Herbarium specimens are an important source of DNA for plant research but current sampling methods require the removal of material for DNA extraction. This is undesirable for irreplaceable specimens ...such as rare species or type material. Here I present the first non-destructive sampling method for extracting DNA from herbarium specimens. DNA was successfully retrieved from robust leaves and/or stems of herbarium specimens up to 73 years old.
Genetic analyses provide a powerful tool with which to identify the biological components of historical objects. Te Tiriti o Waitangi | The Treaty of Waitangi is New Zealand's founding document, ...intended to be a partnership between the indigenous Māori and the British Crown. Here we focus on an archived piece of blank parchment that has been proposed to be the missing portion of the lower parchment of the Waitangi Sheet of the Treaty. However, its physical dimensions and characteristics are not consistent with this hypothesis. We perform genetic analyses on the parchment membranes of the Treaty, plus the blank piece of parchment. We find that all three parchments were made from ewes and that the blank parchment is highly likely to be a portion cut from the lower membrane of the Waitangi Sheet because they share identical whole mitochondrial genomes, including an unusual heteroplasmic site. We suggest that the differences in size and characteristics between the two pieces of parchment may have resulted from the Treaty's exposure to water in the early 20th century and the subsequent repair work, light exposure during exhibition or the later conservation treatments in the 1970s and 80s. The blank piece of parchment will be valuable for comparison tests to study the effects of earlier treatments and to monitor the effects of long-term display on the Treaty.
Hybridization is common in many ferns and has been a significant factor in fern evolution and speciation. However, hybrids are rare between the approximately 30 species of Dicksonia tree ferns ...world-wide, and none are well documented. In this study we examine the relationship of a newly-discovered Dicksonia tree fern from Whirinaki, New Zealand, which does not fit the current taxonomy of the three species currently recognized in New Zealand. Our microsatellite genotyping and ddRAD-seq data indicate these plants are F1 hybrids that have formed multiple times between D. fibrosa and D. lanata subsp. lanata. The Whirinaki plants have intermediate morphology between D. fibrosa and D. lanata subsp. lanata and their malformed spores are consistent with a hybrid origin. The Whirinaki plants-Dicksonia fibrosa × D. lanata subsp. lanata-are an example of hybridization between distantly related fern lineages, with the two parent species estimated to have diverged 55-25 mya. Our chloroplast sequencing indicates asymmetric chloroplast inheritance in the Whirinaki morphology with D. lanata subsp. lanata always contributing the chloroplast genome.
Kiwi are a unique and emblematic group of birds endemic to New Zealand. Deep-time evolutionary relationships among the five extant kiwi species have been difficult to resolve, in part due to the ...absence of pre-Quaternary fossils to inform speciation events. Here, we utilise single representative nuclear genomes of all five extant kiwi species (great spotted kiwi, little spotted kiwi, Okarito brown kiwi, North Island brown kiwi, and southern brown kiwi) and investigate their evolutionary histories with phylogenomic, genetic diversity, and deep-time (past million years) demographic analyses. We uncover relatively low levels of gene-tree phylogenetic discordance across the genomes, suggesting clear distinction between species. However, we also find indications of post-divergence gene flow, concordant with recent reports of interspecific hybrids. The four species for which unbiased levels of genetic diversity could be calculated, due to the availability of reference assemblies (all species except the southern brown kiwi), show relatively low levels of genetic diversity, which we suggest reflects a combination of older environmental as well as more recent anthropogenic influence. In addition, we suggest hypotheses regarding the impact of known past environmental events, such as volcanic eruptions and glacial periods, on the similarities and differences observed in the demographic histories of the five kiwi species over the past million years.
Prions are small petrels that are abundant around the Southern Ocean. Here we use mitochondrial DNA (COI and cytochrome b) and nuclear reduced representation sequencing (ddRADseq) to examine the ...relationships within and between fairy (Pachyptila turtur) and fulmar (P. crassirostris) prions from across their distributions. We found that neither species was recovered as monophyletic, and that at least three species were represented. Furthermore, we detected several genetic lineages that are also morphologically distinct occurring in near sympatry at two locations (Snares Islands and Chatham Islands). The factors that have driven diversification in the fairy/fulmar prion complex are unclear but may include philopatry, differences in foraging distribution during breeding, differences in non-breeding distributions and breeding habitat characteristics. The observed distribution of genetic variation in the fairy/fulmar prion complex is consistent with population expansion from ice-free Last Glacial Maximum refugia into previously glaciated areas.
We examined the genetic structuring of rengarenga (Arthropodium cirratum; Asparagaceae), an endemic New Zealand coastal herb, using nuclear microsatellite markers. This species was brought into ...cultivation by Māori within the last 700-800 years for its edible roots and was transplanted beyond its natural distribution as part of its cultivation. We found very high levels of genetic structuring in the natural populations (FST = 0.84), indicating low levels of gene flow. Reduced genetic diversity was found in the translocated populations, suggesting a large loss of genetic diversity early in the domestication process. The data indicates that rengarenga was brought into cultivation independently at least three times, with the sources of these introductions located within a narrow area encompassing about 250km of coastline. Hybridization was inferred between A. cirratum and the closely related A. bifurcatum, despite A. birfucatum not occurring in the vicinity.
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•The New Zealand wattlebirds (Callaeidae) show significant variation in bill shape with the extinct huia also exhibiting extreme sexual dimorphism in bill morphology.•Phylogenies ...based on genomic data recover the relationships within the family.•Molecular dating indicates that the family radiated within 5.3–8.6 Ma, similar to other endemic New Zealand avian families.•The large range of bill morphologies is not a consequence of longer divergence times but likely relates to the expansion of the huia into the wood foraging niche.
The New Zealand wattlebirds (Callaeidae) are an endemic New Zealand passerine family whose species show extreme variation in bill morphology. In particular, the extinct huia (Heteralocha acutirostris) has attracted considerable attention because it exhibited extreme sexual dimorphism in bill morphology. However, the phylogenetic relationships within the Callaeidae, crucial for understanding bill evolution in the family, have not been resolved to date. Here we present phylogenies based on complete mitochondrial genome sequences and nuclear ultraconserved elements. Kōkako (Callaeas spp.) is strongly supported as sister taxon to saddleback/tīeke (Philesturnus spp.) and huia, diverging around 6.8 Ma. Saddleback and huia are estimated to have split from each other 5 Ma, indicating that the extreme sexual bill dimorphism in huia has evolved within this time frame. Our estimates for the divergences within the Callaetidae are similar to, or younger than, those of most other endemic New Zealand avian families, therefore the observed bill variation is not a consequence of a longer divergence time. Instead, the expansion of the huia into the wood-foraging niche, combined with the sexual dimorphism it evolved in order to optimise feeding on this resource, has been the main contributor to the large variation of bill morphologies within this family.
Sophora sect. Edwardsia is a group of 19 species largely confined to the South Pacific, with New Zealand the centre of species diversity. We used DNA and morphological analyses to investigate the ...origins of six uncurated Sophora sect. Edwardsia specimens from the herbarium of John G. Baker and Silvanus Thompson housed at the Museum of New Zealand Te Papa Tongarewa. These specimens derive from Sophora plants in cultivation in Germany and France between 1796 and 1822. Unexpectedly, our analyses identified one of the specimens as the Rapa Nui (Easter Island) endemic S. toromiro. This species has been extinct in the wild since 1960 but survives in cultivation in botanic and private gardens. The S. toromiro plants in cultivation today are thought to descend from seeds collected during the 1920s-1950s but our specimen was collected from a cultivated specimen in 1800. We suggest that the Baker and Thompson Herbarium S. toromiro specimen likely grew from seed collected during Captain Cook's second voyage (1772-1775). This would give sufficient time for the tree to have grown to a large enough size for a specimen to be removed by 1800. The provenance of the other Sophora specimens was uncertain but they most likely originate from New Zealand and were collected on either Cook's first or second voyages.
Lycopods are tracheophytes in the Kingdom Plantae and represent one of the oldest lineages of living vascular plants. Symbiotic interactions between these plants with fungi and bacteria, including ...fine root endophytes in Endogonales, have been hypothesized to have helped early diverging plant lineages colonize land. However, attempts to study the lycopod rhizobiome in its natural environment are still limited. In this study, we used Illumina amplicon sequencing to characterize fungal and bacterial diversity in nine Lycopodiaceae (club moss) species collected in New Zealand. This was done with generic fungal ITS rDNA primers, as well as Endogonales- and arbuscular mycorrhizal fungi (AMF)-selective primer sets targeting the 18S rDNA, and generic bacterial primers targeting the V4 region of the 16S rDNA. We found that the Lycopodiaceae rhizobiome was comprised of an unexpected high frequency of Basidiomycota and Ascomycota coincident with a low abundance of Endogonales and Glomerales. The distribution and abundance of Endogonales varied with host lycopod, and included a novel taxon as well as a single operational taxonomic unit (OTU) that was detected across all plant species. The Lycopodiaceae species with the greatest number and also most unique OTUs was
, while the plant species that shared the most fungal OTUs were
and
. The bacterial OTU distribution was generally not consistent with fungal OTU distribution. For example, community dissimilarity analysis revealed strong concordance between the evolutionary histories of host plants with the fungal community but not with the bacterial community, indicating that Lycopodiaceae have evolved specific relationships with their fungal symbionts. Notably, nearly 16% of the ITS rDNA fungal diversity detected in the Lycopodiaceae rhizobiome remained poorly classified, indicating there is much plant-associated fungal diversity left to describe in New Zealand.
Understanding the movements of animals that spend much of their life at sea is difficult but important for effective conservation. Determining the at-sea distributions of Macaroni (
Eudyptes ...chrysolophus
) and Royal (
Eudyptes schlegeli
) Penguins poses particular challenges, including their occurrence in remote locations and difficulties in species identification owing to overlap in morphological characters, particularly in immature birds. Here we use DNA sequencing to examine vagrant Macaroni and Royal Penguins from Antarctica and New Zealand in order to improve understanding of their non-breeding distributions. Our sampling included samples from living birds, museum specimens and scavenged penguin remains recovered from the stomachs of Antarctic toothfish (
Dissostichus mawsoni
) caught north of the Ross Sea. Mitochondrial control region (HVRI) sequences indicated that the two samples from New Zealand were likely Royal Penguins as were the scavenged penguins. Both Macaroni and Royal Penguins were detected at Terre Adélie, Antarctica, despite the nearest breeding colony of Macaroni Penguins being 4000 km away. We provide the first evidence of Royal Penguins reaching the Ross Dependency. All but one of the vagrants were immature birds, supporting suggestions that this age group is the most likely to disperse large distances from the breeding colonies. Our study demonstrates how DNA sequences can assist in identifying taxa with similar or overlapping morphologies, as well as fragmentary bird remains.
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