Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation

Abstract Background Baleen whales (Mysticeti) are the largest animals on earth and their evolutionary history has been studied in detail, but some relationships still remain contentious. In particular, reconstructing the phylogenetic position of the gray whales (Eschrichtiidae) has been complicated by evolutionary processes such as gene flow and incomplete lineage sorting (ILS). Here, whole-genome sequencing data of the extant baleen whale radiation allowed us to identify transposable element (TE) insertions in order to perform phylogenomic analyses and measure germline insertion rates of TEs. Baleen whales exhibit the slowest nucleotide substitution rate among mammals, hence we additionally examined the evolutionary insertion rates of TE insertions across the genomes. Results In eleven whole-genome sequences representing the extant radiation of baleen whales, we identified 91,859 CHR-SINE insertions that were used to reconstruct the phylogeny with different approaches as well as perform evolutionary network analyses and a quantification of conflicting phylogenetic signals. Our results indicate that the radiation of rorquals and gray whales might not be bifurcating. The morphologically derived gray whales are placed inside the rorqual group, as the sister-species to humpback and fin whales. Detailed investigation of TE insertion rates confirm that a mutational slow down in the whale lineage is present but less pronounced for TEs than for nucleotide substitutions. Conclusions Whole genome sequencing based detection of TE insertions showed that the speciation processes in baleen whales represent a rapid radiation. Large genome-scale TE data sets in addition allow to understand retrotransposition rates in non-model organisms and show the potential for TE calling methods to study the evolutionary history of species

Recovery of Cryptococcus gattii from an Infected Ventriculo-Peritoneal Shunt, Illinois, USA

Cryptococcus gattii is a fungal pathogen endemic in tropical and subtropical regions. Isolated cases and outbreaks have been reported in areas of North America and Europe, expanding the distribution pattern beyond warmer regions. We describe a case of ventriculo-peritoneal shunt infection by C. gattii in an immunocompetent person in Illinois

A camera trapping survey of mammals in the mixed landscape of Bolivia’s Chiquitano region with a special focus on the jaguar

At a site in the Bolivian Chiquitano region composed by a mosaic of pastureland and primary Chiquitano Dry Forest (CDF) we conducted a camera-trapping study to (1) survey the mammals, and (2) compare individual Jaguar numbers with other Chiquitano sites. Therefore, we installed 13 camera stations (450 ha polygon) over a period of six months. On 1,762 camera-days and in 1,654 independent capture events, we recorded 24 mammalian species that represent the native fauna of large and medium-sized mammals including apex-predators (Puma, Jaguar), meso-carnivores (Ocelot, Jaguarundi, Margay), and large herbivores (Tapir, Collared and White lipped Peccary). We identified six adult Jaguars and found indications of successful reproductive activity. Captures of Jaguars were higher in CDF than in altered habitats. In summary, we believe that (1) the mammal species richness, (2) the high capture numbers of indicator species, and (3) the high capture numbers of Jaguar indicate that our study area has a good conservation status. Future efforts should be undertaken to keep this, and monitoring programs in this region are necessary to further evaluate the potential importance of the Chiquitano region as a possible key region for mammals, especially Jaguars, in South America

A camera trapping survey of mammals in the mixed landscape of Bolivia’s Chiquitano region with a special focus on the Jaguar

At a site in the Bolivian Chiquitano region composed by a mosaic of pastureland and primary Chiquitano Dry Forest (CDF) we conducted a camera-trapping study to (1) survey the mammals, and (2) compare individual Jaguar numbers with other Chiquitano sites. Therefore, we installed 13 camera stations (450 ha polygon) over a period of six months. On 1,762 camera-days and in 1,654 independent capture events, we recorded 24 mammalian species that represent the native fauna of large and medium-sized mammals including apex-predators (Puma, Jaguar), meso-carnivores (Ocelot, Jaguarundi, Margay), and large herbivores (Tapir, Collared and White lipped Peccary). We identified six adult Jaguars and found indications of successful reproductive activity. Captures of Jaguars were higher in CDF than in altered habitats. In summary, we believe that (1) the mammal species richness, (2) the high capture numbers of indicator species, and (3) the high capture numbers of Jaguar indicate that our study area has a good conservation status. Future efforts should be undertaken to keep this, and monitoring programs in this region are necessary to further evaluate the potential importance of the Chiquitano region as a possible key region for mammals, especially Jaguars, in South America

Much effort, little success: causes for the low ecological efficacy of restoration measures in German surface waters

Abstract Background For more than 20 years, restoration measures have been conducted on watercourses in Germany to increase habitat diversity and thus promote biodiversity. However, their ecological efficacy often proved to be limited. While some studies report an increase in species diversity, others show little evidence of improvement even many years after the implementation of restoration measures. In general, ecological efficacy of hydromorphological restoration measures is highest for terrestrial and semiaquatic groups of organisms such as floodplain vegetation and ground beetles. According to the literature, macrophytes responded most strongly to in-stream restoration measures, while fish stocks showed little improvement and macroinvertebrates showed little or no effect in terms of species richness and diversity. These findings raise the question of reasons for the low ecological efficacy of hydromorphological restoration measures, especially for macroinvertebrate communities. The following literature review and a case study for the river Horloff will provide possible indications for failing success of intensive restoration measures. Results One reason for the inadequate ecological status of many restored river stretches is the inappropriate scaling of restoration measures. Often, small-scale restoration measures are planned, although the respective water bodies exhibit stressors at the catchment scale that impair the ecological efficacy of restoration measures. In particular, chemical contamination of running waters is often insufficiently addressed in the planning and implementation of restoration measures and hampers efficacy of hydromorphological restoration measures. For a holistic water resource management, the planning and implementation of measures should therefore be more closely coordinated and harmonized between federal states and neighboring countries. For this purpose, the establishment of so-called river basin communities is suitable, as they already exist today on the rivers Rhine, Danube, Meuse, Weser, Elbe, Ems, Eider, Schlei/Trave, Warnow/Peene. Conclusion The literature review indicated that for a successful recolonization of restored river stretches by macroinvertebrates and the enhancement of the ecological status, large-scale stressors, i.e., stressors acting at the catchment scale, should be eliminated initially by restoration measures focusing on the chemical contamination and the surrounding land use. Structural restoration measures acting on the reach or local scale should ideally be implemented contemporarily to the removal of large-scale stressors like chemical contamination

Habitat destruction threatens jaguars in a mixed land-use region of eastern Bolivia

Large carnivores such as the jaguar Panthera onca are particularly susceptible to population decline and local extinction as a result of habitat loss. Here we report on the long-term monitoring of a local jaguar population in a mixed land-use area in the eastern lowlands of Bolivia from March 2017 to December 2019. We recorded 15 jaguar individuals and four reproduction events (five offspring from three females), suggesting that our study area harbours a resident breeding population. Seven iterations of spatially explicit capture–recapture models provided density estimates of 1.32–3.57 jaguars per 100 km2. Jaguar capture rates were highest in forested areas, with few to no jaguar captures in pastures used for livestock. Massive deforestation after the survey period reduced the proportion of dense forest cover by 33%, shrinking the availability of suitable jaguar habitat and placing the resident jaguar population at risk. We use the jaguar as an indicator species to highlight the threat of habitat destruction in the Chiquitano region and we emphasize the importance of intact forest patches for jaguar conservation

Integrating gene annotation with orthology inference at scale

Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method that integrates structural gene annotation and orthology inference. TOGA implements a different paradigm to infer orthologous loci, improves ortholog detection and annotation of conserved genes compared with state-of-the-art methods, and handles even highly fragmented assemblies. TOGA scales to hundreds of genomes, which we demonstrate by applying it to 488 placental mammal and 501 bird assemblies, creating the largest comparative gene resources so far. Additionally, TOGA detects gene losses, enables selection screens, and automatically provides a superior measure of mammalian genome quality. TOGA is a powerful and scalable method to annotate and compare genes in the genomic era

Habitat destruction threatens jaguars in a mixed land-use region of eastern Bolivia

Large carnivores such as the jaguar Panthera onca are particularly susceptible to population decline and local extinction as a result of habitat loss. Here we report on the long-term monitoring of a local jaguar population in a mixed land-use area in the eastern lowlands of Bolivia from March 2017 to December 2019. We recorded 15 jaguar individuals and four reproduction events (five offspring from three females), suggesting that our study area harbours a resident breeding population. Seven iterations of spatially explicit capture-recapture models provided density estimates of 1.32-3.57 jaguars per 100 km(2). Jaguar capture rates were highest in forested areas, with few to no jaguar captures in pastures used for livestock. Massive deforestation after the survey period reduced the proportion of dense forest cover by 33%, shrinking the availability of suitable jaguar habitat and placing the resident jaguar population at risk. We use the jaguar as an indicator species to highlight the threat of habitat destruction in the Chiquitano region and we emphasize the importance of intact forest patches for jaguar conservation