Modeling the Ecology and Evolution of Biodiversity

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Biodiversity Loss & Dynamics".

Deadline for manuscript submissions: closed (31 July 2022) | Viewed by 13113

Special Issue Editor

Department of Statistics, Feng-Chia University, Taichung 40724, Taiwan
Interests: mathematical modeling; trait evolution; stochastic modeling; phylogenetics comparative method; numerical analysis; approximate bayesian computation; statistical phylogenetics; evolutionary biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Comparative analysis is broadly applied in the fields of biodiversity, ecology, evolutionary biology, genetic diversity, paleoecology, phylogenetic, toxicology, zoology, etc.

The purpose of this Special Issue is to propose to the scientific community a collection of articles on the application of phylogenetic comparative analysis for these fields. Special attention will be paid to the use of various types of mathematical models or statistical methods, associated with applications for the empirical analysis of the biological variety and variability of life.

Potential topics include but are not limited to:

  • General ecological data analysis using the phylogenetic comparative method;
  • Statistical phylogenetic methods for comparative data analyses;
  • Mathematical models for explaining evolutionary phenomenon;
  • The application of mathematical models to study biodiversity;
  • The study of phylogenetic trait evolution.

Dr. Dwueng-Chwuan Jhwueng
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diversity is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • biodiversity
  • comparative analysis
  • ecological data analysis
  • phylogeny
  • statistical modeling
  • mathematical ecology
  • trait evolution

Published Papers (6 papers)

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Editorial

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2 pages, 161 KiB  
Editorial
Modeling the Ecology and Evolution of Biodiversity: Introduction to the Special Issue
by Dwueng-Chwuan Jhwueng
Diversity 2023, 15(1), 24; https://doi.org/10.3390/d15010024 - 23 Dec 2022
Viewed by 854
Abstract
Applying relevant statistical models to empirical data analysis has been considered a very important procedure for scientists to answer research questions in the fields of biodiversity, phylogeography, evolutionary biology, paleoecology, phylogenetics, and geography [...] Full article
(This article belongs to the Special Issue Modeling the Ecology and Evolution of Biodiversity)

Research

Jump to: Editorial

22 pages, 12617 KiB  
Article
Effect of Polytomy on the Parameter Estimation and Goodness of Fit of Phylogenetic Linear Regression Models for Trait Evolution
by Dwueng-Chwuan Jhwueng and Feng-Chi Liu
Diversity 2022, 14(11), 942; https://doi.org/10.3390/d14110942 - 02 Nov 2022
Cited by 2 | Viewed by 2892
Abstract
Phylogenetic regression models for trait evolution incorporate phylogenetic trees for the analysis of comparative data, in order to study trait relationships among a group of related species. However, as such trees are estimated, it is unlikely that there will be no errors when [...] Read more.
Phylogenetic regression models for trait evolution incorporate phylogenetic trees for the analysis of comparative data, in order to study trait relationships among a group of related species. However, as such trees are estimated, it is unlikely that there will be no errors when describing the relationships among species. In particular, for polytomy trees, where the relationships within a particular clade of species are more/less certainly determined (hard/soft polytomy, respectively), results of comparative analyses obtained from models based on those phylogenetic trees may also be affected. In this study, through extensive simulations, the performances of several popular Gaussian process-based regression models (Brownian motion, BM; Ornstein–Uhlenbeck process, OU; early burst, EB), as well as branch-stretching models (Pagel’s λ,δ,κ), were evaluated by assessing their fit and parameter estimation performance when soft polytomies are presented on either the root or a clade with insufficient phylogenetic information. Comparisons of the models are conducted by either assessing the accuracy of the estimator of regression and model parameters, or using a measure of fit (AIC, r2, and mean square error). It is found that, although polytomy does not significantly impact the fit and parameter estimate within a specified model, distinguishable differences and effects may be observed among trees and models. In particular, Pagel λ model and the OU model yield more accurate estimates and provide better fitting effects than the other models (BM, EB, δ, κ). While correcting phylogeny is an essential step prior to analysis, users may also consider using more appropriate models when encountering the polytomy issue. Full article
(This article belongs to the Special Issue Modeling the Ecology and Evolution of Biodiversity)
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14 pages, 2258 KiB  
Article
Phylogeographic Structuring of the Kuroshio-Type Prawn Macrobrachium japonicum (Decapoda: Palaemonidae) in Taiwan and Ryukyu Islands
by Chiao-Chuan Han, Chien-Hung Lai, Chi-Chun Huang, I-Chen Wang, Hung-Du Lin and Wei-Kuang Wang
Diversity 2022, 14(8), 617; https://doi.org/10.3390/d14080617 - 30 Jul 2022
Cited by 3 | Viewed by 1529
Abstract
Oceanic currents, biological traits, and geological evidence from historical climate change have shaped the distribution of genetic diversity and demographic history in Macrobrachium japonicum. In this study, we investigated the phylogeographic structures and demographic history of M. japonicum in Taiwan and the [...] Read more.
Oceanic currents, biological traits, and geological evidence from historical climate change have shaped the distribution of genetic diversity and demographic history in Macrobrachium japonicum. In this study, we investigated the phylogeographic structures and demographic history of M. japonicum in Taiwan and the Ryukyu Islands by the partial mitochondrial COI gene. The topology of the haplotype minimum-spanning network revealed a star-like structure, which suggested a recent range expansion. With the apparent lack of strong dispersal barriers to gene flow between ocean basins, amphidromous prawns, as marine organisms with larvae of high dispersal abilities, are generally expected to show genetic homogeneity. Divergence data suggested that M. japonicum populations diverged 0.462 ± 0.164 myr. Complex patterns of asymmetrical gene flow indicate that variation in dispersal ability is affected by the dominant Kuroshio Current systems of the Pacific Ocean. Analysis of its demographic history revealed that M. japonicum underwent a decline in size following a recent population expansion based on ABC analysis. Bayesian skyline plot analyses of all populations indicated that the expansion of M. japonicum was estimated to have occurred in 175 Kya and that the effective population size rapidly increased by approximately 50 Kya. The results of this study may offer both practical and theoretical value for the further study of conservation genetics, management, and sustainable resource utilization. Full article
(This article belongs to the Special Issue Modeling the Ecology and Evolution of Biodiversity)
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10 pages, 5436 KiB  
Article
Evaluation of Climate Change Impacts on the Global Distribution of the Calliphorid Fly Chrysomya albiceps Using GIS
by Eslam M. Hosni, Areej A. Al-Khalaf, Randa M. Naguib, Abdalrahman E. Afify, Ashraf A. Abdalgawad, Ehab M. Faltas, Mohamed A. Hassan, Mohamed A. Mahmoud, Omar M. Naeem, Yossef M. Hassan and Mohamed G. Nasser
Diversity 2022, 14(7), 578; https://doi.org/10.3390/d14070578 - 20 Jul 2022
Cited by 11 | Viewed by 2901
Abstract
Climate change is expected to influence the geographic distribution of many taxa, including insects. Chrysomya albiceps is one of the most pervasive calliphorid fly with apparent ecological, forensic, and medical importance. However, the global habitat suitability is varied due to climate change. Models [...] Read more.
Climate change is expected to influence the geographic distribution of many taxa, including insects. Chrysomya albiceps is one of the most pervasive calliphorid fly with apparent ecological, forensic, and medical importance. However, the global habitat suitability is varied due to climate change. Models that forecast species spatial distribution are increasingly being used in wildlife management, highlighting the need for trustworthy techniques to assess their accuracy. So, we used the maximum entropy implemented in Maxent to predict the current and future potential global geographic distribution of C. albiceps and algorithms of DIVA-GIS to confirm the predicted current model. The Maxent model was calibrated using 2177 occurrence records. Based on the Jackknife test, four bioclimatic variables along with altitude were used to develop the final models. For future models, two representative concentration pathways (RCPs), 2.6 and 8.5, for 2050 and 2070 were used. The area under curve (AUC) and true skill statistics (TSS) were used to evaluate the resulted models with values equal to 0.92 (±0.001) and 0.7, respectively. Two-dimensional niche analysis illustrated that the insect can adapt to low and high temperatures (9 °C to 27 °C), and the precipitation range was 0 mm to 2500 mm. The resulted models illustrated the global distribution of C. albiceps with alteration to its distribution in the future, especially on the Mediterranean coasts of Europe and Africa, Florida in the USA, and the coasts of Australia. Such predicted shifts put decision makers against their responsibilities to prevent destruction in economic, medical, and ecological sectors. Full article
(This article belongs to the Special Issue Modeling the Ecology and Evolution of Biodiversity)
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13 pages, 3497 KiB  
Article
Phylogenetic Tree Selection by Testing Substitution Number in Clade
by Weishan Chen and Hsiuying Wang
Diversity 2022, 14(7), 543; https://doi.org/10.3390/d14070543 - 06 Jul 2022
Cited by 3 | Viewed by 2105
Abstract
The phylogenetic tree is a widely-used tool to show the evolutionary relationship between taxa. There are many types of phylogenetic trees proposed in the literature such as maximum likelihood, neighbor-joining, and UPGMA trees. The topologies of different types of trees are not the [...] Read more.
The phylogenetic tree is a widely-used tool to show the evolutionary relationship between taxa. There are many types of phylogenetic trees proposed in the literature such as maximum likelihood, neighbor-joining, and UPGMA trees. The topologies of different types of trees are not the same. Even for the same type of tree, the topologies are different when they embed different nucleotide substitution models, such as the JC69 model, K80 model, TN93 model, and so on. Although each type of tree has its advantages, selecting a suitable tree among these choices becomes a challenging problem. In this study, we propose a method based on testing the nucleotide substitution number between sequences to select trees. An Ebolavirus example is used to illustrate the method. In addition, this approach can select a suitable nucleotide substitution model for a particular type of tree. For this ebolavirus example, the JC69 model is the selected substitution model for the maximum likelihood tree. Full article
(This article belongs to the Special Issue Modeling the Ecology and Evolution of Biodiversity)
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16 pages, 2228 KiB  
Article
Spatial Shifts in Species Richness in Response to Climate and Environmental Change: An Adaption of the EUROMOVE Model in the Czech Republic
by Elvis Tangwa, Vilem Pechanec, Jan Brus and Pavel Vyvlecka
Diversity 2022, 14(4), 235; https://doi.org/10.3390/d14040235 - 24 Mar 2022
Cited by 2 | Viewed by 1866
Abstract
Climate change has greatly altered plant habitats, resulting in greater biodiversity loss at different scales. Therefore, it is important to quantify such changes for better monitoring and conservation. In this study, we adapt the EUROMOVE model and its mean stable area indicator (MSAi) [...] Read more.
Climate change has greatly altered plant habitats, resulting in greater biodiversity loss at different scales. Therefore, it is important to quantify such changes for better monitoring and conservation. In this study, we adapt the EUROMOVE model and its mean stable area indicator (MSAi) to the conditions in the Czech Republic. Our objective was to predict change in species richness from a representative pool of 687 species from 1990 to 2100 under the RCP 8.5 climate scenario, focusing on the current period (2018). Another objective was to assess the effectiveness of the MSAi as a tool for quantifying landscape vulnerability. Our result shows that species habitat expanded between 1990 and 2018, although about 2 per cent of species were lost. The average MSAi of the most favourable highland habitats may decrease from 0.85 to 0.65 by 2100 as >20% of baseline species may be lost. Indicator species of Alnus (alder) and Festuca (fescue), typical of lowland habitats, are among the most vulnerable, already showing a net loss of their current habitat extent. The MSAi can be applied as a comprehensive tool to quantify the impact of climate change on landscape vulnerability as more survey data becomes available. Full article
(This article belongs to the Special Issue Modeling the Ecology and Evolution of Biodiversity)
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