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Research article
Evolutionary pattern of Macaca fascicularis in Southeast Asia inferred using Y-chromosomal gene
Faisal Ali Anwarali Khan
Universiti Malaysia Sarawak (UNIMAS)
Corresponding Author
ORCiD: https://orcid.org/0000-0001-7585-4885
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Ecology and Evolution.
Background: We analyzed a combined segment (2,032-bp) of the sex-determining region and the testis-specific protein of the Y-chromosome (Y-DNA) gene to clarify the gene flow and phylogenetic relationships of the long-tailed macaques (Macaca fascicularis) in Southeast Asia. Phylogenetic relationships were constructed using the maximum likelihood, Bayesian inference, and the median-joining network from a total of 164 adult male M. fascicularis from 62 localities in Malaysia, including sequences from the other regions from previous studies.
Results: Based on Y-DNA, we confirm the presence of two lineages of M. fascicularis: the Indochinese and Sundaic lineages. The Indochinese lineage is represented by M. fascicularis located northwards of the Surat Thani-Krabi depression region and is introgressed by the Macaca mulatta Y-DNA. The Sundaic lineage is free from such hybridization event, thus defined as the original carrier of the M. fascicularis Y-DNA. We further revealed that the Sundaic lineage differentiated into two forms: the insular and the continental forms. The insular form, which represents the ancestral form of M. fascicularis, consists of two haplotypes: a single homogenous haplotype occupying the island of Borneo, Philippines, and southern Sumatra; and the Javan haplotype. The more diverse continental form consists of 17 haplotypes in which a dominant haplotype was shared by individuals from southern Thai Peninsular (south of Surat Thani-Krabi depression), Peninsular Malaysia, and Sumatra. Uniquely, Sumatra contains both the continental and insular Y-DNA which can be explained by a secondary contact hypothesis.
Conclusions: Overall, the findings in this study are important: 1) to help authority particularly in Malaysia on the population management activities including translocation and culling of conflict M. fascicularis, 2) to identify the unknown origin of captive M. fascicularis used in biomedical research, and; 3) the separation between the continental and insular forms warrants for the treatment as separate management units.
Keywords
TSPY, SRY, Indochinese, continental and insular Sundaic, hybridization, secondary contact
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This is a list of supplementary files associated with this preprint. Click to download.
- Additonalfile1.xlsx
• Additional file 1 • File format: Excel (.xls) • Title of data: Table S1 • Description of data: Sample identification, localities, haplotypes designation, and the GenBank Accession Numbers for each of the samples used in this study.
- Additonalfile2.xlsx
• Additional file 2 • File format: Excel (.xls) • Title of data: Table S2 • Description of data: Species, Sample identification, localities, haplotypes designation, and the GenBank Accession Numbers for downloaded sequences from GenBank used in this study.
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Posted 08 Jan, 2021
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On 15 Feb, 2021
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Editorial decision: Minor revision
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Received 26 Dec, 2020
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On 25 Dec, 2020
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Invitations sent on 25 Dec, 2020
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On 24 Dec, 2020
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Editorial decision: Major revision
On 08 Nov, 2020
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Received 07 Nov, 2020
Reviewer #2 agreed
On 12 Oct, 2020
Review #1 received
Received 07 Oct, 2020
Reviewer #1 agreed
On 17 Aug, 2020
Editor assigned
On 17 Aug, 2020
Reviewers invited
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On 13 Aug, 2020
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This preprint is under consideration at BMC Ecology and Evolution. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Evolutionary pattern of Macaca fascicularis in Southeast Asia inferred using Y-chromosomal gene
Faisal Ali Anwarali Khan
Universiti Malaysia Sarawak (UNIMAS)
Corresponding Author
ORCiD: https://orcid.org/0000-0001-7585-4885
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
Version 2
Posted 08 Jan, 2021
Published
On 15 Feb, 2021
No community comments so far
Editorial decision: Minor revision
On 19 Jan, 2021
Review #2 received
Received 17 Jan, 2021
Review #1 received
Received 26 Dec, 2020
Reviewer #2 agreed
On 25 Dec, 2020
Reviewers invited
Invitations sent on 25 Dec, 2020
Reviewer #1 agreed
On 25 Dec, 2020
Editor assigned
On 24 Dec, 2020
Submission checks complete
On 24 Dec, 2020
Editor invited
On 24 Dec, 2020
No comments provided
Editorial decision: Major revision
On 08 Nov, 2020
Review #2 received
Received 07 Nov, 2020
Reviewer #2 agreed
On 12 Oct, 2020
Review #1 received
Received 07 Oct, 2020
Reviewer #1 agreed
On 17 Aug, 2020
Editor assigned
On 17 Aug, 2020
Reviewers invited
Invitations sent on 17 Aug, 2020
Submission checks complete
On 14 Aug, 2020
Editor invited
On 13 Aug, 2020
First submitted
On 04 Aug, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Ecology and Evolution.
Background: We analyzed a combined segment (2,032-bp) of the sex-determining region and the testis-specific protein of the Y-chromosome (Y-DNA) gene to clarify the gene flow and phylogenetic relationships of the long-tailed macaques (Macaca fascicularis) in Southeast Asia. Phylogenetic relationships were constructed using the maximum likelihood, Bayesian inference, and the median-joining network from a total of 164 adult male M. fascicularis from 62 localities in Malaysia, including sequences from the other regions from previous studies.
Results: Based on Y-DNA, we confirm the presence of two lineages of M. fascicularis: the Indochinese and Sundaic lineages. The Indochinese lineage is represented by M. fascicularis located northwards of the Surat Thani-Krabi depression region and is introgressed by the Macaca mulatta Y-DNA. The Sundaic lineage is free from such hybridization event, thus defined as the original carrier of the M. fascicularis Y-DNA. We further revealed that the Sundaic lineage differentiated into two forms: the insular and the continental forms. The insular form, which represents the ancestral form of M. fascicularis, consists of two haplotypes: a single homogenous haplotype occupying the island of Borneo, Philippines, and southern Sumatra; and the Javan haplotype. The more diverse continental form consists of 17 haplotypes in which a dominant haplotype was shared by individuals from southern Thai Peninsular (south of Surat Thani-Krabi depression), Peninsular Malaysia, and Sumatra. Uniquely, Sumatra contains both the continental and insular Y-DNA which can be explained by a secondary contact hypothesis.
Conclusions: Overall, the findings in this study are important: 1) to help authority particularly in Malaysia on the population management activities including translocation and culling of conflict M. fascicularis, 2) to identify the unknown origin of captive M. fascicularis used in biomedical research, and; 3) the separation between the continental and insular forms warrants for the treatment as separate management units.
Figure 1
Figure 2
Figure 3
Figure 4