Defining null expectations for animal site fidelity

Site fidelity—the tendency to return to previously visited locations—is widespread across taxa. Returns may be driven by several mechanisms, including memory, habitat selection, or chance; however, pattern-based definitions group different generating mechanisms under the same label of ‘site fidelity’, often assuming memory as the main driver. We propose an operational definition of site fidelity as patterns of return that deviate from a null expectation derived from a memory-free movement model. First, using agent-based simulations, we show that without memory, intrinsic movement characteristics and extrinsic landscape characteristics are key determinants of return patterns and that even random movements may generate substantial probabilities of return. Second, we illustrate how to implement our framework empirically to establish ecologically meaningful, system-specific null expectations for site fidelity. Our approach provides a conceptual and operational framework to test hypotheses on site fidelity across systems and scales.     

Maximal ecological diversity exceeds evolutionary diversity in model ecosystems

Understanding community saturation is fundamental to ecological theory. While investigations of the diversity of evolutionary stable states (ESSs) are widespread, the diversity of communities that have yet to reach an evolutionary endpoint is poorly understood. We use Lotka–Volterra dynamics and trait-based competition to compare the diversity of randomly assembled communities to the diversity of the ESS. We show that, with a large enough founding diversity (whether assembled at once or through sequential invasions), the number of long-time surviving species exceeds that of the ESS. However, the excessive founding diversity required to assemble a saturated community increases rapidly with the dimension of phenotype space. Additionally, traits present in communities resulting from random assembly are more clustered in phenotype space compared to random, although still markedly less ordered than the ESS. By combining theories of random assembly and ESSs we bring a new viewpoint to both the saturation and random assembly literature.     

The complex genome and adaptive evolution of polyploid Chinese pepper (Zanthoxylum armatum and Zanthoxylum bungeanum)

Zanthoxylum armatum and Zanthoxylum bungeanum, known as ‘Chinese pepper’, are distinguished by their extraordinary complex genomes, phenotypic innovation of adaptive evolution and species-special metabolites. Here, we report reference-grade genomes of Z. armatum and Z. bungeanum. Using high coverage sequence data and comprehensive assembly strategies, we derived 66 pseudochromosomes comprising 33 homologous phased groups of two subgenomes, including autotetraploid Z. armatum. The genomic rearrangements and two whole-genome duplications created large (~4.5 Gb) complex genomes with a high ratio of repetitive sequences (>82%) and high chromosome number (2n = 4x = 132). Further analysis of the high-quality genomes shed lights on the genomic basis of involutional reproduction, allomones biosynthesis and adaptive evolution in Chinese pepper, revealing a high consistent relationship between genomic evolution, environmental factors and phenotypic innovation. Our study provides genomic resources and new insights for investigating diversification and phenotypic innovation in Chinese pepper, with broader implications for the protection of plants under severe environmental changes.     

Elastic priors to dynamically borrow information from historical data in clinical trials

Use of historical data and real-world evidence holds great potential to improve the efficiency of clinical trials. One major challenge is to effectively borrow information from historical data while maintaining a reasonable type I error and minimal bias. We propose the elastic prior approach to address this challenge. Unlike existing approaches, this approach proactively controls the behavior of information borrowing and type I errors by incorporating a well-known concept of clinically significant difference through an elastic function, defined as a monotonic function of a congruence measure between historical data and trial data. The elastic function is constructed to satisfy a set of prespecified criteria such that the resulting prior will strongly borrow information when historical and trial data are congruent, but refrain from information borrowing when historical and trial data are incongruent. The elastic prior approach has a desirable property of being information borrowing consistent, that is, asymptotically controls type I error at the nominal value, no matter that historical data are congruent or not to the trial data. Our simulation study that evaluates the finite sample characteristic confirms that, compared to existing methods, the elastic prior has better type I error control and yields competitive or higher power. The proposed approach is applicable to binary, continuous, and survival endpoints.     

Phylogeny of Saxifraga section Saxifraga subsection Arachnoideae (Saxifragaceae) and the origin of low elevation shade-dwelling species

Saxifraga section Saxifraga subsection Arachnoideae is a lineage of 12 species distributed mainly in the European Alps. It is unusual in terms of ecological diversification by containing both high elevation species from exposed alpine habitats and low elevation species from shady habitats such as overhanging rocks and cave entrances. Our aims are to explore which of these habitat types is ancestral, and to identify the possible drivers of this remarkable ecological diversification. Using a Hybseq DNA-sequencing approach and a complete species sample we reconstructed and dated the phylogeny of subsection Arachnoideae. Using Landolt indicator values, this phylogenetic tree was used for the reconstruction of the evolution of temperature, light and soil pH requirements in this lineage. Diversification of subsection Arachnoideae started in the late Pliocene and continued through the Pleistocene. Both diversification among and within clades was largely allopatric, and species from shady habitats with low light requirements are distributed in well-known refugia. We hypothesize that low light requirements evolved when species persisting in cold-stage refugia were forced into marginal habitats by more competitive warm-stage vegetation. While we do not claim that such competition resulted in speciation, it very likely resulted in adaptive evolution.     

Phylogeny and adaptive radiation within the Anomopoda: a preliminary exploration

The distinctness of the Anomopoda and the polyphyletic nature of the so-called Cladocera are emphasized.An attempt is made to reconstruct the ancestral anomopod, which probably lived in Palaeozoic times. This task is facilitated by the availability of detailed information on extant forms, which includes functional as well as purely morphological considerations and enables us to understand the means whereby complex mechanisms were transformed during evolution. Comparative studies on the ecology and habits of extant forms also throw light on the probable way of life of the ancestral anomopod.Adaptive radiation within the Anomopoda is briefly surveyed and an outline of the suggested phylogeny of the order is indicated.Institute of Environmental and Biological Sciences, University of Lancaster     

Islands: stability, diversity, conservation

Islands present both a diversity and a stability paradox. They are often highly species-poor but have considerable biological interest in terms of extraordinary endemic genera and taxonomically isolated groups. They appear to be stable, as in some cases these organisms have persisted for many millions of years, and having an oceanic climate, extreme climatic events may be comparatively rare. However, when subject to extrinsic (anthropogenic) disturbance they do not appear to be stable, but often suffer catastrophic ecological change. These apparent paradoxes are resolved when it is realized that all these features are consequences of the same island characteristics: biotic isolation and oceanicity. As a result of these two characteristics, far oceanic islands are quantitatively different from continental systems in the nature of their ecological processes, which appear to give rise to an extreme punctuated equilibrium model of evolutionary change. Endemics may be ancient relict endemics displaying prolonged stasis and persistence, or products of adaptive radiation representing rapid punctuational events. A process-based definition of a relict endemic (palaeoendemic) is one whose founding lineage (i.e. the original continental source taxon) has not left any descendents. A corollary of this definition is that the time of divergence between an endemic and its continental sister-group should predate the colonization of the island by the now endemic lineage. An example is Dicksonia arborescens which has been on St Helena for at least 9 Myrs and no longer occurs in the likely source area of Africa. These relict endemics, frequent on islands, are important as the last remnants of tranches of biodiversity that have vanished elsewhere. Island conservation strategies require an integrated understanding of both sides of the diversity and stability paradox so that both island processes and island organisms can be conserved.     

The random walk description for isotope exchange in a polypeptide

Isotope exchange in a polypeptide is considered from the point of view in which the boundary point between helix and coil regions of a polypeptide behaves like a weakly asymmetric random walker. We assume that the boundary point is reflected completely at the ends of a polypeptide. The equilibrium fraction of helix region is obtained under this assumption, and this is also confirmed by computer simulation. The experimental results of isotope exchange can be explained in this situation. On the other hand. the rate constant of exchange of a residue given by experiments can also be explained by another assumption, as considered before (M. Fujiwara and N. Saitô, Polym. J. 9 (1977) 625.), in which the nucleations of coil states take place in the helix region. Which of the two is of major importance is left to further studies.     

Adaptive Admixture of HLA Class I Allotypes Enhanced Genetically Determined Strength of Natural Killer Cells in East Asians

Human natural killer (NK) cells are essential for controlling infection, cancer, and fetal development. NK cell functions are modulated by interactions between polymorphic inhibitory killer cell immunoglobulin-like receptors (KIR) and polymorphic HLA-A, -B, and -C ligands expressed on tissue cells. All HLA-C alleles encode a KIR ligand and contribute to reproduction and immunity. In contrast, only some HLA-A and -B alleles encode KIR ligands and they focus on immunity. By high-resolution analysis of KIR and HLA-A, -B, and -C genes, we show that the Chinese Southern Han (CHS) are significantly enriched for interactions between inhibitory KIR and HLA-A and -B. This enrichment has had substantial input through population admixture with neighboring populations, who contributed HLA class I haplotypes expressing the KIR ligands B*46:01 and B*58:01, which subsequently rose to high frequency by natural selection. Consequently, over 80% of Southern Han HLA haplotypes encode more than one KIR ligand. Complementing the high number of KIR ligands, the CHS KIR locus combines a high frequency of genes expressing potent inhibitory KIR, with a low frequency of those expressing activating KIR. The Southern Han centromeric KIR region encodes strong, conserved, inhibitory HLA-C-specific receptors, and the telomeric region provides a high number and diversity of inhibitory HLA-A and -B-specific receptors. In all these characteristics, the CHS represent other East Asians, whose NK cell repertoires are thus enhanced in quantity, diversity, and effector strength, likely augmenting resistance to endemic viral infections.