Genome evolution of the psammophyte Pugionium for desert adaptation and further speciation.

Deserts exert strong selection pressures on plants, but the underlying genomic drivers of ecological adaptation and subsequent speciation remain largely unknown. Here, we generated de novo genome assemblies and conducted population genomic analyses of the psammophytic genus Pugionium (Brassicaceae). Our results indicated that this bispecific genus had undergone an allopolyploid event, and the two parental genomes were derived from two ancestral lineages with different chromosome numbers and structures. The postpolyploid expansion of gene families related to abiotic stress responses and lignin biosynthesis facilitated environmental adaptations of the genus to desert habitats. Population genomic analyses of both species further revealed their recent divergence with continuous gene flow, and the most divergent regions were found to be centered on three highly structurally reshuffled chromosomes. Genes under selection in these regions, which were mainly located in one of the two subgenomes, contributed greatly to the interspecific divergence in microhabitat adaptation.

Species Tree Estimation and the Impact of Gene Loss Following Whole-Genome Duplication.

Whole-genome duplication (WGD) occurs broadly and repeatedly across the history of eukaryotes and is recognized as a prominent evolutionary force, especially in plants. Immediately following WGD, most genes are present in two copies as paralogs. Due to this redundancy, one copy of a paralog pair commonly undergoes pseudogenization and is eventually lost. When speciation occurs shortly after WGD; however, differential loss of paralogs may lead to spurious phylogenetic inference resulting from the inclusion of pseudoorthologs-paralogous genes mistakenly identified as orthologs because they are present in single copies within each sampled species. The influence and impact of including pseudoorthologs versus true orthologs as a result of gene extinction (or incomplete laboratory sampling) are only recently gaining empirical attention in the phylogenomics community. Moreover, few studies have yet to investigate this phenomenon in an explicit coalescent framework. Here, using mathematical models, numerous simulated data sets, and two newly assembled empirical data sets, we assess the effect of pseudoorthologs on species tree estimation under varying degrees of incomplete lineage sorting (ILS) and differential gene loss scenarios following WGD. When gene loss occurs along the terminal branches of the species tree, alignment-based (BPP) and gene-tree-based (ASTRAL, MP-EST, and STAR) coalescent methods are adversely affected as the degree of ILS increases. This can be greatly improved by sampling a sufficiently large number of genes. Under the same circumstances, however, concatenation methods consistently estimate incorrect species trees as the number of genes increases. Additionally, pseudoorthologs can greatly mislead species tree inference when gene loss occurs along the internal branches of the species tree. Here, both coalescent and concatenation methods yield inconsistent results. These results underscore the importance of understanding the influence of pseudoorthologs in the phylogenomics era. [Coalescent method; concatenation method; incomplete lineage sorting; pseudoorthologs; single-copy gene; whole-genome duplication.].

Conservation priorities for endangered trees facing multiple threats around the world.

Trees are vital to the survival of numerous species and to forest ecosystem functioning. However, the current distribution, vulnerability to extinction, and conservation priorities of globally endangered trees are not well known. We mapped the global distribution of 1686 tree species listed as endangered on the International Union for the Conservation of Nature Red List and identified conservation priority for them based on species richness, life-history traits, evolutionary distinctiveness, future climate change, and intensity of human activities. We also evaluated the impacts of various threats to these endangered tree species and evaluated the effectiveness of their protection based on the percentage of the species' range inside protected areas. The worldwide distribution of endangered trees, from the tropics through temperate zones, was uneven. Most endangered tree species were not protected in their native ranges, and only 153 species were fully protected. Hotspots of tree diversity occurred primarily in the tropics, and 79.06% of these were highly vulnerable to threats. We identified 253 areas of high priority for the conservation of endangered trees that are highly threatened and insufficiently protected. In particular, 43.42% of unprotected tree species in priority areas lacked recommended conservation measures or had no associated conservation plan. The priority conservation areas and unprotected trees we identified serve as a guideline for future management underpinning the post-2020 global biodiversity framework.

Prioridades de conservación para los árboles amenazados que enfrentan múltiples amenazas en todo el mundo Resumen Los árboles son vitales para la supervivencia de numerosas especies y para el funcionamiento de los ecosistemas forestales. Sin embargo, no se conoce muy bien la distribución actual, vulnerabilidad a la extinción y prioridades de conservación de los árboles amenazados a nivel mundial. Mapeamos la distribución global de 1686 especies de árboles catalogadas como en peligro por la Lista Roja de la Unión Internacional para la Conservación de la Naturaleza e identificamos su prioridad de conservación con base en la riqueza de especies, características de historia de vida, singularidad evolutiva, cambio climático futuro e intensidad de las actividades humanas. También evaluamos el impacto de varias amenazas sobre estas especies y analizamos la efectividad de su protección con base en el porcentaje de la distribución de la especie ubicado dentro de un área protegida. La distribución mundial de árboles en peligro, desde los trópicos y hasta las zonas templadas, fue desigual. La mayoría de las especies no estaban protegidas dentro de su distribución nativa y sólo 153 especies contaban con protección completa. Los puntos calientes de diversidad de árboles se ubicaron principalmente en los trópicos, y el 79.06% de estos tenían una vulnerabilidad alta ante las amenazas. Identificamos 253 áreas de gran prioridad para la conservación de los árboles en peligro que están amenazados y con poca protección. En particular, el 43.42% de las áreas sin protección dentro de las áreas prioritarias no contaban con las medidas recomendadas de conservación o no tenían asociado un plan de conservación. Las áreas prioritarias de conservación y los árboles sin protección que identificamos son una pauta para futuros manejos que apuntalan el marco de trabajo post-2020 para la biodiversidad.

Water lily (Nymphaea thermarum) genome reveals variable genomic signatures of ancient vascular cambium losses.

For more than 225 million y, all seed plants were woody trees, shrubs, or vines. Shortly after the origin of angiosperms ∼140 million y ago (MYA), the Nymphaeales (water lilies) became one of the first lineages to deviate from their ancestral, woody habit by losing the vascular cambium, the meristematic population of cells that produces secondary xylem (wood) and phloem. Many of the genes and gene families that regulate differentiation of secondary tissues also regulate the differentiation of primary xylem and phloem, which are produced by apical meristems and retained in nearly all seed plants. Here, we sequenced and assembled a draft genome of the water lily Nymphaea thermarum, an emerging system for the study of early flowering plant evolution, and compared it to genomes from other cambium-bearing and cambium-less lineages (e.g., monocots and Nelumbo). This revealed lineage-specific patterns of gene loss and divergence. Nymphaea is characterized by a significant contraction of the HD-ZIP III transcription factors, specifically loss of REVOLUTA, which influences cambial activity in other angiosperms. We also found the Nymphaea and monocot copies of cambium-associated CLE signaling peptides display unique substitutions at otherwise highly conserved amino acids. Nelumbo displays no obvious divergence in cambium-associated genes. The divergent genomic signatures of convergent loss of vascular cambium reveals that even pleiotropic genes can exhibit unique divergence patterns in association with independent events of trait loss. Our results shed light on the evolution of herbaceousness-one of the key biological innovations associated with the earliest phases of angiosperm evolution.

Phylotranscriptomics of Swertiinae (Gentianaceae) reveals that key floral traits are not phylogenetically correlated.

Establishing how lineages with similar traits are phylogenetically related remains critical for understanding the origin of biodiversity on Earth. Floral traits in plants are widely used to explore phylogenetic relationships and to delineate taxonomic groups. The subtribe Swertiinae (Gentianaceae) comprises more than 350 species with high floral diversity ranging from rotate to tubular corollas and possessing diverse nectaries. Here we performed phylogenetic analysis of 60 species from all 15 genera of the subtribe Swertiinae sensu Ho and Liu, representing the range of floral diversity, using data from the nuclear and plastid genomes. Extensive topological conflicts were present between the nuclear and plastome trees. Three of the 15 genera represented by multiple species are polyphyletic in both trees. Key floral traits including corolla type, absence or presence of lobe scales, nectary type, nectary position, and stigma type are randomly distributed in the nuclear and plastome trees without phylogenetic correlation. We also revealed the likely ancient hybrid origin of one large clade comprising 10 genera with diverse floral traits. These results highlight the complex evolutionary history of this subtribe. The phylogenies constructed here provide a basic framework for further exploring the ecological and genetic mechanisms underlying both species diversification and floral diversity.

Comparative analysis of the complete chloroplast genomes of six threatened subgenus Gynopodium (Magnolia) species.

BACKGROUND: The subgenus Gynopodium belonging to genus Magnolia have high ornamental, economic, and ecological value. Subgenus Gynopodium contains eight species, but six of these species are threatened. No studies to date have characterized the characteristics of the chloroplast genomes (CPGs) within subgenus Gynopodium species. In this study, we compared the structure of CPGs, identified the mutational hotspots and resolved the phylogenetic relationship of subgenus Gynopodium. RESULTS: The CPGs of six subgenus Gynopodium species ranged in size from 160,027 bp to 160,114 bp. A total of 131 genes were identified, including 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. We detected neither major expansions or contractions in the inverted repeat region, nor rearrangements or insertions in the CPGs of six subgenus Gynopodium species. A total of 300 large repeat sequences (forward, reverse, and palindrome repeats), 847 simple sequence repeats, and five highly variable regions were identified. One gene (ycf1) and four intergenic regions (psbA-trnH-GUG, petA-psbJ, rpl32-trnL-UAG, and ccsA-ndhD) were identified as mutational hotspots by their high nucleotide diversity (Pi) values (≥ 0.004), which were useful for species discrimination. Maximum likelihood and Bayesian inference trees were concordant and indicated that Magnoliaceae consisted of two genera Liriodendron and Magnolia. Six species of subgenus Gynopodium clustered as a monophyletic clade, forming a sister clade with subgenus Yulania (BS = 100%, PP = 1.00). Due to the non-monophyly of subgenus Magnolia, subgenus Gynopodium should be treated as a section of Magnolia. Within section Gynopodium, M. sinica diverged first (posterior probability = 1, bootstrap = 100), followed by M. nitida, M. kachirachirai and M. lotungensis. M. omeiensis was sister to M. yunnanensis (posterior probability = 0.97, bootstrap = 50). CONCLUSION: The CPGs and characteristics information provided by our study could be useful in species identification, conservation genetics and resolving phylogenetic relationships of Magnoliaceae species.

Abiotic Niche Divergence of Hybrid Species from Their Progenitors.

AbstractAlthough more frequently discussed recently than previously, the role of ecology in homoploid hybrid and allopolyploid speciation has not been subjected to comparative analysis. We examined abiotic niche divergence of 22 assumed homoploid hybrid species and 60 allopolyploid species from that of their progenitors. Ecological niche modeling was employed in an analysis of each species' fundamental niche, and ordination methods were used in an analysis of realized niches. Both analyses utilized 100,000 georeferenced records. From estimates of niche overlap and niche breadth, we identified for both types of hybrid species four niche divergence patterns: niche novelty, niche contraction, niche intermediacy, and niche expansion. Niche shifts involving niche novelty were common and considered likely to play an important role in the establishment of both types of hybrid species, although more so for homoploid hybrid species than for allopolyploid species. Approximately 70% of homoploid hybrid species versus 37% of allopolyploid species showed shifts in the fundamental niche from their parents, and ∼86% versus ∼52%, respectively, exhibited shifts in the realized niche. Climate was shown to contribute more than soil and landform to niche shifts in both types of hybrid species. Overall, our results highlight the significance of abiotic niche divergence for hybrid speciation, especially without genome duplication.

The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales.

The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data set including 423 single-copy loci from 64 taxa representing 39 families to infer the species tree of the flowering plant order Malpighiales. This order includes 9 of the top 10 most unstable nodes in angiosperms, which have been hypothesized to arise from the rapid radiation during the Cretaceous. Here, we show that coalescent-based methods do not resolve the backbone of Malpighiales and concatenation methods yield inconsistent estimations, providing evidence that gene tree heterogeneity is high in this clade. Despite high levels of ILS and gene tree estimation error, our simulations demonstrate that these two factors alone are insufficient to explain the lack of resolution in this order. To explore this further, we examined triplet frequencies among empirical gene trees and discovered some of them deviated significantly from those attributed to ILS and estimation error, suggesting gene flow as an additional and previously unappreciated phenomenon promoting gene tree variation in Malpighiales. Finally, we applied a novel method to quantify the relative contribution of these three primary sources of gene tree heterogeneity and demonstrated that ILS, gene tree estimation error, and gene flow contributed to 10.0$\%$, 34.8$\%$, and 21.4$\%$ of the variation, respectively. Together, our results suggest that a perfect storm of factors likely influence this lack of resolution, and further indicate that recalcitrant phylogenetic relationships like the backbone of Malpighiales may be better represented as phylogenetic networks. Thus, reducing such groups solely to existing models that adhere strictly to bifurcating trees greatly oversimplifies reality, and obscures our ability to more clearly discern the process of evolution. [Coalescent; concatenation; flanking region; hybrid enrichment, introgression; phylogenomics; rapid radiation, triplet frequency.].

Contrasting temporal variations in responses of leaf unfolding to daytime and nighttime warming.

Earlier spring phenological events have been widely reported in plants under global warming. Recent studies reported a slowdown in the warming-induced advanced spring phenology in temperate regions. However, previous research mainly focused on daily mean temperature, thus neglecting the asymmetric phenological responses to daytime and nighttime temperature. Using long-term records of leaf unfolding in eight deciduous species at 1300 sites across central Europe, we assessed and compared the effects of daytime temperature, nighttime temperature, and photoperiod on leaf unfolding during 1951-1980 and 1981-2013. Although leaf unfolding was advanced by daytime warming during 1951-2013, the advancing responses of leaf unfolding significantly decreased from 1951-1980 to 1981-2013 due to a lower accumulation of chilling units by daytime warming. Nighttime warming delayed leaf unfolding during 1951-1980 but advanced it during 1981-2013 due to a higher accumulation of chilling units by nighttime warming. In contrast, critical daylength and plasticity of leaf unfolding dates remained unchanged between 1951 and 2013. Our study provided evidence that daytime warming instead of nighttime warming accounts for the slowdown in the advancing spring phenology and implied that nighttime warming-induced earlier spring phenology may be buffering the slowdown of the advanced spring phenology by daytime warming. The response of spring phenology to nighttime temperature may override that to daytime temperature under the actual trends in global warming.

Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex.

How genome divergence eventually leads to speciation is a topic of prime evolutionary interest. Genomic islands of elevated divergence are frequently reported between diverging lineages, and their size is expected to increase with time and gene flow under the speciation-with-gene-flow model. However, such islands can also result from divergent sorting of ancient polymorphisms, recent ecological selection regardless of gene flow, and/or recurrent background selection and selective sweeps in low-recombination regions. It is challenging to disentangle these nonexclusive alternatives, but here we attempt to do this in an analysis of what drove genomic divergence between four lineages comprising a species complex of desert poplar trees. Within this complex we found that two morphologically delimited species, Populus euphratica and Populus pruinosa, were paraphyletic while the four lineages exhibited contrasting levels of gene flow and divergence times, providing a good system for testing hypotheses on the origin of divergence islands. We show that the size and number of genomic islands that distinguish lineages are not associated with either rate of recent gene flow or time of divergence. Instead, they are most likely derived from divergent sorting of ancient polymorphisms and divergence hitchhiking. We found that highly diverged genes under lineage-specific selection and putatively involved in ecological and morphological divergence occur both within and outside these islands. Our results highlight the need to incorporate demography, absolute divergence measurement, and gene flow rate to explain the formation of genomic islands and to identify potential genomic regions involved in speciation.

Machine learning predicts large scale declines in native plant phylogenetic diversity.

Though substantial effort has gone into predicting how global climate change will impact biodiversity patterns, the scarcity of taxon-specific information has hampered the efficacy of these endeavors. Further, most studies analyzing spatiotemporal patterns of biodiversity focus narrowly on species richness. We apply machine learning approaches to a comprehensive vascular plant database for the United States and generate predictive models of regional plant taxonomic and phylogenetic diversity in response to a wide range of environmental variables. We demonstrate differences in predicted patterns and potential drivers of native vs nonnative biodiversity. In particular, native phylogenetic diversity is likely to decrease over the next half century despite increases in species richness. We also identify that patterns of taxonomic diversity can be incongruent with those of phylogenetic diversity. The combination of macro-environmental factors that determine diversity likely varies at continental scales; thus, as climate change alters the combinations of these factors across the landscape, the collective effect on regional diversity will also vary. Our study represents one of the most comprehensive examinations of plant diversity patterns to date and demonstrates that our ability to predict future diversity may benefit tremendously from the application of machine learning.

Phylogenomics of the genus Populus reveals extensive interspecific gene flow and balancing selection.

Phylogenetic analysis is complicated by interspecific gene flow and the presence of shared ancestral polymorphisms, particularly those maintained by balancing selection. In this study, we aimed to examine the prevalence of these factors during the diversification of Populus, a model tree genus in the Northern Hemisphere. We constructed phylogenetic trees of 29 Populus taxa using 80 individuals based on re-sequenced genomes. Our species tree analyses recovered four main clades in the genus based on consensus nuclear phylogenies, but in conflict with the plastome phylogeny. A few interspecific relationships remained unresolved within the multiple-species clade because of inconsistent gene trees. Our results indicated that gene flow has been widespread within each clade and also occurred among the four clades during their early divergence. We identified 45 candidate genes with ancient polymorphisms maintained by balancing selection. These genes were mainly associated with mating compatibility, growth and stress resistance. Both gene flow and selection-mediated ancient polymorphisms are prevalent in the genus Populus. These are potentially important contributors to adaptive variation. Our results provide a framework for the diversification of model tree genus that will facilitate future comparative studies.

Widespread ancient whole-genome duplications in Malpighiales coincide with Eocene global climatic upheaval.

Whole-genome duplications (WGDs) are widespread and prevalent in vascular plants and frequently coincide with major episodes of global and climatic upheaval, including the mass extinction at the Cretaceous-Tertiary boundary (c. 65 Ma) and during more recent periods of global aridification in the Miocene (c. 10-5 Ma). Here, we explore WGDs in the diverse flowering plant clade Malpighiales. Using transcriptomes and complete genomes from 42 species, we applied a multipronged phylogenomic pipeline to identify, locate, and determine the age of WGDs in Malpighiales using three means of inference: distributions of synonymous substitutions per synonymous site (Ks ) among paralogs, phylogenomic (gene tree) reconciliation, and a likelihood-based gene-count method. We conservatively identify 22 ancient WGDs, widely distributed across Malpighiales subclades. Importantly, these events are clustered around the Eocene-Paleocene transition (c. 54 Ma), during which time the planet was warmer and wetter than any period in the Cenozoic. These results establish that the Eocene Climatic Optimum likely represents a previously unrecognized period of prolific WGDs in plants, and lends further support to the hypothesis that polyploidization promotes adaptation and enhances plant survival during episodes of global change, especially for tropical organisms like Malpighiales, which have tight thermal tolerances.

Intergeneric Relationships within the Family Salicaceae s.l. based on Plastid Phylogenomics.

Many Salicaceae s.l. plants are recognized for their important role in the production of products such as wood, oils, and medicines, and as a model organism in life studies. However, the difference in plastid sequence, phylogenetic relationships, and lineage diversification of the family Salicaceae s.l. remain poorly understood. In this study, we compare 24 species representing 18 genera of the family. Simple sequence repeats (SSRs) are considered effective molecular markers for plant species identification and population genetics. Among them, a total of 1798 SSRs were identified, among which mononucleotide repeat was the most common with 1455 accounts representing 80.92% of the total. Most of the SSRs are located in the non-coding region. We also identified five other types of repeats, including 1750 tandems, 434 forward, 407 palindromic, 86 reverse, and 30 complementary repeats. The species in Salicaceae s.l. have a conserved plastid genome. Each plastome presented a typical quadripartite structure and varied in size due to the expansion and contraction of the inverted repeat (IR) boundary, lacking major structural variations, but we identified six divergence hotspot regions. We obtained phylogenetic relationships of 18 genera in Salicaceae s.l. and the 24 species formed a highly supported lineage. Casearia was identified as the basal clade. The divergence time between Salicaceae s.l. and the outgroup was estimated as ~93 Mya; Salix, and Populus diverged around 34 Mya, consistent with the previously reported time. Our research will contribute to a better understanding of the phylogenetic relationships among the members of the Salicaceae s.l.

Taxon sampling effects on the quantification and comparison of community phylogenetic diversity.

Ecologists are increasingly making use of molecular phylogenies, especially in the fields of community ecology and conservation. However, these phylogenies are often used without full appreciation of their underlying assumptions and uncertainties. A frequent practice in ecological studies is inferring a phylogeny with molecular data from taxa only within the community of interest. These "inferred community phylogenies" are inherently biased in their taxon sampling. Despite the importance of comprehensive sampling in constructing phylogenies, the implications of using inferred community phylogenies in ecological studies have not been examined. Here, we evaluate how taxon sampling affects the quantification and comparison of community phylogenetic diversity using both simulated and empirical data sets. We demonstrate that inferred community trees greatly underestimate phylogenetic diversity and that the probability of incorrectly ranking community diversity can reach up to 25%, depending on the dating methods employed. We argue that to reach reliable conclusions, ecological studies must improve their taxon sampling and generate the best phylogeny possible.

The Impact of Missing Data on Species Tree Estimation.

Phylogeneticists are increasingly assembling genome-scale data sets that include hundreds of genes to resolve their focal clades. Although these data sets commonly include a moderate to high amount of missing data, there remains no consensus on their impact to species tree estimation. Here, using several simulated and empirical data sets, we assess the effects of missing data on species tree estimation under varying degrees of incomplete lineage sorting (ILS) and gene rate heterogeneity. We demonstrate that concatenation (RAxML), gene-tree-based coalescent (ASTRAL, MP-EST, and STAR), and supertree (matrix representation with parsimony [MRP]) methods perform reliably, so long as missing data are randomly distributed (by gene and/or by species) and that a sufficiently large number of genes are sampled. When data sets are indecisive sensu Sanderson et al. (2010. Phylogenomics with incomplete taxon coverage: the limits to inference. BMC Evol Biol. 10:155) and/or ILS is high, however, high amounts of missing data that are randomly distributed require exhaustive levels of gene sampling, likely exceeding most empirical studies to date. Moreover, missing data become especially problematic when they are nonrandomly distributed. We demonstrate that STAR produces inconsistent results when the amount of nonrandom missing data is high, regardless of the degree of ILS and gene rate heterogeneity. Similarly, concatenation methods using maximum likelihood can be misled by nonrandom missing data in the presence of gene rate heterogeneity, which becomes further exacerbated when combined with high ILS. In contrast, ASTRAL, MP-EST, and MRP are more robust under all of these scenarios. These results underscore the importance of understanding the influence of missing data in the phylogenomics era.

Long-term morphological stasis maintained by a plant-pollinator mutualism.

Many major branches in the Tree of Life are marked by stereotyped body plans that have been maintained over long periods of time. One possible explanation for this stasis is that there are genetic or developmental constraints that restrict the origin of novel body plans. An alternative is that basic body plans are potentially quite labile, but are actively maintained by natural selection. We present evidence that the conserved floral morphology of a species-rich flowering plant clade, Malpighiaceae, has been actively maintained for tens of millions of years via stabilizing selection imposed by their specialist New World oil-bee pollinators. Nine clades that have lost their primary oil-bee pollinators show major evolutionary shifts in specific floral traits associated with oil-bee pollination, demonstrating that developmental constraint is not the primary cause of morphological stasis in Malpighiaceae. Interestingly, Malpighiaceae show a burst in species diversification coinciding with the origin of this plant-pollinator mutualism. One hypothesis to account for radiation despite morphological stasis is that although selection on pollinator efficiency explains the origin of this unique and conserved floral morphology, tight pollinator specificity subsequently permitted greatly enhanced diversification in this system.

Coalescent methods are robust to the simultaneous effects of long branches and incomplete lineage sorting.

It is well known that species with elevated substitution rates can give rise to disproportionately long branches in the species tree. This combination of long and short branches can contribute to long-branch artifacts (LBA). Despite efforts to remedy LBA via increased taxon sampling and methodological improvements in gene tree estimation, it remains unclear how long and short branches affect species tree estimation in the presence of incomplete lineage sorting (ILS). Here, we examine the combined influence of long external and short internal branches on concatenation and coalescent methods using both simulated and empirical data. Our results demonstrate that the presence of long and short branches alone does not obviously confound the consistency of concatenation and coalescent methods. However, when long external and short internal branches occur simultaneously with high ILS, concatenation methods can be misled, especially when two of these long branches are sister lineages. In contrast, coalescent methods are more robust under these circumstances. This is particularly relevant because this topological pattern also characterizes numerous ancient rapid radiations across the tree of life. Because short internal branches can increase the potential for ILS and gene tree discordance, our results collectively suggest that coalescent methods are more likely to infer the correct species tree in cases of ancient rapid radiations where long external and short internal branches are in close phylogenetic proximity.

Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics.

In recent articles published in Molecular Phylogenetics and Evolution, Mark Springer and John Gatesy (S&G) present numerous criticisms of recent implementations and testing of the multispecies coalescent (MSC) model in phylogenomics, popularly known as "species tree" methods. After pointing out errors in alignments and gene tree rooting in recent phylogenomic data sets, particularly in Song et al. (2012) on mammals and Xi et al. (2014) on plants, they suggest that these errors seriously compromise the conclusions of these studies. Additionally, S&G enumerate numerous perceived violated assumptions and deficiencies in the application of the MSC model in phylogenomics, such as its assumption of neutrality and in particular the use of transcriptomes, which are deemed inappropriate for the MSC because the constituent exons often subtend large regions of chromosomes within which recombination is substantial. We acknowledge these previously reported errors in recent phylogenomic data sets, but disapprove of S&G's excessively combative and taunting tone. We show that these errors, as well as two nucleotide sorting methods used in the analysis of Amborella, have little impact on the conclusions of those papers. Moreover, several concepts introduced by S&G and an appeal to "first principles" of phylogenetics in an attempt to discredit MSC models are invalid and reveal numerous misunderstandings of the MSC. Contrary to the claims of S&G we show that recent computer simulations used to test the robustness of MSC models are not circular and do not unfairly favor MSC models over concatenation. In fact, although both concatenation and MSC models clearly perform well in regions of tree space with long branches and little incomplete lineage sorting (ILS), simulations reveal the erratic behavior of concatenation when subjected to data subsampling and its tendency to produce spuriously confident yet conflicting results in regions of parameter space where MSC models still perform well. S&G's claims that MSC models explain little or none (0-15%) of the observed gene tree heterogeneity observed in a mammal data set and that MSC models assume ILS as the only source of gene tree variation are flawed. Overall many of their criticisms of MSC models are invalidated when concatenation is appropriately viewed as a special case of the MSC, which in turn is a special case of emerging network models in phylogenomics. We reiterate that there is enormous promise and value in recent implementations and tests of the MSC and look forward to its increased use and refinement in phylogenomics.

Unraveling the biogeographical history of Chrysobalanaceae from plastid genomes.

PREMISE OF THE STUDY: The complex geological and climatic history of the Neotropics has had major implications on the diversification of plant lineages. Chrysobalanaceae is a pantropical family of trees and shrubs with 75% of its 531 species found in the Neotropics, and a time-calibrated phylogeny of this family should shed light on the tempo of diversification in the Neotropical flora. Previously published phylogenetic hypotheses of this family were poorly supported, and its biogeography remains unclear. METHODS: We assembled the complete plastid genome of 51 Chrysobalanaceae species, and increased taxon sampling by Sanger-sequencing of five plastid regions for an additional 88 species. We generated a time-calibrated tree including all 139 Chrsyobalanaceae species and 23 outgroups. We then conducted an ancestral area reconstruction analysis and estimated diversification rates in the family. KEY RESULTS: The tree generated with the plastid genome alignment was almost fully resolved. It supports the polyphyly of Licania and Hirtella. The family has diversified starting around the Eocene-Oligocene transition. An ancestral area reconstruction confirms a Paleotropical origin for Chrysobalanaceae with several transoceanic dispersal events. The main Neotropical clade likely resulted from a single migration event from Africa around 28 mya ago, which subsequently underwent rapid diversification. CONCLUSIONS: Given the diverse ecologies exhibited by extant species, we hypothesize that the rapid diversification of Chrysobalanaceae following the colonization of the Neotropics was triggered by habitat specialization during the complex geological and paleoclimatic history of the Neotropics.