Global Phylogeny Research Articles

A Review of the Fossil Record of North American Turtles of the CladePan-Testudinoidea

Turtles of the clade Pan-Testudinoidea have a rich fossil record in North America, including the Caribbean, ranging from the late Paleocene to the Holocene. All earlier reports cannot be substantiated herein. The earliest members of this clade probably immigrated in multiple waves from Asia. Current phylogenies of crown Testudinoidea recognize four primary clades: Pan-Emydidae, Pan-Geoemydidae, Pan-Testudinidae, and the lineage leading to Platysternon megacephalum. An updated global phylogeny allows attribution of fossils to these lineages with confidence that allows the discernment of new diversity trends and biogeographic patterns. The diversity of North American Pan-Testudinidae increased consistently throughout the Cenozoic and reached its peak in the early Miocene. The extinction of many testudinids at the end of the Pleistocene, however, decreased tortoise diversity toward its extant levels. The diversity of North American Pan-Emydidae and Pan-Geoemydidae shows opposite patterns. Pan-Emydidae are remarkably diverse today, but their diversity was low in the Eocene and only increased dramatically from the Oligocene and onwards. Pan-Geoemydidae, on the other side, were diverse in the late Paleocene to Eocene, but their diversity decreases to their extremely low present levels starting with the Oligocene. A taxonomic review of 191 named North and Central American pan-testudinoid taxa finds 57 nomina valida, 69 nomina invalida, 64 nomina dubia, and 1 nomen nudum.

The curious case of Hemidactylus gujaratensis (Squamata: Gekkonidae).

Hemidactylus Oken, 1817 is one of the most speciose genera of the family Gekkonidae with more than 140 described species (Uetz et al. 2016). While this genus naturally occurs across the tropics and subtropics, a substantial part of its distribution also results from human-mediated dispersal. Carranza Arnold (2006) retrieved five broad clades in a global phylogeny of Hemidactylus, one of which has species distributed in tropical Asia. Subsequent work by Bauer et al. (2010) and Bansal Karanth (2010) revealed that the species from tropical Asia fell into two deeply divergent and potentially non-sister sub-clades-one comprising a large radiation confined to peninsular India and Sri Lanka (the Indian radiation, IR), and the other comprising species largely distributed in Southeast (SE) Asia.

Frugivory-related traits promote speciation of tropical palms.

Animal-mediated seed dispersal by frugivorous birds and mammals is central to the ecology and functioning of ecosystems, but whether and how frugivory-related traits have affected plant speciation remains little explored. Fruit size is directly linked to plant dispersal capacity and therefore influences gene flow and genetic divergence of plant populations. Using a global species-level phylogeny with comprehensive data on fruit sizes and plant species distributions, we test whether fruit size has affected speciation rates of palms (Arecaceae), a plant family characteristic of tropical rainforests. Globally, the results reveal that palms with small fruit sizes have increased speciation rates compared with those with large (megafaunal) fruits. Speciation of small-fruited palms is particularly high in the understory of tropical rainforests in the New World, and on islands in the Old World. This suggests that frugivory-related traits in combination with geography and the movement behaviour of frugivores can influence the speciation of fleshy-fruited plants.

Systematic investigations of gene effects on both topologies and supports: An Echinococcus illustration.

In this paper, we propose a high performance computing toolbox implementing efficient statistical methods for the study of phylogenies. This toolbox, which implements logit models and LASSO-type penalties, gives a way to better understand, measure, and compare the impact of each gene on a global phylogeny. As an application, we study the Echinococcus phylogeny, which is often considered as a particularly difficult example. Mitochondrial and nuclear genomes (19 coding sequences) of nine Echinococcus species are considered in order to investigate the molecular phylogeny of this genus. First, we check that the 19 gene trees lead to 19 totally different unsupported topologies (a topology is the sister relationship when both branch lengths and supports are ignored in a phylogenetic tree), while using the 19 genes as a whole are not sufficient for estimating the phylogeny. In order to circumvent this issue and understand the impact of the genes, we computed 43,796 trees using combinations ranging from 13 to 19 genes. By doing so, 15 topologies are obtained. Four particular topologies, appearing more robust and frequent, are then selected for more precise investigation. Refining further our statistical analysis, a particularly robust topology is extracted. We also carefully demonstrate the influence of nuclear genes on the likelihood of the phylogeny.

Phylogeny and systematics of the brake fern genus Pteris (Pteridaceae) based on molecular (plastid and nuclear) and morphological evidence

The brake fern genus Pteris belongs to Pteridaceae subfamily Pteridoideae. It is one of the largest fern genera and has been estimated to contain 200–250 species distributed on all continents except Antarctica. Previous studies were either based on plastid data only or based on both plastid and nuclear data but the sampling was small. In addition, an infrageneric classification of Pteris based on morphological and molecular evidence has not been available yet. In the present study, based on molecular data of eight plastid markers and one nuclear marker (gapCp) of 256 accessions representing ca. 178 species of Pteris, we reconstruct a global phylogeny of Pteris. The 15 major clades identified earlier are recovered here and we further identified a new major clade. Our nuclear phylogeny recovered 11 of these 16 major clades, seven of which are strongly supported. The inclusion of Schizostege in Pteris is confirmed for the first time. Based on the newly reconstructed phylogeny and evidence from morphology, distribution and/or ecology, we classify Pteris into three subgenera: P. subg. Pteris, P. subg. Campteria, and P. subg. Platyzoma. The former two are further divided into three and 12 sections, respectively.

The shrimp superfamily Sergestoidea: a global phylogeny with definition of new families and an assessment of the pathways into principal biotopes.

The phylogenetic analysis of Sergestoidea based on 253 morphological characters and encompassing all 99 valid species confirmed all previously recognized genus-level clades. Analysis retrieved five major robust clades that correspond to families Luciferidae, Sergestidae, Acetidae fam.n., Sicyonellidae fam.n. and Petalidiumidae fam.n. Synonymy, emended diagnoses and composition of revealed family-level clades are provided. Three types of morphological characters were important in the phylogeny of the Sergestoidea: general external characters, copulatory organs, and photophores. Novel metrics to quantify the contribution of these character types were tested. General external characters were significant in supporting the major clades (80% of the families and nearly half of the genera). Copulatory organ characters and photophores greatly supported the medium-level clades: Lucifer, Belzebub, Petalidium, Neosergestes, Challengerosergia (copulatory organ characters) and Lucensosergia, Challengerosergia, Gardinerosergia, Phorcosergia (photophores). An evolutionary model of the Sergestoidea showing their pathways into their principal biotopes is proposed: the major clades evolved in a vertical direction (from epi- to bathypelagic); further divergence at the genus level occurred within vertical zones in a horizontal direction, with the invasion of the benthopelagic and neritic (shelf and estuarine) habitats and speciation within these domains.

Phylogeography of Coxsackievirus A16 Reveals Global Transmission Pathways and Recent Emergence and Spread of a Recombinant Genogroup.

Coxsackievirus A16 (CV-A16; Picornaviridae) is an enterovirus (EV) type associated with hand, foot, and mouth disease (HFMD) in children. To investigate the spatial spread of CV-A16, we used viral sequence data sampled during a prospective sentinel surveillance of HFMD in France (2010 to 2014) and phylogenetic reconstruction. A data set of 168 VP1 sequences was assembled with 416 publicly available sequences of various geographic origins. The CV-A16 sequences reported were assigned to two clades, genogroup B and a previously uncharacterized clade D. The time origins of clades B and D were assessed in 1978 (1973 to 1981) and 2004 (2001 to 2007), respectively. The shape of the global CV-A16 phylogeny indicated worldwide cocirculation of genetically distinct virus lineages over time and across geographic regions. Phylogenetic tree topologies and Bayes factor analysis indicated virus migration. Virus transportation events in clade B within Europe and Asia and between countries of the two geographic regions were assessed. The sustained transmission of clade D viruses over 4 years was analyzed at the township level in France and traced back to Peru in South America. Comparative genomics provided evidence of recombination between CV-A16 clades B and D and suggested an intertype recombinant origin for clade D. Time-resolved phylogenies and HFMD surveillance data indicated that CV-A16 persistence is sustained by continuing virus migration at different geographic scales, from community transmission to virus transportation between distant countries. The results showed a significant impact of virus movements on the epidemiological dynamics of HFMD that could have implications for disease prevention.IMPORTANCE Coxsackievirus A16 is one of the most prevalent enterovirus types in hand, foot, and mouth disease outbreaks reported in Southeast Asia. This study is based on epidemiological and viral data on HFMD caused by CV-A16 in a European country. The phylogeographic data complemented the syndromic surveillance with virus migration patterns between geographic regions in France. The results show how viral evolutionary dynamics and global virus spread interact to shape the worldwide pattern of an EV disease. CV-A16 transmission is driven by movements of infected individuals at different geographic levels: within a country (local dynamics), between neighboring countries (regional dynamics), and between distant countries (transcontinental dynamics). The results are consistent with our earlier data on EV-A71 and confirm the epidemiological interconnection of Asia and Europe with regard to EV infections.

First global molecular phylogeny and biogeographical analysis of two arachnid orders (Schizomida and Uropygi) supports a tropical Pangean origin and mid‐Cretaceous diversification

AbstractAimWe sought to illuminate the history of the arachnid orders Schizomida and Uropygi, neither of which have previously been subjected to global molecular phylogenetic and biogeographical analyses.LocationSpecimens used in this study were collected in all major tropical and subtropical areas where they are presently found, including the Americas, Africa, Australia and the Indo‐Pacific region.MethodsFrom field‐collected specimens, we sequenced two nuclear and two mitochondrial markers, combined these with publicly available data, and conducted multi‐gene phylogenetic analyses on 240 Schizomida, 24 Uropygi and 12 other arachnid outgroups. Schizomid specimens included one specimen from the small family Protoschizomidae; other schizomid specimens were in Hubbardiidae, subfamily Hubbardiinae, which holds 289 of the order's 305 named species. We inferred ancestral areas using the Dispersal‐Extinction‐Cladogenesis model of range evolution, and we used fossil calibrations to estimate divergence times.ResultsWe recovered monophyletic Schizomida and Uropygi as each other's sister group, forming the clade Thelyphonida, and terminals from the New World were usually positioned as the earliest diverging lineages. The ancestral area for schizomids reconstructed unambiguously to the region comprised of Mexico, Southern California and Florida (the xeric New World subtropics). Optimal trees suggested a single colonization of the Indo‐Pacific in both orders, although this did not receive bootstrap support. Molecular dating gave an Upper Carboniferous origin for each order, and a mid‐Cretaceous expansion of Schizomida, including the origin and initial diversification of those in the Indo‐Pacific.Main conclusionsAncestral area reconstructions, molecular dating and fossil evidence all support an Upper Carboniferous, tropical Pangean origin for Thelyphonida, Schizomida and perhaps Uropygi. Much of this region became unsuitable habitat for these arachnids during the breakup of Pangea, but they persisted in the area that is now Meso‐ and South America. From there they then expanded to the Indo‐Pacific, where schizomids today display an idiosyncratic combination of microendemism and long‐range dispersal.

An integrative approach to untangling species delimitation in the Cataglyphis bicolor desert ant complex in Israel

Although extensive research has been carried out on the desert ants in the genus Cataglyphis in recent years, some of the specific intra- and interspecific relationships remain elusive. The present study disentangles the phylogenetic relationships among the C. bicolor complex in Israel using an integrative approach based on genetic markers, morphometric measurements, and chemical analyses (cuticular hydrocarbons). Several species delimitation approaches based on four nuclear, two mitochondrial, and eleven microsatellite markers, as well as 16 body measurements and 56 chemical variables, were employed to deciphering the occurrence of cryptic species in our data set.Our findings support the occurrence of at least four distinct species in the C. bicolor group in Israel, one of which may be a complex of three more recent species. The findings confirm the distinctiveness of C. isis and C. holgerseni. They attest the presence of a recently discovered species, C. israelensis, in the central mountain ridge and the occurrence of another clade distributed from the Negev to the Mediterranean coast, comprising the species C. niger, C. savignyi, and C. drusus. Although these three species are separated on the basis of mtDNA, this subgrouping was not supported by any of the nuclear sequence markers nor by the microsatellite analysis. This genetic structure may thus either reflect a possible recent speciation, or a geographical structuring of a single species. Overall, using these different sources of evidence we locate our samples within a global phylogeny of the bicolor group and discuss the processes that underlie speciation in this group.

Geographic structure in two highly diverse lineages of Tillandsia (Bromeliaceae)

The Neotropical genus Tillandsia (Bromeliaceae) is an excellent model system for macroevolutionary and biogeographic studies owing to its remarkable species diversity (ca. 650 spp.) and varied morphological and ecological adaptations to epiphytic and saxicolous habitats. Recent phylogenetic studies have greatly improved our knowledge about generic limits and infrageneric classification of Tillandsia. These studies have identified two clades of Tillandsia characterized by a distinct geographic distribution: (i) a North and Central American clade that includes species from subgenus Tillandsia; and (ii) a central South American clade containing species from subgenera Aerobia, Anoplophytum, Diaphoranthema, and Phytarrhiza. Our study aimed to determine the size, composition, and potential geographic structure of these two clades within the context of a global phylogeny of Tillandsioideae. With the addition of 100 newly sequenced species to previous studies to cover the now ca. 30% of the known species diversity of Tillandsia, our analyses found both clades to be strongly supported, and revealed that their species richness is much greater than previously known. Ancestral area estimation suggests that most of the diversification of the first of these clades took place in North and Central America, whereas within the second, most of the migratory events occurred from the Andes to the Brazilian shield.

A global phylogeny of the fern genus Tectaria (Tectariaceae: Polypodiales) based on plastid and nuclear markers identifies major evolutionary lineages and suggests repeated evolution of free venation from anastomosing venation

Tectaria (Tectariaceae) is one of the most confusing fern genera in terms of its circumscription and phylogeny. Since its original description, a number of genera had been moved into or related with this genus, while others had been segregated from it. Tectaria is also among the largest fern genera, comprising 150–210 mostly tropical species. Previous molecular studies have been far from comprehensive (sampling no more than 76 accessions from 52 species), limited in geographic scope (mainly restricted to Asia), and based exclusively on plastid markers. In the present study, DNA sequences of eight plastid and one nuclear marker of 360 accessions representing ca. 130 species of Tectaria, ca. 36 species of six non-Tectaria genera in Tectariaceae, 12 species of Davalliaceae, Oleandraceae, and Polypodiaceae, and 13 species of Lomariopsidaceae were used to infer a phylogeny with maximum likelihood, Bayesian inference, and maximum parsimony approaches. Our major results include: (1) the most recently proposed circumscription of Tectaria is strongly supported as monophyletic; (2) the genera Lenda, Microbrochis, Phlebiogonium, and Sagenia, sampled here for the first time, are resolved as part of Tectaria; (3) four superclades representing early splits in Tectaria are identified, with the Old World species being sister to the New World species; (4) 12 well-supported major clades in Tectaria are revealed, differing from one another in molecular, morphological, and geographical features; (5) evolution of 13 morphological characters is inferred in a phylogenetic context and morphological synapomorphies of various clades are identified; and in particular (6) free venation in Tectaria is inferred to be repeatedly derived from anastomosing venation, an evolutionary phenomenon not documented previously in vascular plants in a phylogenetic context based on both plastid and nuclear evidence.

A curated database of cyanobacterial strains relevant for modern taxonomy and phylogenetic studies

The dataset herein described lays the groundwork for an online database of relevant cyanobacterial strains, named CyanoType (http://lege.ciimar.up.pt/cyanotype). It is a database that includes categorized cyanobacterial strains useful for taxonomic, phylogenetic or genomic purposes, with associated information obtained by means of a literature-based curation. The dataset lists 371 strains and represents the first version of the database (CyanoType v.1). Information for each strain includes strain synonymy and/or co-identity, strain categorization, habitat, accession numbers for molecular data, taxonomy and nomenclature notes according to three different classification schemes, hierarchical automatic classification, phylogenetic placement according to a selection of relevant studies (including this), and important bibliographic references. The database will be updated periodically, namely by adding new strains meeting the criteria for inclusion and by revising and adding up-to-date metadata for strains already listed. A global 16S rDNA-based phylogeny is provided in order to assist users when choosing the appropriate strains for their studies.

Whole genome sequencing of Shigella sonnei through PulseNet Latin America and Caribbean: advancing global surveillance of foodborne illnesses

ObjectivesShigella sonnei is a globally important diarrhoeal pathogen tracked through the surveillance network PulseNet Latin America and Caribbean (PNLA&C), which participates in PulseNet International. PNLA&C laboratories use common molecular techniques to track pathogens causing foodborne illness. We aimed to demonstrate the possibility and advantages of transitioning to whole genome sequencing (WGS) for surveillance within existing networks across a continent where S. sonnei is endemic. MethodsWe applied WGS to representative archive isolates of S. sonnei (n = 323) from laboratories in nine PNLA&C countries to generate a regional phylogenomic reference for S. sonnei and put this in the global context. We used this reference to contextualise 16 S. sonnei from three Argentinian outbreaks, using locally generated sequence data. Assembled genome sequences were used to predict antimicrobial resistance (AMR) phenotypes and identify AMR determinants. ResultsS. sonnei isolates clustered in five Latin American sublineages in the global phylogeny, with many (46%, 149 of 323) belonging to previously undescribed sublineages. Predicted multidrug resistance was common (77%, 249 of 323), and clinically relevant differences in AMR were found among sublineages. The regional overview showed that Argentinian outbreak isolates belonged to distinct sublineages and had different epidemiologic origins. ConclusionsLatin America contains novel genetic diversity of S. sonnei that is relevant on a global scale and commonly exhibits multidrug resistance. Retrospective passive surveillance with WGS has utility for informing treatment, identifying regionally epidemic sublineages and providing a framework for interpretation of prospective, locally sequenced outbreaks.

The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis

Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range. Our dataset includes 54 previously unpublished mitochondrial genomes and significantly increases the coverage of the Eurasian range of the species. The resulting global phylogeny confirms that the Late Pleistocene mammoth population comprised three distinct mitochondrial lineages that began to diverge ~1.0–2.0 million years ago (Ma). We also find that mammoth mitochondrial lineages were strongly geographically partitioned throughout the Pleistocene. In combination, our genetic results and the pattern of morphological variation in time and space suggest that male-mediated gene flow, rather than large-scale dispersals, was important in the Pleistocene evolutionary history of mammoths.

Global Kinetoplastea phylogeny inferred from a large-scale multigene alignment including parasitic species for better understanding transitions from a free-living to a parasitic lifestyle.

All members of the order Trypanosomatida known to date are parasites that are most likely descendants of a free-living ancestor. Trypanosomatids are an excellent model to assess the transition from a free-living to a parasitic lifestyle, because a large amount of experimental data has been accumulated for well-studied members that are harmful to humans and livestock (Trypanosoma spp. and Leishmania spp.). However, recent advances in our understanding of the diversity of trypanosomatids and their close relatives (i.e., members of the class Kinetoplastea) have suggested that the change in lifestyle took place multiple times independently from that which gave rise to the extant trypanosomatid parasites. In the current study, transcriptomic data of two parasitic kinetoplastids belonging to orders other than Trypanosomatida, namely Azumiobodo hoyamushi (Neobodonida) and Trypanoplasma borreli (Parabodonida), were generated. We re-examined the transition from a free-living to a parasitic lifestyle in the evolution of kinetoplastids by combining (i) the relationship among the five orders in Kinetoplastea and (ii) that among free-living and parasitic species within the individual orders. The former relationship was inferred from a large-scale multigene alignment including the newly generated data from Azumiobodo and Trypanoplasma, as well as the data from another parasitic kinetoplastid, Perkinsela sp., deposited in GenBank; and the latter was inferred from a taxon-rich small subunit ribosomal DNA alignment. Finally, we discuss the potential value of parasitic kinetoplastids identified in Parabodonida and Neobodonida for studying the evolutionary process that turned a free-living species into a parasite.

Transmission patterns and evolution of respiratory syncytial virus in a community outbreak identified by genomic analysis.

Detailed information on the source, spread and evolution of respiratory syncytial virus (RSV) during seasonal community outbreaks remains sparse. Molecular analyses of attachment (G) gene sequences from hospitalized cases suggest that multiple genotypes and variants co-circulate during epidemics and that RSV persistence over successive seasons is characterized by replacement and multiple new introductions of variants. No studies have defined the patterns of introduction, spread and evolution of RSV at the local community and household level. We present a whole genome sequence analysis of 131 RSV group A viruses collected during 6-month household-based RSV infection surveillance in Coastal Kenya, 2010 within an area of 12 km2. RSV infections were identified by regular symptom-independent screening of all household members twice weekly. Phylogenetic analysis revealed that the RSV A viruses in nine households were closely related to genotype GA2 and fell within a single branch of the global phylogeny. Genomic analysis allowed the detection of household-specific variation in seven households. For comparison, using only G gene analysis, household-specific variation was found only in one of the nine households. Nucleotide changes were observed both intra-host (viruses identified from same individual in follow-up sampling) and inter-host (viruses identified from different household members) and these coupled with sampling dates enabled a partial reconstruction of the within household transmission chains. The genomic evolutionary rate for the household dataset was estimated as 2.307 × 10 − 3 (95% highest posterior density: 0.935–4.165× 10 − 3) substitutions/site/year. We conclude that (i) at the household level, most RSV infections arise from the introduction of a single virus variant followed by accumulation of household specific variation and (ii) analysis of complete virus genomes is crucial to better understand viral transmission in the community. A key question arising is whether prevention of RSV introduction or spread within the household by vaccinating key transmitting household members would lead to a reduced onward community-wide transmission.

Phylogeny and Haplotype Analysis of Fungi Within the Fusarium incarnatum-equiseti Species Complex

Fusarium spp. are ranked among the top 10 most economically and scientifically important plant-pathogenic fungi in the world and are associated with plant diseases that include fruit decay of a number of crops. Fusarium isolates infecting bell pepper in Trinidad were identified based on sequence comparisons of the translation elongation factor gene (EF-1a) with sequences of Fusarium incarnatum-equiseti species complex (FIESC) verified in the FUSARIUM-ID database. Eighty-two isolates were identified as belonging to one of four phylogenetic species within the subclades FIESC-1, FIESC-15, FIESC-16, and FIESC-26, with the majority of isolates belonging to FIESC-15. A comparison of the level of DNA polymorphism and phylogenetic inference for sequences of the internal transcribed spacer region (ITS1-5.8S-ITS2) and EF-1a sequences for Trinidad and FUSARIUM-ID type species was carried out. The ITS sequences were less informative, had lower haplotype diversity and restricted haplotype distribution, and resulted in poor resolution and taxa placement in the consensus maximum-likelihood tree. EF-1a sequences enabled strongly supported phylogenetic inference with highly resolved branching patterns of the 30 phylogenetic species within the FIESC and placement of representative Trinidad isolates. Therefore, global phylogeny was inferred from EF-1a sequences representing 11 countries, and separation into distinct Incarnatum and Equiseti clades was again evident. In total, 42 haplotypes were identified: 12 were shared and the remaining were unique haplotypes. The most diverse haplotype was represented by sequences from China, Indonesia, Malaysia, and Trinidad and consisted exclusively of F. incarnatum isolates. Spain had the highest haplotype diversity, perhaps because both F. equiseti and F. incarnatum sequences were represented; followed by the United States, which contributed both F. equiseti and F. incarnatum sequences to the data set; then by countries representing Southeast Asia (China, Indonesia, Malaysia, Thailand, and Philippines) and Trinidad; both of these regions were represented by only F. incarnatum sequences. Trinidad shared two haplotypes with China and one haplotype with the United States for only F. incarnatum isolates. The findings of this study are important for devising disease management strategies and for understanding the phylogenetic relationships among members of the FIESC.

South Asia as a Reservoir for the Global Spread of Ciprofloxacin-Resistant Shigella sonnei: A Cross-Sectional Study.

BackgroundAntimicrobial resistance is a major issue in the Shigellae, particularly as a specific multidrug-resistant (MDR) lineage of Shigella sonnei (lineage III) is becoming globally dominant. Ciprofloxacin is a recommended treatment for Shigella infections. However, ciprofloxacin-resistant S. sonnei are being increasingly isolated in Asia and sporadically reported on other continents. We hypothesized that Asia is a primary hub for the recent international spread of ciprofloxacin-resistant S. sonnei.Methods and FindingsWe performed whole-genome sequencing on a collection of 60 contemporaneous ciprofloxacin-resistant S. sonnei isolated in four countries within Asia (Vietnam, n = 11; Bhutan, n = 12; Thailand, n = 1; Cambodia, n = 1) and two outside of Asia (Australia, n = 19; Ireland, n = 16). We reconstructed the recent evolutionary history of these organisms and combined these data with their geographical location of isolation. Placing these sequences into a global phylogeny, we found that all ciprofloxacin-resistant S. sonnei formed a single clade within a Central Asian expansion of lineage III. Furthermore, our data show that resistance to ciprofloxacin within S. sonnei may be globally attributed to a single clonal emergence event, encompassing sequential gyrA-S83L, parC-S80I, and gyrA-D87G mutations. Geographical data predict that South Asia is the likely primary source of these organisms, which are being regularly exported across Asia and intercontinentally into Australia, the United States and Europe. Our analysis was limited by the number of S. sonnei sequences available from diverse geographical areas and time periods, and we cannot discount the potential existence of other unsampled reservoir populations of antimicrobial-resistant S. sonnei.ConclusionsThis study suggests that a single clone, which is widespread in South Asia, is likely driving the current intercontinental surge of ciprofloxacin-resistant S. sonnei and is capable of establishing endemic transmission in new locations. Despite being limited in geographical scope, our work has major implications for understanding the international transfer of antimicrobial-resistant pathogens, with S. sonnei acting as a tractable model for studying how antimicrobial-resistant Gram-negative bacteria spread globally.

Shedding new light on old algae: Matching names and sequences in the brown algal genus Lobophora (Dictyotales, Phaeophyceae)

AbstractThe existence of massive cryptic diversity in algae makes linking DNA‐based lineages to existing taxa exceedingly difficult. A better integration of historical collections into modern taxonomic research is therefore highly desirable. Using the brown algal genus Lobophora as a test case, we explore the feasibility of linking taxonomic names to clades in modern phylogenies. Despite Lobophora being a pantropical genus with probably more than 100 species, traditionally only a handful of species have been recognized. In this study we reevaluated the identity of 17 historical taxa thought to belong to Lobophora by attempting DNA amplification of herbarium material as well as specimens recently collected from the type localities (epitypes). In an attempt to assign them to Molecular Operational Taxonomic Units, the obtained sequences were integrated in a global Lobophora phylogeny based upon data derived from more than 650 specimens. Our results indicate that although five sequences were obtained from type specimens, exclusive reliance on information preserved in type specimens is problematic. Epitype material proved a more successful way forward, but this route often comes with a considerable degree of uncertainty, especially in tropical regions where the extent of sympatry among Lobophora lineages is often considerable. More problematic from a broader perspective is the fact that for 35% of historical taxa, either the type could not be traced or permission was not granted to extract DNA from the types. Such a low accessibility rate may reduce our reliance on type material and jeopardize future efforts to integrate historical taxa into a framework of a modern DNA‐based taxonomy.

Commensal associations and benthic habitats shape macroevolution of the bivalve clade Galeommatoidea.

The great diversity of marine life has been shaped by the interplay between abiotic and biotic factors. Among different biotic interactions, symbiosis is an important yet less studied phenomenon. Here, we tested how symbiotic associations affected marine diversification, using the bivalve superfamily Galeommatoidea as a study system. This superfamily contains large numbers of obligate commensal as well as free-living species and is therefore amenable to comparative approaches. We constructed a global molecular phylogeny of Galeommatoidea and compared macroevolutionary patterns between free-living and commensal lineages. Our analyses inferred that commensalism/sediment-dwelling is likely to be the ancestral condition of Galeommatoidea and that secondary invasions of hard-bottom habitats linked to the loss of commensalism. One major clade containing most of the free-living species exhibits a 2-4 times higher diversification rate than that of the commensals, likely driven by frequent niche partitioning in highly heterogeneous hard-bottom habitats. However, commensal clades show much higher within-clade morphological disparity, likely promoted by their intimate associations with diverse hosts. Our study highlights the importance of interactions between different ecological factors in shaping marine macroevolution and that biotic factors cannot be ignored if we wish to fully understand processes that generate marine biodiversity.