Insight into Central Asian flora from the Cenozoic Tianshan montane origin and radiation of Lagochilus (Lamiaceae).

The Tianshan Mountains play a significant role in the Central Asian flora and vegetation. Lagochilus has a distribution concentration in Tianshan Mountains and Central Asia. To investigate generic spatiotemporal evolution, we sampled most Lagochilus species and sequenced six cpDNA locations (rps16, psbA-trnH, matK, trnL-trnF, psbB-psbH, psbK-psbI). We employed BEAST Bayesian inference for dating, and S-DIVA, DEC, and BBM for ancestral area/biome reconstruction. Our results clearly show that the Tianshan Mountains, especially the western Ili-Kirghizia Tianshan, as well as Sunggar and Kaschgar, was the ancestral area. Ancestral biome was mainly in the montane steppe zone of valley and slope at altitudes of 1700-2700 m, and the montane desert zone of foothill and front-hill at 1000-1700 m. Here two sections Inermes and Lagochilus of the genus displayed "uphill" and "downhill" speciation process during middle and later Miocene. The origin and diversification of the genus were explained as coupled with the rapid uplift of the Tianshan Mountains starting in late Oligocene and early Miocene ca. 23.66~19.33 Ma, as well as with uplift of the Qinghai-Tibetan Plateau (QTP) and Central Asian aridification.

Himalayan uplift shaped biomes in Miocene temperate Asia: evidence from leguminous Caragana.

Caragana, with distinctive variation in leaf and rachis characters, exhibits three centers of geographic distribution, i.e., Central Asia, the Qinghai-Tibetan Plateau (QTP), and East Asia, corresponding to distinct biomes. Because Caragana species are often ecologically dominant components of the vegetation in these regions, it is regarded as a key taxon for the study of floristic evolution in the dry regions of temperate Asia. Based on an expanded data set of taxa and gene regions from those previously generated, we employed molecular clock and biogeographical analyses to infer the evolutionary history of Caragana and link it to floristic patterns, paleovegetation, and paleoclimate. Results indicate that Caragana is of arid origin from the Junggar steppe. Diversification of crown group Caragana, dated to the early Miocene ca. 18 Ma and onwards, can be linked to the Himalayan Motion stage of QTP uplift. Diversification of the major clades in the genus corresponding to taxonomic sections and morphological variation is inferred to have been driven by the uplift, as well as Asian interior aridification and East Asian monsoon formation, in the middle to late Miocene ca. 12~6 Ma. These findings demonstrate a synchronous evolution among floristics, vegetation and climate change in arid Central Asia, cold arid alpine QTP, and mesophytic East Asia.

Young dispersal of xerophil Nitraria lineages in intercontinental disjunctions of the Old World.

Many cases of intercontinental disjunct distributions of seed plants have been investigated, however few have concerned the continents of Eurasia (mainly Central Asia), Africa, and Australia, especially the xerophytic lineages are lacking. Nitraria (Nitrariaceae) is just one of these xerophytic lineages. Previous Nitraria studies have hypothesized either Africa as the ancient center, with dispersals to Australia and Eurasia, or alternatively Central Asia, due to a concentration of endemism and diversity there. Our findings show eastern Central Asia, i.e. the eastern Tethys, to be the correct place of origin. Dispersal westward to Africa occurred during the late Oligocene to Pliocene, whereas dispersal to Australia from western Central Asia was young since Pliocene 2.61 Ma. Two related tetraploids are indicated to have diversified in eastern Central Asia at approximately 5.89 Ma, while the Australian tetraploid N. billardieri, is an independently derived, recent dispersal from western Central Asia.

Molecular Biogeography of Tribe Thermopsideae (Leguminosae): A Madrean-Tethyan Disjunction Pattern with an African Origin of Core Genistoides.

Thermopsideae has 45 species and exhibits a series of interesting biogeographical distribution patterns, such as Madrean-Tethyan disjunction and East Asia-North America disjunction, with a center of endemism in the Qinghai-Xizang Plateau (QTP) and Central Asia. Phylogenetic analysis in this paper employed maximum likelihood using ITS, rps16, psbA-trnH, and trnL-F sequence data; biogeographical approaches included BEAST molecular dating and Bayesian dispersal and vicariance analysis (S-DIVA). The results indicate that the core genistoides most likely originated in Africa during the Eocene to Oligocene, ca. 55-30 Ma, and dispersed eastward to Central Asia at ca. 33.47 Ma. The origin of Thermopsideae is inferred as Central Asian and dated to ca. 28.81 Ma. Ammopiptanthus is revealed to be a relic. Birth of the ancestor of Thermopsideae coincided with shrinkage of the Paratethys Sea at ca. 30 Ma in the Oligocene. The Himalayan motion of QTP uplift of ca. 20 Ma most likely drove the diversification between Central Asia and North America. Divergences in East Asia, Central Asia, the Mediterranean, and so forth, within Eurasia, except for Ammopiptanthus, are shown to be dispersals from the QTP. The onset of adaptive radiation at the center of the tribe, with diversification of most species in Thermopsis and Piptanthus at ca. 4-0.85 Ma in Tibet and adjacent regions, seems to have resulted from intense northern QTP uplift during the latter Miocene to Pleistocene.

Spatiotemporal evolution of Calophaca (fabaceae) reveals multiple dispersals in central Asian mountains.

BACKGROUND: The Central Asian flora plays a significant role in Eurasia and the Northern Hemisphere. Calophaca, a member of this flora, includes eight currently recognized species, and is centered in Central Asia, with some taxa extending into adjacent areas. A phylogenetic analysis of the genus utilizing nuclear ribosomal ITS and plastid trnS-trnG and rbcL sequences was carried out in order to confirm its taxonomic status and reconstruct its evolutionary history. METHODOLOGY/PRINCIPAL FINDING: We employed BEAST Bayesian inference for dating, and S-DIVA and BBM for ancestral area reconstruction, to study its spatiotemporal evolution. Our results show that Calophacais monophyletic and nested within Caragana. The divergence time of Calophaca is estimated at ca. 8.0 Ma, most likely driven by global cooling and aridification, influenced by rapid uplift of the Qinghai Tibet Plateau margins. CONCLUSIONS/SIGNIFICANCE: According to ancestral area reconstructions, the genus most likely originated in the Pamir Mountains, a global biodiversity hotspot and hypothesized Tertiary refugium of many Central Asian plant lineages. Dispersals from this location are inferred to the western Tianshan Mountains, then northward to the Tarbagatai Range, eastward to East Asia, and westward to the Caucasus, Russia, and Europe. The spatiotemporal evolution of Calophaca provides a case contributing to an understanding of the flora and biodiversity of the Central Asian mountains and adjacent regions.

Himalayan origin and evolution of Myricaria (Tamaricaeae) in the neogene.

BACKGROUND: Myricaria 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 FINDINGS: Twelve 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/SIGNIFICANCE: Myricaria 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.

Tertiary montane origin of the Central Asian flora, evidence inferred from cpDNA sequences of Atraphaxis (Polygonaceae).

Atraphaxis has approximately 25 species and a distribution center in Central Asia. It has been previously used to hypothesize an origin from montane forest. We sampled 18 species covering three sections within the genus and sequenced five cpDNA spacers, atpB-rbcL, psbK-psbI, psbA-trnH, rbcL, and trnL-trnF. BEAST was used to reconstruct phylogenetic relationship and time divergences, and S-DIVA and Lagrange were used, based on distribution area and ecotype data, for reconstruction of ancestral areas and events. Our results appear compatible with designation of three taxonomic sections within the genus. The generic stem and crown ages were Eocene, approximately 47 Ma, and Oligocene 27 Ma, respectively. The origin of Atraphaxis is confirmed as montane, with an ancestral area consisting of the Junggar Basin and uplands of the Pamir-Tianshan-Alatau-Altai mountain chains, and ancestral ecotype of montane forest. Two remarkable paleogeographic events, shrinkage of the inland Paratethys Sea at the boundary of the late Oligocene and early Miocene, and the time intervals of cooling and drying of global climate from 24 (22) Ma onward likely facilitated early diversification of Atraphaxis, while rapid uplift of the Tianshan Mountains during the late Miocene may have promoted later diversification.

Retreating or standing: responses of forest species and steppe species to climate change in arid Eastern Central Asia.

BACKGROUND: The temperature in arid Eastern Central Asia is projected to increase in the future, accompanied by increased variability of precipitation. To investigate the impacts of climate change on plant species in this area, we selected two widespread species as candidates, Clematis sibirica and C. songorica, from montane coniferous forest and arid steppe habitats respectively. METHODOLOGY/PRINCIPAL FINDINGS: We employed a combined approach of molecular phylogeography and species distribution modelling (SDM) to predict the future responses of these two species to climate change, utilizing evidence of responses from the past. Genetic data for C. sibirica shows a significant phylogeographical signal (N ST > F ST, P<0.05) and demographic contraction during the glacial-interglacial cycles in the Pleistocene. This forest species would likely experience range reduction, though without genetic loss, in the face of future climate change. In contrast, SDMs predict that C. songorica, a steppe species, should maintain a consistently stable potential distribution under the Last Glacial Maximum (LGM) and the future climatic conditions referring to its existing potential distribution. Molecular results indicate that the presence of significant phylogeographical signal in this steppe species is rejected and this species contains a high level of genetic differentiation among populations in cpDNA, likely benefiting from stable habitats over a lengthy time period. CONCLUSIONS/SIGNIFICANCE: Evidence from the molecular phylogeography of these two species, the forest species is more sensitive to past climate changes than the steppe species. SDMs predict that the forest species will face the challenge of potential range contraction in the future more than the steppe species. This provides a perspective on ecological management in arid Eastern Central Asia, indicating that increased attention should be paid to montane forest species, due to their high sensitivity to disturbance.

Polyploidy enhances the occupation of heterogeneous environments through hydraulic related trade-offs in Atriplex canescens (Chenopodiaceae).

Plant hydraulic characteristics were studied in diploid, tetraploid and hexaploid cytotypes of Atriplex canescens (Chenopodiaceae) to investigate the potential physiological basis underlying the intraspecific habitat differentiation among plants of different ploidy levels. Populations of A. canescens from different habitats of the Chihuahuan Desert (New Mexico, USA) were analyzed using flow cytometry to determine ploidy levels. Traits related to xylem water transport efficiency and safety against drought-induced hydraulic failure were measured in both stems and leaves. At the stem level, cytotypes of higher ploidy showed consistently lower leaf-specific hydraulic conductivity but greater resistance to drought-induced loss of hydraulic conductivity. At the leaf level, comparisons in hydraulics between cytotypes did not show a consistent pattern, but exhibited high plasticity to proximal environmental conditions related to soil water availability. The results suggest that a trade-off between stem hydraulic efficiency and safety across ploidy levels underlies niche differentiation among different cytotypes of A. canescens. Polyploidization may have been facilitated by environmental heterogeneity related to water availability, and variation in water-related physiology found in the present study suggests an important functional basis for the niche differentiation and coexistence of A. canescens cytotypes in desert environments.

Deep sequencing of amplicons reveals widespread intraspecific hybridization and multiple origins of polyploidy in big sagebrush (Artemisia tridentata; Asteraceae).

PREMISE OF THE STUDY: Hybridization has played an important role in the evolution and ecological adaptation of diploid and polyploid plants. Artemisia tridentata (Asteraceae) tetraploids are extremely widespread and of great ecological importance. These tetraploids are often taxonomically identified as A. tridentata subsp. wyomingensis or as autotetraploids of diploid subspecies tridentata and vaseyana. Few details are available as to how these tetraploids are formed or how they are related to diploid subspecies. • METHODS: We used amplicon sequencing to assess phylogenetic relationships among three recognized subspecies: tridentata, vaseyana, and wyomingensis. DNA sequence data from putative genes were pyrosequenced and assembled from 329 samples. Nucleotide diversity and putative haplotypes were estimated from the high-read coverage. Phylogenies were constructed from Bayesian coalescence and neighbor-net network analyses. • KEY RESULTS: Analyses support distinct diploid subspecies of tridentata and vaseyana in spite of known hybridization in ecotones. Nucleotide diversity estimates of populations compared to the total diversity indicate the relationships are predominately driven by a small proportion of the amplicons. Tetraploids, including subspecies wyomingensis, are polyphyletic occurring within and between diploid subspecies groups. • CONCLUSIONS: Artemisia tridentata is a species comprising phylogenetically distinct diploid progenitors and a tetraploid complex with varying degrees of phylogenetic and morphological affinities to the diploid subspecies. These analyses suggest tetraploids are formed locally or regionally from diploid tridentata and vaseyana populations via autotetraploidy, followed by introgression between tetraploid groups. Understanding the phylogenetic vs. ecological relationships of A. tridentata subspecies will have bearing on how to restore these desert ecosystems.

Widespread triploidy in Western North American aspen (Populus tremuloides).

We document high rates of triploidy in aspen (Populus tremuloides) across the western USA (up to 69% of genets), and ask whether the incidence of triploidy across the species range corresponds with latitude, glacial history (as has been documented in other species), climate, or regional variance in clone size. Using a combination of microsatellite genotyping, flow cytometry, and cytology, we demonstrate that triploidy is highest in unglaciated, drought-prone regions of North America, where the largest clone sizes have been reported for this species. While we cannot completely rule out a low incidence of undetected aneuploidy, tetraploidy or duplicated loci, our evidence suggests that these phenomena are unlikely to be significant contributors to our observed patterns. We suggest that the distribution of triploid aspen is due to a positive synergy between triploidy and ecological factors driving clonality. Although triploids are expected to have low fertility, they are hypothesized to be an evolutionary link to sexual tetraploidy. Thus, interactions between clonality and polyploidy may be a broadly important component of geographic speciation patterns in perennial plants. Further, cytotypes are expected to show physiological and structural differences which may influence susceptibility to ecological factors such as drought, and we suggest that cytotype may be a significant and previously overlooked factor in recent patterns of high aspen mortality in the southwestern portion of the species range. Finally, triploidy should be carefully considered as a source of variance in genomic and ecological studies of aspen, particularly in western U.S. landscapes.

A molecular phylogenetic approach to western North America endemic Artemisia and allies (Asteraceae): untangling the sagebrushes.

PREMISE OF THE STUDY: Artemisia subgenus Tridentatae plants characterize the North American Intermountain West. These are landscape-dominant constituents of important ecological communities and habitats for endemic wildlife. Together with allied species and genera (Picrothamnus and Sphaeromeria), they make up an intricate series of taxa whose limits are uncertain, likely the result of reticulate evolution. The objectives of this study were to resolve relations among Tridentatae species and their near relatives by delimiting the phylogenetic positions of subgenus Tridentatae species with particular reference to its New World geographic placement and to provide explanations for the relations of allied species and genera with the subgenus with an assessment of their current taxonomic placement. METHODS: Bayesian inference and maximum parsimony analysis were based on 168 newly generated sequences (including the nuclear ITS and ETS and the plastid trnS(UGA)-trnfM(CAU) and trnS(GCU)-trnC(GCA)) and 338 previously published sequences (ITS and ETS). Genome size by flow cytometry of species from Sphaeromeria was also determined. KEY RESULTS: The results support an expanded concept and reconfiguration of Tridentatae to accommodate additional endemic North American Artemisia species. The monotypic Picrothamnus and all Sphaeromeria species appear nested within subgenus Tridentatae clade. CONCLUSIONS: A redefinition of subgenus Tridentatae to include other western North American endemics is supported. We propose a new circumscription of the subgenus and divide it into three sections: Tridentatae, Filifoliae, and Nebulosae. The position of the circumboreal and other North American species suggests that subgenus Artemisia is the ancestral stock for the New World endemics, including those native to South America.

NARROW HYBRID ZONE BETWEEN TWO SUBSPECIES OF BIG SAGEBRUSH (ARTEMISIA TRIDENTATA: ASTERACEAE). IV. RECIPROCAL TRANSPLANT EXPERIMENTS.

Does endogenous or exogenous selection stabilize the big sagebrush (Artemisia tridentata) hybrid zone? After two years of study, our reciprocal transplant experiments showed significant genotype by environment interactions for a number of fitness components, including germination, growth, and reproduction. Hybrids were the most fit within the hybrid garden. In the parental gardens, the native parental taxon was more fit than either the alien parental or hybrids. These results are consistent with the bounded hybrid superiority model, which assumes exogenous selection, but are clearly at odds with the dynamic equilibrium model, which assumes endogenous selection and universal hybrid unfitness.

The influence of topography on male and female fitness components of Atriplex canescens.

The influence of environmental heterogeneity on components of male and female fitness is examined using Atriplex canescens growing on steep slopes and alluvium at the slope base as a model system. Female fitness is estimated as the grams of fruit produced per plant and the grams of fruit per gram leaf tissue. Male fitness is estimated as the grams of stamens produced, the number of pollen grains dispersed to a given distance, and the potential number of grams of fruit sired taking into consideration the number and distribution of mates and competing pollen donors. The influence of increased plant size on male and female fitness components, the cost of reproduction (as measured by biomass, joules and nitrogen) on a gross level and a per offspring basis are also examined. The results indicate that the female function is more limited on the slope than the male function. The efficiency of pollen dispersal (the number of pollen grains per unit donor plant volume dispersed to a given distance) is enhanced by growing on slopes. Males become less efficient at dispersing pollen as they increase in size, while the efficiency of female reproduction (grams of fruit per volume or gram leaf tissue) is unaffected by increasing plant size. The cost to a male of siring a gram of fruit is about the same as the cost to a female of producing the gram of fruit. Implications for the evolution of sexual lability and dioecy are discussed.

RESURRECTION OF THE GENUS ENDOLEPIS AND CLARIFICATION OF ATRIPLEX PHYLLOSTEGIA (CHENOPODIACEAE).

The genus Endolepis was first described by Torrey in 1860 with E. suckleyi (E. dioica [Nutt.] Standley) as the only species, noting that it differed from species of Atriplex by the presence of perianth parts in the female flowers. Later, Standley described two additional species: E. covillei and E. monilifera. H. M. Hall and Clements merged Endolepis with Atriplex because they thought that the presence of perianth parts in female flowers was variable in Atriplex phyllostegia. It is now clear that this observation was erroneous; A. phyllostegia never has perianth parts in its female flowers. The plants that they examined that had female flowers with perianth parts were specimens of Endolepis covillei; only those with female flowers devoid of perianth parts were specimens of Atriplex phyllostegia. These two taxa differ by several other major attributes including differences in leaf shape, leaf anatomy, fruiting-bract size and shape, fruiting-bract appendages, and flowering habit, and therefore justify taxonomic separation. Also, because the presence of perianth parts in bracteolate female flowers is a rare attribute in the tribe Atripliceae, consistently absent in Atriplex, but always present in Endolepis, the retention of the genus Endolepis, separate from Atriplex, is deemed warranted. We propose that the genus Endolepis comprise two species, E. dioica and E. covillei. The species named E. monilifera by Standley is based on a specimen of Atriplex serenana Nels.

ARE TRIOECY AND SEXUAL LABILITY IN ATRIPLEX CANESCENS GENETICALLY BASED?: EVIDENCE FROM CLONAL STUDIES.

Prior studies have alternatively considered floral phenotypes in Atriplex canescens as trioecious (having three sexual genders) and/or dioecious and having a "leaky genetical switch." Clones transplanted from three populations and grown in common gardens reveal the existence of two distinctly different genetic controls regulating gender expression. In some clones gender is fixed as male (staminate) or female (pistillate), while in other clones gender varies, ranging from a mixture of male and female ramets to simultaneous hermaphrodites with various proportions of male and female flowers. For clones which vary their sex expression, variation occurs within irrigation treatments, between treatments and over time, as a consequence of the combined effects of genotype plus environment. The magnitude of sex change is also a product of the interaction of genetics and environment. Some clones have been repeatedly examined for 20 years.