Divergence Times Of Lineages Research Articles

Five new unexpected populations of endangered tuco-tuco Ctenomys rionegrensis (Rodentia, Ctenomyidae) help understanding its distribution and historical biogeography

In this study, we conducted a survey of newly discovered populations of tuco-tuco (subterranean rodents of the genus Ctenomys) in the Entre Ríos province, in an area characterized by its unexplored nature and its climatic and biogeographic complexity within Argentina, which includes two National Parks. We characterize the nucleotide sequences of the cytochrome-b gene, revealing the presence of seven novel haplotypes within Ctenomys rionegrensis, a species known to inhabit both sides of the Uruguay River. Through Bayesian analyses, we estimated the divergence times of the oldest lineages of C. rionegrensis, as well as those of the haplotypes located east of the Uruguay River, dating back approximately 630,000 years before present (ybp) and 526,000 ybp, respectively. These estimates correspond with significant paleogeographic events in the region. Our findings may raise questions regarding the taxonomic classification of the species and suggest potential modifications to its current endangered status as designated by the International Union for Conservation of Nature (IUCN). Consequently, this research provides valuable insights that may inform future revisions of the species' conservation status and guide the development of informed management strategies/policies.

Comparative phylogeography shows congruent co‐divergence in Neotropical seasonally dry forest and savanna tree species

AbstractAimThe response of South American seasonally dry tropical forest (SDTF) and savanna species to the Quaternary climate changes is still poorly understood. Here we use multi‐model inference approach to compare the phylogeography and demographic history of five trumpet tree species (also known as pau‐d'arco) and draw general biogeographical patterns: Handroanthus impetiginosus, H. ochraceus, H. serratifolius, Tabebuia aurea and T. roseoalba.LocationAmazonia, Atlantic Forest, Cerrado and Caatinga ecoregions, South America and Brazil.TaxaBignoniaceae, Tabebuia Alliance, trees.MethodsWe compiled genetic data, occurrence records and ecological niche modelling (ENM) from published articles. We used coalescent modelling to test patterns of co‐divergence, and analysed niche breadth and overlap and spatial patterns in genetic diversity using quantile regressions.ResultsSpecies showed concordant lineage divergence times in the Pleistocene. Lineage diversification and phylogeographical patterns are more related to species niche breadth than to biome (savanna or SDTF). Differences in genetic diversity among species matches the expected for the demographic scenarios obtained with coalescent simulations and ENMs: species with wider range expansion during the Last Glacial Maximum had higher diversity than species with range retraction or multiple refugia.Main ConclusionsDiversification burst in the Pliocene, and major diversification of lineages during the Pleistocene seems to be a general pattern in SDTF and savannas in the South America. The high number of haplotypes at the Central Brazil, corresponding to the Cerrado ecoregion, highlights the importance of Protected Areas for SDTFs and savannas, highly threatened biomes in Brazil.

Biogeographic Origin of Kurixalus (Anura, Rhacophoridae) on the East Asian Islands and Tempo of Diversification within Kurixalus.

The ancestral area of Kurixalus on the East Asian islands is under dispute, and two hypotheses exist, namely that distribution occurred only on the Asian mainland (scenario of dispersal) and that wide distribution occurred on both the Asian mainland and the East Asian islands (scenario of vicariance). In this study, we conducted biogeographic analyses and estimated the lineage divergence times based on the most complete sampling of species, to achieve a more comprehensive understanding on the origin of Kurixalus on the East Asian islands. Our results revealed that the process of jump dispersal (founder-event speciation) is the crucial process, resulting in the distribution of Kurixalus on the East Asian islands, and supported the model of the Asian mainland origin: that Kurixalus on the East Asian islands originated from the Asian mainland through two long-distance colonization events (jump dispersal), via the model of vicariance of a widespread ancestor on both the Asian mainland and the East Asian islands. Our results indicated that choices of historical biogeography models can have large impacts on biogeographic inference, and the procedure of model selection is very important in biogeographic analysis. The diversification rate of Kurixaus has slightly decreased over time, although the constant-rate model cannot be rejected.

Cryptic species diversity in a widespread neotropical tree genus: The case of Cedrela odorata.

Reconciling the use of taxonomy to partition morphological variation and describe genetic divergence within and among closely related species is a persistent challenge in phylogenetics. We reconstructed phylogenetic relationships among Cedrela odorata (Meliaceae) and five closely allied species to test the genetic basis for the current model of species delimitation in this economically valuable and threatened genus. We prepared a nuclear species tree with the program SNPhylo and 16,000 single-nucleotide polymorphisms from 168 Cedrela specimens. Based on clades present and ancestral patterns ADMIXTURE, we designed nine species delimitation models and compared each model to current taxonomy with Bayes factor delimitation. Timing of major lineage divergences was estimated with the program SNAPP. The resulting analysis revealed that modern C. odorata evolved from two genetically distinct ancestral sources. All species delimitation models tested better fit the data than the model representing current taxonomic delimitation. Models with the greatest marginal likelihoods separated Mesoamerican C. odorata and South American C. odorata into two species and lumped C. angustifolia and C. montana as a single species. We estimated that Cedrela diversified in South America within the last 19 million years following one or more dispersal events from Mesoamerican lineages. Our analyses show that the present taxonomic understanding within the genus obscures divergent lineages in C. odorata due in part to morphological differentiation and taxonomic distinctions that are not predictably associated with genetic divergence. A more accurate application of taxonomy to C. odorata and related species may aid in its conservation, management, and restoration efforts.

Variation in the Mitochondrial Genome of the Chagas Disease Vector Triatoma infestans (Hemiptera: Reduviidae).

Chagas' disease is transmitted mainly by members of the subfamily Triatominae (Hemiptera: Reduviidae). Among them, Triatoma infestans (Klug) is the main vector of the disease in Southern Cone of Latin America. In order to contribute to knowledge of the genetic variation between triatomine vectors, in the present study, we analyzed the intraspecific and interspecific variations of the seven mitogenomes available from Triatominae. In addition, in order to examine their evolutionary relationships with others species of Reduviidae and to estimate the divergence time of the main lineages, we constructed phylogenetic trees including mitogenome sequences of 30 species from Reduviidae. Comparative analysis between mitochondrial DNA sequences from two specimens of T. infestans revealed a total of 54 variable sites. Triatoma infestans, Triatoma dimidiata (Latreille), Triatoma rubrofasciata (De Geer), Triatoma migrans (Breddin), Rhodnius pictipes (Stål), and Panstrongylus rufotuberculatus (Champion) present similar mitogenome organization and the length differences observed among these species are primarily caused by variations in control region (CR) and intergenic spacers (IGS). The relative synonymous codon usage values (RSCU) were similar in the six species of Triatominae, and in agreement with the observed in other insects, a biased use of A and C nucleotides in the majority strand was detected. The monophyly of five subfamilies was strongly supported (Phymatinae, Peiratinae, Triatominae, Stenopodainae, and Harpactorinae), while the sampled species of Reduviinae were grouped with one specie from the Salyavatinae subfamily. The oldest subfamily is Phymatinae at 100.3 Mya (99.6-102.2 Mya) and the youngest is Triatominae and Stenopodainae at 52.6 Mya (42.5-63.7 Mya). The estimated diversification time for the Triatominae subfamily agrees with the Andean uplift geological event. An analysis with more mitogenomes from more Triatominae species would be necessary to provide sufficient evidence to support this finding.

PHYLOGENY AND EVOLUTIONARY HISTORY OF VIETNAMESE Arisaema (ARACEAE)

In the family Araceae, Arisaema Mart is one of the largest genera with 200 species in the world, and mainly distributed in the temperate and warm-temperate areas from the East to South-East of North America to northern Mexico, from tropical East and North-East Africa to the Arabian Penisula, and from temperate East Asia to South and South-East Asia and Malesia. Several species of Arisaema are used as food and local medicine in India, China and Vietnam. Exploring the relationship between plants and explaining where plants originated and how they migrated between regions in the world and Vietnam is still challenging. Construction of molecular phylogeny, estimations of the divergence time and ancestral area of lineages based on evidences of molecular data, fossils, geology have provided major insights into plant evolution. This study was conducted based on comprehensive taxon sampling and molecular data from four chloroplast DNA regions of Arisaema to determine the phylogeny and evolutionary history of Vietnamese Arisaema (Araceae). The phylogeny of Arisaema was studied by using ML and BI methods. Our results indicated that Arisaema originated in Southeast Asia at ca. 31 Ma during the Oligocene and that Vietnamese Arisaema was derived from the Southeast Asia Arisaema during climate optimum period of Mid-Miocene with the presence and development of the tropical rainforest. Whereas, Vietnamese Arisaema likely does not have any connection with Arisaema from India, North China, Japan and the Korean Peninsula regions

Estimating the Divergence Times of Alphaproteobacteria Based on Mitochondrial Endosymbiosis and Eukaryotic Fossils.

Alphaproteobacteria is one of the most abundant bacterial lineages that successfully colonize diverse marine and terrestrial environments on Earth. In addition, many alphaproteobacterial lineages have established close association with eukaryotes. This makes Alphaproteobacteria a promising system to test the link between the emergence of ecologically important bacteria and related geological events and the co-evolution between symbiotic bacteria and their hosts. Understanding the timescale of evolution of Alphaproteobacteria is key to testing these hypotheses, which is limited by the scarcity of bacterial fossils, however. Based on the mitochondrial endosymbiosis which posits that the mitochondrion originated from an alphaproteobacterial lineage, we propose a new strategy to estimate the divergence times of lineages within the Alphaproteobacteria by leveraging the fossil records of eukaryotes. In this chapter, we describe the workflow of the mitochondria-based method to date Alphaproteobacteria evolution by detailing the software, methods, and commands used for each step. Visualization of data and results is also described. We also provide related notes with background information and alternative options. All codes used to build this protocol are made available to the public, and we strive to make this protocol user-friendly in particular to microbiologists with limited practical skills in bioinformatics.

Complex co-evolutionary relationships between cicadas and their symbionts.

Previous evidence suggests that cicadas lacking Hodgkinia may harbour the yeast-like fungal symbionts (YLS). Here, we reinforce an earlier conclusion that the pathogenic ancestor of YLS independently infected different cicada lineages instead of the common ancestor of Cicadidae. Five independent replacement events in the loss of Hodgkinia/acquisition of YLS and seven other replacement events of YLS (from an Ophiocordyceps fungus to another Ophiocordyceps fungus) are hypothesised to have occurred within the sampled cicada taxa. The divergence time of YLS lineages was later than that of corresponding cicada lineages. The rapid shift of diversification rates of YLS and related cicada-parasitizing Ophiocordyceps began at approximately 32.94 Ma, and the diversification rate reached the highest value at approximately 24.82 Ma, which corresponds to the cooling climate changes at the Eocene-Oligocene boundary and the Oligocene-Miocene transition respectively. Combined with related acquisition/replacement events of YLS occurred during the cooling-climate periods, we hypothesise that the cooling-climate changes impacted the interactions between cicadas and related Ophiocordyceps, which coupled with the unusual life cycle and the differentiation of cicadas may finally led to the diversification of YLS in Cicadidae. Our results contribute to a better understanding of the evolutionary transition of YLS from entomopathogenic fungi in insects.

Contribution of historical herbarium small RNAs to the reconstruction of a cassava mosaic geminivirus evolutionary history

Emerging viral diseases of plants are recognised as a growing threat to global food security. However, little is known about the evolutionary processes and ecological factors underlying the emergence and success of viruses that have caused past epidemics. With technological advances in the field of ancient genomics, it is now possible to sequence historical genomes to provide a better understanding of viral plant disease emergence and pathogen evolutionary history. In this context, herbarium specimens represent a valuable source of dated and preserved material. We report here the first historical genome of a crop pathogen DNA virus, a 90-year-old African cassava mosaic virus (ACMV), reconstructed from small RNA sequences bearing hallmarks of small interfering RNAs. Relative to tip-calibrated dating inferences using only modern data, those performed with the historical genome yielded both molecular evolution rate estimates that were significantly lower, and lineage divergence times that were significantly older. Crucially, divergence times estimated without the historical genome appeared in discordance with both historical disease reports and the existence of the historical genome itself. In conclusion, our study reports an updated time-frame for the history and evolution of ACMV and illustrates how the study of crop viral diseases could benefit from natural history collections.

Phylogeny, Historical Biogeography, and Divergence Time Estimates of Eucnide (Loasaceae)

Abstract— Eucnide (Loasaceae) consists of about 15 species distributed across Mexico, Guatemala, and the North American Southwest, a geographically complex landscape made up of floristically unique deserts, large mountain ranges, and a large, geographically isolated peninsula. This complex geography is credited for high levels of biodiversity and endemism in the region and we examine relationships between geography and cladogenesis in Eucnide. In the most recent treatment of the genus, Thompson and Ernst recognize three sections of Eucnide differentiated based on floral morphology. To date, no molecular phylogenetic studies have broadly sampled species in this genus. We used Bayesian and maximum-likelihood phylogenetic analyses of one plastid marker (matK) and one nuclear marker (ITS) to: 1) test the monophyly of Eucnide sections and assess whether the existing taxonomy sufficiently circumscribes diversity within the genus; 2) assess the divergence times of Eucnide lineages to determine when the major clades diversified; and 3) estimate the ancestral range of Eucnide and hypothesize patterns of geographical diversification of the genus. We found that not all infrageneric units of Eucnide are monophyletic and the taxonomy needs revision. Additionally, the major clades of Eucnide are predominantly restricted to geographic regions, suggesting that species have frequently diversified within geographic areas. The ancestral range of Eucnide was inferred to be widespread, and the divergence times of the major clades coincide with major geological events, particularly, the formation of the North American warm deserts, the isolation of the Baja Peninsula, and the uplift of the Trans Mexican Volcanic Belt. This suggests that major geological/climatic events may have contributed to the diversification of the genus.

Late Neogene megariver captures and the Great Amazonian Biotic Interchange

Recently published time-calibrated molecular phylogenies have brought to light a large-scale biotic interchange between the Western and Eastern Amazon basins, associated with the late Neogene (c. 10–4.5 Ma) uplift of the Northern Andes and formation of the modern transcontinental Amazon river. This important macroevolutionary event was previously overlooked due to poor understanding of alpha taxonomy and geographic distributions, lack of species-dense phylogenetic analyses, and insufficient methods for estimating biogeographic range evolution and lineage divergence times. Rapid improvements in all these areas have now provided the community with a corpus of historical biogeographic studies using species-dense and time-calibrated molecular phylogenies of plant and animal taxa distributed across Greater Amazonia. In this study we present historical biogeographic analyses of two clades of freshwater fishes (potamotrygonid stingrays and apteronotid electric fishes), and synthesize these results with those of 18 other published studies of Amazonian taxa, including riverine and upland (terra firme) clades of plants (n = 5), insects (n = 2), and representatives of all five vertebrate classes; i.e. fishes (n = 4) amphibians (n = 3), non-avian reptiles (n = 2), birds (n = 2), and mammals (n = 2). Our results support the hypothesis that tectonically-driven megariver capture events facilitated a massive biotic interchange between the Western and Eastern Amazon basins, which we name the Great Amazonian Biotic Interchange. These same megacapture events also separated the modern Amazon and Orinoco basins, contributing to the biotic distinctiveness of these megadiverse regions, and thereby elevating the total biodiversity of Greater Amazonia. The results highlight the role of large and rare (Black Swan) landscape evolution events in preserving and promoting biodiversity that had accumulated over tens of millions of years and across the whole of the South American continental platform.

Rare and widespread: integrating Bayesian MCMC approaches, Sanger sequencing and Hyb-Seq phylogenomics to reconstruct the origin of the enigmatic Rand Flora genus Camptoloma.

Genera that are widespread, with geographically discontinuous distributions and represented by few species, are intriguing. Is their achieved disjunct distribution recent or ancient in origin? Why are they species-poor? The Rand Flora is a continental-scale pattern in which closely related species appear codistributed in isolated regions over the continental margins of Africa. Genus Camptoloma (Scrophulariaceae) is the most notable example, comprising three species isolated from each other on the northwest, eastern, and southwest Africa. We employed Sanger sequencing of nuclear and plastid markers, together with genomic target sequencing of 2190 low-copy nuclear genes, to infer interspecies relationships and the position of Camptoloma within Scrophulariaceae by using supermatrix and multispecies-coalescent approaches. Lineage divergence times and ancestral ranges were inferred with Bayesian Markov chain Monte Carlo (MCMC) approaches. The population history was estimated with phylogeographic coalescent methods. Camptoloma rotundifolium, restricted to Southern Africa, was shown to be a sister species to the disjunct clade formed by C. canariense, endemic to the Canary Islands, and C. lyperiiflorum, distributed in the Horn of Africa-Southern Arabia. Camptoloma was inferred to be sister to the mostly South African tribes Teedieae and Buddlejeae. Stem divergence was dated in the Late Miocene, while the origin of the extant disjunction was inferred as Early Pliocene. The current disjunct distribution of Camptoloma across Africa was likely the result of fragmentation and extinction and/or population bottlenecking events associated with historical aridification cycles during the Neogene; the pattern of species divergence, from south to north, is consistent with the "climatic refugia" Rand Flora hypothesis.

Phylogenetics and phylogeography of red deer mtDNA lineages during the last 50 000 years in Eurasia

AbstractThe present phylogeographic pattern of red deer in Eurasia is not only a result of the contraction of their distribution range into glacial refugia and postglacial expansion, but probably also an effect of replacement of some red deer s.l. mtDNA lineages by others during the last 50 000 years. To better recognize this process, we analysed 501 sequences of mtDNA cytochrome b, including 194 ancient and 75 contemporary samples newly obtained for this study. The inclusion of 161 radiocarbon-dated samples enabled us to study the phylogeny in a temporal context and conduct divergence-time estimation and molecular dating. Depending on methodology, our estimate of divergence between Cervus elaphus and Cervus canadensis varied considerably (370 000 or 1.37 million years BP, respectively). The divergence times of genetic lineages and haplogroups corresponded to large environmental changes associated with stadials and interstadials of the Late Pleistocene. Due to the climatic oscillations, the distribution of C. elaphus and C. canadensis fluctuated in north–south and east–west directions. Some haplotypes dated to pre-Last Glacial Maximum periods were not detected afterwards, representing possibly extinct populations. We indicated with a high probability the presence of red deer sensu lato in south-eastern Europe and western Asia during the Last Glacial Maximum.

Mitochondrial Genomes of the United States Distribution of Gray Fox (Urocyon cinereoargenteus) Reveal a Major Phylogeographic Break at the Great Plains Suture Zone

We examined phylogeographic structure in gray fox (Urocyon cinereoargenteus) across the United States to identify the location of secondary contact zone(s) between eastern and western lineages and investigate the possibility of additional cryptic intraspecific divergences. We generated and analyzed complete mitochondrial genome sequence data from 75 samples and partial control region mitochondrial DNA sequences from 378 samples to investigate levels of genetic diversity and structure through population- and individual-based analyses including estimates of divergence (FSTand SAMOVA), median joining networks, and phylogenies. We used complete mitochondrial genomes to infer phylogenetic relationships and date divergence times of major lineages ofUrocyonin the United States. Despite broad-scale sampling, we did not recover additional major lineages ofUrocyonwithin the United States, but identified a deep east-west split (∼0.8 million years) with secondary contact at the Great Plains Suture Zone and confirmed the Channel Island fox (Urocyon littoralis) is nested withinU. cinereoargenteus. Genetic diversity declined at northern latitudes in the eastern United States, a pattern concordant with post-glacial recolonization and range expansion. Beyond the east-west divergence, morphologically-based subspecies did not form monophyletic groups, though unique haplotypes were often geographically limited. Gray foxes in the United States displayed a deep, cryptic divergence suggesting taxonomic revision is needed. Secondary contact at a common phylogeographic break, the Great Plains Suture Zone, where environmental variables show a sharp cline, suggests ongoing evolutionary processes may reinforce this divergence. Follow-up study with nuclear markers should investigate whether hybridization is occurring along the suture zone and characterize contemporary population structure to help identify conservation units. Comparative work on other wide-ranging carnivores in the region should test whether similar evolutionary patterns and processes are occurring.

Phylogeny, evolution and ecological speciation analyses of Imperata (Poaceae: Andropogoneae) in the Neotropics

Imperata is a ubiquitous grass genus of the tribe Andropogoneae (Poaceae), distributed throughout the world. Previous systematic studies had established that the genus encompasses nine species although no phylogenetic molecular studies are available in which all the taxa have been included. The American continent has the largest number of species, encouraging research into how these taxa have evolved. Here we present a phylogenetic analysis based on three plastids (ndhF, trnL-F, and atpB-rbcL) and one nuclear (ITS) marker that cover the most extensive geographic distribution of the genus. We use this phylogeny to test the monophyly of Imperata within tribe Andropogoneae, analyze the infrageneric relationships of the genus, and estimate lineage divergence time. Additionally, ecological niche models (ENM) of the American lineages are presented to recognize the abiotic factors that constraint their potential geographic distribution and allow an understanding of the ecological drivers for species diversification. Our results yield a fully supported tree where monophyly is confirmed for the genus and exposes the existence of two clades, one encompassing five American lineages and the other encompassing those of the rest of the world. In parallel, molecular dating, ENM, and ecological speciation tests suggest that American lineages underwent speciation during the Quaternary associated with conservatism and niche divergence. Our results contribute to both the taxonomic and to the evolutionary knowledge of grasses, and also to the understanding of the biological diversity in the Neotropics.

Out of the Pan‐Himalaya: Evolutionary history of the Paeoniaceae revealed by phylogenomics

AbstractPeonies (the Paeoniaceae, Paeonia L.) are famous garden flowers, medicinal plants, and edible oil crops, but their evolutionary history largely remains unknown. To probe into their phylogenetic relationships, evolutionary history, formation of present distribution pattern, and origins of tetraploids, we sequenced 25 fragments belonging to 20 single copy nuclear genes and 14 chloroplast regions of all species in the genus to reconstruct phylogenetic relationships, date the divergence times of lineages, infer the ancestral biogeographical regions, and document the parents of tetraploids. Our results show that Paeoniaceae separated from the other members in Saxifragales in the Campanian of the late Cretaceous and diverged into two clades, woody and herbaceous clades, in the late Oligocene or early Miocene. They survived and early diverged in the Pan‐Himalaya where they migrated eastwards to East Asia and further to NW America, and northwards to Middle Asia, and further to Europe. The woody lineage differentiated into two sublineages with accelerated root or floral disk evolution, while the herbaceous lineage diverged into five sublineages. Multiple glacial and interglacial cycles in Europe in the late Pliocene and early Pleistocene created opportunities for the peony species to meet and hybridize in the Mediterranean refugia, giving rise to eight allotetraploid species and four infraspecific tetraploids. Paeonia daurica Andrews, P. obovata Maxim., and P. tenuifolia L. served as the most important parents. The phylogeny of Paeonia L. implies that a new taxonomic system with two subgenera and seven sections should be proposed.

Plastid phylogenomics and biogeography of the medicinal plant lineage Hyoscyameae (Solanaceae)

The cosmopolitan family Solanaceae, which originated and first diversified in South America, is economically important. The tribe Hyoscyameae is one of the three clades in Solanaceae that occurs outside of the New World; Hyoscyameae genera are distributed mainly in Europe and Asia, and have centers of species diversity in the Qinghai-Tibet Plateau and adjacent regions. Although many phylogenetic studies have focused on Solanaceae, the phylogenetic relationships within the tribe Hyoscyameae and its biogeographic history remain obscure. In this study, we reconstructed the phylogeny of Hyoscyameae based on whole chloroplast genome data, and estimated lineage divergence times according to the newly reported fruit fossil from the Eocene Patagonia, Physalis infinemundi, the earliest known fossil of Solanaceae. We reconstructed a robust phylogeny of Hyoscyameae that reveals the berry fruit-type Atropa is sister to the six capsule-bearing genera (Hyoscyameae sensu stricto), Atropanthe is sister to the clade (Scopolia, Physochlaina, Przewalskia), and together they are sister to the robustly supported Anisodus–Hyoscyamus clade. The stem age of Hyoscyameae was inferred to be in the Eocene (47.11 Ma, 95% HPD: 36.75–57.86 Ma), and the crown ages of Hyoscyameae sensu stricto were estimated as the early Miocene (22.52 Ma, 95% HPD: 15.19–30.53 Ma), which shows a close correlation with the rapid uplift of the Qinghai-Tibet Plateau at the Paleogene/Neogene boundary. Our results provide insights into the phylogenetic relationships and the history of the biogeographic diversification of the tribe Hyoscyameae, as well as plant diversification on the Qinghai-Tibet Plateau.

A Total-Evidence Dated Phylogeny of Echinoidea Combining Phylogenomic and Paleontological Data.

Phylogenomic and paleontological data constitute complementary resources for unraveling the phylogenetic relationships and divergence times of lineages, yet few studies have attempted to fully integrate them. Several unique properties of echinoids (sea urchins) make them especially useful for such synthesizing approaches, including a remarkable fossil record that can be incorporated into explicit phylogenetic hypotheses. We revisit the phylogeny of crown group Echinoidea using a total-evidence dating approach that combines the largest phylogenomic data set for the clade, a large-scale morphological matrix with a dense fossil sampling, and a novel compendium of tip and node age constraints. To this end, we develop a novel method for subsampling phylogenomic data sets that selects loci with high phylogenetic signal, low systematic biases, and enhanced clock-like behavior. Our results demonstrate that combining different data sources increases topological accuracy and helps resolve conflicts between molecular and morphological data. Notably, we present a new hypothesis for the origin of sand dollars, and restructure the relationships between stem and crown echinoids in a way that implies a long stretch of undiscovered evolutionary history of the crown group in the late Paleozoic. Our efforts help bridge the gap between phylogenomics and phylogenetic paleontology, providing a model example of the benefits of combining the two. [Echinoidea; fossils; paleontology; phylogenomics; time calibration; total evidence.].

Two New Species of Gymnotus (Gymnotiformes: Gymnotidae) from Brazil and Historical Biogeography of the Subgenus Lamontianus

Gymnotus is the most species-rich and geographically widespread genus of gymnotiform electric fishes and has been widely explored to understand mechanisms of diversification in Neotropical freshwater fishes at a continental scale. Within Gymnotus, the subgenus Lamontianus is a phenotypically distinctive clade with an elongate, cylindrical body shape currently known from four valid species (G. anguillaris, G. cataniapo, G. pedanopterus, and G. tiquie) restricted to rivers draining the Guiana Shield. Here we use aspects of body-surface coloration, meristic, morphological, and osteological data, including cranial, laterosensory pore, and postcranial characters, to diagnose two new species of Lamontianus that inhabit the Aripuanã and Arapiuns rivers that drain the Brazilian Shield. We also use geometric morphometric analyses of head shape to separate the new species from one another and other species of Lamontianus. We report biogeographic distributions for all species of Lamontianus and estimate ancestral geographic ranges and range evolution using the parametric biogeographic program BioGeoBEARS. We use the phylogeny of Lamontianus to test alternative hypotheses regarding lineage divergence times, before or after the formation of the modern East-draining Amazon at c. 10 Ma. Our analysis suggests that diversification in Lamontianus occurred primarily by geographic range fragmentation (vicariance) from an ancestral species distributed across the Western Guiana Shield. These results are similar to those of other Gymnotus and gymnotiform clades, where allopatric speciation and secondary contact due to geographic range expansion are commonly observed. This study brings to 46 the number of valid species of the genus Gymnotus, and to six the number of valid species of the subgenus Lamontianus.

Molecular analysis of Spiophanes bombyx complex (Annelida: Spionidae) with description of a new species.

Spiophanes bombyx (Claparède, 1870) from the Gulf of Naples, Tyrrhenian Sea, Italy, was the first described Spiophanes with fronto-lateral horns on the prostomium. It was also considered the only horned species occurring in European waters. Our sequence data of five gene fragments suggest the presence of two horned sibling Spiophanes species in northern Europe: S. cf. bombyx in the North and the Norwegian seas, and S. cf. convexus in Brittany, northern France, and Bay of Biscay, northern Spain. Spiophanes cf. bombyx worms are genetically close to a single examined specimen of S. bombyx from Venice Lagoon, Italy but their conspecificity should be verified by further study. Our sequence data show that horned Spiophanes from the North Pacific are genetically distant from horned European species, and that S. uschakowi Zachs, 1933, originally described from the Sea of Japan (East Sea) is a valid species. The data also suggest the presence of two horned sibling Spiophanes species in the North East Pacific: S. hakaiensis Radashevsky & Pankova, n. sp. distributed from Alaska south to about Point Conception, and S. norrisi Meißner & Blank, 2009, distributed from San Francisco Bay south to Baja California Sur, Mexico. Spiophanes from South America, morphologically similar to S. norrisi, are suggested to belong to a new species. Molecular data also suggest the presence of two sibling species among the worms from northern Europe identified by morphology as S. kroyeri Grube, 1860. Worms from the Barents Sea and northern part of the North Sea are tentatively referred to as S. cf. kroyeri; worms from the northern and central parts of the North Sea and from the Bay of Biscay, northern Spain, are tentatively referred to as S. cf. cirrata M. Sars in G.O. Sars, 1872. Sequence data also show that S. duplex from California is genetically different from morphologically similar worms from South America. The South American worms are referred to resurrected S. soederstroemi Hartman, 1953 which was originally described from off Rio Grande do Sul, Brazil, and then considered as a junior synonym of S. duplex. Analysis of divergence times of Spiophanes lineages suggested that the origin of the most recent common ancestor of horned Spiophanes with metameric nuchal organs was around 11.1 mya (95% HPD: 5.1–19.0 mya) and that the divergence of the North Atlantic and North Pacific lineages was around 7.9 mya (95% HPD: 4.1–13.3 mya). The North Atlantic lineage was estimated to have diverged 4.8 mya (95% HPD: 2.2–8.6 mya), resulting in the origin of S. cf. bombyx and S. cf. convexus. The North Pacific lineage was estimated to have diverged first by the isolation and speciation of S. norrisi 1.7 mya (95% HPD: 2.3–1.0 mya), and then by the isolation and speciation of S. uschakowi and S. hakaiensis n. sp. 1.3 mya (95% HPD: 2.0–0.7 mya). The estimates place the divergences soon after maximum glacial period in the North Pacific (2.4–3.0 mya).