This study is one of the first to utilise PD, PWE and CANAPE in analyses of the entire vascular flora of an archipelago at two taxonomic ranks, with previous studies having focused on species within genera or genera within families in continental Australia.
The results of this study are generally consistent with current understanding of New Zealand areas of vascular plant endemism and regional biogeographic patterns. However, the analyses presented here importantly provide new insights into the positions of some of the major biogeographic boundaries and to the types of endemism observed. New centres of endemism can be revealed using the sophisticated analyses in Biodiverse, and patterns of endemism can be identified at a finer scale of resolution and more accurately than in earlier studies. The types of analyses presented here have wide application, including: 1) new hypotheses of areas, boundaries and types of endemism; 2) enabling significant areas to be identified to plan and prioritise conservation efforts; and 3) the phylogenetic metrics can be utilised for environmental reporting to provide insights to and measures of biodiversity at genetic scales not previously possible.
In conclusion, Biodiverse provides a valuable framework for objectively analysing and visualising biodiversity data for the entire vascular flora of the widely dispersed New Zealand archipelago. Further research is needed to better understand the behaviour of endemism metrics with regard to the effects of data biases, taxonomic rank and geographic scale.
Additional rbcL sequencing requirements
Complete the sequencing for the 10 samples with a sequence gap between internal 3′ and 5′ primers and obtain the complete sequence for the 14 samples missing either the 5′ or 3′ half of rbcL.
18For the 31 genera for which we have not obtained DNA sequences from New Zealand indigenous species, this missing data should be obtained to complete the dataset of rbcL sequences representative of all New Zealand genera. This is achievable and loans from other herbaria with recent collections of these genera and some field work is required to obtain suitable plant material for sequencing. It should be noted that the orchids Gastrodia and Molloybas and the parasitic Dactylanthus do not have chlorophyll and therefore are not able to be sequenced for rbcL.
19Having almost completed the construction of an rbcL phylogeny for New Zealand indigenous vascular plant genera, consideration should be given to expanding this to include indigenous non-vascular moss, liverwort and hornwort genera (bryophytes).
20Discussions have been held with Dr Robbie Holdaway (Landcare Research) about utilising the New Zealand indigenous genus rbcL phylogeny as part of the environmental DNA project (A national framework for biological heritage assessment across natural and productive landscapes) in The National Science Challenge, New Zealand’s Biological Heritage. Completing the rbcL sequencing for the missing genera is a priority as the resulting dataset would have multiple uses.
Laffan, S.W., Lubarsky, E. and Rosauer, D.F., 2010. Biodiverse, a tool for the spatial analysis of biological and related diversity. Ecography, 33, 643–647. doi:10.1111/j.1600-0587.2010.06237.x
Mishler, B.D., Knerr, N.J., Gonzalez-Orozco, C.E., Thornhill, A.H., Laffan, S. and Miller, J.T., 2014. Phylogenetic measures of biodiversity and neo- and palaeo-endemism in Australian Acacia. Nature Communications, 4, 4473.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, and Kumar S (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution, 28, 2731-2739.
A. Richness, main New Zealand islands. B. Corrected Weighted Endemism, main New Zealand islands. C. Corrected Weighted Endemism, New Zealand archipelago. Dark blue: primary endemism (top 1%) CWE values; light blue: secondary endemism (top 5%) CWE values; +: greater CWE than expected from random; •: less CWE than expected from random; white: empty cell.
Appendix 4. Genus-level patterns of PD, PWE and neo- and palaeo-endemism
Genus-level patterns and types of neo- and palaeo-endemism. A. Relative phylogenetic diversity significance levels resulting from a randomization test. B. Relative phylogenetic endemism significance levels resulting from a randomization test. C. CANAPE areas of neo-, mixed- and palaeo-endemism. D. Barplot of CANAPE analysis for New Zealand archipelago. E. Barplot of CANAPE analysis for North Island. F. Barplot of CANAPE analysis for South Island. G. Barplot of CANAPE analysis for offshore islands. A, B: red values indicate cells that contain significantly less RPD and RPE than expected; blue values indicate cells that contain significantly more RPD and RPE than expected.
Appendix 5. Species-level patterns of PD, PWE and neo- and palaeo-endemism
A. Relative phylogenetic diversity significance levels resulting from a randomization test. B. Relative phylogenetic endemism significance levels resulting from a randomization test. C. CANAPE areas of neo-, mixed- and palaeo-endemism. D. Barplot of CANAPE analysis for New Zealand archipelago. E. Barplot of CANAPE analysis for North Island. F. Barplot of CANAPE analysis for South Island. G. Barplot of CANAPE analysis for offshore islands. A, B: red values indicate cells that contain significantly less RPD and RPE than expected; blue values indicate cells that contain significantly more RPD and RPE than expected.