Search

A comprehensive study was conducted in the Cuatro Ciénegas Basin (CCB) in Coahuila, Mexico, which is known for its diversity of microorganisms and unique physicochemical properties. The study focused on the "Archaean Domes" (AD) site in the CCB, which is characterized by an abundance of hypersaline, nonlithifying microbial mats. In AD, we analyzed the small domes and circular structures using metagenome assembly genomes (MAGs) with the aim of expanding our understanding of the prokaryotic tree of life by uncovering previously unreported lineages, as well as analyzing the diversity of bacteria and archaea in the CCB. A total of 325 MAGs were identified, including 48 Archaea and 277 Bacteria. Remarkably, 22 archaea and 104 bacteria could not be classified even at the genus level, highlighting the remarkable novel diversity of the CCB. Besides, AD site exhibited significant diversity at the phylum level, with Proteobacteria being the most abundant, followed by Desulfobacteria, Spirochaetes, Bacteroidetes, Nanoarchaeota, Halobacteriota, Cyanobacteria, Planctomycetota, Verrucomicrobiota, Actinomycetes and Chloroflexi. In Archaea, the monophyletic groups of MAGs belonged to the Archaeoglobi, Aenigmarchaeota, Candidate Nanoarchaeota, and Halobacteriota. Among Bacteria, monophyletic groups were also identified, including Spirochaetes, Proteobacteria, Planctomycetes, Actinobacteria, Verrucomicrobia, Bacteroidetes, Candidate Bipolaricaulota, Desulfobacteria, and Cyanobacteria. These monophyletic groups were possibly influenced by geographic isolation, as well as the extreme and fluctuating environmental conditions in the pond AD, such as stoichiometric imbalance of C:N:P of 122:42:1, fluctuating pH (5-9.8) and high salinity (5.28% to saturation). [ABSTRACT FROM AUTHOR]

Candida auris is an emerging multidrug-resistant and opportunistic pathogenic yeast. Whole-genome sequencing analysis has defined five major clades, each from a distinct geographic region. The current study aimed to examine the genome of the C. auris 20–1498 strain, which is the first isolate of this fungus identified in Mexico. Based on whole-genome sequencing, the draft genome was found to contain 70 contigs. It had a total genome size of 12.86 Mbp, an N50 value of 1.6 Mbp, and an average guanine-cytosine (GC) content of 45.5%. Genome annotation revealed a total of 5432 genes encoding 5515 proteins. According to the genomic analysis, the C. auris 20–1498 strain belongs to clade IV (containing strains endemic to South America). Of the two genes (ERG11 and FKS1) associated with drug resistance in C. auris, a mutation was detected in K143R, a gene located in a mutation hotspot of ERG11 (lanosterol 14-α-demethylase), an antifungal drug target. The focus on whole-genome sequencing and the identification of mutations linked to the drug resistance of fungi could lead to the discovery of new therapeutic targets and new antifungal compounds. [ABSTRACT FROM AUTHOR]

We used nuclear genomic data and statistical models to evaluate the ecological and evolutionary processes shaping spatial variation in species richness in Calochortus (Liliaceae, 74 spp.). Calochortus occupies diverse habitats in the western United States and Mexico and has a center of diversity in the California Floristic Province, marked by multiple orogenies, winter rainfall, and highly divergent climates and substrates (including serpentine). We used sequences of 294 low-copy nuclear loci to produce a time-calibrated phylogeny, estimate historical biogeography, and test hypotheses regarding drivers of present-day spatial patterns in species number. Speciation and species coexistence require reproductive isolation and ecological divergence, so we examined the roles of chromosome number, environmental heterogeneity, and migration in shaping local species richness. Six major clades--inhabiting different geographic/climatic areas, and often marked by different base chromosome numbers (n = 6 to 10)--began diverging from each other ~10.3 Mya. As predicted, local species number increased significantly with local heterogeneity in chromosome number, elevation, soil characteristics, and serpentine presence. Species richness is greatest in the Transverse/Peninsular Ranges where clades with different chromosome numbers overlap, topographic complexity provides diverse conditions over short distances, and several physiographic provinces meet allowing immigration by several clades. Recently diverged sister-species pairs generally have peri-patric distributions, and maximum geographic overlap between species increases over the first million years since divergence, suggesting that chromosomal evolution, genetic divergence leading to gametic isolation or hybrid inviability/sterility, and/or ecological divergence over small spatial scales may permit species co-occurrence. [ABSTRACT FROM AUTHOR]

Reconstructing a robust species phylogeny and disentangling the evolutionary and biogeographic history of the gymnosperm genus Ephedra, which has a large genome and rich polyploids, remain a big challenge. Here we reconstructed a transcriptome‐based phylogeny of 19 diploid Ephedra species, and explored evolutionary reticulations in this genus represented by 50 diploid and polyploid species, using four low‐copy nuclear and nine plastid genes. The diploid species phylogeny indicates that the Mediterranean species diverged first, and the remaining species split into three clades, including the American species (Clade A), E. rhytidosperma, and all other Asian species (Clade B). The single‐gene trees placed E. rhytidosperma sister to Clade A, Clade B, or Clades A + B in similar proportions, suggesting that radiation and gene flow likely occurred in the early evolution of Ephedra. In addition, reticulate evolution occurred not only among the deep nodes, but also in the recently evolved South American species, which further caused difficulty in phylogenetic reconstruction. Moreover, we found that allopolyploid speciation was pervasive in Ephedra. Our study also suggests that Ephedra very likely originated in the Tethys coast during the late Cretaceous, and the South American Ephedra species have a single origin by dispersal from Mexico or North America. [ABSTRACT FROM AUTHOR]

Symphyotrichum (Asteraceae) is a well-circumscribed genus on the basis of morphological and molecular data, but species boundaries remain poorly understood. Here, the species delimitation of the contentious Symphyotrichum subulatum group (Symphyotrichum subg. Astropolium) is illuminated using morphometric, phylogenomic, and geographical analyses. Symphyotrichum mexicanum sp. nov., a new species endemic to central Mexico, is described and distinguished from Symphyotrichum expansum based on its morphometric attributes, phylogenetic placement, geographic range, and ecological specialization. [ABSTRACT FROM AUTHOR]

Simple Summary: Cacti account for nearly 1440 species, most of them native to the American continent. These succulent plants are the most ubiquitous elements of the arid ecosystems. Mexico harbors the highest number of cacti species in the world (45%). Unfortunately, many of them are threatened by human activities. Although having this biodiversity relevance, presently the evolutionary processes of cacti have been poorly studied. Because the biological and conservation unit is the species, evolutionary studies provide relevant information. In this study, we analyzed how and when past events shaped the evolutionary relationships of 103 species. Our results showed that from 4.5 million years ago the arid regions of Mexico were the locations for abundant cacti speciation. From these lands, cacti have colonized most of the Mexican territories, the southern regions of the United States, as well as the Caribbean. The evolution of these plants was probably promoted by past temperatures that were comparable to the present ones. We identified different speciation and dispersal events in these fascinating plants. This study identified the Mexican Plateau as the place where the early stages of the evolutionary history of cacti occurred. Mexico harbors ~45% of world's cacti species richness. Their biogeography and phylogenomics were integrated to elucidate the evolutionary history of the genera Coryphantha, Escobaria, Mammillaria, Mammilloydia, Neolloydia, Ortegocactus, and Pelecyphora (Mammilloid Clade). We analyzed 52 orthologous loci from 142 complete genomes of chloroplast (103 taxa) to generate a cladogram and a chronogram; in the latter, the ancestral distribution was reconstructed with the Dispersal-Extinction-Cladogenesis model. The ancestor of these genera arose ~7 Mya on the Mexican Plateau, from which nine evolutionary lineages evolved. This region was the site of 52% of all the biogeographical processes. The lineages 2, 3 and 6 were responsible for the colonization of the arid southern territories. In the last 4 Mya, the Baja California Peninsula has been a region of prolific evolution, particularly for lineages 8 and 9. Dispersal was the most frequent process and vicariance had relevance in the isolation of cacti distributed in the south of Mexico. The 70 taxa sampled as Mammillaria were distributed in six distinct lineages; one of these presumably corresponded to this genus, which likely had its center of origin in the southern part of the Mexican Plateau. We recommend detailed studies to further determine the taxonomic circumscription of the seven genera. [ABSTRACT FROM AUTHOR]

Whole-genome sequencing has advanced our understanding of the population structure of the pathogenic species complex Cryptococcus gattii, which has allowed for the phylogenomic specification of previously described major molecular type groupings and novel lineages. Recently, isolates collected in Mexico in the 1960s were determined to be genetically distant from other known molecular types and were classified as VGVI. We sequenced four clinical isolates and one veterinary isolate collected in the southwestern United States and Argentina from 2012 to 2021. Phylogenomic analysis groups these genomes with those of the Mexican VGVI isolates, expanding VGVI into a clade and establishing this molecular type as a clinically important population. These findings also potentially expand the known Cryptococcus ecological range with a previously unrecognized endemic area. [ABSTRACT FROM AUTHOR]

Recent phylogenomic analyses of sequence data from chloroplast and nuclear genomes as well as morphological and cytological analyses resolved long standing phylogenetic uncertainty in the rock daisy tribe (Perityleae; Asteraceae) and support reclassification at the generic level to reflect evolutionary relationships. The previously recognized genera Eutetras and Pericome were upheld as clades and continue to be recognized in the new classification. The large genus Perityle as treated in previous taxonomies was found not to be monophyletic and is thus reclassified in four genera, using the available names Laphamia (in an expanded sense), Galinsogeopsis (in an expanded sense), Nesothamnus, and Perityle (in a newly restricted sense). The type species of Perityle belongs to an early diverging lineage of the rock daisy tribe, in a clade with varied chromosome numbers of x = 11, 12, 13, 16, 18, or 19. In addition to the type (Perityle californica), Perityle now includes six other minimum-rank taxa of Perityle, all three taxa of Amauria, and the Desventuradas Islands endemic Lycapsus tenuifolius. Nesothamnus is reinstated as a monotypic genus for the Guadalupe Island endemic shrub Nesothamnus incana. Laphamia and Galinsogeopsis together constitute a clade of woody and herbaceous perennials or annuals with a stabilized base chromosome number of x = 17 (n = 17, 34, 51, 68) that have diversified throughout the Basin and Range Province and the Sierra Madre Occidental of the southwest US and northern Mexico. Laphamia and Galinsogeopsis have overlapping geographic distributions but can be distinguished by a combination of fruit and flower traits. This new generic classification of Perityleae resolves long standing conflict about the circumscription of Perityle without expanding the genus to encompass the entire subtribe Peritylinae and recognizes two independent evolutionary radiations onto island-like rocky habitats in western North America as taxonomically distinct components of this fascinating tribe of composites. To allow for this revised taxonomy, 46 new combinations in Galinsogeopsis, Laphamia, and Perityle are provided, and one new name, Laphamia sanchezii, is adopted. [ABSTRACT FROM AUTHOR]

Genomic data continue to advance our understanding of species limits and biogeographic patterns. However, there is still no consensus regarding appropriate methods of phylogenomic analysis that make the best use of these heterogeneous data sets. In this study, we used thousands of ultraconserved element (UCE) loci from alligator lizards in the genus Gerrhonotus to compare and contrast species trees inferred using multiple contemporary methods and provide a time frame for biological diversification across the Mexican Transition Zone (MTZ). Concatenated maximum likelihood (ML) and Bayesian analyses provided highly congruent results, with differences limited to poorly supported nodes. Similar topologies were inferred from coalescent analyses in Bayesian Phylogenetics and Phylogeography and SVDquartets, albeit with lower support for some nodes. All divergence times fell within the Miocene, linking speciation to local Neogene vicariance and/or global cooling trends following the mid-Miocene Climatic Optimum. We detected a high level of genomic divergence for a morphologically distinct species restricted to the arid mountains of north-eastern Mexico, and erected a new genus to better reflect evolutionary history. In summary, our results further advocate leveraging the strengths and weaknesses of concatenation and coalescent methods, provide evidence for old divergences for alligator lizards, and indicate that the MTZ continues to harbour substantial unrecognized diversity. [ABSTRACT FROM AUTHOR]

Heptapteridae is composed of 228 valid species allocated in 24 genera, making it the most diverse family within superfamily Pimelodoidea, a clade endemic to the Neotropical freshwaters. Heptapterids are widely distributed from southern Mexico to the Pampas of Argentina and occupy a variety of habitats generally in small‐ to medium‐sized rivers. To evaluate the phylogenetic relationships of Heptapteridae, we used a matrix with 1,319 ultraconserved elements (UCEs) from the genome from 56 specimens spanning 42 species and 24 genera of Heptapteridae and 19 related siluriform taxa. Maximum likelihood, Bayesian and coalescent‐based analyses strongly supported the monophyly of Heptapteridae and confirmed previous hypotheses of a sister relationship between Heptapteridae and Conorhynchos conirostris. We provide the evidence to recognize two subfamilies: (1) Rhamdiinae (Goeldiella, Rhamdella, Rhamdia, Brachyrhamdia, Pimelodella) and (2) Heptapterinae; with two tribes: Brachyglaniini new tribe (Gladioglanis, Myoglanis, Brachyglanis and Leptorhamdia) and Heptapterini (Mastiglanis, Chasmocranus, Cetopsorhamdia, Pariolius, Phenacorhamdia, Nemuroglanis, Imparfinis, Taunayia, Rhamdioglanis, Acentronichthys, Rhamdiopsis and Heptapterus). Inside Heptapterini, we recognize five subclades and provide putative morphological synapomorphies. This paper represents the first molecular hypothesis of intergeneric and interspecific relationships helping to better delineate heptapterid taxa. [ABSTRACT FROM AUTHOR]

Rock daisies (Perityleae; Compositae) are a diverse clade of seven genera and ca. 84 minimum‐rank taxa that mostly occur as narrow endemics on sheer rock cliffs throughout the southwest United States and northern Mexico. Taxonomy of Perityleae has traditionally been based on morphology and cytogenetics. To test taxonomic hypotheses and utility of characters emphasized in past treatments, we present the first densely sampled molecular phylogenies of Perityleae and reconstruct trait and chromosome evolution. We inferred phylogenetic trees from whole chloroplast genomes, nuclear ribosomal cistrons, and hundreds of low‐copy nuclear genes using genome skimming and target capture. Discordance between sources of molecular data suggests an underappreciated history of hybridization in Perityleae. Phylogenies support the monophyly of subtribe Peritylinae, a distinctive group possessing a four‐lobed disc corolla; however, all of the phylogenetic trees generated in this study reject the monophyly of the most species‐rich genus, Perityle, as well as its sections: Perityle sect. Perityle, Perityle sect. Laphamia, and Perityle sect. Pappothrix. Using reversible jump MCMC, our results suggest that morphological characters traditionally used to classify members of Perityleae have evolved multiple times within the group. A base chromosome number x = 9 gave rise to higher base numbers in subtribe Peritylinae (x = 12, 13, 16, 17, 18, and 19) through polyploidization, followed by ascending or descending dysploidy. Most taxa constitute a monophyletic lineage with a base chromosome number of x = 17, with multiple neo‐polyploidization events. These results demonstrate the advantages and obstacles of next‐generation sequencing approaches in synantherology while laying the foundation for taxonomic revision and comparative study of the evolutionary ecology of Perityleae. [ABSTRACT FROM AUTHOR]

The coronavirus disease 2019 (COVID-19) pandemic has affected most countries in the world. Studying the evolution and transmission patterns in different countries is crucial to enabling implementation of effective strategies for disease control and prevention. In this work, we present the full genome sequence for 17 SARS-CoV-2 isolates corresponding to the earliest sampled cases in Mexico. Global and local phylogenomics, coupled with mutational analysis, consistently revealed that these viral sequences are distributed within 2 known lineages, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage A/G, containing mostly sequences from North America, and lineage B/S, containing mainly sequences from Europe. Based on the exposure history of the cases and on the phylogenomic analysis, we characterized 14 independent introduction events. Additionally, three cases with no travel history were identified. We found evidence that two of these cases represented local transmission cases occurring in Mexico during mid-March 2020, denoting the earliest events described for the country. Within this local transmission cluster, we also identified an H49Y amino acid change in the Spike protein. This mutation represents a homoplasy occurring independently through time and space and may function as a molecular marker to follow any further spread of these viral variants throughout the country. Our results provide a general picture of the SARS-CoV-2 variants introduced at the beginning of the outbreak in Mexico, setting the foundation for future surveillance efforts. [ABSTRACT FROM AUTHOR]

Incomplete or geographically biased sampling poses significant problems for research in phylogeography, population genetics, phylogenetics, and species delimitation. Despite the power of using genome-wide genetic markers in systematics and related fields, approaches such as the multispecies coalescent remain unable to easily account for unsampled lineages. The Empidonax difficilis / Empidonax occidentalis complex of small tyrannid flycatchers (Aves: Tyrannidae) is a classic example of widely distributed species with limited phenotypic geographic variation that was broken into two largely cryptic (or "sibling") lineages following extensive study. Though the group is well-characterized north of the US Mexico border, the evolutionary distinctiveness and phylogenetic relationships of southern populations remain obscure. In this article, we use dense genomic and geographic sampling across the majority of the range of the E. difficilis/E. occidentalis complex to assess whether current taxonomy and species limits reflect underlying evolutionary patterns, or whether they are an artifact of historically biased or incomplete sampling. We find that additional samples from Mexico render the widely recognized species-level lineage E. occidentalis paraphyletic, though it retains support in the best-fit species delimitation model from clustering analyses. We further identify a highly divergent unrecognized lineage in a previously unsampled portion of the group's range, which a cline analysis suggests is more reproductively isolated than the currently recognized species E. difficilis and E. occidentalis. Our phylogeny supports a southern origin of these taxa. Our results highlight the pervasive impacts of biased geographic sampling, even in well-studied vertebrate groups like birds, and illustrate what is a common problem when attempting to define species in the face of recent divergence and reticulate evolution. [ABSTRACT FROM AUTHOR]

Salvia hispanica is an annual food and oil crop native to Mexico and Guatemala. In this study, we report the complete chloroplast genome (plastome) of S. hispanica. The plastome was 150,980 bp in length and comprises a large single-copy region (82,274 bp), a small single-copy region (17,534 bp), and a pair of inverted repeats (25,586 bp). It encodes 114 unique genes, including 80 protein-coding genes (PCGs), 30 tRNAs, and 4 rRNAs. The overall GC content of this plastome was 38.0%. Phylogenomic analysis of all PCGs revealed that S. hispanica was closely related to S. bulleyana. [ABSTRACT FROM AUTHOR]

Aim The aim of our study was to reconstruct ancestral geographic distributions from time-calibrated phylogenies generated from phylogenomic data to answer three broad questions about the biogeography of skinks in the Plestiodon brevirostris group: (1) Are biogeographic patterns correlated with the formation of the Trans-Mexican Volcanic Belt? (2) Do different methods of phylogenetic estimation result in different topologies? If so, (3) are biogeographic reconstructions impacted by the use of different phylogenetic trees? Location Mexico. Methods We used target enrichment of ultraconserved elements ( UCEs) to obtain sequence data from 58 skinks representing 11 of the 13 described species in the group. We estimated time-calibrated phylogenies using concatenated and multispecies coalescent phylogenetic approaches. We used these phylogenies to reconstruct ancestral geographic distributions. Results The final dataset contained 3,282 UCEs from each skink. Samples of each putative species formed well-supported clades in phylogenetic trees. Time-calibrated phylogenies estimated using concatenated and multispecies coalescent methods were generally congruent, but differed in the placement of one basal relationship. Divergences in the P. brevirostris group were temporally and spatially congruent with the pre-Pleistocene formation of the Trans-Mexican Volcanic Belt. The group most likely colonized the Mexican highlands from east to west during the Late Miocene and Pliocene. Inferences about the early biogeographic history of the group were confounded by the unresolved placement of a key phylogenetic relationship deep in the phylogeny. Conclusions Skinks in the P. brevirostris group represent another example of a widespread montane Mexican taxon with a long history of pre-Pleistocene diversification associated with the primary formation of the Trans-Mexican Volcanic Belt. This mountain range seems to have been both a cradle of diversification for P. brevirostris group species and a land bridge facilitating dispersal across the Mexican highlands. Our results highlight the probable existence of new species within the P. brevirostris complex and suggest that querying a large portion of the genome may be critically important for studying the biogeographic history of these skinks. However, inferred differences between the concatenated and multispecies coalescent phylogenies, and the different biogeographic histories of the P. brevirostris group reconstructed from these phylogenies, caution that methods of estimating phylogenetic trees used in biogeographic reconstructions need to be carefully considered. [ABSTRACT FROM AUTHOR]

The first week of September 2013, the National Epidemiological Surveillance System identified two cases of cholera in Mexico City. The cultures of both samples were confirmed as Vibrio cholerae serogroup O1, serotype Ogawa, biotype El Tor. Initial analyses by PFGE and by PCR-amplification of the virulence genes, suggested that both strains were similar, but different from those previously reported in Mexico. The following week, four more cases were identified in a community in the state of Hidalgo, located 121 km northeast of Mexico City. Thereafter a cholera outbreak started in the region of La Huasteca. Genomic analyses of the four strains obtained in this study confirmed the presence of Pathogenicity Islands VPI-1 and -2, VSP-1 and -2, and of the integrative element SXT. The genomic structure of the 4 isolates was similar to that of V. cholerae strain 2010 EL-1786, identified during the epidemic in Haiti in 2010. [ABSTRACT FROM AUTHOR]

• We provide the first comprehensive and dated phylogeny of Myrmecocystus ants, using UCE markers. • We identify cryptic diversity and inconsistencies in the current taxonomic classification. • The genus diversified during aridification of the American Southwest, starting about 14 Ma ago. • The ancestral foraging behavior of Myrmecocystus ants was most likely nocturnal. • UCE data from ant museum specimens can be used to resolve clades with poor sample coverage. The New World ant genus Myrmecocystus Wesmael, 1838 (Formicidae: Formicinae: Lasiini) is endemic to arid and semi-arid habitats of the western United States and Mexico. Several intriguing life history traits have been described for the genus, the best-known of which are replete workers, that store liquified food in their largely expanded crops and are colloquially referred to as "honeypots". Despite their interesting biology and ecological importance for arid ecosystems, the evolutionary history of Myrmecocystus ants is largely unknown and the current taxonomy presents an unsatisfactory systematic framework. We use ultraconserved elements to infer the evolutionary history of Myrmecocystus ants and provide a comprehensive, dated phylogenetic framework that clarifies the molecular systematics within the genus with high statistical support, reveals cryptic diversity, and reconstructs ancestral foraging activity. Using maximum likelihood, Bayesian and species tree approaches on a data set of 134 ingroup specimens (including samples from natural history collections and type material), we recover largely identical topologies that leave the position of only few clades uncertain and cover the intra- and interspecific variation of 28 of the 29 described and six undescribed species. In addition to traditional support values, such as bootstrap and posterior probability, we quantify genealogical concordance to estimate the effects of conflicting evolutionary histories on phylogenetic inference. Our analyses reveal that the current taxonomic classification of the genus is inconsistent with the molecular phylogenetic inference, and we identify cryptic diversity in seven species. Divergence dating suggests that the split between Myrmecocystus and its sister taxon Lasius occurred in the early Miocene. Crown group Myrmecocystus started diversifying about 14.08 Ma ago when the gradual aridification of the southwestern United States and northern Mexico led to formation of the American deserts and to adaptive radiations of many desert taxa. [ABSTRACT FROM AUTHOR]

• A phylogenomic analysis of the lizard genera Abronia and Mesaspis was performed. • Abronia and Mesaspis are both non-monophyletic. • Abronia + Mesaspis species formed clades in several different biogeographic regions. • A single origin of arboreality in the clade (Abronia + Mesaspis) was not supported. Abronia and Mesaspis are two of the five anguid lizard genera in the subfamily Gerrhonotinae. Their members are restricted to Mesoamerica, and most have allopatric distributions. Species of Abronia are primarily arboreal and occur in cloud and seasonally dry pine-oak forests, whereas those of Mesaspis are terrestrial and inhabit mesic microhabitats of montane forests. Recent molecular studies suggest that although these genera together form a monophyletic group, neither genus is monophyletic. Here we performed a phylogenetic study of Abronia and Mesaspis based on the most comprehensive taxonomic sampling of these genera to date and double digest restriction site-associated (ddRADseq) data. Our reconstructed phylogeny differed considerably from all previously published topologies, consistently recovering multiple independent clades of arboreal and terrestrial species and Abronia and Mesaspis as non-monophyletic. Geography, rather than current taxonomy, provides the best explanation of their phylogenetic relationships. Our analyses consistently recovered two main clades, distributed on the highlands of Middle America east and west of the Isthmus of Tehuantepec, respectively, and each composed of subclades of Abronia and Mesaspis. In the former main clade, members of the subgenus Auriculabronia formed the sister taxon to the Mesaspis moreletii complex, whereas the main clade west of the Isthmus was composed of two clades with a subclade of Abronia and another of Mesaspis each (one clade on the Atlantic versant of the main mountain ranges of eastern Mexico and another one on the Sierra Madre del Sur exclusive of its Atlantic versant) and a third clade with species of the subgenera Abronia and Scopaeabronia. We discuss the taxonomic implications of our results for the classification of the examined taxa and list the morphological characters that diagnose the recovered clades. This study highlights the utility of ddRADseq data to reconstruct the evolutionary history of supraspecific vertebrate taxa. [ABSTRACT FROM AUTHOR]

The coronavirus disease 2019 (COVID-19) pandemic has affected most countries in the world. Studying the evolution and transmission patterns in different countries is crucial to enabling implementation of effective strategies for disease control and prevention. In this work, we present the full genome sequence for 17 SARS-CoV-2 isolates corresponding to the earliest sampled cases in Mexico. Global and local phylogenomics, coupled with mutational analysis, consistently revealed that these viral sequences are distributed within 2 known lineages, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage A/G, containing mostly sequences from North America, and lineage B/S, containing mainly sequences from Europe. Based on the exposure history of the cases and on the phylogenomic analysis, we characterized 14 independent introduction events. Additionally, three cases with no travel history were identified. We found evidence that two of these cases represented local transmission cases occurring in Mexico during mid-March 2020, denoting the earliest events described for the country. Within this local transmission cluster, we also identified an H49Y amino acid change in the Spike protein. This mutation represents a homoplasy occurring independently through time and space and may function as a molecular marker to follow any further spread of these viral variants throughout the country. Our results provide a general picture of the SARS-CoV-2 variants introduced at the beginning of the outbreak in Mexico, setting the foundation for future surveillance efforts. IMPORTANCE Understanding the introduction, spread, and establishment of SARS-CoV-2 within distinct human populations as well as the evolution of the pandemics is crucial to implement effective control strategies. In this work, we report that the initial virus strains introduced in Mexico came from Europe and the United States and that the virus was circulating locally in the country as early as mid-March. We also found evidence for early local transmission of strains with a H49Y mutation in the Spike protein, which could be further used as a molecular marker to follow viral spread within the country and the region., (Copyright © 2020 American Society for Microbiology.)

Clostridium difficile B1/NAP1/RT027/ST01 has been responsible for outbreaks of antibiotic-associated diarrhoea in clinical settings worldwide and is associated with severe disease presentations and increased mortality rates. Two fluoroquinolone-resistant (FQR) lineages of the epidemic B1/NAP1/RT027/ST01 strain emerged in the USA in the early 1990s and disseminated trans continentally (FQR1 and FQR2). However, it is unclear when and from where they entered Latin America (LA) and whether isolates from LA exhibit unique genomic features when compared to B1/NAP1/RT027/ST01 isolates from other regions of the world. To answer the first issue we compared whole-genome sequences (WGS) of 25 clinical isolates typed as NAP1, RT027 or ST01 in Costa Rica ( n =16), Chile ( n =5), Honduras ( n =3) and Mexico ( n =1) to WGS of 129 global isolates from the same genotype using Bayesian phylogenomics. The second question was addressed through a detailed analysis of the number and type of mutations of the LA isolates and their mobile resistome. All but two B1/NAP1/RT027/ST01 isolates from LA belong to the FQR2 lineage ( n =23, 92 %), confirming its widespread distribution. As indicated by analysis of a dataset composed of 154 WGS, the B1/NAP1/RT027/ST01 strain was introduced into the four LA countries analysed between 1998 and 2005 from North America (twice) and Europe (at least four times). These events occurred soon after the emergence of the FQR lineages and more than one decade before the first report of the detection of the B1/NAP1/RT027/ST01 in LA. A total of 552 SNPs were identified across all genomes examined (3.8-4.3 Mb) in pairwise comparisons to the R20291 reference genome. Moreover, pairwise SNP distances were among the smallest distances determined in this species so far (0 to 55). Despite this high level of genomic conservation, 39 unique SNPs (7 %) in genes that play roles in the infection process (i.e. slpA ) or antibiotic resistance (i.e. rpoB , fusA ) distinguished the LA isolates. In addition, isolates from Chile, Honduras and Mexico had twice as many antibiotic resistance genes (ARGs, n =4) than related isolates from other regions. Their unique set of ARGs includes a cfr -like gene and tetM , which were found as part of putative mobile genetic elements whose sequences resemble undescribed integrative and conjugative elements. These results show multiple, independent introductions of B1/NAP1/RT027/ST01 isolates from the FQR1 and FQR2 lineages from different geographical sources into LA and a rather rapid accumulation of distinct mutations and acquired ARG by the LA isolates.