1
|
Subramanian S, Kumar M. The Association between the Abundance of Homozygous Deleterious Variants and the Morbidity of Dog Breeds. BIOLOGY 2024; 13:574. [PMID: 39194512 DOI: 10.3390/biology13080574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 07/26/2024] [Accepted: 07/27/2024] [Indexed: 08/29/2024]
Abstract
It is well known that highly inbred dogs are more prone to diseases than less inbred or outbred dogs. This is because inbreeding increases the load of recessive deleterious variants. Using the genomes of 392 dogs belonging to 83 breeds, we investigated the association between the abundance of homozygous deleterious variants and dog health. We used the number of non-routine veterinary care events for each breed to assess the level of morbidity. Our results revealed a highly significant positive relationship between the number of homozygous deleterious variants located within the runs of homozygosity (RoH) tracts of the breeds and the level of morbidity. The dog breeds with low morbidity had a mean of 87 deleterious SNVs within the RoH, but those with very high morbidity had 187 SNVs. A highly significant correlation was also observed for the loss-of-function (LoF) SNVs within RoH tracts. The dog breeds that required more veterinary care had 2.3 times more homozygous LoF SNVs than those that required less veterinary care (112 vs. 50). The results of this study could be useful for understanding the disease burden on breed dogs and as a guide for dog breeding programs.
Collapse
Affiliation(s)
- Sankar Subramanian
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
- School of Science, Technology, and Engineering, University of the Sunshine Coast, Moreton Bay, QLD 4502, Australia
| | - Manoharan Kumar
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, QLD 4502, Australia
| |
Collapse
|
2
|
Mei X, Wang X, Wu X, Liu G, Chen Y, Zhou S, Shang Y, Liu Z, Yang X, Sha W, Zhang H. Mitochondrial Genomic Evidence of Selective Constraints in Small-Bodied Terrestrial Cetartiodactyla. Animals (Basel) 2024; 14:1434. [PMID: 38791652 PMCID: PMC11117313 DOI: 10.3390/ani14101434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Body size may drive the molecular evolution of mitochondrial genes in response to changes in energy requirements across species of different sizes. In this study, we perform selection pressure analysis and phylogenetic independent contrasts (PIC) to investigate the association between molecular evolution of mitochondrial genome protein-coding genes (mtDNA PCGs) and body size in terrestrial Cetartiodactyla. Employing selection pressure analysis, we observe that the average non-synonymous/synonymous substitution rate ratio (ω) of mtDNA PCGs is significantly reduced in small-bodied species relative to their medium and large counterparts. PIC analysis further confirms that ω values are positively correlated with body size (R2 = 0.162, p = 0.0016). Our results suggest that mtDNA PCGs of small-bodied species experience much stronger purifying selection as they need to maintain a heightened metabolic rate. On the other hand, larger-bodied species may face less stringent selective pressures on their mtDNA PCGs, potentially due to reduced relative energy expenditure per unit mass. Furthermore, we identify several genes that undergo positive selection, possibly linked to species adaptation to specific environments. Therefore, despite purifying selection being the predominant force in the evolution of mtDNA PCGs, positive selection can also occur during the process of adaptive evolution.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Honghai Zhang
- School of Life Science, Qufu Normal University, Qufu 273165, China; (X.M.)
| |
Collapse
|
3
|
Patterson EC, Lall GM, Neumann R, Ottolini B, Batini C, Sacchini F, Foster AP, Wetton JH, Jobling MA. Mitogenome sequences of domestic cats demonstrate lineage expansions and dynamic mutation processes in a mitochondrial minisatellite. BMC Genomics 2023; 24:690. [PMID: 37978434 PMCID: PMC10655372 DOI: 10.1186/s12864-023-09789-1] [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: 06/23/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND As a population genetic tool, mitochondrial DNA is commonly divided into the ~ 1-kb control region (CR), in which single nucleotide variant (SNV) diversity is relatively high, and the coding region, in which selective constraint is greater and diversity lower, but which provides an informative phylogeny. In some species, the CR contains variable tandemly repeated sequences that are understudied due to heteroplasmy. Domestic cats (Felis catus) have a recent origin and therefore traditional CR-based analysis of populations yields only a small number of haplotypes. RESULTS To increase resolution we used Nanopore sequencing to analyse 119 cat mitogenomes via a long-amplicon approach. This greatly improves discrimination (from 15 to 87 distinct haplotypes in our dataset) and defines a phylogeny showing similar starlike topologies within all major clades (haplogroups), likely reflecting post-domestication expansion. We sequenced RS2, a CR tandem array of 80-bp repeat units, placing RS2 array structures within the phylogeny and increasing overall haplotype diversity. Repeat number varies between 3 and 12 (median: 4) with over 30 different repeat unit types differing largely by SNVs. Five SNVs show evidence of independent recurrence within the phylogeny, and seven are involved in at least 11 instances of rapid spread along repeat arrays within haplogroups. CONCLUSIONS In defining mitogenome variation our study provides key information for the forensic genetic analysis of cat hair evidence, and for the first time a phylogenetically informed picture of tandem repeat variation that reveals remarkably dynamic mutation processes at work in the mitochondrion.
Collapse
Affiliation(s)
- Emily C Patterson
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Gurdeep Matharu Lall
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Rita Neumann
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Barbara Ottolini
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
- Present Address: Oxford Nanopore Technologies Plc., Oxford Science Park, Edmund Halley Rd, Oxford, OX4 4DQ, UK
| | - Chiara Batini
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
- Present Address: Department of Population Health Sciences, University of Leicester, Leicester, UK
- Biomedical Research Centre, Leicester National Institute for Health and Care Research, Glenfield Hospital, Leicester, UK
| | - Federico Sacchini
- IDEXX Laboratories Italia S.R.L., Via Guglielmo Silva, 36-20149, Milano, MI, Italy
| | - Aiden P Foster
- Bristol Veterinary School, University of Bristol, Langford House, Langford, BS40 5DU, North Somerset, UK
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK.
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK.
| |
Collapse
|
4
|
Wei Q, Wang X, Dong Y, Shang Y, Sun G, Wu X, Zhao C, Sha W, Yang G, Zhang H. Analysis of the Complete Mitochondrial Genome of Pteronura brasiliensis and Lontra canadensis. Animals (Basel) 2023; 13:3165. [PMID: 37893890 PMCID: PMC10603698 DOI: 10.3390/ani13203165] [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: 07/21/2023] [Revised: 09/25/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023] Open
Abstract
P. brasiliensis and L. canadensis are two otter species, which successfully occupied semi-aquatic habitats and diverged from other Mustelidae. Herein, the full-length mitochondrial genome sequences were constructed for these two otter species for the first time. Comparative mitochondrial genome, selection pressure, and phylogenetic independent contrasts (PICs) analyses were conducted to determine the structure and evolutionary characteristics of their mitochondrial genomes. Phylogenetic analyses were also conducted to confirm these two otter species' phylogenetic position. The results demonstrated that the mitochondrial genome structure of P. brasiliensis and L. canadensis were consistent across Mustelidae. However, selection pressure analyses demonstrated that the evolutionary rates of mitochondrial genome protein-coding genes (PCGs) ND1, ND4, and ND4L were higher in otters than in terrestrial Mustelidae, whereas the evolutionary rates of ND2, ND6, and COX1 were lower in otters. Additionally, PIC analysis demonstrated that the evolutionary rates of ND2, ND4, and ND4L markedly correlated with a niche type. Phylogenetic analysis showed that P. brasiliensis is situated at the base of the evolutionary tree of otters, and then L. canadensis diverged from it. This study suggests a divergent evolutionary pattern of Mustelidae mitochondrial genome PCGs, prompting the otters' adaptation to semi-aquatic habitats.
Collapse
Affiliation(s)
- Qinguo Wei
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.W.); (G.Y.)
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| | - Xibao Wang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| | - Yuehuan Dong
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| | - Yongquan Shang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| | - Guolei Sun
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| | - Xiaoyang Wu
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| | - Chao Zhao
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| | - Weilai Sha
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.W.); (G.Y.)
| | - Honghai Zhang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| |
Collapse
|
5
|
Ballard JWO, Field MA, Edwards RJ, Wilson LAB, Koungoulos LG, Rosen BD, Chernoff B, Dudchenko O, Omer A, Keilwagen J, Skvortsova K, Bogdanovic O, Chan E, Zammit R, Hayes V, Aiden EL. The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology. Gigascience 2023; 12:giad018. [PMID: 36994871 PMCID: PMC10353722 DOI: 10.1093/gigascience/giad018] [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: 09/26/2022] [Revised: 01/13/2023] [Accepted: 02/28/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND One difficulty in testing the hypothesis that the Australasian dingo is a functional intermediate between wild wolves and domesticated breed dogs is that there is no reference specimen. Here we link a high-quality de novo long-read chromosomal assembly with epigenetic footprints and morphology to describe the Alpine dingo female named Cooinda. It was critical to establish an Alpine dingo reference because this ecotype occurs throughout coastal eastern Australia where the first drawings and descriptions were completed. FINDINGS We generated a high-quality chromosome-level reference genome assembly (Canfam_ADS) using a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. Compared to the previously published Desert dingo assembly, there are large structural rearrangements on chromosomes 11, 16, 25, and 26. Phylogenetic analyses of chromosomal data from Cooinda the Alpine dingo and 9 previously published de novo canine assemblies show dingoes are monophyletic and basal to domestic dogs. Network analyses show that the mitochondrial DNA genome clusters within the southeastern lineage, as expected for an Alpine dingo. Comparison of regulatory regions identified 2 differentially methylated regions within glucagon receptor GCGR and histone deacetylase HDAC4 genes that are unmethylated in the Alpine dingo genome but hypermethylated in the Desert dingo. Morphologic data, comprising geometric morphometric assessment of cranial morphology, place dingo Cooinda within population-level variation for Alpine dingoes. Magnetic resonance imaging of brain tissue shows she had a larger cranial capacity than a similar-sized domestic dog. CONCLUSIONS These combined data support the hypothesis that the dingo Cooinda fits the spectrum of genetic and morphologic characteristics typical of the Alpine ecotype. We propose that she be considered the archetype specimen for future research investigating the evolutionary history, morphology, physiology, and ecology of dingoes. The female has been taxidermically prepared and is now at the Australian Museum, Sydney.
Collapse
Affiliation(s)
- J William O Ballard
- School of Biosciences, University of Melbourne, Royal Parade, Parkville, Victoria 3052, Australia
- Department of Environment and Genetics, SABE, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Matt A Field
- Centre for Tropical Bioinformatics and Molecular Biology, College of Public Health, Medical and Veterinary Science, James Cook University, Cairns, Queensland 4870, Australia
- Immunogenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Laura A B Wilson
- School of Archaeology and Anthropology, The Australian National University, Acton, ACT 2600, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Loukas G Koungoulos
- Department of Archaeology, School of Philosophical and Historical Inquiry, the University of Sydney, Sydney, NSW 2006, Australia
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA, Beltsville, MD 20705, USA
| | - Barry Chernoff
- College of the Environment, Departments of Biology, and Earth & Environmental Sciences, Wesleyan University, Middletown, CT 06459, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA
| | - Arina Omer
- Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA
| | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Quedlinburg 06484, Germany
| | - Ksenia Skvortsova
- Developmental Epigenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Ozren Bogdanovic
- Developmental Epigenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Eva Chan
- Developmental Epigenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Statewide Genomics, New South Wales Health Pathology, Newcastle, NSW 2300, Australia
| | - Robert Zammit
- Vineyard Veterinary Hospital,Vineyard, NSW 2765, Australia
| | - Vanessa Hayes
- Developmental Epigenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Charles Perkins Centre, Faculty of Medical Sciences, University of Sydney, Camperdown, NSW 2006, Australia
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| |
Collapse
|
6
|
Sosale MS, Songsasen N, İbiş O, Edwards CW, Figueiró HV, Koepfli KP. The complete mitochondrial genome and phylogenetic characterization of two putative subspecies of golden jackal (Canis aureus cruesemanni and Canis aureus moreotica). Gene 2023; 866:147303. [PMID: 36854348 DOI: 10.1016/j.gene.2023.147303] [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: 11/15/2022] [Revised: 02/07/2023] [Accepted: 02/17/2023] [Indexed: 02/27/2023]
Abstract
The golden jackal (Canis aureus) is a canid species found across southern Eurasia. Several subspecies of this animal have been genetically studied in regions such as Europe, the Middle East, and India. However, one subspecies that lacks current research is the Indochinese jackal (Canis aureus cruesemanni), which is primarily found in Southeast Asia. Using a genome skimming approach, we assembled the first complete mitochondrial genome for an Indochinese jackal from Thailand. To expand the number of available Canis aureus mitogenomes, we also assembled and sequenced the first complete mitochondrial genome of a golden jackal from Turkey, representing the C. a. moreotica subspecies. The mitogenomes contained 37 annotated genes and are 16,729 bps (C. a. cruesemanni) and 16,669 bps (C. a. moreotica) in length. Phylogenetic analysis with 26 additional canid mitogenomes and analyses of a cytochrome b gene-only data set together support the Indochinese jackal as a distinct and early-branching lineage among golden jackals, thereby supporting its recognition as a possible subspecies. These analyses also demonstrate that the golden jackal from Turkey is likely not a distinct lineage due to close genetic relationships with golden jackals from India and Israel.
Collapse
Affiliation(s)
- Medhini S Sosale
- Department of Bioengineering, Volgenau School of Engineering, George Mason University, Fairfax, VA, USA; Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA.
| | - Nucharin Songsasen
- Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, USA
| | - Osman İbiş
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey; Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey; Vectors and Vector-Borne Diseases Implementation and Research Center, Erciyes University, Kayseri, Turkey
| | - Cody W Edwards
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA; Department of Biology, George Mason University, Fairfax, VA, USA
| | - Henrique V Figueiró
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA; Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, USA.
| |
Collapse
|
7
|
Ballard JWO, Field MA, Edwards RJ, Wilson LAB, Koungoulos LG, Rosen BD, Chernoff B, Dudchenko O, Omer A, Keilwagen J, Skvortsova K, Bogdanovic O, Chan E, Zammit R, Hayes V, Aiden EL. The Australasian dingo archetype: De novo chromosome-length genome assembly, DNA methylome, and cranial morphology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525801. [PMID: 36747621 PMCID: PMC9900879 DOI: 10.1101/2023.01.26.525801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Background One difficulty in testing the hypothesis that the Australasian dingo is a functional intermediate between wild wolves and domesticated breed dogs is that there is no reference specimen. Here we link a high-quality de novo long read chromosomal assembly with epigenetic footprints and morphology to describe the Alpine dingo female named Cooinda. It was critical to establish an Alpine dingo reference because this ecotype occurs throughout coastal eastern Australia where the first drawings and descriptions were completed. Findings We generated a high-quality chromosome-level reference genome assembly (Canfam_ADS) using a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. Compared to the previously published Desert dingo assembly, there are large structural rearrangements on Chromosomes 11, 16, 25 and 26. Phylogenetic analyses of chromosomal data from Cooinda the Alpine dingo and nine previously published de novo canine assemblies show dingoes are monophyletic and basal to domestic dogs. Network analyses show that the mtDNA genome clusters within the southeastern lineage, as expected for an Alpine dingo. Comparison of regulatory regions identified two differentially methylated regions within glucagon receptor GCGR and histone deacetylase HDAC4 genes that are unmethylated in the Alpine dingo genome but hypermethylated in the Desert dingo. Morphological data, comprising geometric morphometric assessment of cranial morphology place dingo Cooinda within population-level variation for Alpine dingoes. Magnetic resonance imaging of brain tissue show she had a larger cranial capacity than a similar-sized domestic dog. Conclusions These combined data support the hypothesis that the dingo Cooinda fits the spectrum of genetic and morphological characteristics typical of the Alpine ecotype. We propose that she be considered the archetype specimen for future research investigating the evolutionary history, morphology, physiology, and ecology of dingoes. The female has been taxidermically prepared and is now at the Australian Museum, Sydney.
Collapse
Affiliation(s)
- J William O Ballard
- School of Biosciences, University of Melbourne, Royal Parade, Parkville, Victoria 3052, Australia
- Department of Environment and Genetics, SABE, La Trobe University, Melbourne Victoria 3086, Australia
| | - Matt A Field
- Centre for Tropical Bioinformatics and Molecular Biology, College of Public Health, Medical and Veterinary Science, James Cook University, Cairns, Queensland 4870, Australia
- Immunogenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney NSW 2052, Australia
| | - Laura A B Wilson
- School of Archaeology and Anthropology, The Australian National University, Acton, ACT 2600, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Loukas G Koungoulos
- Department of Archaeology, School of Philosophical and Historical Inquiry, the University of Sydney, Sydney, Australia 2006
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA, Beltsville, MD 20705
| | - Barry Chernoff
- College of the Environment, Departments of Biology, and Earth & Environmental Sciences, Wesleyan University, Middletown, CT 06459, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030 USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA
| | - Arina Omer
- Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA
| | - Jens Keilwagen
- Julius Kühn-Institut, Erwin-Baur-Str. 27 06484 Quedlinburg, Germany
| | | | - Ozren Bogdanovic
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Eva Chan
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Statewide Genomics, New South Wales Health Pathology, 45 Watt St, Newcastle NSW 2300, Australia
| | - Robert Zammit
- Vineyard Veterinary Hospital, 703 Windsor Rd, Vineyard, NSW 2765, Australia
| | - Vanessa Hayes
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Charles Perkins Centre, Faculty of Medical Sciences, University of Sydney, Camperdown, NSW, Australia
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030 USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| |
Collapse
|
8
|
Loss of Mitochondrial Genetic Diversity despite Population Growth: The Legacy of Past Wolf Population Declines. Genes (Basel) 2022; 14:genes14010075. [PMID: 36672816 PMCID: PMC9858670 DOI: 10.3390/genes14010075] [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: 11/18/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/28/2022] Open
Abstract
Gray wolves (Canis lupus) in the Iberian Peninsula declined substantially in both range and population size in the last few centuries due to human persecution and habitat fragmentation. However, unlike many other western European populations, gray wolves never went extinct in Iberia. Since the minimum number was recorded around 1970, their numbers have significantly increased and then stabilized in recent decades. We analyzed mitochondrial genomes from 54 historical specimens of Iberian wolves from across their historical range using ancient DNA methods. We compared historical and current mitochondrial diversity in Iberian wolves at the 5' end of the control region (n = 17 and 27) and the whole mitochondrial genome excluding the control region (n = 19 and 29). Despite an increase in population size since the 1970s, genetic diversity declined. We identified 10 whole mitochondrial DNA haplotypes in 19 historical specimens, whereas only six of them were observed in 29 modern Iberian wolves. Moreover, a haplotype that was restricted to the southern part of the distribution has gone extinct. Our results illustrate a lag between demographic and genetic diversity changes, and show that after severe population declines, genetic diversity can continue to be lost in stable or even expanding populations. This suggests that such populations may be of conservation concern even after their demographic trajectory has been reversed.
Collapse
|
9
|
Bergström A, Stanton DWG, Taron UH, Frantz L, Sinding MHS, Ersmark E, Pfrengle S, Cassatt-Johnstone M, Lebrasseur O, Girdland-Flink L, Fernandes DM, Ollivier M, Speidel L, Gopalakrishnan S, Westbury MV, Ramos-Madrigal J, Feuerborn TR, Reiter E, Gretzinger J, Münzel SC, Swali P, Conard NJ, Carøe C, Haile J, Linderholm A, Androsov S, Barnes I, Baumann C, Benecke N, Bocherens H, Brace S, Carden RF, Drucker DG, Fedorov S, Gasparik M, Germonpré M, Grigoriev S, Groves P, Hertwig ST, Ivanova VV, Janssens L, Jennings RP, Kasparov AK, Kirillova IV, Kurmaniyazov I, Kuzmin YV, Kosintsev PA, Lázničková-Galetová M, Leduc C, Nikolskiy P, Nussbaumer M, O'Drisceoil C, Orlando L, Outram A, Pavlova EY, Perri AR, Pilot M, Pitulko VV, Plotnikov VV, Protopopov AV, Rehazek A, Sablin M, Seguin-Orlando A, Storå J, Verjux C, Zaibert VF, Zazula G, Crombé P, Hansen AJ, Willerslev E, Leonard JA, Götherström A, Pinhasi R, Schuenemann VJ, Hofreiter M, Gilbert MTP, Shapiro B, Larson G, Krause J, Dalén L, Skoglund P. Grey wolf genomic history reveals a dual ancestry of dogs. Nature 2022; 607:313-320. [PMID: 35768506 PMCID: PMC9279150 DOI: 10.1038/s41586-022-04824-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 04/28/2022] [Indexed: 01/01/2023]
Abstract
The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1–8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located. DNA from ancient wolves spanning 100,000 years sheds light on wolves’ evolutionary history and the genomic origin of dogs.
Collapse
Affiliation(s)
- Anders Bergström
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.
| | - David W G Stanton
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden.,School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ulrike H Taron
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Laurent Frantz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.,Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
| | - Mikkel-Holger S Sinding
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.,The Qimmeq Project, University of Greenland, Nuuk, Greenland.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Erik Ersmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Saskia Pfrengle
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Molly Cassatt-Johnstone
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Ophélie Lebrasseur
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Linus Girdland-Flink
- Department of Archaeology, School of Geosciences, University of Aberdeen, Aberdeen, UK.,School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Morgane Ollivier
- University of Rennes, CNRS, ECOBIO (Ecosystèmes, biodiversité, évolution)-UMR 6553, Rennes, France
| | - Leo Speidel
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.,Genetics Institute, University College London, London, UK
| | | | - Michael V Westbury
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.,The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Tatiana R Feuerborn
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,The Qimmeq Project, University of Greenland, Nuuk, Greenland.,Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Joscha Gretzinger
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Max Planck Institute for the Science of Human History, Jena, Germany
| | - Susanne C Münzel
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Pooja Swali
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Nicholas J Conard
- Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Christian Carøe
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - James Haile
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Anna Linderholm
- Centre for Palaeogenetics, Stockholm, Sweden.,The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.,Texas A&M University, College Station, TX, USA.,Department of Geological Sciences, Stockholm University, Stockholm, Sweden
| | | | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Chris Baumann
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.,Department of Geosciences and Geography, Faculty of Science, University of Helsinki, Helsinki, Finland
| | | | - Hervé Bocherens
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.,Biogeology, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Ruth F Carden
- School of Archaeology, University College Dublin, Dublin, Ireland
| | - Dorothée G Drucker
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Sergey Fedorov
- North-Eastern Federal University, Yakutsk, Russian Federation
| | | | | | | | - Pam Groves
- University of Alaska, Fairbanks, AK, USA
| | - Stefan T Hertwig
- Naturhistorisches Museum Bern, Bern, Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | | | | | - Richard P Jennings
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Aleksei K Kasparov
- Institute for the History of Material Culture, Russian Academy of Sciences, St Petersburg, Russian Federation
| | - Irina V Kirillova
- Ice Age Museum, Shidlovskiy National Alliance 'Ice Age', Moscow, Russian Federation
| | - Islam Kurmaniyazov
- Department of Archaeology, Ethnology and Museology, Al-Farabi Kazakh State University, Almaty, Kazakhstan
| | - Yaroslav V Kuzmin
- Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | | | | | | | - Pavel Nikolskiy
- Geological Institute, Russian Academy of Sciences, Moscow, Russian Federation
| | | | - Cóilín O'Drisceoil
- National Monuments Service, Department of Housing, Local Government and Heritage, Dublin, Ireland
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR 5288, CNRS, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - Alan Outram
- Department of Archaeology, University of Exeter, Exeter, UK
| | - Elena Y Pavlova
- Arctic & Antarctic Research Institute, St Petersburg, Russian Federation
| | - Angela R Perri
- PaleoWest, Henderson, NV, USA.,Department of Anthropology, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Małgorzata Pilot
- Museum & Institute of Zoology, Polish Academy of Sciences, Gdańsk, Poland
| | - Vladimir V Pitulko
- Institute for the History of Material Culture, Russian Academy of Sciences, St Petersburg, Russian Federation
| | | | | | | | - Mikhail Sablin
- Zoological Institute of the Russian Academy of Sciences, St. Petersburg, Russian Federation
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR 5288, CNRS, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - Jan Storå
- Stockholm University, Stockholm, Sweden
| | | | - Victor F Zaibert
- Institute of Archaeology and Steppe Civilizations, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Grant Zazula
- Yukon Palaeontology Program, Whitehorse, Yukon Territories, Canada.,Collections and Research, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | | | - Anders J Hansen
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Eske Willerslev
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden.,Stockholm University, Stockholm, Sweden
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Verena J Schuenemann
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland.,Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - M Thomas P Gilbert
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,University Museum, NTNU, Trondheim, Norway
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Pontus Skoglund
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.
| |
Collapse
|
10
|
Recurrent erosion of COA1/MITRAC15 exemplifies conditional gene dispensability in oxidative phosphorylation. Sci Rep 2021; 11:24437. [PMID: 34952909 PMCID: PMC8709867 DOI: 10.1038/s41598-021-04077-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 12/15/2021] [Indexed: 11/08/2022] Open
Abstract
Skeletal muscle fibers rely upon either oxidative phosphorylation or the glycolytic pathway with much less reliance on oxidative phosphorylation to achieve muscular contractions that power mechanical movements. Species with energy-intensive adaptive traits that require sudden bursts of energy have a greater dependency on glycolytic fibers. Glycolytic fibers have decreased reliance on OXPHOS and lower mitochondrial content compared to oxidative fibers. Hence, we hypothesized that gene loss might have occurred within the OXPHOS pathway in lineages that largely depend on glycolytic fibers. The protein encoded by the COA1/MITRAC15 gene with conserved orthologs found in budding yeast to humans promotes mitochondrial translation. We show that gene disrupting mutations have accumulated within the COA1 gene in the cheetah, several species of galliform birds, and rodents. The genomic region containing COA1 is a well-established evolutionary breakpoint region in mammals. Careful inspection of genome assemblies of closely related species of rodents and marsupials suggests two independent COA1 gene loss events co-occurring with chromosomal rearrangements. Besides recurrent gene loss events, we document changes in COA1 exon structure in primates and felids. The detailed evolutionary history presented in this study reveals the intricate link between skeletal muscle fiber composition and the occasional dispensability of the chaperone-like role of the COA1 gene.
Collapse
|
11
|
Zhang L, Sun K, Csorba G, Hughes AC, Jin L, Xiao Y, Feng J. Complete mitochondrial genomes reveal robust phylogenetic signals and evidence of positive selection in horseshoe bats. BMC Ecol Evol 2021; 21:199. [PMID: 34732135 PMCID: PMC8565063 DOI: 10.1186/s12862-021-01926-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 10/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In genus Rhinolophus, species in the Rhinolophus philippinensis and R. macrotis groups are unique because the horseshoe bats in these group have relatively low echolocation frequencies and flight speeds compared with other horseshoe bats with similar body size. The different characteristics among bat species suggest particular evolutionary processes may have occurred in this genus. To study the adaptive evidence in the mitochondrial genomes (mitogenomes) of rhinolophids, especially the mitogenomes of the species with low echolocation frequencies, we sequenced eight mitogenomes and used them for comparative studies of molecular phylogeny and adaptive evolution. RESULTS Phylogenetic analysis using whole mitogenome sequences produced robust results and provided phylogenetic signals that were better than those obtained using single genes. The results supported the recent establishment of the separate macrotis group. The signals of adaptive evolution discovered in the Rhinolophus species were tested for some of the codons in two genes (ND2 and ND6) that encode NADH dehydrogenases in oxidative phosphorylation system complex I. These genes have a background of widespread purifying selection. Signals of relaxed purifying selection and positive selection were found in ND2 and ND6, respectively, based on codon models and physicochemical profiles of amino acid replacements. However, no pronounced overlap was found for non-synonymous sites in the mitogenomes of all the species with low echolocation frequencies. A signal of positive selection for ND5 was found in the branch-site model when R. philippinensis was set as the foreground branch. CONCLUSIONS The mitogenomes provided robust phylogenetic signals that were much more informative than the signals obtained using single mitochondrial genes. Two mitochondrial genes that encoding proteins in the oxidative phosphorylation system showed some evidence of adaptive evolution in genus Rhinolophus and the positive selection signals were tested for ND5 in R. philippinensis. These results indicate that mitochondrial protein-coding genes were targets of adaptive evolution during the evolution of Rhinolophus species, which might have contributed to a diverse range of acoustic adaptations in this genus.
Collapse
Affiliation(s)
- Lin Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China.
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China.
| | - Gábor Csorba
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
| | - Alice Catherine Hughes
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla County, 666303, Yunnan, China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China
| | - Yanhong Xiao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China.
- College of Life Science, Jilin Agricultural University, Changchun, 130118, China.
| |
Collapse
|
12
|
Axelsson E, Ljungvall I, Bhoumik P, Conn LB, Muren E, Ohlsson Å, Olsen LH, Engdahl K, Hagman R, Hanson J, Kryvokhyzha D, Pettersson M, Grenet O, Moggs J, Del Rio-Espinola A, Epe C, Taillon B, Tawari N, Mane S, Hawkins T, Hedhammar Å, Gruet P, Häggström J, Lindblad-Toh K. The genetic consequences of dog breed formation-Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels. PLoS Genet 2021; 17:e1009726. [PMID: 34473707 PMCID: PMC8412370 DOI: 10.1371/journal.pgen.1009726] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
Selective breeding for desirable traits in strictly controlled populations has generated an extraordinary diversity in canine morphology and behaviour, but has also led to loss of genetic variation and random entrapment of disease alleles. As a consequence, specific diseases are now prevalent in certain breeds, but whether the recent breeding practice led to an overall increase in genetic load remains unclear. Here we generate whole genome sequencing (WGS) data from 20 dogs per breed from eight breeds and document a ~10% rise in the number of derived alleles per genome at evolutionarily conserved sites in the heavily bottlenecked cavalier King Charles spaniel breed (cKCs) relative to in most breeds studied here. Our finding represents the first clear indication of a relative increase in levels of deleterious genetic variation in a specific breed, arguing that recent breeding practices probably were associated with an accumulation of genetic load in dogs. We then use the WGS data to identify candidate risk alleles for the most common cause for veterinary care in cKCs–the heart disease myxomatous mitral valve disease (MMVD). We verify a potential link to MMVD for candidate variants near the heart specific NEBL gene in a dachshund population and show that two of the NEBL candidate variants have regulatory potential in heart-derived cell lines and are associated with reduced NEBL isoform nebulette expression in papillary muscle (but not in mitral valve, nor in left ventricular wall). Alleles linked to reduced nebulette expression may hence predispose cKCs and other breeds to MMVD via loss of papillary muscle integrity. As a consequence of selective breeding, specific disease-causing mutations have become more frequent in certain dog breeds. Whether the breeding practice also resulted in a general increase in the overall number of disease-causing mutations per dog genome is however not clear. To address this question, we compare the amount of harmful, potentially disease-causing, mutations in dogs from eight common breeds that have experienced varying degrees of intense selective breeding. We find that individuals belonging to the breed affected by the most intense breeding—cavalier King Charles spaniel (cKCs)—carry more harmful variants than other breeds, indicating that past breeding practices may have increased the overall levels of harmful genetic variation in dogs. The most common disease in cKCs is myxomatous mitral valve disease (MMVD). To identify variants linked to this disease we next characterize mutations that are common in cKCs, but rare in other breeds, and then investigate if these mutations can predict MMVD in dachshunds. We find that variants that regulate the expression of the gene NEBL in papillary muscles may increase the risk of the disease, indicating that loss of papillary muscle integrity could contribute to the development of MMVD.
Collapse
Affiliation(s)
- Erik Axelsson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- * E-mail:
| | - Ingrid Ljungvall
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Priyasma Bhoumik
- Translational Medicine, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Laura Bas Conn
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Eva Muren
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Åsa Ohlsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Lisbeth Høier Olsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Karolina Engdahl
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ragnvi Hagman
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jeanette Hanson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Dmytro Kryvokhyzha
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mats Pettersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Olivier Grenet
- Translational Medicine, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Jonathan Moggs
- Translational Medicine, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Christian Epe
- Elanco Animal Health, Greenfield, Indiana, United States of America
| | - Bruce Taillon
- Elanco Animal Health, Greenfield, Indiana, United States of America
| | - Nilesh Tawari
- Elanco Animal Health, Greenfield, Indiana, United States of America
| | - Shrinivas Mane
- Elanco Animal Health, Greenfield, Indiana, United States of America
| | - Troy Hawkins
- Elanco Animal Health, Greenfield, Indiana, United States of America
| | - Åke Hedhammar
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Jens Häggström
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| |
Collapse
|
13
|
Núñez-León D, Cordero GA, Schlindwein X, Jensen P, Stoeckli E, Sánchez-Villagra MR, Werneburg I. Shifts in growth, but not differentiation, foreshadow the formation of exaggerated forms under chicken domestication. Proc Biol Sci 2021; 288:20210392. [PMID: 34130497 DOI: 10.1098/rspb.2021.0392] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Domestication provides an outstanding opportunity for biologists to explore the underpinnings of organismal diversification. In domesticated animals, selective breeding for exaggerated traits is expected to override genetic correlations that normally modulate phenotypic variation in nature. Whether this strong directional selection affects the sequence of tightly synchronized events by which organisms arise (ontogeny) is often overlooked. To address this concern, we compared the ontogeny of the red junglefowl (RJF) (Gallus gallus) to four conspecific lineages that underwent selection for traits of economic or ornamental value to humans. Trait differentiation sequences in embryos of these chicken breeds generally resembled the representative ancestral condition in the RJF, thus revealing that early ontogeny remains highly canalized even during evolution under domestication. This key finding substantiates that the genetic cost of domestication does not necessarily compromise early ontogenetic steps that ensure the production of viable offspring. Instead, disproportionate beak and limb growth (allometry) towards the end of ontogeny better explained phenotypes linked to intense selection for industrial-scale production over the last 100 years. Illuminating the spatial and temporal specificity of development is foundational to the enhancement of chicken breeds, as well as to ongoing research on the origins of phenotypic variation in wild avian species.
Collapse
Affiliation(s)
- Daniel Núñez-León
- Paläontologisches Institut und Museum, Universität Zürich, Karl Schmid-Strasse 4, 8006, Zürich, Switzerland
| | - Gerardo A Cordero
- Senckenberg Centre for Human Evolution and Palaeoenvironment (HEP) an der Eberhard Karls, Universität Tübingen, Tübingen, Germany.,Fachbereich Geowissenschaften, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Xenia Schlindwein
- Senckenberg Centre for Human Evolution and Palaeoenvironment (HEP) an der Eberhard Karls, Universität Tübingen, Tübingen, Germany.,Fachbereich Geowissenschaften, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Per Jensen
- IFM Biologi, AVIAN Behavioural Genomics and Physiology group, Linköping University, SE-58183 Linköping, Sweden
| | - Esther Stoeckli
- Department of Molecular Life Sciences, Universität Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Marcelo R Sánchez-Villagra
- Paläontologisches Institut und Museum, Universität Zürich, Karl Schmid-Strasse 4, 8006, Zürich, Switzerland
| | - Ingmar Werneburg
- Senckenberg Centre for Human Evolution and Palaeoenvironment (HEP) an der Eberhard Karls, Universität Tübingen, Tübingen, Germany.,Fachbereich Geowissenschaften, Eberhard Karls Universität Tübingen, Tübingen, Germany
| |
Collapse
|
14
|
Taron UH, Paijmans JLA, Barlow A, Preick M, Iyengar A, Drăgușin V, Vasile Ș, Marciszak A, Roblíčková M, Hofreiter M. Ancient DNA from the Asiatic Wild Dog ( Cuon alpinus) from Europe. Genes (Basel) 2021; 12:144. [PMID: 33499169 PMCID: PMC7911384 DOI: 10.3390/genes12020144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 01/11/2023] Open
Abstract
The Asiatic wild dog (Cuon alpinus), restricted today largely to South and Southeast Asia, was widespread throughout Eurasia and even reached North America during the Pleistocene. Like many other species, it suffered from a huge range loss towards the end of the Pleistocene and went extinct in most of its former distribution. The fossil record of the dhole is scattered and the identification of fossils can be complicated by an overlap in size and a high morphological similarity between dholes and other canid species. We generated almost complete mitochondrial genomes for six putative dhole fossils from Europe. By using three lines of evidence, i.e., the number of reads mapping to various canid mitochondrial genomes, the evaluation and quantification of the mapping evenness along the reference genomes and phylogenetic analysis, we were able to identify two out of six samples as dhole, whereas four samples represent wolf fossils. This highlights the contribution genetic data can make when trying to identify the species affiliation of fossil specimens. The ancient dhole sequences are highly divergent when compared to modern dhole sequences, but the scarcity of dhole data for comparison impedes a more extensive analysis.
Collapse
Affiliation(s)
- Ulrike H. Taron
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany; (J.L.A.P.); (A.B.); (M.P.); (M.H.)
| | - Johanna L. A. Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany; (J.L.A.P.); (A.B.); (M.P.); (M.H.)
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany; (J.L.A.P.); (A.B.); (M.P.); (M.H.)
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Michaela Preick
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany; (J.L.A.P.); (A.B.); (M.P.); (M.H.)
| | - Arati Iyengar
- Department of Biological Sciences, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA;
| | - Virgil Drăgușin
- Emil Racoviţă Institute of Speleology, Romanian Academy, 31 Frumoasă Street, 010986 Bucharest, Romania;
- Research Institute of the University of Bucharest, Earth, Environmental and Life Sciences Division, Panduri 90–92, 050663 Bucharest, Romania
| | - Ștefan Vasile
- Department of Geology, Faculty of Geology and Geophysics, University of Bucharest, 1 Nicolae Bălcescu Avenue, 010041 Bucharest, Romania;
| | - Adrian Marciszak
- Department of Paleozoology, Faculty of Biological Sciences, University of Wrocław, Sienkiewicza 21, 50-335 Wrocław, Poland;
| | - Martina Roblíčková
- Moravian Museum, Anthropos Institute, Zelný trh 6, 65937 Brno, Czech Republic;
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany; (J.L.A.P.); (A.B.); (M.P.); (M.H.)
| |
Collapse
|
15
|
He W, Chen C, Xiang K, Wang J, Zheng P, Tembrock LR, Jin D, Wu Z. The History and Diversity of Rice Domestication as Resolved From 1464 Complete Plastid Genomes. FRONTIERS IN PLANT SCIENCE 2021; 12:781793. [PMID: 34868182 PMCID: PMC8637288 DOI: 10.3389/fpls.2021.781793] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/27/2021] [Indexed: 05/19/2023]
Abstract
The plastid is an essential organelle in autotrophic plant cells, descending from free-living cyanobacteria and acquired by early eukaryotic cells through endosymbiosis roughly one billion years ago. It contained a streamlined genome (plastome) that is uniparentally inherited and non-recombinant, which makes it an ideal tool for resolving the origin and diversity of plant species and populations. In the present study, a large dataset was amassed by de novo assembling plastomes from 295 common wild rice (Oryza rufipogon Griff.) and 1135 Asian cultivated rice (Oryza sativa L.) accessions, supplemented with 34 plastomes from other Oryza species. From this dataset, the phylogenetic relationships and biogeographic history of O. rufipogon and O. sativa were reconstructed. Our results revealed two major maternal lineages across the two species, which further diverged into nine well supported genetic clusters. Among them, the Or-wj-I/II/III and Or-wi-I/II genetic clusters were shared with cultivated (percentage for each cluster ranging 54.9%∼99.3%) and wild rice accessions. Molecular dating, phylogeographic analyses and reconstruction of population historical dynamics indicated an earlier origin of the Or-wj-I/II genetic clusters from East Asian with at least two population expansions, and later origins of other genetic clusters from multiple regions with one or more population expansions. These results supported a single origin of japonica rice (mainly in Or-wj-I/II) and multiple origins of indica rice (in all five clusters) for the history of rice domestication. The massive plastomic data set presented here provides an important resource for understanding the history and evolution of rice domestication as well as a genomic resources for use in future breeding and conservation efforts.
Collapse
Affiliation(s)
- Wenchuang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Caijin Chen
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Kunli Xiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, China
| | - Ping Zheng
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Luke R. Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
- Luke R. Tembrock,
| | - Deming Jin
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Deming Jin,
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- *Correspondence: Zhiqiang Wu,
| |
Collapse
|
16
|
Bergström A, Frantz L, Schmidt R, Ersmark E, Lebrasseur O, Girdland-Flink L, Lin AT, Storå J, Sjögren KG, Anthony D, Antipina E, Amiri S, Bar-Oz G, Bazaliiskii VI, Bulatović J, Brown D, Carmagnini A, Davy T, Fedorov S, Fiore I, Fulton D, Germonpré M, Haile J, Irving-Pease EK, Jamieson A, Janssens L, Kirillova I, Horwitz LK, Kuzmanovic-Cvetković J, Kuzmin Y, Losey RJ, Dizdar DL, Mashkour M, Novak M, Onar V, Orton D, Pasarić M, Radivojević M, Rajković D, Roberts B, Ryan H, Sablin M, Shidlovskiy F, Stojanović I, Tagliacozzo A, Trantalidou K, Ullén I, Villaluenga A, Wapnish P, Dobney K, Götherström A, Linderholm A, Dalén L, Pinhasi R, Larson G, Skoglund P. Origins and genetic legacy of prehistoric dogs. Science 2020; 370:557-564. [PMID: 33122379 PMCID: PMC7116352 DOI: 10.1126/science.aba9572] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 09/10/2020] [Indexed: 12/11/2022]
Abstract
Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry.
Collapse
Affiliation(s)
- Anders Bergström
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.
| | - Laurent Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
| | - Ryan Schmidt
- School of Archaeology and Earth Institute, University College Dublin, Dublin, Ireland
- CIBIO-InBIO, University of Porto, Campus de Vairão, Portugal
| | - Erik Ersmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Svante Arrhenius väg 18C, Stockholm, Sweden
| | - Ophelie Lebrasseur
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
| | - Linus Girdland-Flink
- Department of Archaeology, University of Aberdeen, Aberdeen, UK
- Liverpool John Moores University, Liverpool, UK
| | - Audrey T Lin
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Jan Storå
- Stockholm University, Stockholm, Sweden
| | | | - David Anthony
- Hartwick College, Oneonta, NY, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Ekaterina Antipina
- Institute of Archaeology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Sarieh Amiri
- Bioarchaeology Laboratory, Central Laboratory, University of Tehran, Tehran, Iran
| | | | | | | | | | - Alberto Carmagnini
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Tom Davy
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Sergey Fedorov
- North-Eastern Federal University, Yakutsk, Russian Federation
| | - Ivana Fiore
- Bioarchaeology Service, Museo delle Civiltà, Rome, Italy
- Environmental and Evolutionary Biology Doctoral Program, Sapienza University of Rome, Rome, Italy
| | | | | | - James Haile
- University of Copenhagen, Copenhagen, Denmark
| | - Evan K Irving-Pease
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Lundbeck GeoGenetics Centre, The Globe Institute, Copenhagen, Denmark
| | - Alexandra Jamieson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | | | | | | | | | - Yaroslav Kuzmin
- Sobolev Institute of Geology and Mineralogy of the Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russian Federation
- Tomsk State University, Tomsk, Russian Federation
| | | | | | - Marjan Mashkour
- Bioarchaeology Laboratory, Central Laboratory, University of Tehran, Tehran, Iran
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Paris, France
| | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
| | - Vedat Onar
- Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | | | - Maja Pasarić
- Institute of Ethnology and Folklore Research, Zagreb, Croatia
| | | | | | | | - Hannah Ryan
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Mikhail Sablin
- Zoological Institute of the Russian Academy of Sciences, Saint Petersburg, Russian Federation
| | | | | | | | - Katerina Trantalidou
- Hellenic Ministry of Culture & Sports, Athens, Greece
- University of Thessaly, Argonauton & Philellinon, Volos, Greece
| | - Inga Ullén
- National Historical Museums, Stockholm, Sweden
| | - Aritza Villaluenga
- Consolidated Research Group on Prehistory (IT-1223-19), University of the Basque Country (UPV-EHU), Vitoria-Gasteiz, Spain
| | - Paula Wapnish
- Pennsylvania State University, University Park, PA, USA
| | - Keith Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
- Department of Archaeology, University of Aberdeen, Aberdeen, UK
- Department of Archaeology, Simon Fraser University, Burnaby, BC, Canada
- School of Philosophical and Historical Inquiry, Faculty of Arts and Social Sciences, University of Sydney, Sydney, NSW, Australia
| | - Anders Götherström
- Centre for Palaeogenetics, Svante Arrhenius väg 18C, Stockholm, Sweden
- Stockholm University, Stockholm, Sweden
| | | | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Svante Arrhenius väg 18C, Stockholm, Sweden
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.
| | - Pontus Skoglund
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.
| |
Collapse
|
17
|
Brassard C, Merlin M, Guintard C, Monchâtre-Leroy E, Barrat J, Bausmayer N, Bausmayer S, Bausmayer A, Beyer M, Varlet A, Houssin C, Callou C, Cornette R, Herrel A. Bite force and its relationship to jaw shape in domestic dogs. J Exp Biol 2020; 223:jeb224352. [PMID: 32587065 DOI: 10.1242/jeb.224352] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/18/2020] [Indexed: 08/26/2023]
Abstract
Previous studies based on two-dimensional methods have suggested that the great morphological variability of cranial shape in domestic dogs has impacted bite performance. Here, we used a three-dimensional biomechanical model based on dissection data to estimate the bite force of 47 dogs of various breeds at several bite points and gape angles. In vivo bite force for three Belgian shepherd dogs was used to validate our model. We then used three-dimensional geometric morphometrics to investigate the drivers of bite force variation and to describe the relationships between the overall shape of the jaws and bite force. The model output shows that bite force is rather variable in dogs and that dogs bite harder on the molar teeth and at lower gape angles. Half of the bite force is determined by the temporal muscle. Bite force also increased with size, and brachycephalic dogs showed higher bite forces for their size than mesocephalic dogs. We obtained significant covariation between the shape of the upper or lower jaw and absolute or residual bite force. Our results demonstrate that domestication has not resulted in a disruption of the functional links in the jaw system in dogs and that mandible shape is a good predictor of bite force.
Collapse
Affiliation(s)
- Colline Brassard
- Mécanismes Adaptatifs et Evolution (MECADEV), Muséum National d'Histoire Naturelle, CNRS, 55 rue Buffon, 75005 Paris, France
- Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), Muséum National d'Histoire Naturelle, CNRS, CP55, 57 rue Cuvier, 75005 Paris, France
| | - Marilaine Merlin
- Mécanismes Adaptatifs et Evolution (MECADEV), Muséum National d'Histoire Naturelle, CNRS, 55 rue Buffon, 75005 Paris, France
| | - Claude Guintard
- ANSES, Laboratoire de la Rage et de la Faune Sauvage, Station Expérimentale d'Atton, CS 40009 54220 Malzéville, France
- Laboratoire d'Anatomie Comparée, Ecole Nationale Vétérinaire, de l'Agroalimentaire et de l'Alimentation, Nantes Atlantique - ONIRIS, Nantes Cedex 03, France
| | - Elodie Monchâtre-Leroy
- GEROM, UPRES EA 4658, LABCOM ANR NEXTBONE, Faculté de Santé de l'Université d'Angers, 49933 Angers Cedex, France
| | - Jacques Barrat
- GEROM, UPRES EA 4658, LABCOM ANR NEXTBONE, Faculté de Santé de l'Université d'Angers, 49933 Angers Cedex, France
| | - Nathalie Bausmayer
- Club de Chiens de Défense de Beauvais, avenue Jean Rostand, 60 000 Beauvais, France
- Société Centrale Canine, 155 Avenue Jean Jaurès, 93300 Aubervilliers, France
| | - Stéphane Bausmayer
- Club de Chiens de Défense de Beauvais, avenue Jean Rostand, 60 000 Beauvais, France
- Société Centrale Canine, 155 Avenue Jean Jaurès, 93300 Aubervilliers, France
| | - Adrien Bausmayer
- Club de Chiens de Défense de Beauvais, avenue Jean Rostand, 60 000 Beauvais, France
- Société Centrale Canine, 155 Avenue Jean Jaurès, 93300 Aubervilliers, France
| | - Michel Beyer
- Club de Chiens de Défense de Beauvais, avenue Jean Rostand, 60 000 Beauvais, France
- Société Centrale Canine, 155 Avenue Jean Jaurès, 93300 Aubervilliers, France
| | - André Varlet
- Société Centrale Canine, 155 Avenue Jean Jaurès, 93300 Aubervilliers, France
| | - Céline Houssin
- Institut de Systématique, Evolution, Biodiversité (ISYEB), CNRS, Muséum National d'Histoire Naturelle, Sorbonne Université, Ecole Pratique des Hautes Etudes, Université des Antilles, CNRS, CP 50, 57 rue Cuvier, 75005 Paris, France
| | - Cécile Callou
- Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), Muséum National d'Histoire Naturelle, CNRS, CP55, 57 rue Cuvier, 75005 Paris, France
| | - Raphaël Cornette
- Institut de Systématique, Evolution, Biodiversité (ISYEB), CNRS, Muséum National d'Histoire Naturelle, Sorbonne Université, Ecole Pratique des Hautes Etudes, Université des Antilles, CNRS, CP 50, 57 rue Cuvier, 75005 Paris, France
| | - Anthony Herrel
- Mécanismes Adaptatifs et Evolution (MECADEV), Muséum National d'Histoire Naturelle, CNRS, 55 rue Buffon, 75005 Paris, France
| |
Collapse
|
18
|
Amiri Ghanatsaman Z, Wang GD, Asadollahpour Nanaei H, Asadi Fozi M, Peng MS, Esmailizadeh A, Zhang YP. Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication. BMC Genomics 2020; 21:207. [PMID: 32131720 PMCID: PMC7057629 DOI: 10.1186/s12864-020-6619-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 02/25/2020] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and three dogs from Iran which covers the eastern part of the Fertile Crescent located in Southwest Asia where the independent domestication of most of the plants and animals has been documented and also high haplotype sharing between wolves and dog breeds has been reported. RESULTS Higher diversity was found within the wolf genome compared with the dog genome. A total number of 12.45 million SNPs were detected in all individuals (10.45 and 7.82 million SNPs were identified for all the studied wolves and dogs, respectively) and a total number of 3.49 million small Indels were detected in all individuals (3.11 and 2.24 million small Indels were identified for all the studied wolves and dogs, respectively). A total of 10,571 copy number variation regions (CNVRs) were detected across the 6 individual genomes, covering 154.65 Mb, or 6.41%, of the reference genome (canFam3.1). Further analysis showed that the distribution of deleterious variants in the dog genome is higher than the wolf genome. Also, genomic annotation results from intron and intergenic regions showed that the proportion of variations in the wolf genome is higher than that in the dog genome, while the proportion of the coding sequences and 3'-UTR in the dog genome is higher than that in the wolf genome. The genes related to the olfactory and immune systems were enriched in the set of the structural variants (SVs) identified in this work. CONCLUSIONS Our results showed more deleterious mutations and coding sequence variants in the domestic dog genome than those in wolf genome. By providing the first Iranian dog and wolf variome map, our findings contribute to understanding the genetic architecture of the dog domestication.
Collapse
Affiliation(s)
- Zeinab Amiri Ghanatsaman
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
- Yong Researchers Society, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China
| | - Hojjat Asadollahpour Nanaei
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
- Yong Researchers Society, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Masood Asadi Fozi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China.
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China.
| |
Collapse
|
19
|
Development of a mitochondrial DNA marker that distinguishes domestic dogs from Washington state gray wolves. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01130-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
20
|
Thomas F, Giraudeau M, Dheilly NM, Gouzerh F, Boutry J, Beckmann C, Biro PA, Hamede R, Abadie J, Labrut S, Bieuville M, Misse D, Bramwell G, Schultz A, Le Loc'h G, Vincze O, Roche B, Renaud F, Russell T, Ujvari B. Rare and unique adaptations to cancer in domesticated species: An untapped resource? Evol Appl 2020. [DOI: 10.1111/eva.12920] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Frédéric Thomas
- CREECUMR IRD 224‐CNRS 5290‐Université de Montpellier Montpellier France
| | - Mathieu Giraudeau
- CREECUMR IRD 224‐CNRS 5290‐Université de Montpellier Montpellier France
| | - Nolwenn M. Dheilly
- School of Marine and Atmospheric Sciences Stony Brook University Stony Brook NY USA
| | - Flora Gouzerh
- CREECUMR IRD 224‐CNRS 5290‐Université de Montpellier Montpellier France
| | - Justine Boutry
- CREECUMR IRD 224‐CNRS 5290‐Université de Montpellier Montpellier France
| | - Christa Beckmann
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Waurn Ponds VIC Australia
- School of Science Western Sydney UniversityParramatta NSW Australia
| | - Peter A. Biro
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Waurn Ponds VIC Australia
| | - Rodrigo Hamede
- School of Natural Sciences University of Tasmania Hobart TAS Australia
| | | | | | - Margaux Bieuville
- CREECUMR IRD 224‐CNRS 5290‐Université de Montpellier Montpellier France
| | - Dorothée Misse
- CREECUMR IRD 224‐CNRS 5290‐Université de Montpellier Montpellier France
| | - Georgina Bramwell
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Waurn Ponds VIC Australia
| | - Aaron Schultz
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Waurn Ponds VIC Australia
| | - Guillaume Le Loc'h
- Clinique des NAC et de la Faune Sauvage, UMR IHAP École Nationale Vétérinaire de Toulouse Toulouse France
| | - Orsolya Vincze
- Hungarian Department of Biology and Ecology Evolutionary Ecology Group Babeş‐Bolyai University Cluj‐Napoca Romania
- Department of Tisza Research MTA Centre for Ecological Research‐DRI Debrecen Hungary
| | - Benjamin Roche
- CREECUMR IRD 224‐CNRS 5290‐Université de Montpellier Montpellier France
- Unité mixte Internationale de Modélisation Mathématique et Informatique des Systèmes Complexes UMI IRD/Sorbonne UniversitéUMMISCO Bondy France
| | - François Renaud
- CREECUMR IRD 224‐CNRS 5290‐Université de Montpellier Montpellier France
| | - Tracey Russell
- School of Life and Environmental Sciences The University of Sydney Sydney NSW Australia
| | - Beata Ujvari
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Waurn Ponds VIC Australia
- School of Natural Sciences University of Tasmania Hobart TAS Australia
| |
Collapse
|
21
|
Wang Q, Jia Y, Wang Y, Jiang Z, Zhou X, Zhang Z, Nie C, Li J, Yang N, Qu L. Evolution of cis- and trans-regulatory divergence in the chicken genome between two contrasting breeds analyzed using three tissue types at one-day-old. BMC Genomics 2019; 20:933. [PMID: 31805870 PMCID: PMC6896592 DOI: 10.1186/s12864-019-6342-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 11/27/2019] [Indexed: 11/10/2022] Open
Abstract
Background Gene expression variation is a key underlying factor influencing phenotypic variation, and can occur via cis- or trans-regulation. To understand the role of cis- and trans-regulatory variation on population divergence in chicken, we developed reciprocal crosses of two chicken breeds, White Leghorn and Cornish Game, which exhibit major differences in body size and reproductive traits, and used them to determine the degree of cis versus trans variation in the brain, liver, and muscle tissue of male and female 1-day-old specimens. Results We provided an overview of how transcriptomes are regulated in hybrid progenies of two contrasting breeds based on allele specific expression analysis. Compared with cis-regulatory divergence, trans-acting genes were more extensive in the chicken genome. In addition, considerable compensatory cis- and trans-regulatory changes exist in the chicken genome. Most importantly, stronger purifying selection was observed on genes regulated by trans-variations than in genes regulated by the cis elements. Conclusions We present a pipeline to explore allele-specific expression in hybrid progenies of inbred lines without a specific reference genome. Our research is the first study to describe the regulatory divergence between two contrasting breeds. The results suggest that artificial selection associated with domestication in chicken could have acted more on trans-regulatory divergence than on cis-regulatory divergence.
Collapse
Affiliation(s)
- Qiong Wang
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.,Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Yaxiong Jia
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan Wang
- Department of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Zhihua Jiang
- Department of Animal Sciences, Center for Reproductive Biology, Veterinary and Biomedical Research Building, Washington State University, Pullman, USA
| | - Xiang Zhou
- College of Animal Sciences and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zebin Zhang
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Changsheng Nie
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Junying Li
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ning Yang
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lujiang Qu
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
| |
Collapse
|
22
|
The selective constraints of ecological specialization in mustelidae on mitochondrial genomes. MAMMAL RES 2019. [DOI: 10.1007/s13364-019-00461-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
23
|
Reale S, Randi E, Cumbo V, Sammarco I, Bonanno F, Spinnato A, Seminara S. Biodiversity lost: The phylogenetic relationships of a complete mitochondrial DNA genome sequenced from the extinct wolf population of Sicily. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2019.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
24
|
Ruiz-García M, Jaramillo MF, Shostell JM. Mitochondrial phylogeography of kinkajous (Procyonidae, Carnivora): maybe not a single ESU. J Mammal 2019. [DOI: 10.1093/jmammal/gyz109] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
AbstractKnowledge of how a species is divided into different genetic units, and the structure among these units, is fundamental to the protection of biodiversity. Procyonidae was one of the families in the Order Carnivora with more success in the colonization of South America. The most divergent species in this family is the kinkajou (Potos flavus). However, knowledge of the genetics and evolution of this species is scarce. We analyzed five mitochondrial genes within 129 individuals of P. flavus from seven Neotropical countries (Mexico, Guatemala, Honduras, Colombia, Ecuador, Peru, and Bolivia). We detected eight different populations or haplogroups, although only three had highly significant bootstrap values (southern Mexico and Central America; northern Peruvian, Ecuadorian, and Colombian Amazon; and north-central Andes and the southern Amazon in Peru). Some analyses showed that the ancestor of the southern Mexico–Central America haplogroup was the first to appear. The youngest haplogroups were those at the most southern area analyzed in Peru and Bolivia. A “borrowed molecular clock” estimated the initial diversification to have occurred around 9.6 million years ago (MYA). All the spatial genetic analyses detected a very strong spatial structure with significant genetic patches (average diameter around 400–500 km) and a clinal isolation by distance among them. The overall sample and all of the haplogroups we detected had elevated levels of genetic diversity, which strongly indicates their long existence. A Bayesian Skyline Plot detected, for the overall sample and for the three most significant haplogroups, a decrease in the number of females within the last 30,000–50,000 years, with a strong decrease in the last 10,000–20,000 years. Our data supported an alignment of some but not all haplogroups with putative morphological subspecies. We have not discounted the possibility of a cryptic kinkajou species.
Collapse
Affiliation(s)
- Manuel Ruiz-García
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, DC, Colombia
| | - Maria Fernanda Jaramillo
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, DC, Colombia
| | - Joseph Mark Shostell
- Math, Science and Technology Department, University of Minnesota Crookston, Crookston, MN, USA
| |
Collapse
|
25
|
Gering E, Incorvaia D, Henriksen R, Wright D, Getty T. Maladaptation in feral and domesticated animals. Evol Appl 2019; 12:1274-1286. [PMID: 31417614 PMCID: PMC6691326 DOI: 10.1111/eva.12784] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 01/10/2019] [Accepted: 02/07/2019] [Indexed: 12/14/2022] Open
Abstract
Selection regimes and population structures can be powerfully changed by domestication and feralization, and these changes can modulate animal fitness in both captive and natural environments. In this review, we synthesize recent studies of these two processes and consider their impacts on organismal and population fitness. Domestication and feralization offer multiple windows into the forms and mechanisms of maladaptation. Firstly, domestic and feral organisms that exhibit suboptimal traits or fitness allow us to identify their underlying causes within tractable research systems. This has facilitated significant progress in our general understandings of genotype-phenotype relationships, fitness trade-offs, and the roles of population structure and artificial selection in shaping domestic and formerly domestic organisms. Additionally, feralization of artificially selected gene variants and organisms can reveal or produce maladaptation in other inhabitants of an invaded biotic community. In these instances, feral animals often show similar fitness advantages to other invasive species, but they are also unique in their capacities to modify natural ecosystems through introductions of artificially selected traits. We conclude with a brief consideration of how emerging technologies such as genome editing could change the tempos, trajectories, and ecological consequences of both domestication and feralization. In addition to providing basic evolutionary insights, our growing understanding of mechanisms through which artificial selection can modulate fitness has diverse and important applications-from enhancing the welfare, sustainability, and efficiency of agroindustry, to mitigating biotic invasions.
Collapse
Affiliation(s)
- Eben Gering
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior ProgramMichigan State UniversityEast LansingMichigan
| | - Darren Incorvaia
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior ProgramMichigan State UniversityEast LansingMichigan
| | - Rie Henriksen
- IIFM Biology and AVIAN Behavioural Genomics and Physiology GroupLinköping UniversitySweden
| | - Dominic Wright
- IIFM Biology and AVIAN Behavioural Genomics and Physiology GroupLinköping UniversitySweden
| | - Thomas Getty
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior ProgramMichigan State UniversityEast LansingMichigan
| |
Collapse
|
26
|
Hu Y, Xing W, Song H, Zhu H, Liu G, Hu Z. Evolutionary Analysis of Unicellular Species in Chlamydomonadales Through Chloroplast Genome Comparison With the Colonial Volvocine Algae. Front Microbiol 2019; 10:1351. [PMID: 31275275 PMCID: PMC6591512 DOI: 10.3389/fmicb.2019.01351] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 05/31/2019] [Indexed: 11/13/2022] Open
Abstract
This study is the first determination of six chloroplast genomes of colonial volvocine algae, Colemanosphaera charkowiensis, Volvulina compacta, Pandorina colemaniae, Pandorina morum, Colemanosphaera angeleri, and Yamagishiella unicocca. Based on 55 chloroplast protein-coding genes, we compared the nonsynonymous (dN) and synonymous (dS) substitution rates between colonial volvocine algae and the other unicellular Chlamydomonadales species. When refer to the dN, we found 27 genes were significantly different, among them, 19 genes were significant higher in unicellular species (FDR-adjusted P < 0.05). When refer to the dS, we found 10 genes were significantly different, among them, 6 genes were significant higher in unicellular species (FDR-adjusted P < 0.05). Then we identified 14 putative fast-evolving genes and 11 putative positively selected genes of unicellular species, we analyzed the function of positively selected sites of the overlap genes of putative fast-evolving and positively selected genes, and found some sites were close to the important functional region of the proteins. Photosynthesis is the process to transform and store solar energy by chloroplast, it plays a vital role in the survival of algae, this study is the first to use the chloroplast genomes to analysis the evolutionary relationship between colonial and unicellular species in Chlamydomonadales. We found more genes have higher substitution rates in unicellular species and proposed that the fast-evolving and positively selected two genes, psbA and psbC, may help to improve the photosynthetic efficiency of unicellular species in Chlamydomonadales.
Collapse
Affiliation(s)
- Yuxin Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Weiyue Xing
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Huiyin Song
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Huan Zhu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Guoxiang Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Zhengyu Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| |
Collapse
|
27
|
Zhou L, Xiao Q, Bi J, Wang Z, Li Y. RabGTD: a comprehensive database of rabbit genome and transcriptome. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:5053987. [PMID: 30010730 PMCID: PMC6047408 DOI: 10.1093/database/bay075] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/22/2018] [Indexed: 12/28/2022]
Abstract
The rabbit is a very important species for both biomedical research and agriculture animal breeding. They are not only the most-used experimental animals for the production of antibodies, but also widely used for studying a variety of human diseases. Here we developed RabGTD, the first comprehensive rabbit database containing both genome and transcriptome data generated by next-generation sequencing. Genomic variations coming from 79 samples were identified and annotated, including 33 samples of wild rabbits and 46 samples of domestic rabbits with diverse populations. Gene expression profiles of 86 tissue samples were complied, including those from the most commonly used models for hyperlipidemia and atherosclerosis. RabGTD is a web-based and open-access resource, which also provides convenient functions and friendly interfaces of searching, browsing and downloading for users to explore the big data. Database URL: http://www.picb.ac.cn/RabGTD/
Collapse
Affiliation(s)
- Lu Zhou
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Xuhui District, Shanghai 200031, China.,University of Chinese Academy of Sciences, 52 Sanlihe Rd., Xicheng District, Beijing 100049, China
| | - Qingyu Xiao
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Xuhui District, Shanghai 200031, China.,University of Chinese Academy of Sciences, 52 Sanlihe Rd., Xicheng District, Beijing 100049, China
| | - Jie Bi
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Xuhui District, Shanghai 200031, China.,University of Chinese Academy of Sciences, 52 Sanlihe Rd., Xicheng District, Beijing 100049, China
| | - Zhen Wang
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Xuhui District, Shanghai 200031, China
| | - Yixue Li
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Xuhui District, Shanghai 200031, China.,Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, 1278 Keyuan Rd., Pudong District, Shanghai 201203, China.,Collaborative Innovation Center for Genetics and Development, Fudan University, 2005 Songhu Rd., Yangpu District, Shanghai 200433, China
| |
Collapse
|
28
|
Werhahn G, Senn H, Ghazali M, Karmacharya D, Sherchan AM, Joshi J, Kusi N, López-Bao JV, Rosen T, Kachel S, Sillero-Zubiri C, Macdonald DW. The unique genetic adaptation of the Himalayan wolf to high-altitudes and consequences for conservation. Glob Ecol Conserv 2018. [DOI: 10.1016/j.gecco.2018.e00455] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
|
29
|
Chen J, Ni P, Tran Thi TN, Kamaldinov EV, Petukhov VL, Han J, Liu X, Šprem N, Zhao S. Selective constraints in cold-region wild boars may defuse the effects of small effective population size on molecular evolution of mitogenomes. Ecol Evol 2018; 8:8102-8114. [PMID: 30250687 PMCID: PMC6144961 DOI: 10.1002/ece3.4221] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 04/25/2018] [Accepted: 05/11/2018] [Indexed: 12/15/2022] Open
Abstract
Spatial range expansion during population colonization is characterized by demographic events that may have significant effects on the efficiency of natural selection. Population genetics suggests that genetic drift brought by small effective population size (Ne) may undermine the efficiency of selection, leading to a faster accumulation of nonsynonymous mutations. However, it is still unknown whether this effect might be balanced or even reversed by strong selective constraints. Here, we used wild boars and local domestic pigs from tropical (Vietnam) and subarctic region (Siberia) as animal model to evaluate the effects of functional constraints and genetic drift on shaping molecular evolution. The likelihood-ratio test revealed that Siberian clade evolved significantly different from Vietnamese clades. Different datasets consistently showed that Siberian wild boars had lower Ka/Ks ratios than Vietnamese samples. The potential role of positive selection for branches with higher Ka/Ks was evaluated using branch-site model comparison. No signal of positive selection was found for the higher Ka/Ks in Vietnamese clades, suggesting the interclade difference was mainly due to the reduction in Ka/Ks for Siberian samples. This conclusion was further confirmed by the result from a larger sample size, among which wild boars from northern Asia (subarctic and nearby region) had lower Ka/Ks than those from southern Asia (temperate and tropical region). The lower Ka/Ks might be due to either stronger functional constraints, which prevent nonsynonymous mutations from accumulating in subarctic wild boars, or larger Ne in Siberian wild boars, which can boost the efficacy of purifying selection to remove functional mutations. The latter possibility was further ruled out by the Bayesian skyline plot analysis, which revealed that historical Ne of Siberian wild boars was smaller than that of Vietnamese wild boars. Altogether, these results suggest stronger functional constraints acting on mitogenomes of subarctic wild boars, which may provide new insights into their local adaptation of cold resistance.
Collapse
Affiliation(s)
- Jianhai Chen
- Key Lab of Agricultural Animal Genetics and BreedingMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- The Cooperative Innovation Center for Sustainable Pig ProductionHuazhong Agricultural UniversityWuhanChina
- Department of Ecology and EvolutionUniversity of ChicagoChicagoIllinois
| | - Pan Ni
- Key Lab of Agricultural Animal Genetics and BreedingMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- The Cooperative Innovation Center for Sustainable Pig ProductionHuazhong Agricultural UniversityWuhanChina
| | - Thuy Nhien Tran Thi
- Key Lab of Agricultural Animal Genetics and BreedingMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- The Cooperative Innovation Center for Sustainable Pig ProductionHuazhong Agricultural UniversityWuhanChina
- National Institute of Animal SciencesHanoiVietnam
| | - Evgeniy Varisovich Kamaldinov
- Federal State Budgetary Educational Institution of Higher EducationNovosibirsk State Agrarian UniversityNovosibirskRussia
| | - Valeriy Lavrentyevich Petukhov
- Federal State Budgetary Educational Institution of Higher EducationNovosibirsk State Agrarian UniversityNovosibirskRussia
| | - Jianlin Han
- International Livestock Research Institute (ILRI)NairobiKenya
- CAAS‐ILRI Joint Laboratory on Livestock and Forage Genetic ResourcesInstitute of Animal ScienceChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Xiangdong Liu
- Key Lab of Agricultural Animal Genetics and BreedingMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- The Cooperative Innovation Center for Sustainable Pig ProductionHuazhong Agricultural UniversityWuhanChina
| | - Nikica Šprem
- Department of Fisheries, Beekeeping, Game Management and Special ZoologyFaculty of AgricultureUniversity of ZagrebZagrebCroatia
| | - Shuhong Zhao
- Key Lab of Agricultural Animal Genetics and BreedingMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- The Cooperative Innovation Center for Sustainable Pig ProductionHuazhong Agricultural UniversityWuhanChina
| |
Collapse
|
30
|
Xie X, Yang Y, Ren Q, Ding X, Bao P, Yan B, Yan X, Han J, Yan P, Qiu Q. Accumulation of deleterious mutations in the domestic yak genome. Anim Genet 2018; 49:384-392. [DOI: 10.1111/age.12703] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2018] [Indexed: 12/19/2022]
Affiliation(s)
- X. Xie
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - Y. Yang
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - Q. Ren
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - X. Ding
- Key Laboratory of Yak Breeding Engineering Gansu Province; Lanzhou Institute of Husbandry and Pharmaceutical Sciences; Chinese Academy of Agricultural Science; Lanzhou 730050 China
| | - P. Bao
- Key Laboratory of Yak Breeding Engineering Gansu Province; Lanzhou Institute of Husbandry and Pharmaceutical Sciences; Chinese Academy of Agricultural Science; Lanzhou 730050 China
| | - B. Yan
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - X. Yan
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - J. Han
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - P. Yan
- Key Laboratory of Yak Breeding Engineering Gansu Province; Lanzhou Institute of Husbandry and Pharmaceutical Sciences; Chinese Academy of Agricultural Science; Lanzhou 730050 China
| | - Q. Qiu
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| |
Collapse
|
31
|
Ní Leathlobhair M, Perri AR, Irving-Pease EK, Witt KE, Linderholm A, Haile J, Lebrasseur O, Ameen C, Blick J, Boyko AR, Brace S, Cortes YN, Crockford SJ, Devault A, Dimopoulos EA, Eldridge M, Enk J, Gopalakrishnan S, Gori K, Grimes V, Guiry E, Hansen AJ, Hulme-Beaman A, Johnson J, Kitchen A, Kasparov AK, Kwon YM, Nikolskiy PA, Lope CP, Manin A, Martin T, Meyer M, Myers KN, Omura M, Rouillard JM, Pavlova EY, Sciulli P, Sinding MHS, Strakova A, Ivanova VV, Widga C, Willerslev E, Pitulko VV, Barnes I, Gilbert MTP, Dobney KM, Malhi RS, Murchison EP, Larson G, Frantz LAF. The evolutionary history of dogs in the Americas. Science 2018; 361:81-85. [PMID: 29976825 PMCID: PMC7116273 DOI: 10.1126/science.aao4776] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 12/26/2017] [Accepted: 05/10/2018] [Indexed: 01/01/2023]
Abstract
Dogs were present in the Americas before the arrival of European colonists, but the origin and fate of these precontact dogs are largely unknown. We sequenced 71 mitochondrial and 7 nuclear genomes from ancient North American and Siberian dogs from time frames spanning ~9000 years. Our analysis indicates that American dogs were not derived from North American wolves. Instead, American dogs form a monophyletic lineage that likely originated in Siberia and dispersed into the Americas alongside people. After the arrival of Europeans, native American dogs almost completely disappeared, leaving a minimal genetic legacy in modern dog populations. The closest detectable extant lineage to precontact American dogs is the canine transmissible venereal tumor, a contagious cancer clone derived from an individual dog that lived up to 8000 years ago.
Collapse
Affiliation(s)
- Máire Ní Leathlobhair
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Angela R Perri
- Department of Archaeology, Durham University, Durham, UK
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Evan K Irving-Pease
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Kelsey E Witt
- School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana-Champaign, IL, USA
| | - Anna Linderholm
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Department of Anthropology, Texas A&M University, College Station, TX, USA
| | - James Haile
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ophelie Lebrasseur
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Carly Ameen
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
| | - Jeffrey Blick
- Department of Government and Sociology, Georgia College and State University, Milledgeville, GA, USA
| | - Adam R Boyko
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | | | | | | | - Evangelos A Dimopoulos
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | | | - Jacob Enk
- Arbor Biosciences, Ann Arbor, MI, USA
| | - Shyam Gopalakrishnan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Kevin Gori
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Vaughan Grimes
- Department of Archaeology, Memorial University, Queen's College, St. John's, Canada
| | - Eric Guiry
- Department of Anthropology, University of British Columbia, Vancouver, Canada
| | - Anders J Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
| | - Ardern Hulme-Beaman
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
| | - John Johnson
- Department of Anthropology, Santa Barbara Museum of Natural History, Santa Barbara, CA, USA
| | - Andrew Kitchen
- Department of Anthropology, University of Iowa, Iowa City, IA, USA
| | - Aleksei K Kasparov
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Young-Mi Kwon
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Pavel A Nikolskiy
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
- Geological Institute, Russian Academy of Sciences, Moscow, Russia
| | | | - Aurélie Manin
- Department of Archaeology, BioArCh, University of York, York, UK
- UMR 7209, Archéozoologie, Archéobotanique, Muséum National d'Histoire Naturelle, Paris, France
| | - Terrance Martin
- Research and Collections Center, Illinois State Museum, Springfield, IL, USA
| | - Michael Meyer
- Touray & Meyer Veterinary Clinic, Serrekunda, Gambia
| | - Kelsey Noack Myers
- Glenn A. Black Laboratory of Anthropology, Indiana University Bloomington, Bloomington, IN, USA
| | - Mark Omura
- Department of Mammalogy, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Jean-Marie Rouillard
- Arbor Biosciences, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Elena Y Pavlova
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
- Arctic & Antarctic Research Institute, St. Petersburg, Russia
| | - Paul Sciulli
- Department of Anthropology, Ohio State University, Columbus, OH, USA
| | - Mikkel-Holger S Sinding
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Andrea Strakova
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Christopher Widga
- Center of Excellence in Paleontology, East Tennessee State University, Gray, TN, USA
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Vladimir V Pitulko
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, UK
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Norwegian University of Science and Technology, University Museum, Trondheim, Norway
| | - Keith M Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
- Department of Archaeology, University of Aberdeen, Aberdeen, UK
| | - Ripan S Malhi
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana-Champaign, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana-Champaign, IL, USA
| | - Elizabeth P Murchison
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.
| | - Laurent A F Frantz
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| |
Collapse
|
32
|
Ni P, Bhuiyan AA, Chen JH, Li J, Zhang C, Zhao S, Du X, Li H, Yu H, Liu X, Li K. De novo assembly of mitochondrial genomes provides insights into genetic diversity and molecular evolution in wild boars and domestic pigs. Genetica 2018; 146:277-285. [PMID: 29748765 DOI: 10.1007/s10709-018-0018-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 04/21/2018] [Indexed: 11/29/2022]
Abstract
Up to date, the scarcity of publicly available complete mitochondrial sequences for European wild pigs hampers deeper understanding about the genetic changes following domestication. Here, we have assembled 26 de novo mtDNA sequences of European wild boars from next generation sequencing (NGS) data and downloaded 174 complete mtDNA sequences to assess the genetic relationship, nucleotide diversity, and selection. The Bayesian consensus tree reveals the clear divergence between the European and Asian clade and a very small portion (10 out of 200 samples) of maternal introgression. The overall nucleotides diversities of the mtDNA sequences have been reduced following domestication. Interestingly, the selection efficiencies in both European and Asian domestic pigs are reduced, probably caused by changes in both selection constraints and maternal population size following domestication. This study suggests that de novo assembled mitogenomes can be a great boon to uncover the genetic turnover following domestication. Further investigation is warranted to include more samples from the ever-increasing amounts of NGS data to help us to better understand the process of domestication.
Collapse
Affiliation(s)
- Pan Ni
- College of Life Science, Foshan University, Foshan, 528231, Guangdong, People's Republic of China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Ali Akbar Bhuiyan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.,Bangladesh Livestock Research Institute, Savar, Dhaka, 1341, Bangladesh
| | - Jian-Hai Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jingjin Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Cheng Zhang
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Xiaoyong Du
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.,College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Hua Li
- College of Life Science, Foshan University, Foshan, 528231, Guangdong, People's Republic of China
| | - Hui Yu
- College of Life Science, Foshan University, Foshan, 528231, Guangdong, People's Republic of China
| | - Xiangdong Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
| | - Kui Li
- College of Life Science, Foshan University, Foshan, 528231, Guangdong, People's Republic of China.
| |
Collapse
|
33
|
Zhang Y, Sun J, Rouse GW, Wiklund H, Pleijel F, Watanabe HK, Chen C, Qian PY, Qiu JW. Phylogeny, evolution and mitochondrial gene order rearrangement in scale worms (Aphroditiformia, Annelida). Mol Phylogenet Evol 2018; 125:220-231. [PMID: 29625228 DOI: 10.1016/j.ympev.2018.04.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 01/16/2018] [Accepted: 04/02/2018] [Indexed: 01/07/2023]
Abstract
Next-generation sequencing (NGS) has become a powerful tool in phylogenetic and evolutionary studies. Here we applied NGS to recover two ribosomal RNA genes (18S and 28S) from 16 species and 15 mitochondrial genomes from 16 species of scale worms representing six families in the suborder Aphroditiformia (Phyllodocida, Annelida), a complex group of polychaetes characterized by the presence of dorsal elytra or scales. The phylogenetic relationship of the several groups of scale worms remains unresolved due to insufficient taxon sampling and low resolution of individual gene markers. Phylogenetic tree topology based on mitochondrial genomes is comparable with that based on concatenated sequences from two mitochondrial genes (cox1 and 16S) and two ribosomal genes (18S and 28S) genes, but has higher statistical support for several clades. Our analyses show that Aphroditiformia is monophyletic, indicating the presence of elytra is an apomorphic trait. Eulepethidae and Aphroditidae together form the sister group to all other families in this suborder, whereas Acoetidae is sister to Iphionidae. Polynoidae is monophyletic, but within this family the deep-sea subfamilies Branchinotogluminae and Macellicephalinae are paraphyletic. Mitochondrial genomes in most scale-worm families have a conserved gene order, but within Polynoidae there are two novel arrangement patterns in the deep-sea clade. Mitochondrial protein-coding genes in polynoids as a whole have evolved under strong purifying selection, but substitution rates in deep-sea species are much higher than those in shallow-water species, indicating that purifying selection is relaxed in deep-sea polynoids. There are positive selected amino acids for some mitochondrial genes of the deep-sea clade, indicating they may involve in the adaption of deep-sea polynoids. Overall, our study (1) provided more evidence for reconstruction of the phylogeny of Aphroditiformia, (2) provided evidence to refute the assumption that mitochondrial gene order in Errantia is conserved, and (3) indicated that the deep-sea extreme environment may have affected the mitochondrial genome evolution rate and gene order arrangement in Polynoidae.
Collapse
Affiliation(s)
- Yanjie Zhang
- Department of Biology, Hong Kong Baptist University, 224 Waterloo Road, Hong Kong, China.
| | - Jin Sun
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay Road, Hong Kong, China
| | - Greg W Rouse
- Scripps Institution of Oceanography, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Helena Wiklund
- Zoology Department, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Fredrik Pleijel
- Department of Marine Sciences, University of Gothenburg, Tjärnö, SE-452 96 Strömstad, Sweden.
| | - Hiromi K Watanabe
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan.
| | - Chong Chen
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan.
| | - Pei-Yuan Qian
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay Road, Hong Kong, China.
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, 224 Waterloo Road, Hong Kong, China.
| |
Collapse
|
34
|
Chen J, Ni P, Li X, Han J, Jakovlić I, Zhang C, Zhao S. Population size may shape the accumulation of functional mutations following domestication. BMC Evol Biol 2018; 18:4. [PMID: 29351740 PMCID: PMC5775542 DOI: 10.1186/s12862-018-1120-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 01/09/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Population genetics theory predicts an important role of differences in the effective population size (N e ) among species on shaping the accumulation of functional mutations by regulating the selection efficiency. However, this correlation has never been tested in domesticated animals. RESULTS Here, we synthesized 62 whole genome data in eight domesticated species (cat, dog, pig, goat, sheep, chicken, cattle and horse) and compared domesticates with their wild (or ancient) relatives. Genes with significantly different selection pressures (revealed by nonsynonymous/synonymous substitution rate ratios, Ka/Ks or ω) between domesticated (Dω) and wild animals (Wω) were determined by likelihood-ratio tests. Species-level effective population sizes (N e ) were evaluated by the pairwise sequentially Markovian coalescent (PSMC) model, and Dω/Wω were calculated for each species to evaluate the changes in accumulation of functional mutations after domestication relative to pre-domestication period. Correlation analysis revealed that the most recent (~ 10.000 years ago) N e (s) are positively correlated with Dω/Wω. This result is consistent with the corollary of the nearly neutral theory, that higher N e could boost the efficiency of positive selection, which might facilitate the overall accumulation of functional mutations. In addition, we also evaluated the accumulation of radical and conservative mutations during the domestication transition as: Dradical/Wradical and Dconservative/Wconservative, respectively. Surprisingly, only Dradical/Wradical ratio exhibited a positive correlation with N e (p < 0.05), suggesting that domestication process might magnify the accumulation of radical mutations in species with larger N e . CONCLUSIONS Our results confirm the classical population genetics theory prediction and highlight the important role of species' N e in shaping the patterns of accumulation of functional mutations, especially radical mutations, in domesticated animals. The results aid our understanding of the mechanisms underlying the accumulation of functional mutations after domestication, which is critical for understanding the phenotypic diversification associated with this process.
Collapse
Affiliation(s)
- Jianhai Chen
- Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Pan Ni
- Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Xinyun Li
- Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Jianlin Han
- International Livestock Research Institute (ILRI), Nairobi, 00100 Kenya
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193 People’s Republic of China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Wuhan Institute of Biotechnology, Wuhan, 430075 People’s Republic of China
| | - Chengjun Zhang
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 People’s Republic of China
| | - Shuhong Zhao
- Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| |
Collapse
|
35
|
Makino T, Rubin CJ, Carneiro M, Axelsson E, Andersson L, Webster MT. Elevated Proportions of Deleterious Genetic Variation in Domestic Animals and Plants. Genome Biol Evol 2018; 10:276-290. [PMID: 29325102 PMCID: PMC5786255 DOI: 10.1093/gbe/evy004] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2018] [Indexed: 12/12/2022] Open
Abstract
A fraction of genetic variants segregating in any population are deleterious, which negatively impacts individual fitness. The domestication of animals and plants is associated with population bottlenecks and artificial selection, which are predicted to increase the proportion of deleterious variants. However, the extent to which this is a general feature of domestic species is unclear. Here, we examine the effects of domestication on the prevalence of deleterious variation using pooled whole-genome resequencing data from five domestic animal species (dog, pig, rabbit, chicken, and silkworm) and two domestic plant species (rice and soybean) compared with their wild ancestors. We find significantly reduced genetic variation and increased proportion of nonsynonymous amino acid changes in all but one of the domestic species. These differences are observable across a range of allele frequencies, both common and rare. We find proportionally more single nucleotide polymorphisms in highly conserved elements in domestic species and a tendency for domestic species to harbor a higher proportion of changes classified as damaging. Our findings most likely reflect an increased incidence of deleterious variants in domestic species, which is most likely attributable to population bottlenecks that lead to a reduction in the efficacy of selection. An exception to this pattern is displayed by European domestic pigs, which do not show traces of a strong population bottleneck and probably continued to exchange genes with wild boar populations after domestication. The results presented here indicate that an elevated proportion of deleterious variants is a common, but not ubiquitous, feature of domestic species.
Collapse
Affiliation(s)
- Takashi Makino
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden
| | - Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Portugal
| | - Erik Axelsson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden
| |
Collapse
|
36
|
Theofanopoulou C, Gastaldon S, O’Rourke T, Samuels BD, Messner A, Martins PT, Delogu F, Alamri S, Boeckx C. Self-domestication in Homo sapiens: Insights from comparative genomics. PLoS One 2017; 12:e0185306. [PMID: 29045412 PMCID: PMC5646786 DOI: 10.1371/journal.pone.0185306] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/11/2017] [Indexed: 02/07/2023] Open
Abstract
This study identifies and analyzes statistically significant overlaps between selective sweep screens in anatomically modern humans and several domesticated species. The results obtained suggest that (paleo-)genomic data can be exploited to complement the fossil record and support the idea of self-domestication in Homo sapiens, a process that likely intensified as our species populated its niche. Our analysis lends support to attempts to capture the "domestication syndrome" in terms of alterations to certain signaling pathways and cell lineages, such as the neural crest.
Collapse
Affiliation(s)
- Constantina Theofanopoulou
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
- Universitat de Barcelona Institute for Complex Systems, Barcelona, Spain
| | - Simone Gastaldon
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
- School of Psychology, University of Padova, Padova, Italy
| | - Thomas O’Rourke
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
| | - Bridget D. Samuels
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, United States of America
| | - Angela Messner
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
| | | | - Francesco Delogu
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Saleh Alamri
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
| | - Cedric Boeckx
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
- Universitat de Barcelona Institute for Complex Systems, Barcelona, Spain
- ICREA, Barcelona, Spain
| |
Collapse
|
37
|
Size Variation under Domestication: Conservatism in the inner ear shape of wolves, dogs and dingoes. Sci Rep 2017; 7:13330. [PMID: 29042574 PMCID: PMC5645459 DOI: 10.1038/s41598-017-13523-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 09/25/2017] [Indexed: 11/08/2022] Open
Abstract
A broad sample of wolves, dingoes, and domesticated dogs of different kinds and time periods was used to identify changes in size and shape of the organs of balance and hearing related to domestication and to evaluate the potential utility of uncovered patterns as markers of domestication. Using geometric morphometrics coupled with non-invasive imaging and three-dimensional reconstructions, we exposed and compared complex structures that remain largely conserved. There is no statistically significant difference in the levels of shape variation between prehistoric and modern dogs. Shape variance is slightly higher for the different components of the inner ear in modern dogs than in wolves, but these differences are not significant. Wolves express a significantly greater level of variance in the angle between the lateral and the posterior canal than domestic dog breeds. Wolves have smaller levels of size variation than dogs. In terms of the shape of the semicircular canals, dingoes reflect the mean shape in the context of variation in the sample. This mirrors the condition of feral forms in other organs, in which there is an incomplete return to the characteristics of the ancestor. In general, morphological diversity or disparity in the inner ear is generated by scaling.
Collapse
|
38
|
Campana MG. BaitsTools: Software for hybridization capture bait design. Mol Ecol Resour 2017; 18:356-361. [PMID: 28941033 DOI: 10.1111/1755-0998.12721] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/12/2017] [Accepted: 09/14/2017] [Indexed: 12/01/2022]
Abstract
Nucleic acid hybridization capture is a principal technology in molecular ecology and genomics. Bait design, however, is a nontrivial task and few resources currently exist to automate the process. Here, I present baitstools, an open-source, user-friendly software package to facilitate the design of nucleic acid baits for hybridization capture.
Collapse
Affiliation(s)
- Michael G Campana
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA
| |
Collapse
|
39
|
Sun S, Li Q, Kong L, Yu H. Limited locomotive ability relaxed selective constraints on molluscs mitochondrial genomes. Sci Rep 2017; 7:10628. [PMID: 28878314 PMCID: PMC5587578 DOI: 10.1038/s41598-017-11117-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 08/18/2017] [Indexed: 01/13/2023] Open
Abstract
Mollusca are the second largest phylum in the animal kingdom with different types of locomotion. Some molluscs are poor-migrating, while others are free-moving or fast-swimming. Most of the energy required for locomotion is provided by mitochondria via oxidative phosphorylation. Here, we conduct a comparative genomic analysis of 256 molluscs complete mitochondrial genomes and evaluate the role of energetic functional constraints on the protein-coding genes, providing a new insight into mitochondrial DNA (mtDNA) evolution. The weakly locomotive molluscs, compared to strongly locomotive molluscs, show significantly higher Ka/Ks ratio, which suggest they accumulated more nonsynonymous mutations in mtDNA and have experienced more relaxed evolutionary constraints. Eleven protein-coding genes (CoxI, CoxII, ATP6, Cytb, ND1-6, ND4L) show significant difference for Ka/Ks ratios between the strongly and weakly locomotive groups. The relaxation of selective constraints on Atp8 arise in the common ancestor of bivalves, and the further relaxation occurred in marine bivalves lineage. Our study thus demonstrates that selective constraints relevant to locomotive ability play an essential role in evolution of molluscs mtDNA.
Collapse
Affiliation(s)
- Shao'e Sun
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| |
Collapse
|
40
|
Li YX, Gao YL, He XL, Cao SX. Exploration of mtDNA control region sequences in Chinese Tibetan Mastiffs. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:800-804. [PMID: 28756720 DOI: 10.1080/24701394.2017.1357714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The control region of mitochondrial DNA (mtDNA) was obtained from 40 purebred Chinese Tibetan Mastiffs (TMs). Sequence structure and genetic diversity were analyzed, and a phylogenetic tree was constructed. The TM mtDNA control region was composed of ETAS (extended termination associated sequences), CD (a central domain) and CSBs (conserved sequenced blocks) and sequence length showed some diversity, which was mainly caused by the number of 10 nucleotide repeat units [5'-GTA CAC GT (G/A) C-3'] between CSB I and CSB II, which ranged from 27 to 35 among individuals. Seventy-five polymorphic sites were identified, which defined 37 haplotypes; the haplotype diversity was 0.990, and the nucleotide diversity was 1.201. Based on the control region sequences, Chinese TMs were divided into three categories, which were consistent with the origin and geographical classification of TMs. Phylogenetic analysis of 538-bp HVR-I sequences revealed that TMs were most closely related to Labrador Retrievers.
Collapse
Affiliation(s)
- Yin-Xia Li
- a Institute of Animal Science , Jiangsu Academy of Agricultural Sciences , Nanjing , Jiangsu , China.,b Key Laboratory of Animal Breeding and Reproduction , Jiangsu Academy of Agricultural Sciences , Nanjing , Jiangsu , China
| | - Yi-Long Gao
- c Policedog Technology Key Laboratory of the Ministry of Public Security , Nanjing Policedog Research Institute of the Ministry of Public Security , Nanjing , Jiangsu , China
| | - Xing-Liang He
- c Policedog Technology Key Laboratory of the Ministry of Public Security , Nanjing Policedog Research Institute of the Ministry of Public Security , Nanjing , Jiangsu , China
| | - Shao-Xian Cao
- a Institute of Animal Science , Jiangsu Academy of Agricultural Sciences , Nanjing , Jiangsu , China.,b Key Laboratory of Animal Breeding and Reproduction , Jiangsu Academy of Agricultural Sciences , Nanjing , Jiangsu , China
| |
Collapse
|
41
|
Kemp BM, Judd K, Monroe C, Eerkens JW, Hilldorfer L, Cordray C, Schad R, Reams E, Ortman SG, Kohler TA. Prehistoric mitochondrial DNA of domesticate animals supports a 13th century exodus from the northern US southwest. PLoS One 2017; 12:e0178882. [PMID: 28746407 PMCID: PMC5528258 DOI: 10.1371/journal.pone.0178882] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/19/2017] [Indexed: 01/24/2023] Open
Abstract
The 13th century Puebloan depopulation of the Four Corners region of the US Southwest is an iconic episode in world prehistory. Studies of its causes, as well as its consequences, have a bearing not only on archaeological method and theory, but also social responses to climate change, the sociology of social movements, and contemporary patterns of cultural diversity. Previous research has debated the demographic scale, destinations, and impacts of Four Corners migrants. Much of this uncertainty stems from the substantial differences in material culture between the Four Corners vs. hypothesized destination areas. Comparable biological evidence has been difficult to obtain due to the complete departure of farmers from the Four Corners in the 13th century CE and restrictions on sampling human remains. As an alternative, patterns of genetic variation among domesticated species were used to address the role of migration in this collapse. We collected mitochondrial haplotypic data from dog (Canis lupus familiaris) and turkey (Meleagris gallopavo) remains from archaeological sites in the most densely-populated portion of the Four Corners region, and the most commonly proposed destination area for that population under migration scenarios. Results are consistent with a large-scale migration of humans, accompanied by their domestic turkeys, during the 13th century CE. These results support scenarios that suggest contemporary Pueblo peoples of the Northern Rio Grande are biological and cultural descendants of Four Corners populations.
Collapse
Affiliation(s)
- Brian M. Kemp
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Kathleen Judd
- Laboratory of Molecular Anthropology and Ancient DNA, Washington State University, Pullman, Washington, United States of America
| | - Cara Monroe
- Department of Anthropology, Washington State University, Pullman, Washington, United States of America
| | - Jelmer W. Eerkens
- Department of Anthropology, University of California, Davis, California, United States of America
| | - Lindsay Hilldorfer
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Connor Cordray
- Laboratory of Molecular Anthropology and Ancient DNA, Washington State University, Pullman, Washington, United States of America
| | - Rebecca Schad
- Laboratory of Molecular Anthropology and Ancient DNA, Washington State University, Pullman, Washington, United States of America
| | - Erin Reams
- Laboratory of Molecular Anthropology and Ancient DNA, Washington State University, Pullman, Washington, United States of America
| | - Scott G. Ortman
- Department of Anthropology, University of Colorado, Boulder, Colorado, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Crow Canyon Archaeological Center, Cortez, Colorado, United States of America
| | - Timothy A. Kohler
- Department of Anthropology, Washington State University, Pullman, Washington, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Crow Canyon Archaeological Center, Cortez, Colorado, United States of America
| |
Collapse
|
42
|
Pires AE, Amorim IR, Borges C, Simões F, Teixeira T, Quaresma A, Petrucci‐Fonseca F, Matos J. New insights into the genetic composition and phylogenetic relationship of wolves and dogs in the Iberian Peninsula. Ecol Evol 2017; 7:4404-4418. [PMID: 28649351 PMCID: PMC5478058 DOI: 10.1002/ece3.2949] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 02/17/2017] [Accepted: 03/05/2017] [Indexed: 12/26/2022] Open
Abstract
This study investigates the gene pool of Portuguese autochthonous dog breeds and their wild counterpart, the Iberian wolf subspecies (Canis lupus signatus), using standard molecular markers. A combination of paternal and maternal molecular markers was used to investigate the genetic composition, genetic differentiation and genetic relationship of native Portuguese dogs and the Iberian wolf. A total of 196 unrelated dogs, including breed and village dogs from Portugal, and other dogs from Spain and North Africa, and 56 Iberian wolves (wild and captive) were analyzed for nuclear markers, namely Y chromosome SNPs, Y chromosome STR loci, autosomal STR loci, and a mitochondrial fragment of the control region I. Our data reveal new variants for the molecular markers and confirm significant genetic differentiation between Iberian wolf and native domestic dogs from Portugal. Based on our sampling, no signs of recent introgression between the two subspecies were detected. Y chromosome data do not reveal genetic differentiation among the analyzed dog breeds, suggesting they share the same patrilineal origin. Moreover, the genetic distinctiveness of the Iberian wolf from other wolf populations is further confirmed with the description of new mtDNA variants for this endemism. Our research also discloses new molecular markers for wolf and dog subspecies assignment, which might become particularly relevant in the case of forensic or noninvasive genetic studies. The Iberian wolf represents a relic of the once widespread wolf population in Europe and our study reveals that it is a reservoir of unique genetic diversity of the grey wolf, Canis lupus. These results stress the need for conservation plans that will guarantee the sustainability of this threatened top predator in Iberia.
Collapse
Affiliation(s)
- Ana Elisabete Pires
- Biotechnology and Genetic Resources UnitNational Institute of Agrarian and Veterinary Research, I.P. (INIAV)OeirasPortugal
- Centre for Ecology, Evolution and Environmental Changes (cE3c)Faculty of SciencesUniversity of LisbonLisbonPortugal
| | - Isabel R. Amorim
- Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos AçoresFaculdade de Ciências Agrárias e do AmbienteAçoresPortugal
| | - Carla Borges
- Biotechnology and Genetic Resources UnitNational Institute of Agrarian and Veterinary Research, I.P. (INIAV)OeirasPortugal
| | - Fernanda Simões
- Biotechnology and Genetic Resources UnitNational Institute of Agrarian and Veterinary Research, I.P. (INIAV)OeirasPortugal
| | - Tatiana Teixeira
- Biotechnology and Genetic Resources UnitNational Institute of Agrarian and Veterinary Research, I.P. (INIAV)OeirasPortugal
| | - Andreia Quaresma
- Centre for Ecology, Evolution and Environmental Changes (cE3c)Faculty of SciencesUniversity of LisbonLisbonPortugal
| | - Francisco Petrucci‐Fonseca
- Centre for Ecology, Evolution and Environmental Changes (cE3c)Faculty of SciencesUniversity of LisbonLisbonPortugal
| | - José Matos
- Biotechnology and Genetic Resources UnitNational Institute of Agrarian and Veterinary Research, I.P. (INIAV)OeirasPortugal
- Centre for Ecology, Evolution and Environmental Changes (cE3c)Faculty of SciencesUniversity of LisbonLisbonPortugal
| |
Collapse
|
43
|
Montana L, Caniglia R, Galaverni M, Fabbri E, Ahmed A, Bolfíková BČ, Czarnomska SD, Galov A, Godinho R, Hindrikson M, Hulva P, Jędrzejewska B, Jelenčič M, Kutal M, Saarma U, Skrbinšek T, Randi E. Combining phylogenetic and demographic inferences to assess the origin of the genetic diversity in an isolated wolf population. PLoS One 2017; 12:e0176560. [PMID: 28489863 PMCID: PMC5425034 DOI: 10.1371/journal.pone.0176560] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 04/12/2017] [Indexed: 11/18/2022] Open
Abstract
The survival of isolated small populations is threatened by both demographic and genetic factors. Large carnivores declined for centuries in most of Europe due to habitat changes, overhunting of their natural prey and direct persecution. However, the current rewilding trends are driving many carnivore populations to expand again, possibly reverting the erosion of their genetic diversity. In this study we reassessed the extent and origin of the genetic variation of the Italian wolf population, which is expanding after centuries of decline and isolation. We genotyped wolves from Italy and other nine populations at four mtDNA regions (control-region, ATP6, COIII and ND4) and 39 autosomal microsatellites. Results of phylogenetic analyses and assignment procedures confirmed in the Italian wolves a second private mtDNA haplotype, which belongs to a haplogroup distributed mostly in southern Europe. Coalescent analyses showed that the unique mtDNA haplotypes in the Italian wolves likely originated during the late Pleistocene. ABC simulations concordantly showed that the extant wolf populations in Italy and in south-western Europe started to be isolated and declined right after the last glacial maximum. Thus, the standing genetic variation in the Italian wolves principally results from the historical isolation south of the Alps.
Collapse
Affiliation(s)
- Luca Montana
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia, Bologna, Italy
- * E-mail:
| | - Romolo Caniglia
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia, Bologna, Italy
| | - Marco Galaverni
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia, Bologna, Italy
| | - Elena Fabbri
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia, Bologna, Italy
| | - Atidje Ahmed
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Barbora Černá Bolfíková
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | | | - Ana Galov
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Raquel Godinho
- CIBIO/InBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Maris Hindrikson
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Pavel Hulva
- Department of Zoology, Charles University in Prague, Prague, Czech Republic
- Department of Biology and Ecology, Ostrava University, Ostrava, Czech Republic
| | | | - Maja Jelenčič
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Miroslav Kutal
- Department of Forest Ecology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic
- Friends of the Earth Czech Republic, Olomouc Branch, Olomouc, Czech Republic
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Tomaž Skrbinšek
- Department of Forest Ecology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic
| | - Ettore Randi
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia, Bologna, Italy
- Department 18/ Section of Environmental Engineering, Aalborg University, Aalborg, Denmark
| |
Collapse
|
44
|
Montana L, Caniglia R, Galaverni M, Fabbri E, Randi E. A new mitochondrial haplotype confirms the distinctiveness of the Italian wolf (Canis lupus) population. Mamm Biol 2017. [DOI: 10.1016/j.mambio.2017.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
45
|
Vasemägi A, Sulku J, Bruneaux M, Thalmann O, Mäkinen H, Ozerov M. Prediction of harmful variants on mitochondrial genes: Test of habitat-dependent and demographic effects in a euryhaline fish. Ecol Evol 2017; 7:3826-3835. [PMID: 28616179 PMCID: PMC5468147 DOI: 10.1002/ece3.2989] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 03/10/2017] [Accepted: 03/21/2017] [Indexed: 11/27/2022] Open
Abstract
Both effective population size and life history may influence the efficacy of purifying selection, but it remains unclear if the environment affects the accumulation of weakly deleterious nonsynonymous polymorphisms. We hypothesize that the reduced energetic cost of osmoregulation in brackish water habitat may cause relaxation of selective constraints at mitochondrial oxidative phosphorylation (OXPHOS) genes. To test this hypothesis, we analyzed 57 complete mitochondrial genomes of Pungitius pungitius collected from brackish and freshwater habitats. Based on inter‐ and intraspecific comparisons, we estimated that 84% and 68% of the nonsynonymous polymorphisms in the freshwater and brackish water populations, respectively, are weakly or moderately deleterious. Using in silico prediction tools (MutPred, SNAP2), we subsequently identified nonsynonymous polymorphisms with potentially harmful effect. Both prediction methods indicated that the functional effects of the fixed nonsynonymous substitutions between nine‐ and three‐spined stickleback were weaker than for polymorphisms within species, indicating that harmful nonsynonymous polymorphisms within populations rarely become fixed between species. No significant differences in mean estimated functional effects were identified between freshwater and brackish water nine‐spined stickleback to support the hypothesis that reduced osmoregulatory energy demand in the brackish water environment reduces the strength of purifying selection at OXPHOS genes. Instead, elevated frequency of nonsynonymous polymorphisms in the freshwater environment (Pn/Ps = 0.549 vs. 0.283; Fisher's exact test p = .032) suggested that purifying selection is less efficient in small freshwater populations. This study shows the utility of in silico functional prediction tools in population genetic and evolutionary research in a nonmammalian vertebrate and demonstrates that mitochondrial energy production genes represent a promising system to characterize the demographic, life history and potential habitat‐dependent effects of segregating amino acid variants.
Collapse
Affiliation(s)
- Anti Vasemägi
- Department of Biology University of Turku Turku Finland.,Department of Aquaculture Estonian University of Life Sciences Tartu Estonia
| | - Janne Sulku
- Department of Biology University of Turku Turku Finland
| | - Matthieu Bruneaux
- Department of Biology University of Turku Turku Finland.,Department of Biological and Environmental Science Centre of Excellence in Biological Interactions University of Jyväskylä Jyväskylä Finland
| | - Olaf Thalmann
- Department of Biology University of Turku Turku Finland.,Department of Pediatric Gastroenterology and Metabolic Diseases Poznan University of Medical Sciences Poznan Poland
| | - Hannu Mäkinen
- Department of Biology University of Turku Turku Finland
| | | |
Collapse
|
46
|
Hua X, Bromham L. Darwinism for the Genomic Age: Connecting Mutation to Diversification. Front Genet 2017; 8:12. [PMID: 28224003 PMCID: PMC5293951 DOI: 10.3389/fgene.2017.00012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/19/2017] [Indexed: 12/30/2022] Open
Abstract
A growing body of evidence suggests that rates of diversification of biological lineages are correlated with differences in genome-wide mutation rate. Given that most research into differential patterns of diversification rate have focused on species traits or ecological parameters, a connection to the biochemical processes of genome change is an unexpected observation. While the empirical evidence for a significant association between mutation rate and diversification rate is mounting, there has been less effort in explaining the factors that mediate this connection between genetic change and species richness. Here we draw together empirical studies and theoretical concepts that may help to build links in the explanatory chain that connects mutation to diversification. First we consider the way that mutation rates vary between species. We then explore how differences in mutation rates have flow-through effects to the rate at which populations acquire substitutions, which in turn influences the speed at which populations become reproductively isolated from each other due to the acquisition of genomic incompatibilities. Since diversification rate is commonly measured from phylogenetic analyses, we propose a conceptual approach for relating events of reproductive isolation to bifurcations on molecular phylogenies. As we examine each of these relationships, we consider theoretical models that might shine a light on the observed association between rate of molecular evolution and diversification rate, and critically evaluate the empirical evidence for these links, focusing on phylogenetic comparative studies. Finally, we ask whether we are getting closer to a real understanding of the way that the processes of molecular evolution connect to the observable patterns of diversification.
Collapse
Affiliation(s)
- Xia Hua
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra ACT, Australia
| | - Lindell Bromham
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra ACT, Australia
| |
Collapse
|
47
|
Ersmark E, Klütsch CFC, Chan YL, Sinding MHS, Fain SR, Illarionova NA, Oskarsson M, Uhlén M, Zhang YP, Dalén L, Savolainen P. From the Past to the Present: Wolf Phylogeography and Demographic History Based on the Mitochondrial Control Region. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00134] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
|
48
|
A cryptic mitochondrial DNA link between North European and West African dogs. J Genet Genomics 2016; 44:163-170. [PMID: 28302420 DOI: 10.1016/j.jgg.2016.10.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/17/2016] [Accepted: 10/21/2016] [Indexed: 01/25/2023]
Abstract
Domestic dogs have an ancient origin and a long history in Africa. Nevertheless, the timing and sources of their introduction into Africa remain enigmatic. Herein, we analyse variation in mitochondrial DNA (mtDNA) D-loop sequences from 345 Nigerian and 37 Kenyan village dogs plus 1530 published sequences of dogs from other parts of Africa, Europe and West Asia. All Kenyan dogs can be assigned to one of three haplogroups (matrilines; clades): A, B, and C, while Nigerian dogs can be assigned to one of four haplogroups A, B, C, and D. None of the African dogs exhibits a matrilineal contribution from the African wolf (Canis lupus lupaster). The genetic signal of a recent demographic expansion is detected in Nigerian dogs from West Africa. The analyses of mitochondrial genomes reveal a maternal genetic link between modern West African and North European dogs indicated by sub-haplogroup D1 (but not the entire haplogroup D) coalescing around 12,000 years ago. Incorporating molecular anthropological evidence, we propose that sub-haplogroup D1 in West African dogs could be traced back to the late-glacial dispersals, potentially associated with human hunter-gatherer migration from southwestern Europe.
Collapse
|
49
|
Freedman AH, Lohmueller KE, Wayne RK. Evolutionary History, Selective Sweeps, and Deleterious Variation in the Dog. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-121415-032155] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The dog is our oldest domesticate and has experienced a wide variety of demographic histories, including a bottleneck associated with domestication and individual bottlenecks associated with the formation of modern breeds. Admixture with gray wolves, and among dog breeds and populations, has also occurred throughout its history. Likewise, the intensity and focus of selection have varied, from an initial focus on traits enhancing cohabitation with humans, to more directed selection on specific phenotypic characteristics and behaviors. In this review, we summarize and synthesize genetic findings from genome-wide and complete genome studies that document the genomic consequences of demography and selection, including the effects on adaptive and deleterious variation. Consistent with the evolutionary history of the dog, signals of natural and artificial selection are evident in the dog genome. However, conclusions from studies of positive selection are fraught with the problem of false positives given that demographic history is often not taken into account.
Collapse
Affiliation(s)
- Adam H. Freedman
- Informatics Group, Faculty of Arts and Sciences, Harvard University, Cambridge, Massachusetts 02138
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095
| |
Collapse
|
50
|
Hindrikson M, Remm J, Pilot M, Godinho R, Stronen AV, Baltrūnaité L, Czarnomska SD, Leonard JA, Randi E, Nowak C, Åkesson M, López-Bao JV, Álvares F, Llaneza L, Echegaray J, Vilà C, Ozolins J, Rungis D, Aspi J, Paule L, Skrbinšek T, Saarma U. Wolf population genetics in Europe: a systematic review, meta-analysis and suggestions for conservation and management. Biol Rev Camb Philos Soc 2016; 92:1601-1629. [PMID: 27682639 DOI: 10.1111/brv.12298] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 08/01/2016] [Accepted: 08/26/2016] [Indexed: 01/04/2023]
Abstract
The grey wolf (Canis lupus) is an iconic large carnivore that has increasingly been recognized as an apex predator with intrinsic value and a keystone species. However, wolves have also long represented a primary source of human-carnivore conflict, which has led to long-term persecution of wolves, resulting in a significant decrease in their numbers, genetic diversity and gene flow between populations. For more effective protection and management of wolf populations in Europe, robust scientific evidence is crucial. This review serves as an analytical summary of the main findings from wolf population genetic studies in Europe, covering major studies from the 'pre-genomic era' and the first insights of the 'genomics era'. We analyse, summarize and discuss findings derived from analyses of three compartments of the mammalian genome with different inheritance modes: maternal (mitochondrial DNA), paternal (Y chromosome) and biparental [autosomal microsatellites and single nucleotide polymorphisms (SNPs)]. To describe large-scale trends and patterns of genetic variation in European wolf populations, we conducted a meta-analysis based on the results of previous microsatellite studies and also included new data, covering all 19 European countries for which wolf genetic information is available: Norway, Sweden, Finland, Estonia, Latvia, Lithuania, Poland, Czech Republic, Slovakia, Germany, Belarus, Russia, Italy, Croatia, Bulgaria, Bosnia and Herzegovina, Greece, Spain and Portugal. We compared different indices of genetic diversity in wolf populations and found a significant spatial trend in heterozygosity across Europe from south-west (lowest genetic diversity) to north-east (highest). The range of spatial autocorrelation calculated on the basis of three characteristics of genetic diversity was 650-850 km, suggesting that the genetic diversity of a given wolf population can be influenced by populations up to 850 km away. As an important outcome of this synthesis, we discuss the most pressing issues threatening wolf populations in Europe, highlight important gaps in current knowledge, suggest solutions to overcome these limitations, and provide recommendations for science-based wolf conservation and management at regional and Europe-wide scales.
Collapse
Affiliation(s)
- Maris Hindrikson
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014, Tartu, Estonia
| | - Jaanus Remm
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014, Tartu, Estonia
| | - Malgorzata Pilot
- School of Life Sciences, University of Lincoln, Green Lane, LN6 7DL, Lincoln, UK
| | - Raquel Godinho
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Astrid Vik Stronen
- Department of Chemistry and Bioscience, Section of Biology and Environmental Science, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg Øst, Denmark
| | - Laima Baltrūnaité
- Laboratory of Mammalian Biology, Nature Research Centre, Akademijos 2, 08412, Vilnius, Lithuania
| | - Sylwia D Czarnomska
- Mammal Research Institute Polish Academy of Sciences, Waszkiewicza 1, 17-230, Białowieża, Poland
| | - Jennifer A Leonard
- Department of Integrative Ecology, Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Avd. Americo Vespucio s/n, 41092, Seville, Spain
| | - Ettore Randi
- Department of Chemistry and Bioscience, Section of Biology and Environmental Science, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg Øst, Denmark
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), 40064, Ozzano dell'Emilia, Bologna, Italy
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystrasse 12, 63571, Gelnhausen, Germany
| | - Mikael Åkesson
- Department of Ecology, Grimsö Wildlife Research Station, Swedish University of Agricultural Sciences, SE-730 91, Riddarhyttan, Sweden
| | | | - Francisco Álvares
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Luis Llaneza
- ARENA Asesores en Recursos Naturales S.L. c/Perpetuo Socorro, n° 12 Entlo 2B, 27003, Lugo, Spain
| | - Jorge Echegaray
- Department of Integrative Ecology, Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Avd. Americo Vespucio s/n, 41092, Seville, Spain
| | - Carles Vilà
- Department of Integrative Ecology, Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Avd. Americo Vespucio s/n, 41092, Seville, Spain
| | - Janis Ozolins
- Latvian State Forest Research Institute "Silava", Rigas iela 111, LV-2169, Salaspils, Latvia
| | - Dainis Rungis
- Latvian State Forest Research Institute "Silava", Rigas iela 111, LV-2169, Salaspils, Latvia
| | - Jouni Aspi
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland
| | - Ladislav Paule
- Department of Phytology, Faculty of Forestry, Technical University, T.G. Masaryk str. 24, SK-96053, Zvolen, Slovakia
| | - Tomaž Skrbinšek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Vecna pot 111, 1000, Ljubljana, Slovenia
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014, Tartu, Estonia
| |
Collapse
|