scholarly journals Evolutionary genomics of endangered Hawaiian tree snails (Achatinellidae: Achatinellinae) for conservation of adaptive capacity

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10993
Author(s):  
Melissa R. Price ◽  
Michael G. Hadfield ◽  
Ingrid S.S. Knapp ◽  
Robert J. Toonen ◽  
Zac H. Forsman
Keyword(s):  
Adaptive Radiation ◽  
Environmental Gradients ◽  
Model System ◽  
Species Level ◽  
Conservation Strategies ◽  
Evolutionary Relationships ◽  
Evolutionary Potential ◽  
Snp Data ◽  
Genome Wide ◽  
In The Wild

Phylogenomic studies can provide insights into speciation, adaptation, and extinction, while providing a roadmap for conservation. Hawaiian tree snails are a model system for an adaptive radiation facing an extinction crisis. In the last 5 years, nearly all populations of Hawaiian tree snails across the 30 remaining species in the subfamily Achatinellinae (Achatinellidae) have declined from hundreds or thousands in the wild down to undetectable levels. Nearly 100 species historically occurred across dramatic environmental gradients on five of the Hawaiian Islands, but habitat loss, overcollection, and predation by invasive species have decimated populations. As such, this system offers the opportunity to integrate efforts to conserve evolutionary potential into conservation planning for a rapidly declining subfamily. Here, we used genome-wide, restriction-site associated DNA sequencing (RADseq), along with mitochondrial genome reconstruction, to resolve evolutionary relationships to inform conservation efforts. Phylogenetic analysis of nearly 400k genome-wide SNPs from 59 populations and 25 species across six genera in the family Achatinellidae, was generally concordant with taxonomy, geography, and mtDNA with several notable exceptions; mtDNA was unable to resolve some deeper nodes (e.g., the monophyly of Achatinella), while SNP data did not resolve as many shallow nodes. Both phylogenetic and coalescent analysis revealed deep divergences between populations within Achatinella mustelina that were consistent with species-level differences. Given cryptic species-level divergence within populations that are geographically proximate, they are at higher risk of extirpation from invasive predators and climate change than previously assumed. This study clarifies evolutionary relationships within this model system for adaptive radiation, forming the basis for conservation strategies such as translocation, captive rearing, and hybridization trials to prevent the loss of capacity to adapt to rapidly changing environmental conditions.

scholarly journals Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kyung Seok Kim ◽  
Kevin J. Roe
Keyword(s):  
Phylogenetic Analyses ◽  
Freshwater Mussel ◽  
Conservation Strategies ◽  
Nucleotide Polymorphisms ◽  
Conservation Units ◽  
Genetic Structuring ◽  
The North ◽  
Snp Data ◽  
Genome Wide ◽  
Significant Difference

AbstractDetailed information on species delineation and population genetic structure is a prerequisite for designing effective restoration and conservation strategies for imperiled organisms. Phylogenomic and population genomic analyses based on genome-wide double digest restriction-site associated DNA sequencing (ddRAD-Seq) data has identified three allopatric lineages in the North American freshwater mussel genus Cyprogenia. Cyprogenia stegaria is restricted to the Eastern Highlands and displays little genetic structuring within this region. However, two allopatric lineages of C. aberti in the Ozark and Ouachita highlands exhibit substantial levels (mean uncorrected FST = 0.368) of genetic differentiation and each warrants recognition as a distinct evolutionary lineage. Lineages of Cyprogenia in the Ouachita and Ozark highlands are further subdivided reflecting structuring at the level of river systems. Species tree inference and species delimitation in a Bayesian framework using single nucleotide polymorphisms (SNP) data supported results from phylogenetic analyses, and supports three species of Cyprogenia over the currently recognized two species. A comparison of SNPs generated from both destructively and non-destructively collected samples revealed no significant difference in the SNP error rate, quality and amount of ddRAD sequence reads, indicating that nondestructive or trace samples can be effectively utilized to generate SNP data for organisms for which destructive sampling is not permitted.

scholarly journals Population genetics of the coral Acropora millepora: Towards a genomic predictor of bleaching

2019 ◽  
Author(s):  
Zachary L. Fuller ◽  
Veronique J.L. Mocellin ◽  
Luke Morris ◽  
Neal Cantin ◽  
Jihanne Shepherd ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Balancing Selection ◽  
Genome Wide Association ◽  
Conservation Strategies ◽  
Genome Sequences ◽  
Acropora Millepora ◽  
Genome Wide ◽  
A Genome ◽  
In The Wild

AbstractAlthough reef-building corals are rapidly declining worldwide, responses to bleaching vary both within and among species. Because these inter-individual differences are partly heritable, they should in principle be predictable from genomic data. Towards that goal, we generated a chromosome-scale genome assembly for the coral Acropora millepora. We then obtained whole genome sequences for 237 phenotyped samples collected at 12 reefs distributed along the Great Barrier Reef, among which we inferred very little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin. We further used 213 of the samples to conduct a genome-wide association study of visual bleaching score, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for the use of genomics-based approaches in conservation strategies.

scholarly journals Genetic and epigenetic signatures associated with the rapid radiation of Aquilegia species

2019 ◽  
Author(s):  
Tianyuan Lu ◽  
Ming-Rui Li ◽  
Ning Ding ◽  
Zhen-Hui Wang ◽  
Li-Zhen Lan ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Adaptive Radiation ◽  
North American ◽  
Model System ◽  
Epigenetic Factors ◽  
Epigenetic Variability ◽  
Species Diversification ◽  
Genome Wide ◽  
Cell Reproduction ◽  
Epigenetic Signatures

AbstractElucidating how the diverse evolutionary mechanisms interact to determine species diversification is crucial to understanding the evolution and persistence of biodiversity. The genus Aquilegia (columbine) is a model system to identify genetic and epigenetic signatures underpinning the rapid adaptive radiation. In this study, we surveyed the genomes and DNA methylomes of ten worldwide Aquilegia species to investigate whether specific genomic architectures were associated with rapid species diversification in the Asian, European and North American lineages. The resulting phylogenies and population structure inferences revealed clearly high genetic and DNA methylomic divergence among the three lineages. Genome-wide scanning demonstrated significantly higher positive and purifying selection pressures among the Asian species compared to the European and North American lineages. More importantly, candidate genes identified at the genetic and epigenetic levels are functionally related to diverse adaptation-related traits, such as stress tolerance, photosynthesis and cell reproduction. While a considerable proportion of the candidate genes share hotspots of intra- and inter-lineage divergence, genetic and epigenetic factors were found to act on complementary biological pathways. By assessing the interaction between genetic variations and epigenetic variability, we found that epigenetic variability is a partially independent factor that intertwines with genetic mechanism to facilitate the diversification of the Aquilegia species. Taken together, these findings suggest that specific genetic architectures have been involved in vital biological pathways in response to diverse environmental conditions and epigenetic modifications may play a complementary role in the process of adaptive speciation. Our study provides an exploratory overview of how the established genetic and epigenetic signatures are associated with the rapid species diversification of Aquilegia species.Author SummaryDisentangling the genetic and epigenetic bases underpinning species diversification is crucial to understanding the evolution and persistence of biodiversity. The columbine (genus Aquilegia) is a model system to address biological mechanisms associated with rapid adaptive radiation. We surveyed the genomes and DNA methylomes of ten worldwide columbine species to investigate whether specific genetic and epigenetic architectures were involved in the diversification of Asian, European and North American columbine species. We pinpointed candidate genes featuring rapid adaptive radiation identified at either the genetic or the epigenetic levels. These candidate genes are functionally associated with diverse adaptation-related traits such as cell reproduction, plant growth, and stress tolerance. Such genetic and epigenetic signatures have potential contributed adaptabilities to the columbine species to cope with diverse environmental conditions. In addition, we also showed that epigenetic modifications could act as a complementary factor that intertwined with genetic mechanism to facilitate the diversification of the columbine species. In all, our study provides a genome-wide view of how the genetic and epigenetic factors are associated with the rapid species diversification of the columbine species.

scholarly journals Adaptive radiation and burst speciation of hillstream cyprinid fish Garra in African river

2021 ◽  
Author(s):  
Boris Levin ◽  
Evgeniy Simonov ◽  
Paolo Franchini ◽  
Nikolai Mugue ◽  
Alexander Golubtsov ◽  
...  
Keyword(s):  
Adaptive Radiation ◽  
Phenotypic Diversity ◽  
Wide Distribution ◽  
Hybrid Origin ◽  
Feeding Strategies ◽  
Ecological Opportunity ◽  
Western Africa ◽  
Snp Data ◽  
Genome Wide ◽  
Genome Wide Data

Adaptive radiation of fishes was long thought to be possible only in lacustrine environments. Recently, several studies have shown that also riverine and stream environments provide the ecological opportunity for adaptive radiation. In this study, we report on a riverine adaptive radiation of six ecomorphs of cyprinid hillstream fishes of the genus Garra in a river located in the Ethiopian Highlands in East Africa. Garra are predominantly highly specialized algae-scrapers with a wide distribution ranging from Southeastern Asia to Western Africa. However, adaptive phenotypic diversification in mouth type, sucking disc morphology, gut length and body shape have been found among these new species in a single Ethiopian river. Moreover, we found two novel phenotypes of Garra (‘thick-lipped’ and ‘predatory’) that were not described before in this species-rich genus (>160 species). Mitochondrial and genome-wide data suggest monophyletic, intra-basin evolution of Garra phenotypic diversity with signatures of gene flow from other local populations. Although sympatric ecomorphs are genetically distinct and can be considered to being young species as suggested by genome-wide SNP data, mtDNA was unable to identify any genetic structure suggesting a recent and rapid speciation event. Furthermore, we found evidence for a hybrid origin of the novel ‘thick-lipped’ phenotype, as being the result of the hybridization of two other sympatrically occurring species. Here we highlight how, driven by ecological opportunity, an ancestral trophically highly specialized lineage is likely to have rapidly adaptively radiated in a riverine environment, and that this radiation was promoted by the evolution of novel feeding strategies.

scholarly journals Genomic comparisons of Persian Kurdish, Persian Arabian and American Thoroughbred horse populations

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0247123
Author(s):  
Navid Yousefi-Mashouf ◽  
Hassan Mehrabani-Yeganeh ◽  
Ardeshir Nejati-Javaremi ◽  
Ernest Bailey ◽  
Jessica L. Petersen
Keyword(s):  
Principal Component ◽  
Conservation Strategies ◽  
Horse Population ◽  
Snp Data ◽  
Thoroughbred Horses ◽  
Genome Wide ◽  
Distinct Cluster ◽  
Shared Ancestry ◽  
Genetic Clusters ◽  
Cluster 2

The present research aimed to characterize the Persian Kurdish horse population relative to the Persian Arabian and American Thoroughbred populations using genome-wide SNP data. Fifty-eight Kurdish, 38 Persian Arabian and 83 Thoroughbred horses were genotyped across 670,796 markers. After quality control and pruning to eliminate linkage disequilibrium between loci which resulted in 13,554 SNPs in 52 Kurdish, 24 Persian Arabian and 58 Thoroughbred horses, the Kurdish horses were generally distinguished from the Persian Arabian samples by Principal Component Analyses, cluster analyses and calculation of pairwise FST. Both Persian breeds were discriminated from the Thoroughbred. Pairwise FST between the two Persian samples (0.013) was significantly greater than zero and several fold less than those found between the Thoroughbred and Kurdish (0.052) or Thoroughbred and Persian Arabian (0.057). Cluster analysis assuming three genetic clusters assigned the Kurdish horse and Thoroughbred to distinct clusters (0.942 in cluster 2 and 0.953 in cluster 3 respectively); the Persian Arabian was not in a distinct cluster (0.519 in cluster 1), demonstrating shared ancestry or recent admixture with the Kurdish breed. Diversity as quantified by expected heterozygosity was the highest in the Kurdish horse (0.342), followed by the Persian Arabian (0.328) and the Thoroughbred (0.326). Analysis of Molecular Variance showed that 4.47% of the genetic variation was present among populations (P<0.001). Population-specific inbreeding indices (FIS) were not significantly different from zero in any of the populations. Analysis of individual inbreeding based on runs of homozygosity using a larger SNP set suggested greater diversity in both the Kurdish and Persian Arabian than in the Thoroughbred. These results have implications for developing conservation strategies to achieve sound breeding goals while maintaining genetic diversity.

Population genetics of the coral Acropora millepora: Toward genomic prediction of bleaching

Science ◽  
2020 ◽  
Vol 369 (6501) ◽  
pp. eaba4674 ◽  
Author(s):  
Zachary L. Fuller ◽  
Veronique J. L. Mocellin ◽  
Luke A. Morris ◽  
Neal Cantin ◽  
Jihanne Shepherd ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Balancing Selection ◽  
Conservation Strategies ◽  
Genome Sequences ◽  
Acropora Millepora ◽  
Genome Wide ◽  
A Genome ◽  
Bleaching Response ◽  
In The Wild

Although reef-building corals are declining worldwide, responses to bleaching vary within and across species and are partly heritable. Toward predicting bleaching response from genomic data, we generated a chromosome-scale genome assembly for the coral Acropora millepora. We obtained whole-genome sequences for 237 phenotyped samples collected at 12 reefs along the Great Barrier Reef, among which we inferred little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin. We conducted a genome-wide association study of visual bleaching score for 213 samples, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for genomics-based approaches in conservation strategies.

scholarly journals Heritability Estimates of Antler and Body Traits in White-Tailed Deer (Odocoileus virginianus) From Genomic-Relatedness Matrices

2020 ◽  
Vol 111 (5) ◽  
pp. 429-435
Author(s):  
Aidan Jamieson ◽  
Spencer J Anderson ◽  
Jérémie Fuller ◽  
Steeve D Côté ◽  
Joseph M Northrup ◽  
...  
Keyword(s):  
Odocoileus Virginianus ◽  
Single Nucleotide ◽  
Snp Data ◽  
Genome Wide ◽  
Data Completion ◽  
In The Wild ◽  
Hind Foot ◽  
Anticosti Island ◽  
Free Ranging ◽  
Genomic Relatedness

Abstract Estimating heritability (h2) is required to predict the response to selection and is useful in species that are managed or farmed using trait information. Estimating h2 in free-ranging populations is challenging due to the need for pedigrees; genomic-relatedness matrices (GRMs) circumvent this need and can be implemented in nearly any system where phenotypic and genome-wide single-nucleotide polymorphism (SNP) data are available. We estimated the heritability of 5 body and 3 antler traits in a free-ranging population of white-tailed deer (Odocoileus virginianus) on Anticosti Island, Quebec, Canada. We generated classic and robust GRMs from &gt;10,000 SNPs: hind foot length, dressed body mass, and peroneus muscle mass had high h2 values of 0.62, 0.44, and 0.55, respectively. Heritability in male-only antler features ranged from 0.07 to 0.33. We explored the influence of filtering by minor allele frequency and data completion on h2: GRMs derived from fewer SNPs had reduced h2 estimates and the relatedness coefficients significantly deviated from those generated with more SNPs. As a corollary, we discussed limitations to the application of GRMs in the wild, notably how skewed GRMs, specifically many unrelated individuals, can increase variance around h2 estimates. This is the first study to estimate h2 on a free-ranging population of white-tailed deer and should be informative for breeding designs and management as these traits could respond to selection.

scholarly journals Genome-wide SNP data unravel the ancestry and signatures of divergent selection in Ghurrah pigs of India

2021 ◽  
pp. 104587
Author(s):  
Arnav Mehrotra ◽  
Bharat Bhushan ◽  
Karthikeyan A ◽  
Akansha Singh ◽  
Snehasmita Panda ◽  
...  
Keyword(s):  
Divergent Selection ◽  
Snp Data ◽  
Genome Wide

scholarly journals On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Gabriele Senczuk ◽  
Salvatore Mastrangelo ◽  
Paolo Ajmone-Marsan ◽  
Zsolt Becskei ◽  
Paolo Colangelo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Diversity Indices ◽  
Melting Pot ◽  
Cattle Breeds ◽  
Snp Data ◽  
Early Migration ◽  
Genome Wide ◽  
European Colonization ◽  
Approximate Bayesian ◽  
European Cattle

Abstract Background During the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, through an approximate Bayesian computation random forest (ABC-RF) approach. Results Our results indicate that European Podolian cattle display higher values of genetic diversity indices than both African taurine and Asian indicine breeds. Clustering analyses show that Podolian breeds share close genomic relationships, which suggests a likely common genetic ancestry. Among the simulated and tested scenarios of the colonization of Europe from taurine cattle, the greatest support was obtained for the model assuming at least two waves of diffusion. Time estimates are in line with an early migration from the domestication centre of non-Podolian taurine breeds followed by a secondary migration of Podolian breeds. The best fitting model also suggests that the Italian Podolian breeds are the result of admixture between different genomic pools. Conclusions This comprehensive dataset that includes most of the autochthonous cattle breeds belonging to the so-called Podolian trunk allowed us not only to shed light onto the origin and diversification of this group of cattle, but also to gain new insights into the diffusion of European cattle. The most well-supported scenario of colonization points to two main waves of migrations: with one that occurred alongside with the Neolithic human expansion and gave rise to the non-Podolian taurine breeds, and a more recent one that favoured the diffusion of European Podolian. In this process, we highlight the importance of both the Mediterranean and Danube routes in promoting European cattle colonization. Moreover, we identified admixture as a driver of diversification in Italy, which could represent a melting pot for Podolian cattle.

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