Rooting and dating maples (Acer) with an uncorrelated-rates molecular clock: implications for north American/Asian disjunctions

QR-STAR: A Polynomial-Time Statistically Consistent Method for Rooting Species Trees Under the Coalescent

We address the problem of rooting an unrooted species tree given a set of unrooted gene trees, under the assumption that gene trees evolve within the model species tree under the multispecies coalescent (MSC) model. Quintet Rooting (QR) is a polynomial time algorithm that was recently proposed for this problem, which is based on the theory developed by Allman, Degnan, and Rhodes that proves the identifiability of rooted 5-taxon trees from unrooted gene trees under the MSC. However, although QR had good accuracy in simulations, its statistical consistency was left as an open problem. We present QR-STAR, a variant of QR with an additional step and a different cost function, and prove that it is statistically consistent under the MSC. Moreover, we derive sample complexity bounds for QR-STAR and show that a particular variant of it based on "short quintets" has polynomial sample complexity. Finally, our simulation study under a variety of model conditions shows that QR-STAR matches or improves on the accuracy of QR. QR-STAR is available in open-source form on github.

Identification and Analysis of the CBF Gene Family in Three Species of Acer under Cold Stress

The C-Repeat Binding Factor (CBF) gene family has been identified and characterized in multiple plant species, and it plays a crucial role in responding to low temperatures. Presently, only a few studies on tree species demonstrate the mechanisms and potential functions of CBFs associated with cold resistance, while our study is a novel report on the multi-aspect differences of CBFs among three tree species, compared to previous studies. In this study, genome-wide identification and analysis of the CBF gene family in Acer truncatum, Acer pseudosieboldianum, and Acer yangbiense were performed. The results revealed that 16 CBF genes (five ApseCBFs, four AcyanCBFs, and seven AtruCBFs) were unevenly distributed across the chromosomes, and most CBF genes were mapped on chromosome 2 (Chr2) and chromosome 11 (Chr11). The analysis of phylogenetic relationships, gene structure, and conserved motif showed that 16 CBF genes could be clustered into three subgroups; they all contained Motif 1 and Motif 5, and most of them only spanned one exon. The cis-acting elements analysis showed that some CBF genes might be involved in hormone and abiotic stress responsiveness. In addition, CBF genes exhibited tissue expression specificity. High expressions of ApseCBF1, ApseCBF3, AtruCBF1, AtruCBF4, AtruCBF6, AtruCBF7, and ApseCBF3, ApseCBF4, ApseCBF5 were detected on exposure to low temperature for 3 h and 24 h. Low expressions of AtruCBF2, AtruCBF6, AtruCBF7 were detected under cold stress for 24 h, and AtruCBF3 and AtruCBF5 were always down-regulated under cold conditions. Taken together, comprehensive analysis will enhance our understanding of the potential functions of the CBF genes on cold resistance, thereby providing a reference for the introduction of Acer species in our country.

Structural Characterization of the Acer ukurunduense Chloroplast Genome Relative to Related Species in the Acer Genus

Acer ukurunduense refers to a deciduous tree distributed in Northeast Asia and is a widely used landscaping tree species. Although several studies have been conducted on the species’ ecological and economic significance, limited information is available on its phylo-genomics. Our study newly constitutes the complete chloroplast genome of A. ukurunduense into a 156,645-bp circular DNA, which displayed a typical quadripartite structure. In addition, 133 genes were identified, containing 88 protein-coding genes, 37 tRNA genes, and eight rRNA genes. In total, 107 simple sequence repeats and 49 repetitive sequences were observed. Thirty-two codons indicated that biased usages were estimated across 20 protein-coding genes (CDS) in A. ukurunduense. Four hotspot regions (trnK-UUU/rps16, ndhF/rpl32, rpl32/trnL-UAG, and ycf1) were detected among the five analyzed Acer species. Those hotspot regions may be useful molecular markers and contribute to future population genetics studies. The phylogenetic analysis demonstrated that A. ukurunduense is most closely associated with the species of Sect. Palmata. A. ukurunduense and A. pubipetiolatum var. pingpienense diverged in 22.11 Mya. We selected one of the hypervariable regions (trnK-UUU/rps16) to develop a new molecular marker and designed primers and confirmed that the molecular markers could accurately discriminate five Acer species through Sanger sequencing. By sequencing the cp genome of A. ukurunduense and comparing it with the relative species of Acer, we can effectively address the phylogenetic problems of Acer at the species level and provide insights into future research on population genetics and genetic diversity.

Tree functional traits, forest biomass, and tree species diversity interact with site properties to drive forest soil carbon

Forests constitute important ecosystems in the global carbon cycle. However, how trees and environmental conditions interact to determine the amount of organic carbon stored in forest soils is a hotly debated subject. In particular, how tree species influence soil organic carbon (SOC) remains unclear. Based on a global compilation of data, we show that functional traits of trees and forest standing biomass explain half of the local variability in forest SOC. The effects of functional traits on SOC depended on the climatic and soil conditions with the strongest effect observed under boreal climate and on acidic, poor, coarse-textured soils. Mixing tree species in forests also favours the storage of SOC, provided that a biomass over-yielding occurs in mixed forests. We propose that the forest carbon sink can be optimised by (i) increasing standing biomass, (ii) increasing forest species richness, and (iii) choosing forest composition based on tree functional traits according to the local conditions.

Forests constitute important ecosystems in the global carbon cycle. This study investigates how tree species influence soil organic carbon using a global dataset, showing the importance of tree functional traits and forest standing biomass to optimise forest carbon sink.

Genetic variation of the relict maple Acer miyabei: uncovering its history of disjunct occurrence and the role of mountain refugia in shaping genetic diversity

PREMISE

Relict species provide valuable insights into the origin and formation of extant vegetation. Here, we aimed to elucidate the genetic structure and diversity of a riparian relic, Acer miyabei, in Japan. Once widely distributed, it now occurs in three isolated regions. The most northern regional group is located at low elevation on Hokkaido Island, whereas the southernmost group in central Honshu Island is at high elevation in a mountainous landscape. This contrastive distribution enables us to examine the effects of climate oscillations on genetic diversity in relation to topographic variation.

METHODS

We collected 604 individuals of A. miyabei from 43 sites. Their genetic structure and diversity were analyzed using 12 microsatellite markers and cpDNA sequences.

RESULTS

According to structure analyses, ∆K was lowest at K = 2; the clustering essentially separated many of the individuals in the most northern regional group from the others. In contrast, the two southern groups were not clearly differentiated from each other, despite their geographic discontinuity. The proportion of private alleles was high in populations from the mountain terrain in the southern group although the number of extant populations is limited.

CONCLUSIONS

Genetic clustering of A. miyabei is not perfectly congruent with the current patterns of geographic distribution. We infer that disjunction of the two southern groups occurred more recently than that between these groups and the northern group. The mountainous landscape in the most southern region likely provided multiple refugia and contributed to the retention of distinctive genetic variation.

Insights Into Comparative Analyses and Phylogenomic Implications of Acer (Sapindaceae) Inferred From Complete Chloroplast Genomes

Acer L. (Sapindaceae) is one of the most diverse and widespread plant genera in the Northern Hemisphere. It comprises 124-156 recognized species, with approximately half being native to Asia. Owing to its numerous morphological features and hybridization, this genus is taxonomically and phylogenetically ranked as one of the most challenging plant taxa. Here, we report the complete chloroplast genome sequences of five Acer species and compare them with those of 43 published Acer species. The chloroplast genomes were 149,103-158,458 bp in length. We conducted a sliding window analysis to find three relatively highly variable regions (psbN-rps14, rpl32-trnL, and ycf1) with a high potential for developing practical genetic markers. A total of 76-103 SSR loci were identified in 48 Acer species. The positive selection analysis of Acer species chloroplast genes showed that two genes (psaI and psbK) were positively selected, implying that light level is a selection pressure for Acer species. Using Bayes empirical Bayes methods, we also identified that 20 cp gene sites have undergone positive selection, which might result from adaptation to specific ecological niches. In phylogenetic analysis, we have reconfirmed that Acer pictum subsp. mono and A. truncatum as sister species. Our results strongly support the sister relationships between sections Platanoidea and Macrantha and between sections Trifoliata and Pentaphylla. Moreover, series Glabra and Arguta are proposed to promote to the section level. The chloroplast genomic resources provided in this study assist taxonomic and phylogenomic resolution within Acer and the Sapindaceae family.

Phylogenetic relationships and molecular evolution of woody forest tree family Aceraceae based on plastid phylogenomics and nuclear gene variations

The forest tree family Aceraceae is widespread in the northern hemisphere and it has ecological and economic importance. However, the phylogenetic relationships and classifications within the family are still controversial due to transitional intraspecific morphological characteristics and introgression hybridization among species. In this study, we determined the evolutionary relationships and molecular evolution of Aceraceae based on plastid phylogenomics and two nuclear gene variations. Phylogenetic analysis based on the plastid genomes suggested that Aceraceae species can be divided into two larger sub-clades corresponding to the two genera Acer and Dipteronia. Conjoint analysis of the plastid and nuclear gene sequences supported the classification with two genera in the family. Molecular dating showed that the two genera diverged 60.2 million years ago, which is generally consistently with previously reported results. Divergence hotspots and positively selected genes identified in the plastid genomes could be useful genetic resources in Aceraceae.

Evidence of Constrained Divergence and Conservatism in Climatic Niches of the Temperate Maples (Acer L.)

Research highlights: The availability of global distribution data and new, fossil-calibrated phylogenies has made it possible to compare the climatic niches of the temperate maple (Acer L.) taxa and assess phylogenetic and continental patterns in niche overlap. Background and Objectives: The maples have radiated from East Asia into two other temperate continental bioregions, North America and Eurasia (Europe and West Asia), over a roughly 60-million-year period. During this time, the Earth’s climate experienced pronounced cooling and drying, culminating in cyclic periods of widespread temperate glaciation in the Pliocene to Pleistocene. The objective of this study is to use newly available data to model the climatic niches of 60% of the temperate maples and assess patterns of niche divergence, constraint, and conservatism in the genus’s radiation out of East Asia. Materials and Methods: I assembled global occurrence data and associated climatic information for 71 maple taxa, including all species endemic to temperate North America and Eurasia and their closely related East Asian congeners. I constructed Maxent niche models for all taxa and compared the climatic niches of 184 taxa pairs and assessed phylogenetic signal in key niche axes for each taxon and in niche overlap at the continental and global scale. Results: Maxent models define a fundamental climatic niche for temperate maples and suggest that drought-intolerant taxa have been lost from the Eurasian maple flora, with little continental difference in temperature optima or breadth. Niche axes and niche overlap show minimal evidence of phylogenetic signal, suggesting adaptive evolution. Pairwise niche comparisons reveal infrequent niche overlap continentally and globally, even among sister pairs, with few taxa pairs sharing ecological niche space, providing evidence for constrained divergence within the genus’s fundamental climatic niche. Evidence of niche conservatism is limited to three somewhat geographically isolated regions of high maple diversity (western North America, the Caucasus, and Japan). Conclusions: Over 60 million years of hemispheric radiation on a cooling and drying planet, the maple genus experienced divergent, though constrained, climatic niche evolution. High climatic niche diversity across spatial and phylogenetic scales along with very limited niche overlap or conservatism suggests that the radiation of the genus has largely been one of adaptive diversification.

The tree of life describes a tripartite cellular world

The canonical view of a 3-domain (3D) tree of life was recently challenged by the discovery of Asgardarchaeota encoding eukaryote signature proteins (ESPs), which were treated as missing links of a 2-domain (2D) tree. Here we revisit the debate. We discuss methodological limitations of building trees with alignment-dependent approaches, which often fail to satisfactorily address the problem of ''gaps.'' In addition, most phylogenies are reconstructed unrooted, neglecting the power of direct rooting methods. Alignment-free methodologies lift most difficulties but require employing realistic evolutionary models. We argue that the discoveries of Asgards and ESPs, by themselves, do not rule out the 3D tree, which is strongly supported by comparative and evolutionary genomic analyses and vast genomic and biochemical superkingdom distinctions. Given uncertainties of retrodiction and interpretation difficulties, we conclude that the 3D view has not been falsified but instead has been strengthened by genomic analyses. In turn, the objections to the 2D model have not been lifted. The debate remains open. Also see the video abstract here: https://youtu.be/-6TBN0bubI8.

Genome-wide supermatrix analyses of maples (Acer, Sapindaceae) reveal recurring inter-continental migration, mass extinction, and rapid lineage divergence

Acer (Sapindaceae) is an exceptional study system for understanding the evolutionary history, divergence, and assembly of broad-leaved deciduous forests at higher latitudes. Maples stand out due to their high diversity, disjunct distribution pattern across the northern continents, and rich fossil record dating back to the Paleocene. Using a genome-wide supermatrix combining plastomes and nuclear sequences (~585 kb) for 110 Acer taxa, we built a robust time-calibrated hypothesis investigating the evolution of maples, inferring ancestral ranges, reconstructing diversification rates over time, and exploring the impact of mass-extinction on lineage accumulation. Contrary to fossil evidence, our results indicate Acer first originated in the (north)eastern Palearctic region, which acted as a source for recurring outward migration. Warm conditions favored rapid Eocene-onward divergence, but ranges and diversity declined extensively as a result of the Plio-Pleistocene glacial cycles. These signals in genome-wide sequence data corroborate paleobotanical evidence for other major woody north-temperate groups, highlighting the significant (disparate) impact of climatic changes on the evolution, composition, and distribution of the vegetation in the northern hemisphere.

Historical biogeography of Acer L. (Sapindaceae): genetic evidence for Out-of-Asia hypothesis with multiple dispersals to North America and Europe

Biogeography is the study of where, when, and how modern species evolved and diversified. Acer L. (maple) is one of the most diverse and widespread genera in the Northern Hemisphere. It comprises 124–156 species in the world, approximately 80% species of Acer are native in Asia. The current diversity center of Acer is not congruent with the distribution of the oldest fossils of the genus. Therefore, we herein used 84 species and subspecies to reconstruct the phylogeny and investigate the biogeographic history of Acer using nuclear ITS and three cpDNA fragments (psbA-trnH spacer, rpl16 intron, and trnL-trnF spacer) with maximum likelihood, maximum parsimony, and Bayesian inference methods. The analyses showed that the current diversity center and the origin center of Acer is Asia. Additionally, the North American and Euro-Mediterranean species originated from multiple sources from Asia via the North Atlantic Land Bridge and the Bering Land Bridge, and intercontinental migration has mainly occurred since the Miocene. This study not only provides a novel insight of the origin and dispersal routes of Acer but also exemplifies how past climatic changes affect the diversification-rates of Northern Hemisphere forest trees.

Evolutionary history of endangered and relict tree species Dipteronia sinensis in response to geological and climatic events in the Qinling Mountains and adjacent areas

Geological and climatic events are considered to profoundly affect the evolution and lineage divergence of plant species. However, the evolutionary histories of tree species that have responded to past geological and climate oscillations in central China's mountainous areas remain mostly unknown. In this study, we assessed the evolutionary history of the endangered and relict tree species Dipteronia sinensis in the Qinling Mountains (QM) and adjacent areas in East Asia based on variations in the complete chloroplast genomes (cpDNA) and reduced-genomic scale single nucleotide polymorphisms (SNPs). Population structure and phylogenetic analysis based on the cpDNA variations suggested that D. sinensis could be divided into two intraspecific genetic lineages in the eastern and western sides of the QM (EQM and WQM, respectively) in East Asia. Molecular dating suggested that the intraspecific divergence of D. sinensis occurred approximately 39.2 million years ago during the later Paleogene. It was significantly correlated with the orogeny of the QM, where the formation of this significant geographic barrier in the region may have led to the divergence of independent lineages. Bayesian clustering and demographic analysis showed that intraspecific gene flow was restricted between the EQM and WQM lineages. Isolation-with-migration analysis indicated that the two genetic lineages experienced significant demographic expansions after the Pleistocene ice ages. However, the genetic admixture was determined in some populations between the two lineages by the large scale of SNP variations due to DNA incompatibility, the large significant population size, and rapid gene flow of nuclear DNA markers. Our results suggest that two different conservation and management units should be constructed for D. sinensis in the EQM and WQM areas. These findings provide novel insights into the unprecedented effects of tectonic changes and climatic oscillations on lineage divergence and plant population evolution in the QM and adjacent areas in East Asia.

Plastome comparative genomics in maples resolves the infrageneric backbone relationships

Maples (Acer) are among the most diverse and ecologically important tree genera of the north-temperate forests. They include species highly valued as ornamentals and as a source of timber and sugar products. Previous phylogenetic studies employing plastid markers have not provided sufficient resolution, particularly at deeper nodes, leaving the backbone of the maple plastid tree essentially unresolved. We provide the plastid genome sequences of 16 species of maples spanning the sectional diversity of the genus and explore the utility of these sequences as a source of information for genetic and phylogenetic studies in this group. We analyzed the distribution of different types of repeated sequences and the pattern of codon usage, and identified variable regions across the plastome. Maximum likelihood and Bayesian analyses using two partitioning strategies were performed with these and previously published sequences. The plastomes ranged in size from 155,212 to 157,023 bp and had structure and gene content except for Acer palmatum (sect. Palmata), which had longer inverted repeats and an additional copy of the rps19 gene. Two genes, rps2 and rpl22, were found to be truncated at different positions and might be non-functional in several species. Most dispersed repeats, SSRs, and overall variation were detected in the non-coding sequences of the LSC and SSC regions. Fifteen loci, most of which have not been used before in the genus, were identified as the most variable and potentially useful as molecular markers for barcoding and genetic studies. Both ML and Bayesian analyses produced similar results irrespective of the partitioning strategy used. The plastome-based tree largely supported the topology inferred in previous studies using cp markers while providing resolution to the backbone relationships but was highly incongruous with a recently published nuclear tree presenting an opportunity for further research to investigate the causes of discordance, and particularly the role of hybridization in the diversification of the genus. Plastome sequences are valuable tools to resolve deep-level relationships within Acer. The variable loci and SSRs identified in this study will facilitate the development of markers for ecological and evolutionary studies in the genus. This study underscores the potential of plastid genome sequences to improve our understanding of the evolution of maples.

Involucre fossils of Carpinus, a northern temperate element, from the Miocene of China and the evolution of its species diversity in East Asia

East Asia has long been recognized as a major center for temperate woody plants diversity. Although several theories have been proposed to explain how the diversity of these temperate elements accumulated in the region, the specific process remains unclear. Here we describe six species of Carpinus, a typical northern hemisphere temperate woody plant, from the early Miocene of the Maguan Basin, southwestern China, southern East Asia. This constitutes the southernmost, and the earliest occurrence that shows a high species diversity of the genus. Together with other Carpinus fossil records from East Asia, we show that the genus had achieved a high diversity in East Asia at least by the middle Miocene. Of the six species here described, three have become extinct, indicating that the genus has experienced apparent species loss during its evolutionary history in East Asia. In contrast, the remaining three species closely resemble extant species, raising the possibility that these species may have persisted in East Asia at least since the early Miocene. These findings indicate that the accumulation of species diversity of Carpinus in East Asia is a complex process involving extinction, persistence, and possible subsequent speciation.

Freezing and water availability structure the evolutionary diversity of trees across the Americas

The historical course of evolutionary diversification shapes the current distribution of biodiversity, but the main forces constraining diversification are still a subject of debate. We unveil the evolutionary structure of tree species assemblages across the Americas to assess whether an inability to move or an inability to evolve is the predominant constraint in plant diversification and biogeography. We find a fundamental divide in tree lineage composition between tropical and extratropical environments, defined by the absence versus presence of freezing temperatures. Within the Neotropics, we uncover a further evolutionary split between moist and dry forests. Our results demonstrate that American tree lineages tend to retain their ancestral environmental relationships and that phylogenetic niche conservatism is the primary force structuring the distribution of tree biodiversity. Our study establishes the pervasive importance of niche conservatism to community assembly even at intercontinental scales.

Comparative Plastome Analyses and Phylogenetic Applications of the Acer Section Platanoidea

The Acer L. (Sapindaceae) is one of the most diverse and widespread genera in the Northern Hemisphere. Section Platanoidea harbours high genetic and morphological diversity and shows the phylogenetic conflict between A. catalpifolium and A. amplum. Chloroplast (cp) genome sequencing is efficient for the enhancement of the understanding of phylogenetic relationships and taxonomic revision. Here, we report complete cp genomes of five species of Acer sect. Platanoidea. The length of Acer sect. Platanoidea cp genomes ranged from 156,262 bp to 157,349 bp and detected the structural variation in the inverted repeats (IRs) boundaries. By conducting a sliding window analysis, we found that five relatively high variable regions (trnH-psbA, psbN-trnD, psaA-ycf3, petA-psbJ and ndhA intron) had a high potential for developing effective genetic markers. Moreover, with an addition of eight plastomes collected from GenBank, we displayed a robust phylogenetic tree of the Acer sect. Platanoidea, with high resolutions for nearly all identified nodes, suggests a promising opportunity to resolve infrasectional relationships of the most species-rich section Platanoidea of Acer.

Combined LM and SEM study of the middle Miocene (Sarmatian) palynoflora from the Lavanttal Basin, Austria: Part V. Magnoliophyta 3 - Myrtales to Ericales

The continued investigation of the middle Miocene palynoflora from the Lavanttal Basin reveals numerous additional angiosperm taxa. The Myrtales to Ericales pollen record documented here comprises 46 different taxa belonging to Onagraceae (Ludwigia), Ericaceae (Craigia, Reevesia, Tilia), Anacardiaceae (Pistacia), Rutaceae (Zanthoxylum), Sapindaceae (Acer), Santalaceae (Arceuthobium), Amaranthaceae, Caryophyllaceae, Polygonaceae (Persicaria, Rumex), Cornaceae (Alangium, Cornus, Nyssa), Ebenaceae (Diospyros), Ericaceae (Andromeda, Arbutus, Empetrum, Erica), Sapotaceae (Pouteria, Sideroxylon), Styracaceae (Rehderodendron) and Symplocaceae (Symplocos). Köppen signatures of potential modern analogues of the additional fossil woody elements confirm the hypothesis of a subtropical (Cfa, Cwa) climate at lower elevations and subsequent transition into a temperate climate with altitudinal succession (Cfa → Cfb/Dfa → Dfb; Cwa → Cwb → Dwb-climate). The fossil plants represent different vegetation units, from wetland lowlands to well-drained montane forests. Many of the fossil taxa have potential modern analogues that can be classified as nemoral and/or meridio-nemoral and/or semihumid-meridional vegetation elements. New is the recognition of oreotropical elements, which are direct indicators for a substantial altitudinal gradient.

Combined LM and SEM study of the middle Miocene (Sarmatian) palynoflora from the Lavanttal Basin, Austria: Part V. Magnoliophyta 3 - Myrtales to Ericales

The continued investigation of the middle Miocene palynoflora from the Lavanttal Basin reveals numerous additional angiosperm taxa. The Myrtales to Ericales pollen record documented here comprises 46 different taxa belonging to Onagraceae (Ludwigia), Ericaceae (Craigia, Reevesia, Tilia), Anacardiaceae (Pistacia), Rutaceae (Zanthoxylum), Sapindaceae (Acer), Santalaceae (Arceuthobium), Amaranthaceae, Caryophyllaceae, Polygonaceae (Persicaria, Rumex), Cornaceae (Alangium, Cornus, Nyssa), Ebenaceae (Diospyros), Ericaceae (Andromeda, Arbutus, Empetrum, Erica), Sapotaceae (Pouteria, Sideroxylon), Styracaceae (Rehderodendron) and Symplocaceae (Symplocos). Köppen signatures of potential modern analogues of the additional fossil woody elements confirm the hypothesis of a subtropical (Cfa, Cwa) climate at lower elevations and subsequent transition into a temperate climate with altitudinal succession (Cfa → Cfb/Dfa → Dfb; Cwa → Cwb → Dwb-climate). The fossil plants represent different vegetation units, from wetland lowlands to well-drained montane forests. Many of the fossil taxa have potential modern analogues that can be classified as nemoral and/or meridio-nemoral and/or semihumid-meridional vegetation elements. New is the recognition of oreotropical elements, which are direct indicators for a substantial altitudinal gradient.

Combined LM and SEM study of the middle Miocene (Sarmatian) palynoflora from the Lavanttal Basin, Austria: Part V. Magnoliophyta 3 - Myrtales to Ericales

The continued investigation of the middle Miocene palynoflora from the Lavanttal Basin reveals numerous additional angiosperm taxa. The Myrtales to Ericales pollen record documented here comprises 46 different taxa belonging to Onagraceae (Ludwigia), Ericaceae (Craigia, Reevesia, Tilia), Anacardiaceae (Pistacia), Rutaceae (Zanthoxylum), Sapindaceae (Acer), Santalaceae (Arceuthobium), Amaranthaceae, Caryophyllaceae, Polygonaceae (Persicaria, Rumex), Cornaceae (Alangium, Cornus, Nyssa), Ebenaceae (Diospyros), Ericaceae (Andromeda, Arbutus, Empetrum, Erica), Sapotaceae (Pouteria, Sideroxylon), Styracaceae (Rehderodendron) and Symplocaceae (Symplocos). Köppen signatures of potential modern analogues of the additional fossil woody elements confirm the hypothesis of a subtropical (Cfa, Cwa) climate at lower elevations and subsequent transition into a temperate climate with altitudinal succession (Cfa → Cfb/Dfa → Dfb; Cwa → Cwb → Dwb-climate). The fossil plants represent different vegetation units, from wetland lowlands to well-drained montane forests. Many of the fossil taxa have potential modern analogues that can be classified as nemoral and/or meridio-nemoral and/or semihumid-meridional vegetation elements. New is the recognition of oreotropical elements, which are direct indicators for a substantial altitudinal gradient.

De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan Province, China

BACKGROUND

Acer yangbiense is a newly described critically endangered endemic maple tree confined to Yangbi County in Yunnan Province in Southwest China. It was included in a programme for rescuing the most threatened species in China, focusing on "plant species with extremely small populations (PSESP)".

FINDINGS

We generated 64, 94, and 110 Gb of raw DNA sequences and obtained a chromosome-level genome assembly of A. yangbiense through a combination of Pacific Biosciences Single-molecule Real-time, Illumina HiSeq X, and Hi-C mapping, respectively. The final genome assembly is ∼666 Mb, with 13 chromosomes covering ∼97% of the genome and scaffold N50 sizes of 45 Mb. Further, BUSCO analysis recovered 95.5% complete BUSCO genes. The total number of repetitive elements account for 68.0% of the A. yangbiense genome. Genome annotation generated 28,320 protein-coding genes, assisted by a combination of prediction and transcriptome sequencing. In addition, a nearly 1:1 orthology ratio of dot plots of longer syntenic blocks revealed a similar evolutionary history between A. yangbiense and grape, indicating that the genome has not undergone a whole-genome duplication event after the core eudicot common hexaploidization.

CONCLUSION

Here, we report a high-quality de novo genome assembly of A. yangbiense, the first genome for the genus Acer and the family Aceraceae. This will provide fundamental conservation genomics resources, as well as representing a new high-quality reference genome for the economically important Acer lineage and the wider order of Sapindales.

Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions

Phylogenetic methods unearth evolutionary history when supported by three starting points of reason: (1) the continuity axiom begs the existence of a "model" of evolutionary change, (2) the singularity axiom defines the historical ground plan (phylogeny) in which biological entities (taxa) evolve, and (3) the memory axiom demands identification of biological attributes (characters) with historical information. Axiom consequences are interlinked, making the retrodiction enterprise an endeavor of reciprocal fulfillment. In particular, establishing direction of evolutionary change (character polarization) roots phylogenies and enables testing the existence of historical memory (homology). Unfortunately, rooting phylogenies, especially the "tree of life," generally follow narratives instead of integrating empirical and theoretical knowledge of retrodictive exploration. This stems mostly from a focus on molecular sequence analysis and uncertainties about rooting methods. Here, we review available rooting criteria, highlighting the need to minimize both ad hoc and auxiliary assumptions, especially argumentative ad hocness. We show that while the outgroup comparison method has been widely adopted, the generality criterion of nesting and additive phylogenetic change embodied in Weston rule offers the most powerful rooting approach. We also propose a change of focus, from phylogenies that describe the evolution of biological systems to those that describe the evolution of parts of those systems. This weakens violation of character independence, helps formalize the generality criterion of rooting, and provides new ways to study the problem of evolution.

On merging Acer sections Rubra and Hyptiocarpa: Molecular and morphological evidence

In this study, we expanded Acer sect. Rubra Pax to include A. sect. Hyptiocarpa Fang. Traditionally, section Rubra comprises two iconic species, Acer rubrum Linnaeus (red maple) and A. saccharinum Linnaeus (silver maple), of eastern North American forests as well as the rare Japanese montane species, A. pycnanthum K. Koch. Section Hyptiocarpa consists of A. laurinum Hasskarl and A. pinnatinervium Merrill, which occur in subtropical and tropical regions of southwestern China to southeast Asia. Here, we confirm prior phylogenetic results showing the close relationship between sects. Rubra and Hyptiocarpa, and we use scanning electron microscopy to demonstrate that leaves of species within these sections have similar arrangements of cuticular waxes, which account for the silvery color of their abaxial surfaces. We describe that the sections also share labile sex expression; inflorescences that range from compound racemose thyrses, to racemes or umbels and that may have undergone evolutionary reduction; and several features of their fruits, such as seed locules without keels, basal portion of wings straight, acute attachment angle between mericarps, and production of some mericarps that are seedless and partially developed at maturity. Our expansion of sect. Rubra to include sect. Hyptiocarpa better elucidates the biogeographic and evolutionary history of these species. Additionally, we show that A. laurinum and A. pinnatinervium have intergrading morphology and are probably synonymous, but we note that further studies are required to conclude their taxonomic status.

Eocene Loranthaceae pollen pushes back divergence ages for major splits in the family

BACKGROUND

We revisit the palaeopalynological record of Loranthaceae, using pollen ornamentation to discriminate lineages and to test molecular dating estimates for the diversification of major lineages.

METHODS

Fossil Loranthaceae pollen from the Eocene and Oligocene are analysed and documented using scanning-electron microscopy. These fossils were associated with molecular-defined clades and used as minimum age constraints for Bayesian node dating using different topological scenarios.

RESULTS

The fossil Loranthaceae pollen document the presence of at least one extant root-parasitic lineage (Nuytsieae) and two currently aerial parasitic lineages (Psittacanthinae and Loranthinae) by the end of the Eocene in the Northern Hemisphere. Phases of increased lineage diversification (late Eocene, middle Miocene) coincide with global warm phases.

DISCUSSION

With the generation of molecular data becoming easier and less expensive every day, neontological research should re-focus on conserved morphologies that can be traced through the fossil record. The pollen, representing the male gametophytic generation of plants and often a taxonomic indicator, can be such a tracer. Analogously, palaeontological research should put more effort into diagnosing Cenozoic fossils with the aim of including them into modern systematic frameworks.

Population structure and historical demography of Dipteronia dyeriana (Sapindaceae), an extremely narrow palaeoendemic plant from China: implications for conservation in a biodiversity hot spot

Inferring past demography is a central question in evolutionary and conservation biology. It is, however, sometimes challenging to disentangle their roles of contemporary versus historical processes in shaping the current patterns of genetic variation in endangered species. In this study, we used both chloroplast microsatellite (cpSSR) loci and nuclear microsatellite (nSSR) loci to assess the levels of genetic differentiation, genetic effective population size, contemporary/historical levels of gene flow and demographic history for five populations sampled across the range of Dipteronia dyeriana, an endangered palaeoendemism from Southwestern China. We found that D. dyeriana had a mixed pattern of moderate genetic diversity and high inbreeding. Bayesian clustering divided D. dyeriana populations into two nSSR genetic clusters. Coalescent-based approximate Bayesian computation analyses suggest the western and eastern groups of D. dyeriana likely persisted in a long-term refuge in Southern China since the beginning of the last glacial period, whereas increasingly colder and arid climates at the onset of the last glacial maximum might have fostered the fragmentation of D. dyeriana within refugia. Following their divergence, the western group kept relatively stable effective population size, whereas the eastern group had experienced 500-fold population expansion during the Holocene. Although clear loss of genetic diversity by human activities was not suggested, recent habitat fragmentation has led to a reduction of population connectivity and increased genetic differentiation by ongoing genetic drift in isolated populations, possibly owing to decreased population size in recent dozen years. Finally, we discussed the implications of these results on conservation policies.

Evolutionary histories determine DNA barcoding success in vascular plants: seven case studies using intraspecific broad sampling of closely related species

Background

Four plastid regions, rpoB, rpoC1, matK, and trnH-psbA, have been recommended as DNA barcodes for plants. Their success in delimiting species boundaries depends on the existence of a clear-cut difference between inter- and intraspecific variability. We tested the ability of these regions to discriminate among closely related species in seven genera of flowering plants with different generation times (trees, perennials, and annuals). To ensure a maximum coverage of intraspecific diversity, and therefore to better evaluate the resolution power of each barcode, we applied a population genetics approach by sampling three to 45 individuals per species over a wide geographical range.

Results

All possible combinations between loci were analysed, which showed that using more than one locus does not always improve the resolution power. The trnH-psbA locus was most effective at discriminating among closely related species (Acer, Lonicera, Geranium, and Veronica), singly or in combination. For Salix, Adenostyles, and Gentiana, the best results were obtained with the combination of matK, rpoB, and trnH-psbA. No barcoding gap was found within six genera analysed, excepting Lonicera. This is due to shared polymorphisms among species, combined with very divergent sequences within species. These genetic patterns reflect incomplete lineage sorting and hybridization events followed by chloroplast capture.

Conclusions

Our results strongly suggest that adding trnH-psbA to the two obligate DNA barcodes proposed by the CBOL plant-working group (matK and rbcL) should be mandatory for closely related species. In our sampling, generation time had no influence on DNA barcoding success, as the best and worst identification successes were found for the two tree genera (Acer, 64 % success and Salix, 86 % failure). Evolutionary histories are the main factor influencing DNA barcoding success in the studied genera.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0678-0) contains supplementary material, which is available to authorized users.

Large scale patterns of genetic variation and differentiation in sugar maple from tropical Central America to temperate North America

Background

Geological events in the latter Cenozoic have influenced the distribution, abundance and genetic structure of tree populations in temperate and tropical North America. The biogeographical history of temperate vegetation that spans large ranges of latitude is complex, involving multiple latitudinal shifts that might have occurred via different migration routes. We determined the regional structuring of genetic variation of sugar maple (Acer saccharum subsp. saccharum) and its only subspecies in tropical America (Acer saccharum subsp. skutchii) using nuclear and chloroplast data. The studied populations span a geographic range from Maine, USA (46°N), to El Progreso, Guatemala (15°N). We examined genetic subdivisions, explored the locations of ancestral haplotypes, analyzed genetic data to explore the presence of a single or multiple glacial refugia, and tested whether genetic lineages are temporally consistent with a Pleistocene or older divergence.

Results

Nuclear and chloroplast data indicated that populations in midwestern USA and western Mexico were highly differentiated from populations in the rest of the sites. The time of the most recent common ancestor of the western Mexico haplotype lineage was dated to the Pliocene (5.9 Ma, 95 % HPD: 4.3–7.3 Ma). Splits during the Pleistocene separated the rest of the phylogroups. The most frequent and widespread haplotype occurred in half of the sites (Guatemala, eastern Mexico, southeastern USA, and Ohio). Our data also suggested that multiple Pleistocene refugia (tropics-southeastern USA, midwestern, and northeastern USA), but not western Mexico (Jalisco), contributed to post-glacial northward expansion of ranges. Current southern Mexican and Guatemalan populations have reduced population sizes, genetic bottlenecks and tend toward homozygosity, as indicated using nuclear and chloroplast markers.

Conclusions

The divergence of western Mexican populations from the rest of the sugar maples likely resulted from orographic and volcanic barriers to gene flow. Past connectivity among populations in the southeastern USA and eastern Mexico and Guatemala possible occurred through gene flow during the Pleistocene. The time to the most common ancestor values revealed that populations from the Midwest and Northeast USA represented different haplotype lineages, indicating major divergence of haplotypes lineages before the Last Glacial Maximum and suggesting the existence of multiple glacial refugia.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0518-7) contains supplementary material, which is available to authorized users.

Biogeographic analysis of the woody plants of the Southern Appalachians: Implications for the origins of a regional flora

PREMISE OF THE STUDY

We investigated the origins of 252 Southern Appalachian woody species representing 158 clades to analyze larger patterns of biogeographic connectivity around the northern hemisphere. We tested biogeographic hypotheses regarding the timing of species disjunctions to eastern Asia and among areas of North America.

METHODS

We delimited species into biogeographically informative clades, compiled sister-area data, and generated graphic representations of area connections across clades. We calculated taxon diversity within clades and plotted divergence times.

KEY RESULTS

Of the total taxon diversity, 45% were distributed among 25 North American endemic clades. Sister taxa within eastern North America and eastern Asia were proportionally equal in frequency, accounting for over 50% of the sister-area connections. At increasing phylogenetic depth, connections to the Old World dominated. Divergence times for 65 clades with intercontinental disjunctions were continuous, whereas 11 intracontinental disjunctions to western North America and nine to eastern Mexico were temporally congruent.

CONCLUSIONS

Over one third of the clades have likely undergone speciation within the region of eastern North America. The biogeographic pattern for the region is asymmetric, consisting of mostly mixed-aged, low-diversity clades connecting to the Old World, and a minority of New World clades. Divergence time data suggest that climate change in the Late Miocene to Early Pliocene generated disjunct patterns within North America. Continuous splitting times during the last 45 million years support the hypothesis that widespread distributions formed repeatedly during favorable periods, with serial cooling trends producing pseudocongruent area disjunctions between eastern North America and eastern Asia.

How tree species fill geographic and ecological space in eastern North America

BACKGROUND AND AIMS

Ecologists broadly accept that the number of species present within a region balances regional processes of immigration and speciation against competitive and other interactions between populations that limit distribution and constrain diversity. Although ecological theory has, for a long time, addressed the premise that ecological space can be filled to 'capacity' with species, only with the availability of time-calibrated phylogenies has it been possible to test the hypothesis that diversification slows as the number of species in a region increases. Focusing on the deciduous trees of eastern North America, this study tested predictions from competition theory concerning the distribution and abundance of species.

METHODS

Local assemblages of trees tabulated in a previous study published in 1950 were analysed. Assemblages were ordinated with respect to species composition by non-metric multidimensional scaling (NMS). Distributions of trees were analysed by taxonomically nested analysis of variance, discriminant analysis based on NMS scores, and canonical correlation analysis of NMS scores and Bioclim climate variables.

KEY RESULTS

Most of the variance in species abundance and distribution was concentrated among closely related (i.e. congeneric) species, indicating evolutionary lability. Species distribution and abundance were unrelated to the number of close relatives, suggesting that competitive effects are diffuse. Distances between pairs of congeneric species in NMS space did not differ significantly from distances between more distantly related species, in contrast to the predictions of both competitive habitat partitioning and ecological sorting of species.

CONCLUSIONS

Eastern deciduous forests of North America do not appear to be saturated with species. The distributions and abundances of individual species provide little evidence of being shaped by competition from related (i.e. ecologically similar) species and, by inference, that diversification is constrained by interspecific competition.

Clock Rooting Further Demonstrates that Guinea 2014 EBOV is a Member of the Zaïre Lineage

While initial phylogenetic analyses concluded to Guinea 2014 EBOV falling outside the Zaïre lineage (ZEBOV), a recent re-analysis of the same dataset by Dudas and Rambaut (2014) suggested that Guinea 2014 EBOV actually is ZEBOV. Under the same hypothesis as used by these authors (the molecular clock hypothesis), we reinforce their conclusion by providing a statistical assessment of the location of the root of the Zaïre lineage. Our analysis unambiguously supports Guinea 2014 EBOV as a member of the Zaïre lineage. In addition, we also show that some uncertainty exists so as to the location of the root of the genus Ebolavirus. We release the software we used for these re-analyses. RootAnnotator allows for the easy determination of branch root posterior probability from any posterior sample of clocked trees and is freely available at http://sourceforge.net/projects/rootannotator/.

The timetable for allopolyploidy in flowering plants

BACKGROUND

Our understanding of the processes and dynamics of allopolyploid speciation, the long-term consequences of ploidal change, and the genetic and chromosomal changes in new emerged allopolyploids has substantially increased during the past few decades. Yet we remain uncertain about the time since lineage divergence when two taxa are capable of spawning such entities. Indeed, the matter has seemed intractable. Knowledge of the window of opportunity for allopolyploid production is very important because it provides temporal insight into a key evolutionary process, and a temporal reference against which other modes of speciation may be measured.

SCOPE

This Viewpoint paper reviews and integrates published information on the crossability of herbaceous species and the fertility of their hybrids in relation to species' divergence times. Despite limitations in methodology and sampling, the estimated times to hybrid sterility are somewhat congruent across disparate lineages. Whereas the waiting time for hybrid sterility is roughly 4-5 million years, the waiting time for cross-incompatibility is roughly 8-10 million years, sometimes considerably more. Strict allopolyploids may be formed in the intervening time window. The progenitors of several allopolyploids diverged between 4 and 6 million years before allopolyploid synthesis, as expected. This is the first study to propose a general temporal framework for strict allopolyploidy. This Viewpoint paper hopefully will stimulate interest in studying the tempo of speciation and the tempo of reproductive isolation in general.

A total-evidence approach to dating with fossils, applied to the early radiation of the hymenoptera

Phylogenies are usually dated by calibrating interior nodes against the fossil record. This relies on indirect methods that, in the worst case, misrepresent the fossil information. Here, we contrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian total-evidence analysis. As a test case, we focus on the early radiation of the Hymenoptera, mostly documented by poorly preserved impression fossils that are difficult to place phylogenetically. Specifically, we compare node dating using nine calibration points derived from the fossil record with total-evidence dating based on 343 morphological characters scored for 45 fossil (4--20 complete) and 68 extant taxa. In both cases we use molecular data from seven markers (∼5 kb) for the extant taxa. Because it is difficult to model speciation, extinction, sampling, and fossil preservation realistically, we develop a simple uniform prior for clock trees with fossils, and we use relaxed clock models to accommodate rate variation across the tree. Despite considerable uncertainty in the placement of most fossils, we find that they contribute significantly to the estimation of divergence times in the total-evidence analysis. In particular, the posterior distributions on divergence times are less sensitive to prior assumptions and tend to be more precise than in node dating. The total-evidence analysis also shows that four of the seven Hymenoptera calibration points used in node dating are likely to be based on erroneous or doubtful assumptions about the fossil placement. With respect to the early radiation of Hymenoptera, our results suggest that the crown group dates back to the Carboniferous, ∼309 Ma (95% interval: 291--347 Ma), and diversified into major extant lineages much earlier than previously thought, well before the Triassic. [Bayesian inference; fossil dating; morphological evolution; relaxed clock; statistical phylogenetics.].

Multigene phylogenetic analyses to delimit new species in fungal plant pathogens

Supporting the identification of unknown strains or specimens by sequencing a genetic marker commonly used for phylogenetics or DNA barcoding is now standard practice for mycologists and plant pathologists. Does one have a new species when a strain differs by a few base pairs when compared to reference sequences from taxonomically well-characterized species that do not differ morphologically from this new strain? If variation at the intra- and interspecific levels for the locus used for identification is already understood for all the closely related species, it is possible to make a reliable prediction of a new species status, but ultimately this question can only be properly addressed by determining the presence or absence of gene flow among a group of strains of the putative new species and strains of previously delimited species. The Phylogenetic Species Concept (PSC) and its assessment using multigene phylogeny and Genealogical Concordance Phylogenetic Species Recognition (GCPSR) are the basis for this chapter. The theoretical framework and a variety of tools to apply these concepts are explained, to assist in the assessment of whether a species is distinct or new when confronted with some sequence divergence from reference data.

The timing and the mode of evolution of wild grapes (Vitis)

Wild grapes are woody climbers, found mostly in temperate regions of the northern hemisphere, comprising the genus Vitis. Despite its importance, the evolutionary history of Vitis is still contentious. Past studies have led to conflicting hypotheses about the phylogeny, speciation events, and biogeographic history of the genus. Here we investigate the evolutionary history of Vitis using data from four chloroplast spacers (trnH-psbA, trnK-rps16, trnF-nahJ, and rpl32-trnL) and the nuclear gene RPB2-I, and we explore mechanisms that could have shaped the observed distribution of current species. Maximum likelihood and Bayesian analyses provided similar results, strongly supporting the presence of two subgenera and suggesting a species clustering within subgenus Vitis that mainly mirrors the disjunction between the Old and New World. Vitis vinifera subsp. sylvestris was found to be sister to the Asian species while three major clades were found in the American species. A network approach confirmed the main geographic groups and highlighted different chloroplast haplotype patterns between Asian and American species. Molecular dating analysis provided the time boundaries to discuss our results. Our study shows wild grape diversification to be a continuous and complex process that concerned the Tertiary as well as the Quaternary, most likely involving both geographical and climatic forces. Local variations in extent and timing of these forces were discussed based on observed differences between groups. In the context of the Tertiary-Quaternary debate, we provide evidence in favor of the "continuous hypothesis" to explain present diversity. Finally, two directions for future research are highlighted: (i) was the earliest grape American or Asian? and (ii) are all modern grape species real?

Rerooting the evolutionary tree of malaria parasites

Malaria parasites (Plasmodium spp.) have plagued humans for millennia. Less well known are related parasites (Haemosporida), with diverse life cycles and dipteran vectors that infect other vertebrates. Understanding the evolution of parasite life histories, including switches between hosts and vectors, depends on knowledge of evolutionary relationships among parasite lineages. In particular, inferences concerning time of origin and trait evolution require correct placement of the root of the evolutionary tree. Phylogenetic reconstructions of the diversification of malaria parasites from DNA sequences have suffered from uncertainty concerning outgroup taxa, limited taxon sampling, and selection on genes used to assess relationships. As a result, inferred relationships among the Haemosporida have been unstable, and questions concerning evolutionary diversification and host switching remain unanswered. A recent phylogeny placed mammalian malaria parasites, as well as avian/reptilian Plasmodium, in a derived position relative to the avian parasite genera Leucocytozoon and Haemoproteus, implying that the ancestral forms lacked merogony in the blood and that their vectors were non-mosquito dipterans. Bayesian, outgroup-free phylogenetic reconstruction using relaxed molecular clocks with uncorrelated rates instead suggested that mammalian and avian/reptilian Plasmodium parasites, spread by mosquito vectors, are ancestral sister taxa, from which a variety of specialized parasite lineages with modified life histories have evolved.

Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns

Background

The chloroplast-localized ribulose-1, 5-biphosphate carboxylase/oxygenase (Rubisco), the primary enzyme responsible for autotrophy, is instrumental in the continual adaptation of plants to variations in the concentrations of CO₂. The large subunit (LSU) of Rubisco is encoded by the chloroplast rbcL gene. Although adaptive processes have been previously identified at this gene, characterizing the relationships between the mutational dynamics at the protein level may yield clues on the biological meaning of such adaptive processes. The role of such coevolutionary dynamics in the continual fine-tuning of RbcL remains obscure.

Results

We used the timescale and phylogenetic analyses to investigate and search for processes of adaptive evolution in rbcL gene in three gymnosperm families, namely Podocarpaceae, Taxaceae and Cephalotaxaceae. To understand the relationships between regions identified as having evolved under adaptive evolution, we performed coevolutionary analyses using the software CAPS. Importantly, adaptive processes were identified at amino acid sites located on the contact regions among the Rubisco subunits and on the interface between Rubisco and its activase. Adaptive amino acid replacements at these regions may have optimized the holoenzyme activity. This hypothesis was pinpointed by evidence originated from our analysis of coevolution that supported the correlated evolution between Rubisco and its activase. Interestingly, the correlated adaptive processes between both these proteins have paralleled the geological variation history of the concentration of atmospheric CO₂.

Conclusions

The gene rbcL has experienced bursts of adaptations in response to the changing concentration of CO₂ in the atmosphere. These adaptations have emerged as a result of a continuous dynamic of mutations, many of which may have involved innovation of functional Rubisco features. Analysis of the protein structure and the functional implications of such mutations put forward the conclusion that this evolutionary scenario has been possible through a complex interplay between adaptive mutations, often structurally destabilizing, and compensatory mutations. Our results unearth patterns of evolution that have likely optimized the Rubisco activity and uncover mutational dynamics useful in the molecular engineering of enzymatic activities.

Reviewers

This article was reviewed by Prof. Christian Blouin (nominated by Dr W Ford Doolittle), Dr Endre Barta (nominated by Dr Sandor Pongor), and Dr Nicolas Galtier.

Species delimitation under the general lineage concept: an empirical example using wild North American hops (Cannabaceae: Humulus lupulus)

There is an emerging consensus that the intent of most species concepts is to identify evolutionarily distinct lineages. However, the criteria used to identify lineages differ among concepts depending on the perceived importance of various attributes of evolving populations. We have examined five different species criteria to ask whether the three taxonomic varieties of Humulus lupulus (hops) native to North America are distinct lineages. Three criteria (monophyly, absence of genetic intermediates, and diagnosability) focus on evolutionary patterns and two (intrinsic reproductive isolation and niche specialization) consider evolutionary processes. Phylogenetic analysis of amplified fragment length polymorphism (AFLP) data under a relaxed molecular clock, a stochastic Dollo substitution model, and parsimony identified all varieties as monophyletic, thus they satisfy the monophyly criterion for species delimitation. Principal coordinate analysis and a Bayesian assignment procedure revealed deep genetic subdivisions and little admixture between varieties, indicating an absence of genetic intermediates and compliance with the genotypic cluster species criterion. Diagnostic morphological and AFLP characters were found for all varieties, thus they meet the diagnosability criterion. Natural history information suggests that reproductive isolating barriers may have evolved in var. pubescens, potentially qualifying it as a species under a criterion of intrinsic reproductive isolation. Environmental niche modeling showed that the preferred habitat of var. neomexicanus is climatically unique, suggesting niche specialization and thus compliance with an ecological species criterion. Isolation by distance coupled with imperfect sampling can lead to erroneous lineage identification using some species criteria. Compliance with complementary pattern- and process-oriented criteria provides powerful corroboration for a species hypothesis and mitigates the necessity for comprehensive sampling of the entire species range, a practical impossibility in many systems. We hypothesize that var. pubescens maintains its genetic identity, despite substantial niche overlap with var. lupuloides, via the evolution of partial reproductive isolating mechanisms. Variety neomexicanus, conversely, will likely persist as a distinct lineage, regardless of limited gene flow with vars. lupuloides and pubescens because of ecological isolation--adaptation to the unique conditions of the Rocky Mountain cordillera. Thus, we support recognition of vars. neomexicanus and pubescens as species, but delay making a recommendation for var. lupuloides until sampling of genetic variation is complete or a stable biological process can be identified to explain its observed genetic divergence.

A molecular genetic timescale for the diversification of autotrophic stramenopiles (Ochrophyta): substantive underestimation of putative fossil ages

BACKGROUND

Stramenopiles constitute a large and diverse eukaryotic clade that is currently poorly characterized from both phylogenetic and temporal perspectives at deeper taxonomic levels. To better understand this group, and in particular the photosynthetic stramenopiles (Ochrophyta), we analyzed sequence data from 135 taxa representing most major lineages. Our analytical approach utilized several recently developed methods that more realistically model the temporal evolutionary process.

METHODOLOGY/PRINCIPAL FINDINGS

Phylogenetic reconstruction employed a Bayesian joint rate- and pattern-heterogeneity model to reconstruct the evolutionary history of these taxa. Inferred phylogenetic resolution was generally high at all taxonomic levels, sister-class relationships in particular receiving good statistical support. A signal for heterotachy was detected in clustered portions of the tree, although this does not seem to have had a major influence on topological inference. Divergence time estimates, assuming a lognormally-distributed relaxed molecular clock while accommodating topological uncertainty, were broadly congruent over alternative temporal prior distributions. These data suggest that Ochrophyta originated near the Proterozoic-Phanerozoic boundary, diverging from their sister-taxon Oomycota. The evolution of the major ochrophyte lineages appears to have proceeded gradually thereafter, with most lineages coming into existence by ∼200 million years ago.

CONCLUSIONS/SIGNIFICANCE

The evolutionary timescale of the autotrophic stramenopiles reconstructed here is generally older than previously inferred from molecular clocks. However, this more ancient timescale nevertheless casts serious doubt on the taxonomic validity of putative xanthophyte/phaeophyte fossils from the Proterozoic, which predate by as much as a half billion years or more the age suggested by our molecular genetic data. If these fossils truly represent crown stramenopile lineages, then this would imply that molecular rate evolution in this group proceeds in a fashion that is fundamentally incompatible with the relaxed molecular clock model employed here. A more likely scenario is that there is considerable convergent morphological evolution within Heterokonta, and that these fossils have been taxonomically misdiagnosed.

Comparison of methods for rooting phylogenetic trees: a case study using Orcuttieae (Poaceae: Chloridoideae)

DNA sequence data (cpDNA trnL intron and nrDNA ITS1 and ITS2) were analyzed to identify relationships within Orcuttieae, a small tribe of endangered grasses endemic to vernal pools in California and Baja California. The tribe includes three genera: Orcuttia, Tuctoria, and Neostapfia. All three genera carry out C(4) photosynthesis but aquatic taxa of Orcuttia lack Kranz anatomy. The unusual habitat preference of the tribe is coupled with the atypical development of C(4) photosynthesis without Kranz anatomy. Furthermore, the tribe has no known close relatives and has been noted to be phylogenetically isolated within the subfamily Chloridoideae. In this study we examine the problem of inferring the root of the tribe in the absence of an identified outgroup, analyze the phylogenetic relationships of the constituent taxa, and evaluate the evolutionary development of C(4) photosynthesis. We compare four methods for inferring the root of the tree: (1) the outgroup method, (2) midpoint rooting, the imposition of a molecular clock for both (3) maximum likelihood (ML) and (4) Bayesian analysis. We examine the consequences of each method for the inferred phylogenetic relationships. Three of the methods (outgroup rooting and the ML and Bayesian molecular clock analyses) suggest that the root of Orcuttieae is between Neostapfia and the Tuctoria/Orcuttia lineage, while midpoint rooting gives a different root. The Bayesian method additionally provides information about probabilities associated with other possible root locations. Assuming that the true root of Orcuttieae is between Neostapfia and the Tuctoria/Orcuttia lineage, our data indicate Neostapfia and Orcuttia are both monophyletic, while Tuctoria is paraphyletic (with no synapomorphies in either dataset) and forming a grade between the other two genera and needs taxonomic revision. Our data support the hypothesis that Orcuttieae was derived from a terrestrial ancestor and evolved specializations to an aquatic environment, including C(4) photosynthesis without Kranz anatomy.

Conservatism and diversification of plant functional traits: Evolutionary rates versus phylogenetic signal

The concepts of niche conservatism and adaptive radiation have played central roles in the study of evolution and ecological diversification. With respect to phenotypic evolution, the two processes may be seen as opposite ends of a spectrum; however, there is no straightforward method for the comparative analysis of trait evolution that will identify these contrasting scenarios. Analysis of the rate of phenotypic evolution plays an important role in this context and merits increased attention. In this article, independent contrasts are used to estimate rates of evolution for continuous traits under a Brownian motion model of evolution. A unit for the rate of phenotypic diversification is introduced: the felsen, in honor of J. Felsenstein, is defined as an increase of one unit per million years in the variance among sister taxa of ln-transformed trait values. The use of a standardized unit of measurement facilitates comparisons among clades and traits. Rates of diversification of three functional traits (plant height, leaf size, and seed size) were estimated for four to six woody plant clades (Acer, Aesculus, Ceanothus, Arbutoideae, Hawaiian lobeliads, and the silversword alliance) for which calibrated phylogenies were available. For height and leaf size, rates were two to approximately 300 times greater in the Hawaiian silversword alliance than in the other clades considered. These results highlight the value of direct estimates of rates of trait evolution for comparative analysis of adaptive radiation, niche conservatism, and trait diversification.

Bayesian hypothesis testing supports long-distance Pleistocene migrations in a European high mountain plant (Androsace vitaliana, Primulaceae)

Colonization of the south-western European mountain ranges is suggested to have predominantly progressed from the Iberian Peninsula eastwards, but this hypothesis has never been tested in a statistical framework. Here, we test this hypothesis using Androsace vitaliana, a high elevation species with eight mostly allopatric subspecies, which is widely but disjunctly distributed across all major south-western European mountain ranges. To this end, we use plastid and nuclear sequence data as well as fingerprint (amplified fragment length polymorphisms) data and employ Bayesian methods, which allow co-estimation of genealogy and divergence times using explicit demographic models, as well as hypothesis testing via Bayes factors. Irrespective of the ambiguity concerning where A. vitaliana started to diversify -- both the Alps and the mountain ranges of the Iberian Peninsula outside the Pyrenees were possible -- colonization routes were not simply unidirectional, but involved Pleistocene connections between the Alps and mountain ranges of the Iberian Peninsula bypassing the interjacent Pyrenees via long-distance dispersal. In contrast, the species' post-glacial history is shaped by regional gene pool homogenization resulting in the genetic pattern showing good congruence with geographical proximity in agreement with a vicariance model, but only partly supporting current taxonomy.

Episodic evolution and adaptation of chloroplast genomes in ancestral grasses

Background

It has been suggested that the chloroplast genomes of the grass family, Poaceae, have undergone an elevated evolutionary rate compared to most other angiosperms, yet the details of this phenomenon have remained obscure. To know how the rate change occurred during evolution, estimation of the time-scale with reliable calibrations is needed. The recent finding of 65 Ma grass phytoliths in Cretaceous dinosaur coprolites places the diversification of the grasses to the Cretaceous period, and provides a reliable calibration in studying the tempo and mode of grass chloroplast evolution.

Methodology/Principal Findings

By using chloroplast genome data from angiosperms and by taking account of new paleontological evidence, we now show that episodic rate acceleration both in terms of non-synonymous and synonymous substitutions occurred in the common ancestral branch of the core Poaceae (a group formed by rice, wheat, maize, and their allies) accompanied by adaptive evolution in several chloroplast proteins, while the rate reverted to the slow rate typical of most monocot species in the terminal branches.

Conclusions/Significance

Our finding of episodic rate acceleration in the ancestral grasses accompanied by adaptive molecular evolution has a profound bearing on the evolution of grasses, which form a highly successful group of plants. The widely used model for estimating divergence times was based on the assumption of correlated rates between ancestral and descendant lineages. However, the assumption is proved to be inadequate in approximating the episodic rate acceleration in the ancestral grasses, and the assumption of independent rates is more appropriate. This finding has implications for studies of molecular evolutionary rates and time-scale of evolution in other groups of organisms.