Search

Two species of Leopoldamys long-tailed giant rats are found in Peninsular Malaysia. They are currently referred to as Leopoldamys ciliatus which inhabits montane habitat, and Leopoldamys vociferans which usually inhabits the lowland forest. To date, there is no report on the phylogenetic relationship of L. ciliatus with the other Leopoldamys taxa. The present study was carried out to determine its relationship, based on the mitochondrial cytochrome b (cyt b) gene sequence, with L. vociferans of Peninsular Malaysia and other congeners. Phylogenetic analysis shows that L. ciliatus is a sister-species to the lineage L1 of L. herberti and L. revertens, and is distantly related to L. edwardsi. L. vociferans, and L. sabanus form a distinct clade (lineage L5) from the other Leopoldamys taxa from Indochina. The Sumatra taxon currently known as L. sabanus is genetically distinct to L. vociferans with K2P distances between 0.065 and 0.069. Contrary to previous opinions, L. herberti, L. revertens, and L. neilli of Indochina are valid species based on more than 2.5% threshold genetic distance. Both the L. edwardsi and L. neilli species complexes are represented by several sibling species. A more extensive taxon sampling from various regions (particularly Sumatra and other regions of Indonesia) as well as the use of morphological and molecular (mitogenomes or multiple genes) data sets are needed to provide a robust phylogeny and systematics.

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics., Trends in Genetics, 39 (7), ISSN:0168-9525

Gray wolves (Canis lupus) in the Iberian Peninsula declined substantially in both range and population size in the last few centuries due to human persecution and habitat fragmentation. However, unlike many other western European populations, gray wolves never went extinct in Iberia. Since the minimum number was recorded around 1970, their numbers have significantly increased and then stabilized in recent decades. We analyzed mitochondrial genomes from 54 historical specimens of Iberian wolves from across their historical range using ancient DNA methods. We compared historical and current mitochondrial diversity in Iberian wolves at the 5′ end of the control region (n = 17 and 27) and the whole mitochondrial genome excluding the control region (n = 19 and 29). Despite an increase in population size since the 1970s, genetic diversity declined. We identified 10 whole mitochondrial DNA haplotypes in 19 historical specimens, whereas only six of them were observed in 29 modern Iberian wolves. Moreover, a haplotype that was restricted to the southern part of the distribution has gone extinct. Our results illustrate a lag between demographic and genetic diversity changes, and show that after severe population declines, genetic diversity can continue to be lost in stable or even expanding populations. This suggests that such populations may be of conservation concern even after their demographic trajectory has been reversed.

Purpose The purpose of this research project was to improve public awareness to improve public awareness of the importance of energy conservation and to improve the use of simple conservation strategies. A thorough evaluation of the net gain from the numerous energy campaigns rolled out to the public every year is lacking. This study conducted pre- and post-campaign surveys and focus groups to evaluate one campaign’s impact on self-reported energy behaviors. Design/methodology/approach The campaign used television public service announcements and a website to improve awareness of the city’s efforts to conserve energy and to increase individual energy conservation practices. Focus groups (n = 40) were used to identify common barriers to conservation, and pre- and post-surveys (n = 533, 479) were conducted to evaluate the campaign’s effectiveness. Findings Results indicated that the campaign increased positive changes in changing light bulbs and confidence in taking action to turn down thermostats, unplug devices and turn off lights. While follow-up research is needed on the precise mechanism of the psychological process at work, the findings are consistent with the concepts of self and response efficacy as needed components of any behavior change. The authors advocate the adoption of research-informed message design to maximize communication campaign effects. Originality/value This paper demonstrates how the combination of three prominent persuasion theories can be used to develop behavior change campaigns. Also, it is one of the few studies to evaluate the effectiveness of the Energy Star campaign.

The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1–8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located. © 2022, The Author(s). 8028-00005B; IP DKRVO 2019-2023, MK000094862; 220457/Z/20/Z, ERC-2013-StG-337574-UNDEAD, ERC-2019-StG-853272-PALAEOFARM; 075-15-2021-1069; European Molecular Biology Organization, EMBO: 217223/Z/19/Z; Vallee Foundation; Velux Fonden; Wellcome Trust, WT; Francis Crick Institute, FCI: FC001595; Horizon 2020 Framework Programme, H2020: 796877; Medical Research Council, MRC; Natural Environment Research Council, NERC: 210119/Z/18/Z, NE/K003259/1, NE/K005243/1, NE/S00078X/1, NE/S007067/1; Cancer Research UK, CRUK; European Research Council, ERC: 852558; Grantová Agentura České Republiky, GA ČR: 15-06446S; Svenska Forskningsrådet Formas: 2018-01640; Knut och Alice Wallenbergs Stiftelse; Vetenskapsrådet, VR: 681396, BELSPO B2/191/P2/ICHIE; Russian Science Foundation, RSF: 16-18-10265-RNF, 20-17-00033, 21-18-00457-RNF, 310763; Science for Life Laboratory, SciLifeLab; Narodowa Agencja Wymiany Akademickiej, NAWA: PPN/PPO/2018/1/00037 This work was supported by grants to P. Skoglund from the European Research Council (grant no. 852558), the Erik Philip Sörensen Foundation and the Science for Life Laboratory, Swedish Biodiversity Program, made available by support from the Knut and Alice Wallenberg Foundation. A.B., L.S., P. Swali and P. Skoglund were supported by Francis Crick Institute core funding (FC001595) from Cancer Research UK, the UK Medical Research Council and the Wellcome Trust. P. Skoglund was also supported by the Vallee Foundation, the European Molecular Biology Organisation and the Wellcome Trust (217223/Z/19/Z). Computations were supported by SNIC-UPPMAX. We also acknowledge support from Science for Life Laboratory, the Knut and Alice Wallenberg Foundation, the National Genomics Infrastructure funded by the Swedish Research Council and the Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. We thank the Yukon gold mining community and First Nations, including the Tr’ondëk Hwëch’in, for continued support of our palaeontology research in the Yukon Territories, Canada. We thank the Danish National High-Throughput Sequencing Centre and BGI-Europe for assistance in sequencing data generation and the Danish National Supercomputer for Life Sciences–Computerome ( https://computerome.dtu.dk ) for computational resources. We thank National Museum Wales for continued sampling support. M. Germonpré acknowledges support from the Brain.be 2.0 ICHIE project (BELSPO B2/191/P2/ICHIE). M.T.P.G. was supported by the European Research Council (grant no. 681396). M.-H.S.S. was supported by the Velux Foundations through the Qimmeq Project, the Aage og Johanne Louis-Hansens Fond and the Independent Research Fund Denmark (8028-00005B). L.D. acknowledges support from FORMAS (2018-01640). D.W.G.S. received funding for this project from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 796877. M.P. was supported by the Polish National Agency for Academic Exchange–NAWA (grant no. PPN/PPO/2018/1/00037). V.J.S. was supported by the University of Zurich’s University Research Priority Program ‘Evolution in Action: From Genomes to Ecosystems’. This research was done with the participation of ZIN RAS (grant no. 075-15-2021-1069). We are grateful to the museum of the Institute of Plant and Animal Ecology UB RAS (Ekaterinburg, Russia) for provision of samples. R.P.J. and C.O’D. were supported by the Standing Committee for Archaeology of the Royal Irish Academy through the Archaeological Excavation Research Grant Scheme. E.Y.P., P.N. and V.V.P. are supported by the Russian Science Foundation (grant no. 16-18-10265-RNF and 21-18-00457-RNF). Y.V.K. was supported by the Russian Science Foundation (grant no. 20-17-00033). M.H. was supported by the European Research Council (consolidator grant GeneFlow no. 310763). M.L.-G. was supported by the Czech Science Foundation GAČR (grant no. 15-06446S) and institutional financing of the Moravian Museum from the Czech Ministry of Culture (IP DKRVO 2019-2023, MK000094862). L.S. is supported by the Sir Henry Wellcome fellowship (220457/Z/20/Z). We thank Staatliches Museum für Naturkunde Stuttgart for sample access. L.F. and G.L. were supported by European Research Council grants (ERC-2013-StG-337574-UNDEAD and ERC-2019-StG-853272-PALAEOFARM) and Natural Environmental Research Council grants (NE/K005243/1, NE/K003259/1, NE/S007067/1 and NE/S00078X/1). L.F. was also supported by the Wellcome Trust (210119/Z/18/Z). This research was funded in whole, or in part, by the Wellcome Trust (FC001595). For the purpose of open access, the author has applied a CC-BY public copyright licence to any author accepted manuscript version arising from this submission.

Background Successful trauma resuscitation relies on multi-disciplinary collaboration. In most academic programs, general surgery (GS) and emergency medicine (EM) residents rarely train together before functioning as a team. Methods In our Multi-Disciplinary Trauma Evaluation and Management Simulation (MD-TEAMS), EM and GS residents completed manikin-based trauma scenarios and were evaluated on resuscitation and communication skills. Residents were surveyed on confidence surrounding training objectives. Results Residents showed improved confidence running trauma scenarios in multi-disciplinary teams. Residents received lower communication scores from same-discipline vs cross-discipline faculty. EM residents scored higher in evaluation and planning domains; GS residents scored higher in action processes; groups scored equally in team management. Strong correlation existed between team leader communication and resuscitative skill completion. Conclusion MD-TEAMS demonstrated correlation between communication and resuscitation checklist item completion and communication differences by resident specialty. In the future, we plan to evaluate training-related resident behavior changes and specialty-specific communication differences by residents.

Bandicoot rats (genus Bandicota) are distributed widely across the Indomalay biogeographic realm of tropical East Asia. One widely distributed species, the greater bandicoot rat (Bandicota indica), has a disjunct distribution including both north and south of the biogeographic break at the Isthmus of Kra. We compared genetic variation of greater bandicoot rats from north and south of the Isthmus of Kra using mitochondrial cytochrome b (cyt b, 1140 bp) and nuclear interphotoreceptor retinoid binding protein (IRBP, 801 bp) sequences. We found that the greater bandicoot rat (B. indica) is not native to Sundaland, the region south of the Isthmus of Kra. The species was introduced to the region recently as the genetic divergence with other regions is very low and phylogenies of both genes showed Malaysian greater bandicoot rat very closely related to conspecifics from Lao PDR. Haplotype data revealed all individuals from Malaysia are homogenous, which implied that the species was introduced recently. The greater bandicoot rats in Malaysia are so far only reported in the rice producing regions of Kedah and Perlis, but they may be increasing in number and distribution. A more detailed survey on the distribution and population demographics of Malaysian greater bandicoot rats are needed to support a management plan for this invasive species.

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics., Trends in Ecology & Evolution, 37 (3), ISSN:0169-5347, ISSN:1872-8383

Background: Fungal infections are associated with increased morbidity and death. Few studies have examined risk factors associated with post-operative fungal intra-abdominal infections (FIAIs) in t...

Long‐chain fatty‐acyl CoA dehydrogenase deficiency (LCHADD) is an inborn error of long chain fatty acid oxidation with various features including hypoketotic hypoglycemia, recurrent rhabdomyolysis, pigmentary retinopathy, peripheral neuropathy, cardiomyopathy, and arrhythmias. Various stresses trigger metabolic decompensation. Coronavirus disease 2019 (COVID‐19) is a pandemic caused by the RNA virus SARS‐CoV‐2 with diverse presentations ranging from respiratory symptoms to myocarditis. We report a case of a patient with LCHADD who initially presented with typical metabolic decompensation symptoms including nausea, vomiting, and rhabdomyolysis in addition to mild cough, and was found to have COVID‐19. She developed acute respiratory failure and refractory hypotension from severe cardiomyopathy which progressed to multiple organ failure and death. Our case illustrates the need for close monitoring of cardiac function in patients with a long‐chain fatty acid oxidation disorder.

Towards high–throughput analyses of fecal samples from wildlife. High–throughput sequencing offers new possibilities in molecular ecology and conservation studies. However, its potential has not yet become fully exploited for noninvasive studies of free–ranging animals, such as those based on feces. High–throughput sequencing allows sequencing of short DNA fragments and could allow simultaneous genotyping of a very large number of samples and markers at a low cost. The application of high throughput genotyping to fecal samples from wildlife has been hindered by several labor–intensive steps. We evaluate alternative protocols which could allow higher throughput for two of these steps: sample collection and DNA extraction. Two different field sampling and seven different DNA extraction methods are tested here on grey wolf (Canis lupus) feces. There was high variation in genotyping success rates. The field sampling method based on surface swabbing performed much worse than the extraction from a fecal fragment. In addition, there is a lot of room for improvement in the DNA extraction step. Optimization of protocols can lead to very much more efficient, cheaper and higher throughput noninvasive monitoring. Selection of appropriate markers is still of paramount importance to increase genotyping success.., Hacia análisis genéticos de alto rendimiento de muestras fecales de fauna silvestre. La secuenciación de alto rendimiento ofrece nuevas posibilidades en ecología molecular y biología de la conservación. Sin embargo, el potencial de esta técnica no ha sido totalmente explotado para estudios no invasivos, a partir de muestras fecales, de fauna en libertad. La secuenciación de alto rendimiento permite la secuenciación de fragmentos de ADN cortos y podría permitir el genotipado simultáneo de un gran número de muestras y marcadores a un bajo coste. La aplicación de estas técnicas a muestras fecales de fauna silvestre ha sido obstaculizada por la gran cantidad de trabajo requerido en varios pasos, desde la recolección de muestras hasta la secuenciación. Aquí evaluamos protocolos alternativos que podrían permitir un mayor rendimiento en dos de estos pasos: muestreo de campo y extracción de ADN. En este trabajo comparamos dos métodos distintos de conservación de las muestras obtenidas en el campo y siete métodos de extracción de ADN para heces de lobos (Canis lupus). Observamos una gran variación en el éxito de genotipado según los protocolos que se sigan. El método de muestreo de campo basado en frotado superficial de los excrementos dio resultados peores que la recolección de un fragmento del excremento. Por otro lado, los protocolos para la extracción de ADN mostraban resultados muy variables y ofrecen mucho margen de optimización y mejora. La optimización de protocolos puede llevar a un monitoreo no invasivo mucho más eficiente, económico y con mayor rendimiento. La selección de marcadores apropiados sigue siendo de importancia vital para incrementar el éxito de genotipado.

Recurring glacial cycles through the Quaternary period drastically altered the size and distribution of natural populations of North American flora and fauna. The “southerly refugia model” has been the longstanding framework for testing the effects of glaciation on contemporary genetic patterns; however, insights from ancient DNA have contributed to the reconstruction of more complex histories for some species. The American badger, Taxidea taxus, provides an interesting species for exploring the genetic legacy of glacial history, having been hypothesized to have postglacially emerged from a single, southerly refugium to recolonize northern latitudes. However, previous studies have lacked genetic sampling from areas where distinct glacial refugia have been hypothesized, including the Pacific Northwest and American Far North (Yukon, Alaska). In order to further investigate the phylogeographic history of American badgers, we collected mitochondrial DNA sequence data from ancient subfossil material collected within the historical range (Alaska, Yukon) and combined them with new and previously published data from across the species' contemporary distribution (n = 1,207). We reconstructed a mostly unresolved phylogenetic tree and star‐like haplotype network indicative of emergence from a largely panmictic glacial refugium and recent population expansion, the latter further punctuated by significantly negative Tajima's D and Fu's Fs values. Although directionality of migration cannot be unequivocally inferred, the moderate to high levels of genetic variation exhibited by American badgers, alongside the low frequency of haplotypes with indels in the Midwest, suggest a potential recolonization into central North America after the hypothesized ice‐free corridor reopened ~13,000 years ago. Overall, the expanded reconstruction of phylogeographic history of American badgers offers a broader understanding of contemporary range‐wide patterns and identifies unique genetic units that can likely be used to inform conservation of at‐risk populations at the northern periphery., Recurring glacial cycles through the Quaternary period drastically altered the size and distribution of natural populations of North American fauna, leaving distinct signatures in contemporary gene pools. Here, we combined newly acquired sequencing information from contemporary, historical, and ancient DNA samples of the American badger (Taxidea taxus) with exemplar sequences across the species' range (total n = 1,207) to reconstruct the phylogeographic history of the species in North America. Recovered patterns of variation revealed little discrete geographic structuring indicative of a largely panmictic glacial refugium and recent population expansion, while also suggesting a potential recolonization into central North America after the hypothesized ice‐free corridor reopened. Photo credit: Emma Walker.

The hyperdiverse shrew genus Crocidura is one of few small mammal genera distributed across Sundaland and all of its boundaries. This represents a rare opportunity to study the geological history of this region through the evolutionary history of these shrews. We generate a phylogeny of all recognized species of Sundaland Crocidura and show that most speciation events took place during the Pleistocene, prior to the inundation of the Sunda Shelf around 400 000 years ago. We find east–west differentiation within two separate lineages on Borneo, and that the current taxonomy of its two endemic species does not reflect evolutionary history, but ecophenotypic variation of plastic traits related to elevation. Sulawesi shrews are monophyletic, with a single notable exception: the black-footed shrew (C. nigripes). We show that the black-footed shrew diverged from its relatives on Borneo recently, suggesting a human-assisted breach of Wallace’s line. Overall, the number of Crocidura species, especially on Borneo, probably remains an underestimate.

BACKGROUND Forty percent of critically ill trauma patients will develop an infectious complication. Pneumonia is the most common cause of death of trauma patients surviving their initial insult. We previously demonstrated that polytrauma (PT), defined as two or more severe injuries in at least two areas of the body, induces emergency hematopoiesis characterized by accelerated myelopoiesis in the bone marrow and increased myeloid cell frequency in the peripheral tissues. We hypothesized that PT alone induces priming of neutrophils, resulting in hyperactivation upon secondary exposure to bacteria and causing acute lung injury and increased susceptibility to secondary exposure to Pseudomonas aeruginosa pneumonia. METHODS C57BL/6 mice were subjected to PT consisting of a lower extremity pseudofracture, liver crush injury, and 15% blood-volume hemorrhage. Pneumonia was induced by intratracheal injection of 5 × 106 CFU live P. aeruginosa or 1 × 107 of heat-killed P. aeruginosa (HKPA). For reactive oxygen species (ROS), studies polymorphonuclear neutrophils (PMNs) were isolated by immunomagnetic bead negative selection and stimulated ex-vivo with HKPA. Reactive oxygen species production was measured by immunofluorescence. For histology, lung sections were stained by hematoxylin-eosin and analyzed by a blinded grader. RESULTS Polytrauma induced persistent changes in immune function at baseline and to secondary infection. Pneumonia after injury resulted in increased mortality (60% vs. 5% p < 0.01). Blood neutrophils from PT mice had higher resting (unstimulated) ROS production than in naive animals (p < 0.02) demonstrating priming of the neutrophils following PT. After intratracheal HKPA injection, bronchoalveolar lavage PMNs from injured mice had higher ROS production compared with naive mice (p < 0.01), demonstrating an overexuberant immunopathologic response of neutrophils following PT. CONCLUSION Polytrauma primes neutrophils and causes immunopathologic PMN ROS production, increased lung injury and susceptibility to secondary bacterial pneumonia. These results suggest that trauma-induced immune dysfunction can cause immunopathologic response to secondary infection and suggests neutrophil-mediated pulmonary damage as a therapeutic target for posttrauma pneumonia.

A nonimmunocompromised patient developed life-threatening soft tissue infection with Trichosporon asahii, Fusarium, and Saksenaea that progressed despite maximum antifungal therapies and aggressive debridement. Interleukin-7 immunotherapy resulted in clinical improvement, fungal clearance, reversal of lymphopenia, and improved T-cell function. Immunoadjuvant therapies to boost host immunity may be efficacious in life-threatening fungal infections.

Nasogastric/nasoenteric (NG/NE) feeding tube placements are associated with adverse events and, without proper training, can lead to devastating and significant patient harm related to misplacement. Safe feeding tube placement practices and verification are critical. There are many procedures and techniques for placement and verification; this paper provides an overview and update of techniques to guide practitioners in making clinical decisions. Regardless of placement technique and verification practices employed, it is essential that training and competency are maintained and documented for all clinicians placing NG/NE feeding tubes. This paper has been approved by the American Society for Parenteral and Enteral Nutrition (ASPEN) Board of Directors.

Objective To explore the relationship between abortion restrictions and maternal mortality in the United States. Study design This was a retrospective study examining maternal mortality in the United States from 1995 to 2017. We used the Global Health Data Exchange and the Centers for Disease Control and Prevention WONDER databases to extract maternal mortality data for all 50 states for each year from 1995 to 2017. We categorized states as restrictive, neutral, or protective of abortion access according to policy information published by the Guttmacher Institute. We assessed associations between abortion restrictions and maternal mortality ratios (maternal deaths per 100,000 live births). Results In 1995, the mean maternal mortality ratios were similar across all groups of states (Restrictive 12.6, 95% CI 11.4-13.6; Neutral 12.2, 95% CI 10.9-13.4; Protective 10.9, 95% CI 9.6-11.9). Maternal mortality ratios increased for each group of states over time and in 2017, the mean maternal mortality ratio was higher in restrictive states than in protective states (Restrictive 28.5, 95% CI 20.7-35.1; Neutral 22.9, 95% CI 16.1-28.6; Protective 15.7, 95% CI 10.7-19.9). Regressions accounting for policy, state and year showed a statistically significant increase in maternal mortality ratios in restrictive states relative to neutral states (1.06, 95% CI 1.01-1.11) and a non-significant decrease associated with protective states (0.89, 95% CI 0.78-1.01). Conclusions States that restrict abortion have higher maternal mortality than states that either protect or are neutral towards abortion. Further investigation is needed to determine how abortion restrictions are associated with increased maternal mortality. Implications The association between abortion restrictions and maternal mortality may reflect the overall legislative priorities of individual states as restrictive states are less likely to pass proactive legislation demonstrated to improve maternal outcomes.

Ecological and conservation genetic studies often use noninvasive sampling, especially with elusive or endangered species. Because microsatellites are generally short in length, they can be amplified from low quality samples such as feces. Microsatellites are highly polymorphic so few markers are enough for reliable individual identification, kinship determination, or population characterization. However, the genotyping process from feces is expensive and time consuming. Given next-generation sequencing (NGS) and recent software developments, automated microsatellite genotyping from NGS data may now be possible. These software packages infer the genotypes directly from sequence reads, increasing throughput. Here we evaluate the performance of four software packages to genotype microsatellite loci from Iberian wolf (Canis lupus) feces using NGS. We initially combined 46 markers in a single multiplex reaction for the first time, of which 19 were included in the final analyses. Megasat was the software that provided genotypes with fewer errors. Coverage over 100X provided little additional information, but a relatively high number of PCR replicates were necessary to obtain a high quality genotype from highly unoptimized, multiplexed reactions (10 replicates for 18 of the 19 loci analyzed here). This could be reduced through optimization. The use of new bioinformatic tools and next-generation sequencing data to genotype these highly informative markers may increase throughput at a reasonable cost and with a smaller amount of laboratory work. Thus, high throughput sequencing approaches could facilitate the use of microsatellites with fecal DNA to address ecological and conservation questions

The endangered Mexican wolf (Canis lupus baileyi) is known to carry exceedingly low levels of genetic diversity. This could be (i) the result of long-term evolutionary patterns as they exist at the southernmost limit of the species distribution at a relatively reduced effective size, or (ii) due to rapid population decline caused by human persecution over the last century. If the former, purifying selection is expected to have minimized the impact of inbreeding. If the latter, rapid and recent declines in genetic diversity may have resulted in severe fitness consequences. To differentiate these hypotheses, we conducted comparative whole-genome analyses of five historical Mexican wolves (1907–1917) and 18 contemporary Mexican and grey wolves from North America and Eurasia. Based on whole-genome data, historical and modern Mexican wolves together form a discrete unit. Moreover, we found that modern Mexican wolves have reduced genetic diversity and increased inbreeding relative to the historical population, which was widespread across the southwestern United States and not restricted to Mexico as previously assumed. Finally, although Mexican wolves have evolved in sympatry with coyotes (C. latrans), we observed lower introgression between historical Mexican wolves and coyotes than with modern Mexican wolves, despite similarities in body size. Taken together, our data show that recent population declines probably caused the reduced level of genetic diversity, but not the observed differentiation of the Mexican wolves from other North American wolves

Mountain ranges offer opportunities for understanding how species evolved and diversified across different environmental conditions. Neotropical frogs of the genus Oreobates (Anura: Craugastoridae) are adapted to highland and lowland habitats along the Andes, but many aspects of their evolution remain unknown. We studied their evolutionary history using ~18,000 exons enriched by targeted sequence-capture. Since capture success was very variable across samples, we evaluated to what degree differing data filtering produced robust inferences. The inferred evolutionary framework evidenced phylogenetic discordances among lowland species that can be explained by taxonomic misidentification or admixture of ancestral lineages. Highland species showed smaller effective populations than lowland frogs, probably due to greater habitat fragmentation in montane environments. Stronger genetic drift likely decreased the power of purifying selection and led to an increased proportion of nonsynonymous mutations in highland populations that could play an important role in their adaptation. Overall, our work sheds light on the evolutionary history and diversification of this group of Neotropical frogs along elevational gradients in the Andes as well as on their patterns of intraspecific diversity., This research was supported by grants from the Spanish Government (Ministerio de Economía y Competitividad) to C.V. (CGL2013-47547-P and CGL2016-75227-P), I.D.l.R (CGL2011-30393), and an FPI (Formación de Personal Investigador) fellowship (BES‐2014‐069006) as well as three travel grants (EEBB‐I‐16‐10576, EEBB‐I‐17‐12168, and EEBB‐I‐18‐12878) to S.M.-M.

Pleistocene climate change impacted entire ecosystems throughout the world. In the northern hemisphere, the distribution of Arctic species expanded during glacial periods, while more temperate and mesic species contracted into climatic refugia, where isolation drove genetic divergence. Cycles of local cooling and warming in the Sahara region of northern Africa caused repeated contractions and expansions of savannah‐like environments which connected mesic species isolated in refugia during interglacial times, possibly driving population expansions and contractions; divergence and geneflow in the associated fauna. Here, we use whole genome sequences of African golden wolves (Canis lupaster), a generalist mesopredator with a wide distribution in northern Africa to estimate their demographic history and past episodes of geneflow. We detect a correlation between divergence times and cycles of increased aridity‐associated Pleistocene glacial cycles. A complex demographic history with responses to local climate change in different lineages was found, including a relict lineage north of the High Atlas Mountains of Morocco that has been isolated for more than 18,000 years, possibly a distinct ecotype. CS was supported by a PhD fellowship from Programa Internacional de Becas “La Caixa-Severo Ochoa” of the Spanish Ministerio de Economía y Competitividad and La Caixa bank (BES-2015-074331). This project was funded by the Frontera grant P18-FR-5099 from the Junta de Andalucia. EBD-CSIC received support from the Spanish Ministry of Economy and Competitiveness under the ‘Centro de Excelencia Severo Ochoa 2013-2017’ program, SEV-2012-0262.

The global COVID-19 pandemic has claimed the lives of more than 450,000 US citizens. Dysregulation of the immune system underlies the pathogenesis of COVID-19, with inflammation mediated local tissue injury to the lung in the setting of suppressed systemic immune function. To define the molecular mechanisms of immune dysfunction in COVID-19 we utilized a systems immunology approach centered on the circulating leukocyte phosphoproteome measured by mass cytometry. COVID-19 is associated with wholesale activation of a broad set of signaling pathways across myeloid and lymphoid cell populations. STAT3 phosphorylation predominated in both monocytes and T cells and was tightly correlated with circulating IL-6 levels. High levels of STAT3 phosphorylation was associated with decreased markers of myeloid cell maturation/activation and decreased ex-vivo T cell IFN-gamma production, demonstrating that during COVID-19 dysregulated cellular activation is associated with suppression of immune effector cell function. Collectively, these data reconcile the systemic inflammatory response and functional immunosuppression induced by COVID-19 and suggest STAT3 signaling may be the central pathophysiologic mechanism driving immune dysfunction in COVID-19.

Background Gun violence (GV) is a complex public health issue, and the management of GV as a disease engages the surgeon in technical and nontechnical skills. The Anatomy of Gun Violence (AGV) curriculum was developed to teach surgical trainees these seemingly disparate skills, training residents to manage the multiple aspects of firearm injury. Study Design The AGV curriculum was delivered over 6 weeks in the 2017–2018 and 2018–2019 academic years (AY), and used multiple educational methods including didactic lectures, mock oral examinations, a Bleeding Control training session, a GV survivor’s personal story, a Resuscitative Endovascular Balloon Occlusion of the Aorta (REBOA) training session, and the Surgery for Abdominal-thoracic ViolencE (SAVE) simulation lab. As surgical residents were involved over both AYs, components of the curriculum were available every other year to provide variety. As proof of concept, this novel curriculum was objectively evaluated by residents’ improvement in knowledge and overall experience using pre- and post-surveys. Results Sixty surgical residents participated in the AGV curriculum in both AYs, with 41 and 36 residents completing the survey regarding their experiences with the curriculum. The curriculum was well received by residents overall in both AYs (median ± IQR 5 ± 0 and 5 ± 0.1, respectively), with the SAVE simulation lab being the most highly favored portion. Additionally, residents had an average 7.5% improvement in knowledge attributed to the curriculum, with a larger effect seen in the junior residents. Conclusions This novel AGV curriculum created a well-received learning experience involving the technical and nontechnical skills necessary to care for GV victims. This comprehensive approach to GV may represent a unique opportunity to engage surgical trainees in both the treatment and prevention of firearm injury.

Janzen's influential "mountain passes are higher in the tropics" hypothesis predicts restricted gene flow and genetic isolation among populations spanning elevational gradients in the tropics. Few studies have tested this prediction, and studies that focus on population genetic structure in Southeast Asia are particularly underrepresented in the literature. Here, we test the hypothesis that mountain treeshrews (Tupaia montana) exhibit limited dispersal across their broad elevational range which spans ~2,300 m on two peaks in Kinabalu National Park (KNP) in Borneo: Mt Tambuyukon (MT) and Mt Kinabalu (MK). We sampled 83 individuals across elevations on both peaks and performed population genomics analyses on mitogenomes and single nucleotide polymorphisms from 4,106 ultraconserved element loci. We detected weak genetic structure and infer gene flow both across elevations and between peaks. We found higher genetic differentiation on MT than MK despite its lower elevation and associated environmental variation. This implies that, contrary to our hypothesis, genetic structure in this system is not primarily shaped by elevation. We propose that this pattern may instead be the result of historical processes and limited upslope gene flow on MT. Importantly, our results serve as a foundational estimate of genetic diversity and population structure from which to track potential future effects of climate change on mountain treeshrews in KNP, an important conservation stronghold for the mountain treeshrew and other montane species.

Background and aims Wildlife conservation has focused primarily on species for the last decades. Recently, popular perception and laws have begun to recognize the central importance of genetic diversity in the conservation of biodiversity. How to incorporate genetic diversity in ongoing monitoring and management of wildlife is still an open question. Methods We tested a panel of multiplexed, high-throughput sequenced introns in the small mammal communities of two UNESCO World Heritage Sites on different continents to assess their viability for large-scale monitoring of genetic variability in a spectrum of diverse species. To enhance applicability across other systems, the bioinformatic pipeline for primer design was outlined. Results The number of loci amplified and amplification evenness decreased as phylogenetic distance increased from the reference taxa, yet several loci were still variable across multiple mammal orders. Conclusions Genetic variability found is informative for population genetic analyses and for addressing phylogeographic and phylogenetic questions, illustrated by small mammal examples here., Conservation, Genetics, Intron, High-throughput sequencing NGS, Multiplex, Wildlife management, Agricultural science, Environmental science, Earth sciences, Biological sciences, Veterinary medicine.

Tropical mountains are cradles of biodiversity and endemism. Sundaland, tropical Southeast Asia, hosts 3 species of Rattus endemic to elevations above 2000 m with an apparent convergence in external morphology: Rattus korinchi and R. hoogerwerfi from Sumatra, and R. baluensis from Borneo. A fourth one, R. tiomanicus, is restricted to lowland elevations across the whole region. The origins of these endemics are little known due to the absence of a robust phylogenetic framework. We use complete mitochondrial genomes from the 3 high altitude Rattus, and several related species to determine their relationships, date divergences, reconstruct their history of colonization, and test for selection on the mitochondrial DNA. We show that mountain colonization happened independently in Borneo (

Genetic variability has been widely neglected as a measure of biodiversity for conservation and management over the last decades. However, major technical advances in molecular biology coupled with increased public awareness have recently marked the opening of a new era. Estimates and tracking of genetic variability in species and populations are now mandates for governments. However, this obligation is difficult to implement. There is no agreement on the most appropriate way to assess genetic diversity, yet the urgent need for comparability among different studies calls for the adoption of standardized molecular tools in biodiversity monitoring. Here, we take stock of the plethora of techniques and tools that have been historically adopted for monitoring genetic diversity in mammals and evaluate their strengths and weaknesses. We focus on the opportunities offered by new genomic approaches and touch upon the major bioinformatics challenges posed by the impressive amount of data that they deliver, suggesting current trends and future prospects.

Summary The presence of population-specific phenotypes often reflects local adaptation or barriers to gene flow. The co-occurrence of phenotypic polymorphisms that are restricted within the range of a highly mobile species is more difficult to explain. An example of such polymorphisms is in the common quail Coturnix coturnix, a small migratory bird that moves widely during the breeding season in search of new mating opportunities, following ephemeral habitats, 1 , 2 and whose females may lay successive clutches at different locations while migrating. 3 In spite of this vagility, previous studies reported a higher frequency of heavier males with darker throat coloration in the southwest of the distribution (I. Jimenez-Blasco et al., 2015, Int. Union Game Biol., conference). We used population genomics and cytogenetics to explore the basis of this polymorphism and discovered a large inversion in the genome of the common quail. This inversion extends 115 Mbp in length and encompasses more than 7,000 genes (about 12% of the genome), producing two very different forms. Birds with the inversion are larger, have darker throat coloration and rounder wings, are inferred to have poorer flight efficiency, and are geographically restricted despite the high mobility of the species. Stable isotope analyses confirmed that birds carrying the inversion have shorter migratory distances or do not migrate. However, we found no evidence of pre- or post-zygotic isolation, indicating the two forms commonly interbreed and that the polymorphism remains locally restricted because of the effect on behavior. This illustrates a genomic mechanism underlying maintenance of geographically structured polymorphisms despite interbreeding with a lineage with high mobility.