Dating nodes on molecular phylogenies: a critique of molecular biogeography

Aim To evaluate competing views on the origin and distribution of the New Zealand flora by testing the hypothesis that the geographical distribution of species is unrelated to ecological traits such as habitat requirements and dispersal capabilities. Location The New Zealand archipelago. Methods An analysis of the factors correlated with distribution and endemism for alpine plants within New Zealand, and for the New Zealand biota as a whole. Results Woody plants are highly endemic; nonendemic plants tend to be herbaceous and are concentrated among the highly dispersible ferns and fern allies, orchids and wetland plants. These groups make up 32% of the total flora but contribute 78% of nonendemics. Alpine plants with wide spatial distribution tend to have greater altitudinal ranges, a broader habitat preference and better dispersal ability. Main conclusions Most vascular plants reached New Zealand by long-distance transoceanic dispersal, probably during the Late Miocene to early Pleistocene period. During the Miocene and Pliocene, similar climates and landscapes to those of Australia and northern island groups, and highly invasible terrain, permitted dispersal of woody plants. Cooling climates and formation of a more mountainous, more compact landscape after that time reduced dispersal of woody plants and favoured herbaceous, wetland and highly dispersible plant groups. The prominence of dispersal has led to intense selective immigration, and is responsible for many characteristic features of the flora. Species selection by glacial‐ interglacial cycles has restricted acquisition or retention of cool or arid climate adaptations, particularly in the lowland flora. Endemic and range disjunction patterns in the New Zealand mainland are not, in general, directly caused by Pliocene inundations or the faulting and associated horizontal displacement of terrain that has continued since the Miocene. They have arisen mainly through Pleistocene extinctions, speciation and dispersal, and some patterns are strongly linked to repeated glaciation. Endemic centres are associated with differentiated terrain and climates providing isolation, distinctive environments, and habitat continuity conducive to speciation.

Endemism, species selection and the origin and distribution of the vascular plant flora of New Zealand.

New Zealand has long been a conundrum to biogeographers, possessing as it does geophysicalandbioticfeaturescharacteristicofbothanislandandacontinent.Thisschism is reflected in provocative debate among dispersalist, vicariance biogeographic and panbiogeographic schools. A strong history in biogeography has spawned many hypotheses, which have begun to be addressed by a flood of molecular analyses. The time is now ripe to synthesize these findings on a background of geological and ecological knowledge. It has become increasingly apparent that most of the biota of New Zealand has links with othersouthernlands(particularlyAustralia)thataremuchmorerecentthanthebreakupof Gondwana. A compilation of molecular phylogenetic analyses of ca 100 plant and animal groups reveals that only 10% of these are even plausibly of archaic origin dating to the vicariant splitting of Zealandia from Gondwana. Effects of lineage extinction and lack of goodcalibrationsinmanycasesstronglysuggestthattheactualproportionisevenlower,in keeping with extensive Oligocene inundation of Zealandia. A wide compilation of papers covering phylogeographic structuring of terrestrial, freshwater and marine species shows some patterns emerging. These include: east–west splits across the Southern Alps, east– west splits across North Island, north–south splits across South Island, star phylogenies of southern mountain isolates, spread from northern, central and southern areas of high endemism, and recent recolonization (postvolcanic and anthropogenic). Excepting the last ofthese,mostofthesepatternsseemtodatetolatePliocene,coincidingwiththerapiduplift of the Southern Alps. The diversity of New Zealand geological processes (sinking, uplift, tilting, sea level change, erosion, volcanism, glaciation) has produced numerous patterns, making generalizations difficult. Many species maintain pre-Pleistocene lineages, with phylogeographic structuring more similar to the Mediterranean region than northern Europe. This structure reflects the fact that glaciation was far from ubiquitous, despite the topography. Intriguingly, then, origins of the flora and fauna are island-like, whereas phylogeographic structure often reflects continental geological processes.

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New Zealand phylogeography: evolution on a small continent.

A reappraisal of the conservation status of the indigenous New Zealand vascular plant flora is presented. The list comprises 792 taxa (34% of New Zealand's total indigenous vascular flora) in the following categories: Extinct 4 taxa, Acutely Threatened 122 taxa (comprising 47 taxa Nationally Critical, 54 Nationally Endangered, 21 Nationally Vulnerable), Chronically Threatened 96 taxa (comprising Serious Decline 26 taxa, Gradual Decline 70 taxa), At Risk 499 taxa (comprising Sparse 126 taxa, Range Restricted 373 taxa), Non‐resident Native 26 taxa (comprising Vagrant 16 taxa, Colonist 10 taxa), and Data Deficient 45 taxa. A further 208 plants are listed as Taxonomically Indeterminate, being those which might warrant further conservation attention once their taxonomic status is clarified. A further 31 named taxa and 18 rated as Taxonomically Indeterminate, and previously considered to be threatened and/or uncommon, are removed from this updated listing. A concordance of plant names is provided. The ...

/pdf/threatened-and-uncommon-plants-of-new-zealand-4mktiiwfs7.pdf

Threatened and uncommon plants of New Zealand

Areas of endemism are central to cladistic biogeography. The concept has been much de- bated in the past, and from this has emerged the generally accepted definition as an area to which at least two species are endemic. Protocols for locating areas of endemism have been neglected, and to date no attempt has been made to develop optimality criteria against which to evaluate competing hypotheses of areas of endemism. Here various protocols for finding areas of endemism are evaluated-protocols based on both phenetic and parsimony analyses, on both unweighted data and data weighted by various criteria. The optimality criteria used to compare the performance of the methods include the number of species included in the areas of endemism, the number of areas delim- ited, and the degree of distributional congruency of the species restricted to each area of endemism. These methods are applied to the African Restionaceae in the Cape Floristic Region. Parsimony meth- ods using weighted data are shown to perform best on the combination of all three optimality criteria. By varying the weighting parameters, the size of the areas of endemism can be varied. This provides a very useful tool for locating areas of endemism that satisfy prespecified scale criteria. (Area of en- demism; biogeography; Cape Floristic Region; centers of endemism; parsimony analysis of endemism; Restionaceae.) Areas of endemism are central to the study of historical biogeography (Henderson, 1991). In the search for explanations of earth history based on biological patterns, ar- eas of endemism are the entities compared. Nelson and Platnick (1981:56) stated, "The most elementary questions of historical bio- geography concern areas of endemism and their relationships." By analogy to phyloge- netic systematics, where species or higher taxa are grouped, in cladistic biogeography the units grouped are areas of endemism. Humphries and Parenti (1999) maintained the same position almost 20 years later, when they described the basic question addressed in cladistic biogeography by asking, "Are areas of endemism interrelated among them- selves in a way analogous to the interrela- tionships of the species of a certain group of organisms?" Areas of endemism are proba- bly less important in the branch of histori- cal biogeography that seeks a geographical history of a particular taxon (Hovenkamp, 1997), because the distributions of individ- ual species can be used instead of areas of endemism. Even so, using areas of en- demism, rather than distributions of individ-

On Areas of Endemism, with an Example from the African Restionaceae

Attention is drawn to the parallel arc patterns permeating much of New Zealand biogeographic structure. The fracturing and creation of such parallel arcs by tectonic movement and erosion has brought about vast disjunctions in many plant and animal groups. The major arcs of distribution correlate with zones of tectonic activity such as plate and terrane margins, fracture zones, and belts of granitic intrusion. Other arcs may be the result of evolution along the Tertiary shores of inland bodies of water. The altitude of many communities in New Zealand also appears to conform to biogeographic and tectonic trends, with higher altitude communities having been derived by the uplift of mid-Tertiary lowland-coastal communities. Evolution is interpreted here as proceeding largely by phases of population reorganisation, for example in the formation of Cretaceous hybrid swarms, and “recrystallisation” in which ancient ranges are “frozen”, even in weedy taxa. Such processes correlate spatially with zones of ...

https://www.tandfonline.com/doi/pdf/10.1080/03014223.1989.10422922

Integrating earth and life sciences in New Zealand natural history: The parallel arcs model

Eighty taxa (subspecies, species, species groups, genera and families) showing disjunction along the New Zealand Alpine fault (Australian/Pacific plate boundary) are documented and mapped. Four plant divisions, including 14 seed plant families, and four animal phyla, including 13 orders of insects, are represented. The disjunction has usually been explained by glaciers having wiped out central populations. However, the gap is often occupied by a related taxon and many alpine taxa are involved, and so extinction by glaciation seems unlikely as an explanation. It is proposed that the disjunction has been caused by the 480 km of lateral displacement on the fault.

Biogeographic disjunction along the Alpine fault, New Zealand

The species ofAbrotanella(Compositae) form mats and cushions a few centimetres high and up to a metre or more in diameter. The flowers are less complex than those of most Compositae and lack a pappus, the usual means of dispersal in the family. There are 20 species, all restricted to mountains of Australasia and southern South America. The putative affinities ofAbrotanellainvolve several tribes of Compositae and the genus is not considered derived within the family. A comparative analysis of areas of endemism inAbrotanellashows clear patterns of vicariance and disjunction shared with many plants and animals, and long-distance dispersal is rejected as an explanation.Abrotanellaand the three genera related to it are all restricted to lands bordering the Pacific. Areas previously accepted as areas of endemism, such as New Guinea, Tasmania, New Zealand and southern South America, are shown to be polyphyletic complexes, rather than simple areas. Use of such areas in area cladograms leads to the erroneous interpretation of taxa-area relations as incongruent. Distributions of the taxa inAbrotanellaare correlated with tectonic features such as plate margins, transform faults and fracture zones, and processes such as continental rifting, terrane accretion, granite emplacement and orogeny.Abrotanella patearoasp. nov., a high-alpine cushion-plant, is described from mountains of eastern Central Otago: Rock and Pillar Range, Lammerlaw Range, Umbrella Mountains and Garvie Mountains.

Vicariance biogeography and terrane tectonics in the South Pacific: analysis of the genus Abrotanella (Compositae)

Regional patterns of biodiversity in New Zealand are illustrated by showing numbers of species in 1° latitude × 1° longitude grid squares. Biodiversity maps are given for twelve speciose groups of lichens, plants and animals which have been recently taxonomically revised. Centres of biodiversity are evident in Nelson and Otago. Other groups would probably highlight Canterbury/north Otago. The different roles of location and environment in the origin and preservation of these patterns of biodiversity are discussed.

https://www.tandfonline.com/doi/pdf/10.1080/03014223.1997.9517542

Michael Heads

Papers

Integrating earth and life sciences in New Zealand natural history: The parallel arcs model

Biogeographic disjunction along the Alpine fault, New Zealand

Vicariance biogeography and terrane tectonics in the South Pacific: analysis of the genus Abrotanella (Compositae)

Regional patterns of biodiversity in New Zealand: One degree grid analysis of plant and animal distributions

Biodiversity in the New Zealand divaricating tree daisies: Olearia sect. nov. (Compositae)