
Lars NauheimerAustralian Tropical Herbarium | ATH
Lars Nauheimer
Dr. rer. nat.
About
37
Publications
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Introduction
Target Capture Phylogenomics
Detection and phasing of hybrid accessions
Additional affiliations
October 2013 - March 2015
Publications
Publications (37)
The generation and analysis of genome-scale data—genomics—is driving a rapid increase in plant biodiversity knowledge. However, the speed and complexity of technological advance in genomics presents challenges for its widescale use in evolutionary and conservation biology. Here, we introduce and describe a national-scale collaboration conceived to...
Derris Lour. and Brachypterum (Wight & Arn.) Benth. (Leguminosae subfamily Papilionoideae) in Australia are revised on the basis of examination of fresh, dried and spirit-preserved specimens and phylogenetic analysis of plastid matK and nuclear internal transcribed spacer (ITS) sequence data. Three species of Derris and four species of Brachypterum...
The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most phylogenetic trees of the family are incompletely sampled and often contain poorly supported branches. Here, we present the most...
Sapindales is an angiosperm order of high economic and ecological value comprising nine families, c. 479 genera, and c. 6570 species. However, family and subfamily relationships in Sapindales remain unclear, making reconstruction of the order’s spatio-temporal and morphological evolution difficult. In this study, we used Angiosperms353 target captu...
The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most published family phylogenies are incompletely sampled, generally contain massive polytomies, and/or show incongruent topologies b...
Australia harbours a rich and highly endemic orchid flora with over 90% of native species found nowhere else. However, little is known about the assembly and evolution of Australia’s orchid flora. Here, we used a phylogenomic approach to infer evolutionary relationships, divergence times and range evolution in Pterostylidinae (Orchidoideae), the se...
Hybridisation has been proposed to play an important role in fern evolution, but has been difficult to investigate. This study explores the utility of target sequence capture and read-to-reference phasing of putative hybrids to investigate the role of evolutionary reticulation in ferns using Australian Thelypteridaceae as a model. The bioinformatic...
Australia harbours a rich and highly endemic orchid flora with over 90% of native species found nowhere else. However, little is known about the assembly and evolution of Australia's orchid flora. Here, we used a phylogenomic approach to infer evolutionary relationships and range evolution in Pterostylidinae (Orchidoideae), the second largest subtr...
Hybridisation can lead to reproductive isolation and consequently speciation. It has been proposed to play an important role in fern evolution, but has been difficult to investigate. This study explores the utility of target sequence capture and reference guided read phasing to investigate the role of evolutionary reticulation in ferns using Austra...
Premise:
Hybrids contain divergent alleles that can confound phylogenetic analyses but can provide insights into reticulated evolution when identified and phased. We developed a workflow to detect hybrids in target capture data sets and phase reads into parental lineages using a similarity and phylogenetic framework.
Methods:
We used Angiosperms...
Premise:
Universal target enrichment kits maximize utility across wide evolutionary breadth while minimizing the number of baits required to create a cost-efficient kit. The Angiosperms353 kit has been successfully used to capture loci throughout the angiosperms, but the default target reference file includes sequence information from only 6-18 ta...
Heterotrophic plants provide intriguing examples of reductive evolution. This is especially evident in the reduction of their plastid genomes, which can potentially proceed toward complete genome loss. Several milestones at the beginning of this path of degradation have been described; however, little is known about the latest stages of plastome re...
Premise of the study: Hybrids contain divergent alleles that can confound phylogenetic analyses but can provide insights into parental lineages when identified and phased. We developed HybPhaser to detect hybrids in target capture datasets and to phase reads according to haplotypes based on similarity and a phylogenetic framework.
Methods and Resul...
Universal target enrichment kits maximise utility across wide evolutionary breadth while minimising the number of baits required to create a cost-efficient kit. Locus assembly requires a target reference, but the taxonomic breadth of the kit means that target references files can be phylogenetically sparse. The Angiosperms353 kit has been successfu...
Nepenthes is a genus of carnivorous plants consisting of ~160 species that are distributed in the paleotropics. Molecular systematics has so far not been able to resolve evolutionary relationships of most species because of the limited genetic divergence in previous studies. In the present study, we used a genome-skimming approach to infer phylogen...
A review of Austrocallerya J.Compton & Schrire and Pongamia Adans. (Leguminosae subfamily Papilionoideae) in Australia, and the description of a new monotypic genus, Ibatiria W.E.Cooper, is presented with the support of fresh, dried, spirit-preserved specimens, molecular phylogenetic analysis of plastid and nuclear data, and illustrations. Three Au...
Abstract for Monocots VI - 6. International Conference on Comparative Biology of Monocotyledones in 2018
Australia harbours a rich and highly endemic orchid flora, with c. 90 % of species endemic to the country. Despite that, the biogeographic history of Australasian orchid lineages is only poorly understood. Here we examined evolutionary relationships and the spatio-temporal evolution of the sun orchids (Thelymitra, 119 species), which display disjun...
Background and aims:
Many African genera of the Amaranthaceae exhibit unique inflorescences that include sterile flowers modified to hooks or spines. Considering that the abundance of large terrestrial herbivores increased on the African continent with the expansion of grassland and savannah ecosystems, modified sterile flowers could have been an...
Phylogenetic relationships in Calochilus (~30 species) were inferred based on a supermatrix of 81 loci including 22 species. To examine the spatio-temporal evolution of Calochilus, divergence-time estimations were conducted within a Bayesian framework using an uncorrelated relaxed molecular-clock model, followed by maximum-likelihood ancestral-rang...
Mycoheterotrophs, i.e. plants that acquire carbon from root-associated soil fungi, often have highly degraded plastomes, reflecting relaxed selective constraints on plastid genes following the loss of photosynthesis. Geosiris Baill. is the only mycoheterotrophic genus in Iridaceae and comprises two species in Madagascar and nearby islands, and a th...
The plastid genomes of early-diverging angiosperms were among the first land plant plastomes investigated. Despite their importance to understanding angiosperm evolution, no investigation has so far compared gene content or gene synteny of these plastid genomes with a focus on the Nymphaeales. Here, we report an evaluation and comparison of gene co...
This study focuses on reconstructing the time-calibrated phylogeny of the nine families comprising the order Sapindales, representing a diverse and economically important group of eudicots including citrus, mahogany, tree-of-heaven, cashew, mango, pistachio, frankincense, myrrh, lychee, rambutan, maple, and buckeye. We sampled three molecular marke...
Plastid genomes exhibit different levels of variability in their sequences, depending on the respective kinds of genomic regions. Genes are usually more conserved while noncoding introns and spacers evolve at a faster pace. While a set of about thirty maximum variable noncoding genomic regions has been suggested to provide universally promising phy...
Fig. S1 Phylogenies of the Pistia-clade based on chloroplast data without (a) and with (b) indel coding. Statistical support is shown by node numbers. Only bootstrap values of 70 or higher are displayed. Scale bars show substitutions per site
The new monotypic genus Englerarum Nauheimer & P.C.Boyce, with the only species Englerarum hypnosum (J.T.Yin, Y.H.Wang & Z.F.Xu) Nauheimer & P.C.Boyce, is here described. The new combination of Alocasia
hypnosa J.T.Yin, Y.H.Wang & Z.F.Xu, with exclusion of Alocasia (Schott) G.Don and transfer into Englerarum, is based on molecular phylogenies using...
The family Araceae (3790 species, 117 genera) has one of the oldest fossil records among angiosperms. Ecologically, members of this family range from free-floating aquatics (Pistia and Lemna) to tropical epiphytes. Here, we infer some of the macroevolutionary processes that have led to the worldwide range of this family and test how the inclusion o...
Alocasia comprises over 113 species of rainforest understorey plants in Southeast Asia, the Malesian region, and Australia. Several species, including giant taro, Alocasia macrorrhizos, and Chinese taro, Alocasia cucullata, are important food plants or ornamentals. We investigated the biogeography of this genus using plastid and nuclear DNA sequenc...
The taxonomic composition of the vascular epiphyte flora at the Río Changuinola, Panama, was examined and complemented with an analysis of biogeographic affinities and physiological parameters related to plant water and nutrient relations. In an area of ca. 1000 ha, we found a total of 476 species of vascular epiphytes. This marks a new diversity r...
Questions
Question (1)
Alleles should vary in heterozygous genes, i.e. have some amount of SNPs. This of course very much depends on the gene and the species and such, but is there an estimate or an average or a general idea how much that would/could be.
I somehow try to "draw a line" or get in idea howto distinguish the variation in alleles of a species to the variation between alleles of a hybrid between species.
I understand that this is a very difficult question to answer and do not expect one value. But if anyone could point me to information on the amount of variation found in alleles of a species, that would be very much appreciated.
Cheers!