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Report2024Open access

Community phylogenetics in the era of DNA-barcoding: potentials and challenges

Orsholm, Johanna


The evolutionary history of taxa in a community reflects the ecological processes which have been particularly crucial in shaping the communities of today. Integrating phylogenetic relationships among taxa in ecological analysis thus offer valuable insight into the underlying mechanisms governing community assembly and biodiversity patterns. Recent advancement in molecular techniques have drastically popularized a method known as DNA barcoding, where a short genetic marker is sequenced. For animals, the most common marker is the COI barcode region. The primary use of COI barcodes is taxonomic classification, but much potential remains untapped in deriving community phylogenetic information from this data. However, rapid saturation and strong functional constraints limits the phylogenetic information of the COI barcode, especially for older divergences. Inferring phylogenetic relationships thus become challenging for taxonomic groups older than a few million years. To improve phylogenetic inference from barcodes, additional information can be included to guide the analysis. Such information can be additional genetic markers or topological constraints drawn from previously known evolutionary relationships. Using such strategies have, in several studies, resulted in trees comparable to those inferred from more comprehensive genetic data. It is also possible to infer community phylogenetic information using phylogenetic placement, where single barcodes are fitted within a reference tree. The reference tree can be based on another available genetic resource. These methods show great promise for the continued integration of barcode-derived phylogenetic information in community ecology. A key aspect for future development is however to adapt methods to handle datasets with a substantial number of taxa, as global datasets covering a wide range of taxa are becoming increasingly achievable with the continued development of barcoding techniques.

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Introductory research essay (Department of Ecology, SLU)
Publisher: Department of Ecology, Swedish University of Agricultural Sciences

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