Genetic diversity of a species is significantly associated with its distribution range, population size, genetic structure, fragmentation, mating system, gene flow patterns (pollen/seed dispersal), etc. It reflects the ability of the species to cope up with the changing environment (Jump and Penuelas 2005) Our study analyzed the impact of population decline due to overharvesting on the population genetic parameters of four threatened Calamus species’, endemic to the two distinct biodiversity hotspots in India. All the four species have a restricted distribution limited to a few pockets in the reserve forests, which are characterized by a prolonged history of resource harvesting. The overexploitation could lead to reductions in populations size, lack of population connectivity and increased population genetic structuring, which are detrimental for the viability of populations. Given the comparable life histories, reproductive strategies and pollination systems of these species, it is expected that the population decline via harvesting influenced the genetic properties of these species to a similar extent.
Most of the loci analyzed for C. brandisi, C. acanthospathus, and C. andamanicus showed divergence from the Hardy-Weinberg proportions. A substantial deficit of homozygotes indicated by the negative Fis value (Fis = -0.1 to − 0.2) and high observed heterozygosity were observed in populations of C. nambariensis and C. acanthospathus. Even though the heterozygosity is interpreted as a measure of genetic diversity, heterozygosity excess could equally arise from negative assortative mating, heterozygote selection, asexual reproduction, recent migration from previously isolated populations, etc. (Stoeckel et al. 2006). This is also identified as a characteristic of small populations in species with obligatory outcrossing (dioecy and self-incompatible monoecy) (Wright 1984; Balloux 2004). The heterozygote excess observed in the study could have arisen from a small number of individuals contributing to reproduction, and dissimilar allele frequency in the two sexes, resulting in a homozygote deficit (Robertson 1962). In concordance with this observation, a similar homozygosity deficit was earlier reported in fragmented populations of C. nagbettai, a highly endemic dioecious threatened rattan species in the Western Ghats (Dev et al. 2019).
Similarly, positive Fis values (Fis = 0.1 to 0.5) and heterozygote deficit observed in the populations of C. andamanicus, might have arisen from the combined effect of small population size and a long history of isolation among the insular populations, which could have imparted restrictions to the gene flow. Similarly, high genetic differentiation of the LA population is likely to be a consequence of the isolated distribution of the insular population. The analysis also revealed a recent genetic bottleneck (Supplementary Table 2) in this population, likely stemming either from a founder effect or reduction in population size coupled with least migration from other populations.
Allelic richness is a more sensitive genetic parameter to population reduction than heterozygosity (Allendorf and Servheen 1986). Among the studied species, C. acanthospathus and C. nambariensis showed lesser values for allelic richness (1.9 to 2.9) as compared to other two species (4 for C. brandisii and 2.8 to 4.38 for C. andamanicus) indicating a past reduction in population size for C. acanthospathus and C. nambariensis. Likewise, north Andaman population of C. anadamanicus must have experienced a large population decline than Baratang population (4.3) as indicated by lower mean allelic richness (NA, mean allelic richness = 2.8).
Despite the it is predicted that a 1:1 sex ratio will be maintained by negative frequency-dependent selection, as found in natural populations of other plants, the sex ratio in the studied populations largely varies from this value (Delph 1999). The populations of northeastern India species C. acanthospathus and C. nambariensis are highly female-skewed in all surveyed populations, whereas the sex ratio in C. brandisi varies according populations, only Agasthyamala population is female skewed and the other two populations showing male skewness. The large deviation from the predicted sex ratio in these species could affect the reproductive success of the species.
Population genetic divergence and structure
Low genetic divergence and genetic structure, as well as high admixture among populations are generally observed in outcrossing species (Finkeldey and Hattemer 2007; Kettle et al. 2011). But contrary to this expectation high genetic divergence (Wright’s Fixation Index, [Fst]) and discrete genetic structuring was found in populations of the studied species, indicating restricted population connectivity.
In C. brandisii, pairwise Fst values indicated genetic divergence of AgM from the rest of the populations. Population genetic structure analysis with two different admixture patterns, also concurred with the differentiation of AgM with limited admixtures. Even though PaP and AgM populations are geographically closer (spatial distance of 8 km), PaP showed more genetic proximity with PadM population in both the analyses. The high divergence and unique genetic structure of AgM population along with a high number of private alleles (Table 3) indicates restricted gene flow and probable adaptation of the population to the local environment (Slatkin 1985; 1987). The local environment of AgM population is quite different from the rest and is characterized by rocky mountains, low soil depth and open canopy. PaP and PadM are canopy-rich habitats where rattans are understorey species. During the field survey, low seedling recruitment and seed predation by microlepidoptera larvae were also observed in AgM population.
The genetic differentiation of MaW population of C. acanthospathus with a discrete genetic structure and little genetic admixture, was evident in the genetic structure analysis, while other populations showed similar levels of genetic admixtures and structure patterns. The discrete genetic structuring and recent bottleneck identified in the MaW population (Supplementary Table 2) pointed out the restricted population connectivity along with a large reduction in population size. The recent bottleneck and clustering of Frcbr (ex situ population) with Nag and PhLui populations could be explained by the founder effect during early establishment years and seed sourcing.
In C. nambariensis, KaW population is well differentiated as compared to other populations. Genetic structure analysis also identified the discreteness of KaW with strong population structuring, while other populations showed similar structuring (at K = 2). The Frcbr and Dih populations of C. nambariensis showed similar admixture patterns, indicating seed sourcing from Dih population for the establishment of Frcbr population. Therefore, bottleneck could be the founder effect in Frcbr population. The ex-situ conserved populations of C. acanthospathus (Frcbr) and C. nambariensis (Frcbr) originated from a single population, leading to inadequate representation of genetic diversity in these species.
Ecological niche modelling
When compared to other Calamus species such as C. Lakshmana with wider predicted niches in the Western Ghats (Sreekumar and Sasi 2019), ENM found a smaller potential ecological niche suitable for C. brandisii. The predicted ecological niche completely falls under the protected range of Agasthyamala Biosphere Reserve. The Precipitation of Coldest Quarter (bio19), Precipitation of Driest Month (bio14), Max Temperature of Warmest Month (bio5) and Elevation are the bioclimatic variables that contributed to the highly restricted distribution of the species to this small pocket. The ENM prediction reported earlier for C. nambariensis and C. adamanicus revealed wider niches for both the species. However, the high-elevation humid tropical and subtropical forests of Assam, and evergreen forest of Andaman and Nicobar Islands are the most suitable area for these species, respectively (Sreekumar et al. 2016; Deka et al. 2018)
Conservation and management strategies for endemic rattan resources
Most rattan species endemic to the Western Ghats, northeast India and Andaman exhibit confined distributions characterized by limited population sizes. The prolonged resource harvesting has exacerbated the decline in population sizes, resulting in the scarcity of mature reproductive individuals, leading to inevitable genetic consequences. However, the dioecious reproductive strategies played a crucial role in retaining the genetic variability within the surviving populations of C. brandisii, C. acanthospathus, C. nambariensis, C. nagbettai, (Dev et al. 2019). Long-term sustenance of populations in these species requires conservation strategies and management actions focused on enhancing population size, fostering genetic connectivity among populations and augmentation of genetically deprived populations. Furthermore, habitat protection and controlled harvesting can help regain the viability of these populations.
Ex-situ conservation can be used as a tool to conserve a significant proportion of genetic variability in highly threatened species (Guerrant et al. 2004; Hoban 2019). Populations with unique alleles and private alleles in environmentally or geographically differentiated/isolated populations need to be prioritised for improving the genetic diversity via assisted migration and augmentation as well as to enhance the adaptive potential of the species. Along with population decline, the skewed sex ratio in certain Calamus species has adversely impacted their reproductive success (Kurian and Sabu 2017; Dev et al. 2019). Gender-specific molecular markers to differentiate the individual sexes have also been reported in different rattan species (Sarmah and Sarma 2011; Sarmah et al. 2016; Kurian et al. 2018). Implementing strategies that can identify the gender of individuals at the juvenile stage can be employed to restore the skewed sex ratio in populations, thereby supporting the long-term endurance of the species.