Taxon sampling effects in molecular clock dating: An example from the African Restionaceae

Young evolutionary origins of dioecy in the genus Asparagus

PREMISE

Dioecy (separate sexes) has independently evolved numerous times across the angiosperm phylogeny and is recently derived in many lineages. However, our understanding is limited regarding the evolutionary mechanisms that drive the origins of dioecy in plants. The recent and repeated evolution of dioecy across angiosperms offers an opportunity to make strong inferences about the ecological, developmental, and molecular factors influencing the evolution of dioecy, and thus sex chromosomes. The genus Asparagus (Asparagaceae) is an emerging model taxon for studying dioecy and sex chromosome evolution, yet estimates for the age and origin of dioecy in the genus are lacking.

METHODS

We use plastome sequences and fossil time calibrations in phylogenetic analyses to investigate the age and origin of dioecy in the genus Asparagus. We also review the diversity of sexual systems present across the genus to address contradicting reports in the literature.

RESULTS

We estimate that dioecy evolved once or twice approximately 2.78-3.78 million years ago in Asparagus, of which roughly 27% of the species are dioecious and the remaining are hermaphroditic with monoclinous flowers.

CONCLUSIONS

Our findings support previous work implicating a young age and the possibility of two origins of dioecy in Asparagus, which appear to be associated with rapid radiations and range expansion out of Africa. Lastly, we speculate that paleoclimatic oscillations throughout northern Africa may have helped set the stage for the origin(s) of dioecy in Asparagus approximately 2.78-3.78 million years ago.

New insights into polyploid evolution and dynamic nature of Ludwigia section Isnardia (Onagraceae)

BACKGROUND

While polyploids are common in plants, the evolutionary history and natural dynamics of most polyploid groups are still unclear. Owing to plentiful earlier systematic studies, Ludwigia sect. Isnardia (comprising 22 wetland taxa) is an ideal allopolyploid complex to investigate polyploid evolution and natural dynamics within and among taxa. With a considerable sampling, we concentrated on revisiting earlier phylogenies of Isnardia, reevaluating the earlier estimated age of the most recent common ancestor (TMRCA), exploring the correlation between infraspecific genetic diversity and ploidy levels, and inspecting interspecific gene flows among taxa.

RESULTS

Phylogenetic trees and network concurred with earlier phylogenies and hypothesized genomes by incorporating 192 atpB-rbcL and ITS sequences representing 91% of Isnardia taxa. Moreover, we detected three multi-origin taxa. Our findings on L. repens and L. sphaerocarpa were consistent with earlier studies; L. arcuata was reported as a multi-origin taxon here, and an additional evolutionary scenario of L. sphaerocarpa was uncovered, both for the first time. Furthermore, estimated Isnardia TMRCA ages based on our data (5.9 or 8.9 million years ago) are in accordance with earlier estimates, although younger than fossil dates (Middle Miocene). Surprisingly, infraspecific genetic variations of Isnardia taxa did not increase with ploidy levels as anticipated from many other polyploid groups. In addition, the exuberant, low, and asymmetrical gene flows among Isnardia taxa indicated that the reproductive barriers may be weakened owing to allopolyploidization, which has rarely been reported.

CONCLUSIONS

The present research gives new perceptions of the reticulate evolution and dynamic nature of Isnardia and points to gaps in current knowledge about allopolyploid evolution.

No phylogenomic support for a Cenozoic origin of the "living fossil" Isoetes

PREMISE

The isoetalean lineage has a rich fossil record that extends to the Devonian, but the age of the living clade is unclear. Recent results indicate that it is young, from the Cenozoic, whereas earlier work based on less data from a denser taxon sampling yielded Mesozoic median ages.

METHODS

We analyzed node ages in Isoetes using two genomic data sets (plastome and nuclear ribosomal cistron), three clock models implemented in MrBayes (ILN, WN, and TK02 models), and a conservative approach to calibration.

RESULTS

While topological results were consistently resolved in Isoetes estimated crown group ages range from the latest Paleozoic (mid-Permian) to the Mesozoic depending on data type and clock model. The oldest estimates were retrieved using the autocorrelated TK02 clock model. An (early) Cenozoic age was only obtained under one specific condition (plastome data analyzed with the uncorrelated ILN clock model). That same plastome data set also yielded the oldest (mid-Permian) age estimate when analyzed with the autocorrelated TK02 clock model. Adding the highly divergent, recently established sister species Isoetes wormaldii to the data set approximately doubled the average median node depth to the Isoetes crown group.

CONCLUSIONS

There is no consistent support for a Cenozoic origin of the living clade Isoetes. We obtained seemingly well-founded, yet strongly deviating results depending on data type and clock model. The single most important future improvement is probably to add calibration points, which requires an improved understanding of the isoetalean fossil record or alternative bases for calibration.

Sequence Capture From Historical Museum Specimens: Maximizing Value for Population and Phylogenomic Studies

The application of high-throughput, short-read sequencing to degraded DNA has greatly increased the feasibility of generating genomic data from historical museum specimens. While many published studies report successful sequencing results from historical specimens; in reality, success and quality of sequence data can be highly variable. To examine predictors of sequencing quality, and methodological approaches to improving data accuracy, we generated and analyzed genomic sequence data from 115 historically collected museum specimens up to 180 years old. Data span both population genomic and phylogenomic scales, including historically collected specimens from 34 specimens of four species of Australian rock-wallabies (genus Petrogale) and 92 samples from 79 specimens of Australo-Papuan murine rodents (subfamily Murinae). For historical rodent specimens, where the focus was sampling for phylogenomics, we found that regardless of specimen age, DNA sequence libraries prepared from toe pad or bone subsamples performed significantly better than those taken from the skin (in terms of proportion of reads on target, number of loci captured, and data accuracy). In total, 93% of DNA libraries from toe pad or bone subsamples resulted in reliable data for phylogenetic inference, compared to 63% of skin subsamples. For skin subsamples, proportion of reads on target weakly correlated with collection year. Then using population genomic data from rock-wallaby skins as a test case, we found substantial improvement in final data quality by mapping to a high-quality “closest sister” de novo assembly from fresh tissues, compared to mapping to a sample-specific historical de novo assembly. Choice of mapping approach also affected final estimates of the number of segregating sites and Watterson's θ, both important parameters for population genomic inference. The incorporation of accurate and reliable sequence data from historical specimens has important outcomes for evolutionary studies at both population and phylogenomic scales. By assessing the outcomes of different approaches to specimen subsampling, library preparation and bioinformatic processing, our results provide a framework for increasing sequencing success for irreplaceable historical specimens.

Integrated phylogenomics and fossil data illuminate the evolution of beetles

Beetles constitute the most biodiverse animal order with over 380 000 described species and possibly several million more yet unnamed. Recent phylogenomic studies have arrived at considerably incongruent topologies and widely varying estimates of divergence dates for major beetle clades. Here, we use a dataset of 68 single-copy nuclear protein-coding (NPC) genes sampling 129 out of the 193 recognized extant families as well as the first comprehensive set of fully justified fossil calibrations to recover a refined timescale of beetle evolution. Using phylogenetic methods that counter the effects of compositional and rate heterogeneity, we recover a topology congruent with morphological studies, which we use, combined with other recent phylogenomic studies, to propose several formal changes in the classification of Coleoptera: Scirtiformia and Scirtoidea sensu nov., Clambiformia ser. nov. and Clamboidea sensu nov., Rhinorhipiformia ser. nov., Byrrhoidea sensu nov., Dryopoidea stat. res., Nosodendriformia ser. nov. and Staphyliniformia sensu nov., and Erotyloidea stat. nov., Nitiduloidea stat. nov. and Cucujoidea sensu nov., alongside changes below the superfamily level. Our divergence time analyses recovered a late Carboniferous origin of Coleoptera, a late Palaeozoic origin of all modern beetle suborders and a Triassic-Jurassic origin of most extant families, while fundamental divergences within beetle phylogeny did not coincide with the hypothesis of a Cretaceous Terrestrial Revolution.

Seeing through the hedge: Phylogenomics of Thuja (Cupressaceae) reveals prominent incomplete lineage sorting and ancient introgression for Tertiary relict flora

The Eastern Asia (EA) - North America (NA) disjunction is a well-known biogeographic pattern of the Tertiary relict flora; however, few studies have investigated the evolutionary history of this disjunction using a phylogenomic approach. Here, we used 2369 single copy nuclear genes and nearly full plastomes to reconstruct the evolutionary history of the small Tertiary relict genus Thuja, which consists of five disjunctly distributed species. The nuclear species tree strongly supported an EA clade Thuja standishii-Thuja sutchuenensis and a "disjunct clade", where western NA species T. plicata is sister to an EA-eastern NA disjunct Thuja occidentalis-Thuja koraiensis group. Our results suggested that the observed topological discordance among the gene trees as well as the cytonuclear discordance is mainly due to incomplete lineage sorting, probably facilitated by the fast diversification of Thuja around the Early Miocene and the large effective population sizes of ancestral lineages. Furthermore, approximately 20% of the T. sutchuenensis nuclear genome is derived from an unknown ancestral lineage of Thuja, which might explain the close resemblance of its cone morphology to that of an ancient fossil species. Overall, our study demonstrates that single genes may not resolve interspecific relationships for disjunct taxa, and that more reliable results will come from hundreds or thousands of loci, revealing a more complex evolutionary history. This will steadily improve our understanding of their origin and evolution.

Redefining the Distributional Boundaries and Phylogenetic Relationships for Ctenomids From Central Argentina

With about 68 recognized living species, subterranean rodents of the genus Ctenomys are found in a multiplicity of habitats, from the dunes of the Atlantic coast to the Andes Mountains, including environments ranging from humid steppes of Pampas to the dry deserts of Chaco region. However, this genus needs an exhaustive reevaluation of its systematic and phylogenetic relationships regarding the different groups that compose it. This knowledge is essential to propose biodiversity conservation strategies both at species level and at higher hierarchical levels. In order to clarify the taxonomy and the recent evolutionary history from populations of Ctenomys in the Pampas region, Argentina, phylogenetic relationships among them were evaluated using mitochondrial DNA sequences: gene encoding cytochrome b protein (1,140 bp) and the non-coding D-loop region (434 bp). To infer the divergence times inside the Ctenomys clade, a Bayesian calibrate tree using fossil remains data from different families within Caviomorpha was performed at first. Secondly, that calibration data was used as priors in a new Bayesian phylogenetic inference within the genus Ctenomys. This phylogenetic tree emphasized on species currently distributed on the Pampas region, more precisely considering both the talarum and mendocinus groups. Bayesian inferences (BI) were integrated with the results of a Maximum Likelihood approach (ML). Based on these results, the distributional limits of the mendocinus and talarum groups appear to be related to the physiognomy of the Pampas region soils. On the other hand, the validity of C. pundti complex as a differentiated species of C. talarum is debated. According to previous evidence from morphological and chromosomal studies, these results show a very low divergence between those species that originally were classified within the talarum group. Mitochondrial DNA sequences from populations associated with these putative species have not recovered as reciprocal monophyletic groups in the phylogenetic analyses. In conclusion, C. talarum and C. pundti complex might be considered as the same biological species, or lineages going through a recent or incipient differentiation process. The results obtained in this study have important implications for conservation policies and practices, since both species are currently categorized as Vulnerable and Endangered, respectively.

Biogeography of the monocotyledon astelioid clade (Asparagales): A history of long-distance dispersal and diversification with emerging habitats

The astelioid families (Asteliaceae, Blandfordiaceae, Boryaceae, Hypoxidaceae, and Lanariaceae) have centers of diversity in Australasia and temperate Africa, with secondary centers of diversity in Afromontane Africa, Asia, and Pacific Islands. The global distribution of these families makes this an excellent lineage to test if current distribution patterns are the result of vicariance or long-distance dispersal and to evaluate the roles of Tertiary climatic and geological drivers in lineage diversification. Sequence data were generated from five chloroplast regions (petL-psbE, rbcL, rps16-trnK, trnL-trnLF, trnS-trnSG) for 104 ingroup species sampled across global diversity. The astelioid phylogeny was inferred using maximum parsimony, maximum likelihood, and Bayesian inference methods. Divergence dates were estimated with a relaxed clock applied in BEAST. Ancestral ranges were reconstructed in the R package 'BioGeoBEARS' applying the corrected Akaike information criterion to test for the best-fit biogeographic model. Diversification rates were estimated in Bayesian Analysis of Macroevolutionary Mixtures (BAMM). Astelioid relationships were inferred as Boryaceae(Blandfordiaceae(Asteliaceae(Hypoxidaceae plus Lanariaceae))). The crown astelioid node was dated to the Late Cretaceous (75.2 million years; 95% highest posterior density interval 61.0-90.0 million years) and an Antarctic-Australasian origin was inferred. Astelioid speciation events have not been shaped by Gondwanan vicariance. Rather long-distance dispersal since the Eocene is inferred to account for current distributions. Crown Asteliaceae and Boryaceae have Australian ancestral ranges and diversified since the Eocene. In Hypoxidaceae, Empodium, Hypoxis, and Pauridia have African ancestral ranges, while Curculigo and Molineria have an Asian ancestral range. Diversification of Pauridia and the Curculigo clade occurred steadily, while diversification of Astelia and Hypoxis was punctuated over time. Diversification of Hypoxis and Astelia coincided temporally with the expansion of the habitat types occupied by extant taxa, e.g., grassland habitat in Africa during the Late Miocene and alpine habitat in New Zealand during the Pliocene, respectively.

Fossil-calibrated time tree of Podarcis wall lizards provides limited support for biogeographic calibration models

Podarcis wall lizards are endemic to the Mediterranean Basin where they represent the predominant reptile group. Despite being extensively used as model organisms in evolutionary and ecological studies their phylogeny and historical biogeography are still incompletely resolved. Moreover, molecular clock calibrations used in wall lizard phylogeography are based on the assumption of vicariant speciation triggered by the abrupt Mediterranean Sea level rise at the end of the Messinian salinity crisis (MSC). However, the validity of this biogeographic calibration remains untested. In this study we inferred a robust time tree based on multilocus data and fossil calibrations using both gene concatenation and species-tree approaches and including models with gene-flow. We found five deeply divergent, geographically coherent, and well-supported clades comprising species from i) Iberian Peninsula and North Africa; ii) Western Mediterranean islands, iii) Sicilian and Maltese islands; and iv-v) Balkan region and Aegean islands. The mitochondrial tree shows some inconsistencies with the species tree that warrant future investigation. Diversification of main clades is estimated in a short time frame during the Middle Miocene and might have been associated with a period of global climate cooling with the establishment of a marked climatic zonation in Europe. Cladogenetic events within the main clades are scattered throughout the time tree, from the Late Miocene to the Early Pleistocene, suggesting that speciation events in wall lizards reflect a complex interplay between regional topography, climate and geological history rather than a shared major climatic or paleogeographic event. Our absolute time estimates, as well as a relative dating approach, demonstrate that the assumption of a causal link between sea-level rise at the end of the MSC and the diversification of many island endemics is not justified. This study reinforces the notion that multiple dispersal and vicariant events, at different time frames, are required to explain current allopatric distributions and to account for the historical assembly of Mediterranean biota, and cautions against the use of biogeographic calibrations based on the assumption of vicariance.

The implications of interrelated assumptions on estimates of divergence times and rates of diversification

Phylogenies are increasingly being used as a basis to provide insight into macroevolutionary history. Here, we use simulation experiments and empirical analyses to evaluate methods that use phylogenies as a basis to make estimates of divergence times and rates of diversification. This is the first study to present a comprehensive assessment of the key variables that underpin analyses in this field - including substitution rates, speciation rates, and extinction, plus character sampling and taxon sampling. We show that in unrealistically simplistic cases (where substitution rates and speciation rates are constant, and where there is no extinction), increased character and taxon sampling lead to more accurate and precise parameter estimates. By contrast, in more complex but realistic cases (where substitution rates, speciation rates, and extinction rates vary), gains in accuracy and precision from increased character and taxon sampling are far more limited. The lack of accuracy and precision even occurs when using methods that are designed to account for more complex cases, such as relaxed clocks, fossil calibrations, and models that allow speciation rates and extinction rates to vary. The problem also persists when analysing genomic scale datasets. These results suggest two interrelated problems that occur when the processes that generated the data are more complex. First, methodological assumptions are more likely to be violated. Second, limitations in the information content of the data become more important.

Mind the Outgroup and Bare Branches in Total-Evidence Dating: a Case Study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae)

Taxon sampling is a central aspect of phylogenetic study design, but it has received limited attention in the context of total-evidence dating, a widely used dating approach that directly integrates molecular and morphological information from extant and fossil taxa. We here assess the impact of commonly employed outgroup sampling schemes and missing morphological data in extant taxa on age estimates in a total-evidence dating analysis under the uniform tree prior. Our study group is Pimpliformes, a highly diverse, rapidly radiating group of parasitoid wasps of the family Ichneumonidae. We analyze a data set comprising 201 extant and 79 fossil taxa, including the oldest fossils of the family from the Early Cretaceous and the first unequivocal representatives of extant subfamilies from the mid-Paleogene. Based on newly compiled molecular data from ten nuclear genes and a morphological matrix that includes 222 characters, we show that age estimates become both older and less precise with the inclusion of more distant and more poorly sampled outgroups. These outgroups not only lack morphological and temporal information but also sit on long terminal branches and considerably increase the evolutionary rate heterogeneity. In addition, we discover an artifact that might be detrimental for total-evidence dating: "bare-branch attraction," namely high attachment probabilities of certain fossils to terminal branches for which morphological data are missing. Using computer simulations, we confirm the generality of this phenomenon and show that a large phylogenetic distance to any of the extant taxa, rather than just older age, increases the risk of a fossil being misplaced due to bare-branch attraction. After restricting outgroup sampling and adding morphological data for the previously attracting, bare branches, we recover a Jurassic origin for Pimpliformes and Ichneumonidae. This first age estimate for the group not only suggests an older origin than previously thought but also that diversification of the crown group happened well before the Cretaceous-Paleogene boundary. Our case study demonstrates that in order to obtain robust age estimates, total-evidence dating studies need to be based on a thorough and balanced sampling of both extant and fossil taxa, with the aim of minimizing evolutionary rate heterogeneity and missing morphological information. [Bare-branch attraction; ichneumonids; fossils; morphological matrix; phylogeny; RoguePlots.].

Global Diversification of Anelosimus Spiders Driven by Long-Distance Overwater Dispersal and Neogene Climate Oscillations

Vicariance and dispersal events, combined with intricate global climatic history, have left an imprint on the spatiotemporal distribution and diversity of many organisms. Anelosimus cobweb spiders (Theridiidae), are organisms ranging in behavior from solitary to highly social, with a cosmopolitan distribution in temperate to tropical areas. Their evolutionary history and the discontinuous distribution of species richness suggest that 1) long-distance overwater dispersal and 2) climate change during the Neogene (23-2.6 Ma), may be major factors in explaining their distribution and diversification. Here, we test these hypotheses, and explicitly test if global Miocene/Pliocene climatic cooling in the last 8 Ma affected Anelosimus radiation in parallel in South America and Madagascar. To do so, we investigate the phylogeny and spatiotemporal biogeography of Anelosimus through a culmination of a 20-year comprehensive global sampling at the species level (69 species, including 84% of the known 75 species worldwide, represented by 268 individuals) using nucleotide data from seven loci (5.5 kb). Our results strongly support the monophyly of Anelosimus with an Oligocene ($\sim $30 Ma) South American origin. Major clades on other continents originate via multiple, long-distance dispersal events, of solitary or subsocial-but not social-lineages, from the Americas. These intercontinental dispersals were to Africa, Madagascar (twice), and SE Asia/Australasia. The early diversification of Anelosimus spiders coincides with a sudden thermal increase in the late Oligocene ($\sim $27-25 Ma), though no causal connection can be made. Our results, however, strongly support the hypothesis that global Neogene climatic cooling in the last 8 Ma drove Anelosimus radiation in parallel in South America and Madagascar, offering a rare empirical evidence for diversification of a socially diverse group driven by an interplay between long-distance dispersal and global Neogene climatic changes. [Cobweb spiders; diversification; global biogeography; long-distance dispersal; molecular phylogenetics; neogene climate changes; sociality; vicariance.].

Phylogenomics indicates the "living fossil" Isoetes diversified in the Cenozoic

The fossil record provides an invaluable insight into the temporal origins of extant lineages of organisms. However, establishing the relationships between fossils and extant lineages can be difficult in groups with low rates of morphological change over time. Molecular dating can potentially circumvent this issue by allowing distant fossils to act as calibration points, but rate variation across large evolutionary scales can bias such analyses. In this study, we apply multiple dating methods to genome-wide datasets to infer the origin of extant species of Isoetes, a group of mostly aquatic and semi-aquatic isoetalean lycopsids, which closely resemble fossil forms dating back to the Triassic. Rate variation observed in chloroplast genomes hampers accurate dating, but genome-wide nuclear markers place the origin of extant diversity within this group in the mid-Paleogene, 45-60 million years ago. Our genomic analyses coupled with a careful evaluation of the fossil record indicate that despite resembling forms from the Triassic, extant Isoetes species do not represent the remnants of an ancient and widespread group, but instead have spread around the globe in the relatively recent past.

Estimating rates and patterns of diversification with incomplete sampling: a case study in the rosids

PREMISE

Recent advances in generating large-scale phylogenies enable broad-scale estimation of species diversification. These now common approaches typically are characterized by (1) incomplete species coverage without explicit sampling methodologies and/or (2) sparse backbone representation, and usually rely on presumed phylogenetic placements to account for species without molecular data. We used empirical examples to examine the effects of incomplete sampling on diversification estimation and provide constructive suggestions to ecologists and evolutionary biologists based on those results.

METHODS

We used a supermatrix for rosids and one well-sampled subclade (Cucurbitaceae) as empirical case studies. We compared results using these large phylogenies with those based on a previously inferred, smaller supermatrix and on a synthetic tree resource with complete taxonomic coverage. Finally, we simulated random and representative taxon sampling and explored the impact of sampling on three commonly used methods, both parametric (RPANDA and BAMM) and semiparametric (DR).

RESULTS

We found that the impact of sampling on diversification estimates was idiosyncratic and often strong. Compared to full empirical sampling, representative and random sampling schemes either depressed or inflated speciation rates, depending on methods and sampling schemes. No method was entirely robust to poor sampling, but BAMM was least sensitive to moderate levels of missing taxa.

CONCLUSIONS

We suggest caution against uncritical modeling of missing taxa using taxonomic data for poorly sampled trees and in the use of summary backbone trees and other data sets with high representative bias, and we stress the importance of explicit sampling methodologies in macroevolutionary studies.

Evolution of Lomandroideae: Multiple origins of polyploidy and biome occupancy in Australia

Asparagaceae: Lomandroideae are a species-rich and economically important subfamily in the monocot order Asparagales, with a center of diversity in Australia. Lomandroideae are ecologically diverse, occupying mesic and arid biomes in Australia and possessing an array of key traits, including sexual dimorphism, storage organs and polyploidy that are potentially adaptive for survival in seasonally arid and fire-dependent habitats. The Lomandroideae phylogeny was reconstructed using maximum likelihood and Bayesian inference criteria, based on plastome data from genome-skimming to infer relationships. A fossil-calibrated chronogram provided a temporal framework for understanding trait transitions. Ancestral state reconstructions and phylogenetic comparative trait correlation analyses provided insights into the evolutionary and ecological drivers associated with Lomandroideae diversification. Lomandroideae diverged from the other Asparagaceae ca. 56.61 million years ago (95% highest posterior density values 70.31-45.34 million years) and the major lineages diversified since the Oligocene. The most recent common ancestor of the clade likely occupied the mesic biome, was hermaphroditic and geophytic. Biome occupancy transitions were correlated with polyploidy and the presence of storage roots. Polyploidy potentially serves as an "enabler" trait, generating novel phenotypes, which may confer tolerance to climatic ranges and soil conditions putatively required for expansion into and occupation of new arid biomes. Storage roots, as a key factor driving biome transitions, may have been associated with fire rather than with aridification events in the Australian flora. This study contributes significantly to our understanding of biome evolution by identifying polyploidy and storage organs as key factors associated with transitions in biome occupancy in this lineage.

Multilocus phylogeny of Paratelmatobiinae (Anura: Leptodactylidae) reveals strong spatial structure and previously unknown diversity in the Atlantic Forest hotspot

The Brazilian Atlantic Forest harbors high levels of anuran diversity and endemism, including several taxa restricted to small geographic ranges. Here, we provide a multilocus phylogeny for Paratelmatobiinae, a leptodactylid subfamily composed of small-ranged species distributed in the Brazilian Atlantic Forest and in the campo rupestre ecosystem. We performed Bayesian inference and maximum likelihood analyses using three mitochondrial and five nuclear markers, and a matrix comprising a broad taxonomic sampling. We then delimitated independently evolving lineages within the group. We recovered Paratelmatobiinae and each of its four genera as monophyletic and robustly supported. Five putatively new species included in our analyses were unambiguously supported in the phylogenetic trees and delimitation analyses. We also recovered other deeply divergent and geographically structured lineages within the four genera of Paratelmatobiinae. Our estimation of divergence times indicates that diversification in the subfamily began in the Eocene and continued until the Pleistocene. We discuss possible scenarios of diversification for the four genera of Paratelmatobiinae, and outline the implications of our findings for taxonomy and conservation.

Priors and Posteriors in Bayesian Timing of Divergence Analyses: The Age of Butterflies Revisited

The need for robust estimates of times of divergence is essential for downstream analyses, yet assessing this robustness is still rare. We generated a time-calibrated genus-level phylogeny of butterflies (Papilionoidea), including 994 taxa, up to 10 gene fragments and an unprecedented set of 12 fossils and 10 host-plant node calibration points. We compared marginal priors and posterior distributions to assess the relative importance of the former on the latter. This approach revealed a strong influence of the set of priors on the root age but for most calibrated nodes posterior distributions shifted from the marginal prior, indicating significant information in the molecular data set. Using a very conservative approach we estimated an origin of butterflies at 107.6 Ma, approximately equivalent to the latest Early Cretaceous, with a credibility interval ranging from 89.5 Ma (mid Late Cretaceous) to 129.5 Ma (mid Early Cretaceous). In addition, we tested the effects of changing fossil calibration priors, tree prior, different sets of calibrations and different sampling fractions but our estimate remained robust to these alternative assumptions. With 994 genera, this tree provides a comprehensive source of secondary calibrations for studies on butterflies.

Major lineages of Loasaceae subfam. Loasoideae diversified during the Andean uplift

The Loasoideae is the largest clade in the Loasaceae. This subfamily is widespread throughout the Neotropics and centered in the Andes, presenting an excellent opportunity to study diversification across much of temperate and mid to high-elevation areas of South America. Despite that, no studies have addressed the historical biogeography of the Loasoideae to date, leaving an important knowledge gap in this plant group. Here, we used four plastid markers (i.e., trnL-trnF, matK, trnS-trnG, and rps16) and sequenced 170 accessions (134 ingroup taxa) to infer the phylogeny of Loasoideae. We then used this phylogeny as basis to estimate divergence times using an uncorrelated relaxed molecular clock approach and seven fossils as primary calibration points. We employed the Dispersal-Extinction-Cladogenesis (DEC) approach to reconstruct the ancestral ranges of the subfamily. Our results indicate that stem Loasoideae diverged from its sister group in the Late Cretaceous to Early Paleocene (ca. 83-62 Ma). The crown node of the whole clade goes back to the Middle Paleocene to Middle Eocene (ca. 60-45 Ma), corresponding to the earliest diversification events of the extant groups, prior to most of the Andean orogeny and roughly coinciding with the Paleocene-Eocene Thermal Maximum. On the other hand, the crown nodes of most genera appear to have originated in the Oligocene and Miocene (median ages: 28-10 Ma). The diversification of some extant lineages appears to have happened in parallel to Andean uplift pulses that seem to have had an effect on the orogeny and concomitant establishment of new habitats and latitudinal corridors. The most likely ancestral areas retrieved for crown Loasoideae, are the tropical Andes and Pacific arid coast. Most of the extant clades have remained restricted to their ancestral areas. Transoceanic Long Distance Dispersal appears to have been involved in the arrival of Loasoid ancestors to South America, and in the distribution of the small clades Kissenia in Africa and Plakothira on the Marquesas Archipelago. The results presented here suggest that the historical biogeography of the continental scale radiation of Loasoideae, follows the sequence and timing of the development of temperate and mid to high-elevation habitats across South America during the Tertiary.

Phylogeny, origin and dispersal of Saussurea (Asteraceae) based on chloroplast genome data

Saussurea is one of the largest genera of the tribe Cardueae of Asteraceae, comprising about 460 species from the Northern Hemisphere with most species distributed in QTPss and adjacent areas. Here, we established a well-supported phylogenetic framework for Saussurea based on whole chloroplast genomes of 136 taxa plus 16 additional taxa of Cardueae using Bayesian inference and Maximum Likelihood. Our phylogenetic results are inconsistent with previous subgeneric classifications of Saussurea. We nearly completely delimited subgen. Eriocoryne, and found that subgen. Theodorea, subgen. Saussurea section Laguranthera and Rosulascentes are closely related to each other. Based on our phylogenetic results, we performed biogeographic analyses and inferred that the genus Saussurea arose during early-middle Miocene within the Hengduan Mountains. We expect that landscape heterogeneity within the QTPss and adjacent areas, such as the Hengduan Mountains, played an important role in the evolution of Saussurea. Following its evolutionary origin, the genus underwent rapid diversification in situs and dispersed northwards in several migrational patterns. Both continuous uplift of the QTPss and adjacent areas as well as global cooling since mid-Miocene probably led to geographic expansion and diffusion of Saussurea, with the latter, in particular, resulting in the northward dispersal.

Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics

The amount and patterns of phylodiversity in a community are often used to draw inferences about the local and historical factors affecting community assembly and can be used to prioritize communities and locations for conservation. Because measures of phylodiversity are based on the topology and branch lengths of phylogenetic trees, which are affected by the number and diversity of taxa in the tree, these analyses may be sensitive to changes in taxon sampling and tree reconstruction methods.To investigate the effects of taxon sampling and tree reconstruction methods on measures of phylodiversity, we investigated the community phylogenetics of the Ordway-Swisher Biological Station (Florida), which is home to over 600 species of vascular plants. We studied the effects of (a) the number of taxa included in the regional phylogeny; (b) random versus targeted sampling of species to assemble the regional species pool; (c) including only species from specific clades rather than broad sampling; (d) using trees reconstructed directly for the taxa under study compared to trees pruned from a larger reconstructed tree; and (e) using phylograms compared to chronograms.We found that including more taxa in a study increases the likelihood of observing significantly nonrandom phylogenetic patterns. However, there were no consistent trends in the phylodiversity patterns based on random taxon sampling compared to targeted sampling, or within individual clades compared to the complete dataset. Using pruned and reconstructed phylogenies resulted in similar patterns of phylodiversity, while chronograms in some cases led to significantly different results from phylograms.The methods commonly used in community phylogenetic studies can significantly impact the results, potentially influencing both inferences of community assembly and conservation decisions. We highlight the need for both careful selection of methods in community phylogenetic studies and appropriate interpretation of results, depending on the specific questions to be addressed.

Molecular phylogeny and biogeography of the land snail subfamily Leptaxinae (Gastropoda: Hygromiidae)

The subfamily Leptaxinae is included within the highly diverse land snail family Hygromiidae. In the absence of clear diagnostic morphological differences, the subfamily status is currently based solely on molecular information and includes three disjunctly distributed tribes, Leptaxini, Cryptosaccini and Metafruticicolini. However, the phylogenetic relationships among these tribes are not fully resolved and the clustering of some of the genera to the tribes is not statistically supported. To resolve the relationships within Leptaxinae and their position within Hygromiidae, we reconstructed their phylogeny using a multi-locus approach with two mitochondrial genes and eight nuclear markers. The phylogeny was further calibrated and an analysis of ancestral area estimation was carried out to infer the biogeographic history of the group. We elevated Metafruticicolini to subfamily level (Metafruticicolinae) and we restricted Leptaxinae to Cryptosaccini and Leptaxini. The Lusitanian genus Portugala was moved to Leptaxini, previously containing only the Macaronesian genus Leptaxis. Within Cryptosaccini, a new genus strictly confined to the Sierra de la Cabrera (Spain) is described, Fractanella gen. nov. According to our results, Leptaxinae originated in the Early Miocene in the Iberian Peninsula, from which the Macaronesian Islands were colonized. Due to the old split recovered for the divergence between Macaronesian and Iberian lineages, we hypothesize that this colonization may have occurred via the once emerged seamounts located between the archipelagos and the European and African continents, although this could also have occurred through the oldest now emerged islands of Macaronesia. In the Iberian Peninsula, the climatic shift that began during the Middle Miocene, changing progressively from subtropical climate towards the present-day Mediterranean climate, was identified as an important factor shaping the subfamily's diversification, along with Pleistocene climatic fluctuations.

Recent range expansion in Australian hummock grasses (Triodia) inferred using genotyping-by-sequencing

The Australian arid zone (AAZ) has undergone aridification and the formation of vast sandy deserts since the mid-Miocene. Studies on AAZ organisms, particularly animals, have shown patterns of mesic ancestry, persistence in rocky refugia and range expansions in arid lineages. There has been limited molecular investigation of plants in the AAZ, particularly of taxa that arrived in Australia after the onset of aridification. Here we investigate populations of the widespread AAZ grass Triodia basedowii to determine whether there is evidence for a recent range expansion, and if so, its source and direction. We also undertake a dating analysis for the species complex to which T. basedowii belongs, in order to place its diversification in relation to changes in AAZ climate and landscapes. We analyse a genomic single nucleotide polymorphism data set from 17 populations of T. basedowii in a recently developed approach for detecting the signal and likely origin of a range expansion. We also use alignments from existing and newly sequenced plastomes from across Poaceae for analysis in BEAST to construct fossil-calibrated phylogenies. Across a range of sampling parameters and outgroups, we detected a consistent signal of westward expansion for T. basedowii, originating in central or eastern Australia. Divergence time estimation indicates that Triodia began to diversify in the late Miocene (crown 7.0-8.8 million years (Ma)), and the T. basedowii complex began to radiate during the Pleistocene (crown 1.4-2.0 Ma). This evidence for range expansion in an arid-adapted plant is consistent with similar patterns in AAZ animals and likely reflects a general response to the opening of new habitat during aridification. Radiation of the T. basedowii complex through the Pleistocene has been associated with preferences for different substrates, providing an explanation why only one lineage is widespread across sandy deserts.

Molecular phylogeny and diversification timing of the Nemouridae family (Insecta, Plecoptera) in the Japanese Archipelago

The generation of the high species diversity of insects in Japan was profoundly influenced by the formation of the Japanese Archipelago. We explored the species diversification and biogeographical history of the Nemouridae Billberg, 1820 family in the Japanese Archipelago using mitochondrial DNA and nuclear DNA markers. We collected 49 species among four genera: Indonemoura Baumann, 1975; Protonemura Kempny, 1898; Amphinemura, Ris 1902 and Nemoura Latreille, 1796 in Japan, China, South Korea and North America. We estimated their divergence times-based on three molecular clock node calibrations-using Bayesian phylogeography approaches. Our results suggested that Japanese Archipelago formation events resulted in diversification events in the middle of the Cretaceous (<120 Ma), speciation in the Paleogene (<50 Ma) and intra-species diversification segregated into eastern and western Japan of the Fossa Magna region at late Neogene (20 Ma). The Indonemoura samples were genetically separated into two clades-that of Mainland China and that of Japan. The Japanese clade clustered with the Nemouridae species from North America, suggesting the possibility of a colonisation event prior to the formation of the Japanese Archipelago. We believe that our results enhanced the understanding both of the origin of the species and of local species distribution in the Japanese Archipelago.

A transcriptome-based resolution for a key taxonomic controversy in Cupressaceae

BACKGROUND AND AIMS

Rapid evolutionary divergence and reticulate evolution may result in phylogenetic relationships that are difficult to resolve using small nucleotide sequence data sets. Next-generation sequencing methods can generate larger data sets that are better suited to solving these puzzles. One major and long-standing controversy in conifers concerns generic relationships within the subfamily Cupressoideae (105 species, approx. 1/6 of all conifers) of Cupressaceae, in particular the relationship between Juniperus, Cupressus and the Hesperocyparis-Callitropsis-Xanthocyparis (HCX) clade. Here we attempt to resolve this question using transcriptome-derived data.

METHODS

Transcriptome sequences of 20 species from Cupressoideae were collected. Using MarkerMiner, single-copy nuclear (SCN) genes were extracted. These were applied to estimate phylogenies based on concatenated data, species trees and a phylogenetic network. We further examined the effect of alternative backbone topologies on downstream analyses, including biogeographic inference and dating analysis.

RESULTS

Based on the 73 SCN genes (>200 000 bp total alignment length) we considered, all tree-building methods lent strong support for the relationship (HCX, (Juniperus, Cupressus)); however, strongly supported conflicts among individual gene trees were also detected. Molecular dating suggests that these three lineages shared a most recent common ancestor approx. 60 million years ago (Mya), and that Juniperus and Cupressus diverged about 56 Mya. Ancestral area reconstructions (AARs) suggest an Asian origin for the entire clade, with subsequent dispersal to North America, Europe and Africa.

CONCLUSIONS

Our analysis of SCN genes resolves a controversial phylogenetic relationship in the Cupressoideae, a major clade of conifers, and suggests that rapid evolutionary divergence and incomplete lineage sorting probably acted together as the source for conflicting phylogenetic inferences between gene trees and between our robust results and recently published studies. Our updated backbone topology has not substantially altered molecular dating estimates relative to previous studies; however, application of the latest AAR approaches has yielded a clearer picture of the biogeographic history of Cupressoideae.

Pleistocene diversification in an ancient lineage: a role for glacial cycles in the evolutionary history of Dioon Lindl. (Zamiaceae)

PREMISE OF THE STUDY

Recent estimates of crown ages for cycad genera (Late Miocene) challenge us to consider what processes have produced the extant diversity of this ancient group in such relatively little time. Pleistocene climate change has driven major shifts in species distributions in Mexico and may have led to speciation in the genus Dioon by forcing populations to migrate up in elevation, thereby becoming separated by topography.

METHODS

We inferred orthologs from transcriptomes of five species and sequenced these in 42 individuals representing all Dioon species. From these data and published plastid sequences, we inferred dated species trees and lineage-specific diversification rates.

KEY RESULTS

Analyses of 84 newly sequenced nuclear orthologs and published plastid data confirm four major clades within Dioon, all of Pleistocene age. Gene tree analysis, divergence dates, and an increase in diversification rate support very recent and rapid divergence of extant taxa.

CONCLUSIONS

This study confirms the Pleistocene age of Dioon species and implicates Pleistocene climate change and established topography in lineage spitting. These results add to our understanding of the cycads as evolutionarily dynamic lineages, not relicts or evolutionary dead ends. We also find that well-supported secondary calibration points can be reliable in the absence of fossils. Our hypothesis of lineage splitting mediated by habitat shifts may be applicable to other taxa that are restricted to elevation specific ecotones.

Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case

Primates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the Cretaceous-Paleogene (K-Pg) boundary and the timing of diversification of the main crown groups remain controversial. Here, we analysed a data set of 372 taxa (367 Primates and 5 outgroups, 3.4 million aligned base pairs) that includes nine primate genomes. We systematically explore the effect of different interpretations of fossil calibrations and molecular clock models on primate divergence time estimates. We find that even small differences in the construction of fossil calibrations can have a noticeable impact on estimated divergence times, especially for the oldest nodes in the tree. Notably, choice of molecular rate model (autocorrelated or independently distributed rates) has an especially strong effect on estimated times, with the independent rates model producing considerably more ancient age estimates for the deeper nodes in the phylogeny. We implement thermodynamic integration, combined with Gaussian quadrature, in the program MCMCTree, and use it to calculate Bayes factors for clock models. Bayesian model selection indicates that the autocorrelated rates model fits the primate data substantially better, and we conclude that time estimates under this model should be preferred. We show that for eight core nodes in the phylogeny, uncertainty in time estimates is close to the theoretical limit imposed by fossil uncertainties. Thus, these estimates are unlikely to be improved by collecting additional molecular sequence data. All analyses place the origin of Primates close to the K-Pg boundary, either in the Cretaceous or straddling the boundary into the Palaeogene.

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.

Historical Biogeography of endemic seed plant genera in the Caribbean: Did GAARlandia play a role?

The Caribbean archipelago is a region with an extremely complex geological history and an outstanding plant diversity with high levels of endemism. The aim of this study was to better understand the historical assembly and evolution of endemic seed plant genera in the Caribbean, by first determining divergence times of endemic genera to test whether the hypothesized Greater Antilles and Aves Ridge (GAARlandia) land bridge played a role in the archipelago colonization and second by testing South America as the main colonization source as expected by the position of landmasses and recent evidence of an asymmetrical biotic interchange. We reconstructed a dated molecular phylogenetic tree for 625 seed plants including 32 Caribbean endemic genera using Bayesian inference and ten calibrations. To estimate the geographic range of the ancestors of endemic genera, we performed a model selection between a null and two complex biogeographic models that included timeframes based on geological information, dispersal probabilities, and directionality among regions. Crown ages for endemic genera ranged from Early Eocene (53.1 Ma) to Late Pliocene (3.4 Ma). Confidence intervals for divergence times (crown and/or stem ages) of 22 endemic genera occurred within the GAARlandia time frame. Contrary to expectations, the Antilles appears as the main ancestral area for endemic seed plant genera and only five genera had a South American origin. In contrast to patterns shown for vertebrates and other organisms and based on our sampling, we conclude that GAARlandia did not act as a colonization route for plants between South America and the Antilles. Further studies on Caribbean plant dispersal at the species and population levels will be required to reveal finer-scale biogeographic patterns and mechanisms.

Frequent and parallel habitat transitions as driver of unbounded radiations in the Cape flora

The enormous species richness in the Cape Floristic Region (CFR) of Southern Africa is the result of numerous radiations, but the temporal progression and possible mechanisms of these radiations are still poorly understood. Here, we explore the macroevolutionary dynamics of the Restionaceae, which include 340 species that are found in all vegetation types in the Cape flora and are ecologically dominant in fynbos. Using an almost complete (i.e., 98%) species-level time calibrated phylogeny and models of diversification dynamics, we show that species diversification is constant through the Cenozoic, with no evidence of an acceleration with the onset of the modern winter-wet climate, or a recent density-dependent slowdown. Contrary to expectation, species inhabiting the oldest (montane) and most extensive (drylands) habitats did not undergo higher diversification rates than species in the younger (lowlands) and more restricted (wetland) habitats. We show that the rate of habitat transitions is more closely related to the speciation rate than to time, and that more than a quarter of all speciation events are associated with habitat transitions. This suggests that the unbounded Restionaceae diversification resulted from numerous, parallel, habitat shifts, rather than persistence in a habitat stimulating speciation. We speculate that this could be one of the mechanisms resulting in the hyperdiverse Cape flora.

Adaptive radiations should not be simplified: The case of the danthonioid grasses

Although much of extant diversity is probably the product of evolutionary radiations, the special case of adaptive radiations has not yet been thoroughly explored. Adaptive radiations are postulated to occur when a lineage is exposed to new ecological opportunities, where it can diversify ecologically. We argue that adaptive radiations have two characteristics. Firstly, the diversification rate accelerates initially, and is then followed by a density-dependent slow-down. Secondly, traits relevant to the new ecological opportunity should evolve at or just before the radiation. We also argue that a correct identification of adaptive radiations is dependent on the phylogenies underlying the diversification dynamics being sampled adequately (i.e. comprehensive species sampling), and that the traits should be treated continuously if they exhibit a biological continuum and not be over-simplified into binary traits. Here, we test the hypothesis that much of the extant diversity of the south-temperate grass subfamily Danthonioideae is the result of two geographically separated but contemporaneous adaptive radiations, in response to Late-Miocene-Pliocene aridification and increasingly seasonal climates. We show that both Pentameris (83 African species) and Rytidosperma (73 Australasian-South American species) exhibit accelerations in diversification rates followed by linear density-dependent declines. We also show that two selected traits show differential evolutionary regimes with different evolutionary optima, and that these are linked to changes in the diversification rate. These results are consistent with these being adaptive, and putatively parallel, radiations. However, by mapping traits over the whole danthonioid phylogeny, it is evident that no identified trait or trait combination is sufficient and necessary for adaptive radiations. Furthermore, we show that simplifying the traits to binary gives a strong but potentially erroneous link between trait shift and diversification rate shift.

Historical biogeography and ecological niche modelling of the Asimina-Disepalum clade (Annonaceae): role of ecological differentiation in Neotropical-Asian disjunctions and diversification in Asia

BACKGROUND

The Asimina-Disepalum clade (Annonaceae subfam. Annonoideae tribe Annoneae) includes a major Neotropical-Asian biogeographical disjunction. We evaluate whether this disjunction can be explained by the Eocene boreotropics hypothesis, which relies on the existence of extensive boreotropical forests during the Late Palaeocene-Early Eocene thermal maximum (52-50 Ma), followed by disruption of boreotropical vegetation during post-Eocene cooling. Molecular dating using an uncorrelated relaxed molecular clock (UCLD) model with two fossil calibrations, ancestral range estimation, and ecological niche modelling across evolutionary time were performed. Our focus was the geographical origin of Disepalum and general biogeographic patterns within this genus. Comparison of ecological tolerance among extant species and niche reconstructions at ancestral nodes within the clade enabled insights in likely migration routes of lineages, as well as evaluating the role of bioclimatic ecological differentiation in the diversification of Disepalum within Southeast Asia.

RESULTS

The inferred vicariance event associated with the Asimina-Disepalum disjunction is estimated to have originated ca. 40 Mya [95% highest posterior density (HPD): 44.3-35.5 Mya]. The Disepalum crown lineage is estimated to have originated ca. 9 Mya (95% HPD: 10.6-7.6), either in western Malesia and continental Southeast Asia, or exclusively in western Malesia. Ecological niche modelling shows that seasonality of temperature and precipitation are major contributors determining the geographical range of species. Ancestral niche modelling furthermore indicates that the ancestor of the Asimina-Disepalum clade likely had bioclimatic preferences close to conditions found in current tropical and subtropical climates across Asia, whereas the ancestors of the Asimina and Disepalum crown groups are projected onto the more subtropical and tropical regions, respectively.

CONCLUSIONS

The vicariance event associated with the Neotropical-Asian disjunction within the Asimina-Disepalum clade likely coincided with climatic deterioration at the Eocene-Oligocene boundary. Although detrended component analyses (DCA) indicate that altitude and seasonality of temperature and precipitation have the greatest influence in determining the geographical range of species, isolation due to palaeogeographic and palaeoclimatic events appears to be of greater significance than climate niche differentiation in driving diversification in Disepalum.

Phylogenetic relationships among tribes of the green lacewing subfamily Chrysopinae recovered based on mitochondrial phylogenomics

Chrysopidae (green lacewings) is the second largest family in Neuroptera, and it includes medium-size lacewings largely recognized by the presence of golden-colored eyes, bright green bodies and delicate wings with dense venation patterns. The subfamily Chrysopinae includes 97% of the species diversity in the family and it is currently divided into four tribes: Ankylopterygini, Belonopterygini, Chrysopini and Leucochrysini. Here we sequenced and annotated the nearly complete mitochondrial genomes of four species of each these tribes: Abachrysa eureka, Italochrysa insignis, Leucochrysa pretiosa, Parankyloteryx sp. We then reconstructed the phylogenetic relationships with estimated divergence times among tribes of Chrysopinae based on the mt genomic data. Our results suggest that Chrysopinae sans Nothancyla verreauxi evolved as two reciprocally monophyletic lineages formed by stem members of the tribes Leucochrysini plus Belonopterygini on one hand, and the stem members of Ankylopterygini plus Chrysopini on the other. Our estimations of divergence times place the diversification of stem Chrysopinae into the extant tribes during the Middle Jurassic to Late Cretaceous. The relatively young ages previously estimated for the green lacewing divergences were probably underestimated due to false inferences of homology between non-sister taxa that are later correctly identified as homoplasy after more taxa are added.

Arrival and diversification of mabuyine skinks (Squamata: Scincidae) in the Neotropics based on a fossil-calibrated timetree

BACKGROUND

The evolution of South American Mabuyinae skinks holds significant biogeographic interest because its sister lineage is distributed across the African continent and adjacent islands. Moreover, at least one insular species, Trachylepis atlantica, has independently reached the New World through transoceanic dispersal. To clarify the evolutionary history of both Neotropical lineages, this study aimed to infer an updated timescale using the largest species and gene sampling dataset ever assembled for this group. By extending the analysis to the Scincidae family, we could employ fossil information to estimate mabuyinae divergence times and carried out a formal statistical biogeography analysis. To unveil macroevolutionary patterns, we also inferred diversification rates for this lineage and evaluated whether the colonization of South American continent significantly altered the mode of Mabuyinae evolution.

METHODS

A time-calibrated phylogeny was inferred under the Bayesian framework employing fossil information. This timetree was used to (i) evaluate the historical biogeography of mabuiyines using the statistical approach implemented in BioGeoBEARS; (ii) estimate macroevolutionary diversification rates of the South American Mabuyinae lineages and the patterns of evolution of selected traits, namely, the mode of reproduction, body mass and snout-vent length; (iii) test the hypothesis of differential macroevolutionary patterns in South American lineages in BAMM and GeoSSE; and (iv) re-evaluate the ancestral state of the mode of reproduction of mabuyines.

RESULTS

Our results corroborated the hypothesis that the occupation of the South American continent by Mabuyinae consisted of two independent dispersion events that occurred between the Oligocene and the Miocene. We found significant differences in speciation rates between the New World and the remaining Mabuyinae clades only in GeoSSE. The influence of phenotypic traits on diversification rates was not supported by any method. Ancestral state reconstruction suggested that the ancestor of South American mabuyine was likely viviparous.

DISCUSSION

Our analyses further corroborated the existence of a transoceanic connection between Africa and South America in the Eocene/Oligocene period (Atlantogea). Following colonization of the isolated South America and subsequent dispersal through the continent by the ancestral mabuyine stock, we detected no difference in macroevolutionary regimes of New World clades. This finding argued against the ecological opportunity model as an explanation for the diversity of living mabuyines.

Fossils matter: improved estimates of divergence times in Pinus reveal older diversification

BACKGROUND

The taxonomy of pines (genus Pinus) is widely accepted and a robust gene tree based on entire plastome sequences exists. However, there is a large discrepancy in estimated divergence times of major pine clades among existing studies, mainly due to differences in fossil placement and dating methods used. We currently lack a dated molecular phylogeny that makes use of the rich pine fossil record, and this study is the first to estimate the divergence dates of pines based on a large number of fossils (21) evenly distributed across all major clades, in combination with applying both node and tip dating methods.

RESULTS

We present a range of molecular phylogenetic trees of Pinus generated within a Bayesian framework. We find the origin of crown Pinus is likely up to 30 Myr older (Early Cretaceous) than inferred in most previous studies (Late Cretaceous) and propose generally older divergence times for major clades within Pinus than previously thought. Our age estimates vary significantly between the different dating approaches, but the results generally agree on older divergence times. We present a revised list of 21 fossils that are suitable to use in dating or comparative analyses of pines.

CONCLUSIONS

Reliable estimates of divergence times in pines are essential if we are to link diversification processes and functional adaptation of this genus to geological events or to changing climates. In addition to older divergence times in Pinus, our results also indicate that node age estimates in pines depend on dating approaches and the specific fossil sets used, reflecting inherent differences in various dating approaches. The sets of dated phylogenetic trees of pines presented here provide a way to account for uncertainties in age estimations when applying comparative phylogenetic methods.

Plastome phylogeny and early diversification of Brassicaceae

Background

The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies.

Results

Bayesian and maximum likelihood phylogenetic analyses using a partitioned supermatrix of 77 protein coding genes resulted in nearly identical tree topologies exemplified by highly supported relationships between clades. All four lineages were well identified and interrelationships between them were resolved. The previously defined Clade C was found to be paraphyletic (the genus Megadenia formed a separate lineage), while the remaining clades were monophyletic. Clade E (lineage III) was sister to clades B + C rather than to all core Brassicaceae (clades A + B + C or lineages I + II), as suggested by a previous transcriptome study. Molecular dating based on plastome phylogeny supported the origin of major lineages or clades between late Oligocene and early Miocene, and the following radiative diversification across the family took place within a short timescale. In addition, gene losses in the plastomes occurred multiple times during the evolutionary diversification of the family.

Conclusions

Plastome phylogeny illustrates the early diversification of cruciferous species. This phylogeny will facilitate our further understanding of evolution and adaptation of numerous species in the model family Brassicaceae.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3555-3) contains supplementary material, which is available to authorized users.

Plastome phylogeny and early diversification of Brassicaceae

BACKGROUND

The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies.

RESULTS

Bayesian and maximum likelihood phylogenetic analyses using a partitioned supermatrix of 77 protein coding genes resulted in nearly identical tree topologies exemplified by highly supported relationships between clades. All four lineages were well identified and interrelationships between them were resolved. The previously defined Clade C was found to be paraphyletic (the genus Megadenia formed a separate lineage), while the remaining clades were monophyletic. Clade E (lineage III) was sister to clades B + C rather than to all core Brassicaceae (clades A + B + C or lineages I + II), as suggested by a previous transcriptome study. Molecular dating based on plastome phylogeny supported the origin of major lineages or clades between late Oligocene and early Miocene, and the following radiative diversification across the family took place within a short timescale. In addition, gene losses in the plastomes occurred multiple times during the evolutionary diversification of the family.

CONCLUSIONS

Plastome phylogeny illustrates the early diversification of cruciferous species. This phylogeny will facilitate our further understanding of evolution and adaptation of numerous species in the model family Brassicaceae.

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

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

Dispersal largely explains the Gondwanan distribution of the ancient tropical clusioid plant clade

PREMISE OF THE STUDY

The clusioid clade (Malpighiales) has an ancient fossil record (∼90 Ma) and extant representatives exhibit a pantropical distribution represented on all former Gondwanan landmasses (Africa, Australia, India, Madagascar, and South America) except Antarctica. Several biogeographers have hypothesized that the clusioid distribution is an example of Gondwanan vicariance. Our aim is to test the hypothesis that the modern distribution of the clusioid clade is largely explained by Gondwanan fragmentation.

METHODS

Using a four gene, 207-taxon data set we simultaneously estimated the phylogeny and divergence times of the clusioid clade using a Bayesian Markov chain Monte Carlo approach. Ancestral Area Reconstructions (AARs) were then conducted on a distribution of 1000 trees and summarized on a reduced phylogeny.

KEY RESULTS

Divergence time estimates and AARs revealed only two or four cladogenic events that are potentially consistent with Gondwanan vicariance, depending on the placement of the ancient fossil Paleoclusia. In contrast, dispersal occurred on > 25% of the branches, indicating the current distribution of the clade likely reflects extensive recent dispersal during the Cenozoic (< 65 Ma), most of which occurred after the beginning of the Eocene (∼56 Ma).

CONCLUSIONS

These results support growing evidence that suggests many traditionally recognized angiosperm clades (families and genera) are too young for their distributions to have been influenced strictly by Gondwanan fragmentation. Instead, it appears that corridors of dispersal may be the best explanation for numerous angiosperm clades with Gondwanan distributions.