Glaciation-based isolation contributed to speciation in a Palearctic alpine biodiversity hotspot: Evidence from endemic species

Wang, Pengcheng; Yao, Hongyan; Gilbert, Kadeem J.; Lu, Qingshan; Yu, Hao; Zhang, Zhengwang; Wang, Nan

doi:10.1016/j.ympev.2018.09.006

Cited by 23 publications

(24 citation statements)

References 69 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As new methods can infer genealogies better and faster (Kelleher, Wong, et al, 2019; Mirzaei and Wu, 2017; Palamara et al, 2018; Speidel et al, 2019), the estimated transition matrix could become a powerful summary statistic in the future. HMM can be a computational burden depending on the model and model parameters, and estimating genealogy through more efficient methods would still allow the use of SMC theory for parameter estimation or hypothesis testing (as in Gattepaille et al (2016), Johndrow and Palacios (2019), and P Wang et al (2018)). In addition, using the work of K Wang et al (2020), one could (to some extent Kim et al (2020)) extend our approach to account for population structure and migration.…”

Section: Discussionmentioning

confidence: 99%

Limits and Convergence properties of the Sequentially Markovian Coalescent

Sellinger

Awad

Tellier

2020

Preprint

View full text Add to dashboard Cite

Many methods based on the Sequentially Markovian Coalescent (SMC) have been and are being developed. These methods make use of genome sequence data to uncover population demographic history. More recently, new methods even allow the simultaneous estimation of the demographic history and other biological variables, extending the original theoretical frameworks. Those methods can be applied to many different species, under different model assumptions, in hopes of unlocking the population/species evolutionary history. Although convergence proofs in particular cases have been given using simulated data, a clear outline of the performance limits of these methods is lacking. We here explore the limits of this methodology, as well as present a tool that can be used to help users quantify what information can be confidently retrieved from given datasets. In addition, we study the consequences for inference accuracy of the violation of hypotheses and assumptions of SMC approaches, such as the presence of transposable elements, variable recombination and mutation rates along the sequence and SNP call errors. We also provide a new interpretation of the SMC through the use of the estimated transition matrix and offer recommendations for the most efficient use of these methods under budget constraints, notably through the building of data sets that would be better adapted for the biological question at hand.

show abstract

Section: Discussionmentioning

confidence: 99%

Limits and Convergence properties of the Sequentially Markovian Coalescent

Sellinger

Awad

Tellier

2020

Preprint

View full text Add to dashboard Cite

show abstract

“…A substantially different modeled LIG distribution compared with those during the present interglacial period is not unique to the Emei mustache toad. Around the Sichuan Basin, such results have been commonly obtained for various animal [49,50,[68][69][70][71] and plant groups [45,55,72,73]. Because the LIG period at1 40-120 ka is relatively recent on an evolutionary scale, it is unlikely that the corresponding effects have been erased.…”

Section: Climatic Suitabilitymentioning

confidence: 86%

Dynamics behind disjunct distribution, hotspot-edge refugia, and discordant RADseq/mtDNA variability: insights from the Emei mustache toad

Dai

Guo

et al. 2020

BMC Evol Biol

View full text Add to dashboard Cite

Background: The distribution of genetic diversity and the underlying processes are important for conservation planning but are unknown for most species and have not been well studied in many regions. In East Asia, the Sichuan Basin and surrounding mountains constitute an understudied region that exhibits a "ring" of high species richness overlapping the eastern edge of the global biodiversity hotspot Mountains of Southwest China. We examine the distributional history and genetic diversification of the Emei mustache toad Leptobrachium boringii, a typical "ring" element characterized by disjunct ranges in the mountains, by integrating time-calibrated gene tree, genetic variability, individual-level clustering, inference of population splitting and mixing from allele frequencies, and paleoclimatic suitability modeling. Results: The results reveal extensive range dynamics, including secondary contact after long-term isolation via westward dispersal accompanied by variability loss. They allow the proposal of a model that combines recurrent contractions caused by Quaternary climatic changes and some failed expansions under suitable conditions for explaining the shared disjunct distribution pattern. Providing exceptional low-elevation habitats in the hotspot area, the eastern edge harbors both long-term refugial and young immigrant populations. This finding and a synthesis of evidence from other taxa demonstrate that a certain contributor to biodiversity, one that preserves and receives low-elevation elements of the east in this case, can be significant for only a particular part of a hotspot. By clarifying the low variability of these refugial populations, we show that discordant mitochondrial estimates of diversity can be obtained for populations that experienced admixture, which would have unlikely left proportional immigrant alleles for each locus.

show abstract

“…Many threatened species or lineages became extinct or failed to recover to pre‐LGM population sizes (e.g., Mays et al., 2018; Yang et al., 2018), but others were able to recover at the end of the LGM and rapidly expanded with Holocene climate warming (e.g., Chattopadhyay et al., 2019; Ye et al., 2018). In addition, some species or lineages unaffected by the LGM maintained relatively stable population sizes or even expanded moderately during the LGM (Lu et al., 2020; Wang et al., 2018). However, the factors related to the different sensitivities to the temperature decline during the LGM between species or lineages remain poorly understood.…”

Section: Introductionmentioning

confidence: 99%

“…In addition, some species or lineages unaffected by the LGM maintained relatively stable population sizes or even expanded moderately during the LGM (Lu et al, 2020;Wang et al, 2018). However, the factors related to the different sensitivities to the temperature decline during the LGM between species or lineages remain poorly understood.…”

mentioning

confidence: 99%

Are population isolations and declines a threat to island endemic water striders? A lesson from demographic and niche modelling of Metrocoris esakii (Hemiptera: Gerridae)

Chen

Yuan

et al. 2020

Molecular Ecology

View full text Add to dashboard Cite

Local endemic species are an important part of biodiversity hotspots and are of great significance for biodiversity conservation (Myers et al., 2000). In contrast to widespread and common species, local endemic species are often characterized by narrow geographical ranges and the need for specialized ecological niches (Işik, 2011). Species with narrow distribution areas and specialized niche requirements also tend to have a small population size (Işik, 2011). Genetic stochasticity due to small population size might contribute

show abstract

Glaciation-based isolation contributed to speciation in a Palearctic alpine biodiversity hotspot: Evidence from endemic species

Cited by 23 publications

References 69 publications

Limits and Convergence properties of the Sequentially Markovian Coalescent

Limits and Convergence properties of the Sequentially Markovian Coalescent

Dynamics behind disjunct distribution, hotspot-edge refugia, and discordant RADseq/mtDNA variability: insights from the Emei mustache toad

Are population isolations and declines a threat to island endemic water striders? A lesson from demographic and niche modelling of Metrocoris esakii (Hemiptera: Gerridae)

Contact Info

Product

Resources

About