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Abstract Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in many marine environments and play a major role in global carbon cycling. Species recognition in Foraminifera is mainly based on morphological characters and nuclear 18S ribosomal RNA barcoding. The 18S rRNA contains variable sequence regions that allow for the identification of most foraminiferal species. Still, some species show limited variability, while others contain high levels of intragenomic polymorphisms, thereby complicating species identification. The use of additional, easily obtainable molecular markers other than 18S rRNA will enable more detailed investigation of evolutionary history, population genetics and speciation in Foraminifera. Here we present the first mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences (“barcodes”) of Foraminifera. We applied shotgun sequencing to single foraminiferal specimens, assembled COI, and developed primers that allow amplification of COI in a wide range of foraminiferal species. We obtained COI sequences of 49 specimens from 17 species from the orders Rotaliida and Miliolida. Phylogenetic analysis showed that the COI tree is largely congruent with previously published 18S rRNA phylogenies. Furthermore, species delimitation with ASAP and ABGD algorithms showed that foraminiferal species can be identified based on COI barcodes.
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This content will become publicly available on June 1, 2026
Genome-wide markers test the status of two putative species of North American bumble bees
Abstract Accurate species delimitation is critical to identifying the conservation status of species. Molecular species delimitation methods have revealed previously unrecognized cryptic species across the taxonomic spectrum. However, studies vary in the molecular markers selected, analytical approaches used, and taxon sampling, which sometimes results in conflicting conclusions. One example of such a conflict is seen in the species delimitation analyses of the western bumble bee,Bombus occidentalis. This species was once an abundant insect pollinator in western North America but has declined severely since the mid 1990s and is predicted to continue to diminish under even optimistic future climate scenarios. Complicating this conservation crisis, the species status ofB. occidentalishas varied over time, with most recent studies recognizing one or two species. Previous studies that used molecular methods to address this question focused on a Bayesian phylogeny of the mitochondrialcytochrome oxidase I(COI) gene. Phylogenetic studies that focus on a single gene are criticized for misrepresenting the evolutionary history of species because nuclear and mitochondrial genomes, and even some genes within them, may have different evolutionary patterns. We tested a two species hypothesis of theB. occidentaliscomplex using nuclear (ultraconserved elements) and mitochondrial (COI) markers to infer maximum likelihood and Bayesian phylogenies for the taxa. We present our results and conclusions from eight species delimitation methods. Based on the genomic, morphological and geographic differences between the taxa we find support for the two species hypothesis, withB. occidentalisandB. mckayias separate species. We discuss the strengths and limitations of each genetic dataset and delimitation method, make recommendations for best practices, and highlight opportunities for equitable knowledge and technology development for phylogenomics in conservation biology.
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- Award ID(s):
- 2127744
- PAR ID:
- 10631798
- Publisher / Repository:
- Springer
- Date Published:
- Journal Name:
- Conservation Genetics
- Volume:
- 26
- Issue:
- 3
- ISSN:
- 1566-0621
- Page Range / eLocation ID:
- 429 to 448
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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