An official website of the United States government
ABSTRACT Although the frequency of ancient hybridization across the Tree of Life is greater than previously thought, little work has been devoted to uncovering the extent, timeline, and geographic and ecological context of ancient hybridization. Using an expansive new dataset of nuclear and chloroplast DNA sequences, we conducted a multifaceted phylogenomic investigation to identify ancient reticulation in the early evolution of oaks (Quercus). We document extensive nuclear gene tree and cytonuclear discordance among major lineages ofQuercusand relatives in Quercoideae. Our analyses recovered clear signatures of gene flow against a backdrop of rampant incomplete lineage sorting, with gene flow most prevalent among major lineages ofQuercusand relatives in Quercoideae during their initial radiation, dated to the Early‐Middle Eocene. Ancestral reconstructions including fossils suggest ancestors ofCastanea + Castanopsis,Lithocarpus, and the Old World oak clade probably co‐occurred in North America and Eurasia, while the ancestors ofChrysolepis, Notholithocarpus, and the New World oak clade co‐occurred in North America, offering ample opportunity for hybridization in each region. Our study shows that hybridization—perhaps in the form of ancient syngameons like those seen today—has been a common and important process throughout the evolutionary history of oaks and their relatives. Concomitantly, this study provides a methodological framework for detecting ancient hybridization in other groups.
more »
« less
Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method
Abstract Applications of molecular phylogenetic approaches have uncovered evidence of hybridization across numerous clades of life, yet the environmental factors responsible for driving opportunities for hybridization remain obscure. Verbal models implicating geographic range shifts that brought species together during the Pleistocene have often been invoked, but quantitative tests using paleoclimatic data are needed to validate these models. Here, we produce a phylogeny for Heuchereae, a clade of 15 genera and 83 species in Saxifragaceae, with complete sampling of recognized species, using 277 nuclear loci and nearly complete chloroplast genomes. We then employ an improved framework with a coalescent simulation approach to test and confirm previous hybridization hypotheses and identify one new intergeneric hybridization event. Focusing on the North American distribution of Heuchereae, we introduce and implement a newly developed approach to reconstruct potential past distributions for ancestral lineages across all species in the clade and across a paleoclimatic record extending from the late Pliocene. Time calibration based on both nuclear and chloroplast trees recovers a mid- to late-Pleistocene date for most inferred hybridization events, a timeframe concomitant with repeated geographic range restriction into overlapping refugia. Our results indicate an important role for past episodes of climate change, and the contrasting responses of species with differing ecological strategies, in generating novel patterns of range contact among plant communities and therefore new opportunities for hybridization. The new ancestral niche method flexibly models the shape of niche while incorporating diverse sources of uncertainty and will be an important addition to the current comparative methods toolkit. [Ancestral niche reconstruction; hybridization; paleoclimate; pleistocene.]
more »
« less
- Award ID(s):
- 1930030
- PAR ID:
- 10429732
- Editor(s):
- Eaton, Deren
- Date Published:
- Journal Name:
- Systematic Biology
- ISSN:
- 1063-5157
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Functional traits of vertebrates can be used to infer paleoenvironmental conditions, allowing research into past climate changes and biotic responses. Birds are generally considered poor palaeoclimatic proxies due to their high vagility. Here, we analyze biogeographical and climatic niche information from multiple vertebrate groups including small mammals, reptiles, and birds to infer the paleoclimatic conditions present during the Late Pleistocene (~14,500–17,000 years BP) at Talara, an asphaltic paleontological locality on the northern Peruvian coast. We created Ecological Niche Models for the nearest living relative of each fossil species identified at Talara. We then used the Mutual Ecogeographic Range method, obtaining the overlapping area between distributions for each vertebrate group (birds, reptiles, and small mammals) as well as for combinations of groups, to infer the paleoclimate at Talara and to determinate what taxonomic groups are best for reconstructing climate in this system. Our analyses indicate that conditions at Talara were slightly cooler and significantly wetter than those of the present day. Individually, different vertebrate groups provide different paleoclimatic information. Birds were found to be a poor paleoclimatic proxy. Mammals were good for inferring paleoprecipitation but not paleotemperature. Reptiles were good group for inferring paleotemperature but not paleoprecipitation. While analyzing all vertebrate groups together yields the most robust conclusions, reptiles and small mammals combined are a good proxy for inferring both paleoprecipitation and paleotemperature. Our results suggest an interstadial period that agrees with paleotemperatures inferred from isotopic and sedimentary information. Our research indicates that today, the southern portion of the Cauca biogeographic province (230 km NE from Talara) has comparable climatic conditions to Late Pleistocene Talara. Understanding how the Talara region transitioned from this biodiverse ecosystem to the hyperarid coastal desert of today could have important implications for predicting biotic response and tipping points in the context of modern climate change.more » « less
-
Abstract Co-adaptation of cytoplasmic and nuclear genomes are critical to physiological function for many species. Despite this understanding, hybridization can disrupt co-adaptation leading to a mismatch between maternally-inherited cytoplasmic genomes and biparentally inherited nuclear genomes. Few studies have examined the consequences of cytonuclear interactions to physiological function across environments. Here, we quantify the degree of co-introgression between chloroplast and nuclear-chloroplast (N-cp) genes across repeated hybrid zones and its consequences to physiological function across environments. We use whole-genome resequencing and common garden experiments with clonally replicated genotypes sampled across the natural hybrid zone betweenPopulus trichocarpaandP. balsamifera. We use geographic clines to test for co-introgression of the chloroplast genome with N-cp and non-interacting nuclear genes. Co-introgression of chloroplast and N-cp genes was limited although contact zone-specific patterns suggest that local environments may influence co-introgression. Combining ancestry estimates with phenotypic data across common gardens revealed that mismatches between chloroplast and nuclear ancestry can influence physiological performance, but the strength and direction of these effects vary depending on the environment. Overall, this study highlights the importance of cytonuclear interactions to adaptation, and the role of environment in modifying the effect of those interactions.more » « less
-
Premise: A switch in pollinator can occur when a plant lineage enters a new habitat where the ancestral pollinator is less common and a novel pollinator is more common. Since pollinator communities vary according to environmental tolerances and availability of resources, there may be consistent associations between pollination mode and specific regions and habitats. Such associations can be studied in lineages that have experienced multiple pollinator transitions, representing evolutionary replicates. Methods: Our study focused on a large clade of Penstemon wildflower species in western North America that has repeatedly evolved hummingbird-adapted flowers from ancestral bee-adapted flowers. For each species, we estimated geographic ranges from occurrence data and inferred environmental niches from climate, topographical, and soil data. Using a phylogenetic comparative approach, we investigated whether hummingbird-adapted species occupy distinct geographic regions or habitats relative to beeadapted species. Results: Hummingbird-adapted species occur at lower latitudes and lower elevations than bee-adapted species, resulting in a difference in their environmental niche. Hummingbird-adapted species seem to evolve in lineages that previously adapted to lower latitudes and elevations, since bee-adapted species sister to hummingbird-adapted species also occur in these regions and habitats. Sister species pairs – regardless of whether they differ in pollinator – show relatively little geographic range overlap. Conclusions: Adaptation to a novel pollinator may often occur in geographic and ecological isolation from ancestral populations. The ability of a given lineage to adapt to novel pollinators may critically depend on its ability to colonize regions and habitats associated with novel pollinator communities.more » « less
-
Abstract PremiseA switch in pollinator can occur when a plant lineage enters a new habitat where the ancestral pollinator is less common, and a novel pollinator is more common. Because pollinator communities vary according to environmental tolerances and availability of resources, there may be consistent associations between pollination mode and specific regions and habitats. Such associations can be studied in lineages that have experienced multiple pollinator transitions, representing evolutionary replicates. MethodsOur study focused on a large clade ofPenstemonwildflower species in western North America, which has repeatedly evolved hummingbird‐adapted flowers from ancestral bee‐adapted flowers. For each species, we estimated geographic ranges from occurrence data and inferred environmental niches from climate, topographical, and soil data. Using a phylogenetic comparative approach, we investigated whether hummingbird‐adapted species occupy distinct geographic regions or habitats relative to bee‐adapted species. ResultsHummingbird‐adapted species occur at lower latitudes and lower elevations than bee‐adapted species, resulting in a difference in their environmental niche. Bee‐adapted species sister to hummingbird‐adapted species are also found in relatively low elevations and latitudes, similar to their hummingbird‐adapted sister species, suggesting ecogeographic shifts precede pollinator divergence. Sister species pairs—regardless of whether they differ in pollinator—show relatively little geographic range overlap. ConclusionsAdaptation to a novel pollinator may often occur in geographic and ecological isolation from ancestral populations. The ability of a given lineage to adapt to novel pollinators may critically depend on its ability to colonize regions and habitats associated with novel pollinator communities.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1093/sysbio/syad018
