Phylogenetic Hypothesis Research Articles

Birds that breed exclusively on islands have smaller clutches

Abstract The “island syndrome” refers to similarity in the biology of island organisms, but its generality is questionable, as the scope of species and traits examined are often limited. Here, I show that birds breeding exclusively on islands (breeding island endemics) evolved smaller clutches, using a dataset of 4,530 bird species. Using an inclusive definition of a breeding island endemic, which also encompasses migratory species and seabirds, I examine the evolution of clutch sizes in island breeding species using phylogenetic generalized linear models. Across disparate phylogenetic hypotheses, and after accounting for biological and geographical co-variables, I show that breeding island endemic landbirds (470 species) evolved smaller clutch sizes than continental breeding species (3,818 species). I show that the evolution of clutch size follows the expectations of the island syndrome, as among breeding island endemic landbirds there is a positive relationship between clutch size and breeding range area. Finally, I reinforce the view that the island syndrome is a general pattern in birds, spanning diverse phylogenetic and ecological groups, by showing that in a seabird-only dataset (242 species), breeding island endemic seabirds show evolution of smaller clutch sizes. In a model of the full dataset of both landbirds and seabirds (4,530 species) there was no evidence of an interaction of being a seabird with breeding island endemicity, showing that seabirds and landbirds respond in the same way. This study, using more than 40% of all bird species, provides the first evidence of a general evolutionary response in a life history trait, clearly showing the island syndrome as a general evolutionary tendency associated with island environments.

Spicy food for the egg-cowries: the evolution of corallivory in the Ovulidae (Gastropoda: Cypraeoidea)

IntroductionHost-parasite associations provide very useful models to study adaptive processes. We investigated the interaction between carnivorous marine gastropods, the Ovulidae or egg-cowries, and their cnidarian food targets. Ovulidae (Fleming, 1828), is a family of specialized carnivorous caenogastropods that feed by browsing on octocorals (Anthozoa: Octocorallia: Malacalcyonacea and Scleralcyonacea) or, to a much lesser degree, on antipatharians (Anthozoa: Hexacorallia: Antipatharia) and Stylasteridae (Hydrozoa: Hydroidolina: Anthoathecata). Very scanty information is available on the phylogenetic relationships and the degree of specificity of the relationship with the cnidarians of this corallivorous lineage, especially for deep-water taxa.MethodsTo assess taxonomic identifications and investigate cnidarian/ovulid relationships in the context of their evolution, we generated an extensive molecular dataset comprising two mitochondrial (cox1 and 16S rDNA) and one nuclear gene (28S rDNA) from 524 specimens collected worldwide. The coral hosts of the ovulid species have been identified by integrating literature data with new records, employing morphological and/or molecular (the mitochondrial 16S rDNA and mtMSH, and the nuclear ITS2) markers.ResultsWe obtained a molecular phylogenetic framework for the Ovulidae, time-calibrated with nine reliable fossil records. An ancestral state reconstruction allowed to identify Hexacorallia or Hydroidolina as the most likely ancestral cnidarian host for the Ovulidae.DiscussionOur phylogenetic hypothesis revealed the existence of groups that do not completely correspond to the currently employed subfamilial arrangement. Concerning trophic ecology, while only pediculariines (Pedicularia and allied) are associated with hydrozoans (Stylasteridae), our results suggest that some ovulid lineages shifted independently between octocorals and hexacorals.

Valid publication of names of two domains and seven kingdoms of prokaryotes.

The International Code of Nomenclature of Prokaryotes (ICNP) now includes the categories domain and kingdom. For the purpose of the valid publication of their names under the ICNP, we consider here the two known domains, 'Bacteria' and 'Archaea', as well as a number of taxa suitable for the rank of kingdom, based on previous phylogenetic and taxonomic studies. It is proposed to subdivide the domain Bacteria into the kingdoms Bacillati, Fusobacteriati, Pseudomonadati and Thermotogati. This arrangement reflects contemporary phylogenetic hypotheses as well as previous taxonomic proposals based on cell wall structure, including 'diderms' vs. 'monoderms', Gracilicutes vs. Firmicutes, 'Negibacteria' vs. 'Unibacteria', 'Hydrobacteria' vs. 'Terrabacteria', and 'Hydrobacterida' vs. 'Terrabacterida'. The domain Archaea is proposed to include the kingdoms Methanobacteriati, Nanobdellati and Thermoproteati, reflecting the previous division into 'Euryarchaeota', 'DPANN superphylum' and 'TACK superphylum'.

Taxonomic dissection based on molecular evidence of the Eriosycecurvispina complex (Cactaceae): identifying nine endemic species from Central Chile.

Chile's distinctive flora, geographical isolation, and complex topography collectively contribute to a notable endemic species diversity, particularly within central regions identified as critical areas for biodiversity conservation. The cactus genus Eriosyce, as currently circumscribed, encompasses seven sections, with Eriosycesect.Horridocatus presenting a notably complex species group. This study investigates the E.curvispina complex, a member of the Notocacteae tribe common in central Chile, by incorporating new populations and examining phylogenetic relationships using four plastid and one nuclear molecular marker. The phylogenetic analysis of sampled individuals identified nine independent lineages, each warranting recognition at the species rank. Despite minimal morphological differences among taxa, morphological characters were utilized to support and stabilize the DNA-based phylogenetic hypothesis. The results highlight the high taxonomic diversity in these cactus lineages and have implications for the classification of the E.curvispina complex, including new combinations and proposals of conservation status.

'Out of Africa' origin of the pantropical staghorn fern genus Platycerium (Polypodiaceae) supported by plastid phylogenomics and biogeographical analysis.

The staghorn fern genus Platycerium is one of the most commonly grown ornamental ferns, and it evolved to occupy a typical pantropical intercontinental disjunction. However, species-level relationships in the genus have not been well resolved, and the spatiotemporal evolutionary history of the genus also needs to be explored. Plastomes of all the 18 Platycerium species were newly sequenced. Using plastome data, we reconstructed the phylogenetic relationships among Polypodiaceae members with a focus on Platycerium species, and further conducted molecular dating and biogeographical analyses of the genus. The present analyses yielded a robustly supported phylogenetic hypothesis of Platycerium. Molecular dating results showed that Platycerium split from its sister genus Hovenkampia ~35.2 million years ago (Ma) near the Eocene-Oligocene boundary and began to diverge ~26.3 Ma during the late Oligocene, while multiple speciation events within Platycerium occurred during the middle to late Miocene. Biogeographical analysis suggested that Platycerium originated in tropical Africa and then dispersed eastward to southeast Asia-Australasia and westward to neotropical areas. Our analyses using a plastid phylogenomic approach improved our understanding of the species-level relationships within Platycerium. The global climate changes of both the Late Oligocene Warming and the cooling following the mid-Miocene Climate Optimum may have promoted the speciation of Platycerium, and transoceanic long-distance dispersal is the most plausible explanation for the pantropical distribution of the genus today. Our study investigating the biogeographical history of Platycerium provides a case study not only for the formation of the pantropical intercontinental disjunction of this fern genus but also the 'out of Africa' origin of plant lineages.

Phylogenetic insights into Central European Chorthippus and Pseudochorthippus (Orthoptera: Acrididae) species using ddRADseq data

The evolution of several orthopteran groups, especially within the grasshopper family Acrididae, remains poorly understood. This is particularly true for the subfamily Gomphocerinae, which comprises cryptic sympatric and syntopic species. Previous mitochondrial studies have highlighted major discrepancies between taxonomic and phylogenetic hypotheses, thereby emphasizing the necessity of genome-wide approaches.In this study, we employ double-digest restriction site-associated DNA sequencing (ddRADseq) to reconstruct the evolution of Central European Chorthippus and Pseudochorthippus species, especially C.smardai, P.tatrae and the C.biguttulus group.Our phylogenomic analyses recovered deep discordance with mitochondrial DNA barcoding, emphasizing its unreliability in Gomphocerinae grasshoppers. Specifically, our data robustly distinguished the C.biguttulus group and confirmed the distinctiveness of C.eisentrauti, also shedding light on its presence in the Berchtesgaden Alps. Moreover, our results support the reclassification of C.smardai to the genus Pseudochorthippus and of P.tatrae to the genus Chorthippus.Our study demonstrates the efficiency of high-throughput genomic methods such as RADseq without prior optimization to elucidate the complex evolution of grasshopper radiations with direct taxonomic implications. While RADseq has predominantly been utilized for population genomics and within-genus phylogenomics, its application extends to resolve relationships between deeply-diverged clades representative of distinct genera.

A new perspective on the taxonomy and systematics of Arvicolinae (Gray, 1821) and a new time-calibrated phylogeny for the clade.

Arvicoline rodents are one of the most speciose and rapidly evolving mammalian lineages. Fossil arvicolines are also among the most common vertebrate fossils found in sites of Pliocene and Pleistocene age in Eurasia and North America. However, there is no taxonomically robust, well-supported, time-calibrated phylogeny for the group. Here we present well-supported hypotheses of arvicoline rodent systematics using maximum likelihood and Bayesian inference of DNA sequences of two mitochondrial genes and three nuclear genes representing 146 (82% coverage) species and 100% of currently recognized arvicoline genera. We elucidate well-supported major clades, reviewed the relationships and taxonomy of many species and genera, and critically compared our resulting molecular phylogenetic hypotheses to previously published hypotheses. We also used five fossil calibrations to generate a time-calibrated phylogeny of Arvicolinae that permitted some reconciliation between paleontological and neontological data. Our results are largely congruent with previous molecular phylogenies, but we increased the support in many regions of the arvicoline tree that were previously poorly-sampled. Our sampling resulted in a better understanding of relationships within Clethrionomyini, the early-diverging position and close relationship of true lemmings (Lemmus and Myopus) and bog lemmings (Synaptomys), and provided support for recent taxonomic changes within Microtini. Our results indicate an origin of ∼6.4 Ma for crown arvicoline rodents. These results have major implications (e.g., diversification rates, paleobiogeography) for our confidence in the fossil record of arvicolines and their utility as biochronological tools in Eurasia and North America during the Quaternary.

Testing the Tropical Niche Conservatism Hypothesis: Climatic Niche Evolution of Escallonia Mutis ex L. F. (Escalloniaceae).

We assess the Tropical Niche Conservatism Hypothesis in the genus Escallonia in South America using phylogeny, paleoclimate estimation and current niche modelling. We tested four predictions: (1) the climatic condition where the ancestor of Escallonia grew is megathermal; (2) the temperate niche is a derived condition from tropical clades; (3) the most closely related species have a similar current climate niche (conservation of the phylogenetic niche); and (4) there is a range expansion from the northern Andes to high latitudes during warm times. Our phylogenetic hypothesis shows that Escallonia originated 52.17 ± 0.85 My, in the early Eocene, with an annual mean temperature of 13.8 °C and annual precipitation of 1081 mm, corresponding to a microthermal to mesothermal climate; the species of the northern and central tropical Andes would be the ancestral ones, and the temperate species evolved between 32 and 20 My in a microthermal climate. The predominant evolutionary models were Brownian and Ornstein-Uhlenbeck. There was phylogenetic signal in 7 of the 9 variables, indicating conservation of the climatic niche. Escallonia would have originated in the central and southern Andes and reached the other environments by dispersion.

Morphological and molecular data in the study of the evolution, population genetics and taxonomy of Rhizostomeae.

Rhizostomeae research based on morphological approaches was reinforced and diversified by new techniques after the 1970s, including developing methodologies for phylogenetic analysis, the rise of the polymerase chain reaction, and the emergence of different sequencing technologies. Here, we summarize the contribution of morphological and molecular data to the study of the classification and phylogenetic relationships of Rhizostomeae in addition to the use of molecular data in studies at the population, species, and supraspecific levels. Throughout the history of the study of the Rhizostomeae systematics, morphological data have been neglected when it comes to phylogenetic inferences, which is reflected in the lack of a phylogenetic analysis of the taxa within Rhizostomeae based on phenotypic characters of the adult medusa. Concerning molecular data, ca.3,200 nucleotide sequences are available in GenBank and are mainly used for discovering, delimiting, describing, and identifying species. Molecular approaches have also allowed species monitoring by qPCR and metabarcoding of environmental DNA, as well as unveiling the distribution and genetic diversity of jellyfish populations, shedding light on introduction events, conservation, and health of edible jellyfish stocks. Nucleotide sequences have also been key for the development of phylogenetic hypotheses that serve as basis for investigations on the origin and diversification of morphological, ecological, and behavioral traits within Cnidaria; however, despite the progress achieved, phylogenetic uncertainty still exists, especially within the formerly known superfamily Inscapulatae. Future directions in Rhizostomeae research involve generating molecular and morphological data of neglected taxa, which represents a golden opportunity to understand the evolution of Rhizostomeae.

Unusual rearrangements of mitogenomes in Diptera revealed by comparative analysis of 135 tachinid species (Insecta, Diptera, Tachinidae)

The Tachinidae is one of the most speciose families in Diptera, and the exclusively parasitoid species play an important role in regulating populations of many herbivorous insects in ecosystems, including many agricultural pests. To better comprehend the characteristics and evolution of the mitochondrial genome for the Tachinidae, we are adding a massive amount of new molecular data by assembling the mitogenomes for 71 genera and 135 species from all four tachinid subfamilies through next-generation sequencing, and we are presenting the most comprehensive mitogenomic phylogenetic analysis of this family so far. Extensive rearrangements observed in the mitogenome of Admontia podomyia (Exoristinae) are unique for the entire suborder Cyclorrhapha. The rearrangement pattern suggests that the process involved a tandem duplication of the complete mitogenome, followed by both random and nonrandom loss of one copy of each gene. Additionally, five minor mitogenome rearrangements are discovered and described in three subfamilies. We present the largest species-level phylogenetic hypothesis for Tachinidae to date, based on mitogenomes of 152 species of Tachinidae, representing all four subfamilies and with five non-tachinid outgroups. Our analyses support the monophyly of the Tachinidae and most tribes and genera were recovered with good support, but the higher-level phylogenetic relationships within Tachinidae were poorly resolved, indicating that mitogenome data alone are not enough to unambiguously resolve the deeper phylogenetic relationships within Tachinidae.

A Phylogenetic Analysis of Marcetia (Melastomataceae, Marcetieae) and Three New Sprawling Species from Bahia, Brazil

Abstract— Three new species of the Neotropical genus Marcetia are described and illustrated: Marcetia barbadensis, Marcetia minima, and Marcetia serratifolia. The three species are known from small isolated populations in mountains of the Chapada Diamantina, Bahia, Brazil. The recognition of Marcetia barbadensis and Marcetia serratifolia is confirmed with an updated molecular phylogeny of the tribe Marcetieae (based on ETS, ITS, accD-psaI, atpF-atpH, trnS-trnG, psbK-psbL, ndhF and rbcL), and by morphological and morphometric studies. In turn, the recognition of Marcetia minima, a new species known only from the type gathering collected about 30 yr ago, is based on analyses of leaf and anther connective shape, as well as linear measurements of vegetative and reproductive structures. Based on the new phylogenetic hypothesis for Marcetieae, we reconstructed the evolution of habit and petal color in the tribe, and showed that prostrate plants and white flowers evolved repeatedly from ancestors with an erect habit and pink to magenta petals. We also provide notes on the intergeneric relationships and phylogeny of Marcetia and evaluate the generic placement of the recently described Acisanthera saxatilis.

Systematics and character evolution of capitate hydrozoans.

Capitate hydrozoans are a morphologically and ecologically diverse hydrozoan suborder, currently including about 200 species. Being grouped in two clades, Corynida and Zancleida, these hydrozoans still show a number of taxonomic uncertainties at the species, genus and family levels. Many Capitata species established symbiotic relationships with other benthic organisms, including bryozoans, other cnidarians, molluscs and poriferans, as well as with planktonic dinoflagellates for mixotrophic relationships and with bacteria for thiotrophic ectosymbioses. Our study aimed at providing an updated and comprehensive phylogeny reconstruction of the suborder, at modelling the evolution of selected morphological and ecological characters, and at testing evolutionary relationships between the symbiotic lifestyle and the other characters, by integrating taxonomic, ecological and evolutionary data. The phylogenetic hypotheses here presented shed light on the evolutionary relationships within Capitata, with most families and genera being recovered as monophyletic. The genus Zanclea and family Zancleidae, however, were divided into four divergent clades, requiring the establishment of the new genus Apatizanclea and the new combinations for species in Zanclea and Halocoryne genera. The ancestral state reconstructions revealed that symbiosis arose multiple times in the evolutionary history of the Capitata, and that homoplasy is a common phenomenon in the group. Correlations were found between the evolution of symbiosis and morphological characters, such as the perisarc. Overall, our results highlighted that the use of genetic data and a complete knowledge of the life cycles are strongly needed to disentangle taxonomic and systematic issues in capitate hydrozoans. Finally, the colonization of tropical habitat appears to have influenced the evolution of a symbiotic lifestyle, playing important roles in the evolution of the group.

Systematics of deep-sea starfish order Brisingida (Echinodermata: Asteroidea), with a revised classification and assessments of morphological characters

Brisingida Fisher 1928 is one of the seven currently recognised starfish orders, and one of the least known taxa as being exclusive deep-sea inhabitants. Modern deep-sea expeditions revealed their common occurrences in various deep-sea settings including seamounts, basins and hydrothermal vent peripheral, underlining the necessity of clarifying their global diversity and phylogeny. In this study, we present a comprehensive molecular phylogeny of Brisingida which encompasses the highest taxonomic diversity to date. DNA sequences (COI, 16S, 12S and 28S) were obtained from 225 specimens collected in the global ocean, identified as 58 species spanning 15 of the 17 extant genera. Phylogenetic relationship was inferred using both maximum likelihood and Bayesian inference methods, revealing polyphyletic families and genera and indicating nonnegligible bias in prior morphology-based systematics. Based on the new phylogeny, a novel classification of the order, consisting of 5 families and 17 genera, is proposed. Families Odinellidae, Brisingasteridae and Novodiniidae (sensu Clark and Mah, 2001) were resurrected to encompass the genera Odinella, Brisingaster and Novodinia. Brisingidae and Freyellidae were revised to include 11 and 3 genera, respectively. A new genus and species, two new subgenera and seven new combinations are described and a key to each genus and family is provided. Transformations of morphological traits were evaluated under the present phylogenetic hypothesis. A series of paedomorphic characters were found in many genera and species, which led to a high degree of homoplasy across phylogenetically distant groups. Our results provide new insights in the phylogeny and ontogeny of the order, and highlight the necessity to evaluate character convergence under sound phylogenetic hypothesis.

A new booid snake from the Eocene (Lutetian) Konservat-Lagerstätte of Geiseltal, Germany, and a new phylogenetic analysis of Booidea

Abstract We describe two exceptionally preserved fossil snakes from the Eocene Konservat-Lagerstätte of Geiseltal, located in the state of Saxony-Anhalt, Germany. The two snake specimens, GMH LIX-3-1992 and GMH XXXVIII-20-1964, can be confidently identified as booids based on general morphology and were thus compared to other geographically and/or temporally close fossil booids. We found that GMH LIX-3-1992 is morphologically very similar to Eoconstrictor spinifer, also from Geiseltal, and to Eoconstrictor fischeri, from the middle Eocene of Messel, but differs from both in a number of cranial and vertebral features. Based on these differences we erect the new species Eoconstrictor barnesi sp. nov.; GMH XXXVIII-20-1964 is very similar to GMH LIX-3-1992 and the two differ only in features that are likely ontogenetic. Phylogenetic analyses of snakes using maximum parsimony and Bayesian inference on datasets inclusive of both morphological and molecular data consistently support a close affinity of E. barnesi to E. fischeri and E. spinifer. Our preferred phylogenetic hypothesis places the three species of Eoconstrictor in a clade that is sister to Neotropical Boidae, a result consistent with previous studies. The genus Eoconstrictor could provide an important calibration point for molecular clock studies of booids and snakes in general.

Phylogenomic analyses reveal reticulate evolution between Neomicrocalamus and Temochloa (Poaceae: Bambusoideae).

Neomicrocalamus and Temochloa are closely related to bamboo genera. However, when considered with newly discovered and morphologically similar material from China and Vietnam, the phylogenetic relationship among these three groups was ambiguous in the analyses based on DNA regions. Here, as a means of investigating the relationships among the three bamboo groups and exploring potential sources of genomic conflicts, we present a phylogenomic examination based on the whole plastome, single-nucleotide polymorphism (SNP), and single-copy nuclear (SCN) gene datasets. Three different phylogenetic hypotheses were found. The inconsistency is attributed to the combination of incomplete lineage sorting and introgression. The origin of newly discovered bamboos is from introgressive hybridization between Temochloa liliana (which contributed 80.7% of the genome) and Neomicrocalamus prainii (19.3%), indicating that the newly discovered bamboos are closer to T. liliana in genetics. The more similar morphology and closer distribution elevation also imply a closer relationship between Temochloa and newly discovered bamboos.

Bayesian Total-Evidence Dating Revisits Sloth Phylogeny and Biogeography: A Cautionary Tale on Morphological Clock Analyses.

Combining morphological and molecular characters through Bayesian total-evidence dating allows inferring the phylogenetic and timescale framework of both extant and fossil taxa, while accounting for the stochasticity and incompleteness of the fossil record. Such an integrative approach is particularly needed when dealing with clades such as sloths (Mammalia: Folivora), for which developmental and biomechanical studies have shown high levels of morphological convergence whereas molecular data can only account for a limited percentage of their total species richness. Here, we propose an alternative hypothesis of sloth evolution that emphasizes the pervasiveness of morphological convergence and the importance of considering the fossil record and an adequate taxon sampling in both phylogenetic and biogeographic inferences. Regardless of different clock models and morphological datasets, the extant sloth Bradypus is consistently recovered as a megatherioid, and Choloepus as a mylodontoid, in agreement with molecular-only analyses. The recently extinct Caribbean sloths (Megalocnoidea) are found to be a monophyletic sister-clade of Megatherioidea, in contrast to previous phylogenetic hypotheses. Our results contradict previous morphological analyses and further support the polyphyly of "Megalonychidae," whose members were found in five different clades. Regardless of taxon sampling and clock models, the Caribbean colonization of sloths is compatible with the exhumation of islands along Aves Ridge and its geological time frame. Overall, our total-evidence analysis illustrates the difficulty of positioning highly incomplete fossils, although a robust phylogenetic framework was recovered by an a posteriori removal of taxa with high percentages of missing characters. Elimination of these taxa improved topological resolution by reducing polytomies and increasing node support. However, it introduced a systematic and geographic bias because most of these incomplete specimens are from northern South America. This is evident in biogeographic reconstructions, which suggest Patagonia as the area of origin of many clades when taxa are underrepresented, but Amazonia and/or Central and Southern Andes when all taxa are included. More generally, our analyses demonstrate the instability of topology and divergence time estimates when using different morphological datasets and clock models and thus caution against making macroevolutionary inferences when node support is weak or when uncertainties in the fossil record are not considered.

Lactifluus subg. Lactariopsis (Russulales/Basidiomycota) from Brazilian tropical forests

Lactifluus subg. Lactariopsis is a well-supported group of milkcaps occurring predominantly in tropical and subtropical ecosystems. This subgenus contains agaricoid and pleurotoid representatives and is the only group with members containing a secondary velum. The results of taxonomic and phylogenetic research into Lactifluus subg. Lactariopsis collected in Brazilian tropical forests (Amazon, Atlantic Rainforests, and Caatinga biomes) of the North and Northeast is presented here. Two new species are described: Lf. aurantioceraceus in sect. Neotropici, and Lf. reniformis in sect. Multicipites, newly delimited here . In addition, Lf. neotropicus has had its distribution expanded to the Caatinga biome, Lf. dunensis was confirmed in Lf. sect. Neotropici with new records from French Guiana, and Lf. annulifer was re-collected from the type locality. A combined dataset of nuclear rDNA internal transcribed spacer region and nuclear large subunit amplified sequences was analyzed and, based on its phylogenetic hypothesis, the two novel taxa and the new section were confirmed .

Archangelskyoxylon carlquistii gen. et sp. nov. Taxonomy and phylogeny of an unequivocal gnetoid Jurassic fossil wood from Argentina

Archangelskyoxylon carlquistii gen. et sp. nov. is based on anatomical secondary xylem from the Lower Jurassic (Sinemurian–Toarcian) in the Roca Blanca Formation of Santa Cruz Province, Patagonia, Argentina. The woods are preserved as siliceous permineralization and examined by light and scanning electron microscopy. The new fossil wood shows a set of anatomical features of the secondary xylem (e.g., vessels with simple, scalariform, foraminate, and modified foraminate perforation plates; vessel with bordered pits with outer aperture vestured or non-vestured, and inner aperture vestured; tracheids with bordered pits; septate fiber-tracheids, and uni to biseriate parenchyma rays), that are related to the Gnetidae and closely resembles those of Gnetum. The new taxon was compared with existing Gnetidae species and included in a phylogenetic analysis to test its relationships with fossil and extant genera of Gnetidae. In the resulting phylogenetic hypothesis, Archangelskyoxylon is placed into a clade that is closely related to Weltwitschia and Gnetum. This finding supports the existence of this lineage in the south of Gondwana during the Jurassic and reinforces the hypothesis that lineages related to the Gnetaceae diverged earlier in South America.

A novel target-enriched multilocus assay for sponges (Porifera): Red Sea Haplosclerida (Demospongiae) as a test case.

With declining biodiversity worldwide, a better understanding of species diversity and their relationships is imperative for conservation and management efforts. Marine sponges are species-rich ecological key players on coral reefs, but their species diversity is still poorly understood. This is particularly true for the demosponge order Haplosclerida, whose systematic relationships are contentious due to the incongruencies between morphological and molecular phylogenetic hypotheses. The single gene markers applied in previous studies did not resolve these discrepancies. Hence, there is a high need for a genome-wide approach to derive a phylogenetically robust classification and understand this group's evolutionary relationships. To this end, we developed a target enrichment-based multilocus probe assay for the order Haplosclerida using transcriptomic data. This probe assay consists of 20,000 enrichment probes targeting 2956 ultraconserved elements in coding (i.e. exon) regions across the genome and was tested on 26 haplosclerid specimens from the Red Sea. Our target-enrichment approach correctly placed our samples in a well-supported phylogeny, in agreement with previous haplosclerid molecular phylogenies. Our results demonstrate the applicability of high-resolution genomic methods in a systematically complex marine invertebrate group and provide a promising approach for robust phylogenies of Haplosclerida. Subsequently, this will lead to biologically unambiguous taxonomic revisions, better interpretations of biological and ecological observations and new avenues for applied research, conservation and managing declining marine diversity.

A TIME-CALIBRATED PHYLOGENY OF VERBESINA (HELIANTHEAE – ASTERACEAE) BASED ON NUCLEAR RIBOSOMAL ITS AND ETS SEQUENCES

Verbesina L. is a genus of the tribe Heliantheae, subtribe Verbesininae (Asteraceae), with distribution in the Americas, where Mexico and the Andes harbour the richest concentration of species. The approximately 325 species in the genus are shrubs, subshrubs, trees and rarely herbs. Despite its high species diversity and biogeographical importance, the only available phylogenetic hypothesis for Verbesina was based on chloroplast DNA restriction site data. In the present study, nuclear ITS and ETS DNA sequence data were used with an expanded taxon sampling, particularly among the South American Verbesina species, to improve phylogenetic resolution and support, clarify infrageneric relationships, and resolve biogeographical questions in the genus. The results of our new analysis corroborate the monophyly of Verbesina, but its current classification into 12 taxonomic sections, based on morphological characters such as phyllotaxis, head size, corolla colour, and presence of ray flowers, is not congruent with the molecular phylogeny, in which most sections are polyphyletic. We also show that Verbesina diverged in the late Miocene of North America, about 8 Ma. At least two independent Pleistocene dispersals into South America across the Isthmus of Panama and along the Southern Andes are evident, beginning around 3.23 Ma (1.27–3.23 Ma) in the Middle Pliocene, and resulting in an extra-Amazonian distribution of the genus inSouth America. Diversification in South America began around 2.83 Ma with occupation of the Andes. Colonisation of Brazil is estimated to have occurred around 2.15 Ma, from Andean lineages.