The tropical Andean plant diversity powerhouse

There and back again: historical biogeography of neotropical magnolias based on high-throughput sequencing

BACKGROUND

The Neotropics are considered one of the most biodiverse areas in the world, housing at least one third of all vascular plant species. One of the genera that has diversified in the Neotropics is Magnolia, with about 174 species of three sections (Macrophylla, Magnolia and Talauma) endemic to the Americas. In this work, we study the biogeographic history of the Neotropical Magnolia species using high-throughput sequencing data. Sequences from 39 species (38 from Magnolia and one from the sister genus Liriodendron) were assembled. The dataset contained sequences from 239 nuclear targets and complete chloroplast genomes. Phylogenomic hypotheses and the ancestral distribution range of Magnolia were reconstructed.

RESULTS

The results of the calibrated phylogenetic hypotheses and ancestral range construction suggest that the earliest arrival in the Neotropics were the ancestors of section Talauma (38 million years ago), which colonized the Pacific region. This early presence in South America suggests long-distance, overwater dispersal from North America, the presumed origin of the genus Magnolia. The analysis and the extant Talauma distribution indicate a south to north recolonization. The ancestors of the other two Neotropical sections, Magnolia and Macrophylla, migrated around 19 mya from Asia to North America, radiating southward to the Neotropics afterwards, around 11 mya.

CONCLUSIONS

Our results suggest that Neotropical magnolias originated from a North American ancestor. The current sections arrived at the region independently influenced by climatic processes such as temperature drops or the Miocene Climatic Optimum. Additionally, geological processes, such as the movement of the South and North American land masses and the emergence of the Panama isthmus, facilitated the migration between continents.

Rapid Radiation of a Plant Lineage Sheds Light on the Assembly of Dry Valley Biomes

Southwest China is characterized by high plateaus, large mountain systems, and deeply incised dry valleys formed by major rivers and their tributaries. Despite the considerable attention given to alpine plant radiations in this region, the timing and mode of diversification of the numerous dry valley plant lineages remain unknown. To address this knowledge gap, we investigated the macroevolution of Isodon (Lamiaceae), a lineage commonly distributed in the dry valleys in southwest China and wetter areas of Asia and Africa. We reconstructed a robust phylogeny encompassing nearly 90% of the approximately 140 extant Isodon species using transcriptome and genome-resequencing data. Our results suggest a rapid radiation of Isodon during the Pliocene that coincided with a habit shift from herbs to shrubs and a habitat shift from humid areas to dry valleys. The shrubby growth form likely acted as a preadaptation allowing for the movement of Isodon species into these dry valleys. Ecological analyses highlight drought-related factors as key drivers influencing the niche preferences of different growth forms and species richness of Isodon. The interplay between topography and the development of the East Asian monsoon since the middle Miocene likely contributed to the formation of the dry valley biome in southwest China. This study enhances our understanding of evolutionary dynamics and ecological drivers shaping the distinctive flora of southwest China and reveals the strategies employed by montane plants in response to climate change and dryland expansion, thus facilitating conservation efforts globally.

Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora

The Andes mountains of western South America are a globally important biodiversity hotspot, yet there is a paucity of resolved phylogenies for plant clades from this region. Filling an important gap in our understanding of the World's richest flora, we present the first phylogeny of Freziera (Pentaphylacaceae), an Andean-centered, cloud forest radiation. Our dataset was obtained via hybrid-enriched target sequence capture of Angiosperms353 universal loci for 50 of the ca. 75 spp., obtained almost entirely from herbarium specimens. We identify high phylogenomic complexity in Freziera, including the presence of data artifacts. Via by-eye observation of gene trees, detailed examination of warnings from recently improved assembly pipelines, and gene tree filtering, we identified that artifactual orthologs (i.e., the presence of only one copy of a multicopy gene due to differential assembly) were an important source of gene tree heterogeneity that had a negative impact on phylogenetic inference and support. These artifactual orthologs may be common in plant phylogenomic datasets, where multiple instances of genome duplication are common. After accounting for artifactual orthologs as source of gene tree error, we identified a significant, but nonspecific signal of introgression using Patterson's D and f4 statistics. Despite phylogenomic complexity, we were able to resolve Freziera into 9 well-supported subclades whose evolution has been shaped by multiple evolutionary processes, including incomplete lineage sorting, historical gene flow, and gene duplication. Our results highlight the complexities of plant phylogenomics, which are heightened in Andean radiations, and show the impact of filtering data processing artifacts and standard filtering approaches on phylogenetic inference.

Past climate cooling and orogenesis of the Hengduan Mountains have influenced the evolution of Impatiens sect. Impatiens (Balsaminaceae) in the Northern Hemisphere

BACKGROUND

Impatiens sect. Impatiens is distributed across the Northern Hemisphere and has diversified considerably, particularly within the Hengduan Mountains (HDM) in southwest China. Yet, the infra-sectional phylogenetic relationships are not well resolved, largely due to limited taxon sampling and an insufficient number of molecular markers. The evolutionary history of its diversification is also poorly understood. In this study, plastome data and the most complete sampling to date were used to reconstruct a robust phylogenetic framework for this section. The phylogeny was then used to investigate its biogeographical history and diversification patterns, specifically with the aim of understanding the role played by the HDM and past climatic changes in its diversification.

RESULTS

A stable phylogeny was reconstructed that strongly supported both the monophyly of the section and its division into seven major clades (Clades I-VII). Molecular dating and ancestral area reconstruction suggest that sect. Impatiens originated in the HDM and Southeast China around 11.76 Ma, after which different lineages dispersed to Northwest China, temperate Eurasia, and North America, mainly during the Pliocene and Pleistocene. An intercontinental dispersal event from East Asia to western North America may have occurred via the Bering Land Bridge or Aleutian Islands. The diversification rate was high during its early history, especially with the HDM, but gradually decreased over time both within and outside the HDM. Multiple linear regression analysis showed that the distribution pattern of species richness was strongly associated with elevation range, elevation, and mean annual temperature. Finally, ancestral niche analysis indicated that sect. Impatiens originated in a relatively cool, middle-elevation area.

CONCLUSIONS

We inferred the evolutionary history of sect. Impatiens based on a solid phylogenetic framework. The HDM was the primary source or pump of its diversity in the Northern Hemisphere. Orogeny and climate change may have also shaped its diversification rates, as a steady decrease in the diversification rate coincided with the uplift of the HDM and climate cooling. These findings provide insights into the distribution pattern of sect. Impatiens and other plants in the Northern Hemisphere.

The evolution of extant South American tropical biomes

This review explores the evolution of extant South American tropical biomes, focusing on when and why they developed. Tropical vegetation experienced a radical transformation from being dominated by non-angiosperms at the onset of the Cretaceous to full angiosperm dominance nowadays. Cretaceous tropical biomes do not have extant equivalents; lowland forests, dominated mainly by gymnosperms and ferns, lacked a closed canopy. This condition was radically transformed following the massive extinction event at the Cretaceous-Paleogene boundary. The extant lowland tropical rainforests first developed at the onset of the Cenozoic with a multistratified forest, an angiosperm-dominated closed canopy, and the dominance of the main families of the tropics including legumes. Cenozoic rainforest diversity has increased during global warming and decreased during global cooling. Tropical dry forests emerged at least by the late Eocene, whereas other Neotropical biomes including tropical savannas, montane forests, páramo/puna, and xerophytic forest are much younger, greatly expanding during the late Neogene, probably at the onset of the Quaternary, at the expense of the rainforest.

Species richness and turnover patterns for tropical and temperate plants on the elevation gradient of the eastern Himalayan Mountains

Understanding species’ elevational distributions in mountain ecosystems is needed under climate change, but remote biodiverse mountain areas may be poorly documented. National Forest Inventories (NFIs) offer a potential source of data. We used NFI records from Bhutan to ask three questions about elevational richness patterns of Himalayan woody plant species. First, does the mean elevation for all species differ from those species whose entire elevational distribution is recorded in the survey? Second, how does the elevation of maximum richness differ when combining species originating from temperate and tropical regions vs. analyzing them separately? And third, do the highest species turnover rates adjoin elevation zones of maximum species richness? We used 32,198 species records from 1685 forest plots along a 7570 m gradient to map species elevation ranges. Species whose entire range was documented were those whose lowest records are located above 400 m, while bare rock defined all species’ upper limits. We calculated species richness and turnover using 400 m elevation bands. Of 569 species, 79% of temperate and 61% of tropical species’ elevation ranges were fully sampled within the NFI data. Mean elevation of tree and shrub species differed significantly for temperate and tropical species. Maximum combined species richness is from 1300 to 1700 m (277 species), differing significantly from maximum tropical (900–1300 m, 169) and temperate species richness (2500–2900 m, 92). Temperate tree turnover rate was highest in the bands adjoining its maximum species richness (2500–2900 m). But turnover for tropical trees was highest several bands above their maximum species richness, where turnover and decrease in richness interact. Shrub species turnover patterns are similar, but rates were generally higher than for trees. Bhutan’s NFI records show that woody plant species are arrayed on the Himalaya in part according to floristic origins, and that combining temperate- and tropical-originating floras for gradient-based studies such as species richness and turnover obscures actual elevational patterns. In addition, species whose ranges extend below the Himalayan elevation gradient should be accounted for in future studies that correlate climate and environment factors with elevational species richness patterns.

Genetic markers in Andean Puya species (Bromeliaceae) with implications on plastome evolution and phylogeny

The Andean plant endemic Puya is a striking example of recent and rapid diversification from central Chile to the northern Andes, tracking mountain uplift. This study generated 12 complete plastomes representing nine Puya species and compared them to five published plastomes for their features, genomic evolution, and phylogeny. The total size of the Puya plastomes ranged from 159,542 to 159,839 bp with 37.3%-37.4% GC content. The Puya plastomes were highly conserved in organization and structure with a typical quadripartite genome structure. Each of the 17 consensus plastomes harbored 133 genes, including 87 protein-coding genes, 38 tRNA (transfer RNA) genes, and eight rRNA (ribosomal RNA) genes; we found 69-78 tandem repeats, 45-60 SSRs (simple sequence repeats), and 8-22 repeat structures among 13 species. Four protein-coding genes were identified under positive site-specific selection in Puya. The complete plastomes and hypervariable regions collectively provided pronounced species discrimination in Puya and a practical tool for future phylogenetic studies. The reconstructed phylogeny and estimated divergence time for the lineage suggest that the diversification of Puya is related to Andean orogeny and Pleistocene climatic oscillations. This study provides plastome resources for species delimitation and novel phylogenetic and biogeographic studies.

Evidence for Alternate Stable States in an Ecuadorian Andean Cloud Forest

Tree diversity inventories were undertaken. The goal of this study was to understand changes in tree community dynamics that may result from common anthropogenic disturbances at the Reserva Los Cedros, a tropical montane cloud forest reserve in northern Andean Ecuador. The reserve shows extremely high alpha and beta tree diversity. We found that all primary forest sites, regardless of age of natural gaps, are quite ecologically resilient, appearing to return to a primary-forest-type community of trees following gap formation. In contrast, forests regenerating from anthropogenic disturbance appear to have multiple possible ecological states. Where anthropogenic disturbance was intense, novel tree communities appear to be assembling, with no indication of return to a primary forest state. Even in ancient primary forests, new forest types may be forming, as we found that seedling community composition did not resemble adult tree communities. We also suggest small watersheds as a useful basic spatial unit for understanding biodiversity patterns in the tropical Andes that confound more traditional Euclidean distance as a basic proxy of dissimilarity. Finally, we highlight the conservation value of Reserva Los Cedros, which has managed to reverse deforestation within its boundaries despite a general trend of extensive deforestation in the surrounding region, to protect a large, contiguous area of highly endangered Andean primary cloud forest.

Phylogeography of Iris loczyi (Iridaceae) in Qinghai-Tibet Plateau revealed by chloroplast DNA and microsatellite markers

Quaternary climate oscillations and complex topography have tremendous effects on current distribution and genetic structure of species, and hence the Qinghai-Tibet Plateau (QTP), the largest plateau in the world, has become a hotspot for many phylogeographic studies. However, little is known about the phylogeographic pattern of herbaceous plants in QTP. Here, we investigate the genetic diversity, population structure and historical dynamics of Iris loczyi, using five chloroplast DNA (cpDNA) fragments and seven microsatellite markers. A total of 15 populations, and 149 individuals were sampled throughout the QTP. High genetic diversity was detected both in cpDNA (H _d = 0.820) and SSR (H _o = 0.689, H _e = 0.699). Ten cpDNA haplotypes and 163 alleles were identified. AMOVA and clustering analyses revealed obvious differentiation between regions. The N _st, G _st and Mantel test showed significant phylogeographic structure of I. loczyi. The neutrality test and mismatch distribution analyses indicated that I. loczyi could not have undergone a historical population expansion, but population XS from the Qilian Mountain area could have experienced a local expansion. Bottleneck analyses indicated that I. loczyi had not experienced bottleneck recently. Based on cpDNA and SSR results, the Qilian Mountain area was inferred as a potential glacial refuge, and the southern Tibet valley was considered as a 'microrefugia' for I. loczyi. These findings provided new insights into the location of glacial refuges for the species distributed in QTP, and supplemented more plant species data for the response of QTP species to the Quaternary climate.

Alpine speciation and morphological innovations: revelations from a species-rich genus in the northern hemisphere

A large number of studies have attempted to determine the mechanisms driving plant diversity and distribution on a global scale, but the diverse and endemic alpine herbs found in harsh environments, showing adaptive evolution, require more studies. Here, we selected 466 species from the genus Saussurea, one of the northern hemisphere's highest-altitude plant genera with high species richness and striking morphological traits, to explore the mechanisms driving speciation and adaptative evolution. We conducted phylogenetic signals analysis and ancestral character estimation to explore the phylogenetic significance of ecological factors. Moreover, we used spatial simultaneous autoregressive (SAR) error models, modified t-tests and partial regression models to quantify the relative effects of ecological factors and morphological diversity upon diversity and endemism of Saussurea. Phylogenetic analyses reveal that geological influences and climate stability exhibit significant phylogenetic signals and that Saussurea originated at a relatively high elevation. Regression models indicate that geological influences and climatic stability significantly affect the diversity and endemism patterns of Saussurea and its morphological innovations. Moreover, morphological innovations in an area show significant contributions to the local diversity and endemism of Saussurea. We conclude that geological influences (mean altitude and topographic heterogeneity), glacial-interglacial climate stability and phylogenetic conservatism have together promoted the speciation and adaptive evolution of the genus Saussurea. In addition, adaptively morphological innovations of alpine species also promote diversification in local regions. Our findings improve the understanding of the distribution pattern of diversity/endemism and adaptive evolution of alpine specie in the whole northern hemisphere.

Amazonia is the primary source of Neotropical biodiversity

Amazonia is not only the world’s most diverse rainforest but is also the region in tropical America that has contributed most to its total biodiversity. We show this by estimating and comparing the evolutionary history of a large number of animal and plant species. We find that there has been extensive interchange of evolutionary lineages among different regions and biomes, over the course of tens of millions of years. Amazonia stands out as the primary source of diversity, which can be mainly explained by the total amount of time Amazonian lineages have occupied the region. The exceedingly rich and heterogeneous diversity of the American tropics could only be achieved by high rates of dispersal events across the continent.

The American tropics (the Neotropics) are the most species-rich realm on Earth, and for centuries, scientists have attempted to understand the origins and evolution of their biodiversity. It is now clear that different regions and taxonomic groups have responded differently to geological and climatic changes. However, we still lack a basic understanding of how Neotropical biodiversity was assembled over evolutionary timescales. Here we infer the timing and origin of the living biota in all major Neotropical regions by performing a cross-taxonomic biogeographic analysis based on 4,450 species from six major clades across the tree of life (angiosperms, birds, ferns, frogs, mammals, and squamates), and integrate >1.3 million species occurrences with large-scale phylogenies. We report an unprecedented level of biotic interchange among all Neotropical regions, totaling 4,525 dispersal events. About half of these events involved transitions between major environmental types, with a predominant directionality from forested to open biomes. For all taxonomic groups surveyed here, Amazonia is the primary source of Neotropical diversity, providing >2,800 lineages to other regions. Most of these dispersal events were to Mesoamerica (∼1,500 lineages), followed by dispersals into open regions of northern South America and the Cerrado and Chaco biomes. Biotic interchange has taken place for >60 million years and generally increased toward the present. The total amount of time lineages spend in a region appears to be the strongest predictor of migration events. These results demonstrate the complex origin of tropical ecosystems and the key role of biotic interchange for the assembly of regional biotas.

Spiroides shrubs on Qinghai-Tibetan Plateau: Multilocus phylogeography and palaeodistributional reconstruction of Spiraea alpina and S. Mongolica (Rosaceae)

A common hypothesis for the rich biodiversity found in mountains is uplift-driven diversification. Using a multilocus approach, here we assessed the influence of Qinghai-Tibetan Plateau (QTP) uplift and fluctuating regional climate on genetic diversity of two sister spiroides shrubs, Spiraea alpina and S. mongolica. Combined with palaeodistributional reconstruction modelling, we investigated the current and past-predicted distribution of these species under different climatic episodes. The study demonstrated that continuous pulses of retreat and expansion during last glacial-interglacial episodes, combined with the uplifting of QTP shaped the current distribution of these species. All the populations showed high level of genetic diversity based on both cpDNA and SSR markers. The average gene diversity within populations based on cpDNA markers was 0.383 ± 0.052 for S. alpina and 0.477 ± 0.048 for S. mongolica. The observed and expected heterozygosities based on SSR for both Spiraea alpina and S. mongolicawere H_E(0.72-0.90)/H_O(0.35-0.78) and H_E(0.77-0.92)/H_O(0.47-0.77) respectively. Palaeodistributional reconstruction indicated species' preferences at southeastern edge of the plateau during last glacial maximum, at higher altitude areas of QTP and range expansion to central plateau during the interglacial episodes. Assignment tests in STRUCTURE, discriminant analysis of principal coordinates and Immigrants analysis in GENECLASS based on nuclear SSR markers did not support the hypothesis of gene flow between both the species. However, maximum likelihood approach based on cpDNA showed sharing of haplotypes between both species.

Sweet vernal grasses (Anthoxanthum) colonized African mountains along two fronts in the Late Pliocene, followed by secondary contact, polyploidization and local extinction in the Pleistocene

High tropical mountains harbour remarkable and fragmented biodiversity thought to a large degree to have been shaped by multiple dispersals of cold-adapted lineages from remote areas. Few dated phylogenetic/phylogeographic analyses are however available. Here, we address the hypotheses that the sub-Saharan African sweet vernal grasses have a dual colonization history and that lineages of independent origins have established secondary contact. We carried out rangewide sampling across the eastern African high mountains, inferred dated phylogenies from nuclear ribosomal and plastid DNA using Bayesian methods, and performed flow cytometry and AFLP (amplified fragment length polymorphism) analyses. We inferred a single Late Pliocene western Eurasian origin of the eastern African taxa, whose high-ploid populations in one mountain group formed a distinct phylogeographic group and carried plastids that diverged from those of the currently allopatric southern African lineage in the Mid- to Late Pleistocene. We show that Anthoxanthum has an intriguing history in sub-Saharan Africa, including Late Pliocene colonization from southeast and north, followed by secondary contact, hybridization, allopolyploidization and local extinction during one of the last glacial cycles. Our results add to a growing body of evidence showing that isolated tropical high mountain habitats have a dynamic recent history involving niche conservatism and recruitment from remote sources, repeated dispersals, diversification, hybridization and local extinction.

Uplift-driven diversification in the Hengduan Mountains, a temperate biodiversity hotspot

A common hypothesis for the rich biodiversity found in mountains is uplift-driven diversification-that orogeny creates conditions favoring rapid in situ speciation of resident lineages. We tested this hypothesis in the context of the Qinghai-Tibetan Plateau (QTP) and adjoining mountain ranges, using the phylogenetic and geographic histories of multiple groups of plants to infer the tempo (rate) and mode (colonization versus in situ diversification) of biotic assembly through time and across regions. We focused on the Hengduan Mountains region, which in comparison with the QTP and Himalayas was uplifted more recently (since the late Miocene) and is smaller in area and richer in species. Time-calibrated phylogenetic analyses show that about 8 million y ago the rate of in situ diversification increased in the Hengduan Mountains, significantly exceeding that in the geologically older QTP and Himalayas. By contrast, in the QTP and Himalayas during the same period the rate of in situ diversification remained relatively flat, with colonization dominating lineage accumulation. The Hengduan Mountains flora was thus assembled disproportionately by recent in situ diversification, temporally congruent with independent estimates of orogeny. This study shows quantitative evidence for uplift-driven diversification in this region, and more generally, tests the hypothesis by comparing the rate and mode of biotic assembly jointly across time and space. It thus complements the more prevalent method of examining endemic radiations individually and could be used as a template to augment such studies in other biodiversity hotspots.

Population Genetic Differentiation and Taxonomy of Three Closely Related Species of Saxifraga (Saxifragaceae) from Southern Tibet and the Hengduan Mountains

The effects of rapid, recent uplift of the Hengduan Mountains on evolution and diversification of young floristic lineages still remain unclear. Here, we investigate diversification of three closely related Saxifraga species with a distribution restricted to the Hengduan Mountains (HM) and southern Tibet, and comment on their taxonomy based on molecular evidence. Three chloroplast DNA fragments (rbcL, trnL-F, trnS-G) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to study genetic structure across 104 individuals from 12 populations of Saxifraga umbellulata, S. pasumensis, and S. banmaensis. Chloroplast DNA (cpDNA) phylogenies revealed two well supported clades, corresponding to S. umbellulata and S. pasumensis plus S. banmaensis. Topology of the ITS phylogeny was largely congruent with that generated from cpDNA haplotypes, but with minor conflicts which might be caused by incomplete lineage sorting. Analyses of molecular variance of both cpDNA and ITS datasets revealed that most variation was held between S. pasumensis s.l. (with S. banmaensis) and S. umbellulata (92.31% for cpDNA; 69.78% for ITS), suggesting a high degree of genetic divergence between them. Molecular clock analysis based on ITS dataset suggested that the divergence between S. pasumensis s.l. and S. umbellulata can be dated to 8.50 Ma, probably a result of vicariant allopatric diversification associated with the uplift events of the HM. Vicariance associated with HM uplifts may also have been responsible for infraspecific differentiation in S. pasumensis. In contrast, infraspecific differentiation in S. umbellulata was most likely triggered by Quaternary glaciations. The much lower levels of gene diversity within populations of S. pasumensis compared with S. umbellulata could have resulted from both range contractions and human collection on account of its putative medicinal properties. Combining evidence from morphology, geographical distributions and molecular phylogenetic data, we recommend that S. banmaensis should be treated as a synonym of S. pasumensis which in turn, and based on the same sources of evidence, should be treated as a separate species rather than as a variety of S. umbellulata.