Partitioned Bayesian analyses, dispersal-vicariance analysis, and the biogeography of Chinese toad-headed lizards (Agamidae: Phrynocephalus): a re-evaluation

Trophic niche and adaptation in highland lizards: sex has greater influences than species matching

The plateau environments are typically arid, cool, and high altitude, posing formidable challenges to wildlife survival due to resource scarcity and harsh conditions. Unraveling ecological adaptability in severe conditions requires a deeper understanding of the niche characteristics of plateau species. Trophic niche, which is a comprehensive indicator describing the energy acquisition strategy of animals, remains relatively understudied in plateau species. Here, by combining stable isotopes and morphological data, we quantified the trophic niches of two allopatric lizard species (Phrynocephalus vlangalii and P. erythrurus) that live in the hinterland of the Qinghai-Tibetan Plateau, and explored how their trophic niches correlate with morphological and environmental factors. While both trophic niche and morphological traits were similar between species, noteworthy distinctions were observed between male and female Phrynocephalus lizards. The morphological traits associated with predation (i.e. limb length and head size) and reproduction (i.e. abdomen length), annual mean temperature, and sex played influential roles in shifting trophic niches. These results imply that sexual dimorphism may facilitate inter-sex divergence in resource utilization, leading to trophic niche variations in the highland lizards. Furthermore, extreme environmental stress can constrain interspecific divergence in morphological and trophic traits. Our findings illustrate the dynamic variations of trophic niches in highland lizards, contributing to a more comprehensive understanding of the adaptation strategies employed by lizard species in plateau environments.

Species divergence in valleys: the phylogeny of Phrynocephalus forsythii complex and description of a new species

Background

Geographic isolation caused by high-altitude valleys promotes the formation of geographic segregation of species, leading to species differentiation. The subgenus Oreosaura contains viviparous species from the Tibetan Plateau and the vicinity of the Tarim Basin, which can be divided into three species complexes according to their geographical distribution: Phrynocephalus vlangalii, Phrynocephalus theobaldi, and Phrynocephalus forsythii. However, molecular data for the P. forsythii complex are limited and the diversity of this species complex has been greatly underestimated. Therefore, this study aimed to explore the species diversity of Oreosaura and species differentiation within the P. forsythii complex.

Methods

We analysed the species diversity of Oreosaura by combining previous data, constructed a phylogenetic tree of the subgenus based on cytochrome c oxidase subunit I and 16S sequences, and estimated the divergence time.

Results

The results suggest significant genetic differences between the Tarim Basin populations and adjacent mountain valley populations of the P. forsythii complex and that the combination of deep valley landscapes in the high mountains and ice-age events have contributed to the differentiation of the viviparous toad-headed agama lizard, which is a key factor in the phylogenetics of the P. forsythii complex. Furthermore, we identified a population collected from Wuqia County, Xinjiang, as a new species, Phrynocephalus kangsuensis sp. nov. The results will provide data for phylogenetic studies following the P. forsythii complex and help demonstrate that valleys promote the formation of Phrynocephalus species.

Species persistence with hybridization in toad-headed lizards driven by divergent selection and low recombination

Speciation plays a central role in evolutionary studies, and particularly how reproductive isolation (RI) evolves. The origins and persistence of RI are distinct processes that require separate evaluations. Treating them separately clarifies the drivers of speciation and then it is possible to link the processes to understand large-scale patterns of diversity. Recent genomic studies have focused predominantly on how species or RI originate. However, we know little about how species persist in face of gene flow. Here, we evaluate a contact zone of two closely related toad-headed lizards (Phrynocephalus) using a chromosome-level genome assembly and population genomics. To some extent, recent asymmetric introgression from Phrynocephalus putjatai to P. vlangalii reduces their genomic differences. However, their highly divergent regions (HDRs) have heterogeneous distributions across the genomes. Functional gene annotation indicates that many genes within HDRs are involved in reproduction and RI. Compared with allopatric populations, contact areas exhibit recent divergent selection on the HDRs and a lower population recombination rate. Taken together, this implies that divergent selection and low genetic recombination help maintain RI. This study provides insights into the genomic mechanisms that drive RI and two species persistence in the face of gene flow during the late stage of speciation.

A Multilevel Assessment of Plasticity in Response to High-Altitude Environment for Agama Lizards

Upslope range shifting has been documented in diverse species in response to global warming. Plasticity, which refers to the ability of organisms to alter their phenotypes in changing environments, is crucial for the survival of those that newly migrated to a high-altitude environment. The scope and mechanisms of plasticity across biological levels, however, have rarely been examined. We used two agama lizards (genus Phrynocephalus) as model systems and a transplant experiment to comprehensively assess their plasticity on multiple organization levels. Two low-altitude (934 m) agama species, Phrynocephalus axillaris (oviparous) and P. forsythii (viviparous), were transplanted to a high-altitude site (3,400 m). After acclimation for 6 weeks in seminatural enclosures, plasticity was measured from bite force, tail display behavior, gene expression, and metabolome. Both lizards were capable of acclimating to the high-altitude environment without sacrificing their performance in bite force, but they also showed high plasticity in tail display behavior by either decreasing the intensity of a specific display component (P. forsythii) or by the trade-off between display components (P. axillaris). Genes and metabolites associated with lipids, especially fatty acid metabolism, exhibited significant differentiation in expression, compared to individuals from their native habitats. Improved fatty acid storage and metabolism appeared to be a common response among animals at high altitudes. Despite distinct reproductive modes that may differ in response to physiological pressure, the two lizards demonstrated high concordance in plasticity when they faced a novel environment at high altitudes. Taken together, lizards likely acclimate to high-altitude environments by reducing behavioral activity and increasing energy efficiency after range shifting. Our results provide new insights into our understanding of phenotypic plasticity and its importance in today’s changing climate.

Comparative Analysis of Mitochondrial Genomes in Two Subspecies of the Sunwatcher Toad-Headed Agama (Phrynocephalus helioscopus): Prevalent Intraspecific Gene Rearrangements in Phrynocephalus

Intraspecific rearrangements of mitochondrial genomes are rarely reported in reptiles, even in vertebrates. The sunwatcher toad-headed agama, Phryncoephalus helioscopus, can serve as an excellent model for investigating the dynamic mitogenome structure at intraspecific level. To date, seven subspecies of P. helioscopus are well recognized, but little is known about the mitogenomic evolution among different subspecies. In this study, complete mitogenomes of subspecies P. helioscopus varius II and P. helioscopus cameranoi were determined by next-generation sequencing, and another P. helioscopus varius I retrieved from GenBank was compiled for comparative analysis. The nucleotide composition and the codon usage are similar to those previously published from toad-headed agamas. P. helioscopus varius II and P. helioscopus cameranoi have 23 tRNA genes, including standard 22 tRNA genes and one extra tRNA-Phe (tRNA-Phe duplication). Gene order and phylogenetic analyses in the genus Phrynocephalus support prevalent intraspecific gene rearrangement in P. helioscopus and other congener species including P. erythrurus, P. vlangalii, and P. forsythii. Six different mitochondrial gene arrangements are observed in Phrynocephalus. Overall, the occurrence of rearrangements may result from multiple independent structural dynamic events. The split of the two subspecies in P. helioscopus was dated at approximately 2.34 million years ago (Ma). Two types of gene rearrangements are found in the three mitogenomes of P. helioscopus, and this intraspecific rearrangement phenomenon can be explained by the tandem duplication/random loss (TDRL) model. Post duplication, the alternative loss types can occur in 0.23–0.72 Ma, suggesting that the duplication and fixation of these rearrangements can occur quite quickly. These findings highlight the need for more mitogenomes at the population level in order to better understand the potentially rampant intraspecific mitogenomic reorganization in Phrynocephalus.

Geological and climatic influences on population differentiation of the Phrynocephalus vlangalii species complex (Sauria: Agamidae) in the northern Qinghai-Tibet Plateau

Extremely heterogeneous topography and complex paleoclimate history of the Qinghai-Tibet Plateau (QTP) have a key role in promoting genetic divergence and lineage/species formation. Here, we sequenced one nuclear and three mitochondrial markers of 532 individuals from the entire range of the Phrynocephalus vlangalii species complex including two species, P. putjatai and P. vlangalii, endemic to the northern QTP. We integrated multilocus phylogeny, demographic analysis and geographic barrier detection to evaluate the population structure and dynamics. We found a new mitochondrial clade (PV-I) in the Gonghe County population of P. vlangalii, partial mitochondrial DNA replacement within P. vlangalii and complete mitochondrial DNA replacement between P. putjatai and P. vlangalii. Neutrality test, mismatch distribution analysis and Extended Bayesian Skyline Plot (EBSP) analysis all supported a significant expansion of the Qaidam Basin population of P. vlangalii (PV-II-2) from 0.091 to 0.026 Ma after Penultimate Glaciation. The uplift of the Arjin and Anyemanqen Mountains during the Kunhuang Movement (∼1.2 Ma) split populations of P. vlangalii in Akesai, Qaidam Basin and source of the Yellow River. The uplift of the Elashan Mountains during the second phase of the Qingzang Movement (∼2.5 Ma) contributed to the divergence of the Gonghe County population of P. vlangalii from other conspecific populations. The third phase of the Qingzang Movement (∼1.7 Ma) contributed to the divergence of the Xinghai population of P. vlangalii from P. putjatai and to the divergence of the northern populations of P. putjatai from the southern conspecific populations. Our data support the idea that the geological and climatic changes following the orogeny of the QTP may have promoted population differentiation and shaped the current population patterns of the P. vlangalii species complex in the northeastern QTP.

A Re-Assessment of Positive Selection on Mitochondrial Genomes of High-Elevation Phrynocephalus Lizards

Due to their integral roles in oxidative phosphorylation, mitochondrially encoded proteins represent common targets of selection in response to altitudinal hypoxia across high-altitude taxa. While previous studies revealed evidence of positive selection on mitochondrial genomes of high-altitude Phrynocephalus lizards, their conclusions were restricted by out-of-date phylogenies and limited taxonomic sampling. Using topologies derived from both nuclear and mitochondrial DNA phylogenies, we re-assessed the evidence of positive selection on the mitochondrial genomes of high-altitude Phrynocephalus. We sampled representative species from all four main lineages and sequenced the mitochondrial genome of P. maculatus, a putative sister taxon to the high-altitude group. Positive selection was assessed through two widely used branch-site tests: the branch-site model in PAML and BUSTED in HyPhy. No evidence of positive selection on mitochondrial genes was detected on branches leading to two most recent common ancestors of high-altitude species; however, we recovered evidence of positive selection on COX1 on the P. forsythii branch, which represents a reversal from high- to low-elevation environments. A positively selected site therein marked a threonine to valine substitution at position 419. We suggest this bout of selection occurred as the ancestors of P. forsythii re-colonized lower altitude environments north of the Tibetan Plateau. Despite their role in oxidative phosphorylation, we posit that mitochondrial genes are unlikely to have represented historical targets of selection for high-altitude adaptation in Phrynocephalus. Consequently, future studies should address the roles of nuclear genes and differential gene expression.

Morphological function of toe fringe in the sand lizard Phrynocephalus mystaceus

Toe fringe is the most typical morphological feature of lizards adapted to sandy environments, and it is simple in shape, can evolve repeatedly, and has a high degree of repetition; therefore, this feature is suitable for testing the adaptive convergence suggested by form-environment correlations. Phrynocephalus mystaceus mainly lives in dune habitats, has a developed bilateral toe fringe, and exhibits fast sand-burying behavior for predator avoidance. We tested the effects of resecting the medial and bilateral toe fringes on the locomotor performance and sand-burying performance of P. mystaceus. The results showed that the maximum sprint speed and acceleration on sand substrate did not significantly differ under different conditions (P > 0.05). Sand-burying performance scores of the unresected individuals were significantly greater than those of the resected individuals (P < 0.05). A partial least squares (PLS) regression analysis showed that the relative area of toe fringe was the main factor affecting the sand-burying performance of unresected P. mystaceus. For lizards without fringe, the PLS regression showed that the swinging index of the hind-limb was the main factor affecting the sand-burying performance of the lizard. A comparison of the swinging indexes of the hind-limb of the lizard under three states revealed that under the unresected states, the frequency of the swinging of the hind-limb was significantly higher than those of lizards with resected bilateral fringes, further indicating that the lizards compensated for the loss of fringe by increasing the time and frequency of swinging of the hind-limb. A path analysis also showed that the fringe affected the sand-burying performance of P. mystaceus not only directly but also indirectly by affecting the frequency of the swinging of the hind-limb. After the bilateral toe fringe was removed, a significant negative correlation between locomotor and sand-burying performance was observed (P < 0.05). Taken together, these results provide experimental evidence that toe fringe is positively associated with the sand-burying performance of P. mystaceus.

Environmental and geological changes in the Tarim Basin promoted the phylogeographic formation of Phrynocephalus forsythii (Squamata: Agamidae)

Environmental factors can promote genetic divergence among populations. The Tarim Basin has experienced a series of environmental and geological changes since the late Pliocene. Phrynocephalus forsythii (Agamidae) has a continuous and circular distribution around the Tarim Basin, and the evolutionary history of this species remains unclear. In the present study, mitochondrial DNA and single nucleotide polymorphism sequences were obtained from 195 P. forsythii samples in the Tarim Basin to examine the phylogeographic structure and evolutionary history of this species. All populations of P. forsythii formed three distinct clusters: the Minfeng, low-elevation, and high-elevation groups. The Minfeng group was the first to separate from all other groups at 4.26 Ma after the original desert environment emerged in the Tarim Basin. The uplift of the Kunlun Mountains created a new high-altitude environment along the southwestern edge of the basin and promoted the divergence of low-elevation and high-elevation groups at 3.67 Ma. Subsequently, the gradual development of deserts and rivers in the Tarim Basin accelerated the dispersal of P. forsythii, eventually forming the current distribution pattern. Our results indicate that ecological separation caused by environmental and geological changes in the Tarim Basin was the main cause for the genetic divergence of P. forsythii.

Molecular phylogeny and biogeography of Triplophysa stone loaches in the Central Chinese Mountains

The geological structure and history of mountains often cause highly complex patterns of evolution. The origin and diversity of the genus Triplophysa is considered to be closely associated with the rapid and persistent rise of the Qinghai-Tibet Plateau (QTP). Species of the genus are widely distributed in the QTP and adjacent regions, and are strongly adapted to its extreme environments. However, the Central Chinese Mountains (CCM), which are far apart from the QTP, also have many Triplophysa populations and yet their taxonomy, phylogeny and origin are unknown. We used three mitochondrial genes of 266 individuals from 29 sites in the CCM to shed light on the evolution of these Triplophysa populations. Phylogenetic analyses and species delimitation revealed seven distinct molecular operational taxonomic units (mOTUs) in the CCM, each with low genetic diversity. Molecular clock and biogeographic analyses suggested that vicariance events resulting from the rapid uplifting of the Qinling and Taihang Mountains initialized diversification in the Pliocene. During the early Pleistocene, dispersal events in the central parts of the Yellow River drainage altered genetic diversity and led to the currently observed biogeographic patterns. Our results suggest the presence of at least six species of Triplophysa in the CCM and more are likely to be discovered in the future.

Genetic and morphological divergence among three closely related Phrynocephalus species (Agamidae)

Background

The Qinghai-Tibetan Plateau (QTP) is the world’s highest and largest plateau, but the role of its uplift in the evolution of species or biotas still remains poorly known. Toad-headed lizards of the reproductively bimodal genus Phrynocephalus are a clade of agamids, with all viviparous species restricted to the QTP and adjacent regions. The eastern part of the range of the viviparous taxa is occupied by three closely related but taxonomically controversial species, P. guinanensis, P. putjatia and P. vlangalii. Here, we combined genetic (mitochondrial ND4 gene and nine microsatellite loci), morphological (11 mensural and 11 meristic variables), and ecological (nine climatic variables) data to explore possible scenarios that may explain the discordance between genetic and morphological patterns, and to test whether morphological divergence is associated with local adaptation.

Results

We found weak genetic differentiation but pronounced morphological divergence, especially between P. guinanensis and P. vlangalii. Genetically, the species boundary was not so clear between any species pair. Morphologically, the species boundary was clear between P. guinanensis and P. vlangalii but not between other two species pairs. Body size and scale characters accounted best for morphological divergence between species. Morphological divergence was related to habitat types that differ climatically.

Conclusions

Our study provides evidence for genetic and morphological divergence among the three closely related viviparous species of Phrynocephalus lizards, and supports the idea that natural selection in spatially heterogeneous environments can lead to population divergence even in the presence of gene flow. Our study supports the hypothesis that the evolutionary divergence between viviparous Phrynocephalus species was a consequence of environmental change after the uplift of the QTP.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1443-y) contains supplementary material, which is available to authorized users.

Cenozoic aridization in Central Eurasia shaped diversification of toad-headed agamas (Phrynocephalus; Agamidae, Reptilia)

We hypothesize the phylogenetic relationships of the agamid genus Phrynocephalus to assess how past environmental changes shaped the evolutionary and biogeographic history of these lizards and especially the impact of paleogeography and climatic factors. Phrynocephalus is one of the most diverse and taxonomically confusing lizard genera. As a key element of Palearctic deserts, it serves as a promising model for studies of historical biogeography and formation of arid habitats in Eurasia. We used 51 samples representing 33 of 40 recognized species of Phrynocephalus covering all major areas of the genus. Molecular data included four mtDNA (COI, ND2, ND4, Cytb; 2,703 bp) and four nuDNA protein-coding genes (RAG1, BDNF, AKAP9, NKTR; 4,188 bp). AU-tests were implemented to test for significant differences between mtDNA- and nuDNA-based topologies. A time-calibrated phylogeny was estimated using a Bayesian relaxed molecular clock with nine fossil calibrations. We reconstructed the ancestral area of origin, biogeographic scenarios, body size, and the evolution of habitat preference. Phylogenetic analyses of nuDNA genes recovered a well-resolved and supported topology. Analyses detected significant discordance with the less-supported mtDNA genealogy. The position of Phrynocephalus mystaceus conflicted greatly between the two datasets. MtDNA introgression due to ancient hybridization best explained this result. Monophyletic Phrynocephalus contained three main clades: (I) oviparous species from south-western and Middle Asia; (II) viviparous species of Qinghai–Tibetan Plateau (QTP); and (III) oviparous species of the Caspian Basin, Middle and Central Asia. Phrynocephalus originated in late Oligocene (26.9 Ma) and modern species diversified during the middle Miocene (14.8–13.5 Ma). The reconstruction of ancestral areas indicated that Phrynocephalus originated in Middle East–southern Middle Asia. Body size miniaturization likely occurred early in the history of Phrynocephalus. The common ancestor of Phrynocephalus probably preferred sandy substrates with the inclusion of clay or gravel. The time of Agaminae radiation and origin of Phrynocephalus in the late Oligocene significantly precedes the landbridge between Afro-Arabia and Eurasia in the Early Miocene. Diversification of Phrynocephalus coincides well with the mid-Miocene climatic transition when a rapid cooling of climate drove progressing aridification and the Paratethys salinity crisis. These factors likely triggered the spreading of desert habitats in Central Eurasia, which Phrynocephalus occupied. The origin of the viviparous Tibetan clade has been associated traditionally with uplifting of the QTP; however, further studies are needed to confirm this. Progressing late Miocene aridification, the decrease of the Paratethys Basin, orogenesis, and Plio–Pleistocene climate oscillations likely promoted further diversification within Phrynocephalus. We discuss Phrynocephalus taxonomy in scope of the new analyses.

Aridification driven diversification of fan-throated lizards from the Indian subcontinent

The establishment of monsoon climate and the consequent aridification has been one of the most important climate change episodes in the Indian subcontinent. However, little is known about how these events might have shaped the diversification patterns among the widely distributed taxa. Fan-throated lizards (FTL) (Genus: Sitana, Sarada) are widespread, diurnal and restricted to the semi-arid zones of the Indian subcontinent. We sampled FTL in 107 localities across its range. We used molecular species delimitation method and delineated 15 species including six putative species. Thirteen of them were distinguishable based on morphology but two sister species were indistinguishable and have minor overlaps in distribution. Five fossils were used to calibrate and date the phylogeny. Diversification of fan-throated lizards lineage started ~18 mya and higher lineage diversification was observed after 11 my. The initial diversification corresponds to the time when monsoon climate was established and the latter was a period of intensification of monsoon and initiation of aridification. Thirteen out of the fifteen FTL species delimited are from Peninsular India; this is probably due to the landscape heterogeneity in this region. The species poor sister genus Otocryptis is paraphyletic and probably represents relict lineages which are now confined to forested areas. Thus, the seasonality led changes in habitat, from forests to open habitats appear to have driven diversification of fan-throated lizards.

Are viviparous lizards more vulnerable to climate warming because they have evolved reduced body temperature and heat tolerance?

Lizards may experience population declines and extinctions on a similar scale to that experienced by amphibians, and climate warming is one hypothesis proposed to explain these declines and extinctions. Within lizards, viviparous species are hypothesized to be more vulnerable to climate warming, because they have evolved reduced body temperature and heat tolerance, but this idea remains untested. To test this hypothesis, we conducted three temperatures (20, 24, and 28 °C) × two species [Phrynocephalus przewalskii (oviparous) and P. putjatia (viviparous)] factorial design experiment that simulated warming on oviparous versus viviparous lizards. Our manipulation of ambient temperature affected activity and thermal preference in both species, birth date in P. putjatia, and egg mass in P. przewalskii; other examined traits (fecundity, reproductive output, and size, morphology, and sprint speed of offspring) were not affected. Neither in P. putjatia nor in P. przewalskii behavioral responses to rising temperatures differ between the sexes. The viviparous species thermoregulated more actively than did the oviparous species, but the two species did not differ in thermal preference. Warming reduced the activity time allotted for thermoregulation in both species, but the effect was more dramatic in the viviparous species. Our data support one of the central predictions that lead to the hypothesis that viviparous lizards are more vulnerable to climate warming; however, this is not because viviparous lizards have evolved reduced body temperature and heat tolerance, but, because warming constrains activity more dramatically in viviparous species.

Phylogeographic patterns of Lygus pratensis (Hemiptera: Miridae): Evidence for weak genetic structure and recent expansion in northwest China

Lygus pratensis (L.) is an important cotton pest in China, especially in the northwest region. Nymphs and adults cause serious quality and yield losses. However, the genetic structure and geographic distribution of L. pratensis is not well known. We analyzed genetic diversity, geographical structure, gene flow, and population dynamics of L. pratensis in northwest China using mitochondrial and nuclear sequence datasets to study phylogeographical patterns and demographic history. L. pratensis (n = 286) were collected at sites across an area spanning 2,180,000 km², including the Xinjiang and Gansu-Ningxia regions. Populations in the two regions could be distinguished based on mitochondrial criteria but the overall genetic structure was weak. The nuclear dataset revealed a lack of diagnostic genetic structure across sample areas. Phylogenetic analysis indicated a lack of population level monophyly that may have been caused by incomplete lineage sorting. The Mantel test showed a significant correlation between genetic and geographic distances among the populations based on the mtDNA data. However the nuclear dataset did not show significant correlation. A high level of gene flow among populations was indicated by migration analysis; human activities may have also facilitated insect movement. The availability of irrigation water and ample cotton hosts makes the Xinjiang region well suited for L. pratensis reproduction. Bayesian skyline plot analysis, star-shaped network, and neutrality tests all indicated that L. pratensis has experienced recent population expansion. Climatic changes and extensive areas occupied by host plants have led to population expansion of L. pratensis. In conclusion, the present distribution and phylogeographic pattern of L. pratensis was influenced by climate, human activities, and availability of plant hosts.

Thermal ecology of three coexistent desert lizards: Implications for habitat divergence and thermal vulnerability

How ectotherms exploit thermal resources has important implications for their habitat utilization and thermal vulnerability to climate warming. To address this issue, we investigated thermal relations of three sympatric lizard species (Eremias argus, Eremias multiocellata, and Phrynocephalus przewalskii) in the desert steppe of Inner Mongolia, China. We determined the thermoregulatory behavior, body temperature (T _b), operative temperature (T _e), selected body temperature (T _sel), and critical thermal maximum (CT_max) of adult lizards. Based on these physiological parameters, we quantified the accuracy and effectiveness of thermoregulation as well as thermal-safety margin for these species. The three species were accurate and effective thermoregulators. The P. przewalskii preferred open habitats, and had a higher T _b than the two Eremias lizards, which preferred shade habitats and shuttled more frequently between the shade and sun. This indicated that the three sympatric lizards have different thermoregulatory behavior and thermal physiology, which might facilitate their coexistence in the desert steppe ecosystem. In addition, the P. przewalskii had higher T _sel and CT_max, and a wider thermal-safety margin than the two Eremias lizards, suggesting that the two Eremias lizards would be more vulnerable to climate warming than P. przewalskii.

Cyprininae phylogeny revealed independent origins of the Tibetan Plateau endemic polyploid cyprinids and their diversifications related to the Neogene uplift of the plateau

Origin and diversification of the Tibetan polyploid cyprinids (schizothoracins) may help us to explore relationships between diversification of the cyprinids and the Tibetan Plateau uplift. Cyprininae phylogeny was analyzed using mitochondrial and nuclear DNA sequences to trace origins of polyploidy and diversifications of schizothoracins. Ancestral states reconstruction for ploidy levels indicated that the Cyprininae was diploid origin and the schizothoracin clades tetraploid origins. There were two diversification rate shifts along with diversification of the cyprinine fishes in response to the Tibetan uplift. The unusual diversification shifts were located to branches subtending the clades of Tibetan polyploid cyprinids. Our analyses suggested that (i) phylogeny of Cyprininae recovered two independent origins of the Tibetan polyploidy schizothoracins; (ii) diversifications of the schizothoracins were closely related to the Neogene uplift of the Tibetan plateau in the following ways: the relatively ancient Late Oligocene-Middle Miocene adaptive radiation may be associated with the uplift of the southern Tibet and Himalaya; the Middle Miocene-Early Pleistocene lineage-specific diversification broadly coincident with major phase of the Neogene Tibetan uplift; and the most recent Pleistocene diversification shift in Schizothorax closely coincident with the successive Kunlun-Huanghe and Gonghe movements of the Tibetan uplift and the glaciation-induced climate oscillations on the plateau.

Evolution of Asparagus L. (Asparagaceae): Out-of-South-Africa and multiple origins of sexual dimorphism

In the most comprehensive study to date we explored the phylogeny and evolution of the genus Asparagus, with emphasis on the southern African species. We included 211 accessions, representing 77 (92%) of the southern African, 6 (17%) of the tropical African, 10 (56%) of the strictly European and 6 (9%) of the Eurasian species. We analyzed DNA sequences from three plastid regions (trnH-psbA, trnD-T, ndhF) and from the nuclear region phytochrome C (PHYC) with parsimony and maximum likelihood methods, and recovered a monophyletic Asparagus. The phylogeny conflicts with all previous infra-generic classifications. It has many strongly supported clades, corroborated by morphological characters, which may provide a basis for a revised taxonomy. Additionally, the phylogeny indicates that many of the current species delimitations are problematic. Using biogeographic analyses that account for phylogenetic uncertainty (S-DIVA) and take into account relative branch lengths (Lagrange) we confirm the origin of Asparagus in southern Africa, and find no evidence that the dispersal of Asparagus follow the Rand flora pattern. We find that all truly dioecious species of Asparagus share a common origin, but that sexual dimorphism has arisen independently several times.

Comparative transcriptomic analysis revealed adaptation mechanism of Phrynocephalus erythrurus, the highest altitude Lizard living in the Qinghai-Tibet Plateau

BACKGROUND

Organisms living at high altitudes must overcome three major environmental challenges: hypoxia, cold, and intense UV radiation. The molecular mechanisms that enable these challenges to be overcome have mainly been studied in endothermic organisms; relatively little attention has been paid to poikilothermic species. Here, we present deep transcriptome sequencing in two closely related lizards, the high altitude-dwelling Phrynocephalus erythrurus and the lowland-dwelling P. putjatia, to identify candidate genes under positive selection and to explore the convergent evolutionary adaptation of poikilothermic animals to high altitude life.

RESULTS

More than 70 million sequence reads were generated for each species via Illumina sequencing. De novo assembly produced 56,845 and 63,140 transcripts for P. erythrurus and P. putjatia, respectively. P. erythrurus had higher Ka/Ks ratios than P. putjatia, implying an accelerated evolutionary rate in the high altitude lizard lineage. 206 gene ontology (GO) categories with accelerated evolutionary rates and 43 candidate positively selected genes were detected along the P. erythrurus lineage. Some of these GO categories have functions associated with responses to hypoxia, energy metabolism and responses to UV damage. We also found that the high-altitude ranid frog R. kukunoris had higher Ka/Ks ratios than the closely related low-altitude frog R. chensinensis, and that the functional categories with accelerated evolutionary rates in R. kukunoris overlapped extensively with those detected along the P. erythrurus lineage.

CONCLUSIONS

The mechanisms of high altitude adaptation in P. erythrurus were tentatively inferred. By comparing two pairs of low- and high-altitude poikilothermic species, we found that similar functional categories had undergone positive selection in high altitude-dwelling Phrynocephalus and Rana lineages, indicating that similar mechanisms of adaptation to high altitude might have evolved in both genera. Our findings provide important guidance for future functional studies on high altitude adaptation in poikilothermic animals.

The complete mitochondrial genome of Phrynocephalus forsythii (Reptilia, Squamata, Agamidae), a toad-headed agama endemic to the Taklamakan Desert

The complete mitochondrial genome was sequenced from a viviparous toad-headed agama, Phrynocephalus forsythii, which is endemic to the Taklamakan Desert. The mitogenome sequence was 17,542 bp in size, containing 13 protein-coding genes, 22 tRNA genes, two rRNA genes and a control region (D-loop). The gene arrangement and composition of P. forsythii is identical to the mitogenome of P. theobaldi in that tRNA-Pro was translocated immediately downstream of tRNA-Phe. The D-loop comprised two parts, one existing between tRNA-Thr and tRNA-Phe, and another containing 12 copies of 36-bp tandem repeats inserting between tRNA-Pro and 12S rRNA. The complete mitogenome sequence of P. forsythii may provide fundamental data for unveiling the phylogenetic origin and adaptive evolution related to Phrynocephalus viviparity.

Cladistic reanalysis and historical biogeography of the genus Lycinus Thorell, 1894 (Araneae: Mygalomorphae: Nemesiidae) with description of two new species from western Argentina

BACKGROUND

The genus Lycinus includes ten species, one from Argentina, eight from Chile, and one from Brazil. Two new species from western Argentina are described, and some data on natural history are presented. A cladistic reanalysis with the newly described species is carried out, and a reconstruction of ancestral areas and primary Brooks Parsimony Analysis are performed. The origins of the main groups of Lycinusarealso discussed in that light.

RESULTS

Lycinus lagigliai sp. nov. and Lycinus nevadoensis sp. nov. are described. The distribution of these species comprised western Argentina at Mendoza province. The cladistic reanalysis showed Lycinus as monophyletic supported only by the synapomorphy of dorsal spines on male palpal tibia. The tree topology was as follows: (Lycinus epipiptus, Lycinus domeyko ((Lycinus longipes, L. nevadoensis sp. nov.) (Lycinus portoseguro, L. lagigliai sp. nov.))(Lycinuscaldera (Lycinusgajardoi,Lycinuschoros))(Lycinustofo,Lycinusquilicura)).The biogeographical analysis showed a close relationship of the species from the Andean region and the South American Transition Zone. The reconstructionof ancestral areas recognized four vicariant nodes.

CONCLUSIONS

A hitherto two unknown Lycinus species are recognized and formally described, along with a cladistic reanalysis and historical biogeographical hypotheses.

Exploring the genetic basis of adaptation to high elevations in reptiles: a comparative transcriptome analysis of two toad-headed agamas (genus Phrynocephalus)

High elevation adaptation offers an excellent study system to understand the genetic basis of adaptive evolution. We acquired transcriptome sequences of two closely related lizards, Phrynocephalus przewalskii from low elevations and P. vlangalii from high elevations. Within a phylogenetic framework, we compared their genomic data along with green anole, chicken and Chinese softshell turtle, and identified candidate genes and functional categories that are potentially linked to adaptation to high elevation environments. More than 100 million sequence reads were generated for each species via Illumina sequencing. A de novo assembly produced 70,919 and 62,118 transcripts for P. przewalskii and P. vlangalii, respectively. Based on a well-established reptile phylogeny, we detected 143 positively selected genes (PSGs) along the P. vlangalii lineage from the 7,012 putative orthologs using a branch-site model. Furthermore, ten GO categories and one KEGG pathway that are over-represented by PSGs were recognized. In addition, 58 GO categories were revealed to have elevated evolutionary rates along the P. vlangalii lineage relative to P. przewalskii. These functional analyses further filter out PSGs that are most likely involved in the adaptation process to high elevations. Among them, ADAM17, MD, and HSP90B1 likely contributed to response to hypoxia, and POLK likely contributed to DNA repair. Many other candidate genes involved in gene expression and metabolism were also identified. Genome-wide scan for candidate genes may serve as the first step to explore the genetic basis of high elevation adaptation. Detailed comparative study and functional verification are needed to solidify any conclusions. High elevation adaptation requires coordinated changes in multiple genes that involve various physiological and biochemical pathways; we hope that our genetic studies will provide useful directions for future physiological or molecular studies in reptiles as well as other poikilothermic species.

The complete mitochondrial genome of Phrynocephalus helioscopus (Reptilia, Squamata, Agamidae)

The toad-headed lizards of genus Phrynocephalus are one of the most prevalent animals in the central Asian desert. A few studies have investigated molecular phylogenesis of Phrynocephalus, yet yield inconsistent results. Moreover, these studies were only based on a few specific DNA fragments of mitochondrial genome. To facilitate the clarification of molecular phylogenesis of Phrynocephalus, we conducted this study to sequence the entire mitochondrial genome of the Phrynocephalus helioscopus collected from Northwest China. The length of complete mitochondrial DNA is 16,249 nucleotides, consisting of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 2 control regions (CR). The gene arrangement and composition of P. helioscopus resemble those of other Phrynocephalus sand lizard, except for P. przewalskii and P. versicolor. The overall A, T, C, G base composition of the heavy-strand was 35.9%, 26.4%, 25.2%, 12.5%, respectively, which is biased toward AT (about 62.3%). The AT-biased base composition was similar to what observed in most vertebrates. The complete mitochondrial genome of P. helioscopus may help to clarify the phylogenetic relationships related to Phrynocephalus oviparity.

The complete mitochondrial genome of Grumgzimailo's toad-headed agama, Phrynocephalus grumgrizimailoi (Reptilia, Squamata, Agamidae)

Polymerase chain reaction (PCR), long-and-accurate PCR and directly sequencing by primer walking was used to sequenced he complete mitochondrial genome sequence of Grumgzimailo's toad- headed agama, Phrynocephalus grumgrizimailoi. The Genbank accession was KM093859. There was 16,301 bp in length of the entire mitochondrial genome of P. grumgrizimailoi and the content of A, T, C, and G were 36.4%, 26.5%, 25.0% and 12.1%, respectively, that was similar to most vertebrate. The complete mitochondrial genome of P. grumgrizimailoi contain 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, plus 2 control regions and was similar to those of other Phrynocephalus sand lizards in gene arrangement and composition, except P. przewalskii and P. versicolor. The complete mitochondrial genome of P. grumgrizimailoi provided fundamental data for resolving phylogenetic relationship problems related to Agaimidae and genus Phrynocephalus.

The complete mitochondrial genome of the color changeable toad-headed agama, Phrynocephalus versicolor (Reptilia, Squamata, Agamidae)

The complete mitochondrial genome sequence of color changeable toad-headed agama, Phrynocephalus versicolor, was determined using polymerase chain reaction (PCR), long-and-accurate PCR and directly sequencing by primer walking. The entire mitochondrial genome of P. versicolor was 16,429 bp in length, the accession was KJ749841 and the content of A, T, C, and G were 36.1%, 26.5%, 24.9% and 12.5%, respectively, which was similar to most vertebrate. The complete mitochondrial genome of P. versicolor contain 13 protein-coding genes, 2 rRNA genes, 23 tRNA genes, plus one control region and was similar to those of other Phrynocephalus sand lizards in gene arrangement and composition, except that tRNA-Phe and tRNA-Pro were exchanged and tRNA-Phe had two copies. The control region comprised three parts, one between tRNA-Thr and tRNA-Phe, a second between tRNA-Pro and tRNA-Phe, and a third between tRNA-Phe and 12S RNA. The complete mitochondrial genome of P. versicolor provided fundamental data for resolving phylogenetic relationship problems related to Agaimidae and genus Phrynocephalus.

Viviparity in high-altitude Phrynocephalus lizards is adaptive because embryos cannot fully develop without maternal thermoregulation

Viviparous Phrynocephalus lizards (Agamidae) are mainly restricted to the Qinghai-Tibet Plateau of China. In this study, we used Phrynocephalus vlangalii females kept under seven thermal regimes for the whole gestation period to test the hypothesis that viviparity in high-altitude Phrynocephalus lizards is adaptive because embryos cannot fully develop without maternal thermoregulation. All females at 24 °C and 93% of the females at 28 °C failed to give birth or produced stillborns, and proportionally fewer females gave birth at 29 or 35 °C than at 32 °C. Though the daily temperatures encountered were unsuitable for embryonic development, 95% of the females in nature and 89% of the females thermoregulating in the laboratory gave birth. There was no shift in the thermal preferences of females when they were pregnant. Although thermal conditions inside natural burrows were unsuitable for embryonic development, mass and sprint speed were both greater in neonates produced in nature. Our data show that (1) long-term exposure of P. vlangalii embryos to temperatures outside the range of 29-35 °C may result in the failure of development, but daily or short-term exposure may not necessarily increase embryonic mortality; (2) low gestation temperatures slow but do not arrest embryonic development, and females produce high-quality offspring in the shortest possible time by maintaining gestation temperatures close to the upper thermal limit for embryonic development; and (3) viviparity is currently adaptive at high elevations because embryos in nature cannot fully develop without relying on maternal thermoregulation. Our data validate the hypothesis tested.

Species history and divergence times of viviparous and oviparous Chinese toad-headed sand lizards (Phrynocephalus) on the Qinghai-Tibetan Plateau

The Qinghai-Tibetan Plateau (QTP) is an important biogeographical area and has recently become a focus for biodiversity studies. Phyrnocephalus lizards form a widespread Eurasian group with oviparous and viviparous reproductive modes, but two previous mtDNA studies of species from around the QTP have provided different phylogenetic hypotheses. We analysed three loci (mtDNA, RAG-1, AME) from all recognised Chinese Phrynocephalus species to reconstruct the speciation history of the group and to estimate species divergence times. The effects of mtDNA partitioning strategy on phylogenetic inference were examined. Bayes factor comparisons of marginal likelihoods (mLs) estimated using stepping-stone sampling revealed that partitioning strategy had a major impact on mL. Nevertheless, it had a negligible effect on the inferred tree topology. The impact of hard-bound uniform or equivalent soft-bound gamma speciation time calibration priors as well as the use of a fixed topology (as opposed to integration over all possible species histories) on divergence time estimation were also assessed, and found to have little impact on posterior estimates. All three gene trees and the species tree supported the hypothesis that the Chinese species form oviparous and viviparous sister clades. This was in agreement with an early mtDNA study but differed from a subsequent reanalysis of the mtDNA data. Inclusion of mtDNA from more widely distributed Phrynocephalus (from previous studies) indicates that the oviparous P. interscapularis from Central Asia lies outside the clade of Chinese viviparous and oviparous species, but that other Asian oviparous species lie within the Chinese oviparous clade. The median of the posterior on the divergence time of Chinese oviparous and viviparous species was 9.7 Ma ago (95% interval: 7.2-13.0 Ma ago), which coincides with major uplifting of the QTP and indicates that viviparity evolved when this clade became restricted to regions of high elevation. We also found that cladogenesis within the viviparous clade began around 5 Ma ago whereas those in the oviparous clade began around 8.6 Ma ago. We establish more robust estimates of divergence times and relationships within this important group and so provide improved insights into the origins of Phrynocephalus diversity across the QTP.

New insights into the intricate taxonomy and phylogeny of the Sylvia curruca complex

We use the mitochondrial cytochrome b from 213 individuals and the three nuclear introns BRM 15, myoglobin 2 and ODC 6-7 from a smaller subsample to evaluate the taxonomy of the Lesser Whitethroat Sylvia curruca (Aves, Passeriformes, Sylviidae) complex, which has long been controversial. We sequenced type material of the taxa althaea, blythi, margelanica and minula, and used topotypical material of caucasica, chuancheica, curruca and telengitica. The nuclear introns fail to resolve the complex, but cytochrome b recovers six major clades, revealing genetically identifiable populations corresponding to previously named taxa, and we propose that the names althaea, blythi, curruca, halimodendri, margelanica and minula, respectively, should be used for these. The margelanica clade is suggested to have a more extensive distribution than previously known, including both the taxon telengitica and a population in eastern Mongolia. The taxon minula is found to have a more restricted range than generally believed, only breeding in China. According to the mitochondrial gene tree, there is a basal dichotomy, with the taxa althaea, blythi, halimodendri and margelanica being part of one clade, well separated from a clade containing curruca and minula. Dating analysis suggests that a basal divergence separating curruca and minula from the other four taxa occurred between 4.2 and 7.2 mya; these two then diverged between 2.3 and 4.4 mya. The splits between the althaea, blythi, halimodendri and margelanica lineages is inferred to have occurred later, approximately between 1.0 and 2.5 mya (all 95% HPD). The nucleotide data suggest significant departure from demographic equilibrium in blythi (clade 1a), halimodendri (clade 2a) and minula, whereas tendencies are weaker for other clades. We propose that the names althaea, blythi, curruca, halimodendri, margelanica and minula should be used for the major clades. However, whether these are treated as subspecies or species is largely a matter of species definition and is not resolved by our data.

Phylogeny and divergence times of some racerunner lizards (Lacertidae: Eremias) inferred from mitochondrial 16S rRNA gene segments

Eremias, or racerunners, is a widespread lacertid genus occurring in China, Mongolia, Korea, Central Asia, Southwest Asia and Southeast Europe. It has been through a series of taxonomic revisions, but the phylogenetic relationships among the species and subgenera remain unclear. In this study, a frequently studied region of the mitochondrial 16S rRNA was used to (i) reassess the phylogenetic relationships of some Eremias species, (ii) test if the viviparous species form a monophyletic group, and (iii) estimate divergence time among lineages using a Bayesian relaxed molecular-clock approach. The resulting phylogeny supports monophyly of Eremias sensu Szczerbak and a clade comprising Eremias, Acanthodactylus and Latastia. An earlier finding demonstrating monophyly of the subgenus Pareremias is corroborated, with Eremias argus being the sister taxon to Eremias brenchleyi. We present the first evidence that viviparous species form a monophyletic group. In addition, Eremias przewalskii is nested within Eremias multiocellata, suggesting that the latter is likely a paraphyletic species or a species complex. Eremias acutirostris and Eremias persica form a clade that is closely related to the subgenus Pareremias. However, the subgenera Aspidorhinus, Scapteira, and Rhabderemias seem not to be monophyletic, respectively. The Bayesian divergence-time estimation suggests that Eremias originated at about 9.9 million years ago (with the 95% confidence interval ranging from 7.6 to 12 Ma), and diversified from Late Miocene to Pleistocene. Specifically, the divergence time of the subgenus Pareremias was dated to about 6.3 million years ago (with the 95% confidence interval ranging from 5.3 to 8.5 Ma), which suggests that the diversification of this subgenus might be correlated with the evolution of an East Asian monsoon climate triggered by the rapid uplift of the Tibetan Plateau approximately 8 Ma.

Phylogenetic studies of sinipercid fish (Perciformes: Sinipercidae) based on multiple genes, with first application of an immune-related gene, the virus-induced protein (viperin) gene

The sinipercid fish represent a group of 12 species of freshwater percoid fish endemic to East Asia. To date published morphological and molecular phylogenetics hypotheses of sinipercid fish are part congruent, and there are some areas of significant disagreement with respect to species relationships. The present study used separate and combined methods to analyze 7307 bp of data from three mitochondrial genes (cyt b, CO1 and 16S rRNA; approximately 2312 bp) and three nuclear genes (viperin, the first two introns of S7 ribosomal protein gene; approximately 4995 bp) for the attempts to estimate the relationships among sinipercids and to assess the phylogenetic utility of these markers. Phylogenetic trees were reconstructed using maximum parsimony, maximum likelihood and partitioned Bayesian analyses. Despite the detection of significant heterogeneity of phylogenetic signal between the mitochondrial and nuclear partitions, the combined data analysis represented the best-supported topology of all data. The sinipercid fish form a monophyletic group with two distinct clades, one corresponding to the genus Siniperca and the other to Coreoperca. Coreoperca whiteheadi is the sister taxon to Coreoperca herzi plus Coreoperca kawamebari. In the Siniperca, Siniperca undulata is the sister taxon to the other members of Siniperca, within the subclade containing the other members of the genus, Siniperca chuatsi and Siniperca kneri are sister species, next joined by Siniperca obscura, Siniperca roulei, Sinipercascherzeri and finally by Siniperca fortis. The potential utilities of six different genes for phylogenetic resolution of closely related sinipercid species were also evaluated, with special interest in that of the novel virus-induced protein (viperin) gene.