Comparative phylogenetic analysis reveals long-term isolation of lineages on the Three Kings Islands, New Zealand

Ancient relicts or recent immigrants? Different dating strategies alter diversification scenarios of New Zealand aquatic beetles (Coleoptera: Hydrophilidae: Berosus)

Dated species-level phylogenies are crucial for understanding the origin and evolutionary history of modern faunas, yet difficult to obtain due to the frequent absence of suitable age calibrations at species level. Substitution rates of related or more inclusive clades are often used to overcome this limitation but the accuracy of this approach remains untested. We compared tree dating based on substitution rates with analyses implementing fossil data by direct node-dating and indirect root-age constraints for the New Zealand endemic Berosus water beetles (Coleoptera: Hydrophilidae). The analysis based solely on substitution rates indicated a Miocene colonization of New Zealand and Pleistocene origin of species. By contrast, all analyses that implemented fossil data resulted in significantly older age estimates, indicating an ancient early Cenozoic origin of the New Zealand clade, diversification of species during or after the Oligocene transgression and Miocene-Pliocene origin of within-species population structure. Rate-calibrated time trees were incongruent with recently published Coleoptera time trees, the fossil record of Berosus and the distribution of outgroup species. Strong variation of substitution rates among Coleoptera lineages, as well as among lineages within the family Hydrophilidae, was identified as the principal reason for low accuracy of rate-calibrated analyses, resulting in underestimated node ages in Berosus. We provide evidence that Oligocene to Pliocene events, rather than the Pleistocene Glacial cycles, played an essential role in the formation of the modern New Zealand insect fauna.

Phylogenetic divergence of island biotas: Molecular dates, extinction, and "relict" lineages

Island formation is a key driver of biological evolution, and several studies have used geological ages of islands to calibrate rates of DNA change. However, many islands are home to "relict" lineages whose divergence apparently pre-dates island age. The geologically dynamic New Zealand (NZ) archipelago sits upon the ancient, largely submerged continent Zealandia, and the origin and age of its distinctive biota have long been contentious. While some researchers have interpreted NZ's biota as equivalent to that of a post-Oligocene island, a recent review of genetic studies identified a sizeable proportion of pre-Oligocene "relict" lineages, concluding that much of the biota survived an incomplete drowning event. Here, we assemble comparable genetic divergence data sets for two recently formed South Pacific archipelagos (Lord Howe; Chatham Islands) and demonstrate similarly substantial proportions of relict lineages. Similar to the NZ biota, our island reviews provide surprisingly little evidence for major genetic divergence "pulses" associated with island emergence. The dominance of Quaternary divergence estimates in all three biotas may highlight the importance of rapid biological turnover and new arrivals in response to recent climatic and/or geological disturbance and change. We provide a schematic model to help account for discrepancies between expected versus observed divergence-date distributions for island biotas, incorporating the effects of both molecular dating error and lineage extinction. We conclude that oceanic islands can represent both evolutionary "cradles" and "museums" and that the presence of apparently archaic island lineages does not preclude dispersal origins.

Applications of phylogenetics to solve practical problems in insect conservation

Phylogenetic approaches have much promise for the setting of conservation priorities and resource allocation. There has been significant development of analytical methods for the measurement of phylogenetic diversity within and among ecological communities as a way of setting conservation priorities. Application of these tools to insects has been low as has been the uptake by conservation managers. A critical reason for the lack of uptake includes the scarcity of detailed phylogenetic and species distribution data from much of insect diversity. Environmental DNA technologies offer a means for the high throughout collection of phylogenetic data across landscapes for conservation planning.

Evidence of a Strong Domestication Bottleneck in the Recently Cultivated New Zealand Endemic Root Crop, Arthropodium cirratum (Asparagaceae)

We use chloroplast DNA sequencing to examine aspects of the pre-European Māori cultivation of an endemic New Zealand root crop, Arthropodium cirratum (rengarenga). Researching the early stages of domestication is not possible for the majority of crops, because their cultivation began many thousands of years ago and/or they have been substantially altered by modern breeding methods. We found high levels of genetic variation and structuring characterised the natural distribution of A. cirratum, while the translocated populations only retained low levels of this diversity, indicating a strong bottleneck even at the early stages of this species’ cultivation. The high structuring detected at four chloroplast loci within the natural A. cirratum range enabled the putative source(s) of the translocated populations to be identified as most likely located in the eastern Bay of Plenty/East Cape region. The high structuring within A. cirratum also has implications for the conservation of genetic diversity within this species, which has undergone recent declines in both its natural and translocated ranges.