Mitochondrial DNA Profiling Reveals Two Lineages of Sun Bears in East and West Malaysia

Abstract

Sun bear populations are fragmented and at risk from habitat loss and exploitation for body parts. These threats are made worse by significant gaps in knowledge of sun bear population genetic diversity, population connectivity, and taxonomically significant management units. Using a complete sun bear mitochondrial genome, we developed a set of mitochondrial markers to assess haplotype variation and the evolutionary history of sun bears from Peninsular (West) Malaysia, and Sabah (East Malaysia). Genetic samples from 28 sun bears from Peninsular Malaysia, 36 from Sabah, and 18 from Thailand were amplified with primers targeting a 1,800 bp region of the mitochondrial genome including the complete mitochondrial control region and adjacent genes. Sequences were analyzed using phylogenetic methods. We identified 51 mitochondrial haplotypes among 82 sun bears. Phylogenetic and network analyses provided strong support for a deep split between Malaysian sun bears and sun bears in East Thailand and Yunnan province in China. The Malaysian lineage was further subdivided into two clades: Peninsular Malaysian and Malaysian Borneo (Sabah). Sun bears from Thailand occurred in both Sabah and Peninsular Malaysian clades. Our study supports recent findings that sun bears from Sundaland form a distinct clade from those in China and Indochina with Thailand possessing lineages from the three clades. Importantly we demonstrate a more recent and clear genetic delineation between sun bears from the Malay Peninsula and Sabah indicating historical barriers to gene flow within the Sundaic region.

First mitogenome phylogeny of the sun bear Helarctos malayanus reveals a deep split between Indochinese and Sundaic lineages

“…The Sunda clade includes sequences ( N = 15) from Borneo, Sumatra and Peninsular Malaysia (all part of Sundaland), but also from Thailand, and from three archival samples of unknown provenance (sample details in Table S1 ). This clade also gave rise to two major lineages, which diverged ~128 kya (CI 95 : 170–93 kya), that correspond to mtDNA lineages previously identified (Lai, Chew, et al, 2021 ): the Peninsular lineage and Sabah lineage (indicated in Figure 2 ). These two lineages have a large geographic overlap: both include sun bears from Sumatra, Peninsular Malaysia and Thailand.…”

“… Bayesian phylogenetic tree reconstructed using H. malayanus mitogenome sequences ( N = 35). Two main branches are labeled according to clade assignment, and previously reported lineages (Peninsula and Sabah; Lai, Chew, et al, 2021 ) are indicated. Sequences are labeled with sample ID and geographic origin (if known); text color of geographic origin follows the inset map (top left).…”

“…MW316324–MW316405; Lai, Chew, et al, 2021 ). This combined dataset of shorter sequences consisted of 117 mtDNA sequences: 32 from this study, 82 from Lai, Chew, et al ( 2021 ), one from Lai, Ratnayeke, et al ( 2021 ), one from Yu et al ( 2007 ), and one from Krause et al ( 2008 ; Table S4 ). The alignment had a length of 1466 bp after removal of the repetitive portion of the control region.…”

“…Existing studies of H. malayanus using molecular markers (mtDNA sequences and microsatellites) were limited in their geographic scope (Kunde et al, 2020 ; Lai, Chew, et al, 2021 ; Onuma et al, 2006 ), and we thus lack knowledge about the distribution of intraspecific genetic diversity across the species' range. To address this shortcoming, we sequenced mitochondrial genomes from samples across a large portion of the sun bear distribution, utilizing both archival material from natural history museums as well as non‐invasively collected material (mucosal cells from saliva).…”

Design and validation of a 63K genome-wide SNP-genotyping platform for caribou/reindeer (Rangifer tarandus)

“…For decades, population genetics approaches have been deployed to inform species conservation efforts [1]. Molecular markers such as mitochondrial DNA sequences and microsatellites have been used to answer conservation genetic questions such as estimating relatedness between individuals [2,3] or effective population size [4,5], and ascertaining population structure to delineate conservation units [6,7]. In the past decades, genetic studies have also started to rely on the analysis of single nucleotide polymorphisms (SNPs), which are highly abundant across genomes (i.e.…”