scholarly journals Characterization of a pericentric inversion in plateau fence lizards (Sceloporus tristichus): evidence from chromosome-scale genomes

2021 ◽  
Vol 11 (2) ◽  
Author(s):  
Ana M Bedoya ◽  
Adam D Leaché
Keyword(s):  
Hybrid Zone ◽  
Pericentric Inversion ◽  
Population Genomics ◽  
Chromosomal Evolution ◽  
Chromosome 7 ◽  
Squamate Reptiles ◽  
Karyotype Formula ◽  
Dynamic Hybrid ◽  
Genome Assemblies

Abstract Spiny lizards in the genus Sceloporus are a model system among squamate reptiles for studies of chromosomal evolution. While most pleurodont iguanians retain an ancestral karyotype formula of 2n = 36 chromosomes, Sceloporus exhibits substantial karyotype variation ranging from 2n =  22 to 46 chromosomes. We present two annotated chromosome-scale genome assemblies for the Plateau Fence Lizard (Sceloporus tristichus) to facilitate research on the role of pericentric inversion polymorphisms on adaptation and speciation. Based on previous karyotype work using conventional staining, the S. tristichus genome is characterized as 2n =  22 with six pairs of macrochromosomes and five pairs of microchromosomes and a pericentric inversion polymorphism on chromosome 7 that is geographically variable. We provide annotated, chromosome-scale genomes for two lizards located at opposite ends of a dynamic hybrid zone that are each fixed for different inversion polymorphisms. The assembled genomes are 1.84–1.87 Gb (1.72 Gb for scaffolds mapping to chromosomes) with a scaffold N50 of 267.5 Mb. Functional annotation of the genomes resulted in ∼15K predicted gene models. Our assemblies confirmed the presence of a 4.62-Mb pericentric inversion on chromosome 7, which contains 62 annotated coding genes with known functions. In addition, we collected population genomics data using double digest RAD-sequencing for 44 S. tristichus to estimate population structure and phylogeny across the Colorado Plateau. These new genomic resources provide opportunities to perform genomic scans and investigate the formation and spread of pericentric inversions in a naturally occurring hybrid zone.

scholarly journals Characterization of a Large Pericentric Inversion in Plateau Fence Lizards (Sceloporus tristichus): Evidence from Chromosome-scale Genomes

2020 ◽  
Author(s):  
Ana M. Bedoya ◽  
Adam D. Leaché
Keyword(s):  
Hybrid Zone ◽  
Pericentric Inversion ◽  
Chromosomal Evolution ◽  
Squamate Reptiles ◽  
Naturally Occurring ◽  
Karyotype Formula ◽  
Dynamic Hybrid ◽  
Genome Assemblies

AbstractSpiny lizards in the genus Sceloporus are a model system among squamate reptiles for studies of chromosomal evolution. While most pleurodont iguanians retain an ancestral karyotype formula of 2n=36 chromosomes, Sceloporus exhibits substantial karyotype variation ranging from 2n=22 to 2n=46 chromosomes. In this study, we present two annotated chromosome-scale genome assemblies for the Plateau Fence Lizard (Sceloporus tristichus) in order to facilitate research on the role of pericentric inversion polymorphisms on adaptation and speciation. Based on previous karyotype work using conventional staining, the S. tristichus genome is characterized as 2n=22 with 6 pairs of macrochromosomes and 5 pairs of microchromosomes with a large pericentric inversion polymorphism on chromosome seven that is geographically variable. We provide annotated, chromosome-scale genomes for two lizards located at opposite ends of a dynamic hybrid zone that are each fixed for different inversion polymorphisms. The assembled genomes are 1.84 to 1.87 Gb (1.72 Gb for scaffolds mapping to chromosomes) with a scaffold N50 of 267.5 Mb. Functional annotation of the genomes resulted in 65,417 annotated genes, 16,426 of which were deduced to have a function. We confirmed the presence of a 4.62 Mb pericentric inversion on chromosome seven, which contains 59 annotated coding genes with known functions. These new genomic resources provide opportunities to perform genomic scans and investigate the formation and spread of pericentric inversions in a naturally occurring hybrid zone.

A holocenic and dynamic hybrid zone between two cactophilic Drosophila species in a coastal lowland plain of the Brazilian Atlantic Forest

2021 ◽  
Author(s):  
Dora Yovana Barrios‐Leal ◽  
Rodolpho S. T. Menezes ◽  
João Victor Ribeiro ◽  
Luiz Bizzo ◽  
Fabio Melo de Sene ◽  
...  
Keyword(s):  
Atlantic Forest ◽  
Hybrid Zone ◽  
Drosophila Species ◽  
Brazilian Atlantic Forest ◽  
Cactophilic Drosophila ◽  
Coastal Lowland ◽  
Dynamic Hybrid

scholarly journals Maintenance of a hybrid zone: The role of female mate choice

The Auk ◽  
2011 ◽  
Vol 128 (4) ◽  
pp. 688-695 ◽  
Author(s):  
Jane M. Hughes ◽  
Alicia Toon ◽  
Peter B. Mather ◽  
Corinna L. Lange
Keyword(s):  
Mate Choice ◽  
Hybrid Zone ◽  
Female Mate Choice ◽  
Female Mate

scholarly journals Transposable elements contribute to dynamic genome content in maize

2019 ◽  
Author(s):  
Sarah N Anderson ◽  
Michelle C Stitzer ◽  
Alex B. Brohammer ◽  
Peng Zhou ◽  
Jaclyn M Noshay ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Genomic Variation ◽  
Gene Content ◽  
Maize Genome ◽  
Large Scope ◽  
Shared Ancestry ◽  
Dynamic Genome ◽  
Genomic Studies ◽  
Genome Assemblies

AbstractTransposable elements (TEs) are ubiquitous components of eukaryotic genomes and can create variation in genomic organization. The majority of maize genomes are composed of TEs. We developed an approach to define shared and variable TE insertions across genome assemblies and applied this method to four maize genomes (B73, W22, Mo17, and PH207). Among these genomes we identified 1.6 Gb of variable TE sequence representing a combination of recent TE movement and deletion of previously existing TEs. Although recent TE movement only accounted for a portion of the TE variability, we identified 4,737 TEs unique to one genome with defined insertion sites in all other genomes. Variable TEs are found for all superfamilies and are distributed across the genome, including in regions of recent shared ancestry among individuals. There are 2,380 genes annotated in the B73 genome located within variable TEs, providing evidence for the role of TEs in contributing to the substantial differences in gene content among these genotypes. The large scope of TE variation present in this limited sample of temperate maize genomes highlights the major contribution of TEs in driving variation in genome organization and gene content.Significance StatementThe majority of the maize genome is comprised of transposable elements (TEs) that have the potential to create genomic variation within species. We developed a method to identify shared and non-shared TEs using whole genome assemblies of four maize inbred lines. Variable TEs are found throughout the maize genome and in comparisons of any two genomes we find ~20% of the genome is due to non-shared TEs. Several thousand maize genes are found within TEs that are variable across lines, highlighting the contribution of TEs to gene content variation. This study creates a comprehensive resource for genomic studies of TE variability among four maize genomes, which will enable studies on the consequences of variable TEs on genome function.

Extensive hybridization between two Andean warbler species with shallow divergence in mtDNA

The Auk ◽  
2021 ◽  
Vol 138 (1) ◽  
Author(s):  
Laura N Céspedes-Arias ◽  
Andrés M Cuervo ◽  
Elisa Bonaccorso ◽  
Marialejandra Castro-Farias ◽  
Alejandro Mendoza-Santacruz ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Contact Zone ◽  
Hybrid Zone ◽  
Secondary Contact ◽  
Tropical Andes ◽  
Phenotypic Data ◽  
Geographic Ranges ◽  
Intermediate Phenotypes ◽  
Ecological Barriers

Abstract Studying processes acting on differentiated populations upon secondary contact, such as hybridization, is important to comprehensively understand how species are formed and maintained over time. However, avian speciation studies in the tropical Andes have largely focused on the role of topographic and ecological barriers promoting divergence in allopatry, seldom examining hybridization and introgression. We describe a hybrid zone involving 2 closely related Andean warblers (Parulidae), the Golden-fronted Redstart (Myioborus ornatus), and the Spectacled Redstart (Myioborus melanocephalus). Geographic ranges of these species abut near the Colombia-Ecuador border and many specimens from the region exhibit intermediate phenotypes, but a formal description of phenotypic variation in the contact zone was heretofore lacking. We collected specimens across a transect encompassing the area where ranges abut and areas where only “pure” parental phenotypes of M. ornatus chrysops and M. melanocephalus ruficoronatus occur. We described variation in plumage traits including patterns of head and ventral coloration and tail markings based on 321 specimens. To describe genetic variation in the contact zone and over a broader phylogeographic context, we used sequences of the mitochondrial ND2 gene for 219 individuals across the transect and the entire range of both species, including all subspecies, from Venezuela to Bolivia. We documented a hybrid zone ~200 km wide based on head coloration, where intermediate plumage phenotypes are most common and “pure” forms do not overlap geographically, consistent with extensive hybridization. Across the range of the M. ornatus–M. melanocephalus complex, mitochondrial genetic structure was shallow, with genetic breaks only coinciding clearly with one topographic feature. Such a low genetic structure is striking given the high diversity in plumage phenotypes and the current taxonomy of the group. Our phenotypic data suggest that barriers to hybridization are not strong, and allow us to postulate hypotheses to be tested using forthcoming genomic data.

scholarly journals The demography and population genomics of evolutionary transitions to self-fertilization in plants

2014 ◽  
Vol 369 (1648) ◽  
pp. 20130344 ◽  
Author(s):  
Spencer C. H. Barrett ◽  
Ramesh Arunkumar ◽  
Stephen I. Wright
Keyword(s):  
Mating System ◽  
Population Genomics ◽  
Molecular Data ◽  
Reproductive Assurance ◽  
Evolutionary Transitions ◽  
Cast Doubt ◽  
Self Fertilization ◽  
Loss Of Diversity ◽  
Linked Selection

The evolution of self-fertilization from outcrossing has occurred on numerous occasions in flowering plants. This shift in mating system profoundly influences the morphology, ecology, genetics and evolution of selfing lineages. As a result, there has been sustained interest in understanding the mechanisms driving the evolution of selfing and its environmental context. Recently, patterns of molecular variation have been used to make inferences about the selective mechanisms associated with mating system transitions. However, these inferences can be complicated by the action of linked selection following the transition. Here, using multilocus simulations and comparative molecular data from related selfers and outcrossers, we demonstrate that there is little evidence for strong bottlenecks associated with initial transitions to selfing, and our simulation results cast doubt on whether it is possible to infer the role of bottlenecks associated with reproductive assurance in the evolution of selfing. They indicate that the effects of background selection on the loss of diversity and efficacy of selection occur rapidly following the shift to high selfing. Future comparative studies that integrate explicit ecological and genomic details are necessary for quantifying the independent and joint effects of selection and demography on transitions to selfing and the loss of genetic diversity.

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