Fine-scale genetic structure, estuarine colonization and incipient speciation in the marine silverside fish Odontesthes argentinensis

The identification of incipient ecological species represents an opportunity to investigate current evolutionary process where adaptive divergence and reproductive isolation are associated. In this study we analysed the genetic structure of marine and estuarine populations of the silverside fish Odontesthes argentinensis using nine microsatellite loci and 396 bp of the mitochondrial DNA (mtDNA) control region. Our main objective was to investigate the relationship among estuarine colonization, divergent selection and speciation in silversides. Significant genetic structure was detected among all marine and estuarine populations. Despite the low phylogeographic structure in mtDNA haplotypes, there was clear signal of local radiations of haplotypes in more ancient populations. Divergence among marine populations was interpreted as a combined result of homing behaviour, isolation by distance and drift. On the other hand, ecological shifts due to the colonization of estuarine habitats seem to have promoted rapid adaptive divergence and reproductive isolation in estuarine populations, which were considered as incipient ecological species. This conclusion is supported by the existence of a set of environmental factors required for successful reproduction of estuarine ecotypes. The pattern of genetic structure indicates that phenotypic and reproductive divergence evolved in the face of potential gene flow between populations. We suggest that the 'divergence-with-gene-flow' model of speciation may account for the diversification of estuarine populations. The approach used can potentially identify 'incipient estuarine species', being relevant to the investigation of the evolutionary relationships of silversides in several coastal regions of the world.     

Intraspecific differentiation of Pleurospermum hookeri (Apiaceae), and its interspecific relationships with two close relatives in the genus Pleurospermum

In order to clarify the interspecific relationships of a lineage in Pleurospermum, P. hookeri C. B. Clarke, P. yunnanense Franch., and P. giraldii Diels, and to understand intraspecific divergence of P. hookeri, a phylogeographic study was carried out based on 198 individuals from 24 populations. Three chloroplast DNA regions, ndhF-rpl32, trnL-trnF, and trnQ-rps16, were sequenced in the present study. The genetic relationship between P. hookeri and P. giraldii is not as close as previously assumed. Pleurospermum hookeri and P. giraldii may originate from an unknown ancestor located in the Qinling region. Pleurospermum yunnanensewas found to be the closest relative of P. hookeri in all the species included in the phylogenetic analysis. The two haplotypes identified from P. yunnanense are shared with P. hookeri, which is potentially a result of both incomplete linkage sorting and introgression. Three large divergences within P. hookeri were identified, located at the northeastern edge, southeastern edge, and platform of the Qinghai–Tibet Plateau (QTP), respectively. Long-term history can explain the deep intraspecific divergence of P. hookeri. The uplift of the QTP played a key role in that divergence, and then were the climatic changes in the Quaternary. In addition, we found one refugium at the northeastern edge of the QTP, one at the southeastern edge, and at least one in the Hengduan Mountains region on the platform of the QTP.     

Late Pleistocene climate change promoted divergence between Picea asperata and P. crassifolia on the Qinghai–Tibet Plateau through recent bottlenecks

Divergence during the early stage of speciation can be driven by a population bottleneck via reduced gene flow and enhanced lineage sorting. In this study, we aimed to examine whether such bottlenecks occurred during the initial speciation of two closely related spruce species Picea asperata and P. crassifolia occurring on the Qinghai–Tibet Plateau (QTP). We analyzed sequences of three chloroplast, two mitochondrial DNA fragments and a further 13 nuclear loci from 216 individuals of the two species. Both species showed a low level of genetic diversity in contrast to other congeners occurring in the QTP and adjacent regions. The estimated population sizes of P. asperata and P. crassifolia are less than the ancestral population size before splitting. These results together with multiple statistical tests (Tajima's D, Fu and Li's D* and F*) suggest that these two species underwent recent bottlenecks. Based on approximate Bayesian computation (ABC), we also determined that the period of the population shrinkage was consistent with the interspecific divergence during the late Pleistocene. The reduced population sizes and the divergent selection may together have triggered the initial divergence under high gene flow between these two species. Our results therefore highlight the importance of climatic oscillations during the late Pleistocene in promoting speciation through changing demographic sizes of the ancestral species on the QTP and in adjacent regions.     

Quaternary climate change and habitat preference shaped the genetic differentiation and phylogeography of Rhodiola sect. Prainia in the southern Qinghai–Tibetan Plateau

There are two long‐standing biogeographic hypotheses regarding the glacial survival of plant species in the Qinghai–Tibetan Plateau (QTP): the in situ survival hypothesis and the tabula rasa hypothesis. We tested these two hypotheses in a phylogeographic study of Rhodiola sect. Prainia, a monophyletic section with ecologically divergent lineages. Molecular data from the nuclear internal transcribed spacer, six plastid markers and 13 nuclear microsatellite loci were analyzed for 240 individuals from 19 populations of this section. Environmental data were used to analyze the niches of major phylogenetic lineages within this section and to model changes in their distributions since the Last Glacial Maximum (LGM). We found that Rhodiola sect. Prainia consists of three evolutionary lineages: all populations of R. stapfii, R. prainii populations at the southern edge of the QTP, and R. prainii populations in the interior part of the QTP. During the LGM, the survival of R. prainii in the interior part of the QTP corresponded with the in situ survival hypothesis, while R. stapfii most probably survived the LGM in a manner corresponding with the tabula rasa hypothesis. The evolutionary history of different lineages of this section was shaped by topography, climate change, and lineage‐specific habitat preferences.     

Restriction‐site associated DNA sequencing data reveal a radiation of willow species (Salix L., Salicaceae) in the Hengduan Mountains and adjacent areas

The Hengduan Mountains (HDM) in China are an important hotspot of plant diversity and endemism, and are considered to be a secondary diversification center for the woody plant genus Salix L. (Salicaceae). Here we aimed to reconstruct the spatiotemporal evolution of the Salix Chamaetia‐Vetrix clade in the HDM and to test for the occurrence of a local radiation. We inferred phylogenetic relationships based on more than 34 000 restriction‐site associated DNA loci from 27 species. Phylogenetic analyses recovered a well‐resolved tree topology with two major clades, the Eurasian clade and the HDM clade, with a divergence time of ca. 23.9 Ma. Species in the HDM clade originated in the northern part of the range and adjacent areas, and then dispersed into the southern HDM, westwards to the Himalayas and eastwards to the Qinling Mountains. Niche modelling analyses reveal that range contractions occurred in the northern areas during the last glacial maximum, while southward expansions resulted in range overlaps. Reconstructions of character evolution related to plant height, inflorescence, and flower morphology suggest that adaptations to altitudinal distribution contributed to the diversification of the HDM willows. Our data support the occurrence of a radiation in the HDM within the Salix Chamaetia‐Vetrix clade. Dispersal within the mountain system, and to adjacent regions, in addition to survival in glacial refugia shaped the biogeographical history of the clade, while adaptations of the HDM willows along an altitudinal gradient could be important ecological factors explaining the high species diversity of Salix in this area.     

Extinct genus Lagokarpos reveals a biogeographic connection between Tibet and other regions in the Northern Hemisphere during the Paleogene

The biodiversity history on the Qinghai–Tibetan Plateau (QTP) has remained unclear for a long time. Recent paleobotanical investigations provide opportunities for revealing the phytogeographic history on the QTP in deep time and for testing phylogeographic hypotheses. Lagokarpos is an extinct genus with unknown modern affinities. It is easily distinguished by its fruits, which have two long wings and an elliptical fruit body. Previously, Lagokarpos fossils have only been found from North America and Germany, ranging from the latest Paleogene to early middle Eocene. Recently, we found fossil fruits of this genus from the Niubao Formation, near Bangoin County in the central QTP. A new species, namely Lagokarpos tibetensis H. Tang, T. Su & Z. K. Zhou sp. nov., is described. This is the first fossil record of the genus in Asia. The occurrence of L. tibetensis indicates a close floristic linkage between the QTP and other floras in the Northern Hemisphere during the Paleogene. According to the floristic assemblages, we suggest the central QTP experienced a tropical or subtropical humid climate during that period.     

Responses of biomass allocation across two vegetation types to climate fluctuations in the northern Qinghai–Tibet Plateau

The Qinghai–Tibet Plateau (QTP) is particularly sensitive to global climate change, especially to elevated temperatures, when compared with other ecosystems. However, few studies use long‐term field measurements to explore the interannual variations in plant biomass under climate fluctuations. Here, we examine the interannual variations of plant biomass within two vegetation types (alpine meadow and alpine shrub) during 2008–2017 and their relationships with climate variables. The following results were obtained. The aboveground biomass (AGB) and belowground biomass (BGB) response differently to climate fluctuations, the AGB in KPM was dominated by mean annual precipitation (MAP), whereas the AGB in PFS was controlled by mean annual air temperature (MAT). However, the BGB of both KPM and PFS was only weakly affected by climate variables, suggesting that the BGB in alpine ecosystems may remain as a stable carbon stock even under future global climate change. Furthermore, the AGB in PFS was significantly higher than KPM, while the BGB and R/S in KPM were significantly higher than PFS, reflecting the KPM be more likely to allocate more photosynthates to roots. Interestingly, the proportion of 0–10 cm root biomass increased in KPM and PFS, whereas the other proportions both decreased, reflecting a shift in biomass toward the surface layer. Our results could provide a new sight for the prediction how alpine ecosystem response to future climate change.     

Belowground carbon responses to experimental warming regulated by soil moisture change in an alpine ecosystem of the Qinghai–Tibet Plateau

Recent studies found that the largest uncertainties in the response of the terrestrial carbon cycle to climate change might come from changes in soil moisture under the elevation of temperature. Warming‐induced change in soil moisture and its level of influence on terrestrial ecosystems are mostly determined by climate, soil, and vegetation type and their sensitivity to temperature and moisture. Here, we present the results from a warming experiment of an alpine ecosystem conducted in the permafrost region of the Qinghai–Tibet Plateau using infrared heaters. Our results show that 3 years of warming treatments significantly elevated soil temperature at 0–100 cm depth, decreased soil moisture at 10 cm depth, and increased soil moisture at 40–100 cm depth. In contrast to the findings of previous research, experimental warming did not significantly affect NH ₄ ⁺‐N, NO ₃ ⁻‐N, and heterotrophic respiration, but stimulated the growth of plants and significantly increased root biomass at 30–50 cm depth. This led to increased soil organic carbon, total nitrogen, and liable carbon at 30–50 cm depth, and increased autotrophic respiration of plants. Analysis shows that experimental warming influenced deeper root production via redistributed soil moisture, which favors the accumulation of belowground carbon, but did not significantly affected the decomposition of soil organic carbon. Our findings suggest that future climate change studies need to take greater consideration of changes in the hydrological cycle and the local ecosystem characteristics. The results of our study will aid in understanding the response of terrestrial ecosystems to climate change and provide the regional case for global ecosystem models.     

Tracing the first step to speciation: ecological and genetic differentiation of a salamander population in a small forest

Mechanisms and processes of ecologically driven adaptive speciation are best studied in natural situations where the splitting process is still occurring, i.e. before complete reproductive isolation is achieved. Here, we present a case of an early stage of adaptive differentiation under sympatric conditions in the fire salamander, Salamandra salamandra, that allows inferring the underlying processes for the split. Larvae of S. salamandra normally mature in small streams until metamorphosis, but in an old, continuous forest area near Bonn (the Kottenforst), we found salamander larvae not only in small streams but also in shallow ponds, which are ecologically very different from small streams. Common-environment experiments with larvae from both habitat types reveal specific adaptations to these different ecological conditions. Mitochondrial and microsatellite analyses show that the two ecologically differentiated groups also show signs of genetic differentiation. A parallel analysis of animals from a neighbouring much larger forest area (the Eifel), in which larvae mature only in streams, shows no signs of genetic differentiation, indicating that gene flow between ecologically similar types can occur over large distances. Hence, geographical factors cannot explain the differential larval habitat adaptations in the Kottenforst, in particular since adult life and mating of S. salamandra is strictly terrestrial and not associated with larval habitats. We propose therefore that the evolution of these adaptations was coupled with the evolution of cues for assortative mating which would be in line with models of sympatric speciation that suggest a co-evolution of habitat adaptations and associated mating signals.     

Genetic Variation Within and Among Populations of Rhodiola alsia (Crassulaceae) Native to the Tibetan Plateau as Detected by ISSR Markers

Genetic variation of 10 Rhodiola alsia (Crassulaceae) populations from the Qinghai–Tibet Plateau of China was investigated using intersimple sequence repeat (ISSR) markers. R. alsia is an endemic species of the Qinghai–Tibet Plateau. Of the 100 primers screened, 13 were highly polymorphic. Using these primers, 140 discernible DNA fragments were generated with 112 (80%) being polymorphic, indicating pronounced genetic variation at the species level. Also there were high levels of polymorphism at the population level with the percentage of polymorphic bands (PPB) ranging from 63.4 to 88.6%. Analysis of molecular variance (AMOVA) showed that the genetic variation was mainly found among populations (70.3%) and variance within populations was 29.7%. The main factors responsible for the high level of differentiation among populations are probably the isolation from other populations and clonal propagation of this species. Occasional sexual reproduction might occur in order to maintain high levels of variation within populations. Environmental conditions could also influence population genetic structure as they occur in severe habitats. The strong genetic differentiation among populations in our study indicates that the conservation of genetic variability in R. alsia requires maintenance of as many populations as possible.     

Contrasting responses to Pleistocene climate changes: a case study of two sister species Allium cyathophorum and A. spicata (Amaryllidaceae) distributed in the eastern and western Qinghai–Tibet Plateau

It has been hypothesized that species occurring in the eastern and the western Qinghai–Tibet Plateau (QTP) responded differently to climate changes during the Pleistocene. Here, we test this hypothesis by phylogeographic analysis of two sister species, Allium cyathophorum and A. spicata. We sequenced two chloroplast DNA (cpDNA) fragments (accD‐psaI and the rpl16 intron) of 150 individuals, and the nuclear (ITS) region of 114 individuals, from 19 populations throughout the distributional ranges of these species. The divergence between the two species was dated at 779 ‐ 714 thousand years before the present and was likely initiated by the most major glaciation in the QTP. Analysis of chlorotype diversity showed that A. spicata, the species occurring in the western QTP, contains much lower genetic diversity (0.25) than A. cyathophorum (0.93), which is distributed in the eastern QTP. Moreover, multiple independent tests suggested that the A. spicata population had expanded recently, while no such expansion was detected in A. cyathophorum, indicating a contrasting pattern of responses to Pleistocene climate changes. These findings highlight the importance of geographical topography in determining how species responded to the climate changes that took place in the QTP during the Pleistocene.     

基于1980—2018年土地利用变化的福建省生境质量时空演变

分析土地利用变化引起生境质量的时空演变特征可以为区域生态文明建设提供科学依据。本研究以生态文明先行示范区福建省为例,以1980—2018年土地利用变化数据为基础,利用InVEST模型对福建省生境质量进行评估,通过地理探测器分析影响因素,结合土地利用变化规律分析福建省生境质量时空演化特征。结果表明: 研究期间,福建省主要土地利用变化类型是耕地转为林地和建设用地,林地转为耕地、草地和建设用地,草地转为林地,分别占总土地利用变化面积的8.4%、14.5%、7.6%、17.1%、6.4%和31.7%。1980—2018年,福建省总体生境质量处于较高级别(0.6～0.8),局部区域呈现生境退化和生境质量降低的趋势。影响福建省生境质量空间分异的第一主导因素是土地利用类型的变化,社会经济因素对沿海县市生境质量的影响显著高于对全域及内陆县市生境质量的影响。沿海地区建设用地快速侵占周边的林草地,使得生境加速退化,且这个过程具有不可逆性;内陆地区中心城区的生境退化会经历相似的过程,只是在速度和规模上可能低于沿海地区。从长远来看,可通过控制城市规模、发展城市生态绿化及构建生态安全格局,以减缓生境退化的速度。     

The genetic basis of intrinsic and extrinsic post-zygotic reproductive isolation jointly promoting speciation in the lake whitefish species complex (Coregonus clupeaformis)

Understanding the genetic architecture of reproductive barriers and the evolutionary forces that drove their divergence represents a considerable challenge towards understanding speciation. The objective of this study was to determine the genetic basis of intrinsic and extrinsic post-zygotic isolation in diverging populations of dwarf and normal lake whitefish with allopatric glacial origins. We found that the rate of embryonic mortality was 5.3-6.5 times higher in dwarf-normal hybrid backcrosses during development than in F1 dwarf and normal crosses. When comparing embryos that died during development against larvae that successfully hatched, patterns of Mendelian segregation at 101 loci whose linkage is known identified 13 loci distributed over seven linkage groups that exhibited significant shifts in segregation ratios leading to significant segregation distortion at these loci in the surviving progeny. Controlled crosses and quantitative trait loci analysis revealed a significant genetic basis for developmental time until emergence, a trait critical to fish larval survival in nature. Hatching backcross progeny exhibited asynchronous emergence and transgressive segregation, suggesting that extrinsic post-zygotic isolation may select against hybridization in specific environmental contexts. Evidence of a genetic basis for increased embryonic mortality followed by asynchronous emergence indicated that intrinsic and extrinsic mechanisms are not mutually exclusive in the formation and maintenance of reproductive isolation, but may be jointly promoting population divergence and ultimately speciation.     

Congruent population genetic structures and divergence histories in anther‐smut fungi and their host plants Silene italica and the Silene nutans species complex

Study of the congruence of population genetic structure between hosts and pathogens gives important insights into their shared phylogeographical and coevolutionary histories. We studied the population genetic structure of castrating anther‐smut fungi (genus Microbotryum) and of their host plants, the Silene nutans species complex, and the morphologically and genetically closely related Silene italica, which can be found in sympatry. Phylogeographical population genetic structure related to persistence in separate glacial refugia has been recently revealed in the S. nutans plant species complex across Western Europe, identifying several distinct lineages. We genotyped 171 associated plant–pathogen pairs of anther‐smut fungi and their host plant individuals using microsatellite markers and plant chloroplastic single nucleotide polymorphisms. We found clear differentiation between fungal populations parasitizing S. nutans and S. italica plants. The population genetic structure of fungal strains parasitizing the S. nutans plant species complex mirrored the host plant genetic structure, suggesting that the pathogen was isolated in glacial refugia together with its host and/or that it has specialized on the plant genetic lineages. Using random forest approximate Bayesian computation (ABC‐RF), we found that the divergence history of the fungal lineages on S. nutans was congruent with that previously inferred for the host plant and probably occurred with ancient but no recent gene flow. Genome sequences confirmed the genetic structure and the absence of recent gene flow between fungal genetic lineages. Our analyses of individual host–pathogen pairs contribute to a better understanding of co‐evolutionary histories between hosts and pathogens in natural ecosystems, in which such studies remain scarce.     

Physiographic and climatic events in the Chihuahuan Desert lead to the speciation and distinct demographic patterns of two sister Sceloporus lizards

The biogeographic history of the Chihuahuan Desert is known to be complex, and there is evidence of the effects of physiographic and climatic events in species diversification and demographic population changes in many taxa. Here, using DNA sequence data, we studied the influence of the physiographic and climatic events that occurred in the Chihuahuan Desert during the Pliocene–Pleistocene transition on the speciation and evolutionary history of the sister lizard species Sceloporus cyanostictus and S. gadsdeni. First, based on mtDNA and nDNA sequences, we estimated the divergence times of the sister species. Then, based on mtDNA sequences, we investigated the demographic history of both species within a phylogeographic framework. The divergence time was inferred to be 1.48 Mya, date that corresponds to the existence of a large lake in the Mapimian subprovince, between the current geographic locations of S. cyanostictus and S. gadsdeni. This lake could have acted as a barrier, leading to the speciation of both species. For the demographic history of the two species, we identified two distinct patterns: the population expansion of S. gadsdeni within the Last Glacial Maximum and the potential population decline of S. cyanostictus. Our results can be used as a guide for the study of other aspects that could be critical to developing conservation actions that ensure the survival of not only S. gadsdeni and S. cyanostictus, but also other co‐occurring lizard species.