Complexity of avian evolution revealed by family-level genomes.

Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method, and the choice of genomic regions 1-3. Here, we address these issues by analyzing genomes of 363 bird species 4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a remarkable degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Paleogene (K-Pg) boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that challenge modeling due to extreme GC content, variable substitution rates, incomplete lineage sorting, or complex evolutionary events such as ancient hybridization. Assessment of the impacts of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates, and relative brain size following the K-Pg extinction event, supporting the hypothesis that emerging ecological opportunities catalyzed the diversification of modern birds. The resulting phylogenetic estimate offers novel insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.

Late Complications after Laparoscopic Longitudinal Gastrectomy - Case Report.

INTRODUCTION: Bariatric surgery is now widely regarded as the most effective treatment for morbid obesity. It aims to enhance patients' health by achieving long-lasting weight loss, reducing associated comorbidities, and improving their quality of life. CASE REPORT: The case involves a 51-year-old female patient who underwent sleeve gastrectomy eight years ago to address morbid obesity (Body Mass Index (BMI) = 43). Subsequently, the patient developed gastric obstructive syndrome, leading to diagnostic investigations including repeated upper digestive endoscopies and native computed tomography. These examinations revealed the presence of a hiatal hernia. In 2021, the patient underwent fundoplication type Dor with anterior hemivalve. However, post-surgery, the patient's condition did not improve, with persistent symptoms including regurgitation, heartburn, difficulty ingesting food, sensation of gastric fullness, and epigastralgia. Further exploratory procedures, including upper digestive endoscopy, abdominal computed tomography with contrast substance, and barium transit with contrast substance, led to the diagnosis of mediogastric stenosis postgastrectomy longitudinal, necessitating surgical intervention. This finding prompted a surgical approach involving distal gastric resection and restoration of digestive tract continuity through Hoffmeister-Finsterer gastro-jejunal anastomosis. Following the surgery, the patient's postoperative symptoms showed improvement. DISCUSSION: Several other studies have demonstrated that the incisura angularis is the most common site of obstruction, as was observed in our study. This particular location appears to be more prone to narrowing, likely attributable to its angular shape. The linear staple line in this area can create a locus minoris resistentiae for kinking, as well as increase the risk of true stenosis if stapling is performed too close to the incisura angularis. CONCLUSIONS: Bariatric surgery should not be considered as the initial treatment option. However, in cases where it becomes necessary, postoperative monitoring is essential to prevent complications or address them promptly.

Harem size should be measured by more than the sum of its parts: Phenology-based measurements reveal joint effects of intrinsic and extrinsic factors on a polygamous herbivore under non-stationary climatic conditions.

Social behaviour is thought to be a major component of survival, reproduction, and resilience of populations. Thus, it is a key component in management and conservation of wild populations. In polygynous breeding species, group size influences the reproductive success of males and females, and hence it is essential to understand the environmental and demographic factors that shape the phenology of group size within populations. Here, we investigate harem size and its determinants using a 15-year dataset of annual harem size phenology-based metrics from a reintroduced population of wild Przewalski horses in Hortobágy National Park, Hungary. From the initial reintroduction of 21 animals in 1997, the population grew to 174 animals in 2012. During that same period, the number of harems increased from three to 23. Despite the 8-fold increase in population size, harem sizes remained stable, and variability among harems within years decreased. The annual phenological cycle of harem size was not consistent over the 15-year period, and the associated annual phenology-based metrics varied differently over the years. The best predictors of our phenology-based harem size metrics were adult sex ratio, annual adult mortality and annual mean number of harems, with some evidence that mean age of harem stallions and drought severity were contributing factors. Our findings reveal that complex interactions between demography, climate, and harem size can emerge in social animals. Taken together, our results demonstrate that intrinsic population processes can regulate group size even in the presence of non-stationary climatic conditions during periods of growth in human-introduced, semi-free ranging animal populations.

Divergent Selection in Low Recombination Regions Shapes the Genomic Islands in Two Incipient Shorebird Species.

Speciation in the face of gene flow is usually associated with a heterogeneous genomic landscape of divergence in nascent species pairs. However, multiple factors, such as divergent selection and local recombination rate variation, can influence the formation of these genomic islands. Examination of the genomic landscapes of species pairs that are still in the early stages of speciation provides an insight into this conundrum. In this study, population genomic analyses were undertaken using a wide range of sampling and whole-genome resequencing data from 96 unrelated individuals of Kentish plover (Charadrius alexandrinus) and white-faced plover (Charadrius dealbatus). We suggest that the two species exhibit varying levels of population admixture along the Chinese coast and on the Taiwan Island. Genome-wide analyses for introgression indicate that ancient introgression had occurred in Taiwan population, and gene flow is still ongoing in mainland coastal populations. Furthermore, we identified a few genomic regions with significant levels of interspecific differentiation and local recombination suppression, which contain several genes potentially associated with disease resistance, coloration, and regulation of plumage molting and thus may be relevant to the phenotypic and ecological divergence of the two nascent species. Overall, our findings suggest that divergent selection in low recombination regions may be a main force in shaping the genomic islands in two incipient shorebird species.

Low-burden TP53 mutations represent frequent genetic events in CLL with an increased risk for treatment initiation.

TP53 aberrations predict chemoresistance and represent a contraindication for the use of standard chemoimmunotherapy in chronic lymphocytic leukaemia (CLL). Recent next-generation sequencing (NGS)-based studies have identified frequent low-burden TP53 mutations with variant allele frequencies below 10%, but the clinical impact of these low-burden TP53 mutations is still a matter of debate. In this study, we aimed to scrutinise the subclonal architecture and clinical impact of TP53 mutations using a sensitive, NGS-based mutation analysis in a 'real-world' cohort of 901 patients with CLL. In total, 225 TP53 mutations were identified in 17.5% (158/901) of the patients; 48% of these alterations represented high-burden mutations, while 52% were low-burden TP53 mutations. Low-burden mutations as sole alterations were identified in 39% (62/158) of all mutated cases with 82% (51/62) of these being represented by a single low-burden TP53 mutation. Patients harbouring low-burden TP53 mutations had significantly lower time to first treatment compared to patients with wild-type TP53. Our study has expanded the knowledge on the frequency, clonal architecture, and clinical impact of low-burden TP53 mutations. By demonstrating that patients with sole low-burden TP53 variants represent more than one-third of patients with TP53 mutations and have an increased risk for treatment initiation, our findings strengthen the need to redefine the threshold of TP53 variant reporting to below 10% in the routine diagnostic setting.

Nesting Habitat Suitability of the Kentish Plover in the Arid Lands of Xinjiang, China.

Understanding the main ecological factors of the nesting habitat of shorebirds is of great significance in relation to their protection and habitat management. Habitat loss and change due to a lack of water threaten the biodiversity of shorebirds, with impacts likely to be most pronounced in arid lands. We collected the data of 144 nesting sites and 10 ecological factors during the breeding season from April to July each year in 2019 and 2020 in nine river districts in Xinjiang. The MaxEnt model was applied to assess the suitability of nesting habitats for Kentish plovers (Charadrius alexandrinus) in the study area to examine the main factors affecting their nesting habitat. The most suitable nesting habitats are mostly distributed in plain reservoirs in the middle part of the Northern Slope of the Tianshan Mountains, Ebinur Lake and its eastern position in the southwestern Junggar Basin, near Ulungur Lake of the Ulungur river area and the southern Irtysh river area. The distance from water, normalized difference vegetation index, mean temperature of the breeding season, slope, and land use were the main factors affecting the nesting habitat selection of Kentish plovers. It was found that the proportion of suitable nesting habitat protected for the Kentish plovers in the study area was low (851.66 km2), accounting for only 11.02% of the total suitable nesting habitat area. In view of the scarcity and importance of water bodies in arid lands and the lack of protection for Kentish plovers at present, it is suggested to strengthen the conservation and management of the regional shorebirds and their habitats by regulating and optimizing the allocation of water resources.

Evolution of reproductive modes in sharks and rays.

The ecological and life history drivers of the diversification of reproductive modes in early vertebrates are not fully understood. Sharks, rays and chimaeras (group Chondrichthyes) have an unusually diverse variety of reproductive modes and are thus an ideal group to test the factors driving the evolution of reproductive complexity. Here, using 960 species representing all major Chondrichthyes taxa, we reconstruct the evolution of their reproduction modes and investigate the ecological and life history predictors of reproduction. We show that the ancestral Chondrichthyes state was egg-laying and find multiple independent transitions between egg-laying and live-bearing via an intermediate state of yolk-only live-bearing. Using phylogenetically informed analysis, we also show that live-bearing species have larger body size and larger offspring than egg-laying species. In addition, live-bearing species are distributed over shallow to intermediate depths, while egg-layers are typically found in deeper waters. This suggests that live-bearing is more closely associated with pelagic, rather than demersal habitats. Taken together, using a basal vertebrate group as a model, we demonstrat how reproductive mode co-evolves with environmental conditions and life-history traits.

Evolution of reproductive strategies: sex roles, sex ratios and phylogenies.

Behavioural variations associated with breeding-termed reproductive strategies-are some of the striking behaviours that have occupied naturalists for 1000s of years. How an animal seeks, competes for and/or chooses a mate? Do they breed with a single partner, or do they change partners between breeding events? How and when do they look after their young? Behavioural biologists, ecologists and evolutionary biologists have investigated these questions using quantitative methods since 1970s. In Debrecen, with the support and mentoring of Prof Zoltán Varga, we are investigating the causes and implications of reproductive strategies since 1988. This article reviews some of the core ideas in reproductive strategies research and explains the influence of Prof Varga on the development of these ideas. My main thesis here is that both integrative thinking and adopting a multi-pronged research approach using an explicit phylogenetic framework-both of these have been spearheaded by Prof Varga throughout his lifetime-can reveal novel aspects of reproductive strategies. Importantly, some of these academic insights have direct implications for preserving species and their habitats in the wild, and thus benefit biodiversity conservation.

Variations in the Reproductive Strategies of Different Charadrius alexandrinus Populations in Xinjiang, China.

Due to the influence of bio-geographical and environmental factors, as well as anthropogenic landscape features, organisms show different reproductive strategies among different populations. There is a lack of detailed information on the reproductive biology of Kentish plover Charadrius alexandrinus in arid lands in Central Asia. In this study, we summarized the characteristics of the reproductive biology of three geographically distinct plover populations in Aibi Lake in northwestern Xinjiang, Taitema Lake in southern Xinjiang and artificial reservoirs around Urumqi City in northern Xinjiang, based on 440 eggs from 158 nests observed and analyzed from April to July of 2019 and 2020. We found that there was no significant difference in clutch size among the three populations. However, the egg size of the Taitema Lake population was significantly larger than those of the other two populations, whilst the egg volume and clutch volume of the artificial reservoirs' populations were significantly larger than that of Aibi Lake. With the postponement of laying dates, the northern and northwestern populations showed the characteristics of a small clutch size and a relatively small egg size, respectively, and a decrease in reproductive output. The heavier female plovers in Taitema Lake laid eggs earlier, and there was a significantly positive correlation between female body mass and clutch size and egg size. The tarsometatarsus length of the female plovers was significantly positively correlated with the reproductive output in all three populations. The model selection results show that female body size and ambient temperature restrict the egg size and reproductive output of Kentish plovers, which is consistent with the upper limit hypothesis of the maternal condition and maternal constraint. Our data support the hypothesis that Kentish plovers show distinct flexibility in their breeding strategies to cope with the harsh natural environment in the arid lands of Xinjiang, China. The results of a relatively high average clutch size and average egg size imply that the saline wetlands of Western China are important breeding habitats for Kentish plovers.

Multiple paternity is related to adult sex ratio and sex determination system in reptiles.

The adult sex ratio (ASR, the proportion of males in the adult population) is an emerging predictor of reproductive behaviour, and recent studies in birds and humans suggest it is a major driver of social mating systems and parental care. ASR may also influence genetic mating systems. For instance male-skewed ASRs are expected to increase the frequency of multiple paternity (defined here as a clutch or litter sired by two or more males) due to higher rates of coercive copulations by males, and/or due to females exploiting the opportunity of copulation with multiple males to increase genetic diversity of their offspring. Here, we evaluate this hypothesis in reptiles that often exhibit high frequency of multiple paternity although its ecological and life-history predictors have remained controversial. Using a comprehensive dataset of 81 species representing all four non-avian reptile orders, we show that increased frequency of multiple paternity is predicted by more male-skewed ASR, and this relationship is robust to simultaneous effects of several life-history predictors. Additionally, we show that the frequency of multiple paternity varies with the sex determination system: species with female heterogamety (ZZ/ZW sex chromosomes) exhibit higher levels of multiple paternity than species with male heterogamety (XY/XX) or temperature-dependent sex determination. Thus, our across-species comparative study provides the first evidence that genetic mating system depends on ASR in reptiles. We call for further investigations to uncover the complex evolutionary associations between mating systems, sex determination systems and ASR.

Egg characteristics vary longitudinally in Arctic shorebirds.

Arctic environments are changing rapidly and if we are to understand the resilience of species to future changes, we need to investigate alterations in their life histories. Egg size and egg shape are key life-history traits, reflecting parental investment as well as influencing future reproductive success. Here we focus on egg characteristics in two Arctic shorebirds, the Dunlin (Calidris alpina) and the Temminck's stint (Calidris temminckii). Using egg photos that encompass their full breeding ranges, we show that egg characteristics exhibit significant longitudinal variations, and the variation in the monogamous species (Dunlin) is significantly greater than the polygamous species (Temminck's stint). Our finding is consistent with the recent "disperse-to-mate" hypothesis which asserts that polygamous species disperse further to find mates than monogamous species, and by doing so they create panmictic populations. Taken together, Arctic shorebirds offer excellent opportunities to understand evolutionary patterns in life history traits.

Polygamy and purifying selection in birds.

Good genes theories of sexual selection predict that polygamy will be associated with more efficient removal of deleterious alleles (purifying selection), due to the alignment of sexual selection with natural selection. On the other hand, runaway selection theories expect no such alignment of natural and sexual selection, and may instead predict less efficient purifying selection in polygamous species due to higher reproductive variance. In an analysis of polymorphism data extracted from 150-bird genome assemblies, we show that polygamous species carry significantly fewer nonsynonymous polymorphisms, relative to synonymous polymorphisms, than monogamous bird species (p = .0005). We also show that this effect is independent of effective population size, consistent with the alignment of natural selection with sexual selection and "good genes" theories of sexual selection. Further analyses found no impact of polygamy on genetic diversity, while polygamy in females (polyandry) had a marginally significant impact (p = .045). We also recapitulate previous findings that smaller body mass and greater geographic range size are associated with more efficient purifying selection, more intense GC-biased gene conversion, and greater genetic diversity.

Remating opportunities and low costs underlie maternal desertion.

Parental care can enhance offspring survival but may impose significant costs to parents. The costs and benefits of care are key to understanding patterns of parental care, where parents can benefit by having their partner increase investment in care, while reducing their own effort. However, investigating the costs and benefits of parental care in wild populations is challenging. Here we use highly detailed behavioral observations in families of a small shorebird, where one parent frequently deserts its offspring, to explore the potential costs and benefits of desertion in a wild population. We first show that females desert their broods more frequently than males. Second, we investigate the benefits of this frequent female desertion in terms of additional mating opportunities, and the costs of desertion to females in terms of the growth and survival of deserted offspring. Our results indicate that female desertion is favored by a combination of remating benefits and a lack of costs to brood growth and survival, as abandoned male parents continue to provide care after desertion. Our results shed light on the costs and benefits underlying natural desertion strategies and suggest that female desertion is a fine-tuned behavior that responds to seasonally changing benefits of desertion.

Myelofibrosis progression grading based on type I and type III collagen and fibrillin 1 expression boosted by whole slide image analysis.

AIMS: The progression of primary myelofibrosis is characterised by ongoing extracellular matrix deposition graded based on 'reticulin' and 'collagen' fibrosis, as revealed by Gomori's silver impregnation. Here we studied the expression of the major extracellular matrix proteins of fibrosis in relation to diagnostic silver grading supported by image analysis. METHODS AND RESULTS: By using automated immunohistochemistry, in this study we demonstrate that the expression of both types I and III collagens and fibrillin 1 by bone marrow stromal cells can reveal the extracellular matrix scaffolding in line with myelofibrosis progression as classified by silver grading. 'Reticulin' fibrosis indicated by type III collagen expression and 'collagen' fibrosis featured by type I collagen expression were parallel, rather than sequential, events. This is line with the proposed role of type III collagen in regulating type I collagen fibrillogenesis. The uniformly strong fibrillin 1 immune signals offered the best inter-rater agreements and the highest statistical correlations with silver grading of the three markers, which was robustly confirmed by automated whole slide digital image analysis using a machine learning-based algorithm. The progressive up-regulation of fibrillin 1 during myelofibrosis may result from a negative feedback loop as fibrillin microfibrils sequester TGF-ß, the major promoter of fibrosis. This can also reduce TGF-ß-induced RANKL levels, which would stimulate osteoclastogenesis and thus can support osteosclerosis in advanced myelofibrosis. CONCLUSIONS: Through the in-situ detection of these extracellular matrix proteins, our results verify the molecular pathobiology of fibrosis during myelofibrosis progression. In particular, fibrillin 1 immunohistochemistry, with or without image analysis, can complement diagnostic silver grading at decent cell morphology.

Adult sex ratios: causes of variation and implications for animal and human societies.

Converging lines of inquiry from across the social and biological sciences target the adult sex ratio (ASR; the proportion of males in the adult population) as a fundamental population-level determinant of behavior. The ASR, which indicates the relative number of potential mates to competitors in a population, frames the selective arena for competition, mate choice, and social interactions. Here we review a growing literature, focusing on methodological developments that sharpen knowledge of the demographic variables underlying ASR variation, experiments that enhance understanding of the consequences of ASR imbalance across societies, and phylogenetic analyses that provide novel insights into social evolution. We additionally highlight areas where research advances are expected to make accelerating contributions across the social sciences, evolutionary biology, and biodiversity conservation.

The evolution of parental care in salamanders.

Complex parenting has been proposed to contribute to the evolutionary success of vertebrates. However, the evolutionary routes to complex parenting and the role of parenting in vertebrate diversity are still contentious. Although basal vertebrates provide clues to complex reproduction, these are often understudied. Using 181 species that represent all major lineages of an early vertebrate group, the salamanders and newts (Caudata, salamanders henceforth) here we show that fertilisation mode is tied to parental care: male-only care occurs in external fertilisers, whereas female-only care exclusively occurs in internal fertilisers. Importantly, internal fertilisation opens the way to terrestrial reproduction, because fertilised females are able to deposit their eggs on land, and with maternal care provision, the eggs could potentially develop outside the aquatic environment. Taken together, our results of a semi-aquatic early vertebrate group propose that the diversity and follow-up radiation of terrestrial vertebrates are inherently associated with a complex social behaviour, parenting.

Evolution of Social Organization: Phylogenetic Analyses of Ecology and Sexual Selection in Weavers.

AbstractCrook published a landmark study on the social organization of weavers (or weaverbirds, family Ploceidae) that contributed to the emergence of sociobiology, behavioral ecology, and phylogenetic comparative methods. By comparing ecology, spatial distribution, and mating systems, Crook suggested that the spatial distribution of food resources and breeding habitats influence weaver aggregation during both the nonbreeding season (flocking vs. solitary foraging) and the breeding season (colonial vs. solitary breeding), and the latter in turn impacts mating systems and sexual selection. Although Crook's study stimulated much follow-up research, his conclusions have not been scrutinized using phylogenetically controlled analyses. We revisited Crook's hypotheses using modern phylogenetic comparative methods on an extended data set of 107 weaver species. We showed that both diet and habitat type are associated with spatial distribution and that the latter predicts mating system, consistent with Crook's propositions. The best-supported phylogenetic path model also supported Crook's arguments and uncovered a direct relationship between nonbreeding distribution and mating system. Taken together, our phylogenetically corrected analyses confirm Crook's conjectures on the roles of ecology in social organizations of weavers; however, our analyses also uncovered an association between nonbreeding distributions and mating systems, which was not envisaged by Crook.