024] Open
Abstract
Coat color and pattern are a distinguished feature in mammalian carnivores, shaped by climatic cycles and habitat type. It can be expressed in various ways, such as gradients, polymorphisms, and rare color variants. Although natural selection explains much of the phenotypic variation found in the wild, genetic drift and heterozygote deficiency, as prominent in small and fragmented populations, may also affect phenotypic variability through the fixation of recessive alleles. The aim of this study was to test whether rare color variants in the wild could relate to a deficiency of heterozygotes, resulting from habitat fragmentation and small population size. We present an overview of all rare color variants in the order Carnivora, and compiled demographic and genetic data of the populations where they did and did not occur, to test for significant correlations. We also tested how phylogeny and body weight influenced the presence of color variants with phylogenetic generalized linear mixed models (PGLMMs). We found 40 color-variable species and 59 rare color variants. In 17 variable phenotypic populations for which genetic diversity was available, the average A R was 4.18, H O = 0.59, and H E = 0.66, and F IS = 0.086. We found that variable populations displayed a significant reduction in heterozygosity and allelic richness compared to non-variable populations across species. We also found a significant negative correlation between population size and inbreeding coefficients. Therefore, it is possible that small effective size had phenotypic consequences on the extant populations. The high frequency of the rare color variants (averaging 20%) also implies that genetic drift is locally overruling natural selection in small effective populations. As such, rare color variants could be added to the list of phenotypic consequences of inbreeding in the wild.
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Affiliation(s)
- Laura Tensen
- Zoology, Institute for Integrated Natural SciencesKoblenz UniversityKoblenzGermany
- Department of Zoology, Centre for Ecological Genomics and Wildlife ConservationUniversity of JohannesburgJohannesburgSouth Africa
| | - Klaus Fischer
- Zoology, Institute for Integrated Natural SciencesKoblenz UniversityKoblenzGermany
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4
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Brandon AA, Almeida D, Powder KE. Neural crest cells as a source of microevolutionary variation. Semin Cell Dev Biol 2023; 145:42-51. [PMID: 35718684 PMCID: PMC10482117 DOI: 10.1016/j.semcdb.2022.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 05/03/2022] [Accepted: 06/03/2022] [Indexed: 11/28/2022]
Abstract
Vertebrates have some of the most complex and diverse features in animals, from varied craniofacial morphologies to colorful pigmentation patterns and elaborate social behaviors. All of these traits have their developmental origins in a multipotent embryonic lineage of neural crest cells. This "fourth germ layer" is a vertebrate innovation and the source of a wide range of adult cell types. While others have discussed the role of neural crest cells in human disease and animal domestication, less is known about their role in contributing to adaptive changes in wild populations. Here, we review how variation in the development of neural crest cells and their derivatives generates considerable phenotypic diversity in nature. We focus on the broad span of traits under natural and sexual selection whose variation may originate in the neural crest, with emphasis on behavioral factors such as intraspecies communication that are often overlooked. In all, we encourage the integration of evolutionary ecology with developmental biology and molecular genetics to gain a more complete understanding of the role of this single cell type in trait covariation, evolutionary trajectories, and vertebrate diversity.
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Affiliation(s)
- A Allyson Brandon
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Daniela Almeida
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Kara E Powder
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA.
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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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6
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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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7
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Greenspan E, Montgomery C, Stokes D, K'lu SS, Moo SSB, Anile S, Giordano AJ, Nielsen CK. Occupancy, density, and activity patterns of a Critically Endangered leopard population on the
Kawthoolei‐Thailand
border. POPUL ECOL 2023. [DOI: 10.1002/1438-390x.12148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Evan Greenspan
- Karen Wildlife Conservation Initiative Willagee Western Australia Australia
| | - Clara Montgomery
- Karen Wildlife Conservation Initiative Willagee Western Australia Australia
| | - Demelza Stokes
- Karen Wildlife Conservation Initiative Willagee Western Australia Australia
| | - Saw Say K'lu
- Kawthoolei Forestry Department Chiang Mai Thailand
| | | | - Stefano Anile
- Forestry Program and Cooperative Wildlife Research Laboratory Southern Illinois University Carbondale Illinois USA
| | | | - Clayton K. Nielsen
- Forestry Program and Cooperative Wildlife Research Laboratory Southern Illinois University Carbondale Illinois USA
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8
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Gibert JM. [Small scale evolution]. Biol Aujourdhui 2022; 216:41-47. [PMID: 35876520 DOI: 10.1051/jbio/2022008] [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: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Small-scale evolution or microevolution concerns evolution at the intra-specific level or between closely related species. At the intra-specific level, it allows the analysis of the evolutionary forces at work: mutation, genetic drift, migration and selection. Moreover, because of the short evolutionary time, it is easier to identify the genetic basis of observed phenotypic differences. Most studies focus on current populations but more and more analyses are performed on ancient DNA. This provides important information for tracing the history of populations and also allows the reconstruction of phenotypes of individuals that disappeared several thousand years ago. In this short review, I present studies showing how pre-zygotic or post-zygotic barriers involved in species formation are set up using the example of the geographical barrier due to the formation of the Isthmus of Panama and that of the heterochromatin divergence in Drosophilidae. I also describe the different approaches that have been used to identify the genetic basis of well known phenotypic variations: candidate gene approach (about melanism in felines), QTL mapping (variation in the number of lateral bone plates in sticklebacks), association study (pigmentation in the Asian ladybird). Finally, I illustrate the key impact of natural selection with the iconic example of the evolution of the beak of Galapagos finches, and the role of certain developmental genes in its morphological diversification.
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Affiliation(s)
- Jean-Michel Gibert
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire de Biologie du Développement, UMR 7622, 9 quai St-Bernard 75005 Paris, France
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9
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Tensen L, Power J, Camacho G, Godinho R, Jansen van Vuuren B, Fischer K. Molecular tracking and prevalence of the red colour morph restricted to a harvested leopard population in South Africa. Evol Appl 2022; 15:1028-1041. [PMID: 35782007 PMCID: PMC9234631 DOI: 10.1111/eva.13423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/05/2022] [Accepted: 05/12/2022] [Indexed: 12/02/2022] Open
Abstract
The red leopard (Panthera pardus) colour morph is a colour variant that occurs only in South Africa, where it is confined to the Central Bushveld bioregion. Red leopards have been spreading over the past 40 years, which raises the speculation that the prevalence of this phenotype is related to low dispersal of young individuals owing to high off-take in the region. Intensive selective hunting tends to remove large resident male leopards from the breeding population, which gives young male leopards the chance to mate with resident female leopards that are more likely to be their relatives, eventually increasing the frequency of rare genetic variants. To investigate the genetic mechanisms underlying the red coat colour morph in leopards, and whether its prevalence in South Africa relates to an increase in genetic relatedness in the population, we sequenced exons of six coat colour-associated genes and 20 microsatellite loci in twenty Wild-type and four red leopards. The results were combined with demographic data available from our study sites. We found that red leopards own a haplotype in homozygosity identified by two SNPs and a 1 bp deletion that causes a frameshift in the tyrosinase-related protein 1 (TYRP1), a gene known to be involved in the biosynthesis of melanin. Microsatellite analyses indicate clear signs of a population bottleneck and a relatedness of 0.11 among all pairwise relationships, eventually supporting our hypothesis that a rare colour morph in the wild has increased its local frequency due to low natal dispersal, while subject to high human-induced mortality rate.
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Affiliation(s)
- Laura Tensen
- Institute for Integrated Natural Sciences, ZoologyUniversity of Koblenz‐LandauKoblenzGermany
- Department of Zoology, Centre for Ecological Genomics and Wildlife ConservationUniversity of JohannesburgJohannesburgSouth Africa
| | - John Power
- Directorate of Biodiversity Management, Department of Economic Development, Environment, Conservation and TourismNorth West Provincial GovernmentMmabathoSouth Africa
| | - Gerrie Camacho
- Mpumalanga Tourism and Parks AgencyNelspruitSouth Africa
| | - Raquel Godinho
- Department of Zoology, Centre for Ecological Genomics and Wildlife ConservationUniversity of JohannesburgJohannesburgSouth Africa
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório AssociadoCampus de Vairão, Universidade do PortoVairãoPortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIO, Campus de VairãoVairãoPortugal
| | - Bettine Jansen van Vuuren
- Department of Zoology, Centre for Ecological Genomics and Wildlife ConservationUniversity of JohannesburgJohannesburgSouth Africa
| | - Klaus Fischer
- Institute for Integrated Natural Sciences, ZoologyUniversity of Koblenz‐LandauKoblenzGermany
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10
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Ross MD, Hargey AS, Smyth LK, Mann GK, O'Riain MJ. New Records of White Phenotype Honey Badgers (Mellivora capensis) from South Africa. AFRICAN JOURNAL OF WILDLIFE RESEARCH 2022. [DOI: 10.3957/056.052.0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
| | | | | | | | - M. Justin O'Riain
- iCWild, Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
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11
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Drouilly M, Horion R, Henschel P. Not all black and white: Records of several melanistic honey badgers in Niokolo‐Koba National Park, Senegal. Afr J Ecol 2022. [DOI: 10.1111/aje.12985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Big spots in a small population: Analyzing characteristics and temporality of coat patterns in Croatian lynx population. ZOOL ANZ 2022. [DOI: 10.1016/j.jcz.2022.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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13
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Anello M, Daverio MS, Rodríguez SS, Romero SR, Renieri C, Vidal Rioja L, Di Rocco F. The ASIP gene in the llama (Lama glama): Alternative transcripts, expression and relation with color phenotypes. Gene 2021; 809:146018. [PMID: 34655720 DOI: 10.1016/j.gene.2021.146018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 07/15/2021] [Accepted: 10/11/2021] [Indexed: 11/27/2022]
Abstract
The Agouti gene (ASIP) is one of the most important genes for coat color determination in mammals. It has a complex structure with several promoters and alternative non-coding first exons that are transcribed into mRNAs with different 5'UTR. These mRNA isoforms regulate the temporal and spatial expression of the gene, producing diverse pigmentation patterns. Here, we studied ASIP transcriptional variants and their expression in the skin of llamas with different coat color phenotypes. We also described the ASIP locus, including promoter usage and the splicing events that originate each transcript variant. Using 5'RACE-PCR we isolated seven ASIP transcripts with alternative 5'UTR, where exons 1A, 1A', 1C, 1D, and a novel non-coding exon 1A" were identified. Additionally, new alternative spliced forms were found. The diversity of ASIP 5'UTRs is originated by a complex pattern of alternative promoter usage, multiple transcription start sites and splicing events that include exon skipping and alternative 3' splicing site selection. We found that ASIP was highly expressed in llamas with white and brown phenotypes while black animals presented very low expression. The main responsible for this difference was a fusion transcript between ASIP and NCOA6 genes, which was present in the skin of white and brown llamas but not in the black ones. The rest of ASIP transcripts presented very low expression in the skin, indicating that the main regulation point for ASIP gene expression is at the transcriptional level. Nevertheless, the characteristics of the 5'UTRs sequences suggest that alternative transcripts could be regulated differently at the protein synthesis level.
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Affiliation(s)
- M Anello
- Instituto Multidisciplinario de Biología Celular (IMBICE), CONICET-UNLP-CIC, La Plata, Buenos Aires, Argentina
| | - M S Daverio
- Instituto Multidisciplinario de Biología Celular (IMBICE), CONICET-UNLP-CIC, La Plata, Buenos Aires, Argentina; Cátedra de Biología, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - S S Rodríguez
- Instituto Multidisciplinario de Biología Celular (IMBICE), CONICET-UNLP-CIC, La Plata, Buenos Aires, Argentina
| | - S R Romero
- Instituto de Investigaciones y Desarrollo Tecnológico para la Agricultura Familiar- Región NOA (IPAF NOA) INTA - Posta de Hornillos, Maimara, Jujuy, Argentina
| | - C Renieri
- School of Pharmacy, University of Camerino, Camerino, Marche, Italia
| | - L Vidal Rioja
- Instituto Multidisciplinario de Biología Celular (IMBICE), CONICET-UNLP-CIC, La Plata, Buenos Aires, Argentina
| | - F Di Rocco
- Instituto Multidisciplinario de Biología Celular (IMBICE), CONICET-UNLP-CIC, La Plata, Buenos Aires, Argentina.
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14
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Rogan JE. First Locality Record of Melanistic Oncilla (Leopardus tigrinus) in Monteverde, Costa Rica. NEOTROPICAL BIOLOGY AND CONSERVATION 2021. [DOI: 10.3897/neotropical.16.e65464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The persistence of the coat color polymorphism melanism has been reported for several tropical felids, but its evolutionary advantages remain an active area of research. Few publications have explored melanism in the elusive species, oncilla (Leopardus tigrinus) within the Neotropical part of their range in Costa Rica. Herein, I present the first record of a melanistic oncilla within the montane cloud forest of Monteverde, Costa Rica. Recent studies have found support for theories (e.g. Temporal Segregation Hypothesis and Gloger’s Rule) explaining the ecological advantages driving melanism in oncilla and tropical felid populations. However, it is unclear what is driving melanism in this Monteverde oncilla population due to the singular observation. Further research investigating whether melanism is occurring at a higher frequency in other individuals in the region is critical to better understanding the occurrence of melanism in local populations of this cryptic species. The montane cloud forest in Monteverde provides critical habitat to this vulnerable species within the small Neotropical part of their range. Melanistic individuals may be particularly threatened by land-use change and increasing human pressure if theories for the evolutionary advantages and ecological conditions motivating melanism are supported.
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15
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Harihar A, Lahkar D, Singh A, Das SK, Ahmed MF, Begum RH. Population density modelling of mixed polymorphic phenotypes: an application of spatial mark‐resight models. Anim Conserv 2021. [DOI: 10.1111/acv.12677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A. Harihar
- Panthera New York NY USA
- Nature Conservation Foundation Mysore Karnataka India
| | - D. Lahkar
- Aaranyak Guwahati Assam India
- Department of Life Science and Bioinformatics Assam University (Diphu Campus) Diphu Assam India
| | | | | | | | - R. H. Begum
- Department of Life Science and Bioinformatics Assam University (Diphu Campus) Diphu Assam India
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16
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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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17
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Elizalde SRFF, Elizalde Castells D, Freitas NMCN, Groom RJ, Durant SM. Several black servals from a single survey at the Luando Strict Nature Reserve, Angola. Afr J Ecol 2020. [DOI: 10.1111/aje.12766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - David Elizalde Castells
- The Range Wide Conservation Program for Cheetah and African Wild Dogs London UK
- Zoological Society of London London UK
| | | | - Rosemary Joy Groom
- The Range Wide Conservation Program for Cheetah and African Wild Dogs London UK
- Zoological Society of London London UK
| | - Sarah M. Durant
- The Range Wide Conservation Program for Cheetah and African Wild Dogs London UK
- Zoological Society of London London UK
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18
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Sauther ML, Bertolini F, Dollar LJ, Pomerantz J, Alves PC, Gandolfi B, Kurushima JD, Mattucci F, Randi E, Rothschild MF, Cuozzo FP, Larsen RS, Moresco A, Lyons LA, Jacky IAY. Taxonomic identification of Madagascar’s free-ranging “forest cats”. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01261-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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19
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Graipel ME, Bogoni JA, Giehl ELH, Cerezer FO, Cáceres NC, Eizirik E. Melanism evolution in the cat family is influenced by intraspecific communication under low visibility. PLoS One 2019; 14:e0226136. [PMID: 31851714 PMCID: PMC6919575 DOI: 10.1371/journal.pone.0226136] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 11/20/2019] [Indexed: 11/18/2022] Open
Abstract
Melanism in the cat family has been associated with functions including camouflage, thermoregulation and parasite resistance. Here we investigate a new hypothesis proposing that the evolution of melanism in cats has additionally been influenced by communication functions of body markings. To evaluate this hypothesis, we assembled a species-level data set of morphological (body marks: white marks on the backs of ears) and ecological (circadian activity: arrhythmic/nocturnal, and environmental preference: open/closed) characteristics that could be associated with communication via body markings, and combined these data with a dated molecular phylogeny. Next, we tested the association between melanism and communication, first by relating species’ body marks with their ecological conditions, using a Bayesian implementation of the threshold model. Second, to explore the evolution of characteristics potentially influencing melanism in cat species, we modeled their evolution relative to melanism using models of coordinated vs. independent character changes. Our results suggest that white marks are associated with intraspecific communication between individuals that have non-melanistic phenotypes, as well as towards melanistic individuals (without white marks). The absence of white marks in a melanistic individual tends to be a limiting condition for intraspecific visual communication at night, resulting in an evolutionary dilemma for these species, i.e. to be almost invisible at night, but not to communicate visually. The comparative analysis of several evolutionary models indicated more support for the evolution of melanism being coordinated with the evolution of arrhythmic activity and white marks on the backs of ears.
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Affiliation(s)
- Maurício Eduardo Graipel
- Departamento de Ecologia e Zoologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
- * E-mail:
| | - Juliano André Bogoni
- Laboratório de Ecologia, Manejo e Conservação de Fauna Silvestre (LEMaC), Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Eduardo Luís Hettwer Giehl
- Programa de Pós-Graduação em Ecologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Felipe O. Cerezer
- Programa de Pós-Graduação em Biodiversidade Animal, CCNE, Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul, Brazil
| | - Nilton Carlos Cáceres
- Departamento de Ecologia e Evolução, CCNE, Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul, Brazil
| | - Eduardo Eizirik
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
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20
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Munishi LK, Courtney‐Mustaphi CJ, Marchant R. Observation of an adult female oribi with leucistic pelage in Lobo, Serengeti National Park, Tanzania. Afr J Ecol 2019. [DOI: 10.1111/aje.12677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Linus K. Munishi
- School of Life Sciences and Bio‐Engineering Nelson Mandela African Institution of Science and Technology Arusha Tanzania
| | - Colin J. Courtney‐Mustaphi
- Geoecology, Department of Environmental Sciences University of Basel Basel Switzerland
- Department of Environment and Geography York Institute for Tropical Ecosystems, University of York York UK
| | - Rob Marchant
- Department of Environment and Geography York Institute for Tropical Ecosystems, University of York York UK
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21
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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: 13] [Impact Index Per Article: 2.6] [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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22
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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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23
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Zafar-ul Islam M, Boug A, Shehri A, da Silva LG. Geographic distribution patterns of melanistic Arabian Wolves, Canis lupus arabs (Pocock), in Saudi Arabia (Mammalia: Carnivora). ZOOLOGY IN THE MIDDLE EAST 2019. [DOI: 10.1080/09397140.2019.1580931] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
| | - Ahmed Boug
- Prince Saud al Faisal Wildlife Research Center, Taif, Saudi Arabia
| | - Abdullah Shehri
- Prince Saud al Faisal Wildlife Research Center, Taif, Saudi Arabia
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24
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Pilfold NW, Letoluai A, Ruppert K, Glikman JA, Stacy‐Dawes J, O’Connor D, Owen M. Confirmation of black leopard (
Panthera pardus pardus
) living in Laikipia County, Kenya. Afr J Ecol 2019. [DOI: 10.1111/aje.12586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nicholas W. Pilfold
- Institute for Conservation Research San Diego Zoo Global San Diego California
| | | | - Kirstie Ruppert
- Institute for Conservation Research San Diego Zoo Global San Diego California
| | - Jenny A. Glikman
- Institute for Conservation Research San Diego Zoo Global San Diego California
| | - Jenna Stacy‐Dawes
- Institute for Conservation Research San Diego Zoo Global San Diego California
| | - David O’Connor
- Institute for Conservation Research San Diego Zoo Global San Diego California
| | - Megan Owen
- Institute for Conservation Research San Diego Zoo Global San Diego California
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25
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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: 5] [Impact Index Per Article: 0.7] [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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26
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Mapping black panthers: Macroecological modeling of melanism in leopards (Panthera pardus). PLoS One 2017; 12:e0170378. [PMID: 28379961 PMCID: PMC5381760 DOI: 10.1371/journal.pone.0170378] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 01/04/2017] [Indexed: 11/19/2022] Open
Abstract
The geographic distribution and habitat association of most mammalian polymorphic phenotypes are still poorly known, hampering assessments of their adaptive significance. Even in the case of the black panther, an iconic melanistic variant of the leopard (Panthera pardus), no map exists describing its distribution. We constructed a large database of verified records sampled across the species’ range, and used it to map the geographic occurrence of melanism. We then estimated the potential distribution of melanistic and non-melanistic leopards using niche-modeling algorithms. The overall frequency of melanism was ca. 11%, with a significantly non-random spatial distribution. Distinct habitat types presented significantly different frequencies of melanism, which increased in Asian moist forests and approached zero across most open/dry biomes. Niche modeling indicated that the potential distributions of the two phenotypes were distinct, with significant differences in habitat suitability and rejection of niche equivalency between them. We conclude that melanism in leopards is strongly affected by natural selection, likely driven by efficacy of camouflage and/or thermoregulation in different habitats, along with an effect of moisture that goes beyond its influence on vegetation type. Our results support classical hypotheses of adaptive coloration in animals (e.g. Gloger’s rule), and open up new avenues for in-depth evolutionary analyses of melanism in mammals.
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27
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Jorge García A, Polidori C, Nieves-Aldrey JL. Pheomelanin in the secondary sexual characters of male parasitoid wasps (Hymenoptera: Pteromalidae). ARTHROPOD STRUCTURE & DEVELOPMENT 2016; 45:311-319. [PMID: 27224206 DOI: 10.1016/j.asd.2016.05.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 05/06/2016] [Accepted: 05/08/2016] [Indexed: 06/05/2023]
Abstract
The occurrence and distribution of eumelanin and pheomelanin, the most prevalent biological pigments, has been rarely investigated in insects. Particularly yellowish to brownish body parts, which in many vertebrates are associated with pheomelanin, are visible in many insects but their chemical nature was rarely examined to a similar detail. Here, by using Dispersive Raman spectroscopy analysis, we found both eumelanin and pheomelanin in different body parts of male parasitoid wasps of three species of the genus Mesopolobus (Hymenoptera: Pteromalidae), which are known to have species-specific spots and coloured stripes on the legs and/or antennae which are displayed to females during courtship. We found a strong eumelanin signal in the antennal clava of all studied Mesopolobus species and in the circular black spot or callosity and the triangular black projection on the outer apical angle of the typically expanded middle tibia of Mesopolobus tibialis and Mesopolobus xanthocerus. Eumelanin was also the predominant pigment in the black thorax of Mesopolobus and other members of the family. Pheomelanin, on the other hand, was detected as predominant only in certain body parts of M. tibialis and M. xanthocerus, precisely in a very narrow, longitudinal brownish stripe on the middle femur and, only in M. tibialis, in a brownish oval-longitudinal stripe on the middle tibia. The two melanin types co-occurred in most pigmented areas, but more often one is clearly predominant relative to the other, according to the variation of Raman signal intensity of their signature peaks. A further tibial yellowish-orange stripe present in both these species did not include melanins of any type. Pheomelanin, could be more widespread than previously known in insects. A convergent evolution of melanin-based male sexual ornaments between vertebrates (e.g. bird feathers) and wasps can be suggested, opening to a new line of comparative evolutionary studies.
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Affiliation(s)
- Alberto Jorge García
- Laboratorio de Microscopía, Museo Nacional de Ciencias Naturales (CSIC), C/ José Gutiérrez Abascal 2, E-28006, Madrid, Spain.
| | - Carlo Polidori
- Instituto de Ciencias Ambientales (ICAM), Universidad de Castilla-La Mancha, Avenida Carlos III, s/n, E-45071 Toledo, Spain.
| | - José Luis Nieves-Aldrey
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (CSIC), C/ José Gutiérrez Abascal 2, E-28006 Madrid, Spain.
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28
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Silva LG, Oliveira TG, Kasper CB, Cherem JJ, Moraes EA, Paviolo A, Eizirik E. Biogeography of polymorphic phenotypes: Mapping and ecological modelling of coat colour variants in an elusive Neotropical cat, the jaguarundi (
Puma yagouaroundi
). J Zool (1987) 2016. [DOI: 10.1111/jzo.12358] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- L. G. Silva
- PUCRS Faculdade de Biociências Laboratório de Biologia Genômica e Molecular Porto Alegre RS Brazil
| | - T. G. Oliveira
- Departamento de Biologia Universidade Estadual do Maranhão São Luís MA Brazil
- Instituto Pró‐Carnívoros Atibaia SP Brazil
| | - C. B. Kasper
- Universidade Federal do Pampa – UNIPAMPA São Gabriel RS Brazil
| | | | | | - A. Paviolo
- Instituto de Biología Subtropical Universidad Nacional de Misiones – CONICET Puerto Iguazú‐Misiones Argentina
| | - E. Eizirik
- PUCRS Faculdade de Biociências Laboratório de Biologia Genômica e Molecular Porto Alegre RS Brazil
- Instituto Pró‐Carnívoros Atibaia SP Brazil
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29
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Amelanism in the corn snake is associated with the insertion of an LTR-retrotransposon in the OCA2 gene. Sci Rep 2015; 5:17118. [PMID: 26597053 PMCID: PMC4657000 DOI: 10.1038/srep17118] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/26/2015] [Indexed: 12/21/2022] Open
Abstract
The corn snake (Pantherophis guttatus) is a new model species particularly appropriate for investigating the processes generating colours in reptiles because numerous colour and pattern mutants have been isolated in the last five decades. Using our captive-bred colony of corn snakes, transcriptomic and genomic next-generation sequencing, exome assembly, and genotyping of SNPs in multiple families, we delimit the genomic interval bearing the causal mutation of amelanism, the oldest colour variant observed in that species. Proceeding with sequencing the candidate gene OCA2 in the uncovered genomic interval, we identify that the insertion of an LTR-retrotransposon in its 11th intron results in a considerable truncation of the p protein and likely constitutes the causal mutation of amelanism in corn snakes. As amelanistic snakes exhibit white, instead of black, borders around an otherwise normal pattern of dorsal orange saddles and lateral blotches, our results indicate that melanocytes lacking melanin are able to participate to the normal patterning of other colours in the skin. In combination with research in the zebrafish, this work opens the perspective of using corn snake colour and pattern variants to investigate the generative processes of skin colour patterning shared among major vertebrate lineages.
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30
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Hedges L, Lam WY, Campos-Arceiz A, Rayan DM, Laurance WF, Latham CJ, Saaban S, Clements GR. Melanistic leopards reveal their spots: Infrared camera traps provide a population density estimate of leopards in malaysia. J Wildl Manage 2015. [DOI: 10.1002/jwmg.901] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Laurie Hedges
- School of Geography; University of Nottingham Malaysia Campus; Semenyih Selangor 43500 Malaysia
- Rimba; 4 Jalan 1/9D; Bandar Baru Bangi Selangor 43650 Malaysia
| | - Wai Yee Lam
- Rimba; 4 Jalan 1/9D; Bandar Baru Bangi Selangor 43650 Malaysia
| | - Ahimsa Campos-Arceiz
- School of Geography; University of Nottingham Malaysia Campus; Semenyih Selangor 43500 Malaysia
| | - D. Mark Rayan
- WWF-Malaysia; 1 Jalan PJS 5/28A; Petaling Jaya Commercial Centre; Petaling Jaya Selangor 46150 Malaysia
| | - William F. Laurance
- Centre for Tropical Environmental and Sustainability Science and College of Marine and Environmental Sciences; James Cook University; Cairns Queensland 4870 Australia
| | - Chris J. Latham
- Department of Chemistry; University of Surrey; GU2 7XH; Guildford United Kingdom
| | - Salman Saaban
- Department of Wildlife and National Parks; Kuala Lumpur 56100 Malaysia
| | - Gopalasamy Reuben Clements
- School of Geography; University of Nottingham Malaysia Campus; Semenyih Selangor 43500 Malaysia
- Rimba; 4 Jalan 1/9D; Bandar Baru Bangi Selangor 43650 Malaysia
- Centre for Tropical Environmental and Sustainability Science and College of Marine and Environmental Sciences; James Cook University; Cairns Queensland 4870 Australia
- Australia and Kenyir Research Institute; Universiti Malaysia; Kuala Terengganu Terengganu 21030 Malaysia
- Panthera; 8 West 40th Street; 18th Floor; New York 10018 USA. School of Science; Monash University; Selangor 46150 Malaysia
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31
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Schneider A, Henegar C, Day K, Absher D, Napolitano C, Silveira L, David VA, O’Brien SJ, Menotti-Raymond M, Barsh GS, Eizirik E. Recurrent evolution of melanism in South American felids. PLoS Genet 2015; 11:e1004892. [PMID: 25695801 PMCID: PMC4335015 DOI: 10.1371/journal.pgen.1004892] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 11/13/2014] [Indexed: 12/04/2022] Open
Abstract
Morphological variation in natural populations is a genomic test bed for studying the interface between molecular evolution and population genetics, but some of the most interesting questions involve non-model organisms that lack well annotated reference genomes. Many felid species exhibit polymorphism for melanism but the relative roles played by genetic drift, natural selection, and interspecies hybridization remain uncertain. We identify mutations of Agouti signaling protein (ASIP) or the Melanocortin 1 receptor (MC1R) as independent causes of melanism in three closely related South American species: the pampas cat (Leopardus colocolo), the kodkod (Leopardus guigna), and Geoffroy’s cat (Leopardus geoffroyi). To assess population level variation in the regions surrounding the causative mutations we apply genomic resources from the domestic cat to carry out clone-based capture and targeted resequencing of 299 kb and 251 kb segments that contain ASIP and MC1R, respectively, from 54 individuals (13–21 per species), achieving enrichment of ~500–2500-fold and ~150x coverage. Our analysis points to unique evolutionary histories for each of the three species, with a strong selective sweep in the pampas cat, a distinctive but short melanism-specific haplotype in the Geoffroy’s cat, and reduced nucleotide diversity for both ancestral and melanism-bearing chromosomes in the kodkod. These results reveal an important role for natural selection in a trait of longstanding interest to ecologists, geneticists, and the lay community, and provide a platform for comparative studies of morphological variation in other natural populations. Color polymorphism in closely related animal species provides an opportunity to study how the balance between natural selection and genetic drift shapes the evolution of appearance and form. The cat family, Felidae, is especially interesting; 13 of 37 extant species exhibit polymorphism for melanism, but evidence for any adaptive role is lacking, in part because the potential benefits of melanism to felid predators are not clear, and in part because the tools for genomic analysis of natural populations are limited. We identify the mutations responsible for melanism in three closely related South American wild felids, the pampas cat, the kodkod, and Geoffroy’s cat, then adapt a new approach for targeted genome sequencing to characterize molecular variation in the region surrounding each melanism mutation. We find that each mutation has developed independently, with strong evidence for natural selection in the black pampas cat, and reduced genetic variation in the entire population of kodkods. Our results demonstrate that some “black cats” are black not by chance, but by selection for a mutation that provides increased fitness.
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Affiliation(s)
- Alexsandra Schneider
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Corneliu Henegar
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Kenneth Day
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Constanza Napolitano
- Laboratorio de Ecología Molecular & Instituto de Ecologia y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Leandro Silveira
- Jaguar Conservation Fund, Instituto Onça-Pintada, Mineiros, Goiás, Brazil
| | - Victor A. David
- Basic Research Laboratory, Frederick National Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Stephen J. O’Brien
- Theodosius Dobzhansky Center for Genome Informatics, St. Petersburg State University, St. Petersburg, Russia
| | - Marilyn Menotti-Raymond
- Basic Research Laboratory, Frederick National Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
- * E-mail: (GSB); (EE)
| | - Eduardo Eizirik
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Instituto Pró-Carnívoros, Atibaia, São Paulo, Brazil
- * E-mail: (GSB); (EE)
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Gershony LC, Penedo MCT, Davis BW, Murphy WJ, Helps CR, Lyons LA. Who's behind that mask and cape? The Asian leopard cat's Agouti (ASIP) allele likely affects coat colour phenotype in the Bengal cat breed. Anim Genet 2014; 45:893-7. [PMID: 25143047 PMCID: PMC4211939 DOI: 10.1111/age.12206] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2014] [Indexed: 11/29/2022]
Abstract
Coat colours and patterns are highly variable in cats and are determined mainly by several genes with Mendelian inheritance. A 2-bp deletion in agouti signalling protein (ASIP) is associated with melanism in domestic cats. Bengal cats are hybrids between domestic cats and Asian leopard cats (Prionailurus bengalensis), and the charcoal coat colouration/pattern in Bengals presents as a possible incomplete melanism. The complete coding region of ASIP was directly sequenced in Asian leopard, domestic and Bengal cats. Twenty-seven variants were identified between domestic and leopard cats and were investigated in Bengals and Savannahs, a hybrid with servals (Leptailurus serval). The leopard cat ASIP haplotype was distinguished from domestic cat by four synonymous and four non-synonymous exonic SNPs, as well as 19 intronic variants, including a 42-bp deletion in intron 4. Fifty-six of 64 reported charcoal cats were compound heterozygotes at ASIP, with leopard cat agouti (A(P) (be) ) and domestic cat non-agouti (a) haplotypes. Twenty-four Bengals had an additional unique haplotype (A2) for exon 2 that was not identified in leopard cats, servals or jungle cats (Felis chaus). The compound heterozygote state suggests the leopard cat allele, in combination with the recessive non-agouti allele, influences Bengal markings, producing a darker, yet not completely melanistic coat. This is the first validation of a leopard cat allele segregating in the Bengal breed and likely affecting their overall pelage phenotype. Genetic testing services need to be aware of the possible segregation of wild felid alleles in all assays performed on hybrid cats.
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Affiliation(s)
- L C Gershony
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California – DavisDavis, CA, 95616, USA
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California – DavisDavis, CA, 95616, USA
| | - M C T Penedo
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California – DavisDavis, CA, 95616, USA
| | - B W Davis
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of HealthBethesda, MD 20892, USA
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M UniversityCollege Station, TX, 77843, USA
| | - W J Murphy
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M UniversityCollege Station, TX, 77843, USA
| | - C R Helps
- Langford Veterinary Services, University of BristolLangford, Bristol, BS40 5DU, UK
| | - L A Lyons
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California – DavisDavis, CA, 95616, USA
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Day K, Song J, Absher D. Targeted sequencing of large genomic regions with CATCH-Seq. PLoS One 2014; 9:e111756. [PMID: 25357200 PMCID: PMC4214737 DOI: 10.1371/journal.pone.0111756] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 09/30/2014] [Indexed: 01/06/2023] Open
Abstract
Current target enrichment systems for large-scale next-generation sequencing typically require synthetic oligonucleotides used as capture reagents to isolate sequences of interest. The majority of target enrichment reagents are focused on gene coding regions or promoters en masse. Here we introduce development of a customizable targeted capture system using biotinylated RNA probe baits transcribed from sheared bacterial artificial chromosome clone templates that enables capture of large, contiguous blocks of the genome for sequencing applications. This clone adapted template capture hybridization sequencing (CATCH-Seq) procedure can be used to capture both coding and non-coding regions of a gene, and resolve the boundaries of copy number variations within a genomic target site. Furthermore, libraries constructed with methylated adapters prior to solution hybridization also enable targeted bisulfite sequencing. We applied CATCH-Seq to diverse targets ranging in size from 125 kb to 3.5 Mb. Our approach provides a simple and cost effective alternative to other capture platforms because of template-based, enzymatic probe synthesis and the lack of oligonucleotide design costs. Given its similarity in procedure, CATCH-Seq can also be performed in parallel with commercial systems.
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Affiliation(s)
- Kenneth Day
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Jun Song
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
- * E-mail:
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