1
|
Marabuto E, Nunes MS, Martins R, Mendes R, Moreira-Pinhal TC, Raimundo J, Seabra SG, Paulo OS. Integrative analysis reveals the divergence and speciation between sister Sooty Copper butterflies Lycaena bleusei and L. tityrus. Mol Phylogenet Evol 2023; 180:107699. [PMID: 36621583 DOI: 10.1016/j.ympev.2022.107699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 12/27/2022] [Accepted: 12/27/2022] [Indexed: 01/07/2023]
Abstract
The comparison of closely related taxa is cornerstone in biology, as understanding mechanisms leading up to differentiation in relation to extant shared characters are powerful tools in interpreting the evolutionary process. Hotspots of biodiversity such as the west-Mediterranean, where many lineages meet are ideal grounds to study these processes. We set to explore the interesting example of Sooty Copper butterflies: widespread Eurasian Lycaena tityrus (Poda, 1761) comes into contact in Iberia with closely related and local endemic, L. bleusei (Oberthür, 1884), which hasn't always been considered a distinct species. An integrative analysis was designed, combining the use of extensive molecular data (five genes), geometric morphometrics analyses, verified and up-to-date distribution data, and environmental niche modelling, aimed at deciphering their true relationship, their placement within European Lycaena and trace their evolutionary history. We revealed several levels of differentiation: L. bleusei and L. tityrus appear to be reciprocally monophyletic independent gene-pools, distinct in all genes analysed, having mutually diverged 4.8 Ma ago. L. tityrus but not L. bleusei, further displays a genetic structure compatible with several glacial refugia, where populations assignable to infraspecific taxa surface. Conversely, L. bleusei shows a loss in mtDNA diversity in relation to nuDNA. Morphological analyses differentiate both species according to size and shape but also discriminate strong seasonal and sexual traits and a geographical phenotype segregation in L. tityrus. Finally, updated distribution and its modelling for current and glacial timeframes reveal both species respond differently to environmental variables, defining a mostly parapatric distribution and an overlapping belt where sympatry was recovered. During the last glacial maximum, a wider expansion in L. bleusei distribution explains current isolated populations. Our study highlights the importance of gathering several lines of evidence when deciphering the relationships between closely related populations in the fringe of cryptic species realm.
Collapse
Affiliation(s)
- Eduardo Marabuto
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; Current affiliation: Leibniz Institute fir the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Bonn & Senckenberg Natural History Collections, Dresden, Germany.
| | - Miguel S Nunes
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Renata Martins
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; Current affiliation: Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Golm, 14476 Potsdam, Germany
| | - Raquel Mendes
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Tatiana C Moreira-Pinhal
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; Associação BioLiving, Rua do Outeiro, 3850-635 Frossos, Albergaria-a-Velha, Portugal
| | - João Raimundo
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Sofia G Seabra
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Octávio S Paulo
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| |
Collapse
|
2
|
Kharzinova VR, Akopyan NA, Dotsev AV, Deniskova TE, Sermyagin AA, Karpushkina TV, Solovieva AD, Brem G, Zinovieva NA. Genetic Diversity and Phylogenetic Relationships of Russian Pig Breeds Based on the Analysis of mtDNA D-Loop Polymorphism. RUSS J GENET+ 2022. [DOI: 10.1134/s102279542208004x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
3
|
Shatokhin KS. Problems of mini-pig breeding. Vavilovskii Zhurnal Genet Selektsii 2021; 25:284-291. [PMID: 34901725 PMCID: PMC8627873 DOI: 10.18699/vj21.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/02/2021] [Accepted: 02/10/2021] [Indexed: 11/19/2022] Open
Abstract
This article provides an overview of some problems of the breeding and reproduction of laboratory minipigs. The most obvious of these are the lack of centralized accounting of breeding groups, uniform selection standards
for reproduction and evaluation of breeding animals, as well as minimizing the accumulation of fitness-reducing
mutations and maintaining genetic diversity. According to the latest estimates, there are at least 30 breeding groups
of mini-pigs systematically used as laboratory animals in the world. Among them, there are both breed formations
represented by several colonies, and breeding groups consisting of a single herd. It was shown that the main selection
strategy is selection for the live weight of adults of 50–80 kg and the adaptation of animals to a specific type of biomedical experiments. For its implementation in the breeding of foreign mini-pigs, selection by live weight is practiced
at 140- and 154-day-old age. It was indicated that different herds of mini-pigs have their own breeding methods to
counteract inbred depression and maintain genetic diversity. Examples are the maximization of coat color phenotypes, the cyclical system of matching parent pairs, and the structuring of herds into subpopulations. In addition,
in the breeding of foreign mini-pigs, molecular genetic methods are used to monitor heterozygosity. Every effort is
made to keep the number of inbred crosses in the breeding of laboratory mini-pigs to a minimum, which is not always
possible due to their small number. It is estimated that to avoid close inbreeding, the number of breeding groups
should be at least 28 individuals, including boars of at least 4 genealogical lines and at least 4 families of sows. The
accumulation of genetic cargo in herds of mini-pigs takes place, but the harmful effect is rather the result of erroneous
decisions of breeders. Despite the fact that when breeding a number of mini-pigs, the goal was to complete the herds
with exclusively white animals, in most breeding groups there is a polymorphism in the phenotype of the coat color
Collapse
Affiliation(s)
- K S Shatokhin
- Novosibirsk State Agrarian University, Novosibirsk, Russia
| |
Collapse
|
4
|
Zhang J, Jiao T, Zhao S. Genetic diversity in the mitochondrial DNA D-loop region of global swine ( Sus scrofa ) populations. Biochem Biophys Res Commun 2016; 473:814-820. [DOI: 10.1016/j.bbrc.2016.03.125] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 03/26/2016] [Indexed: 11/28/2022]
|
5
|
Choi SK, Lee JE, Kim YJ, Min MS, Voloshina I, Myslenkov A, Oh JG, Kim TH, Markov N, Seryodkin I, Ishiguro N, Yu L, Zhang YP, Lee H, Kim KS. Genetic structure of wild boar (Sus scrofa) populations from East Asia based on microsatellite loci analyses. BMC Genet 2014; 15:85. [PMID: 25034725 PMCID: PMC4112609 DOI: 10.1186/1471-2156-15-85] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 07/10/2014] [Indexed: 11/30/2022] Open
Abstract
Background Wild boar, Sus scrofa, is an extant wild ancestor of the domestic pig as an agro-economically important mammal. Wild boar has a worldwide distribution with its geographic origin in Southeast Asia, but genetic diversity and genetic structure of wild boar in East Asia are poorly understood. To characterize the pattern and amount of genetic variation and population structure of wild boar in East Asia, we genotyped and analyzed microsatellite loci for a total of 238 wild boar specimens from ten locations across six countries in East and Southeast Asia. Results Our data indicated that wild boar populations in East Asia are genetically diverse and structured, showing a significant correlation of genetic distance with geographic distance and implying a low level of gene flow at a regional scale. Bayesian-based clustering analysis was indicative of seven inferred genetic clusters in which wild boars in East Asia are geographically structured. The level of genetic diversity was relatively high in wild boars from Southeast Asia, compared with those from Northeast Asia. This gradient pattern of genetic diversity is consistent with an assumed ancestral population of wild boar in Southeast Asia. Genetic evidences from a relationship tree and structure analysis suggest that wild boar in Jeju Island, South Korea have a distinct genetic background from those in mainland Korea. Conclusions Our results reveal a diverse pattern of genetic diversity and the existence of genetic differentiation among wild boar populations inhabiting East Asia. This study highlights the potential contribution of genetic variation of wild boar to the high genetic diversity of local domestic pigs during domestication in East Asia.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Hang Lee
- College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.
| | | |
Collapse
|
6
|
Chen S, Gomes R, Costa V, Santos P, Charneca R, Zhang YP, Liu XH, Wang SQ, Bento P, Nunes JL, Buzgó J, Varga G, Anton I, Zsolnai A, Beja-Pereira A. How immunogenetically different are domestic pigs from wild boars: a perspective from single-nucleotide polymorphisms of 19 immunity-related candidate genes. Immunogenetics 2013; 65:737-48. [PMID: 23846851 DOI: 10.1007/s00251-013-0718-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 06/17/2013] [Indexed: 12/22/2022]
Abstract
The coexistence of wild boars and domestic pigs across Eurasia makes it feasible to conduct comparative genetic or genomic analyses for addressing how genetically different a domestic species is from its wild ancestor. To test whether there are differences in patterns of genetic variability between wild and domestic pigs at immunity-related genes and to detect outlier loci putatively under selection that may underlie differences in immune responses, here we analyzed 54 single-nucleotide polymorphisms (SNPs) of 19 immunity-related candidate genes on 11 autosomes in three pairs of wild boar and domestic pig populations from China, Iberian Peninsula, and Hungary. Our results showed no statistically significant differences in allele frequency and heterozygosity across SNPs between three pairs of wild and domestic populations. This observation was more likely due to the widespread and long-lasting gene flow between wild boars and domestic pigs across Eurasia. In addition, we detected eight coding SNPs from six genes as outliers being under selection consistently by three outlier tests (BayeScan2.1, FDIST2, and Arlequin3.5). Among four non-synonymous outlier SNPs, one from TLR4 gene was identified as being subject to positive (diversifying) selection and three each from CD36, IFNW1, and IL1B genes were suggested as under balancing selection. All of these four non-synonymous variants were predicted as being benign by PolyPhen-2. Our results were supported by other independent lines of evidence for positive selection or balancing selection acting on these four immune genes (CD36, IFNW1, IL1B, and TLR4). Our study showed an example applying a candidate gene approach to identify functionally important mutations (i.e., outlier loci) in wild and domestic pigs for subsequent functional experiments.
Collapse
Affiliation(s)
- Shanyuan Chen
- Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto (CIBIO/UP), Campus Agrário de Vairão, Rua Padre Armando Quintas 7, 4485-661, Vairão, Portugal
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Wang SY, Luo J, Murphy RW, Wu SF, Zhu CL, Gao Y, Zhang YP. Origin of Chinese goldfish and sequential loss of genetic diversity accompanies new breeds. PLoS One 2013; 8:e59571. [PMID: 23527220 PMCID: PMC3602300 DOI: 10.1371/journal.pone.0059571] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 02/19/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Goldfish, Carassius auratus, have experienced strong anthropogenic selection during their evolutionary history, generating a tremendous extent of morphological variation relative to that in native Carassius. To locate the geographic origin of goldfish, we analyzed nucleotide sequences from part of the control region (CR) and the entire cytochrome b (Cytb) mitochondrial DNA genes for 234 goldfish and a large series of native specimens. Four important morphological characteristics used in goldfish taxonomy-body shape, dorsal fin, eye shape, and tailfin-were selected for hypothesis-testing to identify those that better correspond to evolutionary history. PRINCIPAL FINDING Haplotypes of goldfish rooted in two sublineages (C5 and C6), which contained the haplotypes of native C. a. auratus from southern China. Values of F(ST) and N(m) revealed a close relationship between goldfish and native C. a. auratus from the lower Yangtze River. An extraordinary, stepwise loss of genetic diversity was detected from native fish to goldfish and from Grass-goldfish relative to other breeds. Significantly negative results for the tests of Tajima's D and Fu and Li's D* and F* were identified in goldfish, including the Grass breed. The results identified eye-shape as being the least informative character for grouping goldfish with respect to their evolutionary history. Fisher's exact test identified matrilineal constraints on domestication. CONCLUSIONS Chinese goldfish have a matrilineal origin from native southern Chinese C. a. auratus, especially the lineages from the lower Yangtze River. Anthropogenic selection of the native Carassius eliminated aesthetically unappealing goldfish and this action appeared to be responsible for the stepwise decrease in genetic diversity of domesticated goldfish, a process similar to that reported for the domestication of pigs, rice, and maize. The three-breed taxonomy--Grass-goldfish, Egg-goldfish, and Wen-goldfish--better reflected the history of domestication.
Collapse
Affiliation(s)
- Shu-Yan Wang
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Jing Luo
- Laboratory for Conservation and Utilization of Bio-resources, College of Life Sciences, Yunnan University, Kunming, China
| | - Robert W. Murphy
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Canada
| | - Shi-Fang Wu
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
| | - Chun-Ling Zhu
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
| | - Yun Gao
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
- * E-mail: (YG); (Y-PZ)
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
- Laboratory for Conservation and Utilization of Bio-resources, College of Life Sciences, Yunnan University, Kunming, China
- * E-mail: (YG); (Y-PZ)
| |
Collapse
|
8
|
A high throughput genotyping approach reveals distinctive autosomal genetic signatures for European and Near Eastern wild boar. PLoS One 2013; 8:e55891. [PMID: 23460788 PMCID: PMC3584081 DOI: 10.1371/journal.pone.0055891] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 01/07/2013] [Indexed: 11/19/2022] Open
Abstract
The lack of a Near Eastern genetic signature in modern European porcine breeds indicates that, although domestic pigs from the Fertile Crescent entered Europe during the Neolithic, they were completely replaced by their European counterparts in a short window of time. Whilst the absence of such genetic signature has been convincingly demonstrated at the mitochondrial level, variation at the autosomal genomes of European and Near Eastern Sus scrofa has not been compared yet. Herewith, we have explored the genetic relationships among 43 wild boar from Europe (N = 21), Near East (N = 19) and Korea (N = 3), and 40 Iberian (N = 16), Canarian (N = 4) and Mangalitza (N = 20) pigs by using a high throughput SNP genotyping platform. After data filtering, 37,167 autosomal SNPs were used to perform population genetics analyses. A multidimensional scaling plot based on genome-wide identity-by-state pairwise distances inferred with PLINK showed that Near Eastern and European wild boar populations are genetically differentiated. Maximum likelihood trees built with TreeMix supported this conclusion i.e. an early population split between Near Eastern and European Sus scrofa was observed. Moreover, analysis of the data with Structure evidenced that the sampled Iberian, Canarian and Mangalitza pigs did not carry any autosomal signature compatible with a Near Eastern ancestry, a finding that agrees well with previous mitochondrial studies.
Collapse
|
9
|
Ren QP, Fan Z, Zhou XM, Jiang GF, Wang YT, Liu YX. Identification and characterization of anonymous nuclear markers for the double-striped cockroach, Blattella bisignata. BULLETIN OF ENTOMOLOGICAL RESEARCH 2013; 103:29-35. [PMID: 22697889 DOI: 10.1017/s0007485312000375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
During the last decade, multilocus analysis has gradually become a powerful tool for the studies of population genetics and phylogeography. The double-striped cockroach, Blattella bisignata, is endemic to southeast Asia, and there is currently little genetic information available for the species. We chose it as the target species to investigate a biodiversity hotspot in southwest China. Here, we report the identification and characterization of 11 single-copy anonymous nuclear markers with an average length of 378bp. These loci, isolated from a genomic library of B. bisignata, can amplify in two additional Blattella species (B. germanica and B. lituricollis). While testing these markers in representative species of Blattellidae, Blattidae and Epilampridae, some of them can cross-amplify successfully. After sequencing 30 individuals collected from southern China per locus, we found relatively high variability (approximately 3.6 SNPs per 100bp). Finally, a small-scale study was also performed to show that these markers do indeed fulfill the expectations as phylogeographic markers.
Collapse
Affiliation(s)
- Q-P Ren
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | | | | | | | | | | |
Collapse
|