Evolutionary pattern of Macaca fascicularis in Southeast Asia inferred using Y-chromosomal gene
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.
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This is a list of supplementary files associated with this preprint. Click to download.
• 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.
• 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.
Posted 08 Jan, 2021
On 15 Feb, 2021
On 19 Jan, 2021
Received 17 Jan, 2021
Received 26 Dec, 2020
On 25 Dec, 2020
Invitations sent on 25 Dec, 2020
On 25 Dec, 2020
On 24 Dec, 2020
On 24 Dec, 2020
On 24 Dec, 2020
On 08 Nov, 2020
Received 07 Nov, 2020
On 12 Oct, 2020
Received 07 Oct, 2020
On 17 Aug, 2020
On 17 Aug, 2020
Invitations sent on 17 Aug, 2020
On 14 Aug, 2020
On 13 Aug, 2020
On 04 Aug, 2020
Evolutionary pattern of Macaca fascicularis in Southeast Asia inferred using Y-chromosomal gene
Posted 08 Jan, 2021
On 15 Feb, 2021
On 19 Jan, 2021
Received 17 Jan, 2021
Received 26 Dec, 2020
On 25 Dec, 2020
Invitations sent on 25 Dec, 2020
On 25 Dec, 2020
On 24 Dec, 2020
On 24 Dec, 2020
On 24 Dec, 2020
On 08 Nov, 2020
Received 07 Nov, 2020
On 12 Oct, 2020
Received 07 Oct, 2020
On 17 Aug, 2020
On 17 Aug, 2020
Invitations sent on 17 Aug, 2020
On 14 Aug, 2020
On 13 Aug, 2020
On 04 Aug, 2020
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