The evolutionary network of whiptail lizards reveals predictable outcomes of hybridization

Barley, Anthony J.; de, Adrián Nieto‐Montes; Manríquez–Morán, Norma L.; Thomson, Robert C.

doi:10.1126/science.abn1593

Cited by 20 publications

(14 citation statements)

References 80 publications

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“…Phylogenomic data have the potential to be very complex, both in clades that are well-understood to be recalcitrant like Andean plant radiations (Pease et al 2016; Vargas et al 2017), and increasingly in less expected systems like lizards (Barley et al 2022). To best address this complexity, we advocate for the observation of empirical phylogenomic data, including gene tree alignments and topologies, and that data curation be tailored to unique properties of individual datasets.…”

Section: Discussionmentioning

confidence: 99%

Strong phylogenetic signal despite high phylogenomic complexity in an Andean plant radiation (Freziera,Pentaphylacaceae)

Lagomarsino

2021

Preprint

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The Andes mountains in South America are a biodiversity hotspot within a hotspot, the New World Tropics, for seed plants. Much of this diversity is concentrated at middle-elevations in cloud forests, yet the evolutionary patterns underlying this extraordinary diversity remain poorly understood. This is partially due to a paucity of resolved phylogenies for cloud forest plant lineages: the young age of the Andes and generally high diversification rates among Andean systems precludes robust phylogenetic inference, and remote populations, few genomic resources, and generally understudied organisms make acquiring high-quality data difficult. We present the first phylogeny of Freziera (Pentaphylacaceae), an Andean-centered, cloud forest radiation with potential to provide insight into some of the abiotic and extrinsic factors that promote the highest diversity observed on the globe. Our dataset, representing data for 50 of the ca. 75 spp. obtained almost entirely from herbarium specimens via hybrid-enriched target sequence capture with the universal bait set Angiosperms353, included a proportion of poorly assembled loci likely representing multi-copy genes, but with insufficient data to be flagged by paralog filters: cryptic paralogs. These cryptic paralogs likely result from limitations in data collection that are common in herbariomics combined with a history of genome duplication and are likely common in other plant phylogenomic datasets. Standard empirical metrics for identifying poor-quality genes, which typically focus on filtering for genes with high phylogenetic informativeness, failed to identify problematic loci in our dataset where strong but inaccurate signal was a greater problem. Filtering by bipartition support was the most successful method for selecting genes and resulted in a species tree with lower discordance, higher support, and a more accurate topology relative to a consensus tree. Using known paralogs, we investigate the utility of multi-copy genes in phylogenetic inference and find a role for paralogs in resolving deep nodes and major clades, though at the expense of gene tree concordance and support. With the first phylogeny, we infer the biogeographic history of Freziera and identify the northern Andes as a source region. We also identify distinct modes of diversification in the northern and central Andes, highlighting the importance of fine-scale biogeographic study in Andean cloud forest systems.

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Section: Discussionmentioning

confidence: 99%

Strong phylogenetic signal despite high phylogenomic complexity in an Andean plant radiation (Freziera,Pentaphylacaceae)

Lagomarsino

2021

Preprint

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“…However, these same distance-dependent mechanisms also reduce the overall number of gene flow events, potentially mitigating the effects of increased locality. Ultimately, if systems with distance-dependent gene flow ( e.g ., Chapman and Burke, 2007; Tea et al, 2020; Barley et al, 2022) have an abundance of events, it may pose challenges to methods that make certain topological assumptions of the underlying phylogenetic network.…”

Section: Discussionmentioning

confidence: 99%

“…Ultimately, if systems with distance-dependent gene flow (e.g., Chapman and Burke, 2007;Tea et al, 2020;Barley et al, 2022) have an abundance of events, it may pose challenges to methods that make certain topological assumptions of the underlying phylogenetic network.…”

Section: Topological Properties Of Phylogenetic Networkmentioning

confidence: 99%

Exploring the distribution of phylogenetic networks generated under a birth-death-hybridization process

Justison

Heath

2022

Preprint

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Gene-flow processes such as hybridization and introgression play important roles in shaping diversity across the tree of life. Recent studies extending birth-death models have made it possible to investigate patterns of reticulation in a macroevolutionary context. These models allow for different macroevolutionary patterns of gene flow events that can either add, maintain, or remove lineages, thus creating complex diversification scenarios. Further, many reticulate phylogenetic inference methods assume specific reticulation structures or phylogenies belonging to certain network classes. However, the distributions of phylogenetic networks under reticulate birth-death processes are poorly characterized and it is unknown whether they violate common methodological assumptions. We use a combination of analytical and simulation techniques to explore phylogenetic network space under a birth-death-hybridization process. Specifically, we measured the number of lineages through time and role of hybridization in diversification along with the proportion of phylogenetic networks that belong to commonly used network classes (e.g., tree-child, tree-based, or level-1 networks). We find that the growth of phylogenetic networks and class membership is largely affected by the assumptions about macroevolutionary patterns of gene flow. In accordance with previous studies, a lower proportion of networks belonged to these classes based on type and density of reticulate events. However, under a birth-death-hybridization process, these factors form an antagonistic relationship; the type of reticulation events that cause high membership proportions also lead to the highest reticulation density, consequently lowering the overall proportion of phylogenies in some classes. Further, we observed that genetic distance-dependent gene flow and incomplete sampling increase the proportion of class membership, primarily due to having fewer reticulate events. Our results can inform studies if their biological expectations of gene flow are associated with evolutionary histories that satisfy the assumptions of current methodology and aid in finding phylogenetic classes that are relevant for methods development.

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“…This work has shown that the likelihood of behavioural interference decreases with increasing divergence time (e.g. Drury et al ., 2020; Barley et al ., 2022) likely owing to relative similarity in the perceptual systems and agonistic and/or mating signals used in closely related species (Grether et al ., 2009; Orians & Willson, 1964). Consequently, behavioural interference is thought to have a strong impact on the rate of speciation by limiting the rate at which two recently diverged allopatric lineages can coexist in secondary sympatry (Tobias et al ., 2020).…”

Section: Future Directionsmentioning

confidence: 99%

Interspecific behavioural interference and range dynamics: current insights and future directions

Patterson

Drury

2023

Biological Reviews

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Novel biotic interactions in shifting communities play a key role in determining the ability of species' ranges to track suitable habitat. To date, the impact of biotic interactions on range dynamics have predominantly been studied in the context of interactions between different trophic levels or, to a lesser extent, exploitative competition between species of the same trophic level. Yet, both theory and a growing number of empirical studies show that interspecific behavioural interference, such as interspecific territorial and mating interactions, can slow down range expansions, preclude coexistence, or drive local extinction, even in the absence of resource competition. We conducted a systematic review of the current empirical research into the consequences of interspecific behavioural interference on range dynamics. Our findings demonstrate there is abundant evidence that behavioural interference by one species can impact the spatial distribution of another. Furthermore, we identify several gaps where more empirical work is needed to test predictions from theory robustly. Finally, we outline several avenues for future research, providing suggestions for how interspecific behavioural interference could be incorporated into existing scientific frameworks for understanding how biotic interactions influence range expansions, such as species distribution models, to build a stronger understanding of the potential consequences of behavioural interference on the outcome of future range dynamics.

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The evolutionary network of whiptail lizards reveals predictable outcomes of hybridization

Cited by 20 publications

References 80 publications

Strong phylogenetic signal despite high phylogenomic complexity in an Andean plant radiation (Freziera,Pentaphylacaceae)

Strong phylogenetic signal despite high phylogenomic complexity in an Andean plant radiation (Freziera,Pentaphylacaceae)

Exploring the distribution of phylogenetic networks generated under a birth-death-hybridization process

Interspecific behavioural interference and range dynamics: current insights and future directions

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