A CURE for a Major Challenge in Phenomics: A Practical Guide to Implementing a Quantitative Specimen-Based Undergraduate Research Experience

Price, Samantha A.; Larouche, Olivier; Friedman, Sarah T.; Corn, Katherine A.; Wainwright, Peter C.; Martinez, Christopher M.

doi:10.1093/iob/obaa004

Cited by 4 publications

(5 citation statements)

References 33 publications

(30 reference statements)

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“…This study makes use of a large morphological dataset for teleost fishes, collected collaboratively by the authors and a team of undergraduate researchers (see Price et al, 2020, for details on student involvement) on museum specimens from the Smithsonian National Museum of Natural History. Here, we use a subset of these data consisting of marine species with documented depth of occurrence.…”

Section: Methodsmentioning

confidence: 99%

The deep sea is a hot spot of fish body shape evolution

et al. 2021

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Deep‐sea fishes have long captured our imagination with striking adaptations to life in the mysterious abyss, raising the possibility that this cold, dark ocean region may be a key hub for physiological and functional diversification. We explore this idea through an analysis of body shape evolution across ocean depth zones in over 3000 species of marine teleost fishes. We find that the deep ocean contains twice the body shape disparity of shallow waters, driven by elevated rates of evolution in traits associated with locomotion. Deep‐sea fishes display more frequent adoption of forms suited to slow and periodic swimming, whereas shallow living species are concentrated around shapes conferring strong, sustained swimming capacity and manoeuvrability. Our results support long‐standing impressions of the deep sea as an evolutionary hotspot for fish body shape evolution and highlight that factors like habitat complexity and ecological interactions are potential drivers of this adaptive diversification.

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Section: Methodsmentioning

confidence: 99%

The deep sea is a hot spot of fish body shape evolution

et al. 2021

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“…For further details on data collection, measurements and collation methods see Price et al [21]. Notably, a large part of the data collection involved undergraduate researchers through a coursebased undergraduate research experience [22].…”

Section: Materials and Methods (A) Data Collection And Preparationmentioning

confidence: 99%

Body shape diversification along the benthic–pelagic axis in marine fishes

et al. 2020

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Colonization of novel habitats can result in marked phenotypic responses to the new environment that include changes in body shape and opportunities for further morphological diversification. Fishes have repeatedly transitioned along the benthic–pelagic axis, with varying degrees of association with the substrate. Previous work focusing on individual lineages shows that these transitions are accompanied by highly predictable changes in body form. Here, we generalize expectations drawn from this literature to study the effects of habitat on body shape diversification across 3344 marine teleost fishes. We compare rates and patterns of evolution in eight linear measurements of body shape among fishes that live in pelagic, demersal and benthic habitats. While average body shape differs between habitats, these differences are subtle compared with the high diversity of shapes found within each habitat. Benthic living increases the rate of body shape evolution and has led to numerous lineages evolving extreme body shapes, including both exceptionally wide bodies and highly elongate, eel-like forms. By contrast, we find that benthic living is associated with the slowest diversification of structures associated with feeding. Though we find that habitat can serve as an impetus for predictable trait changes, we also highlight the diversity of responses in marine teleosts to opportunities presented by major habitats.

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“…We compared our biogeographic results to ancestral state reconstructions of morphology ( 3 , 49 – 51 ) and pelagic/demersal life habit ( SI Appendix , Table S1 ) to test if deep-sea colonization was related to preexisting ecology and how these relationships changed over time. Early deep-sea colonizations were pelagic (e.g., Argentiniformes, Stomiatiformes) ( Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Conversely, this would imply that some shallow clades do not colonize because they have body plans ill-suited for life in the deep sea. We tested this hypothesis using a morphological dataset spanning teleost fishes based on museum specimens ( 49 , 50 ). This dataset includes eight functionally relevant linear measurements: standard length, maximum body depth, maximum fish width, head depth, lower jaw length, mouth width, minimum caudal peduncle depth, and minimum caudal peduncle width.…”

Section: Methodsmentioning

confidence: 99%

Alternating regimes of shallow and deep-sea diversification explain a species-richness paradox in marine fishes

Miller

Martinez

Friedman

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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The deep sea contains a surprising diversity of life, including iconic fish groups such as anglerfishes and lanternfishes. Still, >65% of marine teleost fish species are restricted to the photic zone <200 m, which comprises less than 10% of the ocean’s total volume. From a macroevolutionary perspective, this paradox may be explained by three hypotheses: 1) shallow water lineages have had more time to diversify than deep-sea lineages, 2) shallow water lineages have faster rates of speciation than deep-sea lineages, or 3) shallow-to-deep sea transition rates limit deep-sea richness. Here we use phylogenetic comparative methods to test among these three non-mutually exclusive hypotheses. While we found support for all hypotheses, the disparity in species richness is better described as the uneven outcome of alternating phases that favored shallow or deep diversification over the past 200 million y. Shallow marine teleosts became incredibly diverse 100 million y ago during a period of warm temperatures and high sea level, suggesting the importance of reefs and epicontinental settings. Conversely, deep-sea colonization and speciation was favored during brief episodes when cooling temperatures increased the efficiency of the ocean’s carbon pump. Finally, time-variable ecological filters limited shallow-to-deep colonization for much of teleost history, which helped maintain higher shallow richness. A pelagic lifestyle and large jaws were associated with early deep-sea colonists, while a demersal lifestyle and a tapered body plan were typical of later colonists. Therefore, we also suggest that some hallmark characteristics of deep-sea fishes evolved prior to colonizing the deep sea.

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A CURE for a Major Challenge in Phenomics: A Practical Guide to Implementing a Quantitative Specimen-Based Undergraduate Research Experience

Cited by 4 publications

References 33 publications

The deep sea is a hot spot of fish body shape evolution

The deep sea is a hot spot of fish body shape evolution

Body shape diversification along the benthic–pelagic axis in marine fishes

Alternating regimes of shallow and deep-sea diversification explain a species-richness paradox in marine fishes

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