Heteroplasmy and Ancient Translocation of Mitochondrial DNA to the Nucleus in the Chinese Horseshoe Bat (Rhinolophus sinicus) Complex

The utility and reliability of mitochondrial DNA sequences in phylogenetic and phylogeographic studies may be compromised by widespread and undetected nuclear mitochondrial copies (numts) as well as heteroplasmy within individuals. Both numts and heteroplasmy are likely to be common across diverse taxa yet few studies have characterised their frequencies and variation at the intra-specific level. Here we report the presence of both numts and heteroplasmy in the mitochondrial control region of the Chinese horseshoe bat Rhinolophus sinicus. In total we generated 123 sequences from 18 bats, which contained two different numt clades (i.e. Numt-1 and Numt-2) and one mtDNA clade. The sequence divergence between Numt-1 and Numt-2 was 16.8% and each numt type was found in all four R. sinicus taxa, suggesting either two ancient translocations of mitochondrial DNA into the nucleus from the same source taxon, or a single translocation from different source taxa that occurred before the split of R. sinicus into different lineages. Within the mtDNA clade, phylogenetic relationships among the four taxa of R. sinicus were similar to those seen in previous results. Based on PCR comparisons, heteroplasmy was inferred between almost all individuals of R. sinicus with respect to sequence variation. Consistent with introgression of mtDNA between Central sinicus and septentrionalis, individuals from these two taxa exhibited similar signatures of repeated sequences in the control region. Our study highlights the importance of testing for the presence of numts and heteroplasmy when applying mtDNA markers to phylogenetic studies.     

辽宁省翼手目分布新记录种大耳菊头蝠

翼手目(蝙蝠)物种独特的飞行能力、夜间活动模式及相近的形态学特征,增大了科研人员在野外对其进行准确鉴别和调查的难度,因此翼手目物种的多样性和分布信息亟需综合多种调查技术开展广泛深入研究。2019年8月,作者在辽宁省朝阳市野外调查发现1种蝙蝠,经分子标记比对、系统发育关系重建及形态学数据鉴定为大耳菊头蝠(Rhinolophus macrotis),是辽宁省翼手目物种新记录。     

中华菊头蝠不同组织基因组DNA甲基化分析

DNA甲基化在动物组织发育和分化等生物过程中发挥至关重要的作用.本研究采用荧光标记甲基化敏感扩增多态性(fluorescence-labeled methylation sensitive amplified polymorphism,F-MSAP)技术分析了中华菊头蝠(Rhinolophus sinicus)脑、心、...     

Sensory Drive Mediated by Climatic Gradients Partially Explains Divergence in Acoustic Signals in Two Horseshoe Bat Species,Rhinolophus swinnyi and Rhinolophus simulator

Geographic variation can be an indicator of still poorly understood evolutionary processes such as adaptation and drift. Sensory systems used in communication play a key role in mate choice and species recognition. Habitat-mediated (i.e. adaptive) differences in communication signals may therefore lead to diversification. We investigated geographic variation in echolocation calls of African horseshoe bats, Rhinolophus simulator and R. swinnyi in the context of two adaptive hypotheses: 1) James’ Rule and 2) the Sensory Drive Hypothesis. According to James’ Rule body-size should vary in response to relative humidity and temperature so that divergence in call frequency may therefore be the result of climate-mediated variation in body size because of the correlation between body size and call frequency. The Sensory Drive Hypothesis proposes that call frequency is a response to climate-induced differences in atmospheric attenuation and predicts that increases in atmospheric attenuation selects for calls of lower frequency. We measured the morphology and resting call frequency (RF) of 111 R. simulator and 126 R. swinnyi individuals across their distributional range to test the above hypotheses. Contrary to the prediction of James’ Rule, divergence in body size could not explain the variation in RF. Instead, acoustic divergence in RF was best predicted by latitude, geography and climate-induced differences in atmospheric attenuation, as predicted by the Sensory Drive Hypothesis. Although variation in RF was strongly influenced by temperature and humidity, other climatic variables (associated with latitude and altitude) as well as drift (as suggested by a positive correlation between call variation and geographic distance, especially in R. simulator) may also play an important role.     

菲菊头蝠不同地理种群回声定位声波差异及其影响因子

回声定位声波地理差异及其形成原因是蝙蝠生态学研究领域一个基本而关键的问题,对于探索物种生存机制、物种形成及其保护具有重要科学意义。本研究从较大地理尺度上(9个地理种群)研究了菲菊头蝠(Rhinolophus pusillus)回声定位声波结构的地理差异,并进一步探讨了影响回声定位声波地理种群差异的因素。结果表明,菲菊头蝠雌性的体型较雄性略大,其主频较高。不同地理种群之间回声定位声波差异明显,包括脉冲持续时间、脉冲间隔、主频以及带宽在不同的地理种群之间均表现出一定程度的差异。进一步分析发现,不同地理种群之间的雌性菲菊头蝠前臂长和体重均与主频呈较弱的负相关,降雨量与雌性的主频呈较强的正相关;而不同地理种群之间的雄性前臂长、体重和降雨量与回声定位声波参数均无相关性;此外,地理距离、温度、湿度均与雌雄回声定位声波参数无相关性。本研究结果表明,菲菊头蝠不同地理种群间的回声定位声波出现明显差异,其中,体型和降雨量为主要影响因子,说明蝙蝠回声定位叫声的进化主要受到了当地生境的影响,表现出动物对不同生境的适应性进化。     

Historical Divergence and Gene Flow in the Genus Zea

Gene flow plays a fundamental role in plant evolutionary history, yet its role in population divergence—and ultimately speciation—remains poorly understood. We investigated gene flow and the modalities of divergence in the domesticate Zea mays ssp. mays and three wild Zea taxa using sequence polymorphism data from 26 nuclear loci. We described diversity across loci and assessed evidence for adaptive and purifying selection at nonsynonymous sites. For each of three divergence events in the history of these taxa, we used approximate Bayesian simulation to estimate population sizes and divergence times and explicitly compare among alternative models of divergence. Our estimates of divergence times are surprisingly consistent with previous data from other markers and suggest rapid diversification of lineages within Zea in the last ~150,000 years. We found widespread evidence of historical gene flow, including evidence for divergence in the face of gene flow. We speculate that cultivated maize may serve as a bridge for gene flow among otherwise allopatric wild taxa.     

Three-Dimensional and Histological Observations on Male Genital Organs of Greater Horseshoe Bat,Rhinolophus ferrumequinum

Journal of Mammalian Evolution - Anatomy of bat genital organs has been conventionally studied by gross and microscopic observations to date. Here, we employ both histological observation and...     

Four New Bat Species (Rhinolophus hildebrandtii Complex) Reflect Plio-Pleistocene Divergence of Dwarfs and Giants across an Afromontane Archipelago

Gigantism and dwarfism evolve in vertebrates restricted to islands. We describe four new species in the Rhinolophus hildebrandtii species-complex of horseshoe bats, whose evolution has entailed adaptive shifts in body size. We postulate that vicissitudes of palaeoenvironments resulted in gigantism and dwarfism in habitat islands fragmented across eastern and southern Africa. Mitochondrial and nuclear DNA sequences recovered two clades of R. hildebrandtii senso lato which are paraphyletic with respect to a third lineage (R. eloquens). Lineages differ by 7.7 to 9.0% in cytochrome b sequences. Clade 1 includes R. hildebrandtii sensu stricto from the east African highlands and three additional vicariants that speciated across an Afromontane archipelago through the Plio-Pleistocene, extending from the Kenyan Highlands through the Eastern Arc, northern Mozambique and the Zambezi Escarpment to the eastern Great Escarpment of South Africa. Clade 2 comprises one species confined to lowland savanna habitats (Mozambique and Zimbabwe). A third clade comprises R. eloquens from East Africa. Speciation within Clade 1 is associated with fixed differences in echolocation call frequency, and cranial shape and size in populations isolated since the late Pliocene (ca 3.74 Mya). Relative to the intermediate-sized savanna population (Clade 2), these island-populations within Clade 1 are characterised by either gigantism (South African eastern Great Escarpment and Mts Mabu and Inago in Mozambique) or dwarfism (Lutope-Ngolangola Gorge, Zimbabwe and Soutpansberg Mountains, South Africa). Sympatry between divergent clades (Clade 1 and Clade 2) at Lutope-Ngolangola Gorge (NW Zimbabwe) is attributed to recent range expansions. We propose an “Allometric Speciation Hypothesis”, which attributes the evolution of this species complex of bats to divergence in constant frequency (CF) sonar calls. The origin of species-specific peak frequencies (overall range = 32 to 46 kHz) represents the allometric effect of adaptive divergence in skull size, represented in the evolution of gigantism and dwarfism in habitat islands.     

形态和声波相似的中华菊头蝠与中菊头蝠的共存机制

研究了同域分布的中华菊头蝠(Rhinolophus sinicus)与中菊头蝠(Rhinolophus affinis)的食性、形态、回声定位声波及捕食时间.中华菊头蝠与中菊头蝠均属于中等体型的菊头蝠,前臂长分别为(51.25±0.22) mm和(52.40±0.37) mm;悬挂状态下的回声定位声波均为典型的调频-恒频-调频(FM-CM-FM)型叫声,峰频分别为(82.07±0.17) kHz和(84.41±0.48) kHz.粪便分析显示中华菊头蝠与中菊头蝠分别捕食9目和7目昆虫,均以鳞翅目(Lepidiptera)和鞘翅目(Coleoptera)昆虫为主要食物(体积百分比总和> 90%),捕食鳞翅目昆虫的体积百分比差异显著,对猎物大小(以鞘翅目昆虫体长衡量)的选择无显著差异.中华菊头蝠与中菊头蝠的营养生态位宽度分别为2.38和2.28,重叠度达0.91,营养生态位未发生明显分化,但充足的食物资源促进了二者的共存.另外,2种菊头蝠的感官生态位和时间生态位未发生明显分化.由2种菊头蝠的翼载和峰频的差异推测二者发生了空间生态位和捕食微生境的分化,这也可能促进了二者的共存.     

The effects of cultural drift on geographic variation in echolocation calls of the Chinese rufous horseshoe bat (Rhinolophus sinicus)

Drift, selection, or their combined effects commonly drive geographic variation in traits. Clarifying the relative roles of each process is a long‐standing research goal in evolutionary biology. Acoustic signals of bats are a phenotypic characteristic that plays an important role in social organization and species recognition. We extensively sampled the Chinese rufous horseshoe bat (Rhinolophus sinicus) throughout China and Vietnam and reconstructed a species phylogeny to better understand the patterns and causes of the geographic variation of acoustic signals. Our results showed that the resting frequency (RF) of calls varied with latitude, sex, and distance among different colony locations. RF differences were not correlated with genetic distance (based on only one nuclear locus and the mitochondrial locus), climatic factors (mean annual temperature and mean annual precipitable water), or body size, although differences in calls increased with distance among various populations. This suggests that cultural drift may play more important roles than genetic drift and acoustic adaptation in shaping acoustic differences within regions in R. sinicus.     

Hidden Historical Habitat-Linked Population Divergence and Contemporary Gene Flow of a Deep-Sea Patellogastropod Limpet

Hydrothermal vents and hydrocarbon seeps in the deep ocean are rare oases fueled by chemosynthesis. Biological communities inhabiting these ecosystems are often distributed in widely separated habitats, raising intriguing questions on how these organisms achieve connectivity and whether habitat types facilitate intraspecific divergence. The deep-sea patellogastropod limpet Bathyacmaea nipponica that colonizes both vents and seeps across ∼2,400 km in the Northwest Pacific is a feasible model to answer these questions. We analyzed 123 individuals from four vents and three seeps using a comprehensive method incorporating population genomics and physical ocean modeling. Genome survey sequencing and genotyping-by-sequencing resulted in 9,838 single-nucleotide polymorphisms for population genomic analyses. Genetic divergence and demographic analyses revealed four habitat-linked (i.e., three seep and one vent) genetic groups, with the vent genetic group established via the opportunistic invasion of a few limpet larvae from a nearby seep genetic group. TreeMix analysis uncovered three historical seep-to-vent migration events. ADMIXTURE and divMigrate analyses elucidated weak contemporary gene flow from a seep genetic group to the vent genetic group. Physical ocean modeling underlined the potential roles of seafloor topography and ocean currents in shaping the genetic connectivity, contemporary migration, and local hybridization of these deep-sea limpets. Our study highlighted the power of integrating genomic and oceanographic approaches in deciphering the demography and diversification of deep-sea organisms. Given the increasing anthropogenic activities (e.g., mining and gas hydrate extraction) affecting the deep ocean, our results have implications for the conservation of deep-sea biodiversity and establishment of marine protected areas.     

Comparison of Brain Transcriptome of the Greater Horseshoe Bats (Rhinolophus ferrumequinum) in Active and Torpid Episodes

Hibernation is an energy-saving strategy which is widely adopted by heterothermic mammals to survive in the harsh environment. The greater horseshoe bat (Rhinolophus ferrumequinum) can hibernate for a long period in the hibernation season. However, the global gene expression changes between hibernation and non-hibernation season in the greater horseshoe bat remain largely unknown. We herein reported a comprehensive survey of differential gene expression in the brain between winter hibernating and summer active greater horseshoe bats using next-generation sequencing technology. A total of 90,314,174 reads were generated and we identified 1,573 differentially expressed genes between active and torpid states. Interestingly, we found that differentially expressed genes are over-represented in some GO categories (such as metabolic suppression, cellular stress responses and oxidative stress), which suggests neuroprotective strategies might play an important role in hibernation control mechanisms. Our results determined to what extent the brain tissue of the greater horseshoe bats differ in gene expression between summer active and winter hibernating states and provided comprehensive insights into the adaptive mechanisms of bat hibernation.     

Development and characterization of novel microsatellite markers from the Chinese rufous horseshoe bat (Rhinolophus sinicus) with cross-species amplification in closely related taxa

We isolated nine polymorphic microsatellite markers from the Chinese rufous horseshoe bat (Rhinolophus sinicus) using an enriched library method. We assessed genetic polymorphism at these loci in 42 individuals from a single population. We recorded high genetic diversity with four to 17 alleles per locus, and estimated expected and observed heterozygosity values ranging from 0.492 to 0.910 and from 0.462 to 0.881, respectively. No locus departed from Hardy-Weinberg equilibrium following Bonferroni correction, and no linkage disequilibrium was detected. Most loci successfully cross-amplified congeneric species. These loci will be used to characterize phylogeographical history of Rhinolophus sinicus in China.     

Origins of Horseshoe Bats (Rhinolophus, Rhinolophidae) in Southern Africa: Evidence from Allozyme Variability

Morphological analyses indicate that horsehose bats in the genus Rhinolophus constitute a monophyletic group which most likely originated in southeastern Asia but which presently inhabits Oriental, Australian, Palaearctic, and Ethiopian zoogeographical provinces. Ten species occur in southern Africa, but it is uncertain which species represent dispersals from Eurasia through North Africa and which have resulted from speciation in Africa. Analyses of 34 allozyme encoding loci in these 10 species and in 2 southern African species of leafnose bats in the sister genus Hipposideros reveal the presence of at least three lineages of Rhinolophus in southern Africa. One lineage includes R. clivosus, R. darlingi, R. fumigatus, and R. hildebrandtii, all of which, except R. clivosus, are endemic to sub-Saharan Africa. Rhinolophus blasii is genetically allied with, but distinct from this group, and appears to be a recent migrant from another lineage centered on the Mediterranean. A third lineage, including at least R. capensis, R. denti, R. simulator, and R. swinnyi, is endemic to sub-Saharan Africa. The phylogenetic position of R. landeri is uncertain, most likely because of the small sample size used to estimate allelic frequencies for this species. The biochemical genetic definitions of these lineages largely agree with previous morphological analyses of Rhinolophus species. Divergences between species within two lineages (R. clivosus, R. darlingi, R. fumigatus, and R. hildebrandtii; and R. capensis, R. denti, R. simulator, and R. swinnyi) appear to reflect two bursts of speciation in the Plio-Pleistocene period within Africa.     

皮氏菊头蝠回声定位声波与年龄的关系

皮氏菊头蝠 (Rhinolophuspearsoni)雌性成体 5只和幼体 2只采自贵州省贞丰县珉谷镇。采用超声波探测仪 (D980 ,ULTRASOUNDDETECTOR)接收皮氏菊头蝠的回声定位声波 ,转换到原频率的 1 / 1 0后导入计算机 ,然后用专业声谱分析软件 (Batsound 3 1 0 )进行分析。成蝠在飞行和悬挂状态下的声波结构相似 ,只是声波各项参数值略有不同 :它们发射FM CF FM型声波 ,具有 2～ 3个谐波 ,主频率在飞行时为 5 6 80± 0 6 2kHz ,悬挂时为 5 8 0 5± 0 2 4kHz ;声脉冲时间和间隔在飞行时分别为 3 4 6 2± 5 2 9ms和 86 5 0± 1 9 72ms ,悬挂时分别为 4 1 0 8± 5 87ms和 1 1 7 2 9± 6 6 4 4ms ;能率环飞行时为 ( 4 4 0 6± 1 2 5 8) % ,悬挂时为 ( 4 6 0 0±2 4 2 5 ) %。幼蝠声波为CF FM型 ,谐波数为 5～ 8个 ,主频率明显低于成体 ,FM带宽窄于成体 ,声脉冲时间和间隔短于成体 ,能率环低于成体。皮氏菊头蝠回声定位声波与年龄有关 ,这可能因成体的声波主要是探测食物和周围环境的详细信息 ,而幼体主要是与母蝠进行交流。     

陕西省翼手类新纪录——大菊头蝠

2010年4月16日,在陕西省安康市镇坪县的一无名岩洞获得1号蝙蝠标本.该标本为雄性,体型较大.马蹄叶发达、覆盖上唇且两侧无小附叶.鞍状叶呈三角形,向两侧明显扩张成翼状.体毛细长柔软而稍卷曲.经鉴定为大菊头蝠(Rhinolophus luctus),属陕西省翼手类新纪录.标本保存于陕西省动物研究所标本室.本文报道了这种...     

Historical introgression and the persistence of ghost alleles in the intermediate horseshoe bat (Rhinolophus affinis)

Phylogenetic conflicts between genetic markers can help to disentangle complex histories of phylogeography and introgression among taxa. We previously proposed that the Chinese mainland subspecies of the intermediate horseshoe bat Rhinolophus affinis himalayanus colonized Hainan Island to form the subspecies R. a. hainanus. Subsequent recolonization of the mainland formed a third taxon, R. a macrurus, and a secondary contact zone with the ancestral himalayanus. To test for historical and recurrent genetic exchange between these mainland subspecies, we sampled populations of each from two parapatric zones and undertook analyses using one mtDNA marker, three nuclear genes and 14 microsatellites. Nuclear DNA, echolocation call frequencies and morphological data all recovered two taxa; however, a mtDNA phylogeny revealed two himalayanus clades, of which one clustered with macrurus, as well as some shared or related mtDNA haplotypes in eastern populations. Isolation‐with‐migration (IM) models suggested some mtDNA gene flow from macrurus to himalayanus. However, strong population structure in himalayanus raises the possibility that macrurus captured mtDNA from a coastal population of himalayanus that has since become rare or extinct. To reconcile these two sets of results, we suggest that the IM estimates might reflect historical mtDNA gene flow among populations of himalayanus, before mtDNA was subsequently captured by macrurus. Finally, microsatellite‐based ABC analyses supported the island origin of macrurus; however, mtDNA‐based ABC analyses suggest this taxon might have evolved on the mainland. Our findings highlight the importance of understanding population history and structure for interpreting hybridization and introgression events.