scholarly journals Implications of Historical and Contemporary Processes on Genetic Differentiation of a Declining Boreal Songbird: The Rusty Blackbird

Diversity ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 103
Author(s):  
Robert E. Wilson ◽  
Steven M. Matsuoka ◽  
Luke L. Powell ◽  
James A. Johnson ◽  
Dean W. Demarest ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genomic Structure ◽  
Natural Disturbance ◽  
Forested Wetland ◽  
Secondary Contact ◽  
Landscape Genomics ◽  
Reduced Representation ◽  
Habitat Features ◽  
Euphagus Carolinus ◽  
Rusty Blackbird

The arrangement of habitat features via historical or contemporary events can strongly influence genomic and demographic connectivity, and in turn affect levels of genetic diversity and resilience of populations to environmental perturbation. The rusty blackbird (Euphagus carolinus) is a forested wetland habitat specialist whose population size has declined sharply (78%) over recent decades. The species breeds across the expansive North American boreal forest region, which contains a mosaic of habitat conditions resulting from active natural disturbance regimes and glacial history. We used landscape genomics to evaluate how past and present landscape features have shaped patterns of genetic diversity and connectivity across the species’ breeding range. Based on reduced-representation genomic and mitochondrial DNA, genetic structure followed four broad patterns influenced by both historical and contemporary forces: (1) an east–west partition consistent with vicariance during the last glacial maximum; (2) a potential secondary contact zone between eastern and western lineages at James Bay, Ontario; (3) insular differentiation of birds on Newfoundland; and (4) restricted regional gene flow among locales within western and eastern North America. The presence of genomic structure and therefore restricted dispersal among populations may limit the species’ capacity to respond to rapid environmental change.

Genetic diversity enhanced by ancient introgression and secondary contact in East Pacific black mangroves

2008 ◽  
Vol 17 (11) ◽  
pp. 2680-2690 ◽  
Author(s):  
ALEJANDRO NETTEL ◽  
RICHARD S. DODD ◽  
ZARA AFZAL-RAFII ◽  
CRISTIAN TOVILLA-HERNÁNDEZ
Keyword(s):  
Genetic Diversity ◽  
Secondary Contact ◽  
East Pacific

Reduced representation genome sequencing reveals patterns of genetic diversity and selection in apple

2017 ◽  
Vol 59 (3) ◽  
pp. 190-204 ◽  
Author(s):  
Baiquan Ma ◽  
Liao Liao ◽  
Qian Peng ◽  
Ting Fang ◽  
Hui Zhou ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genome Sequencing ◽  
Reduced Representation

scholarly journals Parallel adaptations to an altitudinal gradient persist in tetraploid snowtrout (Cyprinidae: Schizothorax), despite extensive genomic exchange within adjacent Himalayan rivers

2021 ◽  
Author(s):  
Tyler K Chafin ◽  
Binod Regmi ◽  
Marlis R. Douglas ◽  
David R. Edds ◽  
Karma Wangchuk ◽  
...  
Keyword(s):  
De Novo ◽  
Genomic Islands ◽  
Secondary Contact ◽  
Evolutionary Patterns ◽  
Ploidy Levels ◽  
Reduced Representation ◽  
Genome Wide ◽  
Genealogical Concordance ◽  
Genomic Approach ◽  
The Ganges

Replicated evolutionary patterns are often attributed to recurrent emergence following parallel selective pressures. However, similar genetic patterns (e.g., 'genomic islands') can also emerge following extensive homogenization in secondary contact, as a by-product of heterogeneous introgression. For example, within Himalayan tributaries of the Ganges/Brahmaputra rivers, drainage-specific mtDNA clades of polyploid snowtrout (Cyprinidae: Schizothorax) are partitioned as co-occurring morphological 'ecotypes,' hypothesized to represent parallel divergence among adjacent streams. To evaluate this scenario, we utilized a reduced-representation genomic approach (N=35,319 de-novo and N=10,884 transcriptome-aligned SNPs) applied to high-altitude Nepali/Bhutanese snowtrout (N=48 each). We unambiguously quantified ploidy levels by first deriving genome-wide allelic depths followed by ploidy-aware Bayesian models that produced genotypes statistically consistent with diploid/tetraploid expectations. When genotyped SNPs were clustering within drainages, the convergence of eco-phenotypes was sustained. However, subsequent partitioned analyses of phylogeny and population admixture instead identified subsets of loci under selection which retained genealogical concordance with morphology, with apparent patterns of parallel ecotype emergence instead driven by widespread genomic homogenization. Here, prior isolation is effectively masked by admixture occurring in secondary contact. We note two salient factors:1) Polyploidy has promoted homogenization in tetraploid Himalayan snowtrout; and 2) Homogenization varies across Himalayan tributaries, presumably in lockstep with extent of anthropogenic modification.

scholarly journals Optimising sampling design and sequencing strategy for the genomic analysis of quantitative traits in natural populations

2021 ◽  
Author(s):  
Jefferson Paril ◽  
David Balding ◽  
Alexandre Fournier-Level
Keyword(s):  
Genetic Diversity ◽  
Natural Populations ◽  
Genomic Analysis ◽  
Complex Trait ◽  
Functional Ecology ◽  
High Genetic Diversity ◽  
Landscape Genomics ◽  
Sequencing Technologies ◽  
Sequencing Strategy ◽  
Study Designs

Mapping the genes underlying ecologically-relevant traits in natural populations is fundamental to develop a molecular understanding of species adaptation. Current sequencing technologies enable the characterisation of a species’ genetic diversity across the landscape or even over its whole range. The relevant capture of the genetic diversity across the landscape is critical for a successful genetic mapping of traits and there are no clear guidelines on how to achieve an optimal sampling and which sequencing strategy to implement. Here we determine through simulation, the sampling scheme that maximises the power to map the genetic basis of a complex trait in an outbreeding species across an idealised landscape and draw genomic predictions for the trait, comparing individual and pool sequencing strategies. Our results show that QTL detection power and prediction accuracy are higher when more populations over the landscape are sampled and this is more cost-effectively done with pool sequencing than with individual sequencing. Additionally, we recommend sampling populations from areas of high genetic diversity. As progress in sequencing enables the integration of trait-based functional ecology into landscape genomics studies, these findings will guide study designs allowing direct measures of genetic effects in natural populations across the environment.

scholarly journals Landscape genomics of an obligate mutualism: discordant population structures between a leafcutter-ant and its fungal cultivars

2018 ◽  
Author(s):  
Chad C. Smith ◽  
Jesse N. Weber ◽  
Alexander S. Mikheyev ◽  
Flavio Roces ◽  
Martin Bollazzi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Abiotic Factors ◽  
Genotyping By Sequencing ◽  
Range Limit ◽  
Range Margin ◽  
Landscape Genomics ◽  
Temperature And Precipitation ◽  
Obligate Mutualism

AbstractTo explore landscape genomics at the range limit of an obligate mutualism, we used genotyping-by-sequencing (ddRADseq) to quantify population structure and the effect of hostsymbiont interactions between the northernmost fungus-farming leafcutter ant Atta texana and its two main types of cultivated fungus. At local scales, genome-wide differentiation between ants associated with either of the two fungal types is greater than the differentiation associated with the abiotic factors temperature and precipitation, suggesting that specific ant-fungus genome-genome combinations may have been favored by selection. For the ant hosts, we found a broad cline of genetic structure across the range, and a reduction of genetic diversity along the axis of range expansion towards the range margin. In contrast, genetic structure was patchy in the cultivated fungi, with no consistent reduction of fungal genetic diversity at the range margins. This discordance in population-genetic structure between ant hosts and fungal symbionts is surprising because the ant farmers co-disperse with their vertically-transmitted fungal symbionts, but apparently the fungi disperse occasionally also through between-nest horizontal transfer or other unknown dispersal mechanisms. The discordance in populationgenetic structure indicates that genetic drift and gene flow differ in magnitude between each partner in this leafcutter mutualism. Together, these findings imply that variation in the strength of drift and gene flow experienced by each mutualistic partner affects adaptation to environmental stress at the range margin, and genome-genome interactions between host and symbiont influences adaptive genetic differentiation of the host during range evolution in this obligate mutualism.

scholarly journals Population genetics reveals cryptic lineages and ongoing hybridization in a declining migratory fish species complex

2021 ◽  
Author(s):  
Quentin Rougemont ◽  
Charles Perrier ◽  
Anne-Laure Besnard ◽  
Isabelle Lebel ◽  
Yann Abdallah ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Life History ◽  
Demographic History ◽  
Life History Strategies ◽  
Secondary Contact ◽  
Allis Shad ◽  
Twaite Shad ◽  
Genetic Diversity And Structure ◽  
Demographic Processes ◽  
Hybridization And Introgression

AbstractDeciphering the effects of historical and recent demographic processes responsible for the spatial patterns of genetic diversity and structure is a key objective in evolutionary and conservation biology. Using genetic analyses, we investigated the demographic history, the contemporary genetic diversity and structure, and the occurrence of hybridization and introgression, of two species of anadromous fish with contrasted life history strategies and which have undergone recent demographic declines, the allis shad (Alosa alosa) and the twaite shad (Alosa fallax). We genotyped 706 individuals from 20 rivers and 5 sites at sea in Southern Europe at microsatellite markers. Genetic structure between populations was lower for the nearly semelparous species allis shad that disperse stronger distance compared to the iteroparous species, twaite shad. Individuals caught at sea were assigned at the river level for twaite shad and at the region level for allis shad. Using an approximate Bayesian computation framework, we inferred that the most likely long term historical divergence scenario between both species implicated historical separation followed by secondary contact accompanied by strong population size decline. Accordingly, we found evidence of contemporary hybridization and introgression between both species. Besides, our results support the existence of cryptic species in the Mediterranean sea. Overall, our results shed light on the interplay between historical and recent demographic processes and life history strategies in shaping population genetic diversity and structure of closely related species. The recent demographic decline of these species’ populations and their hybridization should be carefully considered while implementing conservation programs.

scholarly journals The effects of population size on genetic parameters and mating system of sandalwood in Gunung Sewu, Indonesia

2017 ◽  
Vol 20 (2) ◽  
pp. 182
Author(s):  
Yeni Widyana Nurchahyani ◽  
Sapto Indrioko ◽  
Eny Faridah ◽  
Atus Syahbudin
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Mating Systems ◽  
Natural Disturbance ◽  
Isoenzyme Analysis ◽  
Important Species ◽  
Genetic Base ◽  
Root Suckering ◽  
Genetic Drifts ◽  
Population Demographic

We combined feld observations with isoenzyme analysis to compare population demographic and its effects on genetic diversity and mating systems, among six populations of sandalwood in Gunung Sewu, Indonesia, during March to August 2015. This endangered economic-important species was originated from the southeastern parts of Indonesia, but is recently occured as new landraces in Gunung Sewu, Java island. The observed heterozygosity varied from Ho 0.184 to 0.385 in parents, and from Ho 0.083 to 0.348 in offspring levels, based on the degree of clonality and genetic base. Most of genetic variation is distributed within populations, and only 2.7% were presented among populations, that was indicated by the low DST and FST value (HT 0.30; HS 0.276; DST 2.4%; FST 7.98%). A dendrogram indicated a grouping of populations into three clusters. However, there were seemed to be no association between geographical and genetic distance. Genetic depletion occured due to (i) clonality events as result of heavy-exploitation and/or natural disturbance which induced root suckering, (ii) genetic drifts and bottleneck effects, (iii) the founder effects due to parental low diversity, and (iv) the alteration on mating systems to be more inbreeders. Some of the results confrmed a “reproductive assurance prediction” while some others were contradicting this. It seemed that genetic diversity and mating systems are not much affected by population size, but more by the parental heterozygosity and the degree of clonality. Our results emphasized the importance of populations’ genetic base or parental genetic diversity to naturally maintain the genetic and evolutionary processes under equilibrium conditions.

scholarly journals Novel Genetic Rearrangements Termed “Structural Variation Polymorphisms“ Contribute to the Genetic Diversity of Orthohepadnaviruses

Viruses ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 871
Author(s):  
Kei Fujiwara ◽  
Kentaro Matsuura ◽  
Kayoko Matsunami ◽  
Etsuko Iio ◽  
Yoshihito Nagura ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Structural Variation ◽  
Genomic Structure ◽  
Detailed Examination ◽  
Multiple Alignment ◽  
Structural Variations ◽  
Genetic Changes ◽  
Genetic Sequences ◽  
Genetic Rearrangements

The genetic diversity of orthohepadnaviruses is not yet fully understood. This study was conducted to investigate the role of structural variations (SVs) in their diversity. Genetic sequences of orthohepadnaviruses were retrieved from databases. The positions of sequence gaps were investigated, since they were found to be related to SVs, and they were further used to search for SVs. Then, a combination of pair-wise and multiple alignment analyses was performed to analyze the genomic structure. Unique patterns of SVs were observed; genetic sequences at certain genomic positions could be separated into multiple patterns, such as no SV, SV pattern 1, SV pattern 2, and SV pattern 3, which were observed as polymorphic changes. We provisionally referred to these genetic changes as SV polymorphisms. Our data showed that higher frequency of sequence gaps and lower genetic identity were observed in the pre-S1-S2 region of various types of HBVs. Detailed examination of the genetic structure in the pre-S region by a combination of pair-wise and multiple alignment analyses showed that the genetic diversity of orthohepadnaviruses in the pre-S1 region could have been also induced by SV polymorphisms. Our data showed that novel genetic rearrangements provisionally termed SV polymorphisms were observed in various orthohepadnaviruses.

scholarly journals Population genetic structure and gene flow of rare and endangered Tetraena mongolica Maxim revealed by reduced representation sequencing

2020 ◽  
Author(s):  
Cheng Jin ◽  
Huixia Kao ◽  
Shubin Dong
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Industrial Development ◽  
High Quality ◽  
Reduced Representation ◽  
Rare And Endangered ◽  
Reduced Representation Sequencing

Abstract BackgroundStudying population genetic structure and gene flow of plant populations and their influence factors is crucial in field of conservation biology, especially rare and endangered plants. Tetraena mongolica Maxim (TM), belong to Zygophyllaceae family, a rare and endangered plant with narrow distribution. Due to excessive logging, urban expansion, industrial development and development of the scenic spot in the last decades, has caused habitat fragments and decline.ResultsIn this study, the genetic diversity, the population genetic structure and gene flow of TM populations were evaluated by reduced representation sequencing technology, a total of more than 133.45 GB high-quality clean reads and 38,097 high-quality SNPs were generated. Analysis based on multiple methods, we found existing TM populations have moderate levels of genetic diversity, very low genetic differentiation and high levels of gene flow between populations. Population structure and principal coordinates analysis showed that 8 TM populations can be divided into two groups, Mantel test detected no significant correlation between geographical distances and genetic distance for the whole sampling. The migration model indicated that the gene flow is more of an north to south migration pattern in history.ConclusionsOur study demonstrate that the present genetic structure is mainly due to habitat fragmentation caused by urban sprawl, industrial development and coal mining. For recommendations of conservation management, all 8 populations should be protected as a whole population, rather than just those in the core area of TM nature reserve, especially the populations near the edge of TM distribution in cities and industrial areas deserve our special protection.

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