Shall we all adopt, with no worries, the ‘within a configuration’ approach in geometric morphometrics? A comment on claims that the effect of the superimposition and sliding on shape data is “not an obstacle to analyses of integration and modularity” DOI Open Access
Andrea Cardini

Published: July 17, 2023

The study of modularity and integration using Procrustes geometric morphometrics has become a prominent approach in evolutionary developmental biology. A most popular method is the ‘within configuration’ approach, often used combination with ‘high density’ morphometric data (i.e., large numbers landmarks semilandmarks). In 2019, I realized that this violates basic assumption shape analysis superimposition methods showed violation may increase rate false positives, beyond nominal value, statistical tests. very recent study, however, argues simulations four different datasets indicate theoretical mostly negligible effect on tests, so it “is not an obstacle to analyses modularity” (p. 167, Zelditch Swiderski, 2023). Its authors also claim mischaracterized methods, overstated problem published non-reproducible results. paper, carefully compare their statements mine, as well our results, demonstrate that: 1) always present; 2) overlook importance power p/N ratios (p = number variables; N sample size); 3) results are case-specific but, fact, perfectly congruent single dataset common between both studies; 4) impact especially concerning, based mine findings, precisely ‘high-density’ analyses, claimed be state-of-the-art field; 5) unlike claims external validity generalizes from few cases, explicitly stated multiple times my findings were specific analysed, parameters tests explored. If confirmed by future research, fact fully corroborate original suggestions that, despite undeniable issue, its vary, assessment complex generalizations unlikely easy. However, preliminary work all simulations, semilandmarks slid according minimum bending energy criterion, strongly serious problems might affect highly advertised integration. Given popularity, likely dozens studies high journals have little more than methodological artefacts.

Language: Английский

Morphological evolution in a time of Phenomics DOI Creative Commons
Anjali Goswami, Julien Clavel

Published: Jan. 10, 2024

Organismal morphology has been at the core of study biodiversity for millennia before formalization concept evolution. In early to mid-twentieth century, a strong theoretical framework was developed understanding both pattern and process morphological evolution on macroevolutionary scale. The past half century transformational period evolutionary morphology, in quantification novel analytical tools estimating how why diversity changes through time, with marked increase studies apparent 1990s. We are now another inflection point evolution, availability vast amounts high-resolution data sampling extant extinct allowing ‘omics’-scale analysis. Artificial intelligence is already increasing pace phenomic collection even further. This new reality, where ability obtain quickly outpacing analyse it robust, realistic models, brings set challenges, we here present analyses demonstrating these challenges discussing solutions. Fully transitioning into “Omics” era will involve development automate extraction meaningful, comparable morphometric from images, integrate fossil large phylogenetic trees downstream analyses, generate robust models that accurately reflect complexity processes well-suited high-dimensional data. Combined, advancements solidify emerging field phenomics appropriately center around analysis unambiguously critical deep-time

Language: Английский

Citations

5
Morphological evolution in a time of phenomics DOI Creative Commons
Anjali Goswami, Julien Clavel

Paleobiology, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 19

Published: March 11, 2025

Abstract Organismal morphology was at the core of study biodiversity for millennia before formalization concept evolution. In early to mid-twentieth century, a strong theoretical framework developed understanding both pattern and process morphological evolution, 50 years since founding this journal capture transformational period in quantification analytical tools estimating how diversity changes through time. We are now another inflection point with availability vast amounts high-resolution data sampling extant extinct allowing “omics”-scale analysis. Artificial intelligence is accelerating pace phenomic acquisition even further. This new reality, which ability obtain quickly outpacing analyze it robust, realistic evolutionary models, brings set challenges. Phylogenetic comparative methods have provided insights into processes generating diversity, but reliance on molecular resultant exclusion fossil from most large phylogenetic trees has well-established negative impacts analyses, as we demonstrate examples standard single-rate mode- rate-shift recently described Ornstein-Uhlenbeck climate model. Further development analysis high-dimensional needed, existing can refine our expectations evolution generation under different scenarios, analyses placental skull Cenozoic. Fully transitioning omics era will involve automate extraction meaningful, comparable morphometric images, integrate downstream generate robust models that accurately reflect complexity well-suited data. Combined, these advancements solidify emerging field phenomics appropriately center around deep-time

Language: Английский

Citations

0
Functional modularity and mechanical stress shape plastic responses during fish development DOI
Leandro Lofeu, Felipe C. Montefeltro, Monique Nouailhetas Simon

et al.

Evolution, Journal Year: 2024, Volume and Issue: 78(9), P. 1568 - 1582

Published: June 6, 2024

The adaptive potential of plastic phenotypes relies on combined developmental responses. We investigated how manipulation conditions related to foraging mode in the fish Megaleporinus macrocephalus induces responses at different levels: (a) functional modularity skull bones, (b) biomechanical properties chondrocranium using finite element models, (c) bmp4 expression levels, used as a proxy for molecular pathways involved bone mechanical load. identified new modules experimental groups, suggesting increased integration specific head elements associated with development subterminal and upturned mouths, which are major features morphotypes released lab. Plastic shape differences magnitude stress, seem restricted certain regions. Three bones represent "mechanical unit" changes mouth position induced by mode, that might be enhanced way regions respond Differences levels between indicate associations signaling Our results offer multilevel perspective epigenetic factors responses, expanding our knowledge about mechanisms plasticity originate novel complex phenotypes.

Language: Английский

Citations

3
Topological and variational modularity: A case study using the pectoral girdle across the Chrosomus eos‐neogaeus hybridization complex DOI Creative Commons
Kevin K. Duclos,

Thomas Grünbaum,

Bernard Angers

et al.

The Anatomical Record, Journal Year: 2025, Volume and Issue: unknown

Published: April 24, 2025

Abstract Modularity and integration are key developmental properties have remained central in evo‐devo research because of how they relate to evolvability. While modularity commonly been assessed with landmark‐based geometric morphometrics (GMM), other methods such as anatomical network analysis (AnNA) increasingly being explored. Nonetheless, AnNA has seldom used assess variability within taxa, there no attempts verify whether its results commensurate GMM. We the pectoral girdle members Chrosomus eos‐neogaeus hybridization complex a case study system differences between GMM‐based approaches discuss should be best used. The general anatomy composition do not vary much complex; however, bones show significant diversity morphology presence sutures. Indeed, C. neogaeus displays characteristically enlarged coracoids radials, bone fusion cleithra, coracoids, while eos gracile unfused girdle. Hybrids display morphologies that distinct from both parental species. detected multiple potential patterns modularity, GMM supported similar across but suggested different trajectories morphological variation. Altogether, can valuable tool formulate novel hypotheses understudied which may then tested using GMM, careful descriptions skeletal systems addition interpretation approaches.

Language: Английский

Citations

0
Testing ecological function in the carving of anomalodesmatan morphospace (Mollusca: Bivalvia: Anomalodesmata) DOI
Yue Deng

Journal of Molluscan Studies, Journal Year: 2024, Volume and Issue: 90(4)

Published: Sept. 30, 2024

ABSTRACT Today, the most taxonomically rich bivalve clade is Imparidentia. However, 300 million years ago, Imparidentia's sister clade, Anomalodesmata, was dominant among marine bivalves, while Imparidentia much less diverse. Both clades are ecologically diverse but infaunal suspension-feeding mode of life in each. When taxonomic diversity and morphological disparity plotted through time for each diversified faster Mesozoic than Anomalodesmata until K/Pg boundary, when extinction event interrupts pattern, both then parallel Cenozoic. In this paper, I test hypothesis that has an effect on disparification diversification, by separating themselves from mode, some ‘divergent’ anomalodesmatan lineages may have been able to free direct competition with imparidents once more start rise diversity. During Cenozoic, divergent does increase compared their relatives. not differ between lineages. This suggests functional partitioning drives disparification, diversification.

Language: Английский

Citations

1
Tying the knot between morphology and development: Using enamel-knot determined dental morphology to study the evolution of molarization in hoofed mammals DOI Creative Commons
Austin J. Ashbaugh, Heather A. Jamniczky, Jessica M. Theodor

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: June 13, 2024

Abstract Molariform teeth have fascinated zoologists for as long the field of evolutionary biology has existed, but few mammalian groups show much morphological variation hoofed mammals. Ungulate premolars and molars function together post-canine unit in grinding mastication. The degree similarity to crown complexity varies wildly across dietary ecologies similar morphologies are refered molarized. However, vast majority dental evolution research over past 30 years focused on molar morphogenesis rather than interregional phenomena such molarization. Dental vertebrates is controlled by signalling centers known enamel knots all regions jaw. In this study we tested whether applying current knowledge knot driven shape covariation premolar boundary would inform potential mechanisms molarization We used 2D geometric morphometrics enamel-knot at lower boundaries 16 artiodactyl 18 perissodactyls species. Phylogenetically informed modularity analyses were test several a-priori morphogenetic hypotheses describing different developmental interactions between molars. Our results showed artiodactyls significantly differ their caused heterochronic shifts development. To our knowledge, first contribute a comprehensive yet accesible morphometric method produce heuristic further investigating molarized premolars.

Language: Английский

Citations

0
WingAnalogy: a computer vision-based tool for automated insect wing asymmetry and morphometry analysis DOI Creative Commons
Shahab Eshghi, Hamed Rajabi, Natalia A. Matushkina

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Sept. 27, 2024

Language: Английский

Citations

0
Shall we all adopt, with no worries, the ‘within a configuration’ approach in geometric morphometrics? A comment on claims that the effect of the superimposition and sliding on shape data is “not an obstacle to analyses of integration and modularity” DOI Open Access
Andrea Cardini

Published: July 1, 2023

The study of modularity and integration using Procrustes geometric morphometrics has become a prominent approach in evolutionary developmental biology. A most popular method is the ‘within configuration’ approach, often used combination with ‘high density’ morphometric data (i.e., large numbers landmarks semilandmarks). In 2019, I realized that this violates basic assumption shape analysis superimposition methods showed violation may increase rate false positives, beyond nominal value, statistical tests. very recent study, however, argues simulations four different datasets indicate theoretical mostly negligible effect on tests, so it “is not an obstacle to analyses modularity” (p. 167, Zelditch Swiderski, 2023). Its authors also claim mischaracterized methods, overstated problem published non-reproducible results. paper, carefully compare their statements mine, as well our results, demonstrate that: 1) always present; 2) overlook importance power p/N ratios (p = number variables; N sample size); 3) results are case-specific but, fact, perfectly congruent single dataset common between both studies; 4) impact especially concerning, based mine findings, precisely ‘high-density’ analyses, claimed be state-of-the-art field; 5) unlike claims external validity generalizes from few cases, explicitly stated multiple times my findings were specific analysed, parameters tests explored. If confirmed by future research, fact fully corroborate original suggestions that, despite undeniable issue, its vary, assessment complex generalizations unlikely easy. However, preliminary work all simulations, semilandmarks slid according minimum bending energy criterion, strongly serious problems might affect highly advertised integration. Given popularity, likely dozens studies high journals have little more than methodological artefacts.

Language: Английский

Citations

1
Shall we all adopt, with no worries, the ‘within a configuration’ approach in geometric morphometrics? A comment on claims that the effect of the superimposition and sliding on shape data is “not an obstacle to analyses of integration and modularity” DOI Open Access
Andrea Cardini

Published: July 17, 2023

The study of modularity and integration using Procrustes geometric morphometrics has become a prominent approach in evolutionary developmental biology. A most popular method is the ‘within configuration’ approach, often used combination with ‘high density’ morphometric data (i.e., large numbers landmarks semilandmarks). In 2019, I realized that this violates basic assumption shape analysis superimposition methods showed violation may increase rate false positives, beyond nominal value, statistical tests. very recent study, however, argues simulations four different datasets indicate theoretical mostly negligible effect on tests, so it “is not an obstacle to analyses modularity” (p. 167, Zelditch Swiderski, 2023). Its authors also claim mischaracterized methods, overstated problem published non-reproducible results. paper, carefully compare their statements mine, as well our results, demonstrate that: 1) always present; 2) overlook importance power p/N ratios (p = number variables; N sample size); 3) results are case-specific but, fact, perfectly congruent single dataset common between both studies; 4) impact especially concerning, based mine findings, precisely ‘high-density’ analyses, claimed be state-of-the-art field; 5) unlike claims external validity generalizes from few cases, explicitly stated multiple times my findings were specific analysed, parameters tests explored. If confirmed by future research, fact fully corroborate original suggestions that, despite undeniable issue, its vary, assessment complex generalizations unlikely easy. However, preliminary work all simulations, semilandmarks slid according minimum bending energy criterion, strongly serious problems might affect highly advertised integration. Given popularity, likely dozens studies high journals have little more than methodological artefacts.

Language: Английский

Citations

0