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Sadler DE, Watts PC, Uusi-Heikkilä S. Directional selection, not the direction of selection, affects telomere length and copy number at ribosomal RNA loci. Sci Rep 2024; 14:12162. [PMID: 38802448 PMCID: PMC11130246 DOI: 10.1038/s41598-024-63030-x] [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: 03/14/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024] Open
Abstract
Many fisheries exert directional selection on traits such as body size and growth rate. Whether directional selection impacts regions of the genome associated with traits related to growth is unknown. To address this issue, we characterised copy number variation in three regions of the genome associated with cell division, (1) telomeric DNA, (2) loci transcribed as ribosomal RNA (rDNA), and (3) mitochondrial DNA (mtDNA), in three selection lines of zebrafish reared at three temperatures (22 °C, 28 °C, and 34 °C). Selection lines differed in (1) the direction of selection (two lines experienced directional selection for large or small body size) and (2) whether they experienced any directional selection itself. Lines that had experienced directional selection were smaller, had lower growth rate, shorter telomeres, and lower rDNA copy number than the line that experiencing no directional selection. Neither telomere length nor rDNA copy number were affected by temperature. In contrast, mtDNA content increased at elevated temperature but did not differ among selection lines. Though directional selection impacts rDNA and telomere length, direction of such selection did not matter, whereas mtDNA acts as a stress marker for temperature. Future work should examine the consequences of these genomic changes in natural fish stocks.
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Affiliation(s)
- Daniel E Sadler
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland.
| | - Phillip C Watts
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Silva Uusi-Heikkilä
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
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2
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Roberts M, Josephs EB. Previously unmeasured genetic diversity explains part of Lewontin's paradox in a k-mer-based meta-analysis of 112 plant species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.594778. [PMID: 38798362 PMCID: PMC11118579 DOI: 10.1101/2024.05.17.594778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
At the molecular level, most evolution is expected to be neutral. A key prediction of this expectation is that the level of genetic diversity in a population should scale with population size. However, as was noted by Richard Lewontin in 1974 and reaffirmed by later studies, the slope of the population size-diversity relationship in nature is much weaker than expected under neutral theory. We hypothesize that one contributor to this paradox is that current methods relying on single nucleotide polymorphisms (SNPs) called from aligning short reads to a reference genome underestimate levels of genetic diversity in many species. To test this idea, we calculated nucleotide diversity ( π ) and k-mer-based metrics of genetic diversity across 112 plant species, amounting to over 205 terabases of DNA sequencing data from 27,488 individual plants. We then compared how these different metrics correlated with proxies of population size that account for both range size and population density variation across species. We found that our population size proxies scaled anywhere from about 3 to over 20 times faster with k-mer diversity than nucleotide diversity after adjusting for evolutionary history, mating system, life cycle habit, cultivation status, and invasiveness. The relationship between k-mer diversity and population size proxies also remains significant after correcting for genome size, whereas the analogous relationship for nucleotide diversity does not. These results suggest that variation not captured by common SNP-based analyses explains part of Lewontin's paradox in plants.
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3
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de Jong MJ, van Oosterhout C, Hoelzel AR, Janke A. Moderating the neutralist-selectionist debate: exactly which propositions are we debating, and which arguments are valid? Biol Rev Camb Philos Soc 2024; 99:23-55. [PMID: 37621151 DOI: 10.1111/brv.13010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023]
Abstract
Half a century after its foundation, the neutral theory of molecular evolution continues to attract controversy. The debate has been hampered by the coexistence of different interpretations of the core proposition of the neutral theory, the 'neutral mutation-random drift' hypothesis. In this review, we trace the origins of these ambiguities and suggest potential solutions. We highlight the difference between the original, the revised and the nearly neutral hypothesis, and re-emphasise that none of them equates to the null hypothesis of strict neutrality. We distinguish the neutral hypothesis of protein evolution, the main focus of the ongoing debate, from the neutral hypotheses of genomic and functional DNA evolution, which for many species are generally accepted. We advocate a further distinction between a narrow and an extended neutral hypothesis (of which the latter posits that random non-conservative amino acid substitutions can cause non-ecological phenotypic divergence), and we discuss the implications for evolutionary biology beyond the domain of molecular evolution. We furthermore point out that the debate has widened from its initial focus on point mutations, and also concerns the fitness effects of large-scale mutations, which can alter the dosage of genes and regulatory sequences. We evaluate the validity of neutralist and selectionist arguments and find that the tested predictions, apart from being sensitive to violation of underlying assumptions, are often derived from the null hypothesis of strict neutrality, or equally consistent with the opposing selectionist hypothesis, except when assuming molecular panselectionism. Our review aims to facilitate a constructive neutralist-selectionist debate, and thereby to contribute to answering a key question of evolutionary biology: what proportions of amino acid and nucleotide substitutions and polymorphisms are adaptive?
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Affiliation(s)
- Menno J de Jong
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325, Germany
| | - Cock van Oosterhout
- Centre for Ecology, Evolution and Conservation, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - A Rus Hoelzel
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Strasse 9, Frankfurt am Main, 60438, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14-16, Frankfurt am Main, 60325, Germany
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4
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Sadler DE, van Dijk S, Karjalainen J, Watts PC, Uusi‐Heikkilä S. Does size-selective harvesting erode adaptive potential to thermal stress? Ecol Evol 2024; 14:e11007. [PMID: 38333098 PMCID: PMC10850808 DOI: 10.1002/ece3.11007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 01/12/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024] Open
Abstract
Overharvesting is a serious threat to many fish populations. High mortality and directional selection on body size can cause evolutionary change in exploited populations via selection for a specific phenotype and a potential reduction in phenotypic diversity. Whether the loss of phenotypic diversity that accompanies directional selection impairs response to environmental stress is not known. To address this question, we exposed three zebrafish selection lines to thermal stress. Two lines had experienced directional selection for (1) large and (2) small body size, and one was (3) subject to random removal of individuals with respect to body size (i.e. line with no directional selection). Selection lines were exposed to three temperatures (elevated, 34°C; ambient, 28°C; low, 22°C) to determine the response to an environmental stressor (thermal stress). We assessed differences among selection lines in their life history (growth and reproduction), physiological traits (metabolic rate and critical thermal max) and behaviour (activity and feeding behaviour) when reared at different temperatures. Lines experiencing directional selection (i.e. size selected) showed reduced growth rate and a shift in average phenotype in response to lower or elevated thermal stress compared with fish from the random-selected line. Our data indicate that populations exposed to directional selection can have a more limited capacity to respond to thermal stress compared with fish that experience a comparable reduction in population size (but without directional selection). Future studies should aim to understand the impacts of environmental stressors on natural fish stocks.
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Affiliation(s)
- Daniel E. Sadler
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Stephan van Dijk
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Juha Karjalainen
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Phillip C. Watts
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Silva Uusi‐Heikkilä
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
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5
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Abstract
AbstractEvolutionary biologists have thought about the role of genetic variation during adaptation for a very long time-before we understood the organization of the genetic code, the provenance of genetic variation, and how such variation influenced the phenotypes on which natural selection acts. Half a century after the discovery of the structure of DNA and the unraveling of the genetic code, we have a rich understanding of these problems and the means to both delve deeper and widen our perspective across organisms and natural populations. The 2022 Vice Presidential Symposium of the American Society of Naturalists highlighted examples of recent insights into the role of genetic variation in adaptive processes, which are compiled in this special section. The work was conducted in different parts of the world, included theoretical and empirical studies with diverse organisms, and addressed distinct aspects of how genetic variation influences adaptation. In our introductory article to the special section, we discuss some important recent insights about the generation and maintenance of genetic variation, its impacts on phenotype and fitness, its fate in natural populations, and its role in driving adaptation. By placing the special section articles in the broader context of recent developments, we hope that this overview will also serve as a useful introduction to the field.
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6
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Powell DM. Losing the forest for the tree? On the wisdom of subpopulation management. Zoo Biol 2023; 42:591-604. [PMID: 37218348 DOI: 10.1002/zoo.21776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 03/24/2023] [Accepted: 04/26/2023] [Indexed: 05/24/2023]
Abstract
Animal habitats are changing around the world in many ways, presenting challenges to the survival of species. Zoo animal populations are also challenged by small population sizes and limited genetic diversity. Some ex situ populations are managed as subpopulations based on presumed subspecies or geographic locality and related concerns over genetic purity or taxonomic integrity. However, these decisions can accelerate the loss of genetic diversity and increase the likelihood of population extinction. Here I challenge the wisdom of subpopulation management, pointing out significant concerns in the literature with delineation of species, subspecies, and evolutionarily significant units. I also review literature demonstrating the value of gene flow for preserving adaptive potential, the often-misunderstood role of hybridization in evolution, and the likely overstated concerns about outbreeding depression, and preservation of local adaptations. I argue that the most effective way to manage animal populations for the long term be they in human care, in the wild, or if a captive population is being managed for reintroduction, is to manage for maximum genetic diversity rather than managing subpopulations focusing on taxonomic integrity, genetic purity, or geographic locale because selection in the future, rather than the past, will determine what genotypes and phenotypes are the most fit. Several case studies are presented to challenge the wisdom of subpopulation management and stimulate thinking about the preservation of genomes rather than species, subspecies, or lineages because those units evolved in habitats that are likely very different from those habitats today and in the future.
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Affiliation(s)
- David M Powell
- Department of Reproductive & Behavioral Sciences, Saint Louis Zoo, Saint Louis, Missouri, USA
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7
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Awad MF, Albogami B, Mwabvu T, Hassan MM, Baazeem A, Hassan MM, Elsharkawy MM. Identification and biodiversity patterns of Aspergillus species isolated from some soil invertebrates at high altitude using morphological characteristics and phylogenetic analyses. PeerJ 2023; 11:e15035. [PMID: 37033730 PMCID: PMC10075209 DOI: 10.7717/peerj.15035] [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: 01/17/2023] [Accepted: 02/20/2023] [Indexed: 03/30/2023] Open
Abstract
Background
The carcinogenic, mutagenic, and teratogenic chemicals such as aflatoxin are a worldwide health problem. Aspergillus spp., responsible for most cases of aflatoxin contamination, are common in the environment and spread easily to many different types of food. The objectives of this study were to conduct a survey of fungi associated with three soil invertebrates in Taif, Saudi Arabia, identify these isolates and explore mycotoxins formation.
Methods
In total, 114 fungal isolates were collected from various soil invertebrates (millipedes, Armadillidium vulgare and Porcellio laevis) in Taif, Saudi Arabia, among them, 22 isolates were identified as Aspergillus spp. based on morphological and molecular characteristics followed by both Fusarium and Penicillium.
Results
The sequences of ITS 1 and ITS 4 were utilized. Using bootstrap analysis, phylogenetic tree was split into two distinct clusters. Five sub clusters were included inside the first major cluster, and their bootstrap value was 99%. While, there were two small clusters in the second major cluster. All the tested Aspergillus strains were able to have a single PCR fragment amplified using the primer AspTef. TEF-1 DNA sequence bootstrap analysis with 1,000 replicates revealed two distinct groups. Additionally, the Aspergillus isolates were grouped into two different clusters with about 65% genetic similarity using ISSR-PCR analysis. The standard polymerase chain reaction was used to effectively amplify the Aopks, afl-A and omt-A genes in aflatoxigenic Aspergillus strains. Four Aspergillus strains used in this investigation were shown to generate aflatoxin B1. While, three Aspergillus stains showed ochratoxin genes.
Conclusions
In conclusion, the results indicate significant differences in the fungal community between ecoregions and soil invertebrates. Moreover, mycotoxin detection and identification among Aspergillus isolates were elucidated. This study could shed light on the risk of mycotoxin contamination along the supply chain.
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Affiliation(s)
- Mohamed Fadl Awad
- Department of Biology, College of Science, Taif University, Taif, Saudi Arabia
- High Altitude Research Centre, Taif University, Taif, Saudi Arabia
| | - Bander Albogami
- Department of Biology, College of Science, Taif University, Taif, Saudi Arabia
- High Altitude Research Centre, Taif University, Taif, Saudi Arabia
| | - Tarombera Mwabvu
- School of Biology & Environmental Sciences, University of Mpumalanga, Mbombela, South Africa
| | - Montaser M. Hassan
- Department of Biology, College of Science, Taif University, Taif, Saudi Arabia
- High Altitude Research Centre, Taif University, Taif, Saudi Arabia
| | - Alaa Baazeem
- Department of Biology, College of Science, Taif University, Taif, Saudi Arabia
- High Altitude Research Centre, Taif University, Taif, Saudi Arabia
| | - Mohamed M. Hassan
- Department of Biology, College of Science, Taif University, Taif, Saudi Arabia
- High Altitude Research Centre, Taif University, Taif, Saudi Arabia
| | - Mohsen Mohamed Elsharkawy
- Department of Agricultural Botany, Faculty of Agriculture, Kafrelsheikh University, Kafr Elsheikh, Egypt
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8
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Frankham R. Effects of genomic homozygosity on total fitness in an invertebrate: lethal equivalent estimates for Drosophila melanogaster. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01493-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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9
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Ponnikas S, Sigeman H, Lundberg M, Hansson B. Extreme variation in recombination rate and genetic diversity along the Sylvioidea neo-sex chromosome. Mol Ecol 2022; 31:3566-3583. [PMID: 35578784 PMCID: PMC9327509 DOI: 10.1111/mec.16532] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 04/13/2022] [Accepted: 05/04/2022] [Indexed: 12/03/2022]
Abstract
Recombination strongly impacts sequence evolution by affecting the extent of linkage and the efficiency of selection. Here, we study recombination over the Z chromosome in great reed warblers (Acrocephalus arundinaceus) using pedigree‐based linkage mapping. This species has extended Z and W chromosomes (“neo‐sex chromosomes”) formed by a fusion between a part of chromosome 4A and the ancestral sex chromosomes, which provides a unique opportunity to assess recombination and sequence evolution in sex‐linked regions of different ages. We assembled an 87.54 Mbp and 90.19 cM large Z with a small pseudoautosomal region (0.89 Mbp) at one end and the fused Chr4A‐part at the other end of the chromosome. A prominent feature in our data was an extreme variation in male recombination rate along Z with high values at both chromosome ends, but an apparent lack of recombination over a substantial central section, covering 78% of the chromosome. The nonrecombining region showed a drastic loss of genetic diversity and accumulation of repeats compared to the recombining parts. Thus, our data emphasize a key role of recombination in affecting local levels of polymorphism. Nonetheless, the evolutionary rate of genes (dN/dS) did not differ between high and low recombining regions, suggesting that the efficiency of selection on protein‐coding sequences can be maintained also at very low levels of recombination. Finally, the Chr4A‐derived part showed a similar recombination rate as the part of the ancestral Z that did recombine, but its sequence characteristics reflected both its previous autosomal, and current Z‐linked, recombination patterns.
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Affiliation(s)
- Suvi Ponnikas
- Department of Biology, Lund University, Lund, Sweden.,Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Hanna Sigeman
- Department of Biology, Lund University, Lund, Sweden
| | - Max Lundberg
- Department of Biology, Lund University, Lund, Sweden
| | - Bengt Hansson
- Department of Biology, Lund University, Lund, Sweden
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10
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Ochoa-Zavala M, Osorio-Olvera L, Cerón-Souza I, Rivera-Ocasio E, Jiménez-Lobato V, Núñez-Farfán J. Reduction of Genetic Variation When Far From the Niche Centroid: Prediction for Mangrove Species. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2021.795365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The niche-centroid hypothesis states that populations that are distributed near the centroid of the species' ecological niche will have higher fitness-related attributes, such as population abundance and genetic diversity than populations near the edges of the niche. Empirical evidence based on abundance and, more recently, genetic diversity data support this hypothesis. However, there are few studies that test this hypothesis in coastal species, such as mangroves. Here, we focused on the black mangrove Avicennia germinans. We combined ecological, heterozygosity, and allelic richness information from 1,419 individuals distributed in 40 populations with three main goals: (1) test the relationship between distance to the niche centroid and genetic diversity, (2) determine the set of environmental variables that best explain heterozygosity and allelic richness, and (3) predict the spatial variation in genetic diversity throughout most of the species' natural geographic range. We found a strong correlation between the distance to the niche centroid and both observed heterozygosity (Ho; ρ2 = 0.67 P < 0.05) and expected heterozygosity (He; ρ2 = 0.65, P < 0.05). The niche variables that best explained geographic variation in genetic diversity were soil type and precipitation seasonality. This suggests that these environmental variables influence mangrove growth and establishment, indirectly impacting standing genetic variation. We also predicted the spatial heterozygosity of A. germinans across its natural geographic range in the Americas using regression model coefficients. They showed significant power in predicting the observed data (R2 = 0.65 for Ho; R2 = 0.60 for He), even when we considered independent data sets (R2= 0.28 for Ho; R2 = 0.25 for He). Using this approach, several genetic diversity estimates can be implemented and may take advantage of population genomics to improve genetic diversity predictions. We conclude that the level of genetic diversity in A. germinans is in agreement with expectations of the niche-centroid hypothesis, namely that the highest heterozygosity and allelic richness (the basic genetic units for adaptation) are higher at locations of high environmental suitability. This shows that this approach is a potentially powerful tool in the conservation and management of this species, including for modelling changes in the face of climate change.
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11
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Lettoof DC, Thomson VA, Cornelis J, Bateman PW, Aubret F, Gagnon MM, von Takach B. Bioindicator snake shows genomic signatures of natural and anthropogenic barriers to gene flow. PLoS One 2021; 16:e0259124. [PMID: 34714831 PMCID: PMC8555784 DOI: 10.1371/journal.pone.0259124] [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: 07/28/2021] [Accepted: 10/12/2021] [Indexed: 11/18/2022] Open
Abstract
Urbanisation alters landscapes, introduces wildlife to novel stressors, and fragments habitats into remnant 'islands'. Within these islands, isolated wildlife populations can experience genetic drift and subsequently suffer from inbreeding depression and reduced adaptive potential. The Western tiger snake (Notechis scutatus occidentalis) is a predator of wetlands in the Swan Coastal Plain, a unique bioregion that has suffered substantial degradation through the development of the city of Perth, Western Australia. Within the urban matrix, tiger snakes now only persist in a handful of wetlands where they are known to bioaccumulate a suite of contaminants, and have recently been suggested as a relevant bioindicator of ecosystem health. Here, we used genome-wide single nucleotide polymorphism (SNP) data to explore the contemporary population genomics of seven tiger snake populations across the urban matrix. Specifically, we used population genomic structure and diversity, effective population sizes (Ne), and heterozygosity-fitness correlations to assess fitness of each population with respect to urbanisation. We found that population genomic structure was strongest across the northern and southern sides of a major river system, with the northern cluster of populations exhibiting lower heterozygosities than the southern cluster, likely due to a lack of historical gene flow. We also observed an increasing signal of inbreeding and genetic drift with increasing geographic isolation due to urbanisation. Effective population sizes (Ne) at most sites were small (< 100), with Ne appearing to reflect the area of available habitat rather than the degree of adjacent urbanisation. This suggests that ecosystem management and restoration may be the best method to buffer the further loss of genetic diversity in urban wetlands. If tiger snake populations continue to decline in urban areas, our results provide a baseline measure of genomic diversity, as well as highlighting which 'islands' of habitat are most in need of management and protection.
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Affiliation(s)
- Damian C. Lettoof
- Behavioural Ecology Lab, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Vicki A. Thomson
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Jari Cornelis
- Behavioural Ecology Lab, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Philip W. Bateman
- Behavioural Ecology Lab, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Fabien Aubret
- Station d’Ecologie Théorique et Expérimentale, CNRS, Moulis, France
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Marthe M. Gagnon
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Brenton von Takach
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
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12
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García-Dorado A, Caballero A. Neutral genetic diversity as a useful tool for conservation biology. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01384-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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13
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Filazzola A, Matter SF, MacIvor JS. The direct and indirect effects of extreme climate events on insects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 769:145161. [PMID: 33486167 DOI: 10.1016/j.scitotenv.2021.145161] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/08/2021] [Accepted: 01/09/2021] [Indexed: 06/12/2023]
Abstract
Extreme climate events are predicted to increase in the future, which will have significant effects on insect biodiversity. Research into this area has been rapidly expanding, but knowledge gaps still exist. We conducted a review of the literature to provide a synthesis of extreme climate events on insects and identify future areas of research. In our review, we asked the following questions: 1) What are the direct and indirect mechanisms that extreme climate events affect individual insects? 2) What are the effects of extreme climate events on insect populations and demography? 3) What are the implications of the extreme climate events effects on insect communities? Drought was among the most frequently described type of extreme climate event affecting insects, as well as the effects of temperature extremes and extreme temperature variation. Our review explores the factors that determine the sensitivity or resilience to climate extremes for individuals, populations, and communities. We also identify areas of future research to better understand the role of extreme climate events on insects including effects on non-trophic interactions, alteration of population dynamics, and mediation of the functional the trait set of communities. Many insect species are under threat from global change and extreme climate events are a contributing factor. Biologists and policy makers should consider the role of extreme events in their work to mitigate the loss of biodiversity and delivery of ecosystem services by insects.
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Affiliation(s)
- Alessandro Filazzola
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Canada.
| | - Stephen F Matter
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, United States of America
| | - J Scott MacIvor
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Canada
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14
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Chávez-Cortázar A, Oyama K, Ochoa-Zavala M, Mata-Rosas M, Veltjen E, Samain MS, Quesada M. Conservation genetics of relict tropical species of Magnolia (section Macrophylla). CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01334-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
AbstractSpecial conservation efforts should be made for relict species, as they usually have small population sizes and restricted distributions, placing them in critical extinction risk. To achieve conservation, information about genetic diversity distribution is needed. Here, using nine nuclear microsatellites, we analyzed 23 populations of five recently described species of Magnolia distributed in Mexico, which were previously assigned to Magnolia dealbata. We aimed to determine the level of genetic diversity and the distribution of genetic variation and proposed conservation measures. Compared to other endemic and relict species, we found a moderate level of genetic diversity in most populations; however, we identified two populations with no genetic variation. Additionally, we found evidence of positive values of inbreeding likely due to geitonogamy. We found a strong population structure, low effective population size, and no evidence of bottlenecks. Patterns of genetic differentiation did not support the morphological distinction of five species, so we hypothesized that the gene pools may instead represent well-differentiated populations of a single species. We argue that the pattern of genetic differentiation is explained by the natural fragmentation of the cloud forests after glaciation events, and the effects of genetic drift in small populations poorly connected by gene flow. Despite the moderate levels of genetic diversity, special attention is needed to guarantee conservation, with emphasis on the populations in the central region of the country as well as the valuable populations identified in the southwestern region.
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15
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Wei X, Huang M, Yue Q, Ma S, Li B, Mu Z, Peng C, Gao W, Liu W, Zheng J, Weng X, Sun X, Zuo Q, Bo S, Yuan X, Zhang W, Yang G, Ding Y, Wang X, Wang T, Hua P, Wang Z. Long-term urbanization impacts the eastern golden frog ( Pelophylax plancyi) in Shanghai City: Demographic history, genetic structure, and implications for amphibian conservation in intensively urbanizing environments. Evol Appl 2021; 14:117-135. [PMID: 33519960 PMCID: PMC7819575 DOI: 10.1111/eva.13156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 10/11/2020] [Accepted: 10/20/2020] [Indexed: 11/29/2022] Open
Abstract
Understanding the mechanisms of how urbanization influences the evolution of native species is vital for urban wildlife ecology and conservation in the Anthropocene. With thousands of years of agriculture-dominated historical urbanization followed by 40 years of intensive and rapid urbanization, Shanghai provides an ideal environment to study how the two-stage urbanization process influences the evolution of indigenous wildlife, especially of anuran species. Therefore, in this study, we used mitochondrial Cyt-b gene, microsatellite (SSR), and single nucleotide polymorphism (SNP) data to evaluate the demographic history and genetic structure of the eastern golden frog (Pelophylax plancyi), by sampling 407 individuals from 15 local populations across Shanghai, China. All local populations experienced bottlenecks during historical urbanization, while the local populations in urban areas maintained comparable contemporary effective population sizes (N e) and genetic diversity with suburban and rural populations. Nevertheless, the rapid modern urbanization has already imposed significant negative effects to the integrity of populations. The 15 local populations were differentiated into eight genetic clusters, showing a spatial distribution pattern consistent with the current urbanization gradient and island-mainland geography. Although moderate gene flow still occurred from the rural peripheral cluster to urban and suburban clusters, population fragmentation was more serious in the urban and suburban populations, where higher urbanization levels within 2-km radius areas showed significant negative relationships to the N e and genetic diversity of local populations. Therefore, to protect urban wildlife with limited dispersal ability, improving conditions in fragmented habitat remnants might be most essential for local populations living in more urbanized areas. Meanwhile, we highlight the need to preserve large unfragmented rural habitats and to construct corridor networks to connect discrete urban habitat remnants for the long-term wildlife conservation in intensively urbanizing environments.
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Affiliation(s)
- Xu Wei
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Meiling Huang
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Qu Yue
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Shuo Ma
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Ben Li
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Zhiqiang Mu
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Chuan Peng
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Wenxuan Gao
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Wenli Liu
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Jiaxin Zheng
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Xiaodong Weng
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Xiaohui Sun
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Qingqiu Zuo
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Shunqi Bo
- Shanghai Landscaping & City Appearance Administrative BureauShanghai Forestry BureauShanghaiChina
| | - Xiao Yuan
- Shanghai Landscaping & City Appearance Administrative BureauShanghai Forestry BureauShanghaiChina
| | - Wei Zhang
- Natural History Research Centre of Shanghai Natural History MuseumShanghai Science and Technology MuseumShanghaiChina
| | - Gang Yang
- Natural History Research Centre of Shanghai Natural History MuseumShanghai Science and Technology MuseumShanghaiChina
| | - Youzhong Ding
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Xiaoming Wang
- School of Life SciencesEast China Normal UniversityShanghaiChina
- Shanghai Science and Technology MuseumShanghaiChina
| | - Tianhou Wang
- School of Life SciencesEast China Normal UniversityShanghaiChina
- Institute of Eco‐ChongmingShanghaiChina
| | - Panyu Hua
- School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Zhenghuan Wang
- School of Life SciencesEast China Normal UniversityShanghaiChina
- Joint Translational Science and Technology Research InstituteEast China Normal UniversityShanghaiChina
- Yangtze Delta Estuarine Wetland Ecosystem Observation and Research StationMinistry of Education & Shanghai Science and Technology CommitteeShanghaiChina
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16
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The effects of pollen dispersal and mating pattern on inbreeding depression and hybrid vigor in Balfourodendron riedelianum (Engl.) Engl. (Rutaceae). CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01250-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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17
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Genetic variation across trophic levels: A test of the correlation between population size and genetic diversity in sympatric desert lizards. PLoS One 2019; 14:e0224040. [PMID: 31805058 PMCID: PMC6894812 DOI: 10.1371/journal.pone.0224040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/03/2019] [Indexed: 01/15/2023] Open
Abstract
Understanding the causes of genetic variation in real populations has been elusive. Competing theories claim that neutral vs. selective processes have a greater influence on the genetic variation within a population. A key difference among theories is the relationship between population size and genetic diversity. Our study tests this empirically by sampling two species of herbivorous lizards (Dipsosaurus dorsalis and Sauromalus ater) and two species of carnivorous lizards (Crotaphytus bicinctores and Gambelia wislizenii) that vary in population size at the same locality, and comparing metrics of genetic diversity. Contrary to neutral expectations, results from four independent loci showed levels of diversity were usually higher for species with smaller population sizes. This suggests that selective processes may be having an important impact on intraspecific diversity in this reptile community, although tests showed little evidence for selection on the loci sequenced for this study. It is also possible that idiosyncratic histories of the focal species may be overriding predictions from simple neutral models. If future studies show that lack of correlation between population size and genetic diversity is common, methods using genetic diversity to estimate population parameters like population size or time to common ancestor should be used with caution, as these estimates are based on neutral theory predictions.
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18
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Lu RS, Chen Y, Tamaki I, Sakaguchi S, Ding YQ, Takahashi D, Li P, Isaji Y, Chen J, Qiu YX. Pre-quaternary diversification and glacial demographic expansions of Cardiocrinum (Liliaceae) in temperate forest biomes of Sino-Japanese Floristic Region. Mol Phylogenet Evol 2019; 143:106693. [PMID: 31778814 DOI: 10.1016/j.ympev.2019.106693] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/11/2019] [Accepted: 11/22/2019] [Indexed: 11/27/2022]
Abstract
The Sino-Japanese Floristic Region (SJFR) in East Asia is one of the most diverse temperate floras in the world. However, the relative influence of Neogene palaeogeographical changes and Quaternary climatic fluctuations as causal mechanisms on species diversification remains largely controversial, because most divergence time estimates were inferred from single-locus data and have limited geographic or taxonomic sampling. To evaluate these influences, we use SNP markers from restriction site-associated DNA sequencing (RAD-Seq) loci and expressed sequence tags-simple sequence repeat (EST-SSR) markers to investigate the levels of genetic variation, speciation and demographic history of the temperate-deciduous forest (TDF) endemic Cardiocrinum (Endlicher) Lindley (Liliaceae), a genus comprising three species in China (C. giganteum, C. cathayanum) and Japan (C. cordatum). Phylogenomic and population genomic coalescent-based analyses demonstrated that Late Neogene tectonic/climatic events triggered speciation of Cardiocrinum, and Pleistocene climatic fluctuations had limited influence on its divergence history. Population demographic inference using Approximate Bayesian Computation from EST-SSRs and palaeoclimatic niche models both indicated that all three Cardiocrinum species experienced population expansions during the transition from the LIG to the LGM. We also discussed the implications of these results on the conservation of montane TDF species in the SJFR under ongoing environmental change. Our results improve our understanding of how the constituents of montane TDF across the SJFR responded to previous periods of rapid climate and environmental change in terms of speciation and population demographic processes.
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Affiliation(s)
- Rui-Sen Lu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yang Chen
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ichiro Tamaki
- Gifu Academy of Forest Science and Culture, 88 Sodai, Mino, Gifu 501-3714, Japan
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yan-Qian Ding
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Daiki Takahashi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Pan Li
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yuji Isaji
- Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Jun Chen
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ying-Xiong Qiu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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19
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Guo JL, Cao WJ, Li ZM, Zhang YH, Volis S. Conservation implications of population genetic structure in a threatened orchid Cypripedium tibeticum. PLANT DIVERSITY 2019; 41:13-18. [PMID: 30931413 PMCID: PMC6412106 DOI: 10.1016/j.pld.2018.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 12/22/2018] [Accepted: 12/25/2018] [Indexed: 05/15/2023]
Abstract
Cypripedium tibeticum is a threatened orchid which efficient conservation requires knowledge of its extent and structure of genetic variation. Using two chloroplast DNA fragments (rps16 and trnL-F), we analyzed 157 individuals from 9 populations representing the species range in China. Seven haplotypes were identified. C. tibeticum had high total genetic diversity (H T = 0.80) with major contribution to this diversity made by among-population component (G ST = 0.64, Φ ST = 0.86). However, despite high population differentiation there was no clear phylogeographic structure. The populations CY and DC made the greatest contribution to the total gene diversity as well as allelic richness. The possible mechanisms and implications of these findings for conservation of the species are discussed.
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Affiliation(s)
- Jian-Ling Guo
- Life Science Department, Yunnan Normal University, Kunming 650500, China
| | - Wen-Juan Cao
- Life Science Department, Yunnan Normal University, Kunming 650500, China
| | - Zhi-Min Li
- Life Science Department, Yunnan Normal University, Kunming 650500, China
| | - Yong-Hong Zhang
- Life Science Department, Yunnan Normal University, Kunming 650500, China
| | - Sergei Volis
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
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20
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Ko BJ, An J, Seomun H, Lee MY, Eo SH. Microsatellite DNA analysis reveals lower than expected genetic diversity in the threatened leopard cat (Prionailurus bengalensis) in South Korea. Genes Genomics 2018; 40:521-530. [PMID: 29892957 DOI: 10.1007/s13258-018-0654-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 01/09/2018] [Indexed: 11/25/2022]
Abstract
To optimize conservation efforts, it is necessary to determine the risk of extinction by collecting reliable population information for a given species. We developed eight novel, polymorphic microsatellite markers and used these markers in conjunction with twelve existing markers to measure genetic diversity of South Korean populations of leopard cat (Prionailurus bengalensis), a species for which population size and habitat area data are unknown in the country, to assess its conservation status. The average number of alleles and the observed heterozygosity of the species were 3.8 and 0.41, respectively, and microsatellite diversity was lower than the average genetic diversity of 57 populations of 12 other felid species, and lower than that of other mammal populations occurring in South Korea, including the raccoon dog (Nyctereutes procyonoides), water deer (Hydropotes inermis), and endangered long-tailed goral (Naemorhedus caudatus). Furthermore, analysis of genetic structure in the national leopard cat population showed no clear genetic differentiation, suggesting that it is not necessary to divide the South Korean leopard cat population into multiple management units for the purposes of conservation. These results indicate that the genetic diversity of the leopard cat in South Korea is unexpectedly low, and that the risk of local extinction is, as a result, substantial. Thus, it is necessary to begin appropriate conservation efforts at a national level to conserve the leopard cat population in South Korea.
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Affiliation(s)
- Byung June Ko
- Department of Forest Resources, Kongju National University, Yesan, Chungnam, South Korea
| | - Junghwa An
- National Institute of Biological Resources (NIBR), Incheon, South Korea
| | - Hong Seomun
- National Institute of Biological Resources (NIBR), Incheon, South Korea
| | - Mu-Yeong Lee
- National Institute of Biological Resources (NIBR), Incheon, South Korea
| | - Soo Hyung Eo
- Department of Forest Resources, Kongju National University, Yesan, Chungnam, South Korea.
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21
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Schou MF, Loeschcke V, Bechsgaard J, Schlötterer C, Kristensen TN. Unexpected high genetic diversity in small populations suggests maintenance by associative overdominance. Mol Ecol 2017; 26:6510-6523. [PMID: 28746770 DOI: 10.1111/mec.14262] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/23/2017] [Accepted: 06/28/2017] [Indexed: 12/17/2022]
Abstract
The effective population size (Ne ) is a central factor in determining maintenance of genetic variation. The neutral theory predicts that loss of variation depends on Ne , with less genetic drift in larger populations. We monitored genetic drift in 42 Drosophila melanogaster populations of different adult census population sizes (10, 50 or 500) using pooled RAD sequencing. In small populations, variation was lost at a substantially lower rate than expected. This observation was consistent across two ecological relevant thermal regimes, one stable and one with a stressful increase in temperature across generations. Estimated ratios between Ne and adult census size were consistently higher in small than in larger populations. The finding provides evidence for a slower than expected loss of genetic diversity and consequently a higher than expected long-term evolutionary potential in small fragmented populations. More genetic diversity was retained in areas of low recombination, suggesting that associative overdominance, driven by disfavoured homozygosity of recessive deleterious alleles, is responsible for the maintenance of genetic diversity in smaller populations. Consistent with this hypothesis, the X-chromosome, which is largely free of recessive deleterious alleles due to hemizygosity in males, fits neutral expectations even in small populations. Our experiments provide experimental answers to a range of unexpected patterns in natural populations, ranging from variable diversity on X-chromosomes and autosomes to surprisingly high levels of nucleotide diversity in small populations.
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Affiliation(s)
- Mads F Schou
- Department of Bioscience, Aarhus University, Aarhus C, Denmark
| | | | | | | | - Torsten N Kristensen
- Department of Bioscience, Aarhus University, Aarhus C, Denmark.,Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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22
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Wang S, Liu C, Wilson AB, Zhao N, Li X, Zhu W, Gao X, Liu X, Li Y. Pathogen richness and abundance predict patterns of adaptive major histocompatibility complex variation in insular amphibians. Mol Ecol 2017; 26:4671-4685. [PMID: 28734069 DOI: 10.1111/mec.14242] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 06/01/2017] [Accepted: 06/19/2017] [Indexed: 12/26/2022]
Abstract
The identification of the factors responsible for genetic variation and differentiation at adaptive loci can provide important insights into the evolutionary process and is crucial for the effective management of threatened species. We studied the impact of environmental viral richness and abundance on functional diversity and differentiation of the MHC class Ia locus in populations of the black-spotted pond frog (Pelophylax nigromaculatus), an IUCN-listed species, on 24 land-bridge islands of the Zhoushan Archipelago and three nearby mainland sites. We found a high proportion of private MHC alleles in mainland and insular populations, corresponding to 32 distinct functional supertypes, and strong positive selection on MHC antigen-binding sites in all populations. Viral pathogen diversity and abundance were reduced at island sites relative to the mainland, and islands housed distinctive viral communities. Standardized MHC diversity at island sites exceeded that found at neutral microsatellites, and the representation of key functional supertypes was positively correlated with the abundance of specific viruses in the environment (Frog virus 3 and Ambystoma tigrinum virus). These results indicate that pathogen-driven diversifying selection can play an important role in maintaining functionally important MHC variation following island isolation, highlighting the importance of considering functionally important genetic variation and host-pathogen associations in conservation planning and management.
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Affiliation(s)
- Supen Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Conghui Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Anthony B Wilson
- Department of Biology, Brooklyn College and The Graduate Center, City University of New York, Brooklyn, NY, USA
| | - Na Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xianping Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wei Zhu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xu Gao
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xuan Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yiming Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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23
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Eldridge MDB, Miller EJ, Neaves LE, Zenger KR, Herbert CA. Extensive genetic differentiation detected within a model marsupial, the tammar wallaby (Notamacropus eugenii). PLoS One 2017; 12:e0172777. [PMID: 28257440 PMCID: PMC5336229 DOI: 10.1371/journal.pone.0172777] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 02/09/2017] [Indexed: 11/19/2022] Open
Abstract
The tammar wallaby (Notamacropus eugenii) is one of the most intensively studied of all macropodids and was the first Australasian marsupial to have its genome sequenced. However, comparatively little is known about genetic diversity and differentiation amongst the morphologically distinct allopatric populations of tammar wallabies found in Western (WA) and South Australia (SA). Here we compare autosomal and Y-linked microsatellite genotypes, as well as sequence data (~600 bp) from the mitochondrial DNA (mtDNA) control region (CR) in tammar wallabies from across its distribution. Levels of diversity at autosomal microsatellite loci were typically high in the WA mainland and Kangaroo Island (SA) populations (A = 8.9-10.6; He = 0.77-0.78) but significantly reduced in other endemic island populations (A = 3.8-4.1; He = 0.41-0.48). Autosomal and Y-linked microsatellite loci revealed a pattern of significant differentiation amongst populations, especially between SA and WA. The Kangaroo Island and introduced New Zealand population showed limited differentiation. Multiple divergent mtDNA CR haplotypes were identified within both SA and WA populations. The CR haplotypes of tammar wallabies from SA and WA show reciprocal monophyly and are highly divergent (14.5%), with levels of sequence divergence more typical of different species. Within WA tammar wallabies, island populations each have unique clusters of highly related CR haplotypes and each is most closely related to different WA mainland haplotypes. Y-linked microsatellite haplotypes show a similar pattern of divergence although levels of diversity are lower. In light of these differences, we suggest that two subspecies of tammar wallaby be recognized; Notamacropus eugenii eugenii in SA and N. eugenii derbianus in WA. The extensive neutral genetic diversity and inter-population differentiation identified within tammar wallabies should further increase the species value and usefulness as a model organism.
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Affiliation(s)
- Mark D. B. Eldridge
- Australian Museum Research Institute, Sydney, New South Wales, Australia
- Department of Biological Sciences, Macquarie University, New South Wales, Australia
- * E-mail:
| | - Emily J. Miller
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, New South Wales, Australia
| | - Linda E. Neaves
- Australian Museum Research Institute, Sydney, New South Wales, Australia
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
| | - Kyall R. Zenger
- College of Science and Engineering and Centre of Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
| | - Catherine A. Herbert
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, New South Wales, Australia
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24
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Hua X, Bromham L. Darwinism for the Genomic Age: Connecting Mutation to Diversification. Front Genet 2017; 8:12. [PMID: 28224003 PMCID: PMC5293951 DOI: 10.3389/fgene.2017.00012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/19/2017] [Indexed: 12/30/2022] Open
Abstract
A growing body of evidence suggests that rates of diversification of biological lineages are correlated with differences in genome-wide mutation rate. Given that most research into differential patterns of diversification rate have focused on species traits or ecological parameters, a connection to the biochemical processes of genome change is an unexpected observation. While the empirical evidence for a significant association between mutation rate and diversification rate is mounting, there has been less effort in explaining the factors that mediate this connection between genetic change and species richness. Here we draw together empirical studies and theoretical concepts that may help to build links in the explanatory chain that connects mutation to diversification. First we consider the way that mutation rates vary between species. We then explore how differences in mutation rates have flow-through effects to the rate at which populations acquire substitutions, which in turn influences the speed at which populations become reproductively isolated from each other due to the acquisition of genomic incompatibilities. Since diversification rate is commonly measured from phylogenetic analyses, we propose a conceptual approach for relating events of reproductive isolation to bifurcations on molecular phylogenies. As we examine each of these relationships, we consider theoretical models that might shine a light on the observed association between rate of molecular evolution and diversification rate, and critically evaluate the empirical evidence for these links, focusing on phylogenetic comparative studies. Finally, we ask whether we are getting closer to a real understanding of the way that the processes of molecular evolution connect to the observable patterns of diversification.
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Affiliation(s)
- Xia Hua
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra ACT, Australia
| | - Lindell Bromham
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra ACT, Australia
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25
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Mimura M, Yahara T, Faith DP, Vázquez‐Domínguez E, Colautti RI, Araki H, Javadi F, Núñez‐Farfán J, Mori AS, Zhou S, Hollingsworth PM, Neaves LE, Fukano Y, Smith GF, Sato Y, Tachida H, Hendry AP. Understanding and monitoring the consequences of human impacts on intraspecific variation. Evol Appl 2017; 10:121-139. [PMID: 28127389 PMCID: PMC5253428 DOI: 10.1111/eva.12436] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 09/20/2016] [Indexed: 12/15/2022] Open
Abstract
Intraspecific variation is a major component of biodiversity, yet it has received relatively little attention from governmental and nongovernmental organizations, especially with regard to conservation plans and the management of wild species. This omission is ill-advised because phenotypic and genetic variations within and among populations can have dramatic effects on ecological and evolutionary processes, including responses to environmental change, the maintenance of species diversity, and ecological stability and resilience. At the same time, environmental changes associated with many human activities, such as land use and climate change, have dramatic and often negative impacts on intraspecific variation. We argue for the need for local, regional, and global programs to monitor intraspecific genetic variation. We suggest that such monitoring should include two main strategies: (i) intensive monitoring of multiple types of genetic variation in selected species and (ii) broad-brush modeling for representative species for predicting changes in variation as a function of changes in population size and range extent. Overall, we call for collaborative efforts to initiate the urgently needed monitoring of intraspecific variation.
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Affiliation(s)
- Makiko Mimura
- Department of Bioenvironmental SystemsTamagawa UniversityTokyoJapan
| | - Tetsukazu Yahara
- Department of Biology and Institute of Decision Science for a Sustainable SocietyKyushu UniversityFukuokaJapan
| | - Daniel P. Faith
- The Australian Museum Research InstituteThe Australian MuseumSydneyNSWAustralia
| | | | | | - Hitoshi Araki
- Research Faculty of AgricultureHokkaido UniversitySapporoHokkaidoJapan
| | - Firouzeh Javadi
- Department of Biology and Institute of Decision Science for a Sustainable SocietyKyushu UniversityFukuokaJapan
| | - Juan Núñez‐Farfán
- Instituto de EcologíaUniversidad Nacional Autónoma de MéxicoMéxicoMéxico
| | - Akira S. Mori
- Graduate School of Environment and Information SciencesYokohama National UniversityYokohamaJapan
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary BotanyInstitute of BotanyChinese Academy of SciencesBeijingChina
| | | | - Linda E. Neaves
- Royal Botanic Garden EdinburghEdinburghUK
- Australian Centre for Wildlife Genomics, Australian Museum Research InstituteAustralian MuseumSydneyNSWAustralia
| | - Yuya Fukano
- Department of Biology and Institute of Decision Science for a Sustainable SocietyKyushu UniversityFukuokaJapan
| | - Gideon F. Smith
- Department of BotanyNelson Mandela Metropolitan UniversityPort ElizabethSouth Africa
- Departamento de Ciências da VidaCentre for Functional EcologyUniversidade de CoimbraCoimbraPortugal
| | | | - Hidenori Tachida
- Department of Biology and Institute of Decision Science for a Sustainable SocietyKyushu UniversityFukuokaJapan
| | - Andrew P. Hendry
- Redpath Museum and Department of BiologyMcGill UniversityMontrealQuebecCanada
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26
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Dutoit L, Burri R, Nater A, Mugal CF, Ellegren H. Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher (Ficedula albicollis) genome. Mol Ecol Resour 2016; 17:586-597. [DOI: 10.1111/1755-0998.12602] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 09/02/2016] [Accepted: 09/19/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Ludovic Dutoit
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-752 36 Uppsala Sweden
| | - Reto Burri
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-752 36 Uppsala Sweden
| | - Alexander Nater
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-752 36 Uppsala Sweden
| | - Carina F. Mugal
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-752 36 Uppsala Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-752 36 Uppsala Sweden
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Tinnert J, Hellgren O, Lindberg J, Koch‐Schmidt P, Forsman A. Population genetic structure, differentiation, and diversity in Tetrix subulata pygmy grasshoppers: roles of population size and immigration. Ecol Evol 2016; 6:7831-7846. [PMID: 30128133 PMCID: PMC6093165 DOI: 10.1002/ece3.2520] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/30/2016] [Accepted: 08/31/2016] [Indexed: 12/30/2022] Open
Abstract
Genetic diversity within and among populations and species is influenced by complex demographic and evolutionary processes. Despite extensive research, there is no consensus regarding how landscape structure, spatial distribution, gene flow, and population dynamics impact genetic composition of natural populations. Here, we used amplified fragment length polymorphisms (AFLPs) to investigate effects of population size, geographic isolation, immigration, and gene flow on genetic structure, divergence, and diversity in populations of Tetrix subulata pygmy grasshoppers (Orthoptera: Tetrigidae) from 20 sampling locations in southern Sweden. Analyses of 1564 AFLP markers revealed low to moderate levels of genetic diversity (PPL = 59.5-90.1; Hj = 0.23-0.32) within and significant divergence among sampling localities. This suggests that evolution of functional traits in response to divergent selection is possible and that gene flow is restricted. Genetic diversity increased with population size and with increasing proportion of long-winged phenotypes (a proxy of recent immigration) across populations on the island of Öland, but not on the mainland. Our data further suggested that the open water separating Öland from the mainland acts as a dispersal barrier that restricts migration and leads to genetic divergence among regions. Isolation by distance was evident for short interpopulation distances on the mainland, but gradually disappeared as populations separated by longer distances were included. Results illustrate that integrating ecological and molecular data is key to identifying drivers of population genetic structure in natural populations. Our findings also underscore the importance of landscape structure and spatial sampling scheme for conclusions regarding the role of gene flow and isolation by distance.
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Affiliation(s)
- Jon Tinnert
- Department of Biology and Environmental ScienceEcology and Evolution in Microbial Model Systems, EEMISLinnaeus UniversityKalmarSweden
| | - Olof Hellgren
- Department of Biology and Environmental ScienceEcology and Evolution in Microbial Model Systems, EEMISLinnaeus UniversityKalmarSweden
- Present address:
Department of BiologyLund UniversityLundSweden
| | - Jenny Lindberg
- Department of Biology and Environmental ScienceEcology and Evolution in Microbial Model Systems, EEMISLinnaeus UniversityKalmarSweden
- Present address:
Naturbruksskolan Sötåsen54591TörebodaSweden
| | - Per Koch‐Schmidt
- Department of Biology and Environmental ScienceEcology and Evolution in Microbial Model Systems, EEMISLinnaeus UniversityKalmarSweden
| | - Anders Forsman
- Department of Biology and Environmental ScienceEcology and Evolution in Microbial Model Systems, EEMISLinnaeus UniversityKalmarSweden
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Yang J, Gao Z, Sun W, Zhang C. High regional genetic differentiation of an endangered relict plant Craigia yunnanensis and implications for its conservation. PLANT DIVERSITY 2016; 38:221-226. [PMID: 30159469 PMCID: PMC6112198 DOI: 10.1016/j.pld.2016.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 07/25/2016] [Accepted: 07/29/2016] [Indexed: 05/31/2023]
Abstract
Of the genus Craigia, widespread in the Tertiary, only two relict species survived to modern times. One species is now possibly extinct and the other one, Craigia yunnanensis, is severely endangered. Extensive surveys have located six C. yunnanensis populations in Yunnan province, southwest China. Using fluorescent amplified fragment length polymorphism (AFLP), the genetic diversity and population structure of these populations were examined. It was found that genetic diversity of C. yunnanensis was moderate at the species level, but low at regional and population levels. Analysis of population structure showed significant genetic differentiation between Wenshan and Dehong regions, apparently representing two geographically isolated for long time refuges. There are also clear indications of isolation between populations, which, together with anthropogenically caused decline of population size, will lead to general loss of the species genetic variation with subsequent loss of adaptive potential. To conserve the genetic integrity of C. yunnanensis, we recommend that ex-situ conservation should include representative samples from every population of the two differentiated regions (e.g. Wenshan and Dehong). The crosses between individuals originated from different regions should be avoided because of a high risk of outbreeding depression. As all the extant populations of C. yunnanensis are in unprotected areas with strong anthropogenic impact, there is no alternative to reintroduction of C. yunnanensis into suitable protected locations.
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Affiliation(s)
- Jing Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Zerui Gao
- Yunnan Tobacco Industrial Hi-tech Material CO., LTD, Kunming, 650106, Yunnan, China
| | - Weibang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Changqin Zhang
- Kunming Botanical Garden, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
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Naranjo-Díaz N, Sallum MAM, Correa MM. Population dynamics of Anopheles nuneztovari in Colombia. INFECTION GENETICS AND EVOLUTION 2016; 45:56-65. [PMID: 27553709 DOI: 10.1016/j.meegid.2016.08.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/05/2016] [Accepted: 08/18/2016] [Indexed: 11/27/2022]
Abstract
Anopheles nuneztovari is an important Colombian malaria vector widespread on both sides of the Andean Mountains, presenting morphological, behavioral and genetic heterogeneity throughout the country. The aim of this study was to evaluate whether the population structure and distribution of An. nuneztovari in Colombia are associated with ecological and physical barriers present in a heterogeneous landscape. Further, differences in behavior were addressed. A total of 5392 specimens of An. nuneztovari were collected. Mitochondrial and nuclear marker analyses detected subdivision among the northwest-west, northeast and east populations. For both markers, isolation by distance (~53%) and isolation by resistance (>30%) were determinants of population genetic differentiation. This suggests that physical barriers, geographical distance and ecological differences on both sides of the Andean Mountains promoted the genetic differentiation and population subdivision of An. nuneztovari in Colombia. This species showed the highest biting activity after 20:00h; indoor and outdoor preferences were found in all localities. These results indicated that the most effective interventions for controlling vector populations on both sides of the Andes need to be region-specific.
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Affiliation(s)
- Nelson Naranjo-Díaz
- Grupo de Microbiología Molecular, Escuela de Microbiología, Universidad de Antioquia, Calle 70 No. 52-21, Medellín, Colombia.
| | - Maria Anice M Sallum
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, Brazil.
| | - Margarita M Correa
- Grupo de Microbiología Molecular, Escuela de Microbiología, Universidad de Antioquia, Calle 70 No. 52-21, Medellín, Colombia.
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James JE, Lanfear R, Eyre-Walker A. Molecular Evolutionary Consequences of Island Colonization. Genome Biol Evol 2016; 8:1876-88. [PMID: 27358424 PMCID: PMC4943191 DOI: 10.1093/gbe/evw120] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Island endemics are expected to have low effective population sizes (Ne), first because some may experience population bottlenecks when they are founded, and second because they have restricted ranges. Therefore, we expect island species to have reduced genetic diversity, inefficient selection, and reduced adaptive potential compared with their mainland counterparts. We used both polymorphism and substitution data to address these predictions, improving on the approach of recent studies that only used substitution data. This allowed us to directly test the assumption that island species have small values of Ne We found that island species had significantly less genetic diversity than mainland species; however, this pattern could be attributed to a subset of island species that appeared to have undergone a recent population bottleneck. When these species were excluded from the analysis, island and mainland species had similar levels of genetic diversity, despite island species occupying considerably smaller areas than their mainland counterparts. We also found no overall difference between island and mainland species in terms of the effectiveness of selection or the mutation rate. Our evidence suggests that island colonization has no lasting impact on molecular evolution. This surprising result highlights gaps in our knowledge of the relationship between census and effective population size.
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Affiliation(s)
- Jennifer E James
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Robert Lanfear
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia Division of Evolution Ecology and Genetics, Research School of Biology, the Australian National University, Canberra, Australian Capital Territory, Australia
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
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Abstract
Genetic polymorphism varies among species and within genomes, and has important implications for the evolution and conservation of species. The determinants of this variation have been poorly understood, but population genomic data from a wide range of organisms now make it possible to delineate the underlying evolutionary processes, notably how variation in the effective population size (Ne) governs genetic diversity. Comparative population genomics is on its way to providing a solution to 'Lewontin's paradox' - the discrepancy between the many orders of magnitude of variation in population size and the much narrower distribution of diversity levels. It seems that linked selection plays an important part both in the overall genetic diversity of a species and in the variation in diversity within the genome. Genetic diversity also seems to be predictable from the life history of a species.
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Jaeger CP, Duvall MR, Swanson BJ, Phillips CA, Dreslik MJ, Baker SJ, King RB. Microsatellite and major histocompatibility complex variation in an endangered rattlesnake, the Eastern Massasauga (Sistrurus catenatus). Ecol Evol 2016; 6:3991-4003. [PMID: 27516858 PMCID: PMC4874855 DOI: 10.1002/ece3.2159] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 03/30/2016] [Accepted: 04/01/2016] [Indexed: 01/18/2023] Open
Abstract
Genetic diversity is fundamental to maintaining the long-term viability of populations, yet reduced genetic variation is often associated with small, isolated populations. To examine the relationship between demography and genetic variation, variation at hypervariable loci (e.g., microsatellite DNA loci) is often measured. However, these loci are selectively neutral (or near neutral) and may not accurately reflect genomewide variation. Variation at functional trait loci, such as the major histocompatibility complex (MHC), can provide a better assessment of adaptive genetic variation in fragmented populations. We compared patterns of microsatellite and MHC variation across three Eastern Massasauga (Sistrurus catenatus) populations representing a gradient of demographic histories to assess the relative roles of natural selection and genetic drift. Using 454 deep amplicon sequencing, we identified 24 putatively functional MHC IIB exon 2 alleles belonging to a minimum of six loci. Analysis of synonymous and nonsynonymous substitution rates provided evidence of historical positive selection at the nucleotide level, and Tajima's D provided support for balancing selection in each population. As predicted, estimates of microsatellite allelic richness, observed, heterozygosity, and expected heterozygosity varied among populations in a pattern qualitatively consistent with demographic history and abundance. While MHC allelic richness at the population and individual levels revealed similar trends, MHC nucleotide diversity was unexpectedly high in the smallest population. Overall, these results suggest that genetic variation in the Eastern Massasauga populations in Illinois has been shaped by multiple evolutionary mechanisms. Thus, conservation efforts should consider both neutral and functional genetic variation when managing captive and wild Eastern Massasauga populations.
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Affiliation(s)
- Collin P. Jaeger
- Department of Biological SciencesNorthern Illinois UniversityDeKalbIllinois60115
| | - Melvin R. Duvall
- Department of Biological SciencesNorthern Illinois UniversityDeKalbIllinois60115
| | - Bradley J. Swanson
- Department of BiologyCentral Michigan UniversityMt. PleasantMichigan48859
| | - Christopher A. Phillips
- Illinois Natural History SurveyUniversity of Illinois Urbana‐ChampaignChampaignIllinois61820
| | - Michael J. Dreslik
- Illinois Natural History SurveyUniversity of Illinois Urbana‐ChampaignChampaignIllinois61820
| | - Sarah J. Baker
- Illinois Natural History SurveyUniversity of Illinois Urbana‐ChampaignChampaignIllinois61820
| | - Richard B. King
- Department of Biological SciencesNorthern Illinois UniversityDeKalbIllinois60115
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Wang SH, Bao L, Wang TM, Wang HF, Ge JP. Contrasting genetic patterns between two coexisting Eleutherococcus species in northern China. Ecol Evol 2016; 6:3311-24. [PMID: 27103988 PMCID: PMC4833501 DOI: 10.1002/ece3.2118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Revised: 03/11/2016] [Accepted: 03/21/2016] [Indexed: 11/07/2022] Open
Abstract
Climate oscillations are the key factors to understand the patterns in modern biodiversity. East Asia harbors the most diverse temperate flora, largely because an extensive terrestrial ice cap was absent during repeated Pleistocene glaciation-interglacial cycles. Comparing the demographic histories of species that are codistributed and are close relatives may provide insight into how the process of climate change influences species ranges. In this study, we compared the spatial genetic structure and demographic histories of two coexisting Eleutherococcus species, Eleutherococcus senticosus and E. sessiliflorus. Both species are distributed in northern China, regions that are generally considered to be sensitive to climatic fluctuations. These regions once hosted temperate forest, but this temperate forest was replaced by tundra and taiga forest during the Last Glacial Maximum (LGM), according to pollen records. Using three chloroplast DNA fragments, we assessed the genetic structure of 20 and 9 natural populations of E. senticosus and E. sessiliflorus, respectively. Extremely contrasting genetic patterns were found between the two species; E. sessiliflorus had little genetic variation, whereas E. senticosus had considerably higher levels of genetic variation (15 haplotypes). We speculated that a recent severe bottleneck may have resulted in the extremely low genetic diversity in E. sessiliflorus. In E. senticosus, populations in Northeast China (NEC) harbored all of the haplotypes found in this species and included private haplotypes. The populations in NEC had higher levels of genetic diversity than did those from North China (NC). Therefore, we suggest that both the NC and NEC regions can sustain LGM refugia and that lineage admixture from multiple refugia took place after the LGM elevated the local genetic diversity in NEC. In NEC, multiple genetic hot spots were found in the Changbai Mountains and the Xiaoxing'an Range, which implied that multiple locations in NEC may sustain LGM refugia, even in the Xiaoxing'an Range.
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Affiliation(s)
- Sheng-Hong Wang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University Beijing 100875 China
| | - Lei Bao
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University Beijing 100875 China
| | - Tian-Ming Wang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University Beijing 100875 China
| | - Hong-Fang Wang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University Beijing 100875 China
| | - Jian-Ping Ge
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University Beijing 100875 China
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Santos J, Pascual M, Fragata I, Simões P, Santos MA, Lima M, Marques A, Lopes-Cunha M, Kellen B, Balanyà J, Rose MR, Matos M. Tracking changes in chromosomal arrangements and their genetic content during adaptation. J Evol Biol 2016; 29:1151-67. [PMID: 26969850 DOI: 10.1111/jeb.12856] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 02/23/2016] [Accepted: 02/25/2016] [Indexed: 12/13/2022]
Abstract
There is considerable evidence for an adaptive role of inversions, but how their genetic content evolves and affects the subsequent evolution of chromosomal polymorphism remains controversial. Here, we track how life-history traits, chromosomal arrangements and 22 microsatellites, within and outside inversions, change in three replicated populations of Drosophila subobscura for 30 generations of laboratory evolution since founding from the wild. The dynamics of fitness-related traits indicated adaptation to the new environment concomitant with directional evolution of chromosomal polymorphism. Evidence of selective changes in frequency of inversions was obtained for seven of 23 chromosomal arrangements, corroborating a role for inversions in adaptation. The evolution of linkage disequilibrium between some microsatellites and chromosomes suggested that adaptive changes in arrangements involved changes in their genetic content. Several microsatellite alleles increased in frequency more than expected by drift in targeted inversions in all replicate populations. In particular, there were signs of selection in the O3+4 arrangement favouring a combination of alleles in two loci linked to the inversion and changing along with it, although the lack of linkage disequilibrium between these loci precludes epistatic selection. Seven other alleles increased in frequency within inversions more than expected by drift, but were not in linkage disequilibrium with them. Possibly these alleles were hitchhiking along with alleles under selection that were not specific to those inversions. Overall, the selection detected on the genetic content of inversions, despite limited coverage of the genome, suggests that genetic changes within inversions play an important role in adaptation.
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Affiliation(s)
- J Santos
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - M Pascual
- Department of Genetics and IrBio, Facultat de Biologia, Universitat de Barcelona, Barcelona, España
| | - I Fragata
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - P Simões
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - M A Santos
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - M Lima
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - A Marques
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - M Lopes-Cunha
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - B Kellen
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - J Balanyà
- Department of Genetics and IrBio, Facultat de Biologia, Universitat de Barcelona, Barcelona, España
| | - M R Rose
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - M Matos
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
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Price MR, Sischo D, Pascua MA, Hadfield MG. Demographic and genetic factors in the recovery or demise of ex situ populations following a severe bottleneck in fifteen species of Hawaiian tree snails. PeerJ 2015; 3:e1406. [PMID: 26587358 PMCID: PMC4647602 DOI: 10.7717/peerj.1406] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 10/26/2015] [Indexed: 01/13/2023] Open
Abstract
Wild populations of endangered Hawaiian tree snails have declined precipitously over the last century due to introduced predators and other human impacts. Life history traits, such as very low fecundity (<5 offspring per year across taxa) and maturity at approximately four years of age have made recovery difficult. Conservation efforts such as in situ predator-free enclosures may increase survival to maturity by protecting offspring from predation, but no long-term data existed prior to this study demonstrating the demographic and genetic parameters necessary to maintain populations within those enclosures. We evaluated over 20 years of evidence for the dynamics of survival and extinction in captive ex situ populations of Hawaiian tree snails established from wild-collected individuals. From 1991 to 2006, small numbers of snails (<15) from fifteen species were collected from the wild to initiate captive-reared populations as a hedge against extinction. This small number of founders resulted in a severe bottleneck in each of the captive-reared populations. We identified key demographic parameters that predicted population recovery from this bottleneck. Species with captive populations that produced between two and four offspring per adult per year and had 20–50% of those offspring survive to maturity recovered to numbers above 100 individuals, and maintained viable populations following a decline that occurred between 2009 and 2014. Those populations that had less than two offspring per adult per year and less than 20% survival to maturity did not reach 100 individuals in captivity, and many of these populations died out during the recent decline. We suggest that small reductions in fitness may contribute to extirpation in taxa with inherently low fecundity, by keeping populations below a threshold number essential to long-term recovery. Future ex situ populations should be founded with no less than 15 adults, and maintained in conditions closely approximating the temperature and humidity of source locations to optimize fitness. Permanent translocations of wild populations for conservation purposes will be more likely to succeed with greater than 100 adults, and should be limited to locations with a similar climate to source locations.
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Affiliation(s)
- Melissa R Price
- Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawai'i at Mānoa , Honolulu, HI , USA ; Department of Natural Resources and Environmental Management, University of Hawai'i at Mānoa , Honolulu, HI , USA
| | - David Sischo
- Division of Forestry and Wildlife, Department of Land and Natural Resources , Honolulu, HI , USA
| | | | - Michael G Hadfield
- Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawai'i at Mānoa , Honolulu, HI , USA
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Consuegra S, John E, Verspoor E, de Leaniz CG. Patterns of natural selection acting on the mitochondrial genome of a locally adapted fish species. Genet Sel Evol 2015; 47:58. [PMID: 26138253 PMCID: PMC4490732 DOI: 10.1186/s12711-015-0138-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 06/23/2015] [Indexed: 11/10/2022] Open
Abstract
Background Mitochondrial DNA (mtDNA) is frequently used in population genetic studies and is usually considered as a neutral marker. However, given the functional importance of the proteins encoded by the mitochondrial genome, and the prominent role of mitochondria in cellular energy production, the assumption of neutrality is increasingly being questioned. Results We tested for evidence of selection on the mitochondrial genome of the Atlantic salmon, which is a locally adapted and widely farmed species and is distributed across a large latitudinal cline. We analysed 20 independent regions of the salmon mtDNA that represented nine genes (ND1, ND2, ND3, COX1, COX2, ATP6, ND4, ND5, and CYTB). These 20 mtDNA regions were sequenced using a 454 approach from samples collected across the entire European range of this species. We found evidence of positive selection at the ND1, ND3 and ND4 genes, which is supported by at least two different codon-based methods and also by differences in the chemical properties of the amino acids involved. The geographical distribution of some of the mutations indicated to be under selection was not random, and some mutations were private to artic populations. We discuss the possibility that selection acting on the Atlantic salmon mtDNA genome might be related to the need for increased metabolic efficiency at low temperatures. Conclusions The analysis of sequences representing nine mitochondrial genes that are involved in the OXPHOS pathway revealed signatures of positive selection in the mitochondrial genome of the Atlantic salmon. The properties of the amino acids involved suggest that some of the mutations that were identified to be under positive selection might have functional implications, possibly in relation to metabolic efficiency. Experimental evidence, and better understanding of regional phylogeographic structuring, are needed to clarify the potential role of selection acting on the mitochondrial genome of Atlantic salmon and other locally adapted fishes. Electronic supplementary material The online version of this article (doi:10.1186/s12711-015-0138-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sofia Consuegra
- Department of BioSciences, Swansea University, Swansea, SA2 8PP, UK.
| | - Elgan John
- Department of BioSciences, Swansea University, Swansea, SA2 8PP, UK.
| | - Eric Verspoor
- Inverness College, University of Highlands and Islands, Inverness, IV1 1SA, Scotland, UK.
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Kurbalija Novičić Z, Immonen E, Jelić M, AnÐelković M, Stamenković-Radak M, Arnqvist G. Within-population genetic effects of mtDNA on metabolic rate in Drosophila subobscura. J Evol Biol 2015; 28:338-46. [PMID: 25454557 DOI: 10.1111/jeb.12565] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 11/25/2014] [Accepted: 11/26/2014] [Indexed: 12/22/2022]
Abstract
A growing body of research supports the view that within-species sequence variation in the mitochondrial genome (mtDNA) is functional, in the sense that it has important phenotypic effects. However, most of this empirical foundation is based on comparisons across populations, and few studies have addressed the functional significance of mtDNA polymorphism within populations. Here, using mitonuclear introgression lines, we assess differences in whole-organism metabolic rate of adult Drosophila subobscura fruit flies carrying either of three different sympatric mtDNA haplotypes. We document sizeable, up to 20%, differences in metabolic rate across these mtDNA haplotypes. Further, these mtDNA effects are to some extent sex specific. We found no significant nuclear or mitonuclear genetic effects on metabolic rate, consistent with a low degree of linkage disequilibrium between mitochondrial and nuclear genes within populations. The fact that mtDNA haplotype variation within a natural population affects metabolic rate, which is a key physiological trait with important effects on life-history traits, adds weight to the emergent view that mtDNA haplotype variation is under natural selection and it revitalizes the question as to what processes act to maintain functional mtDNA polymorphism within populations.
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Ferchaud AL, Eudeline R, Arnal V, Cheylan M, Pottier G, Leblois R, Crochet PA. Congruent signals of population history but radically different patterns of genetic diversity between mitochondrial and nuclear markers in a mountain lizard. Mol Ecol 2014; 24:192-207. [PMID: 25410208 DOI: 10.1111/mec.13011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 11/05/2014] [Accepted: 11/14/2014] [Indexed: 10/24/2022]
Abstract
Historical factors, current population size, population connectivity and selective processes at linked loci contribute to shaping contemporary patterns of neutral genetic diversity. It is now widely acknowledged that nuclear and mitochondrial markers react differently to current demography as well as to past history, so the use of both types of markers is often advocated to gain insight on both historical and contemporary processes. We used 12 microsatellite loci genotyped in 13 populations of a mountain lizard (Iberolacerta bonnali) to test whether the historical scenario favoured by a previous mitochondrial study was also supported by nuclear markers and thereby evaluated the consequences of postglacial range movements on nuclear diversity. Congruent signals of recent history were revealed by nuclear and mitochondrial markers using an Approximate Bayesian computation approach, but contemporary patterns of mtDNA and nuclear DNA diversity were radically different. Although dispersal in this species is probably highly restricted at all spatial scales, colonization abilities have been historically good, suggesting capability for reestablishment of locally extinct populations except in fully disconnected habitats.
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Affiliation(s)
- Anne-Laure Ferchaud
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus C, Denmark; EPHE-UMR5175 CEFE, Centre d'Écologie Fonctionnelle et Évolutive, 1919 route de Mende, 34293, Montpellier Cedex 5, France
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Ashoff M, Schmitt T. Are Different Allozyme Genotypes of the ButterflyPolyommatus coridonAdapted to Resist Cold and Heat Shocks? ANN ZOOL FENN 2014. [DOI: 10.5735/086.051.0502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Cullingham CI, Cooke JEK, Coltman DW. Cross-species outlier detection reveals different evolutionary pressures between sister species. THE NEW PHYTOLOGIST 2014; 204:215-229. [PMID: 24942459 PMCID: PMC4260136 DOI: 10.1111/nph.12896] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 05/14/2014] [Indexed: 05/15/2023]
Abstract
Lodgepole pine (Pinus contorta var. latifolia) and jack pine (Pinus banksiana) hybridize in western Canada, an area of recent mountain pine beetle range expansion. Given the heterogeneity of the environment, and indications of local adaptation, there are many unknowns regarding the response of these forests to future outbreaks. To better understand this we aim to identify genetic regions that have adaptive potential. We used data collected on 472 single nucleotide polymorphism (SNP) loci from 576 tree samples collected across 13 lodgepole pine-dominated sites and four jack pine-dominated sites. We looked at the relationship of genetic diversity with the environment, and we identified candidate loci using both frequency-based (arlequin and bayescan) and correlation-based (matsam and bayenv) methods. We found contrasting relationships between environmental variation and genetic diversity for the species. While we identified a number of candidate outliers (34 in lodgepole pine, 25 in jack pine, and 43 interspecific loci), we did not find any loci in common between lodgepole and jack pine. Many of the outlier loci identified were correlated with environmental variation. Using rigorous criteria we have been able to identify potential outlier SNPs. We have also found evidence of contrasting environmental adaptations between lodgepole and jack pine which could have implications for beetle spread risk.
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Affiliation(s)
- Catherine I Cullingham
- Department of Biological Sciences, University of Alberta, Biological Sciences Building, Edmonton, AB, T6G 2E9, Canada
| | - Janice E K Cooke
- Department of Biological Sciences, University of Alberta, Biological Sciences Building, Edmonton, AB, T6G 2E9, Canada
| | - David W Coltman
- Department of Biological Sciences, University of Alberta, Biological Sciences Building, Edmonton, AB, T6G 2E9, Canada
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41
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Estimation of genetic variability level in inbred CF1 mouse lines selected for body weight. J Genet 2014; 93:483-7. [DOI: 10.1007/s12041-014-0374-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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42
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Campos JL, Halligan DL, Haddrill PR, Charlesworth B. The relation between recombination rate and patterns of molecular evolution and variation in Drosophila melanogaster. Mol Biol Evol 2014; 31:1010-28. [PMID: 24489114 PMCID: PMC3969569 DOI: 10.1093/molbev/msu056] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Genetic recombination associated with sexual reproduction increases the efficiency of natural selection by reducing the strength of Hill–Robertson interference. Such interference can be caused either by selective sweeps of positively selected alleles or by background selection (BGS) against deleterious mutations. Its consequences can be studied by comparing patterns of molecular evolution and variation in genomic regions with different rates of crossing over. We carried out a comprehensive study of the benefits of recombination in Drosophila melanogaster, both by contrasting five independent genomic regions that lack crossing over with the rest of the genome and by comparing regions with different rates of crossing over, using data on DNA sequence polymorphisms from an African population that is geographically close to the putatively ancestral population for the species, and on sequence divergence from a related species. We observed reductions in sequence diversity in noncrossover (NC) regions that are inconsistent with the effects of hard selective sweeps in the absence of recombination. Overall, the observed patterns suggest that the recombination rate experienced by a gene is positively related to an increase in the efficiency of both positive and purifying selection. The results are consistent with a BGS model with interference among selected sites in NC regions, and joint effects of BGS, selective sweeps, and a past population expansion on variability in regions of the genome that experience crossing over. In such crossover regions, the X chromosome exhibits a higher rate of adaptive protein sequence evolution than the autosomes, implying a Faster-X effect.
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Affiliation(s)
- José L Campos
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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43
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Wang S, Zhu W, Gao X, Li X, Yan S, Liu X, Yang J, Gao Z, Li Y. Population size and time since island isolation determine genetic diversity loss in insular frog populations. Mol Ecol 2014; 23:637-48. [PMID: 24351057 DOI: 10.1111/mec.12634] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 12/05/2013] [Accepted: 12/11/2013] [Indexed: 12/01/2022]
Affiliation(s)
- Supen Wang
- Key Laboratory of Animal Ecology and Conservation Biology; Institute of Zoology; The Chinese Academy of Sciences; 1 Datun Beichen West Road Chaoyang Beijing 100101 China
- University of Chinese Academy of Sciences; 19 Yuquan Road Shijingshan Beijing 100049 China
| | - Wei Zhu
- Key Laboratory of Animal Ecology and Conservation Biology; Institute of Zoology; The Chinese Academy of Sciences; 1 Datun Beichen West Road Chaoyang Beijing 100101 China
- University of Chinese Academy of Sciences; 19 Yuquan Road Shijingshan Beijing 100049 China
| | - Xu Gao
- Key Laboratory of Animal Ecology and Conservation Biology; Institute of Zoology; The Chinese Academy of Sciences; 1 Datun Beichen West Road Chaoyang Beijing 100101 China
- University of Chinese Academy of Sciences; 19 Yuquan Road Shijingshan Beijing 100049 China
| | - Xianping Li
- Key Laboratory of Animal Ecology and Conservation Biology; Institute of Zoology; The Chinese Academy of Sciences; 1 Datun Beichen West Road Chaoyang Beijing 100101 China
- University of Chinese Academy of Sciences; 19 Yuquan Road Shijingshan Beijing 100049 China
| | - Shaofei Yan
- Key Laboratory of Animal Ecology and Conservation Biology; Institute of Zoology; The Chinese Academy of Sciences; 1 Datun Beichen West Road Chaoyang Beijing 100101 China
- University of Chinese Academy of Sciences; 19 Yuquan Road Shijingshan Beijing 100049 China
| | - Xuan Liu
- Key Laboratory of Animal Ecology and Conservation Biology; Institute of Zoology; The Chinese Academy of Sciences; 1 Datun Beichen West Road Chaoyang Beijing 100101 China
| | - Ji Yang
- Key Laboratory of Animal Ecology and Conservation Biology; Institute of Zoology; The Chinese Academy of Sciences; 1 Datun Beichen West Road Chaoyang Beijing 100101 China
| | - Zengxiang Gao
- College of Environmental Science and Engineering; Ocean University of China; 5 Yushan Road Lao Shan Qingdao 266003 China
| | - Yiming Li
- Key Laboratory of Animal Ecology and Conservation Biology; Institute of Zoology; The Chinese Academy of Sciences; 1 Datun Beichen West Road Chaoyang Beijing 100101 China
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44
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Shinozuka H, Hand ML, Cogan NOI, Spangenberg GC, Forster JW. Nucleotide diversity of vernalization and flowering-time-related genes in a germplasm collection of meadow fescue (Festuca pratensis Huds. syn. Lolium pratense (Huds.) Darbysh.). Ecol Evol 2013; 3:4415-26. [PMID: 24340183 PMCID: PMC3856742 DOI: 10.1002/ece3.828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 09/09/2013] [Accepted: 09/09/2013] [Indexed: 11/28/2022] Open
Abstract
In plant species, control of flowering time is an important factor for adaptation to local natural environments. The Vrn1,CO,FT1 and CK2α genes are key components in the flowering-specific signaling pathway of grass species. Meadow fescue is an agronomically important forage grass species, which is naturally distributed across Europe and Western Asia. In this study, meadow fescue flowering-time-related genes were resequenced to assess nucleotide diversity in European and Western Asian subpopulations. Identified sequence polymorphisms were then converted into PCR-based molecular genetic markers, and a meadow fescue germplasm collection was genotyped to investigate global allelic variation. Lower nucleotide diversities were observed for the Vrn1 and CO orthologs, while relatively higher values were observed for the FT1 and casein kinase II α-subunit (CK2α) orthologs. The nucleotide diversity for FT1 orthologs in the Western Asian subpopulation was significantly higher than those of the European subpopulation. Similarly, significant differences in nucleotide diversity for the remaining genes were observed between several combinations of subpopulation. The global allele distribution pattern was consistent with observed level of nucleotide diversity. These results suggested that the degree of purifying selection acting on the genes differs according to geographical location. As previously shown for model plant species, functional specificities of flowering-time-related genes may also vary according to environmental conditions.
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Affiliation(s)
- Hiroshi Shinozuka
- Biosciences Research Division, Department of Environment and Primary Industries, AgriBio, The Centre for AgriBioscience 5 Ring Road, La Trobe University Research and Development Park, Bundoora, Victoria, 3083, Australia ; Dairy Futures Cooperative Research Centre Bundoora, Victoria, 3086, Australia
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45
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Interspecific hybridization contributes to high genetic diversity and apparent effective population size in an endemic population of mottled ducks (Anas fulvigula maculosa). CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0557-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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46
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Loire E, Chiari Y, Bernard A, Cahais V, Romiguier J, Nabholz B, Lourenço JM, Galtier N. Population genomics of the endangered giant Galápagos tortoise. Genome Biol 2013; 14:R136. [PMID: 24342523 PMCID: PMC4053747 DOI: 10.1186/gb-2013-14-12-r136] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 12/16/2013] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The giant Galápagos tortoise, Chelonoidis nigra, is a large-sized terrestrial chelonian of high patrimonial interest. The species recently colonized a small continental archipelago, the Galápagos Islands, where it has been facing novel environmental conditions and limited resource availability. To explore the genomic consequences of this ecological shift, we analyze the transcriptomic variability of five individuals of C. nigra, and compare it to similar data obtained from several continental species of turtles. RESULTS Having clarified the timing of divergence in the Chelonoidis genus, we report in C. nigra a very low level of genetic polymorphism, signatures of a weakened efficacy of purifying selection, and an elevated mutation load in coding and regulatory sequences. These results are consistent with the hypothesis of an extremely low long-term effective population size in this insular species. Functional evolutionary analyses reveal a reduced diversity of immunity genes in C. nigra, in line with the hypothesis of attenuated pathogen diversity in islands, and an increased selective pressure on genes involved in response to stress, potentially related to the climatic instability of its environment and its elongated lifespan. Finally, we detect no population structure or homozygosity excess in our five-individual sample. CONCLUSIONS These results enlighten the molecular evolution of an endangered taxon in a stressful environment and point to island endemic species as a promising model for the study of the deleterious effects on genome evolution of a reduced long-term population size.
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Affiliation(s)
- Etienne Loire
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, 34095 Montpellier, France
| | - Ylenia Chiari
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, 34095 Montpellier, France
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Aurélien Bernard
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, 34095 Montpellier, France
| | - Vincent Cahais
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, 34095 Montpellier, France
| | - Jonathan Romiguier
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, 34095 Montpellier, France
| | - Benoît Nabholz
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, 34095 Montpellier, France
| | - Joao Miguel Lourenço
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, 34095 Montpellier, France
| | - Nicolas Galtier
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, 34095 Montpellier, France
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47
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Dowling TE, Turner TF, Carson EW, Saltzgiver MJ, Adams D, Kesner B, Marsh PC. Time-series analysis reveals genetic responses to intensive management of razorback sucker (Xyrauchen texanus). Evol Appl 2013; 7:339-54. [PMID: 24665337 PMCID: PMC3962295 DOI: 10.1111/eva.12125] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 09/26/2013] [Indexed: 11/30/2022] Open
Abstract
Time-series analysis is used widely in ecology to study complex phenomena and may have considerable potential to clarify relationships of genetic and demographic processes in natural and exploited populations. We explored the utility of this approach to evaluate population responses to management in razorback sucker, a long-lived and fecund, but declining freshwater fish species. A core population in Lake Mohave (Arizona-Nevada, USA) has experienced no natural recruitment for decades and is maintained by harvesting naturally produced larvae from the lake, rearing them in protective custody, and repatriating them at sizes less vulnerable to predation. Analyses of mtDNA and 15 microsatellites characterized for sequential larval cohorts collected over a 15-year time series revealed no changes in geographic structuring but indicated significant increase in mtDNA diversity for the entire population over time. Likewise, ratios of annual effective breeders to annual census size (N b /N a) increased significantly despite sevenfold reduction of N a. These results indicated that conservation actions diminished near-term extinction risk due to genetic factors and should now focus on increasing numbers of fish in Lake Mohave to ameliorate longer-term risks. More generally, time-series analysis permitted robust testing of trends in genetic diversity, despite low precision of some metrics.
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Affiliation(s)
- Thomas E Dowling
- School of Life Sciences, Arizona State University Tempe, AZ, USA
| | - Thomas F Turner
- Department of Biology and Museum of Southwestern Biology, University of New Mexico Albuquerque, NM, USA
| | - Evan W Carson
- Department of Biology and Museum of Southwestern Biology, University of New Mexico Albuquerque, NM, USA
| | | | - Deborah Adams
- School of Life Sciences, Arizona State University Tempe, AZ, USA
| | | | - Paul C Marsh
- School of Life Sciences, Arizona State University Tempe, AZ, USA ; Marsh & Associates Tempe, AZ, USA
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48
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Kazancıoğlu E, Arnqvist G. The maintenance of mitochondrial genetic variation by negative frequency-dependent selection. Ecol Lett 2013; 17:22-7. [PMID: 24134428 DOI: 10.1111/ele.12195] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 07/05/2013] [Accepted: 09/15/2013] [Indexed: 11/30/2022]
Abstract
Mitochondrial genes generally show high levels of standing genetic variation, which is puzzling given the accumulating evidence for phenotypic effects of mitochondrial genetic variation. Negative frequency-dependent selection, where the relative fitness of a genotype is inversely related to its frequency in a population, provides a potent and potentially general process that can maintain mitochondrial polymorphism. We assessed the change in mitochondrial haplotype frequencies over 10 generations of experimental evolution in 180 seed beetle populations in the laboratory, where haplotypes competed for propagation to subsequent generations. We found that haplotypes consistently increased in frequency when they were initially rare and decreased in frequency when initially common. Our results have important implications for the use of mtDNA haplotype frequency data to infer population level processes and they revive the general hypothesis that negative frequency-dependent selection, presumably caused by habitat heterogeneity, may commonly promote polymorphism in ecologically relevant life history genes.
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Affiliation(s)
- Erem Kazancıoğlu
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Norbyv. 18 D, SE-752 36, Uppsala, Sweden
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49
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Cutter AD, Jovelin R, Dey A. Molecular hyperdiversity and evolution in very large populations. Mol Ecol 2013; 22:2074-95. [PMID: 23506466 PMCID: PMC4065115 DOI: 10.1111/mec.12281] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 01/24/2013] [Accepted: 01/29/2013] [Indexed: 02/06/2023]
Abstract
The genomic density of sequence polymorphisms critically affects the sensitivity of inferences about ongoing sequence evolution, function and demographic history. Most animal and plant genomes have relatively low densities of polymorphisms, but some species are hyperdiverse with neutral nucleotide heterozygosity exceeding 5%. Eukaryotes with extremely large populations, mimicking bacterial and viral populations, present novel opportunities for studying molecular evolution in sexually reproducing taxa with complex development. In particular, hyperdiverse species can help answer controversial questions about the evolution of genome complexity, the limits of natural selection, modes of adaptation and subtleties of the mutation process. However, such systems have some inherent complications and here we identify topics in need of theoretical developments. Close relatives of the model organisms Caenorhabditis elegans and Drosophila melanogaster provide known examples of hyperdiverse eukaryotes, encouraging functional dissection of resulting molecular evolutionary patterns. We recommend how best to exploit hyperdiverse populations for analysis, for example, in quantifying the impact of noncrossover recombination in genomes and for determining the identity and micro-evolutionary selective pressures on noncoding regulatory elements.
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Affiliation(s)
- Asher D Cutter
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.
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50
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Frankham R, Brook BW, Bradshaw CJ, Traill LW, Spielman D. 50/500 rule and minimum viable populations: response to Jamieson and Allendorf. Trends Ecol Evol 2013; 28:187-8. [DOI: 10.1016/j.tree.2013.01.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 12/03/2012] [Accepted: 01/03/2013] [Indexed: 10/27/2022]
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