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Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution

Lamichhaney, Sangeet, Card, Daren C., Grayson, Phil, Tonini, João F. R., Bravo, Gustavo A., Näpflin, Kathrin, Termignoni-Garcia, Flavia, Torres, Christopher, Burbrink, Frank, Clarke, Julia A., Sackton, Timothy B., Edwards, Scott V.·2019·Philosophical Transactions of the Royal Society B: Biological Sciences
DOI 10.1098/rstb.2018.0248
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Abstract

Evolutionary convergence has been long considered primary evidence of adaptation driven by natural selection and provides opportunities to explore evolutionary repeatability and predictability. In recent years, there has been increased interest in exploring the genetic mechanisms underlying convergent evolution, in part, owing to the advent of genomic techniques. However, the current ‘genomics gold rush’ in studies of convergence has overshadowed the reality that most trait classifications are quite broadly defined, resulting in incomplete or potentially biased interpretations of results. Genomic studies of convergence would be greatly improved by integrating deep ‘vertical’, natural history knowledge with ‘horizontal’ knowledge focusing on the breadth of taxonomic diversity. Natural history collections have and continue to be best positioned for increasing our comprehensive understanding of phenotypic diversity, with modern practices of digitization and databasing of morphological traits providing exciting improvements in our ability to evaluate the degree of morphological convergence. Combining more detailed phenotypic data with the well-established field of genomics will enable scientists to make progress on an important goal in biology: to understand the degree to which genetic or molecular convergence is associated with phenotypic convergence. Although the fields of comparative biology or comparative genomics alone can separately reveal important insights into convergent evolution, here we suggest that the synergistic and complementary roles of natural history collection-derived phenomic data and comparative genomics methods can be particularly powerful in together elucidating the genomic basis of convergent evolution among higher taxa. This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.

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  • If a replicated change in phenotype has been achieved through changes in different genetic elements, PhyloG2P methods will fail to identify them unless considerable prior knowledge of the genetic elements involved can be leveraged to identify genetic replication at the network or pathway level.

    “If a replicated change in phenotype has been achieved through changes in different genetic elements, then PhyloG2P methods will fail to identify them unless considerable prior knowledge of the genetic elements involved can be leveraged to identify genetic replication at the network or pathway level (Lamichhaney et al. 2019; Wheeler et al. 2022; Eastment et al. 2024; Shakya et al. 2025).”

    From From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions (2025) · cites this paper as Lamichhaney et al. 2019

  • Presence/absence based studies may oversimplify the biological processes under investigation, limiting the insights gained.

    “they may also oversimplify the biological processes under investigation, limiting the insights gained (Lamichhaney et al. 2019).”

    From From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions (2025) · cites this paper as Lamichhaney et al. 2019

  • To fully characterize the genetic changes associated with evolutionary adaptations involving multiple traits, the traits may need to be investigated individually in addition to studying their collective replicated evolution.

    “Therefore, to fully characterize the genetic changes associated with evolutionary adaptations involving multiple traits, such as those seen in marine mammals, the traits may need to be investigated individually in addition to studying their collective replicated evolution (Speed and Arbuckle 2017; Lamichhaney et al. 2019).”

    From From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions (2025) · cites this paper as Lamichhaney et al. 2019

  • For simple traits with easily quantifiable phenotypes and a simple genetic basis, PhyloG2P studies will have a chance to identify specific genotype-to-phenotype maps.

    “On one end, we can conceptualize “simple” traits with both easily quantifiable phenotypes and a simple genetic basis. Here PhyloG2P studies will have a chance to identify specific genotype to phenotype maps (Lamichhaney et al. 2019; Nagy et al. 2020; Okuyama et al. 2025).”

    From From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions (2025) · cites this paper as Lamichhaney et al. 2019

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Metadata

Authors
Lamichhaney, S., Card, D. C., Grayson, P., Tonini, J. F. R., Bravo, G. A., Näpflin, K., Termignoni-Garcia, F., Torres, C., Burbrink, F., Clarke, J. A., Sackton, T. B., & Edwards, S. V.
Affiliations
  • Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
  • Department of Biology, The University of Texas at Austin, Austin, MA 78712, USA
  • Department of Herpetology, The American Museum of Natural History, New York, NY 10024, USA
  • Informatics Group, Harvard University, Cambridge, MA 02138, USA
ORCID
Venue
Philosophical Transactions of the Royal Society B: Biological Sciences
Publisher
The Royal Society
Published
2019-06-03
Volume
374
Issue
1777
Pages
20180248
ISSN
  • 0962-8436
  • 1471-2970
DOI
10.1098/rstb.2018.0248
Cited by
44
References
10
Language
en
Licence
royalsociety.org/journals/ethics-policies/data-sharing-mining/ (tdm)
Funders
  • Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada
  • Division of Biological Infrastructure (1812310)
  • Division of Environmental Biology (1355343)
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
  • Wenner Gren Foundation
  • Harvard CONACYT (Mexico) Postdoctoral Fellowship Program
  • Division of Earth Sciences (1355292)
  • Lemman Brazil Research Fund at Harvard University

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