A comprehensive molecular phylogeny of the terrestrial Parasitengona (Acariformes, Prostigmata) provides insights into the evolution of their metamorphosis, invasion into aquatic habitats and classification.

Parasitengona (velvet mites, chiggers and water mites) is a highly diverse and globally distributed mite lineage encompassing over 11,000 described species, inhabiting terrestrial, freshwater and marine habitats. Certain species, such as chiggers (Trombiculidae), have a great medical and veterinary importance as they feed on their vertebrate hosts and vector pathogens. Despite extensive previous research, the classification of Parasitengona is still contentious, particularly regarding the boundaries between superfamilies and families, exacerbated by the absence of a comprehensive phylogeny. The ontogeny of most Parasitengona is distinct by the presence of striking metamorphosis, with parasitic larvae being heteromorphic compared to the predatory free-living deutonymphs and adults. The enigmatic superfamily Allotanaupodoidea is an exception, with larvae and active post-larval stages being morphologically similar, suggesting that the absence of metamorphosis may be either an ancestral state or a secondary reversal. Furthermore, there is disagreement in the literature on whether Parasitengona had freshwater or terrestrial origin. Here, we inferred phylogenetic relationships of Parasitengona (89 species, 36 families) and 307 outgroups using five genes (7,838 nt aligned). This phylogeny suggests a terrestrial origin of Parasitengona and a secondary loss of metamorphosis in Allotanaoupodoidea. We recovered the superfamily Trombidioidea (Trombidioidea sensu lato) as a large, well-supported, higher-level clade including 10 sampled families. We propose a new classification for the terrestrial Parasitengona with three new major divisions (epifamilies) of the superfamily Trombidioidea: Trombelloidae (families Audyanidae, Trombellidae, Neotrombidiidae, Johnstonianidae, Chyzeriidae); Trombidioidae (Microtrombidiidae, Neothrombiidae, Achaemenothrombiidae, Trombidiidae, Podothrombiidae); and Trombiculoidae (=Trombiculidae sensu lato). Adding them to previously recognized superfamilies Allotanaupodoidea, Amphotrombioidea, Calyptostomatoidea, Erythraeoidea, Tanaupodoidae and Yurebilloidae.

Molecular phylogeny and divergence time of Harpalyce (Leguminosae, Papilionoideae), a lineage with amphitropical diversification in seasonally dry forests and savannas.

Our knowledge of the systematics of the papilionoid legume tribe Brongniartieae has greatly benefitted from recent advances in molecular phylogenetics. The tribe was initially described to include species marked by a strongly bilabiate calyx and an embryo with a straight radicle, but recent research has placed taxa from the distantly related core Sophoreae and Millettieae within it. Despite these advances, the most species-rich genera within the Brongniartieae are still not well studied, and their morphological and biogeographical evolution remains poorly understood. Comprising 35 species, Harpalyce is one of these poorly studied genera. In this study, we present a comprehensive, multi-locus molecular phylogeny of the Brongniartieae, with an increased sampling of Harpalyce, to investigate morphological and biogeographical evolution within the group. Our results confirm the monophyly of Harpalyce and indicate that peltate glandular trichomes and a strongly bilabiate calyx with a carinal lip and three fused lobes are synapomorphies for the genus, which is internally divided into three distinct ecologically and geographically divergent lineages, corresponding to the previously recognized sections. Our biogeographical reconstructions demonstrate that Brongniartieae originated in South America during the Eocene, with subsequent pulses of diversification in South America, Mesoamerica, and Australia. Harpalyce also originated in South America during the Miocene at around 20 Ma, with almost synchronous later diversification in South America and Mexico/Mesoamerica beginning 10 Ma, but mostly during the Pliocene. Migration of Harpalyce from South to North America was accompanied by a biome and ecological shift from savanna to seasonally dry forest.

Back to the roots, desiccation and radiation resistances are ancestral characters in bdelloid rotifers.

BACKGROUND: Bdelloid rotifers are micro-invertebrates distributed worldwide, from temperate latitudes to the most extreme areas of the planet like Antarctica or the Atacama Desert. They have colonized any habitat where liquid water is temporarily available, including terrestrial environments such as soils, mosses, and lichens, tolerating desiccation and other types of stress such as high doses of ionizing radiation (IR). It was hypothesized that bdelloid desiccation and radiation resistance may be attributed to their potential ability to repair DNA double-strand breaks (DSBs). Here, these properties are investigated and compared among nine bdelloid species collected from both mild and harsh habitats, addressing the correlation between the ability of bdelloid rotifers to survive desiccation and their capacity to repair massive DNA breakage in a phylogenetically explicit context. Our research includes both specimens isolated from habitats that experience frequent desiccation (at least 1 time per generation), and individuals sampled from habitats that rarely or never experienced desiccation. RESULTS: Our analysis reveals that DNA repair prevails in somatic cells of both desiccation-tolerant and desiccation-sensitive bdelloid species after exposure to X-ray radiation. Species belonging to both categories are able to withstand high doses of ionizing radiation, up to 1000 Gy, without experiencing any negative effects on their survival. However, the fertility of two desiccation-sensitive species, Rotaria macrura and Rotaria rotatoria, was more severely impacted by low doses of radiation than that of desiccation-resistant species. Surprisingly, the radioresistance of desiccation-resistant species is not related to features of their original habitat. Indeed, bdelloids isolated from Atacama Desert or Antarctica were not characterized by a higher radioresistance than species found in more temperate environments. CONCLUSIONS: Tolerance to desiccation and radiation are supported as ancestral features of bdelloid rotifers, with a group of species of the genus Rotaria having lost this trait after colonizing permanent water habitats. Together, our results provide a comprehensive overview of the evolution of desiccation and radiation resistance among bdelloid rotifers.

Are dark septate endophytes an ancestral ecological state in the evolutionary history of the order Chaetothyriales?

Dark septate endophytes (DSE) are pigmented fungi that colonize plant roots. They represent a morpho-functional status composed of many species belonging to the phylum Ascomycota, distributed in different orders. The order Chaetothyriales has representatives with diverse lifestyles, among which the rock-inhabiting one has been proposed to be the ancestral ecological character state. However, all taxa have the phenotypic characteristic of being highly melanized. This trait has been considered relevant in most Chaetothyriales because it allows them to tolerate extreme or toxic environmental conditions. In the present study, aiming to reconstruct the evolutionary history of this order, we analyzed the contribution of the DSE habit to the diversification of the Chaetothyriales. We also report the distribution of the DSE habit among the main families and/or clades within the order. Our results suggest that DSE had a key position in the evolution of the order Chaetothyriales, both as an ancestral ecological character and as a character from which other specialized forms such as Domatium probably derived.

A phylogenomic analysis of Lonicera and its bearing on the evolution of organ fusion.

PREMISE: The ~140 species of Lonicera are characterized by variously fused leaves, bracteoles, and ovaries, making it a model system for studying the evolution and development of organ fusion. However, previous phylogenetic analyses, based mainly on chloroplast DNA markers, have yielded uncertain and conflicting results. A well-supported phylogeny of Lonicera will allow us to trace the evolutionary history of organ fusion. METHODS: We inferred the phylogeny of Lonicera using restriction site-associated DNA sequencing (RADSeq), sampling all major clades and 18 of the 23 subsections. This provided the basis for inferring the evolution of five fusion-related traits. RESULTS: RADSeq data yielded a well-resolved and well-supported phylogeny. The two traditionally recognized subgenera (Periclymenum and Chamaecerasus), three of the four sections (Isoxylosteum, Coeloxylosteum, and Nintooa), and half of the subsections sampled were recovered as monophyletic. However, the large and heterogeneous section Isika was strongly supported as paraphyletic. Nintooa, a clade of ~22 mostly vine-forming species, including L. japonica, was recovered in a novel position, raising the possibility of cytonuclear discordance. We document the parallel evolution of fused leaves, bracteoles, and ovaries, with rare reversals. Most strikingly, complete cupules, in which four fused bracteoles completely enclose two unfused ovaries, arose at least three times. Surprisingly, these appear to have evolved directly from ancestors with free bracteoles instead of partial cupules. CONCLUSIONS: We provide the most comprehensive and well-supported phylogeny of Lonicera to date. Our inference of multiple evolutionary shifts in organ fusion provides a solid foundation for in depth developmental and functional analyses.

Global dispersal and diversification in ground beetles of the subfamily Carabinae.

The origin and diversification process of lineages of organisms that are currently widely distributed among continents is an interesting subject for exploring the evolutionary history of global species diversity. Ground beetles of the subfamily Carabinae are flightless except for one lineage, but nevertheless occur on all continents except Antarctica. Here, we used sequence data from ultraconserved elements to reconstruct the phylogeny, divergence time, biogeographical history, ancestral state of hind wings and changes in the speciation rate of Carabinae. Our results show that Carabinae originated in the Americas and diversified into four tribes during the period from the late Jurassic to the late Cretaceous, with two in South America (Celoglossini) and Australasia (Pamborini) and two in Laurasia (Cychrini and Carabini). The ancestral Carabinae were inferred to be winged; three of four tribes (Cychrini, Ceglossini and Pamborini) have completely lost their hind wings and flight capability. The remaining tribe, Carabini, diverged into the subtribes Carabina (wingless) and Calosomina (winged) in the Oligocene. Carabina originated in Europe, spread over Eurasia and diversified into approximately 1000 species, accounting for around 60% of all Carabinae species. Calosomina that were flight-capable dispersed from North America or Eurasia to South America, Australia, and Africa, and then flightless lineages evolved on oceanic islands and continental highlands. The speciation rate increased in the Cychrini and Carabini clades in Eurasia. Within Carabini, the speciation rate was higher for wingless than winged states. Our study showed that the global distribution of Carabinae resulted from ancient dispersal before the breakup of Gondwana and more recent dispersal through flight around the world. These patterns consequently illustrate the causal relationships of geographical history, evolution of flightlessness, and the global distribution and species diversity of Carabinae.

Absence of some cytochrome P450 (CYP) and hydroxysteroid dehydrogenase (HSD) enzymes in hagfishes.

Corticosteroids are synthesized from cholesterol by steroidogenic enzyme catalysts belonging to two main families: the cytochrome p450s (CYPs) and hydroxysteroid dehydrogenases (HSDs). The action of these steroidogenic enzymes allows the genesis of the terminal active corticosteroids 11-deoxycortisol (S), 1ɑ-hydroxycorticosterone (1α-OH-B), or cortisol in different fish species. However, for Cyclostomes like hagfishes, the terminal corticosteroid is still undefined. In this study, we examined the presence or absence of CYPs and HSDs as traits in fishes to gain insight about the primary corticosteroid synthesis pathways of the hagfishes. We used published cytochrome c oxidase I (COXI) amino acid sequences to construct a phylogeny of fishes and then mapped the CYPs and HSDs as morphological traits onto the tree to predict the ancestral character states through ancestral character reconstruction (ACR). There is a clear phylogenetic signal for CYP (i.e., CYP11a1, 17, 21, and 11b) and HSD (i.e., 11-ßHSD and 3ß-HSD) derivatives of interest throughout the more derived fishes. Using trait-based ACR, we also found that hagfishes possess genes for 3ß-HSD, CYP11a1, CYP17, and CYP21. Importantly, the presence of CYP21 implies that hagfish can synthesize 11-deoxycorticosterone (11-DOC) and S. Previous research demonstrated that despite hagfish having CYP21, neither 11-DOC nor S could be detected in hagfish. This discrepancy between the presence of steroidogenic enzymes and products brings into question the expression and/or function of CYP21 in hagfishes.

EvoLaps: a web interface to visualize continuous phylogeographic reconstructions.

BACKGROUND: Phylogeographic reconstructions serve as a basis to understand the spread and evolution of pathogens. Visualization of these reconstructions often lead to complex graphical representations which are difficult to interpret. RESULT: We present EvoLaps, a user-friendly web interface to visualize phylogeographic reconstructions based on the analysis of latitude/longitude coordinates with various clustering levels. EvoLaps also produces transition diagrams that provide concise and easy to interpret summaries of phylogeographic reconstructions. CONCLUSION: The main contribution of EvoLaps is to assemble known numerical and graphical methods/tools into a user-friendly interface dedicated to the visualization and edition of evolutionary scenarios based on continuous phylogeographic reconstructions. EvoLaps is freely usable at www.evolaps.org .

Evolutionary transitions in broad tapeworms (Cestoda: Diphyllobothriidea) revealed by mitogenome and nuclear ribosomal operon phylogenetics.

Broad tapeworms (Diphyllobothriidea) are parasites whose adults are capable of infecting a wide range of freshwater, marine and terrestrial tetrapods including humans. Previous works examining the evolution of habitat and host use in this group have been hampered by the lack of a well-resolved phylogeny. In order to produce a robust phylogenetic framework for diphyllobothriideans, we sequenced the complete mitochondrial genome of 13 representatives, carefully chosen to cover the major clades, and two outgroup species representing the Spathebothriidea and Haplobothriidea. In addition, complementary data from the nuclear ribosomal operon was sequenced for 10 representative taxa. Mitogenomes and ssrDNA and lsrDNA were used towards elucidating the phylogenetic framework for the Diphyllobothriidea. The Cephalochlamydidae is confirmed as the earliest diverging diphyllobothriidean lineage, and Solenophoridae and Diphyllobothriidae are sister groups. We infer a probable freshwater origin of the diphyllobothriideans. The ancestral condition for life cycle complexity could not be unambiguously resolved. However, we infer exclusive use of a three-host life cycle following the origin of the Solenophoridae + Diphyllobothriidae. Regarding definitive host use, although we infer reptiles as the most likely ancestral condition, this result should be revisited with a more densely sampled phylogeny in future studies. Freshwater habitat is used by the early diverging lineages within the Solenophoridae + Diphyllobothriidae clade. For the latter, habitat use shifts between freshwater and marine environments, and definitive host use includes marine and terrestrial mammals and birds. We use mitochondrial genomes to distinguish Schistocephalus species occurring in different species of sticklebacks and demonstrate conspecificity of Ligula cf. intestinalis specimens collected from two Fennoscandian ringed seal subspecies.

Niche partitioning among three snail-eating snakes revealed by dentition asymmetry and prey specialisation.

The level of dentition asymmetry in snail-eating snakes may reflect their prey choice and feeding efficiency on asymmetric land snails. The three species of Pareas snakes (Squamata: Pareidae) in Taiwan, which form partially sympatric distribution on the island, provide a potential case to test the hypothesis of niche partitioning and character displacement with regard to dentition asymmetry and specialisation in feeding behaviour. In this study, behavioural experiments confirmed that P. formosensis feeds exclusively on slugs, whereas P. atayal and P. komaii consumed both. However, P. atayal more efficiently preys on land snails than P. komaii, exhibiting a shorter handling time and fewer mandibular retractions. Micro-CT and ancestral character reconstruction demonstrated the lowest asymmetry in P. formosensis (the slug specialist), the highest dentition asymmetry in P. atayal (the land snail specialist) and flexibility in P. komaii (the niche switcher): increased dentition asymmetry when sympatrically distributed with the slug eater (character displacement), and decreased asymmetry when living alone (ecological niche release). Ecological niche modelling showed that the distribution of P. formosensis is associated with the presence of slugs, while that of P. atayal could be explained by the land snails. Combining the results from morphology, phylogeny, behavioural experiments and ecological niche modelling, we showed that competition in the sympatric region might have facilitated character displacement among congeners, while the absence of competition in allopatric region has led to ecological niche release.

A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios.

The reconstruction of ancestral scenarios is widely used to study the evolution of characters along phylogenetic trees. One commonly uses the marginal posterior probabilities of the character states, or the joint reconstruction of the most likely scenario. However, marginal reconstructions provide users with state probabilities, which are difficult to interpret and visualize, whereas joint reconstructions select a unique state for every tree node and thus do not reflect the uncertainty of inferences. We propose a simple and fast approach, which is in between these two extremes. We use decision-theory concepts (namely, the Brier score) to associate each node in the tree to a set of likely states. A unique state is predicted in tree regions with low uncertainty, whereas several states are predicted in uncertain regions, typically around the tree root. To visualize the results, we cluster the neighboring nodes associated with the same states and use graph visualization tools. The method is implemented in the PastML program and web server. The results on simulated data demonstrate the accuracy and robustness of the approach. PastML was applied to the phylogeography of Dengue serotype 2 (DENV2), and the evolution of drug resistances in a large HIV data set. These analyses took a few minutes and provided convincing results. PastML retrieved the main transmission routes of human DENV2 and showed the uncertainty of the human-sylvatic DENV2 geographic origin. With HIV, the results show that resistance mutations mostly emerge independently under treatment pressure, but resistance clusters are found, corresponding to transmissions among untreated patients.

PastView: a user-friendly interface to explore ancestral scenarios.

BACKGROUND: Ancestral character states computed from the combination of phylogenetic trees with extrinsic traits are used to decipher evolutionary scenarios in various research fields such as phylogeography, epidemiology, and ecology. Despite the existence of powerful methods and software in ancestral character state inference, difficulties may arise when interpreting the outputs of such inferences. The growing complexity of data (trees, annotations), the diversity of optimization criteria for computing trees and ancestral character states, the combinatorial explosion of potential evolutionary scenarios if some ancestral characters states do not stand out clearly from others, requires the design of new methods to explore associations of phylogenetic trees with extrinsic traits, to ease the visualization and interpretation of evolutionary scenarios. RESULT: We developed PastView, a user-friendly interface that includes numerical and graphical features to help users to import and/or compute ancestral character states from discrete variables and extract ancestral scenarios as sets of successive transitions of character states from the tree root to its leaves. PastView provides summarized views such as transition maps and integrates comparative tools to highlight agreements or discrepancies between methods of ancestral annotations inference. CONCLUSION: The main contribution of PastView is to assemble known numerical and graphical methods into a multi-maps graphical user interface dedicated to the computing, searching and viewing of evolutionary scenarios based on phylogenetic trees and ancestral character states. PastView is available publicly as a standalone software on www.pastview.org .

Early consequences of allopolyploidy alter floral evolution in Nicotiana (Solanaceae).

BACKGROUND: Polyploidy has played a major role in angiosperm evolution. Previous studies have examined polyploid phenotypes in comparison to their extant progenitors, but not in context of predicted progenitor phenotypes at allopolyploid origin. In addition, differences in the trends of polyploid versus diploid evolution have not been investigated. We use ancestral character-state reconstructions to estimate progenitor phenotype at allopolyploid origin to determine patterns of polyploid evolution leading to morphology of the extant species. We also compare trends in diploid versus allopolyploid evolution to determine if polyploidy modifies floral evolutionary patterns. RESULTS: Predicting the ancestral phenotype of a nascent allopolyploid from reconstructions of diploid phenotypes at the time of polyploid formation generates different phenotype predictions than when extant diploid phenotypes are used, the outcome of which can alter conclusions about polyploid evolution; however, most analyses yield the same results. Using ancestral reconstructions of diploid floral phenotypes indicate that young polyploids evolve shorter, wider corolla tubes, but older polyploids and diploids do not show any detectable evolutionary trends. Lability of the traits examined (floral shape, corolla tube length, and corolla tube width) differs across young and older polyploids and diploids. Corolla length is more evolutionarily labile in older polyploids and diploids. Polyploids do not display unique suites of floral characters based on both morphological and color traits, but some suites of characters may be evolving together and seem to have arisen multiple times within Nicotiana, perhaps due to the influence of pollinators. CONCLUSIONS: Young polyploids display different trends in floral evolution (shorter, wider corolla tubes, which may result in more generalist pollination) than older polyploids and diploids, suggesting that patterns of divergence are impacted by the early consequences of allopolyploidy, perhaps arising from genomic shock and/or subsequent genome stabilization associated with diploidization. Convergent evolution in floral morphology and color in Nicotiana can be consistent with pollinator preferences, suggesting that pollinators may have shaped floral evolution in Nicotiana.

Reconstructing the ancestral flower of extant angiosperms: the 'war of the whorls' is heating up.

The origin of the angiosperm flower is a long-standing problem of botany and evolutionary biology. One widely accepted milestone towards solving it is the reconstruction of the ancestral flower of extant angiosperms, here termed 'AFEA'. A recent approach employing novel methods gave results that were not anticipated. Most notably the reconstructed phyllotaxis of AFEA soon was criticized and sparked a heated debate in the literature. To better explain, clarify, and perhaps cool the debate, we first summarize the results of previous attempts to reconstruct AFEA and contrast them with the more recent, controversial prediction of its structure. We then outline the major arguments made by contrasting parties in the recent debate. Finally, we discuss two key topics, the molecular mechanism of phyllotaxis and the role of gene regulatory networks during flower development and evolution, that may help to clarify the issue in the intermediate future.

Combining high-throughput sequencing and targeted loci data to infer the phylogeny of the "Adenocalymma-Neojobertia" clade (Bignonieae, Bignoniaceae).

Combining high-throughput sequencing data with amplicon sequences allows the reconstruction of robust phylogenies based on comprehensive sampling of characters and taxa. Here, we combine Next Generation Sequencing (NGS) and Sanger sequencing data to infer the phylogeny of the "Adenocalymma-Neojobertia" clade (Bignonieae, Bignoniaceae), a diverse lineage of Neotropical plants, using Maximum Likelihood and Bayesian approaches. We used NGS to obtain complete or nearly-complete plastomes of members of this clade, leading to a final dataset with 54 individuals, representing 44 members of ingroup and 10 outgroups. In addition, we obtained Sanger sequences of two plastid markers (ndhF and rpl32-trnL) for 44 individuals (43 ingroup and 1 outgroup) and the nuclear PepC for 64 individuals (63 ingroup and 1 outgroup). Our final dataset includes 87 individuals of members of the "Adenocalymma-Neojobertia" clade, representing 66 species (ca. 90% of the diversity), plus 11 outgroups. Plastid and nuclear datasets recovered congruent topologies and were combined. The combined analysis recovered a monophyletic "Adenocalymma-Neojobertia" clade and a paraphyletic Adenocalymma that also contained a monophyletic Neojobertia plus Pleonotoma albiflora. Relationships are strongly supported in all analyses, with most lineages within the "Adenocalymma-Neojobertia" clade receiving maximum posterior probabilities. Ancestral character state reconstructions using Bayesian approaches identified six morphological synapomorphies of clades namely, prophyll type, petiole and petiolule articulation, tendril ramification, inflorescence ramification, calyx shape, and fruit wings. Other characters such as habit, calyx cupular trichomes, corolla color, and corolla shape evolved multiple times. These characters are putatively related with the clade diversification and can be further explored in diversification studies.

Molecular phylogeny of Macrosiphini (Hemiptera: Aphididae): An evolutionary hypothesis for the Pterocomma-group habitat adaptation.

The aphid tribe Macrosiphini Wilson, 1910 (Hemiptera: Aphididae: Aphidinae) is one of the most controversial groups within Aphididae. We sequenced 2876 bp from one nuclear gene (EF-1α) and four mitochondrial genes (COI, tRNA + COII, 16S) from 107 terminal taxa representing 57 genera of Macrosiphini s.l. (the former Macrosiphini + genera in former Pterocommatini), including all of the recognized major genera and outgroups, and reconstructed the phylogeny using maximum likelihood, maximum parsimony and Bayesian methods. The stepping-stone method was used to evaluate various topological hypotheses regarding Macrosiphini s.l. and related groups. Our findings support both the monophyly of Macrosiphini s.l., and of two subordinate groups (Macrosiphini s.str and the Pterocomma-group), as well as the transfer of Capitophorus, Pleotrichophorus, Liosomaphis and Vesiculaphis to the Pterocomma-group-a result not previously suggested by analyses of molecular data. Ancestral state reconstructions for Macrosiphini and the Pterocomma-group suggest an ancestral primary host association with Rosales and Malpighiales, respectively, and other host associations within the tribe. Host transitions independently occurred more than once in Macrosiphini s.str. Furthermore, host-shifts between Rosales and Malpighiales may have occurred at least once in the Pterocomma-group. Additionally, the Macrosiphini phylogeny indicates that host associations are consistent also with host ecology, with a partitioning of aphid-host relationships into riparian and periaquatic habitats versus drier forest/shrubland habitats.

A biogeographic and ecological perspective to the evolution of reproductive behaviour in the family Salamandridae.

Amphibians have a complex reproductive behaviour, which shows the highest diversity among tetrapodes. The family Salamandridae, distributed across the entire Holarctic, is one of the most diverse groups of extant salamanders comprising 114 species in 21 genera. The family has a remarkable diversity of courtship modes, amplexus and sperm transfer. It is often hypothesised that this diversity has evolved in adaptation to a specific mating and/or breeding habitat. We test this hypothesis based upon a phylogenetic reconstruction using the complete mitochondrial genome sequences of 45 Salamandridae species, representing all existing genera. We used ancestral character state reconstruction methods and geographic range models and applied relaxed Bayesian molecular clock models to discuss the results in a temporal framework of Salamandridae evolution. Our results show that the family Salamandridae started to diversify in the Late Cretaceous (ca. 87 mya) and is of Western Palearctic origin. Ancestral character state reconstruction predicts that its common ancestor was oviparous, mated on land without amplexus and probably showed a pin wheel spermatophore transfer, which is still found in the Italian endemic Salamandrina terdigidata. Our results suggest that several colonization of continents with subsequent radiations took place, once to the Nearctic and twice into Eastern Asian realms. However, these events were only in one case associated with a change in mating behaviour (dorsal amplexus in Nearctic newts). Around the Cretaceous-Paleogene boundary (K-Pg boundary) several Salamandridae lineages further diverged, again with no obvious changes in mating behaviour. Overall, there is no significant signal for mating character evolution being caused by changes in habitat type, with only a slight tendency that changes in mating habitat might have led to changes in the type of sperm transfer which in turn was associated with changes in the presence or absence of amplexus.

Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution.

Brassicaceae is one of the most diverse and economically valuable angiosperm families with widely cultivated vegetable crops and scientifically important model plants, such as Arabidopsis thaliana. The evolutionary history, ecological, morphological, and genetic diversity, and abundant resources and knowledge of Brassicaceae make it an excellent model family for evolutionary studies. Recent phylogenetic analyses of the family revealed three major lineages (I, II, and III), but relationships among and within these lineages remain largely unclear. Here, we present a highly supported phylogeny with six major clades using nuclear markers from newly sequenced transcriptomes of 32 Brassicaceae species and large data sets from additional taxa for a total of 55 species spanning 29 out of 51 tribes. Clade A consisting of Lineage I and Macropodium nivale is sister to combined Clade B (with Lineage II and others) and a new Clade C. The ABC clade is sister to Clade D with species previously weakly associated with Lineage II and Clade E (Lineage III) is sister to the ABCD clade. Clade F (the tribe Aethionemeae) is sister to the remainder of the entire family. Molecular clock estimation reveals an early radiation of major clades near or shortly after the Eocene-Oligocene boundary and subsequent nested divergences of several tribes of the previously polytomous Expanded Lineage II. Reconstruction of ancestral morphological states during the Brassicaceae evolution indicates prevalent parallel (convergent) evolution of several traits over deep times across the entire family. These results form a foundation for future evolutionary analyses of structures and functions across Brassicaceae.

Mitochondrial phylogenomics of Hemiptera reveals adaptive innovations driving the diversification of true bugs.

Hemiptera, the largest non-holometabolous order of insects, represents approximately 7% of metazoan diversity. With extraordinary life histories and highly specialized morphological adaptations, hemipterans have exploited diverse habitats and food sources through approximately 300 Myr of evolution. To elucidate the phylogeny and evolutionary history of Hemiptera, we carried out the most comprehensive mitogenomics analysis on the richest taxon sampling to date covering all the suborders and infraorders, including 34 newly sequenced and 94 published mitogenomes. With optimized branch length and sequence heterogeneity, Bayesian analyses using a site-heterogeneous mixture model resolved the higher-level hemipteran phylogeny as (Sternorrhyncha, (Auchenorrhyncha, (Coleorrhyncha, Heteroptera))). Ancestral character state reconstruction and divergence time estimation suggest that the success of true bugs (Heteroptera) is probably due to angiosperm coevolution, but key adaptive innovations (e.g. prognathous mouthpart, predatory behaviour, and haemelytron) facilitated multiple independent shifts among diverse feeding habits and multiple independent colonizations of aquatic habitats.

Molecular phylogeny and forms of photosynthesis in tribe Salsoleae (Chenopodiaceae).

While many C4 lineages have Kranz anatomy around individual veins, Salsoleae have evolved the Salsoloid Kranz anatomy where a continuous dual layer of chlorenchyma cells encloses the vascular and water-storage tissue. With the aim of elucidating the evolution of C4 photosynthesis in Salsoleae, a broadly sampled molecular phylogeny and anatomical survey was conducted, together with biochemical, microscopic, and physiological analyses of selected photosynthetic types. From analyses of photosynthetic phenotypes, a model for evolution of this form of C4 was compared with models for evolution of Kranz anatomy around individual veins. A functionally C3 proto-Kranz phenotype (Proto-Kranz Sympegmoid) and intermediates with a photorespiratory pump (Kranz-like Sympegmoid and Kranz-like Salsoloid types) are considered crucial transitional steps towards C4 development. The molecular phylogeny provides evidence for C3 being the ancestral photosynthetic pathway but there is no phylogenetic evidence for the ancestry of C3-C4 intermediacy with respect to C4 in Salsoleae. Traits considered advantageous in arid conditions, such as annual life form, central sclerenchyma in leaves, and reduction of surface area, evolved repeatedly in Salsoleae. The recurrent evolution of a green stem cortex taking over photosynthesis in C4 clades of Salsoleae concurrent with leaf reduction was probably favoured by the higher productivity of the C4 cycle.