Richard Ian Milne

Richard Ian Milne
The University of Edinburgh | UoE · Institute of Molecular Plant Sciences

About

188
Publications
46,204
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4,657
Citations
Citations since 2016
87 Research Items
2564 Citations
20162017201820192020202120220100200300400
20162017201820192020202120220100200300400
20162017201820192020202120220100200300400
20162017201820192020202120220100200300400

Publications

Publications (188)
Article
Long-distance dispersal (LDD) beyond the range of a species is an important driver of ecological and evolutionary patterns, but insufficient attention has been given to postdispersal establishment. In this review, we summarize current knowledge of the post-LDD establishment phase in plant colonization, identify six key determinants of establishment...
Preprint
Mountainous regions can promote complex speciation scenarios, including hybridization leading to chloroplast capture, revealed by incongruent phylogenetic trees. Four allopatric Taxus lineages from the Hengduan Mountains, southwestern China, exhibit cytonuclear phylogenetic discordance. We use multi-omic data at the population level to investigate...
Article
Background and aims: Rhododendron is a species-rich and taxonomically challenging genus due to recent adaptive radiation and frequent hybridization. A well resolved phylogenetic tree is conducive to understanding the diverse history of Rhododendron in the Himalaya-Hengduan Mountains where the genus is most diverse. Methods: We reconstructed the...
Article
Full-text available
Comparing gene expressions among parasitic plants infecting different host species can have significant implications for understanding host-parasite interactions. Taxillus nigrans is a common hemiparasitic species in Southwest China that parasitizes a variety of host species. However, a lack of nucleotide sequence data to date has hindered transcri...
Article
Full-text available
Persian (Common) walnut (Juglans regia L.) is a famous fruit tree species valued for its nutritious nuts and high-quality wood. Although walnut is widely distributed and plays an important role in the economy and culture of Pakistan, the genetic diversity and structure of its populations in the country remains poorly understood. Therefore, using 31...
Article
Climate change and geological events have long been known to shape biodiversity, implying that these can likewise be viewed from a biological perspective. To study whether plants can shed light on this, and how they responded to climate change there, we examined Oreocnide, a genus widely distributed in SE Asia. Based on broad geographic sampling wi...
Article
Full-text available
Habitat loss induced by climate warming is a major threat to biodiversity, particularly to threatened species. Understanding the genetic diversity and distributional responses to climate change of threatened species are critical to facilitate their conservation and management. Cupressus gigantea, a rare conifer found in the eastern Qinghai‐Tibet Pl...
Article
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Understanding the genetic diversity of wild populations is fundamental to conserving species in-situ and ex-situ. To aid conservation plans and to inform ex-situ conservation, we examined the genetic diversity of the cycad Cycas calcicola (Cycadaceae). Samples were collected from wild populations in the Litchfield National Park and Katherine region...
Article
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Intra-specific genetic diversity is a fundamental component of biodiversity, and is key to species adaptation and persistence. However, significant knowledge gaps still exist in our understanding of the patterns of genetic diversity and their key determinants. Most previous investigations mainly utilized single-species and/or a limited number of ex...
Article
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Urticeae s.l, a tribe of Urticaceae well-known for their stinging trichomes, consists of more than 10 genera and approximately 220 species. Relationships within this tribe remain poorly known due to the limited molecular and taxonomic sampling of previous studies, and chloroplast genome (CP genome/plastome) evolution is still largely unaddressed. T...
Article
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Inferring accurate biogeographic history of plant taxa with an East Asia (EA)-North America (NA) is usually hindered by conflicting phylogenies and a poor fossil record. The current distribution of Chamaecyparis (false cypress; Cupressaceae) with four species in EA, and one each in western and eastern NA, and its relatively rich fossil record, make...
Article
Background and Aims Many angiosperms can secrete both floral (FN) and extrafloral (EFN) nectar. However, much remains unclear about how EFN and FN differ in secretion, composition and ecological function, especially when both FN and EFN are secreted on flowers of the same species. Methods Hemerocallis citrina flowers secrete both FN and EFN. FN an...
Article
Global climate changes during the Miocene may have created ample opportunities for hybridization between members of tropical and subtropical biomes at the boundary between these zones. Yet, very few studies have explored this possibility. The Yunnan-Guizhou Plateau (YGP) in Southwest China is a biodiversity hotspot for vascular plants, located in a...
Article
Full-text available
Recent advancements in whole genome sequencing techniques capable of covering nearly all the nucleotide variations of a genome, would make it possible to set up a conservation framework for threatened plants at the genomic level. Here we applied a whole genome resequencing approach to obtain genome-wide data from 105 individuals sampled from the te...
Article
The Eastern Asia (EA) – North America (NA) disjunction is a well-known biogeographic pattern of the Tertiary relict flora; however, few studies have investigated the evolutionary history of this disjunction using a phylogenomic approach. Here, we used 2369 single copy nuclear genes and nearly full plastomes to reconstruct the evolutionary history o...
Article
Full-text available
Background and aims: Understanding the population genetics and evolutionary history of endangered species is urgently needed in an era of accelerated biodiversity loss. This knowledge is most important for regions with high endemism that are ecologically vulnerable, such as the Qinghai-Tibet Plateau (QTP). Methods: The genetic variation of 84 ju...
Article
Walnuts are highly valued for their rich nutritional profile and wide medicinal applications. This demand has led to the intensification of breeding activities in major walnut production areas such as southwest China, in order to develop more superior cultivars. With the increasing number of cultivars, accurate identification becomes fundamental to...
Article
Extinct taxa may be detectable if they were ancestors to extant hybrid species, which retain their genetic signature. In this study, we combined phylogenomics, population genetics and fluorescence in situ hybridization (GISH and FISH) analyses to trace the origin of the alpine tetraploid Allium tetraploideum (2n = 4x = 32), one of the five known me...
Article
Full-text available
Mountain ecosystems support a significant one-third of all terrestrial biodiversity, but our understanding of the spatiotemporal maintenance of this high biodiversity remains poor, or at best controversial. The Himalaya hosts a complex mountain ecosystem with high topographic and climatic heterogeneity and harbors one of the world's richest floras....
Article
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Understanding processes that generate and maintain large disjunctions within plant species can provide valuable insights into plant diversity and speciation. The butterfly bush Buddleja alternifolia has an unusual disjunct distribution, occurring in the Himalaya, Hengduan Mountains (HDM) and the Loess Plateau (LP) in China. We generated a high‐qual...
Article
Background Leaf functional traits can influence the ability of plants to grow when facing stresses. Climate changes can impose fundamental impacts on plant growth, especially at high mountains. Yet little is known about relationships between leaf functional traits and elevations in tree species above 4000 m a.s.l. Aims Our objective was to investi...
Article
Understanding how species diversify and evolve in species-rich areas like the lowland rain forest in the Neotropics is critical for conservation in times of unprecedented threats. To determine how the Andean uplift, the formation of the Panama land bridge, and Pleistocene climatic fluctuations affected dispersal and diversification in the Sapotacea...
Article
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Many natural systems are subject to profound and persistent anthropogenic influence. Human‐induced gene movement through afforestation and the selective transportation of genotypes might enhance the potential for intraspecific hybridization, which could lead to outbreeding depression. However, the evolutionary legacy of afforestation on the spatial...
Article
Aim There is increasing interest in the role that biological traits, and historical and biogeographic processes, play in the formation of phylogeographic patterns. An arid belt that once existed in northern China might have affected many plants, but this has yet to be tested in an arid‐tolerant, wind‐dispersed species. Here, we tested how intrinsic...
Article
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Debregeasia is an economically important genus of the nettle family (Urticaceae). Previous systematic studies based on morphology, or using up to four plastome regions, have not satisfactorily resolved relationships within the genus. Here, we report 25 new plastomes for Urticaceae, including 12 plastomes from five Debregeasia species and 13 plastom...
Article
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Having a comprehensive understanding of population structure, genetic differentiation and demographic history is important for conservation and management of threatened species. High‐throughput sequencing (HTS) provides exciting opportunities to address a wide range of factors for conservation genetics. Here, we generated HTS data and identified 26...
Article
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Premise: A novel set of microsatellite markers was developed for Juglans sigillata (Juglandaceae), an endemic walnut species in southwestern China, to facilitate cultivar identification and future investigations into the genetic structure and domestication history of this species and its close relatives. Methods and results: We developed 32 micr...
Article
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Full genome sequencing of organisms with large and complex genomes is intractable and cost ineffective under most research budgets. Cycads (Cycadales) represent one of the oldest lineages of the extant seed plants and, partly due to their age, have incredibly large genomes up to ~60Gbp. Restriction site associated DNA sequencing (RADseq) offers an...
Article
Full-text available
Main conclusion: The tobacco nectar proteome mainly consists of pathogenesis-related proteins with two glycoproteins. Expression of nectarins was non-synchronous, and not nectary specific. After secretion, tobacco nectar changed from sucrose rich to hexose rich. Floral nectar proteins (nectarins) play important roles in inhibiting microbial growth...
Article
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The well‐known vicariance and dispersal models dominate in understanding the allopatric pattern for related species and presume the simultaneous occurrence of speciation and biogeographic events. However, the formation of allopatry may postdate the species divergence. We examined this hypothesis using DNA sequence data from 3 chloroplast fragments...
Article
Background and aims: Tertiary relict and Arctic/circumboreal distributions are two major patterns of Northern Hemisphere intercontinental disjunctions with very different histories. Each has been well researched, but members of one biome have generally not been incorporated in the biogeographical analyses of the other, and links or transitions bet...
Article
Honey, as a commercial product, is a target of adulteration through inappropriate production practices and deliberate mislabelling of botanical origin. Floral nectar protein could be a good marker for determining the source flowers of honey, especially monofloral honeys. Here, nectar and monofloral honey from Eriobotrya japonica Lindl. (loquat) wer...
Article
Towards a comprehensive revision of Gesneriaceae in Sri Lanka, 12 names are here typified, of which 11 are lectotypifications, including one second-step lectotypification, and the other is a neotypification.
Article
Non‐bifurcating divergence caused by introgressive hybridization is continuously reported for groups of closely related species. In this study, we aimed to construct genome‐scale classification of deep lineages of the conifer genus Picea, establish their phylogenetic relationships and test the bifurcating hypothesis between deeply branching lineage...
Article
Full-text available
Dispersal is a fundamental ecological process, yet demonstrating the occurrence and importance of long‐distance dispersal (LDD) remains difficult, having rarely been examined for widespread, non‐coastal plants. To address this issue, we integrated phylogenetic, molecular dating, biogeographical, ecological, seed biology and oceanographic data for t...
Article
Dispersal is a fundamental ecological process, yet demonstrating the occurrence and importance of long‐distance dispersal (LDD) remains difficult, having rarely been examined for widespread, non‐coastal plants. To address this issue, we integrated phylogenetic, molecular dating, biogeographical, ecological, seed biology and oceanographic data for t...
Article
Dispersal is a fundamental ecological process, yet demonstrating the occurrence and importance of long‐distance dispersal (LDD) remains difficult, having rarely been examined for widespread, non‐coastal plants. To address this issue, we integrated phylogenetic, molecular dating, biogeographical, ecological, seed biology and oceanographic data for t...
Article
Full-text available
Background and aims: Rapid evolutionary divergence and reticulate evolution may result in phylogenetic relationships that are difficult to resolve using small nucleotide sequence data sets. Next-generation sequencing methods can generate larger data sets that are better suited to solving these puzzles. One major and long-standing controversy in co...
Data
Primers used for MsGulLO and MsGLDH cDNA cloning and qPCR.
Data
Elution profile of MsGulLO on a Superdex-75 size exclusion chromatography column.
Data
MsGulLO peptides identified by mass spectrometry (MALDI-TOF/TOF).
Data
Mucuna sempervirens nectar proteins identified by 2-DE and mass spectrometry.
Article
Full-text available
Floral nectar plays important roles in the interaction between animal-pollinated plants and pollinators. Its components include water, sugars, amino acids, vitamins, and proteins. Growing empirical evidence shows that most of the proteins secreted in nectar (nectarins) are enzymes that can tailor nectar chemistry for their animal mutualists or redu...
Article
Full-text available
Boehmeria is an important genus; however, no plastid genome has been reported to date. Here we report the complete chloroplast genomes for two Boehmeria species. The chloroplast genomes of Boehmeria umbrosa and Boehmeria spicata were found to be 170920 bp and 170958 in length, respectively, and the GC contents were 35.5 and 35.3%, respectively. The...
Article
Full-text available
Rapid and accurate identification of endangered species is a critical component of bio‐surveillance and conservation management, and potentially policing illegal trades. However, this is often not possible using traditional taxonomy, especially where only small or pre‐processed parts of plants are available. Reliable identification can be achieved...
Article
Background and aims: Glacial refugia and inter-/postglacial recolonization routes during the Quaternary of tree species in Europe and North America are well understood, but far less is known about those of tree species in subtropical eastern Asia. Thus, we have examined the phylogeographic history of Populus adenopoda (Salicaceae), one of the few...
Article
Full-text available
The complete chloroplast genome of Cecropia pachystachya Trécul was determined in this study. The total genome size was 153,925 bp in length, containing a pair of inverted repeats (IRs) of 25,443 bp, which were separated by large single copy (LSC) and small single copy (SSC) of 84,947 bp and 18,092 bp, respectively. The GC contents is 36.5%. A tota...
Article
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Background The Cornales is the basal lineage of the asterids, the largest angiosperm clade. Phylogenetic relationships within the order were previously not fully resolved. Fifteen plastid genomes representing 14 species, ten genera and seven families of Cornales were newly sequenced for comparative analyses of genome features, evolution, and phylog...
Article
This study examines genetic relationships among and within the South American species of Oreobolus that span the temperate and tropical Andes hotspots and represent a good case study to investigate diversification in the Páramo. A total of 197 individuals covering the distributional range of most of these species were sequenced for the nuclear ribo...
Article
• Floral nectar can affect the fitness of insect‐pollinated plants, through both attraction and manipulation of pollinators. Self‐incompatible insect‐pollinated plants receive more insect visits than their self‐compatible relatives, and the nectar of such species might face increased risk of infestation by pathogens carried by pollinators than self...
Article
Full-text available
Background and aims: The extent to which hybridization leads to gene flow between plant species depends on the structure of hybrid populations. However, if this varies between locations, species barriers might prove permeable in some locations but not in others. To assess possible variation in hybrid population structure, the magnitude and directi...
Article
Full-text available
Species delimitation in tree species is notoriously challenging due to shared polymorphisms among species. An integrative survey that considers multiple operational criteria is a possible solution, and we aimed to test it in a species complex of aspens in China. Genetic [four chloroplast DNA (cpDNA) fragments and 14 nuclear microsatellite loci (nSS...
Data
Morphological difference between Populus davidiana and P. rotundifolia according to the Flora of China (Fang et al., 1999).
Data
Detailed information for the 76 sampled populations of the Populus davidiana-rotundifolia complex that were adopted for genetic survey using nSSR and cpDNA.
Data
Locations of the five Populus davidiana populations from Korea (Lee et al., 2011) that were used for ecological niche modeling.
Data
The minimum spanning network showing the phylogenetic relationships among the 21 chloroplast DNA (cpDNA) haplotypes in the Populus davidiana-rotundifolia complex, and their occurrence in (A) each species and (B) each range sector. (A) Red and blue on the pie chart of network represent haplotypes that occur in P. rotundifolia and P. davidiana, respe...