Biology subjects

Helmstetter, A. J.

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

17 recordsLinked to original sources

bioRxiv2024

Traits related to pollination and mating result in diverse reproductive strategies in angiosperms

O_LIFlowering plants have many modes of sexual reproduction, notably varying from selfing to outcrossing, and from bisexual flowers to individuals with separate sexes (dioecy). These reproductive modes are associated with floral and life-history traits that have evolved together, making it difficult to interpret correlations between traits. C_LIO_LIWe analysed variation in 21 traits related to flowers, pollination, mating, sexual systems and life history from 361 species representative of flowering plant diversity. C_LIO_LIOutcrossing was mainly found among long-lived, large-stature plants, but hermaphroditic outcrossers and dioecious species appeared as largely non-overlapping strategies in the trait space. Level of floral investment was the main difference between these strategies, with dioecious species having generally smaller, less rewarding flowers, a pattern that also occurred in biotically pollinated species. C_LIO_LIThis multi-trait study shows that pollination can be achieved in many, often contrasting, ways. Despite extensive variation in reproductive traits, dioecy stands out as being linked to floral traits primarily, while correlations with lifespan and dispersal traits appear spurious. We provide a conceptual framework based on lifespan, floral investment, and sexual separation that can be used to integrate pollination, reproduction and plant growth in future research on plant evolution and ecology. C_LI

evolutionary biology↗

bioRxiv2024

Towards a phylogenomic classification of Magnoliidae

PremiseMagnoliidae are a strongly supported clade of angiosperms. Previous phylogenetic studies based primarily on analyses of a limited number of mostly plastid markers have led to the current classification of magnoliids into four orders and 18 families. However, uncertainty remains regarding the placement of several families. MethodsHere we present the first comprehensive phylogenomic analysis of Magnoliidae as a whole, sampling 235 species from 199 (74%) genera and representing all families and most previously accepted subfamilies and tribes. We analyze newly generated data from the Angiosperms353 probe set using both coalescent and concatenation analyses and testing the impact of multiple filtering and alignment strategies. ResultsWhile our results generally provide further support for previously established phylogenetic relationships in both magnoliids as a whole and large families including Annonaceae and Lauraceae, they also provide new evidence for previously ambiguous relationships. In particular, we find support for the position of Hydnoraceae as sister to the remainder of Piperales and, for the first time, resolve the backbone of relationships among most genera of Myristicaceae. ConclusionsAlthough some of our results are limited by low gene recovery for a number of taxa and significant gene tree conflict for some relationships, this study represents a significant step towards reconstructing the evolutionary history of a major lineage of angiosperms. Based on these results, we present an updated phylogenetic classification for Magnoliidae, recognizing 21 families, summarizing previously established subfamilies and tribes, and describing new tribes for Myristicaceae.

evolutionary biology↗

bioRxiv2022

Trait-dependent diversification in angiosperms: patterns, models and data

Variation in species richness across the tree of life, accompanied by the incredible variety of ecological and morphological characteristics found in nature, has inspired many studies to link traits with species diversification. Angiosperms are a highly diverse group that has fundamentally shaped life on earth since the Cretaceous, and illustrate how species diversification affects ecosystem functioning. Numerous traits and processes have been linked to differences in species richness within this group, but we know little about how these interact and their relative importance. Here, we synthesized data from 152 studies that used state-dependent speciation and extinction (SSE) models on angiosperm clades. Intrinsic traits related to reproduction and morphology were often linked to diversification but a set of universal drivers did not emerge as traits did not have consistent effects across clades. Importantly, dataset properties were correlated to SSE model results - trees that were larger, older, or less well-sampled tended to yield trait-dependent outcomes. We compared these properties to recommendations for SSE model use and provide a set of best practices to follow when designing studies and reporting results. Finally, we argue that SSE model inferences should be considered in a larger context incorporating species ecology, demography and genetics.

evolutionary biology↗

bioRxiv2021

Pulled Diversification Rates, Lineage-Through-Time Plots and Modern Macroevolutionary Modelling

AO_SCPLOWBSTRACTC_SCPLOWEstimating time-dependent rates of speciation and extinction from dated phylogenetic trees of extant species (timetrees), and determining how and why they vary, is key to understanding how ecological and evolutionary processes shape biodiversity. Due to an increasing availability of phylogenetic trees, a growing number of process-based methods relying on the birth-death model have been developed in the last decade to address a variety of questions in macroevolution. However, this methodological progress has regularly been criticised such that one may wonder how reliable the estimations of speciation and extinction rates are. In particular, using lineages-through-time (LTT) plots, a recent study (Louca and Pennell, 2020) has shown that there are an infinite number of equally likely diversification scenarios that can generate any timetree. This has lead to questioning whether or not diversification rates should be estimated at all. Here we summarize, clarify, and highlight technical considerations on recent findings regarding the capacity of models to disentangle diversification histories. Using simulations we demonstrate the characteristics of newly-proposed "pulled rates" and their utility. We recognize that the recent findings are a step forward in understanding the behavior of macroevolutionary modelling, but they in no way suggest we should abandon diversification modelling altogether. On the contrary, the study of macroevolution using phylogenetic trees has never been more exciting and promising than today. We still face important limitations in regard to data availability and methodological shortcomings, but by acknowledging them we can better target our joint efforts as a scientific community.

evolutionary biology↗

bioRxiv2020

Phylogenomic relationships and historical biogeography in the South American vegetable ivory palms (Phytelepheae)

The vegetable ivory palms (Phytelepheae) form a small group of Neotropical palms whose phylogenetic relationships are not fully understood. Three genera and eight species are currently recognized; however, it has been suggested that Phytelephas macrocarpa could include the species Phytelephas seemannii and Phytelephas schottii because of supposed phylogenetic relatedness and similar morphology. We inferred their phylogenetic relationships and divergence time estimates using the 32 most clock-like loci of a custom palm bait-kit formed by 176 genes and four fossils for time calibration. We additionally explored the historical biogeography of the tribe under the recovered phylogenetic relationships. Our fossil-dated tree showed the eight species previously recognized, and that P. macrocarpa is not closely related to P. seemanii and P. schottii, which, as a consequence, should not be included in P. macrocarpa. The ancestor of the vegetable ivory palms was widely-distributed in the Choco, the inter-Andean valley of the Magdalena River, and the Amazonia during the Miocene at 19.25 Ma. Early diversification in Phytelephas at 5.27 Ma can be attributed to trans-Andean vicariance between the Choco/Magdalena and the Amazonia. Our results support the role of Andean uplift in the early diversification of Phytelephas under new phylogenetic relationships inferred from genomic data.

evolutionary biology↗

bioRxiv2020

Rapid Parallel Adaptation to Anthropogenic Heavy Metal Pollution

The impact of human mediated environmental change on the evolutionary trajectories of wild organisms is poorly understood. In particular, species capacity to adapt rapidly (in hundreds of generations or less), reproducibly and predictably to extreme environmental change is unclear. Silene uniflora is predominantly a coastal species, but it has also colonised isolated, disused mines with phytotoxic, zinc-contaminated soils. Here, we found that rapid parallel adaptation to anthropogenic pollution has taken place without geneflow spreading adaptive alleles between populations of the mine ecotype. Across replicate ecotype pairs, we identified shared targets of selection with functions linked to physiological differences between the ecotypes, although the genetic response is only partially shared between mine populations. Our results are consistent with a complex, polygenic genetic architecture underpinning rapid adaptation. This shows that even under a scenario of strong selection and rapid adaptation, evolutionary responses to human activities may be idiosyncratic at the genetic level and, therefore, difficult to predict from genomic data.

evolutionary biology↗

bioRxiv2020

Unravelling the phylogenomic relationships of the most diverse African palm genus Raphia (Calamoideae, Arecaceae)

Palms are conspicuous floristic elements across the tropics. In continental Africa, even though there are less than 70 documented species, they are omnipresent across the tropical landscape. The genus Raphia has 20 accepted species in Africa and one species endemic to the Neotropics. It is the most economically important genus of African palms with most of its species producing food and construction material. Raphia is divided into five sections based on inflorescence morphology. Nevertheless, the taxonomy of Raphia is problematic with no intra-generic phylogenetic study available. We present a phylogenetic study of the genus using a targeted exon capture approach sequencing of 56 individuals representing 18 out of the 21 species. Our results recovered five well supported clades within the genus. Three sections correspond to those based on inflorescence morphology. R. regalis is strongly supported as sister to all other Raphia species and is placed into a newly described section: Erectae. Overall, morphological based identifications agreed well with our phylogenetic analyses, with 12 species recovered as monophyletic based on our sampling. Species delimitation analyses recovered 17 or 23 species depending on the confidence level used. Species delimitation is especially problematic in the Raphiate and Temulentae sections. In addition, our clustering analysis using SNP data suggested that individual clusters matched geographic distribution. The Neotropical species R. taedigera is supported as a distinct species, rejecting the hypothesis of a recent introduction into South America. Our analyses support the hypothesis that the Raphia individuals from Madagascar are potentially a distinct species different from the widely distributed R. farinifera. In conclusion, our results support the infra generic classification of Raphia based on inflorescence morphology, which is shown to be phylogenetically useful. Classification and species delimitation within sections remains problematic even with our phylogenomic approach. Certain widely distributed species could potentially contain cryptic species. More in-depth studies should be undertaken using morphometrics, increased sampling and more variable markers. Our study provides a robust phylogenomic framework that enables further investigation on the biogeographic history, morphological evolution and other eco-evolutionary aspects of this charismatic, socially and economically important palm genus.

plant biology↗

bioRxiv2020

The Demographic History of Micro-endemics: Have Rare Species Always Been Rare?

Extinction has increased as human activities impact ecosystems. Conservation assessments for the IUCN red list are a fundamental tool in aiding the prevention of further extinction, yet, relatively few species have been thoroughly assessed. To increase the efficiency of assessments, novel approaches are needed to highlight threatened species that are currently data deficient. Many Madagascan plant species currently have extremely narrow ranges, but this may not have always been the case. To assess this, we used high-throughput DNA sequencing for 2-5 individuals of each species - reflecting the paucity of samples available for rare species. We estimated effective population size (Ne) for each species and compared this to census population (Nc) sizes when known. In each case, Ne was an order of magnitude larger than Nc - a signature of rapid, recent population decline. We then estimated the demographic history of each species, tracking changes in Ne over time. Five out of ten species displayed significant population declines towards the present (68-90% decreases). Our results for palm trees indicate that it is possible to predict extinction risk, particularly in the most threatened species. We performed simulations to show that our approach has the power to detect population decline during the Anthropocene, but performs less well when less data is used. Similar declines to those in palms were observed in data deficient species or those assessed as of least concern. These analyses reveal that Madagascars narrow endemics were not always rare, having experienced rapid decline in their recent history. Our approach offers the opportunity to target species in need of conservation assessment with little prior information, particularly in regions where human modification of the environment has been rapid. SummaryCurrent IUCN conservation assessment methods are reliant on observed declines in species population and range sizes over the last one hundred years, but for the majority of species this information is not available. We used a population genetic approach to reveal historical demographic decline in the rare endemic flora of Madagascar. These results show that it is possible to predict extinction risk from demographic patterns inferred from genetic data and that destructive human influence is likely to have resulted in the very high frequency of narrow endemics present on the island. Our approach will act as an important tool for rapidly assessing the threatened status of poorly known species in need of further study and conservation, particularly for tropical flora and fauna.

evolutionary biology↗

bioRxiv2019

Determinants of growth and body size in Austrolebias South-American annual killifish

Patterns of size variation in fish are supposed to be generated by growth differences, not by egg or hatchling size variation. However, annual killifish live in temporary ponds with a limited time period available for growth and reproduction. It has therefore been hypothesized that among annual killifish, hatchling size variation should be of large relative importance to generate adaptive adult size variation. Using growth curves of 203 individuals from 18 Austrolebias species raised in a common environment, we demonstrate that hatchling size variation indeed is a main determinant of adult size variation in annual killifish, in agreement with the time constraint hypothesis. Furthermore, we find an increased early growth rate in piscivorous species augmenting their difference in size from small congeneric species. This should be adaptive if size differences determine predation success. Environmental effects of spatial location of the population of origin on hatchling size and growth suggest that the time constraint might be weakened in populations occurring near the Atlantic coast. Our study reveals how extreme environments demand specific life history solutions to achieve adaptive size variation and that there might be scope for local adaptations in growth trajectories.

evolutionary biology↗

bioRxiv2019

Introgression in Brownea suggests that reticulate evolution contributes to Amazonian tree diversity

Hybridization has the potential to generate or homogenize biodiversity and is a particularly common phenomenon in plants, with an estimated 25% of species undergoing inter-specific gene flow. However, hybridization in Amazonias megadiverse tree flora was assumed to be extremely rare despite extensive sympatry between closely related species, and its role in diversification remains enigmatic because it has not yet been examined empirically. Using members of a dominant Amazonian tree family (Brownea, Fabaceae) as a model to address this knowledge gap, our study recovered extensive evidence of hybridization among multiple lineages across phylogenetic scales. More specifically, our results uncovered several historical introgression events between Brownea lineages and indicated that gene tree incongruence in Brownea is best explained by introgression, rather than solely by incomplete lineage sorting. Furthermore, investigation of recent hybridization using [~]19,000 ddRAD loci recovered a high degree of shared variation between two Brownea species which co-occur in the Ecuadorian Amazon. Our analyses also showed that these sympatric lineages exhibit homogeneous rates of introgression among loci relative to the genome-wide average, implying a lack of selection against hybrid genotypes and a persistence of hybridization over time. Our results demonstrate that gene flow between multiple Amazonian tree species has occurred across temporal scales, and contrasts with the prevailing view of hybridizations rarity in Amazonia. Overall, our results provide novel evidence that reticulate evolution influenced diversification in part of the Amazonian tree flora, which is the most diverse on Earth.

evolutionary biology↗

bioRxiv2019

Phylogenomic data reveal how a climatic inversion and glacial refugia shape patterns of diversity in an African rain forest tree species

AO_SCPLOWBSTRACTC_SCPLOWThe worlds second largest expanse of tropical rain forest is in Central Africa and it harbours enormous species diversity. Population genetic studies have consistently revealed significant structure across central African rain forest plants, in particular a North-South genetic discontinuity close to the equator at the level of a climatic inversion. Here, we take a phylogeographic approach using 351 nuclear markers in 112 individuals across the distribution of the African rain forest tree species Annickia affinis (Annonaceae). We show for the first time that the North-South divide is the result of a single major colonisation event across the climatic inversion from an ancestral population located in Gabon. We suggest that differences in ecological niche of populations distributed either side of this inversion may have contributed to this phylogenetic discontinuity. We find evidence for inland dispersal, predominantly in northern areas, and variable demographic histories among genetic clusters, indicating that populations responded differently to past climate change. We show how newly-developed genomic tools can provide invaluable insights into our understanding of tropical rain forest evolutionary dynamics.

evolutionary biology↗

bioRxiv2019

Genetic diversity and domestication of hazelnut (Corylus avellana) in Turkey

O_LIAssessing and describing genetic diversity in crop plants is a crucial first step towards their improvement. The European hazelnut, Corylus avellana, is one of the most economically important tree nut crops worldwide. It is primarily produced in Turkey where rural communities depend on it for their livelihoods. Despite this we know little about hazelnuts domestication history and the genetic diversity it holds.\nC_LIO_LIWe use double digest Restriction-site Associated DNA (ddRAD) sequencing to produce genome-wide dataset containing wild and domesticated hazelnut. We uncover patterns of population structure and diversity, determine levels of crop-wild gene flow and estimate the timing of key divergence events.\nC_LIO_LIWe find that genetic clusters of cultivars do not reflect their given names and that there is limited evidence for a reduction in genetic diversity in domesticated individuals. Admixture has likely occurred multiple times between wild and domesticated hazelnut. Domesticates appear to have first diverged from their wild relatives during the Mesolithic.\nC_LIO_LIWe provide the first genomic assessment of Turkish hazelnut diversity and suggest that it is currently in a partial stage of domestication. Our study provides a platform for further research that will protect this crop from the threats of climate change and an emerging fungal disease.\nC_LI

evolutionary biology↗

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↗