Spatial and host related genomic variation in partially sympatric cactophagous moth species

Surveys of patterns of genetic variation in natural sympatric and allopatric populations of recently diverged species are necessary to understand the processes driving intra and interspecific diversification. The South American moths Cactoblastis cactorum, Cactoblastis doddi and Cactoblastis bucyrus are specialized in the use of cacti as host plants. These species have different distribution ranges and differ in patterns of host plant use. However, there are areas in which their ranges overlap, as in northwestern Argentina, where they are largely sympatric. Using a combination of genome-wide SNPs and mitochondrial data we investigated the phylogeographic patterns of these cactophilic moths and searched for footprints of hybridization. Additionally, we evaluated a moth population feeding on Cleistocactus baumannii, a plant never reported as a host for the genus. We identified three well delimited species and detected signs of historical gene flow. Our survey also revealed intraspecific geographic structure in both C. doddi and C. cactorum and showed that the moth population feeding on C. baumannii may be considered as conspecific to C. bucyrus. Overall, our results indicated historical events of genetic interchange occurred in Cactoblastis cactophagous moths, but host plants likely played an important role during divergence limiting gene flow across species.

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Genetic rescue without genomic swamping in wild populations

10.1101/701706 ◽

2019 ◽

Cited By ~ 1

Author(s):

Sarah W. Fitzpatrick ◽

Gideon S. Bradburd ◽

Colin T. Kremer ◽

Patricia E. Salerno ◽

Lisa M. Angeloni ◽

...

Keyword(s):

Gene Flow ◽

Genomic Variation ◽

Adaptive Variation ◽

Genetic Rescue ◽

Genome Wide ◽

Evolutionary Force ◽

Locally Adaptive ◽

Fitness Benefits ◽

Evolutionary Consequences

AbstractGene flow is an enigmatic evolutionary force because it can limit adaptation but can also help populations escape inbreeding depression. Manipulating gene flow for conservation purposes is a controversial, but potentially powerful management strategy. We use multigenerational pedigrees and genomics to test demographic and evolutionary consequences of manipulating gene flow in two isolated wild Trinidadian guppy populations. We found that on average, hybrids lived longer and reproduced more. Despite overall genome-wide homogenization, alleles potentially associated with local adaptation were not entirely swamped by gene flow. Our results suggest that combining new genomic variation from immigrants with potentially adaptive variation from the recipient population resulted in highly fit hybrids and subsequent increases in population size. Contrary to the prevailing view that gene flow constrains adaptation, our study shows that immigration can produce long-term fitness benefits in small populations without swamping locally adaptive variation.

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The counteracting effects of demography on functional genomic variation: the Roma paradigm

Molecular Biology and Evolution ◽

10.1093/molbev/msab070 ◽

2021 ◽

Author(s):

Neus Font-Porterias ◽

Rocio Caro-Consuegra ◽

Marcel Lucas-Sánchez ◽

Marie Lopez ◽

Aaron Giménez ◽

...

Keyword(s):

Gene Flow ◽

Rare Variants ◽

Demographic History ◽

Genomic Variation ◽

Human Populations ◽

History Plays ◽

High Coverage ◽

Roma Population ◽

Genome Wide ◽

Whole Exome

Abstract Demographic history plays a major role in shaping the distribution of genomic variation. Yet the interaction between different demographic forces and their effects in the genomes is not fully resolved in human populations. Here we focus on the Roma population, the largest transnational ethnic minority in Europe. They have a South Asian origin and their demographic history is characterized by recent dispersals, multiple founder events and extensive gene flow from non-Roma groups. Through the analyses of new high-coverage whole exome sequences and genome-wide array data for 89 Iberian Roma individuals together with forward simulations, we show that founder effects have reduced their genetic diversity and proportion of rare variants, gene flow has counteracted the increase in mutational load, runs of homozygosity show ancestry-specific patterns of accumulation of deleterious homozygotes, and selection signals primarily derive from pre-admixture adaptation in the Roma population sources. The present study shows how two demographic forces, bottlenecks and admixture, act in opposite directions and have long-term balancing effects on the Roma genomes. Understanding how demography and gene flow shape the genome of an admixed population provides an opportunity to elucidate how genomic variation is modelled in human populations.

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Selection and gene flow define polygenic barriers between incipient butterfly species

10.1101/2020.04.09.034470 ◽

2020 ◽

Author(s):

Steven M. Van Belleghem ◽

Jared M. Cole ◽

Gabriela Montejo-Kovacevich ◽

Caroline N. Bacquet ◽

W. Owen McMillan ◽

...

Keyword(s):

Gene Flow ◽

Recombination Rate ◽

Genomic Variation ◽

Species Boundaries ◽

Secondary Contact ◽

Butterfly Species ◽

Demographic Modeling ◽

Incipient Species ◽

Genome Wide ◽

Genomic Divergence

AbstractCharacterizing the genetic architecture of species boundaries remains a difficult task. Hybridizing species provide a powerful system to identify the factors that shape genomic variation and, ultimately, identify the regions of the genome that maintain species boundaries. Unfortunately, complex histories of isolation, admixture and selection can generate heterogenous genomic landscapes of divergence which make inferences about the regions that are responsible for species boundaries problematic. However, as the signal of admixture and selection on genomic loci varies with recombination rate, their relationship can be used to infer their relative importance during speciation. Here, we explore patterns of genomic divergence, admixture and recombination rate among hybridizing lineages across the Heliconius erato radiation. We focus on the incipient species, H. erato and H. himera, and distinguish the processes that drive genomic divergence across three contact zones where they frequently hybridize. Using demographic modeling and simulations, we infer that periods of isolation and selection have been major causes of genome-wide correlation patterns between recombination rate and divergence between these incipient species. Upon secondary contact, we found surprisingly highly asymmetrical introgression between the species pair, with a paucity of H. erato alleles introgressing into the H. himera genomes. We suggest that this signal may result from a current polygenic species boundary between the hybridizing lineages. These results contribute to a growing appreciation for the importance of polygenic architectures of species boundaries and pervasive genome-wide selection during the early stages of speciation with gene flow.

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Faculty Opinions recommendation of Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.725563097.793507503 ◽

2015 ◽

Author(s):

Norman Johnson

Keyword(s):

Gene Flow ◽

Experimental Evidence ◽

Early Stages ◽

Ecological Selection ◽

Genome Wide

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Genomic variation in the American pika: signatures of geographic isolation and implications for conservation

BMC Ecology and Evolution ◽

10.1186/s12862-020-01739-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Kelly B. Klingler ◽

Joshua P. Jahner ◽

Thomas L. Parchman ◽

Chris Ray ◽

Mary M. Peacock

Keyword(s):

Genetic Variation ◽

Genetic Structure ◽

Sierra Nevada ◽

Spatial Genetic Structure ◽

Spatial Scales ◽

Thermal Sensitivity ◽

Genomic Variation ◽

Genome Wide ◽

A Genome ◽

American Pika

Abstract Background Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada. Results Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π = 0.0006–0.0009; θW = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θW = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θW = 0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s D was positive for all sites (D = 0.240–0.811), consistent with recent contraction in population sizes range-wide. Conclusions Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.

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Genome diversity in Ukraine

GigaScience ◽

10.1093/gigascience/giaa159 ◽

2021 ◽

Vol 10 (1) ◽

Author(s):

Taras K Oleksyk ◽

Walter W Wolfsberger ◽

Alexandra M Weber ◽

Khrystyna Shchubelka ◽

Olga T Oleksyk ◽

...

Keyword(s):

Sequence Data ◽

Copy Number Variations ◽

Genomic Variation ◽

High Coverage ◽

Genome Data ◽

New Information ◽

Genome Wide ◽

Public Data ◽

Genome Wide Data ◽

Multiple Samples

Abstract Background The main goal of this collaborative effort is to provide genome-wide data for the previously underrepresented population in Eastern Europe, and to provide cross-validation of the data from genome sequences and genotypes of the same individuals acquired by different technologies. We collected 97 genome-grade DNA samples from consented individuals representing major regions of Ukraine that were consented for public data release. BGISEQ-500 sequence data and genotypes by an Illumina GWAS chip were cross-validated on multiple samples and additionally referenced to 1 sample that has been resequenced by Illumina NovaSeq6000 S4 at high coverage. Results The genome data have been searched for genomic variation represented in this population, and a number of variants have been reported: large structural variants, indels, copy number variations, single-nucletide polymorphisms, and microsatellites. To our knowledge, this study provides the largest to-date survey of genetic variation in Ukraine, creating a public reference resource aiming to provide data for medical research in a large understudied population. Conclusions Our results indicate that the genetic diversity of the Ukrainian population is uniquely shaped by evolutionary and demographic forces and cannot be ignored in future genetic and biomedical studies. These data will contribute a wealth of new information bringing forth a wealth of novel, endemic and medically related alleles.

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Unexpected genomic, biosynthetic and species diversity of Streptomyces bacteria from bats in Arizona and New Mexico, USA

BMC Genomics ◽

10.1186/s12864-021-07546-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Cooper J. Park ◽

Nicole A. Caimi ◽

Debbie C. Buecher ◽

Ernest W. Valdez ◽

Diana E. Northup ◽

...

Keyword(s):

New Mexico ◽

Genetic Manipulation ◽

Distinct Species ◽

Biosynthetic Gene Cluster ◽

Genomic Variation ◽

Species Variation ◽

Nucleotide Polymorphisms ◽

Peptide Synthetases ◽

Genome Wide ◽

Diversity Estimates

Abstract Background Antibiotic-producing Streptomyces bacteria are ubiquitous in nature, yet most studies of its diversity have focused on free-living strains inhabiting diverse soil environments and those in symbiotic relationship with invertebrates. Results We studied the draft genomes of 73 Streptomyces isolates sampled from the skin (wing and tail membranes) and fur surfaces of bats collected in Arizona and New Mexico. We uncovered large genomic variation and biosynthetic potential, even among closely related strains. The isolates, which were initially identified as three distinct species based on sequence variation in the 16S rRNA locus, could be distinguished as 41 different species based on genome-wide average nucleotide identity. Of the 32 biosynthetic gene cluster (BGC) classes detected, non-ribosomal peptide synthetases, siderophores, and terpenes were present in all genomes. On average, Streptomyces genomes carried 14 distinct classes of BGCs (range = 9–20). Results also revealed large inter- and intra-species variation in gene content (single nucleotide polymorphisms, accessory genes and singletons) and BGCs, further contributing to the overall genetic diversity present in bat-associated Streptomyces. Finally, we show that genome-wide recombination has partly contributed to the large genomic variation among strains of the same species. Conclusions Our study provides an initial genomic assessment of bat-associated Streptomyces that will be critical to prioritizing those strains with the greatest ability to produce novel antibiotics. It also highlights the need to recognize within-species variation as an important factor in genetic manipulation studies, diversity estimates and drug discovery efforts in Streptomyces.

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