Systematics of Andean Lupinus L. and the origin of L. mutabilis Sweet

Eastwood, RJ

Abstract:: This thesis contributes to the central goals of systematics - the inventory of species, building the tree of life and understanding evolutionary processes - through a descriptive taxonomic study, molecular phylogenetic analysis and morphological survey of the genus Lupinus L.

Lupinus comprises ca. 290 annual and perennial species placed in the Genistoid clade of the Papilionoid legumes. In this study three new DNA sequence datasets are used to reconstruct species relationships. The new phylogeny is used to investigate character evolution, species diversification, domestication and as the basis for a new infrageneric classification.

Approaches to plant species-level phylogeny reconstruction and criteria for selecting DNA sequence loci are evaluated from a theoretical standpoint, and experimental work to develop hypervariable nuclear DNA sequence loci is presented.

The comparative morphology of Lupinus species is investigated and presented. This includesstudies of seed coats, cotyledons, leaves, and chromosomes. Optimisation of these data onto the 3-locus phylogeny reveals congruence between chromosome number and geographyand shows that non-digitate leaves have evolved twice independently within Lupinus.

Evolutionary rates analysis is used to estimate divergence times for clades and to investigate the tempo of species diversification. Notably, a strongly supported clade representing ca. 81 Andean species is estimated to be 1.18-1.76 Myr, implying a diversification rate of 2.49-3.72 species per Myr. This exceeds previous estimates for plants providing the most spectacular example of explosive plant species diversification documented to date.

Lupin species have been independently domesticated as grain legume crops in the Old and New Worlds. The origins of the Andean domesticate, L. mutabilis, are investigated. Lack of resolution amongst the Andean species, attributable to exceptionally rapid species diversification, meant that the progenitor(s) of L. mutabilis could not be firmly established. However, four Andean species are tentatively identified as closely related to L. mutabilis based on morphology. A taxonomic account of these species is presented.

Finally, a new infrageneric classification based on morphological diagnosability monophyly is proposed.

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APA Style

Eastwood, R. J. (2006). Systematics of Andean Lupinus L. and the origin of L. mutabilis Sweet [PhD thesis]. University of Oxford.

MLA Style

Eastwood, R. J. Systematics of Andean Lupinus L. and the Origin of L. Mutabilis Sweet. University of Oxford, 2006.

Chicago Style

Eastwood, RJ. 2006. “Systematics of Andean Lupinus L. and the Origin of L. Mutabilis Sweet.” PhD thesis, University of Oxford.
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Files:: Eastwood_DPhil 2006.pdf

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Authors

+ Eastwood, RJ More by this author

Division:: MPLS
Department:: Plant Sciences
Role:: Author

Contributors

+ Hughes, C

Role:: Supervisor

+ Biotechnology and Biological Sciences Research Council More from this funder

Funding agency for:: Eastwood, RJ

+ The Genetics Society More from this funder

DOI:: 10.5287/ora-erpkqz169
Type of award:: DPhil
Level of award:: Doctoral
Awarding institution:: University of Oxford

Language:: English
Keywords:: Molecular phylogeny

Phylogeny

Seed size

Taxonomic accounts

Evolution

Leaf morphology

Lupin

Lupinus

Species diversification

Character evolution

Radiation

Plant diversification

Andes

Classification

Domestication
Subjects:: Systematics

Botany

Taxonomy
UUID:: uuid:49d11015-d1a2-4893-9df5-02ea08331520
Deposit date:: 2020-03-10

Related item:: Multiple Continental Radiations and Correlates of Diversification in Lupinus (Leguminosae): Testing for Key Innovation with Incomplete Taxon Sampling
Description:: Replicate radiations provide powerful comparative systems to address questions about the interplay between opportunity and innovation in driving episodes of diversification and the factors limiting their subsequent progression. However, such systems have been rarely documented at intercontinental scales. Here, we evaluate the hypothesis of multiple radiations in the genus Lupinus (Leguminosae), which exhibits some of the highest known rates of net diversification in plants. Given that incomplete taxon sampling, background extinction, and lineage-specific variation in diversification rates can confound macroevolutionary inferences regarding the timing and mechanisms of cladogenesis, we used Bayesian relaxed clock phylogenetic analyses as well as MEDUSA and BiSSE birth-death likelihood models of diversification, to evaluate the evolutionary patterns of lineage accumulation in Lupinus. We identified 3 significant shifts to increased rates of net diversification (r) relative to background levels in the genus (r = 0.18-0.48 lineages/myr). The primary shift occurred approximately 4.6 Ma (r = 0.48-1.76) in the montane regions of western North America, followed by a secondary shift approximately 2.7 Ma (r = 0.89-3.33) associated with range expansion and diversification of allopatrically distributed sister clades in the Mexican highlands and Andes. We also recovered evidence for a third independent shift approximately 6.5 Ma at the base of a lower elevation eastern South American grassland and campo rupestre clade (r = 0.36-1.33). Bayesian ancestral state reconstructions and BiSSE likelihood analyses of correlated diversification indicated that increased rates of speciation are strongly associated with the derived evolution of perennial life history and invasion of montane ecosystems. Although we currently lack hard evidence for "replicate adaptive radiations" in the sense of convergent morphological and ecological trajectories among species in different clades, these results are consistent with the hypothesis that iteroparity functioned as an adaptive key innovation, providing a mechanism for range expansion and rapid divergence in upper elevation regions across much of the New World.
Related item:: Lost crops of the Incas: origins of domestication of the Andean pulse crop 'tarwi', Lupinus mutablis
Description:: PREMISE OF THE STUDY: The Andean highlands are a hotspot of domestication, yet our understanding of the origins of early Andean agriculture remains fragmentary. Key questions of where, when, how many times, and from what progenitors many Andean crops were domesticated remain unanswered. The Andean lupine crop tarwi (Lupinus mutabilis) is a regionally important pulse crop with exceptionally high seed protein and oil content and is the focus of modern breeding efforts, but its origins remain obscure.METHODS: A large genome-wide DNA polymorphism data set was generated using nextRADseq to infer relationships among more than 200 accessions of Andean Lupinus species, including 24 accessions of L. mutabilis and close relatives. Phylogenetic and demographic analyses were used to identify the likely progenitor of tarwi and elucidate the area and timing of domestication in combination with archaeological evidence.KEY RESULTS: We infer that tarwi was domesticated once in northern Peru, most likely in the Cajamarca region within, or adjacent to the extant distribution of L. piurensis, which is the most likely wild progenitor. Demographic analyses suggest that tarwi split from L. piurensis around 2600 BP and suffered a classical domestication bottleneck. The earliest unequivocal archaeological evidence of domesticated tarwi seeds is from the Mantaro Valley, central Peru ca. 1800 BP.CONCLUSIONS: A single origin of tarwi from L. piurensis in northern Peru provides a robust working hypothesis for the domestication of this regionally important crop and is one of the first clear-cut examples of a crop originating in the highlands of northern Peru.
Related item:: Diversity and evolutionary history of Lupins - Insights from new phylogenies
Description:: Insights into the diversity and evolutionary and biogeographical history of lupins have been limited by confusion about species delimitation, conflicting nomenclature, as well as sparse sampling and lack of resolution in previous phylogenetic studies. Over the last two years we have published a series of more densely sampled (including c. 40% of lupin species), well-resolved, and robustly supported time calibrated phylogenies, based on DNA sequences from multiple nuclear and plastid genes. In addition, a large number of new chromosome counts have been published for New World species. Here we present an overview of these new phylogenies and the insights they provide into species relationships, the evolution of chromosome number, life history and leaf morphology, in addition to the geographical and temporal patterns of species diversification.Revised estimates suggest that there are c. 280 species in the genus. While some uncertainty remains as to the precise sister group relationships of the 13 Old World species, current data suggest that the ancestral range for the genus is in the Old World, with at least two independent dispersal events to the New World within the last 5-10 million years. The New World species (excluding the unifoliolate species from Florida) are placed in two robustly supported clades: (i) an eastern, largely lowland 2n = 36 clade comprising c. 35 species and (ii) a western, largely montane 2n = 48 clade comprising c. 225 species. These two clades are distributed largely allopatrically with only limited overlap in Texas and the south-central Andes, but both contain ancestral North American and derived South American elements, suggesting at least two independent dispersal events between North America and South America. These new phylogenies also provide clear evidence for two independent evolutionary origins of unifoliolate leaves in Florida and Brazil (congruent with chromosome data), resolving longstanding debate about the relationships of these two groups. Of particular note is the exceptionally high rate of diversification in the western New World 2n = 48 clade. In this group a rapid rate of speciation coincides with the transition from annual to perennial life history and colonisation of montane habitats, permitting the exploitation of novel ecological opportunities following recent uplift of the northern Andes. Further work is needed to confirm whether there have been two independent radiations of the western North American perennials and Andean species, or a single larger radiation of the western New World species. Based on these results a number of well-supported clades which are also diagnosable using non-molecular characters, provide the foundation for development of a new infrageneric classification.
Related item:: Origins of domestication of Lupinus mutabilis in the Andes
Description:: Lupinus mutabilis Sweet is apparently unknown in the wild but is cultivated as an important food crop throughout the Andes and is also the focus of crop breeding and development elsewhere in Australia and Europe. The species exhibits many of the typical legume domestication syndrome traits including indehiscent pods, large seeds, water permeable seed coats, reduced seed pigmentation, rapid and uniform germination and growth, and a nearly annual life history, but retains higher seed alkaloid levels than other lupin domesticates. Despite this importance as a crop, the origins of domestication of L. mutabilis in terms of where, when, how many times and from what wild progenitors it was domesticated remain unknown. Our phylogenetic studies place L. mutabilis in a well-supported Andean clade, ruling out earlier speculations that the crop might have originated from wild North American species. However, within the Andes, research to identify theprogenitors of L. mutabilis is hampered by chaotic taxonomy, the very low levels of DNA sequence divergence amongst the Andean species, and very limited lupin seed remains retrieved from archaeological sites. Low DNA sequence divergencehas been attributed to exceptionally rapid species diversification in the Andes, and makes it difficult to employ conventional DNA sequence data to analysespecies relationships among the ca. 81 species in this Andean group and hence to identify the close relatives and putative progenitors of L. mutabilis.Despite these challenges, recent field, herbarium and laboratory investigation of L. mutabilis provide new evidence from morphology (leaves, indumentum, habit, flower size, flower colour variation, pod and seed size) and DNA sequence data that suggest L. piurensis as the most likely wild progenitor of domesticated L. mutabilis. This species has not previously been proposed as a putative progenitor of L. mutabilis despite its clear morphological similarities and large seeds. L. piurensis is restricted to the western slopes of the Andes between 1650 and 3300 m altitude in northern Peru and southern Ecuador, suggesting that domestication of L. mutabilis may have occurred in northern Peru. A limited number of flower and seed colour variants are documented within L. mutabilis, but in many respects the species is rather uniform.
Related item:: Island radiation on a continental scale: exceptional rates of plant diversification after uplift of the Andes
Description:: Species radiations provide unique insights into evolutionary processes underlying species diversification and patterns of biodiversity. To compare plant diversification over a similar time period to the recent cichlid fish radiations, which are an order of magnitude faster than documented bird, arthropod, and plant radiations, we focus on the high-altitude flora of the Andes, which is the most species-rich of any tropical mountains. Because of the recent uplift of the northern Andes, the upland environments where much of this rich endemic flora is found have been available for colonization only since the late Pliocene or Pleistocene, 2–4 million years (Myr) ago. Using DNA sequence data we identify a monophyletic group within the genus Lupinus representing 81 species endemic to the Andes. The age of this clade is estimated to be 1.18–1.76 Myr, implying a diversification rate of 2.49–3.72 species per Myr. This exceeds previous estimates for plants, providing the most spectacular example of explosive plant species diversification documented to date. Furthermore, it suggests that the high cichlid diversification rates are not unique. Lack of key innovations associated with the Andean Lupinus clade suggests that diversification was driven by ecological opportunities afforded by the emergence of island-like habitats after Andean uplift. Data from other genera indicate that lupines are one of a set of similarly rapid Andean plant radiations, continental in scale and island-like in stimulus, suggesting that the high-elevation Andean flora provides a system that rivals other groups, including cichlids, for understanding rapid species diversification.
Related item:: From famine to feast? Selecting nuclear DNA sequence loci for plant species-level phylogeny reconstruction
Description:: Phylogenetic analyses of DNA sequences have prompted spectacular progress in assembling the Tree of Life. However, progress in constructing phylogenies among closely related species, at least for plants, has been less encouraging. We show that for plants, the rapid accumulation of DNA characters at higher taxonomic levels has not been matched by conventional sequence loci at the species level, leaving a lack of well-resolved gene trees that is hindering investigations of many fundamental questions in plant evolutionary biology. The most popular approach to address this problem has been to use low-copy nuclear genes as a source of DNA sequence data. However, this has had limited success because levels of variation among nuclear intron sequences across groups of closely related species are extremely variable and generally lower than conventionally used loci, and because no universally useful low-copy nuclear DNA sequence loci have been developed. This suggests that solutions will, for the most part, be lineage-specific, prompting a move away from ‘universal’ gene thinking for species-level phylogenetics. The benefits and limitations of alternative approaches to locate more variable nuclear loci are discussed and the potential of anonymous non-genic nuclear loci is highlighted. Given the virtually unlimited number of loci that can be generated using these new approaches, it is clear that effective screening will be critical for efficient selection of the most informative loci. Strategies for screening are outlined.
Related item:: 878. LUPINUS MUTABILIS
Description:: Lupinus mutabilis Sweet is illustrated. The history of its cultivation and domestication is described, nomenclature and typification are discussed, and a full description, two paintings, an illustration and a distribution map are presented.

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