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In the face of anthropogenic change and the potential loss of species, documenting biodiversity – including accurately delimiting species complexes – is of tantamount importance. Genome-wide data are powerful for investigating lineage divergence, though deciding if this divergence represents species-level differentiation remains challenging. Here, we use genome-wide data to investigate species limits in four currently recognized species of Earless Lizards (Phrynosomatidae: Holbrookia), with a focus on H. lacerata and H. subcaudalis, the latter having potentially imperiled populations. This group’s taxonomy has been repeatedly revised; most recently, H. lacerata and H. subcaudalis were elevated to species status using conserved morphological data and a few molecular markers. In this study, we used double-digest restriction-site associated DNA sequencing to delineate species limits for our focal taxa. We recovered five populations that corresponded to five well-supported lineages with very little gene flow among them. Our results support the recognition of H. lacerata and H. subcaudalis as two separate species, based on strong phylogenetic support for these lineages and genetic divergence measures that exceed those of currently recognized species within Holbrookia. Genomic methods for species delimitation offer a promising approach to assess biodiversity in taxonomically confounded taxa or organisms of conservation priority.
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This content will become publicly available on August 19, 2026
Temporal genomics reveal a century of genomic diversity shifts across a biodiversity hotspot avian assemblage
Abstract Biodiversity has experienced tremendous shifts in community, species, and genetic diversity during the Anthropocene. Understanding temporal diversity shifts is especially critical in biodiversity hotspots, i.e., regions that are exceptionally biodiverse and threatened. Here, we use museomics and temporal genomics approaches to quantify temporal shifts in genomic diversity in an assemblage of eight generalist highland bird species from the Ethiopian Highlands (part of the Eastern Afromontane Biodiversity Hotspot). With genomic data from contemporary and historical samples, we demonstrate an assemblage-wide trend of increased genomic diversity through time, potentially due to improved habitat connectivity within highland regions. Genomic diversity shifts in these generalist species contrast with general trends of genomic diversity declines in specialist or imperiled species. In addition to genetic diversity shifts, we found an assemblage-wide trend of decreased realized mutational load, indicative of overall trends for potentially deleterious variation to be masked or selectively purged. Across this avian assemblage, we also show that shifts in population genomic structure are idiosyncratic, with species-specific trends. These results are in contrast with other charismatic and imperiled African taxa that have largely shown strong increases in population genetic structure over the recent past. This study highlights that not all taxa respond the same to environmental change, and generalists, in some cases, may even respond positively. Future comparative conservation genomics assessments on species groups or assemblages with varied natural history characteristics would help us better understand how diverse taxa respond to anthropogenic landscape changes.
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- Award ID(s):
- 1953688
- PAR ID:
- 10629899
- Editor(s):
- Gossmann, Toni
- Publisher / Repository:
- Genome Biology and Evolution
- Date Published:
- Journal Name:
- Genome Biology and Evolution
- ISSN:
- 1759-6653
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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