Species delimitation and evolutionary reconstruction within an integrative taxonomic framework: A case study on Rhinolophus macrotis complex (Chiroptera: Rhinolophidae)

Liu, Tong; Sun, Keping; Csorba, Gábor; Zhang, Kangkang; Zhang, Lin; Zhao, Hanbo; Jin, Longru; Thong, Vu Dinh; Xiao, Yanhong; Jiang, Feng

doi:10.1016/j.ympev.2019.106544

Cited by 19 publications

(23 citation statements)

References 90 publications

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“…For Cyt‐b , phylogenetic relationships were reconstructed based on 29 haplotypes in MRBAYES v.3.2 (Ronquist et al., 2012) and RAXML v.8.2.4 (Stamatakis, 2014) with parameters set from Liu et al. (2019). PARTITIONFINDER v.1.1.1 was used to determine the best nucleotide substitution models and indicated that the K80 + I, HKY, and TrN + G models best fit the first, second, and third positions within codons, respectively.…”

Section: Methodsmentioning

confidence: 99%

“…Based on the PCA results, the first four principal components, which accounted for 39.1%, 26.5%, 17.9%, and 8.5% ( Figure S1) of the variation, were used to build an environmental distance matrix (EDM). We conducted population structure and phylogenetic analysis for microsatellites and Cyt-b, respectively, using the same methods as Liu et al (2019). For microsatellites, Hardy-Weinberg and linkage equilibrium of each population were detected by GENEPOP v.4.3 (Rousset, 2008).…”

Section: Geographic and Environmental Distancementioning

confidence: 99%

“…Sun et al (2016) used extensive sampling, phenotypic data, and multiple genetic markers to investigate the evolutionary history of R. episcopus and its sibling species, and revealed mito-nuclear discordance in these species. Tu et al (2017), Zhang et al (2018), and Liu et al (2019) performed integrative studies and demonstrated phenotypic and genetic divergence among R. episcopus and its closely related species, and revised their taxonomic status, which was debated for a long time (Liu et al, 2019;Sun & Feng, 2009;Sun et al, 2008Sun et al, , 2016Tu et al, 2017;Zhang et al, 2009Zhang et al, , 2018. Those studies revealed geographic variation in population genetic structure and acoustic characteristics within R. episcopus; however, the level of intraspecific differentiation and factors driving such differentiation are still unclear.…”

Section: Introductionmentioning

confidence: 99%

“…(2018), and Liu et al. (2019) performed integrative studies and demonstrated phenotypic and genetic divergence among R. episcopus and its closely related species, and revised their taxonomic status, which was debated for a long time (Liu et al., 2019; Sun & Feng, 2009; Sun et al., 2008, 2016; Tu et al., 2017; Zhang et al., 2009, 2018). Those studies revealed geographic variation in population genetic structure and acoustic characteristics within R. episcopus ; however, the level of intraspecific differentiation and factors driving such differentiation are still unclear.…”

Section: Introductionmentioning

confidence: 99%

“…Rhinolophus episcopus Allen, 1923 ( t.l . : Wanshien, Sichuan, China) has a wide distribution in Southern China that crosses different zoogeographic regions and has varied genetics and phenotypes (Liu et al., 2019; Sun et al., 2016). Most previous studies on R. episcopus focused on genetic differentiation and evolutionary history at the interspecific level.…”

Section: Introductionmentioning

confidence: 99%

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Evolutionary insights intoRhinolophus episcopus(Chiroptera, Rhinolophidae) in China: Isolation by distance, environment, or sensory system?

Liu

Kangkang

Dai

et al. 2020

J. Zool. Syst. Evol. Res.

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Evolutionary processes can be influenced by several factors, such as geographic isolation, environmental selection, and sensory variation. For most nocturnal bats, echolocation is the primary sensory system used to prey and communicate, and plays important roles in chiropteran diversification and evolution. Understanding the relative contribution of geography, the environment, and this sensory system to population genetic divergence can elucidate the processes involved in bat incipient speciation and evolution. In this study, we collected spatial and environmental information, echolocation calls, as well as the previously published genetic data (six microsatellite loci and the mitochondrial cytochrome b gene) of widely distributed Rhinolophus episcopus populations to test three hypotheses for nuclear and mitochondrial divergence (isolation by distance, isolation by environment, and isolation by sensory variation) and unveil the factors that drive intraspecific genetic differentiation. The moderate level of nuclear differentiation was correlated with geographic/ spatial distance and acoustic variation, whereas the relatively high level of mitochondrial differentiation was mainly associated with acoustic divergence. No significant correlation was observed between genetic divergence and environmental variables. Among the three factors, acoustic divergence explained the highest percentage of both nuclear and mitochondrial divergence. Thus, our results indicate that sensory variation may have played important roles in driving population isolation early in bat speciation, which is consistent with the hypothesis of isolation by sensory variation. Our study emphasizes the need to consider more factors, especially sensory traits, and combine multiple statistical methods in landscape genetic studies to test their potential contributions to driving population divergence.

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Section: Methodsmentioning

confidence: 99%

Section: Geographic and Environmental Distancementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Evolutionary insights intoRhinolophus episcopus(Chiroptera, Rhinolophidae) in China: Isolation by distance, environment, or sensory system?

Liu

Kangkang

Dai

et al. 2020

J. Zool. Syst. Evol. Res.

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A turn in species conservation for hairpin banksias: demonstration of oversplitting leads to better management of diversity

Wilson

Rossetto

Bain

et al. 2022

American J of Botany

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Premise: Understanding evolutionary history and classifying discrete units of organisms remain overwhelming tasks, and lags in this workload concomitantly impede an accurate documentation of biodiversity and conservation management. Rapid advances and improved accessibility of sensitive high-throughput sequencing tools are fortunately quickening the resolution of morphological complexes and thereby improving the estimation of species diversity. The recently described and critically endangered Banksia vincentia is morphologically similar to the hairpin banksia complex (B. spinulosa s.l.), a group of eastern Australian flowering shrubs whose continuum of morphological diversity has been responsible for taxonomic controversy and possibly questionable conservation initiatives. Methods: To assist conservation while testing the current taxonomy of this group, we used high-throughput sequencing to infer a population-scale evolutionary scenario for a sample set that is comprehensive in its representation of morphological diversity and a 2500-km distribution. Results: Banksia spinulosa s.l. represents two clades, each with an internal genetic structure shaped through historical separation by biogeographic barriers. This structure conflicts with the existing taxonomy for the group. Corroboration between phylogeny and population statistics aligns with the hypothesis that B. collina, B. neoanglica, and B. vincentia should not be classified as species. Conclusions: The pattern here supports how morphological diversity can be indicative of a locally expressed suite of traits rather than relationship. Oversplitting in the hairpin banksias is atypical since genomic analyses often reveal that species diversity is underestimated. However, we show that erring on overestimation can yield negative consequences, such as the disproportionate prioritization of a geographically anomalous population.

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Exploring the endangerment mechanisms of Hipposideros pomona based on molecular phylogeographic methods

Liu,

Hao,

Song

et al. 2023

Ecology and Evolution

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The endangerment mechanisms of various species are a focus of studies on biodiversity and conservation biology. Hipposideros pomona is an endangered species, but the reasons behind its endangerment remain unclear. We investigated the endangerment mechanisms of H. pomona using mitochondrial DNA, nuclear DNA, and microsatellite loci markers. The results showed that the nucleotide diversity of mitochondria DNA and heterozygosity of microsatellite markers were high (π = 0.04615, HO = 0.7115), whereas the nucleotide diversity of the nuclear genes was low (THY: π = 0.00508, SORBS2: π = 0.00677, ACOX2: π = 0.00462, COPS7A: π = 0.00679). The phylogenetic tree and median‐joining network based on mitochondrial DNA sequences clustered the species into three clades, namely North Vietnam‐Fujian, Myanmar‐West Yunnan, and Laos‐Hainan clades. However, joint analysis of nuclear genes did not exhibit clustering. Analysis of molecular variance revealed a strong population genetic structure; IMa2 analysis did not reveal significant gene flow between all groups (p > .05), and isolation‐by‐distance analysis revealed a significant positive correlation between genetic and geographic distances (p < .05). The mismatch distribution analysis, neutral test, and Bayesian skyline plots revealed that the H. pomona population were relatively stable and exhibited a contraction trend. The results implied that H. pomona exhibits female philopatry and male‐biased dispersal. The Hengduan Mountains could have acted as a geographical barrier for gene flow between the North Vietnam‐Fujian clade and the Myanmar‐West Yunnan clade, whereas the Qiongzhou Strait may have limited interaction between the Hainan populations and other clades. The warm climate during the second interglacial Quaternary period (c. 0.33 Mya) could have been responsible for species differentiation, whereas the cold climate during the late Quaternary last glacial maximum (c. 10 ka BP) might have caused the overall contraction of species. The lack of significant gene flow in nuclear microsatellite loci markers among the different populations investigated reflects recent habitat fragmentation due to anthropogenic activities; thus, on‐site conservation of the species and restoration of gene flow corridors among populations need immediate implementation.

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Species delimitation and evolutionary reconstruction within an integrative taxonomic framework: A case study on Rhinolophus macrotis complex (Chiroptera: Rhinolophidae)

Cited by 19 publications

References 90 publications

Evolutionary insights intoRhinolophus episcopus(Chiroptera, Rhinolophidae) in China: Isolation by distance, environment, or sensory system?

Evolutionary insights intoRhinolophus episcopus(Chiroptera, Rhinolophidae) in China: Isolation by distance, environment, or sensory system?

A turn in species conservation for hairpin banksias: demonstration of oversplitting leads to better management of diversity

Exploring the endangerment mechanisms of Hipposideros pomona based on molecular phylogeographic methods

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