A Highly Contiguous Reference Genome for Northern Bobwhite (<i>Colinus virginianus</i>)

Salter, Jessie F.; Johnson, Oscar W.; Stafford, Norman J; Herrin, William F.; Schilling, Darren; Cedotal, Cody; Brumfield, Robb T.; Faircloth, Brant C.

doi:10.1534/g3.119.400609

Cited by 10 publications

(9 citation statements)

References 27 publications

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“…Long‐read sequencing data have been demonstrated to efficiently fill gaps in genome assemblies that are likely associated with structural variants, repeat regions or phasing errors (Morgan et al., 2022; Salter et al., 2019). We, however, showed that after de novo assembly using long‐read Pacbio data, polishing using Illumina short‐read data and reconstructing polymorphic diploid assembly to a haploid sub‐assembly, the genome assembly of D. maya had an N50 = 17.1 Mb, with the longest scaffold = 59 Mb (Table S3).…”

Section: Discussionmentioning

confidence: 99%

The genomes of Hercules beetles reveal putative adaptive loci and distinct demographic histories in pristine North American forests

Le,

Morgan,

et al. 2023

Molecular Ecology Resources

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Beetles, despite their remarkable biodiversity and a long history of research, remain lacking in reference genomes annotated with structural variations in loci of adaptive significance. We sequenced and assembled high‐quality chromosome‐level genomes of four Hercules beetles which exhibit divergence in male horn size and shape and body colouration. The four Hercules beetle genomes were assembled to 11 pseudo‐chromosomes, where the three genomes assembled using Nanopore data (Dynastes grantii, D. hyllus and D. tityus) were mapped to the genome assembled using PacBio + Hi‐C data (D. maya). We demonstrated a striking similarity in genome structure among the four species. This conservative genome structure may be attributed to our use of the D. maya assembly as the reference; however, it is worth noting that such a conservative genome structure is a recurring phenomenon among scarab beetles. We further identified homologues of nine and three candidate‐gene families that may be associated with the evolution of horn structure and body colouration respectively. Structural variations in Scr and Ebony2 were detected and discussed for their putative impacts on generating morphological diversity in beetles. We also reconstructed the demographic histories of the four Hercules beetles using heterozygosity information from the diploid genomes. We found that the demographic histories of the beetles closely recapitulated historical changes in suitable forest habitats driven by climate shifts.

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Section: Discussionmentioning

confidence: 99%

The genomes of Hercules beetles reveal putative adaptive loci and distinct demographic histories in pristine North American forests

Le,

Morgan,

et al. 2023

Molecular Ecology Resources

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“…The full procedure is described in the Supplemental Methods in Data S1. We aligned reads to the bobwhite reference genome (Salter et al, 2019) using bwa v0.7.17 (Li & Durbin, 2009) and samtools v1.10 (Li et al, 2009), and we called SNPs using a parallel implementation of the Best Practices for Variant Discovery (Salter & Faircloth, 2021; Van der Auwera & O'Connor, 2020) in GATK v4.1.9.0, including base quality score recalibration (McKenna et al, 2010).…”

Section: Methodsmentioning

confidence: 99%

An island ‘endemic’ born out of hybridization between introduced lineages

2023

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Humans have profoundly impacted the distribution of plant and animal species over thousands of years. The most direct example of these effects is human‐mediated movement of individuals, either through translocation of individuals within their range or through the introduction of species to new habitats. While human involvement may be suspected in species with obvious range disjunctions, it can be difficult to detect natural versus human‐mediated dispersal events for populations at the edge of a species' range, and this uncertainty muddles how we understand the evolutionary history of populations and broad biogeographical patterns. Studies combining genetic data with archaeological, linguistic and historical evidence have confirmed prehistoric examples of human‐mediated dispersal; however, it is unclear whether these methods can disentangle recent dispersal events, such as species translocated by European colonizers during the past 500 years. We use genomic DNA from historical museum specimens and historical records to evaluate three hypotheses regarding the timing and origin of Northern Bobwhites (Colinus virginianus) in Cuba, whose status as an endemic or introduced population has long been debated. We discovered that bobwhites from southern Mexico arrived in Cuba between the 12th and 16th centuries, followed by the subsequent introduction of bobwhites from the southeastern USA to Cuba between the 18th and 20th centuries. These dates suggest the introduction of bobwhites to Cuba was human‐mediated and concomitant with Spanish colonial shipping routes between Veracruz, Mexico and Havana, Cuba during this period. Our results identify endemic Cuban bobwhites as a genetically distinct population born of hybridization between divergent, introduced lineages.

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“…The full procedure is described in the Supplemental Methods. We aligned reads to the bobwhite reference genome (56) using bwa v0.7.17 (57) and samtools v1.10 (58), and we called SNPs using a parallel implementation of the Best Practices for Variant Discovery (59, 60) in GATK v4.1.9.0, including base quality score recalibration (61).…”

Section: Methodsmentioning

confidence: 99%

An island “endemic” born out of hybridization between introduced lineages

Salter¹,

Brumfield²,

Faircloth³

2022

Preprint

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Humans have profoundly impacted the distribution of plant and animal species over thousands of years. The most direct example of these effects is human-mediated movement of individuals, either through translocation of individuals within their range or the introduction of species to new habitats. While human involvement may be suspected in species with obvious range disjunctions, it can be difficult to detect natural versus human-mediated dispersal events for populations at the edge of a species' range, and this uncertainty muddles how we understand the evolutionary history of populations and broad biogeographic patterns. Studies combining genetic data with archeological, linguistic, and historical evidence have confirmed prehistoric examples of human-mediated dispersal; however, it is unclear whether these methods can disentangle recent dispersal events, such as species translocated by European colonizers during the past 500 years. We use genomic DNA from historical specimens and historical records to evaluate three hypotheses regarding the timing and origin of Northern Bobwhites (Colinus virginianus) in Cuba, whose status as an endemic or introduced population has long been debated. We discovered that bobwhites from southern Mexico arrived in Cuba between the 12th and 16th centuries, followed by the subsequent introduction of bobwhites from the southeastern USA to Cuba between the 18th and 20th centuries. These dates suggest the introduction of bobwhites to Cuba was human-mediated and concomitant with Spanish colonial shipping routes between Veracruz, Mexico and Havana, Cuba during this period. Our results identify endemic Cuban bobwhites as a genetically distinct population born of hybridization between divergent, introduced lineages.

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A Highly Contiguous Reference Genome for Northern Bobwhite (Colinus virginianus)

Cited by 10 publications

References 27 publications

The genomes of Hercules beetles reveal putative adaptive loci and distinct demographic histories in pristine North American forests

The genomes of Hercules beetles reveal putative adaptive loci and distinct demographic histories in pristine North American forests

An island ‘endemic’ born out of hybridization between introduced lineages

An island “endemic” born out of hybridization between introduced lineages

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