Genomic Analysis of Demographic History and Ecological Niche Modeling in the Endangered Sumatran Rhinoceros Dicerorhinus sumatrensis

Mays, Herman L.; Hung, Chih Ming; Shaner, Pei Jen L.; Denvir, James; Justice, Megan; Yang, Shang Fang; Roth, Terri L.; Oehler, David A.; Fan, Jun; Rekulapally, Swanthana; Primerano, Donald A.

doi:10.1016/j.cub.2017.11.021

Cited by 61 publications

(70 citation statements)

References 70 publications

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“…Nonetheless, our hypothesis of a large glacially-driven expansion event is further supported by population size changes in the Sumatran rhinoceros likely driven by sea level fluctuations (Mays et al, 2018), and opens the possibility that some of the putative 'Toba effects' proposed in past studies (i.e. Luo et al, 2004;Fleischer et al, 2001) Figure 1: Map of the Sunda Shelf showing the four landmasses in the region: Sumatra, Java, Borneo and the Thai-Malay Peninsula.…”

Section: Demographic Impacts Of Forest Expansionsupporting

confidence: 68%

Impacts of the Toba eruption and montane forest expansion on diversification in Sumatran parachuting frogs (Rhacophorus)

O’Connell

Oaks

Hamidy

et al. 2019

Preprint

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2Catastrophic events, such as volcanic eruptions, can have profound impacts on the demographic histories of resident taxa. Due to its presumed effect on biodiversity, the Pleistocene eruption of super-volcano Toba has received abundant attention. We test the effects of the Toba eruption on the diversification, genetic diversity, and demography of three co-distributed species of parachuting frogs (Genus Rhacophorus) on Sumatra. We generate target-capture data (~950 loci and ~440,000 bp) for three species of parachuting frogs and use these data paired with previously generated double digest restriction-site associated DNA (ddRADseq) data to estimate population structure and genetic diversity, to test for population size changes using demographic modeling, and to estimate the temporal clustering of size change events using a full-likelihood Bayesian method. We find that populations around Toba exhibit reduced genetic diversity compared with southern populations, and that these northern populations exhibit a signal of contraction around the time of the eruption (~80 kya). However, we infer a stronger signal of expansion in southern populations around ~400 kya, and at least two of the northern populations may have also expanded at this time. Taken together, this suggests that the Toba eruption precipitated population declines in northern populations, but that the demographic history of these three species was more greatly impacted by mid-Pleistocene forest expansion, supporting local rather than regional effects of the Toba eruption.

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Section: Demographic Impacts Of Forest Expansionsupporting

confidence: 68%

Impacts of the Toba eruption and montane forest expansion on diversification in Sumatran parachuting frogs (Rhacophorus)

O’Connell

Oaks

Hamidy

et al. 2019

Preprint

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“…3b and Supplementary Table S4). The of MJA is similar to those of the endangered golden snub-nosed monkeys (0.042%) [29] and carnivores, including Bengal tiger, White lion, Amur tiger and San Nicolis Island fox (0.040-0.049%) [30][31][32], whereas those of MJB, MPA and MPB were comparable to those in endangered Siamang (0.13-0.15%) [33], giant panda (0.132%) [34], critically endangered Sumatran orangutan (0.12%) [35], Sumatran Rhinoceros (0.13%) [36] and Western lowland gorilla (0.144%) [37], and the extinct Oimyakon woolly mammoth (0.125%) [38].…”

Section: Genetic Diversity Of Pangolinsmentioning

confidence: 95%

Genomic consequences of population decline in critically endangered pangolins and their demographic histories

Hao

Frantz

et al. 2020

National Science Review

110

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Pangolins are among the most critically endangered animals due to heavy poaching and world wild trafficking. However, their demographic histories and the genomic consequences of their recent population declines remain unknown. We generated high-quality de novo reference genomes for critically endangered Malayan (Manis javanica, MJ) and Chinese (M. pentadactyla, MP) pangolins and re-sequencing population genomic data from 74 MJs and 23 MPs. We recovered the population identities of illegally traded pangolins and previously unrecognized genetic populations that should be protected as evolutionarily distinct conservation units. Demographic reconstruction suggested environmental changes have resulted in population size fluctuation of pangolins. Additionally, recent population size declines due to human activities have resulted in an increase in inbreeding and genetic load.Deleterious mutations were enriched in genes related to cancer/diseases and cholesterol homeostasis, which may have increased their susceptibility to diseases and decreased their survival potential to adapt to environmental changes and high-cholesterol diet. This comprehensive study provides not only high-quality pangolin reference genomes, but also valuable information concerning the driving factors of long-term population size fluctuations and the genomic impact of recent population size declines due to human activities, which is essential for pangolin conservation management and global action planning.

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“…However, researchers using coalescent-based full Bayesian methods (e.g. Heled and Drummond 2008) have shown promising results (Fontaine et al 2012; Trucchi et al 2016; Mays et al 2018), especially when used in tandem with ancient DNA (Lorenzen et al 2011; Beland et al 2019). The success of these methods on modern datasets partly depends on the use of appropriate time calibrations, yet despite recent efforts (Crandall et al 2012; Hoareau 2016), adequate mutation rates are still scarce, even for the bowhead whale.…”

Section: Introductionmentioning

confidence: 99%

Whales and Men: genetic inferences uncover a detailed history of hunting in bowhead whale

Hoareau

2020

Preprint

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9After millennia of hunting and a population collapse, it is still challenging to understand the genetic 10 consequences of whaling on the circumarctic bowhead whale. Here I use published modern mtDNA 11 sequences from the Bering-Chukchi-Beaufort population and a new time calibration to show that late-12 glacial climate changes and whaling have been the major drivers of population change. Cultures that 13 hunted in the Arctic Seas from as early as 5000 years ago appear to be responsible for successive 14 declines of the population growth, bringing the effective size down to 38% of its pristine population 15 size. The Thules and the Basques (year 1000-1730) who only hunted in the North Atlantic had a major 16 impact on this North Pacific population, indicating that bowhead whale stocks respond to harvesting as 17 a single population unit. Recent positive growth is inferred only after the end of commercial whaling in 18 1915, and for levels of harvesting that are close to the current annual quota of 67 whales. By unfolding 19 the population history of the bowhead whale, I provide compelling evidence that mtDNA yields critical 20 yet undervalued information for management and conservation of natural populations. 21 22 Population dynamics; Whaling 24 (BCB). This population is showing signs of recovery, has far greater abundance than others (Moore et 48 al. 2019), and has been monitored and studied for several decades (Zeh and Punt 2005). After inferring 49 female effective population size (Ne) using a Bayesian skyline analysis (Heled and Drummond 2008), 50 I calculated population growth rates; a parameter that has a key role in describing population trends and 51 identifying potential drivers of decline (Sibly and Hone 2002). I then applied a molecular clock derived 52 from a single-point calibration and used a clustering method that groups the population growth rates 53 into distinct time periods. Remarkably, I found that bowhead whale demography is strongly influenced 54 by sea-level changes and five millennia of human harvesting. 55 56 Results and discussion 57 Validation of an LGM-based calibration of the molecular clock the following equation [R = dNe /dt = (Ne n -Nen+1)/(tn+1tn)] (with Ne: effective population size, 217 : generation time of the species, t: time and n: number of coalescent events back in time). This provided 218 the rate estimates of the population growth at every point in time associated with the coalescent events 219 recorded in the given dataset (n = 148 coalescent events for a sample size of 149), and this back to the 220 most recent common ancestor of the sequence dataset. 221 222 Calibration of molecular rates 223The calibration relies on the single assumption that the bowhead whale has a first positive population 224 growth rate (R > 0) at 20 ka (Fig. 1A). This assumption is based on the previous palaeoecological results 256 286 surface temperature predicts the movements of an Arctic cetacean: the bowhead whale. Sci Rep. 8:1-12.

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Genomic Analysis of Demographic History and Ecological Niche Modeling in the Endangered Sumatran Rhinoceros Dicerorhinus sumatrensis

Cited by 61 publications

References 70 publications

Impacts of the Toba eruption and montane forest expansion on diversification in Sumatran parachuting frogs (Rhacophorus)

Impacts of the Toba eruption and montane forest expansion on diversification in Sumatran parachuting frogs (Rhacophorus)

Genomic consequences of population decline in critically endangered pangolins and their demographic histories

Whales and Men: genetic inferences uncover a detailed history of hunting in bowhead whale

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