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Abstract Background Engelhardia (Juglandaceae) is a genus of significant ecological and economic importance, prevalent in the tropics and subtropics of East Asia. Although previous efforts based on multiple molecular markers providing profound insights into species delimitation and phylogeography of Engelhardia, the maternal genome evolution and phylogeny of Engelhardia in Juglandaceae still need to be comprehensively evaluated. In this study, we sequenced plastomes from 14 samples of eight Engelhardia species and the outgroup Rhoiptelea chiliantha, and incorporated published data from 36 Juglandaceae and six outgroup species to test phylogenetic resolution. Moreover, comparative analyses of the plastomes were conducted to investigate the plastomes evolution of Engelhardia and the whole Juglandaceae family. Results The 13 Engelhardia plastomes were highly similar in genome size, gene content, and order. They exhibited a typical quadripartite structure, with lengths from 161,069 bp to 162,336 bp. Three mutation hotspot regions (TrnK-rps16, ndhF-rpl32, and ycf1) could be used as effective molecular markers for further phylogenetic analyses and species identification. Insertion and deletion (InDels) may be an important driving factor for the evolution of plastomes in Juglandoideae and Engelhardioideae. A total of ten codons were identified as the optimal codons in Juglandaceae. The mutation pressure mostly contributed to shaping codon usage. Seventy-eight protein-coding genes in Juglandaceae experienced relaxed purifying selection, only rpl22 and psaI genes showed positive selection (Ka/Ks > 1). Phylogenetic results fully supported Engelhardia as a monophyletic group including two sects and the division of Juglandaceae into three subfamilies. The Engelhardia originated in the Late Cretaceous and diversified in the Late Eocene, and Juglandaceae originated in the Early Cretaceous and differentiated in Middle Cretaceous. The phylogeny and divergence times didn’t support rapid radiation occurred in the evolution history of Engelhardia. Conclusion Our study fully supported the taxonomic treatment of at the section for Engelhardia species and three subfamilies for Juglandaceae and confirmed the power of phylogenetic resolution using plastome sequences. Moreover, our results also laid the foundation for further studying the course, tempo and mode of plastome evolution of Engelhardia and the whole Juglandaceae family.

Environmental factors such as mountain tectonic movements and monsoons can enhance genetic differentiation by hindering inter- and intra-specific gene flow. However, the phylogeographic breaks detected within species may differ depending on the different molecular markers used, and biological traits may be a major confounding factor. Pterocarya hupehensis is a vulnerable relict species distributed throughout the Sichuan Basin. Here, we investigated the phylogeographic patterns and evolutionary history of P. hupehensis using chloroplast DNA and restriction site-associated DNA sequencing data from 18 populations around the Sichuan Basin. The 24 chloroplast haplotypes separated into western and eastern lineages at approximately 16.7 Mya, largely coincident with a strengthening of the East Asian monsoon system during the early to middle Miocene. Both cpDNA and nuclear DNA datasets consistently identified distinct western and eastern lineages whose phylogeographic break conformed to the boundary of the Sino-Himalayan and Sino-Japanese forest sub-kingdoms. However, in contrast to the nuclear gene data, the cpDNA data revealed further divergence of the eastern lineage into northern and southern groups along the Yangtze River, a result that likely reflects differences in the extent of pollen vs seed dispersal. During the temperature decline in the penultimate (Riss) glacial period of the Pleistocene epoch, P. hupehensis experienced a genetic bottleneck event, and ecological niche modeling suggests that a subsequent population expansion occurred during the last interglacial period. Our findings not only establish a basis for conservation of this species, but also serve as a case study for the effects of geography and climate change on the evolutionary history of wind-pollinated relict plants.

Nowadays, we are living in a world that is benefiting from biodiversity, although environmental change is dramatic and biodiversity has been influenced by climate changes and human activities [...]

Alseodaphnopsis maguanensis and A. putaoensis, two new species of Alseodaphnopsis (Lauraceae) from southwestern China (Yunnan Province) and northern Myanmar (Kachin State), are here described and illustrated based on both morphological and molecular evidence. They are morphologically similar to Alseodaphnopsis rugosa and phylogenetically closely related to A. rugosa and A. hainanensis respectively. Their preliminary conservation status is also estimated according to the IUCN Red List Categories and Criteria.

Trigonobalanus doichangensis is a rare and endangered species with important evolutionary value and extremely small populations. We investigated the genetic diversity of T. doichangensis to provide information on its effective preservation. We used genotyping-by-sequencing (GBS) technology to assess the genetic diversity, genetic structure and gene flow of the six populations of T. doichangensis. Analysis of SNPs indicated that there was high genetic diversity in the ML and XSBN populations of T. doichangensis. FST values showed moderate genetic differentiation among the populations of T. doichangensis. Meanwhile, admixture, principal components and gene flow analyses indicated that the populations of T. doichangensis are not genetically separated in accordance with their geographical distributions. Habitat destruction and excessive exploitation may have led to a low gene flow, which has in turn resulted in the differences in seed and seedling morphological traits among populations. Based on these findings, we recommend that T. doichangensis be conserved through in situ approaches and artificial seedlings, including preservation of each extant population. Particularly, the ML and XSBN populations have high diversity and more ancestral information, so these two populations should be considered as conservation priorities, and seeds should be collected to obtain germplasm and increase the genetic diversity.

The latitudinal diversity gradient (LDG) is one of the most extensive and important biodiversity patterns on the Earth. Various studies have established that species diversity increases with higher taxa numbers from the polar to the tropics. Studies of multicellular biotas have supported the LDG patterns from land (e.g., plants, animals, forests, wetlands, grasslands, fungi, and so forth) to oceans (e.g., marine organisms from freshwater invertebrates, continental shelve, open ocean, even to the deep sea invertebrates). So far, there are several hypotheses proposed to explore the diversity patterns and mechanisms of LDG, however, there has been no consensus on the underlying causes of LDG over the past few decades. Thus, we reviewed the progress of LDG studies in recent years. Although several explanations for the LDG have been proposed, these hypotheses are only based on species richness, evolution and the ecosystems. In this review, we summarize the effects of evolution and ecology on the LDG patterns to synthesize the formation mechanisms of the general biodiversity distribution patterns. These intertwined factors from ecology and evolution in the LDG are generally due to the wider distribution of tropical areas, which hinders efforts to distinguish their relative contributions. However, the mechanisms of LDG always engaged controversies, especially in such a context that the human activity and climate change has affected the biodiversity. With the development of molecular biology, more genetic/genomic data are available to facilitate the estimation of global biodiversity patterns with regard to climate, latitude, and other factors. Given that human activity and climate change have inevitably impacted on biodiversity loss, biodiversity conservation should focus on the change in LDG pattern. Using large-scale genetic/genomic data to disentangle the diversity mechanisms and patterns of LDG, will provide insights into biodiversity conservation and management measures. Future perspectives of LDG with integrative genetic/genomic, species, evolution, and ecosystem diversity patterns, as well as the mechanisms that apply to biodiversity conservation, are discussed. It is imperative to explore integrated approaches for recognizing the causes of LDG in the context of rapid loss of diversity in a changing world.

Relict species play an important role in understanding the biogeography of intercontinental disjunctions. Pterocarya (a relict genus) is the valuable model taxon for studying the biogeography of East Asian versus southern European/West Asian disjunct patterns. This disjunction has not been as well studied as others (e.g., between Eastern Asia and North America). Several phylogenetic studies on Pterocarya have been conducted, but none have provided a satisfactory phylogenetic resolution. Here, we report the first well-resolved phylogeny of Pterocarya using restriction site-associated DNA sequencing data based on the sampling of all taxa across the entire distribution area of the genus. Taxonomic treatments were also clarified by combining morphological traits. Furthermore, fossil-calibrated phylogeny was used to explore the biogeography of Pterocarya. Our results support the existence of two sections in Pterocarya, which is in accordance with morphological taxonomy. Section Platyptera comprises three species: P. rhoifolia, P. macroptera, and P. delavayi. Section Pterocarya also comprises three species: P. fraxinifolia, P. hupehensis, and P. stenoptera. The divergence between the two sections took place during the early Miocene (20.5 Ma). The formation of the Gobi Desert and climate cooling of northern Siberia in the Middle Miocene (15.7 Ma) might have caused the split of the continuous distribution of this genus and the formation of the East Asian versus southern European/West Asian disjunct pattern. Lastly, the divergence between P. hupehensis and P. stenoptera as well as between P. rhoifolia and P. macroptera/P. delavayi (10.0 Ma) supports the late Miocene diversification hypothesis in East Asia.

BackgroundMyricaria consists of about twelve-thirteen species and occurs in Eurasian North Temperate zone, most species in the Qinghai-Tibet Plateau (QTP) and adjacent areas.Methodology/principal findingsTwelve species of Myricaria plus two other genera Tamarix and Reaumuria in Tamaricaceae, were sampled, and four markers, ITS, rps16, psbB-psbH, and trnL-trnF were sequenced. The relaxed Bayesian molecular clock BEAST method was used to perform phylogenetic analysis and molecular dating, and Diva, S-Diva, and maximum likelihood Lagrange were used to estimate the ancestral area. The results indicated that Myricaria could be divided into four phylogenetic clades, which correspond to four sections within the genus, of them two are newly described in this paper. The crown age of Myricaria was dated to early Miocene ca. 20 Ma, at the probable early uplifting time of the Himalayas. The Himalayas were also shown as the center of origin for Myricaria from the optimization of ancestral distribution. Migration and dispersal of Myricaria were indicated to have taken place along the Asian Mountains, including the Himalayas, Kunlun, Altun, Hendukosh, Tianshan, Altai, and Caucasus etc., westward to Europe, eastward to Central China, and northward to the Mongolian Plateau.Conclusions/significanceMyricaria spatiotemporal evolution presented here, especially the Himalayan origin at early Miocene ca. 20 Ma, and then migrated westward and eastward along the Asian mountains, offers a significant evolutionary case for QTP and Central Asian biogeography.

Background: Given that most species that have ever existed on earth are extinct, it stands to reason that the evolutionary history can be better understood with fossil taxa. Bauhinia is a typical genus of pantropical intercontinental disjunction among the Asian, African, and American continents. Geographic distribution patterns are better recognized when fossil records and molecular sequences are combined in the analyses. Here, we describe a new macrofossil species of Bauhinia from the Upper Miocene Xiaolongtan Formation in Wenshan County, Southeast Yunnan, China, and elucidate the biogeographic significance through the analyses of molecules and fossils. Results: Morphometric analysis demonstrates that the leaf shapes of B. acuminata, B. championii, B. chalcophylla, B. purpurea, and B. podopetala closely resemble the leaf shapes of the new finding fossil. Phylogenetic relationships among the Bauhinia species were reconstructed using maximum parsimony and Bayesian inference, which inferred that species in Bauhinia are well-resolved into three main groups. Divergence times were estimated by the Bayesian Markov chain Monte Carlo (MCMC) method under a relaxed clock, and inferred that the stem diversification time of Bauhinia was ca. 62.7 Ma. The Asian lineage first diverged at ca. 59.8 Ma, followed by divergence of the Africa lineage starting during the late Eocene, whereas that of the neotropical lineage starting during the middle Miocene. Conclusions: Hypotheses relying on vicariance or continental history to explain pantropical disjunct distributions are dismissed because they require mostly Palaeogene and older tectonic events. We suggest that Bauhinia originated in the middle Paleocene in Laurasia, probably in Asia, implying a possible Tethys Seaway origin or an “Out of Tropical Asia”, and dispersal of legumes. Its present pantropical disjunction resulted from disruption of the boreotropical flora by climatic cooling after the Paleocene-Eocene Thermal Maximum (PETM). North Atlantic land bridges (NALB) seem the most plausible route for migration of Bauhinia from Asia to America; and additional aspects of the Bauhinia species distribution are explained by migration and long distance dispersal (LDD) from Eurasia to the African and American continents. [ABSTRACT FROM AUTHOR]

To document arid Northern China as a diversification center for desert plants, and to better understand the mechanisms of desert taxa diversification, we used five cpDNA spacers (trnL-trnF, rps16, psbA-trnH, psbK-psbI and trnS-trnG) to investigate Lagochilus ilicifolius in all distribution areas, including Northern China, Mongolia and Russia. Phylogenetic analyses showed that L. ilicifolius comprises two distinctive lineages, one distributed in China, and another in Mongolia-Russia. Our data confirmed that arid Northern China, is a distinctive area with many endemic genera. Biogeographic inferences, based on a Bayesian uncorrelated lognormal model together with molecular dating, suggested that the main diversification within the species occurred in the Pleistocene (ca. 1.38-0.3 Ma), resulting from the transition of the climate of Eurasia to a dry-cold pattern as well as the desertification caused the vicariance of desert plants. [ABSTRACT FROM AUTHOR]