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AbstractWith the advent of chromatin‐interaction maps, chromosome‐level genome assemblies have become a reality for a wide range of organisms. Scaffolding quality is, however, difficult to judge. To explore this gap, we generated multiple chromosome‐scale genome assemblies of an emerging wild animal model for carcinogenesis, the California sea lion (Zalophus californianus). Short‐read assemblies were scaffolded with two independent chromatin interaction mapping data sets (Hi‐C and Chicago), and long‐read assemblies with three data types (Hi‐C, optical maps and 10X linked reads) following the “Vertebrate Genomes Project (VGP)” pipeline. In both approaches, 18 major scaffolds recovered the karyotype (2n = 36), with scaffold N50s of 138 and 147 Mb, respectively. Synteny relationships at the chromosome level with other pinniped genomes (2n = 32–36), ferret (2n = 34), red panda (2n = 36) and domestic dog (2n = 78) were consistent across approaches and recovered known fissions and fusions. Comparative chromosome painting and multicolour chromosome tiling with a panel of 264 genome‐integrated single‐locus canine bacterial artificial chromosome probes provided independent evaluation of genome organization. Broad‐scale discrepancies between the approaches were observed within chromosomes, most commonly in translocations centred around centromeres and telomeres, which were better resolved in the VGP assembly. Genomic and cytological approaches agreed on near‐perfect synteny of the X chromosome, and in combination allowed detailed investigation of autosomal rearrangements between dog and sea lion. This study presents high‐quality genomes of an emerging cancer model and highlights that even highly fragmented short‐read assemblies scaffolded with Hi‐C can yield reliable chromosome‐level scaffolds suitable for comparative genomic analyses.

Understanding the relationship between life-history variation and population structure in marine invertebrates is not straightforward. This is particularly true of polar species due to the difficulty of obtaining samples and a paucity of genomic resources from which to develop nuclear genetic markers. Such knowledge, however, is essential for understanding how different taxa may respond to climate change in the most rapidly warming regions of the planet. We therefore used over two hundred polymorphic Amplified Fragment Length Polymorphisms (AFLPs) to explore population connectivity at three hierachical spatial scales in the direct developing Antarctic topshell Margarella antarctica. To previously published data from five populations spanning a 1500 km transect along the length of the Western Antarctic Peninsula, we added new AFLP data for four populations separated by up to 6 km within Ryder Bay, Adelaide Island. Overall, we found a nonlinear isolation-by-distance pattern, suggestive of weaker population structure within Ryder Bay than is present over larger spatial scales. Nevertheless, significantly positive F st values were obtained in all but two of ten pairwise population comparisons within the bay following Bonferroni correction for multiple tests. This is in contrast to a previous study of the broadcast spawner Nacella concinna that found no significant genetic differences among several of the same sites. By implication, the topshell's direct-developing lifestyle may constrain its ability to disperse even over relatively small geographic scales.

Summary Increasing levels of anthropogenic noise have the potential to mask signals of acoustically communicating species in their natural habitats. Animals in noise‐polluted habitats typically adjust their signals away from high background noise levels to ensure successful signal transmission under challenging environmental conditions. Earlier we demonstrated that male Chorthippus biguttulus grasshoppers from roadside habitats produce courtship signals with elevated frequency components compared to conspecifics from non‐roadside habitats. Here, we use a common garden approach to study the mechanisms underlying this response. We transferred grasshopper nymphs from seven roadside as well as five non‐roadside habitats to the laboratory to rear half of them under noisy and the other half under quiet conditions in a full factorial two‐by‐two design. Courtship songs of adult males were later recorded under standardized quiet conditions. Males exposed to road noise as nymphs produced signals with higher frequency components compared to males reared under quiet conditions, indicating developmental plasticity as a mechanism underlying the signal adjustment to anthropogenic noise in grasshoppers. In addition, males originating from roadside habitats produced signals with higher frequency components and an increased syllable to pause ratio – a sexually selected signal trait – compared to males from non‐roadside habitats. Our results demonstrate for the first time that developmental plasticity may play an important role in song trait modifications in response to anthropogenic noise. Furthermore, they suggest that multiple roadside populations may have diverged in parallel, possibly in response to selection for minimizing signal masking by road noise.

We present the laboratory results of immersion freezing efficiencies of cellulose particles at supercooled temperature (T) conditions. Three types of chemically homogeneous cellulose samples are used as surrogates that represent supermicron and submicron ice-nucleating plant structural polymers. These samples include microcrystalline cellulose (MCC), fibrous cellulose (FC) and nanocrystalline cellulose (NCC). Our immersion freezing dataset includes data from various ice nucleation measurement techniques available at 17 different institutions, including nine dry dispersion and 11 aqueous suspension techniques. With a total of 20 methods, we performed systematic accuracy and precision analysis of measurements from all 20 measurement techniques by evaluating T-binned (1 ∘C) data over a wide T range (−36 ∘C <T<-4 ∘C). Specifically, we intercompared the geometric surface area-based ice nucleation active surface site (INAS) density data derived from our measurements as a function of T, ns,geo(T). Additionally, we also compared the ns,geo(T) values and the freezing spectral slope parameter (Δlog(ns,geo)/ΔT) from our measurements to previous literature results. Results show all three cellulose materials are reasonably ice active. The freezing efficiencies of NCC samples agree reasonably well, whereas the diversity for the other two samples spans ≈ 10 ∘C. Despite given uncertainties within each instrument technique, the overall trend of the ns,geo(T) spectrum traced by the T-binned average of measurements suggests that predominantly supermicron-sized cellulose particles (MCC and FC) generally act as more efficient ice-nucleating particles (INPs) than NCC with about 1 order of magnitude higher ns,geo(T).

Aim: Understanding the forces that drive range shifts in forest landscapes is imperative for predicting species distributions under anthropogenic climate and land use change. However, empirical studies exploring how these components jointly influence critical early life stages of mountain tree species across environmental gradients are scarce. We used the high mountain tree Polylepis australis as model species to investigate the relative importance of altitude and associated climatic conditions, land use for livestock and microsite characteristics on early life performance. Location: Córdoba Sierras, central Argentina. Methods: We set up an extensive in situ sowing experiment with a robust split-plot design that integrated spatial scales ranging from 0.4 m2 subplots at the microsite level (associated with vegetative and microtopographic structures), to livestock exclosure and enclosure plots of several hectares, to an altitudinal gradient of 1,000 m. Components of early life performance were monitored across two subsequent growing seasons. Results: Microsite characteristics played a fundamental role in P. australis establishment, whereby interactions with altitude and/or land use suggested alternate mechanisms: facilitation (likely reduced desiccation) dominated at low altitude while at high altitude, abiotic stress (likely intensive frost and radiation) overruled any microsite effects. At mid-altitude, benefits of competition release prevailed over facilitation and microsite effects gained importance under livestock presence. Inconsistencies between pre- and post-emergence responses illustrated potential trade-offs between beneficial and detrimental effects of microsite conditions upon performance throughout early life: a favourable location for seeds may abruptly turn adverse for seedlings. Main conclusions: We unravel how changes in altitude, anthropogenic disturbances and microsite characteristics jointly modulate P. australis performance across stages of early establishment. Such information is fundamental when categorizing specific microhabitats as “safe sites” for tree regeneration especially in mountain environments with high spatio-temporal heterogeneity. Fil: Cáceres, Yolanda. German Centre For Integrative Biodiversity Research.; Alemania. Martin Luther Universität Halle Wittenberg; Alemania Fil: Schrieber, Karin. Universitat Bielefeld; Alemania. Martin Luther Universität Halle Wittenberg; Alemania Fil: Lachmuth, Susanne. Martin Luther Universität Halle Wittenberg; Alemania. German Centre For Integrative Biodiversity Research.; Alemania Fil: Auge, Harald. Helmholtz Centre for Environmental Research; Alemania. German Centre For Integrative Biodiversity Research.; Alemania Fil: Argibay, Daihana Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones Biológicas y Tecnológicas. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Instituto de Investigaciones Biológicas y Tecnológicas; Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Centro de Ecología y Recursos Naturales Renovables; Argentina Fil: Renison, Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones Biológicas y Tecnológicas. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Instituto de Investigaciones Biológicas y Tecnológicas; Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Centro de Ecología y Recursos Naturales Renovables; Argentina Fil: Hensen, Isabell. Martin Luther Universität Halle Wittenberg; Alemania. German Centre For Integrative Biodiversity Research.; Alemania

Ecological systems can often be characterised by changes among a finite set of underlying states pertaining to individuals, populations, communities or entire ecosystems through time. Owing to the inherent difficulty of empirical field studies, ecological state dynamics operating at any level of this hierarchy can often be unobservable or 'hidden'. Ecologists must therefore often contend with incomplete or indirect observations that are somehow related to these underlying processes. By formally disentangling state and observation processes based on simple yet powerful mathematical properties that can be used to describe many ecological phenomena, hidden Markov models (HMMs) can facilitate inferences about complex system state dynamics that might otherwise be intractable. However, HMMs have only recently begun to gain traction within the broader ecological community. We provide a gentle introduction to HMMs, establish some common terminology, review the immense scope of HMMs for applied ecological research and provide a tutorial on implementation and interpretation. By illustrating how practitioners can use a simple conceptual template to customise HMMs for their specific systems of interest, revealing methodological links between existing applications, and highlighting some practical considerations and limitations of these approaches, our goal is to help establish HMMs as a fundamental inferential tool for ecologists. International audience WOS:000579175800001

The aim of this work was the identification and molecular characterization of novel sugar beet (Beta vulgaris) repetitive sequences to unravel the impact of repetitive DNA on size and evolution of Beta genomes via amplification and diversification.Genomic DNA and a pool of B. vulgaris repetitive sequences were separately used as probes for a screening of high-density filters from a B. vulgaris plasmid library. Novel repetitive motifs were identified by sequencing and further used as probes for Southern analyses in the genus Beta. Chromosomal localization of the repeats was analysed by fluorescent in situ hybridization on chromosomes of B. vulgaris and two other species of the section Beta.Two dispersed repetitive families pDvul1 and pDvul2 and the tandemly arranged repeat family pRv1 were isolated from a sugar beet plasmid library. The dispersed repetitive families pDvul1 and pDvul2 were identified in all four sections of the genus Beta. The members of the pDvul1 and pDvul2 family are scattered over all B. vulgaris chromosomes, although amplified to a different extent. The pRv1 satellite repeat is exclusively present in species of the section Beta. The centromeric satellite pBV1 by structural variations of the monomer and interspersion of pRv1 units forms complex satellite structures, which are amplified in different degrees on the centromeres of 12 chromosomes of the three species of the Beta section.The complexity of the pBV1 satellite family observed in the section Beta of the genus Beta and, in particular, the strong amplification of the pBV1/pRv1 satellite in the domesticated B. vulgaris indicates the dynamics of centromeric satellite evolution during species radiation within the genus. The dispersed repeat families pDvul1 and pDvul2 might represent derivatives of transposable elements.