A 14th century CE Brucella melitensis genome and the recent expansion of the Western Mediterranean clade.

Brucellosis is a disease caused by the bacterium Brucella and typically transmitted through contact with infected ruminants. It is one of the most common chronic zoonotic diseases and of particular interest to public health agencies. Despite its well-known transmission history and characteristic symptoms, we lack a more complete understanding of the evolutionary history of its best-known species-Brucella melitensis. To address this knowledge gap we fortuitously found, sequenced and assembled a high-quality ancient B. melitensis draft genome from the kidney stone of a 14th-century Italian friar. The ancient strain contained fewer core genes than modern B. melitensis isolates, carried a complete complement of virulence genes, and did not contain any indication of significant antimicrobial resistances. The ancient B. melitensis genome fell as a basal sister lineage to a subgroup of B. melitensis strains within the Western Mediterranean phylogenetic group, with a short branch length indicative of its earlier sampling time, along with a similar gene content. By calibrating the molecular clock we suggest that the speciation event between B. melitensis and B. abortus is contemporaneous with the estimated time frame for the domestication of both sheep and goats. These results confirm the existence of the Western Mediterranean clade as a separate group in the 14th CE and suggest that its divergence was due to human and ruminant co-migration.

A comprehensive genomic history of extinct and living elephants.

Elephantids are the world's most iconic megafaunal family, yet there is no comprehensive genomic assessment of their relationships. We report a total of 14 genomes, including 2 from the American mastodon, which is an extinct elephantid relative, and 12 spanning all three extant and three extinct elephantid species including an ∼120,000-y-old straight-tusked elephant, a Columbian mammoth, and woolly mammoths. Earlier genetic studies modeled elephantid evolution via simple bifurcating trees, but here we show that interspecies hybridization has been a recurrent feature of elephantid evolution. We found that the genetic makeup of the straight-tusked elephant, previously placed as a sister group to African forest elephants based on lower coverage data, in fact comprises three major components. Most of the straight-tusked elephant's ancestry derives from a lineage related to the ancestor of African elephants while its remaining ancestry consists of a large contribution from a lineage related to forest elephants and another related to mammoths. Columbian and woolly mammoths also showed evidence of interbreeding, likely following a latitudinal cline across North America. While hybridization events have shaped elephantid history in profound ways, isolation also appears to have played an important role. Our data reveal nearly complete isolation between the ancestors of the African forest and savanna elephants for ∼500,000 y, providing compelling justification for the conservation of forest and savanna elephants as separate species.

New insight into the motivations of anglers and fish release practices in view of the invasiveness of angling.

The popularity of angling on a global scale reflects the individual needs of people from different social groups in many countries. The socio-economic background and intensity of needs are variable over time and can be modified. These arguments support the development and need to update research among anglers. A new insight into angling research is to link the hierarchy of needs with socio-economic factors concerning and the preferences of anglers in handling fish. These relationships were analyzed using ordinal probit regression and graphically interpreted in an ordination space. The endogenous need for communing with nature is constant in its intensity, regardless of any external factors. Other needs weaken with increasing income, education levels and years engaged in angling. The majority of anglers support releasing fish (66%) and say that the possibility of keeping the fish is not important (62%). It is crucial to identify those anglers for whom the possibility of keeping fish is important and who do not feel extremely negative about releasing fish. The study found that they represent about 25% of the angling population. These findings help to explain the variation in the invasive impact of the identified motivational-preferential profiles of anglers. Cooperation between the associated angling communities and water managers is crucial. By gathering anglers around their own fishing places, they can implement their own educational and organizational solutions.

The Significance of Angling in Stress Reduction during the COVID-19 Pandemic-Environmental and Socio-Economic Implications.

Recreational fishing and other outdoor recreational activities have been proven to have positive effects on mental health, including neutralizing pandemic stress. This study aims to identify the perceptions and behavior of recreational anglers during the COVID-19 pandemic along with identifying the factors that determine attitudes. This study is essential for understanding the complex economic, social, and environmental implications associated with a pandemic. Perceptions of pandemic stress reduction were confirmed by 63.8% of anglers, and nearly 98% felt there was no risk of infection from fishing. These feelings were most strongly positively associated and explained by a preference for fishing with friends and family and the frequency of fishing. Over 26% of respondents fished more frequently during the pandemic. Additional free time and the need to escape the pandemic media hype were the main factors for the increase in angler activity. The balance of benefits from changes in angler pandemic behavior was ambiguous. This was determined by considering the potential increase in pressure on the environmental resources that anglers use. Given the positive effects of angling on stress reduction, it is not advisable for policymakers to restrict recreational fishing access. Instead, best management practices should reduce sanitary bottlenecks to increase safety on fishing grounds.

Impact of Personal Experience of COVID-19 Disease on Recreational Anglers' Attitudes and Behaviors.

BACKGROUND: Anglers are a large social group with access to a "relatively safe" form of recreation, that allows the opportunity to relieve stress. An important question, however, is how they did so, and to what extent their perceived COVID-19 transition status influenced decisions both in life and at the fishing site. AIM: Our study aimed to determine the dynamics of anglers' attitudes and behaviors during the COVID-19 pandemic as a result of the different statuses of their exposure to the SARS-CoV-2 virus. We assumed that the behavior of anglers who have not experienced the disease (were not ill and not sure if ill) will be similar and, on the other hand, different from the behavior of those who have experienced COVID-19. METHODS: The web-assisted interviews survey was used among 586 anglers with different COVID-19 disease experience statuses. Their pandemic behavior and activities by four age groups were studied using non-metric multidimensional scaling. Redundancy analysis has been used to identify the relationship between anglers' life attitudes and socioeconomic and demographic factors, taking into account their preferences and involvement in fishing. RESULTS: We have demonstrated that the behavior of anglers who have not experienced COVID-19 disease and do not present a reckless attitude toward pandemic threats, do not show significant differences from the life attitudes of the group experienced by the SARS-CoV-2 virus. These two groups comprise more than 70% of anglers. However, the rest show a lack of interest in an aware diagnosis of their health and a low level of acceptance of self-restraint in the area of direct social contact. CONCLUSIONS: Unawareness, combined with ignorance, could be a potential factor in the transmission of the virus while fishing. The behaviors of almost 30% of anglers are particularly risky when combined with a strong need to fish in the company of friends and familiar people. Anglers' social identity should be tapped by fishery managers. Targeted educational campaigns should be aimed at groups around specific fishing spots. The need for self-limitation under the pandemic should be promoted for the benefit of the general public and to maintain the reputation of angling as a safe recreational activity.

Potential Factors Conditioning the Compliance to Mandatory Face Covering in the Public Space Due to SARS-CoV-2 Pandemic.

BACKGROUND: During the SARS-CoV-2 pandemic, we could observe different attitudes towards restrictive bans and orders. AIM: The research aimed to examine the potential psychological factors, such as generalized anxiety, fear of COVID-19 or social approval, related to the approach to mandatory face covering in public spaces. METHODS: The web-assisted interviews survey was used among 202 participants, which included socio-demographical data, approach to face covering, the Generalized Anxiety Disorder Scale, the COVID-19 Anxiety Scale, and The Questionnaire of Social Approval. RESULT: The data showed a statistically significant correlation between compliance to the rule of face and nose covering vs. anxiety and compliance to the rule of face and nose covering vs. generalized anxiety. The results indicate differences between vaccinated and non-vaccinated people in the anxiety of COVID-19, generalized anxiety, and compliance with the rule of face and nose covering. CONCLUSIONS: People vaccinated has a higher level of anxiety and more often compliance with the rule of face covering. It is worth noting that an overly pronounced fear of COVID-19 could be a risk factor for mental health. More research about coping with anxiety in the group of vaccinated people is recommended.

Pleistocene mitogenomes reconstructed from the environmental DNA of permafrost sediments.

Traditionally, paleontologists have relied on the morphological features of bones and teeth to reconstruct the evolutionary relationships of extinct animals.1 In recent decades, the analysis of ancient DNA recovered from macrofossils has provided a powerful means to evaluate these hypotheses and develop novel phylogenetic models.2 Although a great deal of life history data can be extracted from bones, their scarcity and associated biases limit their information potential. The paleontological record of Beringia3-the unglaciated areas and former land bridge between northeast Eurasia and northwest North America-is relatively robust thanks to its perennially frozen ground favoring fossil preservation.4,5 However, even here, the macrofossil record is significantly lacking in small-bodied fauna (e.g., rodents and birds), whereas questions related to migration and extirpation, even among well-studied taxa, remain crudely resolved. The growing sophistication of ancient environmental DNA (eDNA) methods have allowed for the identification of species within terrestrial/aquatic ecosystems,6-12 in paleodietary reconstructions,13-19 and facilitated genomic reconstructions from cave contexts.8,20-22 Murchie et al.6,23 used a capture enrichment approach to sequence a diverse range of faunal and floral DNA from permafrost silts deposited during the Pleistocene-Holocene transition.24 Here, we expand on their work with the mitogenomic assembly and phylogenetic placement of Equus caballus (caballine horse), Bison priscus (steppe bison), Mammuthus primigenius (woolly mammoth), and Lagopus lagopus (willow ptarmigan) eDNA from multiple permafrost cores spanning the last 40,000 years. We identify a diverse metagenomic spectra of Pleistocene fauna and identify the eDNA co-occurrence of distinct Eurasian and American mitogenomic lineages.

Examining pathogen DNA recovery across the remains of a 14th century Italian friar (Blessed Sante) infected with Brucella melitensis.

OBJECTIVE: To investigate variation in ancient DNA recovery of Brucella melitensis, the causative agent of brucellosis, from multiple tissues belonging to one individual MATERIALS: 14 samples were analyzed from the mummified remains of the Blessed Sante, a 14 th century Franciscan friar from central Italy, with macroscopic diagnosis of probable brucellosis. METHODS: Shotgun sequencing data from was examined to determine the presence of Brucella DNA. RESULTS: Three of the 14 samples contained authentic ancient DNA, identified as belonging to B. melitensis. A genome (23.81X depth coverage, 0.98 breadth coverage) was recovered from a kidney stone. Nine of the samples contained reads classified as B. melitensis (7-169), but for many the data quality was insufficient to withstand our identification and authentication criteria. CONCLUSIONS: We identified significant variation in the preservation and abundance of B. melitensis DNA present across multiple tissues, with calcified nodules yielding the highest number of authenticated reads. This shows how greatly sample selection can impact pathogen identification. SIGNIFICANCE: Our results demonstrate variation in the preservation and recovery of pathogen DNA across tissues. This study highlights the importance of sample selection in the reconstruction of infectious disease burden and highlights the importance of a holistic approach to identifying disease. LIMITATIONS: Study focuses on pathogen recovery in a single individual. SUGGESTIONS FOR FURTHER RESEARCH: Further analysis of how sampling impacts aDNA recovery will improve pathogen aDNA recovery and advance our understanding of disease in past peoples.

Collapse of the mammoth-steppe in central Yukon as revealed by ancient environmental DNA.

The temporal and spatial coarseness of megafaunal fossil records complicates attempts to to disentangle the relative impacts of climate change, ecosystem restructuring, and human activities associated with the Late Quaternary extinctions. Advances in the extraction and identification of ancient DNA that was shed into the environment and preserved for millennia in sediment now provides a way to augment discontinuous palaeontological assemblages. Here, we present a 30,000-year sedimentary ancient DNA (sedaDNA) record derived from loessal permafrost silts in the Klondike region of Yukon, Canada. We observe a substantial turnover in ecosystem composition between 13,500 and 10,000 calendar years ago with the rise of woody shrubs and the disappearance of the mammoth-steppe (steppe-tundra) ecosystem. We also identify a lingering signal of Equus sp. (North American horse) and Mammuthus primigenius (woolly mammoth) at multiple sites persisting thousands of years after their supposed extinction from the fossil record.

American mastodon mitochondrial genomes suggest multiple dispersal events in response to Pleistocene climate oscillations.

Pleistocene glacial-interglacial cycles are correlated with dramatic temperature oscillations. Examining how species responded to these natural fluctuations can provide valuable insights into the impacts of present-day anthropogenic climate change. Here we present a phylogeographic study of the extinct American mastodon (Mammut americanum), based on 35 complete mitochondrial genomes. These data reveal the presence of multiple lineages within this species, including two distinct clades from eastern Beringia. Our molecular date estimates suggest that these clades arose at different times, supporting a pattern of repeated northern expansion and local extirpation in response to glacial cycling. Consistent with this hypothesis, we also note lower levels of genetic diversity among northern mastodons than in endemic clades south of the continental ice sheets. The results of our study highlight the complex relationships between population dispersals and climate change, and can provide testable hypotheses for extant species expected to experience substantial biogeographic impacts from rising temperatures.

Ancient Mitogenomes Reveal the Evolutionary History and Biogeography of Sloths.

Living sloths represent two distinct lineages of small-sized mammals that independently evolved arboreality from terrestrial ancestors. The six extant species are the survivors of an evolutionary radiation marked by the extinction of large terrestrial forms at the end of the Quaternary. Until now, sloth evolutionary history has mainly been reconstructed from phylogenetic analyses of morphological characters. Here, we used ancient DNA methods to successfully sequence 10 extinct sloth mitogenomes encompassing all major lineages. This includes the iconic continental ground sloths Megatherium, Megalonyx, Mylodon, and Nothrotheriops and the smaller endemic Caribbean sloths Parocnus and Acratocnus. Phylogenetic analyses identify eight distinct lineages grouped in three well-supported clades, whose interrelationships are markedly incongruent with the currently accepted morphological topology. We show that recently extinct Caribbean sloths have a single origin but comprise two highly divergent lineages that are not directly related to living two-fingered sloths, which instead group with Mylodon. Moreover, living three-fingered sloths do not represent the sister group to all other sloths but are nested within a clade of extinct ground sloths including Megatherium, Megalonyx, and Nothrotheriops. Molecular dating also reveals that the eight newly recognized sloth families all originated between 36 and 28 million years ago (mya). The early divergence of recently extinct Caribbean sloths around 35 mya is consistent with the debated GAARlandia hypothesis postulating the existence at that time of a biogeographic connection between northern South America and the Greater Antilles. This new molecular phylogeny has major implications for reinterpreting sloth morphological evolution, biogeography, and diversification history.