scholarly journals Integrated Bayesian Approaches Shed Light on the Dissemination Routes of the Eurasian Grapevine Germplasm

2021 ◽  
Vol 12 ◽  
Author(s):  
Francesco Mercati ◽  
Gabriella De Lorenzis ◽  
Antonio Mauceri ◽  
Marcello Zerbo ◽  
Lucio Brancadoro ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Approximate Bayesian Computation ◽  
Migration Routes ◽  
Bayesian Approaches ◽  
Archaeological Data ◽  
Approximate Bayesian ◽  
Grape Varieties ◽  
First Time ◽  
Shed Light

The domestication and spreading of grapevine as well as the gene flow history had been described in many studies. We used a high-quality 7k SNP dataset of 1,038 Eurasian grape varieties with unique profiles to assess the population genetic diversity, structure, and relatedness, and to infer the most likely migration events. Comparisons of putative scenarios of gene flow throughout Europe from Caucasus helped to fit the more reliable migration routes around the Mediterranean Basin. Approximate Bayesian computation (ABC) approach made possible to provide a response to several questions so far remaining unsolved. Firstly, the assessment of genetic diversity and population structure within a well-covered dataset of ancient Italian varieties suggested the different histories between the Northern and Southern Italian grapevines. Moreover, Italian genotypes were shown to be distinguishable from all the other Eurasian populations for the first time. The entire Eurasian panel confirmed the east-to-west gene flow, highlighting the Greek role as a “bridge” between the Western and Eastern Eurasia. Portuguese germplasm showed a greater proximity to French varieties than the Spanish ones, thus being the main route for gene flow from Iberian Peninsula to Central Europe. Our findings reconciled genetic and archaeological data for one of the most cultivated and fascinating crops in the world.

scholarly journals Genetic Resilience of a Once Endangered Species, Tibetan Antelope (Pantholops hodgsonii)

2019 ◽  
Author(s):  
Yue Shi ◽  
Jiarui Chen ◽  
Jianping Su ◽  
Tongzuo Zhang ◽  
Samuel K. Wasser
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Population Size ◽  
Effective Population Size ◽  
Genetic Bottleneck ◽  
Migration Routes ◽  
Effective Population ◽  
Human Disturbances ◽  
Population Reduction ◽  
Tibetan Antelope

AbstractPopulation reduction is generally assumed to reduce the population’s genetic diversity and hence its ability to adapt to environmental change. However, if life history traits that promote gene flow buffer populations from such impacts, conservation efforts should aim to maintain those traits in vulnerable species. Tibetan antelope (Pantholops hodgsonii) has experienced population reduction by 95% due to poaching during the 20th century. We hypothesize that opportunities for gene flow provided by their sex-specific migration buffered their genetic diversity from the poaching impacts. We measured the mtDNA (control region, CR) and nuDNA (microsatellites or STRs) diversity, population differentiation, along with the change in effective population size (pre-poaching era vs. post-poaching era) and tested for a genetic bottleneck. Our results showed that Tibetan antelope maintained considerable genetic diversity in both mtDNA CR and STR markers (Hd = 0.9970 and Hobs = 0.8446, respectively), despite a marked reduction in post-poaching effective population size 368.9 (95% CI of 249.3 - 660.6) compared to the pre-poaching average (4.93×103 - 4.17×104). Post-poached populations also had low population structure and showed no evidence of a genetic bottleneck. Pairwise Fst values using CR haplotype frequencies were higher than those using STR allele frequencies, suggesting different degrees of gene flow mediated by females and males. This study suggests that the Tibetan antelope’s sex-specific migration buffered their loss of genetic diversity in the face of severe demographic decline. These findings highlight the importance of recognizing the traits likely to maintain genetic diversity and promoting conservation efforts that allow them to be exercised. For Tibetan antelope, this requires assuring that their migration routes remain unobstructed by growing human disturbances while continuing to enforce anti-poaching law enforcement efforts.

scholarly journals Approximate Bayesian computation untangles signatures of contemporary and historical hybridization between two endangered species

2021 ◽  
Author(s):  
Hannes Dittberner ◽  
Aurelien Tellier ◽  
Juliette de Meaux
Keyword(s):  
Gene Flow ◽  
Endangered Species ◽  
Approximate Bayesian Computation ◽  
Bayesian Computation ◽  
Sympatric Population ◽  
Genome Data ◽  
Contemporary Gene Flow ◽  
History Of ◽  
Low Levels ◽  
Approximate Bayesian

ABSTRACTContemporary gene flow, when resumed after a period of isolation, can have crucial consequences for endangered species, as it can both increase the supply of adaptive alleles and erode local adaptation. Determining the history of gene flow and thus the importance of contemporary hybridization, however, is notoriously difficult. Here, we focus on two endangered plant species, Arabis nemorensis and A. sagittata, which hybridize naturally in a sympatric population located on the banks of the Rhine. Using reduced genome sequencing, we determined the phylogeography of the two taxa but report only a unique sympatric population. Molecular variation in chloroplast DNA indicated that A. sagittata is the principal receiver of gene flow. Applying classical D-statistics and its derivatives to whole-genome data of 35 accessions, we detect gene flow not only in the sympatric population but also among allopatric populations. Using an Approximate Bayesian computation approach, we identify the model that best describes the history of gene flow between these taxa. This model shows that low levels of gene flow have persisted long after speciation. Around 10 000 years ago, gene flow stopped and a period of complete isolation began. Eventually, a hotspot of contemporary hybridization was formed in the unique sympatric population. Occasional sympatry may have helped protect these lineages from extinction in spite of their extremely low diversity.

scholarly journals Genetic structure of the threatened West-Pannonian population of Great Bustard (Otis tarda)

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1759
Author(s):  
Jose L. Horreo ◽  
Rainer Raab ◽  
Péter Spakovszky ◽  
Juan Carlos Alonso
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Genetic Structure ◽  
Great Bustard ◽  
Single Population ◽  
Current Conservation ◽  
Otis Tarda ◽  
Hungarian Population ◽  
First Time

The genetic diversity, population structure and gene flow of the Great Bustards (Otis tarda) living in Austria-Slovakia-West Hungary (West-Pannonian region), one of the few populations of this globally threatened species that survives across the Palaearctic, has been assessed for the first time in this study. Fourteen recently developed microsatellite loci identified one single population in the study area, with high values of genetic diversity and gene flow between two different genetic subunits. One of these subunits (Heideboden) was recognized as a priority for conservation, as it could be crucial to maintain connectivity with the central Hungarian population and thus contribute to keeping contemporary genetic diversity. Current conservation efforts have been successful in saving this threatened population from extinction two decades ago, and should continue to guarantee its future survival.

Phylogenomic Data Reveal Widespread Introgression Across the Range of an Alpine and Arctic Specialist

2020 ◽  
Author(s):  
Erik R Funk ◽  
Garth M Spellman ◽  
Kevin Winker ◽  
Jack J Withrow ◽  
Kristen C Ruegg ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genome Sequence ◽  
Population Genetic ◽  
Approximate Bayesian Computation ◽  
Sequence Data ◽  
Species Group ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Approximate Bayesian

Abstract Understanding how gene flow affects population divergence and speciation remains challenging. Differentiating one evolutionary process from another can be difficult because multiple processes can produce similar patterns, and more than one process can occur simultaneously. Although simple population models produce predictable results, how these processes balance in taxa with patchy distributions and complicated natural histories is less certain. These types of populations might be highly connected through migration (gene flow), but can experience stronger effects of genetic drift and inbreeding, or localized selection. Although different signals can be difficult to separate, the application of high-throughput sequence data can provide the resolution necessary to distinguish many of these processes. We present whole-genome sequence data for an avian species group with an alpine and arctic tundra distribution to examine the role that different population genetic processes have played in their evolutionary history. Rosy-finches inhabit high elevation mountaintop sky islands and high-latitude island and continental tundra. They exhibit extensive plumage variation coupled with low levels of genetic variation. Additionally, the number of species within the complex is debated, making them excellent for studying the forces involved in the process of diversification, as well as an important species group in which to investigate species boundaries. Total genomic variation suggests a broadly continuous pattern of allele frequency changes across the mainland taxa of this group in North America. However, phylogenomic analyses recover multiple distinct, well supported, groups that coincide with previously described morphological variation and current species-level taxonomy. Tests of introgression using D-statistics and approximate Bayesian computation reveal significant levels of introgression between multiple North American taxa. These results provide insight into the balance between divergent and homogenizing population genetic processes and highlight remaining challenges in interpreting conflict between different types of analytical approaches with whole-genome sequence data. [ABBA-BABA; approximate Bayesian computation; gene flow; phylogenomics; speciation; whole-genome sequencing.]

scholarly journals Landscape, colonization, and life history: their effects on genetic diversity in four sympatric species inhabiting a dendritic system

2019 ◽  
Vol 76 (12) ◽  
pp. 2288-2302 ◽  
Author(s):  
Daniel E. Ruzzante ◽  
Gregory R. McCracken ◽  
Sarah J. Salisbury ◽  
Hilary T. Brewis ◽  
Donald Keefe ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Lake Trout ◽  
Sympatric Species ◽  
Genetic Structuring ◽  
Colonization History ◽  
Diversity Patterns ◽  
Contemporary Gene Flow ◽  
Approximate Bayesian ◽  
Longnose Sucker

To what degree are patterns of genetic structure in fragmented systems the result of contemporary landscape versus history? We examined the distribution of genetic diversity as a function of colonization history and contemporary landscape in four fish species inhabiting a hierarchically fragmented, unaltered system, the Kogaluk drainage (Labrador): lake trout (Salvelinus namaycush), longnose sucker (Catostomus catostomus), round whitefish (Prosopium cylindraceum), and lake chub (Couesius plumbeus). The footprint of colonization history was still observable in the three species where this issue was examined regardless of the generations since their arrival. Approximate Bayesian computation (ABC) analyses suggest colonization took place from the southwest. The species exhibit similar diversity patterns despite different [Formula: see text] values and generation intervals. Contemporary gene flow was largely negligible except for gene flow from a centrally located lake. These results suggest landscape has driven colonization history, which still has influence on genetic structuring. The species are widespread. Understanding how they behave in the pristine Kogaluk provides a baseline against which to evaluate how other anthropogenically perturbed systems are performing. Improved understanding of historical and contemporary processes is required to fully explain diversity patterns in complex metapopulations.

scholarly journals SUCCESSFUL DEMONSTRATION OF ASSISTED GENE FLOW IN THE THREATENED CORAL ACROPORA PALMATA ACROSS GENETICALLY-ISOLATED CARIBBEAN POPULATIONS USING CRYOPRESERVED SPERM

2018 ◽  
Author(s):  
Mary Hagedorn ◽  
Christopher A. Page ◽  
Keri ONeill ◽  
Daisy M. Flores ◽  
Lucas Tichy ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Global Change ◽  
Direct Evidence ◽  
Acropora Palmata ◽  
Isolated Populations ◽  
Animal Populations ◽  
Caribbean Coral ◽  
Cryopreserved Sperm ◽  
First Time

Global change will compromise the population sizes, species ranges, and survival of economically-important plants and animals, including crops, aquaculture species, and foundational ecosystem builders. Scleractinian reef-building corals are a particular concern because they are slow-growing, long-lived, environmentally-sensitive, and concentrated in the warmest regions of the ocean. Assisted Gene Flow (AGF) is considered a viable tool to help natural plant and animal populations, including corals, adapt to changing environments. Our goal was to test for the first time whether cryopreserved coral sperm could be used to facilitate assisted gene flow between genetically-isolated populations of a Caribbean coral. We collected, pooled, and cryopreserved coral sperm from the threatened Caribbean coral Acropora palmata in the western Caribbean (Key Largo, FL), central Caribbean (Rincon, Puerto Rico), and eastern Caribbean (Curacao). Alongside freshly-collected sperm from Curacao, the cryopreserved sperm from each of these populations was used for in vitro fertilization experiments with freshly-collected eggs from Curacao. Across five egg donors, average fertilization success was 91 to 99% for CUR x CUR (fresh sperm) crosses, 37 to 82% for CUR x CUR (frozen sperm) crosses, 3 to 19% for CUR x FL (frozen sperm) crosses and 0 to 24% for CUR x PR (frozen sperm) crosses. Notably, fertilization was achieved in all four categories of crosses, showing for the first time through direct evidence that populations of A. palmata are reproductively compatible, and that genetic diversity can be transferred from one population to another for the purposes of assisted gene flow. The resulting larvae were reared in Curacao for up to 7 days, then the swimming larvae were transported to Florida for settlement and grow-out at two separate facilities, which achieved larval settlement rates of 37 to 60% across all cohorts. Larvae were reared and settled in Florida to acclimate them to the ambient water quality, microbial environment, and temperature regimes of the western genetic A. palmata population as early in their life cycle as possible. At one month, over 54% all settlers had survived, including over 3500 settlers from CUR x CUR (frozen sperm), 1200 settlers from CUR x FL (frozen sperm), and 230 settlers from CUR x PR (frozen sperm). These experiments represent the first-ever pan-Caribbean coral crosses produced in captivity and the first direct evidence that geographically-separated and genetically-isolated populations of any Caribbean coral are reproductively compatible. Moreover, with over 4700 A. palmata settlers produced using cryopreserved sperm, this represents the largest living wildlife population ever created from cryopreserved material. Together, these findings demonstrate that cryopreservation of coral sperm can enable efficient, large-scale assisted gene flow in corals. This form of assisted migration can not only help to preserve the population-level genetic diversity of extant coral populations but also help to increase population resilience to global change.

scholarly journals Parapatric speciation with recurrent gene flow of two sexual dichromatic pheasants

2021 ◽  
Author(s):  
Zheng Li ◽  
Jie Zhou ◽  
Minzhi Gao ◽  
Wei Liang ◽  
Lu Dong
Keyword(s):  
Sexual Selection ◽  
Gene Flow ◽  
Late Pleistocene ◽  
Approximate Bayesian Computation ◽  
De Novo ◽  
Demographic History ◽  
Population Expansion ◽  
Secondary Contact ◽  
Bayesian Computation ◽  
Approximate Bayesian

Background: Understanding speciation has long been a fundamental goal of evolutionary biology. It is widely accepted that speciation requires an interruption of gene flow to generate strong reproductive isolation between species, in which sexual selection may play an important role by generating and maintaining sexual dimorphism. The mechanism of how sexual selection operated in speciation with gene flow remains an open question and the subject of many research. Two species in genus Chrysolophus, Golden pheasant (C. pictus) and Lady Amherst's pheasant (C. amherstiae), which both exhibit significant plumage dichromatism, are currently parapatric in the southwest China with several hybrid recordings in field. Methods: In this research, we estimated the pattern of gene flow during the speciation of two pheasants using the Approximate Bayesian Computation (ABC) method based on the multiple genes data. With a new assembled de novo genome of Lady Amherst's pheasant and resequencing of widely distributed individuals, we reconstructed the demographic history of the two pheasants by pairwise sequentially Markovian coalescent (PSMC). Results: The results provide clear evidence that the gene flow between the two pheasants were consistent with the prediction of isolation with migration model for allopatric populations, indicating that there was long-term gene flow after the initially divergence (ca. 2.2 million years ago), and further support the secondary contact when included the parapatric populations since around 30 ka ongoing gene flow to now, which might be induced by the population expansion of the Golden pheasant in late Pleistocene. Conclusions: The results of the study support the scenario of speciation between Golden pheasant (C. pictus) and Lady Amherst's pheasant (C. amherstiae) with cycles of mixing-isolation-mixing due to the dynamics of natural selection and sexual selection in late Pleistocene that provide a good research system as evolutionary model to test reinforcement selection in speciation. Keywords: Golden pheasant (Chrysolophus pictus), Lady Amherst's pheasant (Chrysolophus amherstiae), speciation, gene flow, Approximate Bayesian Computation (ABC), Pairwise Sequentially Markovian coalescent (PSMC).

scholarly journals Distinguishing coalescent models - which statistics matter most?

2019 ◽  
Author(s):  
Fabian Freund ◽  
Arno Siri-Jégousse
Keyword(s):  
Genetic Diversity ◽  
Random Forest ◽  
Model Selection ◽  
Exponential Growth ◽  
Approximate Bayesian Computation ◽  
Genetic Data ◽  
Specific Question ◽  
Approximate Bayesian ◽  
Fitting Model ◽  
Kingman’S Coalescent

AbstractModelling genetic diversity needs an underlying genealogy model. To choose a fitting model based on genetic data, one can perform model selection between classes of genealogical trees, e.g. Kingman’s coalescent with exponential growth or multiple merger coalescents. Such selection can be based on many different statistics measuring genetic diversity. A random forest based Approximate Bayesian Computation is used to disentangle the effects of different statistics on distinguishing between various classes of genealogy models. For the specific question of inferring whether genealogies feature multiple mergers, a new statistic, the minimal observable clade size, is introduced. When combined with classical site frequency based statistics, it reduces classification errors considerably.

scholarly journals A study of the genetic polymorphism of Plasmopara viticola in the vineyards of the Krasnodar Territory

2020 ◽  
Vol 23 ◽  
pp. 02005
Author(s):  
Marina V. Makarkina ◽  
Sergey V. Tokmakov ◽  
Elena T. Ilnitskaya
Keyword(s):  
Genetic Diversity ◽  
Downy Mildew ◽  
Prediction Models ◽  
Dna Marker ◽  
Plasmopara Viticola ◽  
Fragment Analysis ◽  
Grapevine Downy Mildew ◽  
Grape Varieties ◽  
First Time ◽  
Different Levels

Plasmopara viticola oomycete is a seasonal pathogen that causes one of the most harmful diseases of the grapevine – downy mildew. The study of the biodiversity of Plasmopara viticola in various zones of viticulture has fundamental goals, as well as practical ones, as it is important for understanding the epidemiological cycle of P. viticola and for refining disease prediction models. The purpose of the work is to study the genetic diversity of P. viticola in the vineyards of the Krasnodar Territory, including on the grape varieties with different levels of resistance to downy mildew. The study was conducted on pathogens samples collected on grape plants of varieties with varying degrees of resistance to downy mildew. The collection of material was carried out in May-August 2019 in various zones of the Krasnodar Territory. 48 samples of P. viticola were analyzed. The DNA markers BER, ISA, CES, GOB, PV91, PV137, PV143, PV144 recommended for studying the genetic diversity of P. viticola were used. The work was performed by PCR. The amplification products were evaluated by the method of fragment analysis. DNA-marker GOB identified 37 alleles of different sizes, PV144 – 20, CES – 10, BER – 3, PV91 – 3, PV137 – 2, ISA – 1, PV143 – 1. It was shown that P. viticola populations are variable on different varieties and in different geographical areas. This study was conducted in the Krasnodar Territory for the first time.

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