Aelys M. Humphreys

Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data

Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The generalised mixed Yule coalescent (GMYC) and the Poisson tree process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such as DNA barcodes. Here, we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothing methods. We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2000 separate species delimitation analyses across 16 empirical data sets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods. The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification. Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model-based gene tree (e.g. RAxML) and GMYC approaches with BEAST trees for obtaining species hypotheses.

Reticulation, data combination, and inferring evolutionary history: an example from Danthonioideae (Poaceae).

We explore the potential impact of conflicting gene trees on inferences of evolutionary history above the species level. When conflict between gene trees is discovered, it is common practice either to analyze the data separately or to combine the data having excluded the conflicting taxa or data partitions for those taxa (which are then recoded as missing). We demonstrate an alternative approach, which involves duplicating conflicting taxa in the matrix, such that each duplicate is represented by one partition only. This allows the combination of all available data in standard phylogenetic analyses, despite reticulations. We show how interpretation of contradictory gene trees can lead to conflicting inferences of both morphological evolution and biogeographic history, using the example of the pampas grasses, Cortaderia. The characteristic morphological syndrome of Cortaderia can be inferred as having arisen multiple times (chloroplast DNA [cpDNA]) or just once (nuclear ribosomal DNA [nrDNA]). The distributions of species of Cortaderia and related genera in Australia/New Guinea, New Zealand, and South America can be explained by few (nrDNA) or several (cpDNA) dispersals between the southern continents. These contradictions can be explained by past hybridization events, which have linked gains of complex morphologies with unrelated chloroplast lineages and have erased evidence of dispersals from the nuclear genome. Given the discrepancies between inferences based on the gene trees individually, we urge the use of approaches such as ours that take multiple gene trees into account.

A Generic Classification of the Danthonioideae (Poaceae)1

Abstract We present a new generic classification of the largely Southern Hemisphere grass subfamily Danthonioideae. This classification is based on an almost completely sampled and well-resolved molecular phylogeny and on a complete morphological data set. We have attempted to delimit monophyletic genera (complicated by the presence of apparent intergeneric hybridization), which are diagnosable, as well as morphologically and ecogeographically coherent. We recognize 17 genera, including five new genera (Austroderia N. P. Barker & H. P. Linder, Capeochloa H. P. Linder & N. P. Barker, Chimaerochloa H. P. Linder, Geochloa H. P. Linder & N. P. Barker, and Tenaxia N. P. Barker & H. P. Linder), and two sections newly designated for Pentameris P. Beauv. (section Dracomontanum H. P. Linder & Galley and section Pentaschistis (Nees) H. P. Linder & Galley). Of the remaining 12 genera, the delimitations of seven are changed: Merxmuellera Conert is much reduced by the segregation of Geochloa, Capeochloa, and Tenaxia; Pentameris is expanded to include Prionanthium Desv. and Pentaschistis (Nees) Spach; Cortaderia Stapf is expanded by the inclusion of Lamprothyrsus Pilg., but reduced by the segregation of its New Zealand species into the new genus Austroderia; a large Rytidosperma Steud. is assembled out of Joycea H. P. Linder, Austrodanthonia H. P. Linder, Notodanthonia Zotov, Erythranthera Zotov, Pyrrhanthera Zotov, and Monostachya Merr.; and the species previously assigned to Karroochloa Conert & Türpe, Schismus P. Beauv., Urochlaena Nees, and Tribolium Desv. have been reassigned to only two genera. Finally, the Himalayan species of Danthonia DC. are transferred to Tenaxia and the remaining African species of Danthonia to Merxmuellera. The 281 species that we recognize in the subfamily are listed under their new genera, which are arranged in the phylogenetic sequence evident from the molecular phylogeny. The 100 necessary new combinations include: Merxmuellera grandiflora (Hochst. ex A. Rich.) H. P. Linder, Geochloa decora (Nees) N. P. Barker & H. P. Linder, G. lupulina (L. f.) N. P. Barker & H. P. Linder, G. rufa (Nees) N. P. Barker & H. P. Linder, Capeochloa arundinacea (P. J. Bergius) N. P. Barker & H. P. Linder, C. cincta (Nees) N. P. Barker & H. P. Linder, C. cincta subsp. sericea (N. P. Barker) N. P. Barker & H. P. Linder, C. setacea (N. P. Barker) N. P. Barker & H. P. Linder, Pentameris praecox (H. P. Linder) Galley & H. P. Linder, P. tysonii (Stapf) Galley & H. P. Linder, P. acinosa (Stapf) Galley & H. P. Linder, P. airoides Nees subsp. jugorum (Stapf) Galley & H. P. Linder, P. alticola (H. P. Linder) Galley & H. P. Linder, P. ampla (Nees) Galley & H. P. Linder, P. andringitrensis (A. Camus) Galley & H. P. Linder, P. argentea (Stapf) Galley & H. P. Linder, P. aristidoides (Thunb.) Galley & H. P. Linder, P. aristifolia (Schweick.) Galley & H. P. Linder, P. aspera (Thunb.) Galley & H. P. Linder, P. aurea (Steud.) Galley & H. P. Linder, P. aurea subsp. pilosogluma (McClean) Galley & H. P. Linder, P. bachmannii (McClean) Galley & H. P. Linder, P. barbata (Nees) Steud. subsp. orientalis (H. P. Linder) Galley & H. P. Linder, P. basutorum (Stapf) Galley & H. P. Linder, P. borussica (K. Schum.) Galley & H. P. Linder, P. calcicola (H. P. Linder) Galley & H. P. Linder, P. calcicola var. hirsuta (H. P. Linder) Galley & H. P. Linder, P. capensis (Nees) Galley & H. P. Linder, P. capillaris (Thunb.) Galley & H. P. Linder, P. caulescens (H. P. Linder) Galley & H. P. Linder, P. chippindalliae (H. P. Linder) Galley & H. P. Linder, P. chrysurus (K. Schum.) Galley & H. P. Linder, P. clavata (Galley) Galley & H. P. Linder, P. colorata (Steud.) Galley & H. P. Linder, P. dentata (L. f.) Galley & H. P. Linder, P. dolichochaeta (S. M. Phillips) Galley & H. P. Linder, P. ecklonii (Nees) Galley & H. P. Linder, P. exserta (H. P. Linder) Galley & H. P. Linder, P. galpinii (Stapf) Galley & H. P. Linder, P. holciformis (Nees) Galley & H. P. Linder, P. horrida (Galley) Galley & H. P. Linder, P. humbertii (A. Camus) Galley & H. P. Linder, P. insularis (Hemsl.) Galley & H. P. Linder, P. juncifolia (Stapf) Galley & H. P. Linder, P. longipes (Stapf) Galley & H. P. Linder, P. malouinensis (Steud.) Galley & H. P. Linder, P. microphylla (Nees) Galley & H. P. Linder, P. minor (Ballard & C. E. Hubb.) Galley & H. P. Linder, P. montana (H. P. Linder) Galley & H. P. Linder, P. natalensis (Stapf) Galley & H. P. Linder, P. oreodoxa (Schweick.) Galley & H. P. Linder, P. pallida (Thunb.) Galley & H. P. Linder, P. pholiuroides (Stapf) Galley & H. P. Linder, P. pictigluma (Steud.) Galley & H. P. Linder, P. pictigluma var. gracilis (S. M. Phillips) Galley & H. P. Linder, P. pictigluma var. mannii (Stapf ex C. E. Hubb.) Galley & H. P. Linder, P. pseudopallescens (H. P. Linder) Galley & H. P. Linder, P. pungens (H. P. Linder) Galley & H. P. Linder, P. pusilla (Nees) Galley & H. P. Linder, P. pyrophila (H. P. Linder) Galley & H. P. Linder, P. reflexa (H. P. Linder) Galley & H. P. Linder, P. rigidissima (Pilg. ex H. P. Linder) Galley & H. P. Linder, P. rosea (H. P. Linder) Galley & H. P. Linder, P. rosea subsp. purpurascens (H. P. Linder) Galley & H. P. Linder, P. scandens (H. P. Linder) Galley & H. P. Linder, P. setifolia (Thunb.) Galley & H. P. Linder, P. tomentella (Stapf) Galley & H. P. Linder, P. trifida (Galley) Galley & H. P. Linder, P. triseta (Thunb.) Galley & H. P. Linder, P. trisetoides (Hochst. ex Steud.) Galley & H. P. Linder, P. velutina (H. P. Linder) Galley & H. P. Linder, P. veneta (H. P. Linder) Galley & H. P. Linder, Cortaderia hieronymi (Kuntze) N. P. Barker & H. P. Linder, C. peruviana (Hitchc.) N. P. Barker & H. P. Linder, Austroderia fulvida (Buchanan) N. P. Barker & H. P. Linder, A. richardii (Endl.) N. P. Barker & H. P. Linder, A. splendens (Connor) N. P. Barker & H. P. Linder, A. toetoe (Zotov) N. P. Barker & H. P. Linder, A. turbaria (Connor) N. P. Barker & H. P. Linder, Chimaerochloa archboldii (Hitchc.) Pirie & H. P. Linder, Tenaxia aureocephala (J. G. Anderson) N. P. Barker & H. P. Linder, T. cachemyriana (Jaub. & Spach) N. P. Barker & H. P. Linder, T. cumminsii (Hook. f.) N. P. Barker & H. P. Linder, T. disticha (Nees) N. P. Barker & H. P. Linder, T. dura (Stapf) N. P. Barker & H. P. Linder, T. guillarmodiae (Conert) N. P. Barker & H. P. Linder, T. stricta (Schrad.) N. P. Barker & H. P. Linder, T. subulata (A. Rich.) N. P. Barker & H. P. Linder, Schismus schismoides (Stapf ex Conert) Verboom & H. P. Linder, Tribolium curvum (Nees) Verboom & H. P. Linder, T. pleuropogon (Stapf) Verboom & H. P. Linder, T. purpureum (L. f.) Verboom & H. P. Linder, T. tenellum (Nees) Verboom & H. P. Linder, Rytidosperma bipartitum (Kunth) A. M. Humphreys & H. P. Linder, R. diemenicum (D. I. Morris) A. M. Humphreys & H. P. Linder, R. fulvum (Vickery) A. M. Humphreys & H. P. Linder, R. lepidopodum (N. G. Walsh) A. M. Humphreys & H. P. Linder, R. pallidum (R. Br.) A. M. Humphreys & H. P. Linder, R. popinensis (D. I. Morris) A. M. Humphreys & H. P. Linder, R. remotum (D. I. Morris) A. M. Humphreys & H. P. Linder. Typifications are designated for the following names: Achneria Munro ex Benth. & Hook. f., Avena aristidoides Thunb., A. elephantina Thunb., Danthonia crispa Nees var. trunculata Nees, Danthonia sect. Himantochaete Nees, D. zeyheriana Steud. var. trichostachya Stapf, Geochloa lupulina, Pentameris aristidoides, and P. holciformis.

The evolutionary reality of higher taxa in mammals

Species are generally regarded as a fundamental unit of biodiversity. By contrast, higher taxa such as genera and families, while widely used as biodiversity metrics and for classification and communication, are generally not believed to be shaped by shared evolutionary processes in the same way as species. We use simulations to show that processes which are important for emergence of evolutionarily significant units (ESUs) at the species level, namely geographical isolation and ecological divergence, can generate evolutionary independence above the species level and thereby lead to emergence of discrete phylogenetic clusters (higher ESUs). Extending phylogenetic approaches for delimiting evolutionarily significant species to broader phylogenetic scales, we find evidence for the existence of higher ESUs in mammals. In carnivores, euungulates and lagomorphs the hierarchical level of units detected correspond, on average, to the level of family or genus in traditional taxonomy. The units in euungulates are associated with divergent patterns of body mass, consistent with occupation of distinct ecological zones. Our findings demonstrate a new framework for studying biodiversity that unifies approaches at species and higher levels, thus potentially restoring higher taxa to their historical status as natural entities.

Absence of mammals and the evolution of New Zealand grasses

Anthropogenic alteration of biotic distributions and disturbance regimes has dramatically changed the evolutionary context for the differentiation of species traits. Some of the most striking examples in recent centuries have been on islands where flightless birds, which evolved in the absence of mammalian carnivores, have been decimated following the widespread introduction of exotic predators. Until now, no equivalent case has been reported for plants. Here, we make use of robust analytical tools and an exceptionally well-sampled molecular phylogeny to show that a majority of New Zealand danthonioid grasses (Poaceae) may have adapted to the relaxed vertebrate herbivore pressure during the late Cenozoic through the development of a distinctive and unusual habit: abscission of old leaves. This feature occurs in only about 3 per cent of the worlds roughly 11 000 grass species and has been empirically shown to increase plant productivity but to reduce protection against mammal grazing. This result suggests that release from a selective pressure can lead to species radiations. This seemingly anachronistic adaptation may represent an overlooked factor contributing to the severe decline in the geographical extent and species diversity of New Zealands indigenous grasslands following the introduction of herbivorous terrestrial mammals in the 19th century.

New insights into the evolutionary history of Gnetum (Gnetales)

Gnetum (Gnetales: Gnetaceae) constitutes an evolutionarily isolated gymnosperm clade, comprising about 40 species that inhabit tropical areas of the world. While its closest living relative, the mo ...

Pollen morphology of Ephedra (Gnetales) and its evolutionary implications

Abstract The Ephedra lineage can be traced at least to the Early Cretaceous. Its characteristically polyplicate pollen is well-represented in the fossil record and is frequently used as an indicator of paleoclimate. However, despite previous efforts, knowledge about variation and evolution of ephedroid pollen traits is poor. Here, we document pollen morphology of nearly all extant species of Ephedra, using a combination of scanning electron microscopy (SEM) and light microscopy (LM), and reconstruct ancestral states of key pollen traits. Our results indicate that the ancestral Ephedra pollen type has numerous plicae interspaced by unbranched pseudosulci, while the derived pollen type has branched pseudosulci and (generally) fewer plicae. The derived type is inferred to have evolved independently twice, once along the North American stem branch and once along the Asian stem branch. Pollen of the ancestral type is common in Mesozoic fossil records, especially from the Early Cretaceous, but it is less commonly reported from the Cenozoic. The earliest documentation of the derived pollen type is from the latest Cretaceous, after which it increases strongly in abundance during the Paleogene. The results of the present study have implications for the age of crown group Ephedra as well as for understanding evolution of pollination syndromes in the genus.

A plastid tree can bring order to the chaotic generic taxonomy of Rytidosperma Steud. s.l. (Poaceae)

Rytidosperma s.l., wallaby grasses and allies, is in dire need of a single, unanimously accepted generic taxonomy. Motivated by the desire to establish a generic classification that complies with phylogeny, we investigated how much phylogenetic signal is contained within a plastid (cpDNA) tree, given that the nrDNA tree (ITS) was uninformative and that a phylogenetic hypothesis based on a single genome may not be reliable. We find that the plastid tree is significantly different from a morphological cladogram and show that this is the result of homoplasy in the morphological dataset. Treated individually, several morphological characters fit the plastid tree very well. Similarly, we find a good fit of the plastid tree with ecological and distribution characters and with biogeographical patterns in the Southern Hemisphere. We conclude that a significant level of the species phylogeny is resolved by the plastid tree and are confident it can form a sound basis for a reconsideration of generic limits. None of the currently recognised seven genera in the Rytidosperma clade is monophyletic. Therefore, we propose combining the segregate genera in Australasia within a broadly construed Rytidosperma, including all the species from Australia, New Guinea, New Zealand and South America.