Bayesian Phylogeny Research Articles

The Tracking of Moist Habitats Allowed Aiphanes (Arecaceae) to Cover the Elevation Gradient of the Northern Andes.

The topographic gradients of the Tropical Andes may have triggered species divergence by different mechanisms. Topography separates species’ geographical ranges and offers climatic heterogeneity, which could potentially foster local adaptation to specific climatic conditions and result in narrowly distributed endemic species. Such a pattern is found in the Andean centered palm genus Aiphanes. To test the extent to which geographic barriers and climatic heterogeneity can explain distribution patterns in Aiphanes, we sampled 34 out of 36 currently recognized species in that genus and sequenced them by Sanger sequencing and/or sequence target capture sequencing. We generated Bayesian, likelihood, and species-tree phylogenies, with which we explored climatic trait evolution from current climatic occupation. We also estimated species distribution models to test the relative roles of geographical and climatic divergence in their evolution. We found that Aiphanes originated in the Miocene in Andean environments and possibly in mid-elevation habitats. Diversification is related to the occupation of the adjacent high and low elevation habitats tracking high annual precipitation and low precipitation seasonality (moist habitats). Different species in different clades repeatedly occupy all the different temperatures offered by the elevation gradient from 0 to 3,000 m in different geographically isolated areas. A pattern of conserved adaptation to moist environments is consistent among the clades. Our results stress the evolutionary roles of niche truncation of wide thermal tolerance by physical range fragmentation, coupled with water-related niche conservatism, to colonize the topographic gradient.

Molecular Phylogenetic Evidence and Biogeographic History of Indian Endemic Portulaca L. (Portulacaceae) Species

The genus Portulaca L. belongs to the monogeneric family Portulacaceae and consists of about 157 species worldwide. In India, it is represented by 11 taxa; among them, Portulaca badamica, Portulaca lakshminarasimhaniana, Portulaca oleracea var. linearifolia, and Portulaca laljii are endemic. So far, the phylogenetic positions of these species have not yet been analyzed. We have reconstructed the Bayesian and maximum likelihood phylogenies based on a combined chloroplast and nuclear DNA sequence dataset to reveal phylogenetic placements of Indian Portulaca. Phylogenetic analyses indicate that all the sampled Indian Portulaca species (except Portulaca wightiana) are placed in the AL clade, which contains most of the known species of the family Portulacaceae. We used reconstructed phylogeny to study the historical biogeography of Indian endemic species by employing S-DIVA analysis. S-DIVA analysis suggested P. lakshminarasimhaniana has origin in India, it may be the result of in situ speciation in India, and P. badamica was dispersed from Africa to India. We have also discussed the systematic placements of endemic species and their morphological relationships with closely allied species. In addition, this study also provides taxonomic treatment for endemic species.

Phylogenetic and Mutation Analysis of the Venezuelan Equine Encephalitis Virus Sequence Isolated in Costa Rica from a Mare with Encephalitis.

Venezuelan Equine Encephalitis virus (VEEV) is an arboviral pathogen in tropical America that causes lethal encephalitis in horses and humans. VEEV is classified into six subtypes (I to VI). Subtype I viruses are divided into epizootic (IAB and IC) and endemic strains (ID and IE) that can produce outbreaks or sporadic diseases, respectively. The objective of this study was to reconstruct the phylogeny and the molecular clock of sequences of VEEV subtype I complex and identify mutations within sequences belonging to epizootic or enzootic subtypes focusing on a sequence isolated from a mare in Costa Rica. Bayesian phylogeny of the VEEV subtype I complex tree with 110 VEEV complete genomes was analyzed. Evidence of positive selection was evaluated with Datamonkey server algorithms. The putative effects of mutations on the 3D protein structure in the Costa Rica sequence were evaluated. The phylogenetic analysis showed that Subtype IE-VEEV diverged earlier than other subtypes, Costa Rican VEEV-IE ancestors came from Nicaragua in 1963 and Guatemala in 1907. Among the observed non-synonymous mutations, only 17 amino acids changed lateral chain groups. Fourteen mutations located in the NSP3, E1, and E2 genes are unique in this sequence, highlighting the importance of E1-E2 genes in VEEV evolution.

Nearctic Species in the Palearctic: Trans-Beringian Range, Phylogeny and Phylogeography of Pterostichus (Cryobius) mandibularoides (Coleoptera, Carabidae)

Subgenus Cryobius is one of the most numerous among the megafauna of tundra soils, but studies on its species distribution, taxonomy, and ecology are lacking. Phylogeny and phylogeography reconstructions of insects with taxonomic complexity have become possible using an integrative approach. Here, we report that specimens of Pterostichus (Cryobius) mandibularoides, described from North America, were detected in Eurasia. Thus, this species has a trans-Beringian range with high distributions in North America, as well as a disjunctive part of the range on the northeastern edge of Asia within Chukotka and Wrangel Island. Eight COI haplotypes with closed relationships (1–2 mutation steps) were detected within the whole range, and one 28S rRNA haplotype was detected for Eurasia. Bayesian phylogeny revealed that P. mandibularoides had the most recent common ancestor with sister species P. brevicornis and P. nivalis. Mean genetic distances of both markers were similar and higher between P. mandibularoides and both P. brevicornis and P. nivalis (>5% ± 1.0%) than between the latter species (<4% ± 1.0%). The obtained results change the previous view about brevicornis group stock differentiation within Cryobius in the Arctic and require a revision of the phylogeny and phylogeography of brevicornis group species and Cryobius altogether.

Spatio‐temporal evolution of the catuaba clade in the Neotropics: Morphological shifts correlate with habitat transitions

AbstractAimThe biotic assembly of one of the most species‐rich savannas, the Brazilian Cerrado, has involved recruitment of lineages from several surrounding regions. However, we lack a clear understanding about the timing and pathways of biotic exchanges among these regions and about the role those interchanges had in the assembly of Neotropical biodiversity. We investigated the timing and routes of species movements between wet or seasonally dry habitats across Neotropical regions and assessed the potential for ecological adaptation by evaluating the habitat transitions correlated with morphological shifts.LocationNeotropics.TaxonThe plant genus Anemopaegma (Bignonieae, Bignoniaceae).MethodsWe inferred a Bayesian molecular phylogeny of Anemopaegma using one nuclear and two chloroplast markers. We sampled more than 90% of the known species diversity of Anemopaegma, covering its full geographical range. We estimated divergence times using a Bayesian relaxed‐clock approach and inferred ancestral ranges as well as shifts in habitat and morphological characters.ResultsPhylogenetic analyses recovered seven main clades within Anemopaegma. The genus likely originated in Amazonia in the late Oligocene. Early‐diverging lineages diversified in situ in Amazonia, particularly during the Miocene, with independent dispersal events to the Andes, Atlantic Forest and Cerrado. Shifts from seasonally dry forest to savanna habitats were correlated with shifts from liana to shrub and the loss of tendrils.Main ConclusionsThe timing of diversification of major lineages within Anemopaegma is consistent with major geological and climatic events that occurred during the late Palaeogene and Neogene, such as the Andean uplift and the Middle Miocene Climatic Optimum. Movements across different regions within the Neotropics were relatively common but shifts between habitats were not. The correlation in the evolution of the shrubby habit, the loss of tendrils and the shifts from forest to savanna are consistent with a scenario of ecological adaptation.

A comprehensive phylogeny helps clarify the evolutionary history of host breadth and lure response in the Australian Dacini fruit flies (Diptera: Tephritidae)

The tribe Dacini (Diptera: Tephritidae) contains over 930 recognised species and has been widely studied due to the economic importance of some taxa, such as the Oriental fruit fly Bactrocera dorsalis. Despite the attention this group has received, very few phylogenetic reconstructions have comprehensively sampled taxa from a single biogeographic region, thereby limiting our capacity to address more targeted evolutionary questions. To study the evolution of diet breadth and male lure response, two key traits fundamental to understanding dacine diversity and the biology of pest taxa, we analysed 273 individuals representing 144 described species from Australia (80% continental coverage), the Pacific, and select close relatives from South-east Asia to estimate a dated molecular phylogenetic reconstruction of the Dacini. We utilised seven loci with a combined total of 4,332 nucleotides, to estimate both Bayesian and Maximum Likelihood phylogenies of the tribe. Consistent with other molecular phylogenies of the tribe, there was a high level of disagreement between the placement of species in the phylogeny and their current subgeneric and species-complex level taxonomies. The Australian fauna exhibit high levels of endemism, with radiations of both exclusively Australian clades, and clades that originate elsewhere (e.g. the Bactrocera dorsalis species group). Bidirectional movement of species has occurred between Papua New Guinea and Australia, with evidence for multiple incursions over evolutionary time. The Bactrocera aglaiae species group emerged sister to all other Bactrocera species examined. Divergence time estimates were ∼ 30 my younger than previously reported for this group, with the tribe diverging from its most recent common ancestor ∼ 43 mya. Ancestral trait reconstruction and tests for trait phylogenetic signal revealed a strong signal for the evolution of male lure response across the tree, with cue-lure/raspberry ketone lure response the ancestral trait. Methyl eugenol response has arisen on multiple, independent occasions. The evolution of host breadth exhibited a weaker signal; yet, basal groups were more likely to be host specialists. Both the evolution of lure response and host fruit use provide predictive information for the outbreak management of understudied pest fruit flies for which direct inference of these features may be lacking. Our results, which parallel those of earlier research into the closely-related African Dacus spp., demonstrate how geographically focussed taxon coverage allows Dacini phylogenetics to more explicitly test evolutionary hypotheses, thereby progressing our understanding of the evolution of this highly diverse and recently-radiated group of flies.

Evolutionary and Biogeographical History of Penguins (Sphenisciformes): Review of the Dispersal Patterns and Adaptations in a Geologic and Paleoecological Context

Despite its current low diversity, the penguin clade (Sphenisciformes) is one of the groups of birds with the most complete fossil record. Likewise, from the evolutionary point of view, it is an interesting group given the adaptations developed for marine life and the extreme climatic occupation capacity that some species have shown. In the present contribution, we reviewed and integrated all of the geographical and phylogenetic information available, together with an exhaustive and updated review of the fossil record, to establish and propose a biogeographic scenario that allows the spatial-temporal reconstruction of the evolutionary history of the Sphenisciformes, discussing our results and those obtained by other authors. This allowed us to understand how some abiotic processes are responsible for the patterns of diversity evidenced both in modern and past lineages. Thus, using the BioGeoBEARS methodology for biogeographic estimation, we were able to reconstruct the biogeographical patterns for the entire group based on the most complete Bayesian phylogeny of the total evidence. As a result, a New Zealand origin for the Sphenisciformes during the late Cretaceous and early Paleocene is indicated, with subsequent dispersal and expansion across Antarctica and southern South America. During the Eocene, there was a remarkable diversification of species and ecological niches in Antarctica, probably associated with the more temperate climatic conditions in the Southern Hemisphere. A wide morphological variability might have developed at the beginning of the Paleogene diversification. During the Oligocene, with the trends towards the freezing of Antarctica and the generalized cooling of the Neogene, there was a turnover that led to the survival (in New Zealand) of the ancestors of the crown Sphenisciform lineages. Later these expanded and diversified across the Southern Hemisphere, strongly linked to the climatic and oceanographic processes of the Miocene. Finally, it should be noted that the Antarctic recolonization and its hostile climatic conditions occurred in some modern lineages during the Pleistocene, possibly due to exaptations that made possible the repeated dispersion through cold waters during the Cenozoic, also allowing the necessary adaptations to live in the tundra during the glaciations.

Comparative Plastome Analysis of Three Amaryllidaceae Subfamilies: Insights into Variation of Genome Characteristics, Phylogeny, and Adaptive Evolution.

In the latest APG IV classification system, Amaryllidaceae is placed under the order of Asparagus and includes three subfamilies: Agapanthoideae, Allioideae, and Amaryllidoideae, which include many economically important crops. With the development of molecular phylogeny, research on the phylogenetic relationship of Amaryllidaceae has become more convenient. However, the current comparative analysis of Amaryllidaceae at the whole chloroplast genome level is still lacking. In this study, we sequenced 18 Allioideae plastomes and combined them with publicly available data (a total of 41 plastomes), including 21 Allioideae species, 1 Agapanthoideae species, 14 Amaryllidoideae species, and 5 Asparagaceae species. Comparative analyses were performed including basic characteristics of genome structure, codon usage, repeat elements, IR boundary, and genome divergence. Phylogenetic relationships were detected using single-copy genes (SCGs) and ribosomal internal transcribed spacer sequences (ITS), and the branch-site model was also employed to conduct the positive selection analysis. The results indicated that all Amaryllidaceae species showed a highly conserved typical tetrad structure. The GC content and five codon usage indexes in Allioideae species were lower than those in the other two subfamilies. Comparison analysis of Bayesian and ML phylogeny based on SCGs strongly supports the monophyly of three subfamilies and the sisterhood among them. Besides, positively selected genes (PSGs) were detected in each of the three subfamilies. Almost all genes with significant posterior probabilities for codon sites were associated with self-replication and photosynthesis. Our study investigated the three subfamilies of Amaryllidaceae at the whole chloroplast genome level and suggested the key role of selective pressure in the adaptation and evolution of Amaryllidaceae.

Fossil coleoid cephalopod from the Mississippian Bear Gulch Lagerstätte sheds light on early vampyropod evolution

We describe an exceptionally well-preserved vampyropod, Syllipsimopodi bideni gen. et sp. nov., from the Carboniferous (Mississippian) Bear Gulch Lagerstätte of Montana, USA. The specimen possesses a gladius and ten robust arms bearing biserial rows of suckers; it is the only known vampyropod to retain the ancestral ten-arm condition. Syllipsimopodi is the oldest definitive vampyropod and crown coleoid, pushing back the fossil record of this group by ~81.9 million years, corroborating molecular clock estimates. Using a Bayesian tip-dated phylogeny of fossil neocoleoid cephalopods, we demonstrate that Syllipsimopodi is the earliest-diverging known vampyropod. This strongly challenges the common hypothesis that vampyropods descended from a Triassic phragmoteuthid belemnoid. As early as the Mississippian, vampyropods were evidently characterized by the loss of the chambered phragmocone and primordial rostrum—traits retained in belemnoids and many extant decabrachians. A pair of arms may have been elongated, which when combined with the long gladius and terminal fins, indicates that the morphology of the earliest vampyropods superficially resembled extant squids.

Bayesian and parsimony phylogeny of Augochlora bees (Hymenoptera: Apoidea) based on morphology: insights for their biogeography and natural history

AugochloraSmith, with 127 valid species, is the most widespread genus of Augochlorini bees, ranging from Argentina to southern Canada, including the Caribbean islands. The genus is divided into three subgenera,Augochloras. str.,OxystoglossellaEickwort, and the fossilElectraugochloraEngel. The extant subgenera were traditionally diagnosed by their nesting substrate, social behavior and morphology. However, accumulating evidence suggests that these features are not reliable for their separation, especially with the discovery of an enigmatic species sharing characteristics from both subgenera. Our objective is to provide a phylogenetic hypothesis to evaluate the monophyly of the extant subgenera and to place a new species, Augochlora (Augochlora) intermedia sp. nov. For this purpose, we compiled 110 unordered characters for 40 species ofAugochloraplus seven outgroup species and analyzed under parsimony and Bayesian inference. Topologies were very similar under both frameworks, allowing us to consistently characterize a few major lineages. Our results demonstrate that the extant subgenera correspond to monophyletic groups and the new species is sister group to remainingAugochloras. str. species. Both subgenera are widespread in the Western Hemisphere, with species groups differing in range and distributional patterns. Our interpretation is thatAugochloraarose in South America, subsequently colonizing Mesoamerica, the Caribbean and North America several times. Facultative social behavior can be found in both subgenera and in most lineages, indicating that the exclusive solitary behavior found inAugochlora purais an exception. Based on morphological clues we interpret that the habit of nesting out of the soil arose once inAugochloras. str.

Ecological and Morphological Differentiation Among COI Haplotype Groups in the Plant Parasitic Nematode Species Mesocriconema Xenoplax.

DNA barcoding with the mitochondrial COI gene reveals distinct haplotype subgroups within the monophyletic and parthenogenetic nematode species, Mesocriconema xenoplax. Biological attributes of these haplotype groups (HG) have not been explored. An analysis of M. xenoplax from 40 North American sites representing both native plant communities and agroecosystems was conducted to identify possible subgroup associations with ecological, physiological, or geographic factors. A dataset of 132 M. xenoplax specimens was used to generate sequences of a 712 bp region of the cytochrome oxidase subunit I gene. Maximum-likelihood and Bayesian phylogenies recognized seven COI HG (≥99/0.99 posterior probability/bootstrap value). Species delimitation metrics largely supported the genetic integrity of the HG. Discriminant function analysis of HG morphological traits identified stylet length, total body length, and stylet knob width as the strongest distinguishing features among the seven groups, with stylet length as the strongest single distinguishing morphological feature. Multivariate analysis identified land cover, ecoregion, and maximum temperature as predictors of 53.6% of the total variation (P = 0.001). Within land cover, HG categorized under “herbaceous,” “woody wetlands,” and “deciduous forest” were distinct in DAPC and RDA analyses and were significantly different (analysis of molecular variance P = 0.001). These results provide empirical evidence for molecular, morphological, and ecological differentiation associated with HG within the monophyletic clade that represents the species Mesocriconema xenoplax.

Analysis of the Origin and Dissemination of HIV-1 Subtype C in Bulgaria.

HIV-1 subtype C is the most abundant strain of HIV-1 infections worldwide and was found in the first known patients diagnosed with HIV/AIDS in Bulgaria in 1986. However, there is limited information on the molecular-epidemiological characteristics of this strain in the epidemic of the country. In this study, we analyze the evolutionary history of the introduction and dissemination of HIV-1 subtype C in Bulgaria using global phylogenetic analysis, Bayesian coalescent-based approach, and molecular clock methods. All available samples with HIV-1 subtype C from individuals diagnosed with HIV/AIDS between 1986 and 2017 were analyzed. Men and women were equally represented, and 24.3% of patients reported being infected abroad. The global phylogenetic analysis indicated multiple introductions of HIV-1 subtype C from various countries of the world. The reconstruction of a Bayesian time-scaled phylogenies showed that several Bulgarian strains segregated together in clusters, while others were intermixed in larger clades containing strains isolated from both European and non-European countries. The time-scale of HIV-1 subtype C introductions in Bulgaria demonstrates the early introduction of these viruses in the country. Our in-depth phylogenetic and phylogeographic analyses are compatible with a scenario of multiple early introductions in the country followed by limited local distribution in the subsequent years. HIV-1 subtype C was introduced in the early years of the epidemic, originating from different countries of the world. Due to the comprehensive measures for prevention and control in the early years of the epidemic in Bulgaria, HIV-1 subtype C was not widely disseminated among the general population of the country.

Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations

In spite of big data and new techniques, the phylogeny and timing of cockroaches remain in dispute. Apart from sequencing more species, an alternative way to improve the phylogenetic inference and time estimation is to improve the quality of data, calibrations and analytical procedure. This study emphasizes the completeness of data, the reliability of genes (judged via alignment ambiguity and substitution saturation), and the justification for fossil calibrations. Based on published mitochondrial genomes, the Bayesian phylogeny of cockroaches and termites is recovered as: Corydiinae + (((Cryptocercidae + Isoptera) + ((Anaplectidae + Lamproblattidae) + (Tryonicidae + Blattidae))) + (Pseudophyllodromiinae + (Ectobiinae + (Blattellinae + Blaberidae)))). With two fossil calibrations, namely,Valditermes brenanaeandPiniblattella yixianensis, this study dates the crown Dictyoptera to early Jurassic, and crown Blattodea to middle Jurassic. Using the ambiguous ‘roachoid’ fossils to calibrate Dictyoptera+sister pushes these times back to Permian and Triassic. This study also shows that appropriate fossil calibrations are rarer than considered in previous studies.

Postulating the Modality of Integrative Taxonomy in Describing the Cryptic Congener Pampus griseus (Cuvier) and Systematics of the Genus Pampus (Perciformes: Stromateidae)

Pomfrets (genus Pampus), a highly commercial fishery resource distributed in the Indo-Western Pacific that includes Lessepsian migrants, have witnessed a series of systematic reforms. In this study, based on comprehensive sampling spanning type localities and coevals in the Northern Indian Ocean, the cryptic and valid species Stromateus griseus is resurrected from the synonymy and re-described as Pampus griseus (New Combination) based on 35 specimens from the Bay of Bengal, corroborated by a molecular analysis, which indicated a confined distribution of the species. The Bayesian phylogeny of the genus was reconstructed, incorporating redressed barcodes (582 nucleotides) and concatenated mitochondrial gene sequence data (1,822 nucleotides) generated from the recorded species P. candidus, P. chinensis and the neophyte along with sequences from GenBank entrusting the latest literature. The phylograms differed in topology as for seven valid species, and the one predicated on the concatenated data erected a highly supported polytomous clade for the P. cinereus complex (P. griseus, P. cinereus, and P. candidus) which shares synapomorphies. Pampus argenteus and P. minor, together, formed a sister clade to the rest. Climate-driven vicariant events during glacial epochs and the Indo-Pacific Barrier effect can be the drivers behind the Indian and Pacific Ocean sister lineages in P. chinensis. A multivariate analysis isolated the cryptic species from its congeners. This article portrays the systematics revision of genus Pampus with an integrative taxonomic approach compiling distinctive molecular, morphological, and anatomical features, revised key for species identification, taxonomic archives of Indian stromateids, and winds up with specific remarks.

Insights on Lulworthiales Inhabiting the Mediterranean Sea and Description of Three Novel Species of the Genus Paralulworthia.

The order Lulworthiales, with its sole family Lulworthiaceae, consists of strictly marine genera found on a wide range of substrates such as seagrasses, seaweeds, and seafoam. Twenty-one unidentified Lulworthiales were isolated in previous surveys aimed at broadening our understanding of the biodiversity hosted in the Mediterranean Sea. Here, these organisms, mostly found in association with Posidonia oceanica and with submerged woods, were examined using thorough multi-locus phylogenetic analyses and morphological observations. Maximum-likelihood and Bayesian phylogeny based on nrITS, nrSSU, nrLSU, and four protein-coding genes led to the introduction of three novel species of the genus Paralulworthia: P. candida, P. elbensis, and P. mediterranea. Once again, the marine environment is a confirmed huge reservoir of novel fungal lineages with an under-investigated biotechnological potential waiting to be explored.

Detection and genetic characterization of the novel torque teno virus group 6 in Taiwanese general population.

Torque teno virus (TTV) is one of the most common human viruses and can infect an individual with multiple genotypes chronically and persistently. TTV group 6 is a recently discovered phylogenetic group first isolated from eastern Taiwan indigenes, but whether the TTV group 6 was also prevalent in the general population still unknown. One hundred and three randomly collected blood samples from general population and 66 TTV positive DNA samples extracted from Taiwan indigenes were included. A group-6-specific PCR was developed for re-screen over TTV positive samples. Two TTV group 6 positive samples from general population were cloned and sequenced for identifying mix-infected TTVs and confirming their classification by maximum-likelihood and Bayesian inference phylogeny. TTV group 6 can be detected in 4.5% (4/89) and 7.6% (5/66) of TTV positive samples from Taiwanese general population and eastern Taiwan indigenes, respectively. Sample VC09 was mix-infected with TTV groups 3 and 6. Sample VC99 was mix-infected with TTV groups 3, 4 and 6. A highly diverse triple overlapping region was observed, which may represent a unique phenomenon of TTV. The group-6-specific PCR can successfully detect TTV group 6. TTV group 6 may be prevalent worldwide regardless of the geographic region and/or ethnic groups.

Multi-Gene Phylogeny and Taxonomy of Hydnellum (Bankeraceae, Basidiomycota) from China.

The genus Hydnellum is an important group of stipitate hydnaceous fungi which can form ectomycorrhiza with many species of woody plants. In recent decades, the frequency and number of basidiocarps observed in China have been declining significantly. So far, however, we know little about the species diversity of Hydnellum in China. In this study, we conducted molecular phylogenetic analyses based on sections of multiple loci, including the large subunit of nuclear ribosomal RNA gene (nLSU), the internal transcribed spacer regions (ITS), the small subunit of nuclear ribosomal RNA gene (SSU) and the second-largest subunit of RNA polymerase II gene (RPB2), as well as morphological studies, of collected samples of Hydnellum from China. We also inferred Maximum Likelihood and Bayesian phylogenies for the order Thelephorales from the dataset of the combined nLSU and ITS. This study has revealed the phylogenetic position of Hydnellum in the order Thelephorales, and phylogenetically confirmed ten major clades in Thelephorales; Twenty-nine taxa are proposed, described or reported, including 10 new subgenera (Hydnellum subgenus Hydnellum, subg. Caesispinosum, subg. Croceum, subg. Inflatum, subg. Rhizomorphum, subg. Scabrosum, subg. Spongiosum, subg. Subindufibulatum, subg. Violaceum and subg. Zonatum), 11 new species (Hydnellum atrorubrum, H. atrospinosum, H. bomiense, H. brunneorubrum, H. fibulatum, H. granulosum, H. inflatum, H. rubidofuscum, H. squamulosum, H. sulcatum and H. yunnanense), 3 newly recorded species (H. caeruleum, H. peckii and H. spongiosipes) and 5 notable specimens (Hydnellum sp 1, H. sp 2, H. sp 3, H. sp 4 and H. sp 5). A classification system based on the morphological characteristics (especially the hyphal structure types) and molecular analyses is proposed to accommodate most species in Hydnellum. The distinguishing characters of the subgenera and the new species with their closely related taxa are discussed. A key to the species of Hydnellum from China is provided.

The role of vicariance and dispersal on the temporal range dynamics of forest vipers in the Neotropical region.

The emergence of the diagonal of open/dry vegetations, including Chaco, Cerrado and Caatinga, is suggested to have acted as a dispersal barrier for terrestrial organisms by fragmenting a single large forest that existed in South America into the present Atlantic and Amazon forests. Here we tested the hypothesis that the expansion of the South American diagonal of open/dry landscapes acted as a vicariant process for forest lanceheads of the genus Bothrops, by analyzing the temporal range dynamics of those snakes. We estimated ancestral geographic ranges of the focal lancehead clade and its sister clade using a Bayesian dated phylogeny and the BioGeoBEARS package. We compared nine Maximum Likelihood models to infer ancestral range probabilities and their related biogeographic processes. The best fitting models (DECTS and DIVALIKETS) recovered the ancestor of our focal clade in the Amazon biogeographic region of northwestern South America. Vicariant processes in two different subclades resulted in disjunct geographic distributions in the Amazon and the Atlantic Forest. Dispersal processes must have occurred mostly within the Amazon and the Atlantic Forest and not between them. Our results suggest the fragmentation of a single ancient large forest into the Atlantic and Amazon forests acting as a driver of vicariant processes for the snake lineage studied, highlighting the importance of the diagonal of open/dry landscapes in shaping distribution patterns of terrestrial biota in South America.

Diversification and distribution of gall crabs (Brachyura: Cryptochiridae: Opecarcinus) associated with Agariciidae corals

Coral reefs are home to the greatest diversity of marine life, and many species on reefs live in symbiotic associations. Studying the historical biogeography of symbiotic species is key to unravelling (potential) coevolutionary processes and explaining species richness patterns. Coral-dwelling gall crabs (Cryptochiridae) live in obligate symbiosis with a scleractinian host, and are ideally suited to study the evolutionary history between heterogeneous taxa involved in a symbiotic relationship. The genus Opecarcinus Kropp and Manning, 1987, like its host coral family Agariciidae, occurs in both Indo-Pacific and Caribbean seas, and is the only cryptochirid genus with a circumtropical distribution. Here, we use mitochondrial and nuclear DNA gene fragments of Opecarcinus specimens sampled from 21 Indo-Pacific localities and one Atlantic (Caribbean) locality. We applied several species delimitation tests to characterise species diversity, inferred a Bayesian molecular-clock time-calibrated phylogeny to estimate divergence times and performed an ancestral area reconstruction. Time to the most recent common ancestor (tMRCA) of Opecarcinus is estimated at 15−6 Mya (middle Miocene—late Miocene). The genus harbours ~ 15 undescribed species as well as several potential species complexes. There are indications of strict host-specificity patterns in certain Opecarcinus species in the Indo-Pacific and Atlantic, however, a robust phylogeny reconstruction of Agariciidae corals—needed to test this further—is currently lacking. The Indo-West Pacific was inferred to be the most probable ancestral area, from where the Opecarcinus lineage colonised the Western Atlantic and subsequently speciated into O. hypostegus. Opecarcinus likely invaded from the Indo-West Pacific across the East Pacific Barrier to the Atlantic, before the full closure of the Isthmus of Panama. The subsequent speciation of O. hypostegus, is possibly associated with newly available niches in the Caribbean, in combination with genetic isolation following the closure of the Panama Isthmus.

Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region.

With c. 2,000 species, Euphorbia is one of the largest angiosperm genera, yet a lack of chloroplast genome (plastome) resources impedes a better understanding of its evolution. In this study, we assembled and annotated 28 plastomes from Euphorbiaceae, of which 15 were newly sequenced. Phylogenomic and comparative analyses of 22 plastome sequences from all four recognized subgenera within Euphorbia revealed that plastome length in Euphorbia is labile, presenting a range of variation c. 42 kb. Large-scale expansions of the inverted repeat (IR) region were identified, and at the extreme opposite, the near-complete loss of the IR region (with only 355 bp left) was detected for the first time in Euphorbiaceae. Other structural variations, including gene inversion and duplication, and gene loss/pseudogenization, were also observed. We screened the most promising molecular markers from both intergenic and coding regions for phylogeny-based utilities, and estimated maximum likelihood and Bayesian phylogenies from four datasets including whole plastome sequences. The monophyly of Euphorbia is supported, and its four subgenera are recovered in a successive sister relationship. Our study constitutes the first comprehensive investigation on the plastome structural variation in Euphorbia and it provides resources for phylogenetic research in the genus, facilitating further studies on its taxonomy, evolution, and conservation.