Matrilineal phylogeny and habitat suitability of the endangered spotted pond turtle (Geoclemys hamiltonii; Testudines: Geoemydidae): a two-dimensional approach to forecasting future conservation consequences

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Biodiversity and Conservation

Main article text

 

Introduction

Materials and Methods

Species identification and sampling

Mitochondrial DNA extraction, sequencing, and mitogenome assembly

Mitogenome characterization and phylogenetic analyses

Species occurrence information

Model covariate selection

Model building and evaluation

Assessment of habitat quality

Results

Mitogenome characterization and comparison

Major phylogenetic relationship

Model execution and habitat suitability

Habitat quality assessment

Discussion

Conclusions

Supplemental Information

List of acquired Testudines species mitogenomes from GenBank database for phylogenetic analysis along with their size and IUCN status.

DOI: 10.7717/peerj.15975/supp-1

Locality information of Geoclemys hamiltonii acquired from previous literature.

DOI: 10.7717/peerj.15975/supp-2

Primary environmental and topographical variables used for ensemble modelling.

DOI: 10.7717/peerj.15975/supp-3

Maximum Likelihood (ML) phylogenetic tree based on the concatenated nucleotide sequences of 13 PCGs showing the phylogenetic position of Geoclemys hamiltonii and other Geoemydidae species.

DOI: 10.7717/peerj.15975/supp-4

Representing the final set of variables maps used for the distribution modelling of Geoclemys hamiltonii.

DOI: 10.7717/peerj.15975/supp-5

Showing the response curves of the all the final selected variable (n = 50) iteration.

Curves show how each environmental variable affects the Maxent prediction. The curves show how the predicted probability of presence changes as each environmental variable is varied, keeping all other environmental variables at their average sample value. The curves show the mean response of the 50 replicate Maxent runs (red) and and the mean +/− one standard deviation (blue, two shades for categorical variables).

DOI: 10.7717/peerj.15975/supp-6

Representing the training omission rate and predicted area as a function of the cumulative threshold, averaged over the replicate runs.

DOI: 10.7717/peerj.15975/supp-7

Additional Information and Declarations

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Shantanu Kundu conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Tanoy Mukherjee performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Manokaran Kamalakannan performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Gaurav Barhadiya performed the experiments, analyzed the data, prepared figures and/or tables, and approved the final draft.

Chirashree Ghosh performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, project administration and funding acquisition, and approved the final draft.

Hyun-Woo Kim conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, project administration and funding acquisition, and approved the final draft.

Animal Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

No animals were encountered or killed from the wild and did not involve harm to the animal, hence no ethics committee or institutional review board approval is required for the present study. The experimental protocols were approved by the host institutions (Pukyong National University, South Korea; Zoological Survey of India, Indian Statistical Institute, and University of Delhi, India) and all procedures were accomplished in accordance with relevant guidelines and regulations of ARRIVE 2.0. (https://arriveguidelines.org).

Data Availability

The following information was supplied regarding data availability:

The nucleotide sequence data is available at GenBank: OP344485.

Funding

This research was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2021R1A6A1A03039211) and a grant from the Institute of Eminence (IOE), Ref. No./IoE/2021/12/FRP, University of Delhi, India. The Korea Institute of Marine Science and Technology Promotion (KIMST), funded by the Ministry of Oceans and Fisheries (Grant No. 20220214) supported the APC. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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