Biology subjects

Helmstetter, A. J.

Publications and source records attributed to Helmstetter, A. J..

5 recordsLinked to original sources

bioRxiv2018

Phylogenomics of the major tropical plant family Annonaceae using targeted enrichment of nuclear genes

Targeted enrichment and sequencing of hundreds of nuclear loci for phylogenetic reconstruction is becoming an important tool for plant systematics and evolution. Annonaceae is a major pantropical plant family with 109 genera and ca. 2450 species, occurring across all major and minor tropical forests of the world. Baits were designed by sequencing the transcriptomes of five species from two of the largest Annonaceae subfamilies. Orthologous loci were identified. The resulting baiting kit was used to reconstruct phylogenetic relationships at two different levels using concatenated and gene tree approaches: a family wide Annonaceae analysis sampling 65 genera and a species level analysis of tribe Piptostigmateae sampling 29 species with multiple individuals per species. DNA extraction was undertaken mainly on silicagel dried leaves, with two samples from herbarium dried leaves. Our kit targets 469 exons (364 653 bp of sequence data), successfully capturing sequences from across Annonaceae. Silicagel dried and herbarium DNA worked eaually well. We present for the first time a nuclear gene-based phylogenetic tree at the generic level based on 317 supercontigs. Results mainly confirm previous chloroplast based studies. However, several new relationships are found and discussed. We show significant differences in branch lengths between the two large subfamilies Annonoideae and Malmeoideae. A new tribe, Annickieae, is erected containing a single African genus Annickia. We also reconstructed a well resolved species-level phylogenetic tree of the Piptostigmteae tribe. Our baiting kit is useful for reconstructing well supported phylogenetic relationships within Annonaceae at different taxonomic levels. The nuclear genome is mainly concordant with plastome information with a few exceptions. Moreover, we find that substitution rate heterogeneity between the two subfamilies is also found within the nuclear compartment, and not just plastomes and ribosomal DNA as previously shown. Our results have implications for understanding the biogeography, molecular dating and evolution of Annonaceae.

evolutionary biology↗

bioRxiv2018

Trait evolution and historical biogeography shape assemblages of annual killifish

Reconstructions of evolutionary and historical biogeographic processes can improve our understanding of how species ssemblages developed and permit inference of ecological drivers affecting coexistence. We explore this approach in Austrolebias, a genus of annual fishes possessing a wide range of body sizes. Regional assemblages composed of different species with similar size distributions are found in four areas of eastern South America. Using phylogenetic trees, species distribution models and size data we show how trait evolution and historical biogeography have affected the composition of species assemblages. We extend age-range correlations to improve estimates of local historical biogeography. We find that size variation principally arose in a single area and infer that ecological interactions drove size divergence. This large-size lineage spread to two other areas. One of these assemblages was likely shaped by adaptation to a new environment, but this was not associated with additional size divergence. We found only weak evidence that environmental filtering has been important in the construction of the remaining assemblage with the smallest range of sizes. The repeated assemblage structures were the result of different evolutionary and historical processes. Our approach sheds light on how species assemblages were built when typical clustering approaches may fall short.

evolutionary biology↗

bioRxiv2018

Rapid, raw-read reference and identification (R4IDs): A flexible platform for rapid generic species ID using long-read sequencing technology.

The versatility of the current DNA sequencing platforms and the development of portable, nanopore sequencers means that it has never been easier to collect genetic data for unknown sample ID. DNA barcoding and meta-barcoding have become increasingly popular and barcode databases continue to grow at an impressive rate. However, the number of canonical genome assemblies (reference or draft) that are publically available is relatively tiny, hindering the more widespread use of genome scale DNA sequencing technology for accurate species identification and discovery. Here, we show that rapid raw-read reference datasets, or R4IDs for short, generated in a matter of hours on the Oxford Nanopore MinION, can bridge this gap and accelerate the generation of useable reference sequence data. By exploiting the long read length of this technology, shotgun genomic sequencing of a small portion of an organisms genome can act as a suitable reference database despite the low sequencing coverage. These R4IDs can then be used for accurate species identification with minimal amounts of re-sequencing effort (1000s of reads). We demonstrated the capabilities of this approach with six vascular plant species for which we created R4IDs in the laboratory and then re-sequenced, live at the Kew Science Festival 2016. We further validated our method using simulations to determine the broader applicability of the approach. Our data analysis pipeline has been made available as a Dockerised workflow for simple, scalable deployment for a range of uses.

bioinformatics↗

bioRxiv2017

A case for sympatric speciation by cannibalism in South-American annual killifish (Austrolebias)

A trophic radiation in the South-American annual killifish genus Austrolebias has led to the evolution of large specialized piscivores from small generalized carnivores. It has been proposed that this occurred in a single series of vicariant speciation events. An alternative hypothesis is denoted giant-dwarf speciation: piscivores would have evolved in sympatry by character displacement and cannibalism. We test the plausibility of both scenarios using size measures combined with distributional data and new phylogenetic trees based on mitochondrial and nuclear molecular markers.\n\nOur analysis uses historical biogeography models and Ornstein-Uehlenbeck processes describing trait evolution across the posterior distributions of phylogenetic trees. Large species most likely evolved three times from small ones. For the clade containing A. elongatus, we argue that vicariance was not involved in the origin of these large and specialized piscivores. They experience stabilizing selection with an optimum shifted towards larger bodies and longer jaws. The branch leading to this clade has the fastest evolving jaw lengths across the phylogeny, in agreement with expectations for giant-dwarf speciation. For A. wolterstorffi, the support for giant-dwarf speciation is weaker. When the species is placed at the root of Austrolebias, ancestral reconstructions are unreliable and vicariance cannot be ruled out. For the remaining large species, we can reject vicariance and giant dwarf speciation. Our results give rise to two new additional scenarios for the evolution of specialized piscivores. In the first, two successive speciation events in sympatry or parapatry produced large and piscivorous species. In the second, the immigration of a different annual killifish genus (Cynopoecilus) in the Patos area of endemism has contributed to in-situ diversification of Austrolebias species.

evolutionary biology↗

bioRxiv2017

Field-based species identification in eukaryotes using single molecule, real-time sequencing.

Advances in DNA sequencing and informatics have revolutionised biology over the past four decades, but technological limitations have left many applications unexplored1,2. Recently, portable, real-time, nanopore sequencing (RTnS) has become available. This offers opportunities to rapidly collect and analyse genomic data anywhere3-5. However, the generation of datasets from large, complex genomes has been constrained to laboratories6,7. The portability and long DNA sequences of RTnS offer great potential for field-based species identification, but the feasibility and accuracy of these technologies for this purpose have not been assessed. Here, we show that a field-based RTnS analysis of closely-related plant species (Arabidopsis spp.)8 has many advantages over laboratory-based high-throughput sequencing (HTS) methods for species level identification-by-sequencing and de novo phylogenomics. Samples were collected and sequenced in a single day by RTnS using a portable, \"al fresco\" laboratory. Our analyses demonstrate that correctly identifying unknown reads from matches to a reference database with RTnS reads enables rapid and confident species identification. Individually annotated RTnS reads can be used to infer the evolutionary relationships of A. thaliana. Furthermore, hybrid genome assembly with RTnS and HTS reads substantially improved upon a genome assembled from HTS reads alone. Field-based RTnS makes real-time, rapid specimen identification and genome wide analyses possible. These technological advances are set to revolutionise research in the biological sciences9 and have broad implications for conservation, taxonomy, border agencies and citizen science.

evolutionary biology↗