Nuclear copies of mitochondrial genes: another problem for ancient DNA

Tex, Robert-Jan den; Maldonado, Jesús E.; Thorington, Richard W.; Leonard, Jennifer A.

doi:10.1007/s10709-010-9481-9

Cited by 40 publications

(31 citation statements)

References 21 publications

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“…The lack of stop codons, indels or significant base composition differences among the sequences and the repeatability of the sequence between multiple amplifications of the same fragment and between overlapping regions of adjacent fragments supports the true mtDNA origin of these sequences as opposed to nuclear inserts (Den Tex et al, 2010b).…”

Section: Resultsmentioning

confidence: 85%

“…Nuclear copies of mitochondrial genes (NUMTs) can be amplified even from historic material, which is of lower quality than fresh tissue (Den Tex et al, 2010b). In order to check for the presence of NUMTs in the data set, the multiple sequences of each fragment and overlapping sections of adjacent fragments were checked for differences.…”

Section: Molecular Methodsmentioning

confidence: 99%

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The phylogeography of red and yellow coppersmith barbets (Aves: Megalaima haemacephala)

Tex

Leonard

2014

Front. Ecol. Evol.

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Understanding the evolution of color in birds is important because it is used for both inter-and intra-specific communication and is often linked to other important traits including life history, behavior, immunology, and mate choice. The coppersmith barbet (Megalaima haemacephala) is widely distributed across southern Asia and many islands of the Sunda shelf and the Philippines. It occurs in two well-differentiated and completely allopatrically distributed color morphs, a red-and a yellow-headed form. We constructed a phylogeny of coppersmith barbets from both color morphs and from across their range using sequences from two mitochondrial and one nuclear loci. Strong geographical patterns were found, in which India and Sri Lanka, the Philippines and mainland tropical east Asia (TE Asia) and the islands on the Sunda shelf (Sundaland) each formed a divergent group. The red birds formed two clades within the diversity of yellow animals. Major clades were dated using a molecular clock calibrated on a larger phylogeny. The phylogeographic patterns suggest that the species likely originated in TE Asia/Sundaland and then colonized the Philippines from the south in the mid-Pleistocene, via a now extinct population on Borneo. More recently, coppersmith barbets colonized India and Sri Lanka, also from TE Asia/Sundaland. Coppersmith barbets were also likely distributed on the Malay Peninsula, but went extinct there too. The population that now inhabits this region derives from a natural recolonization of yellow morph birds about 80 years ago. The red morph evolved at least twice independently from the yellow morph in the late Pleistocene, suggesting that this change does not require very many mutational steps, and thus can arise relatively frequently, on an evolutionary timescale. This system may be ideal for further studies of the genetics of carotenoid coloration.

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Section: Resultsmentioning

confidence: 85%

Section: Molecular Methodsmentioning

confidence: 99%

The phylogeography of red and yellow coppersmith barbets (Aves: Megalaima haemacephala)

Tex

Leonard

2014

Front. Ecol. Evol.

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“…An alternative explanation for COI-1 result is that the primers amplified a numt instead COI-1. The amplification of numts seems to increase with the usage of primers to amplify small fragments and is common in studies with aDNA (Tex et al, 2010).…”

Section: Discussionmentioning

confidence: 99%

Using ancient DNA to unravel taxonomic puzzles: the identity of Deuterodon pedri (Ostariophysi: Characidae)

Silva

Malabarba

2017

Neotrop. ichthyol.

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Accurate identification is essential for any study exploring biodiversity. Unfortunately, museum type specimens preserved for more than a hundred years are often not informative enough for precise identification of the species represented by the name-bearing type. The use of ancient DNA can help solve taxonomic problems when name-bearing types no longer have diagnostic morphological features that allow for an accurate identification of the species involved. That is the case for Deuterodon pedri, an endemic species from a small drainage in the rio Doce basin in Minas Gerais, Brazil, for which the type material is in poor condition. Specimens of D. pedri were collected in 1865 by the Thayer Expedition to Brazil and fixed in spirits, enabling them to yield viable DNA. As the morphology alone of the type material does not allow for an accurate identification, we used both morphological and ancient DNA (aDNA) methods to decisively establish the identity of D. pedri. This identification allowed us to recognize the species among recently collected specimens and then, based on them, redescribe the species. A genetype for the lectotype of D. pedri is presented.Keywords: Lectogenetype, Mini-Barcode, Primers, Rio Doce, Thayer Expedition.Uma identificação acurada é fundamental para qualquer estudo que explora a biodiversidade. Infelizmente, espécimes de museu descritos há mais de cem anos, algumas vezes não são informativos o suficiente para uma identificação precisa da espécie representada pelo tipo. O uso de DNA antigo pode ajudar a resolver problemas taxonômicos, quando espécimes tipos não apresentam mais as características morfológicas diagnósticas que permitem a identificação precisa das espécies. Esse é o caso de Deuterodon pedri, uma espécie endêmica de uma pequena drenagem na bacia do rio Doce, em Minas Gerais, Brasil cujo material tipo encontra-se em condições precárias. Espécimes de D. pedri foram coletados em 1865 pela Expedição Thayer ao Brasil e fixados em "cachaça", o que permite apresentar DNA viável. Como apenas o exame morfológico do material tipo não permitiria a identificação precisa, nós usamos ambos os dados de análises morfológicas e DNA antigo (aDNA) para estabelecer decisivamente a identidade de D. pedri. Esta identificação permitiu reconhecer a espécie entre exemplares coletados recentemente e, com base neles, redescrever a espécie. É apresentado um genetipo para o lectótipo de D. pedri.

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“…This region contains all the variable sites previously reported for California loggerhead shrikes (Mundy et al 1997c). All shrike sequences were checked for evidence of nuclear sequences of mitochondrial origin or ''numts'' (Sorenson and Quinn 1998), although numts are not usually a problem in ancient DNA studies because it is considered more probable for nuclear DNA to be degraded and be present in many less copies per cell than mitochondrial DNA (den Tex et al 2010). To ensure accuracy, we used taxon specific mitochondrial primers and sequencing was performed in both directions in each individual.…”

Section: Laboratory Methodsmentioning

confidence: 99%

Genetic analysis of the endemic island loggerhead shrike, Lanius ludovicianus anthonyi

Caballero

Ashley

2011

Conserv Genet

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Based on limited research, the island loggerhead shrike, Lanius ludovicianus anthonyi has been considered a distinct subspecies endemic to the northern California Channel Islands. We used mtDNA control region sequences and microsatellite genotyping to compare loggerhead shrikes from the southern California mainland (L. l. gambeli), San Clemente Island (L. l. mearnsi), and the northern islands (L. l. anthonyi). Habitats on the islands are recovering due to the removal of non-native ungulates on the islands, but may be transitioning to habitats less supportive of loggerhead shrikes, so this evaluation comes at a critical time. We utilized 96 museum specimens that were collected over a century to evaluate both spatial and temporal genetic patterns. Analysis of multilocus microsatellite genotypes indicated that historical specimens of loggerhead shrikes (collected between 1897 and 1986) from the two northern islands of Santa Rosa and Santa Cruz are genetically distinct from adjacent mainland and island shrikes. Birds from Santa Catalina Island showed mixed ancestry and did not cluster with the northern island birds. Historical specimens of L. l. mearnsi from San Clemente Island also showed mixed ancestry. Our study provides evidence that a genetically distinct form of loggerhead shrikes, L. l. anthonyi, occurred on the islands of Santa Rosa and Santa Cruz.

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Nuclear copies of mitochondrial genes: another problem for ancient DNA

Cited by 40 publications

References 21 publications

The phylogeography of red and yellow coppersmith barbets (Aves: Megalaima haemacephala)

The phylogeography of red and yellow coppersmith barbets (Aves: Megalaima haemacephala)

Using ancient DNA to unravel taxonomic puzzles: the identity of Deuterodon pedri (Ostariophysi: Characidae)

Genetic analysis of the endemic island loggerhead shrike, Lanius ludovicianus anthonyi

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