Phylogenetic relationships and ecological niche conservatism in killifish (Profundulidae) in Mesoamerica

Divergence and reticulation in the Mexican white oaks: ecological and phylogenomic evidence on species limits and phylogenetic networks in the Quercus laeta complex (Fagaceae)

BACKGROUND AND AIMS

Introgressive hybridization poses a challenge to taxonomic and phylogenetic understanding of taxa, particularly when there are high numbers of co-occurring, intercrossable species. The genus Quercus exemplifies this situation. Oaks are highly diverse in sympatry and cross freely, creating syngameons of interfertile species. Although a well-resolved, dated phylogeny is available for the American oak clade, evolutionary relationships within many of the more recently derived clades remain to be defined, particularly for the young and exceptionally diverse Mexican white oak clade. Here, we adopted an approach bridging micro- and macroevolutionary scales to resolve evolutionary relationships in a rapidly diversifying clade endemic to Mexico.

METHODS

Ecological data and sequences of 155 low-copy nuclear genes were used to identify distinct lineages within the Quercus laeta complex. Concatenated and coalescent approaches were used to assess the phylogenetic placement of these lineages relative to the Mexican white oak clade. Phylogenetic network methods were applied to evaluate the timing and genomic significance of recent or historical introgression among lineages.

KEY RESULTS

The Q. laeta complex comprises six well-supported lineages, each restricted geographically and with mostly divergent climatic niches. Species trees corroborated that the different lineages are more closely related to other species of Mexican white oaks than to each other, suggesting that this complex is polyphyletic. Phylogenetic networks estimated events of ancient introgression that involved the ancestors of three present-day Q. laeta lineages.

CONCLUSIONS

The Q. laeta complex is a morphologically and ecologically related group of species rather than a clade. Currently, oak phylogenetics is at a turning point, at which it is necessary to integrate phylogenetics and ecology in broad regional samples to figure out species boundaries. Our study illuminates one of the more complicated of the Mexican white oak groups and lays groundwork for further taxonomic study.

The relationship between niche breadth and phylogenetic characteristics of eight species of rhubarb on the Qinghai-Tibet Plateau, Asia

The relationship between spatial distribution and phylogeny has been widely debated in recent decades. To understand biogeographic and evolutionary history relationships and to explore the interspecific similarities and phylogenetic correlations of niche characteristics, we collected and recorded all distribution points for eight species of rhubarb on the Qinghai-Tibet Plateau, used different methods to describe the ecological niche, and explored the relationship between phylogeny, ecological niche, and distribution range. The results reveal that: (1) the ranges of optimal environmental variables for species with close kinship are not exactly the same, ecologically similar species are not necessarily sister species, and the overlap of rhubarb has no significant correlation with phylogeny. Therefore, the impact of ecological dimensions on species formation is greater than that of geographical latitude for the eight species of rhubarb. (2) Among the eight species of rhubarb, the breadth of ecological niche is positively correlated with the current suitable habitat area and negatively correlated with fluctuations in future suitable habitat area. In the future, except for Rheum tanguticum and Rheum palmatum, the suitable planting areas for the other six species of rhubarb will decrease as greenhouse gas emissions concentrations and time increase. Therefore, species with smaller ecological niches are at a greater risk of habitat loss compared to species with larger ecological niches. (3) In both existing and future distribution prediction models of rhubarb, we observed that both the widely distributed Rheum spiciforme and the niche narrow Rheum nobile, all eight species of rhubarb are present in the Hengduan Mountains, based on our analysis, we propose that the Hengduan Mountains should be regarded as a priority conservation area for rhubarb, to preserve the species' biodiversity. Our study lays the groundwork for identifying evolutionary trends in ecological specialization.

Biomod2 modeling for predicting the potential ecological distribution of three Fritillaria species under climate change

The Fritillaria species ranked as a well-known traditional medicine in China and has become rare due to excessive harvesting. To find reasonable strategy for conservation and cultivation, identification of new ecological distribution of Fritillaria species together with prediction of those responses to climate change are necessary. In terms of current occurrence records and bioclimatic variables, the suitable habitats for Fritillaria delavayi, Fritillaria taipaiensis, and Fritillaria wabuensis were predicted. In comparison with Maxent and GARP, Biomod2 obtained the best AUC, KAPPA and TSS values of larger than 0.926 and was chosen to construct model. Temperature seasonality was indicated to put the greatest influence on Fritillaria taipaiensis and Fritillaria wabuensis, while isothermality was of most importance for Fritillaria delavayi. The current suitable areas for three Fritillaria species were distributed in south-west China, accounting for approximately 17.72%, 23.06% and 20.60% of China's total area, respectively. During 2021-2100 period, the suitable habitats of F. delavayi and F. wabuensis reached the maximum under SSP585 scenario, while that of F. taipaiensis reached the maximum under SSP126 scenario. The high niche overlap among three Fritillaria species showed correlation with the chemical composition (P ≤ 0.05), while no correlation was observed between niche overlap and DNA barcodes, indicating that spatial distribution had a major influence on chemical composition in the Fritillaria species. Finally, the acquisition of species-specific habitats would contribute to decrease in habitat competition, and future conservation and cultivation of Fritillaria species.

Delimitation and species discovery in the Profundulidae fish family: Using genetic, environmental and morphologic data to address taxonomic uncertainty

The family Profundulidae includes some one of the most enigmatic freshwater fishes of Mesoamerica: despite many attempts, a robust phylogenetic framework to delimit species is lacking, mainly due to limited morphological variation within the group. The accumulation of molecular data of profundulid fishes has led to advances in the description of new taxa, but relatively less progress has been made estimating evolutionary and phylogenetic relationships for this fish family. Here, we adopt an integrative taxonomy approach including the use of nuclear and mitochondrial DNA sequences, morphometric and ecological data, to test species boundaries in profundulid fishes in the westernmost area of their known distribution range in the states of Guerrero and Oaxaca, Mexico. Using a combination of methods for species discovery and validation based on Bayesian gene tree topologies, our analyses support the delimitation of 15 valid species of profundulid fishes - a combination of previously described species validated by this study, the synonymy of unsupported taxa, and the description of two new species. Using species delimitation methods, examination of phenotypic variation, and ecological niche characterization, we also identify five potentially new lineages which require further evidence to be erected as new species. We demonstrate that the use of an integrative taxonomy approach provides a robust methodology to delimit species in a taxonomically complex group like Profundulidae. Accurate taxonomic and ecological information is crucial for the conservation of these microendemic fishes, as several species are endangered.

Loss of fungal symbionts and changes in pollinator availability caused by climate change will affect the distribution and survival chances of myco-heterotrophic orchid species

The first comprehensive species distribution models for orchid, its fungal symbionts and pollinator are presented. To evaluate impact of global warming on these organisms three different projections and four various climate change scenarios were analysed. The niche modelling was based on presence-only records of Limodorum abortivum, two species of Russula and three insects pollinating orchid (Anthophora affinis, Bombus terrestris, Rhodanthidium septemdentatum). Two sets of orchid predictions were examined-the first one included only climatic data and the second one was based on climate data and data on future distribution of orchid fungal symbionts. Overall, a poleward range shift is predicted to occur as a result of climate change and apparently global warming will be favorable for L. abortivum and its potential geographical range will expand. However, due to the negative effect of global warming on fungal symbionts of L. abortivum, the actual extension of the suitable niches of the orchid will be much limited. Considering future possibility of cross-pollination, the availability of A. affinis for L. abortivum will decrease and this bee will be available in the worst case scenarios only for 21% of orchid populations. On the other hand, the overlap of orchid and the buff-tailed bumblebee will increase and as much as 86.5% of plant populations will be located within B. terrestris potential range. Also the availability of R. septemdentatum will be higher than currently observed in almost all analysed climate change projections. This study showed the importance of inclusion of ecological factors in species distribution models as the climate data itself are not enough to estimate the future distribution of plant species. Moreover, the availability of pollen vectors which is crucial for long-term survival of orchid populations should be analysed in context of climate changes.

Redescription and diagnoses of the genera Profundulus and Tlaloc (Cyprinodontiformes: Profundulidae), Mesoamerican endemic fishes

Abstract Until recently, the genus Profundulus was classified in two subgenera, Profundulus and Tlaloc, the sole members of the family Profundulidae. Newly discovered molecular data have been used to justify the elevation of these subgenera to genera. Yet morphological analyses to diagnose the two genera are lacking. The aim of this study is to provide a generic diagnosis and a taxonomic key to the species within the family Profundulidae based on morphology. The genus Tlaloc is diagnosed on the basis of five unique characters, among which are the prominent and oval-shaped mesethmoid, exceeding the posterior margins of the vomer; the anterior portion of the parasphenoid making contact with the mesethmoid and extend beyond the center of the mesethmoid; and a reduced autopterotic fossa. Profundulus is diagnosed here based on the following characters: the mesethmoid is small, crescent-shaped, and does not extend beyond the margins of the vomer; the anterior portion of the parasphenoid just contacting the mesethmoid and not extending beyond the center of the mesethmoid; a large autopterotic fossa. For each genus, description and distribution ranges are provided as well as a key for identification of the species.

Climatic niche evolution of a widely distributed Neotropical freshwater fish clade

The role of climate in the speciation process has been documented widely in ectotherms but poorly in freshwater fishes, which represent the richest clade among vertebrates. In this study, we have evaluated the occurrence of phylogenetic niche evolution as a promoter of diversification in the herichthyines (Cichliformes: Cichlidae) clade. We used distributional and bioclimatic data, niche modelling algorithms and phylogenetic comparative methods to study patterns of climatic niche evolution in the herichthyines clade. Our results suggested that herichthyines display signals of phylogenetic niche conservatism, but also signals of niche evolution in the last 14 Myr associated with the availability of new habitats promoting ecological opportunity within the clade. We also concluded that niche conservatism is equally strong in the fundamental and realized niches, which indicates a need to evaluate the potential role of biotic interactions in the evolution of the niche in future studies.

Modeling of the Potential Geographical Distribution of Three Fritillaria Species Under Climate Change

Fritillaria species, a well-known Chinese traditional medicine for more than 2,000 years, have become rare resources due to excessive harvesting. In order to balance the economical requirement and ecological protection of Fritillaria species, it is necessary to determine (1) the important environmental variables that were responsible for the spatial distribution, (2) distribution change in response to climate change in the future, (3) ecological niche overlap between various Fritillaria species, and (4) the correlation between spatial distribution and phylogenies as well. In this study, the areas with potential ecological suitability for Fritillaria cirrhosa, Fritillaria unibracteata, and Fritillaria przewalskii were predicted using MaxEnt based on the current occurrence records and bioclimatic variables. The result indicated that precipitation and elevation were the most important environmental variables for the three species. Moreover, the current suitable habitats of F. cirrhosa, F. unibracteata, and F. przewalskii encompassed 681,951, 481,607, and 349,199 km2, respectively. Under the scenario of the highest concentration of greenhouse gas emission (SSP585), the whole suitable habitats of F. cirrhosa and F. przewalskii reach the maximum from 2021 to 2100, while those of F. unibracteata reach the maximum from 2021 to 2100 under the scenario of moderate emission (SSP370) from 2021 to 2100. The MaxEnt data were also used to predict the ecological niche overlap, and thus high overlap occurring among three Fritillaria species was observed. The niche overlap of three Fritillaria species was related to the phylogenetic analysis despite the non-significance (P > 0.05), indicating that spatial distribution was one of the factors that contributed to the speciation diversification. Additionally, we predicted species-specific habitats to decrease habitat competition. Overall, the information obtained in this study provided new insight into the potential distribution and ecological niche of three species for the conservation and management in the future.