Phylogenomics of white-eyes, a 'great speciator', reveals Indonesian archipelago as the center of lineage diversity
- National University of Singapore, Singapore
- Indonesian Institute of Sciences (LIPI), Indonesia
- Swedish Museum of Natural History, Sweden
- Institute of Zoology (CAS), China
- University of California, Berkeley, United States
- Wildlife Reserves Singapore, Singapore
- University of Western Australia, Australia
- University of Southampton, United Kingdom
- Museums Victoria, Australia
- Universitas Syiah Kuala, Indonesia
- Jiangsu Normal University, China
Abstract
Archipelagoes serve as important 'natural laboratories' which facilitate the study of island radiations and contribute to the understanding of evolutionary processes. The white-eye genus Zosterops is a classical example of a 'great speciator', comprising c. 100 species from across the Old World, most of them insular. We achieved an extensive geographic DNA sampling of Zosterops by using historical specimens and recently collected samples. Using over 700 genome-wide loci in conjunction with coalescent species tree methods and gene flow detection approaches, we untangled the reticulated evolutionary history of Zosterops, which comprises three main clades centered in Indo-Africa, Asia, and Australasia, respectively. Genetic introgression between species permeates the Zosterops phylogeny, regardless of how distantly related species are. Crucially, we identified the Indonesian archipelago, and specifically Borneo, as the major centre of diversity and the only area where all three main clades overlap, attesting to the evolutionary importance of this region.
Data availability
All data generated or analysed during this study are included in Dryad database: https://doi.org/10.5061/dryad.8931zcrmt. Raw FASTQ files of target enriched samples are available on NCBI under BioProject no. PRJNA682287.
-
Phylogenomics of a 'Great Speciator' Reveals Indonesian Archipelago as the Center of Lineage DiversityDryad Digital Repository, doi:10.5061/dryad.8931zcrmt.
-
Zosterops lateralis melanopsNCBI Genome Assembly, 248127.
-
A bird's white-eye view on neosex chromosome evolutionNCBI AccessionSingapore Ministry of Education: PRJNA530916.
Article and author information
Author details
Funding
Singapore Ministry of Education (R-154-000-A59-112)
- Frank E Rheindt
Wildlife Reserved Singapore Conservation Fund (R-154-000-A99-592)
- Frank E Rheindt
Croeni Foundation (R-154-000-A05-592)
- Frank E Rheindt
SEABIG (R-154-000-648-646)
- Balaji Chattopadhyay
SEABIG (R-154-000-648-733)
- Balaji Chattopadhyay
University of Southampton research grant (511206105)
- Kelvin S-H Peh
US National Science Foundation grant (DEB-1441652)
- Rauri CK Bowie
US National Science Foundation grant (DEB-1457845)
- Rauri CK Bowie
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2020, Gwee et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 2,109
- views
-
- 301
- downloads
-
- 19
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Phylogenomics of white-eyes, a 'great speciator', reveals Indonesian archipelago as the center of lineage diversity
eLife 9:e62765.
https://doi.org/10.7554/eLife.62765
Further reading
-
- Ecology
- Evolutionary Biology
Understanding the origins of novel, complex phenotypes is a major goal in evolutionary biology. Poison frogs of the family Dendrobatidae have evolved the novel ability to acquire alkaloids from their diet for chemical defense at least three times. However, taxon sampling for alkaloids has been biased towards colorful species, without similar attention paid to inconspicuous ones that are often assumed to be undefended. As a result, our understanding of how chemical defense evolved in this group is incomplete. Here, we provide new data showing that, in contrast to previous studies, species from each undefended poison frog clade have measurable yet low amounts of alkaloids. We confirm that undefended dendrobatids regularly consume mites and ants, which are known sources of alkaloids. Thus, our data suggest that diet is insufficient to explain the defended phenotype. Our data support the existence of a phenotypic intermediate between toxin consumption and sequestration — passive accumulation — that differs from sequestration in that it involves no derived forms of transport and storage mechanisms yet results in low levels of toxin accumulation. We discuss the concept of passive accumulation and its potential role in the origin of chemical defenses in poison frogs and other toxin-sequestering organisms. In light of ideas from pharmacokinetics, we incorporate new and old data from poison frogs into an evolutionary model that could help explain the origins of acquired chemical defenses in animals and provide insight into the molecular processes that govern the fate of ingested toxins.
-
- Computational and Systems Biology
- Evolutionary Biology
As pathogens spread in a population of hosts, immunity is built up, and the pool of susceptible individuals are depleted. This generates selective pressure, to which many human RNA viruses, such as influenza virus or SARS-CoV-2, respond with rapid antigenic evolution and frequent emergence of immune evasive variants. However, the host’s immune systems adapt, and older immune responses wane, such that escape variants only enjoy a growth advantage for a limited time. If variant growth dynamics and reshaping of host-immunity operate on comparable time scales, viral adaptation is determined by eco-evolutionary interactions that are not captured by models of rapid evolution in a fixed environment. Here, we use a Susceptible/Infected model to describe the interaction between an evolving viral population in a dynamic but immunologically diverse host population. We show that depending on strain cross-immunity, heterogeneity of the host population, and durability of immune responses, escape variants initially grow exponentially, but lose their growth advantage before reaching high frequencies. Their subsequent dynamics follows an anomalous random walk determined by future escape variants and results in variant trajectories that are unpredictable. This model can explain the apparent contradiction between the clearly adaptive nature of antigenic evolution and the quasi-neutral dynamics of high-frequency variants observed for influenza viruses.
