Genomics reveals the origins of ancient specimens

Mapping Intimacies ◽

10.1101/752121 ◽

2019 ◽

Cited By ~ 7

Author(s):

Qian Cong ◽

Jinhui Shen ◽

Jing Zhang ◽

Wenlin Li ◽

Lisa N. Kinch ◽

...

Keyword(s):

Dna Degradation ◽

Species Concepts ◽

Phenotypic Traits ◽

Museum Specimens ◽

Biodiversity Research

Centuries of zoological studies amassed billions of specimens in collections worldwide. Genomics of these specimens promises to rejuvenate biodiversity research. The obstacles stem from DNA degradation with specimen age. Overcoming this challenge, we set out to resolve a series of long-standing controversies involving a group of butterflies. We deduced geographical origins of several ancient specimens of uncertain provenance that are at the heart of these debates. Here, genomics tackles one of the greatest problems in zoology: countless old, poorly documented specimens that serve as irreplaceable embodiments of species concepts. The ability to figure out where they were collected will resolve many on-going disputes. More broadly, we show the utility of genomics applied to ancient museum specimens to delineate the boundaries of species and populations, and to hypothesize about genotypic determinants of phenotypic traits.

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Genomics Reveals the Origins of Historical Specimens

Molecular Biology and Evolution ◽

10.1093/molbev/msab013 ◽

2021 ◽

Author(s):

Qian Cong ◽

Jinhui Shen ◽

Jing Zhang ◽

Wenlin Li ◽

Lisa N Kinch ◽

...

Keyword(s):

Genomic Data ◽

Species Concepts ◽

Morphological Features ◽

Phenotypic Traits ◽

Museum Specimens ◽

Biodiversity Research ◽

Extant Species

Abstract Centuries of zoological studies have amassed billions of specimens in collections worldwide. Genomics of these specimens promises to reinvigorate biodiversity research. However, because DNA degrades with age in historical specimens, it is a challenge to obtain genomic data for them and analyze degraded genomes. We developed experimental and computational protocols to overcome these challenges and applied our methods to resolve a series of long-standing controversies involving a group of butterflies. We deduced the geographical origins of several historical specimens of uncertain provenance that are at the heart of these debates. Here, genomics tackles one of the greatest problems in zoology: countless old specimens that serve as irreplaceable embodiments of species concepts cannot be confidently assigned to extant species or population due to the lack of diagnostic morphological features and clear documentation of the collection locality. The ability to determine where they were collected will resolve many on-going disputes. More broadly, we show the utility of applying genomics to historical museum specimens to delineate the boundaries of species and populations, and to hypothesize about genotypic determinants of phenotypic traits.

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Evaluation of DNA degradation and establishment of a degradation analysis model for Lepidoptera specimens

BioTechniques ◽

10.2144/btn-2019-0166 ◽

2020 ◽

Vol 68 (3) ◽

pp. 138-147

Author(s):

Yao Xu ◽

XueYu Ren ◽

HongBin Wang ◽

Mei Wang ◽

GuoHong Li

Keyword(s):

Dna Sequences ◽

Dna Degradation ◽

Museum Specimens ◽

Analysis Model ◽

Preservation Method ◽

Degradation Analysis ◽

Fragment Distribution ◽

Dna Fragment ◽

Formalin Fixed ◽

Over Time

Millions of museum specimens are integral to biodiversity studies; however, DNA degradation may limit the ability to obtain DNA sequences. In this study, a degradation analysis model for Lepidoptera specimens was established. Based on this model, we revealed the characteristics of DNA fragment distribution caused by external DNA damage factors during specimen preservation. We found that the degree of DNA degradation increased over time; DNA degradation of spread and dried adult specimens was significantly higher than that in the folded and formalin-fixed larval specimens. However, the effects of folding wings on DNA degradation and the effects of the preservation method/stage (formalin-fixed larval vs air-dried adult specimens) were different for different species.

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Phenotypic variation and vocal divergence reveals a species complex in White-eared Ground-sparrows (Cabanis) (Aves: Passerellidae)

Zootaxa ◽

10.11646/zootaxa.4291.1.9 ◽

2017 ◽

Vol 4291 (1) ◽

pp. 155 ◽

Cited By ~ 4

Author(s):

LUIS SANDOVAL ◽

PIERRE-PAUL BITTON ◽

ALANA D. DEMKO ◽

STÉPHANIE M. DOUCET ◽

DANIEL J. MENNILL

Keyword(s):

Maximum Amplitude ◽

Taxonomic Status ◽

Distinct Species ◽

Phenotypic Traits ◽

Museum Specimens ◽

Sound Recordings ◽

Subspecies Level ◽

Morphometric Features ◽

Near Future ◽

The Relationship

The taxonomy of the genus Melozone has recently been analyzed from genus to subspecies level, leading to a significant revision of our understanding of this group of birds. Previous studies quantified differences in phenotypic traits, behavior, and genotypes, to provide a better understanding of the underappreciated diversity within Melozone and the relationship between species within this genus. Yet the relationship between the subspecies of White-eared Ground-sparrows, Melozone leucotis, has not received thorough taxonomic scrutiny. In this study, we evaluate the taxonomic status of the three recognized subspecies of M. leucotis using multiple morphometric characteristics, plumage color features, and vocalizations. We measured plumage patterns and reflectance from museum specimens, morphometric features from museum specimens and live birds, and vocal characteristics from sound recordings. We observed substantial variation between subspecies in plumage, morphometry, and voice, especially between northern and southern birds. The phenotypic and vocal differences exhibited by M. l. occipitalis (from Chiapas, Mexico; Guatemala; and El Salvador) suggest that its taxonomic relationship with the M. l. leucotis and M. l. nigrior complex (from Costa Rica and Nicaragua, respectively) needs to be reevaluated, because these two groups are highly diagnosable from one another. Additionally, M. l. occipitalis is geographically isolated from the other two subspecies, reducing the probability of contact by natural causes in the near future. Based on the clear differences in voice, plumage, and morphometric features reported here, we propose that M. l. occipitalis be recognized as a distinct species, M. occipitalis (Salvin's Ground-sparrow), diagnosed on the basis of its longer tail, longer bill, duller plumage, and songs with a lower frequency of maximum amplitude.

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A SMRT approach for targeted amplicon sequencing of museum specimens (Lepidoptera)—patterns of nucleotide misincorporation

PeerJ ◽

10.7717/peerj.10420 ◽

2021 ◽

Vol 9 ◽

pp. e10420

Author(s):

Jacopo D’Ercole ◽

Sean W.J. Prosser ◽

Paul D.N. Hebert

Keyword(s):

Single Molecule ◽

Large Scale ◽

Dna Degradation ◽

Degraded Dna ◽

Reference Sequence ◽

Coi Gene ◽

Sequence Information ◽

Museum Specimens ◽

Contig Assembly ◽

Evolutionary Diversification

Natural history collections are a valuable resource for molecular taxonomic studies and for examining patterns of evolutionary diversification, particularly in the case of rare or extinct species. However, the recovery of sequence information is often complicated by DNA degradation. This article describes use of the Sequel platform (Pacific Biosciences) to recover the 658 bp barcode region of the mitochondrial cytochrome c oxidase I (COI) gene from 380 butterflies with an average age of 50 years. Nested multiplex PCR was employed for library preparation to facilitate sequence recovery from extracts with low concentrations of highly degraded DNA. By employing circular consensus sequencing (CCS) of short amplicons (circa 150 bp), full-length barcodes could be assembled without a reference sequence, an important advance from earlier protocols which required reference sequences to guide contig assembly. The Sequel protocol recovered COI sequences (499 bp on average) from 318 of 380 specimens (84%), much higher than for Sanger sequencing (26%). Because each read derives from a single molecule, it was also possible to quantify the incidence of substitutions arising from DNA damage. In agreement with past work on sequence changes induced by DNA degradation, the transition C/G → T/A was the most prevalent category of change, but its rate of occurrence (4.58E−4) was so low that it did not impede the recovery of reliable sequences. Because the current protocol recovers COI sequence from most museum specimens, and because sequence fidelity is unaffected by nucleotide misincorporations, large-scale sequence characterization of museum specimens is feasible.

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