Habitat Adaptation Drives Speciation of a Streptomyces Species with Distinct Habitats and Disparate Geographic Origins

Both isolation by distance and isolation by environment occur in bacteria, and different diversification patterns may apply to different species. Streptomyces species, typified by producing useful natural products, are widespread in nature and possess high genetic diversity. However, the ecological processes and evolutionary mechanisms that shape their distribution are not well understood.

Identifying SARS-CoV-2 regional introductions and transmission clusters in real time

The unprecedented SARS-CoV-2 global sequencing effort has suffered from an analytical bottleneck. Many existing methods for phylogenetic analysis are designed for sparse, static datasets and are too computationally expensive to apply to densely sampled, rapidly expanding datasets when results are needed immediately to inform public health action. For example, public health is often concerned with identifying clusters of closely related samples, but the sheer scale of the data prevents manual inspection and the current computational models are often too expensive in time and resources. Even when results are available, intuitive data exploration tools are of critical importance to effective public health interpretation and action. To help address this need, we present a phylogenetic summary statistic which quickly and efficiently identifies newly introduced strains in a region, resulting clusters of infected individuals, and their putative geographic origins. We show that this approach performs well on simulated data and is congruent with a more sophisticated analysis performed during the pandemic. We also introduce Cluster Tracker (https://clustertracker.gi.ucsc.edu/), a novel interactive web-based tool to facilitate effective and intuitive SARS-CoV-2 geographic data exploration and visualization. Cluster-Tracker is updated daily and automatically identifies and highlights groups of closely related SARS-CoV-2 infections resulting from inter-regional transmission across the United States, streamlining public health tracking of local viral diversity and emerging infection clusters. The combination of these open-source tools will empower detailed investigations of the geographic origins and spread of SARS-CoV-2 and other densely-sampled pathogens.

Origin of Symphyotrichum anticostense (Asteraceae: Astereae), an endemic, high polyploid species of the Gulf of St. Lawrence region, based on morphological and nrDNA evidence

Symphyotrichum anticostense (Fernald) G.L.Nesom (Asteraceae: Astereae), a rare endemic of the Gulf of St. Lawrence region is a high allopolyploid (2n=10x=80). It has been hypothesized to be derived from the hybrid between tetraploid (2n=4x=32) individuals of S. boreale (Torr. & A.Gray) Löve & Löve and the hexaploid (2n=6x=48) S. novi-belgii (L.) G.L.Nesom. We investigated this hypothesis using morphological and molecular ITS-sequence data, and we tried to determine the potentially geographic origins of the taxon. Univariate morphological analyses show that 67.5% of the S. anticostense characters are parent-like, 43.5% from S. novi-belgii and 13% from S. boreale, the remainder not differing statistically from either parent; 23.5% are intermediate; and 9% transgressive. Multivariate analyses show that S. anticostense is intermediate between its putative parents. The molecular results support the morphological data, but due to the insufficient resolution among ribotypes on the tree, a more rapidly evolving marker will be needed to ascertain more reliably the origin of S. anticostense. Besides the hypothesis of genetic drift and allele fixation following long-distance dispersals, at least three independent geographic origins may be suggested for S. anticostense; Anticosti Island, Lake St. John, and Gaspé Peninsula-New Brunswick-Maine.

Spatially resolved LA-MC-ICPMS strontium isotope microanalysis of archaeological fauna

The analysis of the strontium isotope composition of archaeological materials can provide important information about the mobility of a range of mammals, including humans. The basis of this method is that, prior to any postburial diagenesis, the Sr87/Sr86 ratio of bone and teeth reflects the geological environment from which food and water were sourced while these biominerals were forming. Teeth are particularly amenable to tracing the geographic origins of humans as they mineralize during the first 12–13 years of life (White and Folkens, 2005) and do not subsequently change strontium composition after this time (Schweissing and Grupe, 2003). Strontium isotope analysis can be used to determine if individuals are local or nonlocal by comparison to the isotopic composition in and around their burial location (i.e., Schweissing and Grupe, 2000; Bentley et al., 2007; Conlee et al., 2009). In order to quantify the extent of faunal mobility, the strontium isotope composition of biominerals from fossil samples needs to be compared with a regional map of values obtained either from local faunal material (Price et al., 2002) or from analysis of the bioavailable component of strontium from plants, regolith, or bedrock (Capo et al., 1998).Strontium isotope analysis has been extensively applied to the determination of archaeological mobility, as reviewed by Price et al. (2002), Budd et al. (2004), Bentley (2006), and Montgomery (2010). Although studies of Paleolithic or older archeological material are rare, some have been undertaken on hominins (Sillen et al., 1995, 1998; Richards et al., 2008; Copeland et al., 2011) and faunal material (Horn et al., 1994; Copeland et al., 2010; Britton et al., 2011).Enamel has been shown to be the most favorable material for strontium isotope analysis based on its ability to resist postburial alteration far better than dentine, cement, or bone (Trickett et al., 2003). Enamel of some species grows over extended periods and, when analyzed with microprofiling or laser ablation analysis, can be used to reconstruct comprehensive life histories. This approach demonstrated the seasonal mobility of cattle in Iron Age Britain (Horstwood et al., 2008), Neolithic Germany (Bentley and Knipper, 2005), and England (Viner et al., 2010).

Plagued by a cryptic clock: Insight and issues from the global phylogeny of Yersinia pestis

Plague has an enigmatic history as a zoonotic pathogen. This potentially devastating infectious disease will unexpectedly appear in human populations and disappear just as suddenly. As a result, a long-standing line of inquiry has been to estimate when and where plague appeared in the past. However, there have been significant disparities between phylogenetic studies of the causative bacterium, Yersinia pestis, regarding the timing and geographic origins of its reemergence. Here, we curate and contextualize an updated phylogeny of Y. pestis using 601 genome sequences sampled globally. We perform a detailed Bayesian evaluation of temporal signal in subsets of these data and demonstrate that a Y. pestis-wide molecular clock model is unstable. To resolve this, we devised a new approach in which each Y. pestis population was assessed independently. This enabled us to recover significant temporal signal in five populations, including the ancient pandemic lineages which we now estimate may have emerged decades, or even centuries, before a pandemic was historically documented from European sources. Despite this, we only obtain robust divergence dates from populations sampled over a period of at least 90 years, indicating that genetic evidence alone is insufficient for accurately reconstructing the timing and spread of short-term plague epidemics. Finally, we identify key historical data sets that can be used in future research, which will complement the strengths and mitigate the weaknesses of genomic data.

Molecular Variability and Host Distribution of ‘Candidatus Phytoplasma solani’ Strains from Different Geographic Origins

The knowledge of phytoplasma genetic variability is a tool to study their epidemiology and to implement an effective monitoring and management of their associated diseases. ‘Candidatus Phytoplasma solani’ is associated with “bois noir” disease in grapevines, and yellowing and decline symptoms in many plant species, causing serious damages during the epidemic outbreaks. The epidemiology of the diseases associated with this phytoplasma is complex and related to numerous factors, such as interactions of the host plant and insect vectors and spreading through infected plant propagation material. The genetic variability of ‘Ca. P. solani’ strains in different host species and in different geographic areas during the last two decades was studied by RFLP analyses coupled with sequencing on vmp1, stamp, and tuf genes. A total of 119 strains were examined, 25 molecular variants were identified, and the variability of the studied genes was linked to both geographic distribution and year of infection. The crucial question in ‘Ca. P. solani’ epidemiology is to trace back the epidemic cycle of the infections. This study presents some relevant features about differential strain distribution useful for disease monitoring and forecasting, illustrating and comparing the phytoplasma molecular variants identified in various regions, host species, and time periods.

The Genetic Landscape of Fiber Flax

Genetic diversity in a breeding program is essential to overcome modern-day environmental challenges faced by humanity and produce robust, resilient crop cultivars with improved agronomic characteristics, as well as to trace crop domestication history. Flax (Linum usitatissimum), one of the first crops domesticated by mankind, has been traditionally cultivated for fiber as well as for medicinal purposes and as a nutritional product. The origins of fiber flax are hidden in the mists of time and can be hypothetically traced back to either the Indo-Afghan region or Fertile Crescent. To shed new light on fiber flax genetic diversity and breeding history, in this study, we presented a comprehensive analysis of the core collection of flax (306 accessions) of different morphotypes and geographic origins maintained by the Russian Federal Research Center for Bast Fiber Crops. We observed significant population differentiation between oilseed and fiber morphotypes, as well as mapped genomic regions affected by recent breeding efforts. We also sought to unravel the origins of kryazhs, Russian heritage landraces, and their genetic relatedness to modern fiber flax cultivars. For the first time, our results provide strong genetic evidence in favor of the hypothesis on kryazh’s mixed origin from both the Indo-Afghan diversity center and Fertile Crescent. Finally, we showed predominant contribution from Russian landraces and kryazhs into the ancestry of modern fiber flax varieties. Taken together, these findings may have practical implications on the development of new improved flax varieties with desirable traits that give farmers greater choice in crop management and meet the aspirations of breeders.

Exploring Dental Modification from Coastal Ecuador from an Unprovenienced Museum Collection

In South America, most examples of dental modification come from Ecuador; however, none have been directly radiocarbon dated and few have associated cultural materials or context. In fact, many modified teeth and crania are housed in museum collections, divorced from their cultural and temporal milieus, and because of this it is generally assumed that this limits the interpretive possibility of these individuals. We used multiple methods to investigate temporal and geographic origins of seven crania with dental modification housed in the Museo Antropológico y Arte Contemporáneo in Guayaquil, Ecuador. We identified diverse forms of dental modification, including dental inlays and appliques, incised lines, and anterior dental avulsion. Additionally, teeth from four modified individuals were sampled for radiocarbon dating and isotopic analyses (Sr, Pb, O). The dates indicate that dental modification persisted for at least 600 years (cal. A.D. 990–1646). The relatively heavy oxygen isotopes in the sampled teeth are consistent with Ecuador as a place of origin for the four individuals assayed, but strontium isotopes are quite varied, from 0.70462 to 0.70777 indicating that they did not reside in the same geographical area. Interestingly, the observed variations in strontium isotopes in the four individuals are lower than the modeled 87Sr/86Sr for the region. The values suggest the individuals resided in terrains with volcanic bedrock, which are abundant in Ecuador, yet their influence on the strontium isoscapes is not well represented by the published regional models. This analysis highlights the utility of multiple methods in bioarchaeology and biogeochemistry to investigate “orphaned” museum collections. En Sudamérica, la mayor parte de los ejemplos de modificación dental surgen de Ecuador; sin embargo, ninguno de estos casos ha sido fechados utilizando análisis de radiocarbono y pocos están asociados con contextos o materiales culturales. De hecho, varios dientes y cráneos modificados están localizados en colecciones museísticas y han sido divorciados de sus entornos culturales y temporales originales, generalmente con la suposición que limitan la posibilidad interpretativa de estos individuos. Nosotros utilizamos varios métodos bioarqueológicos y biogeoquímicos para investigar los orígenes temporales y geográficos de siete cráneos con modificaciones dentales ubicados en el Museo Antropológico y Arte Contemporáneo en Guayaquil, Ecuador. Nosotros identificamos varias formas de modificaciones dentales, incluyendo incrustaciones y aplicaciones dentales, incisiones de líneas y avulsión dental anterior. Adicionalmente, los dientes modificados de cuatro individuos fueron muestreados para fechar con análisis de radiocarbono y análisis isotópico (Sr, Pb, O). Las fechas indican que la modificación dental persistió durante por lo menos 600 años (990–1646 DC). Los isótopos de oxígeno relativamente pesados en los dientes muestreados son consistentes con Ecuador como lugar de origen para los cuatro individuos analizados, pero los isótopos de estroncio son bastante variados, de 0.70462 a 0.70777, lo que indica que no residían en la misma área geográfica. Las variaciones observadas en los isotopos de estroncio son más bajes de los 87Sr/86Sr modeladas para la región e indican que estos individuaos residían en regiones con la roca de fondo volcánica. Las rocas volcánicas son abundadas en Ecuador y aparentemente no está bien representadas en los modelos. Aún más, esta es la primera evidencia bioarqueológica sugerente de avulsión dental en Ecuador prehispánico. Finalmente, este análisis resalta la utilidad de métodos mixtos en bioarqueología y biogeoquímica para investigar colecciones museísticas que han “quedado huérfanas”.

Genetic structure of Eurasian beaver in Romania: insights after two decades from the reintroduction

Once exploited for fur, meat, and extracting the yellowish exudate called castoreum, the Eurasian beaver disappeared from Romania during the eighteenth century. After, the reintroductions carried out two decades ago are currently thriving in the Danube River basin. Using nine nSSR markers, we analysed samples from 98 individuals, and we found no genetic substructure, suggesting high dispersal and gene flow capabilities. The stepwise mutation model (SMM) indicated the existence of a recent genetic bottleneck, though the Eurasian beaver retains high levels of genetic diversity and population growth facilitated variation in nSSR loci. A fine-scale spatial correlation in females was detected, contrasting with males’ dispersal on longer distances. While the movement and establishment of individuals’ new territories were made under natural predation pressure, the mix following natural expansion improved the fitness and could contribute to a higher genetic diversity than the source population. With any reintroduction, a focus on capturing individuals from various geographic origins, as well as securing many and suitable founding individuals (adults, subadults, and juveniles) with mixed origins, could secure the post-genetic bottleneck recovery and higher genetic diversity. Beyond this conservation success, future management strategies should consider building a National Action Plan (NAP) for the species, including a permanent genetic monitoring programme for Eurasian beaver.