Title: Genome‐scale data resolves the timing of divergence in Joshua trees
Premise
Joshua trees (Yucca brevifoliaandY. jaegeriana) and their yucca moth pollinators (Tegeticula syntheticaandT. antithetica) are a model system for studies of plant–pollinator coevolution and, they are thought to be one of the only cases in which there is compelling evidence for cospeciation driven by coevolution. Previous work attempted to evaluate whether divergence between the plant and their pollinators was contemporaneous. That work concluded that the trees diverged more than 5 million years ago—well before the pollinators. However, clear inferences were hampered by a lack of data from the nuclear genome and low genetic variation in chloroplast genes. As a result, divergence times in the trees could not be confidently estimated.
Methods
We present an analysis of whole chloroplast genome sequence data and RADseq data from >5000 loci in the nuclear genome. We developed a molecular clock for the Asparagales and the Agavoideae using multiple fossil calibration points. Using Bayesian inference, we produced new estimates for the age of the genusYuccaand for Joshua trees. We used calculated summary statistics describing genetic variation and used coalescent‐based methods to estimate population genetic parameters.
Results
We find that the Joshua trees are moderately genetically differentiated, but that they diverged quite recently (~100–200 kya), and much more recently than their pollinators.
Conclusions
The results argue against the notion that coevolution directly contributed to speciation in this system, suggesting instead that coevolution with pollinators may have reinforced reproductive isolation following initial divergence in allopatry.
Wenzell, Katherine E.; McDonnell, Angela J.; Wickett, Norman J.; Fant, Jeremie B.; Skogen, Krissa A.(
, American Journal of Botany)
Premise
Divergence depends on the strength of selection and frequency of gene flow between taxa, while reproductive isolation relies on mating barriers and geographic distance. Less is known about how these processes interact at early stages of speciation. Here, we compared population‐level differentiation in floral phenotype and genetic sequence variation among recently divergedCastillejato explore patterns of diversification under different scenarios of reproductive isolation.
Methods
Using target enrichment enabled by the Angiosperms353 probe set, we assessed genetic distance among 50 populations of fourCastillejaspecies. We investigated whether patterns of genetic divergence are explained by floral trait variation or geographic distance in two focal groups: the widespreadC. sessilifloraand the more restrictedC. purpureaspecies complex.
Results
We document thatC. sessilifloraand theC. purpureacomplex are characterized by high diversity in floral color across varying geographic scales. Despite phenotypic divergence, groups were not well supported in phylogenetic analyses, and little genetic differentiation was found across targeted Angiosperms353 loci. Nonetheless, a principal coordinate analysis of single nucleotide polymorphisms revealed differentiation withinC. sessilifloraacross floral morphs and geography and less differentiation among species of theC. purpureacomplex.
Conclusions
Patterns of genetic distance inC. sessiliflorasuggest species cohesion maintained over long distances despite variation in floral traits. In theC. purpureacomplex, divergence in floral color across narrow geographic clines may be driven by recent selection on floral color. These contrasting patterns of floral and genetic differentiation reveal that divergence can arise via multiple eco‐evolutionary paths.
Esque, Todd C; Shryock, Daniel F; Berry, Gabrielle A; Chen, Felicia C; DeFalco, Lesley A; Lewicki, Sabrina M; Cunningham, Brent L; Gaylord, Eddie J; Poage, Caitlan S; Gantz, Gretchen E; et al(
, Frontiers in Ecology and Evolution)
Introduction
Forecasting range shifts in response to climate change requires accurate species distribution models (SDMs), particularly at the margins of species' ranges. However, most studies producing SDMs rely on sparse species occurrence datasets from herbarium records and public databases, along with random pseudoabsences. While environmental covariates used to fit SDMS are increasingly precise due to satellite data, the availability of species occurrence records is still a large source of bias in model predictions. We developed distribution models for hybridizing sister species of western and eastern Joshua trees (Yucca brevifoliaandY. jaegeriana, respectively), iconic Mojave Desert species that are threatened by climate change and habitat loss.
Methods
We conducted an intensive visual grid search of online satellite imagery for 672,043 0.25 km2grid cells to identify the two species' presences and absences on the landscape with exceptional resolution, and field validated 29,050 cells in 15,001 km of driving. We used the resulting presence/absence data to train SDMs for each Joshua tree species, revealing the contemporary environmental gradients (during the past 40 years) with greatest influence on the current distribution of adult trees.
Results
While the environments occupied byY. brevifoliaandY. jaegerianawere similar in total aridity, they differed with respect to seasonal precipitation and temperature ranges, suggesting the two species may have differing responses to climate change. Moreover, the species showed differing potential to occupy each other's geographic ranges: modeled potential habitat forY. jaegerianaextends throughout the range ofY. brevifolia, while potential habitat forY. brevifoliais not well represented within the range ofY. jaegeriana.
Discussion
By reproducing the current range of the Joshua trees with high fidelity, our dataset can serve as a baseline for future research, monitoring, and management of this species, including an increased understanding of dynamics at the trailing and leading margins of the species' ranges and potential for climate refugia.
Quantifying how global change impacts wild populations remains challenging, especially for species poorly represented by systematic datasets. Here, we infer climate change effects on masting by Joshua trees (Yucca brevifoliaandY. jaegeriana), keystone perennials of the Mojave Desert, from 15 years of crowdsourced observations. We annotated phenophase in 10,212 geo‐referenced images of Joshua trees on the iNaturalist crowdsourcing platform, and used them to train machine learning models predicting flowering from annual weather records. Hindcasting to 1900 with a trained model successfully recovers flowering events in independent historical records and reveals a slightly rising frequency of conditions supporting flowering since the early 20th Century. This reflects increased variation in annual precipitation, which drives masting events in wet years—but also increasing temperatures and drought stress, which may have net negative impacts on recruitment. Our findings reaffirm the value of crowdsourcing for understanding climate change impacts on biodiversity.
Population demographic changes, alongside landscape, geographic and climate heterogeneity, can influence the timing, stability and extent of introgression where species hybridise. Thus, quantifying interactions across diverged lineages, and the relative contributions of interspecific genetic exchange and selection to divergence at the genome‐wide level is needed to better understand the drivers of hybrid zone formation and maintenance. We used seven latitudinally arrayed transects to quantify the contributions of climate, geography and landscape features to broad patterns of genetic structure across the hybrid zone ofPopulus trichocarpaandP. balsamiferaand evaluated the demographic context of hybridisation over time. We found genetic structure differed among the seven transects. While ancestry was structured by climate, landscape features influenced gene flow dynamics. Demographic models indicated a secondary contact event may have influenced contemporary hybrid zone formation with the origin of a putative hybrid lineage that inhabits regions with higher aridity than either of the ancestral groups. Phylogenetic relationships based on chloroplast genomes support the origin of this hybrid lineage inferred from demographic models based on the nuclear data. Our results point towards the importance of climate and landscape patterns in structuring the contact zones betweenP. trichocarpaandP. balsamiferaand emphasise the value whole genome sequencing can have to advancing our understanding of how neutral processes influence divergence across space and time.
Straub, Shannon C. K.; Boutte, Julien; Fishbein, Mark; Livshultz, Tatyana(
, Applications in Plant Sciences)
Premise
Apocynaceae is the 10th largest flowering plant family and a focus for study of plant–insect interactions, especially as mediated by secondary metabolites. However, it has few genomic resources relative to its size. Target capture sequencing is a powerful approach for genome reduction that facilitates studies requiring data from the nuclear genome in non‐model taxa, such as Apocynaceae.
Methods
Transcriptomes were used to design probes for targeted sequencing of putatively single‐copy nuclear genes across Apocynaceae. The sequences obtained were used to assess the success of the probe design, the intrageneric and intraspecific variation in the targeted genes, and the utility of the genes for inferring phylogeny.
Results
From 853 candidate nuclear genes, 835 were consistently recovered in single copy and were variable enough for phylogenomics. The inferred gene trees were useful for coalescent‐based species tree analysis, which showed all subfamilies of Apocynaceae as monophyletic, while also resolving relationships among species within the genusApocynum. Intraspecific comparison ofElytropus chilensisindividuals revealed numerous single‐nucleotide polymorphisms with potential for use in population‐level studies.
Discussion
Community use of this Hyb‐Seq probe set will facilitate and promote progress in the study of Apocynaceae across scales from population genomics to phylogenomics.
Smith, Christopher Irwin, McKain, Michael R., Guimond, Austin, and Flatz, Ramona. Genome‐scale data resolves the timing of divergence in Joshua trees. American Journal of Botany 108.4 Web. doi:10.1002/ajb2.1633.
Smith, Christopher Irwin, McKain, Michael R., Guimond, Austin, & Flatz, Ramona. Genome‐scale data resolves the timing of divergence in Joshua trees. American Journal of Botany, 108 (4). https://doi.org/10.1002/ajb2.1633
Smith, Christopher Irwin, McKain, Michael R., Guimond, Austin, and Flatz, Ramona.
"Genome‐scale data resolves the timing of divergence in Joshua trees". American Journal of Botany 108 (4). Country unknown/Code not available: Wiley Blackwell (John Wiley & Sons). https://doi.org/10.1002/ajb2.1633.https://par.nsf.gov/biblio/10237042.
@article{osti_10237042,
place = {Country unknown/Code not available},
title = {Genome‐scale data resolves the timing of divergence in Joshua trees},
url = {https://par.nsf.gov/biblio/10237042},
DOI = {10.1002/ajb2.1633},
abstractNote = {PremiseJoshua trees (Yucca brevifoliaandY. jaegeriana) and their yucca moth pollinators (Tegeticula syntheticaandT. antithetica) are a model system for studies of plant–pollinator coevolution and, they are thought to be one of the only cases in which there is compelling evidence for cospeciation driven by coevolution. Previous work attempted to evaluate whether divergence between the plant and their pollinators was contemporaneous. That work concluded that the trees diverged more than 5 million years ago—well before the pollinators. However, clear inferences were hampered by a lack of data from the nuclear genome and low genetic variation in chloroplast genes. As a result, divergence times in the trees could not be confidently estimated. MethodsWe present an analysis of whole chloroplast genome sequence data and RADseq data from >5000 loci in the nuclear genome. We developed a molecular clock for the Asparagales and the Agavoideae using multiple fossil calibration points. Using Bayesian inference, we produced new estimates for the age of the genusYuccaand for Joshua trees. We used calculated summary statistics describing genetic variation and used coalescent‐based methods to estimate population genetic parameters. ResultsWe find that the Joshua trees are moderately genetically differentiated, but that they diverged quite recently (~100–200 kya), and much more recently than their pollinators. ConclusionsThe results argue against the notion that coevolution directly contributed to speciation in this system, suggesting instead that coevolution with pollinators may have reinforced reproductive isolation following initial divergence in allopatry.},
journal = {American Journal of Botany},
volume = {108},
number = {4},
publisher = {Wiley Blackwell (John Wiley & Sons)},
author = {Smith, Christopher Irwin and McKain, Michael R. and Guimond, Austin and Flatz, Ramona},
}
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