GPSA2: combining landmark-free and landmark-based methods in geometric morphometrics DOI Creative Commons

Benjamin J Pomidor,

Matt Dean

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 6, 2024

ABSTRACT Geometric Morphometrics (GM) revolutionized the way that biologists quantify shape variation among individuals, populations, and species. Traditional GM methods are based on homologous landmarks can be reliably identified across all specimens in a sample. However, landmark-based studies limited by intensive labor required of anatomical experts, regions interest often devoid landmarks. These limitations inspired development many “landmark-free” approaches, but unreliable homology estimation complicated underlying mathematical bases make biological interpretation challenging. Here we present GPSA2, novel method for analyzing surface meshes combines landmark-free methodology within familiar framework Generalized Procrustes Analysis. In major innovation, our incorporate user-defined into otherwise analysis transforming pointwise descriptors exploited during iterative superimposition (i.e. “alignment” objects). GPSA2 also addresses longstanding issue morphometrics – impact variability distribution sampled points over an object introducing area-weighted distance metric cost function. The improved approximation, together with application Taubin smoothing optional resistant-fit technique, ensure robust even when dataset exhibits intense variation. We apply to two empirical datasets: 15 primate skulls 369 mouse bacula. Our analyses show inclusion increases accuracy, produces summaries easy visualize interpret.

Language: Английский

What Doesn't Kill You Makes You Stronger? Examining Relationships Between Early‐Life Stress, Later‐Life Inflammation and Mortality Risk in Skeletal Remains DOI Creative Commons
Ben Wigley, Eleanor Stillman, Elizabeth Craig‐Atkins

et al.

American Journal of Physical Anthropology, Journal Year: 2025, Volume and Issue: 186(2)

Published: Feb. 1, 2025

ABSTRACT Objectives This paper explores conflicting perspectives on the adaptive significance of phenotypic plasticity during fetal and early postnatal development impact that stressors experienced this critical early‐life period have later‐life morbidity mortality risk. Methods The sample ( n = 216) comprised archeologically‐recovered human skeletons. A geometric morphometric (GM) method was employed to evaluate first permanent molar (M1) fluctuating asymmetry (FA) provide a proxy for stress. Shifts in physiology were inferred through two inflammatory lesions: periosteal new bone formation (PNBF) periodontal disease (PD). To explore risk, age‐at‐death estimated dental skeletally immature individuals 104) senescent skeletal changes mature skeletons 112). Results Significant differences found M1 FA between groups, with cohort associated elevated FA. Within‐group analysis revealed group had significant positive relationship PD presence. In group, alongside sex co‐occurrence PNBF, predictor shorter life. Higher also active bilaterally expressed PNBF. Conclusions It is theorized stress, if survived, programmed hyperinflammatory response environmentally‐mediated physiological perturbations which increased chances survival subsequent but Findings demonstrate complicated developmental stress shifts helps illustrate programming support Thrifty Phenotype hypothesis.

Language: Английский

Citations

0
An Integrative Approach of Taxonomic, Morphometric and Ecological Research to Solve the Status of Cryptic Chelonian Taxa—A Case Study With Pelomedusa kobe in Rwanda DOI

Christella Umulisa,

Marko Djurakić, Drew Bantlin

et al.

African Journal of Ecology, Journal Year: 2025, Volume and Issue: 63(1)

Published: Jan. 1, 2025

ABSTRACT Using genetic data, we confirm for the first time presence of Tanzanian helmeted terrapin Pelomedusa kobe in Akagera National Park, Rwanda, extending their known distribution. Our study provides natural history observations, population and morphological data this species from a wild population. As genus are morphologically difficult to distinguish, gain insights into intraspecific interspecific patterns size shape variation plastron morphology between two morphologically‐similar living Eastern Africa, P. subrufa , using geometric morphometrics. Species affiliation, rather than sex, is dominant factor influencing variation. exhibits female‐based sexual dimorphism (SSD), while shows tendency toward male‐based SSD. Furthermore, (SShD) was observed but not . results provide integrative (genetic, history) on however further information distribution park needed effective conservation data‐deficient species. findings lay groundwork future ecological studies potentially revealing unique adaptations needs previously overlooked due its cryptic nature.

Language: Английский

Citations

0
“Visiting scientist effect”? Exploring the impact of time‐lags in the digitization of 2D landmark data DOI Creative Commons
Andrea Cardini

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

Published: March 31, 2025

Abstract Measurement error (ME) in geometric morphometrics has been the subject of countless articles, but none specific to effect time lags on landmark digitization error. Yet, especially for visiting scientists working museum collections, it is not uncommon collect data multiple rounds, with interruptions weeks or years. To explore impact Procrustes shape analysis, I repeatedly digitized same landmarks, photographs crania adult yellow‐bellied marmots, at progressively longer intervals, ranging from a few hours days, and, one case, many Using battery methods, found that there indeed time‐related systematic ME suggesting possibility “visiting scientist effect” biasing patterns. However, relationship between and magnitude bias simple linear, complex. Interestingly, results tests sexual dimorphism allometry modest, mostly negligible, unless design collection highly unbalanced. When this happens, as simulated case where females are first males only later (or vice versa), biological variation becomes important can even lead opposite conclusions group differences. will discuss when more problematic how try mitigate potential analyses.

Language: Английский

Citations

0
Measurement error and effect size in geometric morphometrics: assessing the impact of 2D landmark digitization error in interspecific comparisons of Procrustes shape data DOI Creative Commons
Andrea Cardini

Zoomorphology, Journal Year: 2025, Volume and Issue: 144(2)

Published: April 26, 2025

Language: Английский

Citations

0
Simplifying the Centrolene buckleyi complex (Amphibia: Anura: Centrolenidae): a taxonomic review and description of two new species DOI Creative Commons
Daniela Franco-Mena, Ignacio De la Riva, Mateo A. Vega-Yánez

et al.

PeerJ, Journal Year: 2024, Volume and Issue: 12, P. e17712 - e17712

Published: Aug. 20, 2024

Centrolenidae is a Neotropical family widely distributed in Central and South America, with its species richness concentrated the tropical Andes. Several taxonomic problems have been identified within this family, mostly related to broad geographic distributions. In study, we assessed redefined boundaries of Centrolene buckleyi complex, formally described two new from Andes Ecuador. These taxa are recognized by combination morphometric, osteological, acoustic, genetic data. Following IUCN criteria, propose that should be considered as Endangered (EN), mainly because their small distributions habitat loss. The C. complex provides insights into biogeography closely Andean species. As other glassfrogs, speciation seems mediated linearity Andes, where gene flow can restricted topography and, also, local extinctions.

Language: Английский

Citations

1
GPSA2: combining landmark-free and landmark-based methods in geometric morphometrics DOI Creative Commons

Benjamin J Pomidor,

Matt Dean

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 6, 2024

ABSTRACT Geometric Morphometrics (GM) revolutionized the way that biologists quantify shape variation among individuals, populations, and species. Traditional GM methods are based on homologous landmarks can be reliably identified across all specimens in a sample. However, landmark-based studies limited by intensive labor required of anatomical experts, regions interest often devoid landmarks. These limitations inspired development many “landmark-free” approaches, but unreliable homology estimation complicated underlying mathematical bases make biological interpretation challenging. Here we present GPSA2, novel method for analyzing surface meshes combines landmark-free methodology within familiar framework Generalized Procrustes Analysis. In major innovation, our incorporate user-defined into otherwise analysis transforming pointwise descriptors exploited during iterative superimposition (i.e. “alignment” objects). GPSA2 also addresses longstanding issue morphometrics – impact variability distribution sampled points over an object introducing area-weighted distance metric cost function. The improved approximation, together with application Taubin smoothing optional resistant-fit technique, ensure robust even when dataset exhibits intense variation. We apply to two empirical datasets: 15 primate skulls 369 mouse bacula. Our analyses show inclusion increases accuracy, produces summaries easy visualize interpret.

Language: Английский

Citations

0