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Cao L, Chen P, Hou X, Ma J, Yang N, Lu Y, Huang H. rDNA and mtDNA analysis for the identification of genetic characters in the hybrid grouper derived from hybridization of Cromileptes altivelis (female) × Epinephelus lanceolatus (male). BMC Genom Data 2024; 25:5. [PMID: 38216865 PMCID: PMC10787421 DOI: 10.1186/s12863-023-01188-5] [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: 08/09/2023] [Accepted: 12/20/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Hybridization is a useful strategy to produce offspring with more desirable phenotypic characteristics than those of parents. The hybrid grouper derived from the cross of Cromileptes altivelis (♀, 2n = 48) with Epinephelus lanceolatus (♂, 2n = 48) exhibits improved growth compared with its female parent, which makes it valuable to aquaculture. However, the genetic traits of the hybrid grouper are poorly understood. RESULTS The observations showed that the hybrid grouper was diploid (2n = 48) and displayed intermediate morphology with the parent's measurable characteristics. The ribosomal DNA (rDNA) and mitochondria DNA (mtDNA) were characterized at molecular and phylogenetic level. High similarity and low genetic distance of 5S rDNA and mtDNA sequences between the hybrid grouper and C. altivelis showed that the hybrid grouper had a closer genetic relationship with female parents. The reconstructed phylogenetic tree based on COI gene and D-loop region of mtDNA recovered that mtDNA was maternally inherited in the hybrid grouper. Additionally, the DNA methylation level of 5S rDNA intergenic spacers (IGS) sequence was tested in here. The results showed that the DNA methylation status of the hybrid grouper was significantly lower than that of C. altivelis. CONCLUSION Results of this study provide important data on the genetic characteristics of the hybrid derived from the cross of C. altivelis and E. lanceolatus, and contribute the knowledge of both evolution and marine fish breeding.
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Affiliation(s)
- Liu Cao
- Yazhou Bay Innovation Institute, Sanya, 572022, China
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, 572022, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, 572022, China
- Hainan Tropical Ocean University, Sanya, 572022, China
| | - Pan Chen
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, 572022, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, 572022, China
- Hainan Tropical Ocean University, Sanya, 572022, China
| | - Xingrong Hou
- Yazhou Bay Innovation Institute, Sanya, 572022, China
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, 572022, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, 572022, China
- Hainan Tropical Ocean University, Sanya, 572022, China
| | - Jun Ma
- Yazhou Bay Innovation Institute, Sanya, 572022, China
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, 572022, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, 572022, China
- Hainan Tropical Ocean University, Sanya, 572022, China
| | - Ning Yang
- Yazhou Bay Innovation Institute, Sanya, 572022, China
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, 572022, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, 572022, China
- Hainan Tropical Ocean University, Sanya, 572022, China
| | - Yan Lu
- Hainan Tropical Ocean University, Sanya, 572022, China
| | - Hai Huang
- Yazhou Bay Innovation Institute, Sanya, 572022, China.
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, 572022, China.
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, 572022, China.
- Hainan Tropical Ocean University, Sanya, 572022, China.
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Pfau RS, Kozora AN, Gatica‐Colima AB, Sudman PS. Population genetic structure of a Chihuahuan Desert endemic mammal, the desert pocket gopher, Geomys arenarius. Ecol Evol 2023; 13:e10576. [PMID: 37780089 PMCID: PMC10539045 DOI: 10.1002/ece3.10576] [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: 12/12/2022] [Revised: 08/30/2023] [Accepted: 09/18/2023] [Indexed: 10/03/2023] Open
Abstract
The biogeographic history of the Chihuahuan Desert is complex, driven by numerous physiographic events and climatic changes. This dynamic history would have influenced the flora and fauna of the region including the desert pocket gopher, Geomys arenarius, a subterranean rodent endemic to the northern Chihuahuan Desert. G. arenarius is restricted to sandy soils and are considered to have a disjunct distribution. Two subspecies are recognized: G. a. arenarius and G. a. brevirostris. We used multilocus nuclear (amplified fragment length polymorphisms) and mitochondrial DNA (ND2) sequence data to uncover patterns of genetic diversity within and among populations of G. arenarius. We evaluated correspondence of genetic patterns to traditionally accepted subspecies boundaries, mapped the distribution of potentially suitable soils to identify barriers or corridors to dispersal and to guide future survey efforts, provided evidence that could be used to recognize distinct population segments, and quantified genetic diversity within populations. Both datasets were largely concordant and demonstrated hierarchical patterns of genetic divergence. The greatest divergence was consistent with the two recognized subspecies. Mapping of potentially habitable soils revealed likely barriers to dispersal contributing to the allopatric pattern of geographic distribution and areas, which may be occupied by G. arenarius but not yet documented. Because G. arenarius is restricted to soils with high sand content, and these habitable soils are disjunct within the region occupied by this species, historical factors that impacted soil deposition and deflation likely contributed to the observed patterns of genetic divergence. Genetic diversity was higher within populations of the southern subspecies (G. a. arenarius) compared to G. a. brevirostris. This may be due to a greater availability of continuous suitable soils within the range of G. a. arenarius or higher density due to greater food availability (currently or historically)-both of which could allow for a higher effective population size.
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Affiliation(s)
- Russell S. Pfau
- Department of Biological SciencesTarleton State UniversityStephenvilleTexasUSA
| | | | - Ana B. Gatica‐Colima
- Departamento de Ciencias Químico‐BiológicasInstituto de Ciencias Biomédicas, Universidad Autónoma de Ciudad JuárezCiudad JuarezMexico
| | - Philip S. Sudman
- Department of Biological SciencesTarleton State UniversityStephenvilleTexasUSA
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3
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Hu W, Hao Z, Du P, Di Vincenzo F, Manzi G, Cui J, Fu YX, Pan YH, Li H. Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition. Science 2023; 381:979-984. [PMID: 37651513 DOI: 10.1126/science.abq7487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/11/2023] [Indexed: 09/02/2023]
Abstract
Population size history is essential for studying human evolution. However, ancient population size history during the Pleistocene is notoriously difficult to unravel. In this study, we developed a fast infinitesimal time coalescent process (FitCoal) to circumvent this difficulty and calculated the composite likelihood for present-day human genomic sequences of 3154 individuals. Results showed that human ancestors went through a severe population bottleneck with about 1280 breeding individuals between around 930,000 and 813,000 years ago. The bottleneck lasted for about 117,000 years and brought human ancestors close to extinction. This bottleneck is congruent with a substantial chronological gap in the available African and Eurasian fossil record. Our results provide new insights into our ancestry and suggest a coincident speciation event.
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Affiliation(s)
- Wangjie Hu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Brain Functional Genomics of Ministry of Education, School of Life Science, East China Normal University, Shanghai, China
| | - Ziqian Hao
- College of Artificial Intelligence and Big Data for Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Pengyuan Du
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- College of Artificial Intelligence and Big Data for Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | | | - Giorgio Manzi
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Jialong Cui
- Key Laboratory of Brain Functional Genomics of Ministry of Education, School of Life Science, East China Normal University, Shanghai, China
| | - Yun-Xin Fu
- Department of Biostatistics and Data Science, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
- Key Laboratory for Conservation and Utilization of Bioresources, Yunnan University, Kunming, China
| | - Yi-Hsuan Pan
- Key Laboratory of Brain Functional Genomics of Ministry of Education, School of Life Science, East China Normal University, Shanghai, China
| | - Haipeng Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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Mitochondrial genomes reveal mid-Pleistocene population divergence, and post-glacial expansion, in Australasian snapper (Chrysophrys auratus). Heredity (Edinb) 2023; 130:30-39. [PMID: 36463371 DOI: 10.1038/s41437-022-00579-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 11/17/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
Glacial cycles play important roles in determining the phylogeographic structure of terrestrial species, however, relatively little is known about their impacts on the distribution of marine biota. This study utilised modern (n = 350) and ancient (n = 26) mitochondrial genomes from Australasian snapper (Chrysophrys auratus) sampled in New Zealand to assess their demographic and phylogeographic history. We also tested for changes in genetic diversity using the up to 750-year-old mitochondrial genomes from pre-European archaeological sites to assess the potential impacts of human exploitation. Nucleotide diversity and haplotype diversity was high (π = 0.005, h = 0.972). There was no significant change in nucleotide diversity over the last 750 years (p = 0.343), with no detectable loss of diversity as a result of indigenous and industrial-scale fishing activity. While there was no evidence for contemporary population structure (AMOVA, p = 0.764), phylogeographic analyses identified two distinct mitochondrial clades that diverged approximately 650,000 years ago during the mid-Pleistocene, suggesting the species experienced barriers to gene flow when sea levels dropped over 120 m during previous glacial maxima. An exponential population increase was also observed around 8000 years ago consistent with a post-glacial expansion, which was likely facilitated by increased ocean temperatures and rising sea levels. This study demonstrates that glacial cycles likely played an important role in the demographic history of C. auratus and adds to our growing understanding of how dynamic climatic changes have influenced the evolution of coastal marine species.
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5
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Worden R. The evolution of language by sexual selection. Front Psychol 2022; 13:1060510. [PMID: 36619053 PMCID: PMC9815550 DOI: 10.3389/fpsyg.2022.1060510] [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: 10/03/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Most accounts of the evolution of language assume that language and greater intelligence are beneficial adaptations, leading to increases in survival fitness. These accounts emphasise natural selection, with language as an adaptation to the habitat, placing less emphasis on sexual selection and reproductive fitness. An account of language evolution by natural selection alone faces problems in accounting for the prodigious power and expressivity of human language. Modern language (and its recent antecedents) would appear to offer only small incremental benefits over simpler language, which would require a smaller brain with smaller metabolic costs. Accounts by natural selection also face problems in accounting for the uniqueness of human language and intelligence. I therefore consider a hybrid account, in which both natural selection and sexual selection played a role in the evolution of language and intelligence, probably at different times. Specifically, in this account, early language was driven by natural selection to collaborate. Then later humans became subject to sexual selection for superior intelligence, with language acting as the main display mechanism for intelligence. It is hard to determine the relative roles of natural and sexual selection over the time course of the evolution of language. In the later stages, sexual selection to display intelligence drove a runaway selection process towards powerful modern language. This hybrid account retains the benefits of accounts by natural selection, while also accounting for the prodigious power of human language and intelligence, and for its uniqueness compared to other primates. Sexual selection often leads to traits which are unique to a species, and are exaggerated beyond natural needs. On this account, the capability for language may have evolved in the order: (1) pragmatics and a theory of mind; (2) using single words and constructions; (3) learning and using syntax. In this model, relevance-based pragmatics evolved before language; then, single words and constructions came into use; and later, syntax condensed out of pragmatics, as a codification of some pragmatic rules of inference. This order requires only incremental extensions of primate cognition, and agrees with the order in which children learn language.
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6
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Li B, Yang Z. Multilocus evidence provides insight into the demographic history and asymmetrical gene flow between
Ostrinia furnacalis
and
Ostrinia nubilalis
(Lepidoptera: Crambidae) in the Yili area, Xinjiang, China. Ecol Evol 2022; 12:e9504. [PMID: 36407909 PMCID: PMC9667411 DOI: 10.1002/ece3.9504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 10/10/2022] [Accepted: 10/25/2022] [Indexed: 11/18/2022] Open
Abstract
Tianshan Mountains provide a model for studying biological evolution and speciation. Here we assess the evolutionary history of Ostrinia furnacalis (ACB) and Ostrinia nubilalis (ECB), which are sympatric in the Yili River Valley in Xinjiang, China. Our study is based on the historical gene flow analyses of two species by using three mitochondrial DNA (mtDNA, COI, COII, Cytb) and four nuclear DNA (nuDNA, EF‐1α, Wingless, RPS5, CAD) markers obtained from representatives of HC (Huocheng), YN (Yining), XY (Xinyuan), and MNS (Manasi). Our results reveal that there is an asymmetrical gene flow pattern between the four populations. The population migratory pathways between these different populations show inflow into HC and YN, outflow from XY, and that MNS maintained a flow balance. Bayesian divergence time dating based on the COI gene suggests that the genetic divergence between the two species in this area may have occurred in Holocene at 0.008 Mya. Neutrality tests (Tajima's D, Fu's Fs), and mismatch distribution test results suggest that population expansion events may not have occurred in the recent past. The demographic history and gene flow pattern between ACB and ECB may follow the “mountain isolation” hypothesis. The ML and BI trees of the mtDNA haplotype dataset show that ECB haplotypes are grouped together in a distinct clade and are clearly separate from ACB haplotypes. However, the geographical pattern of haplotype distribution is less clear for both ACB and ECB, supporting that there has been frequent gene flow among the geographic populations in the Tianshan Mountains. These findings indicate that the Tianshan Mountains are less likely a barrier to gene flow of the two species.
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Affiliation(s)
- Bing Li
- College of Plant ProtectionNorthwest A&F UniversityYanglingChina
- Key Laboratory of Plant Protection Resources and Pest MangagementNorthwest A&F UniversityYanglingChina
| | - Zhaofu Yang
- College of Plant ProtectionNorthwest A&F UniversityYanglingChina
- Key Laboratory of Plant Protection Resources and Pest MangagementNorthwest A&F UniversityYanglingChina
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7
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Smith ML, Wallace J, Tank DC, Sullivan J, Carstens BC. The role of multiple Pleistocene refugia in promoting diversification in the Pacific Northwest. Mol Ecol 2022; 31:4402-4416. [PMID: 35780485 DOI: 10.1111/mec.16595] [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: 05/12/2021] [Revised: 06/14/2022] [Accepted: 06/20/2022] [Indexed: 10/17/2022]
Abstract
Pleistocene glacial cycles drastically changed the distributions of taxa endemic to temperate rainforests in the Pacific Northwest, with many experiencing reduced habitat suitability during glacial periods. In this study, we investigate whether glacial cycles promoted intraspecific divergence and whether subsequent range changes led to secondary contact and gene flow. For seven invertebrate species endemic to the PNW, we estimated Species Distribution Models (SDMs) and projected them onto current and historical climate conditions to assess how habitat suitability changed during glacial cycles. Using single nucleotide polymorphism (SNP) data from these species, we assessed population genetic structure and used a machine-learning approach to compare models with and without gene flow between populations upon secondary contact after the Last Glacial Maximum (LGM). Finally, we estimated divergence times and rates of gene flow between populations. SDMs suggest that there was less suitable habitat in the North Cascades and Northern Rocky Mountains during glacial compared to interglacial periods, resulting in reduced habitat suitability and habitat fragmentation during the LGM. Our genomic data identify population structure in all taxa, and support gene flow upon secondary contact in five of the seven taxa. Parameter estimates suggest that population divergences date to the later Pleistocene for most populations. Our results support a role of refugial dynamics in driving intraspecific divergence in the Cascades Range. In these invertebrates, population structure often does not correspond to current biogeographic or environmental barriers. Rather, population structure may reflect refugial lineages that have since expanded their ranges, often leading to secondary contact between once isolated lineages.
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Affiliation(s)
- Megan L Smith
- Department of Evolution, Ecology & Organismal Biology, The Ohio State University, 318 W. 12th Avenue, 300 Aronoff Labs, Columbus, OH 43210-1293, USA
| | - Jessica Wallace
- Department of Evolution, Ecology & Organismal Biology, The Ohio State University, 318 W. 12th Avenue, 300 Aronoff Labs, Columbus, OH 43210-1293, USA
| | - David C Tank
- Department of Botany and Rocky Mountain Herbarium, University of Wyoming, 1000 E. University Ave., Laramie, WY 82071, USA.,Department of Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID 83844-3051, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID 83844-3051, USA
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID 83844-3051, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID 83844-3051, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology & Organismal Biology, The Ohio State University, 318 W. 12th Avenue, 300 Aronoff Labs, Columbus, OH 43210-1293, USA
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A retrotransposon storm marks clinical phenoconversion to late-onset Alzheimer's disease. GeroScience 2022; 44:1525-1550. [PMID: 35585302 PMCID: PMC9213607 DOI: 10.1007/s11357-022-00580-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/26/2022] [Indexed: 12/03/2022] Open
Abstract
Recent reports have suggested that the reactivation of otherwise transcriptionally silent transposable elements (TEs) might induce brain degeneration, either by dysregulating the expression of genes and pathways implicated in cognitive decline and dementia or through the induction of immune-mediated neuroinflammation resulting in the elimination of neural and glial cells. In the work we present here, we test the hypothesis that differentially expressed TEs in blood could be used as biomarkers of cognitive decline and development of AD. To this aim, we used a sample of aging subjects (age > 70) that developed late-onset Alzheimer’s disease (LOAD) over a relatively short period of time (12–48 months), for which blood was available before and after their phenoconversion, and a group of cognitive stable subjects as controls. We applied our developed and validated customized pipeline that allows the identification, characterization, and quantification of the differentially expressed (DE) TEs before and after the onset of manifest LOAD, through analyses of RNA-Seq data. We compared the level of DE TEs within more than 600,000 TE-mapping RNA transcripts from 25 individuals, whose specimens we obtained before and after their phenotypic conversion (phenoconversion) to LOAD, and discovered that 1790 TE transcripts showed significant expression differences between these two timepoints (logFC ± 1.5, logCMP > 5.3, nominal p value < 0.01). These DE transcripts mapped both over- and under-expressed TE elements. Occurring before the clinical phenoconversion, this TE storm features significant increases in DE transcripts of LINEs, LTRs, and SVAs, while those for SINEs are significantly depleted. These dysregulations end with signs of manifest LOAD. This set of highly DE transcripts generates a TE transcriptional profile that accurately discriminates the before and after phenoconversion states of these subjects. Our findings suggest that a storm of DE TEs occurs before phenoconversion from normal cognition to manifest LOAD in risk individuals compared to controls, and may provide useful blood-based biomarkers for heralding such a clinical transition, also suggesting that TEs can indeed participate in the complex process of neurodegeneration.
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Walters AD, Trujillo DA, Berg DJ. Micro-endemic species of snails and amphipods show population genetic structure across very small geographic ranges. Heredity (Edinb) 2022; 128:325-337. [PMID: 35318433 PMCID: PMC9076663 DOI: 10.1038/s41437-022-00521-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/22/2022] [Accepted: 02/22/2022] [Indexed: 11/08/2022] Open
Abstract
Understanding variation in population genetic structure, even across small distances and for species with extremely limited ranges, is critical for conservation planning and the development of effective management strategies for imperiled species. Organisms that occupy the same geographic extent can maintain different population structures, ranging from highly diverged to panmictic. Such differences can result from differences in biological characteristics such as dispersal ability or demographic history. We used microsatellite loci to evaluate population genetic structure and variation of four desert spring invertebrates having high to low dispersal ability: the lung snail Physa acuta, two species of gilled snails (Juturnia kosteri and Pyrgulopsis roswellensis; family Hydrobiidae) and the amphipod Gammarus desperatus. The study location represents entire species ranges for the micro-endemic hydrobiids and G. desperatus, while P. acuta is ubiquitous throughout much of North America. We found little evidence of significant population genetic structure for P. acuta and J. kosteri, but much more for P. roswellensis and G. desperatus. Our results demonstrate differences in habitat preference and/or dispersal ability between the species. This information provides insight into how gene flow shapes varying population genetic structure between species across small spatial scales (<100 km2). Most importantly, our results suggest that conservation agencies should not consider these micro-endemic species to be composed of single populations, but rather, that management plans for such species should account for population genetic variation across the species' ranges.
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Affiliation(s)
| | | | - David J Berg
- Department of Biology, Miami University, Hamilton, OH, USA
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10
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Sun H, Jia F, Zhao W, Zhou Z, Li C, Wang J, Yao Y. Population Genetics Reveals That the Western Tianshan Mountains Populations of Agrilus mali (Coleoptera: Buprestidae) May Have Not been Recently Introduced. Front Genet 2022; 13:857866. [PMID: 35401710 PMCID: PMC8988243 DOI: 10.3389/fgene.2022.857866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Agrilus mali Matsumura is a wood-boring beetle that aggressively attacks species of the genus Malus, that has recently caused serious damage to the wild apple tree M. sieversii (Lebed.) in the western Tianshan Mountains in Xinjiang. It was first detected there in the early 1990s and spread rapidly, being thus considered a regional invasive pest. To explore the possible outbreak mechanism of the local population and characterize the genetic differentiation of A. mali across different regions of China, we used three mitochondrial genes (COI, COII, and CytB) to investigate the genetic diversity and genetic structure of 17 A. mali populations containing 205 individuals collected from five Chinese provinces. Among them, nine populations were from the western Tianshan Mountains. Ultimately, of the 136 pairwise Fst comparisons, 99 showed high genetic differentiation among overall populations, and Tianshan populations exhibited significant differentiation with most of the non-Tianshan populations. Furthermore, A. mali populations represented relatively abundant haplotypes (54 haplotypes). Nine populations from the Tianshan Mountains showed 32 haplotypes (26 of which were unique), displaying relatively high genetic diversity. Additionally, the Mantel test revealed population genetic differentiation among either overall populations or the Tianshan Mountains populations, likely caused by geographical isolation. Phylogenic relationships showed that all populations clustered into three clades, and Tianshan Mountains populations, including CY, occupied one of the three clades. These results suggest that A. mali in the western Tianshan region has possibly been present in the area for a long period, and may not have been introduced recently. Highly frequent gene flows within Tianshan populations are possibly caused by human activities and may enhance the adaptability of A. mali along the western Tianshan Mountains, leading to periodic outbreaks. These findings enhance our understanding of jewel beetle population genetics and provide valuable information for pest management.
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Affiliation(s)
- Huiquan Sun
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Feiran Jia
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Wenxia Zhao
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Zhongfu Zhou
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Chengjin Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Jianjun Wang
- Liaoning Academy of Forest Science, Shenyang, China
| | - Yanxia Yao
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
- *Correspondence: Yanxia Yao,
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11
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Wang X, Tong L, Deng J, Li L, Xiang P, Xu L, Luo Z, Yang K, Song Z. Insights into historical drainage evolution based on the phylogeography of Schizopygopsis malacanthus Herzenstein (Cypriniformes, Cyprinidae) across the upper and middle Yalong River drainage in the Hengduan Mountains region, southwest China. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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12
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Kramina TE, Lysova MV, Samigullin TH, Özbek MU, Sokoloff DD. When Morphology and Biogeography Approximate Nuclear ITS but Conflict with Plastid Phylogeny: Phylogeography of the Lotus dorycnium Species Complex (Leguminosae). PLANTS 2022; 11:plants11030410. [PMID: 35161391 PMCID: PMC8840542 DOI: 10.3390/plants11030410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/29/2022] [Accepted: 01/30/2022] [Indexed: 11/18/2022]
Abstract
Lotus dorycnium s.l. is a complex of taxa traditionally regarded as members of Dorycnium. It has a wide Mediterranean range, extending in the north to Central and Eastern Europe, and in the east to the Crimea, the Caucasus, and the Western Caspian region. Molecular phylogenetic data support placement of the L. dorycnium complex in the genus Lotus. The present study investigated the phylogeny, phylogeography and morphological variability of the L. dorycnium complex across its distribution range to reveal the main trends in genetic and morphological differentiation in this group. The results of the morphological analyses demonstrated some degree of differentiation, with L. d. ssp. herbaceus, ssp. gracilis, and ssp. anatolicus more or less well defined, whereas ssp. dorycnium, ssp. germanicus, and ssp. haussknechtii can be hardly distinguished from each other using morphology. Analyses of the L. dorycnium complex based on nrITS revealed a tendency towards a geographic differentiation into Western, Eastern, and Turkish groups. Phylogenetic and phylogeographic analyses of the same set of specimens using concatenated plastid markers trnL-F, rps16, and psbA-trnH demonstrated a low resolution between the L. dorycnium complex and L. hirsutus, as well as among the taxa within the L. dorycnium complex, which can be interpreted as evidence of an incomplete lineage sorting or hybridization. The evolutionary processes responsible for incongruence in phylogenetic signals between plastid and nuclear sequences of the morphologically well-defined species L. dorycnium and L. hirsutus were most likely localized in the Eastern Mediterranean. A possibility of rare gene exchange between the L. dorycnium complex and the group of L. graecus is revealed for the first time.
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Affiliation(s)
- Tatiana E. Kramina
- Department of Higher Plants, Biological Faculty, Lomonosov Moscow State University, GSP-1, Leninskie Gory, 119234 Moscow, Russia;
- Correspondence: ; Tel.: +7-985-723-0916
| | - Maya V. Lysova
- LLC “Amplitech”, 1-ya Kuryanovskaya Str., 34-8, 109235 Moscow, Russia;
| | - Tahir H. Samigullin
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, GSP-1, Leninskie Gory, 119991 Moscow, Russia;
| | - Mehmet U. Özbek
- Department of Biology, Faculty of Science, Gazi University, Teknikokullar, Ankara 06500, Turkey;
| | - Dmitry D. Sokoloff
- Department of Higher Plants, Biological Faculty, Lomonosov Moscow State University, GSP-1, Leninskie Gory, 119234 Moscow, Russia;
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13
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Hartfield M, Poulsen NA, Guldbrandtsen B, Bataillon T. Using singleton densities to detect recent selection in Bos taurus. Evol Lett 2021; 5:595-606. [PMID: 34917399 PMCID: PMC8645200 DOI: 10.1002/evl3.263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 11/05/2022] Open
Abstract
Many quantitative traits are subject to polygenic selection, where several genomic regions undergo small, simultaneous changes in allele frequency that collectively alter a phenotype. The widespread availability of genome data, along with novel statistical techniques, has made it easier to detect these changes. We apply one such method, the "Singleton Density Score" (SDS), to the Holstein breed of Bos taurus to detect recent selection (arising up to around 740 years ago). We identify several genes as candidates for targets of recent selection, including some relating to cell regulation, catabolic processes, neural-cell adhesion and immunity. We do not find strong evidence that three traits that are important to humans-milk protein content, milk fat content, and stature-have been subject to directional selection. Simulations demonstrate that because B. taurus recently experienced a population bottleneck, singletons are depleted so the power of SDS methods is reduced. These results inform on which genes underlie recent genetic change in B. taurus, while providing information on how polygenic selection can be best investigated in future studies.
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Affiliation(s)
- Matthew Hartfield
- Bioinformatics Research CentreAarhus UniversityAarhusDK‐8000Denmark
- Institute of Evolutionary BiologyUniversity of EdinburghEdinburghEH9 3FLUnited Kingdom
| | | | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and GeneticsAarhus UniversityTjeleDK‐8830Denmark
- Rheinische Friedrich‐Wilhelms‐Universität BonnInstitut für TierwissenschaftenBonnDE‐53115Germany
- Department of Veterinary SciencesCopenhagen UniversityFrederiksberg CDK‐1870Denmark
| | - Thomas Bataillon
- Bioinformatics Research CentreAarhus UniversityAarhusDK‐8000Denmark
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Shilovsky GA, Putyatina TS, Markov AV. Altruism and Phenoptosis as Programs Supported by Evolution. BIOCHEMISTRY. BIOKHIMIIA 2021; 86:1540-1552. [PMID: 34937533 PMCID: PMC8678581 DOI: 10.1134/s0006297921120038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 11/22/2022]
Abstract
Phenoptosis is a programmed death that has emerged in the process of evolution, sometimes taking the form of an altruistic program. In particular, it is believed to be a weapon against the spread of pandemics in the past and an obstacle in fighting pandemics in the present (COVID). However, on the evolutionary scale, deterministic death is not associated with random relationships (for example, bacteria with a particular mutation), but is a product of higher nervous activity or a consequence of established hierarchy that reaches its maximal expression in eusocial communities of Hymenoptera and highly social communities of mammals. Unlike a simple association of individuals, eusociality is characterized by the appearance of non-reproductive individuals as the highest form of altruism. In contrast to primitive programs for unicellular organisms, higher multicellular organisms are characterized by the development of behavior-based phenoptotic programs, especially in the case of reproduction-associated limitation of lifespan. Therefore, we can say that the development of altruism in the course of evolution of sociality leads in its extreme manifestation to phenoptosis. Development of mathematical models for the emergence of altruism and programmed death contributes to our understanding of mechanisms underlying these paradoxical counterproductive (harmful) programs. In theory, this model can be applied not only to insects, but also to other social animals and even to the human society. Adaptive death is an extreme form of altruism. We consider altruism and programmed death as programmed processes in the mechanistic and adaptive sense, respectively. Mechanistically, this is a program existing as a predetermined chain of certain responses, regardless of its adaptive value. As to its adaptive value (regardless of the degree of "phenoptoticity"), this is a characteristic of organisms that demonstrate high levels of kinship, social organization, and physical association typical for higher-order individuals, e.g., unicellular organisms forming colonies with some characteristics of multicellular animals or colonies of multicellular animals displaying features of supraorganisms.
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Affiliation(s)
- Gregory A Shilovsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, Russia
| | - Tatyana S Putyatina
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Alexander V Markov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Borissiak Paleontological Institute, Russian Academy of Sciences, Moscow, 117997, Russia
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15
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Rico Y, León-Tapia MÁ, Zurita-Solís M, Rodríguez-Gómez F, Vásquez-Morales SG. Influence of Pleistocene climatic oscillations on the phylogeography and demographic history of endemic vulnerable trees (section Magnolia) of the Tropical Montane Cloud Forest in Mexico. PeerJ 2021; 9:e12181. [PMID: 34692249 PMCID: PMC8485838 DOI: 10.7717/peerj.12181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 08/29/2021] [Indexed: 11/20/2022] Open
Abstract
The Tropical Montane Cloud Forest (TMCF) is a highly dynamic ecosystem that has undergone frequent spatial changes in response to the interglacial-glacial cycles of the Pleistocene. These climatic fluctuations between cold and warm cycles have led to species range shifts and contractions-expansions, resulting in complex patterns of genetic structure and lineage divergence in forest tree species. In this study, we sequenced four regions of the chloroplast DNA (trnT-trnL, trnK5-matk, rpl32-trnL, trnS-trnG) for 20 populations and 96 individuals to evaluate the phylogeography, historical demography, and paleodistributions of vulnerable endemic TMCF trees in Mexico: Magnolia pedrazae (north-region), M. schiedeana (central-region), and M. schiedeana population Oaxaca (south-region). Our data recovered 49 haplotypes that showed a significant phylogeographic structure in three regions: north, central, and south. Bayesian Phylogeographic and Ecological Clustering (BPEC) analysis also supported the divergence in three lineages and highlighted the role of environmental factors (temperature and precipitation) in genetic differentiation. Our historical demography analyses revealed demographic expansions predating the Last Interglacial (LIG, ~125,000 years ago), while Approximate Bayesian Computation (ABC) simulations equally supported two contrasting demographic scenarios. The BPEC and haplotype network analyses suggested that ancestral haplotypes were geographically found in central Veracruz. Our paleodistributions modeling showed evidence of range shifts and expansions-contractions from the LIG to the present, which suggested the complex evolutionary dynamics associated to the climatic oscillations of the Pleistocene. Habitat management of remnant forest fragments where large and genetically diverse populations occur in the three TMCF regions analyzed would be key for the conservation of these magnolia populations.
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Affiliation(s)
- Yessica Rico
- Red de Diversidad Biológica del Occidente Mexicano, Instituto de Ecología A.C., Pátzcuaro, Michoacán, México
- CONACYT, Ciudad de México, México
| | - M. Ángel León-Tapia
- Laboratorio de Sistemática Filogenética, Red de Biología Evolutiva, Instituto de Ecología A.C., Xalapa, Veracruz, Mexico
| | - Marisol Zurita-Solís
- Red de Diversidad Biológica del Occidente Mexicano, Instituto de Ecología A.C., Pátzcuaro, Michoacán, México
| | - Flor Rodríguez-Gómez
- Departamento de Ciencias Computacionales, División de Electrónica y Computación, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Suria Gisela Vásquez-Morales
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
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16
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Godinez CJP, Dadios PJD, Espina DM, Matsunaga M, Nishibori M. Population Genetic Structure and Contribution of Philippine Chickens to the Pacific Chicken Diversity Inferred From Mitochondrial DNA. Front Genet 2021; 12:698401. [PMID: 34367257 PMCID: PMC8340678 DOI: 10.3389/fgene.2021.698401] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/17/2021] [Indexed: 11/20/2022] Open
Abstract
The Philippines is considered one of the biodiversity hotspots for animal genetic resources. In spite of this, population genetic structure, genetic diversity, and past population history of Philippine chickens are not well studied. In this study, phylogeny reconstruction and estimation of population genetic structure were based on 107 newly generated mitochondrial DNA (mtDNA) complete D-loop sequences and 37 previously published sequences of Philippine chickens, consisting of 34 haplotypes. Philippine chickens showed high haplotypic diversity (Hd = 0.915 ± 0.011) across Southeast Asia and Oceania. The phylogenetic analysis and median-joining (MJ) network revealed predominant maternal lineage haplogroup D classified throughout the population, while support for Philippine-Pacific subclade was evident, suggesting a Philippine origin of Pacific chickens. Here, we observed Philippine red junglefowls (RJFs) at the basal position of the tree within haplogroup D indicating an earlier introduction into the Philippines potentially via mainland Southeast Asia (MSEA). Another observation was the significantly low genetic differentiation and high rate of gene flow of Philippine chickens into Pacific chicken population. The negative Tajima's D and Fu's Fs neutrality tests revealed that Philippine chickens exhibited an expansion signal. The analyses of mismatch distribution and neutrality tests were consistent with the presence of weak phylogeographic structuring and evident population growth of Philippine chickens (haplogroup D) in the islands of Southeast Asia (ISEA). Furthermore, the Bayesian skyline plot (BSP) analysis showed an increase in the effective population size of Philippine chickens, relating with human settlement, and expansion events. The high level of genetic variability of Philippine chickens demonstrates conservation significance, thus, must be explored in the future.
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Affiliation(s)
- Cyrill John P. Godinez
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
- Department of Animal Science, College of Agriculture and Food Science, Visayas State University, Baybay City, Philippines
| | - Peter June D. Dadios
- College of Aquatic and Applied Life Sciences, Southern Leyte State University, Southern Leyte, Philippines
| | - Dinah M. Espina
- Department of Animal Science, College of Agriculture and Food Science, Visayas State University, Baybay City, Philippines
| | - Megumi Matsunaga
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
| | - Masahide Nishibori
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
- Department of Animal Science, College of Agriculture and Food Science, Visayas State University, Baybay City, Philippines
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17
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Liu Y, Yao L, Ci Y, Cao X, Zhao M, Li Y, Zhang X. Genetic differentiation of geographic populations of Rattus tanezumi based on the mitochondrial Cytb gene. PLoS One 2021; 16:e0248102. [PMID: 33735257 PMCID: PMC7971478 DOI: 10.1371/journal.pone.0248102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 02/21/2021] [Indexed: 11/18/2022] Open
Abstract
Rattus tanezumi is a common domestic rat and host of the bubonic plague pathogen in China and Southeast Asia (SEA). The origin, genetic differentiation and dispersal of R. tanezumi have received increasing attention from researchers. The population genetics of R. tanezumi based on its mitochondrial cytochrome b gene have been studied to explain the origin, relationships and dispersal of populations. In this study, we captured a total of 229 rats; morphological and molecular biological identification cytochrome oxidase subunit I (COI) confirmed 131 R. tanezumi individuals collected from 6 provincial areas, and their Cytb gene sequences were analyzed. The results showed that the population in Mohan (MH), Yunnan, had the highest genetic diversity, while that in Ningde (ND), Fujian, had the lowest. Tajima’s D statistic for all populations was negative and nonsignificant, indicating the possible expansion of R. tanezumi populations. Low gene flow occurred between the Zhangmu (ZM) R. tanezumi population and other populations, and the genetic differentiation among them was high. Furthermore, our analyses revealed the ZM lineage was the oldest lineage among the groups and diverged ~1.06 Mya, followed by the Luoyang (LY) lineages (~0.51 Mya) and Yunnan lineage (~0.33 Mya). In southeastern Yunnan, the Jinshuihe (JSH) and MH populations were more closely related to the populations in southeastern China (Fuzhou (FZ), ND, Quanzhou (QZ), Nanchang (NC)) and inland areas (Chongqing (CQ), LY) than to those in other areas of Yunnan (Jiegao (JG) and Qingshuihe (QSH)), indicating that R. tanezumi may have spread from southeastern Yunnan to the interior of China. In summary, R. tanezumi may have originated in ZM and adjacent areas, spread to Yunnan, and then spread from the southeast of Yunnan inland or directly eastward from ZM to inland China.
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Affiliation(s)
- Yingying Liu
- Institute of Health Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Lisi Yao
- Institute of Health Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Ying Ci
- Institute of Health Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Xiaomei Cao
- Institute of Health Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Minghui Zhao
- Jiangxi International Travel Health Care Center, Nanchang, Jiangxi, China
| | - Ying Li
- Institute of Health Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - XiaoLong Zhang
- Institute of Health Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
- * E-mail:
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18
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Dey A, Shashank PR, Meshram NM, Subramanian S, Jeer M, Kalleshwaraswamy CM, Chavan SM, Jindal J, Suby SB. Molecular diversity of Sesamia inferens (Walker, 1856) (Lepidoptera: Noctuidae) from India. 3 Biotech 2021; 11:134. [PMID: 33680699 PMCID: PMC7897588 DOI: 10.1007/s13205-021-02678-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/01/2021] [Indexed: 11/27/2022] Open
Abstract
Pink stem borer, Sesamia inferens (Walker, 1856) (Lepidoptera: Noctuidae) is reported to infest many graminaceous crops and cause significant losses. S. inferens cause damage by killing the central shoot and producing a characteristic symptom called "dead heart". Since graminaceous crops are an important source of food for humans and their livestock, impetus should be given on designing efficient management strategies against pink stem borer. The study of genetic variability of pest populations enables to interpret the ecological investigations correctly and also helps to comprehend the dissimilar response of pest to management tactics. The present study was undertaken to evaluate the diversity in S. inferens populations using mitochondrial cytochrome oxidase subunit I sequences from India, Pakistan, China and Indonesia. Analysis revealed a very low nucleotide diversity in Indian populations (π = 0.00981), as compared to a high nucleotide diversity in the sequences outside India (π = 0.4989). The phylogenetic analysis also did not show any clustering among populations within India and Pakistan. However, the nearest neighbour for the Indian and Pakistan population is a sequence from Indonesia followed by China indicating possible ancestral background. This is the maiden attempt to assess the molecular diversity of Indian populations in comparison to populations from other Asian countries. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02678-y.
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Affiliation(s)
- Adrish Dey
- Division of Entomology, Indian Agricultural Research Institute, New Delhi, India
| | - Pathour R. Shashank
- Division of Entomology, Indian Agricultural Research Institute, New Delhi, India
| | - Naresh M. Meshram
- Division of Entomology, Indian Agricultural Research Institute, New Delhi, India
| | | | - Mallikarjuna Jeer
- ICAR-National Institute of Biotic Stress Management, Raipur, Chhattisgarh State 493225 India
| | - C. M. Kalleshwaraswamy
- Department of Entomology, University of Agricultural and Horticultural Sciences, Shivamogga, Karnataka 577201 India
| | - Sachin Mahadev Chavan
- Krishi Vigyan Kendra, Navsari Agricultural University, Tapi, Vyara, Gujarat 394650 India
| | - Jawala Jindal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | - S. B. Suby
- ICAR-Indian Institute of Maize Research Delhi Unit, New Delhi, 110012 India
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19
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Zhang Y, Manzoor A, Wang X. Mitochondrial DNA analysis reveals spatial genetic structure and high genetic diversity of Massicus raddei (Blessig) (Coleoptera: Cerambycidae) in China. Ecol Evol 2020; 10:11657-11670. [PMID: 33144991 PMCID: PMC7593171 DOI: 10.1002/ece3.6799] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/11/2020] [Accepted: 08/21/2020] [Indexed: 11/11/2022] Open
Abstract
The oak longhorned beetle (OLB), Massicus raddei (Blessig, 1872) (Coleoptera: Cerambycidae), is widely distributed in Asia (China, the Korean Peninsula, Japan, Vietnam and the Russian Far-East), but pest outbreaks have occurred only in Liaoning Province and Jilin Province of China. In order to explore possible mechanisms of local population outbreaks and characterize the genetic diversity and genetic structure of M. raddei across its range in China, three mitochondrial genes (COI, Cytb, and COII) were sequenced and analyzed for seven M. raddei populations collected from six provinces in China. From these different populations, we found a high haplotype and nucleotide diversity. Haplotype networks and phylogenetic analyses both demonstrate apparent genetic diversification between SC (southern China) and NC (northern China) population groups. A set of 21 pairwise comparisons for Fst (pairwise fixation indices) and Nm (genetic flow index) showed significant genetic differentiation and limited gene flow except for two pairs, Shandong (SD) and Liaoning (LN), and Anhui (AH) and Henan (HN). This pattern suggested that the periodic outbreak of the LN population could not be attributed to the absence of genetic flow with other spatial populations and that regional environmental factors might be responsible. AMOVA (Analysis of molecular variance) showed that the greater molecular genetic variation was among populations. Based on Tajima's D statistic, Fu's Fs, and the mismatch distribution test, we determined that the seven populations sampled were stable and had not experienced any recent population expansion. The fact that all the sampled populations showed only unique haplotypes and lacked shared or ancestral haplotypes, as well as the nonstar-like distribution of haplotype network for concatenated genes, collectively provided powerful evidence of the stable and isolated nature of most populations. The high genetic differentiation and spatial genetic structuring among populations are both likely related to the beetle's moderate flight capacity, regional variation in host tree species and microclimate, as well as the geographic distance between sampling sites.
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Affiliation(s)
- Yufan Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland AdministrationResearch Institute of Forest Ecology, Environment and ProtectionChinese Academy of ForestryBeijingChina
| | - Atif Manzoor
- Key Laboratory of Forest Protection of National Forestry and Grassland AdministrationResearch Institute of Forest Ecology, Environment and ProtectionChinese Academy of ForestryBeijingChina
| | - Xiaoyi Wang
- Key Laboratory of Forest Protection of National Forestry and Grassland AdministrationResearch Institute of Forest Ecology, Environment and ProtectionChinese Academy of ForestryBeijingChina
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20
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Cabaña I, Chiaraviglio M, Di Cola V, Guisan A, Broennimann O, Gardenal CN, Rivera PC. Hybridization and hybrid zone stability between two lizards explained by population genetics and niche quantification. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractUnderstanding the factors that affect hybridization is an important issue in the study of species evolution. In this work, we analyse the genetic structure of two lizard species, Salvator merianae and Salvator rufescens, at a microscale within a climatic niche analysis framework, to reveal the main factors that contribute to the stability of their hybrid zone. We assess the effect of climate in hybridization by quantifying and decomposing the niche overlap of both species. Using a mitochondrial and a nuclear marker, we find that hybridization is frequent and is not restricted to the sympatric region. The gene flow is mainly from S. rufescens to S. merianae, with introgression into the range of S. merianae. Also, S. merianae would have long been present in the area, while S. rufescens appears to be a recent colonizer. The climate contributes to the population structure of S. merianae, but not to that of S. rufescens. The niches occupied by S. rufescens in the hybrid zone and the non-hybrid zone are similar, while the niches of S. merianae are different. Our results do not fit previous models of hybrid zone stability, suggesting the need to develop new models that consider the evolutionary factors that can differentially affect parental species and hybrids.
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Affiliation(s)
- Imanol Cabaña
- Instituto de Diversidad y Ecología Animal (IDEA), CONICET-UNC and Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Margarita Chiaraviglio
- Instituto de Diversidad y Ecología Animal (IDEA), CONICET-UNC and Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Valeria Di Cola
- Department of Ecology & Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
| | - Antoine Guisan
- Department of Ecology & Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, Geopolis, University of Lausanne, Lausanne, Switzerland
| | - Olivier Broennimann
- Department of Ecology & Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, Geopolis, University of Lausanne, Lausanne, Switzerland
| | - Cristina N Gardenal
- Instituto de Diversidad y Ecología Animal (IDEA), CONICET-UNC and Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Paula C Rivera
- Instituto de Diversidad y Ecología Animal (IDEA), CONICET-UNC and Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
- Universidad Nacional de Chilecito, La Rioja, Argentina
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21
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Boudali SF, Al-Jumaili AS, Bouandas A, Mahammi FZ, Tabet Aoul N, Hanotte O, Gaouar SBS. Maternal origin and genetic diversity of Algerian domestic chicken ( Gallus gallus domesticus) from North-Western Africa based on mitochondrial DNA analysis. Anim Biotechnol 2020; 33:457-467. [PMID: 32787620 DOI: 10.1080/10495398.2020.1803892] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Local chicken populations are a major source of food in the rural areas of Algeria. However, their origin has not been well characterized. The objectives of this study were to assess genetic diversity and maternal origin of domestic chicken from five agro-ecological regions of western Algeria: coastal (CT), inland plains (IP), highlands (HL), mountains (MT) and sahara (SH, including Oasis, Req and Erg regions). A set of 88 mitochondrial DNA (mtDNA) D-loop sequences including the hypervariable region I (HV1) were analyzed. From the 397 bp D-loop sequence, 20 variable sites that defined 13 haplotypes were identified in Algerian domestic chicken. The haplotype and nucleotide diversity were estimated as 0.597 and 0.003, respectively. Phylogenetic and network analyses indicated the presence of two clades or haplogroups (A and E). Only one clade A haplotype was observed exclusively in the population of mountains, while, Clade E haplotypes were found in almost all Algerian chicken with twelve different haplotypes. These findings suggest that Algerian chickens derived from the most ubiquitous haplogroup which have its root in the Indian subcontinent. Our results provide important information about the origin of the North-West African chicken and the historical dispersal of the first chicken populations into African continent.
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Affiliation(s)
- Selma Farah Boudali
- Laboratoire de Génétique Moléculaire et Cellulaire (LGMC), Université des Sciences et de la Technologie d'Oran Mohamed Boudiaf, USTO-MB, BP 1505, El M'naouer, Oran Algérie
| | - Ahmed S Al-Jumaili
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
| | - Ameur Bouandas
- Physiopathology and biochemical of nutrition (PpBioNut), University of Tlemcen, Tlemcen, Algeria
| | - Fatima Zohra Mahammi
- Laboratoire de Génétique Moléculaire et Cellulaire (LGMC), Université des Sciences et de la Technologie d'Oran Mohamed Boudiaf, USTO-MB, BP 1505, El M'naouer, Oran Algérie.,École Supérieure en Sciences Biologiques d'Oran (ESSBO), BP 1042, Saim Mohamed, Oran, Algeria
| | - Nacera Tabet Aoul
- Laboratoire de Génétique Moléculaire et Cellulaire (LGMC), Université des Sciences et de la Technologie d'Oran Mohamed Boudiaf, USTO-MB, BP 1505, El M'naouer, Oran Algérie.,Department of Biotechnology, University of Oran1 Ahmed Benbella, Oran, Algérie
| | - Olivier Hanotte
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
| | - Semir Bechir Suheil Gaouar
- Laboratoire de Génétique Moléculaire et Cellulaire (LGMC), Université des Sciences et de la Technologie d'Oran Mohamed Boudiaf, USTO-MB, BP 1505, El M'naouer, Oran Algérie.,Physiopathology and biochemical of nutrition (PpBioNut), University of Tlemcen, Tlemcen, Algeria
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22
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Ruiz-Arce R, Todd TN, Deleon R, Barr NB, Virgilio M, De Meyer M, McPheron BA. Worldwide Phylogeography of Ceratitis capitata (Diptera: Tephritidae) Using Mitochondrial DNA. JOURNAL OF ECONOMIC ENTOMOLOGY 2020; 113:1455-1470. [PMID: 32112108 DOI: 10.1093/jee/toaa024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Indexed: 06/10/2023]
Abstract
The Mediterranean fruit fly, Ceratitis capitata (Weidemann), is one of the most economically important tephritid species worldwide. It has spread across six geographic regions as a result of successful invasions and continues to cause substantial losses to agricultural communities. Our study examined 1,864 flies originating from 150 localities, using mitochondrial DNA sequencing methods. We tested for population structure and revealed the genetic diversity for 1,592 specimens gathered from 144 wild fly collections from 46 countries representing the entire geographic range for this species. We also include in this study 272 Sterile Insect Technique (SIT) specimens from four SIT facilities. We recovered 202 haplotypes from the current sampling and updated previously published work to reveal a total of 231 haplotypes for this pest. These data show population structure at and below the regional level for these collections, shedding light on the current demographics for this species. We observed four common haplotypes, seen among 62% of the samples sequenced that have worldwide distribution. Three haplotypes were seen in SIT flies, with one seen as the predominant haplotype. Our work showed that two of the haplotypes were private to SIT flies, not present among wild fly collections. However, a third haplotype common among wild fly collections was also seen in one SIT facility but at a low frequency based on the current sampling. We provide guidance on the interpretation of these methods for the source estimation of current and future infestations.
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Affiliation(s)
| | | | | | | | | | | | - Bruce A McPheron
- Department of Entomology, The Pennsylvania State University, University Park, PA
- The Ohio State University, Columbus, OH
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23
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Syama A, Arun VS, ArunKumar G, Subhadeepta R, Friese K, Pitchappan R. Origin and identity of the Brokpa of Dah-Hanu, Himalayas – an NRY-HG L1a2 (M357) legacy. Ann Hum Biol 2019; 46:562-573. [DOI: 10.1080/03014460.2019.1694700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Adikarla Syama
- The Genographic Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
- Department of Biotechnology, Faculty of Engineering and Technology, Manav Rachana, International University, Faridabad, India
| | | | - GaneshPrasad ArunKumar
- The Genographic Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
- Human Genomics Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thirumalaisamudram, India
| | | | | | - Ramasamy Pitchappan
- The Genographic Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
- Nilgiri Adivasi Welfare Association, Kotagiri, India
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24
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Islam MA, Osman SAM, Nishibori M. Genetic diversity of Bangladeshi native chickens based on complete sequence of mitochondrial DNA D-loop region. Br Poult Sci 2019; 60:628-637. [PMID: 31475858 DOI: 10.1080/00071668.2019.1655708] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
1. The aim of this study was to explore genetic diversity and possible origin of Bangladeshi (BD) native chickens. The complete mtDNA D-loop region was sequenced in 60 chickens representing five populations; naked neck, full feathered, Aseel, Hilly and autosomal dwarf. The 61 reference sequences representing different domestic chicken clades in China, India, Laos, Indonesia, Myanmar, and other Eurasian regions were included. The mtDNA D-loop sequence polymorphism and maternal origin of five BD populations were analysed.2. A total of 35 polymorphic sites, and 21 haplotypes were detected in 60 mtDNA D-loop sequences. The haplotype and nucleotide diversity of the five populations were 0.921 ± 0.018 and 0.0061 ± 0.0019, respectively. Both mtDNA network and phylogenetic analysis indicated four clades (four haplogroups) in BD populations (21 haplotypes) along with 61 reference haplotypes. Clade E contained the most individuals (20) and haplotypes (11) of BD chickens, followed by clade D (17, 6), clade C (12, 2) and clade F (11, 2), respectively.3. The higher number of unique haplotypes found in Yunnan, China, suggested that the origin of BD chickens was in this region. The haplotypes from different haplogroups were introduced in Bangladeshi chickens from India, China and Myanmar. The phylogenetic tree showed a close relationship of BD chickens with the clusters from India, China, Myanmar and Laos, and indicated the dispersion of BD chickens from these sources. The phylogenetic information revealed high genetic diversity of BD chickens because of their origin from different lineages with high genetic variation and distance, which was determined from four cluster and neighbour-joining trees.4. In conclusion, BD populations had high genetic diversity. The mtDNA network profiles and phylogenetic trees showed multiple maternal origins of BD chickens from India, China, Myanmar and Laos.
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Affiliation(s)
- M A Islam
- Department of Dairy and Poultry Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh.,Department of Bio-resource Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - S A M Osman
- Department of Bio-resource Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.,Department of Genetics, Faculty of Agriculture, Minia University, El Minia, Egypt
| | - M Nishibori
- Department of Bio-resource Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
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25
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Hanna ZR, Cicero C, Bowie RCK. Molecular evidence that the Channel Islands populations of the orange-crowned warbler ( Oreothlypis celata; Aves: Passeriformes: Parulidae) represent a distinct evolutionary lineage. PeerJ 2019; 7:e7388. [PMID: 31404458 PMCID: PMC6688592 DOI: 10.7717/peerj.7388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 07/01/2019] [Indexed: 11/23/2022] Open
Abstract
We used molecular data to assess the degree of genetic divergence across the breeding range of the orange-crowned warbler (Oreothlypis celata) in western North America with particular focus on characterizing the divergence between O. celata populations on the mainland of southern California and on the Channel Islands. We obtained sequences of the mitochondrial gene ND2 and genotypes at ten microsatellite data for 192 O. celata from populations spanning all four recognized subspecies. We recovered shallow, but significant, levels of divergence among O. celata populations across the species range. Our results suggest that island isolation, subspecies (delineation by morphology, ecological, and life-history characteristics), and isolation-by-distance, in that order, are the variables that best explain the geographic structure detected across the range of O. celata. Populations on the Channel Islands were genetically divergent from those on the mainland. We found evidence for greater gene flow from the Channel Islands population to mainland southern California than from the mainland to the islands. We discuss these data in the context of differentiation in phenotypic and ecological characters.
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Affiliation(s)
- Zachary R Hanna
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America.,Department of Integrative Biology, University of California, Berkeley, CA, United States of America
| | - Carla Cicero
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America.,Department of Integrative Biology, University of California, Berkeley, CA, United States of America
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26
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Guffanti G, Bartlett A, Klengel T, Klengel C, Hunter R, Glinsky G, Macciardi F. Novel Bioinformatics Approach Identifies Transcriptional Profiles of Lineage-Specific Transposable Elements at Distinct Loci in the Human Dorsolateral Prefrontal Cortex. Mol Biol Evol 2019; 35:2435-2453. [PMID: 30053206 PMCID: PMC6188555 DOI: 10.1093/molbev/msy143] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Expression of transposable elements (TE) is transiently activated during human preimplantation embryogenesis in a developmental stage- and cell type-specific manner and TE-mediated epigenetic regulation is intrinsically wired in developmental genetic networks in human embryos and embryonic stem cells. However, there are no systematic studies devoted to a comprehensive analysis of the TE transcriptome in human adult organs and tissues, including human neural tissues. To investigate TE expression in the human Dorsolateral Prefrontal Cortex (DLPFC), we developed and validated a straightforward analytical approach to chart quantitative genome-wide expression profiles of all annotated TE loci based on unambiguous mapping of discrete TE-encoded transcripts using a de novo assembly strategy. To initially evaluate the potential regulatory impact of DLPFC-expressed TE, we adopted a comparative evolutionary genomics approach across humans, primates, and rodents to document conservation patterns, lineage-specificity, and colocalizations with transcription factor binding sites mapped within primate- and human-specific TE. We identified 654,665 transcripts expressed from 477,507 distinct loci of different TE classes and families, the majority of which appear to have originated from primate-specific sequences. We discovered 4,687 human-specific and transcriptionally active TEs in DLPFC, of which the prominent majority (80.2%) appears spliced. Our analyses revealed significant associations of DLPFC-expressed TE with primate- and human-specific transcription factor binding sites, suggesting potential cross-talks of concordant regulatory functions. We identified 1,689 TEs differentially expressed in the DLPFC of Schizophrenia patients, a majority of which is located within introns of 1,137 protein-coding genes. Our findings imply that identified DLPFC-expressed TEs may affect human brain structures and functions following different evolutionary trajectories. On one side, hundreds of thousands of TEs maintained a remarkably high conservation for ∼8 My of primates’ evolution, suggesting that they are likely conveying evolutionary-constrained primate-specific regulatory functions. In parallel, thousands of transcriptionally active human-specific TE loci emerged more recently, suggesting that they could be relevant for human-specific behavioral or cognitive functions.
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Affiliation(s)
- Guia Guffanti
- Department of Psychiatry, Harvard Medical School, Cambridge, MA.,Division of Depression and Anxiety, McLean Hospital, Belmont, MA
| | - Andrew Bartlett
- Department of Psychology, University of Massachusetts, Boston, MA
| | - Torsten Klengel
- Department of Psychiatry, Harvard Medical School, Cambridge, MA.,Division of Depression and Anxiety, McLean Hospital, Belmont, MA.,Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Georg-August-University, Goettingen, Germany
| | - Claudia Klengel
- Department of Psychiatry, Harvard Medical School, Cambridge, MA.,Division of Depression and Anxiety, McLean Hospital, Belmont, MA
| | - Richard Hunter
- Department of Psychology, University of Massachusetts, Boston, MA
| | - Gennadi Glinsky
- Translational & Functional Genomics, Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA
| | - Fabio Macciardi
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA
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27
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Bradshaw CJA, Ulm S, Williams AN, Bird MI, Roberts RG, Jacobs Z, Laviano F, Weyrich LS, Friedrich T, Norman K, Saltré F. Minimum founding populations for the first peopling of Sahul. Nat Ecol Evol 2019; 3:1057-1063. [PMID: 31209287 DOI: 10.1038/s41559-019-0902-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 04/15/2019] [Indexed: 11/09/2022]
Abstract
The timing, context and nature of the first people to enter Sahul is still poorly understood owing to a fragmented archaeological record. However, quantifying the plausible demographic context of this founding population is essential to determine how and why the initial peopling of Sahul occurred. We developed a stochastic, age-structured model using demographic rates from hunter-gatherer societies, and relative carrying capacity hindcasted with LOVECLIM's net primary productivity for northern Sahul. We projected these populations to determine the resilience and minimum sizes required to avoid extinction. A census founding population of between 1,300 and 1,550 individuals was necessary to maintain a quasi-extinction threshold of ≲0.1. This minimum founding population could have arrived at a single point in time, or through multiple voyages of ≥130 people over ~700-900 years. This result shows that substantial population amalgamation in Sunda and Wallacea in Marine Isotope Stages 3-4 provided the conditions for the successful, large-scale and probably planned peopling of Sahul.
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Affiliation(s)
- Corey J A Bradshaw
- Global Ecology, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia. .,ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia.
| | - Sean Ulm
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia.,College of Arts, Society and Education, James Cook University, Cairns, Queensland, Australia
| | - Alan N Williams
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia.,Climate Change Research Centre, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia.,Extent Heritage Pty Ltd, Sydney, New South Wales, Australia
| | - Michael I Bird
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia.,College of Science and Engineering, James Cook University, Cairns, Queensland, Australia
| | - Richard G Roberts
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia.,Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Zenobia Jacobs
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia.,Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Fiona Laviano
- Global Ecology, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Laura S Weyrich
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia.,Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia
| | - Tobias Friedrich
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Kasih Norman
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia.,Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Frédérik Saltré
- Global Ecology, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia
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28
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Firneno TJ, Townsend JH. Evaluation of species boundaries in sympatric and parapatric populations of Mesoamerican toads. ZOOL SCR 2019. [DOI: 10.1111/zsc.12354] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Thomas J. Firneno
- Department of Biology Indiana University of Pennsylvania Indiana Pennsylvania
| | - Josiah H. Townsend
- Department of Biology Indiana University of Pennsylvania Indiana Pennsylvania
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29
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Nong X, Zhong SN, Li SM, Yang YJ, Liang Z, Xie Y. Genetic differentiation of Pseudoregma bambucicola population based on mtDNA COII gene. Saudi J Biol Sci 2019; 26:1032-1036. [PMID: 31303837 PMCID: PMC6600799 DOI: 10.1016/j.sjbs.2019.04.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/22/2019] [Accepted: 04/22/2019] [Indexed: 11/04/2022] Open
Abstract
mtDNA COII gene sequences were identified and analyzed using different types of software, namely, MEGA5.0, DNAMAN, and DnaSP5.0 in four Chinese provinces, namely, Sichuan, Zhejiang, Guizhou and Shanghai. Analysis of molecular genetic variation and its genetic structure and differentiation, combined with NJ tree, MP tree analysis and analysis of molecular variance (AMOVA), at Fst = 0.0582 conclude that the genetic differentiation is low, gene flow is Nm = 8.0911, and gene exchange is sufficient. However, for the geographic populations of Pseudoregma bambucicola in the four provinces, their gene exchange is relatively weak at Nm = 0.8284, whereas the genetic differentiation is high at Fst = 0.3764. Based on the data, total nucleotide diversity between the populations is 0.00158 ± 0.00021. The results showed that the total population of Tajima’s D and Fu’s Fs results are D = −0.885 and Fs = 0.226, respectively. The experimental numerical results showed that this total population is not significant (P > 0.10), indicating that nine different geographic populations are short-term. No expansion occurred in the internal population. This study provided a theoretical and practical basis for the comprehensive prevention and control of P. bambucicola.
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Affiliation(s)
- Xiang Nong
- Bamboo Diseases and Pest Control and Resources Development Key Laboratory of Sichuan Province, Sichuan 614000, China.,College of Life Science, Leshan Normal University, Leshan 614000, China
| | - Sheng-Nan Zhong
- Bamboo Diseases and Pest Control and Resources Development Key Laboratory of Sichuan Province, Sichuan 614000, China.,College of Life Science, Leshan Normal University, Leshan 614000, China.,College of Food and Biological Engineering, XiHua University, Chengdu 610000, China
| | - Si-Min Li
- Bamboo Diseases and Pest Control and Resources Development Key Laboratory of Sichuan Province, Sichuan 614000, China.,College of Life Science, Leshan Normal University, Leshan 614000, China
| | - Yao-Jun Yang
- Bamboo Diseases and Pest Control and Resources Development Key Laboratory of Sichuan Province, Sichuan 614000, China.,College of Life Science, Leshan Normal University, Leshan 614000, China
| | - Zi Liang
- Bamboo Diseases and Pest Control and Resources Development Key Laboratory of Sichuan Province, Sichuan 614000, China.,College of Life Science, Leshan Normal University, Leshan 614000, China
| | - Yue Xie
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
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30
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Gopal K, Karczmarski L, Tolley KA. Patterns of geographic variation between mitochondrial and nuclear markers in Heaviside's (Benguela) dolphins (Cephalorhynchus heavisidii). Integr Zool 2019; 14:506-526. [PMID: 30688009 DOI: 10.1111/1749-4877.12380] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Heaviside's (or Benguela) dolphin (Cephalorhynchus heavisidii) is endemic to the west coast of southern Africa. The present study investigated the population genetic structure across a large portion of the species distribution using mitochondrial control region and nuclear (microsatellite) markers. A total of 395 biopsy skin samples were analyzed; they were collected from free-ranging Heaviside's dolphins in 7 locations along 1650 km of coast between Table Bay, South Africa and Walvis Bay, Namibia. Both genetic markers rejected the hypothesis of 1 homogenous population but revealed contrasting results in the genetic structuring of putative populations. Mitochondrial DNA suggested either 2 populations or a fine-scale division with 6 (sub) populations, while microsatellite markers were indicative of 2 widespread populations with measurable gene flow between them. Neutrality tests and mismatch distribution of the mitochondrial sequences indicated a departure from mutation-drift equilibrium due to a population expansion at the 2 extremes of the geographic range, but not towards the middle of the distribution. These results highlight the importance of evaluating multiple genetic markers to gain reliable insights into population processes and structure.
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Affiliation(s)
- Keshni Gopal
- Mammal Research Institute, University of Pretoria, Pretoria, South Africa.,South African National Biodiversity Institute, Kirstenbosch Research Centre, Cape Town, South Africa
| | - Leszek Karczmarski
- Mammal Research Institute, University of Pretoria, Pretoria, South Africa.,School of Biological Sciences, University of Hong Kong, Hong Kong, China.,Cetacean Ecology Lab, Cetacea Research Institute, Hong Kong, China
| | - Krystal A Tolley
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Cape Town, South Africa.,Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Johannesburg, South Africa
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31
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Rocha-Méndez A, Sánchez-González LA, Arbeláez-Cortés E, Navarro-Sigüenza AG. Phylogeography indicates incomplete genetic divergence among phenotypically differentiated montane forest populations of Atlapetesalbinucha (Aves, Passerellidae). Zookeys 2019:125-148. [PMID: 30598618 PMCID: PMC6306474 DOI: 10.3897/zookeys.809.28743] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/19/2018] [Indexed: 11/12/2022] Open
Abstract
The White-naped Brushfinch (Atlapetesalbinucha) comprises up to eight allopatric subspecies mainly identified by the color of the underparts (gray vs. yellow belly). Yellow and gray bellied forms were long considered two different species (A.albinucha and A.gutturalis), but they are presently considered as one polytypic species. Previous studies in the genus Atlapetes have shown that the phylogeny, based on molecular data, is not congruent with characters such as coloration, ecology, or distributional patterns. The phylogeography of A.albinucha was analyzed using two mitochondrial DNA regions from samples including 24 different localities throughout montane areas from eastern Mexico to Colombia. Phylogeographic analyses using Bayesian inference, maximum likelihood and haplotype network revealed incomplete geographic structure. The genetic diversity pattern is congruent with a recent process of expansion, which is also supported by Ecological Niche Models (ENM) constructed for the species and projected into three past scenarios. Overall, the results revealed an incomplete genetic divergence among populations of A.albinucha in spite of the species’ ample range, which contrasts with previous results of phylogeographic patterns in other Neotropical montane forest bird species, suggesting idiosyncratic evolutionary histories for different taxa throughout the region.
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Affiliation(s)
- Alberto Rocha-Méndez
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Apartado Postal 70-399, México City 04510, México Universidad Nacional Autónoma de México México City Mexico
| | - Luis A Sánchez-González
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Apartado Postal 70-399, México City 04510, México Universidad Nacional Autónoma de México México City Mexico
| | - Enrique Arbeláez-Cortés
- Grupo de Estudios en Biodiversidad, Escuela de Biología, Facultad de Ciencias, Universidad Industrial de Santander, Carrera 27 Calle 9. Bucaramanga, Santander, Colombia Universidad Industrial de Santander Bucaramanga Colombia
| | - Adolfo G Navarro-Sigüenza
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Apartado Postal 70-399, México City 04510, México Universidad Nacional Autónoma de México México City Mexico
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32
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Li Y, Gao QB, Gengji ZM, Jia LK, Wang ZH, Chen SL. Rapid Intraspecific Diversification of the Alpine Species Saxifraga sinomontana (Saxifragaceae) in the Qinghai-Tibetan Plateau and Himalayas. Front Genet 2018; 9:381. [PMID: 30279701 PMCID: PMC6153349 DOI: 10.3389/fgene.2018.00381] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 08/27/2018] [Indexed: 11/30/2022] Open
Abstract
An increasing number of phylogeographic studies have been conducted for plant species in the Qinghai-Tibetan Plateau (QTP) and its flanking mountains. However, these studies have mainly focused on the determination of glacial refugia and routes of inter-/post-glacial expansions. Rapid intraspecific diversification of plants in this region have not been thoroughly discussed. Herein, we investigate the effects of the Quaternary climate changes on population genetic structure and diversifications of a herbaceous alpine species, Saxifraga sinomontana, which may have an evolutionary time scale <5 million years in the QTP and Himalayan regions. Using a total of 350 individuals from 29 populations, we studied the evolutionary history of S. sinomontana by analyzing cpDNA trnL-trnF, rpl16 and nrDNA ITS sequences. A total of 89 haplotypes and 158 genotypes were detected for cpDNA and ITS sequences, respectively. Only a few haplotypes/genotypes were widespread, while an extremely large number of haplotypes/genotypes were restricted to single populations, which were scattered throughout the current geographical range of S. sinomontana. This suggests the existence of microrefugia of this species during the Quaternary glaciations. In addition, the relationships of the haplotypes/genotypes were almost completely not resolved by phylogenetic reconstruction. Combining characteristics in terms of high haplotype richness, large proportion of private haplotypes, and shallow haplotype divergence, we speculate that recent intraspecific diversification has occurred in S. sinomontana. Molecular clock analysis estimated that the onset diversification within S. sinomontana to be 1.09 Ma (95% HPD = 0.80–1.45), coinciding with the extensive Quaternary glaciations on the QTP which started ca. 1.17 Ma. The Quaternary climatic oscillations may have triggered rapid intraspecific diversification in this QTP-Himalayan species. However, large niche breadth, as well as introgression/hybridization between the studied species and its closely related sympatric saxifrages, may also played a role to some extent on the current genetic structure of S. sinomontana, which need to be further studied.
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Affiliation(s)
- Yan Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qing-Bo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, China
| | - Zhuo-Ma Gengji
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Liu-Kun Jia
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhi-Hua Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
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34
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Comparison of Single Genome and Allele Frequency Data Reveals Discordant Demographic Histories. G3-GENES GENOMES GENETICS 2017; 7:3605-3620. [PMID: 28893846 PMCID: PMC5677151 DOI: 10.1534/g3.117.300259] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Inference of demographic history from genetic data is a primary goal of population genetics of model and nonmodel organisms. Whole genome-based approaches such as the pairwise/multiple sequentially Markovian coalescent methods use genomic data from one to four individuals to infer the demographic history of an entire population, while site frequency spectrum (SFS)-based methods use the distribution of allele frequencies in a sample to reconstruct the same historical events. Although both methods are extensively used in empirical studies and perform well on data simulated under simple models, there have been only limited comparisons of them in more complex and realistic settings. Here we use published demographic models based on data from three human populations (Yoruba, descendants of northwest-Europeans, and Han Chinese) as an empirical test case to study the behavior of both inference procedures. We find that several of the demographic histories inferred by the whole genome-based methods do not predict the genome-wide distribution of heterozygosity, nor do they predict the empirical SFS. However, using simulated data, we also find that the whole genome methods can reconstruct the complex demographic models inferred by SFS-based methods, suggesting that the discordant patterns of genetic variation are not attributable to a lack of statistical power, but may reflect unmodeled complexities in the underlying demography. More generally, our findings indicate that demographic inference from a small number of genomes, routine in genomic studies of nonmodel organisms, should be interpreted cautiously, as these models cannot recapitulate other summaries of the data.
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Hutama A, Dahruddin H, Busson F, Sauri S, Keith P, Hadiaty RK, Hanner R, Suryobroto B, Hubert N. Identifying spatially concordant evolutionary significant units across multiple species through DNA barcodes: Application to the conservation genetics of the freshwater fishes of Java and Bali. Glob Ecol Conserv 2017. [DOI: 10.1016/j.gecco.2017.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Moreira GRP, Eltz RP, Pase RB, Silva GT, Bordignon SAL, Mey W, Gonçalves GL. Cecidonius pampeanus, gen. et sp. n.: an overlooked and rare, new gall-inducing micromoth associated with Schinus in southern Brazil (Lepidoptera, Cecidosidae). Zookeys 2017:37-74. [PMID: 29134006 PMCID: PMC5673834 DOI: 10.3897/zookeys.695.13320] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/07/2017] [Indexed: 11/12/2022] Open
Abstract
Galls induced by the larval stage of cecidosids (Lepidoptera: Cecidosidae) are complex, multi-trophic systems, still poorly studied. They may be associated with other insect feeding guilds, including inquilines, kleptoparasites, cecidophages, parasitoids, and predators. By causing death of the gall inducer early in life and altering the gall phenotype, inquilines may lead to misidentification of the true gall inducers. Here, we describe through light and scanning electron microscopy Cecidonius pampeanus, a new genus and species of cecidosid moth, from the Pampa biome, south Brazil. It induces unnoticed, small galls under swollen stems of Schinus weinmannifolius Mart. ex Engl. (Anacardiaceae). Such galls are severely attacked early in ontogeny either by unidentified parasitoids belonging to Lyrcus Walker (Pteromalidae) that feed upon the inducer, or by inquiline wasps of the genus Allorhogas Gahan (Braconidae). The inquilines modify the galls into large ones that last longer and promptly call attention. Free-living galls are rare and dehiscent, pupation of C. pampeanus occurring on the ground. Due to these reasons the true inducer has been overlooked in this case for more than a century. Additionally we inferred a phylogeny for Cecidosidae using sequences from mitochondrial and nuclear loci, and characterized genetic variation and gene flow across ten populations. Despite its natural history similarities with the African genus Scyrotis, Cecidonius is a much younger lineage, more closely related to the Neotropical cecidosids. C. pampeanus populations, which are now confined to a few mountain areas within its distribution range due to habitat destruction, are also genetically isolated, requiring conservation measures.
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Affiliation(s)
- Gilson R P Moreira
- Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS, Brazil
| | - Rodrigo P Eltz
- Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS, Brazil
| | - Ramoim B Pase
- Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS, Brazil
| | - Gabriela T Silva
- PPG Biologia Animal, Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS, Brazil
| | - Sérgio A L Bordignon
- Programa de Mestrado em Avaliação de Impactos Ambientais, Universidade La Salle, Av. Victor Barreto, 2288, 92010-000 Canoas, RS, Brazil
| | - Wolfram Mey
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
| | - Gislene L Gonçalves
- PPG Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS, Brazil.,Departamento de Recursos Ambientales, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Casilla 6-D, Arica, Chile
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Cutrera AP, Mora MS. Selection on MHC in a Context of Historical Demographic Change in 2 Closely Distributed Species of Tuco-tucos (Ctenomys australis and C. talarum). J Hered 2017; 108:628-639. [PMID: 28605534 DOI: 10.1093/jhered/esx054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 06/07/2017] [Indexed: 11/12/2022] Open
Abstract
Selection necessarily acts within the same current and historical demographic framework as neutral evolutionary processes, and the outcome of the interplay between these forces may vary according to their relative strength. In this study, we compare the variation at a major histocompatibility complex (MHC) locus (DRB exon 2), typically subject to strong diversifying selection, and mitochondrial diversity (D-loop) across populations encompassing the entire distribution of 2 species of South American subterranean rodents: Ctenomys australis and C. talarum (tuco-tucos). Although these species are parapatric along most of their distribution, historically they have followed distinct demographic trajectories associated with sea level changes during the Quaternary. We surveyed 8 populations of C. australis and 15 of C. talarum, from which we analyzed 70 and 212 D-loop haplotypes and 91 and 346 DRB genotypes, respectively. Both species have gone through a recent demographic expansion; however, the signal of this process only encompasses the entire distribution of one of the species: C. australis. While balancing selection on MHC in C. talarum-enhanced DRB diversity at the local level compared to D-loop, although not promoting divergence among populations, in C. australis local diversifying selection may have driven higher population differentiation at DRB than at D-loop. Our findings reinforce the idea that the relative strength of selection acting on MHC genes varies spatially and temporally within and among species, even between species using the same macrohabitat and exposed to similar immune challenges.
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Affiliation(s)
- Ana Paula Cutrera
- Instituto de Investigaciones Marinas y Costeras, CONICET - Universidad Nacional de Mar del Plata, Funes 3350, Mar del Plata (7600), Argentina
| | - Matías Sebastián Mora
- Instituto de Investigaciones Marinas y Costeras, CONICET - Universidad Nacional de Mar del Plata, Funes 3350, Mar del Plata (7600), Argentina
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Petit E, Excoffier L, Mayer F. NO EVIDENCE OF BOTTLENECK IN THE POSTGLACIAL RECOLONIZATION OF EUROPE BY THE NOCTULE BAT (NYCTALUS NOCTULA). Evolution 2017; 53:1247-1258. [PMID: 28565510 DOI: 10.1111/j.1558-5646.1999.tb04537.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/1998] [Accepted: 02/15/1999] [Indexed: 11/29/2022]
Abstract
During the Pleistocene, the habitat of the noctule bat (Nyctalus noctula) was limited to small refuge areas located in Southern Europe, whereas the species is now widespread across this continent. Using mtDNA (control region and ND1 gene) polymorphisms, we asked whether this recolonization occurred through bottlenecks and whether it was accompanied by population growth. Sequences of the second hypervariable domain of the control region were obtained from 364 noctule bats representing 18 colonies sampled across Europe. This yielded 108 haplotypes that were depicted on a minimum spanning tree that showed a starlike structure with two long branches. Additional sequences obtained from the ND1 gene confirmed that the different parts of the MST correspond to three clades which diverged before the Last Glacial Maximum (18,000 yrC14 BP), leading to the conclusion that the noctule bat survived in several isolated refugia. Partitioning populations into coherent geographical groups divided our samples (φCT = 0.17; P = 0.01) into a group of highly variable nursing colonies from central and eastern Europe and less variable, isolated colonies from western and southern Europe. Demographic analyses suggest that populations of the former group underwent demographic expansions either after the Younger Dryas (11,000-10,000 yrC14 BP), assuming a fast mutation rate for HV II, or during the Pleistocene, assuming a conventional mutation rate. We discuss the fact that the high genetic variability (h = 0.69-0.96; π = 0.006-0.013) observed in nursing colonies that are located some distance from potential Pleistocene refugia is probably due to the combined effect of rapid evolution of the control region in growing populations and a range shift of noctule populations parallel to the recovery of forests in Europe after the last glaciations.
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Affiliation(s)
- Eric Petit
- Institut für Zoologie II, Universität Erlangen, Staudtstrasse 5, 91058, Erlangen, Germany
| | - Laurent Excoffier
- Genetics and Biometry Laboratory, Department of Anthropology and Ecology, University of Geneva, CP 511, 1211, Geneva 24, Switzerland
| | - Frieder Mayer
- Institut für Zoologie II, Universität Erlangen, Staudtstrasse 5, 91058, Erlangen, Germany
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Maswanganye KA, Cunningham MJ, Bennett NC, Chimimba CT, Bloomer P. Life on the rocks: Multilocus phylogeography of rock hyrax (Procavia capensis) from southern Africa. Mol Phylogenet Evol 2017; 114:49-62. [PMID: 28411160 DOI: 10.1016/j.ympev.2017.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/31/2017] [Accepted: 04/06/2017] [Indexed: 01/23/2023]
Abstract
Understanding the role of geography and climatic cycles in determining patterns of biodiversity is important in comparative and evolutionary biology and conservation. We studied the phylogeographic pattern and historical demography of a rock-dwelling small mammal species from southern Africa, the rock hyrax Procavia capensis capensis. Using a multilocus coalescent approach, we assessed the influence of strong habitat dependence and fluctuating regional climates on genetic diversity. We sequenced a mitochondrial gene (cytochrome b) and two nuclear introns (AP5, PRKC1) supplemented with microsatellite genotyping, in order to assess evolutionary processes over multiple temporal scales. In addition, distribution modelling was used to investigate the current and predicted distribution of the species under different climatic scenarios. Collectively, the data reveal a complex history of isolation followed by secondary contact shaping the current intraspecific diversity. The cyt b sequences confirmed the presence of two previously proposed geographically and genetically distinct lineages distributed across the southern African Great Escarpment and north-western mountain ranges. Molecular dating suggests Miocene divergence of the lineages, yet there are no discernible extrinsic barriers to gene flow. The nuclear markers reveal incomplete lineage sorting or ongoing mixing of the two lineages. Although the microsatellite data lend some support to the presence of two subpopulations, there is weak structuring within and between lineages. These data indicate the presence of gene flow from the northern into the southern parts of the southern African sub-region likely following the secondary contact. The distribution modelling predictably reveal the species' preference for rocky areas, with stable refugia through time in the northern mountain ranges, the Great Escarpment, as well as restricted areas of the Northern Cape Province and the Cape Fold Mountains of South Africa. Different microclimatic variables appear to determine the distributional range of the species. Despite strong habitat preference, the micro-habitat offered by rocky crevices and unique life history traits likely promoted the adaptability of P. capensis, resulting in the widespread distribution and persistence of the species over a long evolutionary period. Spatio-temporal comparison of the evolutionary histories of other co-distributed species across the rocky landscapes of southern Africa will improve our understanding of the regional patterns of biodiversity and local endemism.
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Affiliation(s)
- K Amanda Maswanganye
- Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa; Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa.
| | - Michael J Cunningham
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa.
| | - Nigel C Bennett
- Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa.
| | - Christian T Chimimba
- Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa.
| | - Paulette Bloomer
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa.
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Gao QB, Li Y, Gengji ZM, Gornall RJ, Wang JL, Liu HR, Jia LK, Chen SL. Population Genetic Differentiation and Taxonomy of Three Closely Related Species of Saxifraga (Saxifragaceae) from Southern Tibet and the Hengduan Mountains. FRONTIERS IN PLANT SCIENCE 2017; 8:1325. [PMID: 28804492 PMCID: PMC5532446 DOI: 10.3389/fpls.2017.01325] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/14/2017] [Indexed: 05/12/2023]
Abstract
The effects of rapid, recent uplift of the Hengduan Mountains on evolution and diversification of young floristic lineages still remain unclear. Here, we investigate diversification of three closely related Saxifraga species with a distribution restricted to the Hengduan Mountains (HM) and southern Tibet, and comment on their taxonomy based on molecular evidence. Three chloroplast DNA fragments (rbcL, trnL-F, trnS-G) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to study genetic structure across 104 individuals from 12 populations of Saxifraga umbellulata, S. pasumensis, and S. banmaensis. Chloroplast DNA (cpDNA) phylogenies revealed two well supported clades, corresponding to S. umbellulata and S. pasumensis plus S. banmaensis. Topology of the ITS phylogeny was largely congruent with that generated from cpDNA haplotypes, but with minor conflicts which might be caused by incomplete lineage sorting. Analyses of molecular variance of both cpDNA and ITS datasets revealed that most variation was held between S. pasumensis s.l. (with S. banmaensis) and S. umbellulata (92.31% for cpDNA; 69.78% for ITS), suggesting a high degree of genetic divergence between them. Molecular clock analysis based on ITS dataset suggested that the divergence between S. pasumensis s.l. and S. umbellulata can be dated to 8.50 Ma, probably a result of vicariant allopatric diversification associated with the uplift events of the HM. Vicariance associated with HM uplifts may also have been responsible for infraspecific differentiation in S. pasumensis. In contrast, infraspecific differentiation in S. umbellulata was most likely triggered by Quaternary glaciations. The much lower levels of gene diversity within populations of S. pasumensis compared with S. umbellulata could have resulted from both range contractions and human collection on account of its putative medicinal properties. Combining evidence from morphology, geographical distributions and molecular phylogenetic data, we recommend that S. banmaensis should be treated as a synonym of S. pasumensis which in turn, and based on the same sources of evidence, should be treated as a separate species rather than as a variety of S. umbellulata.
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Affiliation(s)
- Qing-Bo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of SciencesXining, China
- Key Laboratory of Crop Molecular Breeding of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of SciencesXining, China
| | - Yan Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of SciencesXining, China
- University of Chinese Academy of SciencesBeijing, China
| | - Zhuo-Ma Gengji
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of SciencesXining, China
- University of Chinese Academy of SciencesBeijing, China
| | - Richard J. Gornall
- Department of Genetics, University of LeicesterLeicester, United Kingdom
| | - Jiu-Li Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of SciencesXining, China
- University of Chinese Academy of SciencesBeijing, China
| | - Hai-Rui Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of SciencesXining, China
- University of Chinese Academy of SciencesBeijing, China
| | - Liu-Kun Jia
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of SciencesXining, China
- University of Chinese Academy of SciencesBeijing, China
| | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of SciencesXining, China
- *Correspondence: Shi-Long Chen
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Russell AL, Brown VA, Utzurrum RCB, Brooke AP, Wolf LA, Mccracken GF. Comparative Phylogeography of Pteropus samoensis and P. tonganus (Pteropodidae: Chiroptera) in the South Pacific. ACTA CHIROPTEROLOGICA 2016. [DOI: 10.3161/15081109acc2016.18.2.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Amy L. Russell
- Department of Biology, Grand Valley State University, Allendale, Michigan 49401, USA
| | - Veronica A. Brown
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Ruth C. B. Utzurrum
- Department of Marine and Wildlife Resources, Pago Pago, American Samoa 96899, USA
| | - Anne P. Brooke
- Department of Marine and Wildlife Resources, Pago Pago, American Samoa 96899, USA
| | - Lisa A. Wolf
- Department of Biology, University of Oregon, Eugene, Oregon 97403, USA
| | - Gary F. Mccracken
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
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Gurevitch J, Fox GA, Fowler NL, Graham CH. Landscape Demography: Population Change and its Drivers Across Spatial Scales. QUARTERLY REVIEW OF BIOLOGY 2016; 91:459-85. [DOI: 10.1086/689560] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Cieslak M, Mikkelsen SS, Skall HF, Baud M, Diserens N, Engelsma MY, Haenen OLM, Mousakhani S, Panzarin V, Wahli T, Olesen NJ, Schütze H. Phylogeny of the Viral Hemorrhagic Septicemia Virus in European Aquaculture. PLoS One 2016; 11:e0164475. [PMID: 27760205 PMCID: PMC5070809 DOI: 10.1371/journal.pone.0164475] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 09/26/2016] [Indexed: 12/04/2022] Open
Abstract
One of the most valuable aquaculture fish in Europe is the rainbow trout, Oncorhynchus mykiss, but the profitability of trout production is threatened by a highly lethal infectious disease, viral hemorrhagic septicemia (VHS), caused by the VHS virus (VHSV). For the past few decades, the subgenogroup Ia of VHSV has been the main cause of VHS outbreaks in European freshwater-farmed rainbow trout. Little is currently known, however, about the phylogenetic radiation of this Ia lineage into subordinate Ia clades and their subsequent geographical spread routes. We investigated this topic using the largest Ia-isolate dataset ever compiled, comprising 651 complete G gene sequences: 209 GenBank Ia isolates and 442 Ia isolates from this study. The sequences come from 11 European countries and cover the period 1971–2015. Based on this dataset, we documented the extensive spread of the Ia population and the strong mixing of Ia isolates, assumed to be the result of the Europe-wide trout trade. For example, the Ia lineage underwent a radiation into nine Ia clades, most of which are difficult to allocate to a specific geographic distribution. Furthermore, we found indications for two rapid, large-scale population growth events, and identified three polytomies among the Ia clades, both of which possibly indicate a rapid radiation. However, only about 4% of Ia haplotypes (out of 398) occur in more than one European country. This apparently conflicting finding regarding the Europe-wide spread and mixing of Ia isolates can be explained by the high mutation rate of VHSV. Accordingly, the mean period of occurrence of a single Ia haplotype was less than a full year, and we found a substitution rate of up to 7.813 × 10−4 nucleotides per site per year. Finally, we documented significant differences between Germany and Denmark regarding their VHS epidemiology, apparently due to those countries’ individual handling of VHS.
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Affiliation(s)
- Michael Cieslak
- Institute of Infectology (IMED) of the Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Insel Riems, Germany
- * E-mail:
| | - Susie S. Mikkelsen
- Section for Virology, National Veterinary Institute, DTU, Frederiksberg, Denmark
| | - Helle F. Skall
- Fish Health, Department of Animal Science, Aarhus University, Tjele, Denmark
| | - Marine Baud
- Ploufragan-Plouzané Laboratory (ANSES), Viral Fish Pathology Unit, Université Européenne de Bretagne, Technopôle Brest-Iroise, Plouzané, France
| | - Nicolas Diserens
- Centre for Fish and Wildlife Health (FIWI), Vetsuisse-Faculty, University of Bern, Bern, Switzerland
| | - Marc Y. Engelsma
- Central Veterinary Institute of Wageningen UR, NRL for Fish and Shellfish Diseases, Lelystad, the Netherlands
| | - Olga L. M. Haenen
- Central Veterinary Institute of Wageningen UR, NRL for Fish and Shellfish Diseases, Lelystad, the Netherlands
| | - Shirin Mousakhani
- Institute of Infectology (IMED) of the Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Insel Riems, Germany
| | - Valentina Panzarin
- Istituto Zooprofilattico Sperimentaledelle Venezie, OIE Reference Laboratory for Viral Encephalopathy and Retinopathy, Legnaro, Italy
| | - Thomas Wahli
- Centre for Fish and Wildlife Health (FIWI), Vetsuisse-Faculty, University of Bern, Bern, Switzerland
| | - Niels J. Olesen
- Section for Virology, National Veterinary Institute, DTU, Frederiksberg, Denmark
| | - Heike Schütze
- Institute of Infectology (IMED) of the Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Insel Riems, Germany
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Multi-Phase US Spread and Habitat Switching of a Post-Columbian Invasive, Sorghum halepense. PLoS One 2016; 11:e0164584. [PMID: 27755565 PMCID: PMC5068735 DOI: 10.1371/journal.pone.0164584] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/27/2016] [Indexed: 11/19/2022] Open
Abstract
Johnsongrass (Sorghum halepense) is a striking example of a post-Columbian founder event. This natural experiment within ecological time-scales provides a unique opportunity for understanding patterns of continent-wide genetic diversity following range expansion. Microsatellite markers were used for population genetic analyses including leaf-optimized Neighbor-Joining tree, pairwise FST, mismatch analysis, principle coordinate analysis, Tajima's D, Fu's F and Bayesian clusterings of population structure. Evidence indicates two geographically distant introductions of divergent genotypes, which spread across much of the US in <200 years. Based on geophylogeny, gene flow patterns can be inferred to have involved five phases. Centers of genetic diversity have shifted from two introduction sites separated by ~2000 miles toward the middle of the range, consistent with admixture between genotypes from the respective introductions. Genotyping provides evidence for a 'habitat switch' from agricultural to non-agricultural systems and may contribute to both Johnsongrass ubiquity and aggressiveness. Despite lower and more structured diversity at the invasion front, Johnsongrass continues to advance northward into cooler and drier habitats. Association genetic approaches may permit identification of alleles contributing to the habitat switch or other traits important to weed/invasive management and/or crop improvement.
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Fourdrilis S, Mardulyn P, Hardy OJ, Jordaens K, de Frias Martins AM, Backeljau T. Mitochondrial DNA hyperdiversity and its potential causes in the marine periwinkle Melarhaphe neritoides (Mollusca: Gastropoda). PeerJ 2016; 4:e2549. [PMID: 27761337 PMCID: PMC5068447 DOI: 10.7717/peerj.2549] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/12/2016] [Indexed: 12/18/2022] Open
Abstract
We report the presence of mitochondrial DNA (mtDNA) hyperdiversity in the marine periwinkle Melarhaphe neritoides (Linnaeus, 1758), the first such case among marine gastropods. Our dataset consisted of concatenated 16S-COI-Cytb gene fragments. We used Bayesian analyses to investigate three putative causes underlying genetic variation, and estimated the mtDNA mutation rate, possible signatures of selection and the effective population size of the species in the Azores archipelago. The mtDNA hyperdiversity in M. neritoides is characterized by extremely high haplotype diversity (Hd = 0.999 ± 0.001), high nucleotide diversity (π = 0.013 ± 0.001), and neutral nucleotide diversity above the threshold of 5% (πsyn = 0.0677). Haplotype richness is very high even at spatial scales as small as 100m2. Yet, mtDNA hyperdiversity does not affect the ability of DNA barcoding to identify M. neritoides. The mtDNA hyperdiversity in M. neritoides is best explained by the remarkably high mutation rate at the COI locus (μ = 5.82 × 10−5 per site per year or μ = 1.99 × 10−4 mutations per nucleotide site per generation), whereas the effective population size of this planktonic-dispersing species is surprisingly small (Ne = 5, 256; CI = 1,312–3,7495) probably due to the putative influence of selection. Comparison with COI nucleotide diversity values in other organisms suggests that mtDNA hyperdiversity may be more frequently linked to high μ values and that mtDNA hyperdiversity may be more common across other phyla than currently appreciated.
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Affiliation(s)
- Séverine Fourdrilis
- Directorate Taxonomy and Phylogeny & JEMU, Royal Belgian Institute of Natural Sciences , Brussels , Belgium
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology, Université Libre de Bruxelles , Brussels , Belgium
| | - Olivier J Hardy
- Evolutionary Biology and Ecology, Université Libre de Bruxelles , Brussels , Belgium
| | - Kurt Jordaens
- Department of Biology, Invertebrate Section, Royal Museum for Central Africa , Tervuren , Belgium
| | - António Manuel de Frias Martins
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores, Departamento de Biologia da Universidade dos Açores, University of the Azores , Ponta Delgada , Portugal
| | - Thierry Backeljau
- Directorate Taxonomy and Phylogeny & JEMU, Royal Belgian Institute of Natural Sciences, Brussels, Belgium; Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
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Choudhary JS, Naaz N, Prabhakar CS, Lemtur M. Genetic analysis of oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) populations based on mitochondrial cox1 and nad1 gene sequences from India and other Asian countries. Genetica 2016; 144:611-623. [PMID: 27699519 DOI: 10.1007/s10709-016-9929-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 09/24/2016] [Indexed: 11/25/2022]
Abstract
The study examined the genetic diversity and demographic history of Bactrocera dorsalis, a destructive and polyphagous insect pest of fruit crops in diverse geographic regions of India. 19 widely dispersed populations of the fly from India and other Asian countries were analysed using partial sequences of mitochondrial cytochrome oxidase I (cox1) and NADH dehydrogenase 1 (nad1) genes to investigate genetic diversity, genetic structure, and demographic history in the region. Genetic diversity indices [number of haplotypes (H), haloptype diversity (Hd), nucleotide diversity (π) and average number of nucleotide difference (k)] of populations revealed that B. dorsalis maintains fairly high level of genetic diversity without isolation by distance among the geographic regions. Demographic analysis showed significant (negative) Tajimas' D and Fu's F S with non significant sum of squared deviations (SSD) values, which indicate the possibility of recent sudden expansion of species and is further supported through distinctively star-like distribution structure of haplotypes among populations. Thus, the results indicate that both ongoing and historical factors have played important role in determining the genetic structure and diversity of the species in India. Consequently, sterile insect technique (SIT) could be a possible management strategy of species in the regions.
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Affiliation(s)
- Jaipal S Choudhary
- ICAR Research Complex for Eastern Region, Research Centre, Plandu, Ranchi, Jharkhand, 834010, India.
| | - Naiyar Naaz
- ICAR Research Complex for Eastern Region, Research Centre, Plandu, Ranchi, Jharkhand, 834010, India
| | - Chandra S Prabhakar
- ICAR Research Complex for Eastern Region, Research Centre, Plandu, Ranchi, Jharkhand, 834010, India
- Department of Entomology, Veer Kunwar Singh College of Agriculture, Bihar Agricultural University, Sabour, Dumraon, Buxar, Bihar, 802136, India
| | - Moanaro Lemtur
- ICAR Research Complex for Eastern Region, Research Centre, Plandu, Ranchi, Jharkhand, 834010, India
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Eltanany MA, Hemeda SA. Deeper insight into maternal genetic assessments and demographic history for Egyptian indigenous chicken populations using mtDNA analysis. J Adv Res 2016; 7:615-23. [PMID: 27489728 PMCID: PMC4949740 DOI: 10.1016/j.jare.2016.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 06/19/2016] [Accepted: 06/23/2016] [Indexed: 11/23/2022] Open
Abstract
This study principally sought to reveal the demographic expansion of Egyptian indigenous chickens (EIC) using representative breeds: Sinai (North), Fayoumi (Middle) and Dandarawi (South) of Egypt as well as to deeply clarify their genetic diversity, possible matrilineal origin and dispersal routes. A total of 33 partial mitochondrial DNA sequences were generated from EIC and compared with a worldwide reference dataset of 1290 wild and domestic chicken sequences. Study populations had 12 polymorphic variable sites and 7 haplotypes. A lack of maternal substructure between EIC was detected (F ST = 0.003). The unimodal mismatch distribution and negative values of Tajima's D (-0.659) and Fu's Fs (-0.157) indicated demographic expansion among EIC and pointed to Fayoumi as the oldest EIC population. Egyptian haplotypes were clustered phylogenetically into two divergent clades. Their phylogeography revealed an ancient single maternal lineage of Egyptian chickens likely derived from Indian-Subcontinent. Moreover, a recent maternal commercial heritage possibly originated in Yunnan-Province and/or surrounding areas was admixed restrictedly into Sinai. It is implied that Egypt was an entry point for Indian chicken into Africa and its further dispersal route to Europe. This study provides a clue supporting the previous assumption that urged utilizing consistent founder populations having closely related progenitors for synthetizing a stabilized homogenous crossbreed as a sustainable discipline in breeding program.
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Affiliation(s)
- Marwa A. Eltanany
- Department for Animal Wealth Development, Faculty of Veterinary Medicine, Benha University, 13736 Moshtohor, Toukh, Egypt
| | - Shabaan A. Hemeda
- Department for Animal Husbandry and Animal Wealth Development, Faculty of Veterinary Medicine, Alexandria University, Egypt
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Mora MS, Mapelli FJ, López A, Fernández MJG, Mirol PM, Kittlein MJ. Population genetic structure and historical dispersal patterns in the subterranean rodent Ctenomys “chasiquensis” from the southeastern Pampas region, Argentina. Mamm Biol 2016. [DOI: 10.1016/j.mambio.2016.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Osman SAM, Yonezawa T, Nishibori M. Origin and genetic diversity of Egyptian native chickens based on complete sequence of mitochondrial DNA D-loop region. Poult Sci 2016; 95:1248-56. [PMID: 26994197 DOI: 10.3382/ps/pew029] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 01/08/2016] [Indexed: 11/20/2022] Open
Abstract
Domestic chickens (Gallus gallus) play a significant role, ranging from food and entertainment to religion and ornamentation. However, the details on their domestication process are still controversial, especially the origin and evolution of African chickens. Egypt is thought to be important place for this event because of its geographic location as well as its long history of civilization. However, the genetic component and structure of Egyptian native chicken (ENC) have not been studied so far. The aim of this study is to clarify the origin and evolution of African chickens through assessing the genetic diversities and structure of five ENC breeds using the mitochondrial D-loop sequences. Our results suggest there is genetic differentiation between the pure native breeds and the improved native breeds. The latter breeds were established by the hybridization of the pure native and the exotic breeds. The pure native breeds were estimated to be established about 800 years ago. Subsequently, we extensively analyzed the D-loop sequences from the ENC as well as the globally collected chickens (2,010 individuals in total). Our phylogenetic tree among the regional populations shows African chickens can be separated to two distinct clades. The first clade consists of North African (Egypt), Central African (Sudan and Cameroon), European, and West (and Central) Asian chickens. The second clade consists of East African (Kenya, Malawi, and Zimbabwe) and Pacific chickens. It suggests the dual origins of African native chickens. The first group was probably originated from South Asia, and then migrated to West Asia, and finally arrived to Africa thorough Egypt. The second group migrated from Pacific to East Africa via Indian Ocean probably by Austronesian people. This dual origin hypothesis as well as estimated divergence times in this study is harmonious with the archaeological and historical evidences. Our migration analysis suggests there is limited gene flow within African continent. These obtained findings are important for the better understanding of the diversity and uniqueness of African native chickens.
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Affiliation(s)
- Sayed A-M Osman
- Laboratory of Animal Genetics, Department of Bioresource Science, Graduate School of Biosphere Science, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan Department of Genetics, Faculty of Agriculture, Minia University, El Minia 61517, Egypt
| | - Takahiro Yonezawa
- School of Life Sciences, Fudan University, SongHu Rd. 2005, Shanghai 200438, China The Institute of Statistical Mathematics, Midori-cho 10-3, Tachikawa, Tokyo 190-8562, Japan
| | - Masahide Nishibori
- Laboratory of Animal Genetics, Department of Bioresource Science, Graduate School of Biosphere Science, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan
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Molecular Phylogeography of Harvest Mice (Reithrodontomys megalotis) Based on Cytochrome b DNA Sequences. J MAMM EVOL 2016. [DOI: 10.1007/s10914-015-9318-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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