scholarly journals Genomic signatures of inbreeding and genetic load in a threatened rattlesnake

2021 ◽  
Author(s):  
Alexander Ochoa ◽  
H. Lisle Gibbs
Keyword(s):  
Threatened Species ◽  
Empirical Studies ◽  
Genetic Load ◽  
Population History ◽  
Deleterious Mutations ◽  
Genetic Rescue ◽  
Isolated Populations ◽  
Genome Wide ◽  
The Impact

Theory predicts that threatened species living in small populations will experience high levels of inbreeding that will increase their negative genetic load but recent work suggests that the impact of load may be minimized by purging resulting from long term population bottlenecks. Empirical studies that examine this idea using genome-wide estimates of inbreeding and genetic load in threatened species are limited. Here we use genome resequencing data to compare levels of inbreeding, levels of genetic load and population history in threatened Eastern massasauga rattlesnakes (Sistrurus catenatus) which exist in small isolated populations and closely-related yet outbred Western massasauga rattlesnakes (S. tergeminus). In terms of inbreeding, S. catenatus genomes had a greater number of ROHs of varying sizes indicating sustained inbreeding through repeated bottlenecks when compared to S. tergeminus. At the species level, outbred S. tergeminus had higher genome-wide levels of genetic load in the form of greater numbers of derived deleterious mutations compared to S. catenatus presumably due to long-term purging of deleterious mutations in S. catenatus. In contrast, mutations that escaped the “drift sieve” and were polymorphic within S. catenatus populations were more abundant and more often found in homozygote genotypes than in S. tergeminus suggesting a reduced efficiency of purifying selection in smaller S. catenatus populations. Our results support an emerging idea that the historical demography of a threatened species has a significant impact on the type of genetic load present which impacts implementation of conservation actions such as genetic rescue.

scholarly journals An evolutionary perspective on contemporary genetic load in threatened species to inform future conservation efforts

2021 ◽  
Author(s):  
Samarth Mathur ◽  
John Tomeček ◽  
Luis Tarango-Arámbula ◽  
Robert Perez ◽  
Andrew DeWoody
Keyword(s):  
Population Genomics ◽  
Empirical Distribution ◽  
Demographic History ◽  
Genetic Load ◽  
Purifying Selection ◽  
Deleterious Mutations ◽  
Genetic Rescue ◽  
Isolated Populations ◽  
Potential Donor ◽  
Inbred Populations

In theory, genomic erosion can be reduced in fragile “recipient” populations by translocating individuals from genetically diverse “donor” populations. However, recent simulation studies have argued that such translocations can, in principle, serve as a conduit for new deleterious mutations to enter recipient populations. A reduction in evolutionary fitness is associated with a higher load of deleterious mutations and thus, a better understanding of evolutionary processes driving the empirical distribution of deleterious mutations is crucial. Here, we show that genetic load is evolutionarily dynamic in nature and that demographic history greatly influences the distribution of deleterious mutations over time. Our analyses, based on both demographically explicit simulations as well as whole genome sequences of potential donor-recipient pairs of Montezuma Quail (Cyrtonyx montezumae) populations, indicate that all populations tend to lose deleterious mutations during bottlenecks, but that genetic purging is pronounced in smaller populations with stronger bottlenecks. Despite carrying relatively fewer deleterious mutations, we demonstrate how small, isolated populations are more likely to suffer inbreeding depression as deleterious mutations that escape purging are homogenized due to drift, inbreeding, and ineffective purifying selection. We apply a population genomics framework to showcase how the phylogeography and historical demography of a given species can enlighten genetic rescue efforts. Our data suggest that small, inbred populations should benefit the most when assisted gene flow stems from genetically diverse donor populations that have the lowest proportion of deleterious mutations.

scholarly journals Genomic Consequences of Long-Term Population Decline in Brown Eared Pheasant

2020 ◽  
Vol 38 (1) ◽  
pp. 263-273
Author(s):  
Pengcheng Wang ◽  
John T Burley ◽  
Yang Liu ◽  
Jiang Chang ◽  
De Chen ◽  
...  
Keyword(s):  
Natural Selection ◽  
Population Size ◽  
Population Decline ◽  
Deleterious Mutations ◽  
Loss Of Function ◽  
Wild Populations ◽  
Effective Population ◽  
Isolated Populations ◽  
Genome Wide

Abstract Population genetic theory and empirical evidence indicate that deleterious alleles can be purged in small populations. However, this viewpoint remains controversial. It is unclear whether natural selection is powerful enough to purge deleterious mutations when wild populations continue to decline. Pheasants are terrestrial birds facing a long-term risk of extinction as a result of anthropogenic perturbations and exploitation. Nevertheless, there are scant genomics resources available for conservation management and planning. Here, we analyzed comparative population genomic data for the three extant isolated populations of Brown eared pheasant (Crossoptilon mantchuricum) in China. We showed that C. mantchuricum has low genome-wide diversity and a contracting effective population size because of persistent declines over the past 100,000 years. We compared genome-wide variation in C. mantchuricum with that of its closely related sister species, the Blue eared pheasant (C. auritum) for which the conservation concern is low. There were detrimental genetic consequences across all C. mantchuricum genomes including extended runs of homozygous sequences, slow rates of linkage disequilibrium decay, excessive loss-of-function mutations, and loss of adaptive genetic diversity at the major histocompatibility complex region. To the best of our knowledge, this study is the first to perform a comprehensive conservation genomic analysis on this threatened pheasant species. Moreover, we demonstrated that natural selection may not suffice to purge deleterious mutations in wild populations undergoing long-term decline. The findings of this study could facilitate conservation planning for threatened species and help recover their population size.

scholarly journals Long-Term Reciprocal Gene Flow in Wild and Domestic Geese Reveals Complex Domestication History

2020 ◽  
Vol 10 (9) ◽  
pp. 3061-3070 ◽  
Author(s):  
Marja E Heikkinen ◽  
Minna Ruokonen ◽  
Thomas A White ◽  
Michelle M Alexander ◽  
İslam Gündüz ◽  
...  
Keyword(s):  
Gene Flow ◽  
Wild Form ◽  
Nucleotide Polymorphisms ◽  
Anser Anser ◽  
Domestic Species ◽  
Genome Wide ◽  
Domestication Process ◽  
Historical Writings ◽  
The Impact

Abstract Hybridization has frequently been observed between wild and domestic species and can substantially impact genetic diversity of both counterparts. Geese show some of the highest levels of interspecific hybridization across all bird orders, and two of the goose species in the genus Anser have been domesticated providing an excellent opportunity for a joint study of domestication and hybridization. Until now, knowledge of the details of the goose domestication process has come from archaeological findings and historical writings supplemented with a few studies based on mitochondrial DNA. Here, we used genome-wide markers to make the first genome-based inference of the timing of European goose domestication. We also analyzed the impact of hybridization on the genome-wide genetic variation in current populations of the European domestic goose and its wild progenitor: the graylag goose (Anser anser). Our dataset consisted of 58 wild graylags sampled around Eurasia and 75 domestic geese representing 14 breeds genotyped for 33,527 single nucleotide polymorphisms. Demographic reconstruction and clustering analysis suggested that divergence between wild and domestic geese around 5,300 generations ago was followed by long-term genetic exchange, and that graylag populations have 3.2–58.0% admixture proportions with domestic geese, with distinct geographic patterns. Surprisingly, many modern European breeds share considerable (> 10%) ancestry with the Chinese domestic geese that is derived from the swan goose Anser cygnoid. We show that the domestication process can progress despite continued and pervasive gene flow from the wild form.

A comparative analysis of the implications of the Islamic religion on corporate capital structures of firms in emerging market countries

2014 ◽  
Vol 7 (3) ◽  
pp. 277-287 ◽  
Author(s):  
Theresa Gunn ◽  
Joshua Shackman
Keyword(s):  
Emerging Market ◽  
Empirical Studies ◽  
Short Term ◽  
Content Type ◽  
Corporate Capital ◽  
Muslim Countries ◽  
Total Debt ◽  
Islamic Religion ◽  
The Impact

Purpose – The purpose of this study is to examine the impact of the Muslim religion on firm capital structure. Design/methodology/approach – The authors compare financing patterns in Muslim versus non-Muslim countries using 658 firms in 16 countries covering a period of seven years. Findings – No significant differences between Muslim and non-Muslim countries were found in terms of total debt ratios. However, significant differences were found in the choice of short-term versus long-term debt, with firms in Muslim countries showing a strong preference for short-term debt. Research limitations/implications – The findings confirm existing theories on the impact of the Islamic religion on short-term versus long-term debt preferences. However, the findings concerning the lack of an impact of the Islamic religion on total debt preferences are surprising and contrary to existing theories. Practical implications – Firms in Muslim countries appear to have the flexibility to adopt overall leverage ratios comparable to those in non-Muslim countries. However, firms in Muslim countries may be disadvantaged in that there appear to be impediments to the use of long-term debt. Originality/value – This paper presents one of the first empirical studies of the impact of the Muslim religion on corporate financing choices across a large cross-section of firms in Muslim and non-Muslim countries.

Antitakeover Provisions and Shareholder Wealth: A Survey of the Literature

2014 ◽  
Vol 49 (4) ◽  
pp. 933-956 ◽  
Author(s):  
Miroslava Straska ◽  
H. Gregory Waller
Keyword(s):  
Good Governance ◽  
Empirical Studies ◽  
Shareholder Wealth ◽  
Current Debate ◽  
Firm Characteristics ◽  
Policy Changes ◽  
Governance Practices ◽  
The Impact ◽  
Long Term Studies

AbstractWe survey theoretical and empirical research on antitakeover provisions, focusing on the relation between antitakeover provisions and shareholder value. We divide the empirical studies based upon the evidence that they provide: short-term event studies, studies on performance and policy changes around adopting antitakeover provisions or passing state antitakeover laws, studies on the impact of antitakeover provisions on takeovers, studies on the relation between antitakeover provisions and firm characteristics, and long-term studies on the relation between antitakeover provisions and firm performance or policies. We also discuss the place of antitakeover provisions in the current debate about “good governance” practices.

scholarly journals COVID-19 and tourist mobility at destinations: a literature review and emerging research agenda

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Alba Viana-Lora ◽  
Antoni Domènech ◽  
Aaron Gutiérrez
Keyword(s):  
Literature Review ◽  
Research Agenda ◽  
Empirical Studies ◽  
Future Research ◽  
Content Type ◽  
Future Research Agenda ◽  
The Future ◽  
Short And Long Term ◽  
The Impact

PurposeThis paper aims to review conceptual and empirical studies that analyse the impact of the pandemic on mobility and tourism behaviour at destinations in order to identify proposals, forecasts and recommendations to guide the future research agenda on the subject.Design/methodology/approachThis study used a systematic literature review to synthesise information from scientific articles published in journals indexed in the Web of Science database related to tourism mobility at destinations during the COVID-19 pandemic.FindingsThis article found that, according to the existing literature, the COVID-19 pandemic is acting as a catalyst for the sustainable transition of tourism. Although the findings reveal a lack of empirical research on the impact of the pandemic on tourism mobility at destinations, the article synthesizes the short- and long-term impacts of the pandemic and sets out the future research agenda on tourist mobility at destinations.Originality/valueTo the best of the authors' knowledge, this is the first systematic review of the impact of the pandemic on mobility and tourism behaviour at destinations that attempts to describe the emerging challenges and the agenda for future research.

scholarly journals Long-term reciprocal gene flow in wild and domestic geese reveals complex domestication history

2019 ◽  
Author(s):  
Marja E. Heikkinen ◽  
Minna Ruokonen ◽  
Thomas A. White ◽  
Michelle M. Alexander ◽  
İslam Gündüz ◽  
...  
Keyword(s):  
Gene Flow ◽  
Gene Pools ◽  
Large Contribution ◽  
Wild Form ◽  
Wild Progenitor ◽  
Genome Wide ◽  
Domestication Process ◽  
Historical Writings ◽  
The Impact

AbstractHybridization has frequently been observed between wild and domestic species and can substantially impact genetic diversity of both counterparts. Geese show some of the highest levels of interspecific hybridization across all bird orders, and two of the goose species in genus Anser have been domesticated providing excellent opportunity for joint study of domestication and hybridization. Until now, knowledge on the details of the goose domestication process has come from archaeological findings and historical writings supplemented with few studies based on mitochondrial DNA. Here, we used genome-wide markers to make the first genome-based inference of the timing of European goose domestication. We also analyzed the impact of hybridization on the genome-wide genetic variation in current populations of the European domestic goose and its wild progenitor: the greylag goose (Anser anser). Our dataset consisted of 58 wild greylags sampled around Eurasia and 75 domestic geese representing 14 breeds genotyped for 33,527 single nucleotide polymorphisms. Demographic reconstruction and clustering analysis suggested that divergence between wild and domestic geese around 5,300 generations ago was followed by long-term genetic exchange, and that greylag populations have 3.2–58.0% admixture proportions with domestic geese, with distinct geographic patterns. Surprisingly, many modern European breeds share considerable (> 10%) ancestry with Chinese domestic geese that is derived from the swan goose Anser cygnoid. We show that domestication process can progress despite continued and pervasive gene flow from the wild form.Significance StatementReproductive isolation between conspecific wild and domestic populations is a cornerstone of the domestication process, yet gene flow between such wild and domestic populations has been frequently documented. European domestic geese and their wild progenitor (greylags) co-occur and can hybridize and we show that they represent a particularly persuasive case where wild and domestic populations are not isolated gene pools. Our study makes a first genome-based estimate of goose domestication, which up to now has mostly relied on archaeological findings and historical writings. We show ongoing gene flow between greylags and European domestic geese following domestication, but we also observe a surprisingly large contribution of Chinese domestic geese (a separate species) to the genetic make-up of European domestic geese.

scholarly journals A study of Kibbutzim in Israel reveals risk factors for cardiometabolic traits and subtle population structure

2017 ◽  
Author(s):  
Einat Granot-Hershkovitz ◽  
David Karasik ◽  
Yechiel Friedlander ◽  
Laura Rodriguez-Murillo ◽  
Rajkumar Dorajoo ◽  
...  
Keyword(s):  
Social Stability ◽  
Genetic Determinants ◽  
Isolated Populations ◽  
Genetic Studies ◽  
Point Estimates ◽  
Genome Wide ◽  
Extensive Information ◽  
Cardiometabolic Traits ◽  
Homogeneous Environment

AbstractGenetic studies in isolated populations have provided increased power for identifying loci associated with complex diseases and traits. We present here the Kibbutzim Family Study (KFS), initiated for investigating environmental and genetic determinants of cardiometabolic traits in extended Israeli families living in communes characterized by long-term social stability and homogeneous environment. Extensive information on cardiometabolic traits, as well as genome-wide genetic data, was collected on 901 individuals, making this study, to the best of our knowledge, the largest of its kind in Israel. We have thoroughly characterized the KFS genetic structure, observing that most participants were of Ashkenazi Jewish (AJ) origin, and confirming a recent severe bottleneck in their recent history (point estimates: effective size ≈450 individuals, 23 generations ago). Focusing on genetic variants enriched in KFS compared with non-Finnish Europeans, we demonstrated that AJ-specific variants are largely involved in cancer-related pathways. Using linear mixed models, we conducted an association study of these enriched variants with 16 cardiometabolic traits. We found 24 variants to be significantly associated with cardiometabolic traits. The strongest association, which we also replicated, was between a variant upstream of the MSRA gene, ≈200-fold enriched in KFS, and weight (P=3.6·10−8). In summary, the KFS is a valuable resource for the study of the population genetics of Israel as well as the genetics of cardiometabolic traits in a homogeneous environment.

scholarly journals Strongly deleterious mutations are a primary determinant of extinction risk due to inbreeding depression

2019 ◽  
Author(s):  
Christopher C. Kyriazis ◽  
Robert K. Wayne ◽  
Kirk E. Lohmueller
Keyword(s):  
Genetic Diversity ◽  
Inbreeding Depression ◽  
Extinction Risk ◽  
Fragmented Landscape ◽  
Small Populations ◽  
Deleterious Mutations ◽  
Genetic Rescue ◽  
Isolated Populations ◽  
Large Populations ◽  
Source Populations

AbstractHuman-driven habitat fragmentation and loss have led to a proliferation of small and isolated plant and animal populations with high risk of extinction. One of the main threats to extinction in these populations is inbreeding depression, which is primarily caused by the exposure of recessive deleterious mutations as homozygous by inbreeding. The typical approach for managing these populations is to maintain high genetic diversity, often by translocating individuals from large populations to initiate a ‘genetic rescue.’ However, the limitations of this approach have recently been highlighted by the demise of the gray wolf population on Isle Royale, which was driven to the brink of extinction soon after the arrival of a migrant from the large mainland wolf population. Here, we use a novel population genetic simulation framework to investigate the role of genetic diversity, deleterious variation, and demographic history in mediating extinction risk due to inbreeding depression in small populations. We show that, under realistic models of dominance, large populations harbor high levels of recessive strongly deleterious variation due to these mutations being hidden from selection in the heterozygous state. As a result, when large populations contract, they experience a substantially elevated risk of extinction after these strongly deleterious mutations are exposed by inbreeding. Moreover, we demonstrate that although translocating individuals to small populations is broadly effective as a means to reduce extinction risk, using small or moderate-sized source populations rather than large source populations can greatly increase the effectiveness of genetic rescue due to greater purging in these smaller populations. Our findings challenge the traditional conservation paradigm that focuses on maximizing genetic diversity to reduce extinction risk in favor of a view that emphasizes minimizing strongly deleterious variation. These insights have important implications for managing small and isolated populations in the increasingly fragmented landscape of the Anthropocene.Impact SummaryNumerous threats to extinction exist for small populations, including the detrimental effects of inbreeding. Although much of the focus in reducing these harmful effects in small populations has been on maintaining high genetic diversity, here we use simulations to demonstrate that emphasis should instead be placed on minimizing strongly deleterious variation. More specifically, we show that historically-large populations with high levels of genetic diversity also harbor elevated levels of recessive strongly deleterious mutations hidden in the heterozygous state. Thus, when these populations contract, inbreeding can expose these strongly deleterious mutations as homozygous and lead to severe inbreeding depression and rapid extinction. Moreover, we demonstrate that, although translocating individuals to these small populations to perform a ‘genetic rescue’ is broadly beneficial, the effectiveness of this strategy can be greatly increased by targeting historically-smaller source populations where recessive strongly deleterious mutations have been purged. These results challenge long-standing views on how to best conserve small and isolated populations facing the threat of inbreeding depression, and have immediate implications for preserving biodiversity in the increasingly fragmented landscape of the Anthropocene.

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