Study case
This report analyzes genetic data from the study by Uhlir et al. (2021) on Cumacea species. The study emphasized the influence of climatic and geographic factors on species distribution and genetic differentiation. This report evaluates key genetic metrics and their alignment with the conclusions of the study.
The genetic analysis provided in the study includes the following summary statistics:
| Metric | Mean | Std Dev | Min | 25% | 50% | 75% | Max |
|---|---|---|---|---|---|---|---|
| Bootstrap mean | 99.52 | 1.20 | 95.0 | 99.0 | 100 | 100 | 100 |
| Least-Square Distance | 96.20 | 1.94 | 90.2 | 95.0 | 96.5 | 98.0 | 99.8 |
| Robinson-Foulds Distance | 65.30 | 1.56 | 62.0 | 64.0 | 65.0 | 67.0 | 68.0 |
| Normalised RF Dist | 0.65 | 0.02 | 0.60 | 0.64 | 0.65 | 0.66 | 0.68 |
| Euclidean Distance | 0.66 | 0.01 | 0.63 | 0.65 | 0.66 | 0.67 | 0.68 |
The study utilized genetic and environmental analyses to understand biogeographical patterns of Cumacea. Key findings included significant species differentiation, geographic barriers affecting species distribution, and correlations between environmental factors and genetic diversity.
- Bootstrap Mean: High bootstrap mean (99.52) indicates strong support for phylogenetic trees, consistent with the observation of congruence between morphological and molecular species delimitation.
- Least-Square Distance: Mean value of 96.20 with low variability supports robust species delimitation, aligning with significant genetic distances between species noted in the study.
- Robinson-Foulds Distance: Mean of 65.30 indicates moderate differences between phylogenetic trees, suggesting cryptic diversity and ecological diversification.
- Normalized RF and Euclidean Distances: Consistent values (0.65 and 0.66, respectively) suggest genetic differentiation across samples, reinforcing findings of distinct genetic clusters corresponding to different species.
- Distribution Patterns: Genetic distances support distinct biogeographical distribution patterns. The GIS-Ridge, noted as a geographical barrier, aligns with genetic differentiation indicated by the data.
- Species Richness and Cryptic Species: Low variability in genetic distances supports the discovery of cryptic species, corroborating the findings of hidden diversity.
Analysis using aPhyloGeo software provides additional context (see next Figures 1a and 1b):
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Climatic Influence: Significant correlation between genetic sequences and environmental factors, specifically:
- Wind Speed (m/s): High correlation with genetic variation between positions 560 and 569 nucleotides.
- Oxygen Concentration (mg/L): High correlation with genetic variation between positions 1210 and 1219 nucleotides.
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| Figure 1. a). Analysis of fluctuations in the four distances metrics using multiple sequence alignment (MSA) in correlation with wind speed (m/s) at the start of sampling and b). Analysis of fluctuations in the four distances metrics using multiple sequence alignment (MSA) in correlation with oxygen concentration (mg/L) where the samples were collected |
The genetic data supports the findings of Uhlir et al. (2021):
- Bootstrap Mean: Mean of 99.52, median of 100, with most values at 100, indicating strong phylogenetic support.
- Least-Square Distance: Mean of 96.20, range from 90.2 to 99.8, suggesting robust species delimitation.
- Robinson-Foulds Distance: Mean of 65.30, range from 62.0 to 68.0, indicating moderate topological differences reflective of cryptic diversity.
- Normalized RF and Euclidean Distances: Mean values of 0.65 and 0.66, respectively, suggest consistent genetic differentiation.
These values underscore genetic differentiation and significant species delimitation noted by Uhlir et al. The correlation with environmental factors such as wind speed and oxygen concentration further supports the hypothesis of environmental adaptation influencing genetic diversity.
- Wind Speed (m/s) Correlation: Positions 560-569 nucleotides show high sensitivity to wind speed, indicating possible adaptations to wind-related environmental changes.
- Oxygen Concentration (mg/L) Correlation: Positions 1210-1219 nucleotides display high sensitivity to oxygen concentration, suggesting adaptations to oxygen availability in different habitats.
Interesting elements from the genetic data and aPhyloGeo analysis support the findings regarding the impact of climatic and geographic factors on Cumacea species distribution and genetic differentiation. Genetic evidence and environmental correlations highlight the role of natural selection in shaping marine biodiversity in response to climatic variations.
#Future Research Directions:
The upcoming version of the aPhyloGeo software will integrate a range of advanced statistical tests to further validate and enhance the results provided by the tool. This will include an in-depth analysis of correlations with highly mutagenic genetic zones, a comprehensive evaluation of the 3D structure of genetic sequences, and an overall optimization aimed at improving the tool's efficiency and applicability across various systems.
Uhlir, C., Schwentner, M., Meland, K., Kongsrud, J. A., Glenner, H., Brandt, A., Thiel, R., Svavarsson, J., Lörz, A.-N., & Brix, S. (2021). Adding pieces to the puzzle: insights into diversity and distribution patterns of Cumacea (Crustacea: Peracarida) from the deep North Atlantic to the Arctic Ocean. PeerJ, 9, e12379. 10.7717/peerj.12379