scholarly journals Ancient mitochondrial genomes recovered from small vertebrate bones through minimally destructive DNA extraction: phylogeography of the New Zealand gecko genus Hoplodactylus.

2021 ◽  
Author(s):  
Lachie Scarsbrook ◽  
Alexander Verry ◽  
Kerry Walton ◽  
Rodney Hitchmough ◽  
Nic Rawlence
Keyword(s):  
New Zealand ◽  
Dna Extraction ◽  
Ancient Dna ◽  
Phylogenetic Analyses ◽  
Relative Size ◽  
Distinct Species ◽  
Glacial Refugia ◽  
Extraction Methods ◽  
Mitochondrial Genomes ◽  
Small Vertebrate

Methodological and technological improvements are continually revolutionizing the field of ancient DNA. Most ancient DNA extraction methods require the partial (or complete) destruction of finite museum specimens, which disproportionately impacts small or fragmentary subfossil remains, and future analyses. We present a minimally destructive ancient DNA extraction method optimized for small vertebrate remains. We applied these methods to detect lost mainland genetic diversity in the large New Zealand diplodactylid gecko genus Hoplodactylus, which is presently restricted to predator-free island sanctuaries. We present the first mitochondrial genomes for New Zealand diplodactylid geckos, recovered from 19 modern, six historic/archival (1898 to 2011) and 16 Holocene Hoplodactylus duvaucelii sensu latu specimens, and one modern Woodworthia sp. specimen. No obvious damage was observed in post-extraction micro-CT reconstructions. All ‘large gecko’ specimens examined from extinct populations were found to be conspecific with extant Hoplodactylus species, suggesting their large relative size evolved only once in the New Zealand diplodactylid radiation. Phylogenetic analyses of Hoplodactylus samples recovered two genetically (and morphologically) distinct North and South Island clades, probably corresponding to distinct species. Finer phylogeographic structuring within Hoplodactylus spp. highlighted the impacts of Late-Cenozoic biogeographic barriers, including the opening and closure of Pliocene marine straits, fluctuations in size and suitability of glacial refugia, and eustatic sea-level change. Recent mainland extinction obscured these signals from the modern tissue derived data. These results highlight the utility of minimally destructive DNA extraction in genomic analyses of less well studied small vertebrate taxa, and the conservation of natural history collections.

scholarly journals Evaluation of DNA Extraction Methods Developed for Forensic and Ancient DNA Applications Using Bone Samples of Different Age

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 146
Author(s):  
Catarina Xavier ◽  
Mayra Eduardoff ◽  
Barbara Bertoglio ◽  
Christina Amory ◽  
Cordula Berger ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Ancient Dna ◽  
Extraction Method ◽  
Fragment Size ◽  
Molecular Genetic ◽  
Extraction Methods ◽  
Degraded Dna ◽  
Size Analysis ◽  
Dna Fragments ◽  
Dna Amount

The efficient extraction of DNA from challenging samples, such as bones, is critical for the success of downstream genotyping analysis in molecular genetic disciplines. Even though the ancient DNA community has developed several protocols targeting small DNA fragments that are typically present in decomposed or old specimens, only recently forensic geneticists have started to adopt those protocols. Here, we compare an ancient DNA extraction protocol (Dabney) with a bone extraction method (Loreille) typically used in forensics. Real-time quantitative PCR and forensically representative typing methods including fragment size analysis and sequencing were used to assess protocol performance. We used four bone samples of different age in replicates to study the effects of both extraction methods. Our results confirm Loreille’s overall increased gain of DNA when enough tissue is available and Dabney’s improved efficiency for retrieving shorter DNA fragments that is beneficial when highly degraded DNA is present. The results suggest that the choice of extraction method needs to be based on available sample, degradation state, and targeted genotyping method. We modified the Dabney protocol by pooling parallel lysates prior to purification to study gain and performance in single tube typing assays and found that up to six parallel lysates lead to an almost linear gain of extracted DNA. These data are promising for further forensic investigations as the adapted Dabney protocol combines increased sensitivity for degraded DNA with necessary total DNA amount for forensic applications.

scholarly journals Comparison of two ancient DNA extraction protocols for skeletal remains from tropical environments

2017 ◽  
Author(s):  
Maria A. Nieves-Colón ◽  
Andrew T. Ozga ◽  
William J. Pestle ◽  
Andrea Cucina ◽  
Vera Tiesler ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Ancient Dna ◽  
Extraction Methods ◽  
Optimal Choice ◽  
Skeletal Remains ◽  
Tissue Type ◽  
Dna Fragments ◽  
Illumina Hiseq ◽  
Tropical Environments ◽  
Significant Difference

ABSTRACTObjectivesThe tropics harbor a large part of the world’s biodiversity and have a long history of human habitation. However, paleogenomics research in these climates has been constrained so far by poor ancient DNA yields. Here we compare the performance of two DNA extraction methods on ancient samples of teeth and petrous portions excavated from tropical and semitropical sites in Tanzania, Mexico, and Puerto Rico (N=12).Materials and MethodsAll samples were extracted twice, built into double-stranded sequencing libraries, and shotgun sequenced on the Illumina HiSeq 2500. The first extraction protocol, Method D, was previously designed for recovery of ultrashort DNA fragments from skeletal remains. The second, Method H, modifies the first by adding an initial EDTA wash and an extended digestion and decalcification step.ResultsNo significant difference was found in overall ancient DNA yields or post-mortem damage patterns recovered from samples extracted with either method, irrespective of tissue type. However, Method H samples had higher endogenous content and more mapped reads after quality-filtering, but also higher clonality. In contrast, samples extracted with Method D had shorter average DNA fragments.DiscussionBoth methods successfully recovered endogenous ancient DNA. But, since surviving DNA in ancient or historic remains from tropical contexts is extremely fragmented, our results suggest that Method D is the optimal choice for working with samples from warm and humid environments. Additional optimization of extraction conditions and further testing of Method H with different types of samples may allow for improvement of this protocol in the future.

Morphological description and molecular analyses of Tylodelphys sp. (Trematoda: Diplostomidae) newly recorded from the freshwater fish Gobiomorphus cotidianus (common bully) in New Zealand

2016 ◽  
Vol 91 (3) ◽  
pp. 332-345 ◽  
Author(s):  
I. Blasco-Costa ◽  
R. Poulin ◽  
B. Presswell
Keyword(s):  
New Zealand ◽  
Research Effort ◽  
Phylogenetic Analyses ◽  
Distinct Species ◽  
First Record ◽  
Molecular Data ◽  
Body Cavity ◽  
Morphological Description ◽  
Nominal Species ◽  
Gobiomorphus Cotidianus

AbstractAmong eyeflukes, Tylodelphys Diesing, 1850 includes diverse species able to infect the eyes, but also the brain, pericardial sac and body cavity of their second intermediate host. While the genus shows a cosmopolitan distribution with 29 nominal species in Africa, Asia, Europe and America, a likely lower research effort has produced two records only for all of Australasia. This study provides the first description of a species of Tylodelphys and the first record for a member of the Diplostomidae in New Zealand. Tylodephys sp. metacercaria from the eyes of Gobiomorphus cotidianus McDowall, 1975 is distinguished from its congeners as being larger in all, or nearly all, metrics than Tylodelphys clavata (von Nordmann, 1832), T. conifera (Mehlis, 1846) and T. scheuringi (Hughes, 1929); whereas T. podicipina Kozicka & Niewiadomska, 1960 is larger in body size, ventral sucker and holdfast sizes and T. ophthalmi (Pandey, 1970) has comparatively a very small pharynx and body spination. Tylodelphys sp. exhibits consistent genetic variation for the 28S rDNA, internal transcribed spacer (ITS) and Cox1 genes, and phylogenetic analyses confirm that it represents an independent lineage, closely related to North American species. Morphological and molecular results together support the distinct species status of Tylodephys sp. metacercaria, the formal description and naming of which await discovery of the adult. Furthermore, the validity of T. strigicola Odening, 1962 is restored, T. cerebralis Chakrabarti, 1968 is proposed as major synonym of T. ophthalmi, and species described solely on the basis of metacercariae are considered incertae sedis, except those for which molecular data already exist.

Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing

2015 ◽  
Vol 16 (2) ◽  
pp. 459-469 ◽  
Author(s):  
Cristina Gamba ◽  
Kristian Hanghøj ◽  
Charleen Gaunitz ◽  
Ahmed H. Alfarhan ◽  
Saleh A. Alquraishi ◽  
...  
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
Ancient Dna ◽  
High Throughput Sequencing ◽  
Extraction Methods ◽  
Dna Extraction Methods

scholarly journals Mitochondrial Genomes from New Zealand’s Extinct Adzebills (Aves: Aptornithidae: Aptornis) Support a Sister-Taxon Relationship with the Afro-Madagascan Sarothruridae

Diversity ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 24 ◽  
Author(s):  
Alexander Boast ◽  
Brendan Chapman ◽  
Michael Herrera ◽  
Trevor Worthy ◽  
R. Scofield ◽  
...  
Keyword(s):  
New Zealand ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Sister Taxon ◽  
Mitochondrial Genomes ◽  
Taxonomic Assignment ◽  
Long Distance ◽  
Land Bridge ◽  
The North

The recently extinct New Zealand adzebills (Aptornithidae, Aptornis spp.) were an enigmatic group of large flightless birds that have long eluded precise taxonomic assignment as they do not closely resemble any extant birds. Adzebills were nearly wingless, weighed approximately 16–19 kg, and possessed massive adze-like reinforced bills whose function remains unknown. Using hybridisation enrichment and high-throughput sequencing of DNA extracted from subfossil bone and eggshell, near-complete mitochondrial genomes were successfully assembled from the two Quaternary adzebill species: the North Island Adzebill (Aptornis otidiformis) and South Island Adzebill (A. defossor). Molecular phylogenetic analyses confirm that adzebills are members of the Ralloidea (rails and allies) and are sister-taxon to the Sarothruridae, which our results suggest comprises the Madagascan wood rails (Mentocrex, two likely sp.) in addition to the tiny (<50 gram) rail-like Afro-Madagascan flufftails (Sarothrura, 9 spp.). Node age estimates indicate that the split between adzebills and Sarothruridae occurred ~39.6 Ma, suggesting that the ancestors of the adzebills arrived in New Zealand by long-distance dispersal rather than continental vicariance. This newly identified biogeographic link between physically distant New Zealand and Afro-Madagascar, echoed by the relationship between the New Zealand kiwi (Apterygiformes) and Madagascan elephant-birds (Aepyornithiformes), suggests that the adzebill’s near relatives were formerly more widespread. In addition, our estimate for the divergence time between the two Quaternary adzebill species (0.2–2.3 Ma) coincides with the emergence of a land-bridge between the North and South islands of New Zealand (ca. 1.5–2 Ma). This relatively recent divergence suggests that North Island adzebills are the result of a relatively recent dispersal from the South Island, from which the earliest (Miocene) adzebill fossil has been described.

scholarly journals Assessment of sampling and DNA extraction methods for identification of grapevine trunk microorganisms using metabarcoding

2018 ◽  
Vol 71 ◽  
pp. 10-18 ◽  
Author(s):  
Dion C. Mundy ◽  
Bhanupratap R. Vanga ◽  
Sarah Thompson ◽  
Simon Bulman
Keyword(s):  
New Zealand ◽  
Dna Extraction ◽  
Dna Sequences ◽  
Low Cost ◽  
Pcr Amplification ◽  
Extraction Methods ◽  
Subsequent Work ◽  
Dna Metabarcoding ◽  
Ctab Method ◽  
Dna Extraction Methods

For a deeper understanding of grapevine trunk disease (GTD) in New Zealand, a cheap, rapid, sensitive method for identifying within-vine microbial communities is required. Wood tissue from grapevine trunks was collected and three different DNA extraction methods were compared: a cetyltrimethylammonium bromide (CTAB) method, the Geneaid Plant Genomic DNA Mini Kit and the Qiagen DNeasy Plant Mini Kit. DNA samples from the CTAB and Geneaid methods were used for MiSeq DNA metabarcoding targeting the ribosomal internal transcribed spacer 1 (ITS1) region. DNA produced by the CTAB method was of a greater quantity and quality than for the other two methods, although the majority of the DNA samples provided polymerase chain reaction (PCR) amplification of fungal DNA sequences. Fungal metabarcoding profiles from the CTAB and Geneaid samples indicated the presence of fungi normally associated with GTD in New Zealand. The CTAB method was chosen for subsequent work due to its low-cost, simplicity and effective detection of typical GTD fungi. The complete process of sampling through to metabarcoding is now used annually as part of a wider ecological study, screening more than 600 vines at 12 Marlborough vineyards.

scholarly journals Complete mitochondrial genomes confirm the distinctiveness of the horse-dog and sheep-dog strains of Echinococcus granulosus

Parasitology ◽  
2002 ◽  
Vol 124 (1) ◽  
pp. 97-112 ◽  
Author(s):  
T. H. LE ◽  
M. S. PEARSON ◽  
D. BLAIR ◽  
N. DAI ◽  
L. H. ZHANG ◽  
...  
Keyword(s):  
Echinococcus Granulosus ◽  
Phylogenetic Analyses ◽  
Distinct Species ◽  
Hymenolepis Diminuta ◽  
Mitochondrial Genomes ◽  
Pairwise Comparisons ◽  
Protein Coding ◽  
Specific Level ◽  
Protein Coding Genes ◽  
Complete Mitochondrial Genomes

Unlike other members of the genus, Echinococcus granulosus is known to exhibit considerable levels of variation in biology, physiology and molecular genetics. Indeed, some of the taxa regarded as ‘genotypes’ within E. granulosus might be sufficiently distinct as to merit specific status. Here, complete mitochondrial genomes are presented of 2 genotypes of E. granulosus (G1–sheep-dog strain: G4–horse-dog strain) and of another taeniid cestode, Taenia crassiceps. These genomes are characterized and compared with those of Echinococcus multilocularis and Hymenolepis diminuta. Genomes of all the species are very similar in structure, length and base-composition. Pairwise comparisons of concatenated protein-coding genes indicate that the G1 and G4 genotypes of E. granulosus are almost as distant from each other as each is from a distinct species, E. multilocularis. Sequences for the variable genes atp6 and nad3 were obtained from additional genotypes of E. granulosus, from E. vogeli and E. oligarthrus. Again, pairwise comparisons showed the distinctiveness of the G1 and G4 genotypes. Phylogenetic analyses of concatenated atp6, nad1 (partial) and cox1 (partial) genes from E. multilocularis, E. vogeli, E. oligarthrus, 5 genotypes of E. granulosus, and using T. crassiceps as an outgroup, yielded the same results. We conclude that the sheep-dog and horse-dog strains of E. granulosus should be regarded as distinct at the specific level.

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