Ancient mitochondrial genomes unveil the origins and evolutionary history of New Zealand’s enigmatic takahe and moho
Cite this dataset
Verry, Alexander (2023). Ancient mitochondrial genomes unveil the origins and evolutionary history of New Zealand’s enigmatic takahe and moho [Dataset]. Dryad. https://doi.org/10.5061/dryad.j0zpc86mz
Abstract
Many avian species endemic to Aotearoa New Zealand were driven to extinction or reduced to relict populations following successive waves of human arrival, due to hunting, habitat destruction, and the introduction of mammalian predators. Among the affected species were the large flightless South Island takahe (Porphyrio hochstetteri) and the moho (North Island takahe; P. mantelli), with the latter rendered extinct and the former reduced to a single relictual population. Little is known about the evolutionary history of these species prior to their decline and/or extinction. Here we sequenced mitochondrial genomes from takahe and moho subfossils (12 takahe and four moho) and retrieved comparable sequence data from takahemuseum skins (n = 5) and contemporary individuals (n = 17) to examine the phylogeny and recent evolutionary history of these species. Our analyses suggest that prehistoric takahepopulations lacked deep phylogeographic structure, in contrast to moho, which exhibited significant spatial genetic structure, albeit based on limited sample sizes (n = 4). Temporal genetic comparisons show that takahe have lost much of their mitochondrial genetic diversity, likely due to a sudden demographic decline soon after human arrival (~750 years ago). Time-calibrated phylogenetic analyses strongly support a sister-species relationship between takahe and moho, suggesting these flightless taxa diverged around 1.5 million years ago, following a single colonisation of New Zealand by a flighted Porphyrio ancestor approximately four million year ago. This study highlights the utility of palaeogenetic approaches for informing the conservation and systematic understanding of endangered species whose ranges have been severely restricted by anthropogenic impacts.
README: Ancient mitochondrial genomes unveil the origins and evolutionary history of New Zealand’s enigmatic takahē and moho
https://doi.org/10.5061/dryad.j0zpc86mz
This dataset contains the raw Illumina DNA sequencing reads for DNA libraries prepared as described within the text. DNA libraries prepared from modern blood samples followed the protocol of Meyer & Kircher (2010), while ancient DNA libraries prepared from subfossil bones and and museum skins followed Carøe et al. (2018), except for CM Av30291 and NMNZ S39732, which were prepared following Gansauge et al. (2017). All ancient DNA libraries (subfossils and museum skins) were enriched for takahē mitochondrial DNA, while modern libraries (bloods) were constructed from mitochondrial DNA PCR products.
Carøe, C., Gopalakrishnan, S., Vinner, L., Mak, S. S., Sinding, M. H. S., Samaniego, J. A., ... & Gilbert, M. T. P. (2018). Single‐tube library preparation for degraded DNA. Methods in Ecology and Evolution, 9(2), 410-419.
Gansauge, M. T., Gerber, T., Glocke, I., Korlević, P., Lippik, L., Nagel, S., ... & Meyer, M. (2017). Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase. Nucleic acids research, 45(10), e79-e79
Meyer, M., & Kircher, M. (2010). Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc, 2010(6), t5448.
Description of the data and file structure
Modern DNA libraries were sequencing using paired-end 75 bp sequencing chemistry on the Illumina MiSeq platform, while most ancient DNA libraries (excluding CM Av30291 and NMNZ S39732) were sequenced on one lane of the Illumina HiSeq2500 sequencing platform using 2x75 bp sequencing chemistry. CM Av30291 and NMNZ S39732 were sequenced across four lanes of a single Illumina Nextseq550 flowcell also using 2x75 bp sequencing chemistry.
All libraries (except CM Av30291 and NMNZ S39732) contain two compressed fastq files corresponding to a singular lane of paired-end sequencing.
Files with the suffix R1 contain the forward reads, and those with the suffix R2 contain the reverse reads. Libraries CM Av30291 and NMNZ S39732 contain four R1 files and four R2 files (total = 8) because they were sequenced across four separate flowcell lanes.
Adapter sequences for libraries prepared using the Meyer & Kircher (2010) and Carøe et al. (2018) methodologies (all libraries except CM Av30291 and NMNZ S39732):
P7: CAAGCAGAAGACGGCATACGAGATNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
P5: AATGATACGGCGACCACCGAGATCTACACNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT
Adapter sequences for libraries CM Av30291 and NMNZ S39732:
P7: CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGT
P5: AATGATACGGCGACCACCGAGATCTACACNNNNNNNACACTCTTTCCCTACACGACGCTCTT
Sharing/Access information
Consensus mitochondrial genome sequences for these libraries/samples can be found on Genbank (Accession Numbers: OR753214, OR750879-OR750915).
Methods
This dataset contains the raw Illumina DNA sequencing reads from ancient takahe/moho libraries subject to hybridisation capture of mitochondrial DNA, and from modern takahe libraries constructed from mitochondrial DNA PCR products.
Funding
Royal Society of New Zealand, Award: 16-UOO-096