DOI: 10.5061/dryad.j0zpc86mz
title: Ancient mitochondrial genomes unveil the origins and evolutionary history of New Zealand’s enigmatic takahe and moho

description: 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.
description: 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.
description: # Ancient mitochondrial genomes unveil the origins and evolutionary
 history of New Zealand’s enigmatic takahē and moho
 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).